Many standard oxidants and reductants are non-reusable and toxic, so it is important to pursue cleaner alternatives. In this project, we have synthesized and characterized two metal-bipyridyl supramolecular cages and have studied their application as catalysts for the electrochemical reduction of organic substrates. Supramolecular cages are formed from the self-assembly of organic ligands and metal ions in solution, and they contain internal cavities with unique electronic microenvironments, similar to the interior of enzymes. While these polyhedral structures have been investigated as catalysts for traditional synthetic pathways, their role in electrosynthesis remains underexplored. Electrosynthesis involves the transfer of electrons to and from substrates using an applied potential, rather than chemical redox agents. This method is often hindered by a high kinetic barrier at the electrode-substrate interface, but catalysts can lower this barrier. We hypothesize that redox-active supramolecular cages – cages that can readily interconvert between charge states – can serve as effective electrocatalysts by encapsulating and transferring charge to substrates. To understand the effect of ligand geometry on electrocatalysis, I have synthesized two redox-active ligands with bipyridyl chelating groups. One contains a highly conjugated perylene core, while the other contains a compact core formed from pyromellitic dianhydride. We have metalated these ligands with iron ions to form two tetrahedral supramolecular cages. We then utilized cyclic voltammetry to assess cage-facilitated charge transfer to vicinal dihalide substrates. We observed that the reduction of multiple substrates, including 1,2-dibromo-1,2-diphenylethane, occurred at milder voltages in the presence of the cages, indicating a reduced kinetic barrier. For these substrates, we then performed bulk electrolysis, from which we determined that the percent conversion to the desired product was significantly higher when a cage was present, supporting our hypothesis. Ultimately, we aim to use these cages to enable electrosynthesis of organic feedstocks at lower voltages and with fewer byproducts.

Hypoxia ischemia encephalopathy (HIE) is characterized as a lack of oxygen and blood flow to the brain, and is a leading cause of neonatal mortality and morbidity within the United States. HIE causes immediate cell death and oxidative stress resulting in inflammation, energy failure, and ongoing injury. Though there is a lack of effective therapies for HIE, extracellular vesicles (EVs) have shown incredible potential in attenuating oxidative stress and inflammation. EVs are biological nanoparticles with a lipid membrane containing essential biomolecules. EVs participate in cell-to-cell communication as they travel between membranes of cells within the central nervous system (CNS). Previous studies on adult brain injury models show the potential for EVs to drive neuroprotective and anti-inflammatory processes in the brain. The aim of my project is to evaluate neonatal injury responses to brain-derived EVs (BEVs) following HI injury on ex vivo brain tissues. To mimic an ischemic brain environment, I used an oxygen glucose deprivation (OGD) model to induce hypoxia in neonatal rat brain tissues. I quantified time-dependent changes in the gene expression profiles of brain tissues after BEV treatment by performing RNA extractions and reverse transcription-quantitative polymerase chain reactions (RT-qPCR). This allowed me to compare the expression levels of pro-inflammatory and anti-inflammatory markers to determine the therapeutic efficacy of BEVs on an ischemic model. My results suggested that BEV exposure in OGD-injured models decreased cytotoxicity by encouraging microglia (the brain’s immune cells) to transition from inflammatory to anti-inflammatory phenotypes. Results from the RT-qPCR analysis further suggested that BEVs reduced inflammation through the upregulation of anti-inflammatory cytokines observed in the study. This demonstrates that BEVs play a role in reducing cell death and activating anti-inflammatory pathways in the neonatal brain, providing insight into their potential as a therapeutic tool for future interventions aimed at treating HIE.

Following traumatic spinal cord injuries (SCI), pathological reflexes develop that result in altered bladder function and sphincter discoordination, with accompanying changes in the detrusor, typically hyperreflexia and sphincter dyssynergia. The effects on the bladder following SCI significantly increase the risk of infection as well as permanent kidney deterioration. Oral anticholinergic medications are used to treat neurogenic bladders, but have severe side effects that are not practical for all patients to withstand. Bladder chemodenervation is currently used as a second line of defense after the medication has failed. We hypothesized that acute bladder chemodenervation with BoNT-A application into the detrusor muscle can prevent the onset of bladder wall hypertrophy after spinal cord injury (SCI) thereby improving bladder function and health post-SCI. We used a rodent model of contusion SCI to compare the use of early versus later intervention with BoNT-A following SCI with a number of analytic procedures such as bladder histopathology and collagen deposition to determine the most effective time frame for this treatment. Early histological analyses showed a 46% reduction in bladder wall thickness in SCI + early BoNT-A bladders compared to SCI + early saline (0.86 ± 0.08 mm vs 1.6 mm ± 0.25) treated rats. Bladder cystometry analysis at 6-8 weeks post injury revealed that early BoNT-A bladder injections limited post-SCI bladder capacity over all other SCI groups. Typical mictutition profiles, which indicate normal bladder function, was maintained in all early BoNT-A animals (3/3), whereas no micturitions were observed in SCI-only animals (0/5) and few were observed in late BoNT-A treated animals (2/6). We plan to pilot a limited clinical study to understand the effectiveness of early BoNT-A injections following SCI in humans so that we can gather the necessary data to translate into a full-scale clinical trial.

Over the past 50 years, breast cancer mortality rates in high-income countries have dropped significantly while low and middle-income countries (LMICs) have made few advancements towards early detection and rapid diagnosis. A lack of infrastructure in LMIC healthcare settings causes patients to receive their diagnosis several months after testing, while some never hear back due to travel and communication barriers. We have partnered with Peace and Love Hospitals in Ghana to develop CoreView Imaging on the Needle (ION), a portable, rapid point-of-care (POC) diagnostic system for use in LMIC. Our team developed ION after discovering breast core needle biopsies (CNBs) were too delicate and sticky for transport in our original millifluidic design. Our research is exploring methods of integrating the ION system into CoreView to improve the testing reliability and image quality of biopsies for diagnosis by designing, testing, and iterating fixtures to image CNBs while still on the needle. We modeled our prototypes in Solidworks and printed them using a Prusa 3D printer. Our goal is to load the CNB under a microscope, stain the tissue nuclei, compress its surface against a clear glass window, and image the biopsy surface within 5 minutes. We are using Microscopy with UV Surface Excitation (MUSE) imaging to take panoramic images along the 20 mm biopsy length. The current prototype takes 1 minute to prepare the biopsy (stain and load into ION fixture), 0.5 minutes for each MUSE image and step to the next image (total of 6 images), and 0.5 minutes to unload the biopsy, resulting in 4.5 minutes between biopsy collection and obtaining images for diagnosis. The improved image quality and expected high reliability verifies the success of our ION design for further validation testing to provide earlier breast cancer detection and rapid treatment to rural patients.

A large composition of our universe remains unidentified. Ordinary ‘visible’ matter comprises 5% of the known universe whereas dark matter comprises 27%. The Dark Matter in CCDs (DAMIC) research team hypothesizes that charge-coupled devices (CCDs) may be able to detect weakly interactive massive particles (WIMPs) as a possible candidate for dark matter. The silicon CCDs gather information by measuring the ionized charge from collisions between its silicon atoms and external particles, yet these measurements can become inaccurate in the presence of noise. The leading noise source is leakage current across the CCDs, which can be mitigated by operating the experiment at 100K. Furthermore, CCD performance is highly dependent on temperature so we must assure a constant temperature across the CCDs. Obtaining this temperature is essential in the successful implementation of the DAMIC-M experiment. We started with multiple thermal tests on a single mock CCD module housed in a copper box to ensure proper cooling. We aimed for minimal temperature differences of the box and across the silicon once they reached 110K temperatures. Our initial tests showed large temperature differences leading us to make modifications to the arrangement of the module in the box. Once these modifications were implemented, a consistent trend of minimal temperature differences between the box and silicon was present. Following this development, we began further testing with a new box which holds 13 mock CCD modules. This new arrangement mimics the final DAMIC-M experiment which allows for a more accurate representation for future thermal tests. 

Intermediate metabolism in cells has generally been studied without considering the arrangement of enzymes within the cell. However, recent developments have shown that many metabolic enzymes form organization systems that are made up of oligomers stacking linearly into filaments. The enzyme phosphoribosyl pyrophosphate synthetase (PRPS) makes a precursor required for all de novo nucleotide synthesis in cells, and therefore plays an important role in cellular metabolism. This project aims to characterize the PRPS protein in Xenopus tropicalis and Giardia lamblia. We hypothesize that PRPS from X. tropicalis will have similar biochemical and structural properties as compared to human PRPS, while PRPS from G. lamblia will have different biochemical and structural properties. This hypothesis is supported by the small evolutionary difference between PRPS from humans and X. tropicalis as compared to the large evolutionary difference between PRPS from humans and G. lamblia. This difference would be especially interesting to examine from the perspective of filament formations in the PRPS protein. So far, we have created the Xenopus tropicalis and Giardia lamblia plasmids by cloning. Test expressions of the X. tropicalis yielded protein expression in E. coli cell strains C43 and RIL, while test expressions for G. lamblia have been successful in C43, BL21, pLysS, and Rosetta cell strains. This demonstrates that both X. tropicalis and G. lamblia PRPS can be expressed in E. Coli strains. An analysis of X. tropicalis will allow us to test how filament formation changes with only small evolutionary differences in PRPS. It could also be used for further research in vivo using frog eggs that act as a singular cell system. If it is confirmed that the G. lamblia protein is different from human PRPS, PRPS in G. lamblia could serve as an antibiotic target since current methods of treatment for the organism are very harmful to the human microbiome.

Hemagglutinin (HA) is a glycoprotein found on the surface of the influenza virus. HA binds to sialic acid receptors on host cells and mediates membrane fusion, allowing the virus to enter the cell. This project investigates how mutations associated with species crossover affect viral fusion mechanisms in influenza HA. HA from the past outbreaks of H5N1 influenza strains in Vietnam in 2004 (VN04) and Indonesia in 2005 (IN05), are being compared to an HA from an on-going avian influenza outbreak using a strain isolated in Colorado in 2022 (CO22). Through site-directed mutagenesis, mutations that affect acid stability and affinity for the human receptor were added to HA based on the VN04 and IN05 strains; we are studying these effects in recombinant protein rather than on infectious virus. These mutations are believed to enable the virus to increase transmissibility among mammals including humans. To compare how HA from these H5 isolates with and without the adaptive mutations behave, hydrogen-deuterium exchange mass spectrometry (HDX-MS) is being used to measure changes in deuterium incorporation on the protein backbone for specific peptide segments, giving a profile of local dynamics and structure throughout the HAs. By comparing the dynamic profiles for each as pH is lowered, mimicking acid-activation in host cell endosomes, we can probe how their structure in important fusion and human receptor-binding regions change as the fusion protein becomes activated. By comparing the structural dynamic changes of the WT and mammal-adapted, mutated IN05 and VN04 HA to the new CO22, we will be able to increase our understanding of the effect of the mutations that are associated with species crossover and hopefully be able to gain insight into the potential of this new avian influenza strain’s ability to become transmissible among humans.

In regions with high HIV prevalence, periods of pregnancy and postpartum are associated with higher risk for HIV acquisition. The WHO recommends oral tenofovir (TFV)-based pre-exposure prophylaxis (PrEP) as an effective method of reducing HIV acquisition risk for pregnant people. Although most pregnant patients in Kenya with identified HIV risk factors accept PrEP when offered, >50% discontinue PrEP within the first 30 days.​ Few studies to date examine factors that contribute to PrEP discontinuation in this population and there are no existing intervention studies aimed at improving PrEP adherence during pregnancy/postpartum. We utilized data from the ongoing Mobile Women and Children (mWACh)-PrEP study, a randomized control trial testing a two-way short messaging service (SMS)-based platform to facilitate communication between peripartum patients taking PrEP and remote nurses. In the parent study of 379 HIV-negative, cisgendered Kenyan women taking PrEP, 188 were randomly assigned to the intervention (mWACh-PrEP) group. The purpose of our sub-analysis was to evaluate message contents and identify frequently discussed topics. System messages were tagged into categories based on subject. Of weekly automated messages, 42.1% were responded to by participants, with an average response time of 87 minutes; topics of responses included PrEP concerns (55.1%), antenatal concerns (22.4%), maternal health concerns (17.8%), and infant concerns (17.2%). A total of 366 spontaneous messages were received, with >50% of participants sending at least one spontaneous message; topics of spontaneous messages most frequently included antenatal concerns (22.9%) and PrEP concerns (19.7%). These results indicate that a two-way SMS based intervention provides important support to pregnant and postpartum patients taking PrEP; the mWACh-PrEP system could be an effective solution not only to promote PrEP adherence within this population, but also to increase access to maternal healthcare.

Hexagonal boron nitride (hBN) is essential for nearly all nanoscale two-dimensional (2D) devices, as its flatness and wide bandgap make it an ideal dielectric for applying electrostatic gating. At high electric fields, hBN undergoes electrical breakdown where large currents flow to the sample, damaging the device. Gating fields are therefore limited by hBN’s dielectric strength. While the dielectric properties of hBN have been studied previously, the preparation of those samples differed from that used in practice. I conducted an experiment with the help of my advisors to understand how hBN’s dielectric breakdown characteristics depend on sample thickness and temperature. I began by fabricating three hBN devices, each containing multiple regions of different thicknesses. By measuring the current and varying the voltage on a given region, I was able to locally probe the hBN’s electric breakdown characteristics with thicknesses ranging from 5 to 24 nm. I tested each device multiple times using a cryostat at a range of temperatures from 4 to 300 K. During initial measurements, I observed an increase in the breakdown voltage with temperature in hBN between 15 and 24 nm thick, conflicting with previous reports. I repeated these measurements with a finer resolution which yielded the same result. The thinnest hBN regions showed no temperature dependence, confirming the absence of systematic temperature effects. I am currently fabricating more devices to reproduce this temperature dependence and working with my advisors to find a theoretical basis for this observation. Understanding how thickness and temperature effect hBN’s dielectric strength will allow researchers to construct more resilient devices, facilitating the study of 2D materials at higher electric fields. Moreover, the study of defects in hBN remains an active subject of research for quantum information applications, and a probe of the capacitive properties of hBN may shed light on this topic.

Adoptive T cell therapy is a promising therapeutic strategy for the treatment of many hematologic malignancies, however, its efficacy in solid tumors poses several challenges. Some of these challenges include the limited infiltration and activation of cytotoxic T cells due to the effects of a diverse immunosuppressive environment within the solid tumor. One of the main suppressive immune cells present in several solid tumors are regulatory T cells (Tregs) and high numbers of Tregs within the solid tumor have been correlated with poor prognosis. Therefore, there is a clinical need to develop strategies targeting the suppressive immune cells that limit the efficacy of adoptive T cell therapy. Tumors have highly dysregulated metabolism, which results in the secretion of multiple metabolites into the extracellular space. This allows a buildup within the tumor microenvironment, which may have an effect on the infiltrating immune cells. Our group has identified one metabolite, succinate, that enhances Treg numbers within the tumor microenvironment. Here we further explored the effect of succinate on the function of Tregs. To examine this, we identified tumor cell lines that produce succinate (lung and melanoma) and further altered these to modify the levels of succinate secreted by these cells. We then co-cultured high succinate secreting tumor lines with healthy donor CD4+ T cells that were isolated from PBMCs. We screened these cells and found that the higher levels of succinate resulted in higher numbers of Tregs and increased anti-inflammatory function, as evidenced by TGFb levels in Tregs. Future experiments will validate these findings in in vivo mouse models with the aim of developing synergistic approaches to enhance adoptive T cell therapy.

My project involves making new tools for the genetic manipulation of Staphylococcus aureus. S. aureus is an important and pervasive human pathogen, however, much is still not known about its pathogenesis pathway and virulence genes. To better understand the genes and mutations that make S. aureus successful at causing disease, it is necessary to induce specific genetic changes and assess their impact on the organism’s virulence. However, currently available tools for bacterial genome engineering have yet to be optimized for S. aureus. Building on a successful recombineering system, previously developed by the Salipante lab, that is able to edit the S. aureus genome, we aim to address this need by using a dominant negative mutant protein of the mismatch repair (MMR) system to achieve suppression of DNA repair. Recombineering is the process of incorporating mutagenic DNA molecules into a host genome through the recombinase enzymes. Dominant negative mutations in the highly conserved MutL protein have been shown to disrupt the DNA base MMR pathway in several other microorganisms but have not yet been evaluated in S. aureus. My project aims to construct a temperature sensitive vector that highly expresses a ssDNA recombinase that is active in S. aureus along with a dominant negative mutL mutant able to bypass the MMR pathway. We anticipate that WT mutL should be able to repair a single base mutation since it has a functional MMR, reducing the number of successful recombinants relative to experiments performed with the multiple base pair mutations. The dominant negative mutL strains should not be able to correct a single base pair mutation, resulting in a similar number of drug-resistant transformats when recombineering with either a single base pair or many base pair mutations. This will allow us to better generate custom mutant strains and subsequently test the functions of various S. aureus genes towards a variety of clinically relevant phenotypes.

The main objective of HIV treatment is reducing mortality and morbidity for people living with HIV and preventing new infections. Accessing and maintaining chronic HIV care is critical for patient wellness and preventing new infections. A normal and healthy quality of life with a reduced chance of transmission can be achieved by maintaining a clinically undetectable viral load, which is directly dependent on regular medical appointments with a primary care provider and adherence to antiretroviral therapy. For patients experiencing significant socioeconomic barriers, maintaining an undetectable viral load is difficult. To help overcome these barriers, our clinic provides patients with higher needs interventions to help them regularly attend medical appointments and obtain medications. This descriptive study examines the effectiveness of offering low threshold healthcare by examining viral loads, socioeconomic factors, and experiences of a group of 100 patients with varying levels of need who are receiving treatment at the MAX clinic in Tacoma, WA since August of 2021. We selected consenting participants who met eligibility by being currently enrolled with a detectable viral load within a year of the study start date. One group, designated as having lower levels of need, consists of those with a history of adhering to care and with no significant socioeconomic or circumstantial barriers for accessing treatment. The second group consists of those with higher needs who have a history of non-adherence to care due to socioeconomic factors, substance use, or circumstantial crisis. We are collecting quantitative and qualitative data from regular HIV test results and interviews conducted every six months. Interviews focus on participants’ experiences with HIV healthcare, situational developments, and patient-centered outcomes. Preliminary results of this study support a low-barrier care model contributes to undetectable viral loads by helping patients with higher needs regularly attend medical appointments and adhere to antiretroviral therapy.

Deep mutational scanning is a method to analyze the phenotypic effects of thousands to millions of single mutations in parallel. I will use this approach to perform a scan of the yeast GAL4 gene within the fruit fly Drosophila melanogaster. Scoring the functional effects of mutated GAL4 in D. melanogaster will demonstrate the feasibility of using deep mutational scanning in multicellular organisms; so far, it has been used only in single-cell organisms. Gal4 protein is a transcription factor that binds to its Upstream Activating Sequence (UAS), which I am using to drive the expression of Green Fluorescent Protein (GFP). I will measure the functional effects of single missense mutations in GAL4 by crossing flies containing GAL4 variants with a fly reporter line containing five tandem repeats of UAS upstream of the GFP gene. Thus, I can measure the functional effects of mutations in GAL4 by measuring the intensity of green fluorescence of the resulting fruit fly embryos. A previous deep mutational scan of GAL4 in yeast provides a baseline expectation for the effects of different GAL4 variants. I expect the results I obtain in the fly system will be similar to those from the yeast system; obtaining similar results would validate the potential for mutational scanning in flies. Demonstrating the feasibility of deep mutational scanning in fruit flies will allow future studies to use mutational scanning techniques to study complex phenotypes, including behavioral, developmental, and tissue-specific phenotypes in high-throughput.

Syphilis is a sexually transmitted infection (STI) that is caused by the bacterium Treponema pallidum. STIs within the U.S. remain at a concerning all-time high, with syphilis incidence increasing by 52% since 2016. Syphilis remains endemic in many low- and middle-income regions such as sub-Saharan Africa. A vaccine that’s able to provide complete protection would be an important solution in controlling this infection. To date, there has been a single study producing complete protection that was conducted by immunizing rabbits a total of 60 times, which is impractical in humans patients, but proves that protection can be achieved through immunization. Partial protection has been achieved using recombinant proteins, a method that in our laboratory allowed the identification of possible protective epitopes on T. pallidum specific antigens. Though a vaccine design able to elicit complete protection remains elusive, a chimeric mRNA-based vaccine could breathe new life into the search. This project’s main purpose is to map the immunogenic epitopes of the Tp17 lipoprotein of the syphilis pathogen with the goal of using it as a scaffolding protein for a chimeric vaccine. To this end, we have broken down the Tp17 protein into 23 20-mer peptides overlapping by 10 amino acids and used infected rabbit sera to test and identify the regions of the protein that elicit the most robust humoral response using enzyme-linked immunosorbent assays (ELISA). Preliminary data has shown that the hypothesized external loops in the structure of Tp17 are the regions of highest immunoreactivity. These reactive epitopes were mapped onto the determined Tp17 structure to create a hierarchy of regions that could be replaced with B-cell epitopes protective against syphilis that our lab has previously identified with the future goal to create and test a chimeric mRNA vaccine.

Fire is a fundamental disturbance that drives changes in biome structure. Knowledge of ancient fire regimes may help predict future fire regimes resulting from anthropogenic climate change. Charcoal morphometry (quantified shape of charcoal), particularly charcoal aspect ratio (length:width), is an emerging proxy of ancient fuel type wherein higher mean aspect ratios are associated with grassy fuels. This study aims to experimentally validate this proxy method. Thirty-four modern plant species were sampled from UW Herbarium collections, separating leaf, stem, and reproductive body tissues for each species. Each sample was burned at 500°C for 20 minutes, crushed in a water slurry, and imaged under a binocular microscope. Charcoal particles were enumerated and morphometrics were measured using ImageJ with charcoal particles 125-250 μm and >250 μm analyzed separately to account for differences due to differential particle breakage. Strong evidence was found in the 125-250 μm size fraction through an analysis of variance test (F = 2.66, p = 0.03), that aspect ratio varies as a function of taxonomic group. The strongest evidence for a difference in aspect ratio is found, through Tukey's Honestly Significant Differences to be between graminoid and conifer charcoal (p = 0.03). Evidence is even stronger for a taxonomic effect on aspect ratio in the >250 μm size fraction (F = 3.64, p= 0.007). This variation seems to also be driven by a difference between graminoid and conifer charcoal (p = 0.002), corroborating earlier findings. Future validation of this methodology will be focused on the potential effects of burn temperature and charcoal transport in charcoal morphometric records. Rigorous verification of charcoal morphometry as a proxy of fuel type will help increase confidence in paleo reconstructions of fuel type. 

Sindbis Virus (SINV) is an alphavirus that is transmitted between birds via mosquitos and causes disease in humans after spillover events. While many alphaviruses have potential to cause severe disease such as Venezuelan Equine Encephalitis Virus (VEEV), SINV is known to cause less life-threatening but still severe and debilitating chronic illness predominantly associated with fever, arthralgia, and myalgia. Given its lower morbidity, SINV often serves as a model system for infectivity and pathogenesis studies of alphaviruses. Macrophages are of particular interest for studying pathogenesis as they are important targets of alphavirus infection. Our aim is to identify viral mutations that contribute to differential replication between avirulent and virulent strains of SINV in macrophages. To test this we exchanged sequences between SINV strains Girdwood (avirulent) and AR86 (virulent) to construct reciprocal chimeras which will be tested alongside parent clones. We observed a significant difference in replication between parent AR86 and Girdwood in macrophages and predict that specific RNA structural differences contribute to this variable replication in macrophages, and we are currently mapping determinants of this phenotype. This work could improve our understanding of host-viral interactions of alphaviruses by discerning the mutations required to shift from avirulent to virulent strains which will play an important role in predicting mutations that contribute to greater pathogenicity in human infections.

Structured Interprofessional Bedside Rounds (SIBR) is a hospital communication model that was designed to facilitate collaboration on patient-centered daily plans of care. SIBR is associated with improved teamwork and communication among health professionals, leading to better patient health outcomes and satisfaction. Despite a growing body of evidence in support of SIBR, some healthcare teams find it challenging to consistently use the model and little is known about how this may impact patient satisfaction. The purpose of this study is to compare the level of satisfaction with rounds reported by patients in two ICUs and one acute care floor where SIBR has been adopted as the standard of practice but where variations in fidelity to the model persist. Data is obtained from the Study to Evaluate Associations Between Rounds, Heart Failure Care, and Patient Outcomes (STEAR-HF) through observations, questionnaires, interviews, and electronic health records. STEAR-HF is an in-progress multimethod study involving participants with a diagnosis of advanced heart failure who have been hospitalized at the University of Washington Medical Center. Participant recruitment is ongoing with more than 40 participants recruited to date. Patient satisfaction with rounds is being gathered via a 10-day post-discharge questionnaire and analyzed using descriptive statistics. In preliminary results, 92.3% of participants (n=12) reported that they agreed or strongly agreed with the statement, “I liked morning rounds in the ICU.” Meanwhile, only 57.2% of respondents (n=7) agreed or strongly agreed with the same type of statement for the acute care units (“I liked morning rounds on the acute care floor”). In parallel, rounds observations indicate higher levels of SIBR fidelity in the ICUs compared to the acute care floor. Additional research is needed to more closely compare patient satisfaction between critical care and acute care units and in relation to rounding model fidelity.

Police brutality is a pervasive and traumatic event that has large societal and individual impacts. Research shows that racism is associated with negative health outcomes: impacting living conditions, mental health, and stress levels (Paradeis et al, 2015; Williams & Monnamed, 2009; Williams & Williams-Morris, 2000). Little research exists on how emotions relate to each other during traumatic events. In our study, Black and White college students (N=165) viewed news media of police brutality or car accidents (control) with Black victims, then described their reactions through video recordings. Research assistants (RAs) qualitatively coded the videos in nine emotion categories (anger, anxious, disgust, happy, fear, relaxed, sad, approach, and avoidance). I examined the relationships between the emotions in both traumatic event conditions. In both, approach and avoidance were highly negatively correlated: brutality condition (r = -.79, p < .001) and accident condition (r = -.68, p < .001). The more approach a participant expressed, the less avoidance they expressed. This consistency between contexts might be because RAs were given mutually exclusive behavioral cues to identify those categories, placing them on a single scale continuum. In only the police brutality condition, happiness and sadness (r = -.63, p < .001), as well as approach and relaxation (r = -.59, p < .001) were moderately negatively correlated. These sets of emotions are also often categorized and displayed as opposite emotions with opposing behavioral cues. The difference in correlations between the two conditions may be due to differences in media coverage across the two incident types and the differential levels of political and racial divisiveness regarding the topics. Future research should focus on replication and in more diverse contexts. If emotions can predict when another will be displayed or not displayed, health care teams can better respond to traumatic events and better assist exposed individuals.

In the 400 million years since they first emerged on land, plants have acquired numerous adaptations to the terrestrial environment. One of these adaptations is modification of the photosynthetic pathway, from C3 to C4. The C3 pathway, the ancestral form of photosynthesis found in most plants, has limited efficiency under high temperatures and light intensities, whereas the C4 pathway offers improved productivity. C4 photosynthesis has evolved numerous times in flowering plants in the last 66 million years, with C4 grasses being the most diverse and ecologically dominant. Despite their current importance, we still do not understand exactly when and where the evolution of C4 photosynthesis in grasses occurred because the fossil record of grasses is sparse. Phytoliths (hardened silica structures precipitated within plant cells) offer a novel tool for tracking C4 evolution. We will use phytoliths as a comparative tool to examine morphological changes associated with C4 evolution. All C4 grasses are contained within the PACMAD (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae) clade of grasses. Panicoideae, one of the largest and most diverse subfamilies within PACMAD, containing both C3 and C4 species, is an ideal group to study the ecological and evolutionary factors that drive the distribution of C4 photosynthesis. Through analysis of phytolith morphology, as well as overall density and distribution of phytoliths within leaf tissue using leaf clearings, we will examine a broad sampling of Panicoideae, looking for common trends amongst C4 photosynthesizing groups as compared to their C3 counterparts. To extend the scope of these conclusions beyond Panicoideae, we will seek to confirm these trends by comparison to Aristidoideae, another clade that evolved C4 photosynthesis. Preliminary data indicate that the majority of phytolith morphotypes will be bilobates, crenates, and rondels. We expect these results to correspond between observed leaf clearings and the 3D models.

Schizophrenia is highly heritable and has been associated with many brain structure abnormalities, including significant differences in cortical thickness, surface area, and gray matter volume. It is widely believed that abnormalities in early neurodevelopmental processes contribute to the differences in brain structure observed, and many genetic risk variants associated with schizophrenia influence brain development. Further research is required to understand whether genetic mechanisms underlie the typical pattern of cortical thickness and surface area deficits in schizophrenia or deviations from normal trajectories of cortical thickness and surface area development. Using data collected from 406 participants, including 246 individuals with schizophrenia, 70 unaffected relatives of schizophrenia patients, and 90 healthy controls, the current study will test for associations between polygenic risk for schizophrenia and expected brain measures of cortical thickness and surface area using a Regional Vulnerability Index (RVI) which quantifies the resemblance between an individual’s brain scan to expected brain deficit patterns in people with schizophrenia. Along with that, we will be testing for associations between polygenic risk for schizophrenia and the typical development of cortical thickness and surface area using centile scores which benchmark an individual’s neuroanatomical measurement in the context of the normative age and sex-related trajectories. We hypothesize that polygenic risk for schizophrenia will be positively associated with cortical thickness and surface area RVIs and centile scores for cortical thickness and surface area across all diagnostic groups. Understanding the relationship between genetic risk for schizophrenia and alterations in brain structure and development may facilitate early detection of schizophrenia and aid future efforts to prevent the onset of psychosis in vulnerable individuals.

Since FPGAs (Field-programmable gate arrays) can achieve specific tasks faster and consume less power than general CPUs or GPUs, converting machine learning models to FPGAs has become more popular nowadays. However, people cannot directly deploy a floating-point model onto an FPGA due to resource limits (DSP, BRAM, etc.) on FPGAs. To solve this problem, some processes need to be done to shrink the models' size. Quantization is one method to reduce the models' size by rounding the floating-point calculations into a lower-bit representation. How to quantize a model without losing precision has become an interesting area of study. Our presentation focuses on configuring Qkeras (a tool designed to quantize TensorFlow Keras models) and hls4ml (a package designed to generate equivalent Verilog code based on the original model) to quantize CNN and RNN models before deploying them onto FPGAs. Our results will show that in the hls4ml process, if we quantize the Keras model into a Qkeras model before converting it into an hls model, we will need fewer bits compared to directly converting a Keras model into an hls model. In general, by studying the quantization of machine learning models, we can deploy more powerful AI into hardware such as FPGAs. The need for AI in everyday life has increased significantly, and this is a possible way to deploy AI in small items such as cameras, televisions, or even furniture.

The Janus kinase (JAK) and signal transducer and activator of transcription (STAT) pathway is a crucial regulator of immune responses including tumor and antitumor activities in the human body. Mutations in the JAK-STAT pathway are associated with cancer development. In particular, the JAK2^V617F mutation, a common mutation of the JAK2 protein, has been linked to an increased risk of early death among myeloproliferative cancer patients. Despite this association, much is still unknown about the consequences of this hyperactive JAK-STAT pathway in cancer. The purpose of my project is to gain a clearer understanding of the role of JAK2^V617F in cancer development using the degradation tag (dTAG) system. The dTAG system harnesses the cell’s protein degradation machinery to degrade proteins fused with an FKBP12^F36V tag. After expressing JAK2^V617F in-frame with an FKBP12^F36V-tag (JAK2^V617F-FKBP12^F36V), dTAG molecules can bind to FKBP12^F36V and recruit an E3 ligase complex to induce ubiquitination and proteasomal degradation of JAK2^V617F-FKBP12^F36V. We hypothesize that degrading JAK2^V617F will decrease the activity of downstream pathways that lead to myeloproliferative cancer. To create a system to degrade JAK2^V617F, I first used Gateway cloning to generate a lentiviral plasmid that expresses JAK2^V617F-FKBP12^F36V. I then made lentiviruses with JAK2^V617F-FKBP12^F36V in 293FT cells for delivery into human cells. To express JAK2^V617F-FKBP12^F36V, I transduced human erythroleukemia (HEL) cells with the virus and monitored expression using Western blotting. Once successfully expressed, I will evaluate the degradation of JAK2^V617F-FKBP12^F36V upon treatment with dTAG molecules in a dose-response at various time points. I expect to see lower levels of JAK2^V617F-FKBP12^F36V compared to untagged JAK2^V617F. The ability to selectively degrade JAK2^V617F allows us to uncover the aberrantly activated JAK-STAT pathway’s roles in cancer development. Importantly, this research contributes to future drug discovery by determining whether developing small molecule degraders of JAK2^V617F is a promising therapeutic strategy for myeloproliferative cancer.

Past research found racial diversity in the workplace can increase equity (e.g. Edelman et al., 2001), but could proximity to diversity make White leaders less likely to be held accountable for bias? I conducted two studies examining how having racial diversity near, but not within, the work team may influence people’s perceptions of workplace equity. In Study 1, participants recruited through Prolific (N = 252) rated how equitable they think a White leader would be in two conditions: one where all other leaders are White and one where the other leaders are racially diverse. Participants were informed that the White leader works entirely independently from the other leaders. Results show that participants rated the leader as more equitable in the diverse condition as compared to the all-White condition. Study 2 examines whether proximity to diversity could shield White leaders from accountability in an ambiguous situation where racial bias may have played a role. Results show that participants (N = 234) rated the leader's decision as less likely to be driven by racial bias in the diverse leadership (vs. all-White) condition. Mediation analysis shows that perceiving the leader as more equitable in the diverse leadership condition helps explain the present effect. Implication suggests that people may be less sensitive to detecting bias in diverse environments. Future work should disaggregate the experiences of people of color, examining whether there may be differences among racial groups in how the effect operates. Individual differences may also be moderating factors for the investigated effect. 

In humans, the KRAS protein normally acts as a switch to regulate cell growth. Acquisition of certain mutations result in constant activation of the protein, leading to uncontrollable cell growth. The most frequent such mutations are at the glycine-12 residue of the protein, including changes to valine (G12V). Cells with this mutation can be recognized and eliminated by T cells engineered to express an antigen-specific receptor (TCR), but posttranslational modifications, such as methylation, can interfere with the ability of such engineered T cells to recognize G12V mutant KRAS. The objective of my project is to identify and eventually disrupt mechanisms that lead to methylation of KRAS mutant antigens. I hypothesize specific enzymes are responsible for methylation of mutant KRAS. To accomplish this, I will generate CRISPR-Cas9 gene knockout libraries to screen for potentially responsible enzymes. The CRISPR library will target human genes encoding methyltransferase and demethylase enzymes. I will co-culture these CRISPR-Cas9 knockout cancer cells with T cells engineered with a TCR targeting the unmethylated KRAS mutant antigen. From the tumor cells that have survived this coculture, I will sequence genomic DNA to determine which knockouts are enriched/depleted after the co-culture. Preliminary results show certain gene knockouts are significantly enriched/depleted in co-culture compared to baseline. The sgRNAs that appear from the high-throughput knockout library most likely to be involved in the KRAS methylation pathway will be individually evaluated in additional co-culture experiments. This should allow me to assess the proliferation/susceptibility of these cancer cells in more detail. For confirmation of mechanism, I will evaluate the methylation status of the KRAS mutant antigen in cancer cells rendered susceptible. My goal is to determine the process leading to methylation of KRAS antigen and then target it to allow for more effective targeting of KRAS-driven cancers using TCR-T cell immunotherapy.

We executed an electronic conductance code, TRANSEC, on the supercomputing cluster Hyak to perform real-space atomic-scale electronic transport calculations. TRANSEC is based on the Density Functional Theory (DFT) code PARSEC, with the added capability of computing conductance in nano-scale chemical structures. We used DFT to predict the behavior of valence electrons in these structures with first-principles quantum mechanical computations. We then computed the quantum mechanical electron transmission probability through these structures in order to predict their conductance. Furthermore, the highly parallelizable nature of TRANSEC enables efficient large-scale calculations, thereby reducing computation time. We anticipate this research will result in an enhanced understanding of nano-scale devices relevant to electronics and semiconductor technology.

Chronic non-bacterial osteomyelitis (CNO) is an autoinflammatory disease that predominantly affects children. Osteoclasts are cells that carry out normal bone degradation, and their hyperactivity contributes to pathogenesis of CNO. We do not yet understand how the environment and precursor cells contribute to hyperactivity. We are examining the effects of serum on osteoclastogenesis, the differentiation of osteoclast precursors, from peripheral blood mononuclear cells (PBMCs). Serum from patients with active CNO, inactive CNO, juvenile idiopathic arthritis (JIA), and healthy control participants was collected and used at different concentrations (0.1%, 1%, 10%) to determine their respective effects on osteoclastogenesis. With IRB approval, we sorted PBMCs from ZenBio for monocytes and plated them with media, receptor activator of nuclear factor kappa-B ligand (RANKL) and macrophage colony stimulating factor (M-CSF). Cells were then incubated and media exchanged twice. Tartrate-resistant alkaline phosphatase (TRAP) was used to stain osteoclasts and DAPI was used to stain nuclei. All TRAP positive osteoclasts with three or more nuclei were counted using ImageJ. We then compared counts across serum types and concentrations to identify trends in osteoclastogenesis. Over the course of this project, we encountered issues with the TRAP stain quality and imaging. In response, we modified the procedure at various steps to normalize staining quality across all plates to facilitate the quantification of osteoclast formation. Our results thus far suggest there is a trend of increase in osteoclasts as serum concentration increases with the exception of inactive CNO serum. Given that this study is ongoing and methods are frequently improved, we expect to gain a more comprehensive view of the trends as we progress. The goal of this study is to gain a better understanding of the pathogenesis of CNO, and its results have the potential to guide treatment of CNO and future research.

Microchimerism (Mc) occurs when a small amount of genetically different cells (or DNA) is acquired from another individual. Mc is acquired naturally during pregnancy due to exchange between the mother and child and can be detected decades later. Maternal microchimerism (MMc) is when a person harbors Mc from their mother. MMc is frequently detected in healthy adults but is increased in individuals with some autoimmune diseases, including scleroderma. Few studies have investigated MMc, especially whether it changes in a woman after her own pregnancies. One study tested MMc in peripheral blood of women during the time they were pregnant and occasionally detected MMc, but not if the woman had preeclampsia. No study has addressed whether MMc prevalence and quantities change in healthy women according to the time since the woman’s own childbirths or number of childbirths. This study addresses this knowledge gap. MMc was assayed using a panel of polymorphism-specific real-time polymerase chain reaction (qPCR) assays on DNA from peripheral blood. Most assays employed human leukocyte antigens (HLA)-specific primers and fluorogenic probes targeting non-inherited, non-shared HLA sequences. Each woman and her mother were HLA typed to identify an appropriate target. In total, 142 women were tested, and 266 qPCR experiments were run. Preliminary analysis found evidence of MMc in 59 of the 266 samples and a trend of MMc prevalence being highest within the first year postpartum and ten years after childbirth. Prevalence and quantities of MMc are being analyzed in collaboration with a biostatistician. Pregnancy and childbirth are known to affect some autoimmune diseases and cancer risk. Addressing the knowledge gap about MMc according to the time since birth and the number of births in women could provide further insights about some autoimmune diseases and cancers.

Werner Syndrome is a rare autosomal recessive disorder characterized by premature aging and heightened susceptibility to cancer. The condition is caused by a loss of function in the Werner protein (WRN), a helicase that is essential for maintaining genomic stability by assisting in DNA replication and repair. While much is known about WRN's role in the cell, the mechanisms underlying the acceleration of aging in its absence remain unclear. Recent studies have suggested that aging is associated with a reduced ability to maintain heterochromatic silencing of repetitive DNA sequences in the pericentromeric regions of the genome, also known as satellite repeats. Abnormally high expression of pericentromeric satellites can have a wide range of consequences on the cell, including DNA damage and changes in global gene regulation. Moreover, DNA damage can result in the appearance of satellite DNA fragments in the cytoplasm, leading to pro-inflammatory responses. This study seeks to determine whether WRN-deficient cells transcribe higher levels of satellite RNA and have elevated levels of satellite DNA in the cytoplasm. I focus on SAT II DNA, a class of pericentromeric satellites, using a pair of human fibroblast cell lines, with or without WRN. I isolate, purify and reverse-transcribe RNA from these cells and use qPCR to quantify the levels of SAT II RNA. Additionally, I fractionate WRN-deficient and control cells into cytoplasmic and nuclear fractions, isolate their DNA, and use qPCR to quantify the levels of SAT II DNA in the cytoplasm versus the nucleus. Preliminary results suggest that WRN absence leads to increased expression of SAT II RNA in Werner-depleted cells compared to controls, which may indicate that satellite heterochromatin is not being properly maintained. These findings may impact our understanding of aging and cancer predisposition, along with the mechanisms by which heterochromatic silencing regulates gene expression and cellular function.

This study examines the impact of ease of public transport access on unemployment. Commuting is a significant barrier to work because of its time commitment, expense, and reliance on car ownership. The average commute time in the United States is increasing, rising by 10% from 2006 to 2019. This effect is especially prominent in major cities. As workers travel further to reach their jobs, suburbs far from work centers continue to grow, and affordable urban housing is becoming a rarity, public transportation ridership has seen a decline. Past studies focused on a singular city area showed significant differences in employment between those reliant on public transportation and those with automobiles. With my study I want to see if this applies on a nationwide scale. This study uses a linear regression run on the 2017 US Demographic Census data using the software RStudio for now, as more research is conducted alternate sources may be used. The impacts of variables such as race, economic health of the county, geographical differences, and immigration are isolated to determine the extent to which ease of access to public transport is a cause of unemployment. Tests run on the coefficients of the regression determine statistical significance. A second regression run on the 2020 US Demographic Census determines whether the COVID-19 pandemic had an effect. With the rise in remote workers, it is possible that the impact of ease of access is mitigated. A negative correlation between the ease of public transportation access for a county and its unemployment rate is expected. This study could shed light on another cause of unemployment and the impacts of car-reliant transportation.

As the planet progressively experiences the effects of climate change, the US government is increasingly more interested in limiting the country’s resource consumption with a focus on limiting the footprint of corporations and manufacturers. The US Department of Energy (DoE) created a national network of Industrial Assessment Centers (IAC) within colleges, including the University of Washington, to provide recommendations that will be backed by DOE matching funds to facilities. The mission of the UW IAC is to reduce the energy consumption and emissions, improve overall efficiency, and implement cutting-edge technologies in a minimum of 20 facilities across Washington state and the Pacific Northwest, annually. We hypothesize that, by giving corporations free energy audits with financial incentives and training students to be energy savvy engineers, Washington state will reduce its overall energy consumption and be a leader nationally in resource management. The main methods to my research include initializing our energy audits with companies, preparing preliminary recommendations based on the company’s industry classification, touring the facility while collecting machinery and energy data, and writing detailed DOE-accredited reports entailing the best potential savings for the facility’s overall energy reduction. To date, the UW IAC has provided 250+ recommendations and 50+ assessments to industry, saving 1.49+ TBtu of energy. We have and continue to analyze a breadth of technologies ranging from air compressors, refrigeration, HVAC, lighting, automation, motors, and overhead operations in corporations across a variety of industries including aerospace manufacturing, food production, wastewater treatment, and paper mills. The significance of this pursuit is providing corporations an incentive to reduce their environmental footprint through an increase of revenue and modernization of their practices. We ultimately strive to bring Washington state to the forefront of efficient and clean energy practices.

Regenerative medicine compromises to repair and replace cells, tissues, and organs damaged by disease or aging. To control cell fate in regenerative medicine, methods enabling irreversible and spatiotemporally controlled protein activation would be beneficial, particularly to those that could be applied for both inter- and extracellular activation. Furthermore, an ideal strategy could be applied to virtually any protein and afford rapid activation. In my work, I have sought to develop and exploit such a method through protein photochemistry; in response to mild and cytocompatibile light exposure, user-specified proteins are irreversibly assembled into their bioactive form. I have optimized the processes for hydrogel formation and modifications to increase cell viability. Results further inform that I can biochemically customize the landscape both intra- and extra-cellularly with a photoactivatable mCherry construct. Moving forward, I intend to apply this technique to activate epidermal growth factors and other proteins in multiple physiological systems. Successful protein photoactivation provides a potential, less invasive mechanism for controlling cells in the extracellular matrix for tissue engineering and regenerative medicine.

The trapping of individual ions has allowed physicists to control and observe otherwise inaccessible phenomena. Ion traps have enabled the most precise measurements of fundamental physical constants, mass spectrometry for chemical characterization, atomic clocks that would only lose a fraction of a second over the entire age of the universe, and the direct observation of many core concepts in quantum mechanics. Many crucial developments in ion traps occurred here at the University of Washington in the group of Hans Dehmelt, who shared the 1989 Nobel Prize in physics for that work. Today, techniques in ion trapping continue to be developed because trapped ions are one platform for creating qubits in quantum computers. With the growth of quantum information science in academia and industry, there is a need for inexpensive, scalable educational labs to introduce students to concepts in quantum computing. To fill this need, we developed a reproducible lab, which demonstrates key concepts in ion trapping. Our process utilized, first, a comparative approach with reference to literature and, second, iterative improvement on built components. The lab consists of two, independent quadrupole traps: a four-rod trap and a planar five-rail trap. To reduce cost and complexity, we trap charged particles with 25 µm and 50 µm diameter, rather than atomic ions. The particles are trapped in air, at atmospheric pressure. Due to the damping forces provided by this background gas, the trapped particles are easy to control. The result of our project is a lab capable of several experiments, including controlling the number of particles trapped through voltage modulation at a constant frequency, studying the phase transition between one- and two-dimensional Coulomb crystals, exploring micromotion compensation, observing two- and three-particle secular modes, and demonstrating particle shuttling along the trapping axis of the planar trap.

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 blood cancer. To study T-cell interaction with RCC cells, I utilized a three-dimensional microphysiological system to model RCC, known as RCC-on-a-chip, with RCC spheroids embedded in a 3D collagen extracellular matrix. I observed that RCC spheroids in collagen gradually migrate upwards away from the lower position where the T cells enter, resulting in suboptimal T-cell mediated killing. My hypothesis is that the migration property is intrinsic to the RCC cells/spheroids and that, by inhibiting their upward migration in the collagen, more T-cell mediated killing will be observed. I first assessed treating the spheroids with a panel of eight anti-migratory drugs. Next, I investigated coating the chip surface with polyethyleneimine/glutaraldehyde to cross-link the collagen matrix to the surface of the chip. To efficiently quantify spheroid migration, I wrote and employed novel ImageJ/FIJI macros to automate extracting the migration data from confocal Z-stack images of the RCC-on-a-chip system. Of the eight migration inhibitors tested, three (latrunculin A, blebbistatin, and AT13148) blocked the spheroids’ upward migration without killing the cells. The pre-coating technique was also successful in inhibiting their upward migration. I conclude that the upward migration of the RCC spheroids in collagen is an intrinsic property that can be inhibited using these approaches. However, despite incorporating these changes, the magnitude of T-cell mediated killing remained below our target. Consequently, I am now focusing on how to enhance the migration of T cells into the collagen and their interaction with the spheroids. These studies demonstrate how use of the RCC-on-a-chip model can facilitate the investigation of T-cell immunotherapy for RCC.

The innate immune system must have a rigorous response to many pathogens in order to successfully defend host cells against infections. During infection, inflammasome forming sensors detect pathogen-specific features which release proinflammatory cytokines such as IL-1B for immune activation. The inflammasome forming sensor NLRP1 directly detects multiple signals indicative of infection, including viral protease activity. Recently, it was shown NLRP1 is indirectly activated by bacterial toxins and UV irradiation that disrupt host protein synthesis, demonstrating it can detect environmental stimuli to cause inflammation. However, much of this activation pathway is poorly understood with only one nonpathogenic cause having been investigated. Our goal is to identify the host proteins required for NLRP1 activation and determine whether NLRP1 can broadly detect disrupted protein synthesis. We hypothesize NLRP1 detection of disruption in protein synthesis is a broad strategy to combat infection and may have an important role in causing inflammation in other diseases associated with disrupted protein synthesis, including cancer and neurodegeneration. Knockout cell lines of proteins suspected of activating NLRP1 are produced through lentiviral transduction of Cas-9, a gene editing tool which cleaves off specific nucleotides corresponding to the target gene of each protease sensor in the inflammasome activation pathway. Each cell line is confirmed to be absent of the target sensor via genotyping, and is followed by a functional assay of each knockout line which induces cellular stress targeting the activation of each cleaved protease. We predict that inflammasome activation as defined by IL-1B concentration will be significantly decreased in knockout cell lines targeting key proteases in the inflammasome signal cascade, showing that the overactivation of these proteases is sufficient for inflammasome activation. These results could provide key targets for drug discovery in the treatment of multiple diseases which cause disruption of protein synthesis, including cancer and neurodegeneration.

Youth suicide is a serious mental health and injury prevention issue that is exacerbated through access to firearms. Child Access Protection (CAP) laws are one way to address this critical issue. Previous work suggests a persuasive case for CAP law implementation in all states but is not clear on what makes them effective in the average person’s experience. To fill this gap, the research question I explored in this study is: Are the firearms used in youth suicides stored differently when there is a CAP law in place? This was done to identify if CAP laws were effective in altering storage patterns in cases where the victims are not the firearm owner. Using the National Violent Death Reporting System dataset on youths ages 8-20 who died by firearm suicide between 2003-2018, I conducted data analysis using RStudio to generate descriptive statistics for all demographics and the gun storage variables, “locked” “not-locked” and “missing”. Among all decedents, the majority identified as 88.01% male, 80.49% white, and the mean age reported was 18 (SD = 3). The analysis indicated an association between CAP laws and locked storage; however, it was not strong enough to be conclusive with only a 3.22% higher prevalence of unlocked firearms in no CAP law states. Similarly, for the loaded variable, there was a 0.43% higher prevalence of unloaded firearms in the presence of CAP laws. Although results were inconclusive, this could be due to data limitations such as having 67.59% of total cases missing storage data. Future research should be conducted to explore preventative policy and its effective implementation, including barriers such as various political factors and community norms. Although current data shows minimal impact of the effectiveness of CAP laws, this merits further study on potential policies, community-based methods, and other interventions for this urgent issue.

The extra cellular matrix (ECM) is a complex, heterogenous environment that plays an important role in cellular functions such as proliferation, signaling, movement, and differentiation. The mechanical properties of the ECM vary spatially and temporally, across and within tissues, i.e., during development and disease progression. 3D biomaterial platforms, such as hydrogels – water-swollen polymeric networks—provide a greater understanding of matrix-cell interactions and can be used to study drug delivery and basic disease mechanisms. My research works to create a double network (DN) hydrogel system that allows for spatial control of ECM mechanics in 3D. Our system contains two different polymer networks, one of which uses light polymerization. I have optimized concentrations of multiple gel components and gel light exposure conditions to allow for accurately patterned stiffnesses within the gels. Currently, I am encapsulating live cells to study the amount of cell spreading and movement in the stiff and soft regions of the gels over the course of a week. I then fix, stain, and image each gel to quantify relative cellular spreading. Additionally, I have synthesized multiple components necessary for gel formation, cultured enzyme producing bacteria to degrade formed gels, and performed western blotting to analyze cellular protein concentrations. Imaging results have shown the DNs and the patterning process are cytocompatible. Current experiments have shown differences in fibroblast spreading between stiff and soft regions; future results are expected to show differences in protein expression within mechanosensitive pathways between patterning conditions. Using multiple, intertwined hydrogel networks, I have engineered a dynamic, heterogenous model of the ECM, enabling me to study cellular responses to mechanical stimuli. Accurate modeling of the ECM will allow for a better understanding of how diseases such as breast cancer progress based on differences in environmental stiffness and provide an in vitro platform for future cellular response research.

The prevalence of diabetes has increased dramatically and affects at least 285 million people worldwide. Diabetes is expected to increase to 438 million over the next eight years. Insulin resistance (IR) is a mechanism involved in the development of Type II Diabetes Mellitus (T2DM) that often appears years before diagnosis. The evaluation of IR holds the promise of earlier identification and mitigation of diabetes risk. Acanthosis nigricans (AN) is an early indicator of IR, marked by the velvety thickening and darkening of the skin in areas including the neck, armpits, knuckles, elbows, and knees. In a prior study, Burke et al. (1999) developed a rating system whereby clinicians rate the presence and severity of AN. In the current study, this system was modified to expand its use to non-clinicians working in research and other non-clinical settings. Specifically, in a convenience sample of 43 mother-child dyads recruited from a larger study, a protocol was devised in which photographs of specific views of the neck were taken for later visual inspection and rating by three trained raters. Ratings were then examined in relation to cardiometabolic risk factors. Results showed body mass index (BMI) and BMI percentile were significantly higher among mothers and children, respectively, who exhibited AN (vs. AN absent) (all ps<.01). Glycosylated hemoglobin A1c did not differ between groups. The development, implementation, and testing of this modified AN rating system is a preliminary step in the creation of an alternative approach to the assessment of AN. It can be implemented without clinical expertise, does not require physical contact, and can be used retrospectively. This tool may be useful to researchers, and public health practitioners, making the early identification of IR and other prediabetic conditions more accessible outside traditional clinical settings and increasing opportunities to enhance cardiometabolic health more broadly.

In the era of the internet, numerous individuals participate in fan communities on online social platforms to pursue their interests. Despite all members sharing genuine passions, these communities exhibit varying levels and types of engagement, with some attracting millions if not billions of active users daily, while others show little to no activity. Additionally, users tend to engage in discussions on certain topics more frequently in specific communities. This research aims to explore the reasons behind this difference by investigating the interaction between community size and openness. While previous works focus on the impact of either size or openness, this study develops hypotheses on how their interaction affects member engagement. A survey study is outlined to test these hypotheses, examining members' sense of belonging, level of hostility, and variation of opinions in four distinct communities representing different interactions between community size and openness: large and open, large and closed, small and open, and small and closed. The survey will be distributed among TFBoys fans on Sina Weibo in the Spring of 2023. The expected results will provide insights into how community size and openness interact to influence member engagement in online fan communities, offering recommendations for online social platforms to design features that promote member engagement and contribute to scholarly knowledge in Computer-Mediated Communication and Social Media Studies.

The focus of our research is on digitizing linguistic material from two understudied and endangered Brazilian Amazonian languages, Panãra and Kawaiwete. Panãra (ISO code: kre) is a Northern Jê language with about 600 speakers, and Kawaiwete (ISO code: kyz) is a Tupí-Guaraní language with about 1,000 speakers. Our project focuses on the digital archival of linguistic materials from these communities, the creation of a dictionary, and the study of the morphophonological grammar of these languages. This talk describes the process of data digitization thereby making it usable to a variety of research questions to be answered in future work. Data elicited by Professor Lapierre from field trips in 2018 and 2019 to Kawaiwete speaking communities, and from 2015 to 2019 to Panãra speaking communities forms the foundation for this project. Materials utilized for this research project include elicitation recordings and transcriptions, and field notes obtained through in-situ fieldwork. The initial stage of our research was digitizing handwritten field notes over the course of ten months so the notes could be fully searchable in an online database. We transcribed a total of 16,128 words for the Panãra notebooks and 12,860 words for the Kawaiwete notebooks. The second stage of the project, which is our current stage, is entering lexical items into FieldWorks Language Explorer (FLEx), a software that stores and analyzes lexical and grammatical information. We currently have 351 words entered into the Panãra database, and plan on entering sentences in order to analyze parts of their grammar. The work of this project responds to the lack of an effective writing system in Panãra and the trending language shift towards Portuguese in Kawaiwete. A digital dictionary will help both the creation of written materials by Panãra speakers and the preservation of the current Kawaiwete language.

The aim of the present study is to characterize the morphology of the pharyngeal airway by quantifying the volumetric features in the following four regions: naso-, velo-, and oro- pharyngeal spaces and retroglossal space. Using these volumetric features we will observe how fat composition and the volume of each region of interest play a role in obstructive sleep apnea. A fat composition in the different pharyngeal structures, including the tongue body and base, soft palate, and pharyngeal wall, were quantified as well. Eight 7-8 months old Yucatan minipigs of both genders were sedated and placed in prone to have magnetic resonance imaging (MRI) using dynamic TFE-sequence with synchronized physiological monitoring. The volumes of each region of the pharyngeal airway spaces from MRI images were acquired through anatomical segmentations (VISTA-sequence) and 3D reconstructions using Radiant-DICOM Viewer and ITK-SNAP software. The cross-sectional areas were measured separately and averaged for each region as well. The fat composition was measured using MATLAB for 3D analysis. The script digitized the DICOM image and then parsed giving a relative fat composition for each individual pixel in 3D format. The total volume for each region was computed and fat composition of the tongue base was 13.14%. These results showed that the volume of the 3D segmentations for each region of interest of the pigs with greater weight, displayed more implications within the pharyngeal airway due to the larger fat composition in comparison to pigs that were of normal weight. These results will be later used for further analysis of specific details regarding if there is a certain threshold of fat composition to the onset conditions of obstructive sleep apnea. The measurement of the fat compositions in the tongue body, soft palate, and pharyngeal wall are ongoing.These volumetric results provide the baseline for the following study on the consequences of pharyngeal morphology by the tongue base volume reduction or enlargement. The fat composition characterizes the adipose tissue distributions in the different pharyngeal structures. Together, these data will help to understand the mechanism which regulates the upper airway patency.

Cell death and the processes surrounding it are essential parts of life. Ferroptosis is a distinct type of regulated cell death characterized by increased lipid peroxidation leading to cell membrane damage. The exact mechanism of ferroptotic death is currently unknown, so research is underway to discover pathways that can modulate ferroptosis. The goal of this project is to determine how different isoforms of the ACSL gene impact ferroptosis mediated by non-conjugated and conjugated polyunsaturated fatty acids (PUFAs). ACSL4 (long-chain acyl-CoA synthetase 4) is a gene of importance in ferroptosis because it incorporates PUFAs into the cell membrane. The membrane-incorporated PUFAs can be oxidized via lipid peroxidation in the cell, leading to membrane damage and eventual cell death. It has been found that knocking out or silencing the ACSL4 gene can make cells resistant to ferroptosis. I compare how ACSL4-knockout cells react to different PUFAs, and how these PUFAs sensitize wild-type and ACSL4-knockout cells differently when treated with ferroptosis-inducing drugs. Cell viability assays are a way to measure the amount of cell death in response to a treatment. I perform these assays to create dose-response curves for different lipid and drug treatments and use flow cytometry to quantify the amount of lipid peroxidation. These assays help establish a baseline comparing the response of wild-type and ACSL4-knockout cells to different PUFAs and ferroptotic drugs. Preliminary results demonstrate greater percent viability in two different knockout cell lines compared to wild-type cells when treated with the drug RSL3 and arachidonic acid. ACSL4-knockout cells are expected to have decreased cell death if they are protected from ferroptosis. Results will demonstrate the extent to which knocking out the ACSL4 gene affects cell survival. Ultimately, ferroptosis is a process of interest due to its therapeutic potential in treating tissue damage and as a targeted cancer therapy.

 Although clinical next-generation sequencing is accepted as the gold standard for the accurate and reproducible discovery of genetic variants, using sequencing to guide clinical management is severely limited by these variants of uncertain significance (VUS). In recent years, Saturation Genome Editing technology (SGE) has emerged as a high-throughput solution to reclassify VUS. SGE has strict inclusion criteria, the main one being that only essential genes in the HAP1 cell line (~2,000 genes) are compatible with the assay. Unfortunately, this leaves 18,000+ nonessential genes incompatible with SGE. This begs the question: how do we assess variants in these nonessential genes? This project aims to develop a next-generation SGE method using the principle of synthetic lethality, the genetic interaction where perturbing two co-dependent genes leads to cell death. For this pilot project, I have developed a proof-of-concept assay by searching for synthetic lethal partners of the nonessential gene STK11, a tumor suppressor implicated in cancer with thousands of VUS. I have designed a genome-wide dual combinatorial CRISPR screen, where genes are perturbed in pairs to report if they induce cell death when disrupted together. The results of this experiment will be a comprehensive landscape of STK11’s synthetic lethal interactors. Identifying co-dependent lethal partners of STK11 will further allow STK11 to mimic an essential gene through engineering knockout cell lines of its lethal partners, therefore making it amenable as an SGE target for multiplexed functional reclassification of STK11 VUS. If successful, this method can be generalized to any nonessential gene with synthetic lethal interactors in HAP1 cells. This will expand the potential gene targets for SGE and eventual VUS reclassification in order to prevent, diagnose, and manage clinical care for individuals with genetic diseases.

Microtubules are dynamic polymers of 𝛼- and 𝛽-tubulin subunits instrumental in the organization and division of chromosomes during mitosis. There is an intrinsic structural polarity to microtubules due to the orientation of 𝛼𝛽 heterodimers in the microtubule lattice, so that there is a fast growing plus end and a slower growing minus end. Kinetochores are protein complexes that assemble on chromosome centromeres and attach to microtubules. Proper chromosome segregation relies on kinetochore attachment to the plus ends of microtubules. Kinetochores are thought to initially bind the microtubule lattice and plus end attachments are then achieved by the action of plus end directed motor proteins or microtubule disassembly. While the plus end attachment is essential for mitotic fidelity, it remains unknown if the kinetochores themselves have an intrinsic polarity preference. Using total internal reflectance fluorescence microscopy, we have found that individual kinetochores assembled on centromeric DNA have a strong preference for binding the plus ends of stabilized microtubules in the absence of motor proteins and ATP or microtubule dynamics. Furthermore, using optical trapping we are able to measure the rupture forces of kinetochores on both ends of microtubules and have found that the observed preference for plus ends is matched by a greater binding strength at plus end tips. These results together give insight into how kinetochores could efficiently form plus end tip attachments and how they likely play a part in cell cycle regulation by using tension to sense a correct attachment. A better understanding of the specific mechanisms of kinetochore microtubule binding is valuable for understanding control of mitotic progression and could potentially inform more targeted anti-cancer therapies that focus specifically on dividing cells without impacting regular cell function.

Previous work takes inspiration from 2D metal–organic frameworks to synthesize 0D metal–organic macrocycles which maintain the conductivity of the original material while introducing solution processability. These macrocycles self-assemble into nanotubes through π-π stacking of the aromatic core but, the nanotubes do not have a preferred orientation when imaged by atomic force microscopy (AFM). We hypothesize that by adjusting solvent, drying conditions, and organic ligand functionality we can create a preferred orientation of the macrocycle nanotubes on common substrates which will improve charge carrier mobilities through the aromatic core. This work demonstrates the formation of large domains of nanotube alignment which can lead to greater charge carrier mobility. With unique ambipolar charge carrier transport, metal–organic macrocycles have applications in energy storage, chemical sensing, and electrocatalysis.

With the sharp uptick of diagnosed depression cases since the start of COVID-19, it is likely that someone close to us suffers or has suffered from depression. The standby period when starting a new anti-depressant medication exceeds practical justification when patients must often wait two or more weeks before the efficacy of new medication can be assessed. This waiting game often leads to a loss of hope when other options have been unsuccessful. Predicting the effectiveness of a new medication based on a patient’s individualized makeup is vital to the medication onboarding process. Tests based on metabolizing properties and Pharmacogenomic capabilities provide a pathway into predictive care. The ability to assay target genes while identifying subpopulations can simultaneously reduce the likelihood of potential adverse drug reactions, as well as entice pharmaceutical companies to mass-produce medication directed to those with specific mutations to prevent adverse reactions. This research consists of a literature review detailing forms of potential adverse drug reaction prediction. Methods include the use of information from various scientific articles and the recognition of connections and disconnects between sources. It’s expected that metabolizing genes will be the primary component in efficacy prediction due to drug-gene interactions. The implications of reducing the waiting period for those suffering from depression is crucial to patient well-being. As rates of depression diagnoses increase, the implementation of personalized treatment will aid in decreasing the timespan of treatment. Particular drug manufacturers will lose money if their drug is proven ineffective ahead of time for specific individuals, though patients and physicians alike will benefit from quicker treatment options. Current tests are not mainstream due to ongoing research and strict guidelines that must be followed before clinical implementation. As innovation continues, preventative and personalized medicine will be a prominent supplementation to the treatment of individuals with depression.

Management of muscle-invasive urothelial carcinoma is extremely limited with Anti-FGFR3 (Erdafitinib) being the only kinase-targeting therapy FDA-approved for treating advanced bladder cancer patients. Kinases represent an important family of proteins for drug development due to their well-characterized role in tumor growth and disease progression. Until the last decade, the process of identifying essential proteins was carried out by individually depleting their production using siRNA or shRNA knockdown. To expedite the process of discovery, we’ve applied a machine-learning model that predicts the activity of 428 kinase inhibitors and identifies the most essential kinases associated with promoting viability for five bladder cancer cell lines used in this study (COCAB1, SW780, COCAB11, UMUC5, & SCABER). This technique, known as polypharmacology, leverages the use of non-specific kinase inhibitors that target multiple individual kinases. We have validated the results of this computational method by measuring the effect on cell viability for 7 kinase inhibitors representing strong, moderate, and weak predicted impacts. Using live-cell imaging we quantified relative cell growth over 72 hours and found a positive correlation between predicted and observed effects on viability for all cell lines. The regression identified PTK5 (FRK) and VEGFR2 (KDR) as a common top essential kinase across all five cell lines. Currently, we are exploring validating the essentiality of these kinases by siRNA knockdown. Complete validation of this polypharmacology method would suggest continuing the evaluation of PTK5 and VEGFR2 as candidate novel therapeutic targets to treat advanced bladder cancer patients.

 Different languages only permit certain groups of consonants to be next to each other in speech. These groups are called clusters. In this study, we investigate clusters that aren't present in English. Some consonant clusters are more difficult to perceive than others. One theoretical explanation is that the difficulty is caused by the sonority hierarchy, which is a linguistic concept that places sounds on a relative scale, where vowels have the highest sonority and consonants have the lowest. The present study examines the relationship between the relative difficulty of these clusters and their acoustic and perceptual properties in contrast with their sonority. In our study, participants are exposed to consonant clusters through pictures of characters and objects. We present participants with four pictures on a screen and use an eye-tracking device to follow the movements of their eyes. The eye movements can be interpreted to make inferences about psychological processing. We expect to see that clusters that have poor perceptual salience will be more difficult to perceive. We analyze the data by determining the duration and sequence of each participant’s gaze at each picture, along with how far into the word’s can be identified. The findings contribute to our understanding of how people perceive and produce speech.

Stereotypes are generally harmful, regardless of the content being positive or negative. However, people may perceive certain stereotypes are more acceptable or less harmful than others. We are interested in seeing the varying degree of how people perceive the social acceptability of the stereotypes about women’s interest or ability in computer science. We hypothesize that stereotypes about women being less interested in STEM fields are more socially acceptable than stereotypes about their ability in computer science. For this purpose, we intend to conduct a survey study including 4 scales measuring how much participants, students from University of Washington, believe it is socially acceptable to assume gender stereotypes about women’s interest and ability in computer science. Data will be analyzed using a dependent t-test. We hypothesize that people believe it is less socially acceptable to talk about the stereotypes about women having less ability than being less interested in computer science. The finding may stop the adverse intuition that expressing some stereotypes are tolerated and further motivate women to express their interest in computer science as the stereotypes about their interest should be just as unacceptable as any stereotypes regarding their ability. Future work could develop interventions to spread the awareness that having either types of stereotypes about women on computer science topics, no matter woman’s interest or ability, should be considered harmful.

Nowadays, Diversity, Equity, and Inclusion (DEI) have become buzzwords for many companies. However, some companies promote DEI just for its financial outcome and reputation rather than aiming to establish an inclusive work environment for minority groups. This study defines and differentiates between superficial and authentic diversity in the workplace, specifically gender and racial diversity in the US management consulting industry. I focus on consulting because DEI-related studies were rarely done in this field. Additionally, consulting is a newly-emergent and high-paying industry where if inequality exists and is overlooked, it will influence other businesses for the worse. The research purpose is to validate the thesis that superficial diversity is currently appearing in consulting companies and investigate what factors will contribute to superficial and authentic diversity respectively. Research findings will be based on interviews conducted with consultants coming from different racial and gender backgrounds. Interviews will be recorded, transcribed, and qualitatively analyzed through the thematic method to identify a pattern of what particular behaviors or actions will lead to superficial and authentic diversity across a chain of recruitments, promotions, and retentions. The expected result will tease out the underlying logic that could promote impactful DEI culture and generate practical suggestions based on this insight. Along this line, the research findings will help employees differentiate between superficial and authentic diversity and allow employers to recognize what type of DEI they are committing to so that they can avoid self-deception regarding DEI initiatives. By uncovering the nuances between superficial and authentic diversity, we can make transparent which company is pursuing authentic DEI for a higher level of social equity and which company is just conducting lip service for its own interest. Ultimately, this study intends to reduce racial and gender inequity in the US consulting industry and the entire workplace accordingly.

The mammalian immune system can mount distinct responses depending on the type of pathogen. In the intestine, infections with large parasites trigger a “type 2” immune response. This culminates in fluid secretion into the lumen and increased smooth muscle contractility that pushes the pathogen, intestinal parasites, through the digestive tract and out of the body. Epithelial tuft cells detect worms through their brush-like microvilli projecting from the cells into the lumen and express specific receptors that detect parasites. Once a worm is detected, tuft cells produce IL-25. Binding of IL-25 to receptors on ILC2s causes intestinal ILC2s to proliferate and secrete key cytokines that bind to receptors on intestinal epithelial stem cells and cause a remodeling of the intestinal epithelium. While tuft cells have previously only been associated with parasitic infection, a significant expansion of tuft cells was also found in the distal small intestine of tumor-bearing APC-min mice. In colorectal tumors, IL-25 was found to promote intratumoral ILC2s and suppress anti-tumor immunity, which led to increased tumorigenesis. We used immunofluorescence microscopy to visualize and quantify Flare25, a reporter of Il25 transcription, in tumors and healthy tissue of APC-min mice. The role of IL25 is therefore important to understand, however antibodies for IL25 have failed to detect the protein, so finding another way to visualize it would help determine the role IL25 has in the “weep & sweep” and tumorigenesis pathways. Here we used CRISPR to insert DNA encoding a hemagglutinin (HA) tag at the N-terminal of the IL-25 protein. The presence of the DNA insertion was confirmed through sequencing and genotyping, however we could not detect HA by immunofluorescence microscopy. These studies expand our analysis of Il25 mRNA in the small intestine, but further work is needed to understand why we could not detect HA-tagged IL-25 protein. 

Syphilis is a sexually transmitted infection (STI) caused by the bacterium Treponema pallidum subspecies pallidum (T. pallidum). Syphilis is still a global health concern, as its incidence is rising in high-income countries like the United States and it is still endemic in low-income countries, where it causes significant mortality due to congenital transmission. Our chances at syphilis control would improve if a vaccine against syphilis was available. The past century of research has only yielded experimental vaccines able to produce partial protection, but the use of new techniques could improve this outcome. One possibility would be to use an array of known protective epitopes from other T. pallidum antigens crafted onto a protein carrier to induce a protective immune response. Currently, we are investigating the use of the Tp17 protein of T. pallidum as a scaffolding for a future vaccine. The Tp17 protein has a β-barrel structure with loops around the edges of the barrel. To use this protein as a scaffolding for a vaccine, we will be performing epitope mapping to determine the hierarchy of immunodominant epitopes in Tp17 to find the ideal candidate regions that will be substituted with other epitopes. We are using Enzyme-Linked Immunosorbent Assay (ELISA) to attain these data in combination with human sera to define the reactivity of the different peptides. The results will determine the most immunogenic peptides, thus indicating the ideal areas to be replaced by protective epitopes in a potential vaccine. We anticipate that several of the most reactive peptides will correspond to the protein loops outside of the β-barrel, which should be easily replaceable without affecting Tp17 structure.

Trapped ions are one of the promising candidates for an operating quantum computer. Ions trapped in an electromagnetic trapp serve as a physical qubit, where the qubit states are manipulated by applying lasers to the system. As quantum computers use quantum gates with a given precise angle of rotation of the qubit state within the Bloch sphere, applying a laser with very narrow bandwidth is essential for minimizing errors, and thus stabilization of laser frequency is a required process for trapped ion qubit control. In our project, we stabilize the 1762 nm InfraRed fiber laser by using an optical cavity lock, where we obtain the resonant frequency of the cavity by measuring the intensity of the laser across the Fabry-Perot cavity, while varying the laser frequency. However, this model cannot distinguish between the laser intensity noise and the laser frequency noise. To address this, we eliminate the intensity noise by analyzing the signal reflected back from the cavity, where we observed a frequency dependent signal which reaches zero at resonance, allowing us to stabilize the laser to the desired frequency. A deeper understanding of the laser stabilization techniques may help us to minimize the trapped ion qubit control errors.

Atrial fibrillation (AFib) is the most common sustained cardiac arrhythmia, contributing to significant morbidity and mortality worldwide. Patient-specific computational models of the left atrium are currently studied to predict characteristics of reentrant activity that promotes fibrillation. However, current models’ patient-specificity is limited to anatomical structure and the distribution of disease-related remodeling (fibrosis), whereas electrical properties of cells and tissue are based on literature values. In cases where patients are clinically known to present with either AFib or atrial flutter (AFl), this lack of personalization can lead to inaccuracies in simulation outcomes (e.g., AFib-like behavior in simulations for a patient who actually had AFl, or vice-versa). My goal was to derive parameter sets that favor the initiation of one type of arrhythmia or the other (AFib or AFl). Ten fibrotic left atria were reconstructed from late-gadolinium enhanced (LGE)-MRI scans and the bioelectric parameter space (comprising ion channel expression levels and impulse propagation rates) was explored using a Taguchi L27 Design of Experiments (DoE) approach. Arrhythmias were induced by initializing four atrial regions to different phases of the action potential under each parameter permutation. I ran 300 simulations and manually classified each arrhythmia episode as either AFib- or AFl-like based on prior definitions. I pinpointed a pro-AFl parameter set – bioelectrical conditions under which 89% of all induced arrhythmias were AFl and only 11% were AFib. The pro-AFib parameter set in these preliminary simulations was comparatively less robust (61% vs. 39% for AFib vs. AFl inductions, respectively). My future work on this project will establish stronger relationships between model configurations and simulation outcomes by probing a wider array of possible parameters in a larger population of patient-specific models. Data from the present study will guide future simulations to accurately tailor models to represent the arrhythmic state in patients predisposed to AFl.

The increasing availability of both prescription and illicit opioids has caused substance use disorders to skyrocket. Treatment options such as therapeutics that can inactivate Kappa opioid receptors (KOR) have been shown to reduce drug-seeking behavior through the modulation of intracellular signaling pathways. Downstream KOR activation, G-protein coupled receptor kinase 3 (GRK3)/arrestin-dependent pathway leads to activation of p38 mitogen-activated protein kinase (p38 MAPK) and feelings of dysphoria. In another pathway downstream of KOR receptor activation, a G-protein mediated response and activation of cJun kinase (JNK) leads to the generation of reactive oxygen species (ROS). Selective activation by biased ligands of the JNK mediated pathway result in the release of ROS, which leads to the eventual depalmitoylation of the G-αi/o subunit of the KOR. This results in the long-term inactivation of KOR, which is predicted to improve stress resilience and to prevent drug-seeking behavior. Drugs such as Nalfurafine and Nalmefene can selectively activate KOR such that ROS is produced. Using 2-photon microscopy to detect fluorescence that indicates the release of ROS by Nalmefene and Nalfurafine into the ventral tegmental area of transgenic mice, I can better understand the potential of these drugs for long-term inactivation of KOR. I have observed under a light microscope that when Nalfurafine was washed onto slice, an increase in ROS was observed. Nalmefene showed a similar trend to Nalfurafine but increased ROS to a lesser extent. Additionally, when either Nalfurafine or Nalmefene were added to a solution of naloxone, there was no significant increase in ROS. Using the data collected from slice and behavioral assays such as the tail-flick test, we can illustrate the positive therapeutic effects that KOR inactivators can have on substance use disorders in the long term.

Endophytes are microbes that reside within plants, forming a mutualistic relationship where they improve host physiology in exchange for plant carbohydrates. Inoculating plants with a cultivated consortia of endophytes originally isolated from trees in plant family Salicaceae is proposed as a sustainable strategy for increasing crop yield, plant health, and climate change resilience. However, this plant-microbe relationship may turn parasitic if endophytes become over abundant and their carbohydrate demand exceeds the plant’s capacity. Inoculation method is an important yet underexplored factor in predicting the outcome of this relationship and endophyte colonization success. This study investigates how inoculation methods influence the number of endophytes that colonize different plant tissues. A consortium of Salicaceae endophytes was introduced into hybrid poplar plants grown in sand through different inoculation methods. The methods tested are (1) no inoculation, (2) a pre-planting root soak inoculation, (3) a pre-planting unrooted stem soak inoculation, and (4) a post-planting media soak inoculation. After growth, endophyte density and distribution will be estimated by separately culturing endophytes isolated from leaf, stem, and root tissues and counting their colony forming units per gram. The carbon cost of hosting endophytes will be estimated through in vitro and in planta respiration measurements from the sampled tissue. Epidermal wounding from shoot cutting in the stem-soak inoculation method may increase the amount of entry sites for endophyte colonization. Therefore, it is expected that plants receiving inoculum via stem-soak will show increased endophyte distribution and density and higher respiration rates when compared with other inoculation methods. Comparisons of estimated in planta endophyte densities with plant physiological measurements will establish the relationship between endophyte abundance and host health in poplar. Further research will be needed to create a more generalized model of the effect of individual endophyte distribution and density on the benefits and costs to plant health.  

Benzalkonium Chlorides (BACs) are widely used antimicrobial disinfectants in a variety of settings, including large scale food processing and consumer environments. Persistent usage of BACs raises concerns about the potential disruption of the gastrointestinal microbiota, an increasingly recognized regulator of an individual’s health. Furthermore, the gut microbiota has been shown to regulate drug metabolizing enzymes (DMEs) and the Gut-Liver Axis is a known prominent crosstalk pathway. Previous work in our lab has found BACs are capable of altering gut microbiome composition in BAC exposed C57BL/6 male and female mice, with notable differences between the male and female sexes. Therefore, we hypothesize that exposure to the BACs can alter the composition of gut microbiota, leading to sex specific changes in bile acid homeostasis as well as the metabolic phenotype and DME expression of the liver. In this study, we exposed male and female mice to C12- and C16-BACs at 120 ug/g/day for one week via oral dosing. Additionally, through a targeted bile acid quantitation analysis, we found sex specific decreases in secondary bile acids in BAC-treated mice. This finding is supported by decreases in bacteria known to metabolize primary bile acids into secondary bile acids, such as the families of Ruminococcaceae and Lachnospiraceae. We also aim to elucidate both transcriptomic (RNA sequencing) and functional (enzyme activity assays) analyses of the harvested livers from both male and female cohorts. Upstream pathway analysis from the results of these analyses is expected to yield sex specific differences in the downregulation of genes responsible for a variety of pathways such as protein digestion and absorption and transcriptional regulation in cancer. This study is expected to provide novel insights into the sex specific alterations in the relationship between the gut microbiome and liver caused by BAC exposure and the mechanisms underlying BAC toxicity.

Variants in the genetic risk factor GBA have been shown to increase the risk of developing Parkinson’s disease (PD) and accelerate motor and cognitive decline in PD patients. To better characterize this relationship, this project investigates the mechanisms underlying the onset and exacerbation of Parkinson’s disease in patients with the genetic risk factor GBA through the use of Drosophila and human neuronal cell culture models. We use a GBA deficient Drosophila model, which exhibits symptoms of Parkinson’s disease, including neurodegeneration, motor and cognitive dysfunction, and accelerated protein aggregation. Additionally, we use induced pluripotent stem cells (iPSC) from a PD patient heterozygous for the GBA mutation. Prior work in the lab found that GBA deficiency accelerates protein aggregation, alters lipid metabolism, autophagy, and cell-to-cell propagation of pathogenic protein aggregation via extracellular vesicles (EVs). We also found that restoring wildtype GBA function in glial cells of GBA deficient flies rescues protein aggregation in the brain, leading us to hypothesize that GBA may have a neuroprotective role in glia. Because EVs are formed through the endolysosomal trafficking system, we are examining makers for endolysosomal vesicles in GBA deficient and control astrocytes. We will also observe how GBA deficient versus control astrocytes uptake and traffic neuronal EVs, and eventually test whether co-culturing wildtype astrocytes with GBA deficient neurons may reduce pathogenic protein aggregation in neurons, compared to co-culturing GBA deficient astrocytes with GBA deficient neurons, or GBA deficient astrocytes with control neurons. To perform these experiments, we will be using an automated cell culture system integrated with automated confocal microscopy to observe the survival of the cells over time before fixing and analyzing pathogenic protein aggregation in the cells by Western blot. We hope that this research helps us to better understand the mechanisms underlying the progression of Parkinson’s and explore new therapeutic targets. 

X inactivation is a mechanism of dosage compensation that equalizes gene expression between males (XY) and females (XX). It is mediated by the long non-coding RNA (lncRNA) Xist (X-inactive specific transcript). However, some genes escape X chromosome inactivation(XCI) in females, and thus potentially contribute to sex differences. Escape genes are often identified by allelic expression analysis based on RNA sequences and RNA FISH (fluorescent in situ hybridization) based on imaging. In addition, RNA FISH allows the examination of escape status and the location of the transcript in individual cells. Allelic expression analysis has shown that one X-linked gene Car5b escapes XCI in mouse cells. However, it is not clear whether it escapes XCI in every cell or a portion of the cells. The goal of this project is to use RNA FISH to detect and quantify the escape status of Car5b in wild-type cells and in cells carrying a deletion of an important DNA element required for Car5b escape. In order to achieve the goal, I first prepared the fluorescent probes using the cDNA plasmids of Car5b and Xist. Next, dual RNA FISH was performed for Car5b and Xist in mouse cells to visualize the location of Car5b RNA signals whereas Xist RNA signals serve as the marker of inactivated X chromosome. Analyzing the FISH results is ongoing and we expect to visualize Car5b escape in the wild-type cells but not in the mutated cells. This method can be applied to escape studies in other X-linked genes which could enhance our understanding of X-linked gene regulation and sex difference.

The grass family, Poaceae, dominates over 40% of land ecosystems and is found in every biome except areas covered by ice sheets. Within Poaceae are two major clades, one being the PACMAD clade, named for the six subfamilies: Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonoideae. The PACMAD clade is the only lineage of grasses that evolved C₄ photosynthesis. This derived trait allows plants to efficiently photosynthesize under low CO₂ concentrations and in hot, arid climates. Chloridoideae is the largest subfamily within the PACMAD clade with over 1,500 species across five tribes. Most Chloridoideae species use C₄ photosynthesis and it is likely that some of the first transitions from C₃ to C₄ occurred in this subfamily; however, fossil evidence for this deep history is currently lacking. Phytoliths, which are silica bodies that form in living grass tissues and can be preserved in soils for millions of years, have great potential for filling this gap. We are studying the three-dimensional shape of phytoliths from modern Chloridoideae grasses to better recognize them in the fossil record. By linking modern Chloridoid phytolith shapes to their respective climatic conditions, we will be able to create a robust reference database to be used for future research to identify past Chloridoids and their past growing environments. To do this, we are processing 3D Chloridoid phytolith models from 2D confocal microscope images to analyze and characterize the morphology, abundance, distribution, and diversity of Chloridoid phytoliths. Thus far, preliminary data suggests our findings will be especially useful in making comparisons between past and present bilobate or saddle-shaped phytoliths, though we expect to conduct further analysis on current phytolith shapes. Future studies will be able to compare our 3D modern renderings to fossil phytoliths to infer periods of climatic warming through deep time.

Edentulism, or the loss of all natural teeth, is a condition typically resulting from dental caries and periodontal disease, described as the ultimate manifestation of oral health disease burden. Edentulism has significant effects on masticatory function, such as chewing, swallowing, and speaking, as well as mental health and overall quality of life. Food insecurity has been associated with adverse oral health outcomes. However, this relationship has been insufficiently studied among low-income older adults, who are disproportionately impacted by oral health disparities and more likely to be edentulous. We hypothesized that food insecurity would be associated with increased prevalence of edentulism among low-income older adults in Washington state. To test this hypothesis, we collected data at seven community-based sites across Washington, including the Multi-Service Center in Federal Way and the Pike Market Senior Center. We administered a survey containing a 10-item measure of food insecurity to 218 participants aged 50 years or older. We also conducted dental screenings that involved examination of the mouth, gums, and individual teeth. 45% of participants (n=98) had marginal, low, or very low food security. 7.8% of participants (n=17) had zero teeth. We utilized logistic regression models to examine the association between food security and edentulism. Our preliminary analysis indicates that older adults with low or very low food security had 2.44 times the odds of being edentulous compared to those with high food security, after adjusting for age, sex, and race. Further analysis can help inform the development of feasible and effective interventions to address oral health inequities among low-income older adults.

Cancer is often a life-changing diagnosis that can be extremely difficult to navigate. Parents diagnosed with cancer face not only the burden of their disease, but also the burden of the disease on their children. In addition, previous research has shown a difference in experience for parents diagnosed with terminal cancer compared to those diagnosed with non-terminal cancer, with or without children. These families need support in communicating with their children. However, there is insufficient research about interventions that support parents' engagement in meaningful conversations about the illness. To begin providing these families with the tools they need to endure a cancer diagnosis, one must first discuss what concerns need to be addressed. The purpose of this study is to examine and contrast parent-reported concerns about the children's response to the parent's cancer for parents with early-stage cancer (stage I-III) compared to late-stage cancer (stage IV). Thirty-six mothers from a recently published clinical trial comprised the sample of parents with early-stage cancer. Parents were eligible if they had one or more dependent children five to twelve years of age and were recently diagnosed with stage I-III cancer. Parents' responses to the question "What questions do you have about what your child is thinking or feeling about the cancer?" were transcribed and inductively coded by these authors using content analysis methods adapted from grounded theory. Peer debriefing and an audit trail were established to protect the trustworthiness of results. Four of the resulting domains from parents with early-stage cancer mirrored those of parents with late-stage cancer and there were two major differences found between the two study samples. Contrasting these study results adds to our understanding of the unique or common needs for parents with early-stage versus late-stage cancer and informs future supportive interventions. 

Neonatal hypoxic-ischemic encephalopathy (HIE), caused by a lack of blood flow and oxygen to the brain, is a major cause of infant mortality. Primary and secondary energy failure caused by HIE activates microglia, resulting in morphological changes and inflammatory cascades that mediate ongoing pathology. Proinflammatory microglia release cytokines and reactive oxygen species that damage oligodendrocytes, the myelinating cells in the brain that supports neuronal function, thereby causing demyelination of neurons. Previous studies in term-equivalent in vivo ferret models showed that microglia respond to injury and treatments with region-dependent cell morphology changes. However, the effect of combinatorial therapy on microglia and oligodendrocyte in a preterm model is unknown. This project aims to quantify image-based morphological features of microglia and oligodendrocyte in response to neuroinflammation and separate and combinatorial treatments in different brain regions of an in vivo preterm ferret model. Using machine learning supported image processing, I quantified microglia and oligodendrocyte morphology in the healthy control group, injury group of two hours of oxygen-glucose deprivation, and treatment groups of azithromycin (AZ), erythropoietin (Epo), and combined AZ+Epo treatment followed by injury. The machine learning algorithm clusters microglia and oligodendrocytes into distinct shape modes with different morphological parameters, such as perimeter, circularity, and aspect ratio. Perimeter and circularity of both microglia and oligodendrocytes show regional heterogeneity within each shape mode while aspect ratio is homogeneous. Microglia perimeter decreases upon injury in crescent and rod-like shape modes. Epo treatment reverses the decrease to the level of nontreated control, but AZ+Epo treatment only partially reversed the decrease. By quantifying microglia and oligodendrocyte morphological response to neuroinflammation and treatments across regions, I non-destructively assessed therapeutic performance of separate and combinatorial treatments in the preterm ferret model. The assessed performance informs therapeutic choices for preterm populations and have the potential for translating to larger animal models.

Antiretroviral therapy (ART) prevents the progression of human immunodeficiency virus (HIV) by suppressing viral load, limiting transmission. Of the ~20 million people receiving ART, 30-40% do not maintain adequate medication adherence, resulting in treatment failure and drug resistance. Monitoring HIV medication adherence improves the efficacy of ART but requires bulky and expensive instruments that are not widely accessible at the point-of-need (e.g. doctor’s office or patient’s home), so a rapid and accessible diagnostic alternative is necessary. Our group developed the REverSe TRanscrIptase Chain Termination (RESTRICT) enzymatic assay to provide rapid and inexpensive measurement of HIV drug adherence by measuring antiretroviral drug activity indicated by fluorescence. However, one current limitation of RESTRICT is the need for trained operators to complete multiple precisely timed steps required in the enzymatic activity assay. We aim to create a 3D-printed microfluidic device that will automate the liquid handling steps required for RESTRICT via precisely tuned capillary action for rapid and user-friendly measurement of antiretroviral drugs. To that end, we first demonstrated a proof of concept by creating a microchip with a controlled 15 minute liquid delivery time and consistent liquid extraction. Through optimization of 3D-printing methods, channel geometry, and surface treatment, we created a microchip designed to deliver liquid in 14.64 minutes that ran experimentally in 19.12 ± 2.33 minutes. In the future, we will demonstrate the feasibility of RESTRICT run on-chip and fluorescence measured off-chip by testing clinically-relevant drug concentrations using the controlled liquid delivery time and liquid extraction methods developed. By creating an automated and rapidly fabricated microfluidic chip for therapeutic drug monitoring, we hope to achieve a hands-off device that removes external manipulation to increase the accessibility of RESTRICT-on-a-chip for point-of-need settings without specialized equipment or highly trained operators.

The study of social media usage has become increasingly important in today's digital age as social media has become a central aspect of many people's lives, particularly for entertainment purposes. This is particularly relevant in the context of foreign populations in the United States, as the preferences and habits of individuals from different cultures and backgrounds can provide valuable insights into the changing nature of social media usage. The aim of this research was to study the use of social media for entertainment among international students in the United States. An online survey was conducted with 27 participants around age 16 to 24 to gather data on their social media habits. The survey consisted of five questions regarding their daily use of social media for entertainment purposes. The results of the survey showed that participants spend between 2 to 6 hours daily on social media for entertainment purposes. The most widely used social media platforms among the participants were global platforms such as Instagram, YouTube, and Twitter. Interestingly, participants showed a greater preference for global English-based social media platforms over local, language-specific platforms such as WeChat, Kakao Talk, and LINE. The findings of this research provide valuable insights into the social media habits of international students in the United States. The results suggest that there is a clear preference for global English-based social media platforms. Additionally, the results also indicate the importance of considering gender differences when studying social media usage patterns. This research underscores the need for continued investigation into the changing nature of social media usage, particularly in the context of foreign populations.

The Centers for Disease Control and Prevention recognizes that heart failure (HF) is one of the most complex and expensive health conditions to treat, and affects over 6.2 million Americans. The purpose of this study is to assess health system trust among patients with a diagnosis of advanced heart failure, who were recently discharged from the University of Washington (UW) Medical Center-Montlake. We are also exploring respondent’s reports of trust in the UW ’s healthcare system compared to the general healthcare systems. Data collection for this study is ongoing. Based on the descriptive analyses of reports from 17 respondents, preliminary results suggest that respondents have greater trust in the UW’s healthcare system compared to the general healthcare system. For example, 88.2% (n=15) of respondents agreed or strongly agreed that the UW’s healthcare system provides excellent care, whereas 64.7% (n=11) agreed or strongly agreed that the general healthcare system provides excellent care. In addition, when asked whether patients, regardless of their race or ethnicity, receive equal medical treatment, 58.8% (n=10) agreed or strongly agreed that they received equal medical treatment from the UW’s healthcare system compared to only 35.2% (n=6) who agreed or strongly agreed with the same statement in the general healthcare system. Additional data collection and analysis are needed to confirm whether the findings are similar over time. Further, it is important to explore whether there are differences in responses among study participants from different demographic and socio-economic groups (e.g., race/ethnicity, age, gender, rural/urban residence, education, employment, income, and insurance status) to develop strategies to provide equal health care access in diverse populations and reduce health disparitise. 

Zoom classes or online meetings may be seen as temporary resolutions to COVID-19 restrictions. However, in the mental health field, telehealth continued to represent 20% of outpatient visits when the emergency restrictions of COVID-19 eased in late 2020 (Gentry et al., 2021). Telemental health is a form of online mental health services that can be used to deliver Evidence-Based Practice (EBP) to clients without in-person meetings. Despite the strength, one major barrier to implementation of telemental health services is that some youth may be less engaged in the session (AlRasheed et al., 2022). Limited research indicates that practical organizational support such as trainings, seminars, additional funding for clients, and technology support for clients may improve client engagement, along with a positive organizational climate that promote providing telemental health services (Oetzel & Scherer, 2003). The current study expands on past research to examine the relationship between organizational support and youth engagement in telemental health services among Community Mental health providers (N= 173) who participated in a Washington State-funded EBP training initiative (CBT+). As a part of CBT+, the providers attended a Cognitive Behavioral Therapy for youth training and follow up support and completed self-report surveys. Using survey questions regarding organizational support and youth engagement, we conducted 12 linear models to examine the relationship between organizational climate and practical organizational support with six measures of youth engagement. Results indicated that a positive organizational climate is associated with greater perceived effectiveness of therapy (β = .39, p = .000). The finding suggests that, when perceived effectiveness is low, we encourage organizations to tailor strategies to improve organizational climate for telemental health services, even after COVID-19 restrictions loosen. I will present additional findings and implications regarding practical organizational support in the poster presentation.

Lacking in early emotional support has been associated with emotional dysregulation and impulsivity in adulthood. Although previous research has also demonstrated that emotion dysregulation and impulsivity are both crucial factors associated to alcohol-related problems, to our knowledge there is no study exploring the relationship between early emotional support and alcohol use in adulthood through the mechanisms of emotion dysregulation and urgency. Additionally, previous work has mostly relied on cross-sectional data. The current study aims to explore the association between early emotional support and alcohol use by assessing the role of emotion dysregulation and urgency as mediators. We use pilot data collected via cross-sectional and ecological momentary assessment (EMA) methodology. Emotion dysregulation will be assessed by the Cognitive Emotion Regulation Questionnaire (CERQ; Garnefski & Kraaij, 2001). Urgency was assessed by the averaged values of the negative and positive urgency subscales in the 59-item Impulsive Behavior Scale (UPPS-P; Whiteside & Lynam, 2001; Lynam, Smith, Whiteside, & Cyders, 2006). Early emotional support was assessed by the emotional support subscale in the Multidimensional Neglect Behavior Scale (Dubowitz et al., 2011). Alcohol use was assessed by the Daily Drinking Questionnaire (DDQ-R; Collins, Parks, & Marlatt, 1985). Longitudinal items were gathered from a subset of the above measures. For the purposes of this presentation, we plan to analyze the data using bivariate correlation analyses in preparation for a full mediation analysis in the full study. We expect to find that those lacking in emotional support during adolescence predicts both emotional dysregulation and urgency in adulthood, which leading to alcohol-related problems in adulthood. Results in the expected directions would suggest that low emotional support in adolescence may be a risk factor for substance abuse later in life, showcasing a need for caregivers to better the emotional states of their children.

Urolithin A (UA) is a metabolite produced by gut bacteria from ellagitannin and ellagic acid, which is present in pomegranates, berries, and walnuts. Previous studies have shown that UA supplementation improves skeletal muscle health in both mice and humans. UA supplementation also appears to be beneficial to the heart, resulting in both systolic and diastolic functional improvement in old mice. This study aims to determine a mechanism for the improvements in the aging heart. We hypothesize that the mechanisms behind improved heart function from UA supplementation are related to the pathways that directly improves mitochondria, contractile properties and mitophagy. To investigate the mechanism behind improved heart function with UA supplementation, we split the treatments into two staggered cohorts with 20, 24-month-old mice per cohort (10 control/10 UA treatment). Both the control and the treatment group were kept on the control diet during week 1 for acclimation. In the following 8 weeks, the UA treatment group were moved to a UA 50 mpk supplemented diet. Echocardiography measurements were done pre and post supplementation. At the end of the study, all mice were euthanized under anesthesia after an overnight fast and sample collection was performed. Heart samples were collected from each mouse. Western blots of heart samples on mitophagy, mitochondrial and cardiac contractile protein markers indicate that those pathways remain unaffected by UA supplementation. In future work, we will explore other informatory pathways in order to determine the mechanism behind UA supplementation improvement of heart function.

Increasing mental illness among college students continues to be a critical issue. College life is often a time of great transition, contributing to and potentially exacerbating students' rising stress, anxiety, and other mental struggles. Poor sleep habits may develop during college, and poor sleep quality can amplify stress. To explore how institutions might help students struggling with stress, we conducted a small pilot study examining whether a sleep-focused workshop would reduce stress levels in students at a Pacific Northwest community college. For this pilot study, I helped generate an online pre- and post-workshop survey of demographic questions, the UCLA Loneliness Scale, and the Perceived Stress Scale (PSS). Our results indicated that participants' workshop attendance reduced their stress levels. Before the sleep workshop, participants scored an average of 20.27 (SD=7.41, range=2 to 30) on the PSS, while two weeks after the workshop, the average PSS score had reduced to 16.58 (SD=7.65, range=4 to 27). These results suggest benefits of a sleep-focused wellness workshop for college students. In our present study, we replicated the pilot study. I examined student stress in correlation to sleep quality and assessed these factors through an online survey of demographic questions, sleep quality questions, the Beck Anxiety Inventory, and the PSS. We distributed this survey to participants before and after a sleep workshop run by the Bellevue College psychology department. I hypothesized that poor sleep quality correlates to higher student stress levels. I also hypothesized that the intervention of a sleep workshop would reduce stress levels. I hope that our results provide insight into the utility of wellness workshops for students and whether they are an avenue to help students manage stress and improve their sleep quality, which could improve student mental health by lowering stress and anxiety and improving quality of life and education overall.

Azole drug resistance in fungi is a well-established phenomenon. Previous research through the yEvo (yeast Evolution) program used Saccharomyces cerevisiae as a model organism to study how azole resistance arises using experimental evolution. By growing yeast in increasing doses of azole over time, high school students selected for yeast cells that gained favorable mutations for azole resistance. Sequencing this yeast at UW enabled us to identify specific mutations that contribute to azole resistance. We collaborated with Fred Hutch Science Education Partnership to design a lesson kit that can be checked out by local high school instructors for use in their classrooms. We selected twelve strains from our previous azole evolution experiments that contained a variety of mutations. These included missense and synonymous mutations, copy number gains, transposon insertions, and mitochondrial DNA loss. To develop this kit, I tested the experimental conditions by growing individual strains in a range of azole concentrations. From this, I chose an azole concentration that sufficiently introduces environmental pressure but still allows for strain growth. I then performed a series of competitive growth experiments to confirm replicability and test the procedure as it would be used in the kit. Using the results of my tests, I also contributed to creating the accompanying protocol and curriculum for the kit. Students will have the opportunity to make predictions through a bracket-style match-up, learning about each strain through “trading cards” that I am helping design to contain information about the mutations of each strain. In the final step of this project, I will take part in a training session to support high school instructors interested in teaching the kit. From the implementation of this kit, students will learn broadly about the effects of different types of mutations, and specifically how mutations affect anti-fungal drug resistance.

The presence of methane is known to be one of the most prevalent factors in global warming. Recently, methane has been discovered in the waters of the Pacific Northwest without a credible source. Many of these chemical plumes are scattered throughout the Puget Sound and are concentrated over geological fault lines, such as the Seattle and South Whidbey Fault, and are acting as vents for methane. So far, this release is not considered to be linked to human sources, but instead, either geological or biological sources buried deep on the seafloor. Using a variety of sensors -- sonar, concentration, temperature, depth, and audiovisual -- these plumes have been mapped out and we have received more precise methane readings based on tide, time of day, and other environmental factors. Then, we compare these readings with nearby chemical activity in wells and springs or with prior activity in the area to determine the type of source we are dealing with, either biological or geological, With the data we have gathered, we can identify how the methane bubbles being released are interacting with the phosphorus and nitrogen in the water as it rises to the surface and the rate at which methane is being pumped out. Due to the frequency of the noise that these bubbles make when popping, an accurate estimate can be made about how intense these plumes are. Additionally, knowing whether or not this phenomenon is a result of the last Ice Age will be helpful in conservation efforts as the temperature of the sea is increasing. This project does so to better understand the ocean-atmosphere interaction as it relates to methane gas.

A primary stressor of college students is financial insecurity. Research estimates that 36% of college students are food insecure, 36% lack reliable housing, and 9% experienced homelessness in 2018. Sources of financial stress for college students typically include housing, tuition and other academic expenses, credit card debt, familial responsibilities, and employment status. Furthermore, research has also shown that psychological stress correlates with decreased sleep quality. During periods of intense stress, an individual may have more frequent disturbances during sleep, sleep for fewer hours, and adopt later waking times (Galambos et al., 2013). This study investigates the relationship between financial insecurity and sleep quality of students attending a 2-year college in Washington state. More specifically, this study aims to determine the impact of a sleep wellness workshop on the sleep quality of college students. Data collection will occur through an online Qualtrics survey before and after the sleep wellness workshop. The Qualtrics survey includes modified Sleep Quality Scale questions, the Beck Anxiety Inventory (BAI), and the Perceived Stress Scale (PSS). It is hypothesized that experiencing financial insecurity will positively correlate to poorer sleep quality. It is predicted that this relationship is mediated by stress and that the sleep wellness workshop will improve sleep quality in college students. Understanding factors that contribute to poor sleep quality is vital as sleep plays a key role in maintaining proper cognitive functioning. The results of this study are intended to improve current resources, as well as implement new resources, concerning sleep quality and stress of college students.

College students are notorious for two things, chronic stress and sleep deprivation. To address this, many colleges provide wellness workshops designed to increase awareness and educate students on topics like healthy sleep habits, stress management tips, and ways to avoid burnout. But do these attempted interventions work? Are students experiencing a measurable benefit from attending? This study aims to assess if a sleep-focused wellness workshop effectively improves students' overall sleep and reduces their perceived stress levels. Results from a small initial pilot study recorded a marked improvement in students' levels of perceived stress, measured by the Perceived Stress Scale (PSS), following a sleep-focused wellness workshop. Specifically, the pilot study sample scored an average of 20.27 (n=22, SD=7.41, range=2 to 30) on the PSS before the sleep workshop and 16.58 (n=19, SD=7.65, range=4 to 27) 2 weeks after the workshop. These results suggest that there are measurable benefits to college students from attending sleep workshops. In the present study, we replicated the sleep-focused wellness workshop and measured pre, and post-workshop perceived stress, anxiety, and sleep habits using Qualtrics, an online survey platform. The online pre and post-surveys consist of 31 questions, including the Perceived Stress Scale, Beck’s Anxiety Scale, and demographic questions. This study will be administered by the Psychology Department at a mid-sized 2-year college in the Pacific Northwest. We hypothesize that learning about better sleep habits by attending the sleep-focused wellness workshops correlates with reduced feelings of perceived stress and better overall sleep quality in students. The findings of this study suggest that college students who learn about healthy sleep habits by attending workshops report a reduction in their overall stress and better-quality sleep. 

The geologic record provides opportunity to provide actual examples of how plant communities have responded to climatic changes, providing important perspective for modern anthropogenic-driven climate change. Two important climatic events in the Miocene offer such an opportunity, including a global warming event, the Miocene Climatic Optimum (MCO; 17-14 million years ago), and a global cooling event, the Middle Miocene Climatic Transition (MMCT; 14-12 million years ago). This study is assessing how the diversity and prevalence of ecological strategies within Pacific Northwest (PNW) plant communities changed in response to these events, by analyzing ~6 PNW fossil plant sites that span these events in time. At each site I characterize ecological strategies of taxa comprising these ancient communities by measuring leaf vein density (LVD) of fossil angiosperm leaves, which relates strongly to the maximum photosynthetic rates of the plant. Photosynthetic rates influence ecological strategy by placing plants along a spectrum with fast growth but low tolerance to resource scarcity at one end, and slow growth and high tolerance at the other. I am digitally measuring leaf vein density using microscope images of fossil leaves previously taken at several museums where these fossils are housed. I expect that during the MCO, evergreen plants with slower growth rates become more dominant and the diversity of ecological strategies increased (lower mean and higher variance of LVD). Across the MMCT, I expect that deciduous plants with high growth rates became more dominant and stronger abiotic filtering caused a decrease in the diversity of ecological strategies present (higher mean and lower variance of LVD). This study provides a real-life example of how climatic events reshaped the assembly of plant communities and provide an important perspective for present and future climate change.

Currently, nearly 10% of Americans have Type 2 Diabetes (T2D) and a further 34% have prediabetes - placing it among the most common chronic diseases in the United States. The capacity of the brain to elicit sustained remission of diabetic hyperglycemia in rodent models of T2D following intracerebroventricular (icv) injection of fibroblast growth factor 1 (FGF1) is now well established. Previously, we reported that prolonged (>24 hr) hypothalamic signaling by extracellular signal-related kinases 1 and 2, members of the mitogen-activated protein kinase (MAPK) family, is required for the sustained antidiabetic action of FGF1. Recent studies have now revealed that in addition to FGF1, FGF17 also stimulates the MAPK/ERK signaling pathway, which promotes oligodendrocyte proliferation and overall neurocircuit remodeling. Based on this observation, we hypothesize that FGF17 would have potent antidiabetic actions by activating hypothalamic MAPK/ERK signaling and remodeling hypothalamic neurocircuits. To test this hypothesis, cohorts of adult male C57BL/6J wild-type mice recieved a single icv injection of either FGF17 or saline vehicle. Analysis revealed that FGF17 induced sustained hypothalamic MAPK/ERK signaling, though the magnitude of this induction was less than that obtained with FGF1. We then injected FGF17 or a saline vehicle icv in a cohort of adult, male, diabetic ob/ob mice (diabetic and obese due to mutation in the leptin gene) and took daily measurements of blood glucose, food intake, and body weight. We found that FGF17 induced a transient reduction in food intake and body weight, but was able to normalize diabetic hyperglycemia for 30 days. This data shows that FGF17 is able to induce sustained activation of hypothalamic MAPK/ERK signaling and has antidiabetic actions. This is significant because sustained remission of hyperglycemia can reduce the risk of developing associated chronic diseases such as cardiovascular disease, diabetic nephropathy, and diabetic retinopathy.v Currently, I am performing immunohistochemical studies to identify the specific hypothalamic neurocircuits that FGF17 acts upon to produce these effects.

The ocean and atmosphere interact through air-sea exchanges of heat and energy across the air-sea interface. These air-sea fluxes have important implications on global weather and climate patterns. Because estimation of covarying turbulent variations is not feasible in Numerical Weather Prediction (NWP) models, the turbulent air-sea exchanges are typically estimated using bulk air-sea flux algorithms based on state variables. However there are large differences in the values estimated by different NWP and even when they agree, without a reference data set, it may be that all NWP are equally biased. For this project, I used in situ observations collected by Saildrone Uncrewed Surface Vehicles (USV) in the central tropical Pacific to assess bulk flux estimates from multiple atmospheric reanalyses including NCEP Climate Forecast System Reanalysis (CFSR), ECMWF Reanalysis v5 (ERA5), NCEP/NCAR Reanalysis 1 (NCEP1), and NCEP/DOE Reanalysis 2 (NCEP2). Preliminary results, based upon hourly, spatially-interpolated, co-located values that are then made into 24-hour “daily” averages, indicate that all of the reanalyses had a strong correlation with USV observations for net heat flux and net SWR, but the correlation was much weaker (0.5 to 0.7) for other flux components and very weak (~0.25) for the net longwave radiation for NCEP1 and NCEP2. The root mean square errors for the 24-hour-averaged differences were 55 to 66 W/m^2 for solar radiation and 20 to 30 W/m^2 for latent heat flux. In my analysis of my results, I looked at the differences region by region for each of the flux components and state variables as well as for each of the products. As Saildrone technology becomes more widely used and more intercomparison studies such as this are conducted, observations from Saildrones could eventually be integrated into NWP models, possibly improving forecast accuracy.

When managing our natural resources and assessing human impacts on ecosystems, it is important to understand how plant communities respond to disturbance events. The geologic record has the potential to provide an important source of information for scientists to observe how plant communities of the past have responded to disturbances. Currently, there is a limited ability to recognize disturbance as the primary driver of change because there is limited evidence of how functional traits - plant traits that relate directly with plant function and ecological strategy that are measurable in fossil leaves - vary across succession. To improve this ability, I am measuring the carbon stable isotopic composition (δ¹³C) of bulk organic matter in leaves sampled across a successional gradient. This functional trait is often preserved during leaf fossilization and is representative of a plant's water use efficiency (WUE), an important ecological strategy representing the carbon assimilated per water lost in a plant during photosynthesis. The extent to which carbon isotopes measured at the community scale reflect the successional stage of a plant community is not currently known. To improve this knowledge, I am testing the hypothesis that the WUE of plant species within a community will become more conservative in later successional stages. In support of this hypothesis, I predict that the abundance-weighted community average of leaf δ¹³C will increase through succession. In addition, I hypothesize that δ¹³C as a proxy for WUE will be most confounded in early succession, before a tree canopy forms, due to seedling utilizing water resources more rapidly without having established root systems and thus predict a higher variance of δ¹³C values in this earliest stage of succession. This research is helping develop a method of identifying disturbances within geologic records which can give guidance on management decisions regarding modern ecosystems

This research examines the intricacies surrounding healthcare access for undocumented immigrants in Washington State. Recognizing the role that nationalist, xenophobic, and racist policies play in perpetuating the intentional exclusion of this population, the study explores the three main barriers to access, including ineligibility, socioeconomic status, and psychosocial factors, that compromise equitable and safe care. To gain a comprehensive understanding of the issue, the study employs a combination of primary and secondary sources, including interviews with community leaders, organizations, undocumented immigrants, and social workers, to gain a more personalized and nuanced perspective on the obstacles and systemic barriers faced by this population. Furthermore, the study meticulously evaluates the federal and state legal frameworks that govern healthcare access for undocumented immigrants in Washington State, as well as best practices and policies from other states that have successfully expanded healthcare access for this population. This analysis enables the creation of a policy recommendation that considers the logistics, eligibility criteria, and impacts of expanding healthcare access for undocumented immigrants in the state. The ultimate objective of this study is to provide healthcare providers, policymakers, and undocumented immigrants with a comprehensive analysis of the barriers to healthcare access and contribute to the collective efforts aimed at improving access and equity for this population in Washington State. The conclusions of this study are expected to shed light on the root causes of these barriers and provide a foundation for informed policy decision-making aimed at expanding healthcare to undocumented immigrants.

The rise of illiberal and right-wing nationalist movements poses a clear threat to liberal democracy in Europe. Across the continent, illiberal parties campaign against independent civil society and democratic institutions, while advancing xenophobic, anti-feminist, and anti-immigrant beliefs. In countries where such parties have gained power, illiberal leaders are dismantling checks on government power, protections of civil liberties, and even free elections. Our project explores the rise of illiberalism in Europe across four dimensions: exclusion and resistance to social change; misinformation; nationalism and sovereignty; and the erosion of democratic institutions. Through our analysis, we propose policy recommendations for civil society organizations, regional and national actors, and European Union institutions to proactively defend liberal democracy.

The exact cause of schizophrenia remains unknown however its symptomatology may provide insight into the pathophysiology of the disorder. Cognitive deficits, such as impaired working memory, are a core feature of schizophrenia that precede psychosis onset and remain stable over time. Working memory requires persistent neural activity which is facilitated by N- methyl-D-aspartate glutamate receptors (NMDA-Rs). Large scale genomic studies have revealed that disordered glutamatergic signaling and NMDAR dysfunction are involved in schizophrenia. Additionally, NMDAR antagonists induce symptoms of schizophrenia in healthy humans. Forsyth et al. (2017) explored these connections, finding that the NMDAR agonist D- cycloserine (DCS) improved working memory in schizophrenia patients. The current study will utilize electroencephalogram data collected for the aforementioned study to identify whether changes in brain oscillations underlie this phenomenon. Aberrant gamma oscillations have been observed in schizophrenia patients and NMDAR signaling is essential to generating these rhythms. Theta and alpha rhythms have been implicated in critical components of working memory function. Therefore, we will investigate gamma, theta, and alpha oscillations in schizophrenia patients who received either placebo (n = 16) or D-cycloserine (n = 17) during the n-back task, which assesses working memory. We hypothesize that in patients who received DCS, gamma, theta, and alpha power will mirror patterns observed in healthy individuals in the current literature. Understanding if changes in oscillatory activity subserves NMDAR agonists in boosting working memory function for schizophrenia patients could reveal the etiology of this disorder; this has implications for developing treatments targeting cognitive symptoms and ultimately improving quality of life for individuals with schizophrenia

 Birth control is an important tool to prevent unwanted pregnancies. However, many people who might benefit choose not to use birth control, contributing to a range of negative outcomes, including unwanted pregnancies and sexually transmitted infections. Many factors affect people’s perceptions of birth control options, and ultimately influence their use of contraceptives. Previous research shows racial differences in rates of birth control utilization, but little work has explored why these racial differences exist and if and how culture contributes to birth control attitudes and utilization cross-racially. Furthermore, most previous research in this area focuses exclusively on race, typically reporting only on Black, Hispanic, and White women, with little or no intersectional analysis. The present study investigates how culture influences birth control attitudes, considering both a broader range of racial categories and the impact of multiple intersecting identities on culture. Our goal is to gain insight into the health care decision processes of intersectionally marginalized patients. We accomplish this with a cross-sectional qualitative study. We first pre-screen potential interviewees to recruit participants with diverse cultural backgrounds. Selected participants will participate in structured 1:1 interviews, answering questions about how their cultural background (including race, ethnicity, religion, and family) influences birth control attitudes. We will conduct thematic analysis to determine what aspects of culture impact birth control attitudes. Shedding light on how culture influences the perception and use of birth control provides insight into a broader range of patient populations, allowing for improved contraceptive counseling and education in the medical setting. Recruiting a diverse sample will illuminate the lived experiences of individuals who are typically excluded from research and scholarship, allowing future advancements in birth control to be more representative and sensitive, with the knowledge of all cultural experiences in mind rather than just a select few.

Washington State has 30 counties federally classified as rural, and at least 15 counties are identified as medically underserved areas (MUAs) or Health Professional Shortage Areas (HPSAs) by the Health Resources and Services Administration (HRSA). Individuals who live in rural and underserved areas are at higher risks for poor health outcomes due to the lack of providers serving these areas. Furthermore, the current racial and ethnic make-up of providers do not reflect the population. The Washington Area Health Education Center (WA AHEC) works to improve the diversity, distribution, and quality of the healthcare workforce in Washington. Through its two-year interprofessional certificate program, WA AHEC Scholars, health profession students are educated in topics about rural and medically underserved team-based healthcare. I ask: after students complete WA AHEC Scholars, are they practicing healthcare in a rural location, (MUA), or HPSA? Using students' program applications to extract their demographic data, I conducted an online search of each 2018-2020 graduated student. In my research, I gathered information about what/where they are practicing and if their location is rural/MUA/or a HPSA. Thus far, I have found the practice location of 52 out of 96 AHEC Scholar graduates. Of the 52 students in my study sample, 63% are now working in a rural location, MUA or a HPSA. Out of these students, 45% identify as a racial or ethnic minority. Understanding how to increase recruitment of providers in rural and medically underserved communities in Washington is critical to bettering the health outcomes of these communities. More research needs to be done to help determine additional strategies to address the shortage of providers in vulnerable communities. However, this research suggests that the AHEC Scholars Program has had a positive effect in encouraging diverse healthcare professionals to serve in the communities that need them most.

 In recent decades, various East African countries have experienced changes in precipitation patterns leaving the local communities vulnerable to food and water insecurities. The continent is rich with indigenous knowledges and some of them have proved to be useful in combatting climate change crises. I conducted a case study to explore Massai cattle grazing strategies and the use of sand dams in East Africa. The case study demonstrated that Maasai cattle grazing strategies provide great resilience to spatially and temporally shifting precipitation patterns and that sand dams effectively retain water during droughts. The results have demonstrated the need for further discussion and exploration into the application of these strategies in a larger climate change context.

 Patients with end-stage renal disease (ESRD) are 25 times more likely to be admitted to an intensive care unit (ICU) compared to those without ESRD. About 70% of ICU patients are aged 55 and older. Older ICU survivors may report new impairments in cognitive, physical, and psychological health, referred to as post-intensive care syndrome (PICS). It is unknown whether older ICU survivors with ESRD experience greater severity of PICS symptoms than those without ESRD. We conducted a secondary analysis of pooled data from 2 studies of 51 older ICU survivors. Diagnosis of ESRD was obtained from electronic health records. Assessments from the National Institutes of Health Toolbox (attention, cognitive flexibility, grip strength, dexterity) and Patient-Reported Outcomes Measurement Information System (depression, anxiety) measured PICS symptoms. Wrist actigraphy measured activity and sleep. We conducted independent samples t-tests to compare fully corrected T scores of each PICS symptom between older ICU survivors with ESRD and those without ESRD. Results indicated older ICU survivors with ESRD scored worse on attention (25 ± 10.3) compared to those without ESRD (33.8 ± 6.9), t(48) = 2.76, p = 0.008. Older ICU survivors with ESRD also scored worse on grip strength (24.8 ± 14.9) compared to those without ESRD (39.1 ± 12.6), t(48) = 2.54, p = 0.014. Older ICU survivors with ESRD were less active during the daytime (21.2 ± 10.3 activity counts/minute) compared to those without ESRD (51.9 ± 33.1), t(48) = 2.25, p = 0.03. Older ICU survivors with ESRD slept more during daytime hours (70.5%) compared to those without ESRD (51.2%), t(48) = -2.53, p = 0.015. Older ICU survivors with ESRD may be at risk for PICS throughout recovery from critical illness. Further research with targeted interventions focusing on screening and treating PICS symptoms is needed to improve health in this population.

We are researching adeno-associated viral (AAV) vector based gene therapy for the rare genetic muscle disorder GNE myopathy (GNEM). This disease manifests as progressive skeletal muscle atrophy leading to restricted ambulatory ability and loss of fine motor skills. GNEM is caused by defects in the GNE gene, negatively impacting the sialic acid biosynthesis pathway. The sialylation of muscle fibers does not occur without this pathway, causing a loss of muscle function due to sialic acid deficiency. AAV gene therapy can be used to alternatively express the GNE gene by directly targeting muscle or utilizing liver expression. Sialylated glycoproteins secreted by the liver can be taken up by muscle and the sialic acid recycled. Our lab plans to advance GNEM AAV gene therapy by combining liver- and muscle-specific promoters to reduce the dose of AAV required for sialylation of muscle fibers. We have cloned six tandem promoters and three control promoters that will be tested in human liver cells (HepG2) and murine myoblast cells (C2C12). The tandem promoters combine different regions of liver and muscle promoters. A double (firefly and renilla) luciferase mechanism is used to indicate promoter strength, where the amount of luminescence from firefly luciferase is measured. Our lab is currently recording the promoter strength and level of transfection in the cells. The ratio between these expressions indicate the overall strength of the promoter. We are also cloning these tandem promoters into AAV vectors with the intent of testing the vectors in mice. The aim of our research is to produce a promoter resulting in the expression of the GNE gene in both muscle and liver cells, increasing sialic acid production to aid patients affected by GNEM using a minimal dosage.

When discussing ways to alleviate the effects of poverty, the focal point of policy decisions tend to center on improving material poverty. However, there is a growing recognition that poverty includes temporal constraints as well as material. Time poverty is defined as the lack of discretionary time available for rest, socialization and leisure once accounting for time spent at work and during necessary, committed activities. This study was designed to identify a relationship between time poverty and wellbeing in college students, as well as if race could be a suitable predictor for time poverty. I hypothesized that students with higher perceived and actual time poverty will report lower scores in wellbeing, and that this disparity will also be seen with students of colour. Through a Qualtrics questionnaire, 161 participants completed a modified version of the national American Time Use Scale (ATUS) designed to understand how people spend their daily time. They then answered questions about their perceived general wellbeing, then questions centering their perceived time poverty. The results from a regression analysis suggested that only perceived time poverty (M = -.0068, SD = .64919) negatively predicted wellbeing, R^2 = .325, F(5,150) = 14.41, p < .001, where higher scores predicted lower wellbeing (β = .564, p < .001). Actual time poverty and race were not found to predict well being, nor was there a significant interaction between race and time poverty on wellbeing.​ The results of this study likely stem from low reliability of the materials and indicate a need to create a smaller-scale measure for time poverty in specific demographics (e.g. college students). However, the effect subjective time poverty has on wellbeing supports past literature, and reinforces the importance of improving time constraints.

Most of the current literature on relationships and marriage in the US overlooks the ethnic, religious, and generational variations within the black population. This study explores the nuance in views and attitudes among African American and African immigrant young women toward marriage, especially hypergamous and interracial marriages. This study follows a deductive approach through testing hypotheses developed through four existing theories. First, symbolic interactionism theory suggests African Americans and African immigrants hold different attitudes toward marriage because they developed different meanings of marriage. Second, social exchange theory posits that because people tend to marry those of similar social and economic backgrounds, interracial and hypergamous marriages represent a social exchange of status. Third, classic assimilation theory suggests as the generational status of African immigrants increases, they increasingly develop similar marriage views and attitudes to African Americans. Finally, segmented assimilation theory holds that Muslim African immigrants are selective in their assimilation, thus, would not have similar views to African Americans. This study uses qualitative data collected through interviews, and quantitative data from the public use microdata series, IPUMS USA. The mixed methods approach compares interview participants — black female college students — with the trends in the nationally representative microdata. The expected findings would confirm all of the aforementioned hypotheses. This study aims to enrich the current body of the literature and provide greater depth and breadth into the ethnically, generationally, and religiously diverse black population. A better understanding of marriage views and attitudes in the black community can help shape public policy that fosters more transitions into marriage. Moreover, marriage is among many predictors of the integration of immigrants. Thus, comparing immigrants to Americans can highlight how immigration may play a role in disruptions and delays in the integration process.

 Cystic fibrosis (CF) is a progressive, life-threatening disease, that results from the formation of thick mucus that builds up in the lungs, digestive tract, and other parts of the body. It leads to severe respiratory and digestive problems as well as other complications including opportunistic infections and diabetes. CF is caused by a mutation of the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel. Recently, the initiation of highly effective CFTR modulators including Trikafta (a combination of the medications elexacaftor, tezacaftor, and ivacaftor) has significantly improved the quality of life and life expectancy of patients with CF. However, recent clinical studies have shown that CF patients taking Trikafta have an increased risk of developing obesity and diabetes, though the underlying mechanisms remain unknown. In addition to being expressed in peripheral tissues, the Cftr gene is also expressed in the brain in the arcuate nucleus (ARC), a key brain area involved in metabolic regulation. To begin testing the hypothesis that Trikafta predisposes to metabolic syndrome by altering the activity of signaling of neurocircuits that regulate metabolism in the ARC, I investigated the ability of Trikafta to activate neurons in the ARC of mice (based on histochemical detection of c-Fos, a marker of neuronal activation). Following a single intracerebroventricular injection of Trikafra, compared to vehicle-treated mice, I found that mice treated with Trikafta had significantly increased activation of neurons in the ARC. I am now conducting studies to identify the phenotype of the neurons in the ARC that are activated by Trikafta and predict that successful completion of these studies will advance our understanding of the pathogenesis of obesity and metabolic impairment induced by Trikafta and inform the development of strategies that can avert these deleterious side effects.

To study genetic factors and the molecular mechanism underlying the development rate of mouse embryos, two mouse subspecies were studied. I have collected mouse embryos from crosses between C57BL6/JxCAST/EIJ (B6xCast), CastxB6 (the reciprocal cross), and intercrosses within either strain to examine the effects of maternal and paternal genomes on the developmental rate. I used mouse embryos every 24 hours at gestational stages E11.5-E14.5. Staging by the Embryonic Mouse Ontogenetic Staging System (eMOSS) is used to estimate the actual developmental stage based on limb bud morphology and compared to the gestational stage based on the estimated time of conception by observation of a vaginal plug. I also used gDNA to determine the sex of each embryo to investigate whether sexes play a role in developmental rate. I observed an interesting pattern that the mouse subspecies and the source of each parental genome affect the developmental rate of embryos. I observed embryos with at least one Cast parent, have faster development than B6xB6 starting at gestational stage E13.5. The developmental rate is independent of the sex of embryos or the litter size. Single-cell transcriptomic analysis is ongoing to determine the genes and mechanisms behind the change in developmental rate of mouse embryos. It is important because the result will contribute to human development in early stages, and help to solve problems such as preterm or underdeveloped infants.

 Cancer metastasis, the spread of tumor cells to different parts of the body, significantly increases patient mortality. An early step in the metastasis process is invasion into surrounding tissues. One way that tumor invasion is studied is through tumor organoids. Tumor organoids mimic tumors in vitro through 3D cell culture. While it is generally held that invasion continues to increase monotonically over time, I recently discovered that invasion of tumor organoids has a temporal pattern, where invasion spikes up, then decreases after a certain time. This finding suggests more complex regulation of invasion dynamics than thought previously. The goal of this project is to investigate the temporal dynamics of cell-matrix associated RNAs and proteins during breast tumor organoid invasion. I can perform a qPCR time course of particular genes related to invasion to measure the levels of RNA at specific time points. In addition, I can check for protein levels using a novel method developed in the Cheung lab. This method utilizes bio-orthogonal click-chemistry to perform rapid, selective pairing of intracellular proteins with azidohomoalanine, a clickable methionine analog. Click-chemistry allows us to pick up proteins that cells are either secreted or on the surface of the cells. To define a cancer-specific invasion signature of tumor invasion, I compare RNA and protein dynamics in breast tumor organoids with normal mammary organoids (FVB) migrating in 3D collagen gels. I hypothesize that there will be specific genes associated with increased and decreased invasion levels. In future work we will target those genes by either suppressing those genes that increase with invasion or increasing the expression of invasion suppressors. We expect this work to reveal new regulators of the metastatic process.

The Davis lab is focused on understanding the pathogenesis of Parkinson’s Disease (PD), a neurodegenerative disease characterized by the progressive loss of cognitive functions and motor movements. The mutation in gene glucosidase, beta acid 1 (GBA) is associated with the genetic risk for accelerated PD progression. Prior experiments have shown that GBA deficiency accelerated protein aggregation and affected extracellular vesicles. This has led to our hypothesis that extracellular vesicles are a vehicle for the spread of protein aggregation and mutations in GBA promote this accelerated spread. To investigate this, we developed a Drosophila model of GBA deficiency (GBAdel) and a human neuronal model with induced pluripotent stem cells (iPSCs) from an individual with PD heterozygous for a null GBA mutation. With our fly model, I have conducted genotype recombination to express human Alpha-synuclein (aSyn) in GBA deficient flies in the thorax. If aSyn ended up aggregating in the brain, I compared if this process was accelerated with GBA deficiency versus the control group by measuring high molecular weight oligomers. In addition, prior research has shown that extracellular biogenesis is a result of endolysosomal trafficking which leads to the formation of exosomes in our neuronal culture and spread of protein aggregation in our fly model. We suspect that GBA deficiency affects multiple parts of the endolysosomal pathway. In our human neuronal culture model, we compared endolysosomal trafficking impairments in GBA deficient cells versus controls. To measure this, we stain cells with antibody markers for early endosomes (EEA1,Rab5), late endosomes (Rab11), lysosomes (LAMP1) and conduct confocal imaging for analysis. By understanding the mechanisms of GBA deficiency and progression of protein aggregation, we can determine new therapeutic targets to slow the rate of PD and other neurodegenerative diseases.

Understanding the magnetic properties within novel materials allows for a deeper understanding of electron behavior within solids and can be used to design improved electronics and spintronics. The Kagome 166’s (RT₆X₆, R=rare earth, T= transition metal, X=Sn, Ge, Si) are of particular interest due to their abundant family, easy growth, promising display of charge density waves, and guaranteed interesting properties such as flat bands, Dirac points, and Van Hove singularities. The most accurate mathematical model for the anomalous Hall effect and the associated resistivity expansion is unknown. Adjusting the anomalous Hall effect (AHE) is explored via doping one member of the Kagome 166 family, TbMn₆Sn₆, with Cr. By exchanging some of the Mn for the less magnetic Cr, a tuning knob is created that influences magnetic transitions as well as the AHE. To explore this, I grow, identify, measure, and analyze samples of several different dopings. The analysis of magnetic measurements performed on several samples shows that doping has an impact on the AHE as well as the ferrimagnetic transition temperature. In addition, a novel exchange bias across multiple samples is reported. Identifying a tuning knob for magnetism in Tb(Cr_xMn_1-x)₆Sn₆ allows for a notable contribution to the discussion of the model of the AHE and understanding of the phenomenon itself.

A feature of the criminal legal system of concern to scholars is court-issued monetary sanctions — the fines, fees, and costs imposed on people convicted of crimes. Prior research suggests these debts exacerbate inequality and perpetuate disadvantages for the affected individuals, families, and communities. While previous studies have found that monetary sanctions negatively affect family members of the debt-burdened individual, the impact of these debts on parent-child relationships remains unexplored. Attempting to bridge this gap in knowledge, this study examines monetary sanction’s influence on the nature of parenting. Scholars understand parents play a vital role in shaping and providing emotional and material resources for their children. Given this, it is important to understand the impact of monetary sanction debt on parents’ ability to provide these resources and ultimately how monetary sanctions impact child well-being. Utilizing interview data from a previous multi-state study of over 200 individuals with legal debt and children, supplemented by an analysis of interviews of similar individuals, this study examines how stress and material deprivation resulting from monetary sanction debt reduce the emotional and material capacity of parents to address their child’s needs. Preliminary analyses show parents frame the impact of debt as generating financial and emotional stress for them, and they attempt to minimize its direct effects on their children. In some cases, it is clear that parents are unable to provide important resources for their children, and the stress of debt negatively affects their relationships. These preliminary results suggest one additional avenue as to how monetary sanctions affect individuals. As other researchers have discovered, the impact is not simply resident with the person in debt but has an additional negative reach that should be understood as we look to reform the practice of monetary sanctions.

Morphology of leaves informs plant functions from structure to growth rate, all summing to diverse strategies that plant communities employ to thrive. By analyzing strategy changes over time, morphology can describe the strategic response to disturbance events - particularly those precipitated by human activity. My study aims to develop a framework for characterizing those strategies on a temporal scale during ecological succession based on leaf vein density (LVD), which is the length of vein tissue within a given leaf area. I am accomplishing this through the chemical isolation of vein tissues, analytic microscopy, and image analysis, examining temperate deciduous leaves from 5 sites in North Carolina with varying amounts of time since the plot was clear-cut for timber harvest. Once I prepared slides of 4 cm2 of leaf matter, I began imaging the leaves under 8x magnification and following this, I plan on using image analysis software to measure LVD over 2-3 mm2. Based on correlations between early successional species - species populating a cleared area before slow-growth taxa regenerate - and high vein density organisms demonstrating faster growth, I hypothesize that taxa prioritize growth via resource allocation during initial phases of recovery post-disruption due to the increased availability of sunlight due to altered canopy openness, increasing photosynthetic rate. This would be characterized by higher LVD observed in early successional species. Should this prediction bear out, it indicates that LVD can be used to better understand varying ecological strategies in a community over time. Specifically, we will be able to use it to analyze how that spectrum changes based on environmental changes and determine which strategies are prioritized in which stages of community change. By garnering a clearer grasp on the diversity in early versus late successional strategies, I plan on connecting the prevalence of certain functional traits and environmental changes across time.

Urban trees are an increasingly essential part of the city environment, as lining streets with greenery has been shown to benefit residents’ health and quality of life. Trees especially impact air quality, which has implications for chronic illnesses like asthma, and existing literature suggests a relationship between air quality and children's health. This paper examines the impact of increasing urban tree canopies in a large, evolving city like Chicago on children’s asthma rates over a decade. I use tree census data from the Morton Arboretum to evaluate change in tree cover from 2010 to 2017, and use Chicago health records to track rates of emergency department visits due to pediatric asthma. Testing the strength of correlation through a regression model can determine the existence and strength of a correlation and relationship between tree canopies and health. The results suggest a need for increased tree planting policies to improve local health outcomes, especially in low-income neighborhoods with sparse canopy cover. As the climate gets warmer and air quality decreases, infrastructure that addresses both climate change and public health will become increasingly essential. By continuing to study the impacts of urban forests, we can develop strategies for mitigating these global issues in a local context.

One of the most common sources of hospital-acquired infections and the leading cause of chronic infections in cystic fibrosis patients is the opportunistic pathogen Pseudomonas aeruginosa. Pathogens such as P. aeruginosa exist in structured, bacterial communities encased in a self-produced matrix known as biofilms. These biofilms provide protection to the bacteria, which is largely why P. aeruginosa is so difficult to treat . There are several stages to biofilm development with the final stage being dispersion. During dispersion, bacteria leave the biofilm. Dispersion is a growing area of interest for researchers as dispersed cells are more susceptible to antibiotic treatment and immune cell clearance than biofilm cells. A unique phenotype called the rugose small colony variant (RSCV) develops in P. aeruginosa. This phenotype is characterized by an overproduction of the polysaccharides that make up the matrix. Studies reveal that this phenotype arises in cystic fibrosis patients. Little information is known about RSCVs and dispersion. My research focused on finding out if RSCVs disperse from their biofilms. To investigate this question, biofilms were grown over the course of five days using a tube reactor system. This apparatus supplies bacteria with a constant source of nutrients and flushes out their waste products to create an ideal environment for biofilms to grow. To induce dispersion, the flow of nutrients to the biofilm is stopped. RSCV forming strains were grown in the reactor to compare their dispersion responses to control strains. Samples were collected from the reactor, serial diluted, and colony forming units (CFUs) were counted. I found that biofilms formed from RSCVs release less bacteria when dispersion was induced. The data suggests that RSCVs do not disperse. Future work may be directed towards understanding what aspects of RSCVs cause them to release less bacteria even when signaled to disperse.

Early-onset Alzheimer’s Disease (EOAD) patients have a greater risk of developing seizures. Consequently, EOAD patients who develop seizures have worsened comorbidities, including mortality and behavioral outcomes. The causal relationship between chronic seizures and AD is still unknown. Neuroinflammation has been postulated as one of the links between these two disorders. Our lab has previously demonstrated that young mice with a presenilin 1 (PS1) genetic variant and amyloid precursor protein (APP) overexpression, mimicking an EOAD phenotype and genotype, subjected to chronic seizure are at high risk of mortality. This behavior was not observed in young mice with an EOAD-associated presenilin 2 (PS2) genetic variation. We hypothesize that chronic kindled seizures evoked in 2 months-old APP/PS1 mice worsen neuroinflammation and other neuropathological hallmarks of EOAD, including β-amyloid (Aβ) accumulation in the brain. To address this, 2-month-old male and female APP/PS1 and PS2 mice were subjected to seizures through a corneal kindling model of chronic seizures. The right brain hemisphere was collected before and after mice achieve the kindled criterion (five consecutive 5 Racine scale scores). Brains were harvested and cryopreserved for immunohistochemistry. My role in the project was to process tissues for immunohistochemistry. 20-µm thick sections of hippocampus from each mouse were sectioned on a cryostat and slide-mounted before processing with commercially available antibodies for molecular markers of neuroinflammation and neuropathology. Photomicrographs were collected and images were analyzed as the number of immunoreactive cells for each molecular and protein marker. We anticipate increased neuroinflammation and Aβ accumulation in kindled APP/PS1 mice versus their respective wild types and non-kindled littermates. We do not expect differences in PS2 variant animals. These results add to a larger research study in the laboratory to suggest that targeting seizures, and its inflammatory response, may be a potential therapeutic strategy to mitigate the behavioral and neuropathological burden of AD.

The Middle Miocene (23-5 Ma) represents a period of rapidly changing climate and active volcanism, particularly in the Pacific Northwest. Our understanding of the structure and composition of plant communities during this timeframe is complicated by a limited or degraded leaf fossil record. Plant fossil assemblages are also often time averaged, representing accumulation of plant material over an extended period. A plant community that was preserved because of a single, short-lived event can provide insight into the composition and structure of that community in life. The Watersnake locality of the Sucker Creek Formation in southwestern Idaho contains two thick (8-14 m) ignimbrite tuffs (volcanic ash layers) that preserve charcoal fragments, reflecting plants that were burned when the tuffs were deposited. In order to identify the woody taxa that made up this community, thin section microscopy is used to examine the preserved cellular detail of the fossil charcoal fragments from the lower tuff. Since ignimbrites are deposited as a part of a single event, the impacts of time-averaging are minimized. Although these deposits reflect a short time, they are likely to integrate across space, providing a view of the broader landscape. The results of this study will reveal the structure of this plant community immediately prior to the eruption that caused the ash flow. I hypothesize that the taxa identified within the ash will be very similar to those of the leaf fossil record found in the shale beds below. A lowland community consisting primarily of wetland Glyptostrobus oregonensis, and Quercus simulata found near flowing water will likely be represented. Upland vegetation consisting of conifers (Pinus, Tsuga) were also likely incorporated into the ash flow as it moved downhill. This study will provide insight into the dynamics of plant community change during the Miocene in relation to volcanic disturbance.

Climate change will likely alter the functional composition and diversity of plant communities, including the dominance of particular plant ecological strategies. It is difficult, however, to accurately predict potential vegetation responses due to the complexity of climatic influences. My research uses plant functional traits to reconstruct relative ecological strategies of common plant taxa that lived during the Miocene Climatic Optimum (MCO; warming event 17-14 million years ago) to provide important context for understanding modern climate change. Most prior work has relied on the nearest living relative theory (NLR), which states the ecology of a fossil species can be interpreted from the ecology of its closest extant relative. This theory requires the currently untested assumption that ecological attributes of those species have remained unchanged through time. I hypothesize that fossil species with traits indicating a particular strategy will share those relative traits with their NLR. I am using a sample size of 46 leaves to measure vein density as well as stomatal density and index in order to calculate assimilation rates. With these measurements I am able to characterize relative ecological strategies (e.g., fast growth strategy with high vein density and assimilation rates) and statistically test the significance between genera. Performing similar statistical tests using published vein density and assimilation data acquired from TRY – a large and freely-available plant trait database, I expect the observed strategies of fossil taxa to be reflected in the traits of their NLR’s. This study provides a tool for understanding how climate warming impacts the functional composition of communities by testing the validity of commonly-used NLR-based inferences.

Affordability of housing has been front of mind for policy makers around the country. As population increases in cities around the country, the cost of living has increased vertiginously. As an answer to the problem, cities and states are reshaping residential zoning laws in a process known as upzoning. Minneapolis, Seattle, and Chicago all now allow mixed, middle housing on all land previously zoned for single family residences only. Studies of these cities have found increases in housing and land prices as a result of this policy. In 2019, Oregon passed Oregon House Bill 2001 which allowed duplexes in all residential areas in cities over 10,000 in population, and all forms of mixed-middle housing in cities over 25,000. I hypothesize a detected increase in housing prices as landowners in Oregon cities now have more options for whom to sell estates to. This paper uses difference-in-difference and regressions discontinuity methods to illustrate the effect of this policy on housing prices in large, medium, and small cities. With the Washington Legislature considering a very similar policy, this paper will inform debate by illustrating upzoning’s effect on housing prices in cities of various sizes.

Phytoliths, silica bodies formed within and around plant cells, are a key part of a plant's physiological structure that can vary in shape between species. These phytolith shapes (so-called morphotypes) can be found abundantly within grasses and vary between taxa within a subfamily either in shape or in their relative abundances and could therefore provide important evolutionary data on how specific grass subfamilies may be related. Previous work has been done on certain grass subfamilies, including Bambusoideae, to identify similarities and differences in shape within a grass subfamily. This study aims to investigate the distribution of phytolith morphotypes among three closely related grass subfamilies (Arundinoideae, Danthonioideae, and Micrairoideae). To collect this data, we conducted a morphological study on over 300 phytoliths in samples from many species within our three subfamilies. The samples were taken from leaf clearings wherein the phytoliths were isolated through chemical treatment and centrifuging to remove other organic material before staining. Samples are imaged using a confocal microscope and then patched together with computer processing to form three-dimensional phytolith images. These sample objects were compared based on phytolith morphotype three-dimensional shape, their relative abundance, location in plant tissues, and size. In addition to the morphological study of individual phytoliths, we studied cleared leaves to obtain a greater sense of the composition of morphotypes within the tissue of the grasses. The results are expected to show an overlap in similar phytolith morphotypes across clades that have similar ecological niches such as photosynthetic systems. Overall, this research aims to find a link between these three close modern subfamilies that could be compared to fossil phytoliths in order to document their evolutionary history and past distribution.

Microphysiological systems (MPS) are novel in vitro models used to understand human disease and support drug development. Using a Kidney MPS, we are investigating a class of immunosuppressants termed calcineurin inhibitors (CNIs). CNIs are used in organ transplants to prevent rejection. CNIs have been found to induce nephrotoxicity that manifests as either acute kidney injury (AKI) or chronic kidney disease (CKD). AKI can be reversed with lower dosages of CNI, whereas CKD is irreversible. Our research focuses on the following CNIs: Cyclosporine A (CsA) and Voclosporin (Voc). The mechanism(s) of toxicities for CNIs are pleiotropic with a novel observation involving development of dysmorphic lysosomes. To address this, we have conducted experiments on 2D cultures treating primary human tubule epithelial cells (PTECs) with varying concentrations of CsA and Voc for 48 and 72 hours. The relative toxicities of these CNIs were assessed to determine the amount of cell death at designated time points. Subsequently, we assessed CNI induced toxicity in our kidney MPS via treatment with these CNIs for 48 hours. RNAseq analysis revealed differential toxicity between CsA and Voc. We observed 444 differentially expressed genes (DEG) in CsA MPS, while we only observed 45 DEGs in Voc treated MPS, suggesting significantly less toxicity for Voc versus CsA. Ongoing work to determine what is happening at the protein level involves doing immunohistochemistry (IHC) on the MPS. IHC allows for the staining of apical and basolateral proteins that may be indicative of kidney injury as well to assess for the presence of dysmorphic lysosomes. Ongoing work involves longer term exposure to CNIs as organ transplant patients require these drugs for the rest of their lives. By understanding the mechanism of CNI toxicity, further interventions may be explored to prevent the development of CKD in organ transplant recipients.

3D printing is a popular manufacturing method due to its ability to efficiently produce intricate and lightweight parts but it comes with the drawback of parts being too brittle to be used in load bearing applications. At the Laboratory for Advanced Materials and Processing, my research centers around making printed parts more ductile by studying fiber treatments for continuous-fiber filament. Printing with this filament produces parts with high ductility because they distribute load through the printed part more evenly than chopped carbon fiber or polymer filament. The heat applied during the manufacturing and printing process of the filament makes the continuous fibers to group together, or agglomerate, which decreases the performance of the printed part because it causes applied load to not spread evenly within the filament. I am researching the effect of heat transfer on interfaces in the continuous fiber filament by using sputter deposition equipment. Depositing sputter onto a sample involves taking a disc of extremely pure source material and using a large magnetic field to displace individual atoms from the disc onto the specimen. In my experiment, I coat the yarn with aluminum and ceramic sputter. The thermally conductive aluminum sputtered yarn is expected to fail faster in a tensile test compared to the insulative ceramic sputtered yarn, because the aluminum should theoretically increase heat flow within the filament. Increased heat flow causes agglomeration of yarn in the filament, which results in a decrease of part integrity. By determining how the distribution of heat affects the mechanical behavior of continuous-fiber filament, the manufacturing and printing processes can be improved upon to avoid damage prior to use of the parts. The overall goal of my research is to improve the process of 3D printing parts with low-modulus continuous fiber filaments and therefore aid in reliably printing ductile materials.
 

Melanoma is the leading, most deadly, cause of skin cancer. The survival rate of melanoma was observed from 2011-2017 to drop to 68% for patients with regional spread, and less than 30% for distant, metastatic tumours. Treatment is possible, and therapies such as immune checkpoint blockade (ICB) have been developed, increasing 5-year survival rates to over 50%. Current research has just begun to understand the importance of the tumour microenvironment (TME) for cancer survival. To address the hypothesis that specific gene expression within the TME influences the depth and quality of T-cell infiltration, and thus is a tumour-intrinsic property, I will be investigating infiltration across different subtypes of melanoma to assess whether T-cell exclusion can be predicted by transcriptional signatures. Tumours can be classified as immune-inflamed, (a result of CD8 T-cell infiltration), immune-excluded (CD8 T-cells localized around the border), or as an immune desert, entirely void of CD8 T-cells. A better understanding of these phenotypical and genotypical distinctions, propensities, and consequences is integral to healthcare. By implementing clinically relevant in vivo models, I am able to rigorously investigate TME effects on immunotherapies. The development of innovative humanized mouse models of melanoma, using genetically engineered ‘MISTRG’ recipient mice, has allowed us to mimic an entirely functional human immune system to respond to human melanoma tumours in vivo. Results from my lab suggest that the positioning of T cells in the tumour microenvironment is a tumour-intrinsic property, and modelling of the difference between infiltrated (hot) and excluded (cold) tumours is made possible with extensive modelling software, flow cytometry, epigenetics, and data analytics. The data that TME is intrinsic to patient success are thrilling, and future developments within the immunological field are sure to increase patient success even further. 

Freezing of Gait (FoG) is a disabling symptom of Parkinson's disease that prevents movement of feet despite one’s intention to walk. Virtual reality (VR) has potential in simulating real-life environments that cause FoG, eliminating safety risks. In this project, we extended VR environments that can be used as a rehabilitation tool to assess and treat FoG. To enhance previously developed environments, we added 1) visual cues that enable the person to compensate for FoG, 2) optic flow manipulation that enables researchers to quantify the effect of visual flow on FoG (i.e., how fast or slow the world moves with respect to the person), and 3) an avatar that enhances realism of the virtual environment. We observe how the participant interacts with these features within the virtual environment and how this affects the frequency of FoG. We anticipate that these developments will improve usability when deployed in a clinical setting and enhance the realism of the VR environment for the patient.

Highest adhesion medical tapes are necessary to maintain secure attachment of medical devices, like intravenous (IV) lines. However many nurses desire higher adhesion which is currently impossible without causing additional pain and skin stripping, referred to as Medical Adhesive Removal Skin Injury (MARSI). ThermoTape is a novel medical tape featuring switchable adhesion that provides nurses with a tape option that greatly reduces its contribution to MARSI among at-risk patients, such as children. ThermoTape delivers this multi-functionality with a new release mechanism that utilizes a temperature-sensitive polymer (TSP) additive within a matrix FDA-approved pressure-sensitive adhesive (PSA). The additive lowers the matrix-to-skin adhesion when warmed to 40-43°C using a warm compress. My major contribution is developing the ThermoTape manufacturing process. An automated slot die coater is used with a mechanical syringe pump to deposit a thin-film coating of the PSA and TSP mixture onto a 4.5μm clear plastic film. After oven drying in nitrogen atmosphere for 10 minutes at 120°C, a release film is applied before trimming to final strips for peel-force testing and atomic force microscopy (AFM) phase-contrast imaging. Automated AFM optical particle size analysis measured the average radius of the TSP nano-domains to be about 25nm at the surface. Optical profilometry was used to verify the film thickness was about 50μm for the original prototype. The change in peel force was measured over a 20°C temperature range for the pure PSA and three prototype variations. Formulations with 1% (w/w) TSP additive provide the largest reduction of ~80% peel force compared to pure PSA. The fabricated tapes supported our team’s clinical study of ThermoTape wear on UW students. Compared to a leading commercial tape Tegaderm, our ThermoTape provided higher skin adhesion with equivalent skin compatibility, while providing significantly lower pain levels upon removal, demonstrating both clinical and statistically significant performance.

With the war in Ukraine and President Biden’s announcement in 2022 sponsoring resettlement for 100,000 Ukrainians, approximately 14,000 refugees have entered Washington State. However, there has been insufficient research on the needs specific to this community, such as differing vaccination practices in their home country stemming from inadequate vaccine procurement and mistrust in vaccinations among the general population. Mental health issues also pose a concern in Ukrainian refugees who will need care for PTSD, anxiety, and depression to prevent long-term consequences. The aim of this project is to create a cultural profile for Ukrainian immigrants and refugees for EthnoMed, an ethnic medicine resource website by the University of Washington and Harborview Medical Center to inform healthcare providers in delivering culturally-appropriate care. In exploring the experiences of the community with the U.S. healthcare system and services in Washington, the project will involve identification of community approaches to healthcare and barriers to care, as well as background information about Ukrainian values, beliefs, and perceptions that impact their approaches to health. Research will be conducted in the form of a literature review, conversations with community members, and a review of community surveys conducted by students from the University of Washington in partnership with Nashi Immigrants Health Board – a registered non-profit organization serving Ukrainian communities in Washington – and the WA Department of Health Former Soviet Union workgroup. The profile will be published on the EthnoMed website and will provide healthcare workers with guidance regarding cultural considerations and needs of the community with input from community members. The work is intended to improve the community's use of the healthcare system and services leading to improved health outcomes, and identify barriers that may be improved to support the community's resettlement in the U.S.

Despite a generally held belief that protest is an essential tool of citizen participation in democracy, different protest methodologies can result in dramatically different social responses. Protests involving the destruction of property are often subject to particularly harsh backlash, despite a meaningful body of academic work proposing that such protests are a valuable tool for pulling media attention to a social cause. My work aimed to create a better understanding of this relationship between destructive protests and media. Specifically, I answered this question: how much more heavily did digital print coverage of the 2020 Black Lives Matter protests favor stories that included destruction of property over those that did not. To that end, I performed a quantitative content analysis on a sample of digital print articles published in response to these protests. Ten major online publications were chosen to be studied, with data being collected from all protest-covering articles published by those organizations in the period from May to August of 2020. Coding was done to identify passages of text that discussed destructive and non-destructive protest, and articles were examined for the volume of text dedicated to each subject. It is anticipated that destructive protest methods will receive more discussion in articles that non-destructive methods, indicating that destructive protests do generate more coverage than non-destructive. By generating specific and recent data to support or refute this, I can help to illustrate the effectiveness or lack thereof in property destruction as a tool for generating media attention. This should better equip future scholars to answer more actionable questions: is the destruction of property an effective tool for protestors and is the destruction of property a valid tool for protesters. In the practical decision-making of future protesters, the answers to these questions will decide the methods and tactics taken to seek change.

Saccharomyces cerevisiae is a model organism that is essential in the production of products such as wine, bread, beer, and bioethanol. The process of domestication through selection of desired traits for beer brewing has led to genomic changes in these S. cerevisiae strains. Specifically, the brewing process creates conditions that favor asexual reproduction as opposed to sexual reproduction, allowing genomic changes detrimental to meiosis to accumulate. Some genomic changes resulting from domestication include aneuploidy, genome decay, and high copy number variation. Decreased ability to undergo meiosis makes genetic linkage studies like quantitative trait loci (QTL) mapping incredibly difficult compared to lab strains. Meiosis is a key part of QTL mapping, where a parental strain for a phenotype of interest undergoes meiosis to generate progeny with variation in the phenotypic trait and in their genotypes. My work aims to find and develop genetically tractable brewing yeast strains in order to perform QTL mapping on unique brewing traits. The brewing trait of interest to my work is thermotolerance, as higher temperatures around the globe result in harsher selection conditions on brewing yeast. Previous work on Norwegian kveik strains revealed high thermotolerance and the ability to undergo meiosis and produce viable offspring. My project aims to understand the genetic basis of increased thermotolerance in kveik strains. I will conduct heat tolerance assays to determine the effect a select range of temperatures has on growth. I expect to see variation between individuals in a population and the variation will allow me to conduct bulk segregant analysis–the specific type of QTL mapping I aim to do–for the genotypes associated with the increased thermotolerance trait. As global temperatures are rising more rapidly, it is essential to understand how organisms use thermotolerance as an adaptive response.

Social risk factors, such as lack of access to medical resources, housing insecurities, economic instability, family disruption, and education, have a profound effect on mental health and general well-being. Unfortunately, these factors often disproportionately affect individuals with minority status, as well as those from lower socioeconomic backgrounds. The aim of this study is to shed light on the relationship between the race and ethnicities of public mental health clinicians and the degree of their support for clients presenting with clinically significant social risk factors. By examining the tailoring of treatment and provision of direct support, this study provides valuable insight into the potential disparities in mental health care based on clinician background. A sample of 172 clinicians participated in the study through a baseline survey and a follow-up survey. The preliminary analysis showed that 70.1% of the participants were Caucasian, while the remaining participants represented a range of races, including Asian (12.1%), Hispanic/Latinx/Spanish (11.5%), Black/African American (8.6%), and American Indian/Alaska Native (5.2%). The results showed that while 58.6% of the clinicians tailored their treatment based on the level of social risk, 44.3% provided direct support, however, a significant portion of 22.4% never tailored their treatment and 29.3% never provided direct support. The next level of analysis will examine the distribution of treatment tailoring and direct support across clinicians' race and ethnicity. This study highlights the importance of considering social risk factors and socioeconomic status in the treatment of clients, especially those from lower socioeconomic background, to reduce disparities in mental health. 

905,700 people were diagnosed with liver cancer globally in 2020, and this number is projected to rise more than 55% by 2040. The primary treatment for liver cancer is a partial hepatectomy, in which up to two-thirds of the liver is removed and then subsequently allowed to regenerate. The liver is the only organ that has this regenerative capacity, and while the regeneration process has been evaluated, the triggers of the intracellular pathways are not clear. Further research would be beneficial to the improvement of liver disease treatment. A primary hypothesis suggests a trigger of regeneration is the increased shear stress on liver sinusoidal endothelial cells(LSECs) after a partial hepatectomy channels portal vein flow through the reduced liver. However, current in vitro models that display liver regeneration do not have the ability to model the effects of flow on the liver, due to unrepresentative vasculature, no incorporation of constant flow, and a lack of organ specific endothelial cells. The development of a representative in vitro model to display this process is key, and to address the current limitations, I use the Zheng lab’s previously developed, perfusable, vascularized collagen “vessels.” In this project we 1) create a perfusable model of liver regeneration and analyze the survival of hepatocyte aggregates within it and 2) screen donor LSECs to identify their productivity through albumin production measurements and immunofluorescent staining to identify cell purity and presence of LSEC markers, which is essential if we are to use them in our vessels. Based on previous research, we expect to see greater hepatocyte function (quantified by higher albumin production) within the vascularized vessel due to the more physically representative environment. This model provides a baseline to test the effects of flow on regeneration and has many future applications including drug testing and disease modeling.

In this study, we present a dexterous implementation of the Rubber Hand Illusion (RHI) in virtual reality (VR). The RHI is a classic perceptual illusion in which a sense of embodiment of a non-self object is elicited by synchronously and congruously stroking both a visible non-self object (i.e., a rubber hand) and the subject’s actual hand, hidden from view. While powerful, the classic RHI experiment is constrained by physical reality. Here, we present a new VR-RHI implementation that integrates Unity’s collider-based physics system and SteamVR’s hand pose estimation algorithm to achieve real-time rendering of real-world collisions. This enables precise visuotactile concordance and thus induction of the RHI over a virtual hand. Data from healthy, right-handed human VR-RHI participants (n=17) demonstrated a strong, bounded, linear correlation between VR render offset and proprioceptive drift till a certain threshold. We have designed and validated a new gaze drift metric that uses integrated eye-tracking hardware and SDK support for gaze-object collision to allow gaze-based self-localization. Based on preliminary results, we believe using gaze may refine the proprioceptive drift metric by minimizing the required movement of the subject’s body and contralateral hand while self-localizing after RHI induction. In addition, we have implemented a new feature of the experiment to separate the visual and tactile sensations by showing the subject the actual hand location rendered in the virtual environment during the induction. During these trials, the subject is aware of the offset, but preliminary results suggest that we are still able to induce the illusion. Furthermore, we have also implemented a new induction method where we use movement to induce the illusion rather than tactile sensations. Finally, we have improved the experiment protocol by automating data collection and experimental loops so that the experiment can run without a third party.

Neurological trauma, from a spinal cord injury (SCI), can have devastating effects on the quality of life of individuals, often resulting in a significant loss of motor function and accompanying bowel and bladder complications. Recent research has combined use-dependent physical rehabilitation, which is the current gold standard of treatment, with the delivery of neuromodulators or electrical stimulation to improve motor-recovery outcomes after SCI. However, little work has been done to understand the scope of psychological changes that occur after SCI, or how these changes may, in turn, affect an individual's ability to recover from the trauma. To fill this gap, our project examined changes in motivation levels after a chronic cervical contusion of the spinal cord that produces impairments in forelimb-motor function. We also studied how subsequent motor recovery altered motivation. Our experiments were conducted in an adult rodent contusion model of chronic cervical SCI. We used a skilled forelimb reach-and-grasp behavioral task to assess the motor performance and injury severity of rats. To assess motivation, we recorded the duration that rats attempted to complete the reach-and-grasp task over a thirty-minute time window. Motivation levels and motor performance were assessed pre-and post-SCI and before, during, and after therapy. Our results show that motivation levels were significantly impacted by the SCI, with motivation loss positively correlated to injury severity. Surprisingly, despite significant motor recovery, motivation levels continued to remain low months after the injury. These results provide new insights into the effect of SCI on psychological factors, which will inform future investigations and the design of therapies targeting neurological trauma.

This presentation discusses a unique grammatical phenomenon surrounding person marking on transitive verbs in Kawaiwete, an endangered Tupi-Guarani language spoken in Mato Grosso, Brazil. Like many related languages, Kawaiwete exhibits complex variation in how it conjugates verbs (i.e. changes verbs to fit grammatical context). Transitive verbs, i.e. verbs that need both a subject and an object, require a prefix on the verb. This prefix denotes the role of the sentence’s component parts, called arguments. Whether the subject prefix or object prefix is selected depends on the grammatical role of the arguments and word order of the sentence, which is flexible. I analyzed data collected by Professor Lapierre by comparing sentences with first and third person arguments (i.e. “I/me” and “he/him”). I surveyed (i) the verbal prefixes used, and (ii) the order of the sentence’s arguments. Consider sentences (1a) /miara jemiwara je a-esat/ ‘I see the jaguar eating’, (1b) /miara jemiwara je w-esat/ ‘I see the jaguar eating’, (2a) /a-esat je miara jemiwara/ ‘I see the jaguar eating’, (2b) */w-esat je miara jemiwara/ (ungrammatical). When /je/ ‘I’ appears before /-esat/ ‘see’, its role as the subject is unambiguous, meaning the verb may take either the prefix /a-/, matching with the subject (1a), or the prefix /w-/, matching with the object (1b). However, when /je/ does not precede /-esat/ (2a), the verb must take /a-/, marking /je/ as the subject (2a). This implies that in situations where the role of the sentence’s arguments is unambiguous due to word order, the verbal prefix may select to match either of the verb’s arguments. Crucially, when word order results in ambiguity, the verbal prefix must match with the subject to disambiguate the sentence. This finding suggests that Kawaiwete verbs mark more than simply the verb’s subject or object, a unique phenomenon rarely observed.

Uridine-5'-triphosphate (UTP) is a precursor for RNA synthesis. Ura3 catalyzes the conversion of orotidine-5'-phosphate (OMP) into uridine monophosphate (UMP) and is commonly used as a selection marker to characterize mutation rates of S. cerevisiae. URA3 can be positively selected for by growing cells in the absence of uracil and can be selected against by growing cells in the presence of the toxic fluorinated UTP precursor, 5-Fluoroorotic acid (5-FOA). While mutations in URA3 make up the majority of 5-FOA-resistant mutants, mutations in a small number of other loci can also cause this phenotype. We whole genome sequenced the 5-FOA-resistant mutants with a wild type URA3 and identified mutations to URA6 in each of these individuals. URA6 is an essential gene that encodes an enzyme that catalyzes the conversion of uridine monophosphate (UMP) into uridine-5'-diphosphate (UDP). Here, we describe 41 non-synonymous mutations to URA6 that permit growth in both the absence of uracil and in the presence of 5-FOA. It remains unclear how the URA6 mutants can maintain a functioning UTP synthesis pathway while remaining resistant to the toxic fluorinated precursors. We hypothesize that these mutations alter the protein structure in a manner that decreases the affinity for fluorinated substrates while maintaining the affinity for UDP. To test this, we will evaluate the structural changes to URA6 resulting from these non-synonymous mutations. Our goal is that our findings can benefit our understanding of the UTP biosynthesis pathway and encourage further investigation of the mechanisms involving fluorinated substrate analogues.

Inequities still exist despite efforts to address racism and reduce racial disparities in mental health care. One reason for this may be clinician’s limited knowledge and guidelines on addressing and exploring the consequences of racism in clients' lives. The current study is a mixed-method study using secondary data from the Applying Theatre-Based Training Methods to Address Racism in Community-Based Mental Health Services, which surveyed 119 community mental health clinicians across Washington State in 2021. The first aim of this analysis was to examine qualitative data on clinician's perceived barriers and facilitators in broaching racial issues with clients. The second aim was to explore how these barriers and facilitators are correlated with quantitative measures of multicultural counseling knowledge and awareness. Three significant barriers emerged: 1) Clinicians not engaging in racial topics unless clients initiated; 2) Clinicians avoiding discussions of race and racism because of feeling uncomfortable or unconfident; 3) Clinician's assumptions that their racial identities would be a barrier to discussions. Three significant facilitators included: 1) Client's initiation, emotional openness, and availability to have racial conversations; 2) Relevant social events that provided an avenue to prompt discussion; 3) Clinician's willingness and intentions to address racism through asking or actively listening. There was no statistically significant correlation between either the count of perceived barriers or facilitator themes and clinician's multicultural counseling knowledge and awareness. The present research can supplement and support efforts to train clinicians in broaching racial discussions and inform clinical practice with clients from diverse backgrounds.

The emergence of SARS-CoV-2 (CoV-2) and the rapid growth of the global pandemic has necessitated more than ever the need for fully comprehensive studies of viral pathogenesis. Previous studies of CoV-2 highlight the importance of its viral proteins in transmission and adaptability into human hosts, but few have delved into the role that viral RNA structure plays in emergence and pathogenesis. Viral RNA structure is a known contributor to host-jumping replication as seen in related coronaviruses (CoVs), Flaviviruses, and Alphaviruses. Given this phenomenon and that all human CoVs originated from bat CoVs, we hypothesize that genomic and structural differences in the human CoV-2 RNA compared to the bat RatG13 CoV RNA, the believed progenitor of CoV-2, may have contributed to the species-jumping event from bats to humans that caused the emergence of human CoV-2. To test this hypothesis, I used a CoV-2 replicon system to compare replication of the wildtype (WT) replicon versus a mutant replicon (RaTG13-N/3’UTR(syn)) that contains a firefly luciferase reporter gene and synonymous mutations from the 3’ end of RaTG13. In preliminary replication experiments, RaTG13-N/3’UTR(syn) had notably higher replication than the WT replicon in primate fibroblasts. Based on this result, I used electroporation techniques and Renilla luciferase assays to determine the replication kinetics involved in differential replication of these viral replicons in human versus bat epithelial lung cells. I anticipate increased replication of the RaTG13-N/3’UTR(syn) replicon in bat cells compared to human cells when compared against the WT which would entail a mechanistic study of how RNA structures contribute to viral fitness in the two species using genomic and proteomic approaches. If this data supports our hypothesis, this could enhance our understanding of CoVs to allow us to target and survey zoonotic viruses that threaten species-jumping into the human population.

People living with epilepsy (PWE) often have a poorer quality of life (QoL) compared to the general population. Anti-seizure medicines (ASMs) are used to control seizures in PWE but are often associated with side-effects that lead to reduced adherence. Poor adherence is associated with reduced seizure control which can also negatively impact QoL. A rat model of acquired epilepsy was used to evaluate how poor adherence to the ASM, perampanel (PER), impacts an animal’s engagement with environmental enrichment, which is provided to promote species-specific behaviors and general well-being. Cardboard enrichment was provided to single-housed male Sprague Dawley rats with acquired epilepsy and I scored their level of engagement at the start of each day: i.e.,1 being no engagement; 4 being completely engaged. Animals were observed for 8 weeks: 4 weeks without PER and 4 weeks with PER in a fully adherent (100%) or variably nonadherent (50%) dosing paradigm (10 mg/kg/day, p.o.). I recorded data on the number of days till first engagement with the enrichment, days till max, and max enrichment score. After compiling the data, I found no significant differences in the max enrichment score or days till max score amongst the 100% or 50% treatment groups. Interestingly, when compared to their pretreatment baseline, fully adherent rats took less time to initially engage with their enrichment, i.e., 6-9 days, compared to 9-12 days, respectively. In contrast, nonadherent rats did not show a similar improvement in their enrichment behavior when treatment was initiated. These results suggest that fully adherent rats were more willing to interact with their enrichment whereas, poor medication adherence may have a direct negative impact on QoL. Further investigation is necessary to determine if this is due to a difference in seizure control between the groups.

Aging is an important problem in biomedical research. Given the increased risk of death with age, techniques to delay aging hold substantial promise for human well-being. The premise of my research is that rapamycin, a drug commonly used in transplant patients which is hypothesized to have development-slowing effects, can slow development of fruit flies. One finding from a previous study, however, is that there is enormous genetic variation within the Drosophila population (akin to the variation between dog breeds) which results in varying sensitivity to rapamycin. Earlier measurements indicated that strains of fruit flies that were sensitive to rapamycin had higher levels of histamine, a molecule that participates in metabolism, when on the drug. We set out to determine whether histamine could effectively extend sensitivity to the drug to a wider range of genotypes within Drosophila. Thus, I hypothesize that introducing histamine to the food that fruit fly strains that are genetically resistant to rapamycin are consuming will increase sensitivity. To test this hypothesis, I added solutions with different concentrations of histamine to food with or without rapamycin. I then placed eggs from a resistant strain onto the food to observe the time it takes from egg to pupa. Because I hypothesize that increasing histamine levels will make a resistant strain of Drosophila sensitive to rapamycin, the strain should become sensitive and consequently show an increase in development time compared to the conditions without histamine. Each test condition of a histamine solution and rapamycin has a corresponding control with no rapamycin. Hence, if the histamine-treated conditions show slower pupation times than the histamine-free controls, the hypothesis is validated. If validated, this work could help researchers understand ways to provide the benefits of rapamycin to individuals who might otherwise be genetically resistant to its impact in both aging and medical contexts.

Endophytes are mutualistic microbes that promote plant growth and stress tolerance by improving host nutrient uptake and producing phytohormones. Plants grown under drought or nutrient limitations have benefited from inoculation with endophytes isolated from wild poplar. Previously, tissue culture-grown poplar has received a pre-planting inoculation to successfully promote growth under abiotic stress. However, a lag in plant growth and initial negative physiological and morphological response has also been observed in plants inoculated early in their development. These results suggest that a favorable plant-endophyte interaction may depend on the method of inoculation. To further understand the best method to maximize plant growth promotion with endophyte inoculation, I have explored how the timing of inoculum delivery impacts plant physiological processes. In a greenhouse experiment, hybrid poplar plants were split into three treatment groups: an uninoculated control group, a pre-planting group inoculated with an endophyte consortium via a root soak, and a post-planting group inoculated via a soil soak. Measuring changes in root system architecture, plant height, and biomass will determine how the plants allocate their resources in response to inoculation treatments. Leaf chlorophyll fluorescence will be measured to assess the stress put on plants from the association with endophytes, while measurements of leaf photosynthetic and root respiration rates will be used as a proxy for changes in the host’s carbon budget. I anticipate that allowing plants to acclimate to greenhouse conditions before inoculation will allow them to have greater above- and belowground productivity due to the photosynthetic cost of establishing symbiosis. Host plant physiology will be correlated with additional measurements of endophyte density and distribution throughout the plant to relate inoculation timing to estimated intracellular endophyte concentrations. This information will provide a greater understanding of the initial costs and benefits of endophyte-plant symbiosis and optimal timing of inoculation.

Cystic fibrosis (CF) is a common inherited disease. People with CF develop chronic lung infections with the bacterium Pseudomonas aeruginosa (Pa), and these infections are a major cause of lung dysfunction. Treatment often includes the inhaled antibiotic Tobramycin (TOB) and the anti-inflammatory Azithromycin (AZM), as it is hoped that these medicines would have increased efficacy in combination. However, clinical observations suggest that TOB may actually have reduced efficacy in patients taking AZM, suggesting that the drugs may antagonize each other’s effects. We hypothesized that TOB-AZM antagonism occurs because AZM exposure induces expression Pa genes that have the collateral effect of causing TOB resistance. To test this, we identified 51 genes Pa which have been shown to be induced by AZM, and tested the TOB sensitivity of Pa mutants in which these genes had been inactivated. Consistent with our hypothesis, we found 2 genes (mexX and mexY) that increased Pa TOB sensitivity when disrupted. We then compared these mutants to wild type (WT) in a TOB-AZM antagonism assay and found that the mutants exhibited decreased antagonism. Measuring the expression of these gene in sputum of patients taking AZM could provide additional information about their effects on their combined effects in vivo. Results of this work could suggest changes in CF treatment and increase understanding of antibiotic action in chronic infections.

Glutamine synthetase (GS) is a highly regulated enzyme that catalytically converts glutamate to glutamine which is associated with ammonia assimilation. One of the effects of dysregulation in the GS inter-conversion process is hyperammonemia, which can cause death or brain damage. GS is conserved across all prokaryotes and eukaryotes. Among enzymes, glutamine synthetase's ability to polymerize is still a structural mystery and the functional characteristics of its self-assembling filaments remain unknown. The aim is to understand the occurrence of filament formation in GS and the effects on enzyme activity. We hypothesized that filaments may influence the association of GS substrates or allosterically regulate GS. I purified the GS of Pseudomonas aeruginosa, Mycobacterium tuberculosis, and Helicobacter pylori by using Ni-column and size exclusion chromatography (SEC). Then, I examined the GS of pseudomonas under different buffer conditions (Mg2+, Co2+) using negative staining. Under Magnesium (10mM) conditions, the known dodecamer structure of GS was observed. Under Cobalt (10mM) conditions, the filament was being induced. To better investigate the structural mechanism of filament formation we turned to cryogenic electron microscopy (Cryo-EM). The next step is to create a model of the filament interface of GS and identify the residues involved. This research has broad implications in the field of metabolic engineering, as understanding the structure and the role of filament formation in GS could help develop new therapeutic targets in metabolism.

Metabolites are small organic compounds that are the products of cellular metabolism and the building blocks of macromolecules. The analysis of a multitude of metabolites in a sample simultaneously is known as metabolomics and is a powerful tool for understanding microbial interactions in the ocean. In particular, metabolomics provides a way to investigate how marine communities vary in composition during shifts in environmental conditions. The North Pacific Subtropical Gyre (NPSG) is a region where inorganic nitrogen availability limits phytoplankton productivity and microorganisms rely partially on diazotrophs for fixed nitrogen in the surface ocean. Because N2 fixation is often iron-limited, bioavailable iron should control fixed nitrogen levels in the gyre. Here, we tested this hypothesis by collecting metabolomic samples during a large-volume incubation in which tanks were amended with various nutrient combinations of iron, nitrogen, and phosphate during a month-long incubation. It was expected to stimulate a diazotroph bloom by limiting the incubation for nitrogen. In these nitrogen-limited tanks, we expect to see a strong metabolic response to the absence of fixed nitrogen, followed by the ingrowth of nitrogen fixers with their own metabolite fingerprints as the experiment progresses. I will compare metabolomes of incubations to those of phytoplankton cultures, including the nitrogen-fixing cyanobacteria UCYN-A and Trichodesmium. I will also use the incubation's nutrient concentration and microbial community metabolomics to test the hypothesis that altering nutrient supply ratios (Fe: N: P) in the NPSG microbial population will result in metabolite shifts. As the critical link between inorganic matter and the formation of the organic material that powers the ocean’s food chains and biological carbon pump, metabolomics provides a way to better understand the critical role that nitrogen fixation plays in regulating the taxonomy and biochemistry of the world’s largest biomes.

The development of software applications has increasingly incorporated auditory components such as music and sound effects. Game development is a field in which this is particularly prevalent as in-game musical elements can directly influence or be influenced by users. Often, this music is designed primarily around the context or plot of the game, containing melodic and harmonic ideas that are continually developed throughout the game. Existing research in ludomusicology and human-computer interaction have explored these topics, but few span both areas of study. This work investigates how specific elements of a game’s sound or music are perceived by a user, and how it impacts decision-making. Participants complete a digital maze in which the music progressively adapts in response to their selected path but the adaptation method is not explicitly revealed to the user. Actions that bring a user closer or further to finishing the maze have opposing adaptations, though it is left to the user to observe and interpret these adaptations correctly. Through analyzing quantitative data tracked during user gameplay as well as conducting follow-up interviews with participants about their experience, I seek out what types of auditory changes are perceived by and influential to players of games. Findings from this work may inform the development of software with effective and meaningful auditory elements for users.

Quasars are compact regions at the center of a galaxy that have much higher than normal luminosity. Gas outflowing in winds is common in quasars, and it might play a role in regulating the black hole growth and star formation in the host galaxies. In particular, the ones with extremely high speeds (>~0.1c) have not been thoroughly studied and might pose the biggest challenges to the simulations of how these outflows are driven. A 2020 study by Rodríguez Hidalgo et al. identified 40 quasars with Extremely high-velocity outflows (EHVOs) in the 9th data release of the Sloan Digital Sky Survey by detecting absorption in quasar spectra. The C iv emission properties of this sample were examined in a 2022 study by Rodríguez Hidalgo & Rankine. Compared to the general population as a whole, these extreme outflows seem to be more predominant in quasars with large blueshifts of the C iv emission line, an indication of outflows in emission, but the sample was small. My project aims to answer the question: do EHVO quasars show distinct emission features compared with the general population of quasars? To answer this question, I carried out an extension of a 2022 study, but using a larger sample of 98 new EHVOs that we identified from the latest data release. I built on the python code that our team has previously created, which cross-correlates the sample of 6743 quassars from the 2020 study with measurements calculated by a 2020 study by Rankine et al and allows us to place the EHVO quasars in the C IV emission line parameters space (blueshifts vs emission intensity). Potential connection between the maximum EHVO velocity and increasing C IV blueshifts is also explored.

Mobility models, which stimulates movement patterns of individuals or groups, play pivotal roles in assisting urban planning, transportation, and public health. As these mobility models are progressively used to create new government policies and allocate resources in cities, it is crucial to consider the impact of amplifying or perpetuating existing biases or unfairness. Currently, the existing research is aimed at generating synthetic traces from real historical data and protecting the privacy of traces, but rarely on the fairness dimension of these mobility traces. This research specifically investigates the fairness dimension of mobility models. The fairness will be determined by analyzing the Common Part of Commuters (CPC) for different sensitive groups. CPC is the metric that is used in measuring how accurate the synthetic traces are compared to the real data. The different sensitive groups will be created by grouping the extremities of CDC’s Social Vulnerability Index (SVI), which considers a range of factors including socioeconomic status, household composition, race/ethnicity/language, and housing/transportation. The research will result in a package extension that will allow all users to analyze for fairness in Mobility Models between the wealthy and less privileged regions. We anticipate that mobility models will have a higher average and higher distribution of CPC in the more privileged regions.

Autoantibodies that bind self-antigens are a component of autoimmune diseases in which the immune system attacks the host organism rather than foreign pathogens. Interstitial Lung Disease (ILD) is an autoimmune condition that presents in conjunction with autoantibodies that bind Melanoma differentiation-associated protein 5 (MDA5). Presence of anti-MDA5 antibodies knowingly serve a predictor of clinical mortality for ILD patients. MDA5 is a cytoplasmic protein that recognizes viral RNA and induces synthesis of type 1 interferons. It is unclear whether the MDA5 autoantibodies directly associate with MDA5 to alter immune function and cause disease, or merely serve as an indication of the disease’s presence. One hypothesis is that anti-MDA5 antibodies activate MDA5 inappropriately in the absence of viral infection. Another is that the autoantibodies interrupt MDA5’s response to viral RNA, in which case ILD would result from uninhibited infection. To examine these hypotheses, the Fink lab purified anti-MDA5 antibodies from the plasma of an ILD patient. They then used electroporation to introduce MDA5 autoantibodies or Immunoglobulin G (IgG) antibodies to cultured cells with varied exposure to Polyinosinic: polycytidylic acid (Poly IC), a synthetic RNA that activates MDA5. I used mRNA from these experimental cells to synthesize cDNA and run quantitative real-time reverse transcription PCR. I measured expression of IFIT3, an interferon stimulated gene (ISG) transcribed in the MDA5 pathway, relative to the RPS18 housekeeping gene. IFIT3 was upregulated in conditions with Poly IC, particularly when incubated with anti-MDA5 antibodies. This preliminarily indicates the virally activated immune response is amplified when autoantibodies are present, suggesting that blocking the MDA5 signaling pathway could be a therapeutic treatment for ILD patients. I will be analyzing expression of other ISGs to further test the validity of early results. This project will help define the mechanism of anit-MDA5 autoimmune disease in order to identify treatment strategies.

The Miocene Climatic Optimum (MCO) was a period of global warming 17-14 million years ago, where temperatures increased 2-4°C and CO₂ levels increased to ~400-600 ppm. Overlapping with the MCO were the Columbia River Basalt eruptions (CRB: 6.6-15.9 Ma), where extensive lava flows spread across the Pacific Northwest, resulting in primary succession. My study is focused on reconstructing the vegetation across the MCO and during CRB eruptions using epidermal phytoliths (i.e., Microscopic Biosilica) to understand how these conditions impacted plant communities. Epidermal phytoliths are formed within living plant matter reflecting the current environmental conditions in their size and undulation. The plant matter then falls to the forest floor and decays leaving behind the resilient Microscopic Biosilica, which is preserved within that sediment. Leaves formed in ecosystems with an abundance of sunlight reflect open-canopy vegetation, with small circular phytoliths; while large-undulated phytoliths come from closed-canopy, shady environments. Previous work has shown a correlation between the average size and undulation of epidermal phytoliths with leaf area index (LAI; i.e., a measure of canopy openness). I am using this process with sediment samples collected across four sites in Central Oregon to calculate ancient reconstructed LAI (rLAI), and thus reconstruct the canopy cover. Each site was chosen due to the time period it represents, with different exposure to increasing variations of CO₂ and CRB impacts. I hypothesize increased temperature and atmospheric CO₂ concentrations during the MCO created favorable conditions for plant communities, which promoted a productive closed-canopy forest structure. Additionally I hypothesize, the primary succession induced by CRB volcanism prevented the re-establishment of forests, leading to open-canopy vegetation structure. As modern day anthropogenic-driven climate change invokes alterations in our planet's ecosystems, we need to better predict and anticipate future responses of plant communities to these environmental perturbations. 

Millions of people go hungry and are insecure about their access to food. Charities and non-profit organizations run numerous food assistance programs to help those in need. Previous research suggests that public services are positively associated with housing prices, demonstrating that intra-jurisdictional differences are capitalized through market processes. However, food assistance services bring negative externalities, such as attracting non-residents to gather in the community, disrupting our previous understanding of housing prices. In this research, we employed a hedonic price modeling approach to estimate the impact of the presence of food assistance centers on housing sales, controlling for property attributes, neighborhood, and city characteristics in Baltimore City, Maryland. Two main measurement methods were used to label the attributes of a property: marking all properties within a neighborhood where the food pantry is present as accessible properties and marking all properties within a one-kilometer radius around the food pantry as accessible properties. We tested two hypotheses in this study. The first hypothesized that the presence of a food assistance center is an important indicator of housing prices. The second hypothesized that the impact of food assistance centers varies by the type of property: condo, townhouse, and single-family residents. Under the one-kilometer radius measurement method, the overall effect of the food pantry on house prices is negative, showing that housing prices are lower for accessible properties than properties without food pantry service. Single-family residents and townhomes are the types of properties that are most affected by the presence of food pantries. These findings have the potential to inform urban economics research devoted to the nature of public services. In particular, they show that the food pantry, as one kind of public service, is important not only in the public health field but also plays a role in affecting housing markets and urban planning.

When talking about computational linguistics, what usually comes to mind is mass-processing of language data for better understanding languages, and improving the algorithms that do the job of analysis. The AGGREGATION project at the UW Linguistics Department builds on previous linguistics resources like the LinGO Grammar Matrix and interlinear glossed text (IGT) to automate the construction of grammar fragments and create computational resources that facilitate the preservation of endangered languages. My task is to create treebanks (syntactic representations of sentences’ grammar) by analyzing data sets in given languages. Through generating treebanks and selecting correctly generated trees, my role helps developers determine the capability, generalizability and effectiveness of the methods within the structure used for inferring grammatical information. Currently, the ongoing developing module is for the linguistic phenomena called valence-changing morphology. For example, currently I am treebanking the Abui language (ISO 639-3 code: abz) spoken in East Indonesia, which is endangered because the only assigned language of education instruction in the region is Malay. By analyzing this language, my mentor and I specifically try to identify valence-changing morphology and evaluate the grammar generated by the AGGREGATION pipeline on its correctness. The more correct results it generates, the more it can be applied generally onto other typologically diverse languages. Ultimately, this works to preserve the otherwise lost beauty of complex grammar found in endangered languages.

In response to acute genotoxic insult, cancer stem cells undergo quiescence, a state of temporary cell cycle arrest, to avoid apoptosis (programmed cell death) and later re-enter the cycle to generate daughter cells under suitable conditions. This event is also observed in the irradiated germline stem cells (GSCs) of female Drosophila melanogaster. Previous studies have shown that quiescence is regulated by various upstream components, including gene silencing by polycomb repressive complex 2 (PRC2) and activation of mitophagy, the selective degradation of damaged mitochondria. Activation of PRC2 is shown to be upstream of mitophagy in regulating quiescence. However, the PRC2 target genes that get silenced in this process remain largely unknown. In humans, a downstream target of PRC2 is microRNA-200 (miR-200), which can enhance mitochondrial elongation by downregulating mitochondrial fission factor (MFF). Here, we hypothesize that the miR-8 gene, the Drosophila ortholog of the human miR-200 family, is a downstream target of PRC2 and is required for stress-induced quiescence to take place. To investigate the role of miR-8 in governing quiescence following stress, we overexpress miR-8 in female Drosophila GSCs under UAS-GAL4 control and study the spectrosome and mitochondrial morphology of the immunostained GSCs. We predict that miR-8 overexpression will prevent mitophagy and entry into quiescence after irradiation. We anticipate that our findings will characterize the role of miR-8 and strengthen our understanding of mechanisms that govern the cell cycle and quiescence. This study is critical as our proposed mechanism of quiescence can be applied to other stem cell types, and may present new therapeutic strategies for cell cycle-related diseases.

Heart attacks are a leading cause of mortality and morbidity worldwide. When the flow of oxygenated blood to the heart is blocked, affected tissue dies and becomes non-contractile scar tissue, often leading to fatal heart failure. One potential therapy is implanting pluripotent stem cell-derived cardiomyocytes (PSC-CM) to remuscularize scar. However, implanted PSC-CMs have been strongly associated with dangerous ventricular arrhythmias, hindering scientists from testing this technology in clinical trials. In our study, we use computational modeling to examine the efficacy of arrhythmia suppression enabled by light-induced bioelectric currents (optogenetics). Specifically, we examined expression of a repolarizing light-sensitive ion channel (GtACR1) to prevent spontaneous action potentials in an induced PSC-CM ionic model. We hypothesized that hastening repolarization using optogenetic GtACR1 currents could suppress spontaneous action potentials in simulated cells and representative organ-scale models. My role involves conducting computational simulations in both simulated PSC-CMs and patient-derived left ventricular models. In the cell-scale simulations, I test different combinations of light irradiance and modeled reversal potentials, then analyze the simulation outcomes to see whether spontaneous activity is suppressed. I observed an inverse relationship where more positive light-sensitive channel reversal potentials necessitate the use of stronger light intensities to achieve effective optogenetic suppression. In the organ-scale simulations, I vary the size, depth, and position in an idealized representation of an engrafted sub-epicardial layer of PSC-CM, as well as the applied light irradiances. I have run approximately 50 simulations across 3 irradiances in a patient-derived model. Ultimately, I hope to conduct 108 total simulations across 3 models and extensively analyze them with the goal of better understanding arrhythmia development mechanisms. The results from our parameter-based study can provide a valuable proof-of-concept method to unleash a potentially ground-breaking medical innovation.

Prostate cancer is the second most prevalent cancer among men in the United States. Characteristic biochemical markers include abundant Androgen Receptor (AR) and Prostate Specific Antigen (PSA), a downstream marker for AR activity. A rare neuroendocrine prostate cancer (NEPC), however, is characterized by low AR and PSA activity and high Synaptophysin (SYP; NEPC marker) expression. AR pathway inhibitors (ARPIs), the first-line treatment for prostate cancer, have minimal therapeutic effects on NEPC. This suggests that suppressed AR activity inhibits ARPI effect, and restoring AR could induce sensitivity to ARPIs, such as Enzalutamide. This study investigates the impact of overexpressing a tRNA, Arg-TCT-1-1, in NEPC. tRNA-sequencing of NEPC cell lines identified reduced expression of the Arg-TCT-1-1 tRNA isodecoder (Arg-TCT). Stable cell lines were generated for adenocarcinoma (AD) and neuroendocrine (NE) phenotypes, with overexpression of Arg-TCT or mutant TCT (mut-TCT). Reverse Transcriptase Quantitative Polymerase Chain Reaction confirmed Arg-TCT and mut-TCT overexpression. Cell lysate was immunoblotted for AR, PSA, and SYP; cell growth assays were then performed with Enzalutamide in DMSO to assess cell proliferation and sensitivity. Enzalutamide inhibited AR activity in LNCaP (1uM) and C4-2B AD (20 uM). Immunoblot suggests that Arg-TCT-1-1 overexpression rescues AR activity in NE cells, while mut-TCT does not affect AR activity. Cell growth assays reveal Arg-TCT-1-1 upregulation induces increased cell proliferation and enzalutamide sensitivity in NE cells. These novel findings demonstrate that upregulated tRNA promotes ARPI sensitivity in NEPC cells. Further research on how Arg-TCT-1-1 regulates AR activity and its transferability to other cancers is needed. These results suggest a promising therapeutic vulnerability if confirmed in murine models.

Iron centers which feature metal ligand multiple bonds can be powerful group transfer agents, for example, terminal Fe-oxo intermediates in soluble methane monooxygenase can perform oxo-atom transfer for the selective oxidation of methane to methanol. Abiologically, ligand constructs which enforce desirable electronic and structural configurations have been shown to enhance group transfer to a range of organic substrates. We developed and studied an iron (Fe) molecular complex with two aminophosphine selenide ligands (Se=PPh₂NTol; Ph=Phenyl, Tol=4-Tolyl) that chelate the metal center via the selenium and nitrogen. The iron complex (FeL₂) was synthesized by a reaction between Fe(HMDS)₂ (HMDS = bis(trimethylsilyl)amide) and the aminophosphine selenide. Characterization shows a tetrahedral, high spin, symmetric compound. We hypothesized that FeL₂ can activate and transfer heteroatoms and explored the reactivity of FeL₂ with oxidants, oxo atom donors, and organic azides. Treatment with iodine (I₂) results in oxidation of the iron center (Fe(II) to Fe(III)) and coordination of the iodide counterion results in structural reorganization to a five-coordinate square pyramidal complex. Reactivity with oxo atom donors shows that either the ligand or Fe center are oxidized, and we identified a µ₂-oxo dimer, which is the first Fe-O-Fe dimer to have selenium in its first coordination sphere. We found that FeL₂ forms Fe-nitrenoid intermediates and can perform nitrene transfer to form diazos or do C-H amination, when treated with aromatic and aliphatic azides, respectively. The presented complexes are characterized by single crystal X-ray diffraction (XRD), Evan’s method, nuclear magnetic resonance (NMR), and Ultraviolet-Visible Spectroscopy (UV-Vis). This research builds upon the knowledge of transition metal complexes for heteroatom transformations.