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

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

Religious nationalism is receiving growing attention because of its current influence in democracies, but it manifests itself differently across countries. Previous research has identified socio-historical characteristics that impact the salience of religion as a factor in an individual’s conception of national identity. However, scholars of these studies have mainly used International Social Survey Programme data to analyze European nations. My study uses World Values Survey (WVS) data from 1981 to 2022 to evaluate democracies from a global perspective. I conduct a multilevel analysis to determine the salience of contextual characteristics that prime religion to be used as a vector through which nationalism is mobilized among individuals. Accounting for individual-level factors, I identify which country-level factors influence the relationship between religion and support for nationalism among individuals surveyed. I determine an individual’s support for religious nationalism using the beliefs and groups they express to support in the WVS. I then compare these results to events of national stress to determine if a relationship can be identified. My results suggest that religions favored in church-state relations are more likely to be included in conceptions of national identity. Additionally, affiliates of favored religions are more likely to support nationalism during times of outgroup threat, such as increases in immigration, socio-economic turmoil, and political/cultural shifts. By completing a global analysis of these phenomena, I am able to identify a more comprehensive pattern, something less expansive studies struggle to achieve due to hyper-partisanship debates that can overshadow case studies and regional analyses. Furthermore, by determining which socio-historical characteristics have the greatest impact on conceptions of a religious national identity, I provide a framework to develop a predictive theory on the circumstances under which a religion is not only primed to mobilize nationalist movements, but then comes to be employed to mobilize these movements.

Marine heatwaves have altered ecosystems globally, including changing community composition and facilitating the spread of invasive species. In south Puget Sound, Washington (USA), non-native Pacific oysters (Magallana gigas) have been farmed extensively for almost a century and grown in enhancement sites, however, they have only recently recruited in the wild. This study explores how the appearance of Pacific oysters was related to spatially (eight sites) and temporally (decade) warmer summer water temperatures in south Puget Sound and compares oyster persistence across five sites where recruitment occurred. The largest recruitment event from 2012-2020 was in the summer of 2015, in the middle of the east Pacific Blob marine heatwave which led to warm water temperatures off the west coast of North America. Throughout the study period, the number of oyster recruits each year was positively correlated with warmer water temperatures. Oyster population densities differed across the five sites where recruitment occurred and generally declined after 2015, but showed no site by year interactions, which is consistent with spatially-variable recruitment and similar post-recrutiment survival. Mean oyster shell heights also differed among sites, which could reflect different growth trajectories or recreational harvest patterns. This study supports the claim that warming sea surface temperatures may interact with species introductions to change modern biogeography. 

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

Phytophthora belongs to a group of plant pathogens found in the Kingdom Protista and is known to be highly destructive to plants. The water mold has been found all over the U.S. but just in Washington and Oregon, there are over 30 different species. This water mold is a significant problem in the Pacific Northwest because it infects Pacific Rhododendron leaves. Comprehending the factors that contribute most to the diversification of the Phytophthora species is essential in sourcing and minimizing its spread. We anticipate that the presence of Phytophthora species in residential areas, influenced by human activities, will procure a higher diversity rate of at least 3 or more species. This expectation is rooted in the understanding that the human influence on these environments contribute to an increase in landscaping that works for the proliferation of diverse Phytophthora species. Our location sampling of choice for the bacteria was Chambers Creek located in Pierce County, WA. Chambers Creek has mostly residentially areas surrounding. We gathered four leaves from a rhododendron plant on the Pierce College Fort Steilacoom. We placed the collected rhododendron leaves into bags which were then submerged in the water and left undisturbed for a duration of approximately nine days for observation and analysis. We plan to inoculate the necrotic tissue into V8 agar. We plan to isolate DNA of the Cox-1 subunit protein and sequence it to then use bioinformatics to identify species of Phytophthora. We will use class data to determine if residential areas have an effect on Phytophthora diversity.

Our undergraduate research project is on Phytophthora. Phytophthora translates to “plant destroyer”. The purpose of our research is to use watershed studies and bioinformatics to find patterns in the diversity of Phytophthora species found in local streams in Washington State. We assessed prior studies to estimate the probability of discovering Phytophthora in Chambers Creek, a local stream. Our hypothesis is, in comparison to freshwater, water sources closer to the ocean will have a higher diversity of Phytophthora species because they have more sources of contamination and higher saltwater concentrations. We chose the stream location based on previous watershed information we had. Additionally, we baited Chambers Creek with Rhododendron leaves in an attempt to grow Phytophthora. We then cultured the lesions on the leaves onto a V8 agar to grow Phytophthora. After that we isolated the DNA and “cleaned” it by using reagents to remove unused primers and deoxynucleoside triphosphates, then sent it off for sequencing. At this time, we used gel electrophoresis to determine the quality and quantity of our DNA. Lastly, we used bioinformatics to become familiar with sequence analysis using the National Center for Biotechnology Information Basic Local Alignment Search Tool. Three out of the four samples we obtained had no sequence matches but one sample was 100% positive for Phytophthora bilorbang. In conclusion our hypothesis was correct. Since our water source was subject to higher saltwater concentrations, it was more contaminated and had a higher diversity of Phytophthora species. Doing this research and discovering this information will help add to the knowledge of Phytophthora in Washington State. This can lead to where Phytophthora treatment is needed to protect our environment.

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

Human Immunodeficiency Virus 1 (HIV-1) is a lentivirus and the causative agent of Acquired Immunodeficiency Syndrome (AIDS). HIV encodes a viral protease, the function of which is required for viral replication. The host innate immune sensor CARD8 detects HIV protease activity, leading to inflammasome activation during HIV infection. Inflammasomes are cytosolic innate immune complexes that recruit Caspase-1 and lead to secretion of pro-inflammatory cytokines and lytic cell death. Humans encode a single CARD8 gene; however Old World Monkeys (OWMs), the hosts of Simian Immunodeficiency Viruses (SIVs) encode two copies of CARD8. The function of the OWM CARD8 is unknown. To characterize the function of OWM CARD8s, I cloned CARD8 from representative OWMs and tested their responses to HIV and SIV protease in two ways. First, I determined if OWM CARD8s are capable of forming an inflammasome in response to HIV-1, a panel of SIVs, or the broad CARD8 activator VbP. I found that most, but not all, OWM CARD8s are functional but not responsive to HIV-1/SIVs. Human CARD8 senses HIV-1 through viral protease cleavage of its N-terminus. To determine if this lack of response of OWM CARD8s is due to the absence of viral protease cleavage, I will next perform western blots comparing human and OWM CARD8 proteolysis in the presence of absence of HIV/SIVs. My data suggests that the species-specific differences in CARD8 alters its capacity to detect viral proteases. We speculate that the absence of HIV-like pathogenesis in OWMs with endemic SIV may in part be due to the absence of CARD8 inflammasome activation to SIV protease.

Sickle cell disease (SCD) is an autosomal recessive disorder caused by the inheritance of two abnormal hemoglobin genes and can present numerous health complications due to the sickling of red blood cells. It can lead to multiple comorbidities, and can have adverse effects on pregnancy. SCD is very common in Sub Saharan Africa in mainly developing countries, but it can pose risks to pregnant women even in developed countries. There has been conflicting information about whether or not the presence of SCD poses a significant risk to pregnancy outcomes. To analyze this, I systematically reviewed previously published evidence on the effects of SCD on maternal pregnancy outcomes in women from multiple hospitals in different countries from 1973 to 2021. I did a matched comparison of the outcomes between mothers with SCD (HbSS genotype) and mothers without SCD (HbAA genotype) using data from 11 studies. For binary variables, I used log risk ratio as the effect size metric, and for continuous variables, I used standardized mean difference. I hypothesized that the presence of SCD would pose a significant risk to pregnancy and lead to higher occurrences of adverse pregnancy outcomes. I found that there was a significantly higher risk of adverse pregnancy outcomes in mothers with SCD and their offspring, compared to mothers without SCD and their offspring. Perinatal mortality and stillbirths increased significantly with SCD, as well as intrauterine growth restriction, urinary tract infection, eclampsia, and occurrences of preterm delivery and c-section. I found that there was not a significantly higher risk of maternal death and premature rupture of membranes in mothers with SCD, although their risk was higher overall. Proper knowledge of the risks of pregnancy with SCD as well as proper management and treatment of the complications associated with it can improve maternal and fetal outcomes.

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

The robotic exploration of Mars has found that the early atmosphere was similar to current day Earth, suggesting that life could have existed on Mars in its past. The former atmospheric conditions and potential ancient rivers and lakes are preserved in the sedimentary rocks found across the surface. Interpretation of the Martian sedimentary record in Gale Crater, a possible ancient lake, requires differentiating between a variety of processes that alter sediment chemistry. Our study will contribute to the reconstruction of source rock composition based on the sedimentary records in ancient river systems on Mars. Iceland is a useful analog to ancient Mars as it has a similar climate and geologic makeup as well as similar environmental features, such as glaciers, volcanoes, rivers, and lakes. Here we characterize the chemical composition of source rocks in a cold, basaltic Mars analog source-to-sink system in Iceland and compare them to adjacent sediments. If the source rocks are primarily composed of palagonite, a glassy product of hydrothermal alteration of volcanic glass that weathers easily, we hypothesize that palagonite is the dominant component of the sediments. We analyzed the samples using Micro X-ray Fluorescence (μXRF) to examine thin sections of rock for changes in the elemental composition, and X-ray Fluorescence (XRF) to measure the bulk chemical composition of rocks and sediments. We used thin section classification to quantify the percent proportion of altered rock (palagonite). In source rocks with relatively high amounts of palagonite (greater than 10%), there was no significant chemical difference. The sediment samples are higher in Al, Si, and Fe and have less Mg and Ca. The difference in sediment and source rock chemistry indicates that another process is occurring, such as chemical weathering, sediment sorting, or that palagonite is a major portion of the sediments.

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

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

The purpose of this study is to understand recent developments regarding curriculum standards for teaching Indigenous histories and contemporary matters, specifically within Michigan’s K-12 Public Schools(MPS). This presentation draws from interviews with a range of stakeholders, including: current and former students and educators within MPS; politicians and government officials involved in relevant legislation; university professors concentrating their work in Native Studies at universities in Michigan; and representatives of Tribal Nations located in Michigan. This project also integrates relational discussions with Washington-based educators involved in the teaching and implementation of Washington’s Since Time Immemorial (STI) Curriculum. This presentation will share research analyses of relevant pieces of legislation and academic sources pertaining to Indigenous-centered curriculum. The objective of this research is to inform a written piece addressing current efforts to expand education on Indigenous histories and contemporary matters in MPS including efforts made in the past, actions currently in progress, suggested plans for the future, and what Michigan may learn from Washington’s efforts to fully implement STI through examining shortcomings in the implementation of STI curriculum and how these failures may serve to inform Michigan’s protocol for introducing revised standards. Given that one of the major proposals to the expansion of Indigenous-related curriculum involves teaching Indian Boarding School histories, the long-term implications of this research contribute to ensuring youth are educated about the devastating consequences of residential schools, which in turn aims to assure similar policies are not introduced in the future. Discussion of these findings will emphasize institutions which allow(ed) destructive policies like that of boarding schools to be implemented, reframing the common narrative perpetuated in schooling systems that such policies are the result of a few “bad actors.” This research is interested in exploring how curricula contribute to the latter perspective, and whether newly implemented standards effectively convey the former viewpoint.

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

The endangered Western Pond Turtle (Actinemys marmarata) was once a broadly distributed species across a large range from Western Washington to as far south as Baja, Mexico. However, unprecedented amounts of population loss driven by exploitation as a food source, wetland development and the destruction of habitat began to plague this species beginning in the early 1900s. As a result, the Washington State Department of Fish and Wildlife (WDFW) and the Woodland Park Zoo created six reestablishment sites that proved to be successful, elevating the number of turtles from 150 in the 1990s to around 900 individuals today. Threats to this species persist, making it more crucial than ever to locate new reintroduction sites to increase population numbers and promote self-sustaining populations. Our analysis is focusing on determining if the Union Bay Natural Area (UBNA) could be a potential 7th reestablishment site through the utilization of a habitat suitability index (HSI) with ArcGIS Pro and comparisons with Klickitat County and Pierce County sites. We anticipate that UBNA displays the habitat characteristics capable of promoting occupancy by the Western Pond Turtle. Furthermore, given UBNA’s popularity as a bird watching hotspot, we will also establish a kiosk intended to raise public awareness, educate the public about its threats, and display a map demonstrating their current and potential re-establishment zones as shown by our analysis. This kiosk includes a website linking the general public to a survey allowing visitors to record turtle sightings that can be accessed by future researchers. This study has widespread implications in terms of wildlife conservation, endangered species recovery and the management of threatened species.

Cryo-electron microscopy (Cryo-EM) plays a crucial role in macromolecular complex structure analysis, which helps to understand the cellular mechanism and pathologies to facilitate drug discovery and delivery. However, due to factors such as the target conformational change, damage during imaging, or improper sample preparation, low-resolution maps could be reconstructed and pose challenges to the structural analysis. Prior studies have employed different generative deep learning models to enhance the resolution or readability, performing well most on medium-resolution maps but failing to operate with even lower ones. Here, we proposed another modified diffusion model to enhance the cryo-EM density map resolution, expanding the input range of up to 10 Å. Based on the latent diffusion models, we enable it to work directly in 3D density maps with the conditioning factor to utilize the local resolution estimation rather than a fixed global resolution value for the attention mechanism. Compared with the previous work, the conditioning factor further improves the model's stability and robustness, especially in cases where the structure undergoes conformational changes. Our ultimate objective is to provide an improved and efficient solution for cryo-EM density map analysis, enhancing the process's accuracy and efficiency.

Chronic nonbacterial osteomyelitis (CNO) is an autoinflammatory bone disease that causes bone pain and destruction in children. Anti-inflammatory treatments for CNO can be effective, but there are not any FDA-approved medications specifically for CNO use, so there is interest in determining the effectiveness of different treatments for CNO. While CNO etiology is unknown, previous pathology studies indicate osteoclastogenesis plays a critical role in CNO pathogenesis. Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) was shown to inhibit osteoclastogenesis derived from peripheral blood mononuclear cells (PBMCs) in adults with active rheumatoid arthritis. Our objectives are to determine whether osteoclastogenesis is altered in children with CNO and the effect of abatacept, a CTLA-4 analog, on osteoclastogenesis. We collected samples of PBMC and serum from healthy subjects and children with active or inactive CNO. We incubated patient serum samples with CD14+ cells isolated from a commercial PBMC pooled sample with MCSF and RANKL, which are necessary for osteoclast proliferation and differentiation, for 7 days before staining for osteoclasts. To determine abatacept’s effect, we incubated PBMCs from patients with MCSF and RANKL with or without abatacept (CTLA-4 analog), performed DAPI and TRAP staining, and counted osteoclasts using the computer software, Image J. Osteoclasts were defined as TRAP-positive cells with 3 or more nuclei. We intend to use multivariable linear and mixed-effects regression models to estimate the average group effect on osteoclast counts from the serum study and PBMC study and the impact of abatacept on osteoclast counts. Expected statistical results of the Serum and PBMC study include an increase in osteoclastogenesis from PBMCs of children with active CNO compared to other groups, and a decrease in osteoclastogenesis with abatacept treatment. This is an ongoing study, and the results will shed light on the effect of abatacept on osteoclastogenesis and its potential therapeutic use in children with CNO.

Chronic nonbacterial osteomyelitis (CNO) is an autoinflammatory bone disease that mainly affects children and adolescents. Disease monitoring is challenging as reported pain is not reliable and imaging is not always obtained at all clinic visits. To date, patient-reported outcomes used in CNO research have not yet been validated in this population. The Patient-Reported Outcomes Measurement Information System (PROMIS) questionnaires, validated in other pediatric rheumatic diseases, are administered to patients enrolled in the prospective multisite Chronic Nonbacterial Osteomyelitis International Registry (CHOIR) since 2018. Our objective was to assess the convergent and responsive validity of the PROMIS instruments in patients with CNO. Patients with CNO consented and enrolled in CHOIR. Self-reported PROMIS questionnaires of fatigue, pain interference (PI), pain behavior (PB), mobility, upper extremity (UE), physical activity (PA), and strength impact (SI) were administered to patients. External validation surveys were administered to assess patients’ perception of the difficulty of use of limb/back/jaw, fatigue, sadness, and worry on a 0-10 scale, disease status, and status change. More than 1,000 clinical visits from 184 patients were associated with self-reported PROMIS questionnaire entries. PROMIS scores correlated significantly (p<0.01) with patient-reported variables and physician global assessment (PHGA). The correlation with function and PHGA was good for Mobility, PB, and PI. All PROMIS scores, except physical activity, correlated significantly (p<0.05) with patient-reported disease status. After effective treatment when the clinical disease activity score improved by at least 2.5 points, the change of PROMIS scores from Mobility, PB, PI, and UE was significant. PROMIS questionnaires provide valuable information about the disease status of children with CNO and correlate well with self-reported functional and other psychosocial domains. Mobility, PI, and PB show sensitivity to change after effective treatment or with disease status change. These instruments are useful for CNO clinical disease monitoring and research.

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

According to the Kaiser Family Foundation, almost half of the US population resides in areas with a shortage of mental health professionals. The United States Census Bureau states that 26 million Americans do not have health insurance. Without insurance, a single mental health session can cost hundreds of dollars. Due to these factors, people are looking for alternative ways to address their mental health issues. The purpose of the research being conducted is to create conversational AIs that provide many benefits that a psychotherapist could offer, such as engaging the user in deep conversations, building relationships with the user, and providing apt responses, while avoiding some demerits like patient disclosure and preconceived bias. The research being conducted makes use of Machine Learning and Natural Language Processing models in its development, which is unlike most other popular mental health chatbots that uses a decision-based approach to find the best responses. The anticipated goal of our study is to better understand user comfortability and challenges with the AI therapist that is in development and how to better optimize it for a wider audience. By developing an AI solution that provides the benefits of a psychotherapist, we can better address the mental health crisis and worker shortage in America that predominantly affects low-income and underrepresented communities. The expected result would be a live chatbot application that can understand the mental health issues of the user, and provide advice and suggestions relevant to the user's concerns and issues.

Prostate cancer is the most common type of cancer amongst men in the U.S. It relies on androgens that bind to the androgen receptor (AR), which increases the transcription of genes associated with the growth and proliferation of the prostate cells. For the AR-driven prostate cancer (ARPC), current treatments involve decreasing androgen levels (Androgen Deprivation Therapy) or inhibiting the ARPI (Androgen Receptor Pathway Inhibitors). However, around 15% of patients develop resistance to these treatments, resulting in a type of prostate cancer called neuroendocrine prostate cancer (NEPC). NEPC cells are no longer dependent on AR activity, which makes this subtype difficult to treat with the current treatment options in the clinic. To better understand the biology of NEPC, we focused on gene expression at the protein synthesis level and found that NEPC has a decreased level of a tRNA called Arg-TCT-1-1. Following Arg-TCT-1-1 tRNA overexpression in NEPC, we detected elevated expression of AR downstream targets via qPCR and western blot. NEPC with high Arg-TCT-1-1 also responded to an AR inhibitor called enzalutamide as measured by cell viability assays. To further investigate the role of Arg-TCT-1-1 in prostate cancer, we used shRNA-mediated knockdown of this tRNA in prostate cancer cells with high AR expression and measured changes in gene expression. This study will provide important insights on the role of Arg-TCT-1-1 during the differentiation process from ARPC to NEPC.

To perform its function as a tumor suppressor, breast cancer 1 (BRCA1) must dimerize with BRCA1-associated RING domain protein 1 (BARD1). Due to this critical interaction, pathogenic BARD1 variants are also associated with increased breast and ovarian cancer risk. Genetic testing has identified many rare single-nucleotide variants (SNVs) that cause missense amino acid substitutions in BARD1. Currently, 93% (1,692 of 1,819) of BARD1 missense SNVs are classified as a variant of uncertain significance (VUS) in ClinVar. A VUS classification prevents clinicians from using genetic test results to guide patient care. Consequently, there is a strong need to functionally assess BARD1 SNVs to help resolve VUS. We applied a multiplex assay for variant effect called saturation genome editing (SGE) to functionally assess all possible 12,000 SNVs and 2,300 3-base deletions in BARD1. In SGE, we use CRISPR-Cas9 to edit all possible SNVs into a region of BARD1 in haploid HAP1 cells. BARD1 is essential for cell growth, therefore cells edited with loss-of-function variants become depleted from the population. We track which SNVs become depleted from the population by sequencing. We then generate functional scores for each variant by calculating the change in the abundance of a variant in the original SNV library versus its abundance in the cell population after 13 days in culture. Thus far, I have generated reagents for all 14,300 variants and 2,400 have completed the full experimental pipeline. Functional scores for the functionally critical BRCA1 interaction domain show depletion of 94% stop-gain, 48% splice-site, and 21% missense variants relative to 5% synonymous and 6% intronic variants. This ultimately demonstrates SGE’s ability to accurately identify functionally normal and loss-of-function BARD1 variants. Generating functional scores for all possible BARD1 variants will provide the functional evidence needed for reclassifying BARD1 VUS and definitive test results for providers treating patients with BARD1 variants.

Using data from the United States Sentencing Commission (2014-2022), this study analyzes the impact of a defendant's gender in the sentencing of federal homicide cases. Previous research shows that female defendants experience leniency in criminal sentencing compared to male counterparts. However, studies also suggest harsher punishments are given to female defendants when the crime is violent. This may be influenced by the social construct of gender, where traits including aggression and violence are perceived to be inherently male, and male violence is often expected and excused. Focusing exclusively on federal homicide cases from fiscal years 2014-2022 (N = 3017), I ran linear regression analyses controlling for legal and extralegal factors to analyze the effect of gender on sentence length. I hypothesize that in the case of federal homicide, male defendants will receive shorter sentences compared to female counterparts. This study focuses how gender influences sentencing outcomes in federal courts. It is crucial to understand how gender influences judicial sentencing in order to promote a just legal system.

Fractal dimension, a measure of geometric complexity, finds application in image analysis, biology and medicine, neuroscience, geology and various other fields, yet existing methods often lack adaptability to finite data sets. Using ideas rooted in geometric measure theory, such as Hausdorff measure and Frostman’s Lemma, this research introduces a novel approach to compute fractal dimensions for finite sets, addressing limitations of traditional methods. Using Python, we developed and tested an algorithm to validate known sets such as the unit interval, square, cube, and fractal objects including the Cantor set and Sierpinski triangle. Comparative analysis was also conducted on established methods, including box-counting and correlation integral algorithms, to demonstrate the algorithm's accuracy in determining fractal dimensions. Pivoting towards data sets, we expect to use the computed fractal dimension of real data as a tool for assessing data and optimizing data compression. Our methods offer an improvement as most existing techniques use statistical methods that are limited to integer dimensions. In addition, recent studies have shown that fractal dimension values can be useful as features in machine learning. We also improve upon the calculation of the local dimension of regions in a data set, allowing for additional insights into complex data sets. This includes identifying regions of high complexity, and we expect to show that this allows for the more effective use of algorithms such as principal component analysis. All of these are increasingly important in our society due to the abundance of high-dimensional datasets in both the physical and social sciences. Overall, the benefits of studying novel ways of calculating the dimension of large data sets include efficient representation of data, improved interpretability, and decreased computational burden, as well as detecting certain features in data such as regions of high complexity.

In mammals, circadian rhythms are regulated by a hierarchy of oscillators governed by a central circadian pacemaker in the suprachiasmatic nucleus (SCN), which is principally entrained by the light-dark (LD) cycle. Recent experiments in our lab have revealed that cyclic 24-h fearful stimuli can act as a potent nonphotic zeitgeber, entraining circadian rhythms of behavior in mice and rats. This discovery utilized a naturalistic rodent cage with a safe nesting area separated from a foraging area where feeding and drinking occur. While foraging behaviors naturally occur at night, when the foraging area is rendered dangerous by nocturnal aversive stimuli (footshocks), animals entrain behaviors to the shock schedule by shifting activity to the daytime. Under conditions of fear-entrainment, SCN clock gene expression remains loyal to the LD cycle and the SCN is necessary but not sufficient for sustaining diurnal activity. Therefore, we propose the existence of extra-SCN fear-entrained oscillators capable of overriding SCN output and influencing behavioral timing. Here, we subjected 16 mice to either diurnal shocks (DS; control) or nocturnal shocks (NS) under a 12:12 LD cycle. Following confirmation of fear-entrainment, animals were released into constant conditions and sacrificed between 24-36h after the last presentation of footshocks, either CT 1 or CT13. Brains were dissected, sliced, prepared for immunohistochemistry processing, and c-Fos protein quantification is currently underway in the SCN, basolateral amygdala, paraventricular nucleus of the thalamus, and dentate gyrus. We hypothesize that c-Fos expression within the SCN will align with the LD cycle, while centers involved in fear processing and memory will exhibit altered levels of c-Fos expression in response to time-specific fear. Results from this study may be useful for identifying putative brain regions containing fear-entrainable oscillator(s).

Alzheimer’s disease (AD) is the most common neurodegenerative disease, with over 6 million Americans suffering from the illness and prevalence increasing each year. My work was conducted as part of an NIH-funded multi-institutional network called TREAT-AD (TaRget Enablement to Accelerate Therapy Development for AD) that aims to find potential therapies for AD. The bioinformatics core of this network identified genetic targets of interest using RNA-sequencing and proteomic analysis of post-mortem tissue from participants with AD. We hypothesized that manipulating expression of these target genes in a relevant human model would influence levels of AD-related biomarkers. To manipulate genetic expression efficiently, I used shRNA technology in human induced pluripotent stem cell (hiPSC) derived neurons. I then analyzed these hiPSC-derived neurons for AD-relevant readouts, such as soluble amyloid beta secretion and intracellular phosphorylation of Tau protein, relevant to the two main neuropathological hallmarks of AD. I ran quantitative polymerase chain reactions (qPCR) to measure neuronal expression levels of each gene target, and compared amyloid beta and phosphorylated tau outputs to control samples using MSD ELISA assays. I found four gene targets that have substantial neuronal expression and found that each affected AD-related output levels when gene expression was knocked down with shRNA. My findings provide direct molecular genetic evidence that links these genes to AD pathways, suggesting that these genes could serve as promising targets for therapeutic development.

6PPD-quinone (6PPDQ), a transformation product of an anti-oxidant used in tire manufacturing, was recently identified as the causal agent of acute mortality in coho salmon. Abrasion on tires by road surfaces create tire wear particles (TWPs). Both TWPs and the accumulation of waste tires pose risks of leaching 6PPDQ into stormwater runoff. Crumb rubbers, which are manufactured to reduce landfill tire waste and applied in turf infills, may also leach 6PPDQ. My research aims to determine the conditions at which crumb rubber can be pyrolyzed to prevent 6PPDQ leaching from tire recycling options. If pyrolysis successfully removes 6PPDQ from crumb rubber, then the resulting material can be applied as an absorbent tire char to remove contaminants from water. Waste tire crumb rubber samples were pyrolyzed in a tube furnace under nitrogen flow for 90 minutes at a range of different temperatures. Methanol-based solvent extraction was used to extract the remaining 6PPDQ from the pyrolyzed samples and diluted until suitable for liquid chromatography-tandem mass spectrometry (LC/MS/MS) analysis. It is observed that as the pyrolysis temperature increases, the mass of 6PPDQ leached from pyrolyzed crumb rubber decreases. The results of this study allow us to understand the limitations of pyrolyzing tire rubber to develop activated carbon. To further investigate the feasibility of waste tire activated carbon, a chemical activation step will be added in pyrolysis to better replicate the creation of activated carbon.

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

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

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

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

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