Tuberculosis (TB) remains a major global health challenge, causing over a million deaths annually despite being a curable disease. A critical issue is treatment non-adherence, as many patients struggle to complete the required six-month regimen due to a lack of support and access to reliable medical guidance. Improving treatment adherence can significantly increase recovery rates and save lives. This project develops an AI-augmented chatbot powered by GPT-based models to assist Spanish-speaking TB patients. This is done by providing accurate medical guidance, fostering empathy, and enhancing communication between patients and healthcare providers. Integrated into a Human-System Interaction (HSI) interface, the system employs three AI models: a two-step pipeline that classifies messages as informational or emotional to tailor responses appropriately, a few-shot model that generates responses based on examples from prior patient interactions, and a Retrieval-Augmented Generation (RAG) + few-shot model that retrieves relevant medical information from guidelines while maintaining conversational fluency. These models leverage the same underlying technology as ChatGPT, optimizing responses for accuracy, linguistic fluency, and empathy. As part of the research team, I contributed to model development and implementation, ensuring alignment with medical guidelines and human-centered design principles. The chatbot is currently undergoing external evaluation by a multidisciplinary team, including healthcare professionals specializing in TB treatment and AI researchers. Evaluators interact with the chatbot using personas as TB patients, asking medical and support-related questions to assess response quality. They rate the system based on medical accuracy, linguistic fluency, empathy, and other key criteria relevant to patient-provider communication. Insights from this evaluation will guide future refinements, with the goal of improving AI-driven patient support systems in clinical settings.

Prenatal lead exposure is associated with learning and behavior problems, reduced growth, and increased risk of miscarriages. The Centers for Disease Control and Prevention and the American College of Obstetricians and Gynecologists recommend lead exposure screening for pregnant women due to the significant health risks lead poses to their developing fetus. However, there is no nationally recognized screening tool, leading to inconsistent practices and potential gaps in care across the country. This project aimed to address this gap by identifying state-specific screening resources for clinicians and creating a tool to help healthcare providers more easily access these resources. Through web searches, emails, and phone calls to 50 state health departments, 20 state-level screening resources were identified, along with county-level resources in three counties with childhood lead poisoning prevention programs. These resources were compiled into an interactive map directing clinicians to screening resources in their region. This tool is being reviewed for potential use by the Pediatric Environmental Health Specialty Units, an organization that provides free pediatric and reproductive environmental health consultation services to clinicians. The tool addresses the barrier to accessing screening resources, ideally increasing lead screening rates and improving pediatric health outcomes. The findings highlight the need for a national screening tool and provide insights into regional differences in recommended screening practices.

Acute Pancreatitis (AP) is a sudden inflammatory condition of the pancreas that can lead to significant mortality. Despite its rising prevalence and associated healthcare burden, treatment options remain limited to supportive care, with mortality rates in severe cases reaching 30%. Activin A is a key contributor to AP, interacting with the ACVR2A receptor to regulate various pathophysiological processes, including inflammation through immune cell recruitment. This study hypothesizes that activin A binds to ACVR2A to activate the ERK pathway, leading to increased NF-κB expression and elevated production of pro-inflammatory cytokines, including TNF-α and IL-1β. Experiments were designed using the 266-6 immortalized pancreatic acinar cell line and RAW 264.7 macrophages. These cells will be cultured for western blot analysis, ELISA assays, and transwell migration assays following activin A stimulation. Lower ERK phosphorylation and reduced NF-κB expression are expected when cells are treated with ACVR2A inhibitors in combination with activin A, compared to activin A treatment alone. ELISA assays are anticipated to confirm increased TNF-α and IL-1β production in 266-6 cells following activin A treatment. Macrophage migratory capacity is expected to increase when exposed to conditioned media from activin A-treated 266-6 cells. These findings will provide insights into the role of activin A in AP pathophysiology, potentially identifying new therapeutic targets for mitigating pancreatic inflammation and immune cell recruitment.

Increased mitochondrial oxidative stress causes fatigue and metabolic dysfunction in muscle tissue. It is unclear whether the oxidative stress is due to elevated production or impaired consumption of reactive oxygen species (ROS). The purpose of this study is to test whether the capacity of the antioxidant defense system is impaired or the mitochondrial ROS production rate is elevated in response to chronic changes in mitochondrial oxidative stress. To experimentally manipulate mitochondrial oxidative stress, we use an inducible mouse model to knockdown superoxide dismutase 2 (SOD2) in skeletal muscle and heart to increase oxidative stress, and exercise training to decrease oxidative stress. Knockdowns (KD) or littermate controls (CON) performed a six-week voluntary wheel running (EX) or sedentary control intervention (SED). Following completion of the intervention, I isolated heart and skeletal muscle mitochondria using differential centrifugation. I measured mitochondrial hydrogen peroxide (H₂O₂) production rate and tested the antioxidant capacity by treating isolated mitochondria with Auranofin (AFN) or 1-chloro-2,4-dintrobenzene (CDNB), which inhibit the thioredoxin and glutathione S-transferase components of the mitochondrial antioxidant defense system, respectively. KD heart and skeletal muscle had similar absolute H₂O₂ production rates compared to CON, but normalized to oxygen consumption the KD had significantly higher H₂O₂ production. Since absolute H₂O₂ production under vehicle conditions was not different, this suggests that the antioxidant capacity adapts to meet the changes in mitochondrial H₂O₂ production. We will collect data from the exercise-trained cohort next month. I expect to see an increase in H₂O₂ production rate and antioxidant capacity in both groups due to the increased mitochondrial biogenesis from exercise training. These results demonstrate that chronic increases in mitochondrial oxidative stress decrease mitochondrial H₂O₂ production capacity from skeletal muscle.

Dementia, a growing global health concern, affects the nervous system and leads to severe cognitive impairment, with Alzheimer’s disease (AD) being the most common form, currently impacting nearly 7 million Americans. As life expectancy increases, the prevalence of dementia increases in corresponding fashion, driving research efforts like those of the Darvas Lab, where we study AD and other related dementias using adeno-associated viruses (AAVs) to induce neuropathologic changes. The TDP43 protein is involved in neuropathologic changes such as those in Frontotemporal Dementia (FTD) and in Amyotrophic Lateral Sclerosis (ALS), a primary motor neuron disorder. TDP43, primarily localized in the nucleus, plays a crucial role in regulating gene expression and RNA metabolism. TDP43 pathology in neurons involves the presence of TDP43 in the cytoplasm and its accumulation in cytoplasmic inclusions. To better understand the role of TDP43 in neurodegeneration, we use a mouse model where TDP43 proteins are introduced via AAV, a genetically engineered viral vector commonly used in research. This approach allows control over the timing of neuropathologic changes. Our prior AAV constructs included the Synapsin I promoter, which led to a severe ALS-like motor phenotype due to its expression in spinal motor neurons. However, this model could not be used to study the more subtle effects of dementia due to the extreme nature of the physical pathology. Therefore, our goal is to produce a new model to overexpress TDP43 using an AAV that is exclusive to the cortical brain regions relevant to FTD by instead including the CamKIIα promoter, which exclusively drives expression in the forebrain. I assessed behavioral phenotypes in our mouse model by conducting a Y-maze to evaluate effects on short-term memory, and analyzing neurological scoring to evaluate neuromuscular dysfunction. The development of a more dementia-focused TDP43 model will allow us to more specifically investigate its neuropathology.

My research project focuses on age-related changes in muscle function. We have previously designed and used novel young and naturally aged in vitro three-dimensional engineered muscle tissues (3D-EMTs) using donated myoblasts from the Study of Muscle, Mobility, and Aging (SOMMA) to investigate this. A question raised in this research is the how closely force measured in 3D-EMTs correlates to in vivo force of intact skeletal muscle. To address this, I stimulated young and aged mice's gastrocnemius muscles to contract (Aurora Instruments) measuring maximum force, contraction/relaxation kinetics, and fatiguability. Mice were then sacrificed and hindlimb muscles dissociated to isolate skeletal muscle myoblasts for cell culture. Myoblasts were amplified and used to generate young and aged rodent 3D-EMT. We tested in vitro 3D-EMT muscle mechanics using a Magnetometric Analyzer for engiNeered Tissue ARRAY (MantARRAY, Curi Bio). In vitro muscle force data was compared to in vivo force data from the same mouse. Results generated by this project helped identify the correlation between in vivo and in vitro force measurements and how they are impacted by age. This study also allowed us to bank multiple cell lines for future high throughput studies to utilize these rodent 3D-EMT models to study the progressive loss of muscle mass and function known as sarcopenia. The results from this project and the cellular models created will be used in the future to investigate potential targets for therapeutic interventions to treat sarcopenia in an ever-expanding aging population.

Pancreatic Ductal Adenocarcinoma (PDAC) is a deadly disease without prognostic tools for early detection or effective therapeutic strategies. Activin A is a cytokine that is upregulated in tumor and stromal cells that surround the tumor in PDAC and acts as a promoter of metastasis. Activin A has also been shown to stimulate the AKT pathway which is proto-oncogenic. Here, we set out to test the hypothesis that activin A drives PDAC development through the AKT pathway. Western blots for proteins of the AKT pathway (phospho-PRAS40 and phospho-β-catenin) and transwell migration assays will be performed on PanC1 pancreatic cancer cells stimulated with activin A. Additionally, inhibitors of the activin A receptor subtype 2A (ACVR2A) and the AKT pathway will be included to delineate receptor-specific effects. Given activin's known role for simulating the AKT pathway, it is expected that activin A stimulation will phosphorylate and trigger increased migratory capacity of PanC1 pancreatic cancer cells. Inhibitor experiments will confirm that these effects are ACVR2A specific. This data will identify if activin A is a novel therapeutic target in late stage PDAC, a disease with limited targeted pharmacological treatments. 

Protein subunit vaccines are highly used today as an alternate vaccine platform to older vaccines such as live-attenuated viruses. They contain a protein antigen of the virus or bacterium that can be recognized and targeted by the immune system, and an adjuvant that amplifies the immune system response to this protein by widely putting the immune system on alert. The most commonly used adjuvants pose the risk of possible adverse reactions and are not created to target specific immune pathways, but rather stimulate general inflammation. To design a vaccine adjuvant that generates a more targeted immune response, we are using the self-assembling protein nanoparticle, I53-dn5, to display a CD40 binder that mimics the T Cell ligand, CD40L, by binding to B cell surface receptor CD40. We aim to create a particle that can replicate the binding interaction between B and T cells in the lymph node responsible for triggering antibody maturation, and B cell proliferation and differentiation. We hypothesize that this multivalent display of CD40 binder will generate potent B cell responses allowing us to respond to an antigen more effectively than current adjuvants. We are utilizing computational protein design methods like RFDiffusion, ProteinMPNN, and AlphaFold2 to optimize this display, and testing these designs in vitro for stability and ability to elicit downstream signaling effects of the CD40/CD40L interaction. This research holds two promising innovation potentials. The first is creating higher potency adjuvants by stimulating specific signaling pathways for use with protein subunit vaccines. Secondly, these materials can be used as a more stable and potent molecule in biochemical assays such as being an alternative to feeder cell lines in B cell support culture.

According to the CDC report in 2022, Indigenous women experience 58% of intimate partner violence cases, which is one of the primary causes of homicide. The Reauthorization of the Violence Against Women Act (VAWA) has been credited for expanding protections for Indigenous women. This included increasing the provision of crimes under Tribal Jurisdiction and creating a pilot program for Alaskan Natives to prosecute non-Native offenders in villages. However, this policy reveals a gap between written law and people's experiences. This study examines the effectiveness of VAWA strategically, what demands were left out, and what those gaps represent in demanding changes through intersectional advocacy. In this qualitative research, I created a codebook to analyze the VAWA Congressional hearings from 2009 to 2022 to track the evolution of policy reforms from Indigenous activists. Applying a high-level textualized analysis by gathering a literature review, I utilized the framework of intersectional advocacy, which identifies the extent to which laws and interventions can create meaningful linkages across issues experienced by multiple marginalized people. VAWA remains to be a product of limitations in representation and holistic change to advance the needs of Indigenous people. Expected findings suggest that future policy reforms move beyond analyzing the issue through the lens of individuals to a community-based perspective. Intersectional frameworks will become a cornerstone of future policy work by propelling conversations centered around restorative well-being and healing. Creating bridges between people's lived experiences and legal institutions is foundational to creating critical correspondence. 

Xylazine is a veterinary sedative that has become a common adulterant in fentanyl products due to its ability to prolong the euphoric effects of fentanyl. Adulterated drug mixtures containing xylazine have been linked to an increased risk for respiratory depression and fatal overdose. Existing treatments for overdose such as naloxone do not work against xylazine and there is currently no FDA approved reversal agent for xylazine toxicity. Monoclonal antibodies (mAbs) are a promising therapeutic option to reverse drug overdose and can be used to target small molecules by sequestering them in the bloodstream and preventing their passage into the brain. Previously, we made a series of xylazine haptens and formulated them into vaccines where they were found to induce strong antibody responses, reduce brain to serum ratio of xylazine, and mitigate respiratory depression in Sprague-Dawley rats. Based on the protective effects of our xylazine conjugate vaccines, we hypothesized that we can create an effective reversal agent by isolating xylazine specific mAbs. In this study, we immunized mice with xylazine conjugate vaccines to generate antibodies specific against xylazine. We then used the secondary lymphoid organs of the vaccinated mice to establish stable mAb producing cell lines using hybridoma technology. Hybridomas were screened with ELISA and lead candidates were selected and sequenced for further characterization. We will conduct in-vitro characterization assays to quantify binding affinity, functional activity, and thermostability of our lead mAbs. Furthermore, in-vivo studies will assess the efficacy of our mAb lead candidates in rodent models.

Cave formations, also called speleothems, are natural archives of past climate conditions. Analysis of these speleothems can provide information about environmental changes over thousands of years. Church Mountain Cave is in the Northeast Cascades and is distinctly characterized by its unusually predominant speleothems, which is relatively unusual for western Washington. This project explores the potential of Church Mountain and other caves as paleoclimate archives. I begin with a characterization of Church Mountain Cave, focusing on cave morphology, stratigraphic and structural position of the cave, and forming a hypothesis of cave formation and fault activity. This classification will allow for a detailed view on Church Mountain Cave and the factors impacting speleothem formation. We also characterize a range of speleothems from other caves using trace element and isotope analysis, with the eventual goal of using uranium-thorium dating to establish precise ages and stable isotope analysis with oxygen isotopes to infer past temperature, precipitation patterns, and other environmental factors. By refining regional paleoclimate reconstructions, we can improve predictions of future climate trends and extreme weather events. Additionally, this study underscores the importance of caves as climate archives and highlights the need for conservation efforts to protect these valuable and fragile environments for continued scientific research. 

Historical archaeologists understand toys in the material record to explicitly mark past activities of children. This project focuses on the play activities of enslaved children on North American plantations through the toys they left behind. We used data from the Digital Archaeological Archive of Comparative Slavery (DAACS) to explore the material evidence for identity formation and socialization of enslaved children based on existing studies on enslaved childhoods. Specifically, we investigated the following questions: what materials and manufacturing techniques were most frequently used in the creation of the toys of enslaved children on North American plantations? Based on the associated costs of these materials, what is the range of expense exhibited by enslaved children's toys? What role might toys have played in enslaved children’s agency or passivity in socialization? To address these questions, we queried the DAACS repository concerning object specifications like material and manufacturing technology for toys excavated from North American plantations. This data was imported into RStudio, where we used programming packages to clean it and create visualizations to convey trends. Our pilot project (48 toys) found that porcelain and a molding technique were most frequently used, materials with varying expenses were present, and some toys exhibited post-manufacture modifications. We now have data on 599 toys from 41 sites on 13 plantations, greatly improving our representation of enslaved children in the material record. In this poster we present the result of our analysis of this large data set and compare the locations. The findings of this research will help to fill in gaps of a larger conversation about the relationship between childhood play and race, and more broadly contribute to archaeology’s attention to past social dynamics.

The Aurignacian, a major cultural phase of the Upper Paleolithic, was characterized by remarkable advancement in the social and cognitive capacities of human beings. This period is marked by technical innovations - such as bone tools and weapons, and artistic developments - in the form of cave paintings and portable art. Evidence from this time period also suggests the emergence of social groups spread across Europe. We investigate interactions between these groups by studying the distribution of objects with engraved geometric signs. We use data from SignBase, a large catalog of archeological data from European Paleolithic sites to quantify group areas and site hierarchies, identifying potential ‘checkpoints’ and ‘central places’. Applying seriation, networks analysis, and measures of sign richness and diversity, we examine how the social dynamics change over the four sub-periods of the Aurignacian. We infer patterns of social group boundaries and interactions, improving our understanding of the structure and complexity of Aurignacian social networks.

Prostate cancer has a significant heritable component. It is estimated that 10-15% of patients with advanced prostate cancer carry an inherited predisposing genetic mutation, and these patients generally present with a younger age of onset and a strong family history of cancer. The standard in the field of oncology is to conduct short-read DNA sequencing on such patients to find predisposing mutations. While short-read sequencing does well to identify simple mutations that cause disease in many families, our lab concluded that short-read sequencing misses critical mutations in many prostate cancer susceptibility genes. We hypothesized that prostate cancer in many families is due to complex inherited mutations such as genomic deletions, inversions, and mobile element insertions that are not detectable by conventional genomic technologies such as short-read sequencing. To test this hypothesis, our lab specifically recruited prostate cancer patients who, despite having family histories of cancer, did not have any mutations detected via conventional genetic sequencing methods. This project utilizes Nanopore long-read DNA sequencing, which reads DNA in longer fragments and can reliably detect complex mutations. My role is to conduct long-read sequencing on DNA samples from these patients, then analyze the DNA sequence for mutations. I have sequenced 32 patients so far and identified 4 complex mutations through long-read sequencing which were missed by other approaches. These complex mutations include insertions of repeat sequences and duplications which disrupt gene function in BRCA1 and BRCA2. This suggests that, consistent with our hypothesis, some patients who do not have mutations found via conventional sequencing methods do indeed carry causative mutations in well-established prostate cancer risk genes. By finding these mutations, patients can receive more targeted and effective cancer treatment, and undiagnosed family members stand a better chance of catching cancers at earlier stages.

The activation of inflammasomes is a crucial component of the early immune response to pathogens and initiates a form of inflammatory programmed cell death called pyroptosis. During infection, a cytosolic inflammasome-forming protein sensor detects a pathogen to assemble the inflammasome complex, which subsequently activates the protease Caspase-1 (CASP1). CASP1 processes Gasdermin D (GSDMD), inducing pyroptosis through pore formation in the plasma membrane, while also facilitating the release of proinflammatory cytokines, such as IL-1β and IL-18. Adenovirus (AdV) is a common pathogen that causes inflammatory symptoms by infecting multiple mucosal epithelial tissues in the respiratory tract and intestinal tract such as the nose, mouth, and eyes. We wanted to test whether AdV infection could activate one of the main inflammasome sensors in human conjunctival epithelial cells (hCjE cells), which is NLRP1. However, we found that upon AdV infection, NLRP1-mediated cytokine release is absent, suggesting that CASP1 signaling is suppressed. Interestingly, despite the loss of IL-1β and IL-18, pyroptosis remains unaffected. Recent studies indicate that in the absence of CASP1, inflammasomes can activate Caspase-8 (CASP8), leading to the cleavage of Caspase-3 (CASP3) and Gasdermin E (GSDME), resulting in an alternative, incomplete form of pyroptosis. Thus, I hypothesize that during AdV infection, host cells are still able to induce pyroptosis by activating the alternative CASP8-GSDME pathway. To test this hypothesis, we generated and validated genetic knockouts of CASP8, GSDMD, GSDME, and CASP3 in hCjE cells to assess their roles in pyroptosis during AdV infection. These findings will provide new insights into viral immune evasion strategies and inflammasome regulation in epithelial cells.

Heart attack survivors experience elevated risk of subsequent events and death, as such there is a clinical need for regenerative techniques to rebuild damaged myocardium and reduce risk. Transplantation of human-induced stem cell-derived cardiomyocytes (hiPSC-CMs) into non-human primate hearts has been shown to significantly improve contractile function after heart attack, however, transplanted hearts were also shown to be at elevated risk for developing potentially lethal arrhythmias. Researchers developed a line of hiPSC-CMs to correct this arrhythmia-promoting behavior by inducing a series of four gene edits to prevent the hiPSC-CM spontaneous beating behavior known as "automaticity", these gene edits spawned the cardiomyocyte cell line dubbed MEDUSA (Modification of Electrophysiological DNA to Understand and Suppress Arrhythmia). I have conducted an in-vitro study of the electrophysiological effects of the MEDUSA edits, knockouts of the sodium-calcium exchanger NCX1, the hyperpolarization-activated pacemaker current channel HCN4, the low voltage Calcium ion channel Cav 3.2, as well as overexpression of the potassium channel Kir 2.1. I have employed immunofluorescence microscopy to analyze sarcomere structures, used lentiviral transduction of calcium-sensitive green fluorescent protein to quantify calcium handling, and constructed engineered heart tissue casts to measure contractile force, to compare the electrical and physiological characteristics of MEDUSA CMs and their wild-type counterparts. Characterizing the MEDUSA cell line is essential for identifying issues that could compromise the cells' ability to function in grafts while uncovering its potential for use in regenerative treatments. Here I show that the MEDUSA gene edits create arrhythmia-resistant cardiomyocytes without compromising the integrity of their structure or function, supporting the development of a regenerative therapy future for the field of cardiology.

There are a vast number of pathogens that impact global public health, necessitating an accessible assay capable of detecting multiple targets simultaneously. Lateral flow assays (LFAs) have the potential to fill this role as a cost-effective, rapid, and simple technology instrumental in the detection of many analytes. However, multiplexed detection using nucleic acid LFAs is difficult due to the increased chance of non-specific binding as more targets are added to the assay. In this work, we aim to increase specificity and multiplexing potential in LFAs. We first showcase the process of developing a nucleic acid LFA by evaluating both fluorophores and gold nanoparticles to generate a visible signal. As fluorophores require a fluorescent light source, we moved forward with gold nanoparticles, which have a readout visible to the naked eye. Additionally, we automated the LFA fabrication process using an Echo Liquid Handler. Finally, we assessed methods to convert double-stranded to single-stranded DNA, required for compatibility with LFAs. In the future, we look to optimize signal visibility while increasing multiplexability. This work highlights the potential of multiplexed LFAs as a robust technology capable of significantly improving public health responses and outcomes.

Abiotic stressors are an important driver of organism survival and community structure of epifauna in aquatic environments. Stressors present in estuaries are found in a gradient, as freshwater from rivers mixes with marine water. Marine epifauna have been shown to have both bottom up and top-down controls on ecosystems, which can promote the health of seagrass meadows ecosystems. In Washington state, eelgrass (Zostera sp.) grows across a gradient from coastal waters to estuaries; do abiotic stressors within this gradient determine what epifauna communities are supported in eelgrass? To consider for structure area, 30cm x 30cm artificial turf squares were placed in eelgrass beds overnight at two sites along an estuarine gradient in Willapa Bay (Washington, USA). Epifauna were collected by rinsing turf mats with freshwater, then preserved in ethanol and identified to family level. Following identification, this data will be used to explore the difference in community abundance (univariate statistics, ANOVA) and community composition (multivariate statistics, PERMANOVA). I hypothesize that there will be a difference in epifauna community structure in eelgrass beds between sites, specifically a shift in community composition with higher richness and abundance at the site closer to the ocean. Knowledge of how abiotic stressors influence community structure over estuarine gradients may act as a model for climate change and what communities are expected to be found as abiotic stressors change. How these communities may change as environmental stressors do is important, as epifauna are prey for many bird and commercial fish species.

Machu Picchu is an archaeological site in Peru that is an important source of information about the Incas. In the middle of the 15th century, Machu Picchu was established as an ancient city by the Inca Empire. However, their lives were disrupted by Spanish contact and disease. Smallpox spread from 1519 to 1520, which killed the emperor of the Inca Empire, Huayna Capac. Spanish contact in 1532 forced the Inca people to abandon Machu Picchu. My research investigates whether there may have been epidemics before Spanish contact and how they may have affected the Inca people. I applied survival analysis statistics to the raw data on human remains and compared the results to a known plague population from Europe. I also analyzed radiocarbon ages to detect epidemics in earlier time periods. The skeletal data analysis did not find strong evidence of pre-contact epidemics. The radiocarbon analysis suggests potential depopulation due to epidemics. I encourage future scientists to investigate with more data and a bigger range of periods before and after Spanish contact to further explore possible past epidemics in this region.

Within the complex landscape of the human genome, even a single mutation can trigger devastating neurological consequences. The reality is exemplified by a single missense mutation p.G192R in the RAB39B gene causing X-linked dominant Parkinson’s disease (PD) with reduced penetrance in females. Previously, loss of function mutations in the gene were associated with X-linked intellectual disability and autism spectrum disorder. RAB39B is a member of the human Rab GTPase family which plays a role in early autophagosome formation and is implicated in intracellular vesicular trafficking. This project investigates how defects in endolysosomal trafficking caused by the p.G192R mutation in RAB39B leads to pathogenic protein aggregates and subsequently, parkinsonism and neurodegeneration. To investigate this, we developed a RAB39 G192R Drosophila model which is characterized by neurodegeneration and protein aggregation using western blot, locomotor deficiency, and lifespans. Complementary to the Drosophila model, we developed a human neuronal model by generating induced pluripotent stem cells (iPSCs) from an affected male and similar age unaffected male from a kindred with X-linked PD due to the p.G192R mutation. Neurons differentiated from the iPSCs are analyzed for endolysosomal trafficking alterations by immunocytochemistry, and western blots for evaluating insoluble ubiquitinated protein aggregates and oligomerized forms of alpha-synuclein. Our preliminary results show increased ubiquitinated protein aggregation when a constitutively active RAB39 transgene was expressed in neuronal tissue. The G196R RAB39 adult flies appear morphologically normal, and the G192R mutation does not seem to affect dRAB39 protein expression in Drosophila. RAB39B G196R neurons also do not have altered expression of RAB39B, but have reduced cellular compartment size of p62-stained autophagolysosomes, and Plin2-stained lipid droplets. Understanding mechanisms underlying the pathogenesis of X-linked PD could reveal novel therapies to slow the rate of progression of neurodegeneration and development of PD.

Birdsong in the Machine is a soundscape composition that explores the evolving relationship between natural and artificial worlds through the story of the Streaked Horned Lark (Eremophila alpestris strigata), a threatened coastal songbird native to the Pacific Northwest. The central research question is: How can artificial intelligence (AI) and machine learning (ML) enhance environmental storytelling to amplify the voices of endangered species and reimagine human-nature-technology relations? By integrating AI-generated audio, wildlife recordings, and digital sound processing, this project critically examines the paradoxical role of technology as both a disruptor and preserver of ecological systems. Inspired by my lifelong connection to technology and deep appreciation for the natural world, Birdsong in the Machine reflects on the impacts of technological progress on the Streaked Horned Lark. The project draws from Donna Haraway’s A Cyborg Manifesto and the works of Bernie Krause and Thom van Dooren, challenging the perceived divide between the natural and artificial. It envisions a future where these realms coexist harmoniously, fostering collaboration rather than conflict. This composition combines recordings of the lark’s song and habitat with AI-generated audio, using machine learning models to emulate and predict natural soundscapes. Digital audio processing techniques integrate these elements into a cohesive narrative. Bibliographic, archival, and ethnographic research reinforce the ecological and artistic focus of the composition. Through its juxtaposition of organic and AI-generated sounds, Birdsong in the Machine illuminates the paradox of technology’s role in ecological degradation and preservation. The soundscape fosters empathy and awareness for endangered species while reimagining relationships between humans, nature, and technology. Future directions will explore the ethical implications of using AI in ecological art and expand collaborations with scientists and digital artists. Ultimately, this piece stands as both environmental advocacy and an artistic experiment, challenging audiences to rethink their place in the interconnected natural and artificial worlds.

Mutations in glucosidase, beta acid 1 (GBA) are the strongest genetic risk factor for Parkinson’s Disease (PD) and are associated with faster progression of cognitive and motor symptoms. We hypothesize that GBA mutations disrupt the endolysosomal pathway, altering extracellular vesicle (EV) biogenesis and impairing autophagy, leading to faster spread of Lewy pathology from cell to cell in the brain and consequently accelerated disease progression. To study this connection, we utilize a Drosophila model of GBA deficiency that exhibits increased protein aggregation and neurodegeneration. We found that expression of WT GBA in the muscle of GBA mutant flies reduces protein aggregation in the brain, and EVs isolated from these flies have normalized levels of EV-intrinsic proteins that were elevated in GBA mutant flies. These findings suggest that GBA deficiency mediates PD pathogenesis by accelerating the propagation of protein aggregation to distant tissues. To complement this fly model, we differentiate induced pluripotent stem cells (iPSCs) from a PD patient carrying a null GBA IVS2+1 mutation (GBA IVS PD), isogenic wildtype iPSCs generated by CRISPR repair of the IVS2+1 mutation (GBA WT PD), and iPSCs from an unrelated healthy age and sex match control into neurons. To further investigate how GBA influences EVs, I extract EVs from the GBA IVS PD, isogenic GBA WT PD, and sex-age-match control iPSC-neurons to determine if there is a difference in protein cargo in EVs from GBA deficient neurons. I hypothesize that higher levels of aggregated alpha-synuclein will be present in EVs from GBA deficient neurons. I utilize size exclusion chromatography to isolate EVs from neuronal conditioned media. I then conduct western blots to determine protein within EVs. Understanding how GBA mutations influence EV dysregulation and whether EVs act as a vehicle for spread of Lewy pathology could help us uncover new therapeutic targets to slow neurodegeneration.

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

In December 2022, the U.S. Department of Health and Human Services approved a State Innovation Waiver under section 1332 of the Affordable Care Act (ACA), allowing Washington State to provide health and dental insurance coverage to all its residents, regardless of immigration status, from 2024 to 2028. The goal of the Section 1332 waiver is to decrease the number of uninsured, minimize the cost burden of healthcare on individuals and the government, improve health outcomes, and address health disparities. Health insurance navigators, who help people select, enroll, and use health insurance coverage, are charged with implementing this policy change. Their contributions to improving access to health insurance for vulnerable communities are often undervalued, even ignored, but will be crucial to ensuring migrant, refugee, and undocumented individuals are able to enroll for health insurance. This project presents key insights gained from interviews with navigators working in public health departments, community-based organizations, non-profit hospitals, and health clinics across the state, as well as, policymakers and activists focused on expanding healthcare access for immigrant communities. Using semi-structured interviews with insurance navigators, I explored their responsibilities and tasks, the process of enrolling immigrant communities for health insurance, and training and resources that support navigators. Additionally, I analyzed official documents used for the section 1332 waiver application to examine the motivations and narratives used to justify this insurance access expansion. My research shows how navigators deal with punitive immigration policies, xenophobic political rhetoric, financial uncertainty, cybersecurity concerns, staffing inadequacies, and high demand. This project advances our understanding of the systemic constraints, decision-making processes, and discretionary power that shape access to and use of healthcare and will inform policies that aim to codify health equity for immigrant communities.

 Marine debris, classified as solid, man-made litter and material that has been lost or discarded in the ocean, is a persistent pollution issue in coastal regions around the world, and Puget Sound is not an exception. This research investigates the distribution and abundance of marine debris across various regions of Puget Sound and how they are changing over time. Since 1987, the Washington Department of Fish and Wildlife (WDFW) has conducted annual trawls to assess bottom fish populations in Puget Sound. The contents of these trawls provide valuable representation of the soft-bottom habitat, including the organisms and debris inhabiting the seafloor. The WDFW’s extensive records of these surveys include the location, depth, type, and abundance of debris collected in each trawl. With this dataset, I explore spatial patterns in different types of debris, examine trends in abundance over the last two decades, and identify hotspots for debris accumulation in Puget Sound. The results of this study contribute to a deeper understanding of the dispersal of aluminum, plastic, glass, fishing gear, and other debris that lie at the bottom of Puget Sound. Insights on these patterns are vital to informing effective clean up and guiding prevention efforts to create cleaner and safer waters for both humans and marine life. 

Discharge planning is an important component of safe and efficient hospital care. We are interested in how patients who live in a baseline unsafe situation conceptualize a “safe” discharge plan. Thus, our study aimed to understand the needs, perspectives, and priorities of patients experiencing homelessness as they prepare to leave the hospital. We conducted qualitative semi-structured interviews in 2023-2024 at a large urban, public, safety-net hospital in the Pacific Northwest. Any adult patient admitted to an acute care general medicine service who was living homeless was eligible. Patients with severe cognitive or mental health disorders that precluded consent process were excluded. This study was approved by our institutional IRB. Patients experiencing homelessness shared their perspectives on discharge planning in three major themes: 1) basic needs, 2) barriers to stability, and 3) role of healthcare systems. Within the theme of basic needs, respondents identified the importance of physical survival: shelter/warmth, protection from violence, and treatment for major injuries or illness. They identified key barriers to stability: loss of property, legal concerns, and financial challenges. While many respondents were hopeful that the role of the healthcare system might be to assist in these issues, they also acknowledged the existence of significant resource constraints. Many reflected on the way that U.S. society views poverty and the impact of policy and funding to what is feasible by healthcare providers. Several participants were aware of interventions that the healthcare system puts into place to achieve better outcomes but noted these may still be out of reach when basic needs are not met. We found that patients experiencing homelessness were overwhelmingly focused on achieving their basic needs, including physical survival and environmental stability. Current discharge processes should be tailored to individual lived experiences, especially with regards to housing status.

How do photographic archives “animalize” or “humanize” animals in enclosed cultural spaces, like museums and zoos? I analyze the work of photographers Eadweard Muybridge, George Wheelhouse, Jill Greenberg, and Britta Jaschinski, and taxidermist Damien Hirst to interrogate the terms “animalize” and “humanize” by attempting to distinguish between animal/animalized and human/humanized couplings. To understand the term “animalize” and our aversion to being likened to animals, I argue what we are so afraid of is not being animal, but occupying the attached social position—being objectified and dehumanized. In visual media, this objectification manifests through the visual capture and frozenness of animals. Meanwhile, there are two approaches to “humanization.” The conventional one—“humanization through familiarization”—engages with the similarities between humans and animals through the anthropomorphized positioning of animals. The second, less conventional approach, which I argue deserves more attention, is what I call “humanization through defamiliarization.” This concept draws on Deleuze and Guattari’s idea of “becoming animal,” entailing a direct addressal of the animal that bypasses its appropriation for aesthetic or symbolic means and presents it outside of familiar contexts. Inspired by Jaschinski whose photography of zoo animals exemplifies the process of “becoming-animal,” I created my own images of animals from the Woodland Park Zoo that are both in accordance with and a direct response to her portrayals. While the animals in her photos draw their ostensible power from the darkness of the exposure, the animals in my photos reclaim the “voracious” and “all-exposing” light with the aid of my compositional and technical choices. Finally, I discuss the politics of looking at captive animals and decenter the very medium of sight to perhaps make space for the multisensorial encounters our bodies (human and other-than-human) are capable of.

Data is the fuel driving AI innovation. Much of the most valuable data is, however, siloed in research centers, hospitals, banks, etc. The onerous processes researchers must go through to access each silo cause a substantial underutilization of AI in many of the most important domains, including healthcare and genomics. AI researchers cannot train models for personalized medicine if they cannot get their hands on enough relevant patient data. One way to provide broader access for research while also retaining the privacy of the original data is with synthetic data generation (SDG), which uses machine learning to generate a set of synthetic data similar enough to the real data to retain its value for research while also anonymizing it. While in some cases a single data custodian (such as a hospital) alone may have enough data to train a generative model, usually, datasets from multiple custodians need to be combined to reach a cumulative size that enables meaningful AI research. The latter is, for example, often the case for rare diseases, with each clinical site having data for only a small number of patients, which is insufficient to train high-quality synthetic data generators. The goal of my research is to generate synthetic genomics data of patients with Neurofibromatosis type 1, a rare genetic condition that causes changes in skin pigment and tumors on nerve tissue. Thanks to our Privacy-Preserving Machine Learning Lab’s inclusion in the National Artificial Intelligence Research Resource (NAIRR) Pilot and our collaboration with Sage Bionetworks, I have access to the TACC Frontera supercomputer at the University of Texas and multiple sets of NF1 patient data. Results of my work on the NAIRR include an empirical evaluation of cross-silo federated SDG algorithms in terms of quality of the generated NF1 data, computational cost, and level of privacy protection.

In this experiment we will look into the relationship between different mushroom species' toxicity and copper concentrations. Due to their wide variety of biochemical characteristics, mushrooms can be either extremely toxic or edible. Mushrooms contain different amounts of copper, an essential trace element that may affect a mushroom's toxicity. Using Atomic Absorption Spectroscopy, we evaluated the amount of copper of several mushrooms. Our early results show that mushrooms with higher copper concentration tend to be more toxic. This shows that copper content may be a useful marker of the toxicity of mushrooms, giving foragers important information and assisting in the development of food safety protocols. Our research is to be continued as we’re going to test on more mushrooms to get a better understanding on how copper could affect the production of toxic compounds.

Recent studies have reported that certain tampon brands contain traces of various metals, raising public safety concerns about regular tampon use. Exposure to metals such as lead may pose detrimental effects on cognitive function, the nervous system, and reproductive health, yet little is known about the extent to which these metals are absorbed into the bloodstream from these products.  This project aims to investigate the presence of heavy metals within tampons. We hypothesized that tampons made from cotton would contain higher traces of metals compared to ones that are made with viscose rayon. We selected five widely available brands of varying absorbances and material, categorizing them as either organic (cotton) or non-organic (viscose rayon). To quantify the total lead content, 0.300 g of each sample was digested using a mixture of hydrogen peroxide and nitric acid. To determine the extractable quantity of lead, each sample was submerged in a simulant solution for 24 hours, replicating the acidity of vaginal fluids. To ensure the presence of lead within the sample, tampons with measurable lead concentration were spiked with known amount of lead quantity. Using AA Spectroscopy, quantifiable total lead contents were found in three out of the five tampon samples; Tampon C exhibited the highest lead content of 1.363 µg/g of tampon. Additionally, only one in five tampon samples was found to have significant extractable lead content, with Tampon C containing 0.2184 µg/g of tampon. Our results indicate a higher proportion of detectable traces of total and extractable lead in non-organic tampons compared to organic tampons. Despite these findings, further research is needed to establish whether there are adverse health effects to lead exposure from tampon use.

Coaching is a collaborative, goal-oriented process aimed at supporting individuals in achieving personal or professional goals. Coaching originated in workplace settings and expanded in the 1990s to include life coaching. Life coaching has been applied to many specialized areas, including attention deficit hyperactivity disorder (ADHD). Contrasting with psychotherapy, coaching is not intended to treat mental disorders. As such, the intersection of coaching and clinical care has sparked debates about the boundaries between coaching and psychotherapy, particularly when clinical conditions such as ADHD are involved. The COVID-19 pandemic was accompanied by an increase in seeking mental health services for ADHD. This coincided with an apparent influx of new ADHD coaches joining the profession to fill the increased demand. We created the U.S. National ADHD Coaching Survey to better understand the activities and behaviors of ADHD coaches in the U.S. and how ADHD coaching might fit into the broader context of ADHD care. We explore the differences between ADHD coaches who began their practice prior to the onset of the COVID-19 pandemic with those who began their practices following the onset of the pandemic. We distributed this survey to ADHD coaches through ADHD coaching professional organizations, in-person at a professional conference, and through targeted invitations based on web searches of ADHD coaches. We hypothesize that newer post-pandemic coaches are less likely to be members of coaching organizations, more likely to market themselves on social media, and cover a greater variety of session content. I document ADHD coaching workforce trends over time. Additionally, I compare the professional identities and training, referral networks and marketing, and session content of ADHD coaches who began offering their services pre vs post pandemic using independent samples t-tests and chi-square tests. I explore how those differences might impact the current landscape of ADHD treatment and support.

A subset of voltage-gated potassium channels, Kv2s, are responsible for the majority of the perisomatic delayed rectifier current in pyramidal neurons of the neocortex. Mutations in these ion channels and their associated proteins cause developmental epilepsy, but the cellular mechanisms underlying this remain less clear. Previously, we have shown that the two members of the Kv2 family of voltage-gated potassium channel α-subunits, Kv2.1 and Kv2.2, are expressed differently depending upon the type of neuron in rodent primary sensory and motor neocortex. There are two major subclasses of layer 5 (L5) pyramidal neurons in the neocortex, extratelencephalic (ET) and intratelencephalic (IT) neurons, that are distinguished by their projection targets and laminar distribution. ET neurons, enriched in L5b of the neocortex, send projections to subcortical structures, whereas IT neurons, primarily located in L5a, project within the telencephalon. In rodents, ET neurons are enriched in Kv2.1, but not Kv2.2. Here, we tested whether these features extend to the association cortices of primates, particularly the prefrontal cortex and temporal cortex, which are essential for various higher-order cognitive functions, including recognition, attention, and planning. Using immunohistochemistry against Kv2.1 and Kv2.2, we showed that these subunits have distinct laminar distributions in the dorsolateral prefrontal cortex (dlPFC) and temporal cortex (TCx). Kv2.1 was predominantly expressed in L5b, whereas Kv2.2 was more concentrated in layer 2 (L2) and L5a. Using a tarantula toxin, Guanxitoxin (GxTx), to block the Kv2-mediated current, we found that, similar to what we observed previously in rodents, the role of Kv2 channels differs depending on the L5 neuron type. GxTx makes L5 ET neurons fire repetitive bursts, whereas GxTx makes L5 IT neurons less excitable. Together, these results support distinct roles for Kv2.1 and Kv2.2 in regulating excitability across ET and IT neurons in the association cortex of the macaque. 

Methane is one of the most attractive targets for controlling near-term climate change due to its short lifespan and high potency (34 times that of CO₂). Methanotrophs are bacteria that can consume methane and convert it into CO₂ and biomass. There is growing interest in using these bacteria to mitigate greenhouse gas emissions from sources such as landfills, agricultural feedlots, and abandoned coal mines. However, a key challenge is that to achieve large scale methane sequestration, as well as economic viability of deploying these in the field, we have to significantly improve the growth of methanotrophs at low concentrations of methane. Regulatory genes play an important role in determining how bacteria allocate energy. By deleting specific regulatory genes and measuring the growth rate of these mutants under low methane conditions, we can assess their importance in helping the bacteria survive and thrive in nutrient-limited environments. Using this approach, we can also replicate mutations that have naturally emerged in strains cultivated for over a year under low methane conditions. This allows us to confirm whether these mutations provide a growth advantage. By identifying and testing key genes involved in low-methane growth, we are guiding efforts to engineer a more efficient and resilient strain for real-world applications.

Landslides are one of the main agents of erosion in wet and mountainous regions and can have a long-lasting impact on the landscape. In the Puget Lowland of Washington, landslides are prevalent, especially along steep coastal bluffs. Despite their common occurrence, their triggers are often unknown. In particular, their connection to strong shaking from seismically active faults versus precipitation events is an outstanding problem. The Southern Whidbey Island Fault (SWIF) stretches from Victoria B.C. across Puget Sound into the mainland near Woodinville. The SWIF has produced at least four earthquakes since the last ice age, with the most recent occurring less than 2,700 years ago, evidencing its capability of generating an earthquake up to M7.5. This work quantifies the area, extent, landslide type, roughness of the surface (as a proxy for age), and location distribution of landslides along the coastal bluffs of Whidbey Island. Our ultimate goal is to understand possible links between the landslide inventories in the coastal Whidbey Island area and the activity of the SWIF. Using high-resolution LIDAR elevation data (3 m) we perform a series of topographic analyses using GIS and Python tools to establish a landslide chronology. We use the Ledgewood-Bonair Landslide triggered by a rainstorm in 2013, as a spatial and temporal reference to calibrate our analysis. Our results will shed light on the dynamics of coastal landslides, the feedback between landslide preservation, wave and tidal erosion, and hillslope processes. This study advances our knowledge of cascading hazards from the SWIF and informs risk assessment for the region.

Restoration practices are crucial to the sustainable management of city parks, constructed wetlands, and natural ecosystems that have been disturbed or invaded. Oftentimes, restoration sites have some level of disturbance, such as soil contaminants in urban parks. Therefore, selecting plants for restoration comes with a list of considerations based on the goal and scale of the restoration project. Commonly, plants transplanted into these disturbed or polluted environments experience shock from transplanting stress, making finding solutions that increase restoration planting success invaluable to these practices. Soil fungi and bacteria have potential to boost the success of these efforts through their synergistic interactions with each other and plants. These microorganisms have high potential for use as biofertilizers in place of conventional nitrogen- and phosphorus-based fertilizers, which both have negative environmental impacts, including greenhouse gas emissions and water contamination. We hypothesize that by enriching plants by encasing these beneficial bacteria and fungi in alginate-based hydrogel beads, both plant biomass and overall fitness would improve. Further, this improved fitness has the potential to increase post-transplantation survival rates for plants used in restoration and/or phytoremediation regimes. To determine the effect of hydrogel biofertilizers on early stage development and transplant success in a contaminated restoration site, we are examining the response of blanketflower (Gaillardia aristata) to our novel biofertilizer. This plant is rapid-growing, used in restoration, and is drought-tolerant. Therefore, we are pursuing two questions: 1) How does our mixed-consortium hydrogel impact early development of these plants in greenhouse conditions; and 2) Does transplant survivability increase when planted in contaminated soils? Based on previous studies showing the strong efficacy of hydrogel-encapsulated biofertilizers, we predict that plants treated with biofertilizers will have better outcomes (improved early-stage growth and higher survival rates post-transplant) due to their supplemented nutrient accessibility and accelerated growth and development in early adolescence.

As of 2025, the United States has the highest incarceration rate in the world, with its incarcerated population making up 25% of the incarcerated individuals worldwide. Mass incarceration inflicts the most harm on the most vulnerable populations, disproportionately affecting racial and ethnic minorities and creating insurmountable barriers to reintegrating into society. Prison education programs provide opportunities for growth that help prevent recidivism and support rehabilitation efforts, and with the reinstatement of Pell Grants for incarcerated individuals in 2023, there has never been a better time to expand educational opportunities than now. However, little research has been done on prison education programs, with even less research focusing on enhancing and expanding them to address the specific needs of incarcerated individuals, particularly in digital literacy. In a rapidly evolving digital world, it becomes imperative to ensure that incarcerated people, many of whom have had limited experiences with technology due to extended sentences, have the skills to confidently return to a digital society. This project explores how integrating computer science curricula into correctional facilities can increase rehabilitation, reduce recidivism outcomes for incarcerated individuals, and further support other pre-existing educational programs in prisons. To answer this question, we examined legal documents, performed literature reviews, analyzed previous studies on the incarcerated population, and conducted a comprehensive analysis of outcomes from prior prison education programs. Our findings reveal that computer science education for incarcerated people increases self-efficacy rates, post-employment opportunities, and facilitates a smoother transition back into society. Additionally, integrating computer science through enhanced digital infrastructure can address challenges with current educational programs, such as accessibility, course expansion, and classroom segregation. Collectively, this project represents one of the first studies to explore the possibilities for computer education and prisons, offering valuable insights into the potential to improve rehabilitation, reduce recidivism, and address the digital divide.

Medical debt is a significant burden with fourteen million Americans owing at least $1,000, and the U.S accumulating at least $220 billion (Rae & Rakshit, 2024). Researchers have developed the concept of financial literacy to help patients understand health insurance and apply this newly-acquired knowledge to actively manage their medical bills. Our research challenges the portrayal of medical debt as the patients’ fault for lack of financial literacy and reframes it as a structural problem that purposefully blocks people’s access to financial aid resources. We conducted seven semi-structured interviews with healthcare workers, representatives from non-profit organizations, and financial counselors who help with medical debt. In the interviews we asked about their work, challenges they may face, and recommendations for improving access to financial aid. We recorded these interviews on Zoom, transcribed, and coded them with qualitative analysis software, Dedoose. Our interviews showed that hospitals mandated to have financial aid policies do not help patients access these policies. The documents contain excessive jargon and lack uniformity across hospital systems. Because of this obscurity, many patients are unaware of financial aid opportunities, unable to understand their eligibility and end up with exorbitantly high medical bills. Furthermore, we discovered that healthcare providers are unable to navigate these policies, leaving patients without adequate support. Our results show that policies solely focusing on improving financial illiteracy among individual patients fail to address that hospitals and insurance companies block patients from resources that mitigate medical debt. We advocate for widespread user-friendly financial aid guides, health financial literacy curricula for healthcare staff, and the public dissemination of financial aid resources across clinical settings. Addressing financial illiteracy as a systemic instead of an individual problem helps create a more equitable and accessible health system that enables patients to prioritize their well-being over managing their medical debt.

Neuropsychiatric disorders lead to devastating impacts on a patient’s life, affecting physical movement, cognition, and behavior. A pattern observed in patients with neurodegenerative disease includes neurofibrillary tangles in the brain, which may be caused by the abnormal accumulation of the microtubule-associated protein tau (MAPT). Tau is encoded for in the MAPT gene locus on chromosome 17, where the locus commonly interacts with an enhancer to boost transcription. However, some patients have one copy of chromosome 17 with an inversion that breaks this interaction, which is associated with lower risk of disease. This raises the question of whether the MAPT locus interacts with other enhancers that increases tau production. Thus, the goal of this project is to identify genetic variants that influence the 3D interactions between the MAPT locus and potential enhancers in patients heterozygous for the MAPT inversion associated with a lower risk of neuropsychiatric disorders. To accomplish this objective, neuronal nuclei extracted from patients are analyzed using fluorescent in-situ hybridization (FISH) to identify interactions in the MAPT gene locus. We will map a 2 Mb region of chromosome 17 centered on the inversion using FISH probes. This region is broken up into ten 200 kb spots to be individually visualized using fluorescent oligonucleotides through a fluidics system, to create a composite image of all spots. Interactions involving the MAPT locus may be identified by comparing distances between spots, in which gene segments that interact would have a shorter distance compared to segments that do not interact. This would allow us to find genetic variants associated with the chromosome 17 inversion that potentially influence MAPT gene regulation.

Ocean eddies contribute significantly to the transfer of heat and energy throughout the world’s oceans, playing a key role in regulating climate. Eddies are observed predominantly through Earth-orbiting satellites that collect data on sea surface height (SSH), a metric that can be used to estimate eddies on a global scale. Historically, satellites could only capture point-wise measurements, resulting in low-resolution SSH maps, which led to underestimations of small-scale eddy strength. Launched in 2022, NASA’s Surface Water and Ocean Topography (SWOT) satellite now provides groundbreaking 2D SSH imagery with higher resolution relative to existing SSH products. However, there are only two years of SWOT data available, unlike other satellites with decades-long records. Here, we considered how the recent SWOT data could be deployed to improve the spatial resolution of SSH products from the preceding 30 years. To achieve this, we trained an image-to-image U-Net neural network to predict the high-resolution SSH from an existing low-resolution product (NeurOST). We used SWOT high-resolution data as a ground truth to train this neural network and minimize the mean squared error of the SSH output with respect to the SWOT data. By evaluating the accuracy of the SSH output maps against an independent withheld satellite, we demonstrated that our method improves the spatial resolution of the SSH product compared to the NeurOST dataset. We next plan to test the accuracy of our method when applied to years before SWOT was launched. Overall, our research highlighted how leveraging deep learning and SWOT can enhance the spatial resolution of a decades-long eddy observation time series, enabling more accurate studies of eddies and their climate impact.

Northern Australian landscapes are dominated by termite mounds, raising questions about how these insects might have bioturbated local archaeological sites. In this research we aimed to investigate termite bioturbation at Madjedbebe, Australia’s oldest archaeological site, located in the Northern Territory. We analyzed stone artefact data from Madjedbebe to investigate possible clustering of artifacts, which could have been influenced by termite activity. Specifically, we explored the following questions: Do mass distributions of lithic materials within each of the phases at Madjebebe reflect a non-uniform redistribution associated with termite bioturbation? How does this affect the reliability of the earliest occupation date of Australia? To address these questions, we visualized trends in artifact location and mass in the strata to evaluate artifact size-sorting in each phase as well as within excavation squares B2, C2, and C6. We contextualized our findings using previous experimental and observational research on termite bioturbation to robustly assess the extent of disturbance caused by termites at Madjedbebe. On both site-wide and excavation square levels, we did not find any significant trends that reflected clustering patterns. Thus, we found that mass distributions do not corroborate size sorting at Madjedbebe. This research will contribute to our broader understanding of termite effects on sites in Northern Australia and help with assessments of the validity of dated artifacts at Madjedbebe, enriching our knowledge of the earliest known human activity in Australia.

Lithic artifacts are global phenomena that prevail throughout the archaeological record. Unretouched lithic flakes, though highly abundant, are often ignored as diagnostic parts of an assemblage. However, a recently developed method, FLEXDIST by Will and Rathmann (2025), handles mixed, correlated, incomplete, and high-dimensional data and so is ideal for revealing detailed information from unretouched flakes. We apply this FLEXDIST method to an assemblage of lithic artifacts from Nguom Rock Shelter in Vietnam to understand how people adapted their technology to climatic changes of the Last Glacial Maximum. During the transition from Marine Isotope Stage 3, to Marine Isotope Stage 2 (Last Glacial Maximum), the climate became cooler and drier. Our results suggest that this shift in climate resulted in people adjusting their lithic technology to make longer, heavier, and thicker flakes. We interpret this as a strategic reduction of mobility, perhaps using the Nguom Rock Shelter as a refuge during the peak glacial conditions of the Last Glacial Maximum. Our application of the FLEXDIST method to a novel dataset validates its use as an analytical tool on unretouched flakes and encourages more investigation into what can be learned from this abundant and under-studied component of the archaeological record. In addition, we hope that the application of this method to the Nguom dataset will further our understanding of not only how ancient humans adapted to climate change, but how modern humans might adapt to our changing climate both in the present and in the future. 

The Lidstrom Lab aims to better understand methane-consuming microbes (also called methanotrophs) so that we can develop technologies to remove anthropogenic methane emissions, which will reduce the severity of global warming. Our research explores how the methanotroph Methylotuvimicrobium buryatense 5GB1C can be bioengineered to grow well at the low methane concentrations found in human-made emission sites, while providing value-added products like biomass from dead bacteria that can be used as animal feed. Understanding bacterial methane utilization will allow us to create effective biocatalysts at a far lower monetary and environmental cost. My research project involves deleting cytochrome genes that may be important for the 5GB1C strain to grow in low methane conditions. Manipulating these genes may allow for further improvement of growth at low methane. My targets are three genes that encode cytochromes, which are electron carriers that take electrons from particular reactions and supply them to other reactions that are otherwise energetically unfavorable. My hypothesis is that these cytochromes are involved directly in supplying 5GB1C with electrons needed for the oxidation of methane into methanol. If these cytochromes supply electrons required for methane consumption at low methane, then deleting them would generate a mutant that would grow poorly on methane because it lacks the electron carrier(s). I have generated two possible cytochrome deletion mutants and continue to work on a third cytochrome. Once the mutants that can be generated are sequenced to verify the deletions, cultures will be grown under low methane and methanol conditions to determine how their ability to grow has been affected by the knockout mutations. In this manner, our lab is building a valuable knowledgebase of genes that are suitable for manipulation to improve growth in low methane for the technologies that one day will help curtail the worsening of global warming.

Adolescents and young adults often experience barriers to accessing inclusive, high-quality, and youth-friendly healthcare. Despite growing attention to these disparities, few standardized tools exist to assess or encourage youth-friendly practices across healthcare settings. This project, conducted under the Adolescent Health Team at the Washington State Department of Health, asks: What criteria define a youth-friendly healthcare environment, and how can these be translated into a sustainable certification model? To answer this, we employed a mixed-methods approach. We conducted a landscape review of existing youth-focused health frameworks, analyzed qualitative feedback from community partners and youth advisory groups, and iteratively developed criteria through stakeholder engagement. Branding materials and an informational flyer were designed to enhance accessibility and understanding of the certification. A draft patient satisfaction survey was also created to capture ongoing youth experiences in certified settings. Preliminary findings highlight key themes in youth feedback, such as the importance of inclusive language, provider relatability, and confidentiality and privacy in care settings. These themes directly shaped the final set of certification criteria and informed outreach materials. This work contributes to the field by piloting a novel framework for Youth-Friendly Certification in Washington State. Findings underscore the value of youth-informed design in public health initiatives and provide a replicable model for other regions seeking to improve healthcare access and equity for young people.

The opioid epidemic remains a critical public health crisis, with opioid use disorder (OUD) affecting millions worldwide. Research indicates significant sex differences in addiction patterns, with women exhibiting faster addiction progression, heightened cravings, and increased relapse rates compared to men. However, the biological mechanisms underlying these differences remain poorly understood. This study aims to investigate how chronic heroin use and withdrawal impact gonadal hormone levels in male and female rats, shedding light onto the role of opioid addiction on hormonal regulation. Using a 20-day heroin treatment followed by a 20-day withdrawal period, we examined changes in locomotor response, fluctuations in key gonadal hormones (testosterone, estradiol, and progesterone), and differences in brain activity patterns. Our preliminary data  suggest that females more consistently develop sensitization to heroin and also do so at an earlier time point compared to males. Our ongoing research is working to quantify serum hormone levels across heroin treatment, as well as developing a way to measure neural estradiol activity in real-time during sensitization. Future work will focus on the long-term effects of hormonal disruptions on brain signaling pathways and opioid receptor regulation, with the ultimate goal of informing sex-specific therapeutic interventions for individuals struggling with opioid addiction. Understanding these hormonal changes is crucial for developing more effective, personalized treatment strategies for OUD. By furthering the research on opioid addiction and endocrine function, this research highlights the need to consider sex as a biological variable in addiction studies.

Methane is an extremely potent greenhouse gas, with a warming potential 86 times greater than that of CO2 on a 20-year timescale, and is therefore a top priority for mitigation efforts to combat climate change. Methanotrophic bacteria, such as M. buryatense 5GB1C, metabolize methane as their main source of carbon and chemical energy, a trait that could help slow climate change by reducing emissions. A major obstacle is the rate at which methane consumption occurs at low methane concentrations, which tends to be too low to be appreciable. This project seeks to answer whether currently unknown genes involved in the growth of M. buryatense 5GB1C on low methane could be discovered by comparing its genome with that of a closely related methanotroph, M. alcaliphilum 20Z. While the two have very similar genomes and metabolisms, M. alcaliphilum is not able to grow at low methane concentrations (500 parts per million), while M. buryatense is. I analyzed the two genomes and isolated all genes present in M. buryatense without homologs in M. alcaliphilum. Because they are unique to M. buryatense, they may be involved in the observed growth difference. I systematically performed targeted deletion mutations on many of these candidate genes, and then tested them for growth on low methane compared to the wild type strain, looking for any defect that would suggest a gene directly essential to growth at 500ppm. I confirmed several genes to have no impact on growth at low methane, as well as one that appears to be essential to growth in any conditions, and anticipate reaching conclusions on several more mutants. These findings will help to develop microbial methane mitigation technologies that can be utilized in a great range situations and at a larger scale, essential characteristics for a global impact.

Understanding and predicting changes in primary productivity depend on both upper ocean warming and nutrient supply from the ocean interior. Fronts, where distinct water masses converge, are hotspots for these vertical exchanges, transporting nutrients upward and supporting diverse ecosystems. These fronts create sharp gradients in temperature and salinity, generating strong vertical velocities that upwell nutrients and biomass. However, the exact dynamics of frontogenesis (the formation of fronts) remain poorly understood. Additionally, these processes occur at scales too fine to be resolved in global climate models and are only marginally captured by high-resolution ocean simulations. This underscores the need for observational studies to characterize frontogenesis and test existing theoretical frameworks. In this study, we diagnose frontal dynamics using Petterson’s frontogenesis function, which quantifies the roles of divergence and strain. Using NcCut, a GUI developed by our group, we compiled a unique dataset capturing the full life cycle of numerous ocean fronts in front-following coordinates from a state-of-the-art ocean simulation. Our results indicate that for mesoscale (~100 km) fronts, strain dominates over divergence, aligning with classical theories. In contrast, submesoscale (~10 km) fronts exhibit shorter life cycles and no clear dominant driver of frontogenesis within the Petterson framework. We also identified key limitations in conventional diagnostics and improved our analysis by masking the front from its surrounding environment before diagnosing its drivers. This enhancement provides a more accurate representation of frontogenesis dynamics. In the future, we plan to apply our method to satellite observations to study real-world ocean fronts, validate ocean models, and improve predictions of primary productivity changes. Our findings highlight the importance of refining frontogenesis diagnostics to better capture the small-scale dynamics critical to ocean biogeochemistry and climate predictions.

This project critically examines online narratives about human and more-than-human cloning, with a focus on the spread of misinformation, radicalization, conspiracies, and their dangerous impact. At first glance, discussions about human vs. more-than-human cloning differ significantly. Human cloning is commonly considered morally objectionable, with supporters often forming part of controversial communities. In contrast, more-than-human cloning frequently sparks curiosity and, in some contexts, is encouraged. It is viewed not as an "act against God" but as a testament to human intelligence and dominance. This difference in responses raises many questions: Why are responses so dissimilar? How does online discourse drive these reactions? And can these distinctions--these different understandings of personhood and "life"--reinforce or perpetuate ideologies that cause harm? To answer these questions, I examine academic explorations of cloning and compare them with ones found all across the digital sphere-from social sites such as Reddit, X (formerly known as Twitter), and 4chan, to YouTube comment sections. Using a digital, “websplorer” approach, I analyze different perspectives on cloning, ranging from the "manosphere"-- interconnected misogynist online communities, scientism, and how they relate to the more-than-human. After a critical interrogation of these perspectives, I invite the user to consider an alternative, perhaps more ethical, approach to discussing cloning, one that does not reinforce heteronormativity, human exceptionalism, or pro-eugenic views. This alternative approach includes an exploration and critique of the Western concept of “personhood” and its limitations regarding cloned life, human and more-than-human.

Neuroendocrine bladder cancer (NEBC) is a rare and aggressive urothelial tract cancer. NEBC is characterized by high metastatic potential and poor clinical prognosis. Neuroendocrine cancers often exhibit characteristic genetic changes including loss of tumor-suppressing genes like TP53 and RB1 and amplification or activating mutations in proto-oncogenes, e.g., MYC. However, not all bladder cancers with these characteristic mutations progress to NEBC, suggesting other occult genetic or epigenetic drivers of disease progression. To investigate the clonal origins of NEBC tumor heterogeneity, our lab developed a genetically engineered mouse model by introducing orthotopic mutations observed in human tumors (TP53, RB1, and MYC) in murine bladders by lentiviral delivery of Cre recombinase. We found some of the resulting tumors had high levels of the pioneer transcription factor, FOXA2. To further explore the role of this gene in NEBC development, we conducted an overexpression experiment in which FOXA2 was expressed in mouse-derived bladder cancer cell lines. We performed RNAseq (RNA sequencing) analysis in a panel of syngeneic murine NEBC lines, including samples with FOXA2 over expression and parental controls. In the course of this work, we developed an informatics pipeline to interrogate clonal heterogeneity at the transcriptional level in genetically identical syngeneic tumor lines – a method which we termed clonal phylogenies from RNAseq (CPR) data. My role in this project involved designing and implementing a bioinformatics pipeline to analyze both single-cell and bulk RNAseq data. By integrating cross-species comparisons with computational analysis, we aim to uncover novel molecular mechanisms driving NEBC emergence. While our research is ongoing, this approach highlights a new bioinformatics method allowing deeper insights into human cancer biology.

Following an extensive history of industrial activity in Commencement Bay, Washington, the health of marine ecosystems continues to be affected by persisting pollutants. Commencement Bay has been identified as a Superfund Site, in which the Environmental Protection Agency (EPA) is tasked with cleaning up locations contaminated with hazardous materials. In an effort to gauge just how effective these recovery efforts have been, this study, part of the Puget Sound Foraminifera Project at the Burke Museum, investigates how the density and diversity of benthic foraminiferal assemblages have changed over time. Foraminifera, a diverse and widespread order of shelled marine protists, can be utilized as a reliable measure of marine ecosystem health due to their innate sensitivity to environmental changes. Samples collected by the Washington Department of Ecology (WDOE) from 2014 and 2022 allow for a comparison of diversity indices that are indicative of the success in the bay’s recovery. To quantify this success, calculations of the Shannon Index and the Simpson Index were completed for each sample, supporting our determination of the Foraminiferal Benthic Index (FBI) of the region. The FBI was defined using measures of abundance, diversity, and percentages of tolerant species present in each sample to quantify the extent of adversity. With 2022 density and diversity averages that are statistically similar to those of 2014, we can conclude that clean up efforts have not yet made sufficient measurable improvements in the Foraminiferal Benthic Index over the previous eight years.

Protein Kinase Inhibitors (PKIs) are a family of heat stable, high-affinity inhibitors of the catalytic subunit of Protein Kinase A (PKAc). In the presence of Mg-ATP, the three isoforms—PKIα, PKIβ, and PKIγ—bind to PKAc with very low dissociation constants: 0.758nm, 1.875nm, and 0.4142nm respectively. In vitro studies have shown that PKIs can translocate PKAc from the nucleus to the cytoplasm, suggesting a role for PKIs in terminating nuclear cAMP-driven PKA activity. Previous research, including studies from our lab, has found that dysregulated PKAc mutants play a significant role in Cushing’s syndrome, a rare and potentially fatal metabolic disorder caused by excessive cortisol production. Building on these findings, we hypothesized that increasing PKI expression could counteract the hyperactivity of PKAc mutants and reduce cortisol production. To test this, we expressed each PKI isoform in adrenal cell lines and assessed their steroidogenic capacity using biochemical assays such as western blots, RNA-seq, qPCR, and ELISA-based cortisol assays. We observed that PKIα and PKIγ led to a general suppression of steroidogenic associated proteins such as StAR, Cyp11a1 and SF1. This altered proteome was accompanied by significantly suppressed cortisol synthesis only in the PKIα and PKIγ expressing cells. The difference between PKIα/γ and PKIβ was surprising given that all PKI isoforms are postulated to potently inhibit PKAc. Thus, we questioned whether PKIα/γ effects are mediated through PKAc. To answer this, we have cloned mutant PKI isoforms that do not bind PKAc, and confirmed the mutant PKIs do not inhibit PKAc through kinase assays. Our next step is to express the mutant PKI isoforms in adrenal cells and assess their effect on steroidogenic capacity of the cells. Our findings suggest that PKIα and PKIγ play key roles in cortisol regulation and may have broader implications for gene regulation in adrenal cells.

All cells have a stochastic component to their gene expression, such that even when in the same environment, there will be cell-to-cell differences in gene expression. Studies of this variability in gene expression dynamics have been limited by technological capabilities for measuring gene expression history with single-cell resolution. We have built a history-dependent integrase recorder of gene expression with single-cell resolution in the model plant Arabidopsis thaliana to study the impact of cell-to-cell gene expression variation in two contexts: development of side or lateral roots (LRD) and root regeneration (RR). The recorder uses integrases, proteins from bacteriophages that mediate permanent, heritable DNA changes based on the presence and orientation of a pair of integrase sites. Fluorescent reporter genes within the target construct allows for expression of fluorescent proteins associated with sequential expression of developmental genes. The recorder allows us to tie the switching to expression of developmental genes by expressing integrases with developmental promoters for genes that guide root differentiation. Utilizing our recorder, we are able to illuminate and evaluate variation in the recorder output among roots growing in different contexts. We hypothesize that regeneration leads to more heterogeneity in gene expression than lateral root development, as the latter has more standardized initial conditions and consistent local cues to constrain transcriptional dynamics. We aim to investigate connections between larger scale anatomical variation and underlying cell-to-cell gene expression heterogeneity. This technology will allow us to further understand the dynamics of gene expression during root development and could unlock new avenues for agricultural research and engineering.

Exposure to air pollution, the fourth leading risk factor for global attributable deaths, has been linked to the development of several noncommunicable diseases. The incidence of thyroid diseases in the United States continues to increase yearly, estimating that over 12% of Americans will develop it during their lifetime. While thyroid disorders are not yet recognized as a noncommunicable disease, they promote the onset of other chronic diseases. Diesel exhaust (DE), an important source of particulate matter and other toxic compounds within traffic-related air pollution, generates reactive oxygen species (ROS) which can lead to oxidative stress in the body. Oxidative stress is the imbalance of ROS and antioxidants in the body and is associated with numerous diseases. The purpose of this study is to assess the effects of DE-induced oxidative stress in plasma and the thyroid, specifically examining how effects differ based on sex and a high-fat diet (HFD). We exposed male and female mice (low-density lipoprotein receptor knockout mice) to filtered air or DE for 18 weeks, while fed HFD or Chow. In plasma, we measured the activity of the antioxidant enzyme paraoxonase-1 (PON1) and the concentration of the acute-phase serum amyloid A (SAA) protein via ELISA. In thyroid tissue, we extracted RNA and used RNA-Seq to assess DE-induced transcriptional reprogramming. We expect that DE exposure will result in higher levels of inflammation (SAA) and lower levels of antioxidants (PON1). We expect that these effects will display sex differences and will be more pronounced in HFD-fed mice fed. Our transcriptomics analysis will help identify new genes and pathways affected by DE, diet, or both. Our results will improve our understanding of the link between air pollution and thyroid disorders, guiding future research and interventions to address the growing health concern of thyroid disorders and related noncommunicable diseases.

Cardiovascular diseases are the leading cause of morbidity and mortality in the United States. Among the many contributing factors, mishandling of intracellular calcium (Ca2+) dynamics plays a crucial role in the etiology of cardiac diseases including heart failure, and arrhythmogenic disorders. Cardiac ryanodine receptor 2 (RyR2) channels play a central role in excitation-contraction coupling by regulating Ca2+ release from the sarcoplasmic reticulum (SR). Abnormal activity of the RyR2 by impairing Ca2+ release from the SR results in sudden death in many cardiac disorders. Thus, regulators of RyR2 could provide a novel therapeutic target in several heart diseases. Our initial studies implicate the role of the chloride intracellular channel, CLIC4 in modulating the activity of RyR2. We identified CLIC4 as a mitochondrial-associated endoplasmic reticulum membrane protein. The absence of CLIC4 induced faster Ca2+ release from SR, indicating abnormal RyR2 activity. Further, co-immunoprecipitation studies indicated an interaction between RyR2 and CLIC4. Moreover, we found that the absence of CLIC4 increased myocardial infarction upon ischemia-reperfusion (IR) injury in mice. Thus, based on our findings we hypothesize that CLIC4 by either stabilizing RyR2 in a closed state or by regulating the anionic gradient across SR modulates the  RyR2 activity. In this study, we will map the domain in CLIC4 specific to interaction with RyR2 and modulate its activity. We will systematically clone and express various N- and C-terminal truncated CLIC4 constructs to investigate their interaction with RyR2. Further, we will determine the effects of these constructs in modulating calcium release from RyR2. Our studies could aid in the development of a peptide-based therapeutic approach to modulate RyR2 activity in cardiac diseases.

Stress resilience, the ability of cells and tissues to adapt to stimuli, declines with age. Skeletal muscle contraction is a physiological stressor when repeated through exercise training enhances stress resilience and mitigates age-related comorbidities. However, as the body's capacity to mount adaptive responses diminishes with age, the extent to which this decline affects physiological adaptation to stress remains unclear. This would guide future therapeutic strategies surrounding muscular degeneration over the lifespan. The goal of this study is to assess the magnitude of stress response activation across metabolic, oxidative, proteostatic, and heat shock stress response pathways. We use gene expression analysis to evaluate the transcriptional response to controlled in vivo muscle stimulation, providing insight into age-related differences in stress resilience. Young (6mo) and old (23-24mo) male and female mice (C57Bl/6JNia) underwent an in vivo fatiguing muscle stimulation (Stim) or served as an unstimulated control (Unstim). Three hours following the stimulation both right and left limb muscles were collected and processed for gene expression analysis. Following stimulation and collection, I performed tissue processing, RNA extractions, and RT-qPCR assays on muscle tissue. There was a significant increase in PGC1a, HMOX1, TRIM63, and HSPa1a genes in response to muscle stimulation when compared to the unstimulated limb within the same animal. The magnitude of these changes in response to stimulation were not different across age or sex. Analysis of basal changes in unstimulated groups across age and sex is planned for next month. These preliminary results suggest no significant age or sex differences across multiple pathways of stress resilience in skeletal muscle. A strength of this study design is that we use a combined within- and between-animal analysis of both stimulated and unstimulated conditions to control for any potential variations associated with each age, sex, and stimulation condition, increasing confidence in our results.

The 4-letter genetic alphabet found in Nature is the fundamental basis of biological information storage. As synthetic biologists continue to manipulate the genetic alphabet, they have begun to push against the boundaries of nature itself. Unnatural base-pairing xenonucleic acids (XNAs) are synthetic nucleotides that can pair orthogonally with the standard bases. By increasing chemical and structural diversity, XNAs are poised to enable a plethora of next-generation biotechnologies, including XNA-containing nucleic acid therapeutics (XNAptamers), catalytic nucleic acids (XNAzymes), and an expanded genetic code through a larger codon table. Although the potential of XNAs is near-limitless, the infrastructure required to study XNAs, notably sequencing, is antiquated. Previously, the Marchand Group leveraged commercial nanopore sequencing devices from Oxford Nanopore Technologies to sequence XNAs. This process outputs characteristic current signals that need to be decoded or “basecalled.” The first XNA basecallers used statistical k-mer models to decode XNA containing current signals, yet, their basecalling accuracy is a far cry from commercial basecallers (k-mer: 60-80%, commercial: >95%). Modeling our approach after commercial DNA basecallers, we have built a binary classification training pipeline that leverages long short-term memory (LSTM) neural networks and commercial nanopore sequencing to achieve more precise sequencing of XNAs. Thus far,  we have built models to effectively basecall three XNA base pairs with varying motivations: B≡Sⁿ for studying XNA replication fidelity in PCR due to high error rates, and P≡Z/Ds:Px for their unnatural functional groups (e.g. nitro groups and hydrophobicity) making them useful for applications such as XNAptamers. Currently, our binary classification models have testing accuracies as high as around 95% and we look to further improve our training methods through new model architectures such as transformers. Moving forward, we look to expand our basecaller to perform multi classification, allowing for generalized, de novo basecalling similar to commercial basecallers.

Approximately 320 million years ago, teleost fish experienced a whole-genome duplication event, which is theorized to have contributed to developmental and morphological innovations that enhanced the reproductive success of their modern descendants. However, the role of duplicated genes in the genesis of novel cell types remains unknown. Here we show that the African Turquoise Killifish (Nothobranchius furzeri) possesses a novel immune lineage specified prior to gastrulation—a far earlier stage than observed in other teleosts. Surprisingly, through single-cell RNA sequencing, we found that this lineage unexpectedly expresses nanos1b, a duplicated paralog of nanos1, a gene well known for its role in germline development across vertebrates. To verify this novel expression of nanos1b in immune cells before gastrulation, I performed RNA in situ hybridization to visualize the expression of nanos1b, eomes (a mesodermal marker), and lcp1 (a marker of mature immune cells). The results revealed co-expression of nanos1b with both eomes and lcp1, supporting the hypothesis that nanos1b expression links the myeloid lineage to the developing mesoderm. These investigations will help elucidate the pathway through which the killifish embryo fast-tracks the production of immune cells during early development.

Metabolic Dysfunction-Associated Fatty Liver Disease (MAFLD) is an emerging global human health concern and a risk factor for cardiovascular diseases and atherosclerosis. While the pathogenesis of MAFLD is complex and multifactorial, scientific evidence suggests environmental factors play a role in the development of the disease. Prior studies indicate exposure to particulate matter (PM) leads to MAFLD. A major constituent of ambient PM is diesel exhaust particles (DEPs). This study aims to explore the association between exposure to DEPs and the development of MAFLD using a murine model vulnerable to MAFLD development. DEPs cause oxidative stress through the generation of reactive oxygen species within the body. Male and female low-density lipoprotein receptor knockout mice were exposed to filtered air or freshly generated DE for 18 weeks while fed a high-fat or Chow diet. Plasma and liver tissue were harvested for biochemical measurements. The levels of a panel of lipid markers (triglycerides, cholesterol, free fatty acids) and glucose were measured in plasma and liver via colorimetric assay kits. Liver oxidative stress (8-isoprostane; nuclear factor erythroid 2-related factor 2, and 3-nitrotyrosine) was quantified via ELISA and Western blot (WB), respectively. Levels of peroxisome proliferator-activated receptor alpha (PPARα) were assessed via WB. We found statistically significant increases in plasma glucose and plasma and liver cholesterol in DE HFD male mice, and plasma triglycerides in DE HFD female mice. We expect to find increased liver oxidative stress and decreased liver PPARα protein, providing insight into the metabolic pathways associated with MAFLD that are disrupted by DE. Our findings will lead to a better understanding of air pollution as a risk factor for MAFLD and inform targeted interventions for affected populations.

The root cause of neurodegenerative diseases such as Alzheimer’s, Parkinson's and dementia is protein misfolding which leads to toxic aggregations in the brain, causing neuron death. At the molecular level, these diseases are offset by chaperone proteins, which have the task of stopping toxic aggregation events which directly causes onset of many neurodegenerative diseases. Understanding interactions between small heat shock proteins (sHSP), which are a class of chaperone proteins, and their client proteins, such as those involved in neurodegeneration is key for preventing these diseases. The sHSPs are a class of chaperone proteins which have the purpose of preventing other proteins from misfolding. The formation of toxic aggregates plays a factor in the first steps to pathology. Prevention of these aggregates and thus the toxic events that follow means understanding the protective mechanism that exists to stop aggregation. The challenge of these mechanisms is their immense complexity and there are not many methods in which small changes in the proteins can be detected. One possible technique that allows these small changes to be detected is Fluorescence Resonance Energy Transfer (FRET), which is a highly sensitive distance-dependent physical process. Fundamentally, energy is transferred non-radiatively via an excited molecular fluorophore (the donor) to another fluorophore (the acceptor). The goal of my work is to incorporate the FRET pairs into sHSP oligomers to probe changes in these oligomers. These changes could be the binding of another protein, such as a client protein, or another sHSP. These changes in the FRET signal will be indicative of how the probes are orientated relative to each other, allowing us to gauge what interactions are happening. My work validates the use of FRET to gauge how sHSP are interacting on a molecular level.

Young adult cannabis use has become increasingly prevalent in the US, particularly among individuals attending four-year colleges. The perceived social acceptability of cannabis use plays a crucial role in shaping attitudes and behaviors towards substance consumption. While societal attitudes towards cannabis have evolved over the last two decades, there is a gap in understanding how these perceptions differ between college students and their non-college peers. My research aims to compare perceptions about the social acceptability of cannabis with the actual frequency of use among young adults who attend four-year colleges, versus same aged individuals that are not attending school. I am using a subsample of young adults using baseline data from a larger longitudinal study on health behaviors, the Washington Young Adult Health Survey (WYAHS), for the analysis. I am conducting the data preparation and analysis using SPSS. I believe that there will be a significant difference in perceived social acceptability of cannabis use between college students and those not attending school, but I also anticipate that actual consumption will not be significantly different. The results of this research could be important for improving substance use education and addressing preconceived notions of cannabis use acceptability among young adults. Previous research on the WYAHS data has shown significant changes in substance use behaviors over the last six years, especially throughout the pandemic. Future research is needed, which focuses on how my findings may change when based on data from before the COVID-19 pandemic.

Heroin, a commonly used opioid, has played a significant role in the escalating opioid crisis, highlighting the urgent need to better understand the neural mechanisms underlying its addictive properties. Despite well-documented sex differences in opioid use disorder (OUD), the majority of preclinical research has been conducted in male animal models, limiting our understanding of how biological sex influences addiction-related behaviors. This study investigates the role of sex differences in heroin-induced locomotor sensitization and hormonal adaptations in a rodent model. Using a rodent model, we administered intravenous heroin and tracked activity to assess sensitization to the effects of heroin on locomotion. Following treatment, the rats underwent 20 days of withdrawal from heroin. Blood samples were collected throughout treatment and withdrawal to track changes in serum hormone levels. Our findings indicate that female rats show locomotor sensitization at an earlier time point and exhibit a greater degree of escalation compared to males. This suggests potential sex-specific mechanisms influencing opioid addiction vulnerability and progression. We aim to continue quantifying gonadal hormone fluctuations throughout heroin exposure and withdrawal with additional cohorts of animals. Future experiments aim to use fiber photometry to image estradiol activity in the brain during sensitization, providing a real-time insight into its role in opioid-induced changes in behaviors.