The Everett Marina is a heavily developed area that has significantly altered water flow from the Snohomish River compared to its natural state. Anthropogenic alteration of this environment led to buildups of sediment, which has required dredging at increasingly shorter intervals leading up to the present. In order to explain sediment accumulation in the marina, this study examines the movement of currents and the abundance of sediment using an Acoustic Doppler Current Profiler (ADCP); data were recorded from June 2020 to August 2021 and compared to recent data I recorded from February and March of 2023. I hypothesized that current direction would be variable and speed would be sluggish due to the shallow depth. In addition, I hypothesized that seasonal changes such as snowmelt in spring and rain in winter would impact the velocity of the currents. Because sediment movement is largely impacted by currents, I hypothesized that sediment abundance would reflect seasonal changes in water flow. Analysis of water current data between June 2020 and August 2021 demonstrates a significant correlation between the velocity of North/South currents and the magnitude of tide stages, but river discharge levels appear to have less of an effect on current speed in the marina. The susceptibility of this area to tides more than river discharge suggests that it is easier for sediments to accumulate in one area as opposed to being swept away. Future analysis will compare this past data to the present and investigate potential correlations with sediment abundance.

Over the last decade, the electrohydrodynamic (EHD) interaction produced by dielectric barrier discharge (DBD) actuators has seen strong interest for active flow control applications. Plasma synthetic-jet actuators (PSJAs) are DBD jets capable of producing zero-net mass flux momentum injection through ionic interactions in air at atmospheric pressure. These devices are of particular interest due to their rapid response time, lack of moving parts, variety of tunable parameters, and repeatably demonstrated efficacy in boundary layer modulation under a range of flow conditions. Due to the edge-normal momentum injection characteristics of PSJAs, previous studies naturally focused on surface wall jet configurations with spanwise cartesian geometries (see straight-edge, serrated, fingered electrodes) in quiescent, co-, counter-, and cross flow external conditions. We present an alternative 2-dimensional polar axisymmetric geometry; a circular ground electrode that is concentric and equal in diameter to the inner edge of an active high-voltage electrode ring. Steady-state inward injection develops an inward impinging jet and a resulting wall-normal net momentum directed away from the surface. A thorough electro-mechanical characterization led to the development of an empirical model of axisymmetric wall-normal plasma synthetic-jet actuators. The actuators utilize 0.0625” quartz glass as the dielectric material and have critical diameters of Dg = 40 mm, 60 mm, and 80 mm with an active electrode ring thickness of 10mm. The actuators are tested over an AC current operating range of Vpp = 8 – 60kV and f = 0.5 – 8 kHz. Direct thrust measurements are taken at all electrical conditions and intermittently validated through pitot-tube flow-profile tests. This provides rapid insight into the voltage-frequency-diameter-thrust relationships for axisymmetric PSJAs as well as finer intricacies, including entrainment patterns, high-Reynolds eddy formation, and jet dissipation. Combined with electrical current analysis, the axisymmetric PSJA is found to be an effective method of producing wall-normal momentum-injection. This research will directly contribute to the furthering of electric propulsion and flow control systems, opening the doors to more capable, more efficient, and greener flight technology.

Massive stars place powerful constraints on stellar evolution and are observed in a menagerie of exotic evolutionary phases. These objects play a crucial role in regulating their environments. They drive the chemical evolution of their host galaxies, and set the energy balance of their surroundings via feedback processes. Due to the importance of massive stars, placing constraints on their evolution serves as a key to understanding galactic ecosystems. Notably, stellar variability is a powerful probe of the poorly-constrained physics of massive star evolution. In particular, variability studies on ensembles of evolved massive stars can significantly constrain stellar evolution. We aim to understand the variability of hot massive stars through a census of these objects. We accomplish this using data from the Gaia mission, cross-matched with light curves from the Zwicky Transient Facility (ZTF). We expect to characterize the evolution of massive star variability timescales and amplitudes along the main sequence and beyond. Our results will place key constraints on the evolution of massive stars. 

The Seattle Coronavirus Assessment Network (SCAN) study is a voluntary SARS-CoV-2 (COVID-19) testing program that enrolled participants across Seattle and King County. We collected self-reported demographic data, vaccination status, SARS-CoV-2 test results, and viral genomes from study participants. The reason visualizing this biological and logistics data is so important is so that we can analyze the Covid 19 pandemic and learn how to put measures in place to prevent future pandemics. In our dashboard, we visualized demographic and molecular data on study participants and circulating pathogens using a mix of data analysis with Python, Amazon Web Services tools, and dynamic Tableau dashboards. With data from ~69,000 swab samples collected from May 1st, 2020, to July 31st, 2022, the result was a robust map of COVID-19 trends across King County. Moving forward, our project seeks to explore what it takes to run a community surveillance program for respiratory disease, looking to answer questions such as: Who the people were who used SCAN? Were there any power users vs one-time participants? How effectively did the study reach low-income participants? How many requests from high-income regions did we have to deny every day to get representative samples? Can we identify any opportunities in kit fulfillment? Additionally, how can we gauge the costs of couriering samples, and can we find a less costly alternative? The results of this analysis looking at the SCAN community surveillance program will influence the design of future public health measures to reduce barriers to healthcare; curb community pathogen spread; better allocate resources to support community health. Our goal is to create a future where we can adequately identify and treat diseases before they become pandemics.

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

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

Oral tolerance to antigens is a mechanism by which immune responses are inhibited to prevent chronic inflammation and tissue damage in response to common exposures, such as dietary antigens or commensal bacteria. Regulatory T cells (Tregs) are an important cell type in such regulation of immune responses, especially in the intestines. There is, however, heterogeneity within Tregs, including a subset that expresses the transcription factor RORgt. However, the mechanisms by which RORgt+ Tregs carry out their suppressive function are currently unknown. Intestinal Tregs are induced in the mesenteric lymph nodes (MLNs) by antigen-presenting dendritic cells (DCs) that migrate from the gut. Antigen transfer from DCs to Tregs is crucial for the development of oral tolerance and DCs are largely regarded as being upstream of Tregs. However, it has also been shown that Tregs play a role in DC migration via a CTLA-4-mediated mechanism. Because this DC-Treg relationship is not fully understood with regard to Treg heterogeneity, I have examined the changes in DC populations in a mouse model where the RORgt+ Treg population alone has been ablated. To do this, I developed a new panel of antibodies to use in flow cytometry in order to characterize the subpopulations of DCs in the intestines and related organs. I harvested and processed murine spleens, MLNs, Peyer's Patches, and small intestine lamina propria in order to compare the populations systemically and locally. I anticipate seeing fewer DCs in the mice lacking RORgt+ Tregs and more DCs in the small intestine and Peyer's patches. This work furthers our understanding of the intricacies of the intestinal immune system. This knowledge can be applied to vaccine research, as RORgt+ Tregs have been implicated as suppressors of immune response to oral vaccines. Intestinal immunity is also of interest in allergy and gut inflammation research.

Risk variants of apolipoprotein L1 gene (APOL1) increase the risk of chronic kidney diseases in populations of African ancestry. We seek to study this disease, which is unique to humans, in human kidney organoids derived from induced pluripotent stem (iPS) cells. However, APOL1 is not expressed in organoids at baseline. While interferon (IFN)-gamma is a potent inducer of APOL1 expression, our prior experiments suggested that IFN-gamma itself disrupts organoid structures, limiting the degree to which the specific effects of APOL1 can be assessed. To improve the kidney organoid system as a better platform to model APOL1-associated nephropathy without IFN-gamma stimulation, I am establishing an APOL1 inducible expression system in kidney organoids. I hypothesize that cell lines with the risk variants will demonstrate an accelerated rate of degradation compared to the non-risk variant, modeling risk variant-dependent cytotoxicity. The inducible expression system will be established by generating iPS cell lines encoding Tet-On system sequences, enabling both tunable and temporal control of APOL1 expression using doxycycline. Plasmids were constructed by PCR amplifying and inserting the targeted sequences into a homology-dependent repair template with a doxycycline-inducible promoter. Ligation had to be done multiple times due to the high prevalence of self-ligation of the backbone vector and backward insert orientation. However, we found that adding alkaline phosphatase to dephosphorylate 5’ ends of the backbone vector significantly improved the integration rate and led to the successful construction of plasmids. Next, CRISPR-Cas9 gene editing will be utilized to introduce the APOL1 gene variants into the AAVS1 safe harbor locus in iPS cell lines, which can be differentiated into kidney organoids. This project aids in isolating the phenotype of APOL1 on human kidney organoids with various cell types, which will be a valuable tool in developing an in-vitro pathophysiological assay such as use in therapeutic drug discovery.

The health of Sockeye salmon (Oncorhyncus Nerka) stocks are of high importance to the cultural well-being and sovereignty of Coast Salish tribes. There are multiple ecotypes of Sockeye that include anadromous, potamodromous Kokanee, and resident Sockeye that all carry distinct and significant cultural value for Indigenous communities, as well as distinct ecological roles within the ecosystems they inhabit. Sockeye are impacted by anthropogenic stressors such as habitat degradation and pollution, which can cause shifts in food web dynamics, population declines, and impact commercial and traditional fisheries. To more effectively manage these diverse life histories for conservation, it is crucial to understand the distinct ecological functions that may cause ecotypes to differ in their vulnerability to anthropogenic stressors, thus requiring different management strategies. We will analyze carbon and nitrogen isotopic signatures of Sockeye from Lake Washington to differentiate their ecological niches. Muscle samples were collected from 46 frozen sockeye samples, freeze dried, and then analyzed using mass spectrometry. Preliminary results suggest that there are significant differences between the isotopic signatures of anadromous and potamodromous ecotypes. We hypothesize further interpretation of the results coupled with genetic analysis will identify differing ecological roles in accordance with the diverse life history strategies Lake Washington Sockeye display. This study has been conducted as part of ongoing collaborative efforts with partners at the Snoqualmie Tribe, and the Kokanee Work Group, which aims to restore the Kokanee and Sockeye populations of Lake Sammamish. The results of this work will directly inform management actions taken by our partners to conserve the native Sockeye populations of King County, Washington.