Parasite burden can vary over time due to a variety of factors, including environmental change, competition, and niche differentiation. Clavinema mariae is a parasitic “blood worm” nematode that affects several species of commercially important fishes in Puget Sound, living below their skin and feeding on their blood. C. mariae burden increased dramatically in English sole, Parophrys vetulus, from 1930 to 2016, but it is unclear whether this same pattern affected other host species, including the southern rock sole, Lepidopsetta bilineata. I used rock sole specimens from the Burke Museum’s Ichthyology Collection to determine whether the burden of C. mariae changed over time in this host species. I examined preserved specimens that were collected from various locations in Puget Sound in the period of 1930 to 2016, taking note of the abundance of C. mariae in each individual. Creating a timeline of the parasite’s abundance helps us to narrow in on the various factors, such as fishing pressure, climate change, and nutrient pollution, that may influence C. mariae abundance. Parasite burden can negatively impact commercial fisheries and the overall health of the environment, making this study important for both economic and conservation purposes.

Antiretroviral therapy (ART) is the standard of care for treating human immunodeficiency virus (HIV) infection and suppresses virus levels but cannot eliminate latent HIV reservoirs. Latently infected cells are a barrier to HIV cure. “Shock and kill” is a strategy that uses latency-reversing agents (LRAs) to reactivate latently infected cells under suppressive ART, making the cells vulnerable for removal by host immune responses or other strategies. However, “shock and kill” fails in clinical studies due to the low potency and high toxicity of LRAs. Here we have developed a lipid-polymer nanoparticle platform that addresses “shock and kill” limitations by incorporating multiple LRAs to increase potency and to reduce toxicity by targeting HIV reservoirs in lymphatic tissues. We have shown that ~200nm nanoparticles sustain LRA release and induce latency reversal in a human T-cell line in vitro. To target lymph nodes, we have synthesized nanoparticles smaller than 100nm in diameter, which literature shows enhances lymph node targeting following subcutaneous injection. By adjusting the polymer and lipid concentrations as well as the organic to aqueous solvent ratio during formulation, we obtained an ultrasmall particle of ~100nm. Ex vivo organ imaging from mice subcutaneously administered these ultrasmall particles shows successful targeting to draining lymph nodes as well as other HIV reservoir locations, including the spleen and the gut-associated lymphatic tissue. The ultrasmall nanoparticles also show similar drug release and latency reversal properties as our previous formulations. The nanoparticle platform demonstrated here is able to target latent HIV reservoirs in multiple areas of the body, which is crucial for eliminating latent HIV reservoirs and achieving a cure.

Geographers generally define sense of place as the meaning an individual ascribes to a particular location. Collectively, sense of place creates the identity and character of a region and is represented through culinary, literary, visual, and many other forms of art unique to the local culture. Technological advancements in communication have changed sense of place by affecting how these cultural differences are maintained, but also offer new ways of capturing and sharing sense of place. What elements and by which means individuals choose to capture personal representations of an environment shape the way communities as a whole perceive, ascribe meaning to, and amass their own descriptions and representations of that place. My project explores this iterative relationship between visual representation and written description of place. I have selected a collection of crowd-sourced pictures of the local landscape using an app that pulls up publicly posted Instagram images that have been geotagged near the location of the user. I consider these pictures to be modern forms of landscape folk art and conducted visual content analysis to code the images with descriptive terms. I have also created an in-person, crowd-sourced cartography installation consisting of three simplified maps of Seattle that was placed in a gallery where patrons were asked to write, directly on the maps, descriptions of their own sense of place associated with the locations. I then compared the language from the installation to that from the analysis of the Instagram images. Strong similarities between the two suggest the possibility of using crowd-sourced visual representations of place from social media to offer a greater understanding of how natural and built environments evolve and what they mean to the people who inhabit them.

Flatfishes of Puget Sound commonly host Clavinema mariae nematode “blood worms”, which reside in the subcutaneous tissue of the host, rendering them unmarketable. Recently, we observed C. mariae in blackbelly eelpout, Lycodes pacificus, which has never before been reported to carry this parasite. Because blackbelly eelpouts have no economic importance, there may have been little incentive for reporting this infection in the past; whether our recent observations of eelpout infection represent a new development or a long-standing host–parasite relationship is therefore unclear. To estimate C. mariae burden in eelpouts from Puget Sound, I am counting subcutaneous parasites in preserved specimens collected between 1911 and 2014, from the University of Washington Ichthyology Collection. If C. mariae appear only in eelpout collected recently, this may indicate a host switch from flatfishes to eelpouts. In the future, DNA sequence analysis will be conducted to determine if C. mariae from flatfishes and eelpouts are indeed the same species. Our work will reveal whether the recent appearance of C. mariae in eelpout is due to host-switching, parasite spillover, or improved observation and reporting.

This study explores the use of media to construct social valuation and devaluation in racial discourse on the internet. The use of social media and on-line platforms contribute to complex power relations that mediate social and racial difference. I am investigating how both news sources and social media are used in relation to the Black Lives Matter movement and All Lives Matter campaign to expose the relational construction of value, race, and the “other.” Through an inductive content and discourse analysis of primary movement resources, news media, and Twitter, I reveal the controversial ways in which the value of Black lives is affirmed and challenged on public platforms. This project is significant for understanding how social media and online news sources have created new opportunities for protest as well as new revelations of how the process of “othering” racialized groups persists in the twenty-first century.

Despite the intense coverage of the Syrian Civil War in US media, consensus about what started the Syrian Civil War is highly debated. The variety of explanations cited as leading to the Syrian Civil War range from: corruption, protests, sectarianism, climate change, and drought. My mixed methods research begins by exploring whether certain conflict explanations like the Arab Spring Protests are overrepresented in discourse whereas conflict explanations using climate change are underrepresented. A manifest content analysis of 134 American newspaper articles of causes for the conflict from the New York Times, Washington Post, and Wall Street Journal yielded that they did indeed favor Arab Spring protests but that the results varied by newspaper. The right-leaning Wall Street Journal failed to mention climate change in a statistically significant manner whereas the Washington Post repeatedly mentioned climate change as a major factor for the Syrian Civil War. Interpretations and analysis of the same conflict produced different ideas about what started the conflict. The second part of my research involved an inductive latent content analysis of these news sources to truly understand the perceptions that drove news organizations to report the way they did. Here I report two key findings: a better understanding of how causal factors for conflict are explained in American media and how media organizations justify and convey narratives of importance to them. Such research is important because climate change and conflict is an issue that is important to the stability of the globe. Understanding how and why it’s importance is overrepresented and underrepresented in news sources can help determine how popular geopolitics shapes perceptions and how to make discussions of climate change in the lens of conflict more acceptable.

Non-vascular epiphytes have been determined to grow in a non-random distribution in the canopies of Acer macrophyllum in the Hoh Rainforest, Washington. Nitrogen (N) source has been suggested as a potention driver of the distribution, and stable isotopic analyses were used to consider the influence of this factor. Three epiphyte species, the lycophyte Selaginella oregana, and bryophytes Rhytidiadelphus loreus, and Neckera douglasii, and four trunk dwelling species, Selaginella oregana, and the bryophytes Hypnum subimponens, Leucolepis acanthoneuron, and Metaneckera menziesii, were selected for analyses on the basis of their distribution on five host trees. Samples of plant tissues, as well as canopy and trunk soil were analyzed using isotope ratio mass spectrometry to identify the N source of each species. N source varied significantly by species and growing location. δ¹⁵N values of all bryophyte species confirmed an atmospheric N source. Results for the lycophyte S. oregana varied significantly in response to its relationship with R. loreus, which grows above it in mats in the inner canopy. Selaginella oregana appears to use canopy soil N in the presence of R. loreus, and atmospheric N in its absence on the trunk. These findings suggest the role of niche partitioning in the coexistence of S. oregana and R. loreus within the canopy, and illustrate the likely ability of S. oregana to vary its N source based on competition for the resource. No study of this kind has been conducted in the Hoh Rainforest to date, and this work highlights the intersection of abiotic and biotic factors in determining epiphyte species distributional patterns in the temperate forest ecosystem. 

Marine mammals are federally-protected species of interest, however their parasites are vastly unexamined. A lack of data regarding this host-parasite relationship hinders the understanding of ecosystem interactions, which poses consequences for successful conservation and management of marine mammals. To better understand the impacts of parasites on their marine mammal hosts, my research assessed the intestinal parasite burden of harbor seals (Phoca vitulina richardsi) in south Puget Sound. Harbor seal scats were collected under permit from the Commencement Bay floating dock haul-out site each month during and after the pupping timeframe. Non-invasive fecal floatation methods were used on scats to quantify the abundance and diversity of parasites from July 2017 to February 2018. An increase in prevalence of parasites within the population is expected following the weaning of seal pups as they begin feeding on invertebrates and fish implicated in parasite lifecycles. This research establishes baseline data on the intestinal parasite assemblage of Pacific harbor seals within Puget Sound, and the data will later be used in conjunction with molecular diet analysis to deduce the source of parasitic infection. My research can be used to assist with conservation efforts of harbor seals and can be broadly applied to other marine mammals within and outside of Puget Sound, serving as an example for future studies that consider the relationship between marine mammal hosts and their parasites.

Public transit is a quasi-public space between the public and private, acting as a fabric connecting the lives of many different types of people. Working within a framework of feminist urban geographies, this research seeks to understand how fear, safety, and emotion are constructed and interpreted within transit space in the city. With a particular focus on the experiences of women and queer individuals, I questioned how geographies of fear and safety impact movement and behavior in the city. Additionally, I examined the role of city officials and policy makers in creating safer transit spaces. Using a synthesis of qualitative research, media analysis, and autoethnography, I present the policies and practices that have, and have not, been successful in cities across the United States. The results of this research have shown that women and queer people consistently report feelings of insecurity and lack of safety in urban spaces. Policies and campaigns introduced in major cities such as New York and Los Angeles have had measurable success in combating harassment and violence, while smaller cities such as Seattle have yet to implement policies to do the same. This research is intended to contribute to the larger discourse surrounding feminist geographies and urban studies.

Conventional diagnostics for tuberculosis use the patient’s sputum, mucus from the lower airways, as the primary sample type. Collecting sputum can be difficult and hazardous and for some patients, especially pediatric cases, sputum must be induced through an invasive procedure. An alternative to sputum samples is oral swabs, which have been used to detect the presence of Mycobacterium tuberculosis DNA in clinical trials. However, the current threshold of oral swabs is not yet sufficient for widespread implementation. In a new phase of assessing the viability of oral swab samples, nine different swab types were compared to improve DNA yield and subsequent qPCR readouts. The comparison was based on qPCR Cq values after spiking the swabs with mTB DNA, and analysis of each swab’s suitability for culturing. Earlier results suggest that oral swabs are a feasible alternative to sputum samples when using swabs that are heavily “flocked”, meaning that they have many small fiber particles deposited across a surface. Moreover, samples performed with dissolvable swabs may be better suited for further molecular and microbiological analysis.

Oral swab analysis (OSA) is a possible alternative sample type for tuberculosis diagnostics. It has been observed that tongue swabs contain greater amounts of Mycobacterium tuberculosis DNA than cheek swabs (p<0.0001). This project investigates whether other oral microbiota follow the same pattern by analyzing oral swabs from healthy controls and TB patients from South Africa. To determine the oral bacterial load, the first step was to optimize a universal bacterial PCR protocol that could be used on real samples. The Com1/769R primer set that amplifies the 16s region of prokaryotic DNA (Dorn-In, 2017) was selected after a literature review and tests with DNA from 5 different bacterial species at known amounts to compare sensitivity. Next, samples were collected from 5 healthy volunteers from Seattle. They provided two swabs each, one from their tongue and one from their cheek, which we then analyzed by PCR. Oral swab samples from South Africa were also analyzed by PCR. We found that the tongue swabs contained greater amounts of total bacterial DNA than the cheek swabs. For the healthy Seattle volunteers, the tongue swabs had an average of 294 times more DNA than the cheek swabs. For the South African samples, the tongue swabs had an average of 13.2 times more DNA than the cheek swabs. Our results suggest that there may be more prokaryotic DNA on the tongue than cheek. Our next steps are to test additional samples from South African subjects. This research could impact the development of future diagnostic tests that detect pathogens within the oral cavity.