I am interested in producing Human Papillomavirus (HPV) type specific monoclonal antibodies (mAbs) from B cells derived from adolescent females and young women vaccinated with the licensed human papillomavirus vaccine, Gardasil 9, which provides protection against HPV types 6, 11, 16, 18, 31, 33, 45, 52, and 58. Fluorescently labeled pseudoviruses for these nine HPV types, as well as phenotypic markers of memory B cells are used to isolate HPV specific memory B cells via fluorescence-activated cell sorting (FACs). Gene transcripts for Immunoglobulin (Ig) heavy and corresponding light chain variable regions are amplified through Reverse Transcription Polymerase Chain Reaction (RT-PCR), cloned into their respective IgG1 backbone vectors, and subsequently transfected into eukaryotic cells to produce antibodies. HPV types [6, 11, 16, and 18] have been previously produced by our lab. I aim to expand on this work by developing antibodies against types 31, 33, 45, 52, and 58. I will characterize these mAbs for HPV binding and neutralization. Production of these well-characterized, type specific antibodies are useful for HPV studies, because they provide standards in HPV serologic assays. 

A product we consume daily, such as honey, may contain heavy metals like copper (Cu). Copper can get into our environment and food from urban sources such as tires, roofing materials, and generators. We therefore expect food products from more urbanized areas to show a higher concentration of copper. To test this hypothesis we evaluated copper levels in raw honey from different regions with different levels of urbanization. The honeys we tested were divided into three different categories according to their source: rural, suburban, and urban. The samples were digested by reflux with HNO₃ and H₂O₂ then it was diluted and filtered in preparation for analysis by Atomic Absorption Spectroscopy. The results suggest that the honey with the highest concentration of Cu was from an urban area, and the honey from a rural setting had the least amount of Cu. A one-way ANOVA analysis confirmed a statistically significant difference in the copper levels in raw honey from the regions (p < 0.01). The concentration of Cu in the samples of honey we analyzed ranged from 0.2 ug/g to 0.4 ug/g which is well within the recommended upper limit of 300 ug/g. Since bees collect pollen and honey from plants within roughly one mile of their hive, evaluation of the levels of copper and other metals in honey can provide a snapshot of the background levels of exposure in that area.

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

Methicillin resistant Staphylococcus aureus (MRSA) is an antibiotic resistant pathogen that causes severe illness and thousands of deaths each year in the US. It spreads within the community through improper hand hygiene and is often found in hospitals and on public transport surfaces. This poses a danger to the public, specifically to vulnerable populations such as the elderly and immunocompromised. This study in Seattle, Washington compares the prevalence of the antibiotic-resistant MRSA bacterium on public transport surfaces both proximate and distant to Harborview Hospital. Swabs from bus stops and pedestrian call buttons were collected outside of Harborview Hospital and urban areas of Capitol Hill, a Seattle neighborhood approximately one mile away from any major hospitals. The swabs were streaked onto Tryptic Soy Agar plates, gram stained, and streaked on Mannitol Salt agar plates;catalase and coagulase tests were run to help further confirm the presence of Staphylococcus aureus. The resulting colonies were then screened for antibiotic resistance using the Kirby Bauer Disk Diffusion method. One instance of potential MRSA was isolated from a crosswalk button in Capitol Hill. A higher MRSA prevalence on surfaces close to hospitals could establish a link between the spread of pathogenic bacteria from hospitals to Seattle's city surfaces but was not found in this study. These results suggest that the spread of MRSA in Seattle may have more to do with foot traffic and public transportation usage. However, the presence of MRSA on urban surfaces puts sensitive populations at risk regardless of its source. Practicing good hand hygiene can help curb the spread of MRSA in the community.

 Nitrogen (N) has an important role in aquatic ecosystems, both as an essential nutrient for plant growth and a limiting factor maintaining the overall health and balance of an ecosystem. N concentrations exceeding 0.3mg/L in streams and rivers and 0.1mg/L in lakes and resevoirs pose risk for eutrophication events and ecosystem destabilization. This study tracks the presence of dissolved inorganic nitrogen (DIN) throughout Puget Sound watersheds to determine if concentrations pose a threat to these ecosystems. Our team collected water samples along streams located in the greater Cedar-Sammamish watershed. Ion chromatography was then used to determine the concentrations of nitrate (NO₃^-), nitrite (NO₂^-), and ammonia (NH₄⁺) in the samples. The DIN concentrations varied throughout samples, allowing us to map N levels throughout the watershed and pinpoint regions that are at-risk of eutrophication, as well as identify trends in the fluctuations of N levels. The results of this study contribute to efforts to monitor stream health in the greater Seattle metropolitan area in order to prevent the ecological cascades caused by direct and indirect effects of nitrogen pollution. 

Fluoride is an important element for dental health as it helps to strengthen tooth enamel. Insufficient fluoride intake can lead to weakened teeth that are more susceptible to cavities, leading to further dental issues. On the other hand, dental fluorosis is a condition that causes white or brown speckling of the teeth due to overexposure to fluoride during the development of permanent teeth. For most people, a large portion of their fluoride intake is through water, but water from different sources is expected to contain different amounts of fluoride. Many Americans consume tap water, but bottled water is a popular choice. In fact, US consumers buy about 50 billion water bottles each year which equates to 13 bottles per person monthly. This mass consumption of bottled water raises important questions: 1) Is bottled water a sufficient source of fluoride? 2) How does it compare to tap water? To answer these questions, we collected tap water samples from six cities in the Puget Sound area, along with samples from six popular brands of bottled water. We then used ion chromatography to determine fluoride concentrations in each sample. We found the levels of fluoride in our six municipal sources averaged 0.702 +/- 0.031 mg/L as advertised, however, the levels within the different bottled water brands averaged +/- 0.282 0.307 mg/L, and none met the CDC recommended levels of 0.7 mg/L. The findings of our research are important for keeping consumers well informed about the possible risks or advantages associated with their preferred source of water and for upholding public trust.
 

Exclusionary zoning laws — which limit population densities and land uses in specific neighborhoods — are a typical feature of American municipal land use regulation. An extensive body of evidence links traffic-related air pollutant (TRAP) exposure to adverse health effects. Using zoning data and a model of TRAP levels in cities across the Seattle metropolitan area, I hypothesize that TRAP exposure will be greater on average in zones where higher-density housing is an allowed use, and lower on average in zones reserved for lower-density housing. I used the software package QGIS to spatially join zoning and air pollution data and used the software package R to perform correlation analyses between zone types (classified by maximum population density) and three common TRAPs (NO₂, black carbon, and ultra-fine particles.) This research highlights the public health implications of normative policy regimes like exclusionary zoning. These results can assist elected officials and planners in pursuing a more geographically distributive approach to increasing housing supply in the Seattle area, in order to minimize the TRAP exposure burden – and associated adverse health effects – faced by residents.

Cannibalism is a widespread phenomenon among arthropods with consequences for population dynamics, stability, pathogen transmission, and epidemiology; while it is common in carnivorous arthropods, incidents of cannibalism among non-carnivorous species are less frequent, and the mechanisms behind cannibalism in these species are still poorly understood. Laboratory observations of Pieris rapae (cabbage white) larvae have found that larvae will engage in cannibalistic behavior under certain conditions. The objective of our research was to better understand the conditions that may cause this herbivorous larva to become cannibalistic. Experiments were conducted on variables of density, food source, food scarcity, instar, instar gaps, sex, and prior experience as possible influencing factors in the likelihood that a larvae will engage in cannibalism. Experiments in density, food source, and food scarcity had groups of larvae monitored for 48 hours at differing densities with a collard leaf, artificial diet, or withheld food. For experiments in sex, instar, and instar gaps inexperienced larvae were monitored in sets of two for 72 hours for cannibalism. For prior experience experiments, larvae that had previously engaged in cannibalism were paired with inexperienced larvae and monitored for another 72 hours. We found that higher larvae densities had a greater percentage of cannibalization. Furthermore, a lack of food source produced significantly higher cannibalization than either artificial or leaf diets. A higher rate of cannibalism was also seen in early instars. Prior cannibalistic behavior increased the rate of new cannibalism events within the first 24 hours of observations.These findings provide insights into cannibalistic behavior in P. rapae, with potential applications to prevent cannibalism in laboratory settings and related disease transmission, understand fluctuations in wild populations, and in agricultural settings to leverage cannibalism as a form of natural population control. Future research aims to isolate other possible factors contributing to cannibalism in P. rapae.

Our research aimed to investigate the microbial diversity in Pieris rapae larvae obtained from three distinct settings: wild-collected larvae, larvae fed with leaves in a laboratory setting, and larvae fed with a standard artificial diet. Additionally, this investigation sought to identify the factors contributing to developmental delays in artificial diet-fed larvae, while also investigating the underlying cause of increased cases of infection and mortality affecting the laboratory colony. Initial observations indicated that wild larvae exhibited the fastest development and appeared healthiest, followed by those fed with leaves, both settings showing the lowest instances of disease and mortality. Conversely, the artificial diet group experienced developmental delays and frequently succumbed to disease before pupation. Based on these observations, we hypothesized that variations in microbial composition within different diets and environments contributed to the disparate outcomes. Furthermore, we speculated the possible identification of bacterial strains with known associations with promoting or hindering larval success. To analyze the larval gut microbiome, a specialized contraption was designed for sterile frass (feces) collection. Frass, skin, artificial diet, and leaf surfaces were swabbed onto TSA media, enabling the isolation of distinct colonies and species. Morphological characteristics, gram staining, and Sanger sequencing data of the 16S rRNA gene were used to identify the bacterial colonies at the species level. The identification of six bacteria at the species level yielded intriguing results, with particular interest surrounding Bacillus subtilis and Bacillus thuringiensis. The presence of B. subtilis exclusively in the artificial diet group suggests its potential involvement in the developmental delay observed in the larval population fed by artificial diet. Conversely, the identification of B. thuringiensis implicates a potential bacterial infection, which could explain symptoms experienced by the colony. These findings have potential implications for enhancing larval outcomes in colonies or, in contrast, pesticidal applications in an agricultural setting. 

The basic reproductive number (R₀) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has varied over the course of the pandemic. Phylodynamic analysis uses genetic samples to estimate R₀ by combining a phylogenetic tree model with an epidemic model. Previous research has used phylodynamic analysis to study how government policies and non-pharmaceutical interventions influence the R₀ of SARS-CoV-2. We collected publicly available phylogenetic tree data from published research on selected island nations during the first two years of the pandemic. We studied island nations due to their stricter travel limitations in order to reduce external variables. We estimated transmission rate, incubation period, and sampling probability of the virus in each nation using a birth-death exposed-infectious (BDEI) model implemented in the Python software package PyBDEI. These estimates were used to calculate R₀ for each nation. We validated our data analysis pipeline with sample data and utilized subsampling methods to reduce compute time. We then conducted a comparative analysis of COVID-19 pandemic intervention responses between the island nations using our estimates of R₀. Lower estimates of R₀ provide evidence that supports the effectiveness of specific policy interventions in decreasing viral spread. Our results can inform policymakers which intervention methods to use in case of future similar outbreaks by coordinating evidence-based policies across regions.

Temperature has been shown to impact the physiology and performance of ectothermic organisms including metabolic rate with enzymatic activity. The majority of studies have focused on thermal performance at constant temperatures although organisms experience a range of fluctuating temperatures. Understanding which aspects of performance are affected by fluctuations in temperature can be crucial for predicting how ectothermic species will respond to changes in their environment. Research has shown that ectotherms are more vulnerable to climate change and their growth rates are often temperature-dependent. Previous studies on the cabbage white butterfly (cabbageworm), Pieris rapae, have shown that caterpillars maximize growth at higher temperatures even when higher temperatures are infrequent. Physiological response of P. rapae on fluctuating temperature change will provide an important insight into its ability to adapt and survive to changing temperature ranges. For our study eggs from a lab colony were reared at two different fluctuating temperature regimes (11-35℃ and 18-24℃) until pupation. Our studies measured the overall performance of P. rapae, including egg hatch percentage, growth rate of 4th instar caterpillars, development time from 4th instar to pupation, percent survival, and mass gain at two fluctuating temperature regimes of 11-35°C and 18-24°C. We found that the percent survival was significantly higher at 18-24°C. There was significant mass gain and shorter development time of 4th instar to pupation at 11-35°C. Our results differed from other studies that found growth rate to be greater at 11-35°C. Many studies have found a significant genetic variation in growth rate, development rate, and pupal mass. Future studies using a split sib-family design, may provide insight into the mechanisms of thermal performance in a fluctuating thermal environment. Understanding how fluctuating temperatures impact ectothermic organisms, such as the cabbageworm, can contribute to a deeper understanding of organismal responses to climate change.

Eutrophication fuels toxic algal blooms that can harm biodiversity and human health. Phosphate is often the limiting nutrient in freshwater ecosystems and, when in excess, causes eutrophication. Our study compares urban lakes prone to algal blooms to rural lakes with fewer anthropogenic sources of pollution to better correlate nutrient dynamics of pacific northwest lakes to population density. We collected sediment and water samples from two lakes in the Seattle area and two lakes in a more remote setting, then measured phosphate uptake and release over time using ion chromatography. To determine the potential for the sediments to uptake phosphate, we placed air-dried sediment samples into a phosphate solution and measured the concentration over time. We also put the sediment in distilled water and measured the phosphate released from the sediment over a 24 hour time period. These two data sets allow us to quantify the capacity of sediment to store and release phosphate into the surrounding environment. Our research shows sediments from urban lakes release more phosphate and have a reduced ability to uptake nutrients from the water. This suggests that the lake will continue to eutrophy whereas the lakes more removed from human activity have a better ability to mitigate excess phosphates. This model for assessing the ability of sediment to store phosphate allows prediction of future eutrophication events.