Phytophthora is a genus of oomycete water molds that harms plants. They are a group of fungi-like microbes responsible for several plant diseases, including blight, canker, dieback, and root rot. Even though approximately 30 species have been identified in Oregon and Alaska, the number of species currently present in Washington is yet to be determined. Our research focuses on the diversity of Phytophthora species. First, in an analysis of previously collected data and US Census data, the Phytophthora species diversity is higher in counties with a higher human population. Based on this analysis, we expected to find more than three species of Phytophthora present in Chambers Creek (our sample site) due to the high human population in Pierce County. Secondly, we sampled Chambers Creek for nine days using Rhododendron leaves, incubated the leaves for two days, then performed a PCR. The PCR product was sequenced using Sanger sequencing and a BLAST was used to identify the species present in our sample. Ultimately, we identified four species of the harmful plant pathogen Phytophthora present in Chambers Creek. From this, we conclude that there is a high diversity of Phytophthora present in this Pierce County water source. Phytophthora can be extremely harmful to trees and crops, and it has caused mass famines in the past. This research is vital because understanding patterns of its diversity allows us to monitor its presence locally; should a particularly harmful species be found, we can work to mitigate its effect on our ecosystems.

High indoor carbon dioxide (CO2) levels have been shown to cause negative symptoms in humans, including dizziness, headaches, and cognitive impairment. Concentrations of indoor CO2 have also been used as an effective proxy for the risk of airborne disease transmission risk. Individuals experiencing poverty may be at increased risk of adverse effects from indoor CO2 concentrations due to historic under-investment in infrastructure, such as high quality HVAC systems, in these communities. Public spaces such as libraries are particularly important for under-resourced communities as they may be the only places with accessible Wi-Fi, reading materials, and indoor bathrooms. This study surveys libraries, in several Seattle neighborhoods with varying rates of poverty. All libraries tested are branches of the Seattle Public Library system. Aranet4 HOME air quality monitors, that measure CO2 levels, were placed in similar central locations in each library for twenty-four hours on weekdays.The highest three recorded CO2 levels in a day were averaged to determine the peak CO2 exposures for library patrons. For instance, at the Ballard Branch, the highest average recorded CO2 levels were 712 ppm +/- 0.577 ppm and the neighborhood has a poverty rating of 2/10 according to the Washington Tracking Network (WTN). At the Magnolia Branch, the highest average recorded CO2 levels were 622 ppm +/- 10.6 ppm and the neighborhood has a poverty rating of 1/10 according to the WTN. Preliminary results thus far do not show significant differences in CO2 levels. The chosen libraries vary in size and may show more CO2 fluctuations once data is collected in additional areas. Documenting air quality differences in public spaces can highlight systemic inequities and help planners allocate limited resources to most effectively and equitably serve all Seattle neighborhood communities.

Phytophthora is a genus of water mold that causes plant disease and spreads quickly. Certain Phytophthora species can wreak havoc among crops and ecosystems. Early detection of the plant pathogen is key to preventing its spread. Based on observed blight on oak trees, we set out to detect Phytophthora in our local watershed, at Clark's Creek Park in Puyallup, Washington. We baited pathogens in the water by placing rhododendron leaves in netted bags, and submerging the bags in one of the park streams for 14 days. We then cultured the infected leaves and extracted deoxyribonucleic acid (DNA) from the cultures. We performed polymerase chain reaction (PCR) to amplify the Phytophthora internal transcribed spacer (ITS) gene, and sent our PCR product out for DNA sequencing. Once we received the results, we used the Basic Local Alignment Search Tool (BLAST), an online tool that matches DNA sequences with available DNA databases. Using BLAST, we identified which species were present in our cultures from Clark’s Creek. We confirmed the presence of two Phytophthora species: P. gonapodyides, P. chlamydospora. These species preferentially infect forest and fruit trees. Scientists and community leaders can use our research to track Phytophthora and focus containment efforts in our local ecosystem.

Coastal fog levels along the Pacific Coast have been declining over the past century, likely due to climate change. Fog plays an important role in coastal ecosystems and supports many species native to the Pacific Coast. Plants native to the California coastline have been shown to benefit from the higher humidity and lower temperature conditions associated with fog. Little research has been done of the implications of fog decline on native vegetation in Washington State. This study measures the effect of varying fog levels on photosynthesis rates in Washington State native plants. Plants were divided into a fog and control group in two isolated chambers. The fog chamber was exposed to humidity typical of Washington coastal conditions. Photosynthesis rates were measured by gas exchange (carbon dioxide uptake) and chrorophyll a fluorescence using the Li-Cor LI-6800 Portable Photosynthesis System. The results suggest decreasing fog could cause a decline in the productivity of coastal vegetation, which in turn affects other members of the ecosystem. A better understanding of the impacts of coastal fog decline can inform habitat restoration to include techniques such as fog collection to help mitigate the impacts.

Classical conditioning is a method of learning in which a neutral stimulus is repeatedly matched with a naturally occurring stimulus to produce a learnt response. Whereas operant conditioning involves utilizing consequences to change behavior. Operant conditioning, developed by B.F. Skinner, uses positive or negative consequences to increase or decrease behavior frequency. It's widely used in animal training, but only operant conditioning is used in numerical recognition tasks. Classical conditioning is often used with negative stimuli to create an aversive response, but it's easier to implement and has not been fully explored as an alternative. Our research investigates the use of both operant and classical conditioning in teaching numeral recognition to the common freshwater angelfish, Pterophylum sclarae. Two fish are housed and trained individually. Tanks were set up with one end displaying two windows for dot arrays; this end of the tank has a divider down the middle so the fish can only swim up to one set of dots at a time. They are presented with a single dot on one side, three on the other. The classically trained fish was offered a food reward in front of the window displaying three dots. The operantly trained fish was trained using free-shaping techniques, receiving a small reward for each movement towards the correct array, getting a “jackpot” reward when arriving at the correct window. Fish were assigned a score on a 100 point scale, where the number of seconds it took the fish to get to the correct side is subtracted from 100 to determine the score. Preliminary results show that the classically trained fish has higher accuracy and speed in determining the correct array. This demonstrates that the simpler method of classical conditioning may be a feasible training method for cognitive tasks in angelfish.
 

Giardia lamblia is a gastrointestinal parasite which causes diarrheal disease and hinders nutrient absorption. G. lamblia colonizes the small intestine by a two-phase life cycle: the reproducing trophozoite stage and the transmissive, infective cyst stage via a fecal-oral route. How G. lamblia detects encystation signals in the encystation process is unknown. Our laboratory discovered EncystR, a seven transmembrane protein which compartmentalizes after perceiving cholesterol depletion and increased pH. Knockdown of EncystR promoted encystation, indicating negative regulation. We hypothesize that EncystR is responsible for perceiving encystation stimuli and de-repressing cAMP signaling to promote encystation. However, the mechanism responsible for triggering cAMP signaling is uncharacterized. This project hopes to identify EncystR transient interactions using proximity labeling and mass spectroscopy (LC-MS/MS). Proximity labeling of EncystR over an early encystation time course will identify proteins involved in downstream signaling. To determine time points of interest, EncystR was endogenously labeled with mNeonGreen (mNG), and imaging of non-encysting cells displayed EncystR-mNG at the plasma membrane. To delineate the EncystR trafficking pattern, we induced encystation and followed EnystR localization for several hours using fluorescent microscopy. Individual cells were categorized by localization to peripheral vesicles, a novel acidic compartment, or non-responsive cells where localization remained on the plasma membrane. Percent peripheral vesicle localization peaked at 1h and percent compartmentalization stabilized after 3 hours. Proximity labeling proteomics at these time points can identify connections to cell trafficking to the novel acidic compartment. While EncystR does not tolerate TurboID proximity labeling, miniTurbo produced significant biotin labeling after 30 minutes in 50 mM biotin. Biotin-tagged proteins are sequestered using Streptavidin-coated columns through liquid chromatography, then cataloged using mass spectroscopy (LC/MS-MS). Proximity-tagged proteins using miniTurbo can inspire drug inhibition candidates of Giardiasis. Due to Giardia’s model nature to other parasites, such as reliance on cholesterol, parallel drugs may be found as well.

Antimicrobial resistance in the environment is a topic of increasing concern in public health. There is evidence in recent literature that wild migratory birds in an urban context can act as a vector and reservoir of antibiotic-resistant bacteria and can spread antimicrobial resistance genes (ARGs) to soils in urban parks. In this project, we hypothesized that migratory waterfowl inhabiting urban parks in Seattle, Washington may be a vector of ARGs to soil in public parks with waterfront habitat. To test this hypothesis, we collected samples of feces from Canada geese at Greenlake and Meadowbrook parks in Seattle and collected topsoil samples from the immediate goose habitat. We are focusing on E. coli as an indicator organism. As a comparison, topsoil was also collected from several playfields in Seattle that do not have waterfront habitat. After diluting samples with sterile water, E. coli in these samples was identified using selective media. Once identified, isolated E. coli colonies were tested for resistance to several common antibiotics using Kirby-Bauer diffusion testing. We expect to see antimicrobial resistance in the Canada goose feces, higher rates of antimicrobial resistance in the goose habitat topsoil as compared to topsoil from playfields, and similar profiles of antimicrobial resistance in the waterfront topsoil and goose feces. As many communities without access to private yards depend on public parks for recreation, this work may have important implications for health equity in the urban environment.

The Pacific Northwest is home to a lush lowland forest that continually changes. Quantitative monitoring is essential in understanding forest health and climate change. The primary task was to help create a comprehensive, multi-year, dataset of floral phenology for Green River College’s learning forest; botany and ecology classes participated together in this endeavor. This quantitative data set allowed us to establish baselines for our forest so we could ask questions about how our forest changed over time. How do the native species compare to the invasive species? How many species are there, and which is most abundant? Using the ArcGIS Survey123 app, we measured floral species, abundance, GPS location, and phenology stages (buds, flower, seed/fruit, and leaves). The data was then analyzed using Qlik, an online visualization software. In 2022 alone, we compiled ~13,000 observations, estimating ~3.2 million inflorescences across ~140 species and are currently curating data from 3+ years. When looking at the floral expression in our forest from the last two dry summers, one native species (Wild Ginger) has disappeared, while many non-native and invasive plants were able to thrive. With our data set we can quantitatively look at entire plant families and monitor ecological change. A secondary benefit of this endeavor was to improve the educational capacity of our classes. Students were fully immersed in the forest and floral details. Photographs from students also helped create a repository for plant images of floral phenology stages which strongly aids in identification and higher level data quality. Our project helped undergraduates contribute scientifically while learning about their world. These contributions can help inform decisions on issues such as mitigating climate change or ecosystem preservation. Future directions include expansion of this to city parks and popular hiking trails to broaden our quantitative understanding of our ecosystems.

Mutations in the genetic sequences of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) has played a major part of the pandemic. This is evidenced by the increasing number of distinct strains that have appeared. Evaluating these mutations and their frequency within genetic sequences offers the opportunity to identify patterns that aid in increased virility for SARS CoV-2. We identified prevalent SARS CoV-2 strains in GISAID and downloaded genetic sequences from the NCBI nucleotide database. We used MAFFT (Multiple Alignment using Fast Fourier Transform) in Seaview to align SARS CoV-2 strains to the reference genome. We also built a custom python script to identify locations of mutations, and their potential effect on the proteins’ amino acid sequence. Preliminary work identified a mutation in the ORF1ab gene of the omicron strain. Part of this gene codes the typically conserved NSP-16, associated with the product 2’-O-ribose methyltransferase, an enzyme that catalyzes the transfer of a methyl group from a methyl donor molecule. The modification could affect the stability, localization, and function of RNA such as RNA splicing and post-transcriptional modification. We then generated a phylogenetic tree using BEAST/BEAuti to estimate the frequency and history of mutation across different strains. Our analysis identifies mutations accumulated over the course of the pandemic. Studying the effects of these mutations offers insights into SARS CoV-2 virology. These insights can be used to build a predictive model to aid in effective and efficient vaccine development.

This study aimed to assess the prevalence of cphA-genes, which encode for a CphA β-metallo lactamase (MBL), in Aeromonas bacteria. Aeromonas isolates investigated were collected from wetland and non-wetland locations within the University of Washington Bothell, where crow fecal matter contamination and runoff from North Creek may contribute Aeromonas spp., among other bacteria. Some of the methods I used involved isolation of Aeromonas by plating fecal samples and water samples (on filters) on Ampicillin-infused blood agar, Meropenem (MERO)-infused LB agar and Cefsulodin-Irgasan-Novobiocin antibiotics (CIN) agar. The 41 collected isolates (26 isolates from fecal samples and 15 isolates from wetland water samples) that tested positive on Meropenem were further tested by Modified Hodge test and Modified Carbapenem Inactivation Method (MCIM) test. Results indicated that two (5%) LB+MERO isolates were cphA-positive, which I tested by PCR with primers directed to the cphA gene. These samples were positive both by the MHT and CphA-PCR. Both the cphA+ isolates originated from stream water samples, and they were collected on two different days, indicating the possibility of an alternative source for the CphA β-lactamase-encoding gene other than crow fecal runoff into North Creek. As MBL-producing species pose a potential health risk to the environment and residential areas in proximity to the river, further investigations must be performed. Future studies will involve testing more fecal and wetland water samples to definitively establish the source of cphA containing Aeromonas.

Many curricula today fail to connect STEM with the issues students and their communities face. This shortcoming can lead to increased dropout rates and equity gaps especially in early STEM courses. With the COVID-19 pandemic and the George Floyd uprising, fostering students’ ability to tie STEM into the issues of social justice have never been more important. In this study, we investigate whether a Course-Based Undergraduate Research Experience (CURE) centered around the public health implications of indoor CO₂ can give students a greater understanding of the relevance of STEM to social issues and help them see STEM as a tool to solve problems in their communities. Students were administered a brief pre-survey before beginning the CURE. They were then introduced to the low-cost CO₂ sensors and the public health implications of high indoor CO₂. Students formed groups, formulated their research questions, and collected data. Students then analyzed their data and presented their research to their peers. A post-survey was administered following the CURE. We are currently analyzing the results of the surveys and post-curriculum interviews. The preliminary results suggest that connecting CUREs to relevant social issues in early STEM courses is a powerful tool that not only teaches students to interpret the world around them but also to change it.