Children with uncontrolled asthma are three to six times more likely to be hospitalized. It is necessary for parents and children to collaborate in order to help the child successfully manage their symptoms, yet few solutions exist to support this parent-child shared management. A novel mobile health application was designed and tested with 54 parent-child dyads in an eight-week pilot randomized controlled trial (RCT). The goal was to see if proper planning, communication and using an asthma monitoring watch would improve symptom monitoring in children with asthma. During this study, the watch detected the children’s asthma-related symptoms as they occurred. On a web application, both the parents and the children were asked to collaborate to enter reminders for medicine, summaries for any symptoms, etc. After 8 weeks, the parents and children completed semi-structured interviews where they reported any improvements in their asthma symptoms and general feedback regarding the app. We conducted qualitative analysis by writing codes based on the patterns observed in the user survey responses analyzed. Finally, we compiled our findings into a code book which serves as a guide for upcoming trials. The interview findings revealed that families found the intervention to be helpful for reducing asthma related flare-ups. However, the sync between the watch and the app, integration of the spirometer results with the app, and making the web application interface more kid-friendly are all recommended refinements to consider before the project is scaled for a larger clinical trial.

Possession Sound, WA, serves as an important foraging area for a group of seasonally resident gray whales Eschrichtius Robustus. This group of predominantly Eastern North Pacific Gray Whales that visit Possession Sound (Sounders) arrive as early as January and continue migrating towards other feeding grounds near May. If the frequency of sounds within the hearing range of these gray whales (50 to 5000 Hz) exceeds comfortable levels, they may have difficulty foraging. To monitor these relationships, we looked at the frequency and amplitude of sound near Mt. Baker Terminal (MBT) in Possession Sound, WA, from January 2021 to May 2021 with a specific focus on sounds from 50 to 5000 Hz. To gather this data, we used a SoundTrap 300 HF hydrophone, which is currently mounted to a dock at MBT. From January 2021 to February 2021, the hydrophone recorded continuously at a 96-kilohertz sampling rate. From March 2021 to May 2021, the hydrophone was set to record the first fifteen minutes of every hour at the same sampling rate. Preliminary research shows that Possession Sound has a consistent prevalence of ambient and intermittent noise within the established frequency range and peak amplitudes as high as 164 dB. This level of noise may have the potential to negatively affect gray whale behavior and foraging success. Future research should be conducted to see how current and future vessel slow-down trials will impact the frequencies and amplitude of local noise. Future research should also include comparing the MBT sound profile to other sites in the Salish Sea to better understand if the amplitude increase is unique to the area or a cause for wider concern.

The interaction between incoming salt water from the ocean, which is driven by tides, and exiting freshwater from rivers drives circulation through estuarine environments. As a result of the interaction between the incoming water and the exiting water, nutrients and sediment are moved around the estuary. This study focuses on the interaction between tides and the Snohomish River as it enters the Possession Sound estuary, located in Everett, Washington. To acquire data, I deployed a boat-mounted acoustic Doppler current profiler (ADCP), which uses sound to measure water current direction and velocity. I collected these data at varying tide stages at three different sites between the Snohomish River’s southern output to nearby Mount Baker Terminal, located 3.6 miles southwest of the river output. I have collected 8 samples over the course of 7 months at both ebb and flood tide stages. Each transect survey lasted 3-6 minutes and collected data from the first 20 meters of the water column. To get accurate analysis of current velocity and direction I split the data into categories based on depth. Preliminary analysis shows a southward current at many sites during all tide stages and depths. This raises questions about the scope of the river influence and the potential for southward currents regardless of tidal stage. However, further analysis of current velocity and river discharge are needed. Due to the complexity of the currents in the area, understanding how the river and the tides are interacting can provide a greater understanding of how these currents are impacting the dispersal of sediment and nutrients throughout the estuary.

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.

Corepressors are proteins recruited by partner proteins to negatively influence transcription of genes. TPL is a corepressor from the model plant Arabidopsis thaliana, and while we understand a lot about how TPL works, there are still many mysteries remaining. My project aims to identify other proteins that work with TPL to form a transcriptional repression complex at a single-engineered promoter site. First, we created a synthetic repressor called dCas9-TPL that binds and represses the transcription of the RUBY reporter. The RUBY reporter is a visual marker designed to express throughout the entire plant, turning the green plant a bright purple. Our engineered RUBY line also carries two guide RNAs in its promoter with sequences not found anywhere else in the Arabidopsis genome. This allows dCas9-TPL to bind to and repress this particular gene and not affect the transcription of other genes. Visual screening of the repressed RUBY line showed these plants turn a faint whitish-pink instead of bright purple, signifying that the repression by TPL is working. I have identified the promising repressed RUBY homozygous line and have generated three mutagenized populations of 40,000 individuals using the chemical Ethyl methanesulfonate (EMS). The EMS protocol creates new point mutations allowing us to identify genes involved in repression that we can map through DNA sequencing. I will use visual screening to search for plants with bright purple organs, meaning that the repression by TPL is broken and that a putative TPL interactor may be mutated. By identifying regulators of corepressor function in plant biology, I hope to learn principles that can inform cellular engineering across many organisms and better understand why certain mutations associated with transcriptional repression cause developmental defects or diseases like cancer in humans. 

Cardiovascular disease is the leading cause of death worldwide. A key reason driving the high mortality of heart disease is that the heart is unable to regenerate any muscle that is lost due to injuries like heart attacks. Furthermore, there are no current therapeutics that promote the creation of new muscle. However, in the past decade, scientists have attempted to address this issue by using stem cell-derived cardiomyocytes (iPSC-CMs) to replace lost heart muscle. A key limitation preventing using this therapy in humans has been that cardiomyocytes derived from stem cells remain immature relative to adult cardiomyocytes, and these immature cells cause several complications when transplanted into an adult heart. Identifying cardiomyocyte maturation regulators is needed in order to further develop this technology and translate it to patients. Previous studies from our lab and others have identified the RNA binding protein Muscleblind-like protein 1 (MBNL1) as a key factor controlling muscle maturation. MBNL1 expression increases as the heart matures after birth and it controls expression of many critical regulators of cardiomyocyte maturation, however, MBNL1 has never been studied directly for promoting iPSC-CM maturation. In this project, I am testing the hypothesis that increasing MBNL1 expression will improve the maturity of iPSC-CMs. I am using a genetically engineered stem cell line in which I can overexpress MBNL1 and an isogenic control line to test my hypothesis. I have found that MBNL1 expression naturally increases over time in iPSC-CMs. Additionally, I have validated the MBNL1 overexpression system in iPSC-CMs. Finally, I have used this system to test my hypothesis that MBNL1 will increase iPSC-CM maturity by measuring well-described transcriptional and structural hallmarks of maturity. Ultimately, this project will aid in identifying MBNL1’s role in controlling cardiomyocyte maturation, helping further develop stem cell-based therapeutics to repair damaged heart tissue in humans.

People embody the joy and pain of nature through their own experiences, and have been sharing and cherishing this interconnectedness from time immemorial through paintings, stories, songs, dance, and more. I am a migrant living in a foreign country. i was eating sushi that day…. is a solo dance and an ethnographic research project, exploring ways in which I connect to, resonate with, and embody nature and personal experiences through performance. The awe-inspiring habit of salmon migration sparks my curiosity about the complex and multifaceted nature of human migration. As anadromous fish, salmon spend their juvenile life in rivers, and migrate to the ocean where they spend their adult life. They return to the upstream rivers to reproduce when they reach sexual maturity. Salmon are able to precisely return to their natal river, and even to the very spawning ground of their birth. This creative research explores my questions around identity and the idea of belonging through examining migrating salmon, and my own migrating experiences. What is the definition of home? Is it where you were born, reproduce, and die? Or where you mature? Salmon migrate to optimize their chance of reproduction as it defines their success. What about humans? What are we migrating for? Are we ultimately going to return to where we were from? My creative process starts with producing a soundscore combining text, breathing, and waves. The choreography is inspired by and generated through filmed improvisations as I experiment with different ways to interact with the soundscore and the props, always keeping my research questions in mind. The piece is a product of my desire to understand and reify the fear, confusion, exhaustion, excitement, and hope in the process of migration.

Without proper genetic regulation, the creation and maintenance of cells within eukaryotic organisms such as yeast, plants, and humans is doomed to fail before it even begins. Protein corepressors are key to the genetic repression in all eukaryotic organisms and are vital for an organism to be able to properly coordinate their development and respond to environmental stimuli. In Arabidopsis thaliana, a model plant for genetic studies, the corepressor TOPLESS (TPL) is one of the main proteins that is used to repress the auxin pathway, which is essential to development and organ creation. Recently, the active domain of TPL has been pinpointed to an 18-amino acid long region named LIS1 homology (LisH) that is sufficient for activity. Previously, we found that the helix H1 of LisH in a plant corepressor functioned as a transcriptional repression domain in yeast. These observations suggest a broad conservation of mechanisms across kingdoms, suggesting this motif could be engineered to be a potent, short, and adaptable protein domain suitable for synthetic biology and therapeutics. My project aims to test the ability of the LisH protein domain to repress gene transcription in metazoans using mammalian cell culture. We will transfect human cancer cell lines with DNA encoding a dCas9-TPL fusion protein, which can be targeted to promoters of endogenous genes such as the cell surface antigen CD4, or synthetic constructs such as fluorescent reporter genes to detect differences in protein levels. Results of the project are expected to show that TPL and other foreign corepressors can function within the human cell just as efficiently if not more than human corepressors. Research into LisH's abilities will provide knowledge of its active domains and mechanisms in mammalian cells while also having the possibility to aid the scientific community by developing TPL as a rapidly deployable synthetic biology tool.

The dynamic expression of genes in an organism creates the biological complexity of life. Many are unique to a given lineage, while other genes are conserved and carry out the essential functions of life. Unsurprisingly, these essential genes are complicated to study, as interfering with their function often leads to death. One critical component of transcription is the multi-protein Mediator complex, which is found at every eukaryotic promoter where it helps coordinate the activation of gene expression. My project focuses on a core component of the Mediator complex, Mediator 21 (MED21). While MED21 is required for gene activation, my lab found that it also plays a role in the repression of gene expression, suggesting a complicated interplay between these two states. This can be challenging as many mutations in MED21 lead to lethal phenotypes. As an alternative, I hypothesize that using an integrase-based molecular switch to create a switchable MED21 will then allow me to differientate the role that MED21 plays in activation through the Mediator complex versus repression through the corepressor protein (TPL) in the model plant Arabidopsis. Integrases are capable of inverting DNA sequences flanked by unique sites, and I am engineering a switch that will turn off MED21 in certain tissues or in response to the addition of a chemical. By expressing an integrase protein from a lateral root-specific promoter, we can engineer a MED21 loss of function only in those specific cells while the rest of the plant is wild type and healthy. Future experiments include a switch from wild-type MED21 to a mutant form incapable of binding to corepessor TPL. This study will help us better understand the role MED21 has in repression versus activation, and also how state switching contributes to organogenesis.

Synthetic promoters are increasingly being used to control and fine-tune gene expression in multicellular organisms as part of engineering novel traits. For this genetic engineering project, we aim to build and activator system that when engaged leads to a statistically significant increase in gene expression compared to the unengaged system. Previously, our lab screened for promoters that are constitutively and ubiquitously expressed in Arabidopsis Thaliana. From this screen, multiple viable promoters were found, and a subset was selected for modification by adding sequences not found anywhere else in the genome (target sites). Our first experiments used the CRISPR-mediated gene regulation system to recruit repressors to create NOR logic gates (where a reporter is only expressed when two different inputs are absent) through the use of guide RNAs (gRNAs) complimentary the engineered target site. Currently, we are working to expand the capabilities of these synthetic promoters by swapping the repressor with an activator to see if we can boost expression from these promoters. Our activator construct has an enzymatically disabled Cas9 connected to an activation domain called EDLL, and an aptamer in the gRNA that attracts a second activation domain, VPR. We are currently generating transgenic plants carrying our synthetic promoters and activator constructs. I will quantify gene expression by measuring the levels of a fluorescent reporter under the control of our synthetic promoter. The use of both activator and repressor approaches will allow for the construction of increasingly complex genetic circuits. These circuits have wide potential applications across the fields of synthetic biology and metabolic engineering.

Many genes involved in different cell differentiation processes are known, however it is more challenging to know the history of transcription in each individual cell within a new organ. To fill that gap, I am building and testing a genetically-encoded recorder that uses two serine integrases to follow expression in developing roots of the model plant Arabidopsis thaliana. An integrase is a protein that binds to unique DNA regions, called integrase sites. Once bound, the integrase can perform an inversion or excision of the DNA between the integrase sites, depending on how the sites are oriented relative to one another. In a one-integrase design, we put a constitutive promoter between two fluorescent reporter genes, flanked by integrase sites. When the integrase is expressed under the control of a promoter for a developmental gene, there is a switch between the reporters only in the cells that are undergoing that developmental program. I am now using molecular cloning techniques to build a recorder that can track the expression of two different genes, using two different integrases. My integrase-based recorder will provide insights into when and where genes are “switched” on and off to promote cell specification. In the future, reporter genes can be replaced by genes that control development, and, in this way, we can engineer plants with different root structures. Control over root architecture could lead to plants that are more resilient to heat and drought.

River otters (Lontara canadensis) are high trophic level opportunistic feeders. Their diet, examined through scat, provides key information about local ecosystems. Previous studies have observed a diet dominated by fish, including studies in California (90%), Utah (96.5%), and North Dakota (83%); however, my preliminary results on otter diet at the mouth of the Snohomish River highlight a greater variation in observed prey. The meeting of the Snohomish River and Possession Sound creates a salt wedge estuary with extensive tide flats, providing access to diverse freshwater and saltwater prey species. From 2012-2015, river otter scat samples were collected, dissected, and identified by students at the Ocean Research College Academy (ORCA). Averages over the three years showed that fish were the dominant prey type in fall, winter, and summer; however, crustaceans dominated the river otter diet in the spring. In this study, I dissected scat samples from fall 2022 through spring 2023 from 2 sample locations in Everett Marina. In the more recent data, fall 2022 has followed the pattern of these historical studies, but the winter samples have indicated a shift of fish and crustaceans. In fall 2022, 5/25 samples showed 50% or fewer fish bones, while winter 2023 showed 11/13 samples with less than 50% fish bones. Given that otters are described as opportunistic feeders, this shift in winter diet, relative to previous years, may suggest a significant environmental shift. Future research must examine physical environmental features such as changes in river discharge and/or water temperature. Identifying specific fish species in samples may also reveal prey availability throughout the seasons.

Phytoplankton production depends on a number of factors including nutrient availability, water chemistry variables, and light penetration. Previous studies have shown light penetration to be important for submerged aquatic vegetation, the primary producers that support the marine food web and the ecosystem. Possession Sound is a productive sub-basin of the Salish Sea with complex influences on local water chemistry and primary productivity. Given the significance of primary production in a salt water estuary, this study looks at the seasonal relationships between water chemistry and light penetration, measured by photosynthetically active radiation (PAR) in the Possession Sound estuary across three sites. I collected Seabird CTD and YSI EXO profile data as well as PAR sensor results, in Possession Sound from July 2022 through March 2023. Accompanied with historical data collected by past Ocean Research College Academy researchers, I analyzed site dependent relationships as well as the seasonal relationships. Preliminary analyses showed PAR decreasing with higher salinity and turbidity, but increasing with temperature. Limited connection was observed with dissolved oxygen. Studying the relationships among light penetration and water chemistry allows us to better understand the complex relationships among the key factors determining seasonal primary production.

Unique relationships between photosynthetic active radiation (“PAR”), turbidity, chlorophyll, and dissolved oxygen (DO) can impact primary productivity levels and directly relate to the health of an estuary. Previous studies show that microbial processes depend on PAR and dissolved oxygen. To some extent, this can govern the rate of near-surface mixing, affecting turbidity and the amount of chlorophyll produced. My preliminary results using data from Possession Sound, a salt wedge estuary, show similar patterns. By examining the previous Ocean Research College Academy’s (ORCA) profile data from 2015-2022, I observed that an increase in chlorophyll corresponded with an increase in turbidity. Further, if there is an increase in chlorophyll, there is an increase in dissolved oxygen. From the fall of 2022 to spring of 2023, I collected additional profiles, including PAR data, from three sample locations in Possession Sound. My results show that when PAR is high, chlorophyll levels and turbidity are also high. However, PAR values are inversely proportional to dissolved oxygen concentrations. This means there are correlations among chlorophyll, turbidity, DO, and PAR values with depth. However, PAR can be affected by many factors, so it is difficult to say that any one of these parameters directly relate to PAR values with depth. Future research can examine different parameters affecting PAR with depth, as availability of sunlight and nutrient levels can also affect PAR data.

A primary stressor of college students is financial insecurity. Research estimates that 36% of college students are food insecure, 36% lack reliable housing, and 9% experienced homelessness in 2018. Sources of financial stress for college students typically include housing, tuition and other academic expenses, credit card debt, familial responsibilities, and employment status. Furthermore, research has also shown that psychological stress correlates with decreased sleep quality. During periods of intense stress, an individual may have more frequent disturbances during sleep, sleep for fewer hours, and adopt later waking times (Galambos et al., 2013). This study investigates the relationship between financial insecurity and sleep quality of students attending a 2-year college in Washington state. More specifically, this study aims to determine the impact of a sleep wellness workshop on the sleep quality of college students. Data collection will occur through an online Qualtrics survey before and after the sleep wellness workshop. The Qualtrics survey includes modified Sleep Quality Scale questions, the Beck Anxiety Inventory (BAI), and the Perceived Stress Scale (PSS). It is hypothesized that experiencing financial insecurity will positively correlate to poorer sleep quality. It is predicted that this relationship is mediated by stress and that the sleep wellness workshop will improve sleep quality in college students. Understanding factors that contribute to poor sleep quality is vital as sleep plays a key role in maintaining proper cognitive functioning. The results of this study are intended to improve current resources, as well as implement new resources, concerning sleep quality and stress of college students.

The emergence of SARS-CoV-2 (CoV-2) and the rapid growth of the global pandemic has necessitated more than ever the need for fully comprehensive studies of viral pathogenesis. Previous studies of CoV-2 highlight the importance of its viral proteins in transmission and adaptability into human hosts, but few have delved into the role that viral RNA structure plays in emergence and pathogenesis. Viral RNA structure is a known contributor to host-jumping replication as seen in related coronaviruses (CoVs), Flaviviruses, and Alphaviruses. Given this phenomenon and that all human CoVs originated from bat CoVs, we hypothesize that genomic and structural differences in the human CoV-2 RNA compared to the bat RatG13 CoV RNA, the believed progenitor of CoV-2, may have contributed to the species-jumping event from bats to humans that caused the emergence of human CoV-2. To test this hypothesis, I used a CoV-2 replicon system to compare replication of the wildtype (WT) replicon versus a mutant replicon (RaTG13-N/3’UTR(syn)) that contains a firefly luciferase reporter gene and synonymous mutations from the 3’ end of RaTG13. In preliminary replication experiments, RaTG13-N/3’UTR(syn) had notably higher replication than the WT replicon in primate fibroblasts. Based on this result, I used electroporation techniques and Renilla luciferase assays to determine the replication kinetics involved in differential replication of these viral replicons in human versus bat epithelial lung cells. I anticipate increased replication of the RaTG13-N/3’UTR(syn) replicon in bat cells compared to human cells when compared against the WT which would entail a mechanistic study of how RNA structures contribute to viral fitness in the two species using genomic and proteomic approaches. If this data supports our hypothesis, this could enhance our understanding of CoVs to allow us to target and survey zoonotic viruses that threaten species-jumping into the human population.

Increasing mental illness among college students continues to be a critical issue. College life is often a time of great transition, contributing to and potentially exacerbating students' rising stress, anxiety, and other mental struggles. Poor sleep habits may develop during college, and poor sleep quality can amplify stress. To explore how institutions might help students struggling with stress, we conducted a small pilot study examining whether a sleep-focused workshop would reduce stress levels in students at a Pacific Northwest community college. For this pilot study, I helped generate an online pre- and post-workshop survey of demographic questions, the UCLA Loneliness Scale, and the Perceived Stress Scale (PSS). Our results indicated that participants' workshop attendance reduced their stress levels. Before the sleep workshop, participants scored an average of 20.27 (SD=7.41, range=2 to 30) on the PSS, while two weeks after the workshop, the average PSS score had reduced to 16.58 (SD=7.65, range=4 to 27). These results suggest benefits of a sleep-focused wellness workshop for college students. In our present study, we replicated the pilot study. I examined student stress in correlation to sleep quality and assessed these factors through an online survey of demographic questions, sleep quality questions, the Beck Anxiety Inventory, and the PSS. We distributed this survey to participants before and after a sleep workshop run by the Bellevue College psychology department. I hypothesized that poor sleep quality correlates to higher student stress levels. I also hypothesized that the intervention of a sleep workshop would reduce stress levels. I hope that our results provide insight into the utility of wellness workshops for students and whether they are an avenue to help students manage stress and improve their sleep quality, which could improve student mental health by lowering stress and anxiety and improving quality of life and education overall.

Schizophrenia is highly heritable and has been associated with many brain structure abnormalities, including significant differences in cortical thickness, surface area, and gray matter volume. It is widely believed that abnormalities in early neurodevelopmental processes contribute to the differences in brain structure observed, and many genetic risk variants associated with schizophrenia influence brain development. Further research is required to understand whether genetic mechanisms underlie the typical pattern of cortical thickness and surface area deficits in schizophrenia or deviations from normal trajectories of cortical thickness and surface area development. Using data collected from 406 participants, including 246 individuals with schizophrenia, 70 unaffected relatives of schizophrenia patients, and 90 healthy controls, the current study will test for associations between polygenic risk for schizophrenia and expected brain measures of cortical thickness and surface area using a Regional Vulnerability Index (RVI) which quantifies the resemblance between an individual’s brain scan to expected brain deficit patterns in people with schizophrenia. Along with that, we will be testing for associations between polygenic risk for schizophrenia and the typical development of cortical thickness and surface area using centile scores which benchmark an individual’s neuroanatomical measurement in the context of the normative age and sex-related trajectories. We hypothesize that polygenic risk for schizophrenia will be positively associated with cortical thickness and surface area RVIs and centile scores for cortical thickness and surface area across all diagnostic groups. Understanding the relationship between genetic risk for schizophrenia and alterations in brain structure and development may facilitate early detection of schizophrenia and aid future efforts to prevent the onset of psychosis in vulnerable individuals.

Sindbis Virus (SINV) is an alphavirus that is transmitted between birds via mosquitos and causes disease in humans after spillover events. While many alphaviruses have potential to cause severe disease such as Venezuelan Equine Encephalitis Virus (VEEV), SINV is known to cause less life-threatening but still severe and debilitating chronic illness predominantly associated with fever, arthralgia, and myalgia. Given its lower morbidity, SINV often serves as a model system for infectivity and pathogenesis studies of alphaviruses. Macrophages are of particular interest for studying pathogenesis as they are important targets of alphavirus infection. Our aim is to identify viral mutations that contribute to differential replication between avirulent and virulent strains of SINV in macrophages. To test this we exchanged sequences between SINV strains Girdwood (avirulent) and AR86 (virulent) to construct reciprocal chimeras which will be tested alongside parent clones. We observed a significant difference in replication between parent AR86 and Girdwood in macrophages and predict that specific RNA structural differences contribute to this variable replication in macrophages, and we are currently mapping determinants of this phenotype. This work could improve our understanding of host-viral interactions of alphaviruses by discerning the mutations required to shift from avirulent to virulent strains which will play an important role in predicting mutations that contribute to greater pathogenicity in human infections.