Alzheimer’s disease (AD) is the most common age associated neurodegenerative disease in humans, with approximately 50 million people living with the condition worldwide. AD is the leading cause of dementia, memory loss, and other symptoms related to cognitive decline. Pathologically, AD is greatly associated with the formation of amyloid-beta plaques (Aβ) forming aggregates within the brain and disrupting critical neurological functions. As current treatments for AD only serve to mitigate symptoms, there is a dire need for new therapeutic drugs that address the causes of AD and more efficiently target Aβ plaque formation. Due to its ease of culturing and short life cycle, Caenorhabditis elegans is well suited for the rapid screening of candidate compounds. In this study, we utilize a C. elegans AD disease model expressing a full-length human Aβ gene for the screening of 26 FDA-approved compounds in a dose-dependent manner. We observe that at least 6 of these compounds result in a robust delay in worm paralysis. To investigate whether these compounds delay paralysis by reducing Aβ protein aggregation, we are staining worms with X-34 – a fluorescent dye that labels amyloid structures – and subsequently comparing staining patterns in worms with and without drug treatment. In addition to recording the timing of worm paralysis, we are studying behavioral changes in drug-treated and control worms to determine the effects our identified drugs on other physiological processes. In our use of a pre-clinical C. elegans model, we can apply our findings to future clinical treatments as most C. elegans genes are also conserved in humans. Therefore, by identifying FDA-approved compounds that reduce the appearance of Aβ plaques within C. elegans, we can fast track drug discovery to better treat AD in humans.

Chronic pain affects 30% of children and adolescents, putting them at risk for physical and psychological impairments. Given poor access to pediatric pain care, psychological treatments such as cognitive behavioral therapy are more accessible through digital health interventions. One intervention our lab created is Web-based Management of Adolescent Pain (WebMAP). In this mobile app, youth with chronic pain develop pain management strategies by progressing through interactive modules. Although digital health interventions like WebMAP are transforming accessibility to chronic pain care, limited information is available to understand how best to enhance youth engagement in a mobile app or whether there are differences in engagement among youth with different background characteristics. Our project aimed to 1) identify barriers to engagement with WebMAP among subgroups defined by user demographics and 2) develop recommendations for enhancing engagement with WebMAP and extending its reach to target underserved populations. In a previous cluster randomized controlled trial, participants assigned to the WebMAP intervention were 73 youth aged 10 to 17 (84.3% female) with various chronic pain conditions. We analyzed the app metadata to assess module completion rates across various subgroups, including groups defined by age, race, sex, and annual household income. We also coded interview and questionnaire responses from users to identify app preferences and areas of improvement. Results indicated that although users liked WebMAP’s design and content, they suggested changes to its display and features. By viewing our findings on usage and perception through a health equity lens, we summarized the accessibility of WebMAP and outlined recommendations to enhance its cultural relevance to different groups. Ultimately, our research identified factors that impacted engagement with WebMAP and offered valuable insight into optimizing digital health psychological interventions for chronic pain management. Moving forward, we hope to apply these findings as we develop the next release of WebMAP.

Compared to polymerase chain reaction with nasopharyngeal swab specimens, lateral flow assays (LFA) for detecting SARS-CoV-2 antigen in saliva are rapid, inexpensive, simple-to-use, and instrument-free, but have low sensitivity (ca. 11-40%) due to limited LFA sample capacities (ca. 50µL) and preparatory saliva sample dilution. To address this challenge, I developed an osmotic processor, a 3D-printed device, to concentrate target analytes through static and spontaneous osmosis for improving salivary-based COVID-19 LFA. The specimens loaded into the device were separated from an aqueous polymer solution using a dialysis membrane. The polymer solution with high mass polymer concentration resulted in an osmotic pressure difference that caused water transport from the saliva to the polymer solution, while the target analyte – SARS-CoV-2 nucleocapsid (N) protein – remained within the membrane. As the final solution contained the same N protein amount in a lower liquid volume, the overall sample was concentrated, thus improving the antigen detection limit ca. 60-fold, from 62.5 to 1 pg/mL. Combining the osmotic processor and saliva based LFA enables rapid, sensitive, simple, and inexpensive POC testing.

To test questions on the evolutionary history of a species, it is important to consider the drivers of genetic diversification that lead to speciation. Species diversification is often driven by the formation of geographical boundaries, ecological diversity, sexual preference, or a combination of these factors. However, for the Western Banded Gecko (Coleonyx variegatus), a species native to the southwestern region of the United States, few of these factors exist. Despite the lack of clear barriers to gene flow, prior research identified several distinct populations of C. variegatus in this region, though there is some uncertainty with these distinctions as they relied solely on the signal from one mitochondrial DNA (mtDNA) locus. The aim of this project is to instead use genomic data to assess the validity of the C. variegatus populations defined by mtDNA, and to investigate how these populations are distributed across the geographic region they inhabit. Using genomic data allows us to more confidently define population boundaries and assess how they have evolved through time. To explore the aim of this project, we sequenced reduced representation genomic data for 224 individuals across the range of the species to determine how populations of C. variegatus are structured. We then built species trees to assess the relatedness of these populations with respect to each other and the overall evolutionary history of the species. Our findings show that there are consistencies between both the genomic and mitochondrial data population definitions, but distinct differences are also present, with mtDNA overestimating the number of populations. Thus, relying on mtDNA data alone may be insufficient for confidently ascribing population boundaries for C. variegatus. Accurately defining populations can have great implications for the conservation of native biodiversity, but as shown by our study, relying on a single mtDNA locus may mislead this crucial process.

From previous clinical cases, doctors found that children with Leigh syndrome are sensitive to volatile anesthetics. Leigh syndrome can be caused by defective Ndufs4, a subunit in complex I of the electron transportation chain. Previously, we used the Ndufs4 knockout C57Bl/6 mice to model Leigh syndrome and noticed that individuals with Ndufs4-knockout astrocytes go under anesthesia at a normal concentration, but require a lower concentration to emerge. We also found that isoflurane inhibits the effect of norepinephrine in astrocytes. Since norepinephrine is associated with individual emergence from an anesthetized state, this might help us to understand the mechanism behind our observations of the astrocyte specific Ndufs4 knockout. We furthered our study by assessing the role of gliotransmitters in the mechanism of mitochondrial disease and volatile anesthesia. Gliotransmitters are chemicals released by glial cells and used by astrocytes to modulate neuronal information processing. A pilot study was conducted in vitro in the wildtype mice assessing the release of different gliotransmitters, including cyclic adenosine monophosphate, adenosine, adenosine triphosphate, gamma-aminobutyric acid, serine, glutamine, and glutamic acid. Previously we found that the level of cAMP increased significantly after the norepinephrine treatment. Thus, we expect to see a larger acceleration in cAMP concenration in knockout mice, compared to wildtype. I am continuing this project studying the effect of the gliotransmitters in astrocyte cell cultures from the Ndufs4-knockout mice, to compare to the wildtype counterparts. Each astrocyte culture will be randomly assigned to a treatment: with or without norepinephrine. The amount of each gliotransmitter released per unit of protein is measured. I will analyze the data generated and compare to the wildtype data. Future study includes the assessment of the relationship between the metabolites within astrocytes, and the response to isoflurane and norepinephrine. This study would accelerate our understanding of the mechanism of volatile anesthesia, as well as the mitochondrial disease, which in turn will benefit numerous patients with safer and wiser treatment plans.

The functional connectivity of the brain evolves throughout the life of every individual. These changes, often referred to as neuroplasticity, can be impacted by a wide range of variables from diseases to eating a favorite dessert. How can these changes be modulated to treat neurological diseases and disorders such as post traumatic stress and major depressive disorder? My colleagues and I are intrigued with the prospects of neuromodulation as a therapeutic for abnormal brain connectivity and network dynamics, leading me to the question “At what rate do these connections accumulate and decay with optogenetic modulation; Optogenetics, a technique that uses light to activate or inhibit genetically targeted neurons, offers high cell-specificity and temporal resolution that allows us to zoom into the network dynamics and find more finely tuned results that can help in the development of neuromodulation therapies. I plan to use both single site and paired-pulse optogenetic inhibition to gain a clearer understanding of how functional connectivity behaves during and after repeated modulation periods followed by extended recordings of spontaneous activity with no modulation. By analyzing the pairwise coherence of the local field potentials collected using electrocorticographic recordings in non-human primates, I anticipate seeing targeted changes in functional connectivity when comparing before and after each inhibition session. By analyzing the rate of change in connectivity I plan to understand the timeline of neuroplasticity following optogenetic modulation, thus informing the development of future neuromodulation therapies. This research could have a profound impact on the future therapeutic paradigms for neurological and neuropsychiatric disorders that can accelerate recovery for individuals with these conditions.

High throughput single cell/nuclei RNA sequencing (scRNA-seq/snRNA-seq) has been used to characterize the gene expression at the cellular level in disease control studies. Differentially gene expression analysis aims to emphasize the biological variation between samples without unwanted technical variation. Batch effect correction is occasionally performed where cells from each individual sample are treated as being generated from a batch. We analyzed snRNA-seq data from ApoE neutral and detrimental mouse models of Alzheimer’s disease (AD) to test whether batch correcting the data using all cells from each individual biological sample as representing a batch would result in 1) loss of disease relevant associations, 2) loss of biologically relevant cell types, and 3) reduced association between cell types and phenotypes. We performed scRNA-seq analysis of seven samples from two ApoE genotypes using Seurat workflow applying Harmony batch correction, using each sample as a batch, and without correction. Since we measured two disease-related phenotypes in mice from the two genotypes, we asked whether cell cluster membership associated with genotypes are also associated with unit changes in brain-diseases related phenotypes. After applying individual sample batch correction, we found differences in number of cell types (clusters) before and after batch correction, we showed loss of cell types/clusters specifically from the detrimental genotype, shrinkage of the differences in cell cluster membership across samples and reduced association between cell type membership, genotypes and phenotypes. In conclusion, batch effect correction should be applied consciously based on the experimental design to avoid over correction of biological variability and an appropriate design should help to avoid unwanted technical variation.

mTOR, the mechanistic target of rapamycin, is a serine/threonine kinase which is an enzyme that phosphorylates the hydroxyl group on a serine or threonine side chain. mTOR kinase regulates protein synthesis, cell growth, and metabolism in response to nutrients and energy in most eukaryotes. mTOR consists of two distinct complexes, mTORC1 and mTORC2. These complexes can be further divided into three components: mTORC1 consists of mTOR, Raptor, and mLST8, and mTORC2 consists of mTOR, Rictor, and mLST8. mTORC1 is critical in metazoan development and has been implicated in aging, cancer, diabetes, cardiovascular disease, and hypoxia, a state in which tissues are deprived of oxygen and can not carry out normal metabolic activity. Previously, the Crowder lab conducted a mutant screen in C. elegans, for hypoxia resistant mutations, and has recently identified a missense (changes one amino acid to another) reduction of function mutation in the daf-15 gene, the C.elegan ortholog of Raptor. A unique feature of this mutation is that the function of Raptor can be turned on and off by varying temperature. It has normal hypoxia resistance at 20 degrees, increased resistance between 21-22, and developmentally arrests at 25 degrees. I and the other authors made use of this conditional developmental arrest phenotype to screen for genetic suppressors, mutations that suppressed developmental arrest. Using genetic mapping, sequencing, and complementation testing, we have identified multiple mutations in three different genes responsible for restoring Raptor function. Preliminary results show mutations in the gene rnf-126 (ring finger protein) suppress the Raptor mutation. Current work by myself and others is designed to answer how these genes control Raptor function and hypoxia sensitivity. Elaborating the function of these genes will define novel mechanisms whereby Raptor and mTORC1 controls metabolism, hypoxic injury, and development.

Cytokines are molecules that mediate cell-to-cell communication in the immune system. Their sensing by immune cells drives their response and differentiation into different functional states, such as into memory or effector states for T cells, to form a proper immune response and combat infections or cancer. Signal transducer and activator of transcription (STAT) family proteins are transcription factors that act downstream of cytokine signaling to regulate the expression of genes driving differential cell functions. Different cytokines phosphorylate and activate different STAT family members to give rise to distinct cellular responses and phenotypic changes. However, there is substantial overlap between STAT members activated by different cytokines. For instance, type I interferon (IFN-I) activates both STAT1 and STAT3 signaling to drive genes associated with growth inhibition, cell death, and anti-microbial responses. Alternatively, Interleukin-2 (IL-2) primarily activates STAT5, but can mediate STAT3, to promote T cell effector differentiation and proliferation. Thus, how different cytokines work through a small common set of STATs to elicit distinct functional phenotypes requires further investigation. Therefore, my project seeks to probe T cell responses and STAT activity with different cytokines. To interrogate this, I will develop an assay to stimulate Jurkat cells, an immortalized T cell line, under various cytokines and analyze STAT1, STAT3, and STAT5 phosphorylation with flow cytometry. We expect Jurkats under IFN-I stimulation to have higher STAT3 and STAT1 phosphorylation than STAT5, but exhibit a more immunosuppressive phenotype, as STAT3 is known to inhibit STAT1-mediated gene expression. With IL-2 stimulation, we expect cells to have higher STAT5 activity with increased proliferation and enhanced effector function. By understanding the complexities of how our T cells differentiate and exhibit certain phenotypes from STAT activity, we can potentially tune the signal a cell interprets and the downstream cellular responses to effectively enhance effector functions, or prevent cell death.

Circadian rhythms are adaptive biological processes that govern the synchronous timing of biological functions and behaviors with the daily light-dark cycle. These rhythms are crucial for the timed regulation of sleep-wake cycles, metabolism, and hormone release, as well as for maintaining harmonious physiological functioning within the body. Within the mammalian brain, a central pacemaker, the Suprachiasmatic Nucleus (SCN), governs the timing of these circadian rhythms. This area contains a subpopulation of neurons that express and release the neurotransmitter Vasoactive intestinal peptide (VIP). These neurons play a role in synchronizing activity across the entire SCN network. Thus, this project is aimed at better understanding how VIP-neurons change shape throughout the day. Preliminary research in the de la Iglesia lab suggests that these neurons change shape across the day, such that VIP neuron fibers-axons and dendrites- are more branched during the day than the night. These results were obtained through the use of mouse models expressing a red fluorescent protein in the VIP neurons (VIP-TdTomato). The mice were perfused at a range of timepoints, and the samples underwent a tissue clearing protocol so that the entire SCN can be captured in one image. Then the software QuPath was used to train a machine learning algorithm to aid in the identification of VIP neuron fibers based on fluorescence expression. However, the performance of the machine learning algorithm has not been validated. To address this issue, I compared the algorithm-generated segmentations with manual annotations from humans, finding agreement 75.3% of the time in terms of fiber location and 77.4% of the time regarding background. These rather promising results demonstrate the usefulness of the algorithm in aiding the investigation of the entire dataset. This research provides a step towards better understanding the structural organization of the SCN, and thus circadian control of essential physiological processes.

The ZaP-HD Experiment combines the research fields of electric space propulsion and nuclear fusion by stabilizing the confinement of high energy density plasmas by accelerating ions to high axial velocities. This is known as the Sheared Flow Stabilized (SFS) Z-pinch, and has potential applications in both clean energy production and interstellar space propulsion. ZaP-HD employs numerous diagnostics to record plasma behavior with the goal of understanding how to improve the SFS Z-pinch. My research on ZaP-HD aims to create spatiotemporally resolved "contour maps" of the radial electron density distributions at fixed axial locations in the plasma flow. To collect data for these maps, I use a method known as Helium-Neon (HeNe) Interferometry, which records the interference experienced by a HeNe laser beam shining through a plasma to create a time-resolved curve of the chord integrated electron density of the plasma along the path of the beam. For each "pulse" of experimental plasma, I record four of these curves using four parallel laser beams which pass through the plasma perpendicular to, and at different distances from, the center axis of the Z-pinch. By recording electron density measurements under different experimental parameters, I can gain insight on how to increase the plasma density in future experiments. Increasing plasma density directly contributes to increasing the fusion reaction rate, and thus the energy output of a fusion plasma. I have recorded chord-integrated electron number densities on the order of 10^21 electrons/m^2, and I have observed a trend of the electron density increasing radially inward towards a peak at the center axis. My research aims to contribute to the global push for the advancement of clean and renewable energy production, as well as the development of spacecraft propulsion systems which could enable humanity to finally achieve interstellar space exploration.

Efforts to find disease-modifying treatments for Alzheimer’s disease (AD) have met with limited success in part because they have focused on identifying a specific pathogenic mechanism targeted by a specific drug. AD is a complex disease mechanistically associated with multiple pathways of aging so the probability of effectively targeting all of them would be greatly increased by using drugs in combination, each targeting different pathways. Previous studies have shown that a novel cocktail of the anti-aging FDA approved drugs rapamycin, acarbose and phenylbutyrate prevents age-related cognitive decline in mice by targeting distinct pathways of aging. These findings provided the rationale to test this drug cocktail for ability to alleviate cognitive impairment in a mouse model of AD. Transgenic 5xFAD male and female mice, with multiple mutant amyloid precursor proteins and expression of pathogenic Aβ42 peptide, were fed diet containing all 3 drugs, while control mice were fed a non-medicated diet. After 8 months of treatment, preliminary observations suggest 5xFAD mice fed the cocktail diet performed better in a spatial navigation learning task compared to mice fed the control diet. Laboratory procedures to confirm these observations will include rtPCR and immunohistochemistry to identify differences in expression of specific protein biomarkers of aging pathways in the brains of treated versus control mice. More work would be needed but observations from this study might be helpful in designing potential investigations to alleviate early phases of AD in patients using drugs already approved for human use.

The Center for Disease Control estimates that one in three Americans do not regularly get enough sleep per night. This is considering people have access to a bed and a reliable place to sleep, highlighting how arduous it may be for the 500,000 individuals experiencing homelessness in the US to obtain a good night of rest. Seattle is facing a homelessness crisis exasperated by the pandemic and on any given night there may be 11,000 individuals in King County without their own place to stay. This project investigates how sleep differs between individuals living in shelters, tent cities, and tiny homes to determine where the best sleep can be achieved throughout the year. Data was collected using actigraphy watches and sleep diaries for four weeks in September 2022 and four weeks in February 2023. These two time points allow for a seasonal comparison due to the drastic change in light availability and temperature between seasons in Seattle. There were 29 participants across four sites in September and 25 participants across the same sites in February. Interviews were completed to establish a baseline of individuals health and sleep habits. The watch data and interviews were analyzed to compare sleep duration, efficiency, disruptions, and individual consistency, all of which are factors that impact sleep quality which is foundational to mental and physical health. The seasonal comparison is expected to show longer sleep duration in the winter and more efficient sleep for those living in tiny houses or shelters. It is more difficult to control these factors without a home, but it is especially important for people experiencing homelessness who face a disproportionately high incidence of chronic mental and physical health issues. There has been little sleep research in this population and especially for individuals not living in an organized community.

Building strong relationships between parents and teachers is critical to supporting young children in developing key social, emotional, and pre-academic skills. Especially in preschool, parent-teacher relationships can support a young child’s development across home and school. Communication is an important aspect of successful parent-teacher relationships; however parents and teachers face interpersonal, intrapersonal, and structural barriers to communicating with one another. This study aims to elevate the voices of racial and ethnic minoritized parents of a preschooler and preschool teachers to understand barriers to communicating and strategies to overcome these barriers. Using a qualitative approach, we conducted semi-structured interviews with 9 parents of a preschool child and 7 preschool teachers at two local early childhood centers. Using a codebook, I am currently analyzing all interviews to answer the following research questions: 1) What type of communication do parents and teachers want? 2) What barriers do parents and teachers face when communicating? and 3) What are some strategies for improving communication between parents and teachers? Preliminary results indicate that both parents and teachers desire open, honest communication. Parents expressed wanting daily communication related to how their child was doing in school. Teachers expressed a desire for parents to understand more about their kids and to be able to speak to parents when they have a concern about their child’s behavior. Despite a desire for communication, both parents and teachers describe feeling unsatisfied by their current level of communication, citing how COVID-19 has limited their ability to communicate. Some strategies discussed included increasing face-to-face contact, having more events at school, and creative ways for daily communication (e.g., interactive platform, daily notes, etc.). Through listening to parents and preschool teachers about their current experiences, we hope to identify ways to improve communication between parents and teachers, ultimately improving young children’s outcomes.

The SirT6 gene is protective against systemic aging by enhancing DNA repair, decreasing inflammation and epigenetic deacetylation, and maintaining efficient lipid and glucose metabolism. Studies have shown that SirT6 function gradually decreases with increasing age with a loss in protective mechanisms. The role of SirT6 in brain aging has not been well established, and would be of interest to determine possible therapeutic targeting for conditions of age-related neurological dysfunction including cognitive impairment and dementia associated with Alzheimer’s disease. A mouse line was obtained from the NIH National Mouse Repository with genetic inactivation of one allele of the SirT6 gene (SirT6-/+) resulting in a partial loss of function. Older aged mice were tested in a spatial navigation learning task for exploratory behavior and memory. SirT6-/+ mice were unable to find escape holes as quickly as unaltered littermates (SirT6+/+) with a P-value of 0.003 significance. This observation suggests that partial absence of SirT6 function is associated with cognitive impairment. Following cognitive testing, mice were humanely euthanized, and brains collected and formalin fixed for immunohistochemistry staining to identify specific biomarkers of aging pathways including gamma H2AX for DNA damage response, HDAC-2 for epigenetic alterations, MCP-1 for inflammation, nitrotyrosine for oxidative stress, and p21 for senescence. Stains will be digitally imaged and heat maps generated for quantitative analysis of specific areas of brains from SirT6-/+ and SirT6+/+ mice. Results are expected to provide new knowledge on the role of aging pathways in the downregulation of SirT6 and age-related decline of learning and memory, and insight into possible conditions for development of more severe neurodegenerative diseases associated with dementia such as Alzheimer’s disease.

Alzheimer’s disease (AD) is a progressive neurological disorder associated with protein deposits in the brain, and causes a decline in memory, cognition, and social skills. There is no cure for AD, and as the disease advances, complications lead to incapacitation and death. Insulin-like growth factor 1 receptor (IGF1r) is a transmembrane receptor that responds to the hormone insulin-like growth factor 1, and is associated with healthy aging. An IGF1r variant in exon 6 (Arg-407-His) was found to be enriched in centenarians compared to shorter-lived relatives. Characterizing the role of this IGF1r variant in the development and progression of AD would provide information into a novel therapeutic target. Older-aged C57BL6 mice expressing a CRISPr-generated human Arg-407-His variant of the IGF1r gene were intravenously injected with a neurogenic AAV vector, consisting of the pathogenic components Aβ42 and p301L tau, or SHAM. After 3 months, mice with the IGF1r variant found escape holes more quickly than mice without the variant, using a spatial navigation learning task. Following humane euthanasia, brains were collected and fixed in formalin for immunohistochemistry (IHC). Brain sections were stained with biomarkers for Aêžµ42, ptau, and inflammatory microglia, and digitally imaged for quantitative analysis. Brains from IGF1r variant mice showed a decrease in expression of Aêžµ42 and ptau in line with improved cognition, and an increase in inflammatory glial cells. These preliminary observations help establish IGF1r Arg-407-His variant mice as a model to better understand the role of IGF1r in AD neuropathology, and provide insight into new potential therapeutic approaches for older human patients with AD.

Using simple behavioral analysis (SimBA) and Deep Lab Cut (DLC), we can create predictive behavior classifiers using pose estimation (PE) data obtained through DLC. PE is a computerized technique to track and predict the location of mice by training the video dataset with labeled frames using specific regions of interest (ROIs). With this, we can create machine-learning (ML) predictive classifiers of complex social behavior in SimBA. Social behaviors and interactions are difficult to manually track due to their rapid successions. To overcome this, I plan to use ML classification using our SimBA pipeline for behavioral classification allowing us to exceed human performance and increase throughput and consistency. I plan to create accurate classifiers for social behaviors that I will use to analyze the behavioral motifs of mice undergoing an operant social stress procedure. First, we train male and female C57BL/6J mice to self-administer (SA) their same sex cage mate. Experimental mice are then subjected to either physical stress for males or witness stress for females. Following social stress, non-reinforced SA is used to assess social reward seeking. Next, social interaction (SI) tests are performed to document time spent approaching the familiar same-sex conspecific cage mates and the aggressive CD-1 mice. All behavior was recorded, and transferred to DLC, followed by frame extraction. Using these frames, we trained the operant behavioral dataset to track the orientation of the mice. Next, we evaluate the dataset for a low error margin as observed by a continuous plateau of iteration loss. Although not complete, I expect to create behavioral classifiers for mice during social decision making in a social reward context following social stress inclusive of sex differences. Providing descriptive statistics of both movement and probability of successive behaviors as they occur in real-time.

Parent-teacher relationships are important in supporting young children’s social and emotional development. Especially in preschool, strong parent-teacher relationships can support a preschooler’s development across home and school. Despite the importance of parent-teacher relationships, parents from racial and ethnic minority backgrounds report having lower-quality relationships with their child’s preschool teacher. In this qualitative study, we sought to evaluate the voices of parents from racial and ethnic minority backgrounds, to understand barriers to and strategies for creating strong parent-teacher relationships. As part of a community-based partnership, we partnered with local preschools that serve a majority of underrepresented students. I assisted in conducting interviews with nine parents, in which three identified as Asian, one identified as Black/African American, three identified as white, and two identified as more than one race. During the interviews we asked parents questions about barriers at the individual, center, and systematic level that stand in the way of establishing close relationships with their child’s teacher, as well as potential solutions. My team is currently in the process of coding and analyzing all transcripts to explore barriers and solutions in more detail. Preliminary results reveal that parents brought up several barriers including time, limited face to face interaction, lack of communication, and feeling unwelcome in their child’s school. These barriers were described as impediments to the parent’s ability to form relationships with their child’s preschool teachers. We are currently analyzing and working with our community partners to identify solutions to improving parent-teacher relationships. The findings of this study are important in understanding how to support parents from racial and ethnic minority backgrounds in forming and maintaining strong relationships with their child’s preschool teacher.

Changes within the body that repeat approximately every 24 hours, called circadian rhythms, are controlled by a central pacemaker in the mammalian brain, the suprachiasmatic nucleus (SCN). Circadian rhythms can synchronize to cues like the light-dark (LD) cycle, allowing them to predict the 24-hour environment. SCN neurons are interconnected and connect to other regions within the brain. Our hypothesis is that SCN neurons have the ability to physically change connections throughout the day and that these changes are essential for it to act as a master clock. I explored this plasticity through the study of vasoactive intestinal peptide (VIP) and polysialylated neural cell adhesion molecules (PSA-NCAM). VIP is a neurotransmitter expressed in a subset of SCN neurons and plays a role in the SCN's ability to respond to light. PSA-NCAM is involved in decreasing cell interactions through facilitating events like cell migration and axon guidance; it is only expressed in areas of the adult brain in which neurons display plasticity in their fiber connectivity. Mice house in a 12 hour:12 hour LD cycle were sacrificed at two times, 12 hours apart. I used immunohistochemistry against VIP and PSA-NCAM to determine the levels of these molecules in the SCN. I found that the expression of VIP is higher 9 hours after lights were turned off (ZT 21) compared to 9 hours after lights were turned on (ZT 9). I found that PSA-NCAM has a higher trend of expression levels at ZT 9 than ZT 21. Although these results are preliminary, we find the implication of the results promising. VIP and PSA-NCAM express in anti-phase; as a negative regulator of cell adhesion, higher levels of PSA-NCAM should correlate with lower levels of VIP. Understanding how mammals keep time is important because circadian rhythms are essential for virtually every aspect of an organism's behavior.

Maladaptive aggression characterizes - or is comorbid with - many neuropsychiatric illnesses, and can have devastating effects on individuals, their caretakers, and healthcare professionals. Human aggression is typically demarcated as exhibiting either reactive (defensive) or appetitive (rewarding) components. Despite a significant clinical awareness of the differences between these aggression presentations, preclinical characterization of their relative circuitry and associated neuronal mechanisms are absent. Using recently established protocols within our lab, we are able to study and compare these aggression phenotypes in outbred male mice in a high throughput manner. Briefly, for appetitive aggression, we train mice to self-administer a novel subordinate intruder over 7 days using a trial design. In the reactive condition, we non-contingently administered intruders with the same frequency distribution as the appetitive mice. In the current experiment, we used CD1xVgat-Cre or CD1xVglut1-Cre mice injected with pGP-AAV-syn-FLEX-jGCaMP7s in the lateral septum (LS) to examine cell-type specific activity via fiber photometry. GABAergic activity in the lateral septum has historically been implicated in the control of reactive aggression, but little is known about the role of excitatory activity in the LS in reactive or appetitive aggression. My roles in this project have included behavioral testing and filming of the mice, as well as scoring these videos for first attacks following intruder presentation. Using these timestamps, I will next analyze the changes in population level dynamics across different time points of aggression motivation, seeking, and consumption using the open source photometry analysis program guPPY. We expect that the photometry results for mice in reactive and appetitive environments will show different patterns of activity, with more glutamatergic activity in the appetitive group, and more GABAergic activity in the reactive groups. I hope to help understand and prevent unnecessary aggression through this research.

Biological age generally occurs earlier or later than chronological age and can be used as a biomarker for aging intervention studies. The rate of wound healing is known to decrease with increasing age, such that a simple skin wound might demonstrate overall aging of all organs and tissues of the body. This concept was tested in a mouse model of wound healing consisting of a 2 mm through and through ear biopsy. Cohorts of male and female C57BL/6 mice at 5, 13, and 21 months of age were biopsied, and the area of closure measured over 3 weeks. Ear biopsy cores were used to obtain DNA methylation signatures to a database of age-related signatures to compare biological age. The 5-month-old mice showed a higher percentage of wound healing than the 21-month-old mice 2.5 weeks following the biopsy with a p-value of 0.04. DNA methylation results used to calculate expected wound healing percentage correlated with measured healing percentage with an R2 value of 0.82. Additional validation of biological age will use a computational paradigm to assess severity of age-related lesions on an inter and intra-organ basis. Preliminary observations from this study indicate that a simple skin biopsy procedure can be used to predict biological age, with important translational implications for the treatment and prevention of aging and age-related diseases.

Alzheimer’s disease (AD) is a complex neurodegenerative condition that commonly affects aged populations; therefore, increasing resilience to aging may increase resilience to age-related diseases including AD. To test this concept, a preclinical mouse study was designed to investigate the effects of anti-aging drugs rapamycin, acarbose, and phenylbutyrate in combination (cocktail) previously shown to delay aging phenotypes in mice. Cohorts of C57BL/6 mice, 22 months of age and of both sexes, were fed standard chow containing the drug cocktail or standard control chow for two months. Mice were then given an intravenous injection of a neuronal-specific adeno-associated virus (AAV) vector consisting of Aβ and phosphorylated (p) tau, the major pathogenic components of AD, or AAV sham, and followed for another three months. Mice were then tested for cognitive function using a spatial navigation learning task. Overall, AD mice treated with the drug cocktail showed faster learning times, specifically in trial 2 for females (p<0.05) and trial 3 for males (p<0.05), compared to AD mice not receiving the drug cocktail. Following humane euthanasia, brain tissues will be assessed for Aβ and ptau neuropathology and pathways of aging using a combination of special stains and digital imaging to determine the cellular and molecular effects of the drug cocktail. The preliminary observation that the drug cocktail can prevent cognitive impairment associated with the early stages of AD suggests that targeting resilience to aging has potential translational implications for the early diagnosis and treatment of AD in human patients. Future efforts will work to establish molecular evidence of these observations and validate results in additional models of AD.

A major technical limitation in the study of complex social behavior of freely moving rodents is the manual annotation of behavior because it is subjective, extremely time-intensive, and prone to observer drift. Simple Behavioral Analysis (SimBA) utilizes machine learning (ML) applications to automate behavioral analysis by using pose estimation to create supervised ML predictive classifiers of rodent social behavior. In a single project, thousands of videos need to be preprocessed, which includes locating individual trials, identifying behavioral events within each trial, and choosing trimming points to focus on specific outcomes or the presence of multiple animals. Manual editing amounts to thousands of hours, often yielding clips with inaccuracies in timing or content, and leads to inaccurate ML predictive classifiers. To address this problem, my research is centered around integrating behavioral metadata into a tool that can automate preprocessing steps with high precision to improve the quality of resulting classifiers. I attempt this via two major improvements. First, to eliminate the reliance on manual record-keeping, I will implement a function that utilizes metadata to link relevant time-stamped events to their corresponding behavioral experiment video. Second, I will leverage ML-based object detection, such as YOLO4, to determine time points when two animals are present, which often indicates that a social reward has been obtained. Through this project, when compared to manual scoring, I expect that: (1) there will be a significant cut in the time necessary to preprocess videos, (2) the yield of usable trials for SimBA will increase, and (3) that there will be an improved accuracy of pose estimation and classifier performance. Overall, these additions will greatly enhance the ease and flexibility of data preparation for highly specific behavioral analyses during the task, enhancing the efficiency of ML procedures to yield powerful behavioral classifiers.
 

Neopterin is a biomarker of non-specific inflammation that may result from infectious or chronic disease. Recent studies have observed declining neopterin from infancy through the juvenile period in non-human primates, as well as associations between higher neopterin levels and lower microbial diversity. These findings suggest that neopterin levels could vary with physiological and immune system development peaking during the time infants rely most heavily on innate defenses such as inflammation. We examined fecal neopterin levels in human infants over their first 16 months and in association with age at complementary feeding to further explore potential developmental patterns of neopterin expression. Samples were collected over 8 months from 35 Tsimane infants in lowland Bolivia. Families were visited every 3 weeks to collect infant stool samples and dietary and health information. Fecal samples were assayed for neopterin concentration at the University of California Santa Barbara Biodemography Laboratory in 2015, using commercial kits (Genway Biotech). Neopterin levels were preliminarily examined in separate linear regression models for infant age and feeding status. Results demonstrated that infant age (in months) was inversely associated with neopterin levels (Est. -16.22 ng/ml, p = 0.02). In the separate feeding status model, infants who had begun complementary feeding trended towards lower neopterin levels as compared to exclusively breastfeeding infants (Est. -119.52ng/ml, p = 0.65). Findings support previous observations of a decline in neopterin levels during infancy. Future work would benefit from longer observation and sample collection periods with more participants. This research has public health implications as it suggests there is age related variance in neopterin, a biomarker of gut inflammation, which should be considered in future studies investigating infant gut health and disease risk.

The Neuropixels (NP) probe is a multielectrode array that can record from large populations of neurons with high temporal and spatial resolution, along a shank spanning multiple brain regions. Identifying specific neural populations recorded along the shank is critical for later determining their structural connectivity, adding further insight into their behavioral function. Due to the shank’s material, fluorescent dyes cannot be used for this purpose as the dye will disperse broadly. To solve this, we will use silk fibroin, a biocompatible molecule derived from the cocoon of Bombyx mori to encapsulate a fluorescent protein-encoding viral vector in a silk film that degrades after a controllable period of time. Viral approaches allow for genetic isolation of specific cell-types and circuits. We will combine herpes simplex virus with the silk film and apply it to discrete sections along the shank before insertion, to induce expression of green fluorescent protein (HSV-GFP) in nearby recorded neurons for visualization. First we will test a range of fibroin/HSV-GFP solutions to optimize targeted expression for acute recording applications. Following optimization, we will test the silk/HSV-GFP solution while recording from the mouse amygdala. Then, we will image the brain to visualize the neural populations that were recorded. We predict that the chosen silk/HSV-GFP solution will yield high expression of HSV-GFP in a localized region of the brain that corresponds to the coated subsection of the probe. In future experiments, we will combine the optimal solution with anterograde and retrograde viral tracers along the probes, allowing us to dissect the connectivity patterns of recorded neuronal populations. These experiments will integrate structure and function to derive greater insight from neurophysiological experiments during behavior in mice.

Current models of pain research involve restrictive forms of resident-intruder pairing where experimental mice are involuntarily placed in social situations. These methods have limited application as the research does not account for individual variability and the dynamic social decision-making characteristic of humans. Our research uses a novel volitional social procedure that more accurately represents human behavior in the context of pain. I conducted social self-administration protocols on C57 strain mus musculus to quantify changes in voluntary social interaction before and after neuropathic pain has been induced via spared nerve injury. In addition, I utilized a Von Frey filament test to measure changes in pain sensitivity over this time period. Two social self-administration (SA) experiments were conducted on separate cohorts of C57 mice. In Experiment I, SA was run intermittently at 3-day intervals following neuropathic injury, providing lapses between voluntary social engagement. In Experiment II, SA was run continuously following neuropathic injury. We found that the continuously run SA group experienced a rebound in social interaction to levels matching their pre-surgery states and sham controls, whereas the intermittent group displayed a stark decline in voluntary social interaction that reached statistical significance from sham controls on day 8. Interestingly, tests of allodynia that were conducted to determine prolonged mechanical sensitivity typical of chronic neuropathic pain showed that both groups were experiencing equal levels of increased pain sensitivity throughout behavioral testing. Our results show promise in revealing the dynamic connection between social interaction and pain perception. Research has already identified key areas of interest such as the medial prefrontal cortex (mPFC) and nucleus accumbens (NAc) as hubs responsible for regulating social behavior. We aim to further examine the physiological changes that occur in these areas as a result of persistent pain using a variety of sophisticated analytical techniques.

The widely accepted theory for how Earth’s moon formed begins with an impact to Earth by a Mars sized protoplanet. This impact creates a disk of debris around the Earth, and the moon is subsequently formed as the debris collides and coalesces. Previous studies have modeled the debris disk in a hydrodynamic environment, but results have found that moon formation is uncommon. This research project models the debris disk after it has cooled and condensed into a collection of solid particles using an N-Body simulation. These simulations are run using the ChaNGa code developed by the University of Washington’s N-Body shop and processed on the Hyak supercomputer. Simulations begin with an initial conditions file that we generate with different parameters, including particle resolution, angular momentum, and coefficient of restitution. From each initial conditions file the simulation runs time-progressions that model each particles position and velocity at every time-step, calculating the collective gravitational forces between all of the particles and recording any collisions that occurred. I analyze the data using plots detailing the eccentricity, mass, and semi-major axis of objects that form. Previous results from work I have completed on this project appear to show robust moon formation, with roughly lunar sized objects forming around the Roche limit. Future work on this project will include running more simulations with similar initial conditions to determine how common moon formation is, as well as analyzing the data using plots of semi-major axis vs. number of collisions/bodies accreted to determine if there are specific regions of the debris disk where the moons’ mass is originating from. While previous studies have found that a moon is only formed at very specific impact angles and sizes, this study looks to see if the moon formation mechanism may be more robust when modeled using N-Body simulations.

Single cell neural activity mapping is a novel experimental approach used to understand the relationship between neural activity and behavior/thought across the intact brain. The current approach utilizes immunodetection of Fos, a reliable and endogenous protein marker for neuronal activity that has unique induction and decay properties. This method combines whole-mount brain tissue clearing, IHC staining, and high speed volumetric imaging. However, whole-mount IHC is incredibly challenging due to many factors including variable antibody lots, lengthy processing protocols, and inconsistent timing. To overcome these limitations, various genetic methods including direct gene modification and replacement have been produced. However, these methods limit brain-wide expression profiles, display inaccurate signal to noise ratios, and yield low signal expression levels. Here, we have developed a novel activity-dependent tool that allows viral vector-compatible Fos-like reporting of neuronal activity. Our strategy relies upon non-promoter-based regulatory sequences that endows downstream genes with Fos-like induction profiles. Here, we present its effectiveness in ectopically labeling Fos+ cells in the mouse brain in-vivo, and report its comparison to other conventional genetic strategies. Further, we extend its range of use with the creation of multiple versions that enables a range of activity level reporting and through multiple wavelengths of fluorescence. In summary, this novel genetic tool can be used to ectopically map single cell neural activity more effectively in order to better understand the anatomical basis of neural coding driven by specific cell-types distributed across the entire brain.

Tornadoes are rare events in the Pacific Northwest and are extremely difficult to predict along the coast, causing much surprise when they do form. After witnessing the destruction and rebuilding of a Port Orchard neighborhood that was ravaged by a F2 tornado in December 2018, I was inspired to explore these uncommon occurrences. For this project, I am investigating the near storm environments of tornadic systems that are generated from cold air outbreaks during the winter months along the coastal Pacific Northwest. This is done by analyzing data from massive tornado datasets, METAR (Aviation Routine Air Report) observations of convective precipitation such as graupel, and piecing together upper air reanalysis data to compare them to weather indexes that have been defined to determine atmospheric instability and can be used to predict extreme weather. The goal is to find patterns that are associated with these tornadic events to create more accurate forecasts and to paint a detailed picture of tornado climatology in the Pacific Northwest. My hope for this project is to shed light onto the factors that are at play for tornadoes, hail, and other severe weather that could potentially save lives.

We recently introduced operant social stress (OSS), a new operant procedure that classifies social motivation in mice as they lever press for volitional social interactions with a familiar partner before, during, and after social stress exposure. For social stress exposures, male mice underwent social defeat and female mice underwent witness defeat. In social defeat procedures, mice are repeatedly exposed to physical antagonistic interactions by an aggressive, larger mouse, while mice exposed to witness defeat mice observe these interactions from across a perforated barrier. Consistent with the literature, male mice exposed to social defeat exhibited reduced social motivation, while female mice exposed to witness defeat displayed an increase in social motivation. These opposing observations suggest different underlying mechanisms, but it remains unclear whether lever pressing during the task truly represents a motivation for affiliative reward. Thus, to rule out the contribution of non-social factors impacting social self-administration, we performed two control experiments to rule out alternative interpretations in this new operant method. In Experiment 1, we removed the familiar partner from the waiting chamber, in turn removing the social aspect of the reward. In Experiment 2, we unpaired the social rewards from the contingent lever, instead randomly delivering them during each trial. We hypothesized, and observed, that these manipulations would prevent mice from acquiring operant responses in the task and rule out non-social factors in driving operant responding. With the inclusion of these control experiments, we can now directly assess the social motivation of both male and female mice, facilitating deeper investigations into the underlying mechanisms in future studies.

 Within the field of neuroscience, optogenetics is an established experimental tool which can be used to alter specific cell function or trigger enzymatic reactions under millisecond time-scale precision. The high temporal precision of optogenetic recombinases allows for precise identification of cell populations which causally regulate specific behaviors in health and disease. Furthermore, the inducible optogenetic control specifically of recombinase activity for cell-type targeting eliminates the use of other inducible methods including exogenous chemicals that operate on lower time-scales and notoriously cause non-specific effects. Currently available optogenetic recombinases are driven by low wavelengths of light (e.g., Yao et al, 2020) which limit their in-vivo use to local and/or superficial areas of the brain in an invasive manner. Our recently engineered optogenetics-based protein pair, NOC (Near-IR Optogenetic Cre recombinase) induces Cre recombinase activity with near-infrared (NIR) light through dimerization of split-Cre fragments. We have previously demonstrated NOC’s capability for functional Cre recombinase activity under 650 nm light administration, and now aim to optimize the inducibility profile of NOC through two additional modifications. These include modifications to Cre split-site locations based off of previously designed blue light-inducible recombinases (Yao et. al, 2020), and a novel 660 nm inducible photoreceptor pair (Zhou et. al, 2022). The inducibility of these new configurations will be tested using our in-vitro fiber optic system. The optimal configuration of NOC will lay the groundwork for NOGen (NIR OptoGenetic ensemble capture), an alternative version of NOC which will include a calcium-sensing domain on one of the protein fragments. This will limit NOGen’s activity to active neurons only, offering greater precision in identifying specific cell-populations which drive particular behaviors. These improved molecular tools can be used to further our understanding of brain anatomy and function, which serve as an important catalyst for the development of improved brain disorder treatment.

Mitochondria are the main oxygen consumers in eukaryotic cells and as such are the primary organelles affected by oxygen deprivation, hypoxia. Hypoxia alters the size and shape of mitochondria (so called mitochondrial dynamics) but the responsible mechanisms and their role in hypoxic cell death is unknown. The Crowder lab has recently discovered that a mutation in the Mechanistic Target of Rapamycin Complex One (mTORC1) protein Raptor confers hypoxia resistance. mTORC1 is a master regulator of metabolism and is known to affect certain aspects of mitochondrial biology. In this work I show that disrupting mitochondrial dynamics with mutants in mitochondrial fission produce hypoxia resistance but that mutants with altered fusion have normal hypoxic sensitivity. I have built compound mutants containing both fission and fusion machinery mutants together with the hypoxia resistant Raptor mutant. Using these mutants, I am testing how Raptor controls fission and fusion and whether either is required for its hypoxia resistance. Our preliminary findings indicate that the hypoxia resistance of the Raptor mutant does not require FZO-1-mediated mitochondrial fusion. By exploring the interaction of mitochondrial fusion and fission with Raptor, we are beginning to understand how these important organelle and metabolic regulators combine to control hypoxic cell death.

In the United States, Black adolescent (10-19 years old) girls have the highest prevalence of pediatric obesity. Despite public attention and public health interventions on obesity, current research has yet to evaluate what weight management recommendations are prevalent in mediums most frequently used by Black adolescent girls. Previous scholars show that Black adolescents primarily consume content on Instagram and Tiktok compared to all other social media platforms. Our research seeks to compare the weight management recommendations present in Instagram and Tiktok with those of public health organization websites. Using the rhetorical themes identified, we move to assess the feasibility of health messaging from public policy organizations compared to social media platforms. Ultimately, we seek to evaluate the efficacy of the recommendations based on the availability of the infrastructure accessible to Black adolescents. We analyze weight management messaging on Instagram, Tik Tok, and public policy organization websites. These primary sources are excerpted through simple random sampling and coded for common weight management themes. We seek to determine the feasibility of such messaging as well as points of convergence and divergence between the platforms. We hypothesize that the weight management themes found in social media will not demonstrate consistency with the recommendations made by public health organizations. In addition, we predict that neither the social media nor public policy weight management recommendations will be attainable for Black adolescent girls when assessing their feasibility in relation to the environmental and socioeconomic resources available to them in the United States. In conclusion, there are insufficient resources for Black adolescent girls to make informed weight management decisions and available resources are not effectively communicated.

Rigorous ethological observation via machine learning techniques, termed computational neuroethology, is a rapidly expanding field. Our lab has created an open-source pipeline for automated behavioral analysis using supervised machine learning called Simple Behavioral Analysis (SimBA), to aid in the high throughput analysis of social behavior. Using pose estimation data of socially interacting animals obtained through open source pipelines such as SLEAP or DeepLabCut, we are able to create large training sets of video frames that are hand scored as positive or negative for a behavior, which we then feed into supervised random forest algorithms. These algorithms then build classifiers which can detect the behaviors in novel videos. My work has focused on building and titrating classifiers for two important social behaviors: face and body sniffing by a dominant mouse toward a subordinate. So far, I have hand-scored a large dataset of social interaction videos to create a sizable training set. I have begun the initial phases of training my classifiers, which involves finding appropriate hyperparameters for the random forest algorithms so that they can differentiate positive and negative behaviors, and refrain from overfitting to our training datasets. Using both machine learning performance metrics as well as hand versus machine comparisons, I am able to understand the generalizability and accuracy of my classifiers. As I continue with this project, I will selectively add more positive and negative examples to correct false positives and boost the confidence of the classifiers through subsequent iterations. This work allows me to gain an understanding of the principles of machine learning techniques, and create classifiers that we openly provide to behavioral neuroscience labs across the world. We expect that the pooling of these classifiers with outside labs will promote a high level of standardization of behavioral definitions in behavioral neuroscience, ultimately increasing reliability and reproducibility.

Cognitive decline with increasing age is an aspect of growing old. Age-related cognitive impairment (ARCI) entails the early stages of decline and is extremely common, affecting millions of older people. However, little is known about why some people have ARCI and some are cognitively normal at older ages. A recently characterized mouse model of naturally occurring ARCI, showing a distribution of affected and non-affected animals similar to older humans, was used to interrogate brain samples for transcriptomic profiles generated by RNA sequencing (RNA-seq). Hippocampal brain samples were collected from 22-month-old male and female C57BL/6 mice with and without ARCI (as determined by a spatial navigation learning task). RNA-seq was done by the NovoGene UC Davis sequencing Center. Preliminary data show a stronger presence of pathways of neurodegeneration and oxidative phosphorylation in the hippocampus of mice with ARCI compared to mice without ARCI. Detailed computational analysis will be done to investigate gene-expression quantifications using sequencing pipelines aligning Differential Gene Expression, KEGG orthology pathways, and Star RNA-seq read mapper in order to more accurately identify unique transcriptomic profiles in the brains of mice with and without ARCI. These findings will help identify genetic pathways that could be therapeutically targeted to ameliorate and possibly reverse the effects of ARCI, and provide insight into internal brain factors responsible for an increased risk in developing more severe conditions of neurodegeneration and dementia such as Alzheimer’s disease.

Neuropsychiatric disorders pose a difficult challenge for healthcare providers. Treatments for such disorders vary in efficacy and come with detrimental costs for patients and their communities. Historically, preclinical animal models have failed to incorporate the nuances of volitional human social behavior. This project used chronic social defeat stress to induce depression-like behaviors in male and female mice, this was followed by self-administered social interactions within an operant chamber in which lever presses were reinforced by social contact. The goal is to develop preclinical animal models that can be assessed to identify mechanisms responsible for stress-induced social motivation. The mice will be injected with a nuclear localized tag (oNLS) and viral retrograde tracer rAAV2-retro-GFP. Male and female mice will train to self-administer social interaction with a sex and age-matched housing partner over the course of ten 12-trial sessions. Next, experimental male and female mice will be subjected to physical and witness defeats followed by operant social self-administration. Before and after the 10-day operant social stress sessions, we will test social reward seeking via non-reinforced self-administration of social reward followed by a progressive ratio test. Brain tissue will be collected and prepared for immunohistochemistry and iDISCO+ whole-brain clearing for cfos labelling. We predict results will show differential cfos activity in sexually dimorphic brain regions such as the hippocampus, prefrontal cortex, amygdala and the bed nucleus of stria terminalis. We determine that operant social stress can be used to discern differences in social motivation in male and female mice as a result of stress-induced factors. There is great potential in using whole-brain activity mapping to identify brain structures activated during social reward following social stress, as this can also serve as a technical resource for the field by identifying relevant non-canonical brain regions and circuits that govern such behaviors.

A keystone bacterium involved in the pathogenesis of chronic periodontitis, commonly known as gum disease, is Porphyromonas gingivalis. This pathogen produces multiple structures on the surface of its cells categorized as virulence factors, including lipopolysaccharides (LPS) and outer membrane vesicles (OMV). Lipopolysaccharides are anchored to the outer membrane of P. gingivalis by Lipid A structures. Previous studies in our lab have found that the abundance and cargo selection of OMVs released from the cell’s surface can be modulated by the structure of Lipid A on P. gingivalis. The virulence factors investigated assist P. gingivalis in the colonization of the host at a cellular level – such as the formation of biofilm, or aggregated bacteria on a surface. OMVs released from the cell's surface operate as a delivery system for the various structures found on the outer membrane of the bacterial cell. We hypothesize that the biofilm density and morphology formed by P. gingivalis are influenced by the changes in OMV abundance and content derived from the modulations in the Lipid A structure. To test this, we utilize biofilm assays, where live cultures from various strains with differing Lipid A structures can grow and aggregate on a glass coverslip for 48-72 hours. Morphology differences are revealed from the analysis of the biofilms and pixel intensity is quantified and compared among strains. Various assays are used to compare the activity and concentrations of protein and lipid cargoes within the OMVs to understand how they are connected to biofilm morphology. The biofilms formed by P. gingivalis contribute to its pathogenesis, therefore it is important to understand the impact that secreted outer membrane vesicles have on its structure and integrity.

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.

Botryllus schlosseri is a non-indigenous species of colonial tunicate commonly found in many marinas of the Puget Sound. Colonies of Botryllus can grow asexually through the process of blastogenesis (also called ‘budding’) which involves the formation of buds which mature into new zooids on a weekly cycle. Apoptosis and oxidative stress are involved in the final stage of blastogenesis, a time when the system resorbs the zooids and the newly matured buds take over. Although nickel has been found to be genotoxic and can induce many aspects of the cellular stress response in animals, little research has characterized these effects on marine invertebrates. In this study, we performed acute exposures of nickel chloride at sublethal concentrations in B. schlosseri collected from the field to identify changes to blastogenic timing, DNA damage, apoptosis, and the oxidative stress response. These data will establish the in vivo tolerance and stress responses of B. schlosseri to nickel exposure. Furthermore, these data will inform future studies which seek to use nickel as an immortalization agent in cell culture with the goal of generating the first continuous cell line for any marine invertebrate species.

Hydrogen sulfide (H₂S) impacts biological systems in multiple ways, including the arrest of aerobic respiration, and thus is mechanistically similar to cyanide. Unlike cyanide, however, H₂S can accelerate as well as end cell growth, including in plants, where it drives germination rates when administered in micromolar concentrations. However, the limited research to date leads to a need to better quantify and contextualize chemical composition changes in plant tissue following H₂S-induced plant growth. This study resulted in the ability to quantify the biophysical impacts of H₂S-induced growth in plants. The novel use of δ³⁴S and δ¹⁵N isotope ratios produced at the IsoLab in University of Washington represent the results of this sampling and its subsequent analysis. They may represent a new means to understanding the effects of H₂S on plant growth, including during the crucial phase of plant germination. The effects were observed on hypocotyl tissues from seedlings of Pisum sativum (pea), Phaseolus vulgaris (bean), and Zea mays L. (corn), all grown in hydroponic H₂S solutions, ranging from 0-100μM. These specific isotopic methods may allow comparison between modern and fossil material, because these isotopic species are known to have been preserved across a wide diversity of plant fossils. This novel application of these classic staples in the biochemical toolbox may have further implications for better understanding past events, because many major mass extinctions have now been linked to excess oceanic and atmospheric H₂S (compared to today), and may also, paradoxically, present new paths toward increased crop yields.

Eelgrass (Zostera marina) is a crucial marine flowering plant that provides intertidal ecosystem services in and outside the Puget Sound. However, eelgrass populations are under threat due to the adverse effects of climate change. Maintaining genetic diversity is essential for their survival. This project aims to enhance our understanding of eelgrass reproduction and how populations will react to climate change by characterizing the molecular mechanisms of flowering in eelgrass. We have identified candidate eelgrass flowering genes that are homologous to genes found in Arabidopsis thaliana, a model organism. These candidate genes were selected based on the clock-regulated model of flowering, in which FLOWERING LOCUS T (FT) encodes for a critical protein that triggers the flowering response pathway. To investigate this model, we created transgenic overexpression lines in Arabidopsis and identified two candidate eelgrass FT genes that exhibit an early flowering phenotype similar to FT overexpression in Arabidopsis. We are also using Yeast 2-Hybrid Assays (Y2H) to confirm the identity of the suspected eelgrass FT. Y2H is a technique for studying protein-protein interactions and allows us to investigate interactions between eelgrass FT and other transcriptional regulators within the flowering response pathway. Based on our data, we expect to see the two candidate eelgrass FT genes result in a simultaneous early flowering phenotype and in interactions with other transcriptional regulators to form a transcription factor complex that enables the expression of a reporter gene. Identifying FT in eelgrass will prompt further study of individual and population-wide flowering patterns, and how these patterns change with shifting ocean conditions.

By 2050, the global human population is expected to reach 9.7 billion. Supporting this rapid growth will challenge global food systems, increasing the demand for healthier affordable foods such as poultry-sourced products (meat and eggs). Improving the accuracy of genotype-to-phenotype predictions for farmed animals could enable better breeding strategies and management practices that are crucial to meeting this goal. By characterizing regulatory genomic regions within various tissues, epigenetic factors which dictate specific cellular phenotypes can be pinpointed: improving phenotype prediction accuracy. To this end, we genetically sequenced (whole-genome bisulfite sequencing) samples of reproductive tissues (magnum, shell gland, isthmus, and ovary) from farmed groups of chickens (G. gallus). Through bioinformatics, we functionally annotated regulatory patterns of DNA methylation to identify tissue-specific epigenetic variation across the female chicken reproductive system. To tackle this, we utilized CGmapTools software to comparatively analyze tissues in a pairwise manner. In order to quantify each pairs’ differentially methylated regions (DMRs), all methylated regions were intersected and filtered through a statistical t-test. We found the pairwise comparison analysis between isthmus and ovary tissues to show the highest number of significant DMRs, being 51% hypermethylated in the isthmus. On the other hand, a comparative analysis between isthmus and shell gland tissues showed the lowest number of significant DMRs, being 54% hypermethylated in the isthmus. Upon annotating and conducting enrichment analyses on the DMRs, we learned that genes related to ECM-receptor interactions and focal adhesion were most prominent. Results of this research will aid the FAANG consortium (an international effort to improve farmed animal production) in improving genotype-to-phenotype predictions, hopefully enabling more sustainable genomic selection practices and genome-enabled management in the future of agriculture.

BRCA1-associated RING domain protein 1 (BARD1) is a key interactor with tumor suppressor BRCA1. Due to this interaction, deleterious variants of BARD1 have been associated with breast and ovarian cancer. In recent years, the use of clinical sequencing technologies to inform and personalize patient care, precision medicine, has skyrocketed. Despite the increased prevalence of clinical sequencing, in many clinically relevant genes, like BARD1, most single-nucleotide variants (SNVs) are cataloged as variants of uncertain significance (VUS). These VUS effectively prevent clinicians from using this data to help patients as it is unknown if the observed variant is pathogenic or benign. Consequently, a strong need to functionally assess BARD1 SNVs exists. To help resolve BARD1 VUS, we are applying saturation genome editing (SGE). SGE is a multiplex assay for variant effect that functionally assesses all SNVs for genes, like BARD1, that are essential in the HAP1 cell line. SGE uses CRISPR-Cas9 gene editing to integrate a plasmid library containing all possible BARD1 SNVs into a HAP1 population. Due to BARD1’s essentiality, cells with deleterious variants become depleted from the population. These changes in cell viability are quantified through next-generation sequencing and bioinformatic analysis comparing the abundance of a variant in the original SNV library versus its abundance in the cell population at the end of the experiment. Functional scores are then calculated for each variant. To date, I have designed targeted SNV libraries for 34 regions that span the entire coding region of BARD1. These libraries are preparing to enter tissue culture as we complete final quality checks. Ultimately, we expect the functional scores for BARD1 SNVs to be bimodally distributed, showing strong separation between deleterious and benign variants. These scores will be directly used to reclassify current BARD1 VUS – allowing clinicians to better guide patient care with respect to BARD1 SNVs.

Trauma-induced coagulopathy is a severe complication of trauma that alters the normal mechanism of blood clotting through a number of complex factors. If clots are hypercoagulable, there is risk for dangerous vascular blockages. Conversely, if the clotting is hypocoagulable, it can lead to fatal hemorrhaging. Prior research indicates that actin has a major impact on platelet activity and blood clot formation. Actin is a highly abundant cytoskeletal protein that forms long, insoluble filaments. When released into the blood during cellular death, these filaments have complex effects on blood clot formation. Actin filaments can be integrated into the scaffolding of the clot, increasing strength. My experiment aims to investigate the roles of actin and on human blood clotting. Healthy donor whole blood in 3.2% sodium citrate was spiked with either a saline control or recombinant human skeletal muscle-derived actin (final concentration 200 nM) and allowed to incubate for 5 min. Samples were then activated with either 10 mM adenosine diphosphate (ADP) or 2 mg/mL collagen. The platelet aggregation response was then measured by impedance aggregometry. Each pair of control and actin conditions was run simultaneously. The impedance area under the curve (AUC) was compared between control and actin groups under each activation condition using a paired t-test with significance at p<0.05. Preliminary results show ADP was no different between the control and actin groups (p=0.400, n=5). The AUC in response to collagen was significantly higher in the presence of actin compared to control (p=0.005, n=7). Exogenous muscle actin appears to increase platelet aggregation through the collagen but not the ADP activation pathway. Further investigation is required to better characterize this interaction. A better understanding of the mechanisms of actin on hemostasis could direct research into pharmaceuticals and therapies that could yield better outcomes for trauma patients.
 

With cardiovascular disease being the leading cause of death worldwide, new and improved disease models are required to facilitate the research and production of new treatments. In this research, we are developing improved methods for modeling hypertension in engineered heart tissues (EHTs) to investigate resulting tissue remodeling at the tissue and cellular levels. We developed a model of hypertension using 3D-printed polylactic acid braces that enable stiffness adjustment of the flexible polydimethylsiloxane (PDMS) EHT platform. The braces were validated by mechanical testing to quantify their stiffening effect. Braces were shown to increase stiffness according to beam bending theory, with bracing half of the post’s length resulting in a 7-fold increase in stiffness. Next, we applied braces to tissues that only contain stromal cells, which are responsible for remodeling the extracellular matrix (ECM). The next steps are to quantify how stiffness affects ECM remodeling, including tissue-wide effects such as changes in tissue length and width, and micro-scale effects such as changes in cell migration, apoptosis, and cytoskeletal structure, which are quantified in 3D using IHC and confocal microscopy. We hypothesize that hypertension results in tissue thinning and lengthening, as well as decreased cell density, increased apoptosis, and increased expression of cytoskeletal markers. Next, the braces are applied to EHTs containing human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). The effect of hypertension on EHT remodeling and hiPSC-CM maturation is then quantified using a custom MATLAB image processing suite. Finally, increasing systolic resistance of novel varieties of EHTs that incorporate hiPSC-derived cardiac fibroblasts (hiPSC-CFs) alongside cardiomyocytes enables evaluation of fibrotic remodeling. We hypothesize that hypertension promotes a hypertrophic response in both hiPSC-CMs and hiPSC-CFs in EHTs, displaying increased sarcomerization and fibrosis respectively. Developing this improved hypertension model will accelerate cardiac regenerative medicine research, and provide new approaches for drug discovery.

Melusin, a chaperone protein expressed in cardiac tissue, induces a protective hypertrophic response in response to chronic mechanical stress. This protective hypertrophic response prevents the progression of cardiomyopathy into heart failure. In previous work done in wild-type (WT) and melusin knockout (melKO) mice, the absence of melusin was correlated with a hypertrophic response indicative of heart failure. I plan to investigate the biomechanical role of melusin in humans using human-engineered heart tissues (EHTs) created from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) that lack melusin and their isogenic controls. EHTs are more representative of the human heart, making them an ideal model for studying the role of melusin in humans. I hypothesize that WT EHTs subjected to mechanical stress, i.e., high afterload, will outperform the melKO EHTs. To measure this, I will increase the stiffness of the EHT posts and measure contractile force. I have successfully differentiated high-purity WT and melKO cardiomyocytes from iPSCs, essential for creating healthy EHTs. I will cast both WT and melKO tissues on a bed of silicone posts that can be stiffened to varying extents to induce different amounts of mechanical stress on the cells. I will conduct a western blot on EHTs from all treatment groups to determine the level of melusin expression and examine the expression of Heat Shock Proteins (Hsp) 70 and 90, due to their coregulation with melusin. The EHTs that undergo mechanical stress are expected to express melusin and these results will work to establish whether melusin expression in humans is activated by mechanical stress. I will measure and compare the contractile force between the WT and melKO tissues. Improving our understanding of the role of melusin in humans can lead to further research into therapies and treatments for heart failure.

Over the last decade-and-a-half, China has seen its financial technology (fintech) industry achieve a level of scale and ubiquity without peer among developed economies — Alibaba’s Alipay and Tencent’s WeChat Pay, to name a few examples, each enjoy over one billion users, and are deeply integrated into daily life. Yet, by its hybrid nature, fintech presents complex challenges novel to both financial and technology regulation, the dramatic collapse of China’s peer-to-peer lending industry being a case in point. In this context, as much as Chinese firms lead the way in fintech development, Chinese regulators also act as innovators in the yet-undeveloped field of fintech regulation. As such, the study of the Chinese regulatory experience may yield insight into how other nations may develop their own regulatory frameworks towards fintech as an emerging industry. This research investigates the characteristics and challenges of Chinese fintech regulation. Specifically, this research considers the current institutional approach to regulation, the financial risks that current regulation seeks to address, and the effects of said regulation on the fintech industry. Given the novelty of fintech as a regulatory field, this research addresses a new and developing niche within the broader study of Chinese economic policymaking. I utilize a combination of general policy analysis and case study of specific regulatory actions to analyze both the regulatory process and its effect on the fintech industry. Qualitative analysis of regulatory documents and materials is complemented by quantitative analysis of industry-level data in examining both regulatory initiatives and their empirical economic effects upon fintech firms.This research is expected to yield the result that, because of its novelty and intersectionality, Chinese fintech regulation is underdeveloped relative to traditional finance or technology regulation. Simultaneously, this research is also expected to indicate a general trajectory towards greater regulatory scrutiny towards fintech firms.

There are an estimated 500,000 people in the U.S. who are deaf and use American Sign Language (ASL). Compared to the general population, deaf people are at greater risk of having chronic health problems and experience significant health disparities and inequities (Sanfacon, Leffers, Miller, Stabbe, DeWindt, Wagner, & Kushalnagar, 2020; Kushalnagar, Reesman, Holcomb, & Ryan, 2019; Kushalnagar & Miller, 2019). The longstanding history of inequitable access to language and education, and a lack of printed information and materials, leave people who are deaf and who use ASL unaware of opportunities to participate in cutting-edge research/clinical trials (Kushalnagar & Miller, 2019; Lesch, Brucher, Chapple, R., & Chapple, K., 2019; Smith & Chin, 2012). An unintended consequence, therefore, is that Principle Investigators (PIs) neglect to include ASL signers who are deaf in their subject sample pools, and this marginalized population continues to be at disparity for both health outcomes and clinical research participation. One barrier is the unavailability of informed consent materials that are accessible in ASL. The current research study conducted by our team at the Center for Deaf Health Equity at Gallaudet University attempts to address the language barrier to the consent process through a careful reconsideration of its traditional English format and the development of an American Sign Language (ASL) informed consent app. As part of the project, I successfully leveraged existing machine learning methods to develop a way to navigate and signature an informed consent process using ASL. I call this new method of navigation and signature “ASL Interactability.” In my findings, I found that deaf people who are primarily college educated felt that the process for obtaining ASL consent through an accessible app is just as fluid and easy to understand as traditional English consent. These findings not only show the potential of ASL Interactability in the informed consent process, but in any other digital application that requires the user to interact (e.g. to move between pages, to provide signature, etc).

Racial and ethnic minority groups are less likely to seek or have access to mental health support services. Despite an increase in the quantity of mental health services nationwide, disparities in usage across racial and ethnic minority groups still exist, leaving resources underutilized and many individuals with unmet needs. Previous studies highlight both structural and non-structural barriers, such as income and stigma, which prevent certain racial groups from fully utilizing health care services. Studies often overlook health outcomes associated with immigrant status and overgeneralize findings to all populations. While scholars have studied the structural barriers to accessing mental health care services, there is a need to understand the cultural contexts preventing racial and ethnic groups from reaching out to these services. Using data from the National Health Interview Survey (NHIS), this study examines differences in access to and utilization of mental health care services of U.S born and immigrant populations from the years 2010-2020. The NHIS allows for the control and determination of effects of both structural and cultural factors such as health insurance coverage, financial instability, racial and ethnic characteristics, and migrant status to further understand the dynamics of access to and use of mental health care services. Foreign-born individuals are expected to show lower access to health care resources with varying levels of moderate mental distress. These differences are expected to vary for those who have spent more time in the U.S with more access to resources and higher levels of mental distress. Understanding trends related to mental health care can help develop better public policy responses and improve the promotion of health care services. This study will help address why services are underutilized and how to minimize health service inequalities among racial and ethnic populations. 

Our research group is exploring the feasibility of utilizing nanopore sensors for protein sequencing, whose compact size and ability to facilitate extremely long, uninterrupted reads of protein strands upstage the current procedure of using complex, expensive mass spectrometry (MS) devices. My project predicts the sensor’s raw signal data using a carefully tested combination of each amino acid’s volume and charge properties. Using my model to generate predictions for a specific database of proteins, I can compare the unknown raw signal to each of the predicted signals to single out the best matching/correct sequence. While the protein space of De Novo sequencing is vast (20 to the power of protein sequence length), this method effectively shrinks the protein space to a group of substantive, feasible sequences. Employing the current predictive model on a database of synthetic and natural proteins, when compared against an unknown protein’s raw signal, I found that, on average, the correct prediction consistently ranked within the 99th percentile of matches among a predicted test set of >20,000 sequences. Advancing single-protein sequencing can revolutionize protein research by enabling the identification of low-abundance proteins. Additionally, the increased sensitivity of the nanopore sensor could shed light on the so-called "human dark proteome," composed of approximately 3,000 human proteins that have not yet been identified despite genetic evidence of their existence.

Hepatocellular Carcinoma (HCC) is an aggressive primary liver cancer that can be characterized with contrast-enhanced ultrasound (CEUS) by blood flow parameters. The most important blood-flow parameters are wash-in and washout, measured by the rate of contrast flow into and out of the liver and tumor. Currently blood flow is observed by eye, assessing the brightness of the contrast agent over time during the scan, and then scored on the Liver Reporting and Data System (LI-RADS) scale. This subjectivity delays diagnosis and treatment, and increases HCC mortality rate. To aid clinicians in a timely diagnosis, we are creating a quantitative Python algorithm to extract blood flow parameters from CEUS videos. I studied the existing MATLAB code our lab has created and translated its functionality into a Python executable. Since the two languages have different syntaxes and functions, I reconfigured the entire script to run in Python. This Python script will run faster than the MATLAB code, be able to accurately compute blood flow measures from CEUS scans, and be easier to distribute outside of academia. To extract parameters from CEUS liver videos of HCC patients, we processed the video using respiratory gating and motion compensation to ensure the tumor is on the scan and not moving around due to breathing. Then we analyzed the pixel brightness of the liver and tumor over the course of the scan to create a time-intensity curve (TIC). Finally, we compared various points on the curve to quantify the blood flow within the tumor and surrounding liver. Further iterations of the algorithm will include machine learning tools available in Python to increase the level of autonomy and thus the objectivity of the parameters. Using this algorithm, HCC diagnosis using LI-RADS will be timelier, allowing patients access to more effective treatment options.

Effective rapid tests have been developed to detect COVID-19 in nasal swabs. However, nasal swabs require a trade-off in which deeper insertion of the swab allows higher accuracy but causes greater patient discomfort. On the other hand, saliva can be collected non-invasively in large volumes. Therefore, this project aims to develop a point-of-care diagnostic device (“DiagnosDisk”) for the rapid and sensitive detection of SARS-CoV-2 nucleocapsid protein (NP) in saliva. The DiagnosDisk is a circular disk (25mm diameter) consisting of three layers, from top to bottom: a plastic adhesive capping sheet with a sample port, a hydroxylated nylon detection membrane, and an absorbent pad. Analytes are efficiently enriched by binding to anti-NP antibodies conjugated to temperature-responsive polymers (poly(N-isopropylacrylamide)) which aggregate upon heating. To prepare the sample, polymer- and gold-conjugated antibodies are mixed with the sample and bind to the target antigen, forming a sandwich immunocomplex. When flowing through the heated detection membrane (>37℃), the sandwich immunocomplexes aggregate and are captured on the membrane, producing a visual signal. I quantify the signal intensity on the membrane using ImageJ software. With this design, I hypothesize that the DiagnosDisk will have higher sensitivity than the lateral flow assay (LFA) by utilizing temperature-responsive polymers for sample enrichment and using larger sample volumes which increases the number of antigens that can be captured. From my initial testing, the DiagnosDisk enabled 2mL of buffer flow-through in 7.5 minutes, demonstrating a sample volume capacity 10-times that of most LFA. Next, I tested the DiagnosDisk with buffer samples spiked with 5ng/mL NP. Heated membrane pads produced signal intensities significantly greater than unheated membranes. I plan to apply the device to saliva samples next. Ultimately, by enabling rapid and sensitive detection of COVID-19 in saliva, the DiagnosDisk can help limit community transmission of the virus.

In the body, cells grow in the extracellular matrix (ECM), which presents biochemical and mechanical signals to the cells inside. Hydrogel biomaterials are water-laden polymer networks that can mimic the properties of the ECM, allowing controlled study of cellular behavior in vitro. Many cells are mechanosensitive, but mechanical cues other than stiffness have not been fully investigated. This project aims to develop a platform in which degradability and strain can be activated by a researcher bio-orthogonally. We have synthesized a cyclic peptide crosslinker for a synthetic poly(ethylene glycol) hydrogel that acts as a Boolean AND-gate: one half is degradable by cell-secreted enzymes, and the other half is degradable by sortase, a bacterial enzyme, added by a researcher. We quantified the degradation of hydrogels made with this crosslink via fluorescence release and demonstrated that degradation only occurs after exposure to both enzymatic inputs. We further demonstrated that cells encapsulated in this material retain strong viability. We predict that cells will be unable to spread in this material until after a researcher adds sortase. After sortase addition, we expect that contractile cells will be able to locally degrade the material, spread, and generate strain. We intend to quantify spreading and strain with encapsulated fibroblasts. We also plan to use this platform to study development, by encapsulating immature cardiac stem cells and investigating the effect of fibroblast driven strain as a model; we predict that strain will trigger further specification of these immature cells. In addition to understanding the pathways for development, this research may help identify new therapeutic targets for disease, and it will also inform new strategies to grow tissue in vitro that more closely mimic the native environment.

Across a variety of signaling pathways, soluble factors in the extracellular matrix bind to protein receptors that span the cell wall, thereby triggering an information cascade that affects cell activity or function. It follows that by controlling the binding of signaling factors to these receptors, cell behavior and activity can be guided with substantial precision. In this project, we aim to design a system that allows de novo-developed protein agonists and antagonists, referred to as binders, to be activated with a high degree of temporal and spatial control within cell-encapsulating hydrogels. Towards this end, we employ methods derived from protein semisynthesis and click chemistry to tether binders to the hydrogel polymer network and then subsequently photo-release them from the network. We expect a difference in the functionality of binders when they are bound to the network compared to when they are released through light exposure and solubilized, thus achieving light-dependent control of the binder-receptor interaction and cell activity. This system will be the first to employ de novo developed agonist and antagonist biomolecules for the interrogation and control of cellular behavior. In so doing, it will expand the tool box of biomaterial engineering to include finer control over cells grown in 3D matrices, with direct implications in fields as diverse as therapeutic development, regenerative medicine, and organ-on-a-chip engineering.

Interstrand crosslinks (ICLs), commonly induced by chemotherapeutic drugs, are a form of DNA damage that results in stalled replication forks during DNA replication. When stalled replication forks occur, Ataxia telangiectasia and Rad3 related (ATR) kinase activates the Checkpoint Kinase 1 protein (Chk1) through phosphorylation. This initiates a signaling cascade that leads to cell cycle arrest. Therefore, checkpoint activation via Chk1 phosphorylation is crucial for the cellular DNA damage response (DDR) and overall genomic stability. Mre11 is another protein involved in DNA damage repair. Alongside two other proteins, Rad50 and Nbs1, it forms the MRN complex. As with ATR, the MRN complex is activated in response to DNA damage mainly in response to double stranded break formation. In our lab, we have now found that inhibition of Mre11 using mirin, a potent Mre11 inhibitor, surprisingly led to decreased phosphorylation of Chk1 (p-Chk1). In this work, we are exploring the relationship between Mre11 and checkpoint activation during replication stress. To study this, we made us of cisplatin (a crosslinking agent used in chemotherapy) as well as other replication stress-inducing drugs. Using western blotting to visualize the phosphorylation levels of Chk1 we are examining how Mre11 inhibition affects Chk1 activation. Results showed increased p-Chk1 in response to DNA damage in the cisplatin treatment compared to the control, but a decreased levels of phospho-Chk1 upon Mirin co-treatment. This suggests that MRE11 plays a role in phosphorylating Chk1 and activating the DDR pathway. Our results provide evidence for MRE11 inhibition as a method of decreasing the DNA damage repair response. It also helps to shed light on a potential mechanism of treatment for cancer patients. Future studies will further examine the nature of this relationship by investigating activation of Chk1 using time-course experiments and MRN inhibition through siRNA transfections.

Meadow and wetland areas serve as critical habitats for many native species in the Pacific Northwest and provide countless ecosystem services such as carbon sequestration, sediment removal, and increased biodiversity. However, most wetland and meadows inventories are incomplete or are biased towards those that have been mapped on the ground and those that are easy to detect directly in aerial and satellite imagery. Furthermore, due to habitat loss and climate change effects, the current state of these ecosystems is highly dynamic and unknown. Remote sensing provides landscape analysis capabilities to map current habitats and compile and analyze variables such as elevation, slope, soil type, wetness, and seasonal glacial recession that may predict where these fragile habitats could be. The goal of our research was to identify and map wetlands and meadows in Mount Rainier National Park. Using topographic, vegetative, hydrologic, and soil indices paired with data points to train the machine learning model, we get an output of wetland and meadow probability. Our work, co-produced with National Park Service biologists, contributes to the database of potential wetland ecosystems in Mount Rainier National Park. and improves remote sensing methodology to predict meadow habitats. WIP tool outputs of predicted wetlands and meadows had a high overall accuracy with documented wetlands and meadows in Mount Rainier National Park. Ultimately, by providing models, processes, and continuing to add to knowledge of wetland and meadow habitats, we anticipate a large potential for expansion to other NPS-protected lands.

Ascidians are invertebrate chordates, with tadpole larvae that metamorphose into sessile adults. Molgulidae are a clade of ascidians where tailless larvae have evolved several times independently and our lab is interested in understanding the molecular mechanisms underlying the evolution of taillessness. There are two closely related Molgulidae species that are sympatric in Roscoff, France: Molgula oculata, a tailed ascidian and Molgula occulta, a tailless ascidian. The tailless M. occulta, have 20 notochord cells that do not converge and extend, called a "notoball", and have evolved a number of larval pseudogenes. During embryonic development, the Wnt planar cell polarity (PCP) pathway plays an essential role in regulating cell fate determination and other cell processes. Previous experiments have found that the Stolidobranch ascidian, Halocynthia roretzi, has a Wnt5 duplication, where Wnt5a is invovled in the notochord development whereas Wnt5ß is involved in muscle development. Bioinformatic analysis has been done on several developmental genes involved in notochord formation and the Wnt pathway which showed that most genes are highly conserved between M. oculata and M. occulta. We have identified two Wnt5 isoforms that may play a role in tail formation, and we are in the process of subcloning the 3'UTR regions to obtain gene specific RNA probes for in-situ hybridization. We expect to find Wnt5a expressed in the notochord and Wnt5ß to be expressed in the muscle cells. We are also cloning Dsh to examine gene expression. This information will allow insight into how the Wnt5 genes in M. occulta and M. oculata are implicated in notochord convergence and extension as well as whether the Wnt/PCP pathway contributes to the evolution of tailless larvae. 

One way to obtain plasma is by using a Direct Current (DC) discharge. Plasma is an ionized gas, meaning the separation of positive ions and electrons in a gas. There are three main variables when it comes to a DC discharge configuration. A gas forms into a plasma in an isolated space of low pressure between 2 electrodes, a cathode and an anode. Voltage must constantly be applied across the cathode and the anode to maintain the plasma. The initial voltage needed to initiate the separation of electrons and protons in a gas to produce a plasma is called the breakdown voltage. Our study investigates the configuration of a DC discharge plasma and the correlation between electrode separation, breakdown voltage, and pressures in a DC discharge environment. We constructed an environment consisting of long oval glass tube housing an anode and cathode on each side. A vacuum pump is attached to the glass container to extract air to reduce pressure in our glass tube. To maintain an ideal pressure, we established a concealed air tube connected to our glass tube with a fine adjust valve to let air into our glass tube at the same rate as our vacuum pump extraction resulting in a stable low pressure in our experimental configuration. We designed and conducted a series of tests to investigate the properties of a DC plasma formation. Moreover, we wanted to establish evidence of the Paschen Curve, which relates the breakdown voltage and the product of electrode distance and pressure in DC discharge. We experimentally determined the optimum pressure and electrode separation distance product for plasma breakdown in air and Argon gas. DC plasmas can be utilized as sputter sources to deposit thin films for solar panels; characterizing the breakdown voltage is significant at low pressures and short spacing to control the sputtering rate.

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.

Racial discrimination can heighten stress for people of color. The self-medication model suggests that people who experience racial discrimination consume alcohol to cope with negative emotions elicited from these experiences. Most existing studies have tended to correlate general alcohol use behaviors with recalled experiences of stressors such as racial discrimination. These methods are limited in understanding the causal effects of stressors on people’s intention to drink. There are very few experimental studies that considered the impact of racial discrimination and other daily stressors on drinking behavior among people of color. This study was aimed to examine the effects of racial discrimination and daily hassles (work, academics, and finances) on people of color’s intentions to drink. Using data from a between-groups experimental study, we used virtual reality technology to simulate typical interpersonal exchanges at a house party where alcoholic and nonalcoholic beverages were available. Participants were recruited from a private four-year university and the general community (N=184; M_age=23.9; 48.9% community adults; 47.8% women; 40.8% Latinx/Hispanic, 28.3% Asian American, 19.6% African American/Black, 11.4% other). They were randomly assigned to experience racial discrimination (n=141) or daily stressors unrelated to racism (n=43) in the simulation. Participants’ responses during the simulation were audio recorded; we coded whether they requested to drink an alcoholic or nonalcoholic beverage immediately before and after exposure to the stressor. Logistic regression will be used to assess group differences in intent to drink. We expected more participants in the racial discrimination condition to express intent to drink alcohol than those in the daily stressors condition. Results can illustrate the unique effects of racial discrimination on drinking intentions among young adults of color, and enhance knowledge on predictors of alcohol use and ways to mitigate negative drinking-related consequences.

Reproductive and developmental toxicology is an area of importance for public health. Current in vivo methods of reproductive and developmental toxicity testing require large cohorts of animals, lengthy experiment times, and high cost. In vitro models using cultured cells align with the three R’s of toxicology: to replace, reduce, and refine the use of animals in toxicity testing. Our group is developing an in-vitro model of neonatal testis to study developmental testis toxicity while reducing animal use. To test the physiological relevance of our in-vitro model, I collected post-natal day five testis for immunohistochemical analyses. I dissected the testis from the surrounding tissue, fixed the tissue in formaldehyde solution, and left in a sucrose solution overnight. The fixed tissues were then frozen for cryosectioning. I sectioned the frozen tissue into 20µm sections using a cryostat and adhered them to microscope slides. To improve staining, I washed the adhered samples and permeabilized the membranes with detergent. I incubated each sample with fluorescent antibodies to target functional proteins and cell type markers. To visualize the targets of interest in the tissue sample, I used a confocal microscope to generate stacks of images through each section. I will next perform the same staining procedure on the in vitro culture samples for comparison. My poster presentation will present confocal microscopy images showing localization of these functional and cell type markers. These images will provide a comparison to our group’s in-vitro models. These images also give insight to healthy testis formation which can be compared to abnormalities in future pathological studies.

Major Depressive Disorder (MDD) is one of the fastest growing causes of global disability and requires a variety of treatment options due to its multifactorial etiology. While it’s long been known that blood levels of the neurotransmitter GABA are predictive of MDD, recent studies have implicated the human microbiome as a potent GABA metabolizer that can affect circulating GABA levels. Our collaborators used bioinformatics to identify bacteria containing putative GABA-synthesizing genes (puuD) that are predictive of host GABA levels and depression scores. However, previous literature indicates that the puu operon is repressed under anaerobic conditions in E. coli and the putative PuuD proteins have low sequence similarity to the model PuuD enzyme. My project seeks to confirm the biochemical activity and substrate-specificity of these genes using in-vitro assays measuring both the putative PuuDs’ chemical reactivity and kinetics. Due to conservation in the active site structures between the putative proteins and the model PuuD, I expect that the novel PuuD-like proteins will have gamma-glutamyl hydrolase activity and substrate specificity for gamma-glutamylated-GABA. This work provides base-level evidence for the use of systems biology techniques to identify enzymatic function and lays the foundation for targeted therapeutics manipulating the microbiome for improved MDD outcomes.

Across 200 psychology undergraduate programs in North America, only 6% makes multicultural courses a requirement for majors. Research remains unclear about the effectiveness of a lower-level and content-general course on undergraduate students; critical understanding of cultural diversity in human Psychology. Our research goals are to examine the effects of multicultural instruction on students' appreciation for diversity, and whether race moderates this effect. Data came from undergraduate students enrolled in Research Methods in Psychology course at a mid-sized, predominantly White private university (N=133, Mage=19.83, 79.8% women; 75.9% White/Euro American). As part of the course, they completed surveys assessing variables such as enrollment motivation, ethnic identity, and self-reported importance of cultural diversity in Psychology in the first and last two weeks of the semester. A separate class is employed to be the control group covering contents in open science rather than cultural diversity as part of the quasi-experimental design. Regression analyses were conducted to test whether students in the cultural diversity condition reported greater appreciation for cultural diversity in their post-term assessment than students in the control condition, with pre-term assessment entered as a covariate. In addition, whether changes in appreciation for cultural diversity were greater among White students than students of color was also tested. Students in the multicultural condition scored higher on critical awareness of current limitations in diversity representation in psychological science at the end of the term than those in the control condition. Students across conditions did not differ in appreciation for the importance of cultural diversity considerations in psychology. Implications for how to integrate multicultural training in undergraduate psychology curriculum will be discussed.

The severity and prevalence of alcohol consumption and alcohol use disorder among the Hispanic/Latinx population in the United States have steadily increased for the past 10 years. With the rise of high alcohol use and the development of alcohol disorders, there is a focus on research for the white population, leaving a gap for group-specific factors and how there is minimal research on efficacy differences in population and risk factors. This literature review aims to examine previous research on Hispanic/Latinx populations with alcohol use and alcohol-related issues and to bring to light the gaps in the literature. The question this literature review is answering is “how do group-specific risk factors hold the Hispanic/Latinx population from seeking alcohol use disorder assistance, and how to increase treatment efficacy for this population?” A critical literature review was conducted using PsychINFO and Google Scholar for articles published in the last 25 years with the following keywords: Hispanic/Latinx, alcohol use disorder, interventions, and treatment barriers. Preliminary results indicate that many people in the Hispanic population face more attitudinal barriers than logistical ones. Additionally, results indicate that there is a lack of Hispanic representation in psychological research, thus, making it difficult for evidence-based intervention to be useful for these populations. Finally, results indicated potential adaptations to existing evidence-based therapies to make them more effective for Hispanic populations. Through the findings from the literature review, we found it necessary to address the risk factors and disparities the Hispanic/Latinx population faces and highlight the urgent need for more culturally adapted interventions and treatment plans. We will discuss future research directions concerning the need for more data from the Hispanic/Latinx populations on group-specific treatment efficacy.

The Developmental Origins of Health and Disease (DOHaD) hypothesis evaluates how the prenatal environment affects health after birth. The placenta is a multi-faceted organ that sustains life during human development and is key to evaluating the DOHaD hypothesis. Glial Cells Missing Transcription Factor 1 (GCM1) is a transcription factor that plays a critical role in placental development. Our goal is to understand the downstream effects of GCM1 on various genes necessary for placental development by evaluating gene expression after GCM1 knockdown. The BeWo choriocarcinoma cell line is a model of placental syncytiotrophoblasts cells which undergo a cell fusion process called syncytialization in the placenta to form multinucleated cells that help exchange nutrients. Previously, we knocked down GCM1 in full-term primary placental cells that spontaneously syncytialize and assessed gene expression using RNA sequencing. We identified 10 differentially expressed genes. Based on those findings, we hypothesized that GCM1 plays a greater role during early pregnancy leading us to repeat the GCM1 knockdown in BeWo cells. BeWo cells were treated with 20µM, 50µM and 100µM forskolin (FSK) for 48hr to induce syncytialization which was confirmed via qPCR of syncytialization markers GCM1 and Syncytin-2 and through fluorescence microscopy. GCM1 expression increased 3.15, 1.3, and 1.2 fold respectively after treatment with 20µM, 50µM, and 100µM FSK, whereas Syncytin-2 increased 78.1 fold after 50µM FSK treatment. We then performed an siRNA knockdown of GCM1 in unsyncytialized BeWo cells with two concentrations of siRNA (25nM and 50nM) for 24hrs and observed a 70% and 80% reduction in GCM1 expression, respectively. Next steps include optimizing the siRNA procedure for syncytialized BeWo cells and comparing these results to our previously conducted experiment. Overall, this will improve understanding of how GCM1 coordinates gene expression in the placenta during pregnancy.

Tropospheric reactive halogens are a sink for ozone and influence the oxidizing capacity of the troposphere. Daily measurements of chloride enrichment, bromide enrichment, and iodine in sub- and super-micron aerosol were collected in June 2022 and January-February 2023 in Bermuda during the Bermuda boundary Layer Experiment on the Atmospheric Chemistry of Halogens (BLEACH) campaign. Gas-phase halogen radicals originate from heterogeneous reactions (chemical reactions involving more than one phase of matter) on the surface of halide-containing aerosol. These reactions lead to enrichment or depletion of aerosol halides (e.g., particle phase chloride, bromide, or iodide) relative to their ratios with sodium in sea water. We compare these measurements with simultaneous observations of ozone and gas-phase halogen concentrations in order to understand the relationship between aerosol and gas-phase halogens and their impact on tropospheric ozone abundance. Observations from these campaigns will aid in improving atmospheric model outputs and environmental policy. I extracted the ions from more than 60 quartz air-filter samples and aided in method development with Ion Chromatography (IC). Inductively Coupled Plasma Mass Spectrometry (ICP-MS) was primarily used for iodine measurements. Data analysis and lab work is still ongoing, therefore only preliminary observations are available. We’ve observed that sodium, iodine, chloride, and bromide agree well with previous observations at Tudor Hill (Arimoto et al., 1995; Sander et al., 2013). Higher depletions of chlorine excess and bromine excess and higher iodine and non-sea salt sulfate concentrations are observed during the first half of the summer campaign.

Pseudomonas aeruginosa is a major cause of opportunistic infections in immunocompromised people. P. aeruginosa uses a cell-cell signaling mechanism called quorum sensing (QS) to regulate virulence functions and cooperative behaviors. QS in P. aeruginosa is regulated by two transcription factors, LasR and RhlR. These proteins control the production of extracellular proteases, “public goods” that benefit the entire population. These public goods create an incentive for individuals to cheat by availing themselves of the proteases without incurring their production cost. In fact, when P. aeruginosa is grown in media that requires QS for growth, cheaters emerge in the population and invariably carry mutations in lasR. We were intrigued by the clinical isolate E94, in which we observed the rapid emergence of cheating. E94 contains an inactive LasR via a transposon insertion. Transposons are DNA segments that move between genomic locations. E94 contains dozens of transposable elements. We hypothesized that transposon movement facilitates the adaptability of the E94 genome. I evolved cheaters from wild-type E94 in casein media, which requires QS for growth. I identified cheaters using a phenotypic assay. I then grew cheaters in non-selective media and identified revertant, protease-producing colonies. I used PCR analysis of the cheaters and their protease-producing progeny to determine if the transposon remains inside the lasR gene. I found no transposon movement from lasR upon cheater reversion to a protease-producing phenotype. We also determined that cheaters display no rhlR activity. We then hypothesized that cheating in E94 occurs by disruption of RhlR QS. We did not find mutations in rhlR itself and are performing whole-genome sequencing to identify other genetic targets. Understanding the mechanism of cheating and reversion in E94 gives us insight into the evolution of cooperation and conflict in populations and, potentially, a non-antibiotic approach to controlling bacterial populations a variety of settings.

Identifying risk factors for alcohol misuse among young adults is a critical public health priority given high rates of heavy drinking and alcohol-related consequences observed in this population. The field of behavioral economics has provided a set of quantifiable metrics that measure individuals’ demand for alcohol, which are important predictors of alcohol use, consequences, and response to treatment. Previous literature has also found that one’s self-reported drinking motives (e.g., drinking to cope with negative affect, to conform to peers, etc.) have important associations with drinking outcomes. Despite this literature, little is known regarding how one’s drinking motives relate to one’s demand. The study aims to investigate how different drinking motives may be differentially related to alcohol demand and whether birth sex moderates these relationships. The current study recruited 220 young adults (18-25 year-olds) from Washington state who report drinking at least twice a week and at least one recent heavy drinking episode (4+/5+ drinks for females/males). Participants completed online assessments that included the alcohol purchase task, which asked how many drinks they would hypothetically purchase and consume at various prices ranging from free to $20. Participants were also asked to report their birth sex and drinking motives (social, coping-anxiety, coping-depression, enhancement, conformity). I will conduct regression analyses to test for associations between drinking motives and alcohol demand, and to examine whether these associations are moderated by sex while controlling for age and discretionary spending. I hypothesize (1) stronger positive associations between coping motives and demand relative to other drinking motives, and (2) this relationship to be stronger for males. Results will improve our understanding of the relationship between drinking motives and demand between sexes and inform interventions focused on reducing alcohol misuse through alternate coping strategies or reducing demand.

The Three Sisters Volcanic Complex is located in Lane County, Oregon, and South Sister is considered an active volcano. The USGS observed gradual deformation and uplift around South Sister during 1996-1997. A previous satellite interferometry study of South Sister found that volcanic activity was ongoing during 2020-2021. The results showed that the input rate of magma into the volcano edifice decreased during 2004-2010. Seismic velocity is sensitive to the pressurization state of the system. We can correlate relative seismic velocity with GPS observations to monitor the dynamics of the subsurface of the volcano. The SeisMIC Model is a Python package that provides functionality to apply concepts of seismic interferometry to elastic wave data, reconstructing continuous Green's functions. The expected findings are the relationship between the inflation of the volcano edifice and the seismic velocity change, which could also reveal the relationship between velocity change and deformation. Seismic velocity change is not dependent on the occurrence and location of seismicity, due to its continuous nature. This study could provide a better understanding of the mechanisms causing seismic velocity changes at South Sister.

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.

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. 

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.

Rensch’s rule suggests that sexual dimorphism increases as body size increases in species where males are larger than females. One hypothesis explaining this pattern is that through sexual selection, male-male competition for food, mating partners, and territory increases with body size. Here, we examine whether mandibular sexual dimorphism follows Rensch’s rule in the feliforms, a clade consisting of Nandiniidae (African palm civets), Felidae, Viverridae (civets and genets), Hyaenidae (hyenas), and Herpestidae (mongooses and meerkats). Although previous work found that few carnivoran families exhibit Rensch’s rule trends for their body size, whether a more consistent signal can be found in a trophic morphology such as the mandible has yet to be investigated. To test the hypothesis that carnivoran mandibles follow Rensch’s rule, we 3D scanned 349 mandibles across 73 species from museum collections and performed geometric morphometrics to quantify shape and size differences between male and female mandibles. We then used ANOVAs to test for mandibular dimorphism in each species, and linear regressions to test for Rensch’s rule. Preliminary analyses have revealed that viverrids, herpestids, and felids all do not follow Rensch’s rule, and that the degree of mandibular sexual dimorphism varies among families. We predict that mandibular sexual dimorphism will be highest in feliform clades with a high degree of dietary specialization because the specialized diet of carnivorous species may lead to greater competition between males and females for food. However, we predict that we will find little support for Rensch’s rule, as mandibular dimorphism may vary more with social system or diet than with body size. Overall, our research will add to the growing body of research on Rensch's rule and help elucidate the effects of niche divergence and sexual selection on the evolution of sexual dimorphism in mammals.

Autism Spectrum Disorder (ASD), a neurodevelopmental disorder (NDD), has been increasingly associated with disruption of ion channel function. The symptoms and etiology of ASD are complex and associated with dysregulation of many brain regions. Recent research suggests that individuals with ASD have disrupted activity in the mesostriatal network, which is well-studied for its contribution to social behavior and social reward. Another developing area in the etiology of ASD are ion channel mutations. Specifically, the Kv7 ion channel family, encoded by the genes KCNQ1-5, have become increasingly implicated with NDDs such as ASD. Though broadly expressed throughout the nervous system, these channels are also expressed in the Ventral Tegmental Area (VTA), a region within the mesostriatal pathway that plays a key role in social behavior and social reward. Here we study the impact of a KCNQ3 mutation identified in multiple ASD patients, KCNQ3-R230C. To do this, we used transgenic mice and viral strategies to drive the expression of human wildtype (hKv7.3/WT) or mutant (hKv7.3/R2C) KCNQ3 in the VTA. I helped to conduct a three-chamber social interaction task wherein these transgenic mice could elect to interact with either a novel mouse or a familiar mouse, and I helped analyze the data therefrom. We observed a loss of social novelty preference in the three-chamber social interaction task in mice expressing hKv7.3/R2C but not in controls expressing hKv7.3/WT. This research contributes to our understanding of the role of ion channel disruptions in the VTA in the context of social behavior and ASD.

The protozoan parasite Giardia lamblia infects hosts via the ingestion of cyst-contaminated water. We recently identified EncystR, a 7-trans membrane protein at the cell surface that acts as a negative regulator of encystation and responds to encystation cues by internalizing. By following the localization of EncystR through an encystation timecourse we discovered a novel compartment of unknown function. The Giardia endocytic pathway was only believed to include hybrid endosome/lysosome compartments statically positioned beneath the plasma membrane. We suspect this newly identified compartment may be a lysosome-like compartment. Using EncystR as a marker for this compartment we found that the compartment is highly acidified based on the florescent reporter pHluoren2. Canonically endomembrane compartments are marked by specific phosphatidylinositol phosphates (PIP). Relevant to endomembrane compartments, PI(3)P marks endosomes and PI(3,5)P2 marks multi-vesicular bodies and lysosomes. To test if this newly identified compartment is evolutionarily related to lysosomes, we will generate reporters for these phosphoinositides. Namely, we utilized the FYVE protein’s PIP binding domain as a sensor for PI(3)P which is located on endocytic membranes, the pH domain of PLC delta as a sensor for PI(4,5)P2 or PIP2 which is necessary for endocytosis and membrane-based cytoskeletal protein regulation, and ML1N for PI(3,5)P2 which is localized to lysosomes. Additionally, a mutant variant of the ML1N protein which is incapable of binding to PIPs is utilized as a negative control. These protein sensors were fused to the fluorescent protein mNeonGreen and imaged via fluorescent microscopy. While the experiment is currently in progress, we hypothesize that the localization of PIPs to the novel compartment will likely feature PI(3,5)P2 due to the previously found acidic nature of the compartment, implying a lysosome-like functionality. This possibly novel or conserved compartment could give insight into the evolution of eukaryotic cellular organisms and could potentially offer treatment routes for Giardia.

Organometallic porous materials can be utilized as highly accurate, effective, and low-energy agents in gas separation. Metal centers bind selectively to gas molecules to fill the pores in the material. This project tests the ability of chromium metal-ligand clusters that are coordinated to one another through hydrogen-bonding networks — as opposed to traditional organic linkages — to create a long-range, high-density, highly selective, porous material. Multiple ditopic ligands have been synthesized using standard organic synthetic procedures, and their structure analyzed with 1H NMR. These ligands were reacted directly with chromium metal compounds, chromium (III) chloride hexahydrate and chromous acetate, to create metal-organic complexes. Analysis through UV-Visible and Infrared spectroscopy indicated successful synthesis of the desired chromium complexes. Preliminary results indicate that the use of bidentate carboxylate ligands with nitrogen-rich substituents is the most effective way to generate a stable metal cluster with a strong hydrogen-bonding ability to ensure long-range rigidity. A ligand synthesized from dicyandiamide and 4-cyano benzoic acid has proven to form stable chromium clusters in both inert and atmospheric conditions. Current research is focused on forming long-range hydrogen-bonding networks with the aforementioned clusters to create a porous material. When this material is synthesized, the metal sites remain bound to one solvent molecule, which is then removed through vacuum to open a highly selective binding site. It is expected that the low oxidation state of the metal center will lend itself to be readily oxidized by gas molecules such as O2; but, critically, will not react with reducing agents such as N2. This highly selective nature of the binding site promises successful use of the material to replace thermal gas separation processes and reduce energy consumption nationwide.

In comparison to the abundance of research focusing on early Paleocene mammalian recovery from the K-Pg mass extinction, the mid-Paleocene (63–58 Ma) is an understudied period of mammalian evolution, particularly at the Mehling Site near Ekalaka, Montana. Previous work suggests this site dates to the mid-Paleocene, but its absolute age is not well established due to limited ash beds for radiometric dating. An isolated mammalian molar tooth specimen from the Mehling Site had been tentatively identified as Microsyopinae, a subfamily of an extinct clade of stem primates called Microsyopidae. However, the first appearance of Microsyopidae in the fossil record is during the late Paleocene (58–55 Ma). The purpose of this study is to investigate the incongruity between the taxonomic identification of this specimen and the age of the locality it was found in. I conducted a comparative analysis of the molar tooth specimen using fossil specimens, casts, and digital 3D models of the dentition of microsyopid mammals and their relatives in order to identify the specimen down to the finest taxonomic level possible. My preliminary results show that this specimen shares some features with Navajovius and Arctodontomys, two of the earliest possible genera of the Microsyopidae. The findings of this study will enhance our understanding of the origin of Microsyopidae and of this stage of mammalian evolution during the mid-Paleocene. If the specimen is confirmed to belong to the Microsyopidae and the geological age of the site is correct, then this fossil would push back the earliest occurrence of Microsyopidae in the fossil record to the mid-Paleocene, extending the temporal range of this clade by several million years. Ultimately, this knowledge informs our understanding of the origin and evolutionary history of stem primates.

Giardia Lamblia is an intestinal parasite known for causing the diarrheal disease giardiasis in host organisms. It commonly infects humans and companion animals such as cats and dogs. Giardia’s life cycle is defined by its infectious cyst stage and proliferative trophozoite stage. GlRac is a small Rho-family GTPase which we recently determined to play a role in regulating encystation in Giardia, the process of transition from a trophozoite to a cyst. Guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs) are key regulatory proteins of GTPase activity. The GEFs and GAPs that regulate GlRac activity are currently unknown, but four candidates for GAPs and three candidates for GEFs have been identified. We are testing these GAP and GEF candidates in Giardia with a two-phase approach. First, we are using the protein-protein interaction reporter NanoBit to determine if the candidate GAPs and GEFs interact with GlRac. We are verifying results for NanoBit assays, a split NanoLuciferase reporter that indicates protein-protein interaction. Nanobit can reveal interaction but not the localization of the interaction, so we are performing co-localization with deconvolution microscopy. Candidate GAP and GEF proteins are being visualized using a mNeonGreen fluorescent tag while GlRac is being followed using the halogenase (HALO) tag labeled with Janeliafluor 646. The microscope assays allow us to determine if and where GlRac co-localizes with candidate proteins. Subsequently we will test the role of the identified GAP and GEF proteins in encystation through transcriptional repression using CRISPRi and translational repression using morpholino-modified antisense oligonucleotides (MOs.) If the candidate proteins are truly GAPs and GEFs, the knockdown cells should not progress through encystation as normal. GAPs and GEFs are potential drug targets for treatment of Giardiasis, as well as important in understanding the process of encystation in Giardia.

Non-Human Primates (NHPs) have gained importance in neural engineering preclinical studies as their brains are relevant models to investigate and better understand neural function. The Yazdan lab uses optogenetics to control neuronal activity in order to develop stimulation-based therapies for neurological disorders such as stroke. These experiments require the implantation of various devices such as headposts, cranial chambers, electrode arrays, and optical windows. The use of head posts and cranial chambers requires customization to the curvature of the skull prior to implantation in order to prevent gaps that could introduce complications, including infection or decreased stability. Using an in-house method of NHP neurosurgery preparation that processes MRI data, we can develop 3D brain and skull models. This technique has allowed for chambers to be customized and implanted chronically in two NHPs. My project builds off of this implementation by creating custom chambers for future implantation surgeries and designing custom-fit headposts, which had never been done before. In order to design these components, I extracted the skull and brain using custom Matlab code which allowed for the craniotomy location to be determined and provided a footprint for the chamber and headpost implants. I then imported the skull extraction into a design software where the chambers and headposts could be built off of to ensure a tight fit to the skull. With the components designed, I will 3D print the brain, skull, chamber, and headpost to be assembled together. This platform will simulate the surgical and experimental setup, which provides a template for various experimental components to be modified and tested. It will provide a simple and affordable solution for neurosurgical planning, reducing in-surgery and in-experiment complications. This model's versatility, ease of use and low cost allow for further expansion to other labs and to a wider scope of surgeries.

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.

Myotonic dystrophy type 1 (DM1) is a genetic disease that causes many serious health conditions in a variety of tissues including skeletal muscle stiffening, weakness, and degeneration. DM1 is caused by a CTG repeat expansion mutation in the myotonic dystrophy protein kinase gene, DMPK. Expression of the mutated DMPK allele binds with the splicing regulator muscle-blind-like 1 (MBNL1), causing DM1 by sequestering and limiting its critical role in splicing mRNA. A main focus of the Chamberlain lab is the development of gene therapy to treat DM1, including increasing protein expression of MBNL1 to reduce the disease effects in muscle. Overexpression of MBNL1 in skeletal muscle could be beneficial but may have negative effects on cardiac tissue. The lab discovered that high, unregulated MBNL1 expression from gene therapy vectors in cardiac tissue can result in cardiac damage. In my study, I will focus on cardiac function when testing adeno-associated viral vector (AAV)-mediated systemic delivery of the MBNL1 gene to increase MBNL1 protein expression in muscle. Using analytical methods such as echocardiography and tissue histological techniques, I will determine whether it is possible to prevent MBNL1 protein production and its damaging effects in the heart while still expressing MBNL1 protein in skeletal muscle for therapeutic disease benefits.

What type of future manufacturing system would satisfy both the economic and environmental needs of the planet? A circular economy could be the answer. A circular economy operates much like a solitary spaceship that must regenerate water, organic nutrients, and technical materials in a constant process to sustain life. We are privileged to live on a much larger, regenerative spaceship, however, running out of resources is still a risk. Opposed to the current linear economy where end-of-life products such as toasters will be disposed of without extraction of the metals, ceramics, and plastic parts, a circular economy would realize the economic and environmental potential of keeping the parts of toasters in circulation. The purpose of this research is to discern the possible advantages and disadvantages of a widely adopted circular economy through critically evaluating peer-reviewed sources on a multitude of circular industrial sectors and applications. Much of the current research focuses on emerging technologies such as the hydrometallurgy process for lithium-ion batteries. These emerging technologies require heavy investment to become activated before the returns may be realized. It is anticipated that further research will describe natural plastic alternatives such as vegetable cellulose, but there will likely be a gap in research covering the amount of arable land required to grow crops to meet demand. Predictions detail larger corporations likely have more capability for designing circular products and a probable lack of small businesses with circular potential. Additionally, public support would be lacking due to the esoteric nature of the system and a lack of real-world circular business models currently. That is why the motivation behind this literature review is to spotlight the circular economies that are already thriving.

Prosocial behavior is important to many species and its disruption is a hallmark symptom of many diseases and disorders including autism, schizophrenia, and depression. The neurotransmitter dopamine modulates neuronal activity in the nucleus accumbens (NAc) and plays a critical role in the regulation of prosocial behavior. While the role of dopamine (DA) is well studied in the context of social behavior, little is known about neuronal activity in the NAc during social behavior. Here we use transgenic mice, viral delivery of genetically encoded fluorescent calcium sensors, and a miniaturized microscope to measure NAc neuronal activity during a series of social behavior assays. We used the 3-chamber assay to investigate NAc encoding of social novelty preference, a 5 minute on-off free social interaction assay, and an operant social task in which mice press a lever to gain access to another mouse. Preliminary data suggests that the technique is feasible to detect neuronal activity in the NAc during social behavior, and that there is no detectable encoding of social novelty preference in the 3-chamber assay. Findings from this study will improve our understanding of how prosocial behavior is encoded and may lead to the development of treatments for diseases and disorders that result in a loss of prosocial behavior.

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.

Additive manufacturing, also referred to as 3D printing, enables the fabrication of objects of any design based on a computer-aided design model. 3D printed structures comprising biodegradable protein-polymer networks have potential use for biomedical applications. The Nelson lab has developed a resin for vat photopolymerization 3D printing based on the protein bovine serum albumin (BSA). In my work, I investigated the response of these materials under different pH environments in order to simulate physiological conditions and gain an understanding of how these hydrogels respond to these different environments. I chose the protein-polymer network MABSA-PEGDA (Methacrylated Bovine Serum Albumin-Poly(ethylene glycol) diacrylate), a functionalized version of BSA that protects the globular structure of the protein. When altering the pH of given MABSA-PEGDA resins they retain their low viscosity, based on rheological measurements, and thus they retain printability. When printed, MABSA-PEGDA hydrogels have altered swelling and water holding capacities in pH 2 conditions as well as altered compressive moduli depending on the pH used to make the resin. Additionally, we performed CD spectroscopy and found that the alpha helicity of the protein was maintained, meaning secondary structure is not altered. The results suggested that there must be a change in the tertiary structure of the protein which induced changes in the protein-polymer matrix and altered the mechanical properties of the hydrogel. The next set of studies will include protein analysis techniques to understand the structure of BSA within the hydrogel constructs. The cumulative results of these studies will enable the use of these BSA-based materials for applications such as oral drug delivery that requires survival in harsh gastrointestinal environments.

The Hell Creek Formation (HCF) of northeastern Montana is known globally for preserving some of the last non-avian dinosaurs, including Tyrannosaurus rex. In addition to T. rex, several other species of theropod dinosaur lived in the HCF. These theropods differ morphologically from each other in a variety of ways; however, given that many of these taxa are represented primarily from dental remains (i.e., teeth), the best diagnostic feature available is dental morphology, with the exception of toothless theropods such as Anzu. In this project, I am utilizing imaging processing software in order to collect diagnostic linear measurements of key aspects of tooth morphology from tooth-bearing theropods of the HCF and plot this data against time to ascertain if changes occurred in the dentition of individual taxa through the approximately 2-million-year time span recorded in the formation, utilizing specimens from the upper, middle, and lower portions of the HCF. My current dataset of 20 teeth is insufficient for statistical analysis, but already possesses great potential for future use tracking the various observed dental morphologies. The amount and precision of this morphometric data will only increase as I continue to grow the dataset through the imaging and measurement of at least 40 additional theropod specimens. Once complete, the morphological data I produce will assist in testing my current taxonomic identifications through the establishment of ranges of individual variation. Additionally, quantifying observed morphological variation relative to time can provide insight into the continuing evolution of HCF theropods due either to speciation or extinction. Through these measurements, I hope to gain clarity on both the community composition and dental evolution in the HCF theropods, which is vital to understanding the evolutionary history of those dinosaurs that are closest to birds and their ecological standing as a group immediately prior to the Cretaceous/Paleogene mass extinction.

This paper describes the expression of a non receptor tyrosine kinase, cymric (Uro-1), a HTK16-like (HydraTyrosineKinase-16) gene in Molgula oculata, an ascidian species with a tadpole larva and proposes that it plays a role in muscle development during the development of the tadpole phase. Cymric is also a member of the SHARK (Src-homology ankyrin-repeat containing tyrosine kinase) family of non-receptor TKs, a group of similar tyrosine kinases that can be found across many invertebrate species, but whose function is not yet known. The role of cymric in the development of the tail in tadpole ascidians was suspected after a subtractive hybridization showed cymric is expressed in M. oculata, a species with a tail and not in Molgula occulta a closely related ascidian whose tadpole is missing a tail. In Situ hybridization shows that in M. oculata embryos, cymric localizes to primordial muscle cells. Through transcriptome and genome analysis using both ANISEED and NCIB we show that the tyrosine kinase of the cymric gene in the M.occulta is disrupted by a large retrotransposon insertion. This indicates that, although the mechanism is still not known, cymric is involved in determination of muscle cells. A better understanding of the role cymric plays in development in ascidian species could provide insight into its importance in the many other invertebrate species which also express SHARK proteins.

Cryptocurrency is a worldwide payment system that has the potential to become a universal exchange since it was first presented as a solution to address the limits of centralized banking systems, including inflation and clunky currency conversions. However, high price volatility, cybersecurity threats, and environmental repercussions are some hazards associated with cryptocurrency. Since the start of the 2008 banking crisis, it has long been a contentious topic in the global economy, especially considering the lack of proper regulatory authorities. Current studies on the topic suggest two extremes, with some claiming that it is just a matter of time before cryptocurrencies take over the financial system as opposed to others claiming that they will eventually die out. In 2021, El Salvador became the first country to make Bitcoin legal tender, offering its citizens fee-free transactions and facilitating fast cross-border payments. In contrast, the Chinese government has banned the trade and mining of cryptocurrencies due to their energy consumption and the use of virtual currencies for fraud and money laundering. Major scandals involving this currency consistently occur, causing widespread mistrust in cryptocurrencies and people to question their long-term viability. My literature review assesses the future of cryptocurrencies from the perspectives of economics and political policy, underscoring the prospective advantages of adopting cryptocurrencies as legal tender, either as a replacement for or in addition to centralized currencies. Comparing cryptocurrency usage in different countries, I aim to cast light on the concept of an accessible currency and present a potentially superior alternative for weak currencies. I expect three issues to appear in my results, namely decentralization, security, and scalability. The concept of a universal currency indisputably has the ability to alter how international trade is conducted and alleviate wealth disparity because it would be accessible to everyone, everywhere.

The migratory songbird Gambel's White-Crowned Sparrow (Zonotrichia leucophrys gambelli) experiences drastic seasonal shifts in its song production and stereotypy, driven by changes in distinct song circuit nuclei, namely increased neurogenesis in the forebrain nucleus HVC and increased electrical excitability in nucleus RA. Manipulating the photoperiod and hormone levels of these sparrows in a laboratory setting results in changes very similar to the seasonally-induced behavioral and neurophysiological changes they experience in the wild. We are interested in reducing the number of birds necessary for our studies by developing a protocol to produce seasonal effects in vitro via organotypic slice culture. Organotypic slice cultures preserve the neural connections and functions involved in the seasonal changes we are interested in, so they can be more directly observed and manipulated. We maintained slices of neural tissue from white crowned sparrows, including HVC and RA, on a membrane that allowed for exchange with the media, a technique initially developed by Stoppini et al., in 1991. After the tissue was cultured, it was fixed and resectioned into thinner slices so it could be Nissl stained and imaged to test for the presence of healthy cells. Organotypic culture is an established technique for neural tissue from juvenile animals; we are attempting to use it on tissue from adult, wild caught, white crowned sparrows. There is currently no protocol for organotypic cultures of this tissue, and the nature of the tissue itself poses a challenge. Adult tissue is less plastic than the juvenile or neonatal tissue that is usually used with this technique, so it has more difficulty surviving the shift to culture. Once the protocol is developed, we plan to manipulate the hormonal environment to try to mimic changes that occur during their breeding season.

The dramatic increase in antibiotic-resistant Pseudomonas aeruginosa infections makes it necessary to find new approaches for treatment. P. aeruginosa employs a communication system called quorum sensing (QS) that uses density-dependent accumulation of small diffusible molecules to mediate the production of factors that benefit the entire bacterial community; creating a potential drug target. P. aeruginosa has two QS systems: las and rhl. A previous analysis of the laboratory strain PAO1 revealed that mutations in the las system result in individuals that act as social cheaters that reap the benefits of communally produced goods without expending energy on their production. lasR mutants have a fitness advantage when cultured in a medium requiring the activity of the community goods for survival. I set out to better understand the rhl QS system. I was interested in determining if ΔrhlR mutants act as social cheaters in co-culture with rhlR-competent strains. To make that determination, I screened 12 clinical isolates from the Early Pseudomonas Infection Control (EPIC) study for the ability of their isogenic ΔrhlR mutants to grow in QS and non-QS selective media and their ability to persist in coculture with the parent strain. I also competed these strains against isogenic ΔrhlR mutants by growing them in coculture and using flow cytometry to determine the relative final frequencies of the parent strain and ΔrhlR mutants. Finally, I aimed to determine if rhlR mutants arise spontaneously from the parent strains in a long-term growth experiment by sequencing and functional analysis of the mutants. My preliminary work demonstrates that a small subset of the ΔrhlR mutants dramatically increase relative to concentrations of EPIC strains in coculture and mutations in rhlR do arise in vitro; however, their exact functional effects are still to be determined.  Understanding ΔrhlR cheater dynamics may provide therapeutic targets for antibiotic-resistant P. aeruginosa infections.

Thin film photovoltaics (PV) present many advantages which enable their potential replacement of traditional silicon PV, but they are not yet scalable. Current research aims to enable their large-scale production to meet growing energy demands. Alongside scalable manufacturing methods and competitive device lifetimes, the transition from small-area cells to large-area modules poses a scalability barrier. I explore a novel fabrication method accelerating this transition. In fabricating thin film PV modules, large-area films are divided into multiple small-area cells by removing, or “scribing,” thin films between adjacent cells for later electrical connection. Existing scribing methods include laser and mechanical scribing, but both have drawbacks which impede device performance and scalability. My research professor and I invented a third scribing method to address these issues. Lines of solvent are printed onto a thin film device to dissolve target thin films underneath the solvent. As the solution evaporates, the “coffee-stain effect” redistributes the dissolved material to the fluid perimeter, exposing linear areas of underlying thin films. This effect is characteristic of drying liquids containing dispersed solids: liquid from the interior flows to restore liquid evaporating at the edge, carrying nearly all dispersed material to the fluid perimeter. This effect enables thin film scribing without forming performance-inhibiting film defects or toxic residues. The technology also requires low capital expenditure and is compatible with scalable roll-to-roll manufacturing. In this work, I demonstrate the invention’s feasibility and competitiveness by producing scribes comparable with existing technologies using electrohydrodynamic inkjet (EHDIJ) printing of solvent on perovskite solar cells. I authored a report, filed a provisional patent application, and now collaborate with another university to advance the technology. This invention poses a scalable solution to the transition from small-area cells to large-area modules in the thin film PV space, breaking a pivotal barrier to meeting growing energy demands.

As interest in diverse voices in German literature grows, the long-overlooked Swiss author Annemarie Schwarzenbach (1908-1942) has begun to attract greater scholarly attention. The purpose of this research is to analyze central themes of Schwarzenbach’s 1929 novella To See a Woman and contextualize this work within Schwarzenbach’s biography and the social history of the German-speaking world. The presentation consists of three parts: First, I draw on academic, journalistic, and primary sources to describe Schwarzenbach’s life story and her unique positionality in interwar Swiss society. Second, I discuss the origin, disappearance, and rediscovery of her 1929 novella To See a Woman, its eventual publication in 2008, and its significance in Swiss literary history. Third, I use methods of close reading and literary analysis to examine the role of the landscape surrounding the Alpine resort town of St. Moritz in the novella. The textual evidence gathered through this methodology indicates that the landscape is essential to the narrator’s experience of desire, functioning as an expression of the individual freedom afforded by entering spaces removed from everyday life. By analyzing Annemarie Schwarzenbach’s life in connection with her novella To See a Woman, this research provides insight into diverse perspectives on interwar Swiss society and their literary representation, offering a basis for further academic inquiry into Schwarzenbach’s work.

On the surface, career warrior Larry Alan Thorne seems a likely candidate to be an anti-hero. He fought in three unpopular wars, voluntarily joined the Waffen-SS twice, and was convicted of treason in his homeland, Finland. A carjacker and three-time prison escapee, Thorne, né Lauri Allan Törni, has become a celebrated folk hero and declared a legend by many. He was awarded Finland’s highest military honor, an Act of Congress was passed to grant him American citizenship, John Wayne portrayed a fictionalized version of him in the iconic 1968 film The Green Berets, and he is the only known Waffen-SS soldier buried in Arlington National Cemetery. My research explores the question, “How is public memory of Larry Thorne a case study of historical revision and rehabilitation?” My presentation analyzes numerous primary and secondary sources, including depictions of Thorne in movies, music and social media, as well as personal correspondence with experts including Michael Cleverley, author of the leading English language biography of Thorne, and Professor Oula Silvennoinen of the University of Helsinki, who co-wrote a Thorne biography in Finnish. This research project reveals the significance and nature of a decades-long historical revisionist campaign with regard to a figure with a dubious past, and how those efforts to shape the public story of Thorne involve, at times, potentially misleading narratives. The current personality cult of Larry Thorne is a case study of historical revision in public memory, and his story is still being written and rewritten.

Titus Livius, better known as Livy, was a Roman historian writing at the beginnings of the Augustan age and the fall of the Roman Republic. Livy wrote his magnum opus, Ab Urbe Condita, as a moralizing history in response to the moral degradation and civil strife he experienced during the collapse of the Republic. The first seven chapters of Book I outline Roman prehistory before Romulus’s reign and contain several imitations and allusions to archaic poetry and Classical historiography. Livy himself believes that the subject of his writing would have been better suited for poetry than prose. This project aims to provide quantitative evidence for Livy's claim by quantifying and analyzing instances of literary devices of earlier poetry such as alliteration and etymologizing to determine whether a poetic influence is implicit in Livy’s prehistory of Rome. Preliminary results based on the quantity of alliteration present in Livy's writings suggest some influence by earlier poetic sources. However, it is difficult to substantiate any conclusions on statistical grounds due to fragmentary literatures. Instead, this project also proposes further hypotheses about source accessibility and poetic inclination that may explain the quantitative phenomena.

The National Institute of Health reports that 11 million family members and other unpaid caregivers provide an estimated 16 billion hours of care to people with Alzheimer's or related dementia each year. This vulnerable population struggles to manage their caregiving responsibilities and daily life, yet these unsung heroes persevere in providing care day-in day-out. The COVID-19 pandemic adds another hurdle for caregivers of people with dementia as they give care and attempt to keep their loved ones safe from illness. To examine the impact of the COVID-19 pandemic on informal caregivers of people with dementia in the United States, I conducted a systematic literature review that looks at studies published since the onset of the pandemic. This examination reveals scant attention paid to the experiences of these informal caregivers. These findings are futher bolstered by my interviews with professional social workers working in direct practice with caregivers and people with dementia. The findings confirm the deleterious impact of increased isolation and reduced support options for these caregivers and the subsequent diminished quality of life fo the people with dementia in their care. Further research is needed to explore the plight of this group and to develop and assess the efficacy of potential interventions proposed by the social workders interviewed for this study. 

The COVID-19 pandemic has changed our society in a rapid, lasting way. In March 2020, a national state of emergency was declared, and restrictions began to be put in place to stop the spread of the virus such as stay-at-home orders, social distancing guidelines, and mask mandates. These restrictions caused a whole host of serious changes to daily life and culture bringing an onslaught of mass death; school and business closures; financial stress/instability; cancellation of important events and milestones; and more. These changes could have potentially put adolescents in a particularly unique, unprecedented, and vulnerable state as they are in a crucial developmental period marked with a newfound drive for independence and various hormonal, cognitive, and behavioral changes that was then disrupted in multiple intersecting ways. For youth in the Black community, who has been affected disproportionately by all aspects of the pandemic, these changes could represent an even greater risk factor for poor mental or socio-emotional health. I conducted a systematic literature review in order to identify and analyze how different aspects of life during the COVID-19 pandemic (mentioned above) have affected Black adolescent mental and socio-emotional health in the U.S. through development of mental disorders, changes in socialization patterns/desires, general psychological affect, etc. This research fills many gaps in the literature, as currently it mainly focuses on the physical disease of COVID-19 with majority non-Latino white participants. This research has implications in demonstrating the intrinsic role of the social determinants of health in the lives of Black Americans; proving the importance of schools as safe spaces and resource centers for adolescents; building our knowledge and evidence base to create interventions to support Black youth; and advancing knowledge on how crisis situations affect adolescents- specifically COVID-19, which has effectively changed our society for the foreseeable future.

The peculiar behavior of vowel hiatus resolution in Biloxi provides a useful test case with which to consider the relative merits of two prominent theories of morphologically conditioned phonology (MCP): Cophonology (Inkelas and Zoll, 2007) and Constraint Indexation (Pater, 2009). Biloxi, an extinct or critically endangered (sources vary) language of the Siouan language family, has received little to no phonological study since the 1974 grammar this project is based on (Einaudi, 1974). Vowel-vowel sequences are generally avoided in Biloxi. When vowel-vowel sequences are formed by affixing, this sequence is repaired by deleting the first vowel, as in (1) /ohi dani-axehe/ → [ohi danaxehe] ‘three sitting on ten’ (=13). When such a sequence is formed by the dative prefix /ki-/ and a vowel-initial verb root, glide epenthesis occurs instead, as in (2) /Ø- ki- ε -tu/ → [kijetu] ‘they said to him’. Yet another exception is observed when /ki-/ specifically precedes the verb root /õ/ ‘to make, do’, resulting in glide fortition and an additional /k/ in the surface form, as in (3) /Ø- ki- õ -tu/ → [kikõtu] ‘they made for him’. This analysis lends support to whichever model of MCP better accounts for the complex vowel hiatus pattern of Biloxi. As an understudied language, a framework’s ability to fit Biloxi, in addition to previously considered languages, gives that model greater explanatory power. Avenues for future research include the consideration of a learnability model for Cophonology as compared to that proposed by Pater (2009) for Constraint Indexation. An updated grammar of Biloxi with more detailed phonological analysis would also extend the scope of modern studies of the language. This work brings new attention to the Biloxi language, and contributes to the ongoing debates over morphologically conditioned phonological processes.

Schools across the country struggle with the issue of meal debt and lunch shaming practices used to discourage the accumulation of negative meal balances. These practices include dumping students’ trays in the trash upon non-payment, requiring students to work off their debt, or publicly shaming them. Although lunch shaming was banned in Washington State in 2018, the impacts of this policy shift have not been studied. High-poverty schools shifted to government-subsidized universal school meal programs (USMP) to address students’ food insecurity. Studies show USMP significantly increase the meal participation of students who were already enrolled in free lunch programs. While scholars speculate stigma might explain this phenomenon, it has not been studied directly. This study explores the role of stigma in school meal participation by studying two populations; students who are considered non-poor with meal debt and students who are enrolled in free and reduced priced meal programs. This study considers the role of stigma as a barrier to school meal participation by studying meal debt and students at the eligibility margins in free lunch programs. This study addresses existing gaps in the literature through a combination of in-depth interviews and observations of schools ineligible for government-subsidized USMP. In-depth interviews with school administrators expand understandings of school-level cultures, mealtime procedures, and experiences with meal debt. Observations at a single school over a 2-month period reveal how students experience mealtime, how kitchen workers execute meal debt policies, and the dynamics between students, their peers, and authority figures in the lunchline. Findings show that stigma is reproduced in the lunch line and act as a barrier to student meal participation. 

Creative coding refers to a method of computer programming that prioritizes artistic expression. Remixing is the iterative behavior of altering an existing artifact. Frameworks such as p5.js support sketching with creative code. Given the focus on expressivity over functionality, code reuse in creative coding practice is distinct from other programming contexts. Additionally, remixing facilitates iteration on existing code, but we have yet understand how creative coders use remixing in practice. To understand creative coder remixing strategies, we studied the community of OpenProcessing, a site dedicated to sharing code-generated artworks. To begin, we conducted a network analysis to determine which datasets of original sketches (also referred to as the antecedent sketch) and their remixes to use in our study. Our visualization consisted of a social network graph in which the nodes represent individuals, and edges showing their relationships. We found that 30% of the 1.2 million sketches in our dataset were involved in remixing. For data analysis, we utilized a code-diff tool to showcase ways the antecedent sketch's code differs from the remix and categorize various types of remixing strategies. Over time, these categories became increasingly focused on changes made visible on our code-diff tool. We present on the diversity of ways that authors remix to curate projects, annotate process, explore variations, and transform existing sketches. Through remixing, artists have already begun to tailor, customize, and explore different ways to use their creative tools, in ways system developers may not have foreseen. We find that remixing also encourages exploratory programming and experiential learning. As creative code is increasingly used to support computational education, we can consider the implications of remixing for understanding and facilitating informal learning. At last, we reflect on the prevalence of these remix types and how future systems could support a multiplicity of remixing strategies for creative work.
 

Kaposi’s Sarcoma (KS) is among the most common tumors in central Africa and AIDS patients and Kaposi’s Sarcoma-associated herpesvirus (KSHV) is the etiologic agent of KS. While all herpesviruses are capable of both lytic and latent replication programs, KSHV is predominantly in the latent state in the main KS tumor cell,the spindle cell, a cell expressing markers of the endothelium. There is limited viral gene expression during latency so it is difficult to target the virus directly. Therefore, our approach is to target host cellular requirements for KSHV latent infection. Previously, the Lagunoff Lab performed a genome wide CRISPR-Cas9 screen targeting over 18,000 human genes to identify cellular genes essential only to cells latently infected with KSHV. CYP27A1, a gene that encodes a member of the cytochrome p450 family, was one of the top hits identified in the screen. It specifically encodes sterol 27-hydroxylase, which is an enzyme involved in the breakdown of cholesterol. I hypothesize that CYP27A1 is an essential gene for survival of KSHV latently infected cells, as there is evidence that cholesterol is antiviral and KSHV is known to regulate cholesterol. I have successfully cloned CRISPR guide RNAs targeting CYP27A1 into lentiviral vectors, transfected 293T cells with the vectors to make lentivirus, and transduced human tert-immortal endothelial (TIME) cells with the lentivirus to create CYP27A1 knockout cells. ICE analysis was used to confirm strong knockout of the CYP27A1 gene. Currently, we are infecting these cells with KSHV to determine if CYP27A1 is required during KSHV latent infection using cell survival and cell proliferation as readouts. I expect that knockout of CYP27A1 will result in cell death in endothelial cells latently infected with KSHV. By determining genes necessary for KSHV latency, we hope to identify potential therapeutic targets for KS tumors.

Joubert syndrome (JS) is a neurodevelopmental condition diagnosed by the appearance of the “molar tooth sign” on axial brain magnetic imaging (MRI). Patients display hypotonia, abnormal eye movements, and ataxia. Substantial progress has been made on identifying the genetic causes of JS, which typically displays recessive inheritance. Nonetheless, the cause cannot be identified in ~25% of our cohort of JS-affected families. The contribution of variants that impact RNA splicing remains unknown. Our goal is to evaluate the role of noncanonical splice variants in the pathogenesis of JS. Canonical splice variants impact RNA splicing by disrupting the splice site directly, whereas noncanonical splice variants may affect it through alternative mechanisms, which need to be validated by RNA analysis. We previously identified genetic causes in 520 of 679 families with JS. To identify additional causes, we used SpliceAI (SpliceAI score >0.5) to identify candidate variants that impact splicing. We extracted RNA from patient cell lines and converted it into complementary DNA (cDNA). Then we used polymerase chain reaction (PCR) to amplify the affected exons with two sets of primers flanking the relevant splice junction. We evaluated PCR product size and sequence using gel electrophoresis and Sanger sequencing. We found 74 families with ≥1 canonical splice variant. An additional 34 families have ≥1 candidate noncanonical splice variant. We confirmed the pathogenicity of two of the candidate noncanonical splice variants by demonstrating an abnormal splicing event in AHI1 and MKS1 in two patient samples. By extrapolation from our data in JS, noncanonical splice variants may contribute as much as 10% to the genetic causes of recessive conditions. A precise genetic diagnosis informs prognosis, avoids unnecessary work-up, guides monitoring for associated complications, and opens the door to gene-specific treatments.

Cannabis use has dramatically increased in response to legalization in the U.S., with total sales in the U.S. jumping 46% from 2019 to 2020. ᐃ9-tetrahydrocannabinol (THC) is the primary psychotomimetic compound in Cannabis and has been shown to modify memory and motivation, processes mediated by the prefrontal cortex (PFC) brain region. I sought to test the effects of THC on PFC activity during appetitive Pavlovian conditioning in mice- a behavior in which a subject learns to associate a non-rewarding stimuli to a reward. THC acts on the endocannabinoid (eCB) CB1 receptor (CB1R), a presynaptic signaling protein responsible for modulating neural activity throughout the brain, with robust expression in the PFC. To monitor neural activity during behavioral trials, we implanted optic fibers into the PFC and virally expressed biological sensors: GCaMP6f to track Calcium activity, and the novel GRABeCB2.0 to measure eCB activity. VGAT-Cre and VGLUT1-Cre animals were presented with a house light prior to a sucrose reward to observe the neuronal GABAergic and glutamatergic activity during the conditioning, respectively. After 5 days of conditioning, I administered vehicle or THC (i.p., 5 mg/kg) to observe behavioral and neural effects of THC. We observed neural activity that transferred from the sucrose reward to the house light cue suggesting these neurons encode for this learning. Endocannabinoid activity also transitioned from sucrose reward to the house light cue suggesting cannabinoid involvement in regulating this association. THC pre-treatment reduced licking and motivation for sucrose while modifying neural activity without eliminating it. This provided much needed insight into the formation of memory during learning and reward motivation under the effect of THC.

Active galactic nuclei (AGN) found at the center of galaxies are a compact region of space that produce significantly higher than normal luminosity. AGN are powered by the accretion of matter into a supermassive black hole and sometimes present winds called outflows. Whether outflows affect the evolution of their host galaxies is still a topic of research. Outflows with speeds of more than 10% the speed of light, called Extremely high-velocity outflows (EHVOs), have not been thoroughly explored, and due to their large energies, they might play a large role in star formation. In the 16th data release of the Sloan Digital Sky Survey, 98 new quasars with EHVOs were identified. With this new sample, I will present the results of my findings on the following questions: (1) What does the average EHVO quasar look like? (2) Do these extreme outflows vary more or less than other previously explored outflows? (3) Can we detect these EHVOs at higher speeds? To answer the first question, I will present a composite of the 16th data release EHVO cases found. To analyze if they vary more often or less than other EHVOs, I will present the results of a longitudinal variability study on the 51 cases that were observed on multiple occasions in the EHVO sample. For the last question, I will show the results of applying code our team has created to remove the Lya lines from our spectra, so the intrinsic ions (such as NV, Lya, OVI) will be easier to analyze at higher speeds.

My project studies Extremely High Velocity Outflows (EHVO) in Quasars. Quasars are particularly interesting due to the fact that they are one the most luminous cosmological objects that we have observed in the universe. They are systems at the centres of galaxies that host supermassive black holes--which have masses that range from millions to billions of solar masses--surrounded by an accretion disk of superheated plasma, gas, and dust. The phenomenon that we are studying are the EHVOs in quasars, which are gas outflows traveling at above 10% of the speed of light from the active central region. My project attempts to answer the question of whether quasars with EHVOs show distinct physical characteristics when compared to Broad Absorption Line Quasi-Stellar Objects (BALQSOs), which are quasars with outflows that show a broad absorption width but at lower outflow speeds, as well as compared to the general parent sample of quasars. We hypothesized that quasars with EHVOs show distinctive physical characteristics when compared to the other quasar categories. To study quasar physical characteristics to test our hypothesis, we used data from the Sloan Digital Sky Survey (SDSS) in the latest data release. Previously, our group has found the measurement values for all quasar samples to be overestimated. Thanks to data provided in Rankine+2020, we developed software and used the data to cross-correlate the values of physical parameters, such as bolometric luminosity (Lbol), Eddington ratio and black hole mass (Mbh). I will present the preliminary results of the analysis on EHVO quasar’s physical properties when compared to BALQSOs and the parent sample. These results suggest that quasars with EHVOs exhibit larger values of their Lbol and Eddington ratio when compared to the other two classes of quasars, while the Mbh parameter does not show significant differences.


 

Diaryliodonium salts have recently been shown to facilitate metal-free mechanoredox free radical polymerizations. Prior literature reports focus on the role of diaryliodoniums as photoinitiators; these salts have well established fragmentation mechanisms and kinetic profiles. However, their use in mechanochemistry has not been extensively investigated. Mechanochemistry is an emerging field of chemistry that uses force as a stimulus for chemical reactions. Compared to traditional stimuli such as light, heat, and electricity, mechanical force avoids the use of transitional metal additives and often has a lesser environmental impact. This report looks to explore functionalized (e.g., electron-rich versus electron-deficient) diaryliodoniums and to determine the impact of reactivity in a mechanoredox polymerization setting. Herein we synthesized a library of salts of diverse electronic structures and tested them within an established mechanoredox ball mill system. We report data on their initiation based on radical trapping as well as changes in polymers molecular weight. The hypothesis is that salts with functionalities that withdraw electron density such as alkyl halogens or cyano groups will initiate faster than salts with electron donating functionalities due to their lower reduction potential as demonstrated in literature. Exploration of these functionalized salts will provide kinetic insight and open new avenues of synthesizing commodity polymers. This is particularly applicable in 3D printing, where having control over the rate of initiation could be used to tune downstream physical properties.

We are researching adeno-associated viral (AAV) vector based gene therapy for the rare genetic muscle disorder GNE myopathy (GNEM). This disease manifests as progressive skeletal muscle atrophy leading to restricted ambulatory ability and loss of fine motor skills. GNEM is caused by defects in the GNE gene, negatively impacting the sialic acid biosynthesis pathway. The sialylation of muscle fibers does not occur without this pathway, causing a loss of muscle function due to sialic acid deficiency. AAV gene therapy can be used to alternatively express the GNE gene by directly targeting muscle or utilizing liver expression. Sialylated glycoproteins secreted by the liver can be taken up by muscle and the sialic acid recycled. Our lab plans to advance GNEM AAV gene therapy by combining liver- and muscle-specific promoters to reduce the dose of AAV required for sialylation of muscle fibers. We have cloned six tandem promoters and three control promoters that will be tested in human liver cells (HepG2) and murine myoblast cells (C2C12). The tandem promoters combine different regions of liver and muscle promoters. A double (firefly and renilla) luciferase mechanism is used to indicate promoter strength, where the amount of luminescence from firefly luciferase is measured. Our lab is currently recording the promoter strength and level of transfection in the cells. The ratio between these expressions indicate the overall strength of the promoter. We are also cloning these tandem promoters into AAV vectors with the intent of testing the vectors in mice. The aim of our research is to produce a promoter resulting in the expression of the GNE gene in both muscle and liver cells, increasing sialic acid production to aid patients affected by GNEM using a minimal dosage.

In response to acute genotoxic insult, cancer stem cells undergo quiescence, a state of temporary cell cycle arrest, to avoid apoptosis (programmed cell death) and later re-enter the cycle to generate daughter cells under suitable conditions. This event is also observed in the irradiated germline stem cells (GSCs) of female Drosophila melanogaster. Previous studies have shown that quiescence is regulated by various upstream components, including gene silencing by polycomb repressive complex 2 (PRC2) and activation of mitophagy, the selective degradation of damaged mitochondria. Activation of PRC2 is shown to be upstream of mitophagy in regulating quiescence. However, the PRC2 target genes that get silenced in this process remain largely unknown. In humans, a downstream target of PRC2 is microRNA-200 (miR-200), which can enhance mitochondrial elongation by downregulating mitochondrial fission factor (MFF). Here, we hypothesize that the miR-8 gene, the Drosophila ortholog of the human miR-200 family, is a downstream target of PRC2 and is required for stress-induced quiescence to take place. To investigate the role of miR-8 in governing quiescence following stress, we overexpress miR-8 in female Drosophila GSCs under UAS-GAL4 control and study the spectrosome and mitochondrial morphology of the immunostained GSCs. We predict that miR-8 overexpression will prevent mitophagy and entry into quiescence after irradiation. We anticipate that our findings will characterize the role of miR-8 and strengthen our understanding of mechanisms that govern the cell cycle and quiescence. This study is critical as our proposed mechanism of quiescence can be applied to other stem cell types, and may present new therapeutic strategies for cell cycle-related diseases.

The focus of our research is on digitizing linguistic material from two understudied and endangered Brazilian Amazonian languages, Panãra and Kawaiwete. Panãra (ISO code: kre) is a Northern Jê language with about 600 speakers, and Kawaiwete (ISO code: kyz) is a Tupí-Guaraní language with about 1,000 speakers. Our project focuses on the digital archival of linguistic materials from these communities, the creation of a dictionary, and the study of the morphophonological grammar of these languages. This talk describes the process of data digitization thereby making it usable to a variety of research questions to be answered in future work. Data elicited by Professor Lapierre from field trips in 2018 and 2019 to Kawaiwete speaking communities, and from 2015 to 2019 to Panãra speaking communities forms the foundation for this project. Materials utilized for this research project include elicitation recordings and transcriptions, and field notes obtained through in-situ fieldwork. The initial stage of our research was digitizing handwritten field notes over the course of ten months so the notes could be fully searchable in an online database. We transcribed a total of 16,128 words for the Panãra notebooks and 12,860 words for the Kawaiwete notebooks. The second stage of the project, which is our current stage, is entering lexical items into FieldWorks Language Explorer (FLEx), a software that stores and analyzes lexical and grammatical information. We currently have 351 words entered into the Panãra database, and plan on entering sentences in order to analyze parts of their grammar. The work of this project responds to the lack of an effective writing system in Panãra and the trending language shift towards Portuguese in Kawaiwete. A digital dictionary will help both the creation of written materials by Panãra speakers and the preservation of the current Kawaiwete language.

The rise of illiberal and right-wing nationalist movements poses a clear threat to liberal democracy in Europe. Across the continent, illiberal parties campaign against independent civil society and democratic institutions, while advancing xenophobic, anti-feminist, and anti-immigrant beliefs. In countries where such parties have gained power, illiberal leaders are dismantling checks on government power, protections of civil liberties, and even free elections. Our project explores the rise of illiberalism in Europe across four dimensions: exclusion and resistance to social change; misinformation; nationalism and sovereignty; and the erosion of democratic institutions. Through our analysis, we propose policy recommendations for civil society organizations, regional and national actors, and European Union institutions to proactively defend liberal democracy.

Early-onset Alzheimer’s Disease (EOAD) patients have a greater risk of developing seizures. Consequently, EOAD patients who develop seizures have worsened comorbidities, including mortality and behavioral outcomes. The causal relationship between chronic seizures and AD is still unknown. Neuroinflammation has been postulated as one of the links between these two disorders. Our lab has previously demonstrated that young mice with a presenilin 1 (PS1) genetic variant and amyloid precursor protein (APP) overexpression, mimicking an EOAD phenotype and genotype, subjected to chronic seizure are at high risk of mortality. This behavior was not observed in young mice with an EOAD-associated presenilin 2 (PS2) genetic variation. We hypothesize that chronic kindled seizures evoked in 2 months-old APP/PS1 mice worsen neuroinflammation and other neuropathological hallmarks of EOAD, including β-amyloid (Aβ) accumulation in the brain. To address this, 2-month-old male and female APP/PS1 and PS2 mice were subjected to seizures through a corneal kindling model of chronic seizures. The right brain hemisphere was collected before and after mice achieve the kindled criterion (five consecutive 5 Racine scale scores). Brains were harvested and cryopreserved for immunohistochemistry. My role in the project was to process tissues for immunohistochemistry. 20-µm thick sections of hippocampus from each mouse were sectioned on a cryostat and slide-mounted before processing with commercially available antibodies for molecular markers of neuroinflammation and neuropathology. Photomicrographs were collected and images were analyzed as the number of immunoreactive cells for each molecular and protein marker. We anticipate increased neuroinflammation and Aβ accumulation in kindled APP/PS1 mice versus their respective wild types and non-kindled littermates. We do not expect differences in PS2 variant animals. These results add to a larger research study in the laboratory to suggest that targeting seizures, and its inflammatory response, may be a potential therapeutic strategy to mitigate the behavioral and neuropathological burden of AD.

To study genetic factors and the molecular mechanism underlying the development rate of mouse embryos, two mouse subspecies were studied. I have collected mouse embryos from crosses between C57BL6/JxCAST/EIJ (B6xCast), CastxB6 (the reciprocal cross), and intercrosses within either strain to examine the effects of maternal and paternal genomes on the developmental rate. I used mouse embryos every 24 hours at gestational stages E11.5-E14.5. Staging by the Embryonic Mouse Ontogenetic Staging System (eMOSS) is used to estimate the actual developmental stage based on limb bud morphology and compared to the gestational stage based on the estimated time of conception by observation of a vaginal plug. I also used gDNA to determine the sex of each embryo to investigate whether sexes play a role in developmental rate. I observed an interesting pattern that the mouse subspecies and the source of each parental genome affect the developmental rate of embryos. I observed embryos with at least one Cast parent, have faster development than B6xB6 starting at gestational stage E13.5. The developmental rate is independent of the sex of embryos or the litter size. Single-cell transcriptomic analysis is ongoing to determine the genes and mechanisms behind the change in developmental rate of mouse embryos. It is important because the result will contribute to human development in early stages, and help to solve problems such as preterm or underdeveloped infants.

X inactivation is a mechanism of dosage compensation that equalizes gene expression between males (XY) and females (XX). It is mediated by the long non-coding RNA (lncRNA) Xist (X-inactive specific transcript). However, some genes escape X chromosome inactivation(XCI) in females, and thus potentially contribute to sex differences. Escape genes are often identified by allelic expression analysis based on RNA sequences and RNA FISH (fluorescent in situ hybridization) based on imaging. In addition, RNA FISH allows the examination of escape status and the location of the transcript in individual cells. Allelic expression analysis has shown that one X-linked gene Car5b escapes XCI in mouse cells. However, it is not clear whether it escapes XCI in every cell or a portion of the cells. The goal of this project is to use RNA FISH to detect and quantify the escape status of Car5b in wild-type cells and in cells carrying a deletion of an important DNA element required for Car5b escape. In order to achieve the goal, I first prepared the fluorescent probes using the cDNA plasmids of Car5b and Xist. Next, dual RNA FISH was performed for Car5b and Xist in mouse cells to visualize the location of Car5b RNA signals whereas Xist RNA signals serve as the marker of inactivated X chromosome. Analyzing the FISH results is ongoing and we expect to visualize Car5b escape in the wild-type cells but not in the mutated cells. This method can be applied to escape studies in other X-linked genes which could enhance our understanding of X-linked gene regulation and sex difference.

This presentation discusses a unique grammatical phenomenon surrounding person marking on transitive verbs in Kawaiwete, an endangered Tupi-Guarani language spoken in Mato Grosso, Brazil. Like many related languages, Kawaiwete exhibits complex variation in how it conjugates verbs (i.e. changes verbs to fit grammatical context). Transitive verbs, i.e. verbs that need both a subject and an object, require a prefix on the verb. This prefix denotes the role of the sentence’s component parts, called arguments. Whether the subject prefix or object prefix is selected depends on the grammatical role of the arguments and word order of the sentence, which is flexible. I analyzed data collected by Professor Lapierre by comparing sentences with first and third person arguments (i.e. “I/me” and “he/him”). I surveyed (i) the verbal prefixes used, and (ii) the order of the sentence’s arguments. Consider sentences (1a) /miara jemiwara je a-esat/ ‘I see the jaguar eating’, (1b) /miara jemiwara je w-esat/ ‘I see the jaguar eating’, (2a) /a-esat je miara jemiwara/ ‘I see the jaguar eating’, (2b) */w-esat je miara jemiwara/ (ungrammatical). When /je/ ‘I’ appears before /-esat/ ‘see’, its role as the subject is unambiguous, meaning the verb may take either the prefix /a-/, matching with the subject (1a), or the prefix /w-/, matching with the object (1b). However, when /je/ does not precede /-esat/ (2a), the verb must take /a-/, marking /je/ as the subject (2a). This implies that in situations where the role of the sentence’s arguments is unambiguous due to word order, the verbal prefix may select to match either of the verb’s arguments. Crucially, when word order results in ambiguity, the verbal prefix must match with the subject to disambiguate the sentence. This finding suggests that Kawaiwete verbs mark more than simply the verb’s subject or object, a unique phenomenon rarely observed.

Hexagonal boron nitride (hBN) is essential for nearly all nanoscale two-dimensional (2D) devices, as its flatness and wide bandgap make it an ideal dielectric for applying electrostatic gating. At high electric fields, hBN undergoes electrical breakdown where large currents flow to the sample, damaging the device. Gating fields are therefore limited by hBN’s dielectric strength. While the dielectric properties of hBN have been studied previously, the preparation of those samples differed from that used in practice. I conducted an experiment with the help of my advisors to understand how hBN’s dielectric breakdown characteristics depend on sample thickness and temperature. I began by fabricating three hBN devices, each containing multiple regions of different thicknesses. By measuring the current and varying the voltage on a given region, I was able to locally probe the hBN’s electric breakdown characteristics with thicknesses ranging from 5 to 24 nm. I tested each device multiple times using a cryostat at a range of temperatures from 4 to 300 K. During initial measurements, I observed an increase in the breakdown voltage with temperature in hBN between 15 and 24 nm thick, conflicting with previous reports. I repeated these measurements with a finer resolution which yielded the same result. The thinnest hBN regions showed no temperature dependence, confirming the absence of systematic temperature effects. I am currently fabricating more devices to reproduce this temperature dependence and working with my advisors to find a theoretical basis for this observation. Understanding how thickness and temperature effect hBN’s dielectric strength will allow researchers to construct more resilient devices, facilitating the study of 2D materials at higher electric fields. Moreover, the study of defects in hBN remains an active subject of research for quantum information applications, and a probe of the capacitive properties of hBN may shed light on this topic.

Regenerative medicine compromises to repair and replace cells, tissues, and organs damaged by disease or aging. To control cell fate in regenerative medicine, methods enabling irreversible and spatiotemporally controlled protein activation would be beneficial, particularly to those that could be applied for both inter- and extracellular activation. Furthermore, an ideal strategy could be applied to virtually any protein and afford rapid activation. In my work, I have sought to develop and exploit such a method through protein photochemistry; in response to mild and cytocompatibile light exposure, user-specified proteins are irreversibly assembled into their bioactive form. I have optimized the processes for hydrogel formation and modifications to increase cell viability. Results further inform that I can biochemically customize the landscape both intra- and extra-cellularly with a photoactivatable mCherry construct. Moving forward, I intend to apply this technique to activate epidermal growth factors and other proteins in multiple physiological systems. Successful protein photoactivation provides a potential, less invasive mechanism for controlling cells in the extracellular matrix for tissue engineering and regenerative medicine.

Most of the current literature on relationships and marriage in the US overlooks the ethnic, religious, and generational variations within the black population. This study explores the nuance in views and attitudes among African American and African immigrant young women toward marriage, especially hypergamous and interracial marriages. This study follows a deductive approach through testing hypotheses developed through four existing theories. First, symbolic interactionism theory suggests African Americans and African immigrants hold different attitudes toward marriage because they developed different meanings of marriage. Second, social exchange theory posits that because people tend to marry those of similar social and economic backgrounds, interracial and hypergamous marriages represent a social exchange of status. Third, classic assimilation theory suggests as the generational status of African immigrants increases, they increasingly develop similar marriage views and attitudes to African Americans. Finally, segmented assimilation theory holds that Muslim African immigrants are selective in their assimilation, thus, would not have similar views to African Americans. This study uses qualitative data collected through interviews, and quantitative data from the public use microdata series, IPUMS USA. The mixed methods approach compares interview participants — black female college students — with the trends in the nationally representative microdata. The expected findings would confirm all of the aforementioned hypotheses. This study aims to enrich the current body of the literature and provide greater depth and breadth into the ethnically, generationally, and religiously diverse black population. A better understanding of marriage views and attitudes in the black community can help shape public policy that fosters more transitions into marriage. Moreover, marriage is among many predictors of the integration of immigrants. Thus, comparing immigrants to Americans can highlight how immigration may play a role in disruptions and delays in the integration process.

Zoom classes or online meetings may be seen as temporary resolutions to COVID-19 restrictions. However, in the mental health field, telehealth continued to represent 20% of outpatient visits when the emergency restrictions of COVID-19 eased in late 2020 (Gentry et al., 2021). Telemental health is a form of online mental health services that can be used to deliver Evidence-Based Practice (EBP) to clients without in-person meetings. Despite the strength, one major barrier to implementation of telemental health services is that some youth may be less engaged in the session (AlRasheed et al., 2022). Limited research indicates that practical organizational support such as trainings, seminars, additional funding for clients, and technology support for clients may improve client engagement, along with a positive organizational climate that promote providing telemental health services (Oetzel & Scherer, 2003). The current study expands on past research to examine the relationship between organizational support and youth engagement in telemental health services among Community Mental health providers (N= 173) who participated in a Washington State-funded EBP training initiative (CBT+). As a part of CBT+, the providers attended a Cognitive Behavioral Therapy for youth training and follow up support and completed self-report surveys. Using survey questions regarding organizational support and youth engagement, we conducted 12 linear models to examine the relationship between organizational climate and practical organizational support with six measures of youth engagement. Results indicated that a positive organizational climate is associated with greater perceived effectiveness of therapy (β = .39, p = .000). The finding suggests that, when perceived effectiveness is low, we encourage organizations to tailor strategies to improve organizational climate for telemental health services, even after COVID-19 restrictions loosen. I will present additional findings and implications regarding practical organizational support in the poster presentation.

Microtubules are dynamic polymers of 𝛼- and 𝛽-tubulin subunits instrumental in the organization and division of chromosomes during mitosis. There is an intrinsic structural polarity to microtubules due to the orientation of 𝛼𝛽 heterodimers in the microtubule lattice, so that there is a fast growing plus end and a slower growing minus end. Kinetochores are protein complexes that assemble on chromosome centromeres and attach to microtubules. Proper chromosome segregation relies on kinetochore attachment to the plus ends of microtubules. Kinetochores are thought to initially bind the microtubule lattice and plus end attachments are then achieved by the action of plus end directed motor proteins or microtubule disassembly. While the plus end attachment is essential for mitotic fidelity, it remains unknown if the kinetochores themselves have an intrinsic polarity preference. Using total internal reflectance fluorescence microscopy, we have found that individual kinetochores assembled on centromeric DNA have a strong preference for binding the plus ends of stabilized microtubules in the absence of motor proteins and ATP or microtubule dynamics. Furthermore, using optical trapping we are able to measure the rupture forces of kinetochores on both ends of microtubules and have found that the observed preference for plus ends is matched by a greater binding strength at plus end tips. These results together give insight into how kinetochores could efficiently form plus end tip attachments and how they likely play a part in cell cycle regulation by using tension to sense a correct attachment. A better understanding of the specific mechanisms of kinetochore microtubule binding is valuable for understanding control of mitotic progression and could potentially inform more targeted anti-cancer therapies that focus specifically on dividing cells without impacting regular cell function.

Past research found racial diversity in the workplace can increase equity (e.g. Edelman et al., 2001), but could proximity to diversity make White leaders less likely to be held accountable for bias? I conducted two studies examining how having racial diversity near, but not within, the work team may influence people’s perceptions of workplace equity. In Study 1, participants recruited through Prolific (N = 252) rated how equitable they think a White leader would be in two conditions: one where all other leaders are White and one where the other leaders are racially diverse. Participants were informed that the White leader works entirely independently from the other leaders. Results show that participants rated the leader as more equitable in the diverse condition as compared to the all-White condition. Study 2 examines whether proximity to diversity could shield White leaders from accountability in an ambiguous situation where racial bias may have played a role. Results show that participants (N = 234) rated the leader's decision as less likely to be driven by racial bias in the diverse leadership (vs. all-White) condition. Mediation analysis shows that perceiving the leader as more equitable in the diverse leadership condition helps explain the present effect. Implication suggests that people may be less sensitive to detecting bias in diverse environments. Future work should disaggregate the experiences of people of color, examining whether there may be differences among racial groups in how the effect operates. Individual differences may also be moderating factors for the investigated effect. 

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.

Antiretroviral therapy (ART) prevents the progression of human immunodeficiency virus (HIV) by suppressing viral load, limiting transmission. Of the ~20 million people receiving ART, 30-40% do not maintain adequate medication adherence, resulting in treatment failure and drug resistance. Monitoring HIV medication adherence improves the efficacy of ART but requires bulky and expensive instruments that are not widely accessible at the point-of-need (e.g. doctor’s office or patient’s home), so a rapid and accessible diagnostic alternative is necessary. Our group developed the REverSe TRanscrIptase Chain Termination (RESTRICT) enzymatic assay to provide rapid and inexpensive measurement of HIV drug adherence by measuring antiretroviral drug activity indicated by fluorescence. However, one current limitation of RESTRICT is the need for trained operators to complete multiple precisely timed steps required in the enzymatic activity assay. We aim to create a 3D-printed microfluidic device that will automate the liquid handling steps required for RESTRICT via precisely tuned capillary action for rapid and user-friendly measurement of antiretroviral drugs. To that end, we first demonstrated a proof of concept by creating a microchip with a controlled 15 minute liquid delivery time and consistent liquid extraction. Through optimization of 3D-printing methods, channel geometry, and surface treatment, we created a microchip designed to deliver liquid in 14.64 minutes that ran experimentally in 19.12 ± 2.33 minutes. In the future, we will demonstrate the feasibility of RESTRICT run on-chip and fluorescence measured off-chip by testing clinically-relevant drug concentrations using the controlled liquid delivery time and liquid extraction methods developed. By creating an automated and rapidly fabricated microfluidic chip for therapeutic drug monitoring, we hope to achieve a hands-off device that removes external manipulation to increase the accessibility of RESTRICT-on-a-chip for point-of-need settings without specialized equipment or highly trained operators.

The extra cellular matrix (ECM) is a complex, heterogenous environment that plays an important role in cellular functions such as proliferation, signaling, movement, and differentiation. The mechanical properties of the ECM vary spatially and temporally, across and within tissues, i.e., during development and disease progression. 3D biomaterial platforms, such as hydrogels – water-swollen polymeric networks—provide a greater understanding of matrix-cell interactions and can be used to study drug delivery and basic disease mechanisms. My research works to create a double network (DN) hydrogel system that allows for spatial control of ECM mechanics in 3D. Our system contains two different polymer networks, one of which uses light polymerization. I have optimized concentrations of multiple gel components and gel light exposure conditions to allow for accurately patterned stiffnesses within the gels. Currently, I am encapsulating live cells to study the amount of cell spreading and movement in the stiff and soft regions of the gels over the course of a week. I then fix, stain, and image each gel to quantify relative cellular spreading. Additionally, I have synthesized multiple components necessary for gel formation, cultured enzyme producing bacteria to degrade formed gels, and performed western blotting to analyze cellular protein concentrations. Imaging results have shown the DNs and the patterning process are cytocompatible. Current experiments have shown differences in fibroblast spreading between stiff and soft regions; future results are expected to show differences in protein expression within mechanosensitive pathways between patterning conditions. Using multiple, intertwined hydrogel networks, I have engineered a dynamic, heterogenous model of the ECM, enabling me to study cellular responses to mechanical stimuli. Accurate modeling of the ECM will allow for a better understanding of how diseases such as breast cancer progress based on differences in environmental stiffness and provide an in vitro platform for future cellular response research.

Structured Interprofessional Bedside Rounds (SIBR) is a hospital communication model that was designed to facilitate collaboration on patient-centered daily plans of care. SIBR is associated with improved teamwork and communication among health professionals, leading to better patient health outcomes and satisfaction. Despite a growing body of evidence in support of SIBR, some healthcare teams find it challenging to consistently use the model and little is known about how this may impact patient satisfaction. The purpose of this study is to compare the level of satisfaction with rounds reported by patients in two ICUs and one acute care floor where SIBR has been adopted as the standard of practice but where variations in fidelity to the model persist. Data is obtained from the Study to Evaluate Associations Between Rounds, Heart Failure Care, and Patient Outcomes (STEAR-HF) through observations, questionnaires, interviews, and electronic health records. STEAR-HF is an in-progress multimethod study involving participants with a diagnosis of advanced heart failure who have been hospitalized at the University of Washington Medical Center. Participant recruitment is ongoing with more than 40 participants recruited to date. Patient satisfaction with rounds is being gathered via a 10-day post-discharge questionnaire and analyzed using descriptive statistics. In preliminary results, 92.3% of participants (n=12) reported that they agreed or strongly agreed with the statement, “I liked morning rounds in the ICU.” Meanwhile, only 57.2% of respondents (n=7) agreed or strongly agreed with the same type of statement for the acute care units (“I liked morning rounds on the acute care floor”). In parallel, rounds observations indicate higher levels of SIBR fidelity in the ICUs compared to the acute care floor. Additional research is needed to more closely compare patient satisfaction between critical care and acute care units and in relation to rounding model fidelity.

Quasars are compact regions at the center of a galaxy that have much higher than normal luminosity. Gas outflowing in winds is common in quasars, and it might play a role in regulating the black hole growth and star formation in the host galaxies. In particular, the ones with extremely high speeds (>~0.1c) have not been thoroughly studied and might pose the biggest challenges to the simulations of how these outflows are driven. A 2020 study by Rodríguez Hidalgo et al. identified 40 quasars with Extremely high-velocity outflows (EHVOs) in the 9th data release of the Sloan Digital Sky Survey by detecting absorption in quasar spectra. The C iv emission properties of this sample were examined in a 2022 study by Rodríguez Hidalgo & Rankine. Compared to the general population as a whole, these extreme outflows seem to be more predominant in quasars with large blueshifts of the C iv emission line, an indication of outflows in emission, but the sample was small. My project aims to answer the question: do EHVO quasars show distinct emission features compared with the general population of quasars? To answer this question, I carried out an extension of a 2022 study, but using a larger sample of 98 new EHVOs that we identified from the latest data release. I built on the python code that our team has previously created, which cross-correlates the sample of 6743 quassars from the 2020 study with measurements calculated by a 2020 study by Rankine et al and allows us to place the EHVO quasars in the C IV emission line parameters space (blueshifts vs emission intensity). Potential connection between the maximum EHVO velocity and increasing C IV blueshifts is also explored.

3D printing is a popular manufacturing method due to its ability to efficiently produce intricate and lightweight parts but it comes with the drawback of parts being too brittle to be used in load bearing applications. At the Laboratory for Advanced Materials and Processing, my research centers around making printed parts more ductile by studying fiber treatments for continuous-fiber filament. Printing with this filament produces parts with high ductility because they distribute load through the printed part more evenly than chopped carbon fiber or polymer filament. The heat applied during the manufacturing and printing process of the filament makes the continuous fibers to group together, or agglomerate, which decreases the performance of the printed part because it causes applied load to not spread evenly within the filament. I am researching the effect of heat transfer on interfaces in the continuous fiber filament by using sputter deposition equipment. Depositing sputter onto a sample involves taking a disc of extremely pure source material and using a large magnetic field to displace individual atoms from the disc onto the specimen. In my experiment, I coat the yarn with aluminum and ceramic sputter. The thermally conductive aluminum sputtered yarn is expected to fail faster in a tensile test compared to the insulative ceramic sputtered yarn, because the aluminum should theoretically increase heat flow within the filament. Increased heat flow causes agglomeration of yarn in the filament, which results in a decrease of part integrity. By determining how the distribution of heat affects the mechanical behavior of continuous-fiber filament, the manufacturing and printing processes can be improved upon to avoid damage prior to use of the parts. The overall goal of my research is to improve the process of 3D printing parts with low-modulus continuous fiber filaments and therefore aid in reliably printing ductile materials.
 

As the planet progressively experiences the effects of climate change, the US government is increasingly more interested in limiting the country’s resource consumption with a focus on limiting the footprint of corporations and manufacturers. The US Department of Energy (DoE) created a national network of Industrial Assessment Centers (IAC) within colleges, including the University of Washington, to provide recommendations that will be backed by DOE matching funds to facilities. The mission of the UW IAC is to reduce the energy consumption and emissions, improve overall efficiency, and implement cutting-edge technologies in a minimum of 20 facilities across Washington state and the Pacific Northwest, annually. We hypothesize that, by giving corporations free energy audits with financial incentives and training students to be energy savvy engineers, Washington state will reduce its overall energy consumption and be a leader nationally in resource management. The main methods to my research include initializing our energy audits with companies, preparing preliminary recommendations based on the company’s industry classification, touring the facility while collecting machinery and energy data, and writing detailed DOE-accredited reports entailing the best potential savings for the facility’s overall energy reduction. To date, the UW IAC has provided 250+ recommendations and 50+ assessments to industry, saving 1.49+ TBtu of energy. We have and continue to analyze a breadth of technologies ranging from air compressors, refrigeration, HVAC, lighting, automation, motors, and overhead operations in corporations across a variety of industries including aerospace manufacturing, food production, wastewater treatment, and paper mills. The significance of this pursuit is providing corporations an incentive to reduce their environmental footprint through an increase of revenue and modernization of their practices. We ultimately strive to bring Washington state to the forefront of efficient and clean energy practices.

Nowadays, Diversity, Equity, and Inclusion (DEI) have become buzzwords for many companies. However, some companies promote DEI just for its financial outcome and reputation rather than aiming to establish an inclusive work environment for minority groups. This study defines and differentiates between superficial and authentic diversity in the workplace, specifically gender and racial diversity in the US management consulting industry. I focus on consulting because DEI-related studies were rarely done in this field. Additionally, consulting is a newly-emergent and high-paying industry where if inequality exists and is overlooked, it will influence other businesses for the worse. The research purpose is to validate the thesis that superficial diversity is currently appearing in consulting companies and investigate what factors will contribute to superficial and authentic diversity respectively. Research findings will be based on interviews conducted with consultants coming from different racial and gender backgrounds. Interviews will be recorded, transcribed, and qualitatively analyzed through the thematic method to identify a pattern of what particular behaviors or actions will lead to superficial and authentic diversity across a chain of recruitments, promotions, and retentions. The expected result will tease out the underlying logic that could promote impactful DEI culture and generate practical suggestions based on this insight. Along this line, the research findings will help employees differentiate between superficial and authentic diversity and allow employers to recognize what type of DEI they are committing to so that they can avoid self-deception regarding DEI initiatives. By uncovering the nuances between superficial and authentic diversity, we can make transparent which company is pursuing authentic DEI for a higher level of social equity and which company is just conducting lip service for its own interest. Ultimately, this study intends to reduce racial and gender inequity in the US consulting industry and the entire workplace accordingly.

The Centers for Disease Control and Prevention recognizes that heart failure (HF) is one of the most complex and expensive health conditions to treat, and affects over 6.2 million Americans. The purpose of this study is to assess health system trust among patients with a diagnosis of advanced heart failure, who were recently discharged from the University of Washington (UW) Medical Center-Montlake. We are also exploring respondent’s reports of trust in the UW ’s healthcare system compared to the general healthcare systems. Data collection for this study is ongoing. Based on the descriptive analyses of reports from 17 respondents, preliminary results suggest that respondents have greater trust in the UW’s healthcare system compared to the general healthcare system. For example, 88.2% (n=15) of respondents agreed or strongly agreed that the UW’s healthcare system provides excellent care, whereas 64.7% (n=11) agreed or strongly agreed that the general healthcare system provides excellent care. In addition, when asked whether patients, regardless of their race or ethnicity, receive equal medical treatment, 58.8% (n=10) agreed or strongly agreed that they received equal medical treatment from the UW’s healthcare system compared to only 35.2% (n=6) who agreed or strongly agreed with the same statement in the general healthcare system. Additional data collection and analysis are needed to confirm whether the findings are similar over time. Further, it is important to explore whether there are differences in responses among study participants from different demographic and socio-economic groups (e.g., race/ethnicity, age, gender, rural/urban residence, education, employment, income, and insurance status) to develop strategies to provide equal health care access in diverse populations and reduce health disparitise. 

Adoptive T cell therapy is a promising therapeutic strategy for the treatment of many hematologic malignancies, however, its efficacy in solid tumors poses several challenges. Some of these challenges include the limited infiltration and activation of cytotoxic T cells due to the effects of a diverse immunosuppressive environment within the solid tumor. One of the main suppressive immune cells present in several solid tumors are regulatory T cells (Tregs) and high numbers of Tregs within the solid tumor have been correlated with poor prognosis. Therefore, there is a clinical need to develop strategies targeting the suppressive immune cells that limit the efficacy of adoptive T cell therapy. Tumors have highly dysregulated metabolism, which results in the secretion of multiple metabolites into the extracellular space. This allows a buildup within the tumor microenvironment, which may have an effect on the infiltrating immune cells. Our group has identified one metabolite, succinate, that enhances Treg numbers within the tumor microenvironment. Here we further explored the effect of succinate on the function of Tregs. To examine this, we identified tumor cell lines that produce succinate (lung and melanoma) and further altered these to modify the levels of succinate secreted by these cells. We then co-cultured high succinate secreting tumor lines with healthy donor CD4+ T cells that were isolated from PBMCs. We screened these cells and found that the higher levels of succinate resulted in higher numbers of Tregs and increased anti-inflammatory function, as evidenced by TGFb levels in Tregs. Future experiments will validate these findings in in vivo mouse models with the aim of developing synergistic approaches to enhance adoptive T cell therapy.

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.

This project examines developmental atypical patterns of visual attention in infants in relation to Autism Spectrum Disorder (ASD). Research in this area could help identify additional, specific risk groups or factors that could facilitate focused research that translates to real-world applications. Specifically, this project examines how cognitive development relates to visual attention to faces versus activities at 12 and 24 months of age among different birth weight groups. Developmental scores will be evaluated through data collected using: the Mullen Scales of Early Learning (Mullen), a developmental test measuring cognitive and motor development, and the Vineland Adaptive Behavior Scales (Vineland), a caregiver-interview measuring child adaptive skills. Visual attention will be quantified using eye tracking data which measured proportions of looking towards faces versus activities in social scenes. Participants in the lab were split into two groups, low birth weight and regular birth weight, and were seen by researchers at both 12 months and 24 months. Mullen, Vineland, and eye tracking tests were conducted at both timepoints. Science shows that as infants grow, they focus less on faces and more on the activities they are doing. I anticipate similar effects in eye tracking, with increasing age associated with a higher mean difference in preference for activities versus faces. Uniquely, I hypothesize that the strength of the relationship between looking at activities and developmental skills will be greater at 24 months than it will be at 12 months, and the opposite will be true for looking at faces. We will test our hypotheses on a linear regression model that predicts developmental skills from factorial effects of time point, birth weight, and region of eye tracking preference. This project hopes to seek to understand the interaction between birth weight, age, and attentiveness to faces versus activities as they relate to developmental skills.

In the spring of 2021, a man suffering from what he called a “sexual addiction” obtained a gun and attacked three different Asian massage parlors in Atlanta, Georgia, killing eight people – six of whom were Asian women. This event, alongside the rise in violence against Asian American women since the beginning of the pandemic, motivated me to investigate the role of stereotypes in portrayals of violence against Asian American women. I first conducted a literature review on the history of Asian American women in the United States, the stereotypes that have arisen, and their lasting impacts. I chose to perform thematic analysis on the coverage of the 2021 Atlanta spa shootings in order to investigate the effect of stereotypes in the portrayal of significant act of violence against Asian American women that received intense media attention. I analyzed 48 articles from 4 different news sources within a 48 hour and 2 week time frame, coding for relevant themes. Ultimately I expect to find that the coverage reinforces historical stereotypes that sexualize, objectify, and dehumanize Asian American women, and fails to address the nuances of the shootings. By becoming aware of the ways that stereotypes of Asian American women inhabit their portrayals, we can begin to confront these stereotypes and prevent their presence when taking action against violence against Asian American women.

In the midst of World War I and the Mexican Revolution, a document known as the Plan de San Diego emerged in South Texas. Discovered by local police in January of 1915 in McAllen, Texas when they arrested a Mexican national, the Plan called for a total racial revolution against Anglo-Texan power. A few months later, raids in support of the Plan broke out. Historians have primarily disputed over whether the Plan was an authentic product of local Tejano radicalism, or part of a wartime master plan by German and Mexican conspirators. The mystery surrounding its authorship and the raids has contributed significantly to this lack of consensus. My research traces the roots of the Plan’s rhetoric and the movement around it through the history of Mexicanos in Texas. I argue that the racial logic of the Plan demonstrates a real grounding in local history, regardless of its authorship. Rather than focusing on the moment in itself, I follow the lineage of the “Mexican race” which it attempted to mobilize. To do so, I closely read the wording and differences across time and space in legal policy, court cases, proclamations, newspapers, and folk music. In particular, I read the operation and formation of social-political categories between the lines of these texts. This approach draws significantly on racial formation theory, which offers a means to understand how such a movement could come about. By incorporating this critical approach, I hope to make a step forward in critically analyzing history as an element in racial history and the development of the identity "la raza," which the Chicanx movement mobilized later in the 20th century.

Large predators are particularly sensitive to human disturbance due to their slower life histories, large home ranges, and persecution by humans. Previous research shows that top predators have the ability to alter trophic relationships from their positions at the top of food webs. Therefore, anthropogenic-mediated behavioral changes in large predators could exert indirect and direct impacts on the entire ecological community. In Washington, cougars (Puma concolor) inhabit landscapes with increasing human disturbance, making this state an ideal place in which to explore how anthropogenic activity shapes their behavior. In this study, we examined cougar feeding behaviors in response to road, trail, and building density. We used camera traps deployed at fifty-five cougar kill sites to detect carcass visitation, and GPS collars on cougars to assess the total time spent at a carcass. A hurdle model was used to predict the probability of observing a cougar on a camera trap in relation to road, trail, and building density. Cougars were found to spend significantly less time feeding in areas of higher road density (p < 0.001) and building density (p < 0.001). This indicates that human infrastructure (proxied by road density) and human presence (proxied by building density) reduce cougar feeding opportunities. Our study shows that as the human footprint continues to expand into cougar habitats, cougars may experience further disruptions to their feeding dynamics. Understanding the behavioral response of large predators to disturbance is critical in the management of intact ecosystems and in mitigating human-wildlife conflict. 

Avian scavengers perform a critical ecosystem service by breaking down dead and decomposing organic matter and recycling nutrients. However, the scavenging dynamics of birds have received relatively little attention compared to the dynamics of scavenging mammals. Carcasses provide an ephemeral food source for avian scavengers, which presents them with the unique challenge of locating the carrion. This makes detection and consumption efficiency a topic of interest as not all avian scavengers follow the same pattern of arrival at a carcass. Here, we examine avian scavenger succession – the order in which species arrive and consume carcasses – through monitoring ungulate carcasses in Washington State. We found that turkey vultures outcompeted all other avian scavengers when they were present in summer months, while black-billed magpies and common ravens outcompeted golden and bald eagles in winter months. This confirms previous studies that have found that turkey vultures have morphological and genetic advantages that enable them to readily find carcasses and that body size does not determine succession in this scavenging guild. Our study highlights how social scavengers outcompete solitary scavengers and reach carcasses sooner, regardless of the physical characteristics of a species.

 Dravet syndrome (DS) is a genetic form of epilepsy characterized by febrile seizures in infancy, developmental delays, and sudden unexpected death in epilepsy (SUDEP) as a result of being drug-resistant. Finding new and innovative treatments is essential to reducing the risk of SUDEP and other symptoms in DS patients. Using a mouse model of DS (SCN1a+/- mouse), I showed that a machine learning-based detection algorithm could be used to detect interictal spikes (IS), which are abnormal neuronal discharges typical of epilepsy. The goal of the current experiment is to see whether the prior findings can be generalized to a larger dataset and whether the detected IS can be used to predict seizures before their onset. Data is collected by implanting two electrocorticographic electrodes and one electromyography electrode, as well as a wireless body temperature sensor in DS mice. Ambient temperature is controlled so that the animal’s core body temperature is initially maintained at 37°C and then is gradually increased by 0.5 °C every 2 min until a seizure is observed or the core body temperature reaches 42.5 °C. A machine learning model previously trained using manually scored data from the de la Iglesia lab is used to autonomously detect IS in the collected data. My results so far showed a moderate yet significant positive correlation between ambient temperature increases and IS frequency and points to a positive correlation between IS frequency and seizure onset. However, these results did not include the continuous recordings of body temperature. In the current experiment, I test if these correlations hold using a larger sample size and including continuously recorded body temperature, which may have more predictive power than ambient temperature. Our long-term plan is to design a closed-loop experiment that uses the algorithm to predict and stop seizures before their onset.

About one-quarter of photosynthetically fixed carbon is cycled through the marine microbial community in the form of metabolites, the intermediate compounds or products of metabolic processes. Marine heterotrophic bacteria are largely responsible for consuming these metabolites as a source of carbon, energy, and nutrients, yet little is known about transporter affinity and uptake kinetics of bacteria for abundant substrates. Homarine is a small, nitrogen-containing, zwitterionic metabolite that is produced by the cyanobacterium Synechococcus as well as some diatoms and haptophytes, where it is thought to function as an osmolyte. Dissolved homarine is present in the ocean at very low concentrations (~1.1 nM in Puget Sound). I hypothesize that these low concentrations are the result of high affinity bacterial transporters for homarine. Homarine can be used as a sole carbon and nitrogen source for OBi1, a marine bacterium isolated from Puget Sound. In this study, I investigate the uptake kinetics of homarine by OBi1 in the lab using the Michaelis-Menten model. I compare the uptake kinetics of OBi1 to similar homarine uptake experiments in the Salish Sea in June 2019. I expect that OBi1 will have a high affinity for homarine uptake and will take up homarine at nanomolar concentrations. I also anticipate that the marine microbial community in Puget Sound will have similar uptake kinetics to those observed with OBi1. Understanding the uptake kinetics of homarine by marine bacteria sheds light on the cycling of homarine in marine environments like Puget Sound and can help us understand the processes that keep the dissolved homarine concentration so low.

Cyanobacteria are tiny photosynthetic microbial organisms responsible for producing roughly an eighth of the oxygen we breathe. Synechococcus is a model cyanobacteria, meaning the species has characteristics making it easy to study and modify. As a scientific community, we don’t know the function or purpose of many genes expressed by Synechococcus. The goal of this project is to determine the function of particular genes hypothesized to be important to the adaptive survival of Synechococcus in different environments. We are approaching this by building a start-to-finish gene characterization method, starting with computational analysis to identify genes of interest, followed by knocking out, or disabling these genes and observing the effect on the growth of the culture. On the computational side, I’m now analyzing residual gene expression, using that information to characterize gene clusters, and analyzing external data to infer genetic context. On the laboratory side, I’ve characterized the growth of the un-modified base strains and developed procedures for genetic modification. Identifying the function of Synechococcus genes allows scientists to better study the response of Synechococcus to varying environments, which is especially important in a changing climate. Increasing understanding of the molecular mechanisms of Synechococcus also opens the door to genome engineering for the production of biofuels, plastics, and other commodities, or for using Synechococcus as a tool for bioremedial carbon sequestration. Additionally, the genes of Synechococcus are similar to those in other related oceanic microbes such as Prochlorococcus, the most ubiquitous photosynthetic organism in the world. For all these reasons, Synechococcus is an important model organism, and a deeper understanding of its biology will bolster our sparse understanding of marine genomics.

As the field of astrophysics continues to grow, the quantity of data to analyze is constantly expanding. With projects like the James Webb Space Telescope each sending back hundreds of gigabytes of data every day, Artificial Intelligence (AI) technologies is needed to assist manual analytical techniques in processing these volumes of information. One of the most apparent tasks for AI in astrophysics is image categorization – identifying what sort of astronomical object a certain body is. If a machine could categorize these bodie in significantly less time than a person, it would free tens of thousands of human hours every year. I created a Machine Learning program using a Deep Neural Network (DNN) implemented in Keras and TensorFlow capable of classifying astronomical images based on photometric data. Built from scratch, it utilizes existing labeled images to “learn” how astronomical bodies differ in appearance and assign them a category. The value of automated classification of astronomical phenomena cannot be understated. DNN allows the model to find unique identifiers in images humans often cannot spot, leading to often-more reliable predictions, recognizing possible discoveries in far less time, and freeing astronomers to undertake higher-cognition tasks only humans can accomplish. As the model is continuouly improved, it will be able to make increasingly accurate classifications and be of ever-growing value.

The existential risk of being unable to control a super-intelligent agent is called the Control Problem. Philosophers argue that an intelligence explosion and the creation of a singularity are inevitable, likening it to a ticking bomb. This fear is also present within the media, with rogue robots and singularities being frequent tropes for science fiction. However, the catastrophizing of sentient computers is not new. When first invented, academics and citizens speculated the computer was a precursor to supernatural thinking machines. Even in the mid-20th century, scientists believed sentient computers were right around the corner. This belief led to widespread computer phobia- the general public was afraid of what they thought were sentient gadgets and their implications. As familiarity with computers grew, along with a redefinition of what qualifies as human intelligence, this fear dwindled, and the public viewed computers as mere tools. Once again, due to the innovation of neural networks, we are experiencing a resurgence of phobia, reviving the belief that computers are supernatural thinking machines. This literature review will compare recent and historical philosophical arguments to current psychology and computer science. I expect to find similarities between the 1950s and present phobia and logical dissonance between the application of computer science and philosophical arguments. By confronting a potentially baseless fear, we can correct and alleviate the issues caused by irrationality and identify policies separate from sentience but still necessary to safeguard against non-sentient AI.

 Children are tasked with listening and learning in noisy environments where many people are talking at the same time every day. Conceptual models of listening under complex conditions posit that working memory plays a role in the ability to extract the target speech from the distracting noise. Hard-of-hearing (HoH) children, in particular, do worse listening in noisy environments. Thus, in this study we investigate the relationship between working memory and multitalker speech perception in HoH children. We hypothesized that we would observe a correlation between working memory and speech perception in both HoH and the typical hearing comparison group. Moreover, we expected that HoH children will have worse multitalker speech perception thresholds overall, suggesting difficulty perceiving speech under complex acoustic conditions. We tested 7-to-18-year-old HoH children and an age- and biological sex-matched typical hearing (TH) comparison group. Working memory was assessed in both visual and auditory domains; participants were asked to recall either a sequence of visually presented letters or auditorily presented numbers. Multitalker speech perception thresholds were obtained under 2 conditions: Collocated noise and Segregated noise. In the Collocated Noise condition, the target speaker spoke sentences from 0° azimuth with two additional distracting talkers, referred to as maskers, collocated from the same location. In the Segregated Noise condition, the distracting talkers were spatially segregated to ±90° azimuth, while the target talker remained at 0°. Preliminary analyses suggest that a relationship between working memory and multitalker speech perception is observed. These results will advance our understanding of why HoH children experience difficulty perceiving speech under noisy conditions and have the potential to lay the groundwork for novel assessment and intervention strategies to improve how TH and HoH children listen and learn in a noisy classroom. All authors participated in data acquisition, analysis, and preparation of this presentation.

Phonemic proficiency refers to the ability to manipulate the phonemes, or unit of sounds, in a word. Speech perception deficits has been linked to lower phonemic proficiency, as children have difficulty isolating, manipulating, and blending sounds that they cannot perceive. Autistic children commonly report difficulty perceiving speech in noisy real-world environments where many people are talking at the same time, such as a classroom or playground. Thus, in this study, we investigate the relationship between phonemic proficiency and multitalker speech perception in autistic children. We hypothesized that we would observe a stronger correlation between speech perception and phonemic proficiency in autistic children compared to the neurotypical comparison group. Moreover, we expected that autistic children will have worse multitalker speech perception thresholds overall, suggesting difficulty perceiving speech under complex conditions. We tested 19 7-to-10-year-old autistic children and a comparison group of 19 age- and biological sex-matched neurotypical children. The Phonemic Proficiency subtest of the Weschler Individual Achievement Test – Fourth Edition was administered to assess phonemic awareness. Multitalker speech perception thresholds were obtained under 2 conditions: Co-located Noise and Segregated Noise. In the Co-located Noise condition, the target speaker spoke sentences from 0° azimuth with two additional distracting talkers, referred to as maskers, co-located from the same location. In the Segregated Noise condition, the distracting talkers were spatially segregated to ±90° azimuth, while the target talker remained at 0°. Preliminary analyses suggest that a relationship between phonemic proficiency and multitalker speech perception is observed. These results will advance our understanding of the difficulty autistic children have perceiving speech and have the potential to lay the groundwork for novel assessment and intervention strategies to improve how children with and without autism listen and learn in a noisy classroom. All authors participated in data acquisition, analysis, and preparation of this presentation.

Research, and evolutionary theory, demonstrates that romantic relationships and platonic friendships fulfill different needs and are necessary for survival and critical for reproductive success. These relationships can be highly gendered with different dynamics. Usually, women’s same and cross-sex friendships are more fulfilling and richer. However, there is limited research looking at romantic relationships and platonic friendships and the individual differences and characteristics within these relationships. The current research explores how gender, sexuality, and heteronormativity impact the assessment, comparison, and characteristics between platonic and romantic relationships. We explore which individuals break out of traditional gendered friendship norms and seek similar interactions within their platonic friendships and romantic relationships. 194 Participants answered a questionnaire measuring the different characteristics desired in platonic friendships and romantic relationships. This survey was answered twice, once while thinking about a platonic friend and again for a romantic partner. Relationship characteristics were measured by scales, created by the researchers, that looked at emotional intimacy, physical intimacy, quality time, action affection, verbal assurance, and relationship perception. Romantic relationships had no difference between genders or sexualities for any of the scales. However, there were significant differences between genders and sexualities found in platonic relationships. Non-heterosexual women and non-binary individuals had higher engagement and support and had the highest overall assessment ratings within their platonic relationships. Heterosexual men and non-heterosexual women differed the most in their ratings for all platonic relationship characteristics, heterosexual men having lower scores on average. This supports previous research that men have less fulfilling relationships than women.

The purpose of this study is to establish biomarker assays for physiological stress linked to arsenic exposure and microbiome perturbation in freshwater snails. The ASARCO smelter in Tacoma, Washington polluted soil and water around Puget Sound with arsenic for nearly 100 years. Previous studies have shown that environmental pollutants can alter the gut microbiome and modulate host-microbe interactions in mice. However, little work has been done to understand how chronic exposure to environmental pollutants can impact the microbiota or physiology of primary consumers in aquatic ecosystems. To address this gap in knowledge, we are studying Chinese Mystery Snails (CMS) collected from three lakes in the Puget Sound region: Lake Killarney (20 ppm As), Steel Lake (2 ppm As), and Pine Lake (trace As). We hypothesized that snails exposed to higher concentrations of As are subject to greater levels of physiological stress than those with lower levels of exposure, and that this physiological stress is impacted by the microbiota of snails living in each environment. We measured relative levels of HSP70 expression in snail gut tissues to determine usefulness as a biomarker in our study. We also used inductively coupled plasma mass spectroscopy to determine the amount of arsenic in the tissues of CMS harvested from each lake. Next, we are isolating DNA from snail guts, water, sediment, and plants from each lake. The purified DNA will be subjected to 16S rRNA amplicon sequencing, allowing us to determine the relative abundances of bacterial taxa in each environmental compartment and the overlap between the snail gut vs local environment. Our future research will focus on validating additional stress induced biomarkers, while assessing microbiome alteration linked to the biomarker(s). This work will lay the foundation to future studies focused on understanding the links between arsenic exposure, chronic physiological stress, and microbiome composition.

Inherited retinal diseases (IRDs) are a diverse family of disorders which cause vision loss and retinal degeneration. With only 1-2% of the genome being protein-encoding, genetic variation within the expansive noncoding genome is critical to the development of disease phenotypes in the retina. Macular Telangiectasia Type II (MacTel) is an IRD resulting in disruption of central vision and greatly impacting vision-related quality of life. MacTel has an estimated prevalence of 1 in 1000 individuals, affecting approximately two million people globally. Though MacTel etiology largely remains unknown, accumulation of improperly degraded lipids within the retina is a leading hypothesis in its pathogenesis. Additionally, genome-wide association studies have implicated numerous loci in the development of MacTel, including the novel gene locus ceramide synthase 4 (CERS4). As CERS4 plays a critical role in the synthesis of lipid precursors and is highly expressed in the retina, it stands as a promising candidate for influencing MacTel development. We hypothesize that cis-regulatory element (CRE) mutations are central to the genetic frameworks underlying MacTel. We aim to characterize the sufficiency of putative enhancer regions to drive gene expression. We have identified potential CERS4 enhancer regions through a machine learning approach using adult human retina ATAC sequencing datasets. Sufficiency of candidate enhancer regions will be evaluated by insertion to a barcoded reporter library and electroporation into mouse retinas. Following proof of sufficiency, we will perform saturation mutagenesis on identified enhancers to investigate the impact of all possible single nucleotide variants (SNVs) within these regions. The results of our investigation will aid in identifying SNVs of interest within the CERS4 locus, potentially implicating specific mutations towards the development of MacTel. Greater understanding of CRE mutations will improve early clinical diagnosis and inform future therapies for patients with MacTel.

 Solid tumor cancers are capable of releasing chemicals that are detectable in body fluids. These cancers can cause severe acidosis within the patient, resulting in the change of structure and function of Complement serum proteins, membrane-bound regulators, and receptors that interact with various cells and mediators. A better understanding of the mechanistic interaction between the complement system and tumor-induced acidosis can provide a new direction in cancer immunotherapy research. Here, we investigate the effect of pH on binding between Heparin, Complement Factor H (CFH), and C3b. We found that in controlled in vitro assays conducted through biolayer interferometry, CFH and Heparin bind better to C3b in pH 6.0 but only in lower concentrations of CFH. As for pH 7.4, the binding between CFH, Heparin, and C3b is lower in comparison; however, the binding between only CFH and Heparin is higher at pH 7.4 than at pH 6.0. Our results demonstrate how Heparin, Complement Factor H, and C3b are likely to function in a tumor microenvironment where the pH is generally lower. We anticipate this research to be a starting point for investigating the role of the Complement System in tumor growth and researching the implications of its biological actions with respect to the development of anticancer therapy.

Glioblastoma Multiforme (GBM) is an aggressive and highly heterogeneous form of brain cancer. Due to the heterogeneity of gene expression in GBM within and across patients, patterns in expression of these genes may provide new insights into targeted drug treatments. In this study, I utilized the predictive computational model built by using the Mechanistic Inference of Node Edge Relationships (MINER) algorithm based on data from The Cancer Genome Atlas (TCGA) and clinical outcomes in order to identify enriched biological pathways that affect GBM patient survival. 3797 gene groups, or regulons, and associated transcription factors were analyzed across the 526 TCGA patients. Of these regulons, the top 10 transcription factors and regulons which were most associated with survival through upregulation or downregulation were identified based on Cox hazard ratios. Additionally, individual gene functions were grouped into higher-level pathways. From there, I created a network map of causal and mechanistic influences to identify known and novel driving mutations of GBM. The resulting network included established GBM-driving mutations such as mutations in TP53 and NF1 genes. Additionally, novel GBM-associated mutations were found, such as mutations in the ATRX, PDGFRA, and CUX2 genes. The results of this exploratory study could be used to identify biological pathways for targeting by candidate chemotherapeutic drugs, incorporating drug interactions into the network map. Furthermore, increased accuracy in GBM prognoses may be achieved by examining regulon activity of newly-diagnosed GBM patients.

Hexokinases (HK) are enzymes that catalyze the first step of glycolysis – the phosphorylation of glucose to glucose-6-phosphate. Hexokinase 3 (HK-3), one of four mammalian HK isoforms, is detected in hematopoietic cells and tissues, especially in cells of myeloid lineage. Previous studies have shown that after myeloid cells undergo CRISPR/Cas9-mediated HK-3 gene disruption and differentiation to neutrophil-like cells, loss of HK-3 leads to no effect on glycolysis, but an increased cell death phenotype during differentiation to neutrophil-like cells. This study aimed to examine if HK-3 gene knockout causes a similar cell death phenotype in monocyte/macrophages cells, which are of myeloid origin. To test directly, THP-1 cells, which are monocyte-like cells that can be differentiated to macrophage-like cells, underwent CRISPR/Cas9-mediated HK-3 gene knockout via electroporation. This is a method that uses electric pulses to make pores within the cell and nuclear membrane. PCRs and DNA sequencing comparing wild-type THP-1 cells and HK-3-null THP-1 cells were done to confirm successful knockout. The HK-3-null THP-1 cells then underwent 48-hour, 250 nM PMA-induced differentiation to macrophage-like cells and were then stained with Trypan Blue to compare viability of wild-type macrophage-like cells and HK-3-null macrophage-like cells. No apparent difference was found in cell viability between wild-type macrophage-like cells and HK-3-null macrophage-like cells during differentiation and over six days post-differentiation. Cell function was not assessed. This suggests that further work should be to: (1) confirm these results by repeating the HK-3-null in THP-1 cell line process and remeasuring cell viability after differentiation, (2) perform the HK-3-null process in other cell lines to differentiate into other cells of myeloid origin to determine if cell death phenotype appears, and (3) determine if loss of HK-3 alters viability under culture conditions mimicking low oxygen conditions, such as found in hypoxic tissue areas during bacterial infection. Understanding cell viability differences from loss of HK-3 could give insight into the potential regulatory function of HK-3 during myeloid hematopoiesis. 

Treatment of individuals with HIV using antiretroviral therapy (ART) is highly effective, but effective clinical management depends on maintaining therapeutic drug concentrations. Antiretroviral (ARV) drug concentrations in patients with HIV can vary due to differences in drug metabolism, medication adherence, or interactions between multiple drugs. These individuals may have subtherapeutic or supratherapeutic drug concentrations, putting them at risk of treatment failure, acquisition of drug resistance, and risk of hospitalization or death. Current measurement of ARV concentration is done through liquid chromatography tandem mass spectrometry, which requires expensive equipment and requires a labor-intensive protocol. This restricts accessibility to specialized laboratories, making it difficult for persons with HIV to have routine measurements of ARV drug concentrations. The goal of the project is to develop an assay that is simple to perform and uses standard equipment to increase access to routine clinic-based drug level monitoring to improve HIV care. We designed an assay using a 2-step process of DNA strand transfer and quantitative polymerase chain reaction (qPCR) to quantify integrase strand transfer inhibitors (INSTIs). We tested for dolutegravir (DTG) and cabotegravir (CAB) in both buffer and plasma -- the latter to simulate patient blood samples. We were able to demonstrate that the assay could quantify clinically relevant drug concentrations of DTG and CAB. By developing an assay that can be readily integrated into most clinical laboratories, we will contribute to increasing access to routine HIV drug level monitoring to improve clinical HIV care and maintaining viral suppression in persons with HIV.

Diffusion-weighted imaging (DWI) shows great potential for improving breast cancer detection and diagnosis. Primary findings from the ECOG-ACRIN A6702 multi-site, multi-vendor clinical trial indicate that DWI apparent diffusion coefficient (ADC) values may help reduce false positives and unnecessary biopsies. Gradient nonlinearity (GNL) correction was previously found to improve the accuracy of ADC mapping within and across MRI vendor systems. In this study, we evaluated the impact of GNL correction on breast lesion ADC measures in the A6702 dataset. The dataset comprised 81 suspicious breast lesions (28/81 malignant) in 67 women. Standardized DWI scans were acquired across 9 different MRI scanners. ADC maps were created from DWI scans, and ADC values were measured for each lesion. Direction-averaged GNL correction maps were constructed based on scanner-specific gradient specifications. ADC map correction was then performed through pixel-wise scaling by the GNL correction maps using custom software developed in MATLAB. Lesion ADCs before and after GNL correction were compared using a two-tailed z-test. ADC diagnostic performance (benign vs. malignant) was evaluated using area under the receiver-operating-characteristic-curve (AUC), and optimal ADC cutoffs were chosen to maximize specificity while maintaining 100% sensitivity. GNL-corrected lesion ADCs were significantly lower than uncorrected ADCs (1.12±0.29 vs 1.17±0.30x10-3mm2/s, p<0.001). GNL error in lesion ADCs varied across gradient systems (mean ∆ADCvendorA=0.14±0.08, ∆ADCvendorB=0.03±0.02, ∆ADCvendorC =0.004±0.01, p<0.001). GNL correction produced a slightly lower optimal ADC cutoff (1.33 vs. 1.35x10-3mm2/sec). However, no overall difference in diagnostic performance was detected: AUCuncorrected=0.78 (95% CI 0.68-0.88), AUCcorrected=0.79 (95% CI:0.69-0.89), p=0.22, and 18% potential biopsy reduction for both. This study showed GNL substantially affects lesion ADC measures, with significant variability across different vendor platforms. These findings suggest that GNL correction should be implemented to ensure uniformity and consistency in diagnostic breast lesion ADC measures across MRI platforms, especially for multi-center clinical studies.

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.

Type 1 Diabetes (T1D) is one of the most prevalent chronic diseases among teens in the United States. Teens with T1D facing socioeconomic disadvantage are disproportionately negatively affected by the burden of T1D and are at-risk for poor mental and physical health outcomes. Limited access to diabetes-related technology may be one factor contributing to these disparities. The purpose is to describe diabetes technology (continuous glucose monitors and insulin pumps) use among teens with T1D according to neighborhood-level socioeconomic disadvantage in Washington. The research also aims to investigate links between neighborhood disadvantage and diabetes outcomes and test whether diabetes technology moderates this relationship. We abstracted demographic, clinical, and psychosocial data from medical records of teens aged 13-18 seen for T1D clinical care at Seattle Children’s Hospital in 2019. We determined state-relative decile scores (1-10) for neighborhood disadvantage using the area deprivation index (ADI) tool, which considers income, education, employment, and housing quality factors. Diabetes management was measured using A1c, a 3-month average of blood sugar levels. Diabetes distress was measured using Problem Areas in Diabetes-Teen, a self-report measure of the emotional burden of living with diabetes. I will perform a descriptive analysis calculating the percentage of participants using diabetes technology for each ADI score and for low and high disadvantaged groups using cutoffs from previous literature to reveal technology use patterns. I will conduct linear regressions exploring relationships between neighborhood disadvantage and outcomes (A1c and diabetes distress) and enter diabetes technology as a moderator. We predict that higher neighborhood disadvantage will be associated with poorer diabetes management and higher distress, but this will vary as a function of technology use. Altogether, this research highlights use of a neighborhood-level tool to identify patterns for an at-risk group of teens and may help to identify intervention targets for public policy addressing health disparities.

Cells communicate with each other and their environment via signaling pathways. When a cell receives a signal, it is processed by several proteins. Oftentimes, the same proteins are used by multiple pathways that process distinct signals and produce distinct cellular outputs. I am investigating how the cell is able to correctly process signals using Wnt signaling as a model pathway. Wnt signaling helps regulate cell growth and differentiation and is therefore tightly associated with many diseases. Both Wnt and insulin signaling processing utilize the enzyme glycogen synthase kinase 3β (GSK3β). Activation of insulin signaling results in the phosphorylation of GKS3β. However, if phosphorylated GSK3β from insulin signaling interacts with Wnt proteins, Wnt signaling can be inappropriately activated in the absence of a Wnt signal. The mechanism by which cells prevent improper activation of Wnt signaling is unknown. I am researching the role scaffold proteins play in signaling pathway insulation. Traditionally, scaffold proteins facilitate reactions by binding enzymes and their substrates, bringing them in close proximity to each other. It has also been shown that scaffold proteins can assist in promoting chemical reactions through mechanisms other than binding. Because the scaffold protein Axin binds GSK3β as well as PP2A, an enzyme that dephosphorylates GSK3β, I propose that Axin promotes insulation of the Wnt pathway. Using in vivo human cell culture assays, I have determined that Axin promotes dephosphorylation of GSK3β by PP2A through a mechanism more complex than bringing the two proteins in close proximity with each other. I will use in vitro kinetic assays to determine the underlying kinetic mechanism of this effect. Determining the kinetics of scaffold-mediated insulation will produce a model that can be applied to other signaling pathways and is important in understanding how to specifically target Wnt signaling for disease treatment without affecting other pathways.
 

Capillary microfluidics devices automate point-of-care diagnostic assays because of their instrument-free operation, small size, and low material cost. However, capillary microfluidics currently require expensive fabrication instruments limiting rapid prototyping and deployment in low-resource settings. State-of-the-art capillary microfluidics are fabricated by using digital light project stereolithography (DLP-SLA) 3D-printers that offer high resolution (40 µm) but are expensive ($10,000 – $20,000). Liquid crystal display (LCD) SLA printers have recently emerged with comparable resolution and much lower cost ($300 – $1000). However, our initial experiments with LCD-SLA printers exhibited defects and post-processing issues. Our goal is to optimize the fabrication process of capillary microfluidics using an inexpensive LCD-SLA printer (Anycubic Photon Mono 6K, ~$400) and calibrate performance relative to a DLP-SLA printer (CADWorks Pr 4K, ~$15,000). By varying printing parameters including UV power, exposure time, layer height, retraction speed, and resin choice, we found optimal conditions that produced microfluidic channels with comparable dimensions on the Anycubic and CADWorks printers (i.e. coefficient of variation <20%). With printer settings of 40% UV Power, 1.8s exposure time, 20 µm layer height, and 0.1 mm/s retraction speed with CADWorks clear resin, the Anycubic 3D printer produced microchannels down to 100 μm, the smallest feature size we achieved with the CADWorks printer. Optimizing 3D-printing of capillary microfluidics using inexpensive LCD-SLA printers like the Anycubic has the potential to enable rapid prototyping of point-of-care diagnostics in low-resource settings. Next steps include printing more complex microfluidic components including domino valves and trigger valves.

Gift-giving is a central component for many people in terms of expressing affection through increasing perceived closeness as well as strengthening relationships. Giving gifts can also facilitate requesting help or asking someone for a favor. According to Aknin and colleagues (2018), these ‘motivated gifts’ decrease recipients’ anticipated satisfaction and willingness to perform the favor which could negatively impact relationships. The current study proposed that this decrease in prosocial tendencies could be explained by the self-determination theory of basic psychological need satisfaction (BPNS), that is, that humans require three psychological needs to flourish and live optimally (autonomy, competence, relatedness; Ryan & Deci, 2000). Fulfilling these needs is said to facilitate the integration of autonomous motivation, which was hypothesized to be the mediating role between motivated gifts and prosocial behavior. Participants (N = 426) were recruited for an online survey in which we randomly assigned them to read a hypothetical scenario where they imagine being asked a favor by a friend either with or without a motivated gift. The current study was unable to replicate the findings from Aknin and colleagues’ (2018) study and found no significant differences in participants’ BPNS, but did find that motivated gifts caused a decrease in autonomous motivation. Additionally, motivated gifts were not found to cause a change in whether a participant would be willing to participate in an unrelated study. Altogether, the findings suggest that motivated gifts do not necessarily have a negative impact on prosocial behavior which, considering the primary reason gifts are given, is good news for relationships and prosocial tendencies.

Cyanobacteria are ancient single-celled photosynthetic organisms, prevalent throughout Earth's oceans. Over billions of years, cyanobacteria have evolved genes that enable them to survive across a diversity of adverse, ever-changing environmental conditions. However, researchers are faced with the problem of not understanding the role of many of these genes. This research project entails tracking down the function of some high variance genes in marine Synechococcus, an important model organism and a genus of cyanobacteria. We will test gene function by generating knockout strains in which a gene of interest is inactivated, and testing the growth of these mutant strains in various conditions. In particular, our project focuses on the importance of the flavodoxin gene, which codes for an electron transport protein that is involved in photosynthesis and is expressed in response to iron scarcity. This gene inactivation is done with a plasmid, which is a genetic structure in bacteria that can replicate itself independent of bacterial chromosomal replication, that’s enabled to knock out the flavodoxin I gene when inserted into Synechococcus cells. We insert the plasmid into our Synechococcus cells and once the DNA is taken up by the cell, we then use CRISPR technology to remove the gene. Successfully creating the flavodoxin knockout of Synechococcus establishes the procedures necessary for generating knockouts of other genes that could be expressed in similar patterns as flavodoxin. Ultimately, this research furthers our understanding of how Synechococcus’ genes allow it to adapt to various environments and contributes to ongoing research on how organisms might withstand the pressures of Earth’s ever-changing climate.

Neutrinos are fundamental particles involved in many important universal processes; however, because they only interact via the weak force and gravity, reliably detecting neutrinos directly is notoriously difficult. A new strategy is to study neutrinos through interactions with enhanced cross-section, like coherent elastic neutrino-nucleus scattering (CEvNS), in which the neutrino interacts with the nucleus as a whole (coherent) while conserving kinetic energy (elastic). However, due to the low energy of nuclear recoil in CEvNS, not all nuclei can produce detectable recoil if the recoil energy is on the order of the noise fluctuations in other background radiative processes, as recoil energies become indiscernible. Sodium iodide (NaI) is a candidate for detectable recoil, and I am characterizing the background spectrum of NaI crystals to see if NaI has low enough rates of background processes to be used in CEvNS studies. I analyzed previously collected NaI background spectra to calibrate the event energies and to perform a waveform analysis to distinguish physics pulses from electronics noise. The resulting spectra are used to determine the background rates in the crystals. These routines were converted into scripts to automate the same analysis for future data. Measuring the energy of CEvNS nuclear recoil can help characterize neutrino-quark interactions, which the coherent nature of CEvNS amplifies, providing unprecedented sensitivity to searches for non-standard interactions between neutrinos and matter. Improved characterization of CEvNS also allows for novel checks of predictions made by the Standard Model of particle physics, and has broader applications in understanding supernovae (which produce large quantities of neutrinos) and searches of dark matter candidates that may interact with neutrinos.

The periodontal ligament is a connective tissue that anchors teeth to the bony socket and is crucial in providing nutrition for the survival and functioning of the human body through the mastication of food by teeth. Because the periodontal ligament is anatomically sealed off from the oral cavity, no non-invasive techniques currently exist to investigate it in-vivo, making the development of sound in vitro models critical for periodontal research. With periodontal disease affecting over 743 million people worldwide, in-vitro research to develop regenerative therapies to replace diseased periodontal tissue is urgently needed. To achieve this, we have developed a novel 3D in-vitro model, which closely mimics the in-vivo periodontal ligament. The 3D tissues are fabricated by inverting an array of silicone posts into silicone molds containing a cell-collagen gel mixture in a 24-well plate. Once the tissues have been incubated and the collagen polymerizes, magnetic mechanical force stretches tissues on posts. The post deflection is used to calculate tissue stiffness and contractility. Preliminary data shows a reduction of contractile force in the tissue constructs after 24 hours of mechanical stretching. I expect to find similar outcomes through additional experimentation. Understanding the periodontal ligament’s response to mechanical force is crucial for its effective restoration and ensuring that it is mechanically sound. The novel in-vitro 3D model that we have developed provides a valuable opportunity to better comprehend the ligament's response to these forces. By performing further experiments with this model, we can gain a deeper understanding of the periodontal ligament, allowing for informed decisions when it comes to replacement and repair in patients. This model offers controlled and repeatable experiments, providing more accurate insights into the biology of the periodontal ligament and contributing to the advancement of periodontal disease treatment.

Cancer cells display dysregulated metabolism to meet the increased metabolic demands of rapid cell proliferation. While cancer cells enact metabolic changes to glucose metabolism, known as the Warburg effect, it is also important to consider the metabolic pathways involved in biomass synthesis which support cellular divisions. For example, the amino acid aspartate is a central facet of proliferating cell metabolism because it is a precursor to both purine and pyrimidine nucleotide synthesis, and essential for asparagine and arginine biosynthesis. Based on research from the Sullivan Lab and others, aspartate biosynthesis is essential for tumor cells to proliferate. However, the cellular mechanisms by which aspartate levels impact the proliferation rate of tumor cells remain unknown. Based on data collected in Sullivan lab, my mentor and I hypothesize that SDH inhibition blocks the production of a metabolic intermediate between succinate and aspartate that has an unknown function in sensing aspartate limitation and therefore dictating cell proliferation. Therefore, my project seeks to investigate how aspartate levels as well as several aspartate precursor metabolites in the TCA cycle govern the proliferation rate of tumor cells. In the first portion of the project, I measure proliferation rates of WT and GOT1/2 (converts oxaloacetate to aspartate) double knock-out (DKO) cells treated with or without the SDH inhibitor Atpenin A5 (AA5) in the presence and absence of aspartate. In the second portion of the project, I examine if modulating fumarate, malate, and OAA levels in the TCA cycle impact the proliferation rate of GOT1/2 DKO cells. I anticipate seeing decreased proliferation rate along with decreased levels of fumarate, malate, and OAA in DKO cells treated with AA5. This research project will contribute to the lab and cancer treatment by providing new insight into aspartate metabolism.

Particle-laden turbulent flows are important in both natural and industrial contexts. The particles in many of these processes, such as the formation of ice crystals in clouds or the paper-making process, are anisotropic, with directionally-dependent drag coefficients. Generally, anisotropic particles are free to rotate as they are advected by the carrier fluid. However, external forcing from gravitational and magnetic fields, the larger scale flow, and active behavior can restrict the particles’ orientation, fixing their anisotropic resistance with respect to the reference frame. The dynamics and statistics of symmetric particles in isotropic turbulence are well-studied, but the effect of anisotropic forcing on the transport and behavior of asymmetric particles is less well-understood. We studied these dynamics by conducting Lagrangian particle tracking in simulated isotropic turbulence from the Johns Hopkins Turbulence Database. Computer simulations of 54,000 randomly-placed particle tracers were run in Python, with anisotropy introduced by directly scaling the velocity of the tracer-particle at each simulation time step. We examine how increasing a particle’s resistance to motion in one direction in isotropic turbulence impacts the transport and dispersion statistics in all three directions. We find that increasing tracer anisotropy decreases diffusivity in the direction of velocity scaling as expected, but the diffusivity in the unscaled directions increases such that the total diffusivity remains roughly constant. Studying the dynamics of these simulated anisotropic particles in turbulence will provide a better understanding of how turbulence mixes both particles and the fluid itself, which can then be applied to particle-turbulence interactions in both environmental and industrial contexts.

CD123 is a cell surface protein expressed on neoplastic cells and underlying cancer stem cells in a variety of hematological malignancies, specifically acute myeloid leukemia (AML), B-cell acute lymphoblastic leukemia, hairy cell leukemia, Hodgkin lymphoma, and blastic plasmacytoid dendritic neoplasm, making it a rational drug target for antigen-specific immunotherapeutic approaches. In some cases, however, cell surface CD123 antigen level may not be high enough to elicit a response with an immunotherapeutic, and so we set out to identify mechanisms of regulation of CD123 expression through genome-wide CRISPR screens, and through testing of CD123 expression level changes following treatment of human AML cell lines with clinically validated AML chemotherapeutic drugs. Using commercial anti-CD123 antibodies, I established baseline CD123 expression level on a variety of AML cell lines. I then treated selected cell lines for various times with chemotherapeutic agents, including azacytidine, histone deacetylase (HDAC) inhibitors, the BCL2 inhibitor venetoclax, all-trans retinoic acid (ATRA), doxorubicin, or cytarabine, and measured for altered CD123 level. Utilizing a FACS-based sorting approach on cells that were lentivirally transduced with a genome-wide CRISPR sgRNA Brunello library covering over 19,000 genes, we identified genes that were associated with either increased or decreased expression of CD123. A subset of these CRISPR screen hits were subsequently validated in a small number of AML cell lines using CRISPR/Cas9 sgRNA against specific targets implicated in CD123 expression changes.

This research project aims to investigate how urban ecological design interventions can contribute to the restoration of the vitality of the Belltown neighborhood in Seattle in a post-Covid world. Specifically, the project will utilize an interdisciplinary framework that bridges the fields of landscape architecture and social science through the lens of urban ecology theory. The research methods that will be utilized in this project include investigation, interpretation, and design projection. Investigation will involve the analysis of the current state of the neighborhood, focusing on revealing the hidden urban ecological systems. Interpretation will involve a critical review of the findings from the investigation and the development of design interventions to address the challenges identified. The hypothesis of this project is that small, incremental design interventions that reveal hidden urban ecological systems will foster creative engagement of users with places and natural processes at play, encouraging the care and stewardship for healthier communities and ecosystems in the long term. To support this hypothesis, the project will conduct a thorough review of existing literature on urban ecology and design interventions, as well as collect data through observations and interviews with community members. The expected results of this project are specific and measurable, including the successful implementation and evaluation of an interactive story map to reveal urban ecological systems at play in the neighborhood, and finding potential locations for proposed design interventions. Ultimately, the project aims to contribute to the broader goal of designing future urban grids using the urban ecology framework to reconcile people with their streets in a post-Covid world.

Nature uses only four nucleobases to store genetic information in DNA. However, additional synthetic bases which use Watson-Crick pairing have been developed and are known as non-standard bases (NSBs). NSBs P, Z, B and S incorporated alongside standard bases A, G, C and T compose DNA strands using a new genetic alphabet. Nanopores offer the potential capability for direct single-molecule sequencing of DNA containing non-standard bases (NSBs). Using a voltage gradient, DNA strands were directed through a nanopore, the biological membrane protein MspA, while we measured the ion current through the pore over time. In studying the effect of NSBs on the ion current through the pore, we observe current measurements corresponding to the Z base have a different noise profile compared to other bases. We hypothesize this noise may be associated with pH-dependent protonation of the base. To test this hypothesis, we conducted experiments with identical sequences in buffers of pH 8 and pH 7, as Z is known to have a pKa of 7.8. I analyzed the noise from the ion current signals to look for signs of protonation. I found increased current noise values associated with the Z NSB in pH 7 compared to pH 8, while the canonical A base had no change in noise values from pH 7 and pH 8, supporting the hypothesis that the increased current noise is due to protonation of the Z base. In addition to indicating potential sensing abilities of nanopores for probing protonation kinetics of DNA, this research contributes to a better understanding of the fundamental mechanisms that control the currents in nanopore sequencing of DNA.