This research is being conducted through the Svoboda Diaries Project (SDP), a digital humanities effort within the University of Washington based on the diaries of a British steamship worker during 19th-century Ottoman Iraq. This study aims to assess how students from varying academic backgrounds think and learn on a conceptual level and analyze how this influences their interactions with a digital humanities resource. We are conducting this research in hopes of improving the SDP website and contributing to generalizable knowledge regarding facilitated learning with digital tools. We are performing an interview study that employs two main methods used in usability testing: concept mapping and the think-aloud protocol. Concept maps are defined as graphical representations of one’s conceptual understanding of a topic, and the information falling within that topic. The think-aloud protocol is a research method involving participant’s verbalizing their thought process concurrently with the tasks being performed. During the interview, participants will create their own concept maps of their area of study, followed by a usability test on the image gallery feature of the SDP website, and lastly a second concept map activity where participants will map out the image gallery itself. The interviews will be analyzed using qualitative data analysis methods, and concept maps will be scored both qualitatively and quantitatively. By examining students from diverse academic backgrounds, we can analyze how they interact differently with our digital humanities resource, apply it to their field, and characterize how they think conceptually about topics. This research will contribute to the Svoboda Diaries Project by enabling us to make quality improvements to our website and gain insights to enhance our efforts within the digital humanities domain. Findings from the study may also be valuable when thinking critically about how students think about and interact with digital humanities resources as a whole.

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.

Skin is a densely innervated sensory organ, populated with various somatosensory receptors that help us perceive touch stimuli. Frequent injuries to the skin cause axon damage and lead to axon degeneration. Degenerating axons leave behind debris that must be cleared before reinnervation can occur and sensation is restored. We use adult zebrafish as a model to study injury and innervation because they have homologous cells and structures to humans and have transparent skin, allowing for high-resolution microscopy. Previous experiments in our lab revealed that skin-resident immune cells known as Langerhans cells (LCs) use highly motile protrusions to engulf axonal debris in the zebrafish epidermis. How are these dynamic protrusions regulated at a molecular level? Calcium signaling regulates phagocytosis and cell motility in other cell types, but the role of calcium signaling in LCs is unstudied. Through scale pluck assays and fluorescent microscopy, I have established a model for monitoring calcium signaling in LCs. I observed transient calcium flashes in LCs that varied in frequency, intensity, and subcellular location. I perturbed calcium flux using a calcium chelator and observed decreased flash intensity and protrusion length in LCs, suggesting that calcium signaling is required for protrusion dynamics. To investigate how calcium signaling affects engulfment, I imaged calcium flux in LCs during phagocytosis of apoptotic cells after laser injury. In contrast to the transient flux normally observed, LCs exhibited sustained high concentrations of cellular calcium during corpse engulfment. Because of the effects of perturbed calcium flux on intracellular calcium and protrusion motility, I hypothesize that perturbing calcium concentrations will inhibit LC phagocytosis. Identifying the molecular mechanisms underlying debris removal, such as calcium signaling in LCs, is relevant to understanding skin repair and disease states in which axon homeostasis is altered, including diabetic and chemotherapy-induced peripheral neuropathies.

The leading causes of hearing and balance disorders are damage and loss of inner ear hair cells. Noise overexposure and aging can damage the fragile synaptic transmission between presynaptic hair cells (HC) and postsynaptic afferent neurons (AN), leading to “hidden” hearing loss. Hidden hearing loss is a condition where one can show normal auditory sensitivity when tested but still have difficulty in situations such as hearing one person in loud environments. Mitochondria might play an essential role in this connection by regulating transmission and energy supply. Mitochondria are known to adapt their morphologies to meet cellular demands. Studying mitochondrial morphology may reveal solutions to hearing preservation and contribute to our overall knowledge of the auditory system and general biology. Our lab has previously found that presynaptic hair cells harbor unique mitochondrial networks localized at the presynaptic HC release sites (ribbons) regulated by activity. However, the synapse requires postsynaptic neurons to function correctly to maintain healthy auditory transmission, so we examined the postsynaptic ANs. Preliminary data of two postsynaptic ANs revealed mitochondrial networks that extend between different HCs, but substantial evidence was lacking. Using the zebrafish lateral line as a model system, I microinjected fluorescent probes that tag AN mitochondria, Ca2+ uptake, and track depolarization via Channelrhodopsin. I used serial block-face scanning electron microscopy (SBFSEM) to reconstruct zebrafish AN and their mitochondria. SBFSEM cuts thin layers of the fluorescently tagged structures and images each layer to generate high-resolution 3D images. Probes successfully tracked the different functional characteristics. We observed distinctive architecture in postsynaptic mitochondria, confirming our preliminary findings. Further research will assess changes in postsynaptic mitochondria and regulation by synaptic activity. Understanding the connection between mitochondrial architecture at the synapse and its functional mechanisms will contribute to our knowledge of proper synaptic transmission and the pursuit of healthy hearing preservation.

 Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder that often results in deficits in communication, social skills, and emotion regulation. Additional concerns include disruptions to the sleep wake cycle that results from circadian rhythm dysfunction. 40% of individuals with ASD also have clinically significant anxiety, which tends to exacerbate pre-existing behavioral issues and social deficits. Previous studies suggest an association between increased sleep dysfunction and increased issues with anxiety in typically developing (TD) adults, and have insinuated a possible bidirectional relationship between the two. This study aims to look at the relationship between sleep quality and anxiety in adults with and without ASD. 89 adults (ASD=39) from a longitudinal five-site NIH-funded study on sex differences in autism were included. Participants completed the Munich Chronotype Questionnaire (MCTQ), a measure of the amount of sleep, based on sleep-wake times, and the Screen for Adult/Child Anxiety Related Disorders for a measure of generalized anxiety. Analysis will include (1) independent sample t-tests to examine group differences in anxiety and sleep duration and (2) correlations between sleep duration (MCTQ) and generalized anxiety subscore from the SCAARED measure for the group with ASD and the typically developing group. I hypothesize that individuals with ASD compared to TD will demonstrate higher anxiety scores and worse sleep quality. I also hypothesize that there will be a correlation between higher anxiety scores and shorter sleep duration. Additionally we will explore sex differences in anxiety and sleep. If sleep quality is related to anxiety, this might support the increased use of sleep behavioral interventions to improve mental health in individuals with autism spectrum disorders.

As diseases like COVID-19 become endemic, it becomes more apparent that access to low-cost, user-conducted tests with high sensitivity and rapid results are necessary to help reduce the spread of disease and mitigate burden on healthcare and laboratory infrastructure. While paper-based colorimetric tests attempt to fill this gap, they have reduced sensitivity when compared to “gold-standard” tests such as RT-qPCR, which typically exhibit results with fluorescent reporters. The goal of this project is to detect fluorophore activity using a smartphone camera and flash, with zero modifications (or as minimal as possible). As many people have smartphones and the ability to take a picture, but fewer possess lab skills or access to a lab, we aim to develop a smartphone-based system with the highest sensitivity and lowest barrier for entry, that is capable of detecting a fluorescent output. We are experimenting with both biological and technological levers, including combinations of time-delay using FRET and long-lasting fluorophores. On the software side, we are looking into whether we can leverage a smartphone’s built-in bayer filter to better delineate between emission wavelengths of fluorophores, and using timed flashing and recording methods to detect the biological time delay. So far, we have collected preliminary data on colorimetric readout reactions and shown that the difference between reactant and negative control is apparent at fairly low concentrations (250 uM). We expect that with a simple filter setup, we will be able to excite and detect the fluorescent output from a fluorophore. Further research will aim to simply things setup further, to reduce the number of external modifications required for use. When coupled with a diagnostic test, these ideas could potentially bring any test that can be coupled to a fluorescent readout from the lab to the user, increasing accessibility and lowering the costs of such tests.

STEM education tends to avoid extensive discussion of ethics on topics such as climate change, treatment of disease, and nutrition. However, as textbooks set the foundation for curricula, it is crucial that they allow students to think critically about the ethics of performing science and societal impacts of biological research. Our work tests the hypothesis that introductory biology textbooks use predictable strategies to humanize science (e.g., inviting the reader to act like a scientist to develop a solution) and that some topics are more likely to have humanizing elements than others (e.g., some topics are better positioned to serve as launching points for instructors who seek to include humanizing elements in their class). Bringing in discussions of ethics into the science classroom is one strategy instructors can use to humanize biology. We define humanization as the act of positioning science in a social context and/or the act of discussing science through the lens of justice and/or injustice. Of the instances of humanization identified in these textbooks, ethics was mentioned in only 4.57% of these quotes. Ethics was discussed in relation to impacts on humans (41.0%), impacts on humans by humans (41.0%), and impact of humans (16.7%). Discussion of ethics was nuanced (43.6%), detailed (30.8%), and rarely included justice (10.3%) and equity/inequity (5.1%). Ethics was most commonly discussed in terms of biotechnology (38.7%), treatment of disease (12.0%), and environment (10.7%). These findings demonstrate that ethics is rarely made reference to in introductory biology textbooks, yet the field of biotechnology is at the forefront of biomedical innovation, thus having nuanced discussions about controversial subjects (e.g., CRISPR, GMOs, and eugenics) rather than only teaching what these subjects are is pertinent to the training of future scientists.

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.

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.

The lateral hypothalamus (LHA) is an important brain region for motivated behaviors including feeding. The LHA contains GABAergic (inhibitory), Glutamatergic (excitatory), and other neuropeptide neuron populations. Previous research demonstrated that optogenetic stimulation of LHA GABA neurons increases food consumption while stimulation of glutamate neurons decreases food consumption, but both populations increase in activity during consumption. The caveats to these previous research experiments are that they do not isolate consummatory behaviors from appetitive behaviors, and they only focus on the role of neuronal stimulation on caloric consumption, not on non-caloric rewards or aversive tastants. In our experiments, we use a multi-spout head-fixed mouse behavioral system to isolate consumption from other behavioral variables, and measure consumption over a range of different concentrations of either rewarding or aversive taste solutions. Using fiber photometry, I recorded calcium dynamics from both neuronal cell types of interest simultaneously, and we found that GABA neuron activity scales with increased lick rate regardless of the solution, while glutamate neuron activity scales with aversive but not rewarding solutions. When I stimulate LHA GABA neurons during consumption using the red-shifted excitatory opsin, Chrimson, we see an increase in licking regardless of solution. Stimulation of LHA vglut2 neurons reduced licking regardless of solution. We also ran inhibition experiments using the red-shifted inhibitory opsin, JAWS, of the two populations and saw that GABA inhibition reduces consumption, while glutamate inhibition increases consumption. Our research has shown how both populations work to drive consummatory behaviors and how their activity level influences consumption. This research is important because it uncovered the function of LHA GABA and Glut neurons in bidirectionally mediating consummatory behaviors for both rewarding and aversive solutions and will contribute to understanding of health issues related to consumption such as obesity.

To navigate their surroundings, migratory cells respond constantly to many signals in their environment, including both chemical and electric cues. These signals are produced locally by other cells, pathogens, and in the context of electrical signals, by disruption to the normal ionic balance across cell boundaries. Disruption to this ionic balance will create a local electric field to which immune cells will respond to guide their movement and prevent infection. How cells sense or respond to this electrical cue is not known. To better understand this phenomenon, we are using HL-60 cells that are a migratory neutrophil-like human leukemia cell line, which we have found migrates to the cathodal pole of an applied DC electric field. We have identified a number of gene candidates related to glycosylation, the modification of proteins with the addition of sugar molecules, that reduce the directionality of HL-60 cells in an electric field. Using CRISPR interference to create cell lines with reduced expression (knockdown) for eleven of the gene candidates, we are studying how the loss of these genes alter migration. We used video microscopy to track their migration in 3D at different intensity levels of current to see how the loss of these genes affected cell movement when cells are exposed to an electric field. All of these knockdown lines showed marked change in the cell's response, with less persistence towards the cathode at higher currents than control HL-60 cells. Of these eleven, knockdown of UXS1, a gene that encodes for UDP-xylose that is used in the attachment of long sugar chains (glycosaminoglycans) to certain proteins on the cell surface, showed the greatest effect. Our results suggest that UXS1 is critical for neutrophils' ability to sense or respond to DC electric fields. 

Lck is a lymphocyte-specific tyrosine kinase involved in T cell activation, which is essential for the human immune response. Upon antigen engagement with the T Cell Receptor (TCR), Lck phosphorylates the CD3ζ chain of the TCR, transducing intercellular signaling that activates T cells. Recent studies have demonstrated that Lck’s phosphotransferase activity is not only important for T cell activation, but that Lck also plays a critical role in scaffolding the interaction between the phosphorylated CD3ζ chain of the TCR and the kinase ZAP70 using its regulatory domains. Lck’s phosphotransferase activity has been shown to be toxic to yeast, with increased activity correlating with decreased yeast-growth rates. Using a yeast growth-based deep mutational scan (DMS), we calculated the activity scores of ~5,000 single amino acid variants of Lck’s kinase domain. Through this DMS, we identified all positions on the kinase domain that are amenable to substitution without perturbing kinase activity. In particular, we focused on positions where we could install cysteine residues on the kinase domain without perturbing kinase activity. Currently, we are expressing these cysteine variants in primary T cells, and applying parallel chemoselective profiling methods to quantify changes in the electrophilic reactivity of the cysteine side chains upon TCR stimulation. The expected changes in alkylation of the cysteine side chains upon TCR stimulation will provide insight into changes in the conformational flexibility of Lck, accessibility of the substituted residue sites, and intramolecular protein-protein interactions (PPIs) of Lck upon TCR stimulation. Ultimately, this insight into the conformational dynamics of Lck can be applied to deepen our understanding of basic immunology and the T cell activation signaling cascade.

Research suggests that recruitment, the number of fish entering a population in a given year, is influenced by the environment. However, environmental drivers are not currently used to refine the recruitment estimates of most statistical models used in fisheries management (hereafter, population assessment models). This is increasingly relevant as fish populations experience long-term productivity shifts due to climate change. One major goal of the National Oceanic and Atmospheric Administration (NOAA) in recent years has been to incorporate environmental drivers into population assessment models. This is achieved by using time series data of environmental drivers to inform model estimates. One ongoing challenge is determining which environmental drivers have potential to improve model estimates. In this project, we aimed to determine how correlated an environmental driver time series must be to historical recruitment deviations to improve key model estimates – recruitment deviations and population depletion – in recent years for a range of species. We used R to simulate mock environmental driver time series with varying correlation levels to recruitment deviations by randomly sampling data from a normal distribution. We then compared errors in estimates between population assessment models fit with and without the simulated environmental data. Our results suggest that the more correlated an environmental driver is to historical recruitment deviations, the more accurate estimates of both recruitment deviations and population depletion become. However, our results also reveal that the correlation level necessary for environmentally-driven models to consistently produce more accurate estimates than the original model varies across species. These correlation thresholds are also generally higher than observed correlations between recruitment deviations and environmental drivers in actual fish populations. We suggest fisheries scientists run similar simulation experiments to determine which correlation levels have the potential to improve population assessment models for their target species.

Conjugative plasmids are extrachromosomal genetic elements commonly found in bacteria and are capable of being shuttled between different bacterial cells via a process called conjugation. The Luria-Delbruck Method (LDM) is a stochastic based modeling framework used to estimate the conjugation rate of a particular plasmid between bacterial strains. In my experiment, I am probing the theoretical experimental assumptions made by the LDM; in particular, I am testing that when there is variation in the precision of the selection assay, the application of a theoretical correction can result in accurate quantification of the conjugation rate. In the early phases of the experiment, I performed experimental assays in liquid medium to determine antibiotic concentrations in which donors (strains hosting a conjugative plasmid) and recipients (strains able to receive plasmids from donors via conjugation) die and transconjugants (recipient cells that have received plasmid from donor) grow. To test the theoretical correction, I chose two antibiotic concentrations that differ in the amounts of extinction occurring in the transconjugant population. I executed the LDM conjugation assay with these two conditions which produced equivalent conjugation rate estimates, as would be predicted if the correction factor is effective at mitigating the bias produced from variable amounts of transconjugant extinction in the selective conditions. My experiments demonstrate that the LDM continues to be robust in the face of violations to experimental assumptions which affirms the viability of applying the method to a wider range of bacterial populations with variable selective conditions and thereby broadens our ability to understand the dynamic movement of conjugative plasmids.

Current sociopolitical climates for LGBTQ+ individuals in South Asian countries are hostile, and South Asian communities within America will often reflect similar beliefs. Likewise, there might be an unfavorable atmosphere for LGBTQ+ individuals at faith-based institutions. As such, for South Asian college students enrolled in Christian institutions, their religious context and South Asian cultural practices and values might combine to shape their attitudes towards LGBTQ+ people. To explore this understudied topic, I utilized semi-structured interviews with South Asian students at a Christian institution. Thus far, I have interviewed four participants and intend to complete at least eight interviews to meet the qualitative analysis standard. Preliminary examination reveals our participants’ tendency to avoid conversations about the LGBTQ+ community, and they connected this tendency to South Asian culture. In contrast, they noted that LGBTQ+ topics were actively discussed on their Christian campus. Our study hopes to expand on the research surrounding intersectional identities and their impact on the individual.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by social communicative impairments and sensory sensitivities. Additionally, the physical and social changes that occur with puberty may be a turbulent time for adolescents. Earlier pubertal timing has been correlated with higher internalizing mental health symptoms for neurotypical girls with earlier onset of menarche in females being tied with higher rates of depression that persists into adulthood. This study investigates the relation between pubertal timing and internalizing mental health problems for autistic and non-autistic female adolescents in a longitudinal study. 23 female ASD participants (ages 8 to 17) and 42 female neurotypical participants (ages 8 to 17) from a NIH-funded project investigating sex and gender differences in individuals with autism are included. Participant data was collected at a second timepoint, 3 to 8 years later. Data on pubertal development was collected using the Pubertal Development Scale, a parent or self-report measure of physical development. Depression and anxiety were assessed using the Child Behavior Check List, a parent-report behavioral checklist of mental health symptoms at the first time point, and a self-report version of the CBCL at the second time point. First, we examine pubertal timing variation by calculating residuals of a pubertal maturation by time regression plot. Second, we will investigate the relationship between puberty timing and depression and anxiety using a correlation test. To further analyze this relationship between pubertal timing predicting future depression and anxiety, we will run a multiple regression test. I predict that the relationship between pubertal timing and depression and anxiety will be greater for autistic girls than for neurotypical girls. This study’s data can add a neurodiverse perspective on how pubertal timing impacts mental health in females and could provide evidence for the need of interventions and additional support to adolescent females with ASD.

Climate change continues to intensify the hazards we, and our civil infrastructure, experience. The 21st century has marked an increase in frequency and severity of flooding, hurricanes, wildfires, and extreme temperature events. Our new dynamic environment, with concurrent risks from multiple natural sources, needs engineering solutions to enable multi-hazard risk reduction efforts. This project investigates using polymers as an adaptable solution to simultaneously tune the behavior of reinforced concrete structures for multiple hazards. This differs from standard practice, where the response of a structure is determined based on a single load scenario. Polymers that exhibit strain-rate- and time-dependent properties are introduced to tailor the bond characteristics between the rebar and concrete in critical regions, producing improved overall structural performance when considering a multi-hazard environment. Through standard testing, polyurethane was chosen as the polymer based on compression and shear modulus results at different strain rates. To investigate the influence of polyurethane layer thickness, shape, and strength on the bond behavior between rebar, polyurethane, and concrete, cylindrical concrete specimens were tested under cyclic displacements at three different strain rates. The specimens were constructed by casting concrete between a central corrugated duct and a steel tube. Rebar was aligned along the central axis and polyurethane was cast between the steel duct and rebar. The testing data was used to determine the effective bond stress on the rebar as a function of material duct size and shape. The bond was shown to vary based on the geometry, induced strain rates, and strength of the polyurethane layer. This is markedly different than in current practice where the bond stress is assumed to be constant. The results of this project will help equip structures to adapt to multiple worsening climate change driven hazards, reducing the risk of building failure under extreme loading therefore improving community safety. 

Glaucoma is a neurodegenerative disease that causes loss of retinal ganglion cells in the retina, resulting in incurable blindness. While current research efforts have largely focused on regenerating RGCs and other retinal neurons, it has been recently shown that inflammation resulting from immune responses to injury/degeneration can negatively impact retinal regeneration. Microglia are part of the innate immune system and are the only resident immune cell in the retina and brain; they are involved in inflammatory signaling, phagocytosis, and monitoring tissue for foreign pathogens. Previously, our lab has shown that microglia restrict regenerative capacity; microglia ablation improves neuronal replacement strategies in a mouse model. Here, we want to determine if we can develop a new method to ablate microglia from the retina via intraperitoneal (IP) injections, and observe if ablation affects invasion of the peripheral immune system (monocytes) during the inflammatory response post injury. To comprehensively ablate microglia from the retina, we test both dosage and treatment length (days) of IP injections of PLX5622, a drug which inhibits a receptor necessary for microglia survival. After specific treatment courses, mouse retinas are harvested and immunostained for microglia markers to determine the level of ablation. To determine the interaction between microglia presence and monocyte invasion in a glaucoma model, we use a CCR2-RFP mouse line to track monocytes. These mice will be injected intraocularly with NMDA, a toxin that kills RGCs. The number of invading monocytes at each time point post-NMDA-injury can be assessed with and without PLX5622 treatment to see if ablation of microglia impacts the invasion of monocytes. We expect monocyte recruitment to drastically decrease after microglia ablation. This work will allow us to investigate the role of microglia in developmental processes and identify immune targets that would be most amenable to immunomodulation interventions in future therapies for glaucoma.
 

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.

Recent studies suggest that errors facilitate learning in certain conditions. Despite this, reinforcement paradigms dominate learning methods, subscribing to the narrative that errorless learning is the foundation of an ideal learning environment. If we continue to view learning from this restrictive perspective, we may fail to capture and apply the benefits of errors. Furthermore, although error learning is now a well-documented phenomenon, research on its underlying mechanisms is sparse. Two prominent theories have arisen out of this research; the elaborative hypothesis, in which meaningful connections are derived from errors, and the mediator hypothesis, in which errors act as secondary cues. To go beyond speculation, both must be examined empirically to successfully leverage error learning. Using a combined approach, data from computational models formulated to reflect different mechanisms of error learning were compared to behavioral data. In the behavioral task, participants (N = 61) learned word pairs in either a study or error trial before taking a final test. Supporting past error learning literature, errors before a study opportunity led to better performance on a final test. Differences in reaction times between conditions support the theory that errors increase learning through mediation by acting as a secondary cue rather than as a way to establish a deeper network between the cue and answer. Furthermore, comparing behavioral results to computational cognitive models provided insight into individual differences in mechanisms of error learning.

Eukaryotic DNA is compacted into cells by wrapping DNA around nucleosomes. Nucleosomes are composed of core or variant histone proteins. Unlike core histones, histone variants enable specialized chromatin functions such as gene transcription or inheritance. Given their crucial and widespread functions, core histones and their variants are typically evolutionarily conserved in sequence and function. Therefore, lineage-specific differences in histone repertoires present unique opportunities to understand their functional consequences on genomic organization and biological processes.

Two such changes, both likely selectively advantageous, have occurred in budding yeast and flies. In budding yeast, the histone variant H2A.X, involved in DNA repair, entirely replaced core histone H2A. A crucial SQ motif on the C-terminal tail of H2A.X is required for its DNA repair mechanism. In flies, the loss of H2A.X and a fusion of the SQ motif from H2A.X with a conserved variant H2A.Z, which is implicated in gene expression, gave rise to a unique H2Av variant. We are recreating the histone H2A compositions of flies in yeast to determine the functional consequences of these evolutionary re-arrangements. Specifically, in S. cerevisiae, we moved the SQ motif or the entire C-terminus of H2A.X to H2A.Z, creating a fusion histone similar to the D. melanogaster H2Av. Therefore, the H2A repertoire in these engineered yeast resembles a fly's. Upon treatment with DNA damage agents, these “Drosophilized” yeast show reduced DNA damage repair efficiencies similar to mutant yeast with no SQ motif. Thus, we hypothesize that the abundance and/or localization of the SQ motif is critical for efficient DNA repair in yeast. Furthermore, we will test if processes like sporulation, meiosis, or resistance to stressful conditions that require DNA damage repair are affected in our “Drosophilized” yeast. These experiments will reveal the biological consequences and potential advantages of the unique yeast H2A repertoire.

Studies have revealed evidence that some humans have increased midfoot dorsiflexion, or a midtarsal "break", which decreases rigidity of the arch structure during gait. This "break" suggests that more of the sole of the foot is in contact with the substrate in terminal stance, effectively shortening the lever arm during propulsion. This prompts us to wonder: does arch stiffness predict the magnitude of lever arm distance or the forces of peak braking and peak propulsion? The Arch Indices (AI) of 77 people were calculated in dynamic conditions. Locations of the center of pressure (CoP) of the foot at heel strike, peak braking, and peak propulsion were recorded using a pressure-sensitive mat (RSScan International, Olen, Belgium). I calculated the distance from the heel strike CoP to those of peak braking and propulsion. I normalized peak propulsion and peak braking forces by dividing each by weight. All statistics were calculated in STATA (Statacorp, College Station, TX, VBe17). Dynamic AI has a relationship with lever arm distances for heel strike CoP to those of peak braking and propulsion (p=0.042, p=0.005, respectively). Dynamic AI did not demonstrate significance with peak braking and peak propulsion forces (p=0.758, p=0.194, respectively). My results demonstrate an association between AI and the distance of the functional lever arms, suggesting the presence of a midtarsal “break” as flatter feet exhibited shorter lever arms. Midfoot dorsiflexion and loss of rigid arch structure associated with the "break" would result in a decreased lever arm for propulsion, since the anterior midfoot and forefoot are in contact with the substrate at a later point during gait. This analysis has broader implications for foot morphology and midtarsal “break” research. Future work can utilize infrared markers and force plates to create models of the human foot with ground reaction force (GRF) data.

Kidney function declines with age and is accompanied by injury to the nephron glomerulus. A critical cell for filtration in the glomerulus are podocytes, which are lost with aging and non-proliferative. However, the parietal epithelial cells (PECs) lining the Bowman’s capsule of the nephron may migrate to the glomerular tuft to replace podocytes through differentiation. The mechanisms by which PECs differentiate into podocytes is still unknown. Using a mitochondrial intervention peptide, we previously showed reduction of glomerular injury and improved PEC numbers in aged mice. Mitochondrial dysfunction increases in all organs with aging; therefore, we hypothesized that mitochondrial aging dysfunction affects PEC-to-podocyte differentiation. To determine whether mitochondrial aging dysfunction plays a role in the differentiation of podocytes from PECs, we used young (18-30 yrs.) and old (50+ yrs.) primary human cells derived from kidney PECs isolated from urine. Human urine progenitor cells (hUPCs) were sorted for makers CD133+ and CD24+. For hUPC progenitor-to-podocyte differentiation, we used ‘VRADD’ medium (100 nm retinoic acid + 100 nm Vitamin D3). Proliferation and oxygen consumption rate (OCR) were measured during differentiation. To determine the differentiation of hUPC, we looked for the loss of progenitor makers CD133+ and CD24+ by qRT-PCR. In both aged and young cells, hUPC-podocyte VRAD differentiation resulted in a significant increase of OCR that peaked at day 2 relative to control. Both proliferation and OCR normalized to cell number were significantly lower in aged vs. young cells. Cells cultured with VRADD showed decreased progenitor markers CD24 and CD133 (PROM1) as compared to controls, suggesting hUPC differentiation. Our results support an aging decline in PEC-podocyte differentiation Future work will confirm whether podocyte fate was achieved with qRT-PCR and immunohistochemistry for expression podocyte specific genes/proteins WT1, SYNPO, NPHS1, and NPHS2 and additional assays to measure mitochondrial function of hUPCs across differentiation.

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.

In this study, we explore the potential of using data from the DECam Deep Drilling program for asteroid science. The program, originally intended for supernovae and variable star science, produces valuable data that can be used to discover and analyze asteroids. Our focus is on the COSMOS fields, which are observed 5 times in each of the g, r, and i filters every 3 nights. We employ Heliolinc to match the data with known asteroids and discover 296 independent rediscoveries of known asteroids, as well as new discoveries that require further analysis. To analyze the known asteroids, we use forced photometry based on JPL ephemerides to measure their colors. Our results show that the average (g-r) color gets bluer and (r-i) gets redder with increasing distance from the sun. We use this information to develop a distance color metric that combines the colors to maximize sensitivity to distance. Additionally, for some of the best measured objects, we determine their rotation periods using Lomb-Scargle analysis. Our preliminary results demonstrate the potential of the DECam Deep Drilling program for asteroid science, particularly in analyzing asteroid colors and rotation periods.

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.

Autism Spectrum Disorders (ASD) refer to neurodevelopmental difficulties in communication and social interaction. It is thought that 94% of autistic adults have used camouflaging behaviors at some point in their lives, meaning that they have developed certain behaviors to blend in the social world and to “hide” their autistic differences. Camouflaging behaviors include: masking - hiding the autistic features; compensation - practicing certain behaviors to compensate for certain social shortcomings; and assimilation - trying to fit in so they are not singled out (Hull et al., 2018). We are interested in the relationship between camouflaging behaviors and social communication in individuals with and without autism. Data from 85 participants (42 ASD, 48 females) ranging from 15 to 23 years old from the NIH funded study on sex and differences in autism were included in the analysis. Autism diagnosis was confirmed via standardized tests and all participants had an IQ of 70 or higher. Participants completed the Camouflaging Autistic Traits Questionnaire (CAT-Q), a 25-item questionnaire that tests the degree of using camouflaging strategies, and Vineland Adaptive Behavior Scales, a parental interview that informs the diagnosis of intellectual and developmental disabilities. We predict significantly higher camouflaging behaviors and lower socialization skills in the autistic group compared to the non-autistic group. We predict a positive correlation between CAT-Q scores and Vineland socialization scores in the autistic group, since by resembling their peers will make their parents report better social skills. We also predict that the correlation between masking and social skills will be higher in females than males in both groups, as females are found to have higher social motivations (Cook, Ogden, & Winstone, 2018). Camouflaging may prevent others from recognizing the symptoms of autism and fail to get diagnosis. Therefore, it is important to detect camouflaging behaviors so autistic children get timely treatments.

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.

Chromatin plays a key role in determining gene expression and cellular states. The basic unit of chromatin is a nucleosome composed of ~147bp of DNA wrapped around a histone core with exposed N-terminal tails that help regulate gene expression programs through their post-translational modifications (PTMs). Facultative heterochromatin inheritance, a type of chromatin containing the repressive trimethylation of histone H3 at lysine 27 (H3K27me3) PTM, is necessary for maintaining cell fate, identity, and plasticity. The parental facultative heterochromatin gene repression is maintained during the S-phase by recycling parental nucleosomes containing H3K27me3 onto the daughter strands of DNA and spreading their PTM onto newly synthesized nucleosomes by the polycomb repressive complex 2 (PRC2). Dr. Escobar found that Nucleophosmin 1 (NPM1), a histone chaperone, assists in facultative heterochromatin domain inheritance through interactions with PRC2 in mouse embryonic stem cells. NPM1 is found mutated in roughly 30% of cases of acute myeloid leukemia (AML). Preliminary data finds a significant presence of cleaved NPM1 product at 20 kDa (p20) within the nucleus of normal hematopoietic stem cells (HSCs), but a lack of this NPM1 modification in AML cell lines. Cathepsin B has been shown to cleave normal NPM1 to produce a fragment at p20. I hypothesize that the lack of cleaved NPM1 product factors into leukemogenesis. To test this hypothesis, I have three aims; Aim 1 identifies the Cathepsin B cleavage site of NPM1 using in vitro cleaving assays; Aim 2 assesses the phenotype of HSCs containing a non-cleavable NPM1 mutant; and Aim 3 monitors the phenotype of AML cell lines when inducibly expressing Cathepsin B. This project allows for future investigations into how NPM1 modifications impact facultative heterochromatin inheritance of HSCs and AML cancer cells.

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.

 Subduction zones are regions where two tectonic plates converge, and one is forced underneath the other. They are the primary driver of plate tectonics, and a source of major earthquakes. These earthquakes occur at shallow depths where plates slide past one another quickly, but at greater depths, with higher pressure and temperature (PT) conditions, rocks behave more ductilely. The transition zone between brittle and ductile regions hosts slow slip events (SSEs), which accommodate motion between the plates during events that last months to years, as opposed to the seconds over which earthquakes occur. SSEs are an important mechanism for accommodating plate motion at depth, thereby affecting the occurrence of larger devastating earthquakes, but currently the processes which facilitate SSEs and the rocks that host SSEs are not well understood. By studying rocks formed in and ancient subduction zone from Santa Catalina Island in California, we can learn more about our own modern counterparts, as the rocks record the conditions where slow slip may have occurred. Using optical petrography and data from x-ray spectroscopy, I examine thin sections of epidote-rich blueschist from SSE PT conditions. Optical petrography allows me to characterize the mineralogy of this rock, and the x-ray data provide the chemical compositions of individual minerals. Using image-analysis software, I will pair these two datasets to estimate the bulk-rock chemical composition of my sample. These data will allow me to constrain the starting material (protolith) of this rock before it was metamorphosed in order to determine if it was originally a sedimentary or basaltic component of the subducting oceanic plate. Doing so will improve our understanding of the way in which rocks at those pressure-temperature conditions deform and chemically change to create the context in which modern SSEs occur.

Despite the brain being a 3D structure with a complex topography and spatial relationships, neuroscientists currently rely on 2D visualizations. These less informative visualizations obscure the distances between 3D regions, and hinder scientists’ ability to perceive functional correlations and anatomical connections. To provide a more decipherable method of exploring the structure and function of the brain, we built neuroscience tools specifically aimed toward exploratory 3D data visualization. I worked on the development of a Universal Renderer for Neuroscience (Urchin) that lets users plot their data in its original 3D anatomical context. Urchin can perform a variety of different functions such as displaying certain features (e.g. neurons, brain regions, or contextual objects such as probes), or interactively exploring the data within context of brain location via mouse and keyboard navigation. This not only paves the way for new methods of data analysis but also creates a deeper understanding of the structure and patterns found within the data. I worked on building Urchin within the Unity platform, implementing features to enhance data exploration and analysis via scripting in C. Some examples of functionality that I built include implementing 3D mesh rendering for brain regions, primitive models, and changing materials. I also established a proxy server that allows for secure communication between client side browser applications and python notebooks. Along with this, I developed a more intuitive and efficient python API that allows people with minimal coding experience to run the renderer visualizations with ease. Urchin enhances neuroscience research and education by providing a more interactive and immersive experience, allowing students and the public to directly engage with diverse data sets and investigate different aspects and features of the brain.

Electrophysiology experiments targeting deep brain structures require extensive training and expertise. However, even experienced researchers face challenges in placing electrodes precisely within a target location, particularly when using multiple electrodes simultaneously. On average, there is a 400-um (standard deviation) of human error when targeting Bregma and navigating to insertion coordinates. Slow setup time and human error can lead to unnecessary stress in experimental animals and prevent scientists from focusing on data collection. Our laboratory developed an experiment planning tool called Pinpoint to address these challenges. However, even with interactive tools, a typical two-probe experiment setup can take over an hour, increasing as more probes are added in complex experiments. To reduce time inefficiencies and lower the risk of human error, we developed an electrode manipulator automation platform for Pinpoint. Our platform consists of a server application called Ephys Link, which unifies communication between Pinpoint and various electrode manipulator platforms. With Ephys Link, scientists can view the electrodes they are using in their experiment live inside the virtual brain and pre-plan insertions for multiple probes. They can then simply press a button to have their probes automatically move to their chosen targets. We expect our automation pipeline to make multi-probe electrophysiology an easier and more accessible task for researchers, enabling them to focus on gathering high-quality data rather than managing the geometry of their experiments. To measure the impact of our automation platform, we plan to use positional logging, timed recordings, and researcher feedback to evaluate the efficacy of the pipeline in speeding up electrophysiology experiments. We expect to see increased targeting precision, reduced time setup time, and overall productivity boosts for researchers. By reducing electrophysiology's difficulty and time-consuming nature, our automation pipeline helps researchers alleviate cumbersome experiment setups and prevent unnecessary stress on experimental animals.

The COVID-19 pandemic has changed prioritization and delivery of public health and health care services. Community health workers (CHWs) are an integral part of the healthcare workforce since they connect the most marginalized communities to health and social services. Although there are currently 11 published reviews about CHWs during the COVID-19 pandemic, none focus on the U.S. In this study, we set out to systematically review the literature on CHWs in the U.S. during the COVID-19 pandemic. Specifically, we aim to describe the: 1) roles and responsibilities of CHWs during COVID-19; and 2) organizational settings of CHW integration. We followed systematic review guidelines and focused our search within two major health sciences databases. Included articles were published in English between January 2020-December 2022 and described U.S.-based CHW programs taking place during COVID-19. The initial search retrieved n=322 articles. After removal of duplicates, abstract and title screening, and full text screening by two reviewers, n=26 articles remained. Of the 26 articles, 13 (50%) described CHWs activities to address COVID-19 (e.g., contract-tracing, vaccination) while 15 articles (57.7%) described CHW activities to address non-COVID health conditions (e.g., food security, diabetes). A total of 22 articles (84.6%) described CHW activities to meet individual-level health and social needs of clients (e.g., language translation, patient outreach) while 12 articles (46.2%) described CHW activities to address structural barriers (e.g., advocating for policy change around COVID-19 data equity, increasing healthy food options in underserved neighborhoods). Articles described CHW work across multiple settings including communities (n=18, 69.2%), clinical (n=9, 34.6%), and research (n=8, 30.8%). This study highlights the scope of CHW activities during the COVID-19 pandemic in the U.S. This is important to generate best practices for CHW-led care coordination and structural advocacy post-pandemic to facilitate the health of individuals and populations within U.S. contexts.

As algal blooms continue to demonstrate a great risk to aquatic ecosystems, it’s important to understand the effects aggressive algal growth can have on the organisms that would normally consume them. In a predator-prey ecosystem, stability between grazers and primary producers is determined by the interactions of the species. This study observes this stability using Closed Ecological Systems (CES) containing the algal species Ankistrodesmus, Scendesmus, and Selenastrum, unknown bacteria, and the grazers Daphnia magna. CES are sealed ecosystems that prevent gas exchange with the atmosphere. CES also carry the advantage of repeatability, uncommon in ecological field research. Past research in the Taub lab suggests that if the population of algae increases too rapidly, photosynthesis will cause a pH increase, associated with the death of Daphnia. Understanding which conditions best support D. magna helps us understand how the environment affects a grazer’s ability to compete against rapid algal growth. To determine the optimal initial concentration of algae with their associated nutrients, we set up CES in 6 treatments with ~10% and ~1% algal concentrations, either with or without D. magna, each with 6 replicates. We measure population dynamics by chlorophyll fluorescence, D. magna count and size, ephippia (sexual eggs) presence, and pH indication. CES without D. magna are used to compare how algal growth proceeds without the consumers. The treatments with lower algae concentrations may allow D. magna to persist longer by controlling the algae population and associated pH increase or may experience starvation. The findings of this experiment will give us a deeper knowledge of how algal growth can pose a threat to grazers, and how this information can be applied to other grazer-algae relationships.

The use of computational models of memory has been effective in adaptive learning environments and in determining the memory capabilities of learners. However, these models have not been widely applied in clinical settings. Evaluation of memory loss still heavily relies on extensive neuropsychological testing performed by neurologists or psychiatrists, especially in the context of progressive neurodegenerative disorders. Current evaluation tools lack the necessary reliability, convenience, and repeatability to effectively capture key dynamics of memory decline, including the unique and changing nature of memory over time. The goal of this study was to predict and monitor memory decline in individuals diagnosed with Mild Cognitive Impairment (MCI) using a model-based adaptive fact learning system. Participants, aged 58 to 78 years, were divided into two groups based on their cognitive classification and completed weekly online learning assessments at home, tracking their individual speed of forgetting (SoF) across various study materials. The results showed that this method was effective in accurately diagnosing mild memory impairment, with a success rate of over 80% after a single 8-minute learning session. The study also demonstrated the model’s ability to distinguish MCI subtypes through computations of participants' SoF. These findings offer novel insights into the progressive nature of memory decline and could have implications for early detection and management of Alzheimer’s disease as well as other forms of dementia and cognitive impairment. Further development of this method could serve as an alternative or complement to established diagnostic procedures and be used in clinical settings.

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.

Human history is marked by intergroup and interpersonal conflict. Over time we have begun to understand that humans, and other animal species, are imperfect decision-makers influenced by learned social biases. Specifically, we are interested in understanding in-group bias: the tendency to favor those of one’s own group over those in other groups. In order to investigate this behavior at the neural circuit and cellular level we developed a social behavior paradigm using male mice. Our paradigm utilizes the resident-intruder assay to determine which social behaviors the resident mouse (C57BL/6J male, n = 16) displays in response to a novel ‘in-group’ (C57BL/6J male) or ‘out-group’ (C57BL/6J albino male) intruder placed in their home cage. We focused on investigative and aggressive behaviors and found that a little over 50% of our resident male mice displayed an out-group aggression bias. This bias was eliminated after early life exposure to a C57BL/6J albino, supporting the hypothesis that this behavior is learned. To better understand the development of in-group bias, our future experiments aim to recapitulate out-group aggression bias without the use of a genetic variant by artificially creating groups with neutral odors. We plan to group-house half of the mice in neutral odor A and the other half in neutral odor B to fabricate an in-group and out-group, and determine whether this model produces out-group aggression bias. These insights will help us to interrogate the neurobiology of aggressive behavior and provide insight on out-group aggression and potential ways to reduce this bias.

Ovarian cancer is the deadliest gynecological malignancy with an estimated 13,270 women in the United States to die from it this year. Because of its nonspecific symptoms, it is often diagnosed at advanced stages, resulting in lower survival rates. The majority of current in vitro models for ovarian cancer use established cancer cell lines that lack clinical and translational relevance due to their inability to capture the high inter- and intra-tumor heterogeneity. To study tumor heterogeneity and cancer initiation, induced pluripotent stem cells (iPSC) have emerged as a new powerful tool that are both amenable to gene editing and differentiation into different cell types. One group has previously reported the generation of fallopian tube organoids from human iPSC. However, the generated organoids lack the characteristic tube-like structure as well as components of the microenvironment that removes the possibility to address structural factors and the functional role of the extracellular matrix. Bioengineered devices can be used for geometric cues and controlled release of biomolecules that can guide spatiotemporal cell and tissue organization. This project focuses on establishing a model by seeding iPSC-derived fallopian tube epithelium into lumenized microfluidic devices for further study on cancer initiation and drug screening. To confirm the generation of relevant cell types, I will benchmark the iPSCs at different time points throughout the differentiation protocol with qPCR and immunostainings. We expect results to show specialization of iPSCs towards the fallopian tube epithelium lineage and their further maturation (cilia beating and mucus secretion) once incorporated in the designed device. Once a model is established, further work can be done on elucidating factors such as substrate curvature, genetic mutations, and infections on tumorigenesis.

 Attention Deficit/Hyperactivity Disorder (ADHD) is one of the most common psychiatric disorders affecting adolescents. Treatment often focuses on managing symptoms, including distractibility, poor concentration, disorganization, hyperactivity, and impulsivity. A successful transition to adulthood requires interpersonal, organizational, and planning skills, making adolescence a critical time to treat ADHD symptoms. Sibley et al. (2014) reviewed treatment literature on ADHD in adolescents and concluded that medication and behavior therapy both produce similar effects on ADHD symptoms in adolescents. This project aims to update the results of the prior review using the past ten years of research. First, an electronic database search was conducted using four categories of terms: (1) sample age, (2) disorder, (3) treatment, and (4) randomized control trial. Experts were also contacted to request additional articles published during the designated period. Inclusion criteria were then applied: (1) published between 2013-present, (2) ages 10-19, (3) ADHD diagnosis, (4) quantitative data reported for at least one ecologically valid outcome measure (e.g., ADHD symptom severity), (5) in studies where individuals not meeting age or diagnostic criteria are included, data for adolescents with ADHD must be presented separately, (6) must evaluate treatment efficacy. 20% of the studies were also randomly selected for an inter-rater reliability probe. Next, data were collected based on the type of study, methodology, and participant demographics for every included study. Effect sizes were also calculated for several outcome measures. This review is still in its preliminary stages but will provide an updated review of the most effective pharmacological and non-pharmacological treatments for ADHD in adolescents. It will demonstrate the considerable growth in the number and highlight the effectiveness of available treatments. The next step will include quantifying data to determine trends for each treatment and conclude the review by summarizing our findings.

Sickle cell disease (SCD), the most common genetic blood disease in North America, is characterized by recurrent episodes of acute severe pain due to blockages of red blood cells. In past studies, digital cognitive-behavioral interventions have been shown to be beneficial in other chronic pain conditions through teaching pain-management skills. Our research investigates the effectiveness of iCanCope SCD (iCC-SCD), a web and mobile-based pain-management program for SCD pain in youth ages 12-18 years. The final enrolled sample for the study was 137 participants, of which 26 participants were excluded because they did not complete pre-treatment assessments. Thus, the final sample consisted of 111 adolescents (107 caregivers), 54 randomized to Education control, and 57 randomized to iCC-SCD. The iCC-SCD program includes modules teaching coping strategies, symptom and goal-tracking, and peer-based social support, while the attentional-control contains static education about SCD. The efficacy of the program is determined through self-report scales at pre-treatment, post-treatment (2 months), and follow-up (6-months) periods, targeting the primary outcomes of adaptive coding, pain reduction, and pain-related disability. A statistically significant effect of treatment group (iCC-SCD vs. Education) on change over time in average pain intensity from baseline to 6-month follow-up was found. While most youth engaged with the program (40/57, 70%), the overall usage was highly variable. Therefore, I will explore the differences between participant website and app engagement from this study, feedback on why participants may or may not have been able to complete the iCanCope program and determine areas to enhance engagement. The information collected in this analysis can help to improve web- and mobile-based interventions for not only youth coping with SCD pain but also those with other pain-related conditions, given the flexibility and universality of cognitive-behavioral frameworks.

Politicians use inflammatory language to manipulate voters via aspects of identity: race, sexuality, gender, religion. Due to differences in values within each of these groups, word choice significantly impacts ideological viewpoints. This literature review’s purpose is to highlight the study of inflammatory language that manipulates the public’s identity. During the World Warâ…¡Era the Nazis used false information to sway the public toward an identity-based agenda. In a stark comparison, representation of race was essential in the fight for civil rights. Thus, where is the moral line drawn in the use of identity politics? If an individual doesn’t have an egalitarian outlook, words are weaponized against different communities. Later in the Reagan Era, Reagan used religious catchphrases to rally the Moral Majority, in which he used the religion of others to his own advantage. Negative tribalism re-occurs as a socio-political trend reaffirmed by trigger concepts. The findings are that politicians from all over the political spectrum use terms that irrationally anger and rally narrow bases. These dog-whistle-like phrases are used in ways that subvert two group identities in one way or another, like the power dynamic between agents and the oppressed. This project investigates the effects of politicians’ diction in contrast with the reaction of different communities. The use of terminology by powerful people, could be a danger to the survival of the democratic process. Political analysts need to be aware of the intersectional relationship between inflammatory language and identity to better understand hostage holding behaviors of each political party. An inflammation of this vocabulary could spark a similar hatred of the past and leave our democracy left in ashes.

Satellite missions generally require real-time knowledge of the satellite’s orientation in space. A star tracker, which operates by identifying constellations of stars in photographs, is generally the most accurate attitude determination system and therefore the preferred method. However, it is not uncommon for small satellite missions to have limited computing resources, such as radiation-hardened CPUs, as well as a limited budget. Commercial star trackers can handle these limitations, but most are prohibitively expensive and do not have public documentation of their software. Existing open-source star trackers exhibit good performance only in specific scenarios or require more powerful computing hardware. In order to reproducibly evaluate star tracking algorithms that are capable of running on low-compute satellite missions, and to provide reusable open-source implementations of these algorithms, we developed LOST: Open-source Star Tracker. We compare a suite of star tracking algorithms on performance metrics such as speed, accuracy, and memory usage, with a testing framework capable of generating realistic star images with various noise sources. Our evaluation determines which algorithms have the strongest performance under varying conditions such as motion blur, centroiding error, and number of false stars. In a scenario representative of a low-cost star tracker, the evaluation finds a set of algorithms that are able to identify over 95% of photos in less than 1 millisecond per image, with a peak memory usage of less than 1 MiB, backed by a database of less than 500 KiB. These results indicate that the algorithms implemented in LOST are suitable for running on embedded or radiation-hardened systems with very limited memory and compute power, while still achieving the high accuracy that is characteristic of star trackers.

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.

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.

Mytilid mussels are foundation species who serve a vital role in temperate coastal ecosystems. As ecosystem engineers, mussels modify the physical and local chemical environment, which can both inhibit or facilitate other species. Through a mussel’s metabolic process (i.e., respiration and calcification) they have the ability to alter their chemical environment which has been suggested to be influenced by their gaping behavior. The objective of this project is to associate a given gape behavior to a known mussel behavior (e.g. active/passive filter feeding or laying byssal threads). We installed Hall effect sensors – a specialized magnetic sensor– on the posterior end of the mussels to analyze how wide a mussel gapes. A video camera filmed the mussels concurrently with the sensors to verify the gape signal with a known behavior. We recorded and captured mussel behavior for three Mytilus mussel species (M. trossulus, M. galloprovincialis and M. californianus) for 24 hours (n=8 for each species). We hypothesize that behaviors in mussels that are more active (e.g. active filtering or laying byssal threads) may have more variation in gaping behavior than behaviors like passive filtering where mussels could be resting. We also expect that gaping behavior will differ among the three species, with M. californianus spending less time closed compared to M. trossulus and M. galloprovincialis. Our project takes the first step in interpreting how valve gaping and its relationship with a given mussel behavior may determine how a mussel’s behavior plays a role in their ability to modify their local chemical environment.

Indoor air pollution is a major issue in urban homes, where hazardous volatile organic carcinogens (VOCs), including formaldehyde, can accumulate in the air. This study aims to investigate the potential of genetically modified Epipremnum aureum (pothos ivy) in reducing indoor air pollution by degrading formaldehyde into the non-harmful chemical formate. The study will use a flow-through bioreactor and spectrophotometer to measure the rate of formaldehyde degradation. Preliminary work includes creating standard curves of different formaldehyde concentrations and analyzing them using a spectrophotometer. Then, during the experiment, a stream of air containing formaldehyde concentrations typically found in homes will be exposed to three experimental groups: no plant, wild-type plant, and genetically modified plant. The genetically modified plants are engineered to express the enzyme formaldehyde dehydrogenase (FALDH) cloned from the bacterium Brevibacillus brevis, which oxidizes formaldehyde to formate. Any remaining formaldehyde will be collected in an effluent trap and derivatized with DNPH for analysis. Its amount will be measured using a spectrophotometer to determine the percentage of removal. The genetically modified pothos ivy is expected to exhibit a higher rate of formaldehyde degradation than the wild-type plant, owing to its FALDH enzyme. The results of this research aim to provide support for the use of plant-based strategies in combating indoor air pollution and improving human health.

Describing genetic variation in deep-sea organisms is key to understanding ecological and evolutionary processes shaping biological diversity in these fragile ecosystems that are vulnerable to anthropogenic activity. Among deep-sea species, tubeworms (Class Polychaeta) often dominate faunal biomass in hydrothermal vents where they tend to grow in towering colonies. As foundation species, tubeworms create structural habitats that support assemblages of diverse biological communities across the seafloor. However, heterogeneous environmental conditions throughout their range, such as pH and temperature, and geographic isolation, may cause population subdivision by restricting connectivity between sites. This study aims to further our understanding of tubeworm population structure by investigating genetic relationships between Ridgeia piscesae subpopulations within a deep-sea hydrothermal vent system. At the Axial Seamount, a regularly surveyed area in the study of hydrothermal vent processes on the Juan de Fuca Ridge, our knowledge of the genetic connectivity of R. piscesae subpopulations remains limited. Here, we examined genetic variation in R. piscesae individuals collected from structurally-different sites within the Axial Seamount. Specifically, we genotyped mitochondrial genes and constructed SNP-based phylogenetic trees to elucidate evolutionary relationships between worms inhabiting a chimney and diffuse-flow locations. Genetic differentiation is expected to be low when gene flow is high between populations, but these outcomes may also be influenced by other aspects, such as environmental conditions. These results allow us to evaluate the degree of genetic diversity in tubeworms within this important area and provide insight into the potential impact of human activities, such as seabed mining, on deep-sea vent dynamics.

One third of patients in America diagnosed with depression or anxiety are resistant to treatment, creating an urgent need to develop improved therapeutics. In such disorders, motivation to seek rewarding outcomes (‘approach’ behavior) is commonly reduced while apathy (‘avoid’ behavior) is often increased, suggesting that circuitry regulating approach-avoidance (Ap-Av) behaviors may become disrupted in these disorders. Previous research in our lab showed that neurons that release the endogenous neuropeptide nociceptin in the paranigral ventral tegmental area (pnVTA) become highly activated when a large amount of effort is required to obtain a reward, and that activation of these neurons drives avoidance behavior. To investigate pnVTA nociceptin circuitry in directing approach and avoidance behavior simultaneously, I am using NOPLight, a nociceptin biosensor, in an Ap-Av task to record nociceptin release in vivo during Ap-Av decision making in mice. The Ap-Av behavioral assay I am using utilizes a head-fixed apparatus with an aversive LED light positioned at the mouse’s eye level and a sucrose sipper positioned at their mouth. At variable time intervals, either a tone indicating a sucrose reward outcome or a tone indicating an aversive light outcome will play. After the tone plays, the mice will have a short response period where the number of times they lick the sucrose sipper determines the magnitude of the outcome (more licks = more sucrose reward/aversive light, less licks = less sucrose/light). Thus, this task includes simultaneous approach and avoidance components that collectively influence decision-making, and it gives us insight into the role of nociceptin in regulating these behaviors. This research is clinically significant as it can help us understand possible mechanisms underlying the expression of symptoms related to motivation in psychiatric disorders and identify new therapeutic targets to treat them.

Memory loss is a debilitating symptom of neurodegenerative diseases. The exact process of memory decline or forgetting in the brain remains unclear. To address this issue, the development of technologies to preserve or improve memory is a continuous objective in translational medicine. This study aimed to uncover the brain networks involved in forgetting and investigate if reducing forgetting was possible through the use of transcranial alternating current stimulation (tACS; 60 Hz or sham) targeted to the dorsolateral prefrontal cortex (dlPFC). The dlPFC was considered a potential target for memory interventions as it had been linked to various aspects of memory function including working memory, executive control, encoding, and retrieval, as well as memory and attention functional connectivity networks. Participants took part in four visits, each consisting of three 8-minute memory tasks using an adaptive fact-learning software. The memory tasks assessed recognition memory (multiple choice), recall memory (fill-in-the-blank), and retrieval learning (response generation). The software used a neurocomputational model that adapted to each participant's performance. This cognitive model is based on established cognitive and biological principles and simulates memory encoding and passive forgetting. The model's α parameter, which represents the speed of forgetting and measures how quickly an individual's memories fade, was used as a dependent variable. Additionally, participants completed two resting state functional MRI (fMRI) scans to evaluate their brain's functional connectivity before and after stimulation. The study compared individual speeds of forgetting to individual patterns of functional connectivity to identify the neural networks most predictive of forgetting, and compared functional connectivity between participants who received tACS and those who received a sham stimulation. We hypothesize that tACS to the dlPFC will decrease forgetting rates and be associated with increases in functional connectivity. In conclusion, tACS has the potential to become a low-cost and non-invasive method to ameliorate memory impairments.

COVID-19 is an infectious viral disease that is caused by the SARS-CoV-2 virus entering host cells through surface spike proteins that bind to surface ACE-2 receptors. Some anti-SARS-CoV-2 antibodies allow SARS-CoV-2 to also have antibody-mediated entry (AME) into immune cells, often via Fcγ receptors. This phenomenon has been correlated with cytokine release syndrome, which occurs when the immune system has a highly inflammatory response to infection and is implicated in severe COVD-19 cases. It has also been shown that other antibodies have demonstrated inhibition of SARS-CoV-2 entry. During binding and viral fusion, all three receptor binding domains (RBD) of the spike protein fold to an upward conformation, which is necessary for binding. Inhibitory anti-SARS-CoV-2 antibodies impede this process through mechanisms such as premature cleavage of the RBD or stabilizing a three-down conformation. I hypothesize that inhibitory antibodies can stop AME from occurring, but it is not yet understood which inhibitory mechanisms are most effective at preventing AME. To understand the dynamic between AME and inhibitory antibodies, I am testing the infection levels of monocytes by SARS-CoV-2 pseudo-virus in the presence of antibodies shown to induce AME combined with varying concentrations of inhibitory anti-SARS-CoV-2 antibodies that have different mechanisms of affecting the spike RBD conformation. Preliminary results suggest that high concentrations of multiple neutralizing antibodies inhibit AME. It has also been observed that an inhibitory antibody that activates the up RBD conformation increases entry at certain concentrations, whereas an inhibitory antibody that stabilizes the down RBD conformation does not enhance AME. This work will contribute to our investigation of the connections between AME, spike conformational regulation, and immune cell inflammation. Studies of this type can aid in continued development of safe vaccines and therapeutics, as well as help understand how antibodies affect SARS-CoV-2 spike conformational regulation and therefore viral entry.

In mammals, hair cell loss or damage leads to permanent loss of auditory and vestibular function due to the inability of mammals to regenerate these cells. The primary function of hair cells is to respond to auditory and vestibular stimuli to facilitate perception of sound, head movement, and gravity. Hair cells are particularly sensitive to changes in their mitochondria, a membrane enclosed organelle that provides ATP in all eukaryotic cells. Disturbances or damages to the mitochondria can be caused by mitochondrial deafness genes, aminoglycoside-induced death, or senescence. Currently, there is very little known about the biology of hair cell mitochondria.The zebrafish neuromasts within the lateral line can serve as a functional model for cochlear hair cells because of its homology with the mammalian inner ear at genetic and structural levels. We use the zebrafish lateral line system in conjunction with the serial-block face scanning electron microscopy (SBFSEM) to produce three dimensional imaging of hair cell mitochondrial morphology. SBFSEM allows us to measure and quantify mitochondrial phenotypes. We have identified structural characteristics of mitochondrial networks adjacent to post-synaptic release sites that interact with afferent neurons and regulate synaptic transmission. The information gained from SBFSEM on hair cell mitochondrial morphologies will provide valuable insight on protective intracellular mechanisms that can prevent synaptopathy and protect against hearing loss. In our future work, we will quantify this mitochondrial networking morphology. These data will further inform functional experiments regarding the role of mitochondria at these synapses.

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.

Plasmodium vivax (P. vivax) is the most widespread malaria species. P. Vivax can lay dormant in hepatocytes and cause recurring malarial infections. Tafenoquine (TQ) is an antimalarial drug approved by the FDA in 2018 for the radical cure of P. vivax. Unfortunately, 8-aminoquinolines like TQ cause hemolytic anemia in G6PD deficient patients. Due to this contraindication, genetic G6PD screening is required before TQ administration. These additional tests pose a significant challenge for broad administration in resource-constrained countries. Our polymer prodrug conjugates (drugamers) are designed to improve TQ delivery to the liver and reduce red blood cell exposure. Using RAFT polymerization, drugamers can be optimized for delivery efficiency and avoidance of hemolytic anemia. Polymer architectures can be further enhanced by utilizing a variety of enzyme cleavable linkers, monomers, and receptor binding cofactors. We previously demonstrated increased liver-to-blood area under the curve ratios in mice using a variety of different polymer architectures. Mice received an IV or subcutaneous dose of drugamer and relevant organs were harvested at previously determined time points up to 48 hours. Pharmacokinetic profiles were created using a plate reader fluorescence assay and tandem LC/MS/MS with tissue samples. These drugamers represent an ongoing effort to iteratively improve our drug-polymer design. The improvement in TQ delivery through our drugamer vehicles could allow for more liberal administration guidelines, completely removing the need for G6PD testing for the treatment of P. vivax.

As tool compounds aimed at profiling drug leads, covalent small molecule probes targeting amino acid residues present great value to the field of chemical proteomics. Recent progress has expanded the search for these irreversible inhibitors to those targeting lysine residues on select kinases. These small molecule probes are typically composed of an aminophilic group that binds lysine, a scaffold that directs the inhibitor to the residue of interest, and a reporter group that facilitates visualization of binding on a gel. Here we present the organic synthesis of numerous novel small molecule inhibitors, as well as their live cell labeling behavior. The inhibitors of choice are designed with a variety of electrophilic groups that serve as aminophiles targeting lysine. Each inhibitor is built around either a Foretinib or Xo44 scaffold, and uses a transcyclooctene (TCO) click handle as the reporter group. The TCO handle rapidly binds tetrazine, allowing for the linking of a fluorophore to the inhibitor, which reports labeling of lysines through SDS-PAGE. An initial live cell labeling assay reveals clear binding activity in a foretinib-based inhibitor with a squarate electrophile, as well as minor bands in select sulfonyl-fluoride based inhibitors. Through mass spec (MS) proteomics, the protein targets of these promising inhibitors will be identified. Assuming MS reveals selective, high affinity binding, these small molecule probes aid the profiling of drug leads, and expand the range of targeted covalent inhibitors available for chemical proteomics. 

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.

Phase separation in phospholipid membranes occurs in living systems like yeast vacuole membranes and consists of domains enriched in specific lipid components. Phase separated domains coalesce and merge together into a singular phase as membranes are heated above the phase transition temperature, T_mix. The phase transition temperature depends on the lipid composition of a membrane. In the lab, it is useful to produce simple, model membranes to isolate phenomena like phase separation from the complexity of biological systems. Emulsion phase transfer is one such technique used to generate giant unilamellar vesicles (GUVs) by using a centrifuge to drive emulsion droplets coated in lipids through a lipid-oil solution and water interface. However, there are several specific challenges for emulsion phase transfer that require optimization: drying the lipids down with nitrogen gas into a lipid film, the time sensitive creation and layering of the lipid-oil emulsion, and finding the optimal centrifugation parameters. Here, we optimize emulsion phase transfer in three ways: 1) evenly coating lipids films via swirling, 2) creating the emulsion and depositing it as quickly as possible, and 3) tuning centrifugation to maximize vescile formation and minimize vesicle aggregation. Further, we measure the phase transition temperature for GUVs made of a ternary lipid mixture consisting of DPPC (16:0 PC), DOPC (18:1 PC), and Cholesterol in a 1:1:3 ratio. To visualize membrane phase separation, a fluorescent lipid that partitions preferentially to only one phase was added to lipid mixtures used to prepare GUVs. Due to the crucial role of cholesterol in membrane phase behavior, the phase transition temperature of GUVs generated through this technique will vary from those produced by other techniques due to poor cholesterol incorporation.

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.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by differences in social interaction and communication, as well as repetitive behaviors (APA 2013). Per Kanne and Mazurek (2011), 56% of 1380 children and adolescents diagnosed with ASD engaged in some form of aggression towards family, teachers, or peers. Aggressive behaviors can prevent youth with ASD from being able to engage in learning opportunities and community events. An important factor in decreasing rates and severity of aggression is through the identification of social and environmental factors that may impact the stability of aggressive behaviors. The aim of this study is to look at factors that may impact the stability of aggressive behaviors in a longitudinal sample of autistic and non-autistic youth. 44 participants (22 ASD) aged 8 to 18 years, from the NIH funded longitudinal study on sex differences in autism were included in the analysis. Aggression was measured using the Child Behavior Checklist (CBCL), a parental report measure on problem behaviors, which includes items related to self aggression (self injurious behaviors) and other-aggression (aggression towards peers and adults). Data was collected at baseline and 3 to 8 years later. We expect low IQ and younger age will be related to higher aggressive scores on CBCL at baseline. We predict that youth with greater social improvement between timepoints and use of psychotropic medication will have lower levels of aggression over time. Identification of factors that impact changes in aggression over time can aid in implementing interventions to aggression and improve quality of life.

Attention deficit/hyperactivity disorder (ADHD) in girls had been largely under researched up until the 21st century, and still much is unknown or unclear about prevalence, symptomatology, associated impairments, longitudinal trajectories, treatment options, and treatment efficacy. In this study I attempt to characterize the ethnically diverse sample of adolescent girls (n=235) from the ADHD Teen Integrative Data Analysis Longitudinal (TIDAL) dataset (Sibley & Coxe, 2020). I investigate how different types of behavior therapy [engagement-focused (ENGAGE), comprehensive (COMP), standard (STANDARD), community-based usual care (UC), no treatment (NOTX)], medication engagement (consistent, inconsistent, negligible), clinical problem profile (simplex, internalizing, disruptive/disorganized), and family adversity predict changes in ADHD symptoms and related impairment (academic functioning, parent-teen conflict, and organizational functioning) over time. To do so I create a series of hierarchical linear regression models to examine the relationship between the predictive variables and the outcomes, and how each added variable affects the relationship using data from the ADHD TIDAL dataset. I predict an overall decline in symptoms and related impairment with the ADHD+internalizing profile predicting a greater decline than ADHD simplex and disruptive/disorganized ADHD. I also hypothesize that higher family adversity scores will predict a lesser decline in symptoms and related impairment. The results of this study will provide insight different into female presentations of ADHD. This information can then be used to optimize ADHD screening methods to reduce demographic disparities in ADHD and determine which combination of treatments are most effective for different subgroups.

My research project aims to combat inflammation and fibrosis caused by biomaterials and implants. Nondegradable biomaterials can provide long-term stability in the body but can elicit a foreign body response, such as inflammation. The project focuses on finding ways to repair and replace damaged tissue at the location of the implant.The project involves engineered M1 cells which were created and published by the Giachelli Lab within the Department of Bioengineering at UW. We have two groups of mice: one control group that has been injected with engineered TLR4 (Toll-Like Receptor 4) cells but not given the CID (Chemically Induced Dimerizers) drug, and another group that has been injected with both the engineered TLR4 cells and given the CID drug. The inside of the cell was isolated in both groups of mice and the extracellular domain was removed. For the group with CID, the inside domain of the cell was bound with CID which is thought to result in dimerization and activation of the M1 phenotype.At this stage in the project, we have tissue samples from both these groups, and I will analyze these samples using H&E staining thus allowing me to measure healing parameters, like how dense the collagen structure is around the material and analyze the effect of CID on the state of the tissue. For expected results, I believe the group with CID will have a denser collagen structure around the material than the group without CID.Conducting the analysis on these tissue samples will help address the effect of CID on healing parameters, such as inflammation. Furthermore, this work will help us develop a better understanding of the roles that M1 and M2 phenotypes play in the healing process which can lead to new therapies that reduce the inflammatory response elicited by biomedical devices. 

The quality and accessibility of greenspaces are positively correlated with urban quality of life. The presence of greenspaces increases mental and physical health, economic activity, air quality, and other critical facets of well-being. In this study, we tested the hypothesis that household income is an indicator of the quality and accessibility of greenspaces in Seattle. Specifically, individuals living in higher average household income areas experience higher quality and accessibility of greenspaces than individuals living in lower income areas. We utilized data from the American Community Survey on King County’s annual average household income, along with geographic information on public parks from the City of Seattle GIS database to relate park accessibility and quality to household income by census tracts. We defined accessibility as the number of parks present in a given tract. A Park Quality Index was used to assign a quality score to each park, allowing us to calculate an average park quality rating for each census tract. Park quality was determined by acreage and the presence of natural and man-made elements. We found a weak positive correlation between average household income and park quality but no correlation between income and the number of parks available in a census tract. While our findings showed only weak support for one part of our hypothesis, we believe the lack of support is in part due to the fact that census tracts are too large a scale for analysis. With growing evidence for micro-segregation by race (and by extension, income) within census tracts in Seattle, it is likely that lower income neighborhoods within larger census tracts do in fact experience reduced access to high quality greenspaces. Future research should investigate this question at the scale of neighborhood or city block in order to further investigate what is likely to be an environmental justice issue in Seattle.

Reducing the considerable carbon emissions of the built environment industry is vital to addressing the current climate crisis. Though there have been substantial advancements in cutting emissions from building operations (operational carbon), addressing buildings’ embodied carbon is a newer focus, with ongoing research driving industry transformations. Embodied carbon refers to the greenhouse gas emissions arising from the manufacturing, transportation, installation, maintenance, and disposal of building materials. Since a large portion of embodied carbon emissions are upfront, rapid adoption of improved practices is critical. Thus, many architecture, engineering, and construction (AEC) firms around Seattle have initiated a focus on reducing the embodied carbon from their designs and practices. We have selected three Seattle-based AEC firms, and are analyzing each firm’s methods of improving emissions from their practices while considering the lessons and applications of these methods going forwards. The team is conducting in-person tours of firm offices and interviewing key sustainability-focused team members about their approach to improving their projects’ environmental impacts with particular focus on embodied carbon. Beyond broad qualitative data about firm practices, quantitative data on specific low-carbon buildings is collected. This is being reviewed, analyzed, and synthesized into deliverables summarizing common trends, best practices, and future research needs. Due to the relatively recent innovations in reducing embodied carbon, many practices are yet to be adopted. For this reason, we expect that many firms will be following longer-term plans as they gradually integrate sustainable practices into their workflows. Through an advanced understanding of the changing landscape around the impacts of embodied carbon, designers and researchers will be better prepared to eliminate carbon emissions from all sectors of the built environment.

Research indicates that ethnic minority groups experience disproportionate exposure to air pollution caused by vehicular transportation. It is well known that differential exposure to air pollution causes increased health risks in vulnerable communities. Disparities in air pollution exposure are significant since they exacerbate comorbidities, increasing the risk of diseases like COVID-19. This study examined the relationship between exposure to Transportation-Related Air Pollution (TRAP) and census tract racial demographics in Seattle, WA. We hypothesized that communities with greater percentages of non-white residents are more likely than white-dominated communities to experience greater exposures to TRAP, because of historical factors such as “redlining”, segregation, and discrimination. This is because they are forced to live in less desirable areas and are unable to resist polluting infrastructure in their neighborhoods. We used the Environmental Protection Agency’s Environmental Justice Database to relate diesel particulate matter (PM), a proxy for TRAP, to census tract demographics, from the 2020 U.S. census. We measured diesel PM concentrations at systematic distances along three North/South transects through Seattle, roughly corresponding with the location of Interstate 5 (I-5). Measurement locations were taken sufficiently far from I-5 so as to not be affected by I-5. We found no correlation between the percent non-white population and diesel PM concentration, thus rejecting our hypothesis. There are several reasons for our unsupported hypothesis: first, our transect did not adequately sample majority non-white neighborhoods. Second, diesel PM is only one proxy for air pollution, and may be distributed relatively evenly throughout our study area irrespective of racial demographics. An analysis of other pollutants may support our hypothesis. While it is optimistic that we failed to find disproportionate exposures to diesel PM in our study area, continued analysis of differential exposure to various forms of pollution is critical to identifying and addressing environmental injustice.

Air pollution is not evenly distributed geographically or demographically. For historical reasons related to race and class, ethnically diverse neighborhoods often have a higher rate of negative health effects related to air pollution, as compared to predominantly white communities. In this study, we explore the relationship between the demographic indicator, "percent people of color," to exposure to air pollution and subsequent cancer risk in the Seattle/Tacoma area. Our analysis utilizes data from the Environmental Protection Agency’s Environmental Justice Screening and Mapping Tool, with the independent variable being the air toxics cancer risk, based on the National Air Toxics Association (NATA) calculated Cancer Risk from inhalation of air toxics and measured in percentiles of risk per million people. Our dependent variable, the percent people of color population, was collected from the 2015-2019 American Community Survey, a subset of the US Census, and is defined as everyone who does not identify as non-hispanic white. We performed our analysis using a disproportionate stratified random sample of census tracts from the King-Snohomish County dividing line in the north to the intersection of I5 and Highway 512 in the south, bounded by 122.05’ W on the east margin and the eastern shoreline of Puget Sound on the west margin. For each selected tract, we recorded percent people of color and NATA Air Toxics Cancer Risk National Percentiles. Our data reveals a positive linear relationship between cancer risk percentile and percentage people of color in the population. These findings highlight the importance of recognizing and addressing the lasting effects of racism on health, and the need for continued work towards securing environmental justice.
 

 Reconstructing past environments can help us understand plant community evolution over time. For example, plant silica (phytoliths) can help us reconstruct canopy openness. Phytoliths are formed when plants uptake monosilicic acid from the surrounding soil through their roots and deposit it as opalized silica in and around cells; they have been used as a tool in paleoecology because they are well-preserved in the fossil record. For phytoliths formed in the outermost layers of leaves (epidermis), there is a relationship between morphology and light availability. A previous method established this correlation using modern soils in Costa Rica to apply to sites in the Eocene-Miocene of Argentina. However, it is unclear whether this model can make accurate inferences in other geographic regions. Here, we expand the method using modern phytolith samples from the Southeastern United States to generate a dataset and apply it to fossil phytolith assemblages from the North American Great Plains Region to reconstruct changes in vegetation during Oligocene-Miocene grassland expansion. For this work, we use an optical microscope to observe and count the phytolith assemblages to reflect a range of vegetation types in North America. We focus on phytolith morphotypes representing silicified epidermal pavement cells and measure their size and shape using ImageJ. We expect a linear trend between LAI (Leaf Area Index, the quantified relationship between morphology and light availability) from phytoliths and observed LAI which can be used to form the model for North American environments and applied to the fossil phytolith record of the Great Plains Region. Expanding on this method could make its use more widespread and lead to similar research in other regions of the world. Current models suggest the persistence of closed forests through this entire interval, a result we wish to further test using this updated model.

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.

One of the most striking adaptations in land plant evolution is the specialization of reproductive structures. LEAFY (LFY) is well characterized in flowering plants (angiosperms) as a transcription factor initiating the development of the flower, which contains the reproductive organs. LFY also regulates the first cell division of the zygote (diploid phase) in mosses (a type of non-vascular plant). The fern Ceratopteris richardii is a type of non-flowering plant that is midway phylogenetically between mosses and flowering plants, in the sister clade to seed plants. With a lab-friendly, independent haploid phase (gametophyte), transgenic protocols and a reference genome, C. richardii is ideal for studying LFY’s functional evolution. Previously, targeted silencing of the two fern LFY homologs CrLFY1/2, demonstrated that it maintains the identity of the apical stem cell in gametophytes. To further characterize the function of fern LFY, I study the effects of its over expression on gametophyte development. To that end, I record gametophyte development using bright-field and fluorescent microscopy. Preliminary results suggest that overexpression of CrLFY may affect development of the sperm-producing gametangia (antheridia) in fern gametophytes, with more antheridia found in transgenic plants late in development. Given that antheridia continue to be produced in wild type gametophytes in the absence of fertilization, I test the hypothesis that CrLFY overexpression causes delayed fertilization (by a yet unknown mechanism) and that increased antheridia represent a secondary effect. Here, I experimentally delay fertilization by withholding water needed for sperm release (“flooding”), and compare the number and pattern of antheridia on transgenic and wild type gametophytes with and without flooding. Functional characterization of LEAFY in a fern, and of other master regulators of development more generally, contributes to a better understanding of the evolution of land plants via the potential repurposing of ancestral genetic pathways into novel functions.

Climate change and global population growth are driving the need for more sustainable methods for growing crops used in agriculture and the production of biofuels. To address these challenges we are exploring the role of that plant microbiome in host plant tolerance to environmental stresses related to climate change. In particular we are investigating whether endophytes, microorganisms that colonize the internal tissues of plants, make the host plants more tolerant to drought or low-nitrogen conditions. We are currently optimizing the process of DNA extractions of fruit and poplar trees which were inoculated with beneficial nitrogen fixing bacteria, and grown in either water-or nitrogen limited conditions. We then purify high quality microbial DNA, and use polymerase-chain reaction (PCR) to optimize strain specific primers (SSP), which target specific DNA sequences in the genomes of our endophytes, and minimize background noise produced by plant and other microbial DNA. This allows us to reisolate our strains from the plants to gain understanding of where they colonize, and to demonstrate that the trees were successfully colonized by our endophytes to support growth and drought tolerance data collected from inoculated and uninoculated controls. By ensuring the SSPs only target our strains of interest, we differentiate our endophytes from other members of the plant microbiome. These primers are then used in Droplet Digital PCR (ddPCR) to quantify their relative abundance. Using this information we hope to contribute to the project objectives of demonstrating that beneficial endophytes can be used as a sustainable method for improving drought and low nitrogen tolerance in plants, both in agricultural and biofuel applications, reducing the consumption of nitrogen fertilizers and water for irrigation in these sectors.

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.

Genomic amplification of specific genes is a common mechanism of adaptation that also underpins many human disorders. We use yeast (Saccharomyces cerevisiae) to investigate the mechanism of one such gene amplification. When yeast are grown in sulfate-limited conditions for many generations, the population becomes dominated by cells possessing an inverted triplication of the SUL1 gene, which produces a sulfate transporter. Because of increased transporter levels, these cells have higher fitness in limited sulfate conditions. The Brewer Lab proposed a model — Origin Dependent Inverted Repeat Amplification (ODIRA) — where this gene amplification is initiated via a DNA replication error. In the ODIRA model, DNA replication fork regression at short inverted repeats leads to template switching of the replication machinery and the extrusion of a replication-competent hairpin molecule, which after replication, recombines at the original locus to produce an inverted triplication. An alternative explanation behind the amplification is that the hairpin molecule is generated by double-stranded DNA breaks (DSB). To distinguish between these possibilities, we used an engineered strain in which the selectable marker gene, URA3, is split into overlapping fragments (“ura” and “ra3”) on two different chromosomes. The complete URA3 gene is only present in yeast that undergo rare direct recombination between chromosomes or by recombination of the replicated hairpin formed by ODIRA or DSB. We used CRISPR-Cas9 to induce DSBs upstream of the ura fragment and identify the type of event that restores URA3 function with contour-clamped homogeneous electric field gels (CHEF gels), Southern blots, and polymerase chain reactions (PCR). If DSBs drive hairpin formation, cutting the chromosome upstream of the ura fragment should increase the frequency of URA3 assembly via hairpin intermediate. We demonstrate that double-stranded DNA breaks do not increase frequency of hairpin intermediates, providing further evidence that ODIRA is responsible for the inverted triplications of SUL1 in yeast.

Chromatin, the complex of DNA-wrapped histone octamers that make up our chromosomes, is decorated with post-translational histone modifications (PTMs) that either increase or decrease transcriptional accessibility. Most regions have either predominantly active or repressive modifications that shape chromatin into euchromatin or heterochromatin, respectively. In addition to euchromatin and heterochromatin, some cells have poised chromatin that is decorated with both permissive and repressive modifications. While much is still unknown about a poised chromatin state, it is thought to permit swift changes in gene expression, which is a feature common in stem cells and lymphoid memory cells. Ultimately, the Escobar lab aims to determine the epigenetic mechanisms involved in maintaining the poised chromatin state of memory CD8+ T cells, and in line with this aim, plans to use a CRISPR-Cas12a biotinylation system to tag and precipitate poised chromatin regions for protein analysis and mechanistic studies. This project details the development and proof of concept of this CRISPR-Cas12a biotinylation system. Using traditional cloning techniques and a one-pot strategy to assemble CRISPR arrays, we will express and purify dCas12a-BirA+gRNA ribonucleoproteins (RNPs), introduce these CRISPR RNPs to mouse embryonic stem cells (mESCs), and perform CUT&RUN to verify effective biotinylation at specific chromatin loci. Preliminary results have demonstrated the successful purification of 5 CRISPR RNPs and a dCas12a-BirA control, as well as verified the presence of these CRISPR RNPs and the biotinylation of H3 upon delivery of this system to mESCs. Upon CUT&RUN analysis, we expect to see biotinylation of H3 at our targeted loci of interest. The completion of this validation step will allow us to apply this technology to any cell of interest, particularly CD8+ T cells, which may support significant insights to the mechanistic determinants of poised chromatin.

The Ubiquitin Proteasome System (UPS) is a molecular recycling machine, responsible for  proteolysis and protein activity regulation. The components of the UPS attach a small protein ubiquitin onto other proteins which directly affects their activity or serves as a signal calling for modification or lysis. Ubiquitin-conjugating enzymes (E2) and ubiquitin ligases (E3) are two classes of proteins that determine which proteins are tagged. Ube2W is an E2 with a unique function—it is the only E2 that places ubiquitin onto disordered N termini and amino acylated side chains. In this study we aim to elucidate the mechanism of reactivity and specificity of the enigmatic Ube2W. What structural and chemical features are responsible for its one-of-a-kind functionality? What does this imply about the role of this E2 on the cellular level? We designed a set of Ube2W mutants that had various putatively important features removed or changed to analogs from different E2s. We performed mutagenesis PCR followed by reactivity assays in the presence of known Ube2W substrates. We plan to collect NMR data for the Ube2W-substrate and Ube2W-ubiquitin interactions. We hope to determine which features are critical for this unique E2’s function by following the changes in reactivity when they are removed or altered. The interactions of substrates with these critical residues will help draft an outline for the precise mechanism. Improving our mechanistic understanding of Ube2W will pave the way for being able to control when and under what circumstances this unique biochemical reaction is used by the cell. This work aims to expand the current understanding of the UPS and aid in taming UPS-related diseases.

The association of eukaryotic DNA with histone proteins serves not only to package entire genomes into the nucleus of a cell, but these histone-DNA functional units, called nucleosomes, are hubs for biochemical signaling that regulates gene expression. In the Chatterjee lab, we are fascinated by the transcriptional biology of the small ubiquitin-like modifier protein 3 (SUMO-3), a posttranslational modification that occurs on histones and has been correlated with reduced gene expression. Previous members have demonstrated that SUMO-3 stimulates the activity of transcriptionally repressive enzymes by binding with a scaffolding protein called CoREST1. Hence, my focus has been to understand the functional details of the SUMO-CoREST interaction, particularly how cancer-associated mutations in the SUMO-interacting motif (SIM) of CoREST1 affect its ability to bind SUMO-3. To answer this question, I started by using solid-phase peptide synthesis to prepare truncated CoREST SIM peptides bearing the mutations of interest. I then utilized these peptides, along with SUMO-3 enriched in nitrogen-15, for two-dimensional nuclear magnetic resonance spectroscopy. By comparing the chemical shifts of [¹⁵N]-SUMO-3 with and without the presence of each peptide, I could assess the effects of mutations on the proportion of bound and unbound species in solution. Of special interest was an acidic residue in the hydrophobic core of the CoREST SIM, which distinguishes it from canonical SIMs found in other proteins. Excitingly, my results indicate that substitution of this amino acid with lysine, a mutation found in gallbladder cancer, ablates binding. I observed a similar effect for other mutations in the hydrophobic core of the CoREST SIM. Using these results to guide studies with full-length CoREST in biochemical assays, my research will identify the effects of these mutations on downstream biochemical pathways that may be misregulated in human cancers.

Deep learning methods for protein sequence and structure generation have shown remarkable success in many design scenarios when combined with structure prediction networks such as AlphaFold2. Despite this advance, many design challenges such as de novo binder design still haven’t been fully solved. Diffusion-based models have demonstrated considerable success in image and language generation yet their application in protein design has not yet been fully explored. Recently, the development of a protein diffusion model called RoseTTAFold Diffusion (RFdiffusion) has shown significant success in protein design and enabled us to explore the challenging problem of designing protein binders. Here I demonstrate utilization of RFdiffusion towards generation of de novo binders to disordered major histocompatibility complex (MHC) peptides. Specifically, we took an MHC peptide from KrasG12D and used RFdiffusion to generate a diverse range of structures that can bind this peptide. To optimize the sequence of these structures we used ProteinMPNN. We used AlphaFold2 to predict the structures of these optimized binders in complex with the peptide and saw promising interaction metrics. Further, structure prediction of the designs in complex with Kras wild type (WT) peptide resulted in lower AlphaFold2 confidence metrics of the interaction occurring. This is a promising preliminary result that RFdiffusion can generate fully de novo MHC-mimics, which can differentiate between neoantigens and WT peptide. Many cancers are caused by a single point mutation such as KrasG12D, thus, designing protein binders with point mutant specificity is exciting as it allows for targeting of disease causing proteins over healthy WT proteins. 

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.
 

The retina is made of mostly neurons and glia. In mammals when neurons degenerate in the brain or retina, they are not replaced. Studying other species, the Reh lab discovered a way to stimulate Muller glia in the retina, using the pro-neural Ascl1 transcription factor, to regenerate retinal neurons. My project focuses on another glial cell in the human retina: the astrocyte. Retinal astrocytes come from different progenitors in the brain and migrate, through the optic nerve, to the retina during development. There are two questions about astrocytes that are addressed in this project. When do astrocytes enter the retina? And can human retinal astrocytes be reprogrammed into neurons using the Ascl1 transcription factor? For the first question, based on immunohistochemistry(IHC) stainings done on sections of the human fetal retina I conclude that astrocytes enter the retina between 62-72 days of fetal development. For the second question, I hypothesize the Ascl1 transcription factor can reprogram human retinal astrocytes and the unique development and migration will affect the types of neurons they regenerate. My IHC stainings on cultures of retinal cells confirms that a lenti-virus I added to the culture with an astrocyte marker(Pax2) sufficiently targets astrocytes. I am currently working on isolating astrocytes from other cells in culture. Afterwards a lentivirus with the pro-neural Ascl1 transcription factor will be added to the astrocytes to begin reprogramming trials. Human retinal astrocytes have not been reprogrammed successfully before. If we can reprogram retinal astrocytes into neurons, it would potentially have implications for neural replacement in the retina. This would contribute to research in gene therapies for neurodegenerative retinal diseases such as: glaucoma, AMD and retinitis pigmentosa.

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.

The retina is a neuronal tissue located on the back of the eye that receives light information, and relays this information to the brain, allowing us to see. The light is received by cells called photoreceptors, which send information through a series of inner-retinal neurons before being relayed to the brain via ganglion cells. My project is investigating the effect of a protein called DICER on retinal cell fate in the developing human retina. DICER is important for the maturation of microRNAs, which influence gene expression of retinal precursors that play a crucial role in the progression from early cell types in the mouse, such as ganglion cells, to later cell types, such as photoreceptors and inner retinal neurons. To understand if DICER is also necessary in human development, I am culturing human retinal organoids derived from embryonic stem cells (ESCs), which recapitulate human development in gene expression and developmental timing. I then preferentially knock out (KO) DICER at different developmental time points depending on the timing of infection. I have knocked out DICER in retinal organoids at an early time point and observed that, like mouse studies, cells without DICER more frequently become the early born cell type, ganglion cells. I am now investigating the necessity of DICER in retinal development at later time points. If DICER plays a similar role in cell fate progression, I expect to see an enrichment of later born cell types in the DICER KO cells. By better understanding human retinal development, we will advance future research of regenerative therapies to mitigate the impacts of retinal degenerative diseases leading to vision loss, such as macular degeneration and glaucoma, which affect photoreceptor cells and ganglion cells, respectively.

In the early stages of pathological hypertrophic cardiomyopathy, stress-induced signal transduction promotes the addition of new contractile units to maintain tensional homeostasis through poorly understood mechanisms. Our previous data shows that tension can be changed by altering the contractions within the cells. Inhibition of contraction by expression of D65A cTnC (point mutation on the calcium-binding site of troponin C) results in complete myofibrillar disarray. The mechanism behind the maintenance of myofibril and passive tension seen in these non-contractile CMs is not explained. Data has shown that microtubules provide resistance in the cell and go through rounds of rapid growth or disassembly based on the cell’s need which could be caused by the change in tensional homeostasis. With this in mind, my goal was to determine the role of microtubules in maintaining tensional homeostasis in response to changes in internal tension in CMs. Here, wild-type human induced pluripotent stem cell-derived cardiomyocytes were transduced to express cardiac troponin C with point mutations L48Q (hyper-contractile), I61Q (hypo-contractile), and D65A to study the effect of varying levels of contractility or internal load on microtubules. It was found that microtubular remodeling occurred where the noncontractile CMs had an increase in microtubule density. These noncontractile CMs were then cultures on nanopatterns that provided external tension via topological cues. In addition to the myofibrillar alignment seen previously, it was observed that microtubule density decreased further confirming that microtubules play a compensatory role in these CMs. The next step is to determine if a similar increase in microtubule density observed in the 2D culture is also seen on a tissue level by developing engineered heart tissues. This new data gives insight into how the microtubule remodeling in non-contractile and dysfunctional cardiomyocytes maintains tension in the early stages and its possible role in myofibril formation.

A “tough on crime” approach in the late 1900s ushered in more punitive sentencing than ever before in American history. As a result of mandatory minimums, three-strikes laws, and other harsh legislation, the American carceral state boomed. Not only were more people incarcerated, but they were incarcerated for longer periods of time. Since then, federal court cases have challenged the constitutionality of life and lengthy sentences, especially for individuals sentenced when they were juveniles. In the wake of these federal decisions, Washington state has enacted a variety of legal pathways towards post-conviction sentence review and early release. This study explores how learning of the possibility of early release affects incarcerated individuals who previously did not expect to have a chance at release. This research will be conducted through qualitative interviews and a survey with a sample of 12-15 individuals who served lengthy sentences and unexpectedly learned of a chance for early release. The findings of the research are expected to make a variety of contributions. First, the research will fill a gap in the literature on the social-psychological dimensions of imprisonment and on the significance of hope for incarcerated individuals. Second, this research will add qualitative insights to the largely policy-related literature on criminal sentencing. Third, the research may influence early-release policy by demonstrating potential benefits of such programs, which may positively contribute to less stringent sentencing and carceral practices. Fourthly, the research may help to shatter preconceived notions that individuals who have served life/lengthy sentences are “burdens” to society and instead replace such negative views with positive, prosocial, and communal experiences.

International criminal justice is often criticized for being unfairly selective in prosecuting cases. For instance, all suspects brought before the International Criminal Court in The Hague have come from Africa. This is despite the fact that human rights violations have been reported in many other parts of the world during this same period of time. Although restrictions in time and resources limit international courts’ and tribunals' capacity to prosecute all meritorious cases, the criteria used by the Prosecutors of these courts to determine which cases to pursue and which to disregard remain largely unknown, compromising the legitimacy of international criminal law in its application. This raises the question of why international criminal cases were only initiated in certain cases and not in others, and against particular suspects? To address these questions, this research examines four of the most prominent theories on selectivity in the application of international criminal law, including state capacity, popularity (that the courts will single out people from countries that have a bad reputation in their global affairs while granting leniency to others), crime severity, and victor's justice (countries with powerful positions within the international arena are most likely to escape international scrutiny). Most empirical research examines a single theory in isolation and employs a case study approach. However, I compiled an original dataset that encompasses all cases of international criminal law, from the Nuremberg Trials to the most recent cases of the International Criminal Court in order to test all four major theories systematically. I expect multivariate analysis to provide substantial support for the theory of victor's justice by showing that the power of a country correlates with the likelihood of international interference in the prosecution of international crimes committed in the country.

The Religious Land Use and Institutionalized Persons Act (RLUIPA) of 2000 was passed to protect the rights of incarcerated individuals in the US to freely practice their religion in federal prisons. However, even 22 years after RLUIPA placed a strict scrutiny standard on reviewing inmates; free exercise claims, community organizations have had to repeatedly advocate for civil rights violations in prisons. This project aims to figure out why the free exercise rights of religious minorities are still threatened in the face of strong legislative protection. I will do so first by determining whether there is a bias in RLUIPA decisions for claims made by majoritarian religions, leaving religious minorities with a lower likelihood of success. Then, I will analyze whether the difference in success rates can be explained by a plaintiff's access to resources. Most incarcerated individuals represent themselves in court as they often lack the financial resources necessary for professional legal representation. Pro se plaintiff's often lack the preparation and legal knowledge that goes into a successful court claim. I hypothesize that prisoners with access to more resources, whether it's financial or community-based support, will be more likely to have a successful free exercise claim. My data will be collected from RLUIPA judgements from 2000 to 2022 and compiled into a dataset that includes variables such as the plaintiff's religion, type of representation, and the outcome of the claim. I expect to find that religious minorities will have lower rates of success, and that they will be less likely to have private representation. I also expect that plaintiffs with private representation will have higher rates of success with their RLUIPA claims as compared to pro se plaintiff's. The findings of this research will reveal the difficulties that individuals face in prison because of their religious identity and speak to broader themes of the trust and authority that our political systems give to prisons at the expense of incarcerated individuals' rights. 

Political scientists have rarely considered the intersection of religious organizations and foreign policy. Currently, there is no literature that investigates why religious organizations decide to either support or oppose American wars overseas and why this support can vary within each organization across conflicts. I attempt to answer these questions by testing whether religions are more likely to favor wars with other countries that have smaller groups of same-faith adherents. The social psychology theory of in-group favoritism and an “open-door” incentive to potential proselytization provide a plausible argument for such a relationship. To test this, I analyzed three different denominations of Christianity with a significant presence in the United States and their public position toward specific military conflicts throughout U.S. history. I created an original dataset containing these public positions of support or opposition to a given war along with the existence or size of like-faith communities (i.e., how many of their own church members were present) in the exterior target state of the conflict. I then utilized a multivariate regression analysis to test my theory and determine the relationship between a church’s support for war and the size of same-creed presence in each target state. I expect to find a positive relationship between these two variables, supporting the theories of in-group favoritism and “open-door” proselytization. These findings will contribute to current literature on American public and religious interest group foreign policy attitudes and offer methods for anticipating faith group positions on future military operations.

The American prison system is notorious for the mistreatment and abuse of the incarcerated people left in their care. In the past ten years there have been large pushes for prison reform; yet, these programs have had varying results across states. Why is it that some states have a much higher frequency of sexual assaults in prisons then others? I expect to find that prisons in Democratic-controlled states will have lower rates of sexual assault then their Republican-controlled counterparts. Literature on racial and social justice initiatives point to several differentiating factors between the two parties that aids in explaining this issue. Democrats are more likely to support social welfare and the Black Lives Matter movement, because racial justice activism is important to the Democratic coalition and subsequently their voter base. Additionally, Republican leadership supports tax and social welfare cuts while prison reform depends on subsidization from the government to work. In order to test this theory, I gathered data on sexual assaults in prisons from each state and compared them against each other, controlling for certain factors such as age, population and prison demographic. I ran a multivariate regression to see if Republican-controlled states experience greater frequencies of assault. This study focuses on an underserved population in the United States which greatly deserves thought and attention. Additionally, learning what factors contribute to violence in prisons helps provide a framework for improvements in our judicial system. Through research my goal is to contribute new information to a critical issue that has so far been largely understudied.

As of 2022 there are 103 million displaced people, of which 32.5 million are refugees, and 4.9 million are asylum seekers recognized by the United Nations High Commissioner for Refugees. As the number of displaced people grows, it becomes even more imperative that the United States offers asylum seekers a fair trial in court to pursue refuge in order to comply with the Universal Declaration of Human Rights, as well as to uphold strong ethical obligations based on foundational liberal values. However, today the right to seek asylum in U.S. immigration courts is undermined by the stark variation of adjudication rates between immigration judges. In this paper, I use original data from the Transactional Records Access Clearinghouse at Syracuse University to examine asylum adjudication variation systemically. Building from social identity theory, I hypothesize that asylum adjudication variation occurs due to the implicit bias exercised by judges based on their personal identities. I define implicit biases as unconscious learned biases that usually take the form of stereotypes and narratives that one automatically associates with particular people. Using a multivariate regression, I examine how the race, gender, political leanings, and religious affiliations of 314 judges correlate with the judges’ adjudication rate as well as the racial makeup of their asylum applicant pool. I expect to find that judges that have the characteristics of white, male, conservative and Christian will be more likely to deny asylum applications and I posit that this will have a disparate impact on asylum seekers who are black, brown, or are coming from majority Muslim countries.

Microfinance institutions are considered pivotal in addressing poverty in low- and middle-income countries and providing financial inclusion through loans, savings, and insurance to those typically excluded from traditional banking. Most microloan recipients are women who own small businesses, and thus microfinance is regarded as pivotal to increasing women’s economic status. Some studies, however, highlight the rather lacking ability of microloans to improve household and business outcomes, as well as measures of women’s empowerment. My research explores if targeting such an agenda is the most effective way to uplift women and therefore help economic conditions in middle-income countries. I do this by examining the impact of microfinance loans on women’s autonomy in Vietnam by constructing a panel dataset from the 2006 and 2010 Vietnam Household Living Standards Surveys and designing a causal model. One channel through which microfinance empowers a woman is through her ability to financially contribute to the household, which in turn increases her decision-making ability, and thus changes gender relations in the household. In order to test increased decision-making, I calculate the share of resources in the household that are allocated to each woman and estimate changes in resource shares as a result of receiving a microloan. I expect results to show little to no increase in resource shares as the outcome of a household obtaining a microloan. In order to test changes in gender relations, I compare the previous results across Vietnam’s eight regions, which display varying levels of intimate partner violence. I expect regions with high rates of intimate partner violence to be negatively correlated with increased resource shares for women as compared to regions that have low rates of intimate partner violence. By addressing both the economic and social status of women, I illustrate a more complete picture of the efficacy of microfinance.

Donald Trump’s presidency and its divisive legacy on the American government and its citizens continues to plague our society years after he has left office. It is crucial that policymakers and social scientists understand what values or grievances resonated with Trump’s voters and drove the rise of the Make America Great Again movement, in order to ensure that his voters do not continue to feel alienated from mainstream US politics. Through this paper I explore the electoral motivations of the US white working class, building on existing research that studies voting patterns and trends in previous presidential elections. I test two popular competing theories, pocketbook voting and social identity voting, and apply these theories to the context of the 2020 US presidential election. Pocketbook voting posits that voters respond to individual economic incentives and vote for who would benefit them economically, while social identity voting theorizes that individuals vote based on their subjective sense of belonging to an in-group and a desire to distinguish their group from others. I expect to find that white working class Trump voters were motivated by social identity voting, voting for Trump because of racial grievances and status anxieties. To conduct this study, I use a racial threat index and an economic well-being index, drawing from survey data to compare the social and economic grievances of white working class Trump voters. I expect to find that social identity voting, driven by factors such as status anxiety and racial threat, is a stronger electoral motivator than economic incentives, such as changes in wages or employment. Understanding such motivations lets us fight polarization and address the concerns of disenfranchised voters in future elections and in politics more broadly.

Year after year, catastrophic hurricanes rip through the mainland United States and its island territories. And yet, year after year, we hear stories of communities going without electricity or running water for months, disastrous temporary housing units and evacuations, and months-long wait times for immediate needs like food and medical care. Why has the Federal Emergency Management Agency (FEMA) failed to improve its distribution of disaster relief, even after three major reform bills? This paper seeks to provide an answer by investigating how corporate lobbying may be influencing FEMA’s allocation of relief funds between public and private actors. Considering the lucrative nature of post-disaster contracts awarded to corporations, they may use their lobbying powers to pressure the government to allocate more funds for private contracts and less to its Public Assistance (PA) program, which provides grants directly to state and local governments. FEMA’s preference for private contractors, despite their extensive history of performing inadequate work and defrauding the government, may be a significant part of the agency’s overall dysfunction. I conduct a multivariate regression analysis to determine the relationship between lobbying expenditures from top contractors and FEMA’s allocation of relief funds among public and private sectors between 2004 and 2021. I expect to find a positive relationship between these variables, suggesting lobbying does interfere with the delivery of post-disaster aid. Identifying the private sector’s influence in this area is critical to ensuring communities are properly supported after hurricanes and other natural disasters, which will only increase in frequency due to climate change.

 The spread of misinformation has increased rapidly in the last few years on many social media platforms. Our understanding of its effects, strategies, and influence is growing along with the information in real time. During political elections, we have seen that misinformation can become contagious and pose harmful threats to many aspects of our society and our political environment. How exactly does misinformation disseminate online, and are these social media posts used as a political strategy? To delve deeper into this study, I examine the relationship between false information online and legal cases that challenge election results. Using a mix of qualitative and quantitative methods, I analyze articles, data, and social media posts concerning the 2020 and 2022 elections in Maricopa County. With this data, I identify recurring narratives and influential political figures, using Python visualizations and codebooks for the empirical evidence found online. I anticipate that my findings reveal a pattern of legal cases being used to spread false political narratives that mislead the public about the voting process in Maricopa County. Since Maricopa County is the fourth most populous county in the United States, this study provides insight into how online users receive information about political elections and voting processes. I also anticipate that utilizing courts and election lawsuits can be an effective strategy to uphold and spread misinformation. Further research into other counties may demonstrate similar patterns and narratives with misinformation and U.S. elections.

Search engines are the primary gateways of information. However, the veracity of search results is often not considered before the search results are promoted to users. As the most popular video search engine, YouTube recommends misinformation on the treatment, spread, and origins of COVID-19, undermining public health efforts. Despite the global effects of COVID-19 misinformation, the majority of research is confined to the Global North, leaving the Global South behind. My research aims to qualitatively and quantitatively compare the exposure to COVID-19 misinformation on YouTube between a country in the Global North and Global South. I focused on the United States and South Africa, both of which have been heavily affected by the pandemic. Using 48 curated COVID-19 misinformation search queries, I systematically audited YouTube search results for 10 consecutive days with 12 programmed bots emulating “real” users in South Africa and the United States. This sock-puppet audit method ethically prevented harmful exposure to misinformation to real users and provided a scalable, controlled way to collect data. Then, I fact-checked the collected video results and trained a machine-learning model to scale the annotation process, allowing for the measurement of misinformation prevalence in different geolocations. My preliminary findings showed that YouTube search results differ by up to 20% between South Africa and the United States. Based on these early findings, I expect to see potential differences in the veracity and rankings of COVID-19 misinformation search results between users in South Africa and the United States. This research is the first to report a comparative investigation of COVID-19 misinformation on YouTube between a country in the Global North and Global South. It also establishes a novel method of conducting geolocation audits in different countries, paving the way for further audit research in the Global South and ensuring accountability for social media platforms.

The amount of online information is rapidly increasing, including an abundance of potentially misleading content. However, fact-checkers rely heavily on manual search methods to identify this content, leading to a significant investment of time and resources. While social media monitoring tools exist for platforms like Twitter and Facebook, such tools still need to be improved for video search platforms like YouTube. We collaborated with Africa's largest indigenous fact-checking organization – PesaCheck, during the 2022 Kenyan general election. The spread of rumors aimed at voter suppression gave an advantage to the tally of a specific presidential candidate, which created an urgent need for automated fact-checking systems. To address this issue, a team of undergraduates from the information school and computer science department developed a tool to automatically generate search queries related to significant events and topics for fact-checkers to monitor while providing them the flexibility to modify or create their queries. I was in charge of developing a method to identify video ids, extract the keywords with Natural Language Understanding (NLU), and the function that allowed users to choose keyword tags to characterize videos and then link them to the top search queries of the day. During the crucial period of the Kenyan election, ten full-time fact-checkers were using our tool to check and report falsities on the internet. During the four months of deploying this fact-checking tool, 42 misinformation discovery annotations were added by various fact-checkers, and over 500 misinformation queries were generated by the tool. As a result, the new Kenyan president emerged from one of the most competitive elections in the nation's history. Our research project will also be published as a case study paper to discover value-sensitive fact-checking systems through participatory design.

International students transition from a controlled environment in their home countries to an unfamiliar one with new culture in their host country. This highly complex change can bring about information seeking needs to navigate everyday life. As a result, international students may turn to their host university for answers and resources. This research study aims to examine the perceptions of undergraduate international students at the University of Washington (UW) with regard to the support they receive from their host university for their everyday life information seeking (ELIS) needs. The question guiding this study is: How do perceptions of support from the host university in everyday-life information seeking of 1st-year international students compare with those of 4th-year international students? Findings will be based on data from a survey of UW undergraduate international students about their perceptions of support from their host university. Results of this research study will contribute to the scholarship of Culture Learning Theory, which concerns the challenges experienced by sojourners in navigating through a new culture. Moreover, the findings have scope to support host universities as well as organizations within the host university that serve international students. I plan to disseminate a findings report to UW institutions such as International Student Services (ISS), Foundation for International Understanding Through Students (FIUTS), Center for International Relations and Cultural Leadership Exchange (CIRLCLE), etc. The report will contain a robust data analysis of the satisfaction of international students at UW, and will detail future recommendations from the participants about what will improve their experience abroad. By conducting research on the perceptions of international students pertaining to the support they receive from the host university for their ELIS needs, both scholars and university staff will gain perspective on how international students experience information-seeking aspects of culture learning.

This study examines how undergraduate students majoring in humanities and social sciences navigate the institutional culture of higher education (HE) through a case study at the University of Washington. I identify two different logics within HE that contribute to its institutional culture — the industry logic and the social institution logic. The industry logic refers to the growing trend of business and industry orientations in HE — especially since the emergence of neoliberalism in the 1970s. The social institution logic is the more traditional ideal of HE that aims to cultivate values of citizenship and morals. The goal of this study is to examine how undergraduate students understand and respond to changes in institutional culture. While the commodification of HE is well studied, scholarly attention neglects its evolution and fails to articulate students’ response to this shift. This study is inductive and qualitative — focusing on undergraduate experiences and how students give cultural meaning to their experiences under varying institutional culture. I will conduct 12 semi-structured interviews with undergraduate students majoring in humanities or social sciences to understand their college experiences. Though the anticipated results of the study have yet to be determined due to the inductive nature, I hope to examine how students reconcile their passions and actual experiences under institutional culture of HE. Any disparities observed between universities as institutions and students as agentic individuals might reveal the neglected demands within society. This research will provide insights to which kind of education system our society needs today, which will lead to better policies about the future development of HE.

Several factors influence students’ ability to access the disability accommodations necessary to complete coursework; one of the main factors, however, is the degree to which instructors are willing or able to accommodate their students’ needs. Crucially, students often need to discern if instructors will accommodate their needs before they can register for class. Students must navigate differences in communication styles and perspectives on what constitutes reasonable accommodation. Further, instructors’ knowledge of their own responsibilities, rights, and the process by which accommodations are accessed, is limited. Instructors are not made aware of their role in providing accommodations or the timeline for their involvement. They are often reluctant to provide assistance for fear of overstepping boundaries set by their institutions. The ambiguity of the instructor’s role in accessibility is actively causing harm. Multiply-marginalized students face a number of additional barriers: students who have less wealth have impaired access to healthcare, and are more likely to face poor healthcare outcomes. Further, the effects of marginalization ensure that students with intersectional identities are less likely to be wealthy. While these facts are rarely officially disputed, it is often difficult to determine what supports are missing, why they are missing, and how support can be provided to the benefit of all stakeholders. In order to establish how students and instructor perceptions differ from each other and from the recommended process, more data is sorely needed; this study utilized a basic survey to identify the areas in which instructors and students need further support. Most queries were designed to have quantifiable responses; freeform responses were evaluated to identify the most common topics and positionality respondents presented. Responses which directly oposed the most common positionalities were then quantified. Expected results largely aligned with known areas of need, specifically the need for more transparency and training surrounding accessibility. 

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. 

Implicit bias refers to unconscious attitudes and stereotypes in patient-provider communication that can lead to discrimination based on race, sexual orientation, gender, or other characteristics. This disproportionately impacts historically marginalized communities, including Black, Indigenous, and People of Color (BIPOC) and Lesbian, Gay, Bisexual, Transgender, Queer, and/or Questioning people (LGBTQ+). Although interventions have been developed to improve provider awareness of implicit bias, there has been little exploration of patient perspectives. With the help of my team, I conducted an analysis of 7 previously conducted co-design workshops with 32 BIPOC and LGBTQ+ people to understand patient perspectives on interventions to mitigate the impact of provider implicit bias in healthcare interactions. These workshops included group discussions about personal experiences with healthcare discrimination and a storyboarding activity to envision solutions for improving patient-provider interactions. Across workshops, participants created 13 storyboards that depict solutions in a primary care setting, several of which focus on improving patient-provider communication and promoting self-advocacy and empowerment. Through our collaborative qualitative analysis, my team and I identified two prominent themes from the workshops: communication tools and patient advocates. Participants shared experiences of feeling dismissed and unheard during healthcare visits, leading to storyboard proposals of communication tools, such as "smart boards" that allow patients to describe their symptoms in a nuanced manner. Another storyboard proposed a "panic button" that helps patients ask for help or request a different provider. Other storyboards focus on strategies to hold providers accountable, such as a "patient advocate" who approaches the provider about the patient's experience of discrimination and recommends a communication training intervention that raises awareness of bias. These findings can inform future research on interventions to address implicit bias in provider-patient communication. By prioritizing patient perspectives, we can create a healthcare system that is equitable and inclusive for all.

Methanotrophs are prokaryotes that naturally consume the potent greenhouse gas methane for energy. Through metabolic engineering at an industrial scale, these microorganisms hold potential to mitigate the contribution of methane emissions to global warming. In particular, Methylotuvimicrobium buryatense can sustain robust growth both in nature and experimental settings; it is a promising engineering candidate. To develop a robust metabolic engineering platform using M. buryatense, biologists require a deeper understanding of the genetic mechanisms by which it functions. Here, I present an open-source software tool designed to interactively explore the transcriptome of M. buryatense. By integrating bulk RNA-seq datasets collected from experiments over the past decade and applying an array of unsupervised machine learning clustering algorithms, we cluster genes by their expression profiles in differing growth conditions. These gene clusters are annotated with gene ontology (GO) terms using statistical enrichment analysis to assist in functional interpretation of the clusters and the genes that comprise them. To enhance domain-expert researchers’ ability to explore and drill-down into specific queries, I unify these cluster-specific analyses in a web-hosted tool using interactive data visualization techniques centered on a ReactJS frontend and Azure Cloud backend. With both exploratory and query-focused use cases, this software tool can support M. buryatense biologist workflows for predicting functions of hypothetical proteins, showcase new or confirming putative regulatory processes, and generate new experimental hypotheses from the presented transcriptomic trends.

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.

The visual system is a critical portion of the sensory arsenal in many animals, since light is a fundamentally important factor that allows animals to assess and navigate their surroundings. Differences in latitude have measured effects on the quality, quantity, and consistency of daylight, and animals have adapted to these varying light levels in different ways. Research has shown that animals with larger eyes, reflected in their bony orbit dimensions, are able to perceive their environments better in more dimly lit settings. Studies have also suggested that animals at higher latitudes exhibit larger eyes for better visual performance. Our group seeks to understand if there is any significant relationship between latitude and orbital size in Canidae (wolves, foxes, and relatives) due to the difference in light levels at different latitudes. I collected several linear measurements using ImageJ and 3D Slicer from skull 3D scans of 29 species of the Canidae family over a latitude range from -104.07° - 99.02°. Additionally, our team collected data on the average tree coverage, diet, and hunting style of species, to test for additional variables that may affect orbital size. We conducted regressions and ANOVAs among the variables collected. The preliminary results show there is no significant relationship between latitude and orbital size. However, we found that both hunting style and skull length have a significant relationship with orbital volume in Canidae. These results potentially impact the field by allowing us to infer the possible evolutionary trajectories of bony orbital dimensions, and how eye size could allow for more complex hunting styles in Canidae. Future research may seek to validate these findings in other carnivore families.

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.

Remote collaboration today rarely involves a single communication channel. Instead, teams frequently juggle a myriad of communication tools, such as video conferencing, group chat, and email. Each of these platforms provides different mechanisms for relaying information and media to ultimately meet the needs and goals of the team. While discussions occurring on different platforms are often related, existing tools used to support each type of communication are disconnected. To research how to bridge this gap and support seamless collaboration and communication across different platforms, we developed a toolkit that connects conversations between three of the most commonly used remote collaboration platforms: Slack, Google Docs, and Zoom, covering both synchronous and asynchronous modes of communication. We iteratively designed and implemented features such as adding information from Slack chat directly to Google Docs notes to build up meeting agendas and selecting specific snippets of Zoom meetings to be embedded into notes or sent to chat. We also plan to evaluate the effectiveness of our toolkit in helping streamline the transfer of information across different team communication sites and enhancing the remote collaboration experience for teams via subsequent qualitative user studies. Specifically, we will be conducting a week-long field study with existing teams, such as teams from industry, teams working on school projects, research groups, committees, etc. We will use a combination of experience sampling, diary study and post-study interviews to understand their experience. The results we expect to get from these exploratory user studies will help us answer the following questions: Which aspects of the tools work best for the users? Does the current UI and design make sense for how the user interacts with the toolkit? In which scenarios is the toolkit being used most effectively? These results will also guide us in designing additional features for the toolkit in the future.
 

Illegal, unreported and unregulated (IUU) fishing violates the rights of Indigenous peoples to traditional fishing grounds; compromises food security of legitimate fishers and coastal populations; and facilitates human labor trafficking. Once caught, tails, fins, and heads are cut off for storage and transportation, which makes identification by phenotype impossible. Polymerase Chain Reaction (PCR) and electrophoresis can detect different tuna species but are time-consuming and require access to a fully equipped laboratory and trained personnel. Thus, I developed a novel biological assay and a 3D printable portable device to detect Ahi tuna, one of the species of interest among three tuna species. The biological assay consists of three steps: DNA extraction by crude lysis method; DNA amplification by Recombinase Polymerase Amplification (RPA); and detection by fluorescence using Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR Cas) 12a. qPCR verified Ahi tuna DNA extraction by crude lysis method, generating 10⁶ copies of DNA per reaction comparable to the standard silica-based capture method. Nested qPCR and Tapestation verified RPA’s successful amplification of Ahi tuna DNA extracted by crude lysis method. Quantification of fluorescence by qPCR verified that one-pot RPA and CRISPR Cas12a reactions could generate up to 6000 Relative Fluorescence Units above the negative control within 15 minutes. The isothermal device keeps the samples at a constant temperature (37-42℃) for the RPA and CRISPR Cas12a reactions. I successfully demonstrated a <50 min sample-to-result assay to detect Ahi tuna DNA, and this protocol will be further adapted for testing other types of tuna including Bluefin tuna. By developing such a rapid and affordable isothermal biological assay and a point-of-need 3D printable portable device for tuna identification, I aim to contribute in helping individuals and ecosystems impacted by IUU fishing.

Wildfire smoke exposure is measured using the surrogate for all pollution by the concentration of particulate matter 2.5 microns wide (PM2.5). According to the CDC, short term exposure to wildfire smoke can result in negative health outcomes. It is highly recommended to stay indoors if your area is experiencing a wildfire smoke event. However, it is inevitable that outdoor air will leak indoors through any holes in the building, open doors, or windows. Occupants can also worsen indoor air quality through the activities they perform in their daily lives. This research is part of an indoor air quality pilot using PurpleAir sensors. We used the statistical methods within R to identify important building and occupant factors that influence IAQ. Participants tracked their IAQ using color changing PA-I monitors and a spike event log noting the time of the event, the color change exhibited, most probable cause, and the action taken to remedy the air quality. Data were analyzed using the tidyverse, caTools, simDesign, and lubridate packages in R. After grouping events across houses by cause, we saw a significant association between cooking and high levels of PM2.5 compared to other short-lived spike causes. The findings of this study will serve to set best occupant practices for indoor air quality within a household both during a wildfire smoke event and under normal atmospheric conditions. While economic barriers may exist when protecting oneself against unhealthy air, it is crucial to be aware of low-cost alternatives to minimize the health threat posed by poor indoor air quality.

The snowball Earth hypothesis states that between ~720-635 Ma Earth underwent glaciations during which the planet was covered completely in ice. Scientists use carbonate deposits, called cap carbonates, which appear atop snowball Earth glacial deposits to mark the end of these glaciations. Cap carbonate deposition is currently thought to have occurred during extreme stages of the chemical weathering (breakdown of rock by chemical reactions) that followed snowball Earth. However, there is insufficient geochemical evidence to confidently determine which stage–extreme, mild, or otherwise–of chemical weathering intensity the carbonates were deposited in. Magnesium, Mg, isotope abundance is useful in tracking chemical weathering events because of magnesium’s sensitivity to chemical weathering intensity. Data collected from rock samples from the Yangtze Formation in South China support the conjecture that chemical weathering was most intense immediately following snowball Earth, but it was not until chemical weathering slowed down that cap carbonates were deposited. This scenario allows time for continental chemical weathering to occur and calcium and magnesium cations to become available for the production of carbonates. To revise the snowball Earth hypothesis with this information, samples from more than one region are needed to apply this timeline globally. I will dissolve rock samples collected from the Amazon Craton in Brazil and study the sample powders using mass spectrometry to collect Mg isotope abundance data. I expect the data collected from these samples to resemble the data collected from the Yangtze Formation cap carbonates. This corroboration will help piece together the puzzle of the Snowball earth timeline.

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.

Prior research suggests that people with obesity commonly have diets with more added sugar and saturated fat, worse sleep quality, emotional eating, and lower physical activity time than people with healthy weight. However, do these lifestyle characteristics predict one’s response to a behavioral weight loss (BWL) intervention? We will explore, in people with obesity, if these lifestyle characteristics, individually and/or jointly, are related to the change in adiposity in response to a 6-month BWL intervention. The methodology consists of data from self-report questionnaires administered to participants (N=63) at baseline in the BWL intervention group in the Weight Effects on Brain Health Study. Adiposity measurements were obtained by dual-energy X-ray absorptiometry. Diet characteristics were determined and Healthy Eating Index was calculated by analyzing 3 unannounced dietary recalls from an automated self-administered 24-hour recall system. Eating behavior was measured through the Three Factor Eating Questionnaire-R18. Sleep quality was determined by The Pittsburgh Sleep Quality Index. Physical activity assessed regular activity during the previous 4 weeks and was calculated as MET-h/wk. A composite score will be generated to include the 4 lifestyle factors described. Statistical analyses are undergoing. Anticipated results are associations between poor diet quality, poor sleep quality, less physical activity, and higher scores for uncontrolled and emotional eating and a greater reduction of adiposity over 6 months, as determined by multiple linear regression. Confounding by age and sex will be explored and models adjusted as needed. Additionally, we anticipate improved predictability of lifestyle characteristics, when considered jointly, to the change in adiposity. Participants were 69.8% female with mean age of 42.2±10.9 years, BMI of 37.2±5.3 kg/m2, and visceral adipose tissue of 1875.6±1027.7 grams. This research may help illuminate if lifestyle measures are able to predict one’s response to a BWL intervention and who could benefit most from it.

Chronic kidney disease is the ninth leading cause of death in the United States. The current process for pathological diagnosis involves pathologists manually reviewing histochemically stained tissue slides. This analysis is also used to inform further treatment and is therefore critical to patient outcomes. In this project, we aim to improve the robustness of the diagnostic process by utilizing machine learning models to identify and classify features indicative of kidney disease on whole slide images. We manually annotate Masson’s Trichrome stained kidney tissue images from our collaborators at the University of Illinois for three functional structures (tubular cytoplasm, tubular basement membrane, glomerulus) and three indicators of damage to the kidney (fibrosis, edema, and inflammation). These annotations are used to train our VGG16 convolutional neural network model to classify patches of unmarked whole slide images into the four categories: tubular cytoplasm, fibrosis, inflammation, and glomerulus. We also address data variability that often comes from differences in the histochemical staining procedure across labs resulting in inconsistency across stains/imaging that can typically affect the generalizability of deep learning models. To address this, we are training a CycleGAN for image-to-image translation as a method of stain normalization and investigating the effect on the accuracy of our VGG16 model. Additionally, I will be training a model to identify the cortex versus medulla regions of the kidney to add to the pipeline for area-specific evaluations. Our research with integrating machine learning models within renal pathology aims to decrease the time and manual labor needed in the process and increase the accuracy of diagnoses.

As part of cellular metabolism, all organisms produce reactive oxygen species (ROS), such as (O₂^– ) and hydrogen peroxide (H₂O₂). ROS can damage multiple cellular organelles and processes, disrupting normal physiology. Proteins, lipids, and nucleic acids can be damaged by ROS molecules, resulting in cell death. Also, several human diseases have been linked to an imbalance between ROS production and antioxidant defenses. Plants' chloroplasts and mitochondria contribute a substantial amount of ROS, as they are responsible for photosynthesis and aerobic respiration. In maize, Whirly ssDNA-binding proteins help to maintain the stability of the plastid genome. We recently demonstrated that maize seedling development is accompanied by increasing oxidative stress to the demise of chloroplasts, mitochondria, and their DNA. We also showed that maize seedlings grown in the light had higher levels of oxidants and lower levels of antioxidants than dark-grown seedlings. Here, our objective is to elucidate the role of Whirly proteins in oxidative damage. We isolated organelles from maize seedlings and performed oxidant and antioxidant assays for both wild-type and whirly-mutant plants. We found a significant difference in oxidation levels between wild-type and mutant plants. Our study should provide a better understanding of the role of ssDNA-binding proteins in oxidative damage to organelles.

Despite heavy exposure to Mycobacterium tuberculosis (Mtb), the bacteria that causes Tuberculosis (TB), some individuals show no evidence of infection and by defining these resistance mechanisms, we may identify novel treatment strategies. Among Mtb resistant individuals, our lab identified the Rab5a protein as differentially expressed as compared to controls with Mtb infection. By regulating vesicle trafficking, Rab proteins modulate a variety of cellular pathways including inflammatory signaling, antigen presentation, and autophagy, likely playing a role in Mtb clearance. We hypothesized that loss of Rab5a would alter IFN-êžµ gene expression. Monocyte-like THP-1 cells were electroporated with siRNA targetting Rab5a and yielded 70-90% knockdown at 24 hours versus scrambled siRNA control. Cells were then stimulated with DNA ligands for four hours before RNA analysis. Loss of Rab5a resulted in lower levels of IFN-êžµ gene expression after stimulation with Sheared Calf Thymus DNA (p=0.002, 53.9% reduction), Poly(I:C) (p=0.01, 42.8% reduction), supercoiled plasmid (p=0.03, 45.3% reduction), and cGAMP (p=0.008, 45.7% reduction). We conclude that Rab5a expression is required for Type I IFN production through the DNA-sensing pathway. By characterizing the pathways by which Rab5a modulates the macrophage Mtb response, we may identify host targets to augment protective responses that may serve as adjuncts to current TB treatments and vaccines.

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.

When the cell undergoes stress, it leads to an increase in protein instability and misfolded states that prevents proper cell functions. Small Heat Shock Proteins (sHSPs) are molecular chaperones that work to maintain a healthy proteome by associating with misfolded proteins to delay aggregation under stress conditions. Other chaperones and co-factors will then refold or degrade the misfolded protein client. HSPB5 is a human sHSP ubiquitously expressed throughout the body. A HSPB5 disease mutant, where arginine is mutated to glycine at residue 120 (R120G), is a defective chaperone associated with cataracts and desmin-related myopathy. HSPB5 comprises three domains but only one domain—the alpha-crystallin domain (ACD)—is folded. My research aims to understand the effect of the R120G mutation on the folded ACD’s structure. HSPB5 creates a dimer through electrostatic and hydrophobic interactions between ACD at the dimer interface. This network of interactions causes the dimer interface to be highly sensitive to electrostatics, working like a sensor for environmental charges. Wild-type HSPB5 is more positive at its dimer interface, likely facilitating interactions with negatively charged compounds. In the R120G mutant, the loss of arginines at the dimer interface site causes it to be less positive, hypothetically lowering HSPB5’s affinity for these compounds. Through site-directed mutagenesis, I obtained HIS-tagged cleavable constructs for wild type and R120G B5 ACD that allowed for easier purification. Using these constructs, I grew isotopically labelled N15 B5 ACD in minimal media and purified my protein sample through nickel affinity, size exclusion and anion exchange chromatography. Through NMR titration experimentation, I investigate how amino acid identity at the R120 site will affect ACD interactions with charged molecules in R120 mutant of HSPB5. Learning how mutations at the R120 site affect protein dynamics and client interactions will be a step forward in understanding the sHSPs’ overall chaperone mechanism.

Seattle Repertory Theatre put on Heidi Schreck's What the Constitution Means to Me as a part of their 2022 season. The play is an illuminating 100 minute almost solo-show of Heidi Schreck recounting her personal story of what the US Constitution, promises and gaps, means to her and the women of her family. This retrieval is prompted by the questions she received at US Constitution debates she attended all over the country, but specifically at the American Legion Hall in Wenatchee, Washington. Struck by Schreck's implementation of "Greek tragedy wailing", I argue that she signals the existence of intergenerational trauma in white American women. More so, that there is little interpersonal communication amongst white American women about their shared cultural traumatic experiences. How does she do this? I draw on theory and evidence around intergenerational trauma put forth by historical and contemporary accounts of the weaponization of white femininity, feminist interpretations of Euripides' Medea, Charlotte Perkins Gilman's The Yellow Wallpaper, literary trauma theory, and trauma theory, all of which may show us how to descend into the next step of dissecting these seemingly patterned behaviors. I formulate this argument from my phenomenological experience with the play, but support it through a semiotic analysis focusing on Heidi's "Greek tragedy wailing", her sock monkey, and the use of yellow for her blazer and promotional material. I wonder: did the play resonate with the white women in the audience? Obviously, not with the woman I passed on my way out, as she said she "didn't understand the point of the sock monkey." Is this an exact example of what Schreck is trying to point to, highlighting the oversight or lack of conversation about this topic? I am interested in theatre as a site of healing and discussion of unresolved trauma. This paper is to help us better understand Schreck and uproot white supremacy, the patriarchy, and the violence this trauma inflicts on white American women and black people in America. 

The emergence of the SARS-CoV-2 vaccine helped shine a light on protein subunit vaccines that use fragments of infectious protein from viruses to trigger protective immune responses. Normally in subunit vaccines, the immune system stimulation is triggered by a separately provided adjuvant. These adjuvants elicit immune responses in a broad and indeterminate manner. We hope to replace this with a molecule that can provide a more specific immune stimulation: CD40Ligand (CD40L). CD40L is an immune protein present on T cells and works to signal B cells to either replicate or create antibodies. For B cells to replicate antibodies, they need a primary signal from the antigen and a secondary signal, which CD40L initiates. To achieve this, we are using the I53-dn5 nanoparticle, which has the ability to display different ligands on its two components by putting both the antigen and adjuvant on either the pentamer or trimer component. We designed 8 different constructs where we tested two versions of CD40L, the placement of CD40L, and the linker length between CD40L and the nanoparticle surface. Out of the five stages of the project - designing, expressing, purifying, assembling, and evaluating - we have completed the first three. The designs that have expressed the best throughout each stage have been those with the CD40L truncated sequence instead of the full sequence. Furthermore, we have seen a trend with the pentamer subunit being more amenable to the addition of CD40L. Future in vitro studies and re-expressions will determine if the particle will retain stability and native CD40L function. We expect CD40L-displaying nanoparticles will promote B-cell proliferation to a greater extent than the nanoparticle vaccine displaying only hemagglutinin antigen. Ultimately, we hope to examine how co-display of CD40L with antigen will change the quality of immune response and memory in vivo.

Documenting plant-animal interactions allows for a better understanding of biodiversity, the behavioral ecology of frugivores, and the coevolution between plants and animals. Bats are important seed dispersers on hundreds of plant species in the tropics, but their patterns of plant use across habitats is still relatively unknown. The overarching goal of my research project is to characterize the interactions between mutualistic fruit bats and plants across different habitats at a site in Costa Rica (La Selva). My hypothesis is that bats will exhibit frequent interactions with Piper plants overall, with more variable interactions across forest Piper species over time because these species have intermittent fruiting peaks. Existing field data consist of 24h camera trap videos and nightly acoustic ultrasonic recordings taken at dozens of forest and gap Piper plants at La Selva during both rainy and dry seasons between 2019-2021. The acoustic data collected is heavy in background noise from organisms and weather conditions; therefore I developed a program in MATLAB to streamline this analysis. I am using RavenPro to identify relevant parameters of bat calls within the filtered files using focal calls as a guide to later identify the species participating in these visitations. I am comparing the number of calls across 10 P. sanctifelicis plants (open habitat) to the number of calls found across 8 P. generalense plants (closed habitat) to observe the frequency of possible fruit-bat interactions across habitats. This project is significant in the field of ecology because of its focus on plant-animal mutualistic interactions: by understanding the frequency of bat visitations to plants across habitats, we can gain a better understanding of the importance of these frugivores for seed dispersal and survival of plants.

Electron paramagnetic resonance (EPR) spectroscopy is a powerful spectroscopic tool for detecting unpaired electrons in molecular systems. By attaching two spin-labels which contain unpaired electrons to different regions of a protein, the distance between the spin labels can be measured, making this technique particularly useful for studying protein structure and dynamics. The signal sensitivity of these measurements is especially sensitive to protons on amino acids adjacent to the spin label. While it is known that the presence of neighboring protons to the spin label decreases the signal intensity, the magnitude in which specific amino acids affect the signal is not well understood. My research aim is to determine how specific neighboring amino acids affect the EPR signal. Here, I design model systems in which spin labels are placed on various parts of maltose-binding protein (MBP) to construct a sample set that contains the spin label in diverse amino acid environments. These spin labels are placed on MBP through a process called site-directed spin labeling. MBP is mutated through site-directed mutagenesis using specific primers, the final plasmid transformed into competent E. coli cells. Through collecting EPR data of these MBP mutants, we can gain insight to which amino acids neighboring the spin label most affect the signal. This project will help us understand how to determine spin-labeling sites to result in maximum EPR signal intensity. Maximizing this signal intensity will enable us to use EPR to study biological systems that could not previously be studied due to lack of sensitivity, such as membrane proteins.

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.

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.

One of the most revolutionary points of Annie Baker’s The Flick is the way it insists that everyday actions, occurrences, and feelings matter. In fact, they do not just matter in a passing, superfluous way - they are deeply significant and meaningful. Art often takes on the role of importance-giving in our society, showing us which aspects of our lives and the world around us are important enough to be recreated and talked about. Annie Baker answers the all important question of what here deserves to be illuminated in a relatively uncommon way. She chooses an atypical topic, three employees of a small town, small time movie theater and chooses to spend the next three hours with them. The Flick, by virtue of its very existence, says that these people, and their experiences matter. This is a radical statement in a world that denies the importance of billions of people’s common, everyday experiences, and audiences have noted that resonance. In this essay I will explore exactly how Baker achieves this effect, and explore various audience reactions to the lifting up of “ordinary” activities through a phenomenological analysis of reception. To do this, I will consider a wide range of reviews of The Flick, with an eye turned towards reactions to the unassuming content and how audiences may have recontextualized their own lives and experiences within the new hierarchy of importance offered by this play. It is my belief that this is a monumental question to consider because art and other forms of representation have an undeniable impact on how people understand themselves and their relation to the world, often in terms of importance. If making powerful, insightful plays about ordinary people can impact our own relationships to ourselves, that has the potential to offer a guiding light for theater in the 21st century.

Mosasaurs are extinct, enormous lizards that dominated the oceans in the Late Cretaceous, from 90 to 66 million years ago. They were important members of Late Cretaceous marine ecosystems, with some species being the top predators. However, there remain many uncertainties about mosasaur diets, which likely varied considerably among species. Therefore, I aim to investigate mosasaur diets to provide more information on lizard evolution and Cretaceous marine ecosystems. To infer the diets of mosasaurs, I examine the lower jaws and teeth of their closest living relatives, modern lizards, and test for correlations between craniodental morphology and diet. For example, a lizard that eats primarily hard-shelled foods will likely have more robust jaws and teeth than a lizard that primarily consumes insects. To quantify the morphologies of the lower jaw and teeth, I measured the width and height of the jaws at three points, and the height, width, length, curvatures, root length, and cusp numbers of the teeth at the same three points (n = 43 species). I then used the jaw measurements to calculate cross sectional shape values that represent the amount of stress the jaws experience during feeding. Finally, I used phylogenetic regressions and multivariate analyses to test the relationship between jaw/tooth shapes and diets. I find evidence that jawbone heights increase among diets in the following order: insectivores, carnivores, herbivores, and durophagous taxa. Further, bone width is greater in herbivores than in non-herbivorous taxa, and durophagous lizards have the most diverse tooth morphologies. These results provide a foundation for future studies to examine the relationship of jaw/tooth shapes and diet more robustly, with the goal of using modern lizards as analogs for inferring diets of mosasaurs.

Mitochondria are organelles responsible for Adenosine triphosphate (ATP) production and are central in biological aging research. Laboratory interventions that extend healthy animal lifespans also work to treat severe animal mitochondrial disease, however, how these interventions work at the molecular level is still unknown. Several longevity interventions extend lifespan and treat a model of Leigh Syndrome, a severe mitochondrial disease, in mice. Among these, rapamycin inhibits the metabolic master regulator mTOR (mechanistic target of rapamycin). This evidence suggests that mitochondrial disease and biological aging share a common cause at the cellular level. When mTOR is inhibited, SIRT3 is upregulated, an enzyme that controls mitochondrial fatty acid oxidation (FAO). We are using the mouse model of Leigh Syndrome, Ndufs4 knockout (KO) mice, to ask the following question: Does rapamycin treatment require SIRT3 activity to increase FAO to treat mitochondrial disease? Preliminary results show that SIRT3 is required for lifespan extension in Ndufs4 KO mice with rapamycin treatment. SIRT3 has also been observed regulating FAO. We are using both etomoxir, a drug that inhibits FAO, and rapamycin to answer this question by measuring lifespan. We are also measuring mitochondrial FAO directly in Ndufs4 Sirt3 double KO animals. Our results are allowing us to better understand how mitochondrial disease and normative aging are related, which will streamline targeting the biology of aging and mitochondrial dysfunction in humans.

Lignocellulosic biomass, composed of cellulose, hemicellulose, and lignin, has become an attractive renewable carbon source for microbial bioproduction of value-added chemicals. Lignin is relatively difficult to depolymerize, and its enzymatic hydrolysate contains mostly aromatic compounds known to inhibit microbial growth when used as a carbon source. Pseudomonas putida (P. putida), a soil bacteria known for its tolerance to aromatics, has been engineered to catabolize lignin hydrolysate. Engineered microbes have also been encapsulated in hydrogels for on-demand bioproduction and exhibited enhanced tolerance to harsh processing conditions, i.e. freeze-drying and exposure to organic solvents. This research aims to create microbe-laden hydrogels from encapsulating engineered P. putida KT2440 cells in F127-bisurethane methacrylate (F127-BUM) hydrogels for robust on-demand bioproduction when using lignin hydrolysate as a substrate. To mimic growth rate inhibition that often happens in hydrolysate environments, we first examine if P. putida-laden hydrogels remain active when grown in a less-ideal medium, such as M9 minimal media (MM9) known to yield a slower microbial growth rate. We find that hydrogel-encapsulated P. putida containing a plasmid for heterologous expression of a green fluorescent protein (sfGFP) maintained its activity in MM9 continuous culture over two days as measured via fluorescence of the expressed sfGFP. This preliminary result on encapsulated P. putida growth and activity in a less desirable culture environment highlights the potential for utilizing aromatics-rich lignin hydrolysate in bioproduction as a more economical and renewable feedstock alternative.

Pangolins are the most widely trafficked mammal in the world. Pangolin scales are smuggled for use in traditional medicine and this is a concern due to all eight species of pangolins; four in Africa and Asia, respectively, currently being in the vulnerable to critically endangered category. My research provides insight into the practices and routes of smugglers using stable isotope analysis to obtain information on locality of origin from scale samples of Smutsia gigantea, Smutsia temminckii, Phataginus tetradactyla, and Phataginus tricuspis, the four species of pangolins native to the African continent. I collected powdered scale samples from the four pangolin species and analyzed the samples using an Elemental Analyzer attached to an Isotope Ratio Mass Spectrometer (EA-IRMS). Scale samples were sourced from recent seizures in multiple ports. Data from the EA-IRMS provide Sulfur, Carbon, Nitrogen and Oxygen stable isotope composition estimates. This information was then used to place individuals into groups and then predict where those groups lived prior to being poached. Better understanding of smuggling routes and poaching habits is an aim of this project. Stable isotope analysis may also help our collaborators identify the pangolin species when scale samples contain insufficient or otherwise poor quality DNA. This project has valuable implications in future forensic studies of organic materials and will lead to better policing and policy making with regards to pangolin conservation.

The Hijra is a South Asian community of genderqueer peoples which perform spiritual rituals and give blessings, typically at births and weddings in return for donations. This ancient community, however, has a long history of invisibilization and criminalization in South Asia. I am studying the Hijras’ physical and literary portrayal as it connects with, and unfolds from, their histories of criminality, invisibility, and mobility under imperial and post-imperial rule. Knowing this history is valuable to the field of colonial and gender/queer studies, as it provides a better understanding of how minoritized peoples navigate – and survive – changes in power and status under shifting power. The Hijra is a good interdisciplinary model for this, as they are minoritized at intersections of gender, religion, sexuality, caste, and class. I am using Indian epics, including the Mahabharata and Ramanayana, to theorize the figure of the Hijra as it exists in the dominant South Asian literary tradition. I am pairing this with articles on Hijra identity, which historicize the community’s legal and social statuses under the Mughal and British imperial formations, up into the decades post-South Asian independence. The purpose of tracing this history is two-fold: (1) to attempt the respectful re-tracing of a genealogy which, until now, has been invisible under various dominant empires and (2) to understand the Hijra peoples’ increasing inclusion into both Western research and South Asian democracy. The urgency and relevance of my inquiry has increased as pro-genderqueer legislation is currently being passed at unprecedented rates in South Asia. This includes India’s 2014 “third gender” law, which officially recognizes the Hijra as the nation’s “third gender.” While many celebrate this inclusionary shift, I argue that the change must be critically assessed, as it represents another incoming shift in global power that minoritized communities will have to navigate and survive.  

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.

Larissa FastHorse originally wrote The Thanksgiving Play in response to theatre-makers' complaints that they could not produce her other works due to a lack of indigenous actors. The Thanksgiving Play, therefore, does not include any indigenous roles and instead centers itself around the very issue of pursuing representation without the people you are trying to represent. Upon first watching the show, audiences may leave the performance having come to the same conclusion as the characters: true representation is impossible to do well, and it’s better to say nothing than to try “too hard.” But is that really what FastHorse is asking of her audience? Is The Thanksgiving Play a snarky way of telling white people to keep their noses and “activism” out of places where they don’t belong and stay as passive spectators? A closer reading of the play reveals the characters to be continually contradicting themselves; they seem to care deeply about social issues, but are completely oblivious of their own ignorance and intolerance; they are attempting to create dialogue, but can’t communicate with one another. I have taken a deconstructive and phenomenological approach to understand how the binary of passivity/activity represented in Larissa FastHorse’s The Thanksgiving Play works against the perceived message around political activism, yet somehow still succeeds in calling audiences to find a space of truly meaningful engagement. The results of my analysis will provide a glimpse into one way that the controversial topic of modern casting practices is being discussed in contemporary theatrical productions. Along with an analysis of the text itself, I will bring in information on historical activist theatre to understand the ways in which The Thanksgiving Play both follows and contradicts the conventions of its genre in order to further its message, especially in relation to Brechtian Epic Theatre. I will also include information from three different receptions of one LA production of the show in order to understand what audiences seemed to get out of it, and how their interpretations interact with each other and the ideas of Cultural Activism.

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.

In low- and middle-income countries (LMICs), human exposure to animals can represent a significant source of enteropathogens. The presence of domestic and non-domestic animals either in the vicinity or in immediate households within LMICs have the potential to contaminate soil and high-touch surfaces leading to enteropathogen transmission and infection. Among LMICs, access to water, sanitation, and hygiene (WASH) is limited and is responsible for contributing to the global disease burden. Lack of WASH regulations and implementation can compound transmission and infection rates of enteropathogens from animal exposures. The objective of this study is to determine the sources and quantities of household animal fecal contamination, an important exposure pathway for enteropathogens, in Ecuadorian households. Quantitative PCR (qPCR) assays were used to identify host-associated fecal contamination by detecting gene fragments of gut microbes that are specific to the feces of a given human or animal host. These microbial source tracking (MST) marker assays were used on environmental samples collected in Ecuador households including floor, mother and child hand rinses, and domestic water to assess the abundance and sources of household fecal contamination. MST marker targets included human feces associated markers (HF183 & HumM2), dog feces makers (DG37), ruminant feces markers (Rum2Bac), pig feces markers (Pic2Bac), bird droppings markers (GFD), and general bacteroidales markers (GenBac). The anticipated results are that the qPCR data will continue to indicate high levels of general and human-associated animal fecal contamination in animal-owning Ecuadorian households as previously observed in Phase 2 of this study. Findings from this study will highlight the need for the development and implementation of relevant public health interventions aimed at reducing animal exposures and improving overall hygiene practices to decrease the global disease burden among LMICs.

Pacific salmon are both an ecological and cultural keystone species, essential to Pacific Northwest ecosystems, Indigenous Peoples, and the economy. Road salts (primarily NaCl), an increasingly common toxic constituent of stormwater runoff, adversely affect salmonids in vulnerable early life stages and mobilize heavy metals found in roadside soils. Dissolved copper (Cu), a ubiquitous nonpoint source pollutant, has been correlated with the impairment of olfactory systems in salmon; the negative effects of Cu decrease pre-smolt survival rates when compounded with NaCl. Our study investigates the concentrations of Cu and Cl^- in urban and rural watersheds home to Pacific salmon. We collected water samples from the Cedar River watershed and the Thornton Creek watershed in the greater Seattle area following storm events. Ion chromatography (IC) and inductively coupled plasma-mass spectrometry (ICP-MS) analysis were performed on our samples to determine the concentration of Cl^- and dissolved Cu, respectively. Our results show levels of Cl^- that have been shown to increase the mortality rate of Atlantic salmon alevin, whereas concentrations of Cu are undetectable in Cedar River and at very low levels in Thornton Creek. Annual returns of salmon runs across the Pacific Northwest are in rapid decline and although the cause is neither singular nor isolated, water quality and habitat degradation are leading concerns. Our results provide insight into how road salts and metal-containing road dust contaminate streams and rivers, altering water quality conditions for salmonids from fertilization to swim-up. We relate our findings to current ecological management practices and research examining the effect of salinization and copper toxicity on salmonids in critical early life stages.

Organic photovoltaic (OPV) solar cells present promising solutions in photovoltaic technology due to their lower cost and the abundance of materials compared to earlier solar technologies. As energy costs rise, OPV’s are increasingly of interest as a source of energy. The development of new curricula using a socio-scientific issues (SSI) framework can encourage students to consider careers in organic chemistry to fill these critical needs in global energy. The SSI framework also allows students in the developing stages of their STEM pathway to engage more deeply in traditionally ‘weed-out’ coursework and develop skills which will allow them to persist through STEM. We have designed a laboratory experiment using a SSI framework to allow undergraduate organic chemistry students to explore OPV’s current energy. Students synthesize poly(3-hexylthiophene) (P3HT), the active layer of an OPV cell and a promising polymer in OPV technology due to its stability and scalability. Undergraduates also build and strengthen skills of fundamental processes of organic chemistry using Grignard monomer formation and gain insight into the benefits and current challenges of organic solar cells, increasing their scientific literacy. Synthesis is conducted without the use of an inert atmosphere, lowering the barrier to implementation in under-resourced learning environments. This laboratory protocol exposes students early in their STEM careers to SSI-based learning in OPV technology and allows them to see connections in coursework to broader global issues.

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

Movements can be externally driven, based on responses to the environment, or internally driven, based on self-initiated triggers. We modeled these systems using saccades, which are rapid eye movements that shift the direction of gaze. We compared visually-guided saccades (VGS) to visible targets and memory-guided saccades (MGS), where a target was transiently presented and its location memorized before a saccade was made. As a result of aging, growth, and skeletomuscular damage, adaptations in brain circuitry are necessary to adjust motor output and maintain accuracy for both types of movement, but their corresponding mechanisms are not well understood. We hypothesize that VGS and MGS employ different adaptation mechanisms. The superior colliculus (SC) is the central structure in creating the saccade command signal, and prior research suggests VGS adaptation occurs downstream of the SC. To compare this to MGS adaptation, we recorded single unit activity from visuomotor neurons in the SC in four Macaca mulatta monkeys as they adapted their saccade amplitude. I analyzed this data, measuring the median number of action potentials during each saccade for both VGS and MGS; the “non-adapted” saccades, which had the largest amplitudes, were compared to the “adapted” saccades with smaller amplitudes. For VGS, neuronal activity remained constant as saccade amplitude decreased, but for MGS, the number of spikes decreased alongside the saccade amplitude, which indicates VGS and MGS adaptations employ different processes. Moreover, as visuomotor neuronal activity in the SC decreased during MGS adaptation, further research can be conducted to determine if MGS adaptation occurs within or upstream of the SC.

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.

Archaeal cellular envelopes are quite simple compared to bacterial surfaces. Unlike bacterial cells, S-layers are the dominant component of most archaeal surfaces. Archaeal S-layers are composed of proteins or glycoproteins symmetrically arranged in an almost crystalline lattice. S-layers are in direct contact with the surrounding environment and facilitate important processes including protection, cell adhesion, molecular sieving, ion trapping, and nutrient adsorption. It is clear that S-layer proteins play an important role in an organism's ability to survive, especially within extreme environments. However, it remains unclear if S-layer proteins change in response to environmental stressors such as increasing temperature. This project is aimed at quantifying variation in bulk protein concentrations within microbial cultures containing a hyperthermophilic deep-sea methanogen (Methanocaldococcus sp. FS406-22) grown at 65, 73, and 85°C. Total protein concentrations were gathered via spectrophotometric analysis after growth. Optimal growth temperature for Methanocaldococcus sp. FS406-22 is 65C but can grow at temperatures up to 92°C, the highest known temperature limit for biological nitrogen fixation. I hypothesize that changes to Methanocaldococcus sp. FS406-22 S-layer proteins will be observed in order for the organism to acclimate to more extreme growth conditions. These data give important preliminary information regarding Methanocaldococcus sp. FS406-22 ability to physically adapt to changing environmental conditions. This project ultimately provides context for future work to be directed at exploring not just if S-layer proteins change but also how.

Increased awareness of the complexity and importance of soil ecosystems has led to a surge in “regenerative” agricultural practices, which build topsoil and improve soil fertility and nutritional quality of produce. Such practices also sequester carbon in soils, reduce topsoil erosion and reliance on synthetic fertilizers, and increase microbial content and water storage capacity of soils, avoiding many of the negative environmental and ecological impacts caused by more conventional forms of agriculture. While there is substantial anecdotal evidence for the success of regenerative farming, quantitative studies that support farmer experiences are limited. This study aims to help bridge this gap by examining soils in the Puget Sound region to evaluate differences between areas managed regeneratively and conventionally. I visited five local regenerative farms and took two sets of soil samples from each: one from a plot managed regeneratively, and one from a portion of the farm that has not yet transitioned from conventional to regenerative management. Each set of soil samples consisted of soil cores to test for soil organic carbon (SOC), and a soil pit to examine soil horizons. I determined SOC using loss-on-ignition tests, and topsoil depth by measuring the thickness of the A-horizon in the soil profile. The data show that topsoil managed with regenerative practices can be up to 4 inches deeper and contain up to 20% more SOC than when managed conventionally. Within the regeneratively managed plots at the UW Student Farm, there is a strong correlation between the age of the plot and topsoil depth, suggesting growth of topsoil over time. While these findings align with the results of other studies, a more nuanced understanding of how topsoil formation processes and soil ecosystems develop under regenerative management is necessary to support large-scale transitions towards more sustainable agriculture.

Crowded farmworker housing conditions are associated with stress and adverse mental health effects. The H-2A program, administered by the Department of Labor (DOL), grants employers the ability to apply for foreign workers to perform temporary agricultural labor. H-2A employers are required to provide housing for workers at no cost. We sought to describe the distribution of H-2A worker housing and crowding within Region 10 (Washington, Oregon, Idaho, and Alaska). We defined crowding as the occasion when the reported total workers certified exceeds the reported total occupancy (the total occupancy capacity for all housing units per the employer H-2A application). Using data gathered by the DOL over 2020 and 2021, we examined 2,315 applications, representing 72,151 workers (54,873 in WA). Across Region 10, 22% (n=15,892) of all workers lived in mobile homes, 12% (n=8,476) in houses, 11% (n=7,832) in temporary worker housing, 9% (n=6,397) in stick-built homes, 8% (n=5,970) in labor camps, and 6% (n=4,054) in apartments. The definition of crowded housing was met by 24% of applications (n=567/2,315). A total of 36,101 workers (50% of total) lived in crowded housing conditions, with 10,569 workers in crowded mobile homes, 6,256 in temporary worker housing, 3,289 in houses, 2,931 in labor camps, 2,534 in stick-built homes, and 1,471 in apartments. Our results suggest crowding is prevalent in Region 10 H-2A worker housing and is especially of concern in mobile homes and temporary worker housing. Our work helps to guide efforts to prevent crowding and its adverse health effects among vulnerable workers.

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.

In every eukaryotic genome, there is a cluster of tandemly repeated ribosomal DNA (rDNA) that is present in high copy numbers. Besides encoding ribosomal RNAs, rDNA is also involved in many non-ribosomal cellular functions. It is still not fully understood how this cluster of rDNA is maintained and how variation in its copy number impacts cellular function. Kobayashi et al found that Fob1, a protein that binds to replication fork blocking (RFB) sequences, is involved in the expansion and contraction of the rDNA region, however, the underlying mechanism of this copy number control is unknown. To explore the interactions between FOB1 and rDNA I would like to utilize CRISPR/Cas9-mediated editing to edit specific sequences in each rDNA repeat in wild-type and fob1Δ strains of Saccharomyces cerevisiae. Previous studies in our lab utilizing CRISPR/Cas9-mediated editing of the rDNA found that the rDNA copy number was initially significantly reduced, resulting in very slow cellular growth, and after many cell generations, rDNA copy number would expand through a proposed mechanism of reintegration of excised repeats and unequal sister recombination. These observations raise an important question: if FOB1 is needed for rDNA expansion, would it even be possible to perform rDNA editing and recover rDNA copy number in a fob1Δ strain? To address this, I am performing CRISPR/Cas9 editing of rDNA in fob1Δ cells alongside a wild-type control. I am characterizing viable transformants by studying their growth rate, ploidy, and rDNA copy number expansion. I am expecting to see no rDNA expansion occur in strains that do not have the presence of FOB1. By understanding the phenotypic impact of rDNA copy variation in a fob1Δ strain of Saccharomyces cerevisiae, we can come closer to understanding the interactions between RFB, FOB1, and rDNA copy number along with its effects on cellular processes.

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 primary goal of post-transplant care is to achieve the optimal balance of immunosuppression between infection and rejection. Physicians currently rely on laboratory markers such as changes in serum creatinine. Physicians use kidney allograft biopsies to detect acute rejection but biopsies are expensive, invasive, and susceptible to sampling error. This study investigates the use of donor-derived cell free DNA (dd-cfDNA) as a biomarker for kidney allograft dysfunction to allow for optimization of immunosuppression. This multicenter prospective study (Caredx) examines the correlation between dd-cfDNA levels and infection and rejection episodes in pediatric kidney transplant recipients. Dd-cfDNA is measured 3 to 12 months post-transplant and compared to the clinical outcomes of major infection events and biopsies. Data is collected from November 2019 to 2023 on 59 participants from Seattle Children’s Hospital, St. Louis Children’s Hospital, and Emory University. Using patient’s charts in EPIC I abstract patient demographics, transplant characteristics, laboratory, and kidney biopsy results. I assist with patient recruitment and retention by keeping track of when patients are within sample windows and ensuring their sample requests are sent. Preliminary data from the first 10 samples revealed that elevated dd-cfDNA levels were associated with viral infection or acute rejection episodes. We observed a decrease in the dd-cfDNA levels following treatment for BK viremia. Following data collection, we plan to submit an abstract to the American Society of Nephrology in May of 2023. Additionally, we will prepare a manuscript to submit to the Journal of Pediatric Transplantation in the Summer of 2023. Use of dd-cfDNA will enable early intervention and minimize damage to allografts leading to improved longevity and quality of life. Furthermore, the biomarker is less expensive, less invasive, and more accessible than reliance on transplant biopsies holding the potential to break down economic and physical barriers to health care.

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.

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 alpine zone has been underrepresented in herbarium collections due to its difficulty in access and short growing season. Despite its underrepresentation, the alpine zone presents a unique opportunity to study climate change impacts due to species; limited ability to migrate to more suitable habitats. For this study, we are examining the Cascades Range from the Canadian border to Mount Adams. Our primary objective is to understand the distribution patterns of alpine species richness and how it is influenced by latitude and elevation. Our secondary objective is to see if these patterns in phytogeography correlate to species; life history characteristics of dispersal, pollination mode, and flower color. To research these questions, we created a species list of Washington's alpine plants using 50 Peaks Project data, historical herbarium records, and literature references. To assess latitudinal course patterns of species richness along the Cascades range, we created three relatively equal zones and scored the presence of each species in it. For statistical analysis, the total number of species per zone will be tallied and Chi-square analysis will be performed to test for significant differences in species richness. We will use regression analysis to quantify the relationships between latitude and the number of peaks, and latitude and average elevation. To compare life history traits across the three zones, we will analyze frequency distribution of those traits. Our preliminary results for latitudinal patterns indicate that the North Cascades have the most species while the Southern and Central Cascades are nearly tied. The final results from this study will inform the selection of future collecting locations and future analysis for species richness among peaks for the 50 Peaks Project. Preliminary Run through the Burke Herbarium, the 50 Peaks Project collects plant specimens to document diversity and distribution in Washington's Cascades Range alpine zone.

The choice to terminate a pregnancy is rarely an easy one. It is critical that the experience of pregnancy termination is made as comfortable and convenient as possible as women grapple with the mental and physical challenges that arise from their choice to abort. The current standard protocol for at-home medical termination of pregnancy involves the patient-mediated oral misoprostol delivery 24-48 hours after mifepristone. This timed delivery ensures that misoprostol can trigger contractions after the cervix is dilated by mifepristone. This presents a challenge for patients, who have to manage the side effects of mifepristone while also timing the delayed dosage window for misoprostol. Combining these two medications into the single dose modality that instantly releases mifepristone and ensures the delayed release of misoprostol will improve the at-home medical abortion process for patients globally. The nanoparticle encapsulation of misoprostol for oral delivery offers the prospect of delayed release and release modulation through the alteration of variables such as molecular weight and co-polymer polymerization and other formulation parameters. Herein, we aim to use established protocols for nanoparticle encapsulation to fabricate and characterize misoprostol nanoparticles. By varying molecular weight and copolymerization parameters, we aim to tailor misoprostol release and evaluate the efficacy of different encapsulation approaches. We intend to investigate the particle size, entrapment efficiency, shelf-stability, and in vitro release of misoprostol nanoparticles in PBS and simulated gastrointestinal fluid. In doing so, we aim to provide a proof-of-concept of formulating misoprostol into nanoparticles to demonstrate encapsulation and sustained release. This understanding can contribute to the development of a single-dosage modality to meaningfully improve the comfort and ease of at-home medical abortions.

The brain is one of the most complex and vital organs in our body. While thousands of people get treated for concussions, our knowledge of the impacts of brain injury is fairly limited. Brain injury caused by concussions occurs in about 1.9 million youth. Coupled with anxiety, this type of injury can become further complicated, which is why a holistic approach is necessary when treating patients, and even more critical when considering pediatric cases. There is research evaluating concussions and anxiety independently, but there is little research analyzing the joint relationship between the two. The Care4Kids study at the Seattle Children's Research Institute is one site in a multi-site study that examines post-concussive symptoms in children between the ages of 11-18; in conjunction with this work, I present the findings of a literature review evaluating the intersectionality between anxiety and concussions, asking the question, “What are the effects of pediatric sports-related concussions on anxiety?” The methodology for this review primarily focuses on synthesizing previously conducted research studies and reviews to present a comprehensive picture on the current discussion in research involving anxiety and concussion, and also its impact in the scientific community. In this review, I analyze the various aspects of pediatric sports concussion symptoms, focusing specifically on the manifestation of anxiety in post-concussive children, the degree of this anxiety faced across all ages, and a comparison of the short and long-term effects. With the findings from this literature review, we can gain a more comprehensive understanding of the relationship between anxiety and concussions in children to better predict and detect concussive symptoms in the future in order to ultimately provide children with efficient and conclusive post-concussive care.

Students in a statistics course made concept models throughout the course. Previous studies suggest that making concept models is a useful way for instructors to assess learning. The growth and changes of these student-constructed models may serve as an indicator of how a student constructs and organizes their cognitive structure. But, little is known about how much impact the Covid-19 disruption has had on a student’s cognitive restructuring in STEM courses. Therefore, we ask the following research question: What factors best explain the changes in the student-made models about statistics as representations of their cognitive structure? To address this research question, we analyzed concept models from three assessment points and two quarters of the same course, one taught before the Covid-19 disruption and the other during the Covid-19 disruption, to estimate the impact that the distributions had on their cognitive structures. After converting the 180 student model into graphs, we calculated the number of concepts in each model to build a linear model to compare a quarter taught before and during the major disruptions. First, we created a box and whisker plot that shows model growth across two different quarters, pre and during, and then we created a model to explain how the disruption term influenced the rate of concepts being added to student models at three different assessment points of the course. Our preliminary results revealed that students in the emergency online environment added concepts to their models at a significantly slower rate. Future directions and limitations will be discussed. This work is important because it helps teachers and professors understand how college students are learning in different environments.

In the ubiquitin-proteasome system, the E2 enzymes are involved in the second step of transferring the ubiquitin (Ub) to a substrate. Specifically, an E2 enzyme receives the ubiquitin from an E1-Ubiquitin(E1-Ub) conjugate and becomes an E2-Ub conjugate. Then, an E3 enzyme can deliver the ubiquitin from the E2-Ub conjugate to a substrate to form a substrate-Ub conjugate. Most of the E2s attach Ub to a substrate lysine residue, but Ubc6, an E2 from yeast, also seems to react with substrate hydroxyl groups on serine/threonine/tyrosine. This project is divided into two parts: first, validate the reactivity of Ubc6 in different amino acid (serine/threonine/lysine/cysteine/tyrosine) conditions. Second, apply a proper machine model to predict the reactivity of Ube2J2-Ub, a mammalian homolog of the Ubc6-Ub conjugate. The quantification analysis on the Ubc6 charge/discharge assays can reveal the rate of the reactivity of the Ubc6 in different amino acid conditions. After validation, three types of E2s with known reactivities: Ubc2D(1/2/3/4)-Ub, Ube2L3-Ub, and Ubc6-Ub, can be used as training sets for the machine learning model. Once the model predicts the reactivity of Ube2J2, the prediction can be validated by performing assays on Ube2J2. We expect that Ubc6 reacts fastest with Cysteine, followed by Threonine, Lysine, Tyrosine, and Serine. Since Ube2J2 is a human homolog of Ubc6, we predict that Ube2J2 has the same reactivity as Ubc6. The implication of this project is whether machine learning can assist with finding the reactivity of a protein enzyme.

Engineered genetic circuits provide an environmentally friendly path to chemical industries, including fine chemicals and therapeutics. To effectively modulate genetic circuits, a programmable tool to control multiple genes is necessary. CRISPR-mediated gene activation (CRISPRa) is an emerging tool suitable for this purpose. In CRISPRa, a nuclease-deficient dCas9 protein is used to deliver a transcriptional activator domain (MCP-SoxS) upstream of genes of interest. A complementary guide RNA (gRNA) enables dCas9 recruitment to any DNA target. Despite the programmability of CRISPRa, the number of genes that can be simultaneously regulated remain unexplored. In this work, we aim to experimentally investigate the number of gRNAs limitation in the chemical bioproduction context. First, we designed CRISPRa circuits with an increasing number of guide RNAs encoded on plasmids constructed with a scalable and high-throughput technique via Golden Gate Assembly. CRISPRa circuit performance was then evaluated by simultaneously regulating multiple fluorescent proteins as a proxy for multi-enzyme cascade in biosynthetic pathways. Increasing the number of gRNAs was found to decrease CRISPRa activity, suggesting competition of CRISPRa components. Furthermore, we applied the constructed circuits for metabolically engineered pathways in P. putida regulating production of p-aminocinnamic acid (pACA), a precursor for polymer synthesis vital in photovoltaic and biomedical applications. Bioproduction of pACA in P. putida was enabled by simultaneously regulating 9 heterologous genes. The outcome of CRISPRa circuits will be analyzed via High-Performance Liquid Chromatography (HPLC).The implication of this work will allow us to construct large scale CRISPR genetic circuits and optimize multi-gRNA CRISPR circuit integrations into other systems such as non-model organisms and cell-free systems, which will expand metabolic engineering capabilities and chemical productions beneficial in a wide range of biosynthetic applications.

 As climate change worsens, flooding from extreme weather and sea-level rise continues to threaten coastal populations and energy infrastructure. Small, isolated island states like Puerto Rico have weaker electrical grids and are especially vulnerable. Coastal habitats such as mangroves and coral reefs buffer shorelines and offer natural protection against these storms. To identify where habitats reduce the risk of flooding and erosion, we used a spatial model that takes in biophysical data and estimates an exposure variable for every 250m of coastline. The model shows that habitats safeguard 250,000 people living on vulnerable coastlines. Most of these people live in major port cities with substations and fuel terminals that deliver power to the entire island. As urbanization and global warming further degrade coastal habitats, Puerto Rico loses its best defense against tropical storms. Our results highlight the importance of sustainable development planning, especially as the island invests in its renewable energy transition. The spatial model can help prioritize which vulnerable communities receive resilience funding and where to avoid siting tourism to preserve ecosystems. Our model also reveals degraded habitats that could be targeted for ecological restoration. In future projects, we will apply the model to other states to explore relationships between communities, energy, and climate across multiple land and seascapes.

People have avoided art therapy for a long time due to the belief that they cannot use it to cope with their mental health problems if they do not have artistic ability. Luckily, people can use this form with or without art skills. In Europe, this type of therapy originated in the 1940s. During a tuberculosis outbreak, art therapy helped patients cope with their illness. It is safe to assume that anyone can benefit from art therapy based on that information alone. A number of studies have examined people's mental health symptoms before and after sessions. That raises the question: How can art therapy affect others in the long term in the mental health field? In a variety of studies, they reported significant symptom improvement after art therapy interventions. It was not only people’s symptoms that improved but it was also shown that their self-esteem was positively oriented. This literature review will help identify the stigma surrounding this form of therapy. It will also help identify how art can be a healthy way to cope and express themselves. 

In flowering plants, LEAFY (LFY) is a key floral developmental gene; homologes of LFY exist in nonflowering plants, where this developmental regulatory role cannot exist. In an effort to understand what role LFY serves in a nonflowering plant I am studying the model fern Ceratopteris Richardii, as ferns produce spores not flowers. My goal is to determine if the two fern LFY homologues, CrLFY1/2, play a role in the reproductive or vegetative development of ferns. To investigate this function, I am characterizing the phenotypes of transgenic plants that overexpress one or both of the fern copies. To that end, I record data on key developmental markers across the diploid generation of the fern, or sporophyte. Given that LFY overexpression has been associated with early flowering and leaf compounding in flowering plants, I anticipate early reproductive development and/or abnormal leaf development in my transgenic ferns sporophytes. Preliminary results suggest that transgenic ferns are producing spores earlier than controls, and are not displaying all expected markers of vegetative development. Here, I present data on the vegetative development and appearance of reproductive structures of C. richardii ferns overexpressing one or both of two gene duplicates, CrLFY1 and CrLFY2 to help elucidate the functional evolution of the this important developmental regulator of flowering.

Road salts are commonly applied as deicer during the winter months in Washington and can enter freshwater systems through run-off. The salinized waters can harm aquatic ecosystems. Zooplankton, specifically Daphnia, play a crucial role in providing food to other trophic levels in many ecosystems and could threaten the stability of these systems if they are unable to tolerate salinized waters. We hypothesized that Daphnia exposed to low levels of salt through several generations would better adapt to salinized water than an untreated population over time. Two populations of Daphnia were cultivated in the lab, one control with standard media and another with low levels of additional salt. We then placed these two groups in varying salt concentrations for one week. Under each condition, the survival rate of Daphnia was recorded. Heart rate was also observed as an indicator of physiological stress. We expect the pre-treated Daphnia to adapt to the road salt while the non-treated will have higher mortality rates. Understanding the impact of road salts on Daphnia can help us predict the possible effects on the overall health of aquatic ecosystems.

Under cellular stress conditions, proteins are destabilized, often causing them to misfold, and in certain cases aggregate. Without protective systems in place, significant cellular dysfunction occurs, often resulting in cell death. One mechanism of molecular stress response is increased expression of small heat shock proteins (sHSPs). sHSPs are ATP-independent chaperones that are thought to keep proteins in a refolding-competent state during stress and work with other chaperone proteins to rescue proteins from irreversible aggregation. Members of the sHSP family are defined by their shared structure: a conserved α-crystallin domain (ACD) flanked by unstructured N-terminal (NTR) and C-terminal (CTR) regions. Transient interactions between the three domains are important regulators in oligomerization. The structured ACD is the building block of sHSP oligomers and provides a framework for studying oligomerization. The ACD dimer contains three grooves into which the NTR and CTR can bind. Though it is clear the ACD plays a major role, the regulation of these domain interactions underlying oligomer formation is not well-defined. HSPB5 and HSPB1 are two human sHSPs that are ubiquitously expressed throughout tissues and can form homo- and hetero-oligomers. My experiments were aimed at studying the effects of mixing the isolated ACD with the full-length protein. To analyze the domain interactions and oligomer size changes upon mixing, I used size-exclusion chromatography (SEC). In these mixing experiments, addition of the ACD to different oligomers increased the number of available grooves with each titration point. The experiments presented here provide glimpses into the hierarchical organization of homo- and hetero-oligomers of HSPB1 and HSPB5. My results indicate that not only does the number of grooves matter, but also their identity. My working hypothesis is that the identity dictated the strength of the interactions between the different binding components and led to differences in the propensity for subunit exchange in oligomers.

 Immune cells make up the body's defense against cancer and observing their spatial distribution in a tumor can provide information about patient prognosis. However, it is difficult and time consuming to identify each immune cell in images from cancer biopsies in order to perform spatial analysis. Additionally, stained immune cells are hard to distinguish by appearance in unprocessed multispectral images due to the overlapping or "mixing" of signals coming from different channels. A computational tool could efficiently identify the immune cells in a tumor. The goal of this project is to build a digital pipeline to identify each immune cell in a multispectral image of a tumor and make it generalizable to multispectral images from any source. First, we use an unsupervised method to break up mixed multispectral images into clusters. The user selects a subset of clusters that do a good job of isolating each type of immune cell. A sample of these user-selected results are used to train a supervised machine learning model. The trained model assigns a label to each cluster to classify the entire image. Preliminary results have shown that clusters can usually be assigned to the correct label with over 50% certainty. We anticipate that the clusters will show good agreement with clinician classifications. This pipeline will allow for immune cell identification with less human involvement than pathologist annotation and without requiring spectral unmixing, a preprocessing step that typically takes hours. In the future, we will test this pipeline with varying amounts of training data coming from different sources and integrate it with spatial analysis to capture immune signatures of disease.

Human brain organoids (HBOs) are multicellular, three-dimensional tissue structures, created from human donor stem cells. Journalists and scientists commonly refer to HBOs as “mini brains” when communicating to lay audiences. Given the brain’s central role in our sense of personal identity, it is important to be thoughtful about the terminology used to describe this research. In this project, I am seeking to understand how terminology impacts lay perceptions of organoid research. We interviewed 59 participants who donated biospecimens for HBO research using the term “brain organoid,” to query their perspectives on HBO research. They were then asked about the alternative term “mini brains.” I qualitatively coded interview transcripts for key themes. Analysis revealed the majority of participants preferred the term “brain organoid.” Perceived benefits of “brain organoid” included sounding more scientific, accurate, and respectful; drawbacks included overcomplication and necessity of explanation. Perceived benefits of “mini brain” included sounding more relatable and matching mental imagery; drawbacks included inaccuracy, over-exaggeration, and feeling misled. Of those who indicated a preference for “mini brain,” most had misconceptions about the level of sophistication of organoids. “Mini brain” was more commonly associated with fears about cloning or misuse. These results suggest the terminology used to describe a novel neurotechnology like HBOs could shape public perception of research. Although “mini brains” may seem like the more accessible term, we believe that properly explaining “brain organoid” promotes scientific literacy and accessibility to neuroscience for the general public. Use of accurate terminology conveys respect for lay audiences and discourages misinformation which could raise undue ethical concerns. Future research will include analyzing data from a survey where participants are randomized to “mini brain” or “brain organoid” versions to assess a large population for differences in responses based on terminology.

Smartphone detection of anemia using patient photos has the potential to provide a non-invasive method of measuring hemoglobin levels, introducing the possibility of increasing the accessibility and cost-effectiveness of current practices. While traditional methods of anemia detection require a complete blood count by a trained healthcare professional, smartphone detection instead relies on the user to take a high quality picture of their fingernails. However, it currently lacks the ability to provide feedback to the user on the quality of their image. For example, an overexposed image or one with low fingernail visibility can lead to inaccurate predictions of hemoglobin levels. We propose that machine learning classification methods can analyze these patient images to estimate the image quality and predict the effectiveness of smartphone detection of anemia for a given image. With various classical machine learning models, we demonstrate and compare the capabilities of each in classifying images of patients’ hands as being of “good” or “bad” quality (or on a more granular numerical scale) when given features of the images. Preliminary results show that a logistic regression model reaches 91.4% accuracy labeling images when compared to empirically assigned labels, and we expect iterative models to achieve improved performance. When completed, we would propose that this classifier could be used in the field to identify if patient image is of high enough quality to produce an accurate measurement of hemoglobin levels in real-time, providing feedback on the phone to adjust or correct the image-taking process.

Ophthalmic drug administration has been increasingly prevalent in recent years, with eyedroppers being utilized to administer costly medication like that for glaucoma. There haven’t been many solutions addressing eyedropper instillation for those with preexisting conditions like arthritis, who often deal with a host of problems when administering them: producing the necessary force to distill a drop, aiming the drop into the eye, and contamination of the eyedropper tip. We are testing the question of whether accessible eye drop aids can significantly improve eyedrop compliance and distillation for the elderly. Solutions to eye drop administration can save money and make the overall process easier for many patients. Existing solutions on the market seem to address the issue of contamination using apparatuses that press onto the lower eyelid, but there is still much to be desired with the force and aim required. Many require the use of gripping or squeezing, motions that many elderly patients can’t apply as much force with. I propose a couple of solutions to these problems in the form of eyedropper aids that each make use of a few different methods, including translating the motion, applying the force with different limbs, and even mechanizing the force required. Through a quantitative study, I hope to eventually test these prototypes through an ophthalmology clinic among a wide variety of elderly. Assessing these prototypes through both questionnaires and observation, I hope to notice an increase in effectiveness from previously existing apparatuses. We will use a survey to ask a variety of questions to around 100 elderly patients with varying expertise in eye drop instillation. The survey will ask whether the tool was more useful, easier, how hard it was to assemble, and we will also monitor quantitatively whether the accuracy of drops actually instilled was better. This work hopefully saves patients money from medication cost from a reduction in wastage, allows for better administration of medicine, and eases the process of distillation.

Alzheimer’s Disease (AD) is a neurodegenerative disorder characterized by the aggregation of the amyloid-β (Aβ) peptide into fibrillar β-sheet plaques. While Aβ plaques have been the historical focus in the study of AD, it has recently been shown that Aβ also forms oligomeric intermediates of a novel α-sheet secondary structure along its aggregation pathway. Furthermore, the formation of these α-sheet oligomers is correlated with the neuronal death and subsequent cognitive impairment seen in AD, and it begins up to 10-20 years before plaque formation or symptom development. In this project, I utilize a novel diagnostic technique known as the soluble oligomer binding (SOBA) assay to characterize the in vitro aggregation of Aβ through α-sheet detection in various timepoints of incubated Aβ. Additionally, I use SOBA to characterize AD phenotypes in transgenic mouse models using α-sheet detection in brain homogenate samples. SOBA selectively detects α-sheet oligomers using plate surfaces functionalized with in-house α-sheet peptide designs, followed by the introduction of amyloid samples and then amyloid-specific primary and secondary antibodies for detection. This research allows for the further elucidation of Aβ's structure and aggregation pathway, paving the way for future treatment methods for AD. Finally, I aim to translate my work with AD to develop SOBA for the system of Type 2 Diabetes (T2D) to detect the presence of toxic islet amyloid polypeptide (IAPP), the amyloid peptide implicated in T2D. This will be achieved through the systematic tuning of antibody systems and other procedural parameters such as plate washing methods. Preliminary results have shown the ability of SOBA to detect α-sheet in synthetic IAPP samples with concentrations as low as 10 pM. This novel method for toxic IAPP detection has the potential for T2D diagnosis earlier in disease progression.

The glymphatic system, which is primarily active during sleep, is a network of astroglial perivascular channels within the brain that allows for cerebrospinal fluid (CSF) influx and exchange. Glymphatic exchange plays a crucial role in the clearance of amyloid, a hallmark in the development of Alzheimer’s. Recently, a bidirectional relationship between Alzheimer's disease and sleep has also been suggested with amyloid deposition associated with mid-life sleep disruption. However, the mechanistic link between sleep disruption, particularly over chronic time scales, and the development of Alzheimer’s pathology remains unclear. This study investigated whether chronic sleep disruption, similar to that experienced in aging population, impacts downstream Alzheimer’s-related neuropathology. We hypothesized chronic sleep disruption will result in decreased glymphatic function and increased amyloid plaque burden. This experiment utilized a chronic sleep disruption model using Lafayette Sleep Fragmentation chambers, where mice underwent either chronic sleep disruption every two minutes during normal sleeping periods (daylight hours) or normal sleeping conditions (sham) from 10 weeks to 18 weeks of age (n=120). After eight weeks of sleep disruption or sham exposure, glymphatic function was assessed by dynamic in vivo near infrared imaging following stereotactic CSF tracer injection. Animals were perfusion fixed, cryosectioned, and glymphatic function was further assessed by measurement of fluorescent cerebrospinal fluid tracers in brain tissue. Aquaporin-4 localization, amyloid plaque deposition, and markers of astroglial and microglial activation were assessed by immunofluorescence. The collected data demonstrated that sleep disruption significantly increased neuropathological outcomes. The measured impact of glymphatic function was also correlated with these downstream pathological effects. These findings could be an indicator of interactions between neurological disease progression and an inflammatory expression after sleep disruption. They can also shed more light on the complex relationship between Alzheimer’s disease progression, the glymphatic system, and chronic sleep disruption.

In the era of Internet of Things, the operation of various kinds of sensors or devices on the shelves in warehouses or supermarkets often requires batteries or complex wire management. To address this issue, we propose a charging solution utilizing the near-field wireless power transfer (WPT) with multiple relay resonators, also known as a multi-hop WPT system. In this study, we designed and simulated several coil geometries for the WPT system to ensure high efficient power can be delivered from a transmitter to a receiver through various coil hopping configurations. After evaluating the trade-off between the coupling coefficient of coils in parallel and series as well as the design complexities, we constructed many unified coils in one geometry. We then measured the coil-to-coil estimated efficiency using the scattering parameter obtained through a Vector Network Analyzer on a foam board shelf. Our results show the efficiency range from 9% to 81% in the worst and best hopping configurations, respectively. Furthermore, we proposed a power efficiency optimization approach to improve the worst hopping configuration by up to 80%. We anticipate that the success of this work will significantly reduce the staff cost associated with the maintenance of wire management and charging systems on each shelf. It will also simplify the assembly process and enhance the accessibility of smart shelves while potentially mitigating environmental impact by reducing battery usage.

In this research project, our multidisciplinary team is developing environmental forensic technology to identify illegally caught seafood, with a focus on high-value species such as bluefin tuna. To tackle the difficult task of immediately detecting illegal, unregulated, and unreported (IUU) fishing, we are developing a rapid, affordable, and portable detection device that uses isothermal amplification and blue LEDs to detect resultant green fluorescent products indicating the presence of tuna DNA. As the lead Electrical Engineer, I designed an electrical circuit to precisely and stably control the temperature of a resistive heater using a microcontroller, thermistor, and PID algorithm along with an LED circuit. The requirement for the process involves the utilization of isothermal amplification technique at a fixed temperature of 37°C (33-42°C range) and green fluorescence detection (at 550 nm) in DNA using blue LEDs (at 470 nm) and an orange acrylic filter to filter the blue wavelength. The result is a circuit that meets the requirements for the biochemical process and enables real-time feedback without the need for shipping samples to a laboratory. With the development of the device finished, the next step is to streamline the user experience. I am leading the software development effort to create a phone application that facilitates the assay setup process and automates image capturing and analysis. With a capable research team, including colleagues shaping the user interface, a junior researcher connecting the device to the phone application, and a Ph.D. candidate in Computer Science and Engineering developing a proprietary camera software, our team's effort culminates in a user-friendly phone app that streamlines the assay workflow and provides real-time sample analysis. With the completion of this project, we will be able to make a difference by helping communities and marine ecosystems.

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.

 When homeless youth turn 26 years of age many of the organizations and resources they have been utilizing for survival, such as food and shelter, become unavailable as many organizations no longer consider them youth. The purpose of this study is to identify gaps in the transition period for homeless youth moving towards adulthood to explore ways to make the transition more efficient and accessible. I conducted a systematic literature review among databases and ten studies are included. Restrictions on studies included were publication dates after the year 2000, publications in English only and studies done in the United States. This study includes data from both currently and previously homeless youth from ages 18 to 30. Several areas are identified as gaps that affect the ease of transition for homeless youth including lack of consistent support in case management or mentorship, preparing the youth ahead of time for exit out of youth programs, housing models being utilized at time youth are aging-out at twenty-six years old, and how the youth values themselves. Recommendations for programs such as a housing first model that collaborates with mentoring and community support and youth preparation programs that begin at least a year before a youth turns 26 years old are discussed in this study.

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.

In the human immune system, there is a coevolutionary arms race occurring between pathogens and the host. Pathogens, especially viruses like HIV and SARS-CoV-2, evolve to escape the immune challenge presented by the human immune system. In return, the human immune system can re-organize and through processes that resemble Darwinian evolution, produce novel antibodies that target and neutralize the evolved pathogens. However, it is unclear who leads and who follows in this coevolutionary arms race. I introduce a bipartite, Markovian model to study a coevolving network of species and investigate causality in stochastically evolving systems. My results include novel analytical expressions for observables that discern causality, e.g., the rate of change of partial mutual information, and characterize how causal relationships change with the dimension and topology of the network. I compare the theory to simulations and describe statistical features of these processes. The tools I develop will be useful for distinguishing drivers of evolution in fitness seascapes and, more broadly, detecting causality in any type of dynamic network that undergoes nonequilibrium stochastic dynamics.

HIV-2 represents approximately 1-2 million of the 38.4 million people living with HIV (PLHIV) worldwide. Existing guidelines and recommendations for the treatment of HIV-2 infection are largely derived from in vitro data and small-scale clinical studies, and are often extrapolated from studies of people living with HIV-1. Furthermore, of the two most common HIV-2 groups (A and B), only a few examples of drug resistance in group B have been reported in literature. As a result, in-depth knowledge about the mutations that arise in group B HIV-2 isolates and the roles that these mutations play in antiretroviral drug resistance is lacking. The aims of my project are (1) to develop a novel approach for creating full-length, infectious HIV-2 group B clones that encode patient-derived integrase sequences, and (2) to demonstrate that this approach can be used to characterize resistance to Integrase Inhibitors (INI), which are an important class of antiretroviral drugs. Specifically, the parental plasmid for cloning and virus expression is 7312A-JK; this plasmid contains a full-length HIV-2 genome with group B gag and pol gene sequences. To facilitate downstream steps, I have replaced the integrase-encoding portion of p7312A-JK pol with a short, synthetic linker. This cassette clone will serve as the acceptor for longer, synthetic DNA fragments that encode patient-derived group B HIV-2 integrases. My ultimate goal is to generate a panel of 10 replication-competent group B clones that can be given to members of the Gottlieb lab for culture-based drug susceptibility testing. This work is an essential step toward a more comprehensive knowledge of drug resistance in HIV-2 which, in turn, is important for evidence-based treatment of all HIV-2–infected individuals, including those infected with group B strains.

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.

It is well-established that mutations have impacts on an organism’s fitness; however, the fitness effects of mutations are not static, and can vary depending on environmental contexts, such as the species in which a mutation is found. Evolution of the same gene in different species could thus lead to the evolution of different phenotypes, as different species would favour different sets of mutations. If that gene could be exchanged between species, it could lead to increased evolutionary possibilities, as high-fitness genotypes that require a prerequisite deleterious mutation in one species could become accessible if the mutation is not deleterious in another. Our research examines how the presence of two bacterial hosts, Escherichia coli and Klebsiella pneumoniae, could affect the evolution of an antibiotic resistance-conferring TEM-1 β-lactamase gene located on a conjugative plasmid. If different hosts confer different mutational effects to TEM-1, the process of horizontal gene transfer (HGT) that allows mutations to be shared between species could open up more mutational possibilities than those accessible in either single-species population alone. We tested this hypothesis through three rounds of experimental evolution in the presence of the antibiotic cefotaxime, where we evolved two single-species E. coli and K. pneumoniae populations and one multi-species population where HGT was simulated with a shared plasmid pool. We are now reconstructing the genotypes found in all three populations after each round to assess how much antibiotic resistance they confer in both species, and hope to see if the genotypes acquired under HGT treatment provide higher resistance compared to the single-species populations. Our results have practical implications for the predictability and nature of antibiotic resistance development in the real world, a current global health crisis, and potentially motivate further study in predicting resistance emergence in clinically encountered multi-species populations.

Merkel cell carcinoma (MCC) is a rare and aggressive skin cancer with a mortality rate of ~30%. In ~80% of cases, MCC development is attributed to the integration of Merkel cell polyomavirus (MCPyV) DNA into the host’s genome, leading to the expression of viral oncoproteins and tumorigenesis. Developing treatments that sustain immunity against MCC is imperative to address recurrent and/or progressive disease. In many cancers, tumor-infiltrating B cells have been associated with better prognosis and response to immunotherapies. However, the mechanisms by which B cells contribute to tumor immunity in humans have been difficult to resolve in part due to the inter-patient heterogeneity of tumor-specific antigens. The shared nature of MCPyV tumor antigens in MCC allows for MCC-specific B cell responses to be studied across patients. Using DNA-barcoded and fluorescently labeled viral oncoprotein tetramers, we analyzed the transcriptome, proteome, and receptor repertoire of MCC tumor-infiltrating B cells in 12 patient samples at single-cell resolution. From paired heavy and light chain sequences, we cloned 8 antibodies from B cells specific for the MCPyV oncoproteins to confirm binding to MCC-specific antigens. Transcriptomic and proteomic analyses of MCPyV-specific B cells revealed heterogeneity of intra-tumoral B cell responses. Interestingly, we found that the absence of MCC-specific germinal center (GC) B cells in MCC tumors associates with disease progression: ~80% of patients with no detectable GC B cells had MCC progression within a year post-surgery, whereas patients with detectable GC B cells remained progression-free a year after surgery (n=12, p=0.0043). These results suggest strong synergy between B cells and T cells may regulate tumor growth, as B cells rely on signals presented by T cells to differentiate into GC cells. Our long-term objective is to identify B cell phenotypes associated with anti-MCC responses to develop therapeutics that boost cancer-specific immunity.

T cells are a crucial part of the human immune system that play a role in the response to diseases from type 1 diabetes to COVID-19. All T cells undergo genomic recombination to create distinct T cell receptor complex (TCR) cell surface molecules that recognize antigens presented by major histocompatibility complex (MHC) molecules, thereby triggering a series of signaling pathways that culminate in T cell activation and cell division. Afterwards, daughter progeny share the same unique TCR molecules. In my project, I will be examining the role TCRs shared within a single individual (private) and between individuals (public) during COVID-19 infection. While the existence of these classes of TCRs is well documented, their functional roles remain unclear. My hypothesis is that the presence of public TCRs is linked to the strength of an immune response and, hence, to different disease severity in humans. We reason that common evolution may have led to the rise of these public TCRs because of their major role in the human body’s antiviral immune response. This hypothesis predicts reduced levels of public TCRs results in an inability to fight disease, whereas high levels of public TCRs will be associated with less severe disease. To test this, I will use a mixture of single cell RNA analysis and statistical tests on a dataset of TCRs acquired from blood samples of 254 SARS-CoV-2 patients and 16 healthy patients. Using a multiomic approach will allow me to also find genetic links between cells of interest. The data includes baseline and acute readings for each patient, and can be subsetted to cells with expanded TRA and TRB junctions individually. This experiment will help advance our knowledge about the function of public TCR chains and their role in fighting disease. Furthermore, our data could have translational applications for disease biomarkers.

Soluble factor signaling between immune cells and fibroblasts is critical in regulating biological processes. However, it is often dysregulated in diseases and leads to physiological changes, including airway inflammation in asthma and allergies. One immune cell type that can be attributed to airway inflammation is eosinophils (EOS). When activated by interleukin-3 and heat-aggregated immunoglobulin G, EOS release certain soluble factors associated with the activation of lung fibroblasts. To investigate the interactions between human lung fibroblasts (HLFs) and EOS, we used the open microfluidic coculture device. This device has two chambers, in which two types of cells can be cocultured in the shared media while being physically separated by a half wall. We found that HLFs in coculture with activated EOS had the highest levels of proinflammatory gene expressions and proinflammatory cytokines. However, the exact mediators responsible for promoting these biological processes are still uncertain. We hypothesize that EOS secrete a cytokine, interleukin-1 alpha (IL-1a), and a protein, transforming growth factor alpha (TGFa), to be consumed by HLFs, triggering proinflammatory responses of HLFs. The goal of this study was to elucidate the roles of IL-1a and TGFa in airway inflammation. HLF-EOS cocultures are seeded in the microfluidic coculture device, then IL-1a, TGFa, and their respective cellular receptors are neutralized using antibodies. Enzyme-linked immunosorbent assays are used to measure the level of EOS-derived neurotoxins after their activation. Then, reverse transcription quantitative-polymerase chain reactions are used to quantify gene expression levels relevant to proinflammatory responses of HLFs, in addition to multiplex immunoassays to analyze the secreted soluble factors from both cell types. We anticipate that HLF-EOS cocultures treated with neutralizing antibodies have lower expression levels of proinflammatory genes than cocultures without antibodies. Findings from this study will help us better understand the key regulators that promote proinflammatory behaviors of HLFs in airway inflammation.

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.

The focus of psychedelic research has been on psilocybin during the last decade, revealing positive implications for the future of psychiatry. Psilocybin has recently emerged as a potential therapeutic breakthrough for major depressive disorder, with a favorable profile of rapid-acting, long-lasting effects, and non-addictive properties. Given the high comorbidity and overlapping symptoms betweeen depression and opiate withdrawal, this recent advancement in depression treatment can be utilized to gain new insights into opiate withdrawal and its potential treatment. Recent research has also assessed psilocybin for treatment of nicotine and alcohol cessation, which showed promising results. The present study hypothesizes that psilocybin treatment alleviates anhedonic behaviors related to naloxone-induced morphine withdrawal and restores baseline behavior in rats. We examine morphine withdrawal symptoms and the efficacy of psilocybin using the open field test and sucrose preference test. Behavioral markers for anhedonic morphine withdrawal symptoms are extracted and quantified using DeepLabCut, a novel deep machine learning algorithm. Our preliminary data showed that psilocybin attenuated the overall effects of morphine withdrawal on locomotor activities, in support of our hypothesis. Since hundreds of thousands of lives are lost and affected by addiction every year in the U.S, there is an urgent call for new, effective treatments for substance use disorders. This study aids our understanding of opiate withdrawal and its untapped potential therapeutic treatment.

Δ⁹-tetrahydrocannabinol (THC) is the primary psychoactive compound found in Cannabis sativa and acts on the cannabinoid-1 receptor (CB₁R). Given its well-documented analgesic effects, THC’s therapeutic value in treating pain such as those associated with motor neuron disease states, muscle spasticity-related pain, chronic pain, and muscular sclerosis has gained traction. THC’s psychotomimetic locomotor impairing effects causes patients to cease treatment. However, this relationship between THC and locomotor control is poorly understood. To address this, we are investigating THC’s effects on Pre-Frontal Cortex (PFC) neural activity during natural, unprompted movement behavior in mice. The PFC historically is known for its role in executive function but is also a target for THC’s psychotomimetic effects. We expressed GRAB_eCB2.0, an endocannabinoid biosensor, or GCaMP6f, a Ca²⁺ biosensor, in the PFC and recorded neural activity through fiber photometry during uninhibited movement behavior. We found a novel, THC- and locomotion-dependent transient of Ca²⁺ and endocannabinoid activity in the PFC at the initiation of movement. I investigated the activity of glutamatergic and GABAergic neuron activity in the PFC by utilizing genetic mouse lines and found the Ca²⁺ activity transients were primarily driven by the GABAergic interneurons that constitute 20% of the anatomical population. I hypothesized that this is due to THC-dependent activation of the CB1R on distinct GABAergic interneuron subpopulations in the PFC, which would disinhibit glutamatergic activity and in turn promote spontaneous movement. I utilized in situ hybridization to examine colocalization of CB₁R with distinct GABAergic interneuron subpopulations. We found that while CB₁R does, in fact, colocalize with GABAergic interneurons, there was no differential localization between subpopulations. Overall, this project furthers our understanding of the ways in which THC modulates neuronal activity and locomotive behaviors.

Massive stars place powerful constraints on stellar evolution and are observed in a menagerie of exotic evolutionary phases. These objects play a crucial role in regulating their environments. They drive the chemical evolution of their host galaxies, and set the energy balance of their surroundings via feedback processes. Due to the importance of massive stars, placing constraints on their evolution serves as a key to understanding galactic ecosystems. Notably, stellar variability is a powerful probe of the poorly-constrained physics of massive star evolution. In particular, variability studies on ensembles of evolved massive stars can significantly constrain stellar evolution. We aim to understand the variability of hot massive stars through a census of these objects. We accomplish this using data from the Gaia mission, cross-matched with light curves from the Zwicky Transient Facility (ZTF). We expect to characterize the evolution of massive star variability timescales and amplitudes along the main sequence and beyond. Our results will place key constraints on the evolution of massive stars. 

Much of cosmology, including the age, shape, and evolution of the universe, depends upon the values of certain parameters. The Hubble Constant is one such parameter and is currently undergoing thorough investigation: our two primary means of measuring it yield two conflicting values. Is this merely a series of errors, or is there new physics to be uncovered? In order to eliminate measurement error as an explanation, we need to reduce uncertainty, but our current methods of measuring the movement of distant galaxies are unlikely to yield the necessary precision. Instead, we are developing a new method that may be able bypass the current reliance on a series of calibrations. Fast Radial Bursts are sufficiently point-like to detect the curvature in their wavefronts; hence the time delay registered between several satellites a sufficient distance apart can be used to determine the curvature of the pulse and hence the distance to the burst. More precise measurements of the distance to Fast Radio Bursts will lead to a better measurement of the Hubble Constant and the evolution of the dark energy. Further, using radio telescopes will require minimal advancement in precision measurement given already active GPS methods. While exploring what configuration will yield the greateat sensitivity, I have found a particular equidistant configuration of satellites that is able to maintain a consistent range of error regardless of what direction the FRB signal is coming from. Currently I am extending this search to additional satellites and numerous FRB sources to show that our model is able to achieve sub-1% precision in the Hubble Constant. If so, our model could be used to resolve the Hubble Tension, or to show that new physics such as new behaviors in dark energy is in fact present. 

The Circumgalactic Medium (CGM) is an extended structure surrounding galaxies, populated with hot diffuse gas and cold dense clouds of gas. The CGM acts as an intermediary between gas within galaxies (Interstellar Medium, or ISM) and gas between galaxies (Intergalactic Medium, or IGM). Insights into its properties and behavior could lead to a connection between the CGM and galaxy evolution, and the transition of a galaxy from star-forming to non-star-forming (quiescent). One standard method of observing the CGM is by measuring the absorption of light by elements in the CGM along its path to Earth, and since elements ionized to different degrees have distinct absorption signatures that can be observed, we can use them to determine the properties of the cool CGM. Our project aims to determine how the radiation from two sources of radiation—the central galaxy and the background—affect the ionization of this gas. Using observational data from the Hubble Space Telescope, we aim to constrain the dominant ionization mechanism of the cool CGM by comparing the data to physically-motivated fits and theoretical models developed by Dr. Faerman and Prof. McQuinn. Preliminary results show that by relating the density of CGM gas to the star-formation rate in the galaxy, the model is more consistent with the data, suggesting a relationship between the two properties. We are currently testing our method with one specific, well-modeled galaxy sample, and our framework allows including other existing samples as well as new, future observations. Modeling the properties of the CGM and how it interacts with galaxies will help us understand how galaxies form and evolve over cosmic times; one of the great open questions in modern astrophysics.

With the ever-increasing interest in new photovoltaic materials, much attention is being given to the study of nanoparticles and their assembly. One of the primary goals in this field is the self-assembly of particles, such that they can be programmed to form a desired structure given only a template and a solution of particles. In my project, I investigate the effect of proteins (specially designed through de novo synthesis) on the aggregation of gold nanoparticles, with samples prepared in buffers of salt and Tris base. The particles used are nanospheres of sizes 100, 50 and 10 nm, as well as nanorods of different aspect ratios which can offer more information on the directionality of the assembly. To obtain the necessary data on these samples I use a number of spectroscopy techniques (ultraviolet-visible, dynamic light scattering and circular dichroism) and microscopy methods (hyperspectral and scanning electron). A stereospecific response is obtained from the protein-particle mixtures if the materials formed are chiral, that is, if they rotate plane polarized light. I have shown that the proteins stabilize the particles in a salt solution, which is an indication of protein-particle binding - similar results have been correlated in literature to the formation of a chiral organic-inorganic complex. Such complexes would potentially benefit from both the plasmonic properties of the nanomaterial by absorbing light at a particular wavelength in the visible range, as well as the stereospecificity imparted by the protein helix. Being able to achieve such a result is an important step towards understanding the optoelectronic properties of biotemplated nanostructures, which has a diverse array of applications, including materials for solar energy production, photodynamic cancer therapy in which tumor cells can be specifically targeted, and drug delivery systems. It would also be invaluable for the customizable design of catalysts, enzymes, probes, sensors and diagnostic tools.

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.

Indium phosphide (InP) magic-size clusters (MSCs) are atomically-precise molecules that can be used as precursors to quantum dots (QDs). In a reaction to form InP MSCs, QDs are the thermodynamic product, whereas MSCs are a kinetic product, so there is a critical temperature below which a reaction will form MSCs but above which a reaction will form QDs. The goal of this project is to explore the effect of ligand identity on the formation and stabilization of InP MSCs and their subsequent conversion to QDs. For carboxylates, which bind weakly to InP surfaces, the critical temperature is about 120 ËšC. For phosphonic acids, which bind strongly to InP surfaces this temperature is so high that cannot be reached via a heating mantle – above about 400 ËšC. I am working to investigate the effects of native thiols/thiolate ligands on the synthesis of InP MSCs. Thiols are intermediate in their binding strength to and are commonly used with InP surfaces. I will probe the concentrations and temperatures at which thiolate-capped InP MSCs form. I hypothesize that the critical temperature for the synthesis of MSCs versus QDs reflects the ligand binding strength. If this is true, thiolate-capped InP MSCs should form readily at temperatures above 120 ËšC, but the temperature at which QDs are formed should be achievable via a heating mantle, opening up new parameter space for QD and cluster synthesis and study.

Since FPGAs (Field-programmable gate arrays) can achieve specific tasks faster and consume less power than general CPUs or GPUs, converting machine learning models to FPGAs has become more popular nowadays. However, people cannot directly deploy a floating-point model onto an FPGA due to resource limits (DSP, BRAM, etc.) on FPGAs. To solve this problem, some processes need to be done to shrink the models' size. Quantization is one method to reduce the models' size by rounding the floating-point calculations into a lower-bit representation. How to quantize a model without losing precision has become an interesting area of study. Our presentation focuses on configuring Qkeras (a tool designed to quantize TensorFlow Keras models) and hls4ml (a package designed to generate equivalent Verilog code based on the original model) to quantize CNN and RNN models before deploying them onto FPGAs. Our results will show that in the hls4ml process, if we quantize the Keras model into a Qkeras model before converting it into an hls model, we will need fewer bits compared to directly converting a Keras model into an hls model. In general, by studying the quantization of machine learning models, we can deploy more powerful AI into hardware such as FPGAs. The need for AI in everyday life has increased significantly, and this is a possible way to deploy AI in small items such as cameras, televisions, or even furniture.

In 2020, inclement weather spoiled over 1,800 pounds of produce at the UW Farm - roughly 15% of annual production. The resilienncy tunnel, our design for a greenhouse is intended to protect crops and extend the production season by multiple months, eliminating the need to quickly harvest spoiling crops in extreme weather using single-use plastic bags to deliver to the UW Food Pantry. The execution and operation of this project will notably contribute towards action VI of the UW Sustainability Action Plan, involving a target that 35% of campus food is from local sources by 2025. Our team shares the ambitious goal of designing an agricultural structure and landscape that sustainably and respectfully gives back to the community and surrounding areas with three key pillars: Resilience, Renewability, and Reciprocity. The Resiliency Tunnel, a 1500 square foot greenhouse and 600 sf educational space, will enable the UW Farm to grow produce with higher nutritional value in greater quantities and ensure that this produce reaches food-insecure populations. The UW Farm supplies dining halls, the UW Food Pantry, and the greater community with produce each year. As the climate changes, however, the increasing discrepancy between high demand during the academic year and high production during the summer growing season results in inadequate supply during the spring and fall. A greenhouse facilitates resilience against these conditions through crop protection and temperature control. Our proposal incorporates passive thermal design, a solar array, and rainwater catchment integrated with the structure and the landscape.