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.

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.

Neurodiverse representation has the power to shape how we view ourselves and others – for better or worse. Recent years have seen increasing accuracy and accountability in the way some mental conditions that differ from cultural norms, like autism and ADHD, are confronted in books and film. Despite this, obsessive-compulsive disorder (OCD), an often debilitating condition defined by unwanted intrusive thoughts and repetitive behaviors, remains a mystery to many. It’s a victim of stereotyping, often reduced to slang for neatness and made light of in shows like The Big Bang Theory and Monk. Conversely, other symptoms of OCD are stigmatized – confusion about the ego-dystonic nature of intrusive thoughts has led to such a wide-reaching news outlet as the New York Post, in 2023, incorrectly and irresponsibly pointing to OCD as the cause of violent extremism. People with OCD have a ten times higher suicide risk and only about 10% receive evidence-based treatment. Shame and unjustified guilt are some of the core emotions associated with OCD, and these intrapersonal factors combined with external stereotyping and stigma have disastrous effects. This project explores the possible literary origins of misconceptions around OCD through a lens of psychoanalytic literary criticism. In a literature review, I’ve identified the successes and failures of representation in the most historically prominent fictional works that feature OCD. I hope to shed light on the importance of representing OCD, provide a groundwork for accurate fictional portrayals, and illustrate how the experience of neurodivergence can be transformed by literature’s capacity for widespread social change.

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.

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.

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

The Khmer Empire was one of the largest preindustrial settlements in the world and is known for its vast temple complexes such as Angkor Wat. Although we have a functional understanding of the Angkor empire, the relationship between the Angkor state expansion as it relates to human-environment dynamics is unclear. Archaeological evidence from the site of Prasat Basaet, northeast of Cambodia demonstrates that there was human activity even before the Angkorian Period. Through our geological analysis of sediment samples excavated from ancient households at Prasat Basaet, we can get insights into the practices and activities of people and the surrounding environment. The preliminary results of our sediment particle analysis and organic matter measurements show change in human activity in Prasat Basaet as it relates to the expanding state. Using geoarchaeological methods such as; loss on ignition, magnetic susceptibility, and color, we have found an early, pre-Angkorian settlement at the site, followed by a long period of little to no activity, and then an increase in activity during the Angkorian period. We anticipate our research to be a pathway for understanding human-environment dynamics during expansion and contraction of the empire.

Trapped ions are proving to be a promising realization of quantum computation; computation is performed with an ion — such as 40Ca+ — contained by an electric potential and irradiated with laser beams of multiple wavelengths for ion cooling and qubit state control. Advantages to other implementations include repeatability and efficiency in state preparation, gate operation, and state readout. However, a number of ions are required for useful operation, and larger systems introduce complexity and possibility for error, which necessitates modular and scalable trap geometries fabricated using common methods pioneered by the semiconductor industry. Two-dimensional surface traps can suffer from low trapping depth, low efficiency, and higher ion motion, complicating high-fidelity operation. We explore alternative geometries, such as traps with multiple surfaces, and elucidate acceptable misalignment or non-ideal geometries. Our method exploits a multipole expansion of electric potentials produced through COMSOL; we expect to use the resulting multipole coefficients, trap depth, and trap frequency to inform fabrication tolerances and parameters such as electrode spacing, size, or shape. Through proper fabrication and optimal design informed by this work, traps with high depth, high efficiency, and low ion motion can aid the push for modular trapped-ion quantum computing.

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

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.

Herpes Simplex Virus (HSV) causes lifelong infections due to the establishment of latency in peripheral nerves. The immune response to HSV infections involves CD8 tissue resident memory T cells (CD8TRM) to sense HSV reactivation, and the innate immune cells to mitigate viral replication and spread. Plasmacytoid dendritic cells (pDC) can produce type-1 interferons (IFN-I) and prime CD8 T cells, yet their role in human HSV infections is unclear. ChipCytometry is a highly multiplexed imaging platform useful in observing cell-cell interactions, cell distribution in a tissue, and cell phenotypes. Using Chip Cytometry, we analyzed a tissue biopsy from a genital herpes lesion with a panel of 24 markers to characterize immune cell infiltration during active HSV reactivation. We showed that CD123+/CD303+ pDCs were located near activated CD8 T cells, many of which were found in lymphoid like structures in the dermis. These lymphoid like structures formed in areas where large nerve bundles and blood vessels were present and were packed with T cells and other immune cells which expressed markers for activation, exhaustion, and proliferation. Further research into pDC functions in HSV infections and cell interactions in these lymphoid like structures may provide insight on mechanisms of immune cell surveillance and response of reactivating HSV infections.

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.

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

 Alzheimer’s disease (AD) is the most prevalent of neurodegenerative diseases, with over 6 million Americans suffering from the illness and cases increasing each year. TREAT-AD (TaRget Enablement to Accelerate Therapy Development for AD) is an NIH-funded, multi-institutional network that identifies and addresses new targets for AD drug development. Genetic targets of interest were identified via RNA-sequencing and proteomic analysis of post-mortem tissue from participants with AD. We tested the effects of inhibiting or overexpressing selected target genes hypothesized to increase the risk of Alzheimer’s. One such target is the CD44 gene, which regulates GABA receptor activity. To efficiently manipulate genetic expression, we used clustered regularly interspaced palindromic repeats (CRISPR) technology to enhance (CRISPRa) or repress (CRISPRi) genetic transcription in neural progenitor cells, stem cells in the process of differentiating into neurons. We used a cell line engineered to harbor CRISPRa and CRISPRi machinery. CRISPRa involves a catalytically inactive Cas9 protein fused to a transcriptional activator. In CRISPRi, the inactivated Cas9 is fused to a transcriptional repressor. This, along with the quantification of molecular pathways linked to Alzheimer’s, permits a window into the conditions that lead to earlier onset of AD, and thereby conditions that might be altered by new drug treatments. Here we report that underexpression of genes related to endosomal trafficking leads to changes in protein buildup that may be related to earlier onset of AD.

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.

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.

Alveolar macrophages are vital immune cells, residing in the distal lung parenchyma. They provide the first line of defense against pathogens like mycobacterium tuberculosis (Mtb). They help initiate immune response within the lung and respond to viral infection. Mtb is the pathogen causes tuberculosis. This disease is fatal, and is the leading cause of death among infectious diseases globally. TOLLIP is a ubiquitin-binding protein that is involved in regulating innate immune responses by interacting with many receptors and the transport of endosomal cargo. Currently, TOLLIP’s role in TB pathogenesis is unknown, however, mice without the TOLLIP gene (Tollip-/-) have more severe Mtb disease. The goal of my project was to measure effects of adding mycolic acid and integrated stress response inhibitor (ISRIB) to macrophages of Tollip-/- and B6 Wild Type mice in vitro. I conducted the Bronchoalveolar Lavage (BAL) technique to extract macrophages from the lung via the trachea of B6 Wild Type and Tollip-/- mice. After macrophages were harvested, I plated them in mycolic acid and ISRIB in according wells with media. The cells were then infected with tuberculosis in the animal BSL-3, and data was collected through enzyme-linked immunosorbent assay technique and critically analyzed. Results illustrate that in both B6 Wild Type and Tollip-/- macrophages, adding ISRIB and mycolic acid results in an increase in production of the cytokine TNF, but Tollip-/- had a higher increase. Furthermore, the Tollip-/- samples had high variation in amount of TNF produced while Wild Type had minor amounts, raising further questions about how TOLLIP-deficient alveolar macrophages react when mycolic acid or ISRIB is added. Ultimately, the findings from this research, which is better understanding what specifically stimulates certain cytokines to help immune response to tuberculosis, is essential, and this is a small stepping stone in the broader goal of developing therapeutics for tuberculosis.

Mycoplasma genitalium (MG) is a sexually transmitted bacteria that causes urethritis in men and cervicitis, pelvic inflammatory disease, and infertility in women. MG infections vary in length: some infections are cleared within a few weeks, while others last for years and are difficult to treat due to antimicrobial resistance observed in MG. Hence, we began looking for novel compounds in fungal extracts and discovered rasfonin. In order to understand how rasfonin may inhibit MG growth, we attempted to select resistant mutants by conducting a serial passage with increasing concentrations of rasfonin. We found that one sample had a slightly higher minimum inhibition concentration. We isolated and sequenced this mutant and looked for mutations and analyzed how these mutations may affect the structure of this strain. Understanding how these mutations affect rasfonin resistance could allow for future studies on rasfonin as a possible treatment for MG.

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.

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

Veterans and Servicemembers experience trauma and chronic stress that lead to psychiatric disorders. Ample research has now demonstrated that blast exposure via detonation of high explosives on the battlefield can result in mild traumatic brain injury (mTBI) and it often occurs in combination with PTSD, depression, and addiction. Recently, Schindler Lab preliminarilly published that activation of dynorphin/kappa opioid receptor (KOR) system mediates stress/trauma-related dysphoria and anxiety-like outcomes. The expectation from this research project is that blast mTBI produces KOR activation to drive executive dysfunction and psychopathology and our aim is to understand the mechanisms underlying the adverse outcomes from blast-mTBI related to impaired executive functioning and determine the effect of blast trauma on the female and male population to understand sex as a biological variable. Prior to sham/blast exposure, mice will be injected with either vehicle (control) or norBNI that blocks activation of the KOR. Utilizing pneumatic shock tube and sophisticated operant paradigm in male and female mice, we modeled battle-field relevant open-field blast forces, detonation of high explosives to produce m-TBI and assessed various aspects of executive function (probability discounting, DRL, reversal learning, and progressive ratio) by monitoring the number and timing of lever presses and head entries into the food magazine of the operant chambers. Researching the chronic executive dysfunction mediated by blast-induced KOR activation during or immediately after repetitive blast exposure will contribute to understanding the underlying mechanisms regarding the effect of blast exposure on executive dysfunction for both females and males and the importance of timing on the effect to optimize further treatment options for veterans with an mTBI history and various psychiatric consequences. In the end, this research hopes to establish a novel understanding of mechanisms and treatment targets with experimental outcomes, giving rise to precision medicine approaches and endophenotype-specific treatment development.

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.

The drug rapamycin can increase lifespan in a variety of model organisms by repressing the activity of the mTOR complex, a cellular component required for growth and development. Other than one small study that looked at genetic variation in the effect of rapamycin on lifespan in fruit flies (Rohde et al., 2021), little is known about how natural genetic variation affects the response to rapamycin. Previous work by the Promislow lab, utilizing developmental time to indicate rapamycin’s affect, has shown that some strains of fruit flies are completely resistant to rapamycin while others are sensitive. These genotypic differences are also reflected in the metabolome, the complete set of small molecules and metabolites present within cells. Metabolome analysis of these strains revealed significant differences in metabolite concentrations between resistant and sensitive lines. Interestingly, when we treated sensitive strains with rapamycin, their metabolome profiles were like those of starved larvae. I hypothesize that rapamycin is affecting larval ability to take up nutrients and that the starved metabolome is a result of actual starvation. To test my hypothesis, I am designing a starvation assay to compare the death rate of sensitive and resistant larvae. Measurement of resistance to starvation is taken two days after rapamycin treatment by transferring larvae to nutrient deficient food. The duration of time for individual larvae to die is recorded, and the death rates between the two populations are compared. If my hypothesis is true, the sensitive larvae will have a higher death rate than the resistant larva. If death rates are similar however, that could mean that rapamycin does not cause a nutrient deficit and there is another explanation for its effects on the metabolome. This study will provide insights to the underlying mechanisms of sensitivity to rapamycin, and why it might differ between individuals.

Semiconductors are integral to many industries. As electronics trend towards more powerful devices, research efforts now focus on developing tools with the ability to achieve higher feature densities, such as the use of extreme ultraviolet (EUV) photolithography. Current photoresist technologies center around the use of 193 nm wavelength light with photo-sensitive organic thin films. However, these tools cannot produce feature sizes smaller than 20 nm. To overcome this limitation, semiconductor manufacturing is exploring 13.5 nm (EUV) wavelength light. Current commercial polymer photoresists lose sensitivity at this wavelength due to their low atomic absorption and photoemission of EUV light. Transition metal atoms have higher EUV absorption and can be incorporated to improve polymer photoresist sensitivity. To that end, molecular layer deposition (MLD) is a promising, scalable tool capable of creating thin films with angstrom-level precision. Unlike other deposition techniques, MLD does not require the use of solvents for deposition, boasts high compositional control, and is area selective deposition capable. In this work, the synthesis, characterization, and stability of novel thin films deposited using MLD are tested to determine their suitability as EUV photoresists, with the goal of improving semiconductor feature density, reducing the use of hazardous solvents, and decreasing energy and material costs in semiconductor production. Six films were studied using diethyl zinc (DEZ) as an inorganic EUV absorbent with six organic reactants: ethylene glycol; cis-2-butene-1,4-diol; 2-Methylene-1,3-propanediol; 1,5-hexadiene-3,4-diol; 1,4-butyne diol; and 3,4-dihydroxy-1-butene. Film thickness was measured using ellipsometry. Photosensitivity was measured upon exposure to 254 nm wavelength UV-C light. Degradation upon solvent exposure in an inert environment was examined using acetone, chloroform, ethanol, toluene, and deionized water, which proved most effective at removing the films, with thickness reductions up to ~90%. Results of solvent stability and light sensitivity will be used to propose new EUV photoresist processes for production-scale semiconductor manufacturing.

Wastewater contamination poses a serious threat to global public health. An emerging way that wastewater is treated is through poplar tree evapotranspiration galleries. In this system, microbiomes in the soil can extract pollution out of wastewater. We are conducting controlled studies to evaluate the ability of microbiomes to extract pollutants from secondary wastewater effluent at high water application rates. Our aim is to understand the microbiomes' pollution extraction capacity by studying their composition at varying soil depths with a focus on nitrogen species removal. I collected soil samples from 9 reactors, at two different depths each, and extracted DNA using a Qiagen DNA extraction kit. 16S gene of the DNA will then be sequenced using MinION, MinION is a third-generation sequencing technology with emerging applications for long-read 16S microbiome composition. In parallel, microbiome nitrogen cycling activity will be measured in the lab. The level of nitrogen processing will be compared from the different depths and with comparison to the community composition. We predict that as the depth of the soil increases, the composition of the microbiome will change, and the ability of the microbiome to extract nitrogen pollutants from wastewater decreases. This study will guide the formation of soil around wastewater facilities to optimize pollutant removal from wastewater.

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.

The Mongol Empire (1206-1368) under Chinggis Khan and his descendants was the largest continuous land empire in history, stretching across 5,000 miles of the Eurasian Steppe. During this period, referred to as the Pax Mongolica (lit. 'Mongol Peace'), the restoration of the Silk Road under a common administration allowed for the trading of goods between the Levant and Orient, and therefore the wider dissemination of technologies, cultures, and religions. This is juxtaposed with the great deal of brutality associated with the Mongol conquests, as evidenced by archaeological and textual records of mass killings during sieges, and modern scholarship regarding the Mongol Empire is tasked with balancing these perspectives. Witness to the Mongols is an upcoming sourcebook which compiles primary source material from all across the known world at the time, creating a complete picture of the life and legacy of Chinggis Khan, from his birth c.1185 to the fall of the last remnants of Chinggisid rule in 1502. Witness aims to compile, translate, and update scholarship for new audiences, both academic and at large, in order to communicate a more nuanced perception of Mongol imperial influence which, in my experience, otherwise propagates in Western education almost exclusively through the writings of Marco Polo. My specific contribution to this project concerns assisting in editing passages to ensure continuity between sources and revising introductory paragraphs and footnote annotations in preparation for publication. My particular fascination within the Mongol imperial sphere focuses on Mongol-Viet relations, especially in interpreting cultural dissonance regarding victory and failure of the Mongol invasions of Vietnam, as the successful defenses of Vietnam are widely celebrated to this day in folk tradition, though largely regarded in scholarship as Mongol victories for establishing a tributary relationship. As such, I am also tasked with investigating these threads for possible inclusion in Witness.

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.
 

Spatial transcriptomics is a set of neuroscience methods that enables the visualization of gene expression patterns across the brain. Using Expansion-Assisted Iterative Fluorescence in situ hybridization (EASI-FISH) protocols, a cutting-edge spatial transcriptomic approach, we can label unique RNA segments with multiple colored fluorescent probes in neurons throughout an extracted ex vivo brain section. Brain sections are then volumetrically imaged using a confocal microscope and collected images undergo analyses to align images and segment cells and fluorescence expression. Current limitations of these analysis techniques include computing resource usage and the lack of parallel dataset analysis which we aim to address by adapting open source software to be compatible with cloud-based computing. Here we utilize the Hyak cluster operated by University of Washington-IT to overcome memory, CPU, and GPU limitations of desktop computers. To benchmark the analysis package, we analyzed 3D volumetric tissue from the medial preoptic area (MPOA) of the mouse brain labeled for the genes Vgat and Esr1, markers for inhibitory neurotransmitter and estrogen receptor expression respectively. Our scientific goal is to understand the enrichment of such genes during female mating behaviors. From previous transcriptomic data, we expect that around 70% of Esr1 positive cells in the MPOA will be Vgat positive and will be located in the nucleus part of the MPOA. These neurons will tend to be activated after mating in female mice. However, how these double positive neurons locate in high resolution 3D space is not known and will provide novel insights. The future goal is to apply the analysis package to whole-brain light sheet microscopy data. The broader impact of this work is the development of a high-throughput open-source analysis pipeline for the quantification of multiplexed gene expression patterns across multiple spatial scales.

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.

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.

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.

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. 

Justice-centered approaches to equitable computer science (CS) education frame CS learning as a means for advancing peace, antiracism, and social justice rather than war, empire, and corporations. However, most research in justice-centered approaches in CS education focus on K--12 learning environments. In this position paper, we review justice-centered approaches to CS education, problematize the lack of justice-centered approaches to CS in higher education in particular, and describe a justice-centered approach for undergraduate Data Structures and Algorithms. Our approach emphasizes three components: (1) ethics: critiques the sociopolitical values of data structure and algorithm design as well as the underlying logics of dominant computing culture; (2) identity: draws on culturally responsive-sustaining pedagogies to emphasize student identity as rooted in resistance to the dominant computing culture; and (3) political vision: ensures the rightful presence of political struggles by reauthoring rights to frame CS learning as a force for social justice. Through a case study of this \emph{Critical Comparative Data Structures and Algorithms} pedagogy, we argue that justice-centered approaches to higher CS education can help all computing students not only learn about the ethical implications of nominally technical concepts, but also develop greater respect for diverse epistemologies, cultures, and experiences surrounding computing that are essential to creating the socially-just worlds we need.

The Black Death began in 1346 AD and had a significant impact on the population of the European continent. We examine the demographic implications of the pandemic through a new proxy: measurements of social and economic health through discretionary “spending” of both labor and capital. One of the most widespread of such efforts includes church-building. By examining church-building rates from the Medieval Ages in relation to the Black Death, we can investigate the economic and demographic implications on the ability for generations of Europeans to build churches. We found that during the century in which Black Death began (1346 - 1446 AD), there was an overall sharp decrease in church construction in Europe during the first 40 years, and then gradual increase in the latter half of the century. However, despite the overall decrease in church building rates, there were variations between individual countries’ construction trends. Several regions such as the Netherlands and areas of Northern France had a significant spike in church building rates during the pandemic despite high mortality rates. Our results show that there are likely several other factors besides mortality rates that influenced the rates of church construction and other demographic implications of the Black Death. Although the drop in population numbers correlates with the numbers of European-built churches in the century following the Black Death, we found that there was also a correlation with a drop in the Clergy’s reputation (Zenter, 2015). Hence, the drop in population health and the accompanying correlation in church-building data could suggest a lack of trust in the church or the lack of economic resources. We anticipate this research to be the starting point of more discussion between the relationship of the church and pandemics in regards to population level health.

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

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.

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.

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.

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

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

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

Climate change coupled with inadequate infrastructure has disproportionately impacted people from underserved communities, as is the case for one village located in rural Alaska. Due to the increasing frequency of microbial water contamination exacerbated by temperature rise, this community experiences water insecurity. Previous research also illustrates that water samples collected from the Kuskokwim River, which is used for subsistence, had excessively high mercury levels compared to the regional baseline levels. Furthermore, our team's preliminary findings from informal interviews with community members indicate that their use of a rainwater cistern is well received by many households. However, community leaders have questioned the cistern's operation from September to March. When the temperature falls below zero degrees Fahrenheit in the winter, the cistern must be shut down to avoid damage to the system, and because it is not possible to collect water. Our work will develop and administer an online household-level survey to understand perceptions about local drinking water conditions. We implement principles derived from Indigenous research methodologies and Community-Based Participatory Research approaches. * Preliminary results gathered from conversations with the tribal council suggested a positive perception of the water quality from the installed water cistern, but we hope to quantify the water quality from survey data. * Our research focused on two areas: we will evaluate the utility of an online survey in collecting data from one remote community to understand their water needs and use the data to help guide future decision-making to improve the cistern operation under extreme temperatures. This work is part of a larger initiative to underscore the self-determination of under-resourced communities in Alaska, offering insights into Indigenous research methods and inspiring future design in the field. Note: * means revison per feedback, but will still need to get tribal approval as they approved for previous version as is

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.

 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.

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.

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.

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.

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

 Increased rates of opioid use have led to an alarming number of overdose deaths in Washington state. The National Center for Health Statistics reported 2,255 overdose deaths in May 2022, compared to 1,913 overdose deaths the previous year. Evidence-based interventions such as take-home naloxone, buprenorphine treatment, and HIV/HCV testing significantly reduce deaths related to opioid use. Unfortunately, opioid-related deaths most often occur outside medical settings, in communities where evidence-based interventions aren't accessible. To bridge this gap, our research team created recommendations for implementing evidence-based interventions by collecting and analyzing qualitative data (from 30 semi-structured interviews with first responders and mobile clinic staff). Few research exists integrating collaboration of community members in the research process. The voices of community members are often discussed in the research but left out in the decision-making process. Using a community-based participatory research (CBPR) approach, members from Research with Expert Advisors on Drug Use (READU), a newly formed group with lived substance abuse experience, were hired to co-conduct research on evidence-based interventions as described above. The recommendations developed by READU (co-researchers), alongside the research team, are currently being implemented to improve overdose response in first responder agencies in King County. This study aims to learn from the process of integrating CBPR into this research environment. READU members (n=8) participated in a 2-hour focus group to discuss topics relating to the research process and feelings/concerns about their experience. A thematic analysis approach is used to analyze the qualitative data from the focus group transcript to investigate reemerging themes. Based on the findings in this study, we expect to integrate the needs and suggestions for the CBPR approach (e.g., supportive environment, equitable participation, capacity building & empowerment, and improved programming & policy) from READU members into future community-based research design and process. 

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.

The Lieber lab is exploring chemotherapy-drug-free in vivo expansion systems that involve knock-out a gene in hematopoietic stem cells (HSCs) by precision genome editors. Part of this system is an immunotoxin that targets non-transduced HSCs and eliminates them, thereby allowing for the selective expansion of edited HSCs. The goal of my project is to test one of our target proteins CD49f, integrin α6, which has been reported to be expressed on primitive HSCs. In my studies, using flow cytometry with a PE-conjugated anti-CD49f antibody, I have confirmed that CD49f is present on 63% of human CD34+ cells, a cell fraction that is enriched for HSCs. PAI Life Sciences then set out to generate a CD49f-targeted immunotoxin. If the immunotoxin works, CD34+ cells should be highly susceptible to the conjugated immunotoxin. I then tested the immunotoxin on tumor cell lines and primary human CD34+ cells. Measured by flow cytometry, nearly 100% of HEK293T, HeLa and MDA-MB231 cells expressed CD49f. Next, I incubated three cell lines with increasing concentrations of the CD49f-peptide-saponin immunotoxin, ranging from 0.5pg/mL to 10µg/mL. The cell viability and total cell number was measured three days later by two methods: i) flow cytometric quantification, using DAPI staining and ii) counting cells in a hemocytometer after Trypan-blue staining. In tumor cell lines, MDA-MB-231 and HeLa cells, only at the highest immunotoxin concentration a ~58% decrease in total cell numbers was found. The number of viable cells was ~ 4.1% lower than that of untreated controls. Then, I performed cytotoxicity studies with primary CD34+ cells. At the highest concentration tested (10µg/mL), around 6.7% cells were killed by the immunotoxin. Overall, the data indicates that the cytotoxic activity of the new CD49f-targeted immunotoxin is suboptimal. Future steps will include the design and testing of new immunotoxin conjugates.

Aperiodic tilings are of interest due to their connection to quasicrystals, which have myriad applications in material science. Instead of a periodic crystalline structure, quasicrystals are structured in ways that can be modeled by aperiodic tilings of Euclidean space. An aperiodic tileset is a tileset which tiles the plane but will never tile the plane periodically. One of the most famous aperiodic tilesets is the Penrose tiles, which have a rich substitutive structure. Building on previous research on applying symbolic dynamical systems theory to the Penrose tilings, we propose a substitution rule for the Penrose Wang shift and show that the shift is closed under such a substitution. We also compare the new substitution rule to that of the vanilla Penrose tiles. Symbolic dynamical systems theory is a way of discretizing the state space of dynamical systems to aid in studying their trajectories. Studying tilings using symbolic dynamics is a relatively new pursuit, and our result which proves the aperiodicity of the Penrose Wang shift via a self-similar shift map on an equivalent tiling provides a solid example in an emerging field of research.

More than two thirds of youth have experienced at least one traumatic event by the age of 16, which may lead to increased internalizing and externalizing behavior concerns among youth, including aggression, truancy, anxiety, and depression. While self report measures can give valuable insights on the respondent’s internal experiences and inform clinical assessments, low levels of agreement between measures from different informants can arise. This discrepancy is referred to as discordance and has been shown to impact the assessment, classification, and treatment of childhood psychopathology among youth and parent self reports. Current literature indicates that discordance exists persistently between parent and child reports of youth exposure to trauma and trauma symptomatology. The guiding question of this research is: How closely do parents and children have concordance on perceptions of child trauma and symptomatology after a traumatic event? Analysis was conducted using preliminary data collected from trauma-exposed children and parents, assessed via the Child PTSD Symptom Scale for DSM-V (CPSS-V) and the Short Mood Feelings Questionnaire (SMFQ). I analyzed parent child discordance using Pearson's r, in which lower r values indicate greater discordance. I hypothesize that parent-child discordance on reports of youth’s externalizing behaviors will be lower than reports of internalizing behaviors. These results may illustrate the importance of alignment between parent and child perceptions of trauma symptomatology, as discordance can buffer access to mental health services and treatment effectiveness. Future research on parent child discordance also needs to investigate social determinants of the phenomenon. Understanding the nuanced causes and implications of parent-child discordance in youth symptomatology after a traumatic event brings light to ways of improving trauma-exposed youth therapeutic outcomes.

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.

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

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

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

The 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.

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.

With rising greenhouse gas emissions, both emissions reductions and greenhouse gas capture and conversion are necessary to mitigate the impacts of climate change. Though carbon dioxide comprises the largest proportion of global greenhouse gas emissions, methane causes over 80 times more global warming per unit than carbon dioxide. While methane can be converted catalytically at high temperatures and pressures, bacteria called methanotrophs transform methane into biomass at ambient temperatures and pressures. Engineering these organisms to consume methane globally can help slow climate change. At the Lidstrom Lab, I study the relationship between the methanotroph genome and metabolic regulation. Through this work, I have focused on finding genes that facilitate responses to environmental conditions and am now looking at genes that impact overall growth rate. I design and construct mutant strains, eliminating genes that appear to use the cell’s energy unnecessarily based on transcriptomics data. We expect that eliminating such genes will allow the cells to devote more energy to methane consumption and growth, improving growth rates under low methane conditions. This work is being extended to experiments in a bioreactor to observe how selected mutations and growth conditions impact growth rate at low methane. For this work, I am setting up the bioreactor to maintain the intended reaction conditions and utilizing a gas chromatogram to monitor methane consumption over time. These experiments reveal how the methanotrophs grow under specific conditions. I am also analyzing the results of the experiments using Python, MATLAB, and Excel. Long-term, this research will help prepare methanotrophs for deployment in the field to consume methane in areas of atmospheric methane release including landfills and agricultural sites.

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.

Walking droplets are a phenomenon in which fluid droplets bounce along the surface of a vertically oscillating fluid bath. Movement of the droplets is generated by interaction between the droplet and waves generated by its bouncing. Studies in this field have revealed the emergence of statistical patterns in the horizontal movement of the droplet which are wave-like. This has led to the use of walking droplets as an analogy to the wave-particle duality of quantum particles. My goal is to expand the analogy between walking droplets and quantum particles by working towards a more robust model of walking droplet dynamics. I investigate how walking droplets behave in baths with various bottom topographies. I aim to find similarities in topographies inducing the behavior of walking droplets and potential fields inducing the behavior of quantum particles. I used 3D-printing and computer-aided design software to create fluid baths. I collected data on the droplets by filming them, and analyzed the videos using our in-house droplet tracking algorithm based on deep learning. I investigated the statistical distribution of a walking droplet in a fluid bath with depth varying linearly from one end to the other. I linearized the plot of the particle’s position distribution to find a function which describes the pattern. This provides me with a starting point for analyzing droplet behavior in highly non-linear bath bottom topographies. In the future I will investigate connections between droplet behavior in highly non-linear topographies and quantum particles in potential fields. The field of walking droplets as an analogy to quantum particles has the potential to improve our understanding of the quantum realm. Furthering our understanding of how quantum particles behave could make impacts in fields such as quantum computing and quantum metrology, allowing engineers, doctors, and researchers to make more precise measurements.

Multiple myeloma (MM) is an incurable malignancy of the B-cell lineage, characterized by neoplastic, monoclonal expansion of plasma cells in the bone marrow. Remarkable progress has been made in the treatment of MM with the anti-CD38 monoclonal antibodies such as Daratumumab and Isatuximab, which can kill MM cells through the induction of complement-dependent cytotoxicity (CDC). The CDC efficacy of Daratumumab and Isatuximab is however limited by membrane complement inhibitors, including CD46 and CD59, which are upregulated in MM cells. We recently developed a small recombinant protein (Ad35K++) capable of blocking CD46 and sensitizing tumor cells to anti-CD20 mAb triggered CDC (e.g Rituximab and Ofatumumab). Here we tested Ad35K++ in combination with Daratumumab and Isatuximab. We show that Ad35K++ increases the CDC efficacy of Daratumumab and Isatuximab on Burkitt’s lymphoma and MM cell lines (MOLP8 and SUDHL-8). Ad35K++ salvaged the efficacy of Daratumumab and Isatuximab at subtherapeutic (“low”) doses in MM lines. Daratumumab and Isatuximab treatment of MM lines (without Ad35K++) resulted in the upregulation of CD46/survival of CD46 high MM cells which escaped a second round of Daratumumab and Isatuximab treatment. Escape was reduced by combining Daratumumab and Isatuximab with Ad35K++. We also tested a small recombinant protein that targets CD59 (rIYD4) in combination with Daratumumab and Isatuximab on MM cells. rIYD4 also increased CDC killing of MM cells by Daratumumab and Isatuximab. The combination of Ad35K++ and rILYD4 additively enhanced the CDC effect of Daratumumab and Isatuximab. Studies with patient MM cells will be reported. Overall, our data demonstrate that Ad35K++ and rILYD4 are efficient co-therapeutics of Daratumumab and Isatuximab and could be used to improve the treatment of multiple myeloma.

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.

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.

Stromatolites are laminated sedimentary constructions that are thought to be built by microbes. These structures have the potential to serve as indicators of environmental or biological change throughout Earth history. Here, I aim to understand how the study of what controls a stromatolite's shape has changed through time. In particular, I am interested in understanding the extent to which missing branches of study, or what I term “ghost literature,” have contributed to the corpus, and if their absence imparts bias in contemporary approaches to the study of stromatolite formation. To this end, I have developed computational tools to analyze the literature. To compile publication data, I utilize a self-authored computational toolset to probe existing literature databases, including xDD (formerly known as GeoDeepDive), and Web of Science. I examine the compiled data using visualizations and statistical analyses. Through these analyses, I uncover publication biases by assessing how references might be over- or under-cited in the corpus. Furthermore, I highlight conceptual frameworks for stromatolite formation that have been lost or understudied by reviewing text from under-cited references. This project is the first step in a much larger project that will attempt to quantitatively link stromatolite shape to both environmental and biological factors, which can unlock their potential as windows into our planet's past.

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.

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

Despite a rise in egalitarian views over the past decade, the trend has recently slowed down and scholars are struggling to understand why. Past research shows an unexpected trend of young millennials, specifically men, reverting to traditional gender norms. Childhood family instability is proposed as one possible explanation, but it has not been examined empirically. The goal of this project is to understand how one form of family instability, divorce, impacts men’s view on love, marriage, and gender norms. The research is driven by two questions. First, how does the experience of divorce affect a father's view on gender? Second, did the father’s post-divorce view on gender affect the son’s attitudes, and, if so, how were these attitudes transmitted from father to son? The data will be collected through individual semi-structured interviews with divorced fathers who had custody of their son and the sons of these fathers who are at least 18. The study expects that children of divorce will reject egalitarian views because they have observed their parents separate through their attempt to uphold egalitarian views. While this project only examines males, future research can expand this study through interviewing single mothers and their female children. This project will help address the puzzling phenomenon of why there is a declining trend toward egalitarian gender views.

Thoracic aortic aneurysms (TAA) are excessive dilations of the aorta, inside the chest. TAA can rupture, causing sudden death. Human TAA are attributed to both decreased and increased TGF-β signaling in aortic smooth muscle cells (SMC). Experimental data from mice clearly shows that decreased SMC TGF-β signaling causes TAA; however, the connection of increased SMC TGF-β signaling with TAA is largely based on correlational data. Some of these data implicate excessive TGF-β signaling in only one of the two SMC embryonic lineages that populate the proximal thoracic aorta: the cardiac neural crest (CNC) lineage. To directly test whether increased SMC TGF-β signaling in either of the two lineages causes TAA, I am generating mice with increased SMC TGF-β signaling in either CNC-derived or second heart field (SHF)-derived SMC. I accomplish this by using a transgene that expresses a constitutively active TGF-β receptor (TBRI-CA) after activation by Cre recombinase. To express TBRI-CA in CNC-derived SMC, I mate mice with a Wnt1-Cre transgene to mice with the TBRI-CA transgene. To express TBRI-CA in SHF-derived SMC, I mate mice with an Mef2c-Cre transgene to mice with the TBRI-CA transgene. I hope to determine whether increased TGF-β signaling in SMC of either lineage causes TAA. However, because SMC TGF-β signaling plays critical roles in embryonic vascular development, I will begin by determining whether activation of TGF-β signaling in either lineage is embryonically lethal. I am analyzing genotypes of pups from each mating, and using Chi Square or Fisher Exact Test to test the null hypothesis that increased TGF-β signaling in embryonic SMC is not lethal. If my hypothesis is supported, I will then be able to determine whether SMC-targeted activation of TGF-β signaling causes TAA. My findings could provide support for development of human therapies that prevent TAA by blocking SMC TGF-β signaling.

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

Cell division is essential to all living organisms, and microtubules are critical for this process. Microtubules in bundled kinetochore-fibers generate forces to move chromosomes by stochastically switching between assembly and disassembly states. Electron tomographs of mammalian mitotic spindles show that microtubule tips maintain a high level of coordination despite stochastic switching between states. The collective behaviors of microtubule bundles give rise to chromosome oscillation, which promotes the alignment and separation of chromosomes along the spindle equator during metaphase. To understand how stochastically-switching microtubules can produce synchronized motions in vivo, we use a mechanical model that describes the force-dependent dynamics of microtubules. The model reproduces the bistability of microtubule bundles observed in vivo and suggests that this coordination could be explained by sufficiently stiff mechanical coupling. We also propose a new way to characterize microtubule bundle state based on the substates of microtubules within the bundle. We will use this characterization to calculate microtubule bundle switch rates, which are technically difficult to distinguish otherwise, thereby laying the groundwork for future comparisons between bundle switch rates in vivo and in silico. In the future, we plan to explore the assumptions on which this model is based by analyzing the relationship between microtubule velocity and forces. We predict that this result will validate the assumed force-velocity relation of microtubule growth and contribute to a more accurate understanding of kinetochore-fiber behaviors. 

The goal of the SQRLab is to develop technologies for a fully fault tolerant quantum computer capable of processing 10,000 qubits of information. One necessary component is a Paul Trap, consisting of two pairs of blades delivering both direct current (DC) and radio frequency (rf) alternating signals in order to trap and stabilize a string of ions. In order for the modes of the quantum states of these ions to be stable, the stability of power delivery to the device is crucial. Given these design specifications a rf resonator circuit is necessary. The goal of my project is to design, simulate, build, and test a low-loss rf resonator to deliver rf signals to the ion Paul Trap efficiently and stably. Using a toroid shape, I experiment with the material of the wiring and the method of winding the toroid to find a wiring scheme that creates the least loss in delivering power to the experiment. The material used in the wire and dielectric material inside the coil directly affects the efficiency of translating signals. It is desirable that this resonator generates a voltage gain at a specified power level, has impedance matching of the coil with the driving circuit, and contains a method of monitoring this voltage. Thus far, I have measured the voltage gain generated by the coil and the quality factor of the coil (the quality of the resonator frequency as it interacts with the rest of the circuit). I have also designed a capacitive “pickup” to sample the voltage level of the delivered rf power. I will produce noise figures to stabilize the trap power to a set-point voltage level. This research contributes to SQRL’s objective of designing useful scalable quantum systems to simulate nature and perform complex algorithms not permitted by classical computers.

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.

The transition to online instruction because of covid-19 necessitated a new way of delivering hands-on lab courses. We created a remote lab where students can remotely access Field Programmable Gate Arrays (FPGA) on Intel's DE1-SoC boards to complete their assignments without the need for shipping lab kits. Studying digital design could be a challenge to pre-college students due to the sheer breadth of the topic and the affordability of equipping students and institutions with expensive lab equipment. A high percentage of lower-income and underrepresented minority high school graduates start their college journey through the community college system and many students begin exploring engineering in high school, with the goal of enrolling in a four-year college to obtain a computer engineering degree. The purpose of BEADLE is to promote equitable access to educational technologies by offering an affordable platform for students to remotely access industry-grade hardware to learn and develop their skills in digital design. In addition, BEADLE aims to create a curriculum for an introductory course on digital logic intended for 2-year community college and high school students using the remote FPGA lab platform. The BEADLE curriculum works to prepare students entering a university in their junior year of a four-year computer engineering degree, where this course is typically completed during the freshman and sophomore years. We evaluated the curriculum by offering it in a sophomore class on digital logic design at a 4-year public university. Through assignments and surveys of students, it has been identified that the BEADLE curriculum has a significant positive correlation with learners understanding a variety of skills.

Large-magnitude earthquakes commonly produce surface deformation, including meter-scale fault and liquefaction scarps. The size of a fault scarp is related to the magnitude of coseismic slip, but liquefaction scarps produced by near-surface slumping can vary in size regardless of magnitude. This study focuses on two subparallel scarps in Dixie Valley, Nevada. We hypothesize (1) liquefaction-related scarps are generated on sub-horizontal layers of loosely consolidated material, accompanied by evidence of lateral spread, subsidence, and low-temperature discharge, and (2) faults can produce scarps that transect topography and access high-temperature fluids. We used remote sensing and field data to describe the distribution of lateral spreading, subsidence, scarp profiles, travertine, and cemented alluvium. We constructed elevation profiles and cross-sections of the subsurface geology across the scarps. We collected travertine samples from calcite-cemented sands and hot springs and ran stable isotope analyses. We found the scarps to be about 9-15 m tall. Moderate flow rates (2-120 L/min) and hot spring temperature (23-49 °C) indicate a deep transect of the subsurface that reaches the heat reservoir (>1 km). Liquefaction features like compression zones and sand boils were not observed in the area. The range of δ¹³C of travertine is -1.73 to 3.10 ‰ VPDB and δ¹⁸O of travertine is -20.27 to -11.49 ‰ VPDB which falls in the ranges associated with thermogenic travertines. The decrease in δ¹⁸O composition corresponds to the sampling site with respect to hot spring surface temperature. The findings support the earthquake-related origin of these scarps. We interpreted the cemented sands to form from geothermally recharged water that flowed through the fault, mixed with meteoric water, explaining the presence of mollusk skeletal remains. The lack of geomorphic features related to liquefaction further supports faulting as the scarp origin. Mapping these features in geothermal settings provides a geological perspective for energy exploitation.

Unprecedented technological growth is upon us. Augmented reality (AR), a technology that enhances our capabilities, is one of the most promising examples. My research shows that AR is often a cost-effective alternative to more widely used technologies such as cell phones and personal computers. It is also seen to be more accessible. Additionally, AR has the potential to be more environmentally friendly, safer, and more efficient than current technology. In this literature review, I attempt to answer the question, "How could AR replace current technology to increase capability and accessibility?" Results and experiments have shown that AR is becoming more capable and cost-effective. This pattern indicates that AR will be adapted more to increase our capabilities as a species. Greater adaptation of AR has correlated with more equity amongst the population, giving equal opportunities for a wider range of abilities and socio-economic status. This is evident with a substantially greater student-to-teacher ratio in schools as well as a much greater potential to train many new individuals in professional careers than would exist otherwise. All of this is done while drastically reducing or even eliminating safety concerns. My research has shown a positive growth and implementation pattern that indicates a future inundated with this technology will soon be on the horizon, if it is not already. This implies a future where AR will help us develop a more equitable society.

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

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.

 Quantum mechanics is inherently a probabilistic theory, wherein the particles it describes are modeled as waves of fluctuating probability densities. In reality, we see these probabilistic outcomes in our experiments. However, while not deterministic, the measurement results are always definite. This hints that there is a physical process by which our probability distributions collapse to single, measurable outcomes. The pertinent question is: How does this physical process occur? This underpins the measurement problem of quantum mechanics. Our research analyzes Klaas Landsman’s ‘flea model’ for quantum measurement. Landsman’s model, outlined in his paper A Flea on Schrodinger’s Cat, showed that given some symmetry-breaking ‘flea’ perturbation to the symmetric double well, superpositions of measurement states would dynamically collapse in the classical limit to a single measurement state. This philosophically explains the lack of classical superposition states as the lack of perfect symmetry in nature. However, Landsman’s formulation relied upon the position of the flea perturbation to determine the classical probabilities predicted, breaking Born’s rule. This rule is an important postulate of quantum mechanics which states that the outcomes of a measurement are determined by the state being measured alone, not the potentials it may reside in. Proving Landsman’s model was in agreement with Born’s rule was the problem we tackled over the past year. By considering the position of the flea as a random variable and applying the method of arbitrary functions (which derives probability distributions invariant of variations in dynamical parameters), our group was able to prove this result held. Given any distribution in Landsman’s flea, the probabilities predicted would converge in the classical limit to those predicted by Born’s rule.

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

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

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.

FKBP51 is a protein that acts as a co-chaperone for glucocorticoid receptors and is active during the stress response. FKBP51 blunts glucocorticoid receptor signaling and can interfere with feedback inhibition of stress responses. Overall, increased levels of FKBP51 and its gene FKBP5 positively correlates with an increased risk of stress-related neuropsychiatric disorders. FKBP5 is expressed in serotonin neurons of the dorsal raphe nucleus (DRN), a brain region and system important to stress and anxiety responses. In order to investigate the function of FKBP5 in the DRN, new plasmids were generated to knock down or overexpress FKBP5, thereby changing FKBP51 expression in serotonin neurons. My first goal was to validate these plasmids using Neuro2A cells which endogenously express FKBP5. In order to do this, I cultured Neuro2A cells so that we could transfect the cells with either a CRISPR plasmid to decrease FKBP5 expression or an overexpression plasmid to increase FKBP5 expression. I used western blots to test for changes in FKBP51 protein, and that data was analyzed using integrated density in ImageJ. I found that the CRISPR knockdown plasmid successfully decreased expression of FKBP51 in cells and that the overexpression virus upregulated FKBP5. My second goal was to validate the CRISPR FKBP5 knockdown in vivo. Using Pet1-CRE mice that express Cre recombinase in serotonin neurons, we injected the CRISPR virus for a control virus into the DRN. I then used fluorescent in situ hybridization to look for changes in FKBP5 mRNA levels. I found that CRISPR successfully reduced FKBP5 relative to controls, indicating this virus is a viable way to reduce FKBP5 expression in vivo. This research is a clear step to better understanding stress-related neuropsychiatric disorders such as depression, anxiety, and PTSD.

Insulin resistance in the Central Nervous System (CNS) is associated with various disease states, such as diabetes mellitus, metabolic syndrome, and even Alzheimer’s disease and age-related cognitive decline. There are several risk factors that are linked with insulin resistance in age-related cognitive decline; among those are apolipoprotein (apoE) E4 genotype, female sex, and high-fat diet (HFD). We expect that apoE4 mice will express a deficiency in CNS insulin regulation, exacerbated by female sex and HFD. Mice have been grouped into 8 cohorts so that sex, apoE isoforms, and HFD can be cross examined and their synergistic effects on insulin resistance can be analyzed. Multiple modes of measuring insulin response are employed to determine whether the deficiency in insulin action is due to decreased insulin transport, decreased insulin retention, increased insulin degradation, or decreases in insulin receptor activation and post-receptor signaling driven predominantly by changes in phosphorylation. Here, we show the brain distribution of radioactive insulin following intranasal administration. Additionally, the levels of insulin degrading enzyme are analyzed to determine the effect of insulin retention and degradation. Lastly, deficiencies in response to intranasal insulin are then measured by changes in protein phosphorylation. Understanding the mechanisms of insulin resistance in the CNS could guide innovations of clinical therapies for related disease states such as Alzheimer’s disease.

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

 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.

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

Traffic related air pollution (TRAP) is comprised of pollutants such as oxides of nitrogen, carbon monoxide, ultrafine particles, and particulate matter emitted from motor vehicles. Research has found associations between TRAP and adverse health effects in older adults, including various aging and health outcomes such as Alzheimer’s disease and dementia. Black carbon (BC), a type of particulate matter pollutant, is commonly found in diesel exhaust. BC is of high concern as it is particularly small in size, making it able to pass through the blood brain barrier. To date, only a few studies have investigated the association between BC pollution and performance-based physical function among older adults. We leverage the Adult Changes in Thought (ACT) study, a Seattle-based cohort of older adults, to evaluate the association between BC exposure and physical performance. Physical performance is a measure calculated from three assessments: gait speed, grip strength, and chair-stand time, each scored on a scale of 0 to 4. The sum of these three tests on a scale of 0 to 12 provides the “physical performance score”, with higher scores serving as an indicator of better physical performance. The average physical performance score at baseline among a cohort of 2,604 participants was a 9.39 with an interquartile range of 8 to 10. We estimated a 0.097-point decrease in physical performance score at baseline for each interquartile range increase in 5-year average BC exposure, adjusted for age, sex, and race (95% CI: -0.200, 0.007). Additionally, we estimated that men had a higher average physical performance score of 10.8, white participants had an average score of 10.7, and that there was a gradual decline in physical performance scores across age of participants at baseline. Our preliminary findings suggest exposure to higher levels of BC may contribute to worse physical functioning among older adults.

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

The Paleolithic era saw the beginning of the development of human language. Furthermore, the Paleolithic is characterized by the appearance of non-figurative, or geometric art. There are extensive examples of signs commonly seen in Paleolithic art, and while over 40 distinct signs have been recorded, we focus on the five most abundant signs in the SignBase dataset (cf. doi: 10.1038/s41597-020-00704-x): notch, line, obline, hatching, and dot. Here we investigate Bacon’s recent (2023, doi: 10.1017/S0959774322000415) hypothesis that geometric signs were a way of recording a phenological calendar. We found an abundance of representation of the notch symbol (254), followed by the line (174). To assess their proposed calendrical function, we report on the distribution of frequencies of the symbols to identify if seasonal patterns are represented. Our study sheds new light not only on the characteristics of geometric art, but also on the likelihood that they encode a phenological calendar as proposed by Bacon et al. (2023).

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.

 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.

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

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.

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.

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.

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.

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

A thoracic aortic aneurysm (TAA) is an expansion of the aorta within the chest. TAA can rupture, often causing sudden death. Mechanisms of TAA formation and growth are incompletely understood, but likely include dysfunction/loss of aortic smooth muscle cells and inflammatory cell accumulation. We hypothesized that quantitative analyses of cell types, transcriptomes, and cell-cell communications in experimental TAA tissue would provide insights into pathogenesis. Because many TAA are caused by heritable mutations, we investigated TAA pathogenesis in a mouse model of TAA caused by a mutation in the type 2 transforming growth factor beta receptor (Tgfbr2^G357W/+ mice). We used single-cell RNA sequencing (scRNA-seq) to quantify cell types and transcriptomes in proximal aortas of Tgfbr2^G357W/+ and wild-type mice. I analyzed transcriptomes with CellChat, a tool that uses scRNA-seq data to quantitatively infer and analyze intercellular communication networks. Tgfbr2^G357W/+ aortas had fewer smooth muscle cells and more macrophages than control aortas. Transcriptome analysis revealed that Tgfbr2^G357W/+ aortas also contained a new subpopulation of fibroblasts (“new fibroblasts”) that was absent in controls. Among all cell types, CellChat identified the new fibroblasts as the strongest source of outgoing cell-cell signals, and smooth muscle cells and macrophages as the major recipients of signals emanating from both the new fibroblasts and from other fibroblast populations. Outgoing signals predicted to emerge from the new fibroblasts are mediated by matrix components (e.g., collagen, laminin), cytokines (e.g., CSF), and other ligands (e.g., angiopoietin). We conclude that TAA in Tgfbr2^G357W/+ mice have fewer smooth muscle cells, more inflammatory cells, and a new population of fibroblasts. These new fibroblasts appear to signal to other aortic cells and may play important roles in inflammation and smooth muscle cell phenotypic alteration/loss. Further characterization of the new fibroblasts and their signaling pathways may reveal new targets for therapies that prevent or stabilize TAA.

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

Alcohol use disorder affects 5.8% of adults in the U.S., incurring a yearly cost of $249 billion annually. The repeated and prolonged use of alcohol creates a variety of physiological and behavioral issues. Acute alcohol withdrawal syndrome encompasses seizures, delirium tremens, and in some cases, death. The dependence and withdrawal cycles lead to neuroinflammation, worsened withdrawal symptom severity, and impaired neuromodulation. The striatum plays an important role in the chronic aspect of addiction. This project focuses on how alcohol alters microglial function in this key brain region. At the Neumaier lab, we found that alcohol withdrawal increased the expression of genes involved in the unfolded protein response (UPR) in striatal microglia, the brain’s immune cells. The UPR is activated when there is an increase of misfolded proteins in the endoplasmic reticulum; which contribute to impaired cell function. The UPR is a protective mechanism in moderation, but when left unchecked, has been shown to increase cell death. We predict that removing CHOP will lead to a decrease in withdrawal symptoms and regulate the need to consume alcohol. Knocking out CHOP involves breeding CHOP fl/fl |Cx3cr1 CreER /eYFPI mice. We observe changes in the offspring via emotional behavioral tests after a 5 week period of CIE (chronic intermittent alcohol exposure). A second cohort’s brains are analyzed using cryosectioning and immunohistochemistry (IHC). My role is preparing the brains for analysis. The first step is removing and perfusing, which prepares the samples for cryosectioning. This is my other specialty, which is freezing and slicing the brains. Lastly, I conduct analysis with IHC, and look for physiological changes in the striatum. We anticipate our findings will have a positive and large impact on treating alcoholism. Our hope is to reduce the stigma surrounding addiction, and instead offer compassionate and scientifically based care.
 

The weathering—or breaking apart by physical and chemical means—of common silicate (silicon dioxide based) minerals is a major mechanism of the freeing and distribution of nutrients into the environment at large, as well as a major component of the planetary carbon cycle. Effective extraction of nutrients by weathering is particularly important to organisms living along bedrock surfaces, such as the bacteria found in the basal ice of the Greenland ice sheet. Microbial surfaces have reactive sites which bind to ions and minerals, and may be a mechanism for internalization of nutrition in the incredibly harsh Greenland ice sheet basal water pores. These reactions may encourage the further dissolution of minerals as their constituent ions are pulled out of solution. Therefore, my research seeks to understand the effects that bacterial surface binding has on the dissolution of gneissic bedrock from the Greenland ice sheet’s base. I hypothesize that the presence of endospores will increase the rate of silica dissolution above control sample rates. To test this hypothesis, two experiments were performed. Ground gneiss obtained from the base of the Greenland ice sheet was placed into dialysis pouches. One dialysis pouch was placed in water containing Bacillus subtilis endospores and the other dialysis pouch was placed in pure water. The dissolution products were monitored over time. Initial results suggest that increased mineral dissolution occurs in samples with endospores present, implying that endospore surface reactivity may have important implications in chemical weathering processes. Better understanding of weathering processes, particularly as they are used to extract nutrients and control climatic conditions, allows us to better understand habitability in our present, past, and changing future.

Garnet-bearing sand has been identified along the coast of Washington at Ruby and Rialto Beach. There is currently no identified local source rock and no conclusion about the provenance of the garnet minerals: are they sourced from glacial sediments or subduction zone rocks? When garnets form, they can contain small inclusions of other minerals that provide constraints on the pressure and temperature of mineral growth. I am investigating the inclusion mineral assemblages found within the garnet to determine their metamorphic facies and match this with possible source rocks in the region. There are two possible locations of provenance for the garnet: the Cascadia Subduction Zone or the North Cascades/British Columbia (BC). I collected samples of the garnet sand from both Ruby and Rialto Beach and used a Frantz Magnetic Separator to isolate the garnet for grain mounts polished to expose the interior of crystals. A scanning electron microscope (SEM) and energy dispersive spectroscopy were used to identify the composition of the index minerals within the garnet to locate their metamorphic facies and provenance region. The results of the SEM analysis will potentially show high-pressure mineral inclusions (lawsonite, glaucophane, omphacite) and provenance from the Cascadia Subduction Zone or higher temperature metamorphic minerals (staurolite, sillimanite, biotite) and provenance from the North Cascades/BC. If subduction zone provenance is determined, this garnet could represent material brought to the surface from an active subduction zone, which can be used to directly compare with active processes in the Cascadia Subduction Zone today. If North Cascades/BC regional metamorphism provenance is determined, a better understanding of glacial ice transport during the last global cooling event can be developed.

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.

Lung-resident type 1 conventional dendritic cells (cDC1s) are critical for initiating immune responses against foreign respiratory viruses and endogenous assaults like cancer cells. Importantly, the cDCs of each tissue display unique phenotypes and functions dictated by the environment they populate. However, our understanding of the factors that regulate cDC1 development and function in the lung is minimal. The cytokines, FMS-like tyrosine kinase 3 ligand (FLT3L), and granulocyte-macrophage stimulating factor (GM-CSF) are essential for the development of tissue-resident cDC1, but in in vitro systems, these factors are insufficient to generate cDC1s with a lung-specific phenotype. RNAseq analysis of lung cDC1 identified a clear enrichment in genes associated with transforming growth factor beta (TGF-β) signaling, a factor also known to be enriched in the airspaces of the lung. TGF-β has been previously reported to maintain DC quiescence in the lung, however, our data suggested it may also play a role in differentiation and lung specification of these cells. Based on this, I hypothesized that adding TGF-β to in vitro bone marrow (BM) cultures alongside established cytokines FLT3L and GM-CSF would generate cDC1s phenotypically and functionally similar to in vivo lung cDC1s. The addition of TGF-β, but not GM-CSF, to optimized FLT3L-BMDC cultures resulted in development of cDC1 which highly resemble lung cDC1. The development of a high throughput in vitro system that differentiates functional lung cDC1s will not only inform the in vivo factors required for development of these cells but also provides a useful platform for interrogation of lung cDC1 function and a stepping-off point to begin models for human lung cDC1 production and study.

Irritable Bowel Syndrome (IBS) is a common, chronic gastrointestinal disorder consisting of three common subtypes; IBS-Constipation (IBS-C), IBS-Diarrhea (IBS-D), and IBS-Mixed (IBS-M) — a combination of the two prior categories. IBS is associated with abdominal pain and changes in bowel habits. Patients may also experience other symptoms such as nausea, anxiety, and depression. It is unknown, however, how the gut microbiome impacts signs and symptoms. This study aims to compare the gut microbiota between adults with IBS and healthy controls and describe the relationship between symptoms and gut microbiota taxa. Fecal microbial communities are examined through stool samples collected from women aged 18 to 45 with 16 S rRNA gene sequencing analyses. We hypothesize that compared to healthy controls, those with IBS will have higher quantities of pathogenic gut bacteria such as Clostridium difficile (C. diff), Escherichia coli (E. coli), and other Firmicutes. Comparing the gut microbiome between those with and without IBS can improve screening of the disease, leading to improvements in symptoms, treatments, and quality of life.

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

TDP is one of the proteins believed to cause ALS, a neurodegenerative disease leading to gradual loss of muscle control and function. Although there are treatments which mitigate symptoms of ALS, this fatal disease remains uncurable. In addition, ALS also contributes to high healthcare costs and pressure on families caring for the afflicted. TDP-43 is a protein with notable aggregation in the motor neurons of 95% of those with ALS. Research has found TDP-43 mutations leading to familial ALS, further implicating its involvement in the development of the disease. There has also been some research suggesting a relationship between TDP-43 and tau, a protein linked to Alzheimer’s Disease and other neurodegenerative diseases. It may be possible for certain genes to control both tau and TDP-43 toxicity. Mutagenesis of C. elegans identified a mutation in suppressor-of-tau (sut) gene sut-6 that caused the amino acid change of W292X. Deletion of sut-6, or sut-6(null), also inhibited tau, but W292X showed greater suppression. Furthermore, a TDP-43 transgenic model expressing mutant TDP-43 protein in C. elegans neurons indicated suppression of TDP-43 by sut-6(null). The goal of this study was to learn whether sut-6(W292X) and sut-6(null) reduce the toxicity of high wildtype human TDP-43 aggregation in C. elegans neurons. I crossed TDP-43 transgenic C. elegans with sut-6 mutation-carrying C. elegans to generate TDP-43 transgenic C. elegans with sut-6 mutations. I then conducted locomotor swimming assays to measure the swimming ability of TDP-43 transgenic C. elegans with and without sut-6 mutations, with increased swimming ability indicating reduced toxicity of wildtype human TDP-43 in C. elegans with the mutations. Investigating the relationship between TDP-43 and sut-6 mutations allows greater understanding of the mechanisms of toxicity caused by TDP-43 and tau in neurodegenerative diseases, providing greater insight into therapies aimed at targeting both proteins.

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.

Infection from Mycobacterium tuberculosis is the second leading infectious cause of death worldwide after COVID-19, with rates of tuberculosis infection greatest in low and middle-income countries (LMICs). Tuberculous meningitis (TBM) is one of the most severe forms of M. tuberculosis disease with over half of all cases resulting in death or neurological consequences. Recent studies in our lab have found that single-nucleotide polymorphisms (SNPs) in MUC5AC, a secretory lung mucin, are associated with increased TBM susceptibility, morbidity, and mortality. The purpose of my study is to identify the functional MUC5AC SNP. Four candidate SNPs were selected within the MUC5AC promoter region based on high linkage-disequilibrium scores across multiple global populations with a SNP in the MUC5AC promoter, rs28737416. I utilized molecular cloning techniques to combine a luciferase-expressing plasmid with isolated regions of the human MUC5AC promoter containing the SNPs of interest, and subsequently transformed this recombinant plasmid into competent cells. Next, I am performing in-vitro, site-directed mutagenesis to investigate how genotypic variation in each candidate SNP influences promoter function by measuring luciferase expression. I anticipate variants in at least one SNP of interest will reduce gene expression (measured by luciferase expression), indicating functionality. Characterization of this genetic mutation will provide insight into TBM susceptibility across populations and could inform studies of novel therapeutics to treat TBM.


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.

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.

Wildfire has been a growing problem in recent years. This paper looks at ways to control wildfire by considering fuel reduction resulting from fire as a self-regulating mechanism. We use the programming language R and spatial statistics to look at the effects of simulated wildfires on future fire spread in a simulated landscape. We simulated scenarios of different numbers of fires, where the total area burned were kept constant, to investigate whether the spatial arrangement of past fires impacts future fire spread. For each fuel scenario, we also investigated conditions of low and high moisture deficit in conjunction with fire pattern. After running the simulations, we analyzed the results to determine the strength of different underlying variables on the spread of our simulated wildfires. We observed what was controlling the size of fires was not the fuel configuration, rather the fuel moisture and the mean fuel loading. This research suggests that in order to control the spread of wildfire, the focus should be on reducing the mean fuel load for a region rather than aiming for a certain spatial arrangement of fuel.

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

Seventy-five years after the forced removal of Palestinians from their homes and villages during the nakba, the permanent effects on the physical and geographical landscape of the region is not entirely understood. I investigate how much of the erasure of Palestinian villages has been made permanent through reforestation and repopulation. Prior work, specifically by Walid Khalidi in All That Remains: The Palestinian Villages Occupied and Depopulated by Israel in 1948, attempted to quantify the loss, but has not been made current. Using quantitative data from aerial photographs and previously collected records as well as qualitative data in the form of narratives from Palestinian refugees, I examine the permanent impact of the forced expulsion of Palestinians from their homes and villages and the destruction of those places. I focus on comparing geographical and population data from 1945 with recent data, and examine in particular the al-Ramla and Jerusalem subdistricts. These results are generalizable to other areas impacted by recent and ongoing wars, expulsions, and genocides and may add to the understanding of the ongoing impact of these events.

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.

Alzheimer’s disease (AD) is characterized by aberrant cleavage of Amyloid Precursor Protein (APP) leading to toxic β-Amyloid (Aβ) peptide aggregates. Presenilin 1 (PSEN1), and presenilin 2 (PSEN2) are intimately involved in this process. We found that alternative splicing of PSEN2 leads to the increased inclusion of a cryptic exon (part of the RNA that codes for a protein), in the typically non-coding intron 9 of PSEN2, titled exon 9B (PS2x9B), which has elevated abundance in individuals with sporadic AD. My aim is to uncover the link between PS2x9B and sporadic AD. I designed a PCR approach to measure the ratio of PS2x9B inclusion compared to non-mutated Wild Type (WT) in cDNA generated from parietal and temporal lobe tissue samples. I distinguished PS2x9B inclusion by amplicon size on a gel and measured the ratio to WT via band intensity using ImageJ. I found that the ratio of PS2x9B inclusion was significantly elevated in sporadic AD cases in the parietal lobe (p = 0.02) and the temporal gyrus (p = <0.001). Next I transfected SH-Sy5y cells with plasmids containing either WT or PS2x9B PSEN2 joined to a Flag-tag. I extracted proteins from these cells and control empty plasmids, and used Western blot to examine size differences between each plasmid’s protein products to research the impact of PS2x9B inclusion on PSEN2 protein levels. I hypothesize that inclusion of PS2x9B will lead to truncated proteins due to an early stop codon. Additionally, I am working to establish the consequences of PS2x9B on APP processing and Aβ cleavage. I expect that PS2x9B could cause either an increase in Aβ production or modify its length. These findings will allow us to expand our understanding of PSEN2 and alternative splicing in sporadic AD which could guide development of novel gene therapy treatments for AD.

 

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.

It is important to characterize air quality within dental clinics because dental professionals experience prolonged worksite exposure; patients, too, should not be exposed to unnecessary levels of particulate matter (PM2.5) or carbon dioxide (CO2). Elevated CO2 levels (>~1,000 parts per million (ppm)) reduces cognitive function and can indicate an increased risk of airborne disease transmission. PM2.5, which is produced during dental procedures, easily passes into the lungs causing adverse cardiovascular health effects and aggravating lung conditions such as asthma. This study explores whether the levels of either CO2 or PM2.5 exceed healthy levels within dental clinics. Healthy air is defined as CO2 below 945 ppm and PM2.5 below 50 on an AQI scale. PocketLab Air sensors that measure PM2.5 and CO2 were deployed in multiple dental clinics in the Seattle area. Data was collected for 1-2 days. These findings can help dental offices and other healthcare providers develop appropriate and effective plans to ensure a safe, healthy environment for both patients and practitioners.

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.

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

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.  

Somewhere in the internal structure of the icy moons in our solar system there is the possibility of stable liquid water. This water would exist as a melt extracted from internal layers of high-pressure ice. Previously, to determine the ideal pressure and temperature (P-T) conditions for this melt to be produced, studies relied on the pure water liquidus model. Now, we instead consider a model with a melting curve influenced by soluble ions found on the moons. Ions within the ice could potentially shift its liquidus from that of the pure water model, therefore changing the internal conditions at which melt could be produced. Our investigation focused on how salt (NaCl) concentrations of 1 and 2 mol/kg within ice affects its melting curve at low temperature and high pressure. Using diamond anvil cells (DAC), we monitored the liquidus behavior of the NaCl-H2O solution(s) under a range of select P-T conditions. Comparing the data to the ideal solution model for NaCl-H2O, we quantified changes from ideality. In our results, we determined a melting curve of the solutions that more accurately reflect those of the high-pressure ices within icy moons. Understanding the conditions at which stable liquid melt could exist within these moons brings the scientific community closer to understanding the potential of life within them, as well as other icy bodies around neighboring stars.

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.

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

Mycobacterium Tuberculosis (M.tb) is a pathogenic bacterium that causes the disease tuberculosis (TB). In 2022, TB was second to COVID-19 in the number of deaths caused worldwide. Most T cells recognize peptide antigens presented by polymorphic antigen-presenting molecules MHC-I and MHC-II. Conversely, lipid antigens, including those derived from the M.tb cell wall, can be presented to T cells by a family of non-polymorphic antigen-presenting molecules called CD1. The glycolipid glucose monomycolate (GMM) is present in mycobacteria and is presented by CD1b. Two synthetic GMM compounds (GMM-1 and GMM-2), differing in the length of their lipid tails, were synthesized and I evaluated their stimulatory effects on human CD1b-GMM-specific T cell lines using intracellular cytokine staining. We hypothesized that lipid tail length has an effect on the ability of T cells to recognize the antigen. GMM-1 led to a higher frequency of interferon-gamma (IFN-g) positive T cells (68.6%) compared to either GMM-2 (49.4%) or the common mycobacterial antigen C₈₀ GMM, which is a synthetic antigen that worked as a great control because it is known for getting a T cell response. I also observed an increased secretion of TNFa and IL-2 after stimulation with GMM-1 (72.7% and 57.8%) compared to GMM-2 (59% and 22.9%). The data suggests having lipid tails at similar lengths versus having one significantly longer than the other has an effect on antigen recogniton. Validation of tools to help us better understand the T cell recognition of antigens could further our ability to dissect the mechanisms of M.tb immune evasion, thus, aiding in the advancement of better therapies for treatment. 

Concurrent fentanyl and methamphetamine use disorders are increasingly responsible for overdose deaths in America. Substance use disorders are driven, in part, by neuroplasticity within the cortico-basal ganglia-thalamic network. In particular, the striatum (i.e., the dorsal striatum and nucleus accumbens) functions as a central node contributing to drug-seeking and drug-taking behaviors. As individuals using opioids and psychostimulants together show high rates of overdose and relapse, it is essential to investigate how polysubstance stimulant-opioid use alters motivations for drug consumption and drug seeking. We will accomplish this by using a response dependent rodent model of fentanyl and methamphetamine self-administration (SA) that can directly assess specific behaviors related to addiction (drug-seeking, motivation, valuation). This SA model incorporates key components of the American Psychiatric Association’s diagnostic criteria for substance use disorders, including difficulty stopping or limiting drug intake (modeled by an escalation of drug intake), high motivation to obtain and consume drugs (modeled by a progressive ratio task), sustained drug craving during periods of abstinence (modeled by extinction), and relapse to drug consumption following abstinence (modeled by cue-induced reinstatement of drug seeking). For each of these behavioral metrics, we will compare rats with a history of chronic polysubstance use (i.e., methamphetamine and fentanyl SA) and rats with a history of chronic single substance use (i.e., either methamphetamine SA or fentanyl SA). We hypothesize that opioid-stimulant polysubstance use will have a unique, synergistic effect on addiction-related behaviors that is not present when either drug is used alone. In the future, we hope to investigate further the underlying neural circuits and striatal recruitment of polysubstance use disorders using this behavioral model. Accordingly, we believe this work has important implications for understanding how and why polysubstance use of opioids and stimulants drives continued drug use and increased relapse.

Voice assistants (VAs) are transforming how humans interact with technology. While promising, state-of-the-art VAs like Siri and Alexa do not incorporate a user’s spatiotemporal context such as their surrounding objects or gestures, which results in degraded performance and unnatural dialogue. Since pronoun usage is inherent to everyday speech, we expect future VAs to support ambiguous speech queries. We introduce GazePointAR, a wearable augmented reality (AR) system that resolves ambiguity in speech queries using eye gaze, pointing gestures, conversation history, real-time computer vision, and a large language model (OpenAI’s text-davinci-003). With GazePointAR, a user can ask “what’s over there?” or “how do I solve this math problem?” simply by looking and/or pointing. Upon voice activation, GazePointAR listens for the query, takes a screenshot, and narrows the focus by incorporating information from eye gaze, replaces the pronoun in the query with the detected objects and texts, and utilizes a language model to answer the modified query. To assist in this project, Liam and I reviewed relevant literature, brainstormed technical solutions for multimodal integration, constructed user study scenarios, and conducted reflexive thematic coding on qualitative data. To evaluate GazePointAR, we conducted a three-part lab study that compared GazePointAR to two other state-of-the-art query systems (Google Voice Assistant and Google Lens), examined GazePointAR’s pronoun disambiguation for three tasks, and concluded with an open-ended component where users could suggest and try their own queries. Participants appreciated the improved simplicity and human-likeness of context-aware queries; however, they preferred faster response times and better explanations for query results. By combining visual and voice inputs to answer a broader range of questions, GazePointAR provides a foundation for future works of VAs, such as designing a more anthropomorphic VA.

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

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

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.

Archaeological sequences are the successive organization of artefact-bearing stratigraphical units spanning thousands of years. Due to vast periods of time represented by each unit, sometimes analysis of the sequence results in the appearance of little cultural change over time. This can make it hard to distinguish between random drift, directional selection, and stabilizing selection of ancient technologies. We demonstrate a new statistical method to test hypotheses about drift and selection using archaeological time series data. Through the analysis of Log-rate log-interval plots computed using R, we compare the median slope values of an archaeological sequence to experimentally determined time series values. We demonstrate this method using a case study from Gua Talimbue, a cave in Southeast Sulawesi, Indonesia. Using the artifact data spanning the late Pleistocene and Holocene, we analyze the rate of artifact change over three depositional phases to determine whether the cultural evolution of the artifacts is indicative of stabilizing, random, or directional selection. Previous work at this site hypothesized stabilizing selection, which is confirmed by the results of our new work. We formally evaluate this using a new statistical method borrowed from palaeontology, originally developed by Gingerich in his book "Rates of Evolution" (https://doi.org/10.1017/9781316711644). This research is vital in the building of a better understanding and deeper insight into rates of change of lithic technologies generally, and more specifically the skills employed by early people, specifically within pre-Neolithic Indonesia.

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

Globally, marine socio-ecological systems are social, economic, and cultural foundations for many coastal communities. In the Broken Group Island Archipelago in Barkley Sound, British Columbia, shellfish–including but not limited to butter (Saxidomus Gigantea) and littleneck (Protothaca Staminea) have supported the Indigenous peoples of the Northwest Coast for millennia. Archaeological assemblages of shellfish are evidence of diet, resource management of communities, and reflect coastal ecosystems from thousands of years ago. This presentation explores archaeological shellfish taxa and abundance at the Tseshaht village of Kakmakimilh (Keith Island), located in Tseshaht Territory with a focus on clam size. In concert with past research on sea-level effects on archaeological shellfish assemblages, I documented column sample data from 3 areas of this site. I estimated proportions of rocky and sandy-associated shellfish and measured clam umbos to estimate size trends over thousands of years of occupation at Kakmakimilh. With limited data in this undergraduate student project, the conclusions are tentative, but my specific research suggests an increase in clam size over time, and no change in relative percentages of shellfish with rocky versus sandy habitats. This data might be able to deepen the conversation around shellfish and clam harvesting over time, and how such relationships differed across time and space with the variance in the coastal landscape.

Blast exposure via detonation of explosives results in symptoms such as mild traumatic brain injury, post-traumatic stress disorder, and chronic pain, serving as a major source of trauma for service members, Veterans, and civilian bystanders. These effects characterize the polytrauma clinical triad and pose a risk factor for increased substance use and substance use disorder (SUD). This polytrauma exposure yields diverse symptom trajectories. To understand the interactions between polytrauma and SUD risk, we use a rodent model that utilizes custom, in-house-built polysubstance self-administration chambers, Socially Integrated Polysubstance (SIP) cages, to measure water, alcohol, and fentanyl intake. Two types of tracking are used to monitor drinking: Radio Frequency Identification (RFID) tracking and the volumetric drinking monitor, and these combined tell us which mouse drinks what liquid for a variable period of time. These SIP cages have the advantage to study both voluntary drinking habits and preferences as well as the effect of group housing on these patterns. For this project, we used 69 C57Bl/6 male and female mice aged 9 weeks on arrival. These mice were then single or group-housed in the SIP cages for 9 days to monitor drinking patterns. Testing multiple substances at once can give us valuable insight into substance preference and polysubstance use, making it more representative of the human experience. These mice had behavioral testing before entrance into the SIP cages, and we will explore different methods to characterize these drinking and anxiety subgroups that emerge. In addition, we plan to look at sex differences and how that changes substance use and preference. These factors combined will give valuable insight into classifying substance use that can lead to more optimized treatment for Veterans with polytrauma.

Breast cancer has attracted tremendous research interest in treatment development as one of the major threats to public health. The use of nanoparticle (NP) for therapeutic DNA delivery has shown promise in treating various cancer types, including breast cancer, due to their high DNA loading capacity, high cell transfection efficiency, and design versatility. However, cytotoxicity and large sizes of NPs often raise safety concerns and hinder their applications in the clinic. Here we report the development of a novel nanoparticle formulation (termed NP-Chi- xPEI) that can safely and effectively deliver DNA into breast cancer cells for successful transfection. The nanoparticle is composed of an iron oxide core coated with low molecular weight (800 Da) polyethyleneimine crosslinked with chitosan via biodegradable disulfide bonds. The NP-Chi-xPEI can condense DNA into a small nanoparticle with the overall size of less than 100 nm and offer full DNA protection. Its biodegradable coating of small-molecular weight xPEI and mildly positive surface charge confer extra biocompatibility. NP-Chi-xPEI-mediated DNA delivery was shown to achieve high transfection efficiency across multiple breast cancer cell lines with significantly lower cytotoxicity as compared to the commercial transfection agent Lipofectamine 3000. With demonstrated favorable physicochemical properties and functionality, NP-Chi-xPEI may serve as a reliable vehicle to deliver DNA to breast cancer cells.