Alzheimer's disease (AD) is a neurodegenerative age-related disease characterized by the presence of amyloid-beta aggregates and hyperphosphorylated tau tangles. It has been well documented that cognitive decline and changes in age-related pathways are associated with disease progression. Mitochondria play an important role in degradation of amyloid protein through a mitochondrial protein-mediated quality control system. This pathway can break down with increasing age and lead to the overwhelming presence of amyloid, disrupting normal mitochondrial activity. This damage leads to the formation of more Aβ plaques and neuroinflammation, contributing to the pathogenesis of AD. Mitochondrial regulators may be potential therapeutic drug targets but models are needed to help identify and characterize them. In this regard, an Adeno-Associated-Viral (AAV) vector was used to induce AD protein expression in the brains of old mice. 40 Male and 40 Females mice aged 24 months were infected with either the AAV-AD or AAV-SHAM vector and given 3 months for expression of the proteins to build. Mice were euthanized and brain tissue collected into formalin, with the hippocampus cut into slides for immunohistochemistry (IHC). Data generated from these mice has shown trends in decreased synaptic integrity, increased inflammation and DNA damage associated with expression of the vector proteins. Utilizing the same model, this experiment aims to understand how expression of the AAV-AD proteins may be associated with known roles of mitochondria and characterized pathways in the early stages of AD. IHC was performed using antibodies specific for PITRM1, a mitochondria protein degradation regulator, and PINK1, responsible for mitochondrial-mediated cell death (mitophagy). Imaging software “ImageJ” will be used for quantitative analysis of the stains. This study will help clarify an association between varying levels of AD protein expression and mitochondrial regulation, providing valuable information for enhancing therapies aimed at preventing the progression of early stage AD.

As our world progresses through technological advancements, much of our planet regresses as an effect of climate change, highlighting a need for underutilized resources to be brought to the forefront of industry. One avenue for transforming abundant resources into useful chemicals for generating sources like fuel is the catalytic upgrading of biomass derived molecules. However, catalysts traditionally used for these reactions are not stable to contaminants in biomass mixtures, such as water or organic acids. For biomass derived molecules to serve as precursors for biofuel and other related energy sources, more stable and efficient catalysts are needed. Our group has recently shown that a bifunctional acid–base MOF with co-localized acidic and basic sites outperforms a MOF with randomly dispersed acid–base sites for the aldol condensation reaction. To further demonstrate the importance of having the acid and base groups co-localized, I synthesized and tested three control frameworks for comparison: (1) a framework with no functionality, (2) a framework with only acidic sites, and (3) a framework with only basic sites. I then tested stability and recyclability of the bifunctional acid–base frameworks by conducting recycling experiments. I resubjected the same sample to reaction conditions for a total of 5 cycles. After each cycle, I used 1H NMR to quantify the conversion of starting material to ensure that there were no changes in catalytic activity. Lastly, I used powder X-ray diffraction (PXRD) to ensure that the catalysts maintained their crystalline structure after 5 cycles. Here I show that metal–organic frameworks (MOFs), a class of porous crystalline solids, can be used as efficient and recyclable catalysts for the aldol condensation, an important reaction for biomass conversion. Overall, this work illustrates the stability and reusability of metal organic frameworks as catalysts and thus their potential for utility in biomass upgrading reactions.

Plants' defense mechanism against herbivory and disease is integral to both natural ecological balance as well as global food supply. Induced plant responses to these threats are often triggered by specific molecules such as Herbivore Associated Molecular Patterns (HAMPS) and Pathogen Associated Molecular Patterns (PAMPS). In this project, we are refining a Luciferase Reporter Assay (LRA) and then using that assay to categorize novel HAMPS and PAMPS. This assay’s first main part is the HAMP/PAMP Receptor (HPR). By inoculating a Nicotiana benthamiana (NB) leaf with an Agrobacterium containing a Plasmid with an HPR, we are expressing specific HPRs. We are then using the second part of the LRA, a Luciferase Reporter, whose promoter is tied to an immune response related gene to measure levels of immune activity without the need for Transcriptomic Analysis. After we have infiltrated the NB leaf with the vector containing Agrobacterium and induced a response by adding a HAMP/PAMP, we are measuring Luminescence as a proxy for immune response via an imaging machine, then using R to run an analysis on the levels of immune response, helping us characterize an HPR and its signal pathway. We recently optimized time points for HPR and Luciferase imaging and have found that infiltration by Agrobacterium only takes 24 hours for sufficient plasmid integration. As such we are using this assay to run an experiment on the molecular mechanisms of an HPR in only a few days. Refining this LRA and the information we have gathered has helped shed light on the underlying mechanisms used in induced plant defense. In the future, we are planning on expressing genes of interest using this technique to seek novel activators and suppressors helping us further understand mechanisms of plant defense.

It is well established that formerly incarcerated individuals face stigma upon their return to society, negatively impacting reintegration efforts and life outcomes. Existing literature highlights the significance of stigma in influencing reentry outcomes, emphasizing gender-specific challenges faced by formerly incarcerated individuals, but fails to quantitatively study how these gender stereotypes impact public stigma. Although some research does address variations in the formerly incarcerated population and their influence on public opinion, these studies rarely focus on gender. My study directly explores how gender and stigma interact throughout reentry, by quantitatively investigating public perceptions of formerly incarcerated individuals in Washington State. I develop vignettes about hypothetical formerly incarcerated individuals that vary key facts between participants to examine the extent to which gender, offense type, and post-release behavior influence the public stigma of incarceration. Respondents are randomly assigned these vignettes to evaluate their varying perceptions, unveiling whether gender leads to differential perceptions and therefore, differential treatment in the daily lives of formerly incarcerated individuals. My preliminary expectations are that the public will value relationship-building (a traditionally feminine ideal) more for formerly incarcerated women than for formerly incarcerated men. Additionally, I hypothesize that respondents will exhibit a greater willingness to interact with formerly incarcerated women as compared to their male counterparts, due to negative stereotypes about male aggression and criminality. The implications of this research extend to a broader understanding of the obstacles faced by individuals with criminal records in achieving successful rehabilitation. My analysis will help create more targeted and effective reintegration support policies by uncovering how public stigma impacts the reentry outcomes for women differently than for men. Addressing these dynamics is crucial for fostering inclusivity and dismantling barriers that impede the social and economic participation of formerly incarcerated individuals.

Brain-derived neurotrophic factor (BDNF) plays a critical role in neuronal function with potential implications for cognitive health, including involvement in adult neurogenesis. A decline in BDNF levels is associated with mild impairments in learning and memory. The hippocampus, known for its involvement in learning and memory processes, serves as a focal point for investigation in the brain due to its responsiveness to environmental stimuli, including exercise. There is an existing knowledge gap concerning whether running promotes an increase in BDNF levels within the hippocampus at very old ages, despite BDNF's importance in neuronal function and its potential implications for cognitive health. This study was designed to investigate whether physical exercise influences BDNF levels in the hippocampus of aged mice. Aged C57BL/6 mice were allowed access to running wheels, or locked running wheels, for three days, after which their brains were collected, post-euthanasia for neuropathology assessment. Immunohistochemistry (IHC) was performed with an anti-BDNF antibody by measuring BDNF presence, since lack of BDNF levels signifies lost neurons. QuPath digital imaging techniques were employed to provide a quantitative measure of the potential impact of running on hippocampal BDNF expression. Both the average and the variance of total distance run during voluntary wheel running decreased with age. Elevated BDNF levels were observed in the hippocampus of running mice compared to sedentary counterparts. The study provides insight into the potential impact of exercise on neurotrophic support in the aging brain. Such findings suggest a beneficial effect of exercise on neurotrophic support in the aging brain, and indicates the need for further investigations into lifestyle stratergies for promoting resilience to brain aging and cognitive decline in older adults.

Alzheimer’s Disease (AD) is a progressive brain disorder that debilitates memory, learning, and decision-making. Early-stage AD represents the initial phase where individuals are still able to function independently, but with increasing age, their condition steadily progresses to dementia and loss of independence. Because a significant number of the aging population is affected by AD, understanding the neuroinflammatory processes would help develop more effective strategies for treatment. Examining markers such as MCP-1 and TNF-alpha, known to be associated with inflammatory response, will help identify the modulatory processes that lead to mild cognitive impairment associated with early-stage AD. Subsequently, higher levels of inflammation markers within the brain leads to mild cognitive impairment. This research study involved 40 C57BL/6 mice, 20 males and 20 females (21 months old), retro-orbitally infected with 80 µL of neurotrophic AAV-AD vector or AAV-Sham for a duration of 2 months before humane euthanasia. Brains were collected, and specific regions were examined by immunohistochemistry (IHC) and digital imaging to assess the expression levels and distribution of the inflammation markers. Preliminary observations showed that hippocampal regions of the brain from mice with early-stage AD had higher staining intensity for MCP-1and TNF-alpha compared to respective areas in Sham mice, suggesting increased inflammation is a very early lesion that develops in the presence of AD pathogenic components that might be controlled by anti-inflammatory drugs. The preliminary data suggests that the characteristics of AD manifest in part due to the neuroinflammatory response of brain factors that change with onset AD.

 The cGAS-STING pathway is a critical component of the innate immune system responsible for the detection of cytosolic DNA, which is key in identifying viral or bacterial infection. Activation results in the transcription of type I interferons (IFN), including IFN-β, and other proinflammatory cytokines that lead to the recruitment of immune cells to help control the infection. To explore this pathway, we use a system of conditionally immortalized macrophages (CIMs) derived from Cas9-transgenic i-TOMCAT mice. The Cas9 transgene allows us to make gene-specific knockout (KO) CIMs using CRISPR, while the i-TOMCAT allele, which drives expression of a fluorescent reporter (TdTomato) from the endogenous Ifnb1 locus, allows us to quantify type I interferon expression using flow cytometry. Using the STING agonist DMXAA, I found that CIMs in the progenitor state undergo rapid cell death upon STING activation, while terminally differentiated CIMs were resistant to cell death and produced high levels of IFN-β. Further experiments using the pan-caspase inhibitor Z-VAD-FMK and the necroptosis inhibitor necrostatin-1 showed that cell death in progenitor CIMs following STING activation is independent of apoptosis and necroptosis. This project aims to explore the signaling pathways downstream of STING that dictate either a cell death of IFN-β response. While considerable progress has been made in understanding how cGAS-STING signaling leads to IFN-β secretion, the cell death pathways associated with this cascade remain enigmatic. With recent studies showing that cGAS-STING activation can lead to tumor suppression by preventing cell division, promoting immunosurveillance, and triggering the release of tumor-specific antigens, research into this pathway may help guide the development of improved cancer immunotherapies.

Plants grow in designated areas known as meristems that contain stem cells. The gene LEAFY (LFY) is a flower meristem identity gene that initiates flower development in flowering plants and its homologs are also found in plants that do not produce flowers. Ferns are a lineage of land plants phylogenetically midway between the non-vascular bryophytes (such as mosses) and the seed plants. The model fern Ceratopteris richardii (Ceratopteris) contains two LFY homologs (CrLFY1/2). Given the described meristematic function of LFY in flowering plants, I am investigating whether CrLFY overexpression affects the development of the multicellular lateral meristem known as the “notch meristem”, the main site of cell division for the heart-shaped Ceratopteris gametophytes (the haploid stage of a plant’s life cycle). It has previously been established that CrLFY maintains cellular division in the apical cell of Ceratopteris gametophytes (a unicellular meristem that initiates development), but it is unknown if CrLFY also plays a role in notch meristem division once the apical cell terminates early in development. Consistent with our hypothesis, qualitative observations suggested that plants over-expressing CrLFY have larger and more U-shaped meristems, whereas wild type meristems appear more V-shaped. I am working to quantify the meristematic region within the notch in wild type compared to CrLFY over-expressing gametophytes using scanning electron microscopy and cell hand-tracing. I measure each traced cell and identify meristematic cells as those thinner and longer than the surrounding cells, with a length-to-width ratio of 3 or above. Additionally, I analyze the meristem angle to determine if there is a correlation between CrLFY expression and notch meristem shape. Understanding the role of LFY in plant meristems has important implications for the overall evolution of land plants, as master regulator genes such as LFY emerged in early plant lineages and evolved their functions over time.

Air pollution is a key component to understanding the Public Health of populations globally, with Diesel Exhaust Particles (DEP) being a significant contributor to traffic-related air pollution. Exposure to DEPs varies across populations and is therefore crucial to understanding the continual impacts of traffic-related air pollution on the public. Prior research has indicated that the formation of Amyloid-𝛽 (A-𝛽) plaques and activation of the  nucleotide-binding domain, leucine-rich–containing family, pyrin domain–containing-3 (NLRP3) inflammasome is linked with the development of Alzheimer’s disease (AD) later in life. AD is a form of progressive disease that impairs memory and other cognitive functions and impacts the lives of tens of millions of people globally. This study aims to confirm the linkage between exposure to DEP and memory impairment through NLRP3 inflammasome activation, utilizing an animal model to investigate a potential increase in AD later in life. We exposed male and female low-density lipoprotein receptor knockout (LDLR KO) mice chronically to inhaled DEP or filtered air as a control for 18 weeks. We then utilized the Object Location Memory (OLM) and Object Recognition Memory (ORM) behavioral tests to investigate the immediate impact of multi-week DEP exposure on short-term memory, another indicator in AD progression. Afterward, we sacrificed the mice and harvested a variety of tissues, including the brain. I conducted Immunohistochemistry (IHC) on cryosections of the exposed and non-exposed brain to assess DEP-induced AD-like brain architectural changes and to quantify the impact of DEP exposure in activating the NLRP3 inflammasome, ultimately leading to neurotoxicity, and to the development and progression of AD. Confirming the association between diesel exhaust and the NLRP3 pathway provides a potential therapeutic target in populations at an elevated risk for AD.

It is well documented that pet cats develop age-related diseases similar to humans with chronic age-related diseases, including Alzheimer’s disease (AD). Since pet cats live in the same environment as their owners and by extension are subjected to the same environmental stressors, older pet cats are an excellent mammalian model to study therapeutic targets to slow or reverse brain aging. However, aging within the brains of pet cats is not well characterized, partly because valid reagents have not been identified. This study was designed to test several human-specific antibody reagents that identify non-neuronal cells, aging pathways, and Aβ amyloid and phosphorylated tau (pTau) seen at autopsy in brains from patients with AD. Archived brain samples, collected from pet cats at autopsy, were graciously provided by the veterinary pathology departments at University of California Davis campus and University of Pennsylvania. Immunohistochemistry staining was done to detect: 1) Microglia, a non-neuronal inflammatory reactive cell type, using an IBA1-specific marker; 2) An inflammatory pathway using an MCP-specific marker; 3) Amyloid plaques using E610, an Aβ42-specific marker; and 4) pTau fibrillary tangles using AT8, a pTau-specific marker. A digital imaging software program was used to generate a heat map to visualize staining and quantify results. It was found that brain samples from older pet cats had increased inflammation as determined by high staining intensity of microglia and MCP1. Brains from several cats showed evidence of amyloid plaques and pTau tangles. These observations suggest that the human-based reagents tested can identify analogous cell types, pathways, and pathogenic components of AD in brains from pet cats. These prototype reagents can now be used to begin the task of characterizing neuropathology in deceased pet cats donated to the Cat Alzheimer’s disease Program at the University of Washington.

While survival rates from breast cancer have notably improved, survivors still face long-term health complications due to the side effects of chemotherapy. A significant concern is that patients can develop lasting cardiovascular problems that are exacerbated by physical inactivity during treatment. This study hopes to address this by identifying the optimal fitness intervention for improved cardiorespiratory fitness (CRF) to enhance the cardiovascular health of breast cancer survivors, particularly in those who showed reduced CRF after breast cancer treatment. This randomized control trial enrolled thirty breast cancer survivors into an aerobic exercise, resistance exercise, or control group. Over six-months, the participants performed their designated training, and MRI scans were taken before and after the training program. I am analyzing the depots of fat, including visceral and subcutaneous fat from MRI images of the thigh and abdomen in order to determine the association with cardiorespiratory fitness. Statistical analysis utilized a paired t-test with an intent-to-treat approach to determine the difference in fat levels and to mitigate bias from non-compliance and dropouts. I expect a marginal difference in levels of overall fat between the separate fitness interventions, however, I anticipate a significant difference between the control and both fitness groups. The interpretation of this data provides a first step towards understanding how exercise interventions can be tailored to breast cancer survivors, potentially improving post-treatment survivorship.

Early-Stage Alzheimer’s Disease (ESAD) is characterized by the development of beta-amyloid aggregates (Aβ42) and phosphorylated tau (pTau) leading to mild cognitive decline and variable personality changes. Because specific diagnostic criteria have not yet been established for ESAD at middle age, there is no way of knowing who might be susceptible and who might be resilient to more severe neuropathology and dementia in later years. The geroscience concept assumes pathways associated with aging are also associated with age-related diseases including ESAD. Therefore, a simple skin biopsy procedure shown to predict resilience to aging in middle-aged mice should be able to predict resilience to ESAD in middle-aged mice. An adeno-associated-viral (AAV) vector system carrying pathogenic components of AD, Aβ42, and pTau, was used to induce ESAD in 23-month-old C57BL/6 mice. Before receiving the AAV vector, 2 mm ear punch biopsies were performed, and the rate of closure was measured over 3 weeks. The study ended when mice were 26 months of age, and the closure rate for each mouse was calculated and correlated with behavioral and neuropathological features of EASD. Preliminary observations will help address the question of whether the healing rate of a simple skin wound can predict susceptibility to the burden of AAV-mediated ESAD. It is expected increases in physical resilience will be associated with increased wound closure, and thus, mice with increased wound closure will have greater resilience to the onset of ESAD neuropathology. This could have highly impactful implications for the early treatment of ESAD in human patients thus preventing the irreversible and fatal progression of dementia associated with late-stage AD. In addition, DNA from skin biopsy cores could be used to obtain DNA methylation signatures for determining biological age thus providing an enriched, translationally relevant data set.
 

Alzheimer's Disease (AD) is incredibly complex such that development of neuropathology and cognitive impairement is driven by multiple pathways. Therefore, targeting these pathways simultaneously, could provide a more effective treatment for AD compared to any single drug. Rapamycin, acarbose, and phenylbutyrate each have independent but overlapping effects on multiple pathways involved in cellular respones to pathogenic beta amyloid such as inflammation, glucose homeostasis, synaptic integrity, autophagy, and DNA damage. To test the safety and effectiveness of a cocktail of these three drugs, a proof of concept experiment was undertaken in transgenic mice carrying mutations for genes associated with early onset AD (5xFAD). These mice express neuronal amyloid plaques, a major feature of AD neuropathlogy. Transgenic and wild type mice were given either a control feed or feed containing the drug cocktail starting at 4 months of age and continued until 12 months of age. Medicated transgenic mice showed significantly less cognitive impairement in a spatial navigation learning task and reduced amyloid plaque levels in the hippocampal brain region compared to untreated transgenic mice. Immunohistochemistry will be used to identify specific biomarkers for inflammation, synaptic integrity, glucose homeostasis, autophagy, and DNA damage in the hippocampus of treated and untreated transgenic mice. Observation from this study will suggest the need to conduct additional preclincial experiments testing this specfic drug combination for a successful approach to treat Alzheimer's Disease. 

The seeds and fruits of all flowering plants derive from female reproductive structures called pistils. At the tip of a pistil is an area called the stigma that is the site of pollen reception, making the structure of stigmas critical for ensuring plants are pollinated and produce seeds. In the genus Thalictrum, stigmas vary widely: short stigmas are present in insect-pollinated Thalictrum species to facilitate closer contact with visiting insects and ensure successful pollen deposition, while longer, more feathery stigmas have evolved from these to take advantage of wind for pollination. However, the evolutionary and genetic basis for this transition is not known. I aim to explore the genetic mechanisms that facilitate the transition from insect-mediated to wind-mediated pollination using Thalictrum thalictroides as a model species. Specifically, I am testing the function of two candidate genes in T. thalictroides stigma development, STYLISH1 and STYLISH2 (STY1/2), which are known to be necessary for stigma development in other plant species. To do so, STY1/2 genes have been silenced and overexpressed by virus-induced gene silencing and virus-mediated overexpression. I collected and imaged floral tissue from transgenic plants and validated them by qPCR. The effects of silencing and overexpressing STY1/2 are then determined using scanning electron microscopy to visualize cellular changes to the pistil and stigma. I predict shortened or loss of stigmas in silenced flowers and elongated stigmas in overexpressed flowers, which would support my hypothesis that STY1/2 are necessary for stigma formation in T. thalictroides. Not only do these findings enhance our knowledge of plant adaptation to environmental changes, but they also create implications for efforts toward conservation and sustainable agriculture, offering potential insights into the prospect of engineering wind-pollinated plants in a changing climate with dwindling pollinator populations.

As the Anthropocene progresses, environmental stressors are becoming more noticeable in their impacts on aquatic ecosystems and the organisms that inhabit them. One such organism of environmental and ecological importance is the Pacific oyster, C. gigas. Under climate change, molluscan shells are likely to become weaker due to lowered calcium carbonate availability which may lead to increased mortalities. In Washington state, C. gigas provides 3200 jobs annually and lowers nitrogenous waste concentrations. Our focus in this work was to determine if temperature and pH would affect shell strength in C. gigas as climate change continues to affect their environment. We used C. gigas samples that grew in Puget Sound, Washington, over the summer months. Samples were tested for maximum load of pressure shells could withstand and correlating that to thickness to determine strength. We found that temperature and pH were not correlated to shell strength. We observed that the shell strength of C. gigas taken from Puget Sound did not depend on temperature or pH changes. Previous molluscan shell strength experiments in other settings and locations show contradictory results, but there is little evidence pertaining specifically to C. gigas. These experiments are typically conducted in laboratory settings as well, not in field settings like ours. Going forward, this concept should be reconsidered to confidently identify what the Anthropocene has in store for C. gigas.

Although the relationship between the structure, function, and physiology of organs is well documented, the mechanisms by which cells collectively coordinate into three-dimensional tissues and organ components remains unknown.The countless factors that inform the morphogenesis of mammalian organs poses a challenge to understand organogenesis from first principles. However, the Malpighian tubules of the fruit fly Drosophila offer an excellent model system for investigating this question due to their rapid development, relative simplicity, and the degree to which scientists can manipulate variables that affect their development. These tubules are the renal equivalent of the fruit fly excretory system; further, many of the genes involved in sculpting these tubules are conserved from flies to humans. One conserved gene is the fly homolog of β-catenin, which is known to play an essential role in cell-cell adhesion. The goal of my research is to define how β-catenin impacts organ morphogenesis. To do this, I use fluorescence microscopy and live imaging to compare wildtype Drosophila to those with decreased β-catenin expression. Using tissue-specific fluorescent protein tagging, I can differentiate Malpighian tubule cells from other embryonic cells under the microscope so that their shapes can be analyzed, and I control the level of β-catenin expression specifically in Malpighian tubule cells using RNAi. Due to β-catenin’s integral role in cell-cell adhesion, I expect to find localization of β-catenin to the cell membranes of the tubules, with high concentration along membranes undergoing the greatest adhesion or motion, and interrupted tubule morphogenesis in reduced-expression lines. I also suspect that cells may completely fail to adhere and will be unable to transmit tension effectively along the tissue. The results of this experiment will contribute to our understanding not only of Malpighian tubule morphogenesis, but of one of the components of morphogenesis in general.

How do organs have such consistent and reproducible shape, form, and volume? One factor of this complex phenomena is cell-cell adhesion. Cell-cell adhesion plays a vital role in organ formation, as it is an essential driver of cell shape, cell arrangements, and tissue structure. To determine the role of adhesion in organ formation, I define the role of E-Cadherin, a cell-cell junction projection that adheres neighboring cells. The developing renal system of Drosophila, Malpighian tubules, are an excellent system because I can selectively manipulate expression of E-Cadherin in the organ and can utilize fluorescence microscopy to observe how these changes affect tubule morphogenesis. I observe where the adhesion protein is located during organ growth, and what happens to organ growth when expression of the adhesion protein is reduced. To track the dynamic localization of E-Cadherin, I take measurements of specific location of E-Cadherin between cells and concentration of E-Cadherin throughout organ development. I expect the concentration of E-Cadherin to increase during elongation, and that it will be enriched in more looped parts of the organ. To define the requirement of E-cadherin during organ formation, I use RNA interference to reduce E-Cadherin expression. Because of how vital E-Cadherin is in other developmental morphogenetic processes, I expect a decrease of expression to have profound impacts, leading to severe organ developmental defects. I measure these defects by comparing cell shape change and organ shape in control and E-Cadherin reduced organs. The results of this study will not only help us understand Malpighian tubule morphogenesis, but it will also help us understand organogenesis more generally. Elucidating the precise mechanisms behind cell behavior, shape, and cell-cell interaction has important human health implications and will enable work in many other fields such as cancer, regenerative treatments, tissue growth, and organ synthesis.

Wastewater pollution is a grave concern for public health worldwide, and the U.S. wastewater treatment system can be improved to extract pollutants to the highest level more adequately. One way to better extract pollution left after treatment is by using the metabolic capacity of microbiomes in the soil. This study tests microbiome pollution extraction potential by measuring functional gene abundance according to soil depth in poplar tree reactors irrigated with synthetic wastewater. I collected and extracted DNA from soil samples from 9 reactors at two different depths. I then performed ddPCR on the extracted DNA to quantify the nitrogen-cycling genes amoA, nifH, and nirK, at different depths. I also tested the 16S gene to quantify total soil microbiome biomass. Biomass and functional gene abundance did not vary by depth, but they did vary by season. Biomass additionally varied by treatment group. Study findings could guide the design of a wastewater facility to maximize pollution extraction.

Sustainable and effective wastewater treatment is a growing field that incorporates biological and environmentally friendly solutions to many stages in the wastewater treatment process. This study explored the tertiary treatment of wastewater through poplar tree bioreactors with a focus on nitrate and other nitrogen compounds. Synthetic secondary wastewater was made and fed to the bioreactors. The bioreactor effluent was then collected and analyzed. Previous work has shown significantly decreased levels of nitrate found in the poplar bioreactor effluent when compared to the control bioreactors. An important aspect of this bioreactor system is its ability to simultaneously produce biomass. To incentivize this project, the biomass produced can be sold to be synthesized into bioethanol. The latter portion of this study was a woody biomass analysis to compare the different growths between the treated and untreated poplar tree bioreactors. The trees were coppiced, processed, and dried at 60C for roughly seven days until there were little to no changes in the mass between hourly measurements. A leaf nutrient analysis of the treated and untreated trees was made to trace nitrogen pathways. Upon visual inspection, the treated trees appeared significantly larger and more developed. The result of the biomass analysis indicated that were was increased growth in the treated poplar bioreactors. Some of the treated trees had produced over five times the biomass of the untreated trees. The results of the leaf analysis showed greater carbon and nitrogen concentrations in the treated poplar leaves. Additionally, a higher percentage of nitrate was found in the leaf composition of the treated poplars. These results demonstrate that the treated bioreactors possessed an increased nitrogen uptake due to the increased presence of nitrate in the wastewater. There also appears to be a strong correlation between the treatment of the poplar tree bioreactors and their increased growth.

The drug resistance in tuberculosis (TB) is a rising concern for the diagnosis and treatment of the disease. Being able to detect the presence of drug resistance accurately and rapidly in the patient strain is essential for improving individual treatment outcomes and reducing further transmission of resistant strains, which are more costly and difficult to treat than drug-susceptible strains. However, the current methods come in short in point-of-care (POC) settings, due to problems such as long processing time, high complexity, and necessity for specialized personnel/equipment. Oligonucleotide ligation assay (OLA) provides a high sensitivity and specificity against TB drug resistance, and here, I have developed a novel lateral flow test (LFT) device that incorporates OLA into it, which have shown comparable specificity and sensitivity against traditional protocol of OLA in lab setting followed by LFT. Moreover, the simplicity of the design enables further incorporation of other techniques such as isothermal DNA amplification, for a compact, one-step TB drug resistance diagnostic device for low-resource environment. 

Anaerobic digesters are specialized vessels that hold microbial communities that decompose organic materials without oxygen present. There are many diverse applications for anaerobic digesters such as the treatment of biodegradable waste and sewer sludge. Specifically, anaerobic vessels that house methanogenic communities have great potential to break down and utilize paper manufacturing waste. In our lab, there are two anaerobic digesters that have been studied for the past two decades. The goal of this research was to design and implement new anaerobic digesters to improve the stability of the anaerobic microbial communities. To complete this task, I did research on methanogenic communities and compared our current anaerobic digesters. After this, there were two versions of the prototype digester created with improvements made to the waste and feeding port. I tested the integrity of the vessel by submerging it under water and then pumping it with nitrogen gas to ensure no oxygen was present. The vessel was then filled with 10 ml of acetate feed with resazurin color indicator which was incubated for 10 days. I concluded that the vessel was able to maintain an anaerobic environment and we ensured that no oxygen could contaminate the vessel by siliconing the tubes and ports. The final vessel included access ports to take samples and more security against oxygen seeping in. We then moved the microbial communities from the current anaerobic vessel to the new anaerobic vessels. Furthermore, we tested how fast the communities processed the acetate feed (which was given daily) and the types of microbial communities in the reactors. We found that the new digesters allow for easy sampling and that they process feed almost immediately. This research can be used to improve how anaerobic digestion is used in the treatment of paper manufacturing wastewater and testing the microbial communities in wastewater.

Substance use disorder (SUD) takes a tremendous toll on human life every year, which makes understanding the underlying neural circuitry behind SUD a very high priority. A key neurotransmitter in the discussion surrounding SUD is dopamine, which has been implicated in mediating reward-seeking and motivational behavior. More specifically, these behaviors are believed to be mediated by the dopaminergic projection from the ventral tegmental area (VTA) to the nucleus accumbens (NAc). Using contemporary technologies like fiber photometry paired with dopamine biosensors, live dopamine dynamics can be viewed in real time and aligned to certain behavior events collected during tasks performed by animals to further understand dopamine dynamics relating to SUD. With this in mind, we injected a cohort of male and female Wistar rats with a viral vector containing the dopamine biosensor dLight, which fluoresces when bound to dopamine, into the NAc and implanted fiber optic cannulas directly above the injection site to monitor the transmission of dopamine in real time during drug consumption. From there, we ran the cohort through a drug self administration cycle consisting of a training period, short access sessions to establish baseline drug consumption (1hr), and finally long access sessions (6hr) which is known to produce escalation of drug consumption, an SUD-like phenotype. Dopamine dynamics were recorded during several time points across this task. We then performed data analysis to assess various relationships between the behavioral and photometry data, along with immunohistochemistry to confirm the injection. Understanding the dopamine dynamics underlying drug consumption and how they change across changing behavior, such as escalation of drug consumption, is essential to building our understanding of SUD, and our current research helps to illuminate the inner workings of that relationship.

Consumption of highly reinforcing drugs, such as cocaine, can result in an escalation of drug consumption. Escalation is related to the most severe consequences associated with substance use disorder (SUD), including overdose. Chronic substance use leads to neurobiological changes including the signaling of the stress-related peptide corticotropin-releasing factor (CRF). Previous work has implicated CRF dysregulation in alcohol, psychostimulant, nicotine, and opioid dependence. CRF release in extrahypothalamic regions contributes to anxiety-like symptoms of withdrawal that can motivate individuals to consume drugs. There is limited evidence addressing whether CRF receptor (CRFR) activation alters cocaine consumption in individuals who have escalated their cocaine consumption. Additionally, the majority of the previous work has primarily been conducted in male subjects. The present study examines the underlying neurobiology of escalated cocaine consumption in male and female rats. Wistar rats were trained on long access (6hr) cocaine self-administration paradigm in which a subset demonstrated an escalation in their cocaine consumption. At the end of this paradigm, rats were subject to systemic administration of one of two CRFR1 antagonists, antalarmin (25mg/kg, i.p.) or N,N-bis(2-methoxyethyl)-3-(4-methoxy-2-methylphenyl)-2,5-dimethyl-pyrazolo[1,5a]pyrimidin-7-amine (MPZP; 10 and 27.5 mg/kg, s.c.). I hypothesize, following previous work, that antalarmin and MPZP will both significantly reduce escalated cocaine consumption in rats classified as escalators but not non-escalators. These results would indicate that CRFR1 activation mediates escalated cocaine consumption in both male and female rats and may be a valuable target of clinical investigation into the neurobiological underpinnings of this dangerous facet of SUDs.

Quantum computers represent data through qubits, as opposed to bits in classical computers. These qubits can be implemented using various physical systems, including trapped ions where they are represented by the internal energy levels of individual ions confined within electromagnetic fields. Trapped ions are an attractive choice for qubit implementation since this system has the potential to meet all the DiVincenzo criteria, which are a set of requirements needed to build a mainstream quantum computer. To facilitate the development of mega-qubit (MQb) trapped-ion quantum technologies, the Scalable Quantum Research Lab is conducting extensive research on the persistent issue of collisions with background gas molecules, an error immune to the standard quantum error correcting codes. My research focused on answering the question, 'Can error rates be controlled through trap design?'. To answer this question, there are 3 parameters to determine: (1) trap height: vertical location of the ions from the surface trap; (2) trap depth: how strong the trap is (i.e., how stable is the trapping potential); and (3) trap anharmonicities: the coefficients associated with polynomial potential. These anharmonic potentials can accelerate ions after collisions, thereby increasing collision errors. These results were found using Particle-in-Cells simulations and computational analysis for error minimization. Optimizing the trap design allowed greater control over the collision error rate for a long ion-chain trap. In short, finding a way to control anharmonicity and trap depth using trap geometric optimization can reduce the additional measured errors in the bigger experiments. The results presented are a model of trapped ion and graphs showing relationship between different trap paramters and the three variables mentioned above. 

Infants perceive speech and acquire language amidst noisy and complex auditory environments. Thus, elucidation of the cognitive mechanisms governing speech perception under noisy conditions is crucial. Cortical encoding of the speech envelope has been one approach used to study speech-in-noise perception in adults. For infants, research shows that Infant Directed Speech (IDS) facilitates cortical encoding of the speech envelope in quiet conditions more than adult direct speech. However, it is unclear whether infants are able to track the IDS speech envelope amidst competing speech. To investigate this, we recorded the neural responses from 40 typically-hearing infants (20 seven-month-olds, 20 eleven-month-olds) to continuous IDS using electroencephalography (EEG) in three conditions: Quiet, Co-located Noise, and Separated Noise. The target stimuli consisted of naturally recorded IDS produced by two female English speakers. The noise stimuli consisted of a four-person babble constructed from audiobooks read by 2 male and 2 female English speakers. We presented stimuli at an overall level of 70 dB SPL via speakers placed at 0°, +90°, and -90° azimuth to infants sitting on a caregiver’s lap in a sound-attenuated booth. Our team analyzed EEG signals using the Multivariate Temporal Response Function (mTRF) toolbox in MATLAB. This backward modeling approach assesses whether the stimulus envelope can be reconstructed based on the recorded neural responses. Reconstruction accuracies greater than chance were observed in all three conditions for the majority of infants, suggesting that we were able to decode the speech envelope in both quiet and noise. Participants demonstrated the capacity to process speech, even amidst competing auditory stimuli, emphasizing speech perception competencies from an early developmental stage. These results support using the envelope model and mTRF method as a feasible method for investigating the development of speech-in-noise perception in infants and young children.

PARP inhibitors are a revolutionary precision cancer therapy that inhibits PARP function and causes synthetic lethality in cells with homologous recombination deficiency (HRD) such as cells with BRCA1/2 loss. As such, BRCA1 presence plays a key role in PARP inhibitor sensitivity, providing a basis to predict treatment response based on BRCA1 expression in patient tumors. In addition to protein loss mutations, hypermethylation of BRCA1 gene may also result in the loss of BRCA1 expression, and subsequent HRD and potential PARP inhibitor sensitivity. The NRG-GY005 clinical trial focuses on the development of a clinically useful predictor of PARP inhibitor sensitivity/resistance to spare toxicities for patients unlikely to derive benefit. I will first characterize BRCA1 expression in randomized and blinded tumor samples as a biomarker for response to PARP inhibitors in patients. I will then relate BRCA1 protein expression to methylation status of BRCA1. Combining these two aims will describe BRCA1 function/presence in tumors, and better define overall homologous recombination deficiency to optimize patient-specific treatment between PARP inhibitors or other precision therapies. I conducted immunohistochemistry (IHC), a targeted staining with antibody MS110, towards BRCA1 to identify protein presence in tumor tissue and have compiled and analyzed droplet digital PCR (ddPCR), IHC, and clinical treatment reports. I am currently working through Aim 1 by performing IHC staining on tissues from the first phase of the NRG-GY005 clinical trial and will continue investigating whether a lack of BRCA1 expression is associated with cancer cells that are responsive to therapies. In combining IHC and ddPCR assays, we can compare BRCA1 presence with methylation to analyze tumor cases without BRCA1 expression and contribute toward identifying biomarkers to inform patient-specific treatment for individuals with recurrent ovarian cancer. I anticipate that cases lacking BRCA1 expression have an increased likelihood of hypermethylation in the tumor, causing loss of BRCA1.

The ventral tegmental area (VTA) is a key region in the brain’s mesolimbic circuitry playing a role in regulating reward processing, aversion, motivation, and stress-related behaviors, housing both dopamine (DA) and GABA-expressing neurons. GABA neurons in the VTA form direct connections with DA neurons, modulating dopamine and influencing reward-related behaviors. This study aims to characterize two distinct VTA GABA populations marked by expression of the nociceptin gene (Pnoc) and corticotropin-releasing hormone binding protein (Crhbp). Using double transgenic mice and viral targeting, we aim to map the projection patterns of these two populations. We anticipate that Crhbp-GABA expressing populations will innervate the Ventral Pallidum and Lateral Habenula brain areas as these neurons also coexpress Vglut2, a marker for glutamate neurons which are known to project to these regions, whereas, Pnoc-GABA expressing populations might represent the local GABA population that synapses onto DA neurons within the VTA. To assess their functional role, we will optically activate these populations during a real-time place preference task (RTPT) using channelrhodopsin-2 (ChR2). We hypothesize that activation of Pnoc-GABA neurons will result in a negative valence response and support real time place aversion. On the other hand, Crhbp-GABA neurons may have a more varied effect on valence response, based on their coexpression of Vglut2, during the RTPP task. By understanding the roles of VTA GABAergic populations marked by Pnoc and Crhbp expression, we can gain insights into the neural mechanisms involved in reward processing, motivation, and stress, often dysregulated in psychiatric disorders. This understanding could ultimately inform the development of targeted therapeutic interventions for psychiatric conditions characterized by maladaptive behavioral responses to stress and other stimuli.

Sporadic inclusion body myositis (sIBM) is an acquired progressive inflammatory muscle disease. It is most commonly seen in individuals over 50 years old and affects more men than women. Symptom onset is generally gradual and characterized by progressive muscle weakness and atrophy. Weakness often starts in the quadriceps and finger flexors but can affect other muscles in the arms and legs as the disease progresses. Difficulty swallowing also can be present. The disease remains challenging to diagnose due to its non-uniform presentation. There is currently no cure or standard treatment for sIBM as it is unresponsive to corticosteroids and immunosuppressive drugs. In this study, we investigated the prevalence of and associations between different features considered in the diagnosis of sIBM. We reviewed the electronic medical records of adult patients diagnosed with sIBM using ICD-10 codes at the University of Washington Medical Center from 2003 to 2023. Data was collected including creatine kinase (CK) levels, presence of the anti-cytosolic 5′-nucleotidase 1A (NT5c1A) antibody, pulmonary function testing, presence of dysphagia, muscle strength testing, muscle biopsy findings, electromyography (EMG)/nerve conduction studies, and magnetic resonance imaging (MRI). Statistical analyses were performed to identify the presence of sIBM phenotypes and correlations between them. This study confirms the heterogenous presentation of sIBM and highlights the associated diagnostic challenges this presents. Understanding both typical and atypical presentations is key to preventing delayed diagnosis and misdiagnosis commonly seen in this patient population. Timely diagnosis allows for more tailored management of disease-related symptoms and can help to eliminate the unnecessary administration of ineffective medication and invasive testing. In addition, further characterization of sIBM phenotypes may lead to improvements in both current diagnostic criteria and considerations for clinical trial outcome measures.

Physics concepts dealing with charges, particles, and electricity are difficult to conceptualize, yet foundational for students' scientific understanding. As an undergraduate researcher at the Novel Observations in Mixed Reality (NOMR) lab, I work on developing virtual reality applications for introductory physics lab courses at UW. To develop tools and scenarios for the labs, we use C# in Unity. One of the tools that I worked on developing was the Charge Tool, a tool that allows students to change particle charges and experiment with the relationship between charge and force according to Coulomb's Law. We conducted usability testing by taking participants with different levels of familiarity with VR, using the “think aloud” method. Through this, we identified user pain points for ease of use and ensuring an easier learning curve for students who are new to using VR. Based on key insights, we improved the particle colors to being more intuitive and color-blind friendly, as well as redesigned the tool to make it more functional and easier to use. I also work on a decay particle project that focuses on the principle of conservation of charge, momentum, and mass-energy, and a tutorial project which allows students to access instructions and lab manuals inside the VR lab scene. Since virtual reality is still pretty new in the field of education, research in it becomes important as it allows students to interact with physics concepts in a way that they never have before.

Artificial intelligence has made significant progress in image classification, an essential task for machine perception to achieve high-level image understanding. Despite recent advances in vision-language fields, image classification is still challenging because classes are inherently multimodal. Traditional approaches provide solely images or descriptions of a given class, but this does not properly encapsulate the entire concept. I aim to understand if utilizing multiple modalities when classifying images will allow for more robust and generalizable image classification. Here, I leverage Ensemble Learning to form a weighted sum of the embeddings produced by my classifiers. The ensemble consists of an image-to-text classifier that utilizes generated class descriptions and an image-to-image classifier that uses generated images for prediction. My results show that this improved conceptual representation from the multimodal approach directly results in higher classification accuracy. Additionally, this approach allows for these improvements without any additional context, training, or fine-tuning, meaning this method is completely zero-shot. Improved image classification directly impacts a myriad of fields, and enhances how humans use computing technology. Whether it be more accurate diagnoses in medical imaging or robust crop monitoring in agriculture, improvements in image classification extend across disciplines and aid the quality of life for all.

Recently there has been interest in two possible sources of mass in the outer solar system. First, observations of recently discovered remote outer solar system objects have suggested the presence of a ninth planet. Different numerical simulations have suggested either a less massive (1.5-3 Earth masses) planet with a semimajor axis of 250-500 AU from the Sun (the Earth orbits at 1 AU), or a more massive (5-15 Earth masses) planet at 400-800 AU. Second, data from the New Horizons spacecraft has suggested that there may be an additional roughly circular belt of objects, similar to the Kuiper Belt, beyond 60 AU. This raises the question of whether this belt would be compatible with some or all of the proposed forms of planet 9. To answer this question, I ran a series of orbital dynamics simulations with randomly generated test particles representing the proposed second Kuiper Belt, and different masses and orbital parameters for planet 9. By looking at how planet 9 changed the orbits of the test particles over the period of the simulation, I concluded that although planet 9 would not significantly affect objects orbiting at 60-100 AU, in the most extreme cases, it would significantly broaden the distribution of orbital inclinations of objects beyond 100 AU. Astronomical deep and wide surveys conducted over the next few years have the potential to detect both planet 9, and objects beyond the Kuiper Belt. If second Kuiper Belt objects are discovered, these objects having a wider-than-expected range or orbital inclinations would point to gravitational disturbances, such as those caused by planet 9. Alternatively, if planet 9 is discovered, these simulations suggest that a second Kuiper Belt would need to be more inclined than has been so far assumed.

Nutrients play a large role in marine primary productivity, and fluctuations in concentrations can have large impacts on the health of both marine life and human populations. Phosphates, silicates, nitrates, nitrites, and ammonium are all nutrients which are naturally present and key to the functioning of marine environments; however, negative consequences such as Harmful Algal Blooms (HABs) can occur if concentrations differ too far from normal ranges. Both natural processes and anthropogenic activities influence nutrient concentrations in marine environments, and in estuarine environments, like Possession Sound–part of the Whidbey Basin–the impacts of anthropogenic activities are further magnified due to unique estuarine hydrodynamics and the close proximity to dense human populations. For this study, I analyzed three sites within Possession Sound, looking at nutrient levels in comparison with dissolved oxygen (DO) and chlorophyll concentrations (as a proxy for primary productivity). I collected data during numerous research cruises and used this in tandem with the Ocean Research College Academy (ORCA) historical data set. Water samples were sent to the University of Washington Marine Chemistry Laboratory to measure nutrient concentrations, and chlorophyll and DO data were collected through the use of a conductivity, temperature, and depth (CTD) sensor. Preliminary results suggest a strong seasonal trend in nutrient values, with the lowest abundance occurring during the summer months. I hypothesize that further analysis will suggest an inverse relationship between primary productivity and nutrients. This study can potentially offer insight into the health of the Possession Sound ecosystem by assessing the extent to which dissolved oxygen, chlorophyll, and nutrient concentrations are within normal limits and following expected seasonal patterns.

The properties of an estuary are driven largely by the vertical circulation and stratification patterns resulting from the convergence of dense salt water and less dense fresh water. These density-driven circulation patterns play an important role in the way vital nutrients are distributed throughout the environment to primary-producers. This study focuses on the seasonal variation in salinity and chlorophyll in comparison with river discharge levels of the Snohomish River, at Mount Baker Terminal, WA, within Possession Sound. This site is located 3.6 miles SW of the Snohomish River output near Mukilteo, WA. Salinity, chlorophyll, and depth data were collected from January 2020 to December 2023 using a boat based CTD (EXO SONDE). I participated in the collections from Fall 2020 to December 2023. I also reference the United States Geological Survey (USGS) streamflow data at site number 12150800. I categorized deployments by season (Winter: Dec-Feb; Spring: Mar-May; Summer: Jun-Aug; Fall: Sept-Nov) and utilized RStudio and GGPLOT2 to visualize and analyze my data. Preliminary analysis suggests well-defined haloclines and increased chlorophyll levels during spring months, corresponding with increases in river flow at this time. Decreased stratification, weak haloclines and low chlorophyll levels are conversely observed during summer months, corresponding with consistently low rates of river discharge. This raises questions concerning the impact that seasonal changes in river flow have on primary production at and around the halocline. Further analysis of chlorophyll ranges at the halocline is required to better understand this relationship. Monitoring the impact of river discharge variability and primary production is especially relevant in light of changes in seasonal weather patterns related to climate change.

As primary producers, plankton play an important role in the marine environment as the basis of the food chain. Because of this, plankton biodiversity can be an indicator of the health of the ecosystem. As weather patterns change, rising salinity has been documented in marine environments across the globe. This has shown harmful effects in several organisms, including plankton. This study focuses on examining the correlation between salinity and plankton biodiversity across different seasons in Possession Sound located in Everett, Washington. For each site and season I compared biodiversity values with halocline salinity data for each plankton tow. Plankton were collected using horizontal plankton net tows at the halocline and identified based on morphology. I used the Shannon Diversity Index to examine biodiversity of phytoplankton and zooplankton. I collected this data on research cruises held by the Ocean Research College Academy and used historical data collected by previous students. The collected data encompass three sites visited from 2014-2024. Preliminary analysis suggests that biodiversity and salinity will have an inverse relationship. By examining the correlation between salinity and plankton biodiversity, we can begin to understand the potential impacts of rising salinity levels in marine ecosystems.

 Primary productivity is the basis of energy production in marine ecosystems and is primarily dependent on nutrients and sunlight to occur, specifically the 400-700nm range of light that is used in photosynthesis, known as photosynthetically active radiation (PAR). In the Possession Sound estuary, nutrient input from the Snohomish River and seasonal daylight patterns lead to high productivity in spring, summer, and fall. These patterns provide an opportunity to investigate the influence of PAR against the influence of nutrients, which would allow for a greater understanding of the potential effects of PAR from artificial light at night (ALAN) in an estuarine system. We utilized existing and ongoing data from the paired deployments of a Seabird 19+ and a YSI EXO 2-Sonde to obtain water column profiles of PAR, chlorophyll, turbidity, and dissolved oxygen from July 2022 to April 2024 at Mt. Baker Terminal (MBT) in Mukilteo, and data from a moored MiniDOT PAR logger at MBT and moored EXO sensors at MBT and the Everett Marina from October 2023 to April 2024. The moored PAR logger and EXO sensors were set to collect data at 1 and 15 minute intervals, respectively. Additionally, we collected a concurrent total of 30 plankton samples at MBT and Everett Marina after sunset using a 1.7L Niskin bottle and a 20µm plankton filter. Preliminary analysis shows no measurable PAR at night, though Marina potentially has more productivity at night than MBT based on plankton data. Due to the small timeframe of our research, future explorations should expand the available analysis of temporal variation along with increasing the scope of sites throughout the Possession Sound and greater Salish Sea.

Escherichia coli (E. coli) abundance is commonly used to indicate water quality and environmental health. The pH of water has been shown to affect the survival of E. coli. Possession Sound is an estuary that faces a wide range of pH (around 7.5-9.0) throughout the year due to alkaline salt water from Puget Sound mixing with acidic fresh water from the Snohomish River. Primary production, organism respiration, nutrient runoff, carbon emissions, and currents also affect pH levels. This study aims to analyze the relationship between pH and E. coli abundance in an estuarine environment. PH and E. coli data was collected from 2018 to 2023 by myself and other Ocean Research College Academy students. PH data was collected with a YSI EXO2 Sonde. E. coli data was collected using a Niskin bottle to obtain water samples which were then transferred to Petri dishes for growing and counting E. coli. My preliminary analysis shows that Possession Sound’s average pH range is around 7.5-8.5, with pH being higher in spring and summer than in fall and winter. Early analysis using Spearman’s Rank Correlation suggests that pH and E. coli have a weak, inverse relationship. There is minimal research on the relationship between pH and E. coli in a marine setting, so my study helps to provide insight into the relationship between E. coli and pH in a unique estuary.

The synthesis of key organic molecules often requires toxic, expensive, non-reusable reduction agents and extreme conditions. In recent years, electrochemistry has emerged as a sustainable alternative to standard methods, but this approach is often hindered by high energy barriers for electron transfer to the substrate. Electrocatalysts address this challenge by shuttling charge between the electrode and dissolved substrates, accessing lower transfer barriers, and reducing the overall energy needed. Current electrocatalysts, however, cannot stabilize reactive intermediates, which often leads to harmful side reactions and degradation of the electrode. We hypothesize that redox-active supramolecular cages can address this limitation by both shuttling charge and providing unique microenvironments capable of stabilizing intermediates. Previously, we synthesized two tetrahedral supramolecular cages that incorporate redox-active perylene diimide (PDI) and pyromellitic diimide (PMDI) motifs. Using cyclic voltammetry, we then showed that both cages can lower the voltages required for the electroreduction of vicinal dihalides to alkenes, indicating electrocatalysis. To better understand these results, I used density-functional theory (DFT) calculations to obtain computer models of the PDI and PMDI cages. These DFT-optimized structures revealed significant differences in charge density between redox centers due to electron-donating functional groups, which may explain why the PMDI cage lowered the substrate reduction voltages more than the PDI cage. With these models, I have also studied the shape and volume of the cages’ internal cavities, thereby providing information about substrate compatibility. I am conducting additional DFT analysis to understand how modifications to the ligand motifs may alter the electrocatalytic behavior. By continuing to investigate supramolecular cages for reductive electrocatalysis, I aim to contribute to the development of low-waste synthetic strategies for the production of alkenes and other commercially significant organic compounds.

More than 53 million adults or 22% of the US suffer from chronic inflammation. Along with being a critical factor in the onset and progression of aging and cell senescence of the central nervous system, inflammation is also a central hallmark of neurodegenerative diseases and brain injury. Modulation of neuroinflammation has the therapeutic potential to decelerate aging processes in the brain. Studies consistently show that cytokines such as Interleukin (IL)-6, Tumor Necrosis factor (TNF)-α, Monocyte Chemoattractant Protein -1 (MCP-1), and their receptors, are upregulated in aged tissues and cells. This study investigated effects of GHK-Cu, a naturally occurring peptide that has regenerative properties, as a potential therapeutic measure to reduce the expression of these proteins. Mouse SIM-A9 microglial cells and N2A neuroblastoma cells were used as a model system, and bacterial endotoxin (Lipopolysaccharide, designated as LPS) was used as a stressor to trigger an inflammatory response. Cell morphology, viability, and cytokine ELISA assays including IL-6, MCP-1, and TNF-α, provided data suggesting that GHK-Cu peptide is a potent factor in enhancing resistance of neuronal and microglial cell lines to LPS-induced stress by reducing the expression of key inflammatory cytokines.Understanding the mechanisms by which GHK-Cu modulates inflammation can pave the way for the development of novel treatments targeting inflammation-associated diseases, aging mechanisms and various forms of dementia.

Saltwater estuaries can experience high turbidity levels due to river input and tidal influences. Turbidity is a measure of inorganic and organic particles suspended in the water column. Reduced light penetration due to higher turbidity levels can contribute to decreased levels of primary production and the introduction of harmful pathogens to the environment. Understanding the relationship between river discharge, tides and turbidity levels could lead to a better understanding of the causes of turbidity in estuaries such as Possession Sound, WA. I hypothesize that higher current velocity contributes to higher turbidity levels. I analyzed data from a moored Acoustic Doppler Current Profiler (ADCP) and a Conductivity, Temperature, Depth (CTD) sensor located in the Everett Marina. ADCP and turbidity data were collected every 15 minutes, 24 hours a day, from 2017 to 2021. Preliminary results suggest that higher current velocity correlates to higher turbidity levels. Future research looks to discover how river discharge, tides and seasonal variance play into turbidity spikes.

Over the last two decades, the threat of climate change has inspired significant research in the Salish Sea. Understanding trends and correlations between water temperature, dissolved oxygen (DO), and chlorophyll levels can help us understand how climate change and other anthropogenic activity has already affected the Salish Sea. My reseach focuses on seasonal and annual trends of water temperature, DO, and chlorophyll levels between 2019 and 2023 in Possession Sound, located in Everett, Washington. This longterm data-stream is generated by the Ocean Research College Academy, collected autonomously every 15 minutes by a pair of EXO sondes that are moored at Mount Baker Terminal and Everett Marina. My goal is to understand the relationship between water temperature, DO, and chlorophyll seasonally and historical trends over multiple years in Possession Sound. Preliminary figures and outside research have shown fairly consistent seasonal cycles for temperature and chlorophyll. DO trends are not as clear and data suggest significant variation is occurring within a short time frame. Future reseach may include comparing river discharge data to water chemistry data, however a more comprehensive understanding of specific inputs to the Snohomish River system is needed to draw solid conclusions about the affects of climate change.

The US education system is a tool used to push the dominant Anglo-American cultures among immigrants and other minoritized cultures within the United States. With their proximity to the US border and historical events, Mexicans living in the United States have faced subjugation and discrimination from the Texas Revolution to the anti-immigrant policies and rhetoric; these educational practices have targeted Mexicans for almost two centuries. This causes a conflict of cultural identity for Mexican youths living in the United States, as they grow up within multiple social spheres that consider them too American to be Mexican yet too Mexican to be American. This conflict of identity has caused multigenerational trauma and is only made worse by the discrimination from the media and the bias of the schools, as these students are forced to look elsewhere to discover their history, such as family or the community. My research study examines the value of ethnic studies and bilingual education practices and how they not only empower these students but gives them the motivation to succeed within an academic setting. This research is based on interviews that I have conducted with Mexican Americans who have experienced the education system during different years, ranging from the 60’s to the early 2000’s. Furthermore, I examine the autobiography of a prominent Mexican American scholar as I draw scholarship on ethnic studies and bilingual education, criticizing the current education system while offering solutions to address those critiques. Through the interviews I conducted, I found that the people who were most connected to their heritage and the Spanish language, not only experienced more success academically, but were also happier, indicating the need for ethnic and bilingual studies within the K-12 curricula.

Understanding human mobility based on location data from smartphones and other digital accessories has become a fundamental part of urban and environmental planning in cities. Through collection of these geo-traces, it has become possible for the scientific community and policy-makers to model citizens’ daily mobility patterns. Because of privacy issues, collection of location based data is rare, sparse and infrequent. To this end generative mobility models are used to create synthetic data. Because this data can be used in big decisions such as resource allocation and planning, if the data is skewed towards privileged groups, existing social and structural inequities can be exacerbated. Therefore, a critical concern that arises is the extent to which such synthetic data is fair and inclusive. Our goal is to create tools that measure whether socioeconomic conditions and geographical location affect individual and group trajectory predictions made by generative models. Using Gravity, Deep Gravity, and other models to generate mobility flow dataframes, we layered census data onto the flow dataframes by census tract to analyze the high income areas against lower income areas. We used this analysis to establish and implement a set of fairness metrics for mobility datasets and models in a python package that’s distribution could identify skewed modality data and hopefully influence other researchers to measure fairness in their generative models.

In this research project, we delved into the realm of gate-based quantum computation with a focus on qudit-based quantum computation. In the era of Noisy Intermediate-Scale Quantum (NISQ) computation, there are many avenues for physical implementations of qudits, such as trapped ions, superconducting circuits, and photonic systems. We primarily studied trapped ion qudit-based computation, investigating the notion of universality and how arbitrary gate operations can be simulated by experimentally realizable transformations in such systems. More quantitatively, we analyzed the fidelity under the assumptions of rotation angle errors in trapped ion implementations of quantum gates. We proved several lower bounds for various connectivity graph designs applicable to the 5-level calcium ion under this model of assumptions. Our techniques also generalize to physical systems with more than 5 levels. Currently, our attention is directed toward understanding the impact of entanglement on the aforementioned dynamics and studying the notion of universality for multi-qudit systems. A related question we are trying to answer is how qubit circuits can be converted into qudit circuits to reduce a well-defined notion of "circuit complexity".

Nickel phosphide (Ni2P) nanoparticles have been gaining attention due to their ability to catalyze various clean energy-relevant reactions, e.g., the hydrogen evolution and carbon dioxide reduction reactions; however, Ni2P has been known to corrode in aqueous electrolytes. Studies have indicated that nickel phosphide alloys have shown a small amount of oxidation to nickel phosphate at oxidizing potentials or complete dissolution at more aggressively oxidizing potentials. However, understanding of the speciation and kinetics of oxidation is limited. Therefore, we aim to understand the corrosion mechanism of Ni2P in neutral buffered electrolyte; which we hypothesize to show significant conversion to nickel phosphate at oxidizing potentials. First, I synthesized colloidal Ni2P nanoparticles from NiCl2 and tris(diethylamino)phosphine [P(NEt2)3] in oleylamine. Techniques such as powder X-ray diffraction, transmission electron microscopy, and thermogravimetric analysis confirmed the formation of uniform 5 nm diameter nanoparticles. Next, we probed the electrochemical corrosion of Ni2P through anodic polarization and operando X-ray absorption spectroscopy (XAS). In order to prevent premature oxidation of Ni2P, all procedures were performed in an air-free environment which posed many challenges for the preparation of the electrochemical cells, especially the operando XAS cell. Finally, we found that Ni2P nanoparticles corrode upwards of 0.4 V vs RHE and can no longer be restored when anodically polarized beyond 0.6 V vs RHE. Future experiments will probe the corrosion of Ni2P in acidic and basic electrolytes. This study aims to understand how Ni2P can be used industrially to replace rare and expensive metals, such as platinum, as electrocatalysts to electrify the petrochemical industry and reduce greenhouse gas emissions.

Malaria, caused by parasites belonging to the genus Plasmodium, accounts for roughly 600,000 deaths per year, with the most vulnerable population being children under 5 years old. The current available malaria vaccines show limited effectiveness in children. After being deposited by the bite of an infected mosquito, Plasmodium travels through the bloodstream and invades liver hepatocytes, causing an asymptomatic infection. Within hepatocytes, Plasmodium multiplies until the hepatocyte bursts, in which they are released into the bloodstream to cause a symptomatic infection. To develop an effective vaccine for children, it is critical to understand the immune response to liver stage Plasmodium infection in children. However, our current understanding of immune responses in children compared to adults, specifically in the liver, is limited. During Plasmodium infection, CD8 T cells in the liver are able to confer sterilizing protection. The main goal of this study is to identify differences in the spatial location of immune cells in human liver tissue across ages. We are currently utilizing a combination of RNAscope and immunofluorescent assay (IFA) staining to visualize CD8αα+ T cells expressing the promyelocytic leukemia zinc finger (PLZF) transcription factor, which distinguish them from conventional CD8+ memory-like cells as innate-like T cells. These unconventional cells play a key role in autoimmune responses in the liver. We are doing further spatial analysis on Imaris to gather quantitative data on these samples. We hypothesize that children would express higher levels of CD8αα+ T cells expressing PLZF because they do not produce memory-like cells as well as adults, and thus lack an efficient response to infections. The results of this study will help us better understand the differences that age may cause in immune cell types and quantities, and how this can be used to develop a more effective malaria vaccine for children.

Each winter, the northeastern U.S. experiences powerful storms that cover cities in snow and ice, which result in millions of dollars in damage, halt travel, and disrupt essential services. Yet, the type, intensity, and distribution of precipitation is unique to each winter storm. This research project aims to provide a greater understanding of the precipitation properties and distribution in snowstorms, through focusing on a major winter storm that occurred over the Midwest on 17 February 2022 and was the target of a research flight conducted during the Investigation of Microphysics and Precipitation for Atlantic Coast-Threatening Snowstorms (IMPACTS) field campaign. Radar data collected during this research flight provides a unique perspective of the vertical cloud and precipitation structure, and numerical model fields provide the environmental context of the structures observed in the radar measurements. This storm had a frontal boundary, or a strong thermal contrast, that provided lift needed for the production of precipitation and had sub-freezing temperatures so that the precipitation fell as snow.This frontal boundary consisted of warm air originating from southern latitudes riding over colder air originating from northern latitudes. Analysis of the vertical cloud and precipitation structure from radar data and the in situ cloud particle measurements collected during the flight revealed that regions of higher reflectivity had larger particles and greater ice water content, compared to regions with lower reflectivity. The analysis also includes examining how the cloud particle properties are different depending on the origin of the air masses (from the north or south) that form the storm. By relating the temporal and spatial information regarding the air masses to the high-resolution radar and microphysics data collected by the IMPACTS airborne instruments, the results of this analysis will ultimately support increasing the accuracy of snow prediction.

Ferrate is an effective technology for water treatment applications because of its capabilities as an oxidant, coagulant, and disinfectant. Furthermore, ferrate is an environmentally benign chemical derived from a ubiquitous mineral on the Earth’s surface. However, ferrate rapid reduction to ferric species reduces its oxidation capacity. Ferrate-coated sand has been proposed as a better deployable method for ferrate in water treatment applications. Sand has a high composition (>80%) of silica (SiO₂) which has been demonstrated to stabilize ferrate reactivity and increase its oxidation capacity. A previous study on the treatment of phenol, a common surface water contaminant, showed that ferrate-coated sand was better at degrading phenol than ferrate only (in the absence of sand). However, the study was conducted in pure water matrices. Here, we are evaluating the oxidation of phenol by ferrate-coated sand in the presence of effluent organic matter and trace metals (i.e. copper). Organic matter is ubiquitous in the environment and can impact contaminant remediation efficiency. Studies have detected trace metals in surface waters which can pose environmental and health risks. Through batch tests, we observed that effluent organic matter hinders the stability of the ferrate-coated media and reduces its oxidation capacity. The results of this study will provide information about the ferrate-coated sand reactivity and capacity for the treatment of complex water matrices.

Inhalation toxicology is a rising field of study as respirable toxicants become increasingly prevalent in our environment. Our research focuses on commonly inhaled toxicants: diesel exhaust (DE) and electronic cigarette aerosols (e-cig). Exposure to traffic-related air pollution and the use of e-cigs has rapidly increased, yet molecular pathways and health effects, and innate factors that impact health outcomes, remain largely unexplored. To assess cardiometabolic and neurodegenerative effects of DE, we exposed male and female mice (low-density lipoprotein receptor knockout, Ldlr KO) to filtered air or freshly generated DE for 18 weeks while fed a high-fat or Chow diet. We then conducted Object-Recognition and Object-Location Memory neurobehavioral tests to assess cognition, specifically hippocampus-independent recognition memory and hippocampus-dependent spatial memory and discrimination, respectively. We sacrificed mice and harvested brain, liver, and lung tissue for histopathological staining and biochemical measurements, including 3-nitrotyrosine, a biomarker of oxidative stress, via Western blot. To assess cardiopulmonary effects of e-cig aerosols, we exposed different mouse strains to acute (5 days) and chronic (3 months) e-cig aerosols with and without nicotine. We then harvested lung tissue and quantified glutathione (reduced and oxidized), an antioxidant and essential nucleophilic scavenger of electrophiles, via high-pressure liquid chromatography; and protein 3-nitrotyrosine. Statistical analyses of all the results obtained were carried out using R. Initial results revealed sex differences in biomarker levels between control and exposed mice. We plan to expand analyses by measuring an additional biomarker of oxidative stress, 8-oxo-dG. Additionally, we will quantify heavy metal accumulation in liver and brain in DE-exposed mice, along with metabolites of carcinogens such as acrolein in e-cig exposed mice. Forthcoming measurements will provide a more comprehensive understanding of biological responses to exposures and elucidate potential health implications. Our research in inhaled toxicants helps reveal critical insights for emerging public health challenges.

Science is rapidly evolving, yet its advances do not enter classrooms at the same rate. Systems Education Experiences (SEE) is a program in the Baliga Lab at the Institute for Systems Biology (ISB) that accelerates the transfer of scientific knowledge and practices to classrooms. One active area of Baliga Lab research is elucidating the level of resilience organisms have, when faced with complex environmental changes. My role is to design laboratory experiments that investigate this with the model organism Halobacterium salinarum (Halo) and to connect this to broader rules governing natural systems for use in high school classrooms. My first experiment probes the resiliency of Halo with the introduction of a combination of stressors (salt and hydrogen peroxide) and its recovery after population collapse. The second measures the long term phenotypic changes in the population. I wanted to see if after being exposed to a new environment if there was an advantage to having gas vesicles and if it is an irreversible trait that allows Halo to be resilient across a variety of environmental conditions. This relates to broadly applicable rules governing resilience across many systems. This project serves as a model for how all organisms respond to stress. Combinations of stressors in human lives can make us less resilient. However, strategies to quickly prepare, respond, and react can improve outcomes for individuals and the overall population. This project connects to a goal of K-12 science education which is to not just teach academic concepts but to equip students with knowledge that can be applied to all parts of life. Our knowledge on the mechanisms that control how organisms respond to stress is extremely limited. By understanding the biological stress response we can promote resilience in the earth's most vulnerable systems in the wake of climate change.

Per- and poly-fluoroalkyl substances (PFAS) are colloquially known as “forever chemicals” due to their long-lasting chemical characteristics that allow them to persist in nature. Specifically, their man-made carbon-fluorine bonds are extremely durable which makes them valuable in coating non-stick cookware and waterproof materials. These compounds are so indestructible that they accumulate in waterways and are eventually found in animal tissue. Firefighting foam is the most prominent source of PFAS pollution in waterways, which can accumulate in shellfish such as mussels, which humans often consume and can potentially lead to cancer formation. However, it remains unclear how much PFAS are actually in shellfish in Washington State. Using liquid chromatography tandem mass spectrometry (LCMSMS), we will analyze the amount of PFAS in homogenized mussel tissue samples collected from many different sites within the Puget Sound and surrounding waterways. PFAS levels have not been significantly monitored in shellfish in Washington State, this novel research which will provide valuable insight on the potential bioaccumulation of these compounds in various marine organisms and potentially find associations between the proximity to centers of high population density and PFAS concentration.

Serratia marcescens is an opportunistic pathogen that can infect multiple human organs and is responsible for many healthcare-associated infections. It has a mortality risk of up to 58% and early diagnosis is crucial for timely treatment. S. marcescens secretes a unique restriction endonuclease, which has been recognized as a virulent factor and thus can be used as a diagnostic biomarker. To detect this restriction enzyme biomarker, I have designed and investigated a model system using novel restriction endonuclease mediated DNA strand displacement (resDSD), adapted from the enzyme-free DNA strand displacement (DSD) reaction. In a typical DSD circuit, a DNA input “invading” strand invades a duplex DNA substrate, replacing the previous incumbent strand through branch migration to reveal a fluorescence molecule. In contrast, my resDSD circuit employs a restriction endonuclease enzyme input. In my design, the toehold region is concealed and blocked by a strand that the restriction enzyme can cleave. Once cleaved, the toehold region is exposed, allowing an invading strand to hybridize and initiate the DSD cascade. This study represents the first demonstration of the resDSD system. To validate the concept, I used commercially-available restriction endonuclease BamHi instead of S marcescens’ endonuclease. I will also modify E. coli 5-alpha competent strain (c2987h) to secrete BamHi in place of S. marcescens. By investigating this innovative resDSD approach, I aim to establish a reliable method for detecting bacterium such as S. marcescens based on its secretion of the restriction endonuclease. Such a diagnostic tool could contribute to early detection and prompt treatment of infection caused by this opportunistic pathogen or similar pathogens in healthcare settings.

In a recent breakthrough, bullvalene, renowned for its “shape-shifting” molecular nature with over 1.2 million degenerate isomers, has been successfully integrated into polymer backbones. This integration addresses challenges in solubility and thermal properties crucial for tailoring polymers used in manufacturing diverse products ranging from phone screens to organic solar cells. This project aims to deepen our understanding of the interplay between fluxionality and thermal properties by examining the thermal stability of small molecule bullvalene models. Through extrapolating insights for bullvalene-substituted polymers, our research seeks to contribute to the advancement of the development of advanced materials suited for varying thermal conditions. We synthesized small molecule bullvalenes to mimic polymer chains, subjecting them to diimide reduction to suppress fluxionality before comparison with their fluxional counterparts. Their thermal properties were characterized using Thermogravimetric Analysis (TGA) and Differential Scanning Calorimetry (DSC). Key findings reveal a decrease in glass transition temperature upon reduction of bullvalene, highlighting the impact of fluxionality on thermal stability. Future work will delve deeper into exploring the thermal properties of small molecule models, providing insights into polymer behavior. We anticipate bullvalene as an internal plasticizer capable of modulating rigidity, solubility, and thermal properties within different classes of polymers, thus enabling a more efficient and cost-effective large-scale industrial production of a wide array of polymeric materials.

Mild cognitive decline with increasing age commonly affects millions of people beginning as early as middle age. It can progress to more severe levels of cognitive impairment including dementia associated with Alzheimer’s disease and irreversible brain damage with eventual death. Therefore, treatment before the onset of dementia would be the most effective way to prevent the devastating loss of normal daily living and death as an outcome. However, few drugs have been shown to be successful in preventing the progression of mild cognitive decline to more severe cognitive dysfunction. One candidate drug we are testing is the naturally occurring peptide GHK (glycyl-L-histidyl-L-lysine), which is known to have regenerative and anti-inflammatory properties in the brain. In order to test this peptide, we treated middle-aged male and female C57BL/6 mice with GHK as a copper complex (GHK-Cu) or saline using a novel intranasal atomizer daily for two months. We then conducted behavioral tests to assess learning and memory, and then mice were euthanized to collect brain samples for special stains for biomarkers of brain aging including the presence of non-neuronal microglia, brain-derived neurotrophic factor, and synapse integrity. Our preliminary observations from behavioral tests show that mice treated with intranasal GHK-Cu performed better in learning and memory tests than mice treated with intranasal saline. The brain aging biomarker tests I completed show that the neuropathology markers associated with aging are less severe in mice treated with intranasal GHK-Cu. Such a positive outcome provides the rationale to do further preclinical testing as a way to move toward clinical studies designed to treat mild cognitive decline and prevent the devastating progression of irreversible neurodegeneration.

Ford Madox Brown's 1865 painting Work depicts a group of laborers digging a sewage line on a busy London street. Widely considered the most important painting of Ford Madox Brown’s career, Work is also one of the most radical paintings of the pre-Raphaelite period. In this presentation, I will argue that the dignity afforded to manual laborers in Work establishes a pride in British identity and a push for social reform in line with Christian socialist values. I will support this argument by analyzing the painting's composition, use of symbolism, and historical context. In the painting’s composition and content, the work of William Hogarth and the Pre-Raphaelite Brotherhood reveal themselves as influences on Brown’s art and politics. I will also discuss how other scholars have interpreted Work’s symbolism and sociopolitical context, especially the writings of John A. Walker and Jenny Plastow. Through the painting and Brown’s accompanying catalog, Work instructs the importance of education and Christian values to social reform. Work is a complex and historically significant painting that celebrates labor during a turbulent time in England’s history. This paper will strengthen understanding of Work’s political rhetoric and symbolism, and in doing so illuminate the context of its creation.

Mirrors have been a contextually important part of architecture and painting since before the Renaissance, but during the Baroque and leading into the Rococo, mirrors became a central aspect to power dynamics in built environments and were utilized as a tool to control self-representations. This paper investigates the ways in which mirrors were activated in interior architecture and paintings, as well as how they underscored the “soft” power of elite women during the Rococo period by analyzing François Boucher’s Madame de Pompadour (1756) as an example of mirrors and expressions of the self and purposeful manifestations of “soft” power. I place Boucher’s painting in the context of contemporary interior spaces, such as the Versailles’ Hall of Mirrors (1678) which illustrates “hard” political power and the Salon de la Princesse room in Paris’ Hôtel de Soubise (1732) which communicates a softer power, as examples to how mirrors enforce performative power in spaces. I explain how power dynamics are reinforced through interior spaces paying special attention to use of space, decoration/motifs, and the location/orientation of the interior architecture and design and exploring Madame de Pompadour’s use of mirrors to subtly control a narrative that elevated her status in the French court.
The implications of this work recontextualize the presence of mirrors in paintings of the Rococo period and give a new view on the roots of the subtly psychological implications of mirrors within the built environment. Mirrors as a topic of specific study within aristocratic interiors lacks robust research, my work aims to fill part of this gap by seeking to understand how mirrors established themselves within architecture through power preformances and psychology.

The human genome is associated with numerous variations, some of which can be pathogenic. Any variations larger than 50 base pairs (bp) are considered structural variants (SVs), and SVs impacting copy number of the genome are termed copy number variants (CNVs). By studying CNVs, we can understand the underlying mechanisms of damage and repair within DNA, which can help work towards prevention and cure in other fields, such as cancer genomics. My project investigates a CNV on chromosome 2 of a pediatric patient, who presents with tetralogy of Fallot, global development delay, and multiple other congenital anomalies. Using array comparative genomics hybridization (aCGH), we identified a 3.2 megabase (Mb) complex genomic rearrangement (CGR) spanning the 2q31 region of the proband’s chromosome 2. Detailed analysis of the short-read whole genome sequencing (WGS) allowed us to locate the exact coordinates of each junction, or the beginning and end points of each extra copy. PacBio long-read genome sequencing and optical genome mapping detected the same junctions and facilitated confirmation of the overall structure. The CGR can be characterized as a duplication-triplication-duplication-triplication-duplication (DUP-TRP-DUP-TRP-DUP), meaning this segment of the genome contains a segment of alternating 1 and 2 extra copies of this region. The CGR is de novo, or not inherited from the proband’s parents. Due to the nature of this variant, it is likely to be impacting the phenotype of our patient. To establish a genotype-phenotype correlation, I did a literature review of patients with overlapping CGRs, comparing their phenotypes to our proband, as well as reviewing any known disease-associated genes in the region using the online catalog of human genes and genetic disorders (OMIM). Patient and disease comparison revealed the extreme rarity of our patient’s CGR, leading us to believe the phenotype of the proband results from impact of multiple genes in the affected region.

Current research on substance use suggests a positive correlation between emotion dysregulation and cannabis misuse or cannabis use disorders (CUD). This study aims to identify which specific facets of emotion dysregulation increase CUD symptom severity. While previous studies using the Difficulties in Emotion Regulation Scale (DERS) have linked overall composite scores of emotion dysregulation to CUD, there is a gap in the understanding of how individual DERS subscales relate to CUD, which limits our ability to develop targeted interventions. Young adults (N=68, Mage=23.7 years, SD=3.05, 54.4% female, 63.2% White) who reported using cannabis 2-3x/week or more in the past month completed measures of emotion dysregulation (DERS) and CUD (Cannabis Use Disorder Identification Test; CUDIT). To test associations between the 6 DERS subscales and CUDIT total score, we will first conduct bivariate correlations. If significant associations are found, we will conduct a multiple linear regression model to test which subscales best predict CUDIT total score. We hypothesize a moderate-to-strong correlation between the DERS and CUDIT scores, with Nonacceptance and Impulse control demonstrating stronger correlations. We also hypothesize that Nonacceptance and Impulse control subscales will most strongly predict CUDIT total scores. Results from the present study could help identify which of the emotion dysregulation subtypes should be targeted in future prevention and intervention efforts for young adults. If these findings are supported, additional efforts may want to teach skills to increase acceptance of emotional responses and improve impulse control. The proposed study is an important step in the treatment of cannabis misuse and CUDs as we will be able to narrow our aim toward isolated treatments to improve the livelihood of those involved.

Bacterial metabolic engineering holds great promise for applications in medicinal, industrial, and climate technologies. A key element of metabolic engineering is the integration of non-native genes and pathways into microorganisms. However, the current state of technology is inefficient and time-intensive. Large cargo sizes of above 2-4 kilobases (kb) reduce integration efficiency, preventing entire metabolic pathways from being integrated into an organism at once. To maintain large heterologous genes and pathways in an organism’s genome, a seamless method for genomic integrations is necessary. A recent breakthrough in genetic engineering uses transposase enzymes and clustered regularly interspaced short palindromic repeat (CRISPR) machinery for more efficient and generalizable genomic integrations. Guided by RNA elements, this genomic integration system improves target site specificity and selection, as well as multiplexing capability (the direct insertion of genes at multiple genomic sites simultaneously). This system is expected to handle cargo insertions of around 10kb, meaning entire metabolic pathways can be implemented into a genome. My research aims to utilize this tool to demonstrate metabolic pathway integrations in non-model organisms and multiplexed knockouts for improved organism engineering. I plan to insert a fluorescent protein in 3 different industrially relevant organisms to demonstrate the generalizability of this genetic engineering toolkit. Additionally, I intend to establish multiplexing capability in multiple organisms by integrating the same genetic cargo at multiple sites using an array of guide RNAs, and determined results using polymerase chain reaction, gel electrophoresis, and DNA sequencing. Finally, using analytical methods such as liquid chromatography-mass spectrometry, I will measure the metabolic effects from integration of complete pathways. I will present the results of ongoing progress for all of the outlined tasks. Overall, my research on CRISPR RNA-guided transposases will enable the targeted, efficient integration of novel genes and pathways in bacteria, leading to significant advancements in therapeutics, biomanufacturing, and sustainable chemical conversion.

Alzheimer's Disease (AD) is clinically characterized as a predominantly amnestic (memory impairment) syndrome at presentation that progresses to affect other cognitive domains. AD is pathologically defined by the presence of amyloid plaques and neurofibrillary tangles of hyperphosphorylated tau (pTau) in stereotypical brain regions. AD shows clinical and pathological diversity, including non-amnestic subtypes, severity of tau pathology across brain regions, and co-pathologies such as aggregates of hyper-phosphorylated transactive response DNA-binding protein 43 (pTDP-43). This study aims to examine the association between pTau and pTDP-43 using new highly quantitative approaches. By examining the combined pathology, we hope to identify patterns of pTau related to pTDP-43 across the different clinical and pathologic subtypes. The University of Washington Alzheimer's Disease Research Center clinical core autopsy cohort was characterized and subdivided into amnestic and non-amnestic syndrome subtypes. The subjects were analyzed to identify the prevalence of pTDP-43 and its correlation to the subject's cognitive data and patterns of progression. This analysis was used to select a subset of 29 cases with non-amnestic dementia and a matched subset with an amnestic subtype for more in-depth neuropathological and molecular profiling of several brain regions. Using the HALO platform, I generated quantitative measures of pTau in the frontal, temporal, and parietal cortex, as well as the hippocampus. The integration of these findings aims to understand how pTDP-43 pathology influences tau distribution based on clinical presentation These results will allow us to select a small set of cases for further work that will include using NanoString GeoMx Digital Spatial Profiling to identify potential pathways relevant to the association between pTDP-43 and pTau severity concerning mechanisms of clinical and pathologic heterogeneity in AD. These insights will allow for further research of these pathways to determine their biological relevance and ways to mitigate their effects.

The heart is one of the most mechanically active organs in the body. In a mechanism known as the “Bainbridge Reflex”, the heart rate accelerates in response to the mechanical stretch induced by the increase in venous return. The cardiac pacemaker controls heart rate, and while stretch-activated channels have been identified in cardiac tissue, their molecular identity remains unknown. We hypothesize that PIEZO channels are the molecular determinant of the stretch-dependent heart rate acceleration responsible for the Bainbridge reflex. Using quantitative polymerase chain reaction (qPCR), we assessed the presence of Piezo1 and Piezo2 transcripts in the pacemaker, atrium, and ventricle of the mouse heart. Our findings revealed that both Piezo1 and Piezo2 are present in the three regions with significantly higher expression in the pacemaker and atria. Combining immunohystochemistry, tissue clearing, and super-resolution microscopy, we analyzed the distribution of Piezo1 and Piezo2 in mouse pacemaker explants. Our results show that Piezo2 is uniformly expressed in the pacemaker and surrounding atrial tissue, whereas Piezo1 exhibits higher expression levels outside the pacemaker. These results were further confirmed at the single-cell level, with immunostaining of Piezo1 and Piezo2 in isolated pacemaker cells (HCN4+) and transitional cells (HCN4-). We observed similar expression levels of Piezo2 in both cell types and increased Piezo1 expression in transitional cells. In addition, we observed distinct localization patterns for Piezo1 and Piezo2 at the subcellular level. Piezo1 predominantly localizes to the sarcolemma, while Piezo2 exhibits a striated distribution that colocalizes alternately with both the Z- and the M- line of the sarcomere. Given this pattern, half of the Piezo2 bands colocalize with the RyR. These results set the starting point to evaluate the functional role of PIEZO channels in the cardiac pacemaker.

The cerebellum, which accounts for 10% of human brain volume, contains approximately 80% of all brain neurons and has long been understudied relative to the cerebral cortex. During development, the cerebellar ventricular zone (VZ) is a transient progenitor zone which generates all cerebellar GABAergic (inhibitory) neurons. This includes Purkinje cells (PCs) and PAX2+ interneuronal progenitors (PIPs). While the mouse cerebellar VZ has been relatively well characterized, there is limited knowledge about its human counterpart. In this study, we investigated organization of progenitors and birth of neurons derived from the human cerebellar VZ, uncovering several notable features. Specifically, I conducted image analysis in conjunction with immunohistology (IHC) assays to (1) identify different cell types and marker gene expression across developmental stages and (2) quantify proliferative cells at different stages of development. We found that a substantial number of PCs are generated during embryonic development, particularly within the first 50 post-conception days, within a compact two-week timeframe. This occurs well before the onset of cerebral neurogenesis, with interneuronal differentiation commencing during early fetal development. Neuronal differentiation predominantly occurs from the inner and outer subventricular zones (SVZ), zones which are completely absent in the mouse developing cerebellum, with the initial wave of differentiation occurring from the outer SVZ. Significantly, relative to mice, we observed variations in migratory patterns and the quantity of PC plates, including a subset of PCs that retain the expression of cell cycle genes several weeks after these cells leave progenitor zones. This work extends our knowledge of human-specific birth and organization of progenitors and neurons originating from the ventricular zone and cellular and molecular differences in ventricular zone progenitors, Purkinje cells, and PIPs across different developmental ages.