Marine sediments are a critical carbon reservoir, locking both inorganic and organic carbon in sediments for thousands to millions of years. This carbon is released in part through the production of methane at methane seeps, places where methane gas is emitted from the seafloor. In this study, I characterized source differences and quantified the amount of inorganic and organic carbon stored in Puget Sound sediments at a methane seep site. A multicorer collected sediment samples at two sites: one at the Alki Point methane vent field and a control site within the Main Basin of Puget Sound. The sediment cores were subsampled in 2 cm sections downcore and stored for later analysis. Analyses included physical parameters (grain size, percent loss on ignition (% LOI), and 210Pb sediment dating) and geochemical parameters (Total Organic Carbon (TOC), Total Carbon (TC), del 13C TOC, del 13C TC). Both sites were silt-dominated (Alki = 37 microns, Control = 30 microns), with a well-mixed layer 15 cm thick. Organic content (% LOI) was high at both sites (Alki = 7.5%, Control = 6.9%). Likewise, TOC and TC showed trends of increased organic material at the methane seep site. Isotope data indicate that methane-influenced sites have lighter del 13C. Given the amount of carbon they store and the potential for these reservoirs to be disturbed by bottom trawling, deep sea mining, and other invasive human activities, understanding how carbon is cycled through marine sediments is critical for preserving these reservoirs and adequately factoring their role in the carbon cycle into global climate models.

In this study I examined the spatial distribution and concentration of various xenobiotic contaminants in the waters of the equatorial Pacific near American Samoa. Using state-of-the-art mass spectral techniques, I determined if pollutant loads increase near urban environments, as well as how individual manmade contaminants present spatially. I collected water samples in the region around American Samoa, then extracted pollutant chemicals from the sample via solid phase extraction using hydrophilic-lipophilic balance (HLB) cartridges and performed analysis of chemical concentrations using gas chromatography-mass spectrometry (GC-MS). This was followed by a detailed spatial comparison of the chemical pollutants. Industrial anthropogenic pollutants such as benzyl butyl phthalate and n-Tridecane were confidently found near the airport and fuel depot in American Samoa. Spatially, compound abundance was generally found to decrease moving away from urban environments. Assessing the spatial distribution of xenobiotic pollutants in relation to urban environments can help improve current understanding of how much manmade pollution is entering and persisting in the ocean, which can endanger ecosystems and human health.

Coccidioidomycosis, also known as Valley Fever (VF) is caused by the fungus Coccidioides. Pigtail macaques (PTMs) bred at the Washington National Primate Research Center (WaNPRC) in Mesa, AZ are naturally infected with Coccidioides and are similar to humans in their physiology, symptoms, and immune responses. Populations with a weakened immune system, notably older individuals, are at risk for severe complications from infection. Additionally, there is evidence that males have a higher incidence of VF than females in endemic areas. I characterized the immune responses in a PTM model across age and sex to better understand how VF affects the immune response of these populations. Forty-two PTMs (2.25-19.24 years, 3.66-18.29 kg, 37 female, 5 male) at the WaNPRC were sampled for blood. The frequencies of immune cell subsets in whole blood were characterized by flow cytometry and compared for significant differences based on age and sex. I analyzed sex-based differences with Brown-Forsythe and Welch ANOVA t-tests and found no statistically significant differences. For age-based differences, we used a simple linear regression to analyze differences by age in immune cell subsets. We found that old PTMs (10.07-19.24 years) have higher activation of CD8+ T cells, myeloid dendritic cells, intermediate monocytes, and higher frequency of γΔ T cells and CD4+ γΔ T cells than young PTMs (2.25-9.69 years). Young PTMs have a higher frequency of CD45+ granulocytes, PD-1 High CD8+ T cells, plasmacytoid dendritic cells, and NK cells. By correlating older PTMs with higher immune cell activation, and younger PTMs with higher immune cell frequency, we have a better understanding of how a vaccine or treatment could be developed to support older individuals, who are at greater risk of severe infection.

In the pursuit of higher density integrated circuits and the increased use of stacked die chips, the importance of wafer die preparation plays a crucial role in the semiconductor manufacturing process, turning silicon wafers into individual dies. An important step of die preparation is wafer backgrinding, which enables wafers to be thinned significantly, thus allowing for higher density packaging of chips. Backgrinding occurs near the end of a chip’s manufacturing process, thus it is important to quantify the surface quality of the wafers after the grinding process to avoid potential damage to the finished product. The most relevant process parameters include chuck speed, wheel speed and vertical feed rate. By systematically varying the process parameters and analyzing their impact on key output metrics including surface roughness, thickness variation and surface damage allows us to study each parameter in greater detail. We expect the tool to preform best when following the default given recipes supplied by the tool manufacturer, however to better understand the affect of each parameter we must vary each variable in a controlled manner. By performing a parameter-based design of experiment (DOE) we can study how each parameter affects our key metrics. At the Washington Nanofabrication Facility, where this project will take place, there are a variety of different processes and products all with different requirements. Understanding the relationship that each parameter of grinding has on the surface of the wafer allows us to develop different recipes for specific use cases depending on the requirements of each process.

Phagocytosis is a primary function of macrophages that facilitates the elimination of pathogens and the clearance of endogenous and exogenous debris from tissues. This function can become impaired by aging or exposure to environmental toxicants, which may contribute to impaired immune responses and wound healing. To determine the involvement of macrophage phagocytosis in different pathophysiological conditions, we developed an in vitro macrophage phagocytosis assay with lung macrophages and brain microglia from CD-1 mice (three male, three female). The tested groups included an untreated control group, a lipopolysaccharide (LPS)-treated positive control group to increase phagocytosis, a cytochalasin D-treated negative control group to inhibit phagocytosis, and an experimental pioglitazone-treated group to stimulate PPAR-g (nuclear hormone receptor and transcription factor that has been shown to stimulate phagocytosis). We used green fluorescent protein (GFP)-labeled dextran beads opsonized with serum to assess the phagocytotic abilities of the macrophages in each treatment group. We are currently analyzing data that will determine the percentage of macrophages that phagocytosed the beads (GFP+ macrophages) and the average number of beads phagocytosed among GFP+ macrophages per treatment. We predict that there will be fewer GFP+ macrophages in the cytochalasin D-treated group vs. controls, indicating that phagocytosis is properly inhibited. We predict that both LPS and the pioglitazone-treated macrophages will present more GFP uptake and GFP+ cells than the control. A comparison of pioglitazone and LPS uptake will indicate the relative efficacy of pioglitazone in enhancing phagocytosis. Because pioglitazone is thought to stimulate phagocytosis without causing a pro-inflammatory response like LPS does, pioglitazone treatment may be a way to improve the helpful functions of macrophages with impaired phagocytic functions, which can occur with aging or following exposures to environmental toxicants.

Human Immunodeficiency Virus 1 (HIV-1) is a lentivirus and the causative agent of Acquired Immunodeficiency Syndrome (AIDS). HIV encodes a viral protease, the function of which is required for viral replication. The host innate immune sensor CARD8 detects HIV protease activity, leading to inflammasome activation during HIV infection. Inflammasomes are cytosolic innate immune complexes that recruit Caspase-1 and lead to secretion of pro-inflammatory cytokines and lytic cell death. Humans encode a single CARD8 gene; however Old World Monkeys (OWMs), the hosts of Simian Immunodeficiency Viruses (SIVs) encode two copies of CARD8. The function of the OWM CARD8 is unknown. To characterize the function of OWM CARD8s, I cloned CARD8 from representative OWMs and tested their responses to HIV and SIV protease in two ways. First, I determined if OWM CARD8s are capable of forming an inflammasome in response to HIV-1, a panel of SIVs, or the broad CARD8 activator VbP. I found that most, but not all, OWM CARD8s are functional but not responsive to HIV-1/SIVs. Human CARD8 senses HIV-1 through viral protease cleavage of its N-terminus. To determine if this lack of response of OWM CARD8s is due to the absence of viral protease cleavage, I will next perform western blots comparing human and OWM CARD8 proteolysis in the presence of absence of HIV/SIVs. My data suggests that the species-specific differences in CARD8 alters its capacity to detect viral proteases. We speculate that the absence of HIV-like pathogenesis in OWMs with endemic SIV may in part be due to the absence of CARD8 inflammasome activation to SIV protease.

Elementary school educators are primary influences on children’s development by helping shape their behavior with peers and in the classroom. Employees in education are deferred to by their newer coworkers regarding student interactions and set precedents for students’ school environment. New and seasoned educators’ disciplinary practices greatly vary when addressing students exhibiting problematic behaviors which may differently affect student-instructor relationships. I use an existing dataset from a larger study testing the impact of a novel implementation strategy on the implementation of a universal social, emotional, and behavioral program in nine elementary schools from one district. Educator participants in this study completed a survey battery when starting and ending the school year and the district provided quarterly discipline records via a universal prevention program. The findings identify trends in student disciplinary actions between new (<5 yrs) and experienced (>5 yrs) instructors. Understanding the relationship between teacher tenure and the treatment of student misbehavior is crucial to demystifying the manifestation of poor student enrichment and hostile student-instructor relationships. These findings could suggest how differential disciplinary practices by educators based on their years of experience influence student learning.

The Allan Hill region of Antarctica has produced the oldest ice core samples ever recovered, which provide insights into Earth’s climate history prior to the existing 800,000 year ice core record. However, the highly disturbed nature of this ice complicates straightforward dating and interpretation. Understanding the scales of preserved climate records in this old ice will enable deeper insights into the variability of climate over the last 2 million years. Here I study a section of ice from ALHIC1901, an ice core recovered from the Allan Hills in 2019. This section has three parallel sets of water isotope measurements, and they all show a small but significant dip. However, the cause of this dip remains unclear. The goal of this study is to test whether this isotope change could be a glacial-interglacial transition preserved for 1.3 million years, or whether diffusion should have eliminated any climate signal. To investigate this question, I apply a simple water isotope diffusion model that takes as inputs temperature, an initial water isotope profile, and a thinning history, and provides as an output the resulting water isotope profile after a given number of years. I identify the range of possible temperature, thinning, and initial water isotope signals for this ice. I use these as inputs for the diffusion model, and compare the results to the ice core record to evaluate if the observed water isotope signal can be climatically driven. Constraining the cause of this water isotope signal will improve our understanding of fine scale paleoclimate proxy changes in the extremely old Allan Hills ice cores, enabling new insights into past climate variability.

Titanium dioxide is a compound that has been used in the realm of nanotechnologies for decades. Titanium dioxide is used as a protective and high-refractive index optical coating. It also has strong mechanical and chemical stability. This is also true of other ceramics throughout the Washington Nanofabrication Facility with compounds such as aluminum oxide, titanium nitride, and aluminum nitride. With this in mind, the goal is to explore the best conditions to reactively sputter titanium dioxide. Thus, I developed a series of experiments including a screening for significant factors, and a following set of experiments using previous results to find an optimum point. In order to produce titanium dioxide in a physical vapor deposition environment such as the sputter tool utilized, the chamber holding the designated surface was pumped down and exposed to a chamber filled with argon, whose function was to hit the target titanium and a percentage of oxygen designed to react with the titanium in order to form titanium dioxide. By generating experiments designed to better understand how titanium and oxygen would react within the sputter tool, there was an aim to better screen for factors and understand the surface composition of the titanium dioxide. The desired outcome of this research is to build a working titanium dioxide recipe that optimizes deposition. Based on preliminary testing, the ideal outcome is likely produced under low pressure and higher power conditions. Future goals may include uniformity and accuracy within titanium dioxide, but also with other materials. With the implementation of this recipe, which is both optimized for the deposition of the material as well as its applicability for the lab, other recipes utilizing similar methods are desired. With a working titanium dioxide recipe, titanium and aluminum nitride recipes can better be developed.
 

Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect, requiring patients to undergo multiple invasive cardiac procedures, including pulmonary valve replacement (PVR). However, with recent clinical advances, new tools are needed to optimize PVR timing. We believe noninvasively collected cardiopulmonary exercise testing (CPET) data can provide insight into a patient’s need for PVR. Specifically, we hypothesize that patients with a more severe stage of pulmonary valve dysfunction have a limited ability to increase their stroke volume during exercise, an abnormal response that can be assessed by analyzing the behavior of the oxygen pulse (O2-pulse) curve during CPET. A ‘flattening’ of this curve suggests impaired augmentation of stroke volume and potentially a more urgent need for PVR. This research aims to identify metrics that can characterize patterns in O2-pulse. Data were collected from 44 participants with TOF undergoing CPET PVR evaluation and 10 healthy individuals. To find a maximum O2-pulse, we fit a penalized bilinear regression model to this curve. We extracted 8 parameters to mathematically describe the O2-pulse curve, as well as 20 traditional CPET performance metrics. One important parameter that was calculated is the ‘lost area under the curve’ (LAUC), defined as the area under the two calculated regression lines over time subtracted from the area under the curve as determined if the first regression line were to continue on the same slope as is typically expected during a maximal CPET. This value captures both the change in slope and when participants transitioned from a steep increase in O2-pulse to a relatively flattened O2-pulse. The LAUC, among our other identified metrics, can potentially provide insight into the optimal timing of PVR in patients with TOF. Unsupervised machine learning may be a useful tool to characterize patterns in these metrics and search for clinically relevant patient phenotypes.

Western U.S. wildfires are a growing threat to human lives, societal infrastructure, and global climate. While it is well known that meteorological factors impact wildfire intensity and growth rate, quantitative relationships between meteorology and wildfire are scale-dependent. For example, a recent study evaluating all recently observed California wildfires found that explosive fire growth was strongly related to short periods of strong winds and dryness. However, that study used data from a global atmospheric reanalysis (which cannot resolve local winds). As such, even the strong relationships found between meteorology and wildfire growth may have been underestimated. Given the potential consequences involved in predicting and mitigating future wildfires, it is important to understand the real-world accuracy of previously determined fire-environment relationships. To do so, this project compares how local meteorological observations from Remote Automated Weather Stations (RAWS) differ from reanalysis observations during known wildfires. The seasonal and spatial variation in the different relationships is also evaluated. Analysis has shown that the RAWS network is dense enough to adequately represent conditions at each fire being examined. Early results indicate that RAWS and reanalyses have similarly timed wind events during the max growth period. These results are promising, as they indicate that global atmospheric reanalyses can be used as a proxy for ground observations in remote terrain when analyzing periods of extreme wildfire growth.

Protein kinases have been found to regulate cell processes such as cell growth and adaptive responses to the environment. Thus, they act as excellent targets for tuberculosis treatment. The Mycobacterium tuberculosis (Mtb) genome encodes 11 separate serine/threonine protein kinases (STPKs). One of those STPKs is PknF, which our lab has previously found to be associated with a survival deficit in Mtb. Since Mtb utilizes multiple carbon sources during its infection in vivo, my research project aims to test the effect of perturbing pknF expression levels on Mtb survival in different carbon source conditions. I grew an avirulent Mycobacterium tuberculosis (aMtb) strain that conditionally overexpresses pknF upon exposure to anhydrotetracycline (pknF OE) in different media formulations that provided different carbon sources: glycerol and acetate. I measured colony-forming units (CFU) to quantify aMtb survival in these different growth conditions. I compared survival measurements of the pknF OE strain relative to an empty vector control strain. I found that the pknF OE strain showed a survival deficit by day 7 in both media conditions, with glycerol showing a higher survival deficit compared to acetate. The extent of the survival deficit seems to be affected by which carbon source is provided by the media. Previous literature has linked pknF to the regulation of glucose transport and phosphorylation of glucose catabolism-associated enzymes in the citric acid cycle. Based on this, we hypothesize that these processes may be involved with pknF's observed survival deficit in different media. In follow-up experiments, we plan to investigate how perturbing glucose transport or catabolism influences pknF's survival deficit. These findings can be used to inform future studies on pknF as a potential target for tuberculosis treatment during infection.