Malaria affects close to half of the world’s population and kills nearly 3,000 children every day. Due to the rapid rise in drug-resistant parasites and insecticide-resistant mosquitoes, we need a vaccine now more than ever before. Malaria is caused when a mosquito infected with the parasite, Plasmodium, bites and injects thousands of sporozoites that infect the liver and replicate without causing symptoms for 7-10 days. After egressing out of the liver, the parasites infect red blood cells and can get taken up by another mosquito during a bite perpetuating disease transmission. In the blood stage, the population of parasites in circulation can reach the billions, symptoms occur, and disease complications can result in death. Our strategy is to develop a pre-erythrocytic malaria vaccine by creating a genetically attenuated parasite (GAP) strain. If infection could be stopped before the parasites break through into the proliferative blood stage, both the disease and transmission could be prevented. Our goal is to make a late-liver stage arresting Plasmodium falciparum GAP conferring a broad antigenic diversity. Based on late-liver stage transcriptomics, we identified genes that could be candidates for knockout. One of these genes is mei2 of which my team already generated a CRISPR/Cas9-mediated knockout. We conducted an analysis of invasion kinetics via a growth competition assay between wild-type and mei2- parasites to ensure the gene deletion did not reduce viability. We proceeded by exposing our human-liver chimeric mice to infectious mei2- sporozoites, tracked liver stage development, and looked for breakthrough into the blood stage as an indication of incomplete attenuation. We then built on the previously established role of mei2 as an RNA binding protein by studying the subcellular localization of Pf mei2 to better understand the effect it has on liver-stage development.

The Methow Valley is a community located in Okanogan County, WA that has experienced wildfires in 4 of the past 5 years. The Methow Valley Clean Air Project (MVCAP) is a local volunteer group that promotes air quality awareness through outreach and programming. MVCAP’s Purple Air Network was designed to provide access to spatial air quality information to help community members make decisions about protective actions, to identify relatively clean air spaces, and to serve as a public health invervention for wildfire smoke. In collaboration with MVCAP, we worked to install a network of 20 purple air monitors in the summer of 2018. The monitors were placed in homes of “Clean Air Ambassadors” who committed to maintain and promote the monitor. For calibration, each monitor was placed according to federal guidelines and two were collocated with nephelometers maintained by Washington Department of Ecology. During the summer of 2018, two wildfires burned nearby which allowed the monitors to be utilized in a wildfire smoke event. The data from the monitors was downloaded and compared to the nephelometer data using linear regression. I worked to establish a correction factor by analyzing the data and found that the Purple Air monitor over reported the PM2.5 concentration by a factor of 0.53 and even more at high concentrations. The network proved the importance of high spatial concentration monitoring by capturing the air quality variation. In some areas, the air quality was good while in others it was hazardous. Having the network is a tool for individuals to know what the air quality is near their homes and other places in their community. It allowed individuals to access local air quality data and make choices about poor air quality. The next step for MVCAP is designing an online interface that applies the correction factor directly to accurately communicate risk.

Whispering Gallery Mode (WGM) sensors have unprecedented sensitivity in the optical detection of label-free biomolecules. These sensors can detect surface adsorption and have been used to detect single molecule adsorption and interaction processes. By observing resonance shifts during molecular interactions, WGM sensors can characterize a molecule’s surface adsorption. The goal of this project is to develop a robust WGM dip sensor array controlled by a three-axis stage in order to perform high-throughput characterization of peptide binding and adsorption within a 96-well plate format. The peak of spectral absorbance is the WGM resonance, and as this changes with surface adsorption we measured a spectral shift. Using this spectral shift in combination with the known concentration of our peptide species, we determined binding kinetics. The WGM sensor was used to characterize different peptide sequences to further understand the effects of peptide mutations on binding kinetics. A single microsphere resonator was used as proof of principle and will eventually be adapted to an array of eight WGM microsphere resonators to generate large amounts of data. This high throughput approach will provide the much needed large amount of quality data that is necessary for the development and adaptation of machine learning and applied statistical analysis algorithms toward the eventual development of artificial intelligence platforms in material science. The project is supported by NSF-DMREF through the Materials Genome Initiative.

 This project will assess how plant-based meat substitutes can most effectively replace animal-based meat. I will be focusing specifically on chicken, the most widely-produced animal in the meat industry. 8,000,000,000 chickens are killed for meat every year in the United States, dwarfing the number of all other animals used for meat combined. Chicken production is a threat to global health, because it contributes to the emissions of greenhouse gases. It is also an environmental justice issue because low-income communities with little political power live near slaughterhouses and experience polluted waterways from the animal waste. The scope of the chicken industry demands that a solution to its problems account for scale of implementation. I am going to be interviewing experts in the fields of plant-based food technology, farm transformation, and poultry industry economics. I plan to discover why poultry is one of the most prominent agricultural industries in the United States, focusing on supply chains and subsidies. I will then compare these factors to corn, wheat, and soy, the most common ingredients in plant-based meat. The current state and levels of production of the meat and animal product industry are financially inefficient, environmentally harmful, and unhealthy for our communities. For plant-based meat to realistically compete with real chicken, it must be widely available, reasonably priced, and equally nutritious. My project aims to explain what this would look like in practice.

Parkinson’s Disease (PD) is a neurological disease that affects motor function. Symptoms include muscle rigidity, tremors, slowed movements, and altered voice. Deep Brain Stimulation (DBS) is a therapeutic intervention addressing PD symptoms, by implanting an electrode into the brain, delivering electrical impulses to areas affected by PD. DBS patients, however, must come into clinic every few months for multi-hour reprogramming sessions to adjust DBS settings according to the progressions of their symptoms, making DBS treatment an arduous and expensive process. This significantly limits the accessibility of DBS, because only limited locations/providers who can offer this service. Our lab has developed a computer algorithm that can derive digital biomarkers, indicators for the severity/presence of a disease, for PD from voice samples. We aim to investigate the correlation between patient voice and physical symptoms, with manipulation of stimulation in the on/off states. Our findings could aid clinicians in their monitoring, management and adjustment of DBS protocol, without the need for patients to come into clinic. We tested this by obtaining motor scores via the Unified Parkinson’s Disease Rating Scale (UPDRS), and gathering voice samples with DBS turned on and off, during patients’ visit at UW clinics. Voice samples were analyzed for specific biomarkers, using our machine learning algorithm. We expected to observe different voice-associated biomarkers present with DBS turned on/off, to demonstrate a correlation between DBS and voice/motor symptoms. Once the relationship between DBS and voice is established, the ultimate goal is to develop a closed looped DBS device which can auto tune itself based on patient voice alone. In an age where audio collection devices, such as smartphones are so accessible, the use of voice data has exciting potential as a clinical tool, optimizing DBS therapy protocol and efficiency for administering clinicians and patients with PD.

 Within archaeology, little research has focused on Native American lithic traditions in colonial contexts, especially over the last two centuries. This project analyzes lithic material from the Molalla encampment, a nineteenth and twentieth century habitation area on the Grande Ronde Reservation in northwestern Oregon. Research teams associated with Field Methods in Indigenous Archaeology, a community-based research project between the UW and confederated Tribes of Grande Ronde Historic Preservation Office, collected the lithics over three field seasons, from 2016-2018. By using methodologies such as macroscopic attribute description analysis and geochemical obsidian sourcing, this research investigates how colonialism impacted the Grande Ronde community’s relationship to lithic traditions, raw material acquisition, and tool manufacturing and use. The care taken to create tools that acted as a central part of community connection during the hardships of the colonial era reflects an effort to stay connected to place and practice despite forced relocation and assimilation pressures. This project expands on research on the analysis of lithic traditions, showing that long-important practices remained features of Native cultural lifeways in colonial contexts.

From November 2015 through March 2016, the Olympic Mountains Experiment (OLYMPEX) was conducted on the Olympic Peninsula to study the evolution of wintertime clouds and precipitation in frontal systems passing over this coastal mountain range and to validate satellite-derived precipitation measurements from the U.S.-Japan Global Precipitation Measurement (GPM) mission. While most OLYMPEX research has focused on precipitation processes on the windward (usually southwest) side of the Olympic Mountains, this study uniquely examines the leeward (usually northeast) side of the mountains where there is climatological rain shadow (i.e. a minimum in precipitation relative to the windward side). The vertical structure of the frontal systems over the northern Olympic Mountains is examined using data from a radar managed by Environment and Climate Change Canada on Vancouver Island (EC-XBAND), including intensity inferred from radar reflectivity. Using environmental data from North American Regional Reanalysis on the windward side of the mountains, this study classifies the leeside radar data based on upstream large-scale conditions. The cloud and precipitation structure on the leeward and windward sides of the mountains are compared utilizing the Doppler on Wheels (DOW) radar in the Quinault River Valley, and the EC-XBAND radar. Cloud and precipitation particles measured by in situ aircraft over the windward and high terrain illuminate situations when particles are lofted over the mountains to the leeward side, reducing the rain shadow. These findings will inform local studies of snowpack and water supply in the Olympic Peninsula as many reservoirs there depend on precipitation that occurs on the leeward side. Outside of the Pacific Northwest, these findings can be applied to other midlatitude coastal mountain ranges on the west side of continents around the world.

Recently, microfluidic technologies have been developed to allow higher throughput collection of yeast replicative lifespan data. Adoption of these devices has been limited, in part, due to the high cost of the motorized microscopy instrumentation from mainline manufacturers. Inspired by recent development of open source microscopy hardware and software, we developed minimal-cost hardware attachments to provide long-term focus stabilization for lower-cost microscopes and open-source software to manage concurrent time-lapse image acquisition from multiple microscopes. This functional 3D printed scaffold along with attached electronics has shown to capture accurate yeast lifespans without costing as much as other third party autofocusing system. We hope that this can help spur the wider adoption of microfluidic technologies for the study of yeast replicative aging.

Natural disasters pose a great threat to power systems. They can cause major damage to power lines and substation equipment, resulting in widespread outages. It can then take days to weeks and millions of dollars to restore power to customers. Power system resilience is concerned with reducing the impact of disasters on power systems. The purpose of this study is to evaluate the resilience of one power utility in southwest Washington, the Grays Harbor PUD (GHPUD), to earthquakes, earthquake liquefaction, and tsunamis. This study will consider the likelihood of these disasters, potential effects on the GHPUD’s electrical system and its customers, and possible mitigation techniques. I have collected seismic hazard curves, response spectra, and liquefaction susceptibility data at GHPUD substation sites from US Geological Survey maps and the M9 project. I have also collected data on tsunami inundation depth at substation sites from Washington Geological Survey maps. With this information I have determined which of their substations are most at risk from these disasters. This data will be used to determine possible impacts on substation equipment and to estimate the probability of equipment failure. When completed, the results of this study can allow the Grays Harbor PUD and other power utilities to be more prepared for future disasters and to be more informed of potential resilience improvements.

Chronic non-bacterial osteomyelitis (CNO), or chronic recurrent multifocal osteomyelitis (CRMO), is an auto-inflammatory bone condition that causes persistent bone pain, poor growth, and other complications. Physical exams, laboratory tests and radiographs are not sensitive in detecting the active disease. MRI is the gold standard assessment for diagnosis. Patient reported outcome (PRO) measurements have not been commonly used to determine the disease impact on the physical health of affected children. Pain score is not accurate in assessing disease activity due to the confounding effects from other associated conditions such as amplified pain syndrome. Consensus treatment plans (CTPs) were developed by the Childhood Arthritis and Rheumatology Research Alliance (CARRA). In this study, a prospective patient registry based on CTPs is used to compare the effects of different treatment plans. This study was approved by the Seattle Children’s Institutional Review Board (#1232). The center is the coordinating site of this multicenter observational study, Chronic nonbacterial Osteomyelitis International Registry (CHOIR). Inclusion criteria are: ≤21 years old at enrollment and CNO diagnosis. Consent and assents are obtained. Standard of care is provided to the subjects and no investigational intervention is performed. Detailed clinical information, laboratory, and imaging data along with patient/parent reported outcome measurements (PROMIS questionnaires) and childhood health assessment questionnaire (CHAQ) are collected at baseline and follow-up visits. We aim to enroll 2,000 subjects worldwide and follow up with subjects for at least 5 years. Our center has enrolled 74 subjects between June 2018-present and collected PROs at baseline visits. Data is being entered into REDCap database for further analysis. PROs collected throughout the course of the study will be correlated with imaging results and expectedly determine the effectiveness of commonly used medications for patients. The data will establish measurements for physicians to estimate disease burden and treatment responses in children with CNO.

In this research project, a method was developed to quantify Gordonia and Microthrix parvicella filamentous bacteria in primary, secondary and digester sludge from three different wastewater treatment facilities in King County. The goal of developing this method was to determine the concentrations of filamentous bacteria for the purpose of relating those values to the foaming process in anaerobic digesters. The method utilized gram staining to identify Gordonia and M. parvicella by microscopy. After visual identification, the method required counting of the filamentous bacteria. These counts were then related to the measurements of biomass to calculate the overall concentrations of Gordonia and Microthrix parvicella in sludge samples. The method was validated by quantitative polymerase chain reaction (qPCR), which used DNA to quantify the filamentous bacteria. This method was successful in determining the concentration of these filamentous bacteria in sludge samples manipulated in the lab. However, it did not succeed with sludge samples directly from wastewater treatment plants. To ensure this method determines the concentration of Gordonia and Microthrix parvicella in samples directly from treatment plants, suggestions for future improvement of the method was made. Suggested improvements include different drying methods, different dilutions or additional preparation to homogenize sludge samples.
 

Primary care (PC) is the foundation of healthcare. Family physicians (FPs) are specialty trained and certified in PC and provide most PC services in the US. General practitioners (GPs), a separate group with no specialty training, are commonly confused with FPs despite differences in demographic, professional and service characteristics. Medical researchers commonly ignore this distinction and report the two groups together. Our study aims to document the rate that research in major medical journals separates or lumps GPs and FPs. We selected 23 journals on impact factor, US focus and relevance to primary care across MedLine categories of primary health care, general internal medicine, pediatrics, public health and health services. Using a MedLine search, we sought all papers published in these journals in 2017-18 that met inclusion criteria: original research, done in US, studying FPs and/or GPs and/or primary care physicians. Two researchers reviewed each article to determine inclusion, study characteristics and whether it lumped FPs with GPs or reported them separately in results. Literature search retrieved 440 total studies, with 104 (23.6%) meeting inclusion criteria. Among these, 42 (40.4%) included family physicians only, leaving 62 (59.6%) that also included GPs. Among studies including GPs, only 3 (2.9%) separated GPs from FPs. Another 23 (22.1%) lumped the GPs and FPs together. In 36 (34.6%) the reporting of GPs, FPs and others was unclear. We identified no studies on GPs only. Further analysis will examine FP-GP lumping vs. splitting by journal type, author specialty and source of specialty information.  In key medical journals, most studies lump together GPs and FPs, masking differences between these distinct groups of physicians. Most research reports fail to explain how they classify PC clinicians. Research reports need to accurately study FPs and primary care in the US.

Mutations in the ND2 gene (mitochondrially encoded NADH dehydrogenase 2) have been linked to a reduction in efficient energy production, shortened lifespan, progressive neurodegeneration, and mitochondrial diseases such as Leigh’s syndrome. The ND2 gene codes for the production of NADH, a crucial portion of the electron transport chain in cellular respiration. Previous studies have hypothesized that mutations within the ND2 gene are responsible for mitochondrial disease development. However, previous studies have not extensively investigated how genetic variation present in a population might affect the mutant ND2 phenotype. This study attempts to understand how nuclear genetic variation can ameliorate or exacerbate the effects of mutations in the mitochondrially encoded gene, ND2. To model genetic variation in a population, the project utilizes the Drosophila Genome Reference Panel (DGRP), a set of 200 fully sequenced, inbred lines with over 4 million single nucleotide polymorphisms (SNPs) throughout the genome. These SNPs are particularly useful for Genome Wide Association Studies (GWAS). To assess the effects other genes might have on the ND2 mutant phenotype, DGRP lines were crossed with a mutant ND2 line that expresses ‘bang sensitivity’, measured as recovery time following paralysis after being vigorously shaken in a test tube. Recorded progeny recovery times varied significantly among DGRP lines, suggesting that nuclear genetic variants influence the ND2 mutant phenotype. After conducting GWAS, a list of identified SNPs associated with varying recovery times was acquired. With further study, we hope to identify which specific genes interact with ND2, what function those genes have, and whether those genes might be part of a larger regulatory pathway involving the ND2 gene.

Marine terraces are geomorphic features created by wave erosion of the land, which is modulated by crustal uplift or past sea level changes. In this study, I consider possible driving mechanisms that could have generated the marine terraces on the archipelago of Haida Gwaii, Canada. Southwest of the island, there is a young subduction zone that was only initiated ~6 Ma. This subduction has generated a M_w 7.8 earthquake in 2012. From this study, we can find out more information about the plate boundary, including uplift and deformation histories. The island has also experienced ice coverage during the last glacial maximum. Since then, the ice has melted. As a result, the island may have uplifted in response to the ice melting during the Holocene. To obtain the data needed, I am using newly released LIDAR data which contain high resolution elevation topography to map the landforms digitally. The purpose of this project is to provide a resource for locations of the terraces and also to find patterns in distribution and in elevation of marine terraces in Haida Gwaii.

Tetramerized viral proteins are a powerful tool for examining the immune response to infection and vaccination. However, the field lacks a clear understanding of the stability of these tetramerized proteins over time and varying temperatures. One such viral protein, Respiratory Syncytial Virus (RSV) fusion (F) protein can degrade from a prefusion (preF) conformation to a postfusion (postF) conformation. The stability of tetramers of the RSV preF protein is tested by 1) freeze-thawing; 2) incubating for 1, 2, 4, 8, and 12 weeks; and 3) storing at -20°C in glycerol, 4°C in PBS, and room temperature in PBS. RSV F in the preF versus the postF conformation is measured using bio-layer interferometry (BLI) to assess how these different variables affect tetramer stability. This study aims to define ideal conditions for the storage of tetramerized viral proteins. This crucial information will ensure reagents used to study the immune response to vaccines and infections are robust and will also help minimize the cost and time of producing these reagents. The findings could also allow the implementation of these reagents in resource-limited settings.

Studying zebrafish embryos allows us to understand features of vertebrate embryonic development. Neuro-mesodermal progenitor cells at the very posterior end, or tailbud, of an embryo are bipotential. This is because the presence or absence of Wnt signaling commits them to either neural or mesodermal fate. Directed by environmental cues, mesodermal cells exit the tailbud, migrate anteriorward, and become somites, structural segments from which muscles differentiate. The Kimelman lab has found that Tbx16/Spadetail, a major driver of mesodermal morphogenesis, downregulates Arhgap29 and Arhgap35, members of Rho family GTPase activating proteins. This suggests Arhgap29 and Arhgap35 may be involved in mesodermal cell movement. My work in the lab is focused on finding out what roles these two genes play. I used heat shock promoter hsp70 to overexpress Arhgap29 and Arhgap35 in transgenic fish lines. Previously, our lab showed that sustained Arhgap35 affected somite morphology, and that sustained Arhgap29 also decreased the number of somites. In my experiments, I carried out in-situ hybridization in wild-type, Arhgap29- and Arhgap35-expressing embryos to examine genes regulating specification/differentiation of muscle cells and genes involved in transmembrane cell adhesion. I will present data on cell tracking and cell protrusions collected from Arhgap29- and Arhgap35-expressing embryos. These results will help me compare cell migration between Arhgap-expressing and wild-type embryos. The purpose of these analyses is to understand how these two proteins control cell movement in the embryo. In the future, I will continue to investigate cellular mechanisms underlying vertebrate posterior elongation.

As anthropogenic climate change progresses and alters our marine ecosystems, it is important to monitor the changes it creates in order to inform plans for mitigation or management. This project, completed as part of the Puget Sound Foraminifera Research Project at The Burke Museum, uses sediment samples collected by the Washington State Department of Ecology and extracts benthic foraminifera from those samples to learn vital information about the health of the Puget Sound. Benthic foraminifera are single-celled organisms that live on or in marine sediment and form shells of calcium carbonate or agglutinated sand grains. This research looks at the dissolution of shells of a species of calcareous foraminifera called Elphidiella hannai in order to establish whether different populations across Puget Sound are affected differently and if dissolution primarily happens before or after the death of individuals. For this research, samples collected from a variety of Puget Sound embayments over four years starting in 2015 were processed and stained with Rose Bengal to ascertain whether the foraminifera were alive at the time they were collected. Following this, foraminifera were sorted and species were grouped. Finally Elphidiella hannai were assessed for dissolution on a 0-3 scale, 0 meaning pristine and 3 heavily damaged. Preliminary results show higher levels of damage in stained individuals and vastly differing amounts of damage in different Puget Sound embayments, suggesting most damage happened while foraminifera were still alive and that changes in acidity of water are impacting populations at different rates.

Global warming is a real threat to our communities and the world at large, yet most publics may under-appreciate the threat, or yet be moved to action. This research explores the level of awareness and motivation at UW Bothell, specifically exploring the questions: What is the level of knowledge about global warming and fossil fuels from students, faculty and staff? Does knowledge or perception of these issues differ among U.S. students versus international students? How does awareness and motivation toward action correlate to having taken environmental coursework? Results will be presented from an anonymous, cross-sectional survey from three groups: students, faculty, and staff at UW Bothell (UWB) regarding knowledge, perception, usage, and interest or engagement in actions to reduce fossil fuel use and reduce climate warming. Based on related prior work, both quantitative and qualitative results are expected to show a range in perception, knowledge, and acceptance of global warming, as well as fossil fuel usage and energy conservation in relation to political affiliation, and prior exposure to environmental coursework. The study serves as a foundation for a future study to increase knowledge about global warming and energy conservation.

Hemoglobin A1c (HbA1c) is an important marker to aid in the diagnosis and monitoring of diabetes, as it is a measurement of average blood glucose concentration over the previous two to three months. The current instrument used at Seattle Children’s Hospital to measure glycated hemoglobin is the DCA™ Vantage Analyzer. The DCA™, being a point of care (POC) device, can only run one sample at a time and requires a significant amount of tech time to run a batch of samples. With that, there is a desire to validate HbA1c on the Vitros 4600 as it would improve utilization of tech time and potentially provide more accurate and precise results. A correlation study was first done by running 30 different samples across the Analytical Measurement Range (AMR <14%) on the Vitros 4600 and compared to the original values run on the DCA™ using the statistical program in EP Evaluator. The overall bias of the two methods was -3.265%, but after closer analysis, the bias <9% HbA1c was -0.509%, while the bias >9% HbA1c was -5.026%. Another method comparison was done by running high HbA1c samples (8-14%) on the DCA™ and Vitros 4600 compared against ion exchange HPLC, which is the gold standard for the measurement of HbA1c. The Vitros 4600 had a better correlation with HPLC (bias of 1.075%) on the high end for HbA1c compared to the DCA™, suggesting the DCA™ actually has a high-end bias with higher HbA1c values compared to HPLC. Thus, by using the Vitros 4600, there can be more accurate results for HbA1c levels especially when managing diabetes, while also increasing productivity by having the ability to run multiple samples compared to a POC device.

With the introduction of new social technology to society, there has been a clear paradigm shift in the way in which we are initiating, maintaining, and facilitating relationships. Technology has no doubt made it easier for people to communicate but has also diminished the need for interpersonal skills. I use multiple interdisciplinary lenses including: communication studies, gender studies, and a generational lens for this systematic literature review. With my findings, I have been able to conclude that people are indeed getting too comfortable hiding behind technology and using it as a mechanism to avoid in-person confrontation and emotional discomfort. A growing phenomenon that is rising in spite of this is ‘ghosting’, in which one party blocks or deletes a person virtually from their life to break off any means of modern communication. Dating apps such as Tinder encourage this sort of behavior and are accelerating the rise of a hookup culture with little means of a true connection. There are a number of generational and gender differences in how people are approaching technology and intimacy in a digital age. My research delves into what exactly is going on with millennials and modern-day dating and aims to dissect the behaviors in order to further understand the driving force behind the hook-up culture.

Through rapid industrialization and development, much of the Green River Valley landscape and townships from the earlier periods of settlement have been obscured. However, several historical cemeteries remain largely preserved. Cemeteries can have an equalizing power when it comes to representation of past populations, while preserving societal ideas of hierarchy. While cemeteries cannot tell the full history and lives of those interred, they do provide names, ages, and the placement of the individual in conversation with other deceased people. A cemetery is not a passive location in a town, but rather a place created with the ability to reflect societal values regarding death and social integration and spiritual significance for the living. My research focuses on what relationships can be rediscovered in the development of the Green River Valley’s townships, as these relationships may speak to the social organization of the Valley townships in development, the role death had in society, and how race, gender, religion or other factors were presented. These relationships will be investigated following three lines of inquiry: a) relationship among the dead in cemeteries, b) relationship between cemeteries and the living in modern and historical times, and c) relationship of the deceased’s identity and their position within the cemetery landscape.  Though each cemetery has been researched and written about separately, conducting a survey of several cemeteries in the region and analyzing them together will allow for a bigger picture of health discrepancies between men and women, white and non-white residents, and differences of land quality broadly associated with members of different social classes, building a more comprehensive history of the Green River Valley.

African-born individuals in the United States face unique barriers in accessing preventative healthcare. We conducted a mixed-methods study to implement community-based health fairs and learn in the process the barriers regarding accessing preventative healthcare. From April to May 2018, we held six health fairs at three apartment complexes with high numbers of African-born residents. Fairs included free point-of-care screening for glucose, cholesterol, BMI, blood pressure, and HIV along with social services and health education. The health fairs were hosted in apartment complex common areas with HIV testing conducted in private rooms. Health fair participants were asked to complete a series of questionnaires to evaluate demographics, access to health services, and HIV testing history. We conducted 18 key informant interviews with health fair participants and community leaders to identify barriers to preventative healthcare among African-born individuals. Of the 111 adults who accessed at least one service at a health fair, 92 completed questionnaires. 61% were female, 52% were born in Africa, and 63% had health insurance. Among the 18 interviewed, the most commonly reported barriers were language, logistical barriers, a distrust of health professionals, and lack of health literacy. These barriers create a disconnect between patients and health providers and impedes access to health-related information. A high prevalence of non-communicable diseases was also identified among participants, including obesity, high blood pressure, and high cholesterol. Residential health fairs are a feasible method to increase engagement of African-born individuals in preventative care. Key considerations are providing culturally-competent care, easily accessible services, and staffing services with healthcare providers who speak the primary languages of the populations being served or have adequate interpretation services. Preventative healthcare services will also be more acceptable if all services (e.g. cardiometabolic and HIV screenings) are incorporated into one package and promoted as routine activities.

The Large Synoptic Survey Telescope (LSST) will be capable of observing objects of 25+ magnitude across the u, g, r, i, z, y broad-band filters. At these extremely dim magnitudes the survey will turn up a large number of unresolvable red point-like sources. With some variation depending on the filter, beyond roughly 25 magnitude these filters will lose the ability to provide data accurate enough for an observer to reconstruct the parameters of the objects being detected. In other words, past that point it will become difficult to tell whether an object is a nearby low mass main sequence star, a far away giant, or a high-redshift galaxy. The simplest possible solution to this problem is to add some more filters, specifically ones with narrower band width. If these narrow band filters allow for accurate data to be collected at higher magnitudes than their broad band counterparts can, it would not only solve the problem, but do so without necessitating a longer survey or requiring any great feat of engineering to implement. A simulated LSST field consisting of roughly 127,000 stars was used to explore this possibility. The (simulated) observed magnitudes and colors of each star were compared to a catalog of each star’s true magnitudes, with a nearest-neighbor algorithm applied in an attempt to recover that star's true effective temperature, surface gravity, and metallicity. This process resulted in accurately-recovered stellar effective temperatures out to far greater magnitudes than allowed by the broad band filters. Unfortunately, improved parameter recovery seems for now to be unique to effective temperature, as this initial test has not shown any great improvement in the recovery of gravity or metallicity over the broad band filters.

Zebrafish are an emerging model for skeletal biology in part because they are amenable to rapid-throughput approaches for applications including identifying possible causal genes of heritable skeletal conditions such as osteoporosis. Previously, a software called FishCuT was developed for measuring the vertebrae of the zebrafish in microCT image stacks; though this software was not conducive to further development. Expanding FishCuT’s measurement content will help researchers characterize the skeletal features of the analyzed fish with more detail to aid in basic research which could lead to clinical applications such as identifying new drug targets. To expand FishCuT’s capabilities, first I reorganized the codebase into a modular architecture that allows for faster and easier development of discrete and specific blocks of code. The new architecture allows developers to create extensions to FishCuT without having to understand the details of the core software. To demonstrate the utility of this structure, I have prototyped an extension for additional measurements on a zebrafish vertebral structure called the neural arch. By implementing this prototyped module retroactively in existing microCT data from a gene-knockout experiment, I have appended the experiment data records with an additional neural arch phenotype for the zebrafish gene bmp1a, which has an analogous gene in humans associated with brittle bone disease. This development strategy facilitates collaborative work, and we aim to make FishCuT an open source project for the zebrafish research community. Expanding FishCuT’s measurements to other skeletal structures and features, in conjunction with retroactive microCT analysis, can greatly increase the knowledge of the zebrafish community and catalyze discoveries and developments for treatments of skeletal conditions.

Carbon storage is an effective and natural way to reduce the excessive carbon dioxide levels in the atmosphere, a leading cause of global climate change. The largest carbon sink could be the soil underneath our feet, therefore, it can be utilized for carbon storage. Biosolids from King County’s wastewater treatment plants are a concentrated mixture of nutrients resulting from anaerobic digestion of organic waste filtered from wastewater inflow. This includes feces and food scraps. When applied to land, biosolids demonstrate an increase in soil carbon storage, making a connection between the geosphere and atmosphere that could be vital for effective carbon sequestration. For over twenty years, King County has applied biosolids to commercial forest plantations. We investigated the potential and effectiveness of biosolids applied to Douglas Fir stands in aiding carbon sequestration. This included measuring the bulk density, total carbon and nitrogen in conifer forest soils that have had biosolids applied and comparing those measurements to those of conifer forest soils that have had no biosolid application. The treatment stands had four rounds of biosolid application in the last fifteen years. These findings could be important in developing better planning strategies, sustainable business products and further research studies to combat the effects of climate change.

In our study, we focus on sugar-sweetened beverage selection mediated by Compensatory Health Beliefs (CHB), participants’ justifications for unhealthy eating habits; Considerations of Future Consequences (CFC), participants’ risk perception; and, personal health perceptions, participants' beliefs about their own general health. Additionally, we look at three Implicit Association Tests (IAT) to see if implicit preferences also mediate sugar-sweetened beverage consumption; Greenwald and colleagues’ (1998) original Traditional IAT (good/ bad), the Personalized IAT (“I like”/ “I don't like”), and our own adaptation, the Extended Personalized IAT (“I want”/ “I don't want”). We predict that 1) participants with higher personal health perception will be less likely to endorse CHB use, 2) participants with a higher regard for future consequences will be less likely to endorse CHB use, and 3) participants’ BMI and Three-Factor Eating Questionnaire (TFEQ; disinhibition, hunger, and restraint) scores will correlate with CHB use, but not their implicit preferences. Participants from the University of Washington, Tacoma campus will complete the study on campus and will receive course credit upon participation. Participants complete three IAT tasks, administered in counterbalanced order, then explicit self-report measures, such as demographical information (which include BMI), the TFEQ, self-reported liking of beverages, questions on personal health perception, and the CHB and CFC scales. Hypotheses 1 and 2 will be analyzed using a one-tailed t-test, which indicates a desired sample of 102 (based off a power analysis using p = 0.05, a power of 0.80, and an effect size of 0.50). Planned analysis for hypothesis 3 is a multiple regression to test the contribution of BMI, TFEQ, and implicit preferences on CHB use with a desired sample of 112 (p = 0.05, power level = 0.80, and and an effect size of 0.10).

The process of gene expression known as transcription is an essential component in all eukaryotic cellular development. TBP Associated Factor 1 (Taf1) is the largest subunit within the the ubiquitously expressed transcription factor complex TFIID and plays an integral role in regulating gene transcription. In neuronal cells, an isoform of Taf1, dubbed N-Taf1, is expressed and is thought to be a key regulator of neuronal development. When under-expressed, N-Taf1 has been hypothesized to be associated with the neurodegenerative disease X-linked Dystonia Parkinsonism, which causes individuals to experience tremors, impaired movement, and uncontrolled rigidity. The goal of this study is to expand our knowledge of the functional role of N-Taf1 in neuron development and how impairment of this function may lead to neurodegenerative disease. To accomplish this, we investigate the expression of N-Taf1 and proteins that signify neuronal differentiation within various cell lines using western blot protocol and fluorescently active antibodies. Once an ideal cell line to study N-Taf1 function is identified, we selectively alter the expression of N-Taf1 using CRISP-Cas9 and compare the expression levels of our proteins of interest when N-Taf1 is under-expressed or unaltered. By analyzing this data, we can begin to draw connections between N-Taf1 expression levels and the process of neuronal development. By understanding this relationship, we hope to move closer to a treatment for X-linked Dystonia Parkinsonism and any other neurological impairments associated with N-Taf1.

Cortical plasticity is the substrate for learning and memory. It is the basis of an organism’s ability to adapt in response to a changing environment and is central to functional recovery after an injury involving the nervous system. Vagus nerve stimulation (VNS) has already been shown to be effective in altering neuroplasticity. Most VNS research has been conducted on epileptic animals and thus offers little information on how VNS may affect a healthy human brain. The final goal of this project is to establish a minimally invasive VNS protocol aiming to augment neuroplasticity and ultimately affect behavioral performance in a cognitive task. Because this study is conducted using non-human primates, and because of the limited invasiveness of the procedure, the outcomes can be directly translated to applications for human subjects. Non-human primates are implanted with cortical electrodes allowing both recording and stimulation of the cortex at select locations. Closed-loop cortical stimulation triggered by the troughs of beta (15-25Hz) oscillations leads to phase-dependent changes in excitability which outlast the oscillatory episodes for a couple of seconds. By delivering current through a clip electrode attached to the right or left cymba concha, we paired the cortical stimulation with auricular branch VNS (abVNS). This stimulation protocol is used to investigate the effects of cycle-triggered cortical stimulation with abVNS. Preliminary results show a suppression of excitability when the abVNS is delivered in phase with cortical stimulation which lasted for minutes after the cycle-triggered stimulation has ended. However, more control experiments need to be run before conclusions can be drawn. These findings of lasting change to cortical plasticity are novel and suggest that vagus nerve stimulation can affect medium-term neural plasticity.

The nitrogen vacancy (NV) center is a point defect in diamond with quantum mechanical spin properties. These properties enable optical nano-scale magnetic field sensing at room temperature, making them highly bio-compatible. To conduct wide-field magnetic field imaging, we require a nano-scale thin surface layer of high NV center density in our diamond samples. We demonstrate optimized sensing capability in our diamonds through growth and processing methods, which create an ensemble of NV centers. With these sensitive samples we use quantum control protocols called double quantum and spin bath driving to reach sensitivities of 60nT/Hz^1/2 over a 0.1 cubic micron pixel. These protocols take advantage of inherent characteristics of the NV center and improve the imaging capability for biological systems.

Fiber-reinforced composites are advanced materials that combine polymeric matrices with fibers to achieve low densities along with high strengths and moduli. These properties make composites invaluable to industries that rely on materials with high strength-to-weight ratios, such as aviation and aerospace. This contribution discusses the structural design of the Hyperloop Prototype built by the University of Washington’s team competing in the SpaceX Hyperloop Competition. As the Structures’ team lead, my work has centered around designing a reinforced sandwich panel c-channel design, for the upcoming fourth competition, to optimize the total structural weight to 16lbs respect to the third competition design’s weight of 60lbs. I then analyzed and optimized this design using 1D beam analysis scripts written in MATLAB as well as 2D composite shell analysis in Femap and Hypersizer software to validate SpaceX’s structural stiffness and strength requirements. The structures team conducted an extensive testing campaign to capture flexural properties and identify limit loads of the design. This campaign included three-point-bend tests to capture sandwich panel properties and insert hardpoint testing to validate performance of the mechanical joints between the primary structure and propulsion, stability and braking modules. Finally, with the support of Boeing composite production advisors, the team manufactured prototype composite structures making use of advanced industry procedures including use of FlexCore, carbon puck hardpoints and autoclave cure cycles. This work serves as a critical example of composite material technology application to student-lead design projects as well as the engineering knowledge that can be developed outside of the traditional classroom setting through research and independent studies.

The Puget Sound is an economically and culturally important marine ecosystem, and insects are a little understood part of this ecosystem. Research suggests that insects are an important food source for near shore juvenile salmon which has wider ecological and conservation implications, including at higher trophic levels; while some work has been done in coastal British Columbia, little work has been done on the insects themselves within the environment of the Puget Sound. To close this biodiversity knowledge gap, field and museum collection surveys were and are being conducted to gain a better understanding of the insects of Puget Sound. Various hand sampling techniques were utilized including net, aspirator and insect vacuum. So far, 15 individual species of 6 families of 2 different orders of insects were confirmed present in Puget Sound in this study. Additionally, 10 species of 2 families of 2 different orders of insects were reported in similar conditions in the literature, but were not observed in this survey or found in museum collections. The most abundant order was Diptera. In all, 14 beaches on the Puget Sound have assessed and some contained unique species. Further studies, in seasonality (and food availability), habitat substrate preference, insect behavior, insect population dynamics and a deeper look at predation of marine insects by juvenile salmon could be investigated based off the work done in this study.

This project is about decision-making systems and in particular, the costs and benefits of consensus. Consensus voting is appealing because, among other reasons, it not only protects the right of minority views that would otherwise be consistently overruled, it also has the potential to completely transform organizational culture - which is good since for many organizations nothing at all could get done by consensus under their current culture. The dynamics that consensus creates teaches us how get along with other people, to create cameraderie, and to change the world or at least reduce the disastrous consequences of our conflict-based status quo. I’ve explored when and why consensus voting does and doesn’t work, and have produced proposals for its wider use in one or more specific groups or situations. First, I analyzing three cases where consensus is currently used, including felony trial by jury, and three cases where it could be added or expanded, such including certain urban planning decisions. I also held a simulation to gather feedback from participants. In certain situations, consensus can allow a broader range of people affected by a decision to participate in it, but it can also be seriously impeded by a small group, and the effects of this depend on whether there is any sort of escape valve or override, as well as the social dynamics of the situation.

Microphysiological systems (MPS), also known as “organs-on-chips,” provide a novel, ex vivo approach for evaluating the risk of drug induced toxicity and the impact of environmental toxins. Evaluating the chronic impact of exposure to environmental toxins in humans is difficult, due to ethical concerns, but the MPS provide an approach to examining the toxicological effects on human cells, without the need for human subjects. Aristolochic acid I (AA-I) is a potent, plant-derived nephrotoxin and carcinogen that has been implicated as the causative agent in both Balkan Endemic Nephropathy and Chinese Herb Nephropathy. The contribution of hepatic metabolism to the bioactivation of AA-I was previously demonstrated by microfluidically linking a hepatocyte containing MPS and a human renal proximal tubule eptileial cell (PTEC) containing MPS. PTECs are kidney cells from the nephron that lie between the glomerulus and the Loop of Henle. We studied the cytotoxic effects of AA-I on PTECs and human hepatocytes in MPS by exposing the MPS to concentrations of AA-I ranging from 0 µM to 10 µM for longer than seven days. AA-I was perfused into the MPS into either a linked hepatocyte-PTEC MPS or an unlinked PTEC only MPS. The chronic, low-dose effect of AA-I resembles Balkan Endemic Nephropathy, where individuals were exposed to low concentrations of Aristolochic acid from tainted wheat. Both PTEC only and linked hepatocyte-PTEC MPS provide experimental methods for further investigating how organ-organ interactions affect drug metabolism and xenobiotic toxicity.

In eukaryotes, conserved mechanisms ensure that cell growth is coordinated with nutrient availability. Overactive growth during nutrient limitation (“nutrient-growth dysregulation”) can lead to rapid cell death. Here, we find that cells can adapt to nutrient-growth dysregulation by evolving major metabolic defects. Specifically, when yeast lysine auxotrophic mutant lys- encountered lysine limitation, an evolutionarily-novel stress, they suffered nutrient-growth dysregulation, and a sub-population repeatedly evolved to lose the ability to synthesize organosulfurs (lys-orgS-). The purpose of this study is to identify the types of yeast cells that recovered by being lys- and orgS- and their frequencies through generations. Using 96-well plates, we inoculated single colonies into three separate conditions (control, +lys, +lys+orgS) to test for auxotrophs. Surprisingly, we found drastically different frequencies of lys-orgS- when lys- evolved as a monoculture in lysine-limited chemostat versus in a coculture with a lysine-releasing strain. We also found mutants defective in synthesizing glutamine and arginine. Our work suggests that under stressful conditions, multiple metabolites are released, which can facilitate the evolution of new interactions and mechanisms. 

The lysosome is a critical organelle affected by the aging process. Changes to lysosomal physiology during aging and their effects on cellular function are poorly understood. Here, we study the lysosome-like vacuole of the budding yeast during replicative aging. Using a microfluidic device, we trap hundreds of mother cells and visualize them over the course of their replicative lifespans. Using strains with fluorescent protein tags we investigate protein abundance, intracellular physiological conditions, and organelle morphology. We find that during aging, the vacuole becomes progressively less acidic. Using a vma mutant as genetic model of vacuolar pH dysfunction, we find that loss of vacuolar acidity triggers a loss of respiratory capacity, loss of iron-sulfur cluster protein activity, and iron starvation response. We find that iron supplementation rescues both the loss of respiratory capacity and shortened replicative lifespan of vma mutant cells. We see that during aging, a similar iron starvation response occurs, correlated on a single-cell level with the loss of vacuolar acidity. We propose that the loss of iron-sulfur cluster synthesis capacity due to loss of vacuolar acidity is a conserved process underlying multiple aging phenotypes.

Hereditary Spastic Paraplegia (HSP) is a classification for a group of neurogenetic diseases that cause affected individuals to have severe contractions and stiffness in the lower limb muscles. This group includes a genetically diverse range of disorders that vary in age of onset, rate of progression, and severity. The purpose of my project is to identify the causal gene involved in this novel form of HSP. My lab acquired DNA samples from affected and unaffected members of a family with an unassigned autosomal dominant HSP. At first, we obtained whole exome sequencing on DNA from three affected family members. In a file containing all the variants (differences from a reference DNA exome) detected in any of these three subjects, we looked for previously identified causal variants to ensure that the family did not have a known HSP subtype. Then we identified potential variants by filtering for those that were present in one copy (heterozygous) in all three family members, since this form is autosomal dominant. We further filtered them for low prevalence in the Genome Aggregation Database, since HSP is not a common disorder. Candidate variants for testing were selected based on their predicted change in the protein, relevance of gene function, and predicted impacts from CADD and GERP models. We are currently in the process of analyzing the candidates. We are amplifying and sequencing them using DNA from all the family members to determine whether these variants are present in all those who are affected and absent from those who are not affected, since that is how the causal variant would present. My project will contribute to our understanding of the pathogenesis of and improve clinical diagnostics for HSP. The implications of my research could also extend to other genetic disorders if a novel genetic mechanism is elucidated.

Alzheimer's disease has been labeled the disease of the 21st Century. Societies around the world have not properly prepared for the expected massive increase in cases projected for the next 30 years. It is unclear who will care for the increase in numbers of people who will not be able to care for themselves.  At present, the vast majority of care is provided in the home by family members. Spouses represent a sizable percent of these family members. Research on spouse caregivers (CGs) has focused mostly on Whites, with relatively little research on minorities.  Research that has examined minorities has mostly examined self-rated measures, with little work on biological indices. The current study compares four groups of spouses: Black CGs (n = 7), Black Non-Caregivers (NCGs) (n = 8), White CGs (n = 115) and White NCGs (n = 108).  We observe differences in perceived stress, coping, burden/distress and physiological measures. The outcome of our research recommends interventions that could be used to mitigate health problems in caregivers that may allow them and their care-recipients to remain in their homes and live independently.

Sexual dimorphism is a characteristic of many organisms that is genetically encoded and typically studied as a binary trait. Biomedical research routinely categorizes subjects into “male” and “female”, and the resulting data are used to establish sex-specific measures of good health and disease. However, this practice overlooks the existence of intersexual phenotypes and oversimplifies the overlapping variation between sex-specific groups. The phenotypic expression of sex is directed by a complex orchestration of many genes. As such, it is reasonable to consider that there are more than just two discrete expressions of sex, and furthermore that the dimorphism of so-called sex-specific traits resides along a continuum. Metabolomics studies the small molecules that make up all the molecular building blocks in the body, and offers a unique opportunity to quantify sex variation that is morphologically invisible. Doublesex (dsx) is a gene that plays a pivotal role in the sex development of Drosophila melanogaster, and its absence results in an intersexual morphological phenotype. This study models sex in Drosophila melanogaster as a continuous trait by comparing metabolomic profiles for wildtype females, males and dsx null mutants using statistical analysis of metabolome data. While many studies have been conducted to understand the role of dsx in sex determination, to our knowledge no one has attempted to use this novel approach to quantify sex variation as a complex trait. Here we measure over 1000 metabolites in fly samples and test a hypothesis that some metabolites exhibit continuity between male, intersex and female phenotypes. Future work could explore the degree to which these metabolic sexual continuities exist in natural fly populations, and provide a powerful model to study factors that are influenced by sex differences more comprehensively.

The PestiSeguro/PestiSafety app aims to give agricultural workers reliable information on pesticide safety by providing accurate Spanish translations. The health and safety information of the app is important because handling pesticides incorrectly may harm workers, crops, and the environment. The PestiSeguro/PestiSafety app was evaluated by the community itself, agricultural workers ranging from workers, supervisors, and farm owners. The app was also evaluated by state wide stakeholders. The evaluation consisted of 15min interviews where we gathered qualitative and quantitative data on demographics, translation quality, and recommendations. The interviews were conducted through phone on early mornings and late afternoons to accommodate agricultural workers schedules. During the Analysis of the qualitative data we started coding the content by topic and codes were generated from the data. This process was repeated 3 times adjusting codes and coding undil they were consistent. Then we identified themes and patterns that told us, what the community was benefiting from the most, errors made in the accessibility of translations, and improvements on user friendly experience, such as adding graphics. Among the testers 94% of them agreed that information in spanish helps to understand how to handle pesticides safely. Another 94% agreed that the translations were clear and understandable. Future work includes, releasing a demonstration app that can be downloaded directly from the app or play store and to continue to disseminate information to valuable stakeholders. 

Biological mineralization is the formation of minerals in hard tissues guided by proteins. Unique aspects of these minerals include the molecular control of hierarchical structure, intricate architectures, and multifunctional properties for inspiration in bionanotechnology and nanomedicine applications. Numerous biomineralization strategies have been developed in hard tissue regeneration therapies. However, there is currently no in-depth understanding of how proteins regulate the synthesis of these inorganics or the physiological formation of the minerals. The ability to control mineral formation for biomedical applications, therefore, is still limited to the use of a few mineral-directing proteins extracted from tissues. Biomineralization can also be controlled using short peptide domains derived from natural proteins known to have a regulatory role in mineralization. Our laboratory has designed peptides derived from amelogenin (ADPs), the key protein in tooth formation, using combinatorial selection and computational design, whose utility in rebuilding hydroxyapatite (HAp) mineral on tooth has been demonstrated in numerous case studies. The goal here is to understand the fundamental mechanisms of biomineralization guided by ADP5 and develop a methodology to form HAp with exclusive control of its growth kinetics and mineral crystallography. We designed mutants of ADP5 to investigate changes in mineralization kinetics, nucleation, and morphology. In the current study, we are establishing the conditions for ion-peptide interactions on the onset pH for mineral nucleation using calcium/phosphate and mutant ADPs. The goal is to gain insights into the correlation between sequence domains and biomineralization outcomes eventually facilitating greater control over the reaction and further optimize remineralization approach. The developed method has a high potential to develop non-invasive oral health care materials and methods by restoring mineral loss, the root cause of dental ailments and, eventually, help bring clinical and over-the-counter dental products into the market with preventive, restorative, therapeutic, and cosmetic characteristics. Sponsored by SoD Spencer Funds.

Mercury (Hg) is widely known to be a neurotoxin. Mercury in our environment is found in many different forms, and the key difference between them is evident in the way they are absorbed by organisms. Hydrophobic methylmercury (Me-Hg) readily bioaccumulates in the tissues of all organisms, leading to Hg exposures involving higher doses. Recent research shows that sulfate-reducing bacteria (SRBs) play a role in methylating mercury only when they possess the hgcAB gene cluster. Gaining a more comprehensive understanding of the aqueous conditions required for SRBs to thrive and consequently methylate inorganic mercury is essential for addressing the ongoing problems associated with Hg toxicity. In the initial phase of this study, ion chromatography was used to quantify sulfate (SO42-) concentrations along an urban river in an industrial region of Seattle (the Duwamish/Green River Watershed). The measurements revealed that SO42- concentrations as high as 5300 ppm were present at several sites along the lower portion of the Duwamish River. A number of previous studies also showed significant amounts of mercury in this region’s sediments and fish tissues. The secondary phase of this study involved an investigation determining whether the measured high sulfate concentrations were related to the production of Me-Hg and additionally examined if SRBs likewise played a role. River sediment was analyzed for the presence of the hgcAB gene cluster. Ongoing studies are focused on quantifying Me-Hg at sites where SRBs were found and on the identification of key indicators for mercury methylation conditions along a watershed. This study provides further insight into the relationship between mercury, sulfates, and SRBs when found in combination in an aqueous environment.

Deposits of windblown silt, or loess, provide information about the wind direction as well as wind speed in the geological past. In general, stronger winds can transport both larger and heavier particles. Loess is also subject to soil formation processes, making it an archive of other paleoclimate variables. In this study, we have collected samples of the Palouse loess along the Columbia River, in southeastern Washington State, to examine the effects of wind transport on heavy (magnetic) minerals. We examine the particle size and composition of magnetic separates using a Scanning Electron Microscope (SEM) and energy dispersive x-ray spectroscopy (EDS) as well as bulk particle size. We expect a relationship between these characteristics and sample distances downwind from the source area, giving us a better understanding of the environmental conditions in which the loess was deposited. We plan to compare our results to physical models to determine wind speed and direction during glacial-interglacial cycles.

Embryonal rhabdomyosarcoma (ERMS) is a devastating pediatric cancer that affects soft tissue such as skeletal muscle and connective tissue. Currently, there is no effective treatment for patients with ERMS. Mutations in the gene PTPN11 are found to have cancer-promoting roles in leukemia, lung, and breast cancers, but its role in ERMS is virtually unknown. PTPN11 codes for the SHP-2 protein, which is a component of the RAS/MAPK (mitogen-activated protein kinase) signaling pathway. Abnormalities in this pathway are known to transform normal cells into cancer cells when certain proteins are upregulated. My central hypothesis is that PTPN11 promotes RMS tumor growth by allowing cells to proliferate and differentiate out of control. To test the hypothesis, I used CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas gene editing technology to disrupt PTPN11 gene function in two models. I designed constructs that express guide RNAs that target the PTPN11 locus in the zebrafish or human genome. If PTPN11 has a tumor-promoting role, I expect targeted disruption of zebrafish PTPN11, delivered via microinjection, to result in reduced RMS tumor formation and growth compared to zebrafish tumor with no PTPN11 gene disruption. In the human ERMS cell lines, I will use virus-mediated transfer to introduce the CRISPR DNA construct in vitro. My hypothesis will be supported if the cells harboring targeted disruption of PTPN11 have reduced growth and less self-renewal capacity compared to the control cells. My findings will elucidate the role of PTPN11 in RMS, which will allow further research into the potential therapeutic benefit of targeting PTPN11 in pre-clinical RMS models.

2-deoxy-ATP (dATP) is a nucleotide used in DNA synthesis and its presence has been seen to improve the magnitude and rate of contractions in heart muscle cells. However, levels of dATP are naturally low in mature cells. As an attempt to develop a novel treatment for heart failure, methods to increase the expression of ribonucleotide reductase (RNR), a key enzyme in the production of dATP are being investigated. RNR is regulated by ubiquitin-proteasome degradation of the small subunit of RNR, the Rrm2 subunit. We constructed a variant version in which two regions were changed to prevent ubiquitination. This new variant should lead to higher levels of RNR in cardiomyocytes, which also indirectly increases levels of dATP. Our preliminary results show a successful increase in levels of both RNR protein and dATP in cultured neonatal rat cardiomyocytes. Although levels of RNR and dATP were increased, the level present in our cultured samples are much higher than expected for adult rat and mice cells. Therefore, we are currently testing this RNR variant in vitro in cultured adult rat cells, as well as in vivo in aged adult mice. These models are more representative of a therapeutic use. Preliminary results have been promising toward identifying a more effective method of increasing dATP levels for improving cardiac function.

The Time-Domain Spectroscopic Survey (TDSS) is the largest spectroscopic survey ever carried out specifically targeting variable objects. In this poster we consider the subsample of some 22,000 TDSS variables characterized spectroscopically as stars, and evaluate best methods for retrieval and analysis of light curve data from the Palomar and Catalina surveys. We analyze light curves using Python and the VARTOOLS code of Hartman & Bakos (2016). A combination of the VARTOOLS output, spectroscopic information from Sloan, and classification of periodic variables in Catalina from Drake et al. (2014) is used to guide future classification of the entire TDSS sample, including some discussion of the larger variable sample for which no significant periodicity is found. The particular patterns of each type of variable star we find can be used to learn more about stellar evolution and the physical processes taking place within stars. The discovery of new and unexplained types of variable stars can also act as a driver that leads astronomers to an explanation of the underlying mechanism behind it. The SAO REU program is funded in part by the National Science Foundation REU and Department of Defense ASSURE programs under NSF Grant no. AST-1659473, and by the Smithsonian Institution.

Neutron stars are extremely dense objects that are the remnant of exploded massive stars. The purpose of this project is to try to discover new neutron stars in orbit with normal stars. These new systems will improve our understanding of the processes of stellar evolution. To conduct the research, I cross-matched data from two different instruments, ROSAT and ZTF. ROSAT provides a comprehensive survey of the X-ray sky, while ZTF provides a real time stream of time varying optical sources. The combination of the two can identify neutron star binaries as they change in brightness. I continue to sift through the data on weekly basis to enhance the chance of finding new binary outbursts. By the end of this project, I expect to construct certain data filters that will result in the most outbursts. I expect to find a few objects that could potentially be what we are searching for.

Physiological and behavioral rhythms are controlled in mammals by a central circadian clock located in suprachiasmatic nuclei of the hypothalamus (SCN). This master clock has outputs to other organs and tissues crucial to keeping the organism properly synchronized. The SCN clock is synchronized by environmental cues, most importantly is the light-dark cycle (LD). Fearful stimuli (i.e. presence of predators) can also present cyclic variations. The de la Iglesia lab has recently shown that timed fearful stimuli during the night can switch the locomotor activity rhythms of mice to the light phase, overriding their natural nocturnal behavior. Interestingly, while the expression of the so-called “clock genes” (which sustain the circadian rhythms at the molecular level) remains unchanged in the SCN, it displays a complete inversion in the amygdala, the brain region that encodes fear. Currently, we aim to determine the pattern of expression of clock-genes in peripheral organs of mice subjected to cycling fear stimuli. Using qPCR, we will assess RNA expression of the clock genes bmal1, per1, and per2 in the adrenal gland, kidney, and liver to determine whether entrainment of activity by cyclic fear also impacts peripheral clocks at the molecular level. We hypothesize that the pattern of expression the clock genes in the liver and kidneys will be modified in mice subjected to nocturnal fear, due to altered feeding and drinking patterns. However, the adrenal gland is difficult to make predictions about the pattern of expression of the clock genes given the fact that preliminary data from our lab showed that cortisol shows two peaks in mice displaying diurnal activity after nocturnal cyclic fear exposure compared to the single peak displayed by nocturnally active mice. Thus, it is unclear if we will observe an inversion peak, much like the amygdala, or a peak similar to the LD cycle.

Chromosome segregation during mitosis and meiosis ensures accurate division of a cell's nucleus to produce daughter cells that each contain a proper set of chromosomes. An important hallmark of mitotic and meiotic cell division is the attachment of microtubules to protein structures called kinetochores. The phenomenon is susceptible to error, causing mis-segregation of chromosomes, which can result in aneuploidy, miscarriage or cancer. During the 1960s, Dr. Bruce Nicklas established the present model for how meiotic error correction transpires. By directly manipulating individual chromosomes in grasshopper spermatocytes, he misaligned individual chromosomes from the metaphase plate and then observed as the chromosomes spontaneously realigned. Dr. Nicklas’ work demonstrated that mechanical tension is required for stabilizing proper kinetochore-microtubule attachments, and that the lack thereof results in detachments that allow the chromosome to reorient correctly. The Asbury Lab aims to further his experiments by using small molecular inhibitors in combination with micromanipulation to determine the role of enzymes such as Aurora B kinase in chromosomal error correction. Here, we tested the impact of Aurora B kinase, using a small molecular inhibitor that has been reported in human cancer models, AZD. Cricket spermatocytes were dissected and soaked in a solution of insect medium and AZD. After treatment, the spermatocytes were spread on a glass slide and filmed under a phase-contrast microscope for three hours. Metaphase cells were filmed because it is expected that Aurora B kinase releases erroneous attachments during this phase of cell division. Our results show that AZD treatment of cricket spermatocytes delays the transition from metaphase to anaphase, confirming that Aurora B kinase plays an important role in chromosome segregation in these cells. Our latest work focuses on fluorescent tagging of chromosomes to better distinguish misaligned chromosomes and to further understand the mechanisms of error correction.

Virtual reality augmentation of therapy has advanced a long way since its beginnings. Virtual reality technologies have been found effective for treatment of post-traumatic stress disorder and phobias as well as a potential aid as an in-treatment distraction for burn patients undergoing dressing changes. The advent of increasingly advanced displays, tracking, and comfort have transformed virtual reality from a novelty into a highly beneficial clinical device. The increasing presence of virtual reality devices in clinical settings necessitates additional investigation into sterilization techniques. The diversity of materials in the devices makes a single method of sterilization difficult. The device’s vulnerable surfaces can be separated into categories: lenses, casing, straps, and facial interface. The delicate electronics preclude the use of autoclave sterilization and the porous nature of the straps and cushioning preclude the use of surface wipes. Finally, the delicate lenses need special care to facilitate cleaning while retaining structure. In the present study UV, steam autoclave, and water-based benzalkonium chloride antibacterial foam were compared to standard procedures by Oculus, one of the leading commercial manufacturers of virtual reality devices. Oculus Go virtual reality headsets were disassembled for testing. After determining baseline presence of environmental bacteria, Staphylococcus Aureus was applied to the tested surfaces. The previously mentioned methods were applied to the newly contaminated surfaces and the surfaces were swabbed and cultured. Effectiveness of sterilization was determined through numerical analysis of colony forming units. While Oculus' standard procedures have adequately disinfected some of the diverse materials tested here, more rigorous methods are needed for complete sterilization. A hospital setting may benefit from a multifaceted and specialized approach that addresses the needs of different materials to prevent increases in resistant strains. Proper sterilization procedures for this rising technology will allow for safe widespread implementation as a medical device.

Archaeologists are increasingly concerned with the long-term preservation and accessibility of research data. However, few have explored the challenges and opportunities of data management in the context of community-based research with Native communities. This project focuses on the data management practices of Field Methods of Indigenous Archaeology (FMIA), a community-based research partnership between UW and the Confederated Tribes of Grand Ronde Historic Preservation Office. It examines how these practices take on special importance when working with Native communities, including how they help bridge gaps between archaeologists’ interpretations of Grand Ronde history and those maintained by the tribal community. To explore this question, I photographed artifacts, digitized field and lab data, and assessed FMIA’s approach to data curation and accessibility. This archive of photographs and digital data ensures that project data remain usable to future researchers and the Grand Ronde community in investigations of tribal history. Thinking through archaeological data management thus facilitates better organization of research data and fosters increased community collaboration.

Youth sports participation can have many benefits, including positive psychosocial development and lifelong healthy activity levels. However, such benefits are often not realized due to attrition from sport. Parents play a key role in shaping youth sport experiences. High pressure sports parenting and disruptive sideline behavior contribute to attrition. Interventions aimed at reducing such parent behaviors exist; however, little is known about their effectiveness. The purpose of this narrative review was to synthesize the extant research on sports parenting interventions. A narrative literature review was conducted between December 2018 and February 2019. Studies were selected if they contained a critically evaluated sports parenting intervention (inclusive, but not limited to education and policies) for parents of children 18 or younger participating in organized sports. Additional articles were obtained via pearling of reference lists. Study quality was appraised using the Downs & Black checklist. Our preliminary search found 13 articles, which included 8 educational interventions and 6 policies. The majority of educational interventions were related to sportsmanship; few included any elements of sports psychology. Many educational interventions were implemented using online videos and non-interactive online modules. Evaluations were of poor methodological quality, consisting primarily of limited-scope qualitative evaluations. No randomized controlled trials have as-yet been published on this topic. High quality research into the effectiveness of sports parenting education and sideline behavior policies is needed to better understand whether existing approaches are effectively changing this important parenting behavior. Future research should seek to use randomized designs and measure behavioral outcomes. Further, studies should move beyond efficacy measures and collect implementation data to understand how policies and educational programs are being used in a range of youth sport settings.

Mental illness is a national concern; for rural residents, the availability of mental health services magnifies the problem. The 2017 National Survey on Drug Use and Health found close to 1.5 million non-urban residents had psychiatric illness or serious thoughts of suicide during 2017. Hypothesis: In Washington State, there is less access for outpatient mental health services in rural areas than in urban areas. The 2018 Washington State Directory of Certified Mental Health, Substance Use Disorder, and Problem & Pathological Gambling Services contains 503 entries of mental health facilities. Using the Office of Community Health Systems Series on Rural-Urban Disparities, facilities with available information were categorized as urban or rural. Statistics were calculated to characterize the availability of individual therapy, and crisis intervention information via public-facing websites for included clinics. The association between rural-urban status and the availability of outpatient psychotherapy and crisis intervention contact information was tested via the chi-squared test of independence. Approximately half (n=131, 50.6%) of clinics with available information regarding outpatient psychotherapy indicated that these services were available. Similarly, nearly half (n=120, 46.1%) of clinics with available information had crisis lifeline information presented via their public-facing website. There was no significant association between urban-rural status and availability of outpatient psychotherapy services (_X²=0.21, p=.647), nor between urban-rural status and publicly available crisis lifeline information on mental health clinic websites (_X²=0.80, p=.371). Washington State rural clinics are not significantly different from urban clinics with respect to saying they provide outpatient psychotherapy and crisis lifeline information. Limitations include methods relying on public reporting of services and limited scope, not allowing the study of other factors that might affect rural residents, such as distance traveled to obtain care. Rural counties in Washington State do not differ from urban counties with respect to the presence of clinics providing outpatient psychotherapy.

2D cell models have traditionally been used in labs to test the effects of new drugs on certain cell types due to the ease and convenience of use. While 2D methods are great, they often simplify the cell-to-cell interactions and may not accurately represent cell systems in humans. 3D methods show the complex cell communication systems and better simulate actual organ systems. Research comparing these two methods can inform scientists on the benefits of 3D models which can help efficiency in creating new drugs. Our lab looked into various 3D models to determine their effectiveness and reliability and looked into the differences in perceived cell mechanics and functionality between 2D and 3D methods. We tried Corning Matrigel and Corning 3D Spheroid microplates for 3D cell modeling using HEK293 cells, which are human embryonic kidney cells that were grown in lab. They are known for being easy to grow and transfect. We used SNAP-Gels, which are protein assays that show the protein levels in the cells, to ensure that the protein levels were similar between the 2D and 3D systems. We then did florescent imaging to determine cell localization and EPIC dynamic mass redistribution (DMR) to determine cell functionality. We found Matrigel to have inconsistent results, so we focused on using the spheroid microplates. Based on our initial results, we saw increased functionality and expression levels for full-length protein cells compared to cells with a truncated N-terminal protein in the 3D method. This increase in functionality and expression levels was not seen in the 2D method. Our results show that 3D modeling methods can be reliable, and do show results that differ from 2D models. This is important for future studies that require cell modeling because 3D models can provide a more accurate and reliable modeling system to create novel therapeutics.

Numerous interventions and genetic modifications have been shown to extend lifespan across a diversity of species. However, these studies often assume that extended lifespan is synonymous with extended healthspan. Recent research in the nematode worm, Caenorhabditis elegans, has questioned this assumption, and suggests that increasing lifespan can prolong the frailty associated with old age. This is particularly important for humans, as increasing lifespan without a corresponding increase in healthspan could spell disaster. The majority of healthcare costs are associated with aging-related pathologies, and prolonging life without prolonging health could radically inflate these costs. To parse out the genetic relationship between healthspan and lifespan, we have turned to Drosophila melanogaster, a well characterized model organism for studies on the genetics of aging. We have collected lifespan data as well as multiple measures of healthspan across these genotypes, and found a strong positive correlation between lifespan and healthspan in these flies. This confirms the importance of lifespan as the primary parameter in aging studies, and suggests that genetic interventions increasing lifespan may generally be accompanied by an increase in healthspan.

Opsins are the light-sensitive proteins in photoreceptors that mediate vision. They are most commonly known to be expressed in rods and cones in the retina of the eye, but some are also expressed in various tissues throughout the body. Because previous research has shown that retinas from OPN3 knockout mice have altered circadian amplitudes, my goal is to further investigate the effects of OPN3 on circadian rhythms of various tissues. In order to determine which tissues actively express OPN3, rtPCR analysis will be done on a variety of Wild-Type (WT) mouse tissues. To determine how circadian amplitude and rhythmicity is affected by OPN3, tissues from both WT and OPN3 knockout mice with the Per2 Luciferase marker are cultured and have their circadian rhythms recorded and analyzed. These cultures are also used to determine the effect of OPN3 on ability to synchronize to light-dark cycles, and to begin investigating the mechanism through which OPN3 works. Preliminary results show that OPN3 knockout mice have significantly decreased amplitudes in tissues actively expressing OPN3, although the lack of OPN3 does not affect rhythmicity or the ability to synchronize to light-dark cycles. So far, I have seen that OPN3 is not acting through a diffusible substance, as other opsins have been shown to do. More investigation should be done in the future to determine the exact mechanism through which OPN3 works, as it will have important consequences for understanding the circadian system. 

Bignoniaceae, also known as the trumpet creeper family, consists of 800 species of trees, shrubs, herbs, and lianas. Bignoniaceae diversity is highest in the Neotropics, but have a worldwide distribution in both tropical and temperate zones. Molecular phylogenetic studies recognize 8 major clades in the family. The goal of this work is to construct an updated Bignoniaceae phylogeny by gathering all available DNA sequence data in the family from previous studies, GenBank, and unpublished sources. I organized, gathered and selected genetic data that I used to create locus alignments for a concatenated matrix. Phylogenetic reconstruction of the concatenated data was done using Maximum Likelihood and Bayesian methods. With these results, we aim to better understand family-wide diversification patterns in the family. Previously recognized clades are supported, additional resolution among them is obtained, and major biogeographic events are reconstructed.

Our Lab, GEMSEC, uses molecular biology, bioinformatics, genome sciences, and engineering for de novo design of short amino acid sequences for various applications such as tooth remineralization strategies in dentistry, biosensing in cancer diagnostics, and bioelectronics in single-molecule detection. Designing and constructing peptides for a desired function begins with selecting the appropriate sequence of amino acids with the predictive conformation that affects the function. In this project we use latent-space representation (matrix factorization) in conjunction with a simple neural network to create a model that is able to predict peptide binding affinity to several alleles of MHC-I protein. Python was used to encode amino acids by creating data frames defining the functional groups within them, differing by n-terminus, intermediate, and c-terminus of each amino acid and their placement along the backbone of each structure. A tensor was created using the data frames describing each amino acid to encode the 9- and 10-length sequences of thousands of unique peptides from the Immune Epitope Database. Each chemical structure and peptide sequence can be described by k attributes, or latent features. Matrix factorization was used to discover the latent features and send this feature encoding to a neural network (NN) to determine binding affinity. The goal is to minimize the mean-squared-error by stochastic gradient descent in a supervised learning protocol. The two modules of matrix factorization and NN provide an optimum between interpretability and predictability simultaneously.The successful prediction of peptide binding affinity towards nanoscale targets provides novel opportunities for drug design towards targeted public health initiatives and in technology applications such as bio/nano hybrid devices. This research is supported by NSF/DMR-DMREF program under the Materials Genome Initiative.

This research focuses on using advanced surveying techniques as well as hand mapping to analyze force distribution during laboratory impacts of man-made projectiles into ice. This is done in the hopes of characterizing substrate damage surrounding an impact crater created by a proposed hard landing system. Knowing where these different deformation zones occur is useful in determining where the lander could sample. The landing system, the Subsurface Ice Plume Sampler (SIPS) utilizes ejecta (broken up debris thrown from the crater) to create a transient atmosphere - decelerating a secondary instrument package through momentum transfer. Small-scale experiments were done on one-ton buckets of ice using scale-sized projectiles. Between two hundred and five hundred images used to 3D models of the ice craters using the structure from motion imaging technique. Hand mapping of the deformation zones (areas of different types of fractures) was conducted to compare to the 3D model to help show the directionality of force distributions through the crater. Using both the 3D models and a hand mapping analysis of the craters, we were able to determine that the crater shapes were atypical. In a typical crater, the force disperses radially outward from the impactor; however, we determined that the majority of the force was focalized directly below the impactor. Future work includes using Rhinoceros 3D computer software to quantitatively analyze each crater’s individual morphology, curvature, and volume and compare them to traditional impact craters.

Secondary nucleotide messengers are used by all domains of life to sense and respond to the changes in their environment. In bacteria these secondary nucleotide messengers play a role in regulating several signaling pathways such as cell wall homeostasis, motility, and the expression of virulence genes. The nucleotide cyclic di- 3, 5’ adenosine monophosphate (c-di-AMP) was recently added to the list of secondary nucleotides. C-di-AMP is found in many bacteria such as S. aureus, S. pneumoniae, B. subtilis, and L. monocytogenes (Lm). C-di-AMP has been best characterized in Lm, a well-studied intracellular pathogen. Lm has adapted to survive and replicate in the host cell cytosol by evading host cell defenses through use of key virulence factors. In Lm, synthesis of c-di-AMP is catalyzed by the diadenylate cyclase dacA and degradation is coordinated by the phosphodiesterases, pdeA and pgpH. Studies using Lm mutants that lack both pdeA and pgpH contain abnormal c-di-AMP levels that cause growth and virulence defects of about four logs compared to wild type Lm. This highlights the importance of c-di-AMP regulation for bacterial virulence and growth, but we still know very little about c-di-AMP regulation and toxicity. Our goal is to further understand the toxicity of high levels of c-di-AMP during bacterial infection. We aim to create a transposon library in the double phosphodiesterase KO (ΔΔ Pde) background to identify suppressor mutations. Previous approaches to analyzing suppressor mutations in the ΔΔ Pde strain has not been thorough or cannot be utilized in vivo. Therefore, we have created an amenable phosphodiesterase mutant that knocks out the phosphodiesterases in Lm (pdeA and pgpH) to grow in vivo successfully to investigate c-di-AMP regulation. Understanding the regulation of c-di-AMP could result in targets for novel treatments against Lm and allow for ways to investigate regulation methods of c-di-AMP in other organisms.

Distal Arthrogryposis (DA) syndromes are a group of disorders with a wide breadth of phenotypic severity. A previous study found that individuals with recessive Spondylocarpotarsal Synostosis Syndrome were compound heterozygous, that is, there was the presence of two different variant alleles at a specific gene locus, for a coding variant found in the gene Myosin Heavy Chain 3 (MYH3) and a non-coding variant found at the location c.-9+1G>A (rs557849165), also in the same gene. We are interested in discovering if individuals with DA and MYH3 variants are carriers for this variant, c.-9+1G>A, to explain more severe phenotypes seen. We hypothesize that rs557849165 has a role in phenotype severity of individuals with DA. We screened our cohort of individuals with DA and MYH3 variants in the previously unscreened non-coding region of exon 2. We did not detect the variant in any individuals screened in our first cohort. Individuals that did not previously produce results for analysis are being re-screened for the same variant. Further investigation is being conducted on additional DA candidates to better identify the genotype-phenotype relationship of various forms within DA1, DA2A, and DA2B. Some cases of DA are more severe than others due to specific variants in MYH3 and we are trying to better understand the effects these variants have on these individuals with DA.

Diet influences mammalian physiology and has been linked to obesity and the development of carotid artery disease. Carotid artery disease (CAD) is a result of plaque buildup in arteries leading to the brain and other parts of the head, reducing blood flow and increasing the risk of stroke. Rates of obesity and carotid artery disease are higher in countries with Western diets (higher saturated fat and carbohydrate composition) compared to those with Mediterranean diets (higher produce and monounsaturated fat composition). Although there is evidence demonstrating the effect of diet on overall health and physiology, the mechanisms by which these changes arise could be better understood. These health consequences of diet are thought to be mediated by changes in gene expression caused by eating different diets. Understanding how diet influences gene regulation in different tissue types could give critical insight into our understanding of diet’s effect on physiology. To this end, I measured gene expression via RNA-Seq in 37 cynomolgus macaques (Macaca fascicularis) that were randomly assigned either a Western or Mediterranean diet. By analyzing gene expression in samples collected from two types of fat (subcutaneous and visceral) as well as two arterial tissue types (iliac and carotid), I aim to gain insight into the transcriptomic changes due to diet. Further, by understanding diet’s role in gene regulation, I aim to construct a clearer picture of the mechanisms through which western diet might heighten the risk of obesity and the development of CAD. I predict that the differentially expressed genes in fat tissues will be associated with obesity and that the differentially expressed genes in the arterial tissues will be associated with plaque build up and CAD. This study will illuminate how diet mediates gene regulation in a variety of tissues, providing a mechanistic link to diet-related diseases such as obesity and CAD.

Analysis of faunal remains provides crucial insight into the subsistence patterns of past groups. This is particularly important for the Grand Ronde community in northwestern Oregon, where past and present populations have balanced traditional practices and lifeways with imposed colonial assimilation pressures and economies. This research examines faunal remains found at the Molalla Encampment and Grand Ronde Agency Schoolhouse, two nineteenth and early twentieth century archaeological sites on the Grand Ronde Reservation. Our research focuses on documenting and analyzing faunal remain attributes such as degree of fragmentation, taxonomic presence, and bone modification at the two sites. In addition to comparative faunal analysis, our research takes a step further by looking into the implications of observed bone modifications. Aided by archival and primary sources, we reconstructed the taphonomic pathways of these remains, determining whether they have been altered by either humans or animals. For example, our analysis of cut marks revealed if meat was butchered commercially at the site, what meat cuts were consumed, and meat prices at Grande Ronde during the early 1900s. Comparing these data by site and stratigraphic level paints a better picture of life at Grand Ronde across space and time. This research provides insight into subsistence patterns within the Grand Ronde community and how they navigated the challenges and opportunities of life on the reservation.

Heritable spinocerebellar ataxias (SCAs) are rare genetic neurological disorders that affect the cerebellum and sometimes the spinal cord. As a result, those with SCA often have problems with movement and coordination. In my experiment, I analyzed a pedigree where several family members had a dominant, late-onset spinocerebellar ataxia. The family tested negative on the tests for all known variants causing dominant spinocerebellar ataxias. Thus, my goal was to find what genetic variant was responsible for the SCA in this pedigree. I began by obtaining exome sequences for two of the affected family members. The exome sequences listed all of the variants present in each individual’s exome. My approach to variant filtering steps were selecting shared heterozygous variant, an assessment of population frequency, functional significance, and evolutionary conservation, and then prioritizing the remaining variants based on candidate gene function and expression, animal models and relevance to neurologic disease. The process resulted in a list of candidate variants. I then created primers for my candidate variants and ran PCRs with DNA samples of both affected and unaffected family member. The DNA fragments generated from the PCR were then sequenced. The only candidate that co-segregated was a variant c.158T>C, p.Ile53Thr in STUB1 a gene known to be associated to a recessive SCA. The pathology study to review the abnormality in the patient autopsy brain was performed by our collaborators. Our finding confirmed that STUB1 can cause autosomal dominant hereditary cerebellar ataxia in addition to recessive form of this disease. It is increasingly apparent that variants once associated only with one form of inheritance are in fact capable of causing both recessive and dominant forms.

 Antibiotic resistance is a growing threat to public health. This resistance, coupled with a dearth of new antibiotics, makes the study and development of antibiotics of critical importance. Many antibiotics derive from microbial pathways that synthesize complex natural products, and engineering these pathways to produce new antibiotics is an exciting prospect. I aim to use such a strategy to produce variants of the klebsidin lasso peptide, known for its distinct lariat knot structure and its antibiotic activity. Klebsidin is produced by three biosynthetic enzymes that modify and export a ribosomally-synthesized precursor peptide. We have developed an assay that relies on cellular growth to (1) investigate how mutation influences the antibiotic activity and biosynthesis of klebsidin, and to (2) identify variants of klebsidin that overcome a known resistance mutation. When expressed in E. coli, klebsidin inhibits growth of its host cell. I expressed a library of approximately 10,000 klebsidin variants, each within a single cell, and used next-generation DNA sequencing to count the frequency of each variant before and after a growth selection. Functional klebsidin variants should decrease in frequency after selection, whereas null variants should increase in frequency. Using these sequencing data, I generated functional scores for a majority of single amino acid mutations within klebsidin, identifying positions that tolerate mutation and positions for which mutation abolishes bioactivity. To better understand these trends, I am performing mass spectrometry experiments to study the biosynthesis of key variants. In addition, we are interested in how mutagenesis of klebsidin can combat known resistance to lasso peptides. By performing the same growth selection in an E. coli strain resistant to wild type klebsidin, we hope to identify variants that overcome this resistance. Together, these studies will provide a framework for understanding lasso peptide engineering and identifying novel peptide-based antibiotics.

Microglia are innate immune cells in the CNS that exhibit a sustained pro-inflammatory response in the Alzheimer's disease (AD) brain. Sustained pro-inflammatory responses by microglia can promote excessive synaptic pruning and neuronal death, exacerbating neurodegeneration. MicroRNAs can regulate microglia inflammatory behaviors by modifying gene expression at the post-transcriptional level by suppressing expression of target genes. MiR-155 is a microRNA that targets suppressors of inflammation and is dysregulated in neurodegenerative disorders. Additionally, miR-155 deletion has been reported to be neuroprotective in several models of neural injury and degeneration. The impact of microglia specific miR-155 regulation on the neuroinflammatory response or behavioral outcomes of AD models has yet to be elucidated. We hypothesize that miR-155 deletion in microglia decreases neuroinflammatory response to AD, thus improving memory impairments typically observed in AD. We use a mouse model expressing a transgene of associated mutant forms of human amyloid precursor protein and presenilin 1 (APP/PS1). We crossed APP/PS1 mice with a tamoxifen-inducible Cre model or a constitutive Cre model to conditionally or constitutively delete miR-155 in microglia. We use open field chambers and T-maze to assess general behavior and spatial memory at 6, 9, and 12 months. When miR-155 was deleted specifically in microglia, no difference was seen in the spatial memory as measured through T-maze tests, compared to APP/PS1 mice. However, increased locomotor activity was seen in open field tests at 6 and 9 months. Similarly, when miR-155 was deleted in microglia and peripheral myeloid cells, there were no significant differences in spatial memory, though increases in locomotor activity at 6 and 9 months and potential decreases in anxiety at 6 months were also seen in open field. These results suggest that miR-155 may play a more complex role in the regulatory response of neuroinflammation during AD.

Previous research on JNK-mediated stress signals demonstrated that stem cells in the posterior midgut of Drosophila Melanogaster only undergo compensatory proliferation or apoptosis. However, our group discovered that the stem cells can also undergo the process of basal extrusion and dissemination, resulting in the cells being eliminated from the tissue into the hemocoel, the blood containing intertissue body cavity. The JNK signal promotes the cells to exit the epithelium of the gut, move through the muscle layer, and be released to the hemocoel, which resembles the process of metastasis in human cancer. In order to understand the mechanism of this extrusion process, we carried out a RNA Interference (RNAi) screen and sought to find genes that are necessary for the stem cell extrusion in the JNK activators, rasv12 and HepCA, expressed flies. We used the ESG-GAL4, UAS-GFP, TUB-GAL80TS(EGT) genetic system to study the knockdown effect from the RNAi of each gene. After 4 days of inducement, which is the sufficient time for the JNK signal to promote complete extrusion of the intestinal stem cells, the intestines were dissected, fixed, mounted, and examined with a fluorescent microscope for any presence of stem cells. Our previous research from last year focused on the first phase of screening of possible RNAi lines involved in cell extrusion. Our results from this year focuses on our second phase of further identifying characteristics of cell movement in rasv12 flies.

Modification of biomolecules is responsible for the regulation of cellular activities in all organisms. A type of enzyme, named ADP-ribosyltransferase (ART), plays a crucial role in such modifications by transferring one or multiple ADP-ribose moieties onto its target molecules. Some bacterial ART proteins are toxins that serve as virulence factors that enable pathogens to disrupt host cell functions during persistent infection. However, it was unclear if ARTs play roles in interbacterial interactions. Here, I report the discovery of the first interbacterial ART toxin encoded by a Serratia proteamaculans strain, a commensal bacterium isolated from plant root. Growth competition assays showed that the toxin is capable of conferring a higher fitness for S. proteamaculans. Subsequent analysis by microscope revealed that target bacterial cells became elongated, leading up to cell lysis. Together, my results offered new insights into the complex question of how bacteria compete against each other. The finding expanded our knowledge of the diverse roles of ART proteins and their cellular activities.

Spinal cord and traumatic brain injuries (SCI and TBI) result in secondary injury causing further damage to neural cells, due to mechanisms of inflammation and cytotoxicity. Though some anti-inflammatory drugs have shown promising results in reducing secondary injury in animal models, their use is controversial in clinical practice due to systematic side effects at the required high dosage with questionable efficacy. An electrically controlled drug release system will allow for spatiotemporal control of drug delivery and might solve some of the issues with systemic dosing. We designed and fabricated a polypyrrole (PPy) microneedle array for control release of dexamethasone for application to the nervous system. Using micro-scale 3D printing, microneedles design were 3D printed in photoresist and sputter coated in gold to form a conductive surface. PPy was electrodeposited onto the microneedle arrays from a monomer solution of pyrrole and dexamethasone. Dexamethasone can then be released from the PPy layers by applying a negative potential. Dexamethasone release was quantified using absorbance spectrometry, after purification through high pressure liquid chromatography. Dexamethasone PPy arrays were then tested in an in vitro model of neuroinflammation. One hour after inflammation activation, cells received treatment. After 48 hours of incubation, cells were assayed for nitric oxide and cytokine production. Experimental results show sufficient release using electronically controlled dexamethasone release from PPy microneedles to decrease nitric oxide. There was a trend towards decreasing inflammatory cytokine release, but future experiments with higher sample sizes will be needed to prove significance.

An increasing number of American adults are participating in consensual non-monogamous practices. Within the umbrella term of consensual non-monogamy lies polyamory. Researchers in fields spanning from Sociology to Neuroscience have researched jealousy, emotional territoriality, and whether or not a person can love more than one person at the same time. Scholars have explored how jealousy and expectations are managed within polyamorous relationships and research has found that polyamorous partners use particularly constructive and honest methods of communication. Polyamorous communities contain diverse populations varying by social class, sexual identities, race, ethnicity, education level and socio-economic status. While some research has been focused on how humans manage jealousy, there is presently no research on jealousy management in people who have various socio-economic backgrounds and diverse sexual and gender identities. The literature, as it presently exists, states that all you have to do to have a 'healthy' (polyamorous) relationship is to communicate your feelings well. My study fills this gap with the following research question. In a romantic polyamorous relationship, how do participants' social experiences and backgrounds influence their expressions of jealousy and expectations in a fulfilling relationship? Through interviews, lasting one hour each, with over ten adult polyamorous individuals, answers to this research question yields a more complete understanding of polyamory. This contributes to our understanding of how intersectional identities matter in intimate relationships. 

We identified an optically varying light source in the night sky labeled PTFS1623al. In our search for interesting stars, this object caught our attention when we found that it was within the X-ray emitting region 1RXS J235728.5+671600. The light that came from the object varied by 2.5 magnitudes over a 96 minute period. An average light source only varies by a tenth of a magnitude over a week, month, or even a year time scale. The large change in magnitude over such a short period sparked our investigation. We confirmed this 2.5 magnitude variability with the Neil Gehrels Swift space based gamma ray observatory using the X-Ray Telescope as well as confirm a correlation between the optically varying source and the X-ray emitting source. Using the Keck telescope on Mauna Kea and the Low Resolution Imaging Spectrometer or LRIS we collected spectroscopic data. Spectroscopic data is a different way of viewing light where the individual molecules in the object radiate light at different wavelength allowing us to identify the specific elements in an object. Geometry of the object can also be identified by the shape of the spectral lines. We identified strong double-peaked Hydrogen and Helium emission lines with phase-dependent morphology. After reading through scientific literature and making comparisons, we concluded that the features present in the spectroscopic data are consistent with a magnetic cataclysmic variable, or a magnetic accreting white dwarf star. Accretion is the process of moving mass from one star to another, so this system is a binary system with an unknown donating star. A white dwarf and cataclysmic variable are two exotic classifications of a star with unique spectral characteristics. We present our observations and discuss their implications for our understanding of the system parameters.

Nuclear magnetic resonance (MR) is a phenomenon which may be harnessed to provide high resolution images of the soft tissues of the body and aid in the diagnosis of many diseases. MR imaging relies on measuring the alignment, perturbation, and realignment of the magnetic dipole moments of hydrogen nuclei composing water molecules. Differing rates of realignment, or relaxation, of the magnetic moments of the hydrogen nuclei after perturbation creates contrast in MR images. This contrast can be enhanced by the introduction of magnetic field disturbances in the vicinity of hydrogen atoms. Clinically, contrast enhancement in MR imaging is achieved with chelates of the strongly paramagnetic metal, gadolinium. However, increasing evidence indicates that gadolinium can cause nephrogenic systemic fibrosis in patients with renal damage. Iron oxide nanoparticles (NPs) may be safer alternatives than gadolinium-based contrast agents given iron’s biodegradability and physiological role in hemoglobin. This research optimizes iron oxide NPs for use as contrast agents in MR imaging. We evaluate two important MR imaging parameters, the transverse and longitudinal relaxivity, of iron oxide NPs as a function of core size at two different magnetic field strengths. Our findings show that both the transverse and longitudinal relaxivities of iron oxide NPs decrease with decreasing core size at a low field strength, but transverse relaxivity decreases while longitudinal relaxivity increases at high field strength. Furthermore, we find that the transverse relaxivity component is more strongly influenced by core size than the longitudinal relaxivity. These trends in MR parameters as a function of core size will allow for the optimization of iron oxide NP as contrast agents for MR imaging.

In the era of new technologies, the functions of mobile apps cover all aspects of our lives. Social networking apps expand our social and business groups, as well as increase job and entertainment opportunities dramatically. Other types of apps, such as travel and buying & selling apps, enable people to get both tangible and intangible products without leaving home. The fast development of mobile apps, however, made it difficult for elders over 65 to understand and learn, and the physical condition of elders presents barriers to operating new technologies. Overall, the lack of accessible design on mobile apps has caused elders to not have the equal opportunity to obtain information and enjoy the same conveniences as other age groups; and new technologies have gradually made the older generation feel abandoned. In the past six months, I conducted a competitive analysis of the current situation of using mobile apps by the elderly to gain a broad view on the user experience of mobile apps for elders. I designed and distributed a questionnaire survey among members of the Yakima Serious Table Tennis Club to understand the barriers they encountered when using various types of mobile apps. I interviewed two retirees from different fields of employment and cultural backgrounds about their views on the usability of different kinds of mobile apps. Ultimately, referring to my collected data and the Web Content Accessibility Guidelines version 2.1, I analyzed possible changes that could be made by some popular apps to improve the accessibility for elders. I created interface templates of an accessible mobile social media for elders using Adobe Experience Design; then I edited it to a final version while doing usability tests on the templates. The conclusions from this research could be used to help design applications that are suitable for more age groups, and to ultimately make society more inclusive by letting elders have equal opportunity to enjoy new technologies.

Proper development of an organism relies on the tight regulation of gene expression in cells and errors can lead to diseases or improper growth. Corepressors interact with DNA-binding proteins and inhibit gene expression. In the model plant Arabidopsis thaliana, the corepressor TOPLESS (TPL) is a member of a deeply conserved Gro/Tup1/TLE family. I am studying which helices in TPL monomers are necessary and sufficient for homotetramerization. Additionally, I’m investigating what proteins TPL interacts with to control repression, especially mediator components and histone deacetylases (HDACs), which previous studies have identified as potential interactors. I am using a protein-protein interaction assay known as the cytoplasmic split-ubiquitin system (Cyto-SUS). In my assay, a bait (TPL) and prey proteins hypothesized to interact with TPL are attached to two halves of ubiquitin. If the bait and prey successfully interact, then ubiquitin is reformed and a ubiquitin-specific protease cleaves a transcription factor to induce expression of genes producing adenine and histidine. Successful interaction is measured qualitatively by observing growth of yeast on plates that lack adenine and histidine. Only certain helices of TPL are observed to interact with full length TPL. Specifically, truncations that are sufficient to drive repression in a synthetic yeast assay are insufficient to multimerize. This means that the multimer state is not required for repression. Secondly, we found that the N-terminus of TPL directly interacts with mediator through MED21, suggesting that TPL regulates recruitment of RNA Polymerase II. Other corepressors of the Gro/Tup1/TLE family, like Tup1 found in yeast, and the mammalian homolog Transducin-like enhancer of split (TLE) are known to homotetramerize and interact with similar regulatory elements like TPL, including: HDACS and mediator components. Understanding homotetramerization of TPL and its role in repressive mechanisms is pivotal for comprehending how corepression works across eukaryotes.

Filoviruses are a family of viruses including the Ebola and Marburg viruses which pose serious threats to global health, as evidenced by the 2013-2016 West African Ebola outbreak. Lloviu virus (LLOV) is a recently discovered filovirus associated with large bat die-offs in Spain and Hungary. Its effects on humans are unknown; however, similarities to other deadly filoviruses suggest it may have similar infectivity. Live LLOV has not been isolated, hindering vaccine research and development. The goal of my project is to develop a model “pseudotype virus” of LLOV using non-pathogenic vesicular stomatitis virus (VSV) as a backbone expressing LLOV viral envelope glycoprotein. I modified and optimized existing methods used to produce VSV pseudotype viruses by transfecting cells with plasmids expressing the VSV genome, modified to produce LLOV viral envelope glycoprotein. This pseudotyped LLOV can now be used to test vaccines against LLOV and provide insights into this understudied virus.

Noncommunicable diseases (NCDs) are responsible for the majority of all global deaths. They reduce quality of life on a mass scale and threatening the United Nation's 2030 Agenda for Sustainable Development while creating massive financial burden in the Global South and developed countries alike. However, in 2017, NCDs received only 2% of total development assistance for health (DAH) in 2017 despite causing 67% of global deaths. This is a signficant lack of alignment between disease burden and funding. Researchers state that donor groups divert DAH to other causes because they are unaware of the impact of NCDs in low and middle income countries. In addition, curbing NCDs on a mass scale requires highly complex responses in comparison to the more cost-effective and evidence-based approaches for many infectious diseases. However, these claims are based on primarily anecdotal studies and there is limited quantitative research on how donor groups allocate foreign aid for NCDs. This report aims to understand how donor groups prioritize economic, political, social, and epidemiological determinants when deciding the level of DAH to provide to countries for NCDs. The master dataset is provided by RTI International and consists of grants for NCDs from 2010 to 2015. It is merged with demographic, economic, geographic, and epidemiological data extracted from publicly available sources. I model correlations between these factors and DAH received using a multiple linear regression. As foundations and NGOs provide the majority of global funding for NCDs, I concentrate on this donor group. I hypothesize that NGOs and foundations concentrate on health indicators and level of corruption when allocating aid for NCDs versus economic indicators, such as level of trade openness. Further research of donor behavior and development assistance for health will contribute to greater transparency in funding processes to better address the emerging NCD pandemic.

Antibiotics are an environmental contaminant increasingly found in aquatic ecosystems, adversely affecting wildlife and contributing to antibiotic drug resistance. Sources include untreated agricultural runoff entering rivers and estuaries, outdated or leaking septic systems in rural areas, and large urban populations excreting unmetabolized medications into sewage systems. Current wastewater treatment methods are unable to effectively mitigate the release of these environmental toxins, thus new approaches are needed. White-rot fungi produce lignin-modifying enzymes which can degrade persistent organic pollutants, including antibiotics. Previous studies have demonstrated that the mycelia of turkey tail (Trametes versicolor) and shiitake (Lentinula edodes) mushrooms can reduce concentrations of the common antibiotics erythromycin and cefuroxime, respectively. In this study, three species of fungus (turkey tail, shiitake, and oyster mushrooms/Pleurotus ostreatus) were combined to create a more dynamic and effective approach to removing antibiotics from wastewater, using commonly available equipment and low-maintenance growth conditions. The fungi were cultivated at room temperature in modular bins, connected in series with removable tubing. The mycelia of the fungi were exposed to antibiotic solutions (erythromycin and cefuroxime dissolved in water) and tested for rates of removal in two phases. The first phase established a baseline rate of removal for each single fungus/antibiotic pair; the second phase optimized the sequence of fungus species and method of exposure (continuous flow vs. batch mode) to improve filtration of a synthetic wastewater solution containing both antibiotics. Results suggest that combining fungal species may be a more efficient method of filtration compared to methods using a single species. This is a promising step towards advancing the practical technologies available for complex wastewater treatment in various settings.

Last year, our team conducted an exploratory study to characterize the prevalence and admittance factors of STEM degrees across the U.S. with Additional Requirements to Entry (ARE). By gathering data on universities with these programs and surveying their administrators, we gained a general understanding of the state of competitive majors across the nation. We found that GPA was the most frequent criteria of admittance for these programs, which were mostly in engineering and life sciences. Furthermore, we determined that the most common reason for the implementation of these programs was limitations on faculty, funding, and administrative support. These findings suggested that further study into these programs is warranted. Thus, our current aim is to characterize the impact of these programs on the student experience at the University of Washington, particularly those of students from minority and low income backgrounds. To this end, we conducted focus groups throughout winter and spring quarter of 2019 to evaluate student experiences with competitive majors and assess whether there are consistent themes across them. We will be supplementing these qualitative data with quantitative data from survey questions administered to a large number of UW undergraduates. Because GPA is often correlated with socioeconomic or minority status, we hypothesize that these programs may discourage students or disproportionally exclude minority groups from entering high-earning STEM fields. The qualitative and quantitative data of this project will further add to our understanding of the effects and scope of competitive majors.

Loss of heterozygosity (LOH) is a form of genomic instability that is common in cancer and can result in loss of function of tumor suppressor genes. LOH can occur as a result of interhomolog recombination (IHR). We are studying the mechanism of IHR using a human cell line engineered to report on the frequency of IHR at the gene encoding the cell surface protein, CD44. In this line, one allele of CD44 carries an inactivating mutation in exon 1 and the other in exon 17, so no surface CD44 protein is produced and the cells are sCD44- by flow cytometry. Our laboratory has shown that double strand breaks (DSBs) targeted by CRISPR/Cas9 to sites between the two mutations will stimulate IHR and generate sCD44+ cells, which are readily quantified by flow cytometry. We are working to identify the factors that regulate IHR. This will enable us to control the frequency of IHR and may help to reduce the frequency of IHR that results in loss of tumor suppressor gene activity in tumors.

Space travel and exploration provides a new perspective of the universe and our place within it. Private companies are taking the leading role in driving the aerospace industry. Many of these companies are looking for new technologies that will lower the cost of spacecraft production and operation. This goal could be achieved through the development of a multi-use modular launch vehicle. This project created a scaled modular rocket utilizing an adjustable ring fin design. The adjustable ring fin allows the user to easily and quickly change the aerodynamics of the rocket to compensate for a variety of payloads. Four test models were created using Callisto rocketry kits. Three of the Callistos were modified with a variety of ring fin diameters, and one was kept as an unmodified control. The live test parameters were based on rail velocity, visual stability, and altitude. After the baseline performance of each ring fin was established, the lengths of the rockets were adjusted to simulate different payloads. This work demonstrates that adjusting the ring fin allows the same base rocket to fly a variety of payloads without needing to construct a new rocket. Successful flights of the test vehicles, with improved performance based on our alterations, provide a new avenue of research into incorporating small modifications to garner a wide array of uses without extensive and costly modification. Further research will involve scaling up to rockets with motors with an impulse up to 10,000 newton seconds, as well as testing other innovative concepts related to modularity and revisions to the ring fin design. The ultimate goal is the design of a single rocket with a changeable ring fin that can be used in a wide variety of applications, saving money on research and development of new launch systems.

Everyone dying at home requires help from a care partner (CP). For most people, these CPs are family members and friends who help their loved ones with daily tasks, medications, and comfort measures. Those who engage hospice services also benefit from the support of experienced medical/social service teams. By definition, the focus of hospice care is on a family unit, although currently there are no broadly disseminated systematic methods for assessing the needs of CPs or offering preventative interventions. My mentors, Dr. Sadak's team, conducted a pragmatic trial of assessing CP needs in hospice by adapting "Managing Your Loved One's Health" (MYLOH), a 29-item self-report measure of CP activation: readiness, knowledge, skills for meeting their care recipient's healthcare needs and maintain personal wellness for use in hospice. I reviewed and thematically coded: 1. Video interviews with RN case managers and administrators, 2. Researcher's field notes, and 3. All other documented communication between the research and the hospice teams; created a timeline and documented the rationale for adaptations that were made in MYLOH. Methods: A Sample of N=50 CP of people receiving hospice care; N=14 RN Case Managers; N=6 Hospice Administrators. MYLOH and several other brief CP assessment measures were administered by RN case managers to CPs on baseline, week 4, and week 12. Measures were used as a guide for conducting CP/Patient needs assessment, and to plan and assess effectiveness of interventions. Case managers took process notes and offered feedback via video-recorded interviews with the research team. Adaptations to MYLOH were made based on this iterative feedback. MYLOH-Hospice is a 12-item measure that is a useful tool for guiding assessment and interventions for CPs in hospice, it has strong face validity and acceptability, but is found to be too long for iterative routine use.

Traditional geotechnical ground improvement processes oftentimes rely on hazardous chemicals and high energy. Microbially Induced Calcite Precipitation (MICP) offers an eco-friendly alternative and is a bio-mediated cementation method that can improve the shear stiffness and strength of soils by cementing particle contacts. In this process, calcite precipitation is initiated by indigenous bacteria through the hydrolysis of urea, which produces solution alkalinity and ammonium. Following treatment, bio-cemented soils contain high concentrations of ammonium by-products that have the potential to harm environmental and human health. Previous research work has been performed to evaluate the ability of rinse injections to remove nitrogen by-products. In this study a meter-scale bio-cementation experiment was performed and developed rinse techniques were examined. Five 3.7-meter, horizontally oriented, rectangular soil columns were cemented and subsequently rinsed with 13 pore volumes of a high pH, calcium chloride solution. Columns varied in applied treatment techniques and soil types. The first received a standard enrichment stimulation solution to achieve a higher bulk ureolytic activity. The second was treated with a reduced enrichment stimulation solution to reduce ureolytic activity and aim for improved uniformity of cementation over the column length. The third column was augmented with Sporosarcina pasteurii to match the ureolytic rate in the standard enrichment column. Fourth and fifth columns both received the reduced enrichment treatment on different soil types, a marine fine sand and a different alluvial sand, respectively. Shear wave velocities, aqueous samples, pore pressure measurements, and soil samples were collected over the course of the experiment. After injecting 13 pore volumes of rinse solution, aqueous samples suggest that ammonium concentrations were reduced from ~500 mM to less than 2 mM in all columns. After a 24 hour retention period, however, increases in concentrations were observed suggesting the potential for ammonium by-product leaching in time. This work moves MICP closer to field implimentation and wider-use.

All around the world, humans depend on cultivating plants for medicine, food, landscaping and building materials. Understanding how plants grow helps people make more informed decisions about what to grow and how best to grow it. The plant hormone auxin plays a key role in determining almost all aspects of plant growth and development. The Nemhauser Lab has previously determined that two versions of the receptors for auxin, TIR1 and AFB2, function at different speeds in the model plant Arabidopsis thaliana. Currently, we do not know how this speed disparity affects specific plant functions. My hypothesis is that there are measurable differences in organism functions caused by this difference in molecular speed. In the past, full knockout mutants for TIR1 and AFB2 did not exist, making it difficult to answer this question. To complete my research, I developed these mutant plant lines, determined functions that can be quantitatively measured, and collected and analyzed the data. Because the auxin-signaling network affects so many plant functions, any additional information we can gain about how this network functions in the model organism helps us move towards a more complete understanding of plant growth. This could positively improve the efficacy of agriculture and other plant-based industries, as well as moving us towards other new discoveries in the field of plant growth.

The identification and characterization of natural and artificial protein-protein interactions are fundamental to science and engineering. Although many technologies have been established to expedite research in this area, all can hardly meet the need to analyze vastly diverse protein-interactome networks, dynamics, evolution, and druggability. To develop a high-throughput quantitative interaction profiling technology, multimeric protein interaction sequencing (mPI-seq), we performed a 20×20-plex binding assay in a single aqueous solution using a set of de novo designed heterodimeric pairs. First, we barcoded the proteins with DNAs by ribosome and mRNA display. Then, barcoded proteins were assayed en masse in aqueous solution and immobilized into an ultrathin polyacrylamide gel layer attached to glass surface for in situ sequencing. DNA barcodes were amplified into discrete DNA clusters (polymerase colonies or polonies) and then sequenced using sequencing by synthesis. Finally, the protein-protein interactions were measured on the basis of the statistics of colocalized polonies arising from barcoding DNAs of interacting proteins. Through this project, we aim to establish a robust quantitative method to measure protein binding affinity massively in parallel and to use the large-scale functional data set to guide computational protein design.

PTEN is a tumor suppressing protein that carries out important cell functions such as inhibiting cell growth and promoting genomic stability. Somatic variants of PTEN can lead to cancer, and PTEN mutational status has shown to be an indicator of patient survival and prognosis. However, it is not clear whether cancer-associated PTEN variants affect cell growth, genome stability, or both. Here, we demonstrate that simple competition assays can quantitatively assess PTEN variants for their effect on these two important cellular functions. Cells expressing cancer-associated PTEN variants tagged to blue fluorescent protein are mixed with cells expressing wild-type (WT) PTEN tagged with a red fluorescent protein. The proportion of blue and red cells are analyzed over several days using flow cytometry. If the variant does not repress cell growth, variant (blue) cells will outcompete their WT (red) counterparts. To modify the competition assay for genome stability assessment, cells are treated with a PI3K inhibitor and the genotoxic chemotherapeutic temozolomide. These drugs isolate the genomic stability function of PTEN by removing its role in cell growth and causing genome instability, respectively. Here, cells harboring variants that cannot repair temozolomide-induced DNA lesions will be outcompeted by their WT counterparts. The assay generates a score that is based on the rate of change of variant populations relative to the WT population to quantitatively define the phenotype. Results can be interpreted to establish a relationship between a PTEN variant and its quantitative effect on the cell growth or genomic stability functionality of PTEN. Furthermore, the growth-based nature of these assays means that in future work they can be adapted to a pooled library format, allowing the simultaneous, quantitative assessment of thousands of PTEN variants. Data from both low-throughput and high-throughput experiments bring clarity to the relationship between specific PTEN functions and patient prognosis.

The recent large number of world-wide disasters has catapulted disaster research to a highly important endeavor. 2017 was the most expensive on record with 16 U.S. climate events’ losses totaling $306 billion. Research suggests the costliest effects may result from emotional and psychosocial health. Those who are: seniors, distressed, and/or experience early-life vulnerabilities are at increased risk for negative health responses. This study addresses the need to reduce vulnerability and increase preparedness by evaluating how older adults perceive/prepare for disasters, including psychological factors that may influence their motivation to prepare. Literature review results from 26 references indicate older adults are: (1) among our most vulnerable populations for natural disasters, (2) underprepared, though resources are available, and (3) preparing close friends/family before themselves. The Socioemotional Selectivity Theory (SST) posits that as we age, our time perceptions become constrained, motivations shift, and we prefer positive over negative information. Therefore, I asked: (1) if older adults are intuitively resistant to negative information, such as impending disasters, how might we reframe it to be congruent with their desire for positive information? (2) If we approach older adults through more positive experiences, will they be receptive and motivated to prepare? I employed a model, namely: disaster preparedness behavior (PB) is a function of vulnerability (V) and resilience (R). To test this, a survey was developed to assess how factors of V and R would interact and influence PB. I will pilot test this survey through the evaluation of community-living older adults. PB is expected to be negatively related to V, positively related to R. This study extends disaster research by using psychological variables to predict preparedness and evaluating motivation to prepare using SST as a guiding framework. Results should increase knowledge about older adults’ perceptions of disaster preparedness and factors to mitigate increased preparedness.

X-ray binaries consist of a star gravitationally bound to a compact object (white dwarf, neutron star, or stellar mass black hole). Matter from the star is pulled onto the compact object and accretes in a disk which emits high-energy X-rays. These objects have variability observable on human time-scales—days and weeks rather than millions of years—and provide insight into high-energy physics. In this project we analyzed the light curves of time-variable objects to identify candidate binary systems. We cross matched data from optical variability surveys such as ASAS-SN, ATLAS and ZTF with the ROSAT all-sky X-ray survey. We were able to confirm known cataclysmic variables (CVs) and active galactic nuclei, and also discovered new CVs. These methods will be useful in identifying these rare objects in LSST’s massive data set in a few years.

In the near future, spectrometers on extremely-large ground-based telescopes will conduct some of the first searches for life beyond the solar system. These telescopes will use high-spectral resolution observations of reflected light from nearby exoplanets to search for abundant oxygen in the exoplanet’s atmosphere. While photosynthesizers produce abundant O₂ on our planet, a planet that has lost its ocean may also have high atmospheric O₂ – even up to many times the Earth’s current abundance. This is because as the ocean evaporates, water vapor high in the atmosphere can be broken up by UV light from the star, allowing the hydrogen to escape to space and leaving the oxygen behind. Here we use a radiative transfer model (SMART) to generate high-resolution synthetic spectra of both Earth-like and ocean loss worlds to determine which spectral features can help distinguish the source of abundant oxygen in an exoplanet’s atmosphere. We compare atmospheric models of Proxima Centauri b, a planet orbiting a nearby star, to quantify the strength of absorption bands of different molecules. Based on these models, we found that the extremely high oxygen atmospheres resulting from ocean loss have strong suppression of oxygen bands due to additional broad absorption caused by the collisions of O₂ molecules, which is not present for the smaller amounts of oxygen generated by photosynthesis. We find that the presence of a strong oxygen band centered at 0.69 micrometers (µm) combined with the suppression of the oxygen band at 1.27 µm would indicate an ocean loss scenario and not a photosynthetic biosphere. These results emphasize the need for accurate models, and ground-based high-resolution spectrometers that are sensitive to wavelengths shorter than 0.7µm to detect diagnostic O₂ collisionally-induced absorption.

Major Depressive Disorder (MDD) has the largest life time prevalence (17%) of mood and anxiety-related disease. The prevalence of MDD is also 1.7 times greater in women than men. Chronic stress and anhedonia are the primary symptoms of depression, and decisions are affected. Our laboratory has shown that corticotropin releasing factor (CRF), the stress hormone, potentiates dopamine release in the core of the nucleus accumbens (NAc), suggesting a relationship between stress and reward processing. While it is known that an individual’s decision making is altered in a depressed state, the precise neurological pathway between stress and reward processing in the brain is unclear. To characterize this “stress-reward” pathway, I used a novel decision-making framework where a cohort of male and female mice performed an operant concurrent-choice task choosing between 0.1M sucrose solution or water. Mice were injected intracranially with α-CRF, a non-selective CRF antagonist, or vehicle in the NAc prior to performing the task. I measured task performance. I hypothesize that mice injected with α-CRF demonstrate less appetitive and reward-seeking behavior compared to the vehicle group, implicating a lower sucrose nosepoke percentage, sucrose choice percentage, and higher sucrose latency during the decision-making task. I also hypothesize that females have a greater reward sensitivity system than males, resulting in an augmented decline in appetitive and reward-seeking behavior compared to males. If these results indicate a significance in further elucidating the “stress-reward pathway” through the decision-making task, this can pave way for potential new treatments targeting this pathway for depression.

During HIV infection, CD8+T-cells are crucial for the control of viral replication. Increased CD8+T-cell polyfunctionality, which is the ability for one cell to perform more than one function within the immune response, was associated with improved clinical outcomes, is now the focus of experimental curative therapies for HIV. One therapy that showed promise is a Conserved Elements DNA (CE) vaccine, which is designed to prime the immune system with essential regions of the virus, thereby eliciting polyfunctionality and circumventing escape mutants. A novel immunotherapeutic combinatorial approach was investigated for the ability to reduce or eliminate viral burden in Simian Human Immunodeficiency Virus (SHIV) infected macaques receiving antiretroviral drug therapy. We evaluated effects of this regimen on CD8+T-cell polyfunctionality and its correlation to viral control after analytical antiretroviral treatment interruption (ATI). Our combinatorial immunotherapy regimen uses the CE vaccine to target highly conserved viral sequences, latency reversal agent GS986, exhaustion reversal agent anti-PD-1, and CCR5 gene editing to delete the co-receptor for viral entry in CD4+T-cells. Analysis of CD8+T-cell polyfunctionality was performed using intracellular cytokine staining and flow cytometry to measure the frequency of CD8+T-cells secreting one or more of the following effector functions: TNFα, IFNγ, IL-2, and both CD107a and Granzyme B. Polyfunctionality induced by the combinatorial regimen was algorithmically quantified and compared to a control group receiving no interventions and a group receiving CE vaccine and CCR5 gene editing alone. Our analysis showed neither significant differences in polyfunctionality between treated and control groups, nor any changes in polyfunctionality within the subset of CD8 targeting conserved regions of the virus. However, we observed diverse viral control post-ATI among all animals, and additional experiments are in progress to determine if CD8 polyfunctionality played a role in improved viral control post-ATI.

Large and complex regions of the human genome (a complete set of genetic material) are difficult to sequence and characterize due to the inherent biases in shotgun sequencing technologies (by far the most prevalent sequencing technology today) or short read length limitations. These regions have also been shown to associate with many human diseases such as neurodevelopmental disorders. One category of such regions is variable number tandem repeat (consecutive repetitive sequences of variable size, aka VNTRs). In previous studies, Chaisson and colleagues discovered a group of complex regions in the human genome that had variable lengths in the human population using single molecule, real-time (SMRT) sequencing. Unlike older DNA sequencing technologies, SMRT can sequence with high accuracy long stretches of complex genomic regions. We compared these regions between human and non-human primates (chimpanzee, gorilla, and orangutan) in order to detect human-specific DNA sequences. We generated six haplotypes (we each have two copies of the genome, one from mom, one from dad, where each copy is a haplotype) resolved non-human primate genomes. We also developed a customizable, automated, Python program which used a variety of sequence analysis methods such as dot plots (a method to visualize repetitive sequences), average length statistics, repeat motif (pattern) analysis, and gene annotation to characterize VNTR size differences and possible human-specific expansions across different samples. We discovered a group of human ab initio VNTR expansions that were enriched in intronic regions of genes with established roles in human early fetal neurodevelopment. This study elucidated for the first time the haplotype-resolved sequence of the rapidly expanded VNTRs of the human genome, which was a vastly under-ascertained form of genetic variation in the human genome. The results of this study could potentially further our understanding of diseases associated with VNTR expansions.

Previous study found that neural oscillations recorded in the resting-state electroencephalogram (EEG) can predict the learning rate of monolinguals. However, it is unknown whether bilinguals’ learning rates can also be predicted by their resting EEG. This study investigatesd to what extent the brain oscillations in the resting-state EEG of bilinguals and monolinguals would predict the learning rates. The resting-state EEG were used to predict the learning rates of native English speakers and Chinese-English speakers in three experiments. In each experiment, an eyes-closed and an eyes-open resting-state EEG were collected for each subject before participants completed two learning tasks (map and vocabulary). The relationship between power oscillations in alpha (8 to 13 Hz), beta (13 to 30 Hz), and theta (4 to 8 Hz) bands and learning task performance were investigated. The differences in bilinguals and monolinguals resting EEG are hypothesized to predict and reveal the variations in individual learning rates. The results of this study can contribute to the research of brain patterns observed in the resting-state EEG on investigating the impacts of individual linguistic abilities on predicting learning rates.

Neurodegenerative diseases, such as Alzheimer’s (AD), Parkinson's, and Huntington’s, affect millions of people. In AD, prior studies indicate the formation and accumulation of amyloid-beta proteins may play a crucial role in the pathology of the disease. The Herpes Simplex Virus (HSV-1) encodes an alkaline nuclease (UL12.5) known to cause degradation of the mitochondrial genome. HSV-1 infection has been previously associated with AD brain pathology. We hypothesize that UL12.5 activity in the brain may predispose an individual to amyloid-beta aggregation and AD neuropathology. Here, we controlledl the amyloid-beta protein aggregation using a degron attached UL12.5, which is induced by the plant hormone auxin through a molecular signaling pathway known as auxin-inducible degron. We have engineered an auxin UL12.5-degron construct in order to precisely control the temporal and cell type expression of UL12.5 in Caenorhabditis elegans (C.elegans). This construct was microinjected into the worms and by using auxin, we controleld the expression of UL12.5 and tested its effects on amyloid-beta and Huntington protein aggregation. Here, we have elucidated the relationship between HSV-1 infection, UL12.5 expression, and neurodegenerative disease which may form the basis of novel treatments.

Plastic debris in large water bodies such as oceans and seas has become a prominent issue. Microplastics (polymers less than 5 mm) can be primary, manufactured (i.e. microbeads from facial exfoliants), entering water bodies through runoff / drainage systems, or secondary (i.e. clothing fibers or fragments) and overtime undergo weathering and breakdown. These microplastics are often small enough to pass through water treatment filters, thus ending up in watersheds. Aquatic organisms are known to ingest microplastics, and while the impacts are currently unknown, interest in the matter is growing. Contaminants in microplastics are also a concern and could have harmful effects on the environment and the organisms that ingest them as well. This study evaluated the concentration and distribution of microplastics collected from sandy beaches on islets (motus) of Tetiaroa, an atoll located in the Pacific Ocean. Thirty-six samples were collected from 8 of the islets. The analysis included density separation using a high-density fluid, filtration to .3-mm, examination under a microscope, and gravimetric analysis to determine concentration and type of microplastics in each sample. Sixty percent of the samples processed contained microplastics including fibers, netting, and a fragment. This preliminary study shows that microplastics continue to be ubiquitous in the natural environment, and continues to heighten the need for disposal management throughout the world.

Contextual word representations derived from large-scale neural language models are successful across a diverse set of natural language processing (NLP) tasks, suggesting that they encode useful and transferable features of language. To shed light on the linguistic knowledge they capture, we study the representations produced by several recent pretrained contextualizers (variants of ELMo, the OpenAI transformer LM, and BERT) with a suite of sixteen diverse probing tasks. We find that linear models trained on top of frozen contextual representations are competitive with state-of-the-art task-specific models in many cases, but fail on tasks requiring fine-grained linguistic knowledge (e.g., conjunct identification). To investigate the transferability of contextual word representations, we quantify differences in the transferability of individual layers within contextualizers, especially between recurrent neural networks (RNNs) and transformers. For instance, higher layers of RNNs are more task-specific, while transformer layers do not exhibit the same monotonic trend. In addition, to better understand what makes contextual word representations transferable, we compare language model pretraining with eleven supervised pretraining tasks. For any given task, pretraining on a closely related task yields better performance than language model pretraining (which is better on average) when the pretraining dataset is fixed. However, language model pretraining on more data gives the best results.

Archaeologists increasingly use three-dimensional modeling to analyze artifact attributes and document in situ relationships. Less attention has been paid to modeling’s potential in strengthening connections between descendant communities and their cultural heritage. In collaboration with the Grand Ronde Historic Preservation Office, we created three-dimensional models of excavation units and belongings associated with the Molalla Encampment, a late nineteenth and early twentieth century settlement area on the Grand Ronde Reservation in northwestern Oregon. This work proceeded in two steps. First, we established a modeling methodology applicable to a variety of excavation contexts and artifact types. This required defining proper artifact handling techniques and modeling procedures, including optimal camera settings and software workflow. Second, we used this methodology to capture hundreds of artifacts photos in order to build each model. Photogrammetry provides an alternative approach to heritage curation, allowing us to share interactive, three-dimensional models of historic belongings within the Grand Ronde community. This not only lends additional transparency to our research process, it can also initiate conversations with tribal members about the functions and meanings of belongings in historic reservation lifeways. Photogrammetry can thus play an important role in the development of community-based research practices.

A positron emission tomography scan (PET scan) can be used to map areas of potential cancer in the body. Cancer cells multiply at an incredibly fast rate, and in doing so, use a greater amount of glucose to fuel their high-energy needs compared to normal tissues. PET scans use radiolabeled fluorodeoxyglucose to quantify cellular metabolic activity, producing visual hotspots that are usually overlayed on computed tomography (CT) images and correlate to cancer sites (“PET/CT”). PET/CTs are often used to follow patients with acute myeloid leukemia (AML) after hematopoetic cell transplantation (HCT). In the lab’s database of over 300 consecutive patients whose AML relapsed after HCT, we found 15 patients who were followed with PET/CT because of extramedullary disease. These patients received a variety of treatments for their AML relapses, including induction chemotherapy, radiation, and/or hypomethylating therapy. We sought to assess if a negative post-treatment PET was helpful in predicting a cure. Through detailed chart review, we found PET scan negativitity is hard to achieve, a negative PET is not reassuring (50% still relapsed) and even a low SUV-positive PET is prognostic of disease progression. Moreover, if any extramedullary disease is present, systemic therapy prolongs life more than local radiation alone, but no treatments are likely to be curative.

Obstructive sleep apnea (OSA) is the condition of repetitive stops of breathing during sleep due to complete or partial occlusion of the upper airway. OSA affects around 34% in men aged 30–70 years and is associated with significant cardiovascular mobility. Studies have indicated that retro-palatal region is the most common site of upper airway collapse leading to OSA. However, few studies have addressed the respiratory dynamics of soft palate, tongue base, and epiglottis during sleep. The purpose of this study is to analyze the respiratory motions of soft palate and its relation to oropharyngeal structures during drug-induced sleep in verified obese/OSA and non-obese/non-OSA minipigs. The hypotheses is that obese/OSA minipigs would have larger variance of soft palate motions and altered motion pattern as compared to non-obese/non-OSA controls, which may contribute to OSA. Four obese and two non-obese minipigs were first revived live sleep monitoring using wireless BioRadio system to verify OSA, and all 4 obese showed different degrees of OSA by apnea/hyponea index (AHI) while 2 non-obese did not. Sleep videofluoroscopy was performed under sedation when subjects were places in the prone and lateral positions. The ImageJ was used to trace the movements of soft palate tip in inhaling and exhaling phases. The static reference was defined to be the intersection of mesial surface and occlusal plane of upper second molar. The purpose of reference is to compare relative location of soft palate tip and its relation to other oropharyngeal structures. Dynamic movement of soft palatal tip presented significantly larger variance in obese/OSA than non-obese minipigs. Going forward, I will further map the dynamic shape changes of the soft palate and to define how spatial relationships between soft palate, tongue base and epiglottis lead to oropharyngeal airway patent or collapse during respiration.

Becoming a mother can be an incredibly beautiful process, but it can also become overwhelming and extremely stressful, especially when lacking support and resources. The chronic and significant stress that low-income, pregnant women experience put them at greater risk for adverse health outcomes and their infant at risk for poor developmental outcomes. At the University of Washington’s Center for Child and Family Well-Being, our research team has developed mindfulness-based interventions to help new moms adjust to their new life. Our goal is to examine the effects of stress on the mother-infant dyad and to evaluate whether these programs are beneficial for moms and their babies. Expecting mothers are randomly assigned to attend one mindfulness-based program that focuses on preparing for childbirth, reducing postpartum stress, or developing parenting skills. Administration of extensive questionnaires to the mother and recordings of the mother and baby completing various tasks, before and after the program, measure the pair’s socioemotional development. We also collect cortisol, a stress hormone, and measure heart rate and breathing during a stress-reactivity paradigm to inform us of the physiological effects of stress. We hypothesize that mothers who exhibit high levels of mindfulness are more likely to engage in consistent, warm, and responsive parenting skills. As a result, these mothers' infants will display better self-regulation and focus. We also predict that mothers and babies who participate in these mindfulness interventions are more likely to show a decrease in cortisol production and have controlled cardiovascular reactivity. Recommendations for future research include establishing a systematic way of identifying mothers at risk so that we may prevent further harms caused by stress. Implications of the findings can be used to advocate for equitable, accessible mental health programs and implementation of public health policy centered around protecting and empowering vulnerable women and children in our community.

Each neuron in the visual cortex of the human brain has an affinity for specific features in our visual field. In early processing stages, these features are simple, like spots or edges of light. In deeper regions of the visual system, the features that excite neurons become complex combinations of lines, curves, color and texture that are not well understood. To better understand how combinations of visual features are encoded in the visual cortex, it is necessary to rapidly and systematically present complex visual stimuli while recording neuronal responses. To address this, we developed an online optimization approach that uses Bayes’ theorem and information theory to select visual stimuli in real time to characterize neurons. Specifically, we calculated mutual information between candidate visual stimuli and a set of hypotheses about the neurons that were derived from a clustering analysis of data from previous studies of cortical area V4. We simulated our optimization system with the assumption that neuronal responses were subject to Poisson noise, and found that we were often able to classify neurons with less than one tenth the number of visual stimuli used in the original studies. We then implemented our system in the experimental lab, ensuring that the optimization calculations are performed fast enough to occur within tens of milliseconds between visual stimulus presentations. We now have a working system where signals from electrodes in the cortex are detected, digitized and transmitted to our optimizer, which then selects the next stimulus and transmits this choice to the visual display program. We are working on refinements of the optimizer algorithm in preparation for final deployment in vivo. We expect our novel system to characterize neurons more rapidly and thoroughly than ever before, and to shed new light on how cortical neurons encode complex conjunctions of visual features.

Alzheimer's Disease (AD) is the 6th leading cause of death in the United States. The rate of AD diagnoses has substantially increased in the last two decades. The direct causes behind the initiation of AD are still unknown; however, genetic heritability is known to be a significant risk factor. The goal of our research is to identify the genetic variants that directly influence resistance to the formation of amyloid plaques, which are believed to lead to the initiation of AD. To investigate this idea, we are performing a genome-wide association study (GWAS) using the model organism Drosophila melanogaster. Female flies expressing the human form of amyloid beta (Aβ) are crossed with male flies from each of the 200 lines that make up the Drosophila Genetic Reference Panel (DGRP), a collection of highly inbred lines. The complete genome sequence is known for each of these lines, enabling researchers to carry out GWAS to identify genes associated with variation in any trait of interest. In our case, the progeny of these crosses all express Aβ, but differ from each other with respect to their inherited DGRP genotype. These progeny undergo image analysis to measure the amount of degeneration caused by the aggregation of amyloid plaques in the eyes. Eye degeneration is scored on a five-point scale, from zero, indicating a wildtype phenotype, to four, indicating an extremely degenerated phenotype. Preliminary results show that there is variation in the level of resistance to the aggregation of amyloid plaques among the DGRP lines, which can be accounted for by the genetic variation among these lines. The ability to identify the single nucleotide polymorphisms and the resulting proteins that cause this resistance could be pivotal in identifying methods to prevent the initiation and progression of AD.

Conditioned pain modulation (CPM) is the alteration of pain sensation upon the application of a separate, conditioning stimulus. In healthy patients CPM is experienced as a pain-inhibits-pain phenomena, but patients living with fibromyalgia (FM) and other chronic pain conditions have been shown to lack this pain inhibitory CPM response. While the deficiency of CPM in chronic pain patients has been widely documented in meta-analysis, the impact of other risk factors on CPM has largely yet to be understood. A limited collection of previously conducted studies has examined the impact of daily activity, depression, and anxiety on CPM in non-FM patients but the low number of participants and studies available warrants further investigation. To do this, we analyzed baseline data from a clinical trial in FM patients underwent thermal stimulus testing to determine CPM, wore an actigraphy watch for seven days to provide objective measurements of daily activity, and completed several questionnaires and psychological assessments. A series of analyses were completed using Stata SE, including bivariate correlations, linear regression, and logistic regression. Results indicate that there were no significant correlations between daily activity level, depression, anxiety, pain catastrophizing, pain intensity, and physical functioning with CPM. However, a significant correlation was observed between CPM and PTSD score, with individuals more likely to be suffering from PTSD experiencing greater hyperalgesia CPM effects. Indeed, the odds of hyperalgesia were 3.1 times higher among those with PTSD than in those without PTSD (95% CI: 1.4, 6.6). This suggests that PTSD contributes to neurological deficits in pain processing. If this result is confirmed in other samples of patients, then future research should evaluate the effectiveness of PTSD-targeted treatments for improving pain outcomes in FM patients with PTSD.

Attention deficit hyperactivity disorder (ADHD) is one of the most prevalent neurodevelopmental disorders to date, affecting 5-7% of school-age children. Characterized by inattention, impulsivity, and hyperactivity, those diagnosed with ADHD often have difficulty in navigating multiple tasks, sustaining attention, and inhibiting impulses. Although prior research suggests increased attention to sensory stimuli enhances task performance temporarily when the stimuli are task-related, little is known about the effect of irrelevant stimuli on task performance. The current study evaluates whether irrelevant stimuli decreases response accuracy and speed during computer tasks among children with ADHD. Children between the ages of seven and eleven, with (n=50) and without (n=30) ADHD, are recruited to participate in comprehensive neurocognitive phenotyping, including completion of two computer games varying in difficulty (i.e. easy and hard versions). The tasks involve ignoring irrelevant visual stimuli that are presented alternatively with task-related visual stimuli. Irrelevant stimuli consist of three stimulus types, including standard (60%; white bracket-shaped image), deviant (20%; white bracket in opposite orientation to standards), and novel (20%; white line drawings of animals and vehicles). The current study hypothesizes that compared to non-ADHD children, children with ADHD will have lower accuracy and slower reaction times in response to task stimuli that immediately follow novel irrelevant stimuli, as compared to standard irrelevant stimuli. Preliminary results (n = 23) support this hypothesis through a variance analysis, indicating children with ADHD show worse accuracy following novel, i.e. more distracting, stimuli than standard stimuli compared to typical, non-ADHD children, F(1, 19) = 5.028, p = .037. Through this study, we will gain a greater understanding of children’s needs of attention maintenance. Implications of this study include reduction in classroom distractions could improve task-related accuracy and processing speed among children with ADHD.

Over the past 15 years, early college students of the Ocean Research College Academy (ORCA), which is offered through Everett Community College, have collected information about fecal coliform levels in Possession Sound. This research is comprehensive spatially and temporally, but does not include information about potentially dangerous antibiotic resistance. Carbapenem-resistant enterobacteriaceae (CRE) are a class of antibiotic-resistant gram-negative bacteria that are specifically resistant to Carbapenem-class antibiotics, which are often considered last-resort antibiotics. As such, CRE pose a major health risk and cases are often difficult to treat. This study will investigate the presence of CRE in Possession Sound at 5 public-access beaches. Samples will be collected using sterile containers and then cultured on selective media containing graduated levels of imipenem using MacConkey agar. Viable CRE colony-forming units will be tested using disc-diffusion for sensitivity against a panel that represented other common antibiotic treatments for enterobacteriaceae on Mueller-Hinton agar and species-identified using a API 20E kit. This study will provide a reference point for future researchers looking to investigate the presence of CRE organisms or other resistant bacteria in the Possession Sound.

How can we improve healthcare in under-served South East Asian Countries? One possibility is via mobile-health technology. Mobile-health or m-health is the practice of medical and public health supported by mobile and wireless devices. This literature review looks at over 20 years of the emergence of m-health and the prediction of future possibilities. The goal is to look at areas of improvement such as cost efficiency, adapting to the specific country’s infrastructure and integration of m-health in healthcare. In countries like Nepal, m-health has helped to eradicate diseases like malaria, improve neonatal health care and empower female health volunteers. It has also helped gather information such as statistics on usage and distribution of drugs, healthcare workers' interactions with patients and disease surveillance. With the rise of mobile users, healthcare facilities can create a structured international framework to regulate and increase the efficiency of m-health. This research will help facilitate conversations about the potential of m-health and where it needs to be improved so that it can play a pivotal role in healthcare of South East Asian countries.

Labeling objects with DNA-based tags can provide a secure, difficult to fake identifier that is particularly useful for objects of high value or those that cannot be physically tagged. In this problem setup, a tag is a bit string, where each bit represents the presence or absence of a DNA strand containing a particular barcode. Our goal is to consistently and accurately identify the tag. These DNA barcodes were designed for use on a MinION nanopore sequencer, which outputs a time series signal corresponding to the DNA sequence. Ideally, each barcode should generate a dissimilar signal, which makes it easier to distinguish from other barcodes. We designed 96 barcodes that are signal orthogonal (i.e the signal output from the MinION was as dissimilar as possible), and detected them using signal processing algorithms. Using this system, I created an error analysis pipeline to ensure that we can identify tags both quickly and accurately. In order to optimize the time it takes to identify a tag, it was important to minimize the number of sequencing reads we needed to observe on the MinION, without sacrificing accuracy. I found that using a subset of the reads produced approximately the same error rate as a full run. Therefore, we can run the MinION for a shorter amount of time, and still identify tags at a similar error rate compared to a longer runtime.

This project examines reproductive output across different wildtype genotypes in the fruit fly, Drosophila melanogaster, and how it correlates with lifespan, activity and age-specific metabolite levels. To answer this question, we used the Drosophila Genome Reference Panel (DGRP), a collection of ~190 fully sequenced Drosophila strains that have been inbred to near homozygosity. Fecundity was measured as the per capita number of adult offspring produced by female flies over 48 hours when they are 4, 8, and 12 days old, using 3-5 replicate vials for each Drosophila strain. We have shown that there is highly significant genetic variation for reproductive output. Reproductive output declines with age in most but not all genotypes. The correlation between reproductive output and lifespan was not statistically significant, suggesting that there is not a direct trade-off between survival and reproduction in this population. A genome wide association study (GWAS) identified statistically significant single nucleotide polymorphisms correlated with variation in reproductive output, although most of them were located in genes of unknown function.

Symbiotic nitrogen fixation (SNF) in the interaction between the soil bacteria Sinorhizobium meliloti and legume plant Medicago sativa is carried out in specialized root organs called nodules. During nodule development, each symbiont must drastically alter their proteins, transcripts and metabolites in order to support nitrogen fixation. Moreover, bacteria within the nodules are under stress, including challenges by plant antimicrobial peptides, low pH, limited oxygen availability, and strongly reducing conditions, all of which challenge proteome integrity. S. meliloti stress adaptation, proteome remodeling and quality control are controlled in part by the large oligomeric protease complexes HslUV and ClpXP1. To improve understanding of the roles of S. meliloti HslUV and ClpXP1 in free-living conditions and in symbiosis with M. sativa, we generated ΔhslU, ΔhslV, ΔhslUV, and ΔclpP1 knockout mutants. Shoot dry weight of M. sativa plants inoculated with each deletion mutant was significantly reduced, suggesting a role in symbiosis. Further, slower free-living growth of ΔhslUV and ΔclpP1 suggest HslUV and ClpP1 were involved in adapting to heat stress, while ΔhslU and ΔclpP1 mutants were sensitive to kanamycin. All deletion mutants produced less exopolysaccharide and succinoglycan, as shown by replicate spot plating and Calcofluor binding. We also generated endogenous C-terminal eGFP fusions to HslU, HslV, ClpX and ClpP1 in S. meliloti. Using anti-eGFP antibodies, native coimmunoprecipitation experiments of proteins from free-living and nodule tissues were performed and analyzed by mass spectrometry. The results suggest HslUV and ClpXP were closely associated with ribosomal and proteome quality control proteins, and identified several novel putative protein-protein interactions.

Climate change is misunderstood and largely ignored because people imagine its impacts as far away and they lack education on how to effectively combat it long term. We built this mobile game to shatter various misconceptions by educating users in a fun and engaging way. We allow players to explore environmental concepts by incorporating story, science and community into a single experience that blends real world images taken from the user's mobile device with 3D graphics. This is done by including various mechanics such as collecting, combat, puzzles and exploration in a way that is easily accessible to everyone. With this game we hope to inspire users to not only be more environmentally conscious but also become more financially supportive of sustainable businesses. We built this application from scratch using the power of Unity3D game engine, augmented reality technology and mobile GPS location. With this technology we can immerse users by placing a fantastical world into the real one and incorporating environmental narratives.

The Osceola Mudflow is one of the largest historic lahars, or volcanic mudflows, from Mount Rainier discovered to date. It flowed from Mount Rainier to the Puget Sound through the White River valley about 5,600 years ago. For this study, samples of the Osceola Mudflow deposit were taken from a vertical profile on an outcrop along the White River and were analyzed using anisotropy of magnetic susceptibility, or AMS. An AMS analysis measures the orientations of magnetic particles too small to see through a microscope in relation to the bulk of the sample. The orientations of submicroscopic magnetic particles have been used in prior studies to determine variations in flow directions and related characteristics in lava flows and sediments; however, little is known about the behavior of clay-rich lahars such as the Osceola Mudflow. In this study, we compare vertical variations in the AMS characteristics of the Osceola Mudflow to expectations based on fluid dynamics. It’s expected that these AMS measurements will indicate lower flow rates at the bottom of a flow compared to the surface of the flow. Measurements of the vertical variations in magnetic properties of clay-rich lahar deposits is expected to allow for better predictions about the flow characteristics of future clay-rich lahars which has implications for hazard mitigation.

Base J is a glycosylated nucleobase found in Trypanosomatids, a family of single celled parasites causing Sleeping Sickness, Chagas Disease, and Leishmaniasis. This modified base is thought to play an important role in transcriptional termination for these organisms. Current methods of analyzing Base J rely solely on chromatin immunoprecipitation experiments, which provide low resolution information pertaining to Base J positions. While previous studies have shown that SMRT-seq interpulse duration (IPD) is associated with the position of Base J, we still lack methods to use this information to produce a genome wide, nucleotide-level map of Base J. Here we explore analytical approaches such as dimensionality reduction, machine learning, and signal processing to determine patterns of IPD and DNA enrichment which correspond to Base J across the entire Leishmania tarentolae genome. We show that many simplified approaches such as peak calling, and dimensionality reduction do not contain enough information to accurately classify Base J. We also utilize signal decomposition with Fourier transforms, machine learning clustering and regression methods to provide a more complex treatment of the data. Our findings are an important step in producing an algorithmic approach to identifying precise locations of Base J and can yield insight into transcriptional regulation in Trypanosomatids.

Quantum systems are building blocks for promising new technologies such as fundamental secure communication, quantum computing, and quantum sensing. One quantum system, the diamond nitrogen-vacancy center, presents many of the best traits among scalable qubit candidates. Preferential lattice orientation of nitrogen-vacancy centers, while technically difficult, would improve signal to noise ratios in quantum sensing and efficiency of quantum repeaters. I report defect orientation changes in diamond through week-long diamond anneals at high temperatures. I discuss my techniques to measure, characterize and spatially track thousands of nitrogen-vacancy defects through confocal microscopy to observe orientation changes as a function of annealing temperature. I show conclusive data supporting a critical temperature for achieving nitrogen-vacancy orientation changes and discuss follow on applications.

A patient’s performance status (PS) is a key determinant of eligibility for enrollment in acute myeloid leukemia (AML) clinical trials, as PS is regarded as a crucial predictor of death as a result of treatment on the trial. PS values range from 0 (minimally symptomatic) to 4 (bed-ridden). It is crucial to account for possible differences in PS when comparing results of different trials. However, the degree of concordance between observers in assessing PS remains unknown. Because of this uncertainty and the clinical significance of PS, my research studies inter-observer concordance in assessing PS. Specifically, I compare PS as assigned in electronic medical records by medical providers, as abstracted by myself given history of present illness and physical exam findings, and the patient’s own evaluation via a health questionnaire. Data was collected from 300 randomly selected patients arriving to Seattle Cancer Care Alliance from January 2015 to December 2017 with newly diagnosed AML. The results of this study may inform similar research within other treatment centers, and development of increasingly precise guidelines for evaluation of PS to improve reliability.

When all goes according to plan, newly synthesized proteins within cells fold down an energetic funnel into a functional, minimal energy configuration. If a protein does not fold properly, it is both energetically unfavorable and nonfunctional, often with hydrophobic parts exposed to the aqueous environment. This creates the potential for misfolded proteins to form insoluble aggregates, which can become toxic to cells. These aggregates can crowd the cellular environment and impair cellular functions, which on a single cell scale can lead to cell death and on a larger organism scale, cause diseases like Alzheimer’s, Parkinson’s, and Huntington’s. To deal with this problem, cells have evolved protein quality control (PQC) systems that comprise two classes of action: chaperones that help proteins fold properly and ubiquitin-protein ligases that tag misfolded proteins with ubiquitin for destruction by the proteasome. Previous studies concluded that chaperones are required protein degradation. In our study, we find that Hsp70 chaperone dependence for protein degradation is variable along a spectrum of independent to dependent. My work specifically examined the function of yeast ubiquitin-protein ligase San1 by comparing degradation of various substrates between strains with or without San1 function, and with or without chaperone activity. By performing degradation whereby protein synthesis was halted and the stability of the synthesized pool of substrate was monitored by Western analyses, we were able to see the degree of substrate degradation by each strain over time. Degradation through San1 has been shown to require chaperones, but San1 also is known to recognize substrates independently without chaperones. From our work, San1 recognizes patches of hydrophobicity on misfolded proteins; a feature that is also recognized by chaperones. By studying the interactions of the folding and degradation enzymes, we are gaining a new understanding of how PQC pathways collaborate and coordinate to achieve optimal protection for the cell.
 

 Technology has evolved in ways that allow healthcare professionals to improve patient outcomes through personal electronic devices such as smartphones or healthcare applications. These advances have allowed patients to manually or automatically record personal health information which can then be sent to their provider for real time assessments. The purpose of this study was to evaluate healthcare providers’ perceptions about the value of digital healthcare technology in improving healthcare outcomes for low-resourced communities. We hypothesized that healthcare providers will report that mobile health technologies can be a valuable innovation to support patient wellness and improve health outcomes. To test our hypothesis, we recruited N=20 healthcare providers from Washington, state. Healthcare providers comprising physicians, medical assistants, nurses, and social workers participated in a 60-minute focus group and asked about the role of technology in improving healthcare services for their patients. Participants received a $75 gift certificate at the end of the session and responses were transcribed for later assessment. We evaluated transcripts by deriving codewords, codewords used more than two times were identified and recorded on three separate trials, codewords with similar information were grouped into codeword clusters, and finally, themes were derived based on a single idea from codeword clusters. Results of our study revealed that providers perceived value of smartphones/mobile health technologies to improve patient health outcome through data tracking and increased accuracy of reported health information. The implication of our finding is that mobile healthcare technologies can support the work of healthcare providers by accurately tracking patient health status and thus support treatment delivery.

During the early stages of vertebrate embryonic development, blocks of muscle tissue called somites form progressively along the anterior-posterior (head to tail) body axis. As the embryo grows in length, new somites are continuously added at the posterior end until the tail reaches its final length. Our work focuses on a subset of genes called the hox genes. These genes encode transcriptional regulatory proteins that are involved in controlling the formation of the body plan along the anterior-posterior (AP) axis. In vertebrates, these genes are present in four major clusters (A, B, C and D) and within a cluster they are expressed temporally from 3’ to 5’ of DNA, with hox13 being at the very 5’ end and thus the most posteriorly expressed hox genes. In this study we use zebrafish as a model organism. Zebrafish embryos are excellent for investigation because: 1) the genome has been fully sequenced to a very high quality allowing the use of CRISPR mutagenesis; 2) the zebrafish embryos are transparent and so very easy to study using live microscope imaging; 3) much of the early development is similar among all vertebrates including humans. The role of the hox genes during the somite-forming states has almost entirely been characterized based on the overexpression of individual hox genes in previous research. We developed a zebrafish loss-of-function hoxa13 CRISPR mutant and are investigating the roles of this gene on the formation of the body plan. My research focuses on understanding how a loss of hoxa13 gene affects cell movement as the AP axis forms using spinning desk confocal microscopy to capture cells and Imaris software to track them, and I will present the results of this analysis. We expect to observe abnormal or reversal of cell movement in the prognitor area of the tailbud.

One of the key challenges of programming robots is the specification of concurrent behaviors. Most simplified programming interfaces involve single-threaded, imperative programming, whereas robots have many actuators that can move simultaneously and sensors that detect environmental changes or user input in parallel. For example, a mobile social robot may need to navigate its surroundings, sense and avoid obstacles, and listen for user speech at the same time. Hence, robot programs require multiple threads as well as the ability to react to environmental events, rather than a single-threaded sequence of commands. Unfortunately, creating such programs requires advanced knowledge of programming languages and is difficult even for professional software developers. In this project we developed ConCodeIt: a block-based visual programming interface that allows easy specification of concurrent robot behavior through two key concepts: (1) the ability to start robot actions and check their status through separate instructions, and (2) "wait" statements that can be injected into the imperative program flow to react to sensed events or action status changes. The design of ConCodeIt is informed by a series of user studies with novice programmers. The first study demonstrates the intuitiveness of our proposed hybrid programming paradigm, in comparison to the current way such programs are created using callbacks in a text-based language. The second study replicates the first study in block-based programming, comparing our approach to a previously proposed block equivalent of callbacks, namely "when" blocks. The last study demonstrates the benefits of an improved visual design for our programming paradigm, exploiting visual parallelism to represent concurrent execution. Each study evaluates program comprehension, debugging, and program creation tasks for real world robot programs. We also illustrate the expressivity of ConCodeIt through use cases by programming a mobile manipulator robot to perform object manipulation and human interaction tasks.

Fragile race avoiding is defined as the tendency to refrain from talking about race or racial issues to hide one’s bias due to sensitivity concerning the topic. Some even demonstrate discomfort or incoherence when directly talking about racial issues. This is common amongst whites who want to avoid conflict regarding racism. Although white people may believe that avoiding racial topics stops disagreements from arising, fragile race avoiding can promote ignorance about stereotypes and inhibit cultural awareness. We believe that this is a method in which individuals suppress their discomfort towards blacks. Therefore, we predict that a higher score on fragile race avoiding will correlate with higher levels in overall racism. We tested this prediction in a study in which UW undergraduate students talked about various scenarios with a research confederate to prompt a discussion about current day racial issues. Coders watched these taped interactions and rated various categories of microaggressions on a scale from zero to three. Scores of zero for fragile race avoiding indicates that the research participant is comfortable talking about racial issues and brings up race without being prompted by the confederate. Meanwhile scores of three indicate that the participant actively avoids mentioning race and shows palpable discomfort throughout the interaction. For the scores on overall racism, coders considered the interaction as a whole and determined how black individuals would feel when in a room with the participant. A score of zero represents comfort and understanding of the racial implications these topics were created to induce, while a three shows that the participant’s racist beliefs are explicit and clear. We hypothesize that there will be a positive correlation between the scores on fragile race avoiding and overall racism, indicating that fragile race avoiding is a modern form of racism in which individuals suppress their discomfort among blacks.

For women to have protection from unintended pregnancy and human immunodeficiency (HIV), current lead prevention options use oral antiretroviral drugs (ARV) for pre-exposure prophylaxis (oral PrEP) along with a form of contraception. Failure to adhere to these drug therapies will increase the risk of contracting HIV or pregnancy. We have proposed to integrate drug-eluting materials onto a copper-intrauterine device (IUD) that could provide both HIV prevention and contraception. We will evaluate two methods to formulate a matrix release drug delivery system. Injection molding is a method to inject material into a mold that can be used for constructing drug-eluting medical devices with low drug degradation. For our purpose, we injected a polymer and drug combination into a mold to construct a solid slab. Whereas, electrospinning is a method that uses electric force to formulate stable and high surface-to-volume ratio nanofibers with high drug encapsulation and porosity compared to the molded slab. Both delivery systems will be used to administer ARV drugs to the female genital tract for a year. We optimized the molded slab and electrospun nanofibers technique for maximum polymer-loading, and used 3-D printing and nanofiber wrapping technique as a process for slab integration and fiber integration onto the IUD respectively. The polymer and drug combinations for both electrospun nanofibers and molded slabs were chosen to have the maximum drug-loading and stable mechanical properties. Drug release was measured in vitro to predict daily release rates out to three years. The ideal matrix release drug delivery system method for the dual HIV prevention and conception IUD is determined based on the mechanical properties and drug release rate of the polymer and system combination. We also investigated the drug delivery systems for cytotoxicity to verify dosage safety.

Dementia impacts 4+ million older adults in the United States. The majority of patients with dementia (PWD) are cared for at home by family/friend care partners (CP). While this caregiving role can be highly meaningful, it is also a demanding responsibility. Resilience, or the ability to recover from stressful situations, has been shown to be protective for CP of PWD. There are three major models of resilience, describing resilience as: 1) an outcome, 2) a trait or 3) a process. Currently, there is no consensus on the best way to operationalize and measure resilience in the context of dementia caregiving. My project focuses on addressing this gap. My hypothesis is that: 1. Resilience in the context of dementia caregiving has specific characteristics, reflecting the complexity of caregiving; 2. CP likely over-estimate their resilience; 3. Resilience is a dynamic process related to positive functioning that fluctuates across time and situation, rather than a personality trait or outcome. 4. Optimal assessment will combine CP self-report with more objective, observable, or CP-reported behaviors. Our initial focus was understanding different approaches of defining and measuring resilience in CP of PWD. We used two data sources to code behaviors linked with resilience: 1. relevant literature; 2. 30 semi-structured interviews with CP of PWD evaluating resilience-related behaviors. We identified relevant behaviors and organized data from both sources using thematic coding. We used key identified behaviors to create a behavior-based model of CP resilience–Care Partner Resilience (CPR). Our hypotheses were confirmed. Our next steps are to validate CRP. Dementia is one of the major health conditions faced by the geriatric population, and CP burden from dementia can take a devastating toll the capacity to continue providing care. Thus, an accurate operational definition of resilience is essential in targeting interventions and developing long-term support tools for CP.

Auxin is a plant hormone that promotes root branching which allows improved anchoring in the soil and nutrient acquisition. At the molecular level, auxin promotes the activity of auxin responsive transcription factors called ARFs. I hypothesize that AGL42, a MADS box transcription factor works with ARFs during lateral root formation. I used CRISPR to remove the entire AGL42 gene from the genome and characterize lateral root phenotypes in the mutant. I characterized that AGL42 is regulated by auxin signaling. This was done by spraying Arabidopsis seedlings with auxin and measure AGL42 expression levels by RT-qPCR. I predict that increasing the levels of auxin will positively impact AGL42 levels. Alternatively, AGL42 may not be an auxin-responsive gene but may itself interact with the ARFs to affect downstream auxin signaling. To test this hypothesis, I performed a co-immunoprecipitation (Co-IP) assay to determine whether the AGL42 and ARFs interact with each other. By better understanding the lateral root specification, specifically the role of AGL42, we can learn how to improve the architecture of different crop plants, increasing their ability to thrive even in harsh environments.

Quantum sensing applications require diamonds with high concentrations of high-fidelity NV centers. Here we find we can significantly increase the NV center density in high-purity diamond by over a factor of ten by simple annealing. We perform fifteen anneals starting with 800 °C up to 1100 °C. Throughout each anneal, we track thousands of individual NV centers in a large experiment volume (350x350x500 um³) using a custom confocal microscope. Peak NV density was observed to occur at 980 °C. Spectroscopy measurements also show near ideal NV quantum characteristics for the newly formed centers. With this process, we can optimize NV formation for magnetic field sensing and quantum entanglement applications.

The study of peptide self-assembly on solid surfaces has the potential to catalyze numerous nanotechnological advances such as biosensors and nanoelectronics. A comprehensive understanding of the factors that influence peptide binding to solids would allow for expansive integration of biomolecules and solid-state devices, and organic-inorganic interface bridging will permit greater information flow between biological systems and technological devices. The Genetically Engineered Materials Science (GEMSEC) lab has engineered peptides that are capable of binding to substrates such as graphene, monolayer molybdenum disulfide, and boron nitride nanosheets. Utilizing experimentally determined binding affinities of these binding peptides alongside a database of biochemical and physicochemical properties of amino acids, we have developed a method to computationally predict short amino acid sequences that preferentially bind to atomically flat surfaces. Matrix factorization and linear regression is used to train a model capable of predicting an experimentally observed peptide count number (observed during sequencing of eluate of phage display biopanning) from 8 Total Similarity Scores (TSS) that are calculated from 8 novel similarity matrices. This model is then used to predict the ranking of actual binding affinities of genetically engineered peptides to monolayer molybdenum disulfide from fluorescence microscopy experiments. The ability to predict solid binding by peptides will facilitate further research into peptide structure and functional properties upon adsorption. Ultimately, these methods will be implemented in a cohesive software platform using machine learning and signal processing tools to allow determination of sequence-property linkages and pattern recognition in a larger bioinformatics context, and allow for nanomedical and nanotechnological advances at the intersection of materials science, biology, and genetics. Supported by the NSF-DMREF program through the Materials Research Initiative.

In the central nervous system, insulin acts as an anorexigenic hormone, regulating the desire for fatty and sugary foods. It also plays an important role in learning and memory. Thus, a malfunctioning insulin transport system across the blood-brain barrier (BBB) could be linked to obesity, the development of type 2 diabetes, and cognitive impairments as occur in Alzheimer’s disease. Studies have shown that insulin binds to insulin receptors (IR) located on the endothelial cells which make up the BBB; the activated insulin-IR complex is then taken up into the cell, where it sets off a signal cascade. Additionally, insulin binds a protein responsible for transport from the luminal to abluminal side of the brain endothelial cell. However, the mechanism by which this occurs is still not understood. Thus, we set out to elucidate the difference between insulin receptor uptake and insulin transcytosis in vivo, focusing on clathrin and caveolin, the two proteins primarily responsible for mediating endocytosis. To do this, we use radiolabeled insulin, the IR antagonist S961 (which binds to IR but is not taken up into the cell), and three pharmacological agents: phorbol 12-myristate 13-actetate (PMA) to promote endocytosis, monensin to disrupt clathrin-mediated endocytosis, and filipin to disrupt caveolin. To eliminate serum factors, cardiac perfusion in male CD-1 mice will be performed. One group will be the vehicle control group, and the other will receive radiolabeled insulin, S961, in addition to one of the three pharmacological agents. Perfusions will last from 1-10 minutes, in which brains are collected and dissected into brain regions. Radioactivity is measured in the hypothalamus and hippocampus as well as whole brain. The data collected will help us better understand the differences between insulin transcytosis versus endocytosis and how insulin transport may go awry in Alzheimer’s disease, diabetes, and obesity conditions.

High-density lipoprotein (HDL) plays an important protective role in development of atherosclerosis, one of the leading causes of cardiovascular disease (CVD) and death. Although HDL is generally believed to exert anti-inflammatory effects in cells, recent data have emerged showing that HDL can enhance the pro-inflammatory effects of inflammatory stimuli under some conditions. However, molecular mechanisms involved in the pro-inflammatory effects of HDL are not well understood. We hypothesized that HDL-mediated cholesterol depletion in macrophages drives the pro-inflammatory effect of HDL in an ADAM metallopeptidase domain 17 (ADAM17)-dependent manner. Bone marrow-derived macrophages (BMDMs) were collected from wild-type mice and from mice deficient in ADAM17 in hematopoietic cells. ADAM17 is a membrane-bound sheddase that cleaves extracellular parts of several membrane proteins. The BMDMs were pretreated with HDL for 18 hours before stimulation with lipopolysaccharide (LPS). At the end of the LPS treatment (10 ng/ml, 6 hours), BMDMs were collected and used for gene expression or protein analysis. We observed that HDL (100 μg/ml) exaggerated the response of LPS on tumor necrosis factor alpha (4-fold over LPS alone) and interleukin 1 beta (2.8-fold over LPS alone) gene expression in BMDMs. This effect was prevented by cholesterol loading of the macrophages. The pro-inflammatory effects of HDL were associated with increases ADAM17 gene expression (50% over LPS alone) and protein (~2.5-fold over LPS alone) levels. Moreover, deletion of ADAM17 in macrophages prevented the pro-inflammatory effects of HDL by inhibiting HDL-mediated cholesterol depletion. We also observed that BMDMs from ADAM17-deficient mice exhibit elevated expression of genes related to fatty acid and cholesterol synthesis. Overall, these data suggest that deficiency of ADAM17 alleviates the pro-inflammatory effects of HDL by preventing cholesterol depletion in macrophages. This research helps us to understand HDL’s functions in inflammatory cells, which become dysfunctional in several pathophysiological states, including diabetes and cardiovascular disease.

One of the open questions in neutrino physics is the absolute mass scale of the neutrino, currently recognized as the only fundamental fermion whose mass scale is not fully known. The Project 8 neutrino experiment employs cyclotron radiation emission spectroscopy (CRES) to probe the neutrino mass spectrum, a method developed to measure electron energy by detecting cyclotron radiation through the acceleration of electrons confined in a magnetic (B) field. CRES data relies on energy precision which is directly related to B-field precision, therefore it is pertinent to monitor the time-varying field vector in which the experiment lies. Initial B-field surveys in our laboratory provided insight into the volatility of the local field environment, showing stray field fluctuations up to .5 microTesla produced by neighboring high field, high ramp-cycle magnets. This discovery motivated the implementation of the ambient magnetic field array measurement (AMFAM) system which monitors the local field environment and helps parse fluctuations in the B-field that could adversely affect the CRES data. The AMFAM system utilizes multiple triple-axis magnetometers placed around our laboratory for strategic B-field investigation. I worked on the development of the Arduino-based software to extract appropriate data from the magnetometers, as well as the hardware and wiring of the array system. I present my plans to execute data analysis and describe how long-term investigation of field conditions will benefit Project 8’s CRES data.

In humans, limb amputation and recovery post-amputation is characterized by inflammation and scarring that lead to poor clinical outcomes. In contrast, amphibians such as the frog Xenopus tropicalis are capable of healing scarlessly and can fully regenerate previously amputated appendages. Successful limb regeneration depends on precisely choreographed expression of genes, directed in part by the deposition and removal of epigenetic markers. The broad aim of this research is to identify the spatiotemporal dynamics of epigenetic modifications and how they play a role in regulating gene expression during regeneration. It is known that histone deacetylases (HDACs) and H3K27-specific methyltransferase EZH2 enzymes limit chromatin accessibility and are necessary for regeneration to occur properly. However, the precise mechanisms and genomic targets of these enzymes remain unknown. We hypothesize that inhibiting these enzymes will leave chromatin in a constitutively accessible state, disrupting the gene expression required for successful regeneration. I am utilizing the drugs Trichostatin A (TSA) and DZNep to inhibit HDACs and EZH2 respectively at differing sequential time points throughout tail regeneration. In addition to characterizing the morphological outcome of regenerating tails that have been treated with these drugs at varying intervals post-amputation, I  also use immunofluorescence to identify the targeted location relative to the injury site and tissue types as they are affected across time. For humans and other mammals with limited regenerative capability, studying these epigenetic changes and their impact on Xenopus tropicalis tadpole tail regeneration is especially significant: it has the potential to determine how changes in gene regulation may enable and facilitate a broader capacity for limb regeneration by informing future therapeutic possibilities.

Glutamylation is a post-translational modification that occurs on tubulin and regulates tubulin function. Microtubules play a role in cell division, cell motility, and the transportation of vesicles and organelles. A family of enzymes called tubulin tyrosine ligase-like (TTLL) enzymes catalyze the glutamylation of tubulin. Eight TTLL enzymes are encoded within the human genome and mutations of these enzymes has been shown to affect cilia mobility. Individual deletions and reduced function of select TTLL enzymes has been shown to impair the mobility of cilia in various cell types in humans, mice, and Caenorhabditis elegans (C. elegans). C. elegans express six of these eight TTLL enzymes and will be used as a model system to investigate the role of tubulin glutamylation in microtubule function. To examine the role of these enzymes, a strain with mutations in multiple TTLL enzymes was generated (ttll-4, ttll-9, and ttll-11) and viability, brood size, male mating, and male mating efficiency assays were preformed. The gathered information on the triple mutant's viability, brood size, observations of behavior(s), and the confirmed triple mutant C. elegan shall be used in continuing studies on TTLL enzymes in C. elegans. This research will yield further insight to the role(s) of TTLL enzymes and glutamylation in regulating microtubule function.

Black bears are the most abundant bear in North America and Washington, but present knowledge is dominated by telemetry studies on home range size or vegetation class preference. Camera trapping data indicating black bear presence were used to build an occupancy model for the two study sites in Washington, one in Okanogan county and one in the northeast. The camera traps are intended for a predator-prey study focused on wolves, cougars, and ungulates, but detected a large number of black bears, suggesting the importance of black bears in these ecosystems. Black bear distribution may be driven by land-use patterns including variables such as elevation, vegetation and habitat type, approximate percent canopy cover, slope, aspect, and land management type. The constructed single season occupancy models of black bear presence can be used to better understand habitat selection by black bears in different regions of the state. This study seeks to fill in gaps of knowledge about black bears in Washington and provides a framework for future occupancy studies on black bear habitat use.

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s Sarcoma (KS), a highly vascularized tumor composed of cells of endothelial origin. KSHV, while possessing both lytic and latent replication programs, predominantly exists in the latent form during infection. While KSHV infects both blood (BECs) and lymphatic (LECs) endothelial cells, LECs are more susceptible to infection and express fewer antiviral genes during infection compared to BECs. Recent experiments have shown that LECs, but not BECs, have a defect in STING, a critical signaling protein that is activated during herpesvirus infections and results in the production of antiviral signaling molecules such as IFN-β. It remains unknown whether the defect in STING plays a direct role in increasing susceptibility to KSHV infection and if the defect impacts the ability of STING to suppress lytic reactivation in LECs. Accordingly, I propose to construct a constitutively active (CA)-STING and express it in LECs. Because CA-STING results in the continuous induction of IFN-β, I hypothesize that CA-STING-LECS will show decreased susceptibility to the establishment of latency by KSHV and have increased ability to suppress lytic reactivation compared to empty vector-expressing (EV)-LECs. First, I will infect EV-LECs and CA-STING-LECs with KSHV and measure the infection rates 48 hours post infection (hpi). I expect the number of infected cells in the CA-STING-LECs to be decreased relative to the EV-LECs. Next, I will infect EV-LECs and CA-STING-LECs with KSHV, and at 48 hpi, I will induce lytic reactivation in the two cell types and quantify the virus produced. If CA-STING suppresses lytic reactivation in LECs, I expect less virion production from CA-STING-LECs than from EV-LECs. The results from these experiments will further elucidate how KSHV exploits defects in innate-immunity to infect and transform host cells.

The mental health of transgender children, children who have socially transitioned to live as the gender “opposite” their assigned sex at birth, have not been researched extensively, although the occurrence of childhood social transitions have increased in recent history. Instances of bullying and discrimination are reported in the LGBTQ community in high rates, which has been known to lead to higher rates of internalized symptoms. Previous studies have looked at the stress buffering hypothesis, which postulates that social support protects against the negative effects of victimization experiences, but the results from those studies are mixed. In the present study, we examine whether social support moderates the association between bullying and discrimination with internalizing symptoms in transgender youth. To test our hypothesis, we had the parents of 265 socially transitioned children, from ages 3-15 (mean age 9.41), answer questions regarding a child’s support structure (family, peer, school) and whether their child has been bullied and/or discriminated against specifically because of their gender. Our results show that the relationship between victimization experiences and internalizing symptoms was moderated by peer support, but not by family support or school support. We found that when participants had less peer support, being victimized more was associated with more internalizing symptoms, while higher levels of peer support do not yield significant results between the two variables, indicating that peer support may act as a buffer between victimization experiences and internalizing symptoms in transgender youth.

The Irrawaddy River is Myanmar’s biggest river system and the world’s third largest river in terms of sediment load. It drains the eastern edge of the Himalayas and flows through the Central Myanmar Basin into the Andaman Sea. Its geological history remains yet poorly documented, and when its modern drainage basin was established is unknown. For my research, I reconstructed the history of the Irrawaddy drainage system by using sedimentary provenance methods. Sediments in the Central Myanmar Basin can be traced back to their source rock by using different geochemical and petrographic proxies; by using these proxies on dated sedimentary rocks in the basin, I aimed at determining when the modern sediment sources were established. My research focused on two proxies: zircon geochronology and petrographic analysis of sandstones. Zircon geochronology is a method of dating zircon minerals from sandstones. The zircon age distribution obtained from a particular sediment sample is a direct insight into the age of the sediment source rock. Sandstone petrographic analysis involves analyzing at least 300 individual sediment grains and classifying them according to their mineralogy to compare them with the known rock characteristics in the potential sediment source areas. Both proxies were applied on sedimentary rocks of different ages previously collected in the field. I compared the results from both analyses with the modern sediments collected from the Irrawaddy river mouth and modern sediment source areas. I looked for consistency in the zircon age distributions and petrography signatures between the modern and older deposits to deduce the maximum age of the river. My preliminary results suggest that the Irrawaddy River was established around Middle Eocene (40Ma), which would make the Irrawaddy one of the oldest drainage systems of Asia.

Mitochondrial dysfunction, characterized by decreased efficiency of the Electron Transport Chain (ETC) and loss of structural integrity, is linked to cellular senescence, an irreversible end to the cell-division cycle that contributes to aging. Minimizing senescence through late age intervention may prevent aging tissue dysfunction. Systematic treatment of old mice with a tetrapeptide, SS-31 reduced mitochondrial dysfunction and senescence in kidneys. We hypothesized that a similar effect would occur in other organs, and with other mitochondrial targeting interventions. These interventions included the SS-31 tetrapeptide which interacts with mitochondrial cardiolipin to improve structure and function, and NMN (Nicotinamide Mononucleotide), which fuels the organelle for more efficient adenosine triphosphate generation through the ETC. We treated old mice at 24 months-of-age for 8 weeks with either SS-31, NMN, or both interventions combined. Control groups included young-untreated mice at 4 months-of-age and old-untreated mice sacrificed with the treatment groups at 26 months-of-age. By comparing tissues, including heart, kidney, liver, skeletal muscle, skin and brain, within individual mice, we were able to account for differing rates of aging between mice. To determine the relative levels of senescence and treatment response in each tissue, we used Immunohistochemistry to quantify known senescence markers p16 and HMGB1, and quantitative-PCR to measure p16 mRNA transcript levels. As expected, preliminary results from p16 staining showed higher overall senescence burden in old as compared to young mice. The staining patterns also revealed senescence susceptible cells, with majority of p16 positivity in liver satellite cells, glomeruli and tubules of kidney, fibrocytes of heart and myocytes of skeletal muscle. Overall, the kidney and liver had more p16 positive senescent cells than did heart and muscle. These tissues are currently under analysis to determine whether intervention treatments can reduce cellular senescence.

The plant hormone Jasmonic acid (JA) interacts with JAZ proteins, proteins that play a crucial role in the regulation of signal cascades triggered by jasmonates, and controls the activity of MYCs, a family of genes that code for transcription factors. In the absence of JA, JAZ proteins bind to downstream MYCs and limit their activity. JA is produced in plant cells in response to tissue damage, and is crucial to plant fitness. The genome of model plant Arabidopsis thaliana encodes 13 JAZ and 5 MYC isoforms, but as of now, it is unclear why this apparent redundancy exists. Such redundancy is a common feature of plant genomes. In the case of JA-signaling, it may be that interaction strengths differ between JAZ and MYC isoforms and that this is important for system behavior. In A. thaliana, there are 65 pairwise combinations alone, which provides many opportunities for engineering incredibly fine-tuned and controlled gene expression. Our past work has been to clone and create a library of JAZ and MYC proteins. Our goal now is to create yeast mini-circuits, which are yeast cells that contain plasmids that carry certain selected JAZ and MYC proteins. After constructing these yeast mini-circuits, we will study the JA-response dynamics of these circuits to better understand the role of each of these proteins and study differences in strengths of interaction between the different proteins. We suspect that the absence of certain JAZ and MYC proteins will lead to different phenotypes in defense mechanisms. Additionally, by investigating this relatively familiar pathway through the construction of yeast mini-circuits, we are attempting to develop an efficient technique which can be used to characterize other unexplored plant systems.

Quantitative PCR (qPCR) is a commonly-used method to analyze gene expression. However, carrying out a qPCR experiment is often daunting to a beginner such as an undergraduate student, as it involves a lot of advance planning, precise pipetting, and is susceptible to contamination. Our goal is to automate laboratory and data analysis protocols so that (1) experiments can be carried out more quickly and more efficiently; (2) data are carefully tracked and recorded; and (3) results are reproducible. Automation involves repeated testing, writing and integrating protocols onto Aquarium, the laboratory operating system developed by our lab. Since Aquarium can keep track of every data point that it is asked to collect, we can define metrics of protocol success (like product quality, time-to-completion and ease of execution) and compare them throughout the automation process to make sure that the final protocols satisfy the three criteria above. For the 2018-2019 school year, we are automating protocols to cultivate Arabidopsis thaliana and study the gene expression of its Jasmonate (JA) signaling pathway. Since the JA pathway in Arabidopsis thaliana involves many genes and has been well-studied by plant biologists, we reason that it would be an appropriate case-study for our automation project. As we apply our qPCR workflow to study the expression of these genes in response to application of exogenous JA, we expect to see results that are consistent between different sets of technical replicates performed by different student technicians, and results that are consistent with those in existing literature.

Cancer is the second leading cause of death in the United States. Advanced treatment techniques and robust research have improved cancer survivorship. However, there is significant cancer treatment related morbidity and mortality with 30% of breast cancer patients presenting with heart failure symptoms that include trouble breathing, poor exercise tolerance, and fatigue. Therefore, research that aims to improve the lives of cancer survivors in this regard is needed. Excess body weight is a significant risk factor for both increased mortality in cancer patients and heart failure symptoms; however, it is unclear how fat is implicated. Intermuscular fat (IMF), fat that is located inside and between muscle groups, is a metabolically active tissue that competes with skeletal muscle for the use of oxygen, blood, and glucose. Elevated IMF has the strongest relationship with breast cancer mortality compared to any other measure of body composition. The purpose of my research is to describe differences in IMF accumulation during treatment in 143 patients receiving chemotherapy for cancer. Abdominal magnetic resonance imaging (MRI) will be used to determine total skeletal muscle, visceral fat, and IMF using Tomovision software. Images will compare total pixel surface area of each tissue to create a ratio of skeletal muscle to IMF at enrollment (0 mos) and end of study (24 mos). I hypothesize that the type of chemotherapy most strongly associated with weight loss will be linked with increased IMF during treatment. The study results will add to one aspect of a larger body of work that aims understand the mechanisms of IMF in cancer patients and its relation to cancer treatment-related symptoms. Future research should investigate interventions that aim to reduce IMF and monitor for reduced fatigue, less severe heart failure symptoms, and improved patient mortality.

Anecdotal evidence suggests patients that undergo Targeted Muscle Reinnervation (TMR) surgery, an operation where nerves are implanted to muscle instead of cut and left between muscle, report less residual and phantom limb pain when compared to standard amputation patients. To our knowledge, this is the first study to investigate this claim. Based on the nature of the TMR procedure, it should facilitate higher pressure thresholds than a severed nerve from a standard amputation, resulting in less pain for the patient. The risk of neuromas, a collection of highly sensitive tissue that can develop on a damaged nerve, should also diminish. To evaluate the efficacy of TMR in relation to pain reduction, a populace upwards of 135 people (comprised of TMR amputees, standard amputees and a control cohort) will have their nerves stimulated using focused ultrasound, allowing the application of focal intense and transient pressure on the nerve and not on the surrounding tissue. In this study, diagnostic ultrasound imaging guided the application of intense focused ultrasound on intact and transected nerve endings in our test subjects. We increased the ultrasound intensity until we either elicited a sensation or reached the maximum output possible by our device. We anticipate TMR amputees to have a higher threshold for ultrasound-induced sensations than standard amputation test subjects, but a lower threshold than the control test subjects. Due to the limited availability of TMR amputees in the area, a definitive conclusion has not been made about the effect TMR has relative to the standard amputation. When analyzing results from standard amputees specifically, there are three subgroups that possess an intriguing feature that distinguish them from each other. This study can potentially influence the types of surgical techniques offered to future amputees if TMR operations do in fact reduce the amount of pain experienced by patients.

Lecture demonstrations have a long history of use in science learning spaces. While extant research in STEM education show that demonstrations can be used to rouse student interest, some studies suggest that demonstrations have little to no effect on improving students’ understanding of the concepts taught in class. In chemistry, demonstrations are commonly used in lectures with the belief that student understanding of chemical concepts improves from observations of chemical phenomena. The purpose of this mixed methods study was to investigate students’ perceptions of lecture demonstrations and their usefulness in preparing for exams. To measure students’ perception of lecture demonstrations, a survey was administered to first year students (n <1500) in nine introductory chemistry classes over two quarters. Initial findings reveal that while students do in fact remember and enjoy lecture demonstrations, they found it difficult to apply demonstration concepts to problems on exams. Results also suggest a strong link between student engagement and exam performance. Overall this study highlights the importance of soliciting student feedback for improving and designing course materials and tools. Various strategies and implications for practice are also addressed.

The Olympic Mountains on the west coast of Washington State are an impressive topographic feature, the emergence timing of which remains poorly documented. The Olympic Peninsula comprises 52 million year old (52 Ma) igneous rocks, and marine sedimentary rocks deposited from 52Ma to present. Here, we use a proxy to model sourcing of sediment called detrital zircon provenance (DZP). We use DZP of sedimentary rocks from the Olympic peninsula and from the Seattle Basin further east to model ancient drainage systems in order to place age constraints on the uplift of the Olympic Mountains. Our data from both areas show that 52 Ma through 23 Ma sandstones display DZP patterns and sediment type in agreement with a direct supply from central Washington. Samples of 13 to 11 Ma sandstones and modern river sands from the west of the Olympic Peninsula display a youngest zircon age population at 17 Ma. These data indicate that this area was still fed by central Washington at that time. 11 Ma sandstones from the eastern part of the Seattle Basin display DZP patterns still in agreement with supply from central Washington. By contrast, contemporary river sandstones from the western part of the basin mostly consist of reworked older sediment. This change in sediment source shows that by 11 Ma, the Olympics had already emerged and reached sufficient topographic prominence to support eastward draining rivers that deposited the 11 Ma river sandstone units of the Seattle Basin. These data allow us to constrain the initial uplift of the Olympic Mountains sometime after 17 Ma but before 11 Ma. The data are in close agreement with previously published ages that establish the exhumation of the Olympic Mountains beginning at 18 Ma, and show that the Olympic Peninsula became an emerged topographic high in less than 6 million years.

Art can be a healthy way to express emotions and bring healing to the hurting mind. Tapping into the creative mind and using art to express oneself can provide a calm that other methods may not. Mental health disorders and substance use disorders are giants that cannot be defeated by one method alone. The safest place to be for an individual suffering in silence is outside the mind in an inclusive, creative, empathetic, and healing environment. The LWTech Lion's Pride Healing Art club is intended to help individuals safely experience and express emotions while bonding and sharing a safe space with like-minded people. To understand the effect that the healing art club has on its participants, I am conducting in-depth interviews with key students and staff. I hypothesize that participation in the healing art club helps express themselves in a therapeutic way, foster feelings of belonging to the community, and contributes to their overall health. The data collected is a helpful start in encouraging college communities to adopt similar programs and to promote positive mental health on campus.

Telomeres represent the structural ends of genomic chromosome molecules and are composed of hexamer repeats of the form [TTAGGG] which play a protective role against DNA damage and genetic information loss. The telomere length of normal diploid cells decreases over time and can be correlated with issues related to cancer and the aging process. Our preliminary work utilizes methods developed initially by Cawthon and O’Callaghan and is applied to DNA samples obtained from research studies involving the elderly as well as those with aneurisms. In contrast to standard measurements which use real-time PCR in order to calculate relative telomere lengths, our method uses absolute quantification through the use of standard curves generated with a synthetic 84-mer telomere (control gene) and another synthetic oligomer (36B4 ‘housekeeping gene’). Through the use of both synthetic standards in a typical RT-PCR experiment utilizing SybrGreen and specific primers for either telomere sequence or housekeeping gene, the true length of a diploid telomere can be calculated by extrapolation from standard curves. Telomere lengths obtained through this method have been compared to results derived from commercially available test kits which used relative RT-PCR as a quantification measure. Results obtained through the use of this technique can be incorporated in research studies encompassing cell apoptosis, processes involved with aging. This technique can also be used to ascertain the effects of environmental impacts involving DNA damage on plants, bacteria, and animal cells.

Isolation of silicon (Si) is a microfabrication technique used to isolate selected areas of silicon from interacting with each other using silicon dioxide (SiO2). This processes is done to separate metal oxide semiconductor (MOS) transistors from each other. MOS is a specific way of fabricating devices that is low cost and easy to integrate. It is a very important step in creating integrated circuits. Circuits must be isolated from each other to perform correctly. The smaller the space to separate the circuits, the more circuits can be placed on a device or the smaller the device can be. There are currently two different techniques for isolating silicon. Local Oxidation of Silicon (LOCOS) is the more widely used technique versus the more modern attempt, Shallow Trench Isolation (STI) that is becoming more popular this decade but has many more process steps. Each technique has its pros and cons. LOCOS is a method in which a thin layer of SiO2 is deposited on a wafer, pad oxide, and then a layer of silicon nitride (SiN) is also then deposited as an etch barrier for later stages.Through photolithography processes, including photoresist application, aligning and exposure, a pattern is transferred onto the wafer. The wafer is then put through a plasma etcher to create space for more oxide. Next is for the thermal oxide to be grown, creating an unfortunate “birds beak” that limits feature size of the circuit . The final step is the removal of the remaining nitride and only oxide is left. I am creating a completely new process flow along with a new wafer mask for photolithography to cater to the labs existing equipment, varying different variables and attempting to optimize the technique for the lab. In doing so I will be our lab’s capabilities are tested to see how efficient it is to run the process in the facility and how accurate the results are. The results will be used to determine if in the future certain design features will be able to be implemented in and then fabricated in the lab. Also the question of the techniques viability is answered, if it is still usable and in tolerance with different standards.

Magnetic Resonance Imaging (MRI) is an invaluable imagining modality that allows physicians to quickly analyze the anatomical and physiological processes of the body. To improve contrast efficiency, MRI contrast agents are frequently administered to patients. However, the most commonly used T1 contrast agent – gadolinium-based contrast agent (GBCA) – has been associated with many adverse health effects, such as reduced white blood cell count, increased serum levels of inflammatory cytokines, and vacuolar degeneration. As such, there is an urgent need to design a T1 contrast agent that has a short half-life and that does not produce toxic endpoints in patients. To address this need, the present study developed an iron-oxide nanoparticle (IONP)-based T1 contrast agent by synthesizing 4 nm oleic acid-coated IONP and reacting them with phosphine oxide-PEG. Next, this study characterized the biological and the magnetic properties of the generated IONP system in vitro in order to determine its suitability as a T1 contrast agent. Finally, this study also analyzed the synthesized contrast agent’s use in other biomedical applications, specifically targeted drug delivery. Previous research has shown that cells can undergo ferroptosis – a regulated form of cell death – upon loss of activity of the lipid repair enzyme glutathione peroxidase 4 (GPX4). As such, a silencing RNA (siRNA) that can mark GPX4 mRNA for degradation was conjugated to these IONPs in order to downregulate GPX4 expression in mesenchymal stem cell – a type of stem cell that are particularly involved in cancer progression and that are especially resistant to radiotherapy – and sensitize them to radiotherapy. Ultimately, the findings of this study not only offer a safer alternative to GBCAs but also provide a foundation for a versatile, tunable IONP system that can be used in a variety of biomedical settings.

This project showcases how the works of organizations and individuals have advanced the efforts to achieve justice for the crimes against humanity committed throughout 20th century Latin America. By conducting in-depth research on how organizations have advanced cases of disappeared persons through forensic anthropology and criminal prosecution, we answer the question of how specific organizations and individuals have revolutionized the fields of forensic anthropology and human rights in the pursuit for justice. Our research investigates newspaper articles, court cases, and other media resources to identify how forensic evidence has been used to hold human rights abusers accountable. We also compare the human rights crises in Latin America to other global human rights crises to identify similarities between their initiation and subsequent movements for justice. We expect to find similarities in the cases of forced disappearances in Latin America and gain detailed information on how different methods of justice have been pursued across the region. Our research will be culminated on a central website that depicts the background, development, and ongoing movements of Latin America’s human rights history. By presenting this information in an accessible form, we hope to increase the public's knowledge of forensics and human rights, and to explain the value of these fields in attaining justice in Latin America and ultimately around the world.

In order to maintain maternal, fetal and neonatal health during pregnancy and lactation, appropriate nutrition is necessary. Both excessive and inadequate intake are associated with significant complications for the mother, fetus and neonate. The objective of this study was to describe nutritional intake during pregnancy and lactation in healthy women (n=13) relative to current recommendations from the National Institute of Health’s Office of Dietary Supplements during pregnancy and lactation as well as compare nutritional intake during pregnancy (25-28 weeks and 28-32 weeks gestation) to >3 months postpartum in lactating women. Individual daily dietary consumption was determined by averaging dietary intake for 3 days during each study window. Nutritional content was determined utilizing Fooducate® (Fooducate Ltd.). Statistical comparison of nutritional intake for study windows were conducted using repeated measures analysis of variance (RStudio). Results are reported as mean ± SD. Significant differences were found in daily sugar intake (25-28 weeks: 82.1±25.1 grams, 28-32 weeks: 97.5±29.7 grams, and postpartum: 62.0±34.8 grams, p<0.03) and daily added sugar intake (25-28 weeks: 39.0±5.7 grams, 28-32 weeks: 54.0±19.7 grams, and postpartum: 32.0±18.0 grams, p<0.02). No significant differences were seen in daily total calories, calories from fat, total fat, saturated fat, trans fat, cholesterol, sodium, potassium, total carbohydrates, dietary fiber, protein, vitamin A, vitamin C, vitamin D, calcium and iron. During pregnancy and lactation, average dietary consumption exceeded recommended daily allowances for carbohydrates (lactation only), sodium, protein, iron (lactation only), vitamin A, and vitamin C (pregnancy only). In contrast, average daily consumption of calories, carbohydrates (pregnancy only), fiber, potassium, calcium, iron (lactation only), vitamin C (pregnancy only), and vitamin D were less than the recommended daily allowances. In conclusion, women consume more sugar during pregnancy than postpartum and average nutritional intake during pregnancy and lactation are inconsistent with current nutritional recommendations from the National Institute of Health’s Office of Dietary Supplements.

Genetic differentiation has long been thought to be low in marine environments, mainly due to higher dispersal potential and low barriers to migration. However, many marine species show population structure on relatively small geographic scales. For example, Pacific cod in the Gulf of Alaska is structured in an isolation-by-distance pattern along the coast. Genome wide surveys also identified genes with particularly strong differentiation, especially the zona pellucida (ZP), a sperm-binding complex in the eggs of Pacific cod that determines what sperm will fertilize the egg. When the outermost region of this complex (ZP3) was sequenced and analyzed it was found that the population of Pacific cod around Kodiak Island had far different ZP3 proteins than the population of Pacific cod residing within Prince William Sound, suggesting that the two populations are reproductively isolated. Our study will expand these results by increasing sample sizes and extending the geographic range of sampling towards the west to assess whether differentiation at this gene can also identify populations in the Aleutian Islands and the Bering Sea. Our results would confirm a split of Gulf of Alaska Pacific cod into two large East-West subpopulations, and may also reveal additional population structure. These findings would not only provide insights into reproductive isolation within marine fishes, but would also have large implications for management, as distinct subpopulations must be managed as such.

This cross-sectional study examined how participants’ NTB (need to belong) moderates the relationship between anxiety and FBSC (Facebook social comparisons). Higher Facebook use has been linked to greater anxiety and increased Facebook social comparisons. Although the literature has demonstrated that people who spend more time on Facebook are more prone to negative consequences, it has yet to demonstrate who might be more vulnerable to comparing themselves to others on social media. Students from a Southern university (N=152, 61.18% female, M=22.55 years) participated in this study. Linear regression analysis was used. Results revealed anxiety and NTB were significantly and positively associated with FBSC. Those with higher levels of anxiety and NTB engaged in the most FBSC, whereas those with higher levels of anxiety and lower NTB engaged in the least FBSC. These results may be useful for clinicians to identify highly anxious clients who are also higher in NTB, as these individuals might be more susceptible to the negative mental consequences associated with FBSC.

Freshwater mussels are one of the most at-risk taxonomic groups in North America with about twenty percent of species and subspecies listed as endangered. Populations are thought to be declining due to habitat loss brought on by invasive species such as the zebra mussel (Dreissena polymorpha), water pollution, and the construction of dams, which prevent the passage of the host fish necessary for mussel reproduction. Freshwater mussels provide vital ecosystem services by acting as biomonitors of stream health, improving water clarity by filter feeding, and providing microhabitats for other freshwater organisms. The focal species of the study is the federally endangered Higgins eye pearlymussel (Lampsilis higginsii) which are found in the Mississippi River and nine of its tributaries, including the Wapsipinicon River. The Wapsipinicon is valuable habitat for Higgins eye due to its lack of zebra mussels, but several dams, now up for removal, have restricted the species to just a few sections of the river. This study compares microhabitat factors and hydraulic parameters at sites with and without Higgins eye pearlymussel populations in five sections of the Wapsipinicon River to determine the habitat requirements of the species. Using GIS, a habitat suitability index was created and potential reintroduction areas in parts of the river that will become accessible following dam removal were mapped. Although the data are limited, there is some indication that Higgins eye prefer sandy substrate at river bottom elevations around 231 meters. All of the sites have significant areas that match this description and could provide habitat for Higgins eye in the future, but more data are necessary to select specific sites and confirm this conclusion. If these inaccessible areas are found to support Higgins eye populations we can encourage dam removals and improve our understanding of a struggling and under researched species.

Microbial toxins are a molecular weapon involved in pathogenesis, immune evasion, and bacterial competition. A prime example of such microbial toolkits are polymorphic toxin systems, which consist of multi-domain proteins and are widespread in all major bacterial lineages. A polymorphic toxin system called MuF has been newly identified and is the first to be discovered in temperate phages and their bacterial hosts. Though it is highly abundant in the human gut microbiome, its biological role has not been defined. To better understand the toxin system, our team is studying a model species Enterococcus faecalis, a commensal bacterium encoding a two-domain MuF toxin protein on one of its phages, consisting of an N-terminal MuF domain and a C-terminal toxin domain. The toxin domain is predicted to be an ADP-ribosyltransferase (ART), which post-translationally attaches ADP-ribose moieties to its target molecules and can profoundly impair cell processes, leading up to cell death. Using genetic approaches to generate phages with malfunctional ART activity, I have found that the mutations change phage infectivity and the morphology of the plaques formed (clear zones in a cell layer formed due to lysis by phage). Moreover, heterologous expression of the toxin domain in E. faecalis results in cell aggregation. From this, I hypothesize that the MuF toxin is delivered by phages to help infection and ensure phage DNA incorporation into host genomes. To further dissect the mechanism by which the MuF toxin system operates, our team is currently developing a fluorescent protein reporter system to investigate and track the detailed process of phage infection. In addition, by applying X-ray crystallography and electron microscopy, I aim to uncover structural information on the toxin, which may lend insight into the mechanism of MuF toxicity and its larger role in the human microbiome.

Single-cell gel electrophoresis, or a Comet Assay, can be used to assess DNA damage in cells as it liberates single-strand DNA breaks (SSB), alkali labile sites (ALS), and DNA cross-links, then uses microscopy to determine levels of chromosome damage. Various methods have been used to detect DNA damage; advantages of this assay include its capacity to detect low levels of DNA damage, the small number of cells required, low cost, and the ability to utilize various cell types. Our lab used lymphocytes withdrawn from elderly patients as we targeted quantifying the effects on an individual’s DNA due to aging, stress, and drugs. Lymphocytes were suspended in low-melting point agarose and placed on a slide pre-coated with regular agarose. Once cells were fixed on the slide, they were placed in lysis solution to remove membranes and liberate DNA. Lymphocytes then went through an alkaline treatment to unwind DNA super-coils. The assay has been tried under neutral conditions however, we used the alkaline method because it is known to increase reproducibility and specificity. The cells were then placed in an electrophoresis chamber at 5 V/cm for 30 minutes, the SSB’s, ALS’s, and DNA cross-link fragments traveled towards the anode, forming a comet like appearance behind the cell. The cells were then neutralized, stained with ethidium bromide, and the comets were visualized. Data can be quantified using software provided by Instem Technologies. A comparison of Comet values derived from varying cell densities as well as untreated control samples are also presented, confirming good reliability using this technique.

Von Willebrand Disease (VWD) is a bleeding disorder in which von Willebrand Factor (VWF), a polymeric blood protein, is either completely absent or in a dysfunctional state within the circulatory system. VWF’s function is to respond to shear force through an unfolding conformational change, and it is this unfolding and consequential exposure of platelet binding sites that initiates the blood clotting cascade. Affecting 1% of the entire population, VWD is the most common inherited bleeding disorder. However, few effective treatments exist. A major barrier to understanding VWF function is the absence of human cellular and vascular models that can accurately reconstitute complex phenotypes and molecular mechanisms. Studies of VWF at the cellular and vascular scale can provide important insight into physiological factors that regulate VWF. Human cells are particularly attractive and provide a highly accessible, species-specific model that can be more flexible than mouse models. Current cellular models for VWF functional studies are primarily limited to endogenous VWF secreted from human umbilical vein endothelial cells (HUVECs), which are not immortal, making it difficult to engineer disease models. This project serves to directly address these barriers through the creation and characterization of stable VWF knock-out human pluripotent stem cell lines (hPSC). These cells are immortal and can differentiate into numerous lineages including endothelia. VWF knock-out cells differentiated normally into endothelial cells, as expected, based on cell morphology and endothelial marker expression. The VWF knock-out cells have been confirmed through immunoblot and immunofluorescence to be deficient in various VWF-associated proteins, such as Factor VIII and Angiopoietin-2. We are currently investigating the mechanisms behind these deficiencies and how they relate to the absence of VWF. These findings will enable us to better understand the function of VWF, which will ultimately guide us to discover effective treatments for VWD.

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by multi-organ inflammation and damage, including skin and kidney. Ultraviolet B light (UVBL) is the only environmental factor known to precipitate both skin and kidney disease. How UVBL-triggered sterile inflammation in the skin influences kidney injury remains a pressing question for SLE patients, about 70% of whom suffer from sensitivity to UVBL. We previously demonstrated that neutrophils are the first immune cells to infiltrate the inflamed skin tissue after exposure to UVBL. To investigate the neutrophils’ role in UVBL-induced kidney injury, C57BL/6J mice were irradiated with a single dose of UVBL (500mJ/cm2). Cells in the bone marrow (BM), skin, blood, and kidney were characterized using flow cytometry. Gene expression of inflammatory mediators and adhesion molecules was evaluated using qPCR. Following acute exposure to UVBL, we observed a 10-fold increase in skin neutrophils, associated with a decline in neutrophils from the BM and a 5-fold increase in circulating neutrophils relative to baseline (no UVL). Relevant to SLE, neutrophils increased up to 10-fold in the kidney after skin UVBL injury (vs. no increase in monocytes/macrophages). Local skin response was characterized by rapid induction in inflammatory cytokines (IL1b, TNFa, IL6, IL33) and neutrophil chemoattractants (G-CSF, CXCL1, LIX) (day 1-2) that returned to baseline by day 6 after UV. Neutrophil infiltration into the kidney was accompanied by endothelial activation and inflammation: increased VCAM1, E-Selectin, IL1b, Ngal, and s1008/9 gene expression, markers of kidney injury in SLE, as well as by transient proteinuria. Neutrophils recruited to the kidney demonstrated two phenotypes: early activated CXCR2hi (day 1-2) and late aged CXCR4hi (day 2-6), which followed expression of CXCR4 ligand CXCL12, another marker of kidney injury. Together, our findings propose a novel neutrophil-dominated skin-kidney axis of pathogenesis and provide a model for UVBL-triggered disease UW flares in SLE.

A study conducted by Dunning and Kruger suggested that people with high skills usually under evaluate their performance, whereas relatively lower skilled individuals tend to over evaluate the performance due to a limited amount of knowledge. This research aims to model the relationship between students’ self-assessed and actual performance on exams in general chemistry courses at the University of Washington. Using a two-stage least squares regression analysis, we examined student’s’ estimation of their test performance following course examinations and their actual performance. The results indicated the magnitude of overestimation was on average greater for students receiving lower exam scores, while high performers tended to under evaluate their performance, consistent with the so-called Dunning-Kruger effect. In addition, the degree of overfidence was more pronounced for men with lower performance; however, higher scoring women tended to underestimate their performance relative to men with equivalent scores. The immense number of external factors that contribute to students’ exam performance threatens the validity of estimates of the Dunning-Kruger effect. Therefore, this research also examined the role of measurement bias in estimating the relationship between students’ self-assessment and actual exam performance.

Implanted biomedical devices are becoming increasingly common for the treatment of organ or tissue loss. The efficacy of these implants, however, is continuously hindered by attempts of the host immune system to eliminate foreign biomaterials, a process termed the foreign body reaction. The long-term outcome is the collagenous encapsulation of the implant that prevents it from integrating into the body. While there are many approaches towards guiding or suppressing the host immune response, we are particularly interested in modulating the macrophage phenotype at the biomaterial-host interface to dampen foreign body reaction and restore tissue homeostasis. Specifically, vascularization, the formation of blood vessels and capillaries, in and around a porous biomaterial is shown to be partially driven by the expression of different macrophage phenotypes which in turn are modulated by the biomaterial pore diameters. Thus, we hypothesize that activating the pro-inflammatory M1 macrophage phenotype in the biomaterial microenvironment promotes vascularization and dampens collagen deposition. To test our hypothesis, I am currently optimizing the seeding and activation of primary inducible engineered pro-inflammatory M1 macrophages (i-M1macs) on biomaterial with different pore diameters in vitro. The focus following the optimization of their M1 phenotype expression will be investigating their effect on the foreign body reaction to biomaterial with different pore diameters in vivo. I will implant the i-M1macs seeded biomaterials in laboratory mice and harvest them at selected time points. Using histology and image analysis, we will determine whether the primary i-M1macs increase vascularization in and around the biomaterial and whether i-M1macs-dependent vascularization is affected by the pore diameters. Obtaining positive results will confirm the potential of our cell therapeutic approach to improve the integration and biocompatibility of various biomedical devices.

Analysis of plant foods and medicines is a growing field within archaeological research. However, few scholars have examined plant foods among Native American communities in colonial settings. This project combined archival and archaeological data to better understand plant use within the Grand Ronde community during the late nineteenth and early twentieth centuries. Field Methods in Indigenous Archaeology (FMIA), a community-based research partnership between UW and the Confederated Tribes of Grand Ronde Historic Preservation Office, has collected macrobotanical remains from the Grand Ronde Reservation in northwestern Oregon. I explored how and why these remains were used within the community. Knowing this information will provide a better sense of local environmental contexts and cultural lifeways. To study this question, I selected ten plants that have been recovered during FMIA’s excavations and examined ethnographic, archaeological, and documentary sources from the region to understand each plant’s cultural context. I found that most plants found on the reservation were used as food sources, though some also had medicinal and spiritual significance. This work sheds new light on the relationships between Native communities and plants in the Pacific Northwest over the past two centuries, helping us understand how people navigated the challenges and opportunities introduced by colonialism.

Autophagy is a fundamental biological pathway that facilitates the degradation and recycling of intracellular components. While it is known to be activated in response to cellular stress, it may also have critical roles in developmental processes. To date, studies in mice have shown that deletion of core autophagy proteins impairs the production of many essential hematopoietic lineages, suggesting that autophagy is critical for blood cell differentiation. In particular red cell production is known to be dependent on autophagy however (1) when does autophagy occur? and (2) how is it regulated? In human erythropoiesis is unknown. Preliminary data from the Doulatov lab has identified a novel negative regulator of autophagy, ATG4A, in human erythropoiesis. The ATG4 family of proteins are cysteine proteases known to regulate LC3B a critical molecule which decorates the outside of the autophagosome. However, whether its expression is confined to erythropoiesis or broadly applies to other hematopoietic lineages is unknown. Therefore, I performed a bioinformatic analysis on a large RNA microarray dataset which profiles gene expression in 38 distinct cell populations in the 7 major hematopoietic lineages. Only ATG4A and ATG4B were detected in the dataset, and when mapped across the hematopoietic hierarchy had differing patterns of expression. In contrast to ATG4B the expression of autophagy protein ATG4A was selectively upregulated in the erythroid lineage. Previous studies have described a critical role BNIP3L(NIX) in erythropoiesis, therefore I compared the expression pattern of ATG4A to BNIP3L. ATG4A and BNIP3L had similar patterns of expression suggesting multiple autophagy proteins may be upregulated during erythroid differentiation. Taken together these data suggest that ATG4A ia a unique regulator in the human erythroid lineage.

The Zwicky Transient Factory (ZTF) is a telescope located at Caltech in southern California. It is part of a new generation of wide field survey telescope programs. With its 47 square degree field of view and the ability to cover 4200 square degrees per hour of the night sky, ZTF is equipt to complete its survey of the Northern hemisphere. ZTF takes photometric data in multiple color bands including visual (r and g) and (i) bands increasing the accuracy of data collected on an observed body. It’s limiting magnitude is ~21 allowing us to see deeper into our universe. We constructed a pipeline of code which pulls photometric data from ZTF and fits light curves for asteroids with previously reported orbital parameters. A light curve is a recorded fluctuation in light intensity of a variable body. As an asteroid rotates its albedo or surface reflectivity varies producing the variation in flux we measure as a light curve. From a light curve you can calculate many properties of the body such as period, diameter, and mass. Our pipeline fits the observed light curve for its period and, for a subset of the asteroids with previously known periods reported in the Light Curve Database (LCDB), we test the accuracy of the fitting process. Of the initial ~4000 asteroid samples, 437 had periods reported in LCDB. In this subset we matched ~60% of the reported rotation periods within 5%. We continue improvements on the pipeline, specifically in outlier rejection, in hopes to use our pipeline in future telescopes like the Large Synoptic Survey Telescope. As well as data collection hoping to fully resolve the Jovian Trojans, two asteroid groups that co-orbit with Jupiter.

As anhedonia, characterized by a blunted sensitivity to reward, is associated with decreased goal-directed behavior, increased risk taking in those with high anhedonia may reflect a lack of concern for the outcomes of risk-related behaviors. Observational studies indicate anhedonia is associated with some risky behaviors, with skydivers endorsing higher levels of anhedonia than non-skydivers and high-risk sports players who report higher anhedonia taking fewer precautions. Gender has also been shown to influence riskiness, with men reporting more recreational and health-related risk taking than women. Despite having behavioral tasks that show predictive validity in assessing real-life risk taking, the relationship between anhedonia and risk taking has not been examined using a controlled, experimental paradigm, which is critical to establishing a predictive association between these constructs. This study aims to characterize the relationship between anhedonia and behavioral risk taking. Sixty individuals, either high in anhedonia (15 female, 15 male) or within a healthy range (15 female, 15 male), were recruited. Risk taking behavior is operationalized with the Game of Dice Task, a gambling task that has shown validity in assessing risk taking in clinical samples. We hypothesized that individuals with high anhedonia would score significantly higher on risk taking compared to those with low anhedonia. Further, we hypothesized a moderating role of gender, such that male participants with high anhedonia would be even riskier than females with high anhedonia. As risk taking often precipitates harm, understanding this association is an important public health concern. Moreover, characterizing the relationship between anhedonia and risk taking may provide insight into high rates of suicidal behavior observed in individuals with high anhedonia.

Deep reactive-ion etching (DRIE) is a highly anisotropic etch used for creating high aspect ratio and steep sidewall etch features in silicon wafers. The etch characteristics of DRIE are desirable for a variety of microelectromechanical systems (MEMS) applications such as through silicon vias for integrated 3 dimensional circuits and MEMS based microneedles. A common problem while trying to etch smaller features using DRIE is that the difficulty of transporting etch gasses and etch byproducts in and out of the deep trenches decreases silicon etch rates. This causes the silicon-to-mask selectivity to decrease with feature size as the etch rate for silicon decreases while the etch rate for the photoresist mask remains unchanged. By manipulating the process variables (including pressure, deposition/etch times, and temperature) and using an oxide hard mask instead of photoresist, we intend to improve the selectivity for DRIE etches of smaller features. Standard recipes are used to deposit a uniform oxide layer on the wafer, then a photoresist mask is used to etch through the deposited oxide. After stripping the photoresist mask, an oxide hard-mask is left patterned on the wafer. The silicon wafers are then etched using the SPTS-DRIE & Oxford-DRIE tools, which utilize alternating steps of C4F8 passivation and SF6 etching, known as the Bosch process, to create the high aspect ratio trenches. The scanning electron microscope (SEM) will be used to characterize the depths and sidewall profiles of trenches containing features of all sizes, while a profilometer will be used to find the depths of large-featured trench depths. Additionally, the SEM will be employed to determine differences in sidewall topography compared to topography achieved with photoresist. The goal is to obtain an etch profile with high selectivity using oxide hard masks, while still maintaining sidewalls close to 90° and typical etch characteristics.

Crops are constantly exposed to pathogens and pests, but being sessile, they cannot physically move away from danger. In order to defend themselves, plants have mechanisms to recognize and respond to threats. One way that plants do this is through the Jasmonic acid pathway, which is specifically activated in response to the wounding of plant tissue. Surprisingly, there are many functionally similar Jasmonate-ZIM domain (JAZ) proteins involved in this response, and the reason for this redundancy is unknown. Studying this pathway in depth presents a challenge when using low-throughput methods. In order to better understand this complex system, we built a workflow, which will be integrated into an automated system using the Aquarium Laboratory Operating System, designed by the Klavins Lab. This will help us track data from high throughput experiments. By developing automated methods to track maintenance of cell cultures, production of protoplasts, and delivery of dCAS9 transcription regulators, we hope to produce sufficient data to better understand the JA-signaling pathway. We anticipate that these experiments will illustrate a relationship between the manipulated activity of JAZ gene regulators and subsequent immune response activity, and have potential implications in the agricultural and food industries, where pests and stress conditions are a significant concern.

 This poster focuses on the relationship between afterschool programs and school discipline rates. I ask how availability of and access to school social programs affects school discipline patterns across school districts in Washington. This poster describes patterns of variation in school discipline, and summarizes how afterschool programs can affect the rate of school discipline. Using publicly available data about school districts (WA Superintendent Office of Public Instruction; U.S. Census Bureau ;), I anaylyzed the rate of school discipline as well as the availability of afterschool programs in different counties in Washington. I used ARC Gis to map the prevalence of each and then compared them in order to determine that the increase in presence of afterschool programs was correlated with a lower school discipline rate. Therefore, this poster argues that school social programs affect school discipline rates.

Studies show that disparities in healthcare access in ethnically diverse underserved communities are linked to healthcare barriers including cost of care and language differences. The purpose of the study was to evaluate the role of technology in improving healthcare access for ethnically diverse and underserved communities and thus helping to reduce healthcare disparities. We hypothesized that ethnically diverse patients’ ready access to mobile health technologies like smartphones and healthcare apps can improve patient care by promoting self-care management and improve doctor-patient communication. To test our hypothesis, we recruited N=20 healthcare providers from Washington, state. Healthcare providers comprising physicians, medical assistants, nurses and social workers participated in a 60-minute focus group session and were asked about the role of technology in increasing access to healthcare services for diverse ethnic communities. Respondents received a $75 gift certificate at the end of the study and responses were transcribed for later assessment. We evaluated transcripts by deriving codewords, codewords used more than two times were identified and recorded on three separate occasions, codewords with similar information were grouped into codeword clusters and finally, themes were derived based on a single idea from codeword clusters. From our analysis, we learned that healthcare providers see the importance of using mobile devices to increase healthcare access for ethnically diverse and underserved communities. They noted that mobile healthcare technologies can improve patient-provider relationships via enhanced communication. The implication of our finding is that mobile health technologies can improve patient-provider communication and help to eliminate barriers to healthcare access for ethnically diverse and underserved communities.

The three year-long civil war in Yemen between Houthi militia, made up of Yemen's Zaidi-Shia Muslim minority, and the Saudi-led coalition over the restoring of each of their respective powers to the Yemeni government has had irreversible impact on both Yemeni people and society. Thousands have died, either directly from bombing or indirectly due to blockades put in place by the opposing forces, and hundreds have gone missing or been forcibly disappeared. Soaring inflation, in combination with years of blockades and bombs, have had disastrous effects on the economy of Yemen. As part of a seminar on Human Rights through UW Bothell, I explored policymakers' response to the ongoing crisis. My research took place in two phases: first was gathering data regarding the war, where I found that current UN reports project that if bombing continues and a resolution between the opposing parties is not reached soon, over 14 million people will die of starvation. Step two was to make a policy recommendation on behalf of the U.S. as a result of this research. Scholars have engaged in long-standing debates over what U.S. response should be to the crisis. In my research, I argue that the United States, as an ally of Saudi Arabia, must act immediately to end support of the Saudi-led coalition in Yemen that is directly responsible for the deaths of thousands and for the dire humanitarian crisis of millions. No administration has gone to Congress to approve the involvement in Yemen's civil war, and thus, Congress must enact the War Powers Resolution of 1973 and end U.S. support of the Saudi-led coalition in Yemen. If the United States wants to be seen as a protector of human rights worldwide, we must stop aiding the blatant human rights abuses in Yemen.

In Arabidopsis thaliana the plant signaling hormone auxin is a major regulator of plant growth and development including the formation of lateral roots. Auxin controls the development of lateral roots by regulating the activity of transcription factors, known as Auxin Response Factors (ARFs). Because ARF7 and ARF19 mutants shows reduced formation of lateral roots, they are identified as master regulators of lateral root development. Using these ARF mutants, my project aims to understand how these regulators control early stages of lateral root development and gain insight into the role of auxin signaling in developmental specification. To investigate this, reporter lines are crossed with plant mutant lines of ARF7, ARF19, and both ARF7/ARF19 exhibiting a range of lateral root phenotypes, enabling accurate identification of lateral root specification and initiation stages. In mutants, we use bend assays to induce the lateral root developmental program in a synchronous manner. Seedlings are grown vertically on agar plates for 4 days, then turned 90° eliciting a gravitropic bend response at the root tip and leads to an eventual emergence of a lateral root at that the bent region. In mutants, temporal dynamics of lateral root program is quantified using fluorescence microscopy of reporters in synchronously induced lateral roots. Based on collected data thus far, the arf7 mutants (compared to wild type) exhibit slower onset of the specification reporter, suggesting the mutation has a temporal delay on developmental processes. As this project progresses, we will focus on temporal differences in expression of reporters that identify early specification and initiation stages of lateral root development via use of bend assays along with microscopy. Insights gained from these experiments will help us focus on stages and events in lateral root development that are impaired in arf mutants and thereby indicate on how auxin controls the developmental processes.

Nanoparticles have been touted to exhibit extraordinary properties, which could ultimately reverse environmental damage thought to be irreparable. However, is their synthesis process scalable? What are their macro-scale impacts? This life cycle analysis looks at the environmental impacts of producing iron-oxide nanoparticles used as an additive to help detect and track gastrointestinal gut bleeding to the microscale. It discusses the environmental impacts of using a nano-scale technology. An attributional life cycle inventory model with geographic specificity in Seattle, WA has been conducted. Data sources include the US GREET database and FineChem, along with the published results in "Synthesis of phase-pure and monodisperse iron oxide nanoparticles by thermal decomposition" in Kemp et al.

The impacts assessed include contribution to climate change, water consumption, resource consumption, and energy consumption. ReCiPe will be used for midpoint and endpoint charaterization. Preliminary results show that in this case, the uncertainty related with required dosage size of nanoparticles for this specific application yielded a large variance for potential impact. However, using the concept of disability-adjusted life years (DALY), it is shown that this technology provides a net benefit for human health.

Eighty-four percent of genes associated with human disease have a zebrafish counterpart. This is one reason that zebrafish are staples for developmental and genetic studies. Recently, there has been an interest in studying genetic control of skeletal phenotype, particularly in the craniofacial skeleton. Experiments typically use micro-computed tomography (micro-CT) to capture skeletal phenotype in 3D, and rely on manually annotated anatomical landmarks for statistical shape analysis of individual bone structures. However, manual segmentation has some fundamental problems. Subtle differences in how anatomical landmarks are recorded create differences between data sets that can influence the fidelity of the work. Varying lab practices can make exchanging data between researchers and reproducing findings difficult. Additionally, the significant time it takes to manually annotate an image makes large data sets an obstacle. Here, we propose the use of a fully segmented synthetic template of the zebrafish skeleton, created from common inbred strains, to segment and isolate cranial structures in a nearly automated procedure. Instead of segmenting each image individually, manual segmentation only needs to occur once on the template. Then, large quantities of images may be segmented by matching their skeletal landmarks to those of the template. This would not only standardize these micro-CT studies but also reduce the time burden of image analysis. We demonstrate an application of nearly automated shape analysis in proof-of-concept studies that compare the template-segmented volumes of 200 zebrafish otoliths with the volumes measured with manual annotation. Further proof-of-concept studies will compare measurements of other skeletal structures, specifically cranial bone width and parasphenoid bone length. Future work will include developing a micro-CT scanning protocol for the zebrafish Weberian apparatus and applying the template segmentation method to studying the relationship between swim bladder defects and the Weberian apparatus by examining the skeletal phenotypes of a number of zebrafish mutants.

The human adaptive immune system is composed of B and T cell lymphocytes. Of the latter, these cells are further differentiated and identified by the presence of CD (cluster of differentiation) molecules. CD molecules are expressed on the surface of the cell and can range from receptors essential to the cell’s functionality to glycoproteins marking distinct stages in their maturation. For example, CD45RA is expressed on naïve T cells while the presence of CCR7 marks the change to effector memory cells. Flow cytometry can be used as a tool to aid in detecting multiple types of T cells in a peripheral blood sample both rapidly and accurately. The use of 10-color flow cytometry in the clinical laboratory can provide simultaneous detection of ten cell markers to help differentiate the populations of T cells in a patient. Seattle Children’s Hospital utilizes this technology to monitor immune status in patients with auto-immune disorders, immunodeficiencies and post transplantation. Extended T-cell immunophenotyping by flow cytometry is not a mainstream clinical test. Since only a few laboratories offer this service, samples are often received from sites outside the hospital. With distance comes the issue of peripheral blood stability, especially regarding the loss of CD markers among the T-cell population over time. This study will compare the stability of T cell subsets through peripheral blood samples collected in EDTA vs sodium heparin collection tubes through four days of daily T cell immunophenotyping testing, as well as to determine the last day of stability for each T cell subset. The results will help form the guidelines regarding specimen stability for transport and the availability of offering this test to both adult and pediatric patients across the globe and help aid the diagnosis and treatment of various diseases and conditions that these patients face.

In the world we live in today, there is a common misconception that men and women have equal opportunity in all aspects of life. Specifically in the science world, women are discriminated against and perceived as less capable compared to their male colleagues. The microaggressions against women scientists greatly impacts their scientific output around the world. In order to gain insight on the effects of discrimination against women, I am distributing an electronic survey to female undergraduate students, graduate students, and professors. This survey contains seven questions that ask about their experiences with gender injustices in their daily life as a female scientist and how it has impacted their career. I am also examining different research articles about how scientific advancement by women scientists in different countries is affected by different forms of inequalities they might face. I expect that I will find a large percentage of women in the science world who have personally experienced gender injustices and that it has made it more difficult for them to achieve the same level of success as a male. This study will further emphasize the importance of achieving women’s rights around the world in order to access the wealth of knowledge that is currently being held back by discrimination. 

Grasslands cover approximately 20% of Earth’s land today and spread gradually worldwide in subtropical areas during the last 40 million years. Pollen data from sedimentary rocks in Myanmar suggest that grasslands might have existed there as early as 25 million years ago but did not spread to other Asian regions until much later, 10-6 million years ago. To fully understand the ecology of these early Asian grasslands, I reconstructed the paleoenvironments of Myanmar during the late Oligocene and early Miocene, 25 to 18 million years ago. I used two paleoenvironmental proxies on paleosol samples from Burmese sedimentary rocks: carbon isotopic composition of bulk sediment and phytolith analysis. The bulk carbon isotopic composition in paleosol is an indirect insight into the local aridity and can help reconstructing soil productivity; phytoliths–silica bodies deposited inside living plant tissue that remain in the soil after the tissue decays, forming fossils—when extracted, can help identify the grass types and their relative abundance in the ecosystem. Documenting the characteristics and paleoenvironmental setting of these early grasslands will help us understanding why they did not spread until millions of years later in Asia –and if this timing of ecological expansion is linked to the regional evolution of monsoonal intensity.

Chemically induced dimerization (CID), in which two proteins dimerize only in the presence of a small molecule, has been widely used to control cell signaling, regulatory, and metabolic pathways, and used as logic gates for biological computation in living mammalian cells. However, few naturally occuring CID systems and their derivatives are currently available. Creating a CID system with desired affinity and specificity for any given small molecule remains an unsolved problem for computational design and other protein engineering approaches. To address this challenge, we have used a novel strategy to select CID binders from a vastly diverse combinatorial nanobody library. We have created new CID systems that can sense cholecalciferol and artemisinin. We are validating CID biosensors by a yeast three-hybrid system and built structural models to understand the small molecule-induced dimerization. Our work is a proof-of-concept that can be generalized to create CID systems for many applications.

Elevated intermuscular fat (IMF) is an indicator of metabolic syndrome and triggers the development of chronic diseases such as diabetes and heart diseases. Metabolic syndrome (MetS) includes insulin resistance, hypertension, dyslipidemia, hypercholesterolemia and abdominal adiposity. A leading hypothesis linking IMF to MetS is because skeletal muscle is the primary site of glucose metabolism. This function is impeded by the presence of IMF due to limited microvasculature perfusion to the muscle. Cancer treatment increases the ratio of intermuscular fat to skeletal muscle (IMF:SM), which indicates an investigation of IMF is warranted in patients treated for cancer. The purpose of this study to investigate the relationship between IMF, diabetes and hypertension in patients treated for cancer. We will perform a secondary analysis to examine IMF composition by magnetic resonance imaging (MRI) leveraging existing data in 143 cancer patients with stage A heart failure. This will inform us of the association between intermuscular fat, hypertension and insulin resistance in cancer patients, which is the first study to investigate this research question. Further study is needed to determine whether increased IMF in cancer patients leads to increased risk of MetS or diabetes. Furthermore, this line of work will inform future research into lifestyle interventions capable of reducing intermuscular fat, which has implications for the development of MetS in individuals treated for cancer.

Often, when rodents are faced with a decision on a maze, they will pause to look back and forth between different paths. This behavior has been termed vicarious trial-and-error (VTE) and has been linked to the reactivation of hippocampal place field sequences as animals look back and forth. Previous research has shown that place field sequences represent a neural map of the paths the animals can potentially take as if they are pre-playing their future path. These reactivation events give merit to the idea that VTEs are reflective of a deliberative process. Additionally, studies show that when animals reach such decision points there is increased communication between the hippocampus (HPC) and medial prefrontal cortex (mPFC) as measured by increased correlates in local oscillatory power. We wanted to further study the mPFC’s role in initiating VTEs during a task that is HPC and mPFC dependent: the spatial delayed-alternation-task. This task was carried out on a plus maze; it required rats to alternate between reward arms every trial while the start arm was pseudo-randomly selected every trial. During this task we used a closed-loop system to optogenetically disrupt the mPFC upon detection of specific phases of HPC theta oscillations. Additionally, disruption was applied across three different task-epochs: delay, choice, and reward in order to determine under which epoch is the mPFC most important for VTE behavior. We hypothesized that mPFC disruption during the choice epoch would reveal the greatest change in the number of VTE’s as the mPFC is thought to initiate retrieval events when decisions are to be made. Because VTE’s are a unique and observable behavior that has clear neural activity correlates, we hope to use this study to better understand the relationship between the hippocampus and mPFC in learning and memory.

Understanding how genetic variation shapes phenotypic variation for complex quantitative traits is fundamental to developing more accurate disease prognoses and therapeutic interventions. Genes that are important in early development contribute to adult quantitative traits, such as height, vision, and health. The fruit fly Drosophila melanogaster is a model organism for studying complex traits, such as aging. Drosophila possesses many well-developed genetic tools and shares evolutionarily conserved age-regulating pathways with our species. One such conserved pathway is the mechanistic Target Of Rapamycin (mTOR) nutrient signaling pathway. Rapamycin is a specific allosteric inhibitor of mTOR signaling that extends lifespan in adult Drosophila melanogaster and delays development in larvae. However, the functional explanation for these effects is incomplete and a genetic association between development and lifespan is unknown. We used the Drosophila Genetic Reference Panel (DGRP), a highly inbred fruit fly population representing natural genetic variation, to measure rapamycin-mediated developmental delay. We used these data to carry out a Genome Wide Association Study (GWAS), and combined our data with data from a screen for the effects of rapamycin on lifespan in the DGRP, also carried out in our lab. GWAS analysis will help us to identify genetic variants associated with rapamycin efficacy and to discover novel variants associated with developmental timing. By connecting lifespan and development genetically, we identified shared candidate genes that modify these two very different molecular genetic programs. Accomplishing this is the first step towards identifying early life biomarkers that are predictive of rapamycin success as a longevity intervention in later years. These pharmacogenomic analyses advance a precision medicine approach where interventions are tailored towards genetic background to maximize human health.

Many of the world’s most important countries are experiencing large increases in their populations of older adults (e.g. Japan, China, Italy, Germany). Such longevity is requiring a greater need for long term care. However, societies can not afford to pay for formal care, so informal (unpaid family) caregivers (CGs) are becoming increasingly important. Unfortunately, many CGs are at high-risk for psychosocial/health problems. Moreover, caregivers with pre-existing health problems are particular risk. Our goal is to examine factors that may make cancer caregivers vulnerable. We used a vulnerability (have a cancer history or not) by exposure (being a caregiver or not) model, and stratified our participants into four groups: Cancer Caregivers, Non-Cancer Caregivers, Cancer Non-Caregivers, and Non-Cancer Non-Caregivers. At baseline and 15-18 months later, we measured indicators of life quality and caregiver demands: satisfaction with support, well-being, perceived support, loneliness, and hours spent caregiving. Cancer Caregivers reported poorer social supports and more time caregiving. This is important because previous work has shown that Cancer Caregivers have more negative and fewer positive life experiences and that these are related to the ability to fight tumor growth. Despite innovations, this study only included white Americans. Also, to increase participation among persons with cancer, we only included those who were not treated for at least one year and who had not suffered from serious forms of cancer. Our results would probably have been stronger had we included persons with more serious cancers, but such individuals might not have participated or been able to be caregivers. Given the rapid rise of cancer in China, we suggest that research examine cancer and caregiving in China and that cross-cultural research be done in the U.S. and China. To understand the dynamics of caregiving, health and well-being, one needs to study these processes cross-culturally.