Cancer, the leading cause of death worldwide, results from a combination of mutagenesis and selection for malignant phenotypes. Mutations from DNA replication errors may initiate as many as two thirds of all human cancers. Accurate DNA replication requires proofreading domains found on the major DNA polymerases as well as mismatch repair (MMR) proteins that detect and repair replication errors after DNA synthesis. Cancer-causing defects in proofreading and/or MMR lead to “mutator phenotypes”, marked by elevated mutation rates and increased cellular mutation burden. Such mutator cells occur spontaneously and drive evolution by generating mutations that enhance population survival. However, mutator cells also accumulate detrimental mutations that compromise fitness. Combined defects in polymerase proofreading and MMR cause error-induced extinction (EEX), which imposes a strong selection for cells with “antimutator” mutations that suppress the mutator phenotype. Using yeast (Saccharomyces cerevisiae), we isolated mutants that survived EEX and mapped the underlying determinants to candidate mutations (APC1, MCM5, PMS1). We are engineering these mutations into yeast strains to test whether they confer an antimutator phenotype. Understanding how mutator cells suppress elevated mutation rates will give us insights into how cancer cells survive and thrive in the face of strong mutagenesis and may suggest novel therapeutic strategies to combat this disease.

UW Solar is an interdisciplinary student-led organization committed to developing solar infrastructure projects at the University of Washington. Solar arrays on campus not only produces clean renewable energy, but also helps the UW meet its carbon neutrality goals of its Climate Action Plan while providing a sustainable return on investment. UW Solar is working with UW Sustainability to maximize solar capacity on campus in support of the first UW Sustainability Plan to achieve the goals of the UW Climate Action Plan. Therefore, UW Solar is proposing a multi-phase plan for solar development at UW Seattle which aims to maximize solar capacity while providing a positive return on investment for Capital projects. UW Solar assessed all buildings on campus, and has identified the top 30 projects to be developed over the next 30 years to meet the UW’s 2050 Carbon Neutrality Goals. UW Solar’s scope of work for the Campus Plan includes the evaluation of all buildings on campus for potential solar installations and ranking them based on a suite of criteria that takes into consideration the following: energy generated, financial value of energy generated, cost of installation, return on investment, identifying funding options, working with campus stakeholders to develop the solar plan and timeline, assisting with schematic design, selection of contractor, oversight of installations, monitoring of energy generated for research and education. The total solar capacity for the Seattle campus could reach 8,000,000 kWh/year, with an annual energy value savings of $600,000. UW Solar will continue evaluating buildings on campus and working with all stakeholders to decide the priority of solar installations over the next 30 years.

ImageJ allows users to create plugins that work with other imported packages and the ImageJ libraries. Using the ImageJ API (application program interface) and the macros recorder built into ImageJ, each image analysis performed within the Lee laboratory at the Department of Radiology was programmed into individual plugins by both Vineeth Narajala and Selina Liu, to be used by research scientists. Before writing each data analysis plugin, the standard operating procedure (SOP) of image analysis created by the Lee lab was practiced manually by both the programmers so we understood the process researchers perform on each data set. After understanding the SOP, we commented a simple outline in Java to start writing the plugin code. After the code was outlined with comments, Selina wrote algorithms for portions of the analysis that required numeric patterns and searched through the ImageJ API to manipulate the image using built-in commands. Methods were created to perform calculations, scale the images, and close extra images that were generated during the analysis. These methods helped generate the final image map used for measurements by the researchers. Plugins were tested for usage and updated when a researcher required other procedures that were not specified in the SOP. We also created a python program in Python 2.7 to automate the data analysis of the dataset. The program can also plot rudimentary graphs of the analyzed results. The python program used pandas to analyze the data and matplotlibs to create the graphs. Overall, each plugin and the automation program save researchers hours of time from importing, calculating, and archiving the images when following a single SOP. The research scientists typically used Microsoft Excel to analyze the data after the images were created and regions of interest were identified. This method was very time consuming and could not be scaled to different input sizes.

Roughly 20% of young adults in the United States experience some sort of mental health disorder. The majority of this research has focused on young adults in general or 4-year college students, however less is known about the mental health and coping strategies of young adults not currently attending school. The purpose of this study was to compare mental health, the use of alcohol and/or other substances as a coping mechanism for stress, and alcohol and marijuana use among young adults who attend 4-year colleges and those not attending school. A subsample (N=552; 56% female, 59.5% White, M age=20.58, SD=1.7) of young adults using baseline data from a larger longitudinal study on health behaviors was used for the current analyses. The subsample included 355 students currently attending 4-year college and 197 young adults not attending school (highest education status of these individuals included less than a high school diploma (1.5%), high school diploma (19.3%), some college (15.2%), 2-year degree (10.1%), 4-year college degree (52.8%), and graduate degree (1%). Findings indicated that young adults not in school reported significantly higher rates of depression, anxiety, and perceived stress in the past month than students in 4-year colleges. Similarly, findings indicated that non-students reported being high from marijuana for more hours, higher rates of alcohol use and coping with stress through alcohol and/or substance use in the past month than 4-year college students. Further research is needed, which focuses on young adults who are not currently attending 4-year colleges as they may face different life stressors and cope differently than 4-year college students.

As demand for accurate evaluation of chemicals and their potential to cause effects on humans increases, we have designed in vitro methods to facilitate such assessments. However, models of in vitro cell cultures are limited in their approach typically using a monoculture of limited cell types. Using a 3 dimensional organotypic approach to culture multiple cell types more reflective of a functioning organ can provide a framework for evaluating systematic interactions minimizing the need for in vivo assessment. We utilized a novel organotypic, in vitro model of testicular development that mirrors the development shown by in vivo studies. Our baseline study isolated testes that were harvested from C57BL/6 male mice on post-natal day 9. Testicular co-cultures were maintained for up to 16 days in 24 well plates with data collections occurring at days in vitro (DIV) 3, 7, and 16. Plates were stained with antibodies providing markers that correspond to morphological features of specific cell type markers. Five different primary antibodies were used as markers to visualize the change in cell populations. Markers for Sertoli cells corresponded to Vimentin, Leydig cells with 3b-HSD, Germ cells to DAZL and c-kit, and proliferation with PCNA. For each well, we used an immunofluorescence dual staining technique with Scanning Laser Image Cytometery (iCys) to observe the percentage of cell types and to determine change in phenotypic distribution of the cell population. From our preliminary observations, we were able to observe changes in Sertoli cells, Leydig cells and Germ cells throughout testicular development. Future studies would further develop and confirm the population and morphological changes observed with the testicular cell cultures. With a baseline model created, this in vitro model can be used to test the lethality of chemicals without the need of in vivo alternatives.

This project was designed to support staff within an early childhood program experiencing major changes. The early childhood program had recently moved to a temporary location while a new learning center is under construction. This program now occupies an elementary school building and has been joined by a previously separate Head Start program and a special education preschool program. Along with the move the program shifted its requirements and curriculum to better match the Head Start program they now share a building with. These changes include in-class meal times, a mandatory rest period, and mixed age classrooms. The physical building move and program changes have created new challenges and added stress for teachers. This includes new challenging behaviors related to new program changes. With this in mind, this project sought to alleviate stress for a teacher who was dealing with persistent challenging behavior for one student. Practical skills training has been shown to improve teacher attitudes towards working with students with challenging behaviors. In this project I compiled a practical skills training using Gail Joseph’s Positive Behavior Supports videos and guided a teacher through writing and implementing a behavioral support plan with the intention of reducing one child’s challenging behavior. The intervention was successful in providing the skills necessary to write and implement a behavior plan as well as reducing the child’s challenging behavior. The frequency of the challenging behavior was reduced from an average of 13.6 times a day to 8.5 times a day after 3 weeks. Future research could examine how effective video skills trainings are in providing teachers with skills to deal with challenging behaviors and could consider the possibility of remote trainings or remote professional development opportunities for teachers.

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 an RNA Interference (RNAi) screen and sought to find genes that are necessary for the stem cell extrusion in the JNK activator, 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. We selected 215 lines of kinases and phosphatases of flies to test if the knocked-down gene results in suppression of cell elimination by the JNK stress signal. After 4 days of inducement, which is the sufficient time for the JNK signal can 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. Through this screen, we could find 33 lines that had strong suppression of cell elimination, 39 lines that had a moderate effect. Our results suggest that the knocked down genes with strong suppression of cell elimination are involved in the mechanism of basal cell extrusion, and future research dictates an investigation into the molecular function of each of these genes.

Interactions between HIV-1 and dendritic cells (DCs) have been suggested to play a role in HIV-1 pathogenesis. DCs are antigen presenting cells that take up, process, and present foreign material to T-cells. Previous research suggests that HIV-1 can exploit this process by binding to DCs, allowing HIV-1 virions to relocate to lymph nodes where infection of T-cells can occur. HIV-1 mediates this interaction through binding of the HIV-1 envelope glycoprotein (Env) to DC-SIGN, a glycan binding protein located on the surface of DCs. Env contains a high amount of oligomannose glycans, enabling Env to act as a binding partner for DC-SIGN. Due to high sequence variation, HIV-1 strains exhibit variability in glycan presentation. A gap remains in our knowledge of where DC-SIGN binding occurs and how glycan presentation across various isolates modulates these interactions. In this study, we applied a combination of biophysical and structural approaches to characterize Env:DC-SIGN interactions across multiple HIV-1 strains. Biolayer interferometry experiments measuring binding affinity demonstrate that DC-SIGN binds with strong affinity towards Env from different isolates. This suggests that DC-SIGN is capable of recognizing different oligomannose glycan presentations and may not have a well defined epitope. However, preliminary results using electron microscopy illustrate that Env glycoprotein structure can be disrupted and altered via binding to DC-SIGN. This appears to be an isolate-specific response, as some strains remain unchanged. Using single particle approaches, we identified potential epitopes in heavily glycosylated regions of Env where additional densities are attributed to DC-SIGN. We infer that in addition to binding HIV Env, DC-SIGN may shield key neutralizing epitopes within these glycosylated regions. Our results provide further insight into the interactions that occur between HIV Env and DC-SIGN, and suggest a mechanism where HIV-1 hijacks DC’s normal immune function allowing HIV-1 trafficking while shielding neutralizing epitopes.

Aerosol particles, solid or liquid particles suspended in the air, can affect Earth’s climate by scattering and absorbing sunlight. PM_2.5, particles less than 2.5 micrometers in diameter, are largely responsible for degraded visibility and easily traverse respiratory system pathways causing adverse health effects in humans. Often, a majority of PM_2.5 is composed of organic matter formed through photo-chemical reactions of hundreds of volatile organic compounds (VOC). This process depends on nitrogen oxide radical (NO_X = NO + NO₂) concentrations in the atmosphere, now predominantly contributed by anthropogenic emissions. NO_X and VOC react to produce organic nitrates, thought to be significant contributors to PM_2.5, but for which measurements are generally lacking. My project involves developing a concrete assessment of the role of organic nitrates as contributors to PM_2.5. I am developing an analytical method to thermally desorb organic nitrates from atmospheric particles collected on filters and promptly decompose them into nitrogen dioxide (NO₂). The resulting NO₂ is measured with a Cavity Attenuated Phase Shift (CAPS) spectroscopy instrument. I am establishing whether there is a direct correlation between the concentration of organic nitrates in PM_2.5 and desorbed NO₂. The goal is to quantify organic nitrates without individually measuring each of the likely hundreds present in the ambient atmosphere. Moreover, the thermal desorption process provides information on the physical properties of organic nitrates, such as effective saturation vapor pressure, needed for air quality computer models to accurately simulate their contribution to PM_2.5. As a result, I will help develop a better understanding of how natural and anthropogenic emissions affect the composition of the atmosphere by allowing assessments of how PM_2.5 levels have changed in response to NO_X emission reductions by the Clean Air Act.

Flowering is crucial to a plant's lifecycle because it determines reproductive success for the plant. Scientific understanding of the molecular mechanisms that direct this process are constantly being revised and expanded as more is discovered about how plants sense their environment and adjust their flowering time in order to optimize reproductive success. In this study we explore the molecular mechanisms involved in the FKF1 photoreceptor signaling pathway. FKF1 is a blue light sensitive photoreceptor that influences FLOWERING LOCUS T (FT) gene expression, which induces flowering in plants. The molecular mechanism of activation of FT expression under high light has not yet been fully characterized. By comparing relative gene expression in cat2 mutants we found six transcription factors that have the potential to bind to the FT promoter and show significantly higher expression levels under high light conditions. Our research focuses on these six transcription factors and their potential impact on flowering time in the plant. To study these transcription factors, we are developing transgenic lines to analyze the effects of knocking down or overexpressing these genes. We will look at the resulting phenotypes of our transgenic plants in order to develop models that explain the suppressive or activating effects of our transcription factors. This will further our understanding of how plants regulate flowering under high light conditions. By achieving a deeper understanding of plant development, we can devise ways to maximize agricultural output in order to feed an ever growing global population.

Aging is a major risk factor for the most common causes of death in the developed world which include cancer, heart disease, and neurological disorders. Because of this, therapies that target the hallmarks of aging are a promising area of study. The mechanistic target of rapamycin (mTOR) kinase is a major regulator of growth, aging, and survival in cells. Inhibition of the mTOR signaling pathway is associated with increased longevity in organisms including yeast, nematode worms, fruit flies, and mice. Inhibition of mTOR can be achieved through pharmacologic intervention, which is a promising strategy to extend healthy lifespan. To better understand how mTOR inhibitor response varies between genetically-diverse populations, we utilized a set of 90 wild and domesticated yeast strains. We tested a set of mTOR inhibitory compounds on these strains to identify strains with increased sensitivity or resistance to mTOR inhibition. We have identified genetic variants that drive drug sensitivity or resistance in these strains. We then engineered mutations into laboratory strains to confirm that these mutations recapitulate the phenotype of interest. By understanding drug response across genetically-diverse populations, we will create the framework for a precision medicine approach to developing healthspan-enhancing compounds that can be translated to humans.

Insights from the study of biosonar (echolocation) in mammals such as bats have applications in developing coordinated autonomous manoeuvres in a variety of environments. However, limited research has studied bat echolocation and flight behaviour in natural habitats, which involves multiple bats competing for a shared prey resource. In a confined space, bats have been observed to emit calls with lower intensity, shorter duration, and broader bandwidth compared to when echolocating in the open. Bats foraging in the wild also experience more complex echo-acoustic scenes created by sounds of all sources in the landscape, such as calls from other bats and echoes from vegetation and obstacles in the environment. Evidence from previous field studies suggest that solo bats engage in stereotypic flight path behaviour to minimise the cost of sensory processing required for spatial orientation, making those resources available for prey localisation. Other studies have observed leader-follower behaviour in pairs of bats, where they coordinate manoeuvres by copying the others’ trajectory through active echolocation. We propose to investigate flight and echolocation behaviour of an even larger number of simultaneously foraging bats over the Central Pond in the Union Bay Natural Area. This 74-acre natural area on the shore of Lake Washington is a prime location for a natural observatory right on the UW campus. We are currently developing an ultrasonic microphone array that is a non-cost-prohibitive alternative to proprietary wildlife recording devices, and we will start data collection when local bats local emerge from winter hibernation. We plan to develop fully automated algorithms for tracking bats and estimating their echolocation directional aim during foraging. These data will serve as a basis for deriving computational principles of coordinated flight and sensing across multiple agents, which can inspire new technology for autonomous vehicles in the air, on the ground, or underwater.

The goal of our project is to create an electronic device capable of early detection of pancreatic cancer (PC) with high selectivity and sensitivity. PC projects a very low survival rate often due to late-stage cancer diagnosis. Recent research has established that there are PC biomarkers prevalent throughout the body for several years before symptoms emerge. The consequent wider time window presents an opportunity for these biomarkers to be detected at their initial low concentrations thus allowing for early diagnosis. Our device uses a modular sensing construct consisting of an immobilized probe molecularly bound to the surface of the sensor device. Detection occurs when a target biomarker specifically binds to the probe and changes the electrical properties of the sensing surface that is measured quantitatively. Validating the functionality of the sensing construct and its properties is accomplished through a variety of molecular adsorption and binding techniques that assess each step; from probe immobilization to target detection. Using this modular design, research is underway to develop an array of sensors, thus potentially revolutionizing rapid medical diagnostics to provide long-term health monitoring of PC and other cancers. 

Abundance estimates are integral to wildlife management. In many cases however, abundance estimates are difficult to obtain due to excessive labor and costs. Alternatively, abundance indices can provide representative measurements of relative abundance. Furthermore, cameras are a convenient tool to obtain estimates of relative abundance using capture frequencies as indices, though are predominantly used on larger animals. Small mammal abundance is commonly used to measure for forest health, diversity, and prey availability, though is generally dependent on the use of live trapping. Broadening the application of camera traps can prove to develop better indices for abundance analyses. Through this study, we examine different indices of small mammal abundance to determine whether camera trap data can be used as an index of small mammal abundance. Using data collected from the field, an abundance estimate based on live trapping of mice, voles, and chipmunks is compared to our camera trap estimates of these three species. We tested three possible small mammal indices, two of which were camera based: proportion of cameras detecting a species, number independent detection events, and number of animals live captured on the first night. Each of the three indices that were tested gave an estimate of abundance which we compared with the live-capture density estimate to determine relative accuracy. The proportion detected estimate and the first night capture estimate were significantly correlated to the estimated population abundance of each species. The low population of voles influenced the results and are discussed further. This data may contribute meaningful data for future wildlife abundance analyses. By gaining an understanding of reliable indices, we are able to make better considerations for wildlife management decisions.

This project aims to ground truth a statistical model created previously by our lab. The model predicts the characteristics of a hyper velocity impact of a projectile into both sea ice and water ice. We compared the modeling program’s simulated results with observed results from both 1.5 inch and 4 inch ice perpetrators on lab created water ice and naturally forming sea ice respectively and studying such characteristics such as peak ejection angle, maximum crater depth, and crater diameter. The experimental results are compared with the simulation presented by Koch 2017. We will apply both our experimental data and our simulation data in the design and creation of a two-stage penetration probe. The first stage is a hyper-velocity penetrator. The second stage is an aero-breaking probe that will use the plume created by the first stage to reduce its velocity before impacting the surface.

Hosted through the Earth and Space Sciences department, HuskySat-1 is a 3U (30cm x 10cm x 10cm) satellite manifested for launch into low earth orbit in late 2018 or early 2019. HuskySat-1 is primarily an undergraduate research effort, but includes graduate students and industry partnerships. It spans many departments including Earth and Space Sciences, Electrical Engineering, Mechanical Engineering, Aerospace Engineering, Physics, Mathematics, and many others. The mission goals are to establish a space presence for the University of Washington, and to test novel hardware fabricated here at the University of Washington. Of particular interest are the Pulsed Plasma Thruster (PPT), a plasma propulsion device designed and fabricated entirely at the University of Washington in the Advanced Propulsion Labratory, and the K-band communication system, a high-frequency, high-gain antenna capable of transmitting data at megabits per second from orbit to Earth. The satellite also includes several other subsystems including power, attitude control, structures, computers and data handling, and low-gain communication. The mission strives to provide experience in real-life engineering to the entire team, and we achieve this by attempting to build as much of each of these subsystems from scratch as possible. Not only does this provide the most possible experience, but we are also able to grow our mission scope and customize our requirements without the excessive budget attached with many pre-made satellite components. We plan to present on the current and planned state of the mission, what we have learned in the process of designing and building this mission, and our next plans for further space exploration at the University of Washington.