Inflammasomes are multimeric protein complexes involved in innate immune responses. Inflammasomes include a protein sensor, such as NLRP3 or pyrin, linked to the enzyme caspase-1 via the adaptor protein, ASC. Active caspase-1 is responsible for release of the cytokine interleukin (IL)-1ß and triggering inflammatory cell death. Inflammasomes are crucial in defense against pathogens. However, excess inflammasome activation is linked to diseases such as Alzheimer's, atherosclerosis, and other inflammatory conditions. Although inflammasomes are linked to several diseases, we do not fully understand how inflammasomes are activated. We are researching the role that potassium plays in inflammasome activation. To detect inflammasome activation, I measured released IL-1ß using enzyme-linked immunosorbent assays (ELISAs). I determined whether inflammasome activation requires potassium efflux by measuring IL-1ß released from cells stimulated in high extracellular potassium, which prevents potassium efflux. I found that IL-1ß release triggered by NLRP3 inflammasome activators is prevented when cells are stimulated in high extracellular potassium. However, IL-1ß release triggered by the pyrin inflammasome was not affected by high extracellular potassium. From these results, we conclude that the NLRP3 inflammasome is dependent on potassium efflux from the cell, whereas the pryin inflammasome is not. The implications of our research are two-fold. First, our findings argue against a long-standing hypothesis that high extracellular potassium blocks ASC binding. Both NLRP3 and pyrin need ASC, but our data show that only NLRP3 is affected by potassium concentration. This suggests that potassium affects NLRP3 activation at an unknown point. Second, understanding the role of potassium in regulating inflammasome activity provides a potential therapeutic target. There are drugs that regulate ion concentrations by controlling ion channel activity. Knowing whether an inflammasome pathway is potassium efflux dependent could be beneficial in limiting excess inflammasome activation that is linked to a variety of human diseases.

As climate change progresses, increasing temperature is expected to have community and population-level consequences. The temperature-size rule predicts shifts in both community and population structure to favor smaller bodied organisms over larger bodied organisms as temperatures increases. We investigated this hypothesis in the context of rocky intertidal invertebrate communities on San Juan Island, and examined changes in community and population structure over the past 45 years. We replicated historical ecology studies on the abundance of six intertidal species; three of which body size data was also collected. These species included grazing and predatory molluscs (Katharina tunicata, Nucella lamellosa), anemones (Anthopleura elegantissima), and crabs (Hemigrapsus nudus, Pugettia gracilis, Pagurus sp). Additional abundance data was collected on smaller molluscs (limpets, littorine snails). Predicted decreases in body size were not apparent in populations of K. tunicata., N. lamellosa, and A. elegantissima. However, when comparing abundances, shifts in community structure towards smaller-bodied organisms were apparent. We observed an increased abundance of smaller-bodied gastropods and crustaceans (limpets and Pagurus sp), but a decrease in K. tunicata abundance, one of the largest grazers in this system. This research highlights the potential for a variety of community and population responses including both stability and variability in the face of climate change.

Ankle range of motion (ROM) is frequently measured in clinical settings for the purpose of diagnosing and treating foot and ankle pathologies. Gastrocnemius equinus (GE), a condition in which isolated gastrocnemius contracture inhibits ankle ROM, contributing to foot pain in otherwise neurologically healthy individuals. Controversy surrounds the definition of GE, however, and the reliability of goniometer-based measurements of dorsiflexion—and consequently identification of gastrocnemius contracture—is untested. This study examines the reliability of using a goniometer to measure ankle dorsiflexion. Two observers (KR and CG) measured ankle dorsiflexion in 14 neurologically healthy individuals (6M/8F; ages 20-56 years; 6 participants measured by both observers) with the knee in fully-extended and flexed positions. Three measurements were taken for each position with the goniometer fulcrum on the lateral malleolus; stationary and moving arms aligned with the fibular head and fifth metatarsal, respectively. Inter- and intra-observer reliability was assessed using Cronbach’s alpha. Intra-observer Cronbach’s alpha was 0.230 (CG) and 0.533 (KR) for dorsiflexion with the knee extended, and 0.805 (CG) and -0.350 (KR) for dorsiflexion with the knee flexed. Inter-observer Cronbach’s alpha was 0.656 for extension and -0.245 for flexion. Little correlation exists within or between observers for goniometer-based ankle dorsiflexion measurements in either a flexed-knee or extended-knee position. The clinically-accepted practice of using a goniometer to determine ankle ROM, and consequently to diagnose and treat GE, may be unreliable and needs further evaluation.

English sole Parophrys vetulus is a species of benthic flatfish that is commercially and tribally exploited off the coast of Washington State. The commercial value of English sole can decrease if the fish is infected with parasites, which degrade their appearance and health; in fact, widespread parasitic infection contributed to the closure of the commercial fishery in south Puget Sound in 1948. Clavinema mariae is a trophically transmitted nematode parasite that has increased in abundance by eight-fold since 1930 in Puget Sound. Since C. mariae is a nematode that infects hosts via ingestion, I used a diet analysis of English sole to: 1) assess the types of prey that sole consume, and 2) correlate the prey type abundance to C. mariae abundance. I evaluated the gut contents of contemporary sole collected in 2017 and historical sole collected over the past 80 years and held in the UW Fish Collection. I categorized gut contents to the lowest taxonomic family. Sole are hypothesized to primarily consume invertebrates, and C. mariae is transmitted by copepods, thus we expect copepods to represent a larger portion of the diet in more recently collected, more heavily infected sole. Knowing the type and number of organisms that English sole consume will improve our understanding of how sole interact with the Puget Sound food web; specifically, how they are initially infected with C. mariae, which would offer insight to their observed increase in abundance in sole over the past 80 years.

Asthma is the most common chronic disease among children, affecting almost 10% of children in the US. Standard treatment for persistent asthma is inhaled daily corticosteroids to reduce airway inflammation. Adherence to these controller medications is poor, with less than 50% of children consistently using them. Poor adherence leads to worsened asthma control, causing increased symptoms, exacerbations, school absences, and decreased quality of life. Poor asthma control has also been associated with impaired family functioning. The purpose of this study was to analyze the relationships between quality of life, family functioning and asthma control among school-age children with asthma and their parents.  Thirty-three child-parent dyads (children ages 6-11 years) were enrolled in this study. Parents and children independently reported on asthma quality of life and the child’s asthma control. Additionally, parents reported on family functioning using the McMaster Family Assessment Device, which assesses numerous family functioning domains. Our hypothesis is that poor asthma control will be associated with impaired family function and decreased asthma quality of life and that parent and child reports of asthma quality of life will differ significantly. Results from this study will provide insight into new potential opportunities for nursing interventions for children with asthma and their families. 

Lift-off is a subtractive process used in wafer fabrication of Micro-Electrical-Mechanical-Systems (MEMS) devices to pattern deposited films, often metal, that are challenging to dry etch. To achieve a successful lift-off, the lift-off process begins by depositing and then patterning a photoresist masking material onto a silicon wafer using photolithographic techniques. An important characteristic of the photoresist is undercutting the resist sidewalls after developing, protecting them from being coated with metal during deposition. After deposition, the photoresist and metal layer is removed via solvent. The purpose of our research is to allow for a more varied range of fabrication using positive tone photoresist. Negative tone photoresist is typically used for this lift-off process because after development, this resist naturally forms the desired undercut. Alternately, positive tone photoresist is characterized by a tapered sidewall that is difficult to not coat with the metal film layer, making the removal step via solvent problematic. We hypothesized an advantageous undercut is possible with positive tone photoresist using a white light diffuser that would allow light to enter at angles through our mask during the exposure step. We evaluated resist undercut using the Nikon microscope and resist/metal sidewall characteristics using the Scanning Electron Microscope. We will assess the new resist exposure technique using both line-of-sight evaporation (physical vapor deposition in which a target material’s atoms precipitate into solid form, when heated up under high vacuum, coating everything in the vacuum chamber) and sputtering (metal deposition involving particle ejection of ions) to deposit a thin metal film. We anticipate evaporated metal to lift-off easily with the new technique, which indicates a crowning demonstration of success.

Conservative estimates suggest that food production must increase by 60-70% by 2050 to keep up with population growth. This challenge to global food security is compounded by a lack of knowledge of how crop species will respond to a changing climate. The Nemhauser Lab has been studying how the photoreceptor Phytochrome B (phyB) directs the allocation of plant resources in response to environmental stimuli like elevated CO2. I have focused on studying this phenomenon in Brassica rapa, a member of the mustard family that includes a large variety of popular vegetables such as broccoli, cauliflower, Brussels sprouts, as well as varieties used for oil production. B. rapa plants with mutations in the phyB gene make fewer seeds, have a lower chloroplast density, photosynthetic rate, total chlorophyll levels, and stomatal index. To better understand how phyB is involved in seed yield, I am characterizing ovules and gynoecia (female reproductive organ) development in phyB deficient B. rapa plants. To understand how phyB plays a role in other processes relating to or impacting resource allocation such as chlorophyll levels, I will identify genes differentially expressed between wild type and phyB deficient B. rapa plants. This will ultimately lead to the identification of potential targets for engineering more resource-efficient and higher-yielding crop varieties.

Springsnails are a broad group of highly diverse North American gastropods, with the most speciose genus being Pyrgulopsis (139 species). These tiny aquatic gastropods are often found in thermally-influenced freshwater springs, where endemism is common. Restricted occurrence and narrow habitat requirements of many species has generated conservation concern because of anthropogenic threats to spring systems and associated aquafers. The Blue Point Pyrg is endemic to Blue Point Spring in Lake Mead National Recreation Area within the eastern Mojave Desert. Two other springsnail species also occupy this unique spring. Little is known, however, about the distribution, abundance, and habitat associations of these springsnails. As a first step in a larger study investigating these parameters, we addressed methodological questions associated with the use of artificial tile samplers for long-term monitoring of springsnail abundance. We determined that the area of our tile samplers was adequate for sampling these springsnails and that our multiple, replicate tiles did not produce significantly different measures of abundance within our one meter sampling areas. These results indicate that monitoring could be accomplished with fewer tile replicates. We identified all three springsnail species within our samples and determined that identification of adult springsnails by shell morphology under magnification appears possible; we are currently developing genetic markers to confirm the morphological assessment. The relative abundance of springsnails peaked at approximately four meters below the springhead, and then dropped precipitously further downstream. Limited numbers of springsnails downstream may be related to the presence of nonnative, predatory fishes. We are currently investigating this hypothesis, and the findings of our methodological assessment have allowed us to use half of our sampler replicates in a fish exclusion experiment to assess the impact of predation.

Asthma affects over 6 million children in the United States. Asthma management requires a high level of executive functioning and self-regulation, including attention, planning, problem solving, and self-control. Executive functioning deficits, therefore, may impair asthma management capacity. Therefore, the purpose of this study is to describe the executive functioning of school aged children with asthma. The executive functioning of 33 children ages 6 to 11 years with asthma was tested using the National Institute of Health Toolbox Cognition Battery. The battery assessed numerous executive functioning processes, including attention, inhibition, shifting, episodic memory, working memory, processing speed, receptive vocabulary, and language. Compared to the reference sample, children in this study exhibited significantly lower age-adjusted scores in attention and inhibition t(33) = 93.06, p = 0.001, shifting t(33) = 92.64, p = 0.003, and processing speed t(30) = 82.37, p = 001. They scored significantly higher in receptive vocabulary t(33) = 113.76, p = 0.000, and language t(30) = 119.80, p = 0.000. This study revealed significant differences in the executive functioning of school aged children with asthma, specifically deficits in attention, inhibition, and shifting. These functions can be instrumental in the consistent use of controller medications and as a result impact the effectiveness of asthma management. Implications of these findings may include developing asthma management strategies within the capacity of the child. Future studies should explore the possible causes for executive functioning deficits as well as interventions that align with the executive functioning capacity of school aged children with asthma.

 Developmental epileptic encephalopathies (DEEs) are a group of severe neurological disorders that present with seizures in early infancy and developmental delays. A genetic cause can be identified in up to 50% of affected individuals and is most commonly a de novo genetic change. However, for some patients a genetic change is not evident through DNA sequencing. In this research project, we are using RNA sequencing to search for and identify abnormal splicing events that may be due to splice-altering variants in the genome of previously undiagnosed patients. Splicing occurs naturally in unaffected and affected individuals; it is the process of introns being removed from mRNA transcripts and exons being joined. The process of RNA sequencing allows us to discover abnormal splicing errors by looking at splice junctions, which are sites on the intron and exon border where splicing normally occurs. We search for abnormal splicing defects using RNA sequencing by comparing the splice-junctions from our patients to a reference database of healthy controls (Genotype-Tissue Expression Project), filtering out common splice junctions, allowing us to identify unique and abnormal splice junctions. If we identify abnormal splicing, we will also investigate the genome of the patient to determine whether there is an underlying DNA change. Using RNA sequencing, we hope to provide a genetic diagnosis for a subset of our undiagnosed patients and for more individuals affected by DEE in the future.

The Lake Washington, and Sammamish basin contains a complex mix of life history strategies of Oncorhynchus nerka. These life history strategies include 1) Anadromous sockeye that remain in the lake for one or two years before migrating to the ocean and returning to fresh water as mature adults; 2) “Residual” sockeye salmon that breed with and are genetically a part of the anadromous population but do not migrate to the ocean, and 3) “kokanee” salmon that are genetically distinct from anadromous and residual sockeye. Kokanee salmon are native to the basin and are thought to have evolved when glaciers or other barriers restricted access to the ocean. Although once extremely abundant throughout the basin, native kokanee are now thought to be found only in Lake Sammamish. Large numbers of kokanee-like fish continue to occasionally migrate from Lake Washington into the Sammamish river and its tributaries. Intriguingly, these “mystery nerka” migrate and spawn later than the sockeye/residual population and may represent a fourth distinct O. nerka population (e.g. a remnant of native Lake Washington kokanee, or a newly evolved kokanee population derived from sockeye ancestors). Sockeye, residuals, and kokanee use gill rakers, bony extensions in the throat, to capture prey. In other cases where kokanee have evolved from sockeye ancestors, the number and size of gill rakers differs – a reflection of the of the different types environments they mature in and the different types of prey available in freshwater vs. saltwater. In this research we document the variation in gill raker number and length in the Lake Washington/Sammamish populations of O. nerka in an attempt to 1) investigate trophic adaptations within the basin associated with life history strategy and location of maturation, and 2) to assess the relationship of “mystery nerka” to the other populations known to occur in the basin.

Spanish is one of the fastest growing spoken languages in the United States. In 2017, the US census reported that about 41 million residents (13.4%) speak Spanish in the home. Since the number of Spanish speakers increases annually in the United States, it is important to research how Spanish heritage language (HL) learners and Spanish second language (L2) learners interact with each other. Many assume that speaking with a Spanish HL learner will improve the quality of the L2 learner’s Spanish. The goal of my project is to analyze the amount of English spoken between the two types of students and the opportunities for learning created during their interaction by correcting each other’s grammar or helping each other to use different vocabulary words. To this end, I have transcribed the Spanish conversations between two Spanish L2 students and formatted them using the F4/F5 transcription software. I am currently coding them using a qualitative data analysis program called Atlas.Ti, with the addition of three other transcriptions that had already been transcribed. I predict that our results will demonstrate that, while some learning will occur between the HL and L2 students, a majority of the learning will occur among Spanish L2 learners. Since the research is still ongoing, I predict that due to the greater level of comfort a Spanish L2 learner has while talking to a fellow Spanish L2 learner, they will work together to solve more language issues than with a Spanish HL learner. This research is important due to its implications for improving how Spanish is taught in schools across the United States.

This work replicates previous research used to criticize the use of principle component (PCA) and exploratory factor analysis (EFA). Factor analysis is often used when research is being conducted in a new area and there is limited background knowledge about what one might expect to find. It’s useful because of its ability to reduce the number of variables in a dataset by examining the correlations between items and identifying latent dimensions that account for measured item variance and covariation. A criticism of this method is that it detects patterns in random data where there is no underlying structure. We tested this criticism by replicating the methods in a 1981 paper by Robert Vierra and David Carlson. We generated random data in R Studio and looked at the variance accounted for by the factors identified by EFA and PCA. We also examined the Type I error rate in sample correlation matrices tested with Bartlett's test. Additionally, we have begun a literature review looking at the modern methods similar to exploratory factor analysis, including machine learning, in order to understand how these criticisms have been addressed by these modern approaches.

Sleep in hospitalized children is disrupted by numerous factors including loud noises, light, assessments, medication administrations, and being away from their usual sleep routine and setting. Inadequate sleep can increase behavioral problems, increase stress, and increase length of stay. The goal of this project is to evaluate if an evidence-based sleep hygiene protocol in the Psychiatric and Behavioral Mental Health Unit at Seattle Children's Hospital promotes better sleep for the patients. The sleep hygiene protocol, a guided routine done prior to bedtime, is derived from a literature review on sleep routines in school aged children. A retrospective chart review will be conducted of seven patients from the unit ages 5-9 who use the sleep hygiene protocol. Data will include usage of sleep medication, hours asleep, and nighttime behavioral problems from before and after implementation of the sleep hygiene protocol. I am focusing on the effectiveness of the newly edited sleep hygiene protocol. Results from this study will be used to refine the sleep hygiene protocol so that it can be widely implemented in the PBMU and other units of the hospital. 

Many children in the United States experience mental health issues that impact their performance in school. Evidence-based practices (EBP) have demonstrated effectiveness at improving student outcomes for students impacted by their mental health. However, many factors affect the successful implementation of these programs. Mental health services, particularly those for youths with the most mental health needs, typically involve multi-organizational processes to implement EBP. The Inter-Organizational Alignment study strives to examine these multi-organizational frameworks, and how they impact the school mental health services provided. The research study examined the association between race and the degree of inter-organizational alignment on climate for EBP implementation. Researchers surveyed 28 school mental health clinicians and 57 school staff in the states of Washington and Minnesota. The sample included 22 white or Caucasian participants and 14 non-white participants. Non-white participants were either American Indian or Alaskan Native, Asian, Black or African American, multiracial, or other. Implementation climate of EBP in school settings was rated on a Likert scale of 0 (not at all) to 3 (great extent) on a standard, multi-item scale. Researchers evaluated schools on a range from an open and positive implementation climate to a closed and negative implementation climate. The degree of alignment was determined between clinician and school staff scores, with misalignment defined as a difference of one standard deviation. Quantitative analysis of the results suggested more alignment in implementation climate between clinician and school staff of different races, which suggests that racial factors impact EBP implementation in racially diverse environments. An independent t-test determined that these differences were statistically significant. Consequently, these findings suggest that EBP may be impacted when implemented by more diverse organizations.

Current methods of drug delivery include the use of antibody drug conjugates (ADCs), lipid and polymeric nanoparticles, and top-down modified viruses. While successful in certain applications, these delivery platforms involve laborious production methods and have limited engineering opportunities. Synthetically designed proteins are viable drug delivery candidates that can be precisely modified to overcome the engineering challenges associated with other delivery platforms. Specifically, synthetic nucleocapsids (synNCs) are computationally designed icosahedral protein assemblies evolved to have virus-like genome packaging. The linkage between the encapsulated mRNA (genotype) and exterior proteins (phenotype) allows for directed evolution to be achieved through library selection. The synNC was evolved to increase the in vivo circulation half-life from less than 5 minutes to over 4.5 hours. The next step is to optimize the targeting ability of synNCs toward specific organs. We performed site-directed mutagenesis to introduce several mutations on the exterior of the synNC, performed two rounds of in vivo library selection, and identified several mutations that favored specific organs. Our current work involves producing five promising synNC mutants, biochemically characterizing the mutants, and examining their biodistribution in mice. The ability to target specific organs will be a successful step towards utilizing nucleocapsids in drug delivery and other biomedical applications.

Abstinence-based treatment has long been considered the standard of care for people with alcohol use disorders (AUD). However, abstinence-based treatment fails to engage severely affected populations (e.g., homeless people affected by AUD) because many are not yet ready, willing or able to stop drinking. A recent randomized controlled trial tested the efficacy of a lower-barrier harm-reduction treatment for alcohol (HaRT-A), in which participants could define their own harm-reduction and quality-of-life (QoL) goals. The aim of this present secondary study was to describe participants’ own harm-reduction and QoL goals and document their achievement of these goals over the course of HaRT-A. Participants were people currently experiencing homelessness and AUD (N = 86) who attended the 4-session HaRT-A, during which interventionists elicited participants’ own harm-reduction and QoL goals. The Safer-drinking and Harm Reduction Efforts (SHaRE) form was administered to elicit and record participant-generated harm reduction goals, which were entirely participant-driven with no suggestions from study interventionists for any specific drinking-related goals. Directed content analysis was performed to classify participant-generated treatment goals. Results indicated that goals fell into 7 primary categories, the top 3 being drinking-related goals, quality of life goals, and health-related goals. These findings suggest that a client-driven, goals-setting approach could inform accessible and appropriate treatment and QoL-enhancing interventions for people experiencing homelessness and AUD.

Self-assembling synthetic nucleocapsids have been at the center of increasing development as a medium for targeted drug delivery. By identifying certain cell markers of tumor cells, researchers at the Baker Lab have been evolving desired characteristics to this protein assembly by attaching different functional domains to specifically target cells. This screening of functional domains is possible because of the nucleocapsid’s ability to encapsulate its mRNA sequence, thereby linking genotype to phenotype. Moreover, this enables us to evolve desirable features in these functional domains through library selection. However, subsequent attachment of functional units to its exterior surface proved to decrease its mRNA packaging efficiency, thus limiting applications like mRNA delivery and evolution of functional units. This project aims to enhance the amount of encapsulated mRNA by mutating certain interior amino acids. Methods include cloning our I53-50-v4 protein assembly gene into Escherichia coli (E.coli) strains and over-expressing the proteins through IPTG induction. After the cells were harvested and lysed, proteins were purified through Immobilized Metal Affinity Chromatography (IMAC). RNA encapsulation levels were measured through Quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR) to compare between the original and mutated nucleocapsid. Promising results would demonstrate an increase in RNA concentration per nucleocapsid when compared to the original assembly across different constructs. The success of this project would allow for attaching multiple domains for evolution without compromising the nucleocapsid’s capacity to retain its biomolecular cargo. This research would greatly expand the utility of these nucleocapsids for evolving displayed proteins for desirable characteristics as well as enhance their efficacy for drug delivery applications.

African Americans may be at increased risk of developing Alzheimer's disease. Decreased social engagement and depression are related; changes in older adult levels of social engagement are associated with dementia. The Sharing History through Active Reminiscence and Photo-Imagery (SHARP) study aims to improve cognitive health among cognitively normal and mildly cognitively impaired older African Americans by employing a culturally celebratory framework integrating walking and community-based social reminiscence. In triads, African Americans aged >55 (n=40) walked 3x/week for 6-months in 2016 and 2017 while engaging in image-prompted conversational reminiscence about neighborhood history. Walks took place in Portland, Oregon’s historically Black neighborhoods. Baseline and end-study surveys had seventeen close-ended questions about physical and mental health and health behaviors. SPSS analytical software will aid in analysis. Focus groups discussed the impact of the program’s culturally celebratory approach on physical activity and mental health. Qualitative data will be thematically coded. Preliminary data highlights self-reported health-related outcomes which include increased activity throughout the day on days that walks occurred, rekindled friendships, increased impromptu social engagement, and heightened sense of community connectedness as a result of increased social engagement and place-based group reminiscence. Participants feel that the program’s social aspect, rather than physical activity, is the primary driver for sustained engagement. Structured socializing and the focus on neighborhood history contributes to improved self-reported mental health, important for sustained cognitive health. Finding innovative, culturally meaningful ways for older adults to be socially engaged may improve mental and cognitive health outcomes.

The delivery of cell and drug-based chemotherapeutics to tumors have presented major challenges in effective cancer treatment. Opportunities to improve current small molecule drug delivery systems exist by increasing overall delivery specificity and decreasing harmful off-target effects. Towards this, we have recently developed a chemical framework for creating user-programmable hydrogels that undergo programmed degradation in response to multiple environmental cues following Boolean logic. Exploiting this methodology, user-specified combinations of environmental inputs (e.g., tumor-presented enzymes, reducing conditions) yield material breakdown and accompanying therapeutic release. To translate these materials for chemotherapeutic delivery in vivo, we established strategies to formulate these stimuli-sensitive materials into nanogels that circulate in the bloodstream before acting on the desired target site. We developed techniques to formulate gels on the 50-250 nanometers size scale, one which should enable circulation in the blood and uptake within tumors based on the enhanced permeability and retention effect. Different ultrasonication conditions allowed us to tune nanogel, size and dispersity. This system is scalable, translational, and simple to recreate. In the future, these materials can effectively hone and selectively deploy small molecule chemotherapeutics to tumors in patients.

Small-angle neutron scattering (SANS) is a powerful tool that provides access to molecular-level structure in a variety of material, such as soft matter, colloids, and biomolecules. Currently, researchers must follow a manual and inefficient procedure to reduce and analyze data due to inconsistent meta-data storage and varying reduction processes. Thus, our project is aimed to improve the automated reduction of SANS data and streamline data flow at the experiment site by the use of machine learning (ML) and data science techniques. We propose a machine learning classification algorithm, trained on a historical SANS dataset, to automatically sort raw data into six categories of scattering profiles and relevant background measurements required for reduction. The first stage of our research project uses a feature reduction model to create a subset of most significant and relevant meta-data in the historical scattering data set. After pre-processing, we then explore different ML models (e.g. neural networks) to sort the data in a comprehensive, accessible, and maintainable form that can be easily applied to sorting data directly from experiment sites. In addition, we incorporate a Postgres database to improve data management as well as an interactive front-end to enable user interaction. Currently, we are building meaningful and useful data processing and management methods by starting with a small SANS dataset from the Pozzo Research Group at the University of Washington. In the future, these methods will be expanded to larger historical SANS datasets to train our machine learning models. By developing this machine learning algorithm that can utilize experimental information and scattering patterns for auto-labeling of raw data and relevant meta-data, we will enable more efficient storage, reduction, and analysis of SANS data for researchers in the future.

 Domestic dogs express individual differences in personality and perception, affecting their behavior towards objects they encounter in the world. One of these differences is a form of cognitive bias called judgement bias. Dogs that approach an ambiguous stimulus at a rate closer to that of approach towards a rewarded stimulus demonstrate a positive judgement bias. Likewise, dogs who approach at a rate closer to that of a non-rewarded (or aversive) stimulus have a negative judgement bias. Some dogs refuse to approach the non-rewarding stimulus entirely, which can be defined as refusal behavior. We analyzed whether refusal behavior was related to companion dogs’ judgement bias and general fear and anxiety. Dog owners completed the Canine Behavioral Assessment and Research Questionnaire (C-BARQ), a previously validated questionnaire measuring a variety of individual differences in dog behavior, and, most importantly, fear and anxiety. Afterwards, dogs were brought in for in-person testing. We measured each dog’s latency to approach ambiguous stimuli and compared this to their latency when approaching rewarded versus non-rewarded stimuli. We would expect that dogs who refuse to approach ambiguous stimuli will also exhibit higher C-BARQ scores in fear and anxiety than dogs who do approach ambiguous stimuli. Refusing to approach may also suggest a negative judgement bias. These findings are extremely useful to not only further understand canine behavior and cognition, as refusal to engage with a stimulus may be a future tool to define a canine’s perception of ambiguous stimuli. They also have practical implications for both animal welfare and training efficacy, as individual cognitive differences among dogs may impact how they will respond in behavioral tests and training regimes.

High rates of early dropout or premature termination in university psychology training clinics adversely affect both patients and clinicians. Prior research suggests that among clients seen at training clinics approximately 70% terminate prematurely and approximately 55% do not report reliable change at the conclusion of treatment. To help assess the generality of this issue, we are investigating the rate of premature termination in a university-based clinical psychology training clinic in the Northwest. Using the Reliable Change Index (RCI) as a marker of recovery, we calculated the RCI for 3 outcome measures: the Patient Health Questionnaire (PHQ-9), Generalized Anxiety Disorder 7 (GAD-7), and the Brief Adjustment Scale-6 (BASE-6). Additionally, the training clinic in this study practices Measurement-Based Care (MBC) which involves the systematic administration of symptom rating scales known to increase treatment efficiency and effectiveness by assisting with clinical decision-making and informing patient progress. The hypothesis was that there would be a higher rate of reliable improvement and lower rate of deterioration at the end of treatment. Our examination of the test-retest reliability within 2 weeks of these outcome measures found the total scores of all three scales to perform adequately. Within the training clinic, 18.18% reliably improved using the GAD-7, 21.51% reliably improved using the PHQ-9, and 27.27% reliably improved using the BASE-6. These results did not support the hypothesis and instead found a lower rate of reliable improvement than the published norms. Potential reasons for the discrepancy will be discussed. This study will benefit those suffering from ineffective treatment outcomes and those struggling with untreated debilitating mental disorders. It will also add to the growing literature on the benefits and obstacles of MBC which has been gaining increasing recognition recently. 

If you're tiling a circular room with square tiles, how many do you need? What if your tiles are parallelograms? As the circle gets larger, is there a pattern? Mathematically, this can be framed as counting integer points in a large circle. We're interested in how this count changes as you change the shape of the tiles, and to understand this better, we started by counting the number of integer vector pairs within a ball of radius R so that the parallelogram they make has a fixed area (determinant). We created a Python program that would generate all of the primitive points out to radius R, which we then extended to count the number of vector pairs with a certain determinant k. We were able to compute the limiting density of this count, extending known results for the case of determinant 1. We are now studying other discrete sets, such as ones generated by objects from hyperbolic geometry, known as Hecke triangle groups. In the future, we plan to use our research for counting pairs of vectors in different spaces and generalize it for counts of k-tuple vectors. Come for floor tilings, stay for beautiful pictures!

Young adults are susceptible to a whole range of psychological disorders. Approximately 39.6% of young adults (ages: 18-25) in the United States have had a heavy drinking episode in the past year, and 9.6% of young adults have had a major depressive episode in the past year. Previous research has shown that young adult males tend to drink more alcohol, while females have higher rates of anxiety and depression. There is, however, limited research about the extent to which certain groups of young adults, based on living situation and college enrollment, may exhibit higher alcohol use and poorer mental health. The purpose of this research is to examine differences in alcohol use, alcohol-related consequences, and mental health by demographic characteristics (i.e. attending 4-year college or not, living with parents or not, biological sex) among a community sample of young adults (ages 18-23). Analyses use baseline data (N=764; 55.9% female, mean age 20.6 (SD = 1.72) from a larger longitudinal study on health behaviors. Outcomes will be alcohol use, alcohol consequences, depression, and anxiety. Separately for each outcome, an analysis of covariance (ANCOVA) will be conducted. The sample includes 352 4-year college students and 412 individuals not attending a 4-year college, 468 individuals not living with parents and 296 individuals living with parents, and 428 females and 336 males. We hypothesize that higher alcohol use and consequences will be found for males, individuals not living with parents, and individuals enrolled in a 4-year college. We also hypothesize poorer mental health for females, individuals not living with parents, and individuals enrolled in a 4-year college. Results from this study will provide a better understanding of which young adults are experiencing poorer mental health and higher alcohol use, thus providing valuable information to guide interventions.

The receptor human protein kinase EphA2 has emerged as a therapeutic drug target for cancer and infectious diseases. However, the dearth of selective EphA2 inhibitors in the field is hampering EphA2-based research and therapies. Our lab recently developed a novel selective small molecule EphA2 inhibitor I268 using medicinal chemistry. Surprisingly, we observed the same inhibitory effects on cell proliferation paradoxically when inhibiting EphA2 with I268 or activating EphA2 with its agonist EphrinA1. We hypothesized that both I268 (inhibitor) and EphrinA1 (agonist) may lead to the same protein-protein interaction network of EphA2 that caused this paradoxical inhibition. We used a chemical proteomic method developed in our lab called “co-clickable precipitation (Co-CP)” to study the interaction network of EphA2 in colon cancer cell line HCT-116. We observed that the onset of inhibitory effect by I268 concurred with the association between EphA2 and a protein interactor called c-RAF, a key player in activating proliferation pathways in cancer cells containing Ras mutations such as HCT-116 cells. We are currently performing confirmatory experiments to characterize whether upon inhibition by I268 or activation by EphrinA1, EphA2 sequesters c-RAF in a form unable to transmit proliferative signals downstream. Our results may demonstrate a possible mechanism for inhibitory effects of EphA2 inhibition on cancer cell growth. These results validated EphA2 as a drug target and may provide novel ways for treating cancer cells by inhibiting cell proliferation pathways indirectly using EphA2 inhibitors.

Dogs have been shown to use the direction of humans’ gaze to infer information about hidden food, a behavior referred to as social referencing. We might expect that social dependency towards a handler will be higher for dogs that are more dependent on humans’ presence, especially when faced with uncertain situations. We tested whether there was a relationship between attachment and dependency behaviors and social referencing in companion dogs. Dog owners completed an intake survey that included the previously validated Canine Behavioral Assessment and Research Questionnaire (C-BARQ), which gives a score for the degree of separation-related distress behaviors dogs exhibit which we used as a measure for dogs’ attachment and dependence on their owners. These owners then brought their dogs to participate on-location for our experimental set up. We taught the dogs a location-based discrimination task, in which subjects learned to expect a food reward in one location (the positive stimulus), and no reward in an opposing location (the negative stimulus). When dogs approached the positive stimulus faster than the negative stimulus, we intermittently presented them with ambiguous stimuli, i.e. intermediate between the positive and negative stimuli. We measured social referencing as the frequency of glancing behavior of dogs toward their owner or the handler for each trial. We analyzed social referencing by stimuli in order to assess whether dogs would treat ambiguous stimuli as they do the rewarded location or the non-rewarded location with respect to glancing behavior. We hypothesized that dogs with higher C-BARQ scores for separation-related behavior would exhibit higher proportions of social referencing behavior, particularly when presented with ambiguous stimuli. Our research has implications regarding potential effects of canine dependency on their owners in their decisions in certain situations, such as those that introduce ambiguity.

Sixty percent of adults in the US have a chronic disease (e.g., heart disease, cancer, diabetes) and forty percent of adults have two or more chronic diseases. Risk for chronic disease is strongly influenced by a short list of health behaviors such as tobacco use, physical activity, diet, and alcohol use. College students, as they become independent from their families, start to establish lifelong habits through their time in school. Students who experience high stress are more likely to engage in less healthful behaviors which can increase their long-term risk of chronic disease. The purpose of this study is to understand how stress and lifestyle behaviors among low-income and international college students impact risk for chronic disease. This is a survey study in which 300 undergraduate international and native students at Portland State University will complete questionnaires about health behaviors, stress, socioeconomic status and demographics. International student participants are recruited from different clubs and programs that provide support for international students. We expect our results to indicate that international students and students from low-income families experience higher than average levels of stress, which may negatively impact their engagement in health behaviors and further increase their risk for chronic disease.

Culturally competent interventions are essential to recruiting and retaining ethnic minority populations. Latino communities are the fastest growing population in the United States. Despite their growing numbers, Latino communities are dramatically underrepresented in clinical trials. As a result, the data from those clinical trials are not representative of the Latino population. There are many factors that make Latino communities very diverse, even amongst themselves. They do not share the same languages, customs, and socioeconomic status. There is a need to investigate the barriers and facilitators of the recruitment of Latinos into research. A survey was developed for Latino families in Oregon. The survey items were informed by a literature search around barriers and facilitators of clinical trial participation for minority and disadvantaged populations. This survey has been translated in both English and Spanish. After finalization of the survey, it was piloted with three representatives from the local community to get qualitative feedback. It will be administered to low-income parents of children enrolled in head-start settings in Oregon over the next five months and expect to have 200 responses. The anticipated results will contribute a better understanding of what commonly impacts recruitment among the Latino families participating in clinical trials and what strategies address those issues. This project can serve as a resource for the wider scientific community that seeks to recruit and study the Latino population for research purposes.

Measurement in Psychology usually assumes continuous dimensions. Correspondingly, theoretical constructs are typically conceptualized as dimensions, meaning that observations differ in degree. However, theoretical constructs may also be categorical, i.e., rather than differing by degree, differing qualitatively. Different construct operationalization’s may lead to different scientific conclusions. Self esteem has long been of interest in Psychology. It has been conceptualized in various different ways, but always dimensional. Some self-esteem measures (for example, the The Rosenberg Self Esteem scale) seek to measure globally how much one values themselves as a person, without focusing on specific domains. On the other hand, other self-esteem measures (for example, the State self esteem scale) focus on perceived capabilities in specific domains, such as performance, social, and appearance. In the National Survey of Youth, participants rated themselves in specific areas, and then again as they would like to be. Using these data, we examined how different operationalization’s of self-esteem are associated with a few psychologically interesting outcomes such as drug use and crime. Specifically, we compared continuous and categorical representations of self-esteem. By examining the assumption of continuous latent variables, we shed light on how scientific conclusions differ based on construct operationalization.
 

Rehabilitation research has demonstrated the benefits of early powered mobility intervention for children with disabilities, from improving developmental skills to empowering children to better participate in family and community life. However, traditional powered mobility devices are often stigmatizing, costly, and require specialized transportation due to their size and weight. One alternative early powered mobility option that has sought to address several of these concerns, The Go Baby Go Mobility and Socialization Project, provides children with disabilities a means of socially welcoming, early independent mobility experiences through custom safety and accessibility modifications to commercially available toy ride-on cars. The Go Baby Go project has resulted in promising pilot research along with community-based outreach and education in collaboration with families, clinicians, and engineers. However, a means to efficiently track car performance in real-world environments without the presence of a researcher has been lacking. Therefore, the purpose of our project was to develop a customized data logger and companion Arduino code with the ability to collect real-time data from the cars as families use them in their homes and communities. Our multidisciplinary team has created and implemented a system which gathers car performance data automatically via integrated sensors, including the number and duration of switch activations, frequency and duration of use, outdoor location, distance traveled, and driving terrain. Housed in a simple, waterproof food storage container, the data logger is integrated into the car’s electronics and powered by the car battery, with data stored on a micro-SD card. Preliminary analysis of results from eight cars in local communities is ongoing and will be shared; initial feasibility of our system for real-world tracking without undue research presence or caregiver reporting burden is promising. Future research goals include full quantitative analysis of car use patterns to improve technology design and implementation in community settings.

c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinases (MAPKs) family that are derived from three genes: Jnk1, Jnk2, and Jnk3. JNKs have been implicated in several cellular responses to homeostatic insults, including inflammation and apoptosis. We previously reported in a chronic epilepsy rat model significant elevated levels of phosphorylated JNKs (pJNKs), which indicate increased JNK activities. Additionally, we demonstrated that pharmacological manipulations of JNK proportionally affected seizure frequency. In this set of experiments, we attempted to identify which of the JNK isoforms (JNK1, JNK2, JNK3) contribute to the overall increased pJNK levels in our animal model of epilepsy. This would provide us insights as to the role(s) of JNKs in this disease. We measured the phosphorylation levels of the individual isoforms after pJNK enrichment from the CA1 hippocampal tissue of chronic epileptic rats and their age controls. The amount of protein was normalized by pJNK levels between experimental and control samples. We found a significant increase in activation levels of JNK2 in chronic epilepsy at 130 ± 9% (n=6, p=0.018) when compared to naïve, nonepileptic controls but insignificant changes in activation levels of JNK1 (97 ± 14%, n=5, p=0.83) and JNK3 (98 ± 17%, n=6, p=0.92). Previously, we had found in rats that JNK1 predominantly exists in the 46kDa size; JNK3 predominantly exists in the 54 kDa; and JNK2 exists in both sizes equally. We further analyze which of the JNK bands (46 kDa and 54 kDa or both) contribute to the elevated phosphorylated JNK levels. Given the previous pharmacological observation that JNK manipulation does influence seizure frequency in epilepsy, this investigation is imperative as it will allow us to narrow our focus to a specific JNK isoform to study further.

Plants take up silica over the course of their lives along with other essential nutrients in the water that they absorb through their roots. The silica becomes deposited within their tissues in the form of solid bodies (phytoliths); when the plant dies and decays, phytoliths are left in the soil where they can fossilize. Fossil phytoliths preserve the original morphology of plant cells and can be used to reconstruct past vegetation. The Middle Miocene Climatic Optimum (MMCO) was a major global warming event that happened ~17-14.5 million years ago. Researcher have reconstructed the climate of the Santa Cruz Formation in Patagonia, Argentina during this period as warmer and drier. While we would expect the vegetation to become more open (i.e., grassy or shrubby versus forested), phytoliths from the Santa Cruz Formation tell a different story; in particular grass phytoliths (and therefore grass abundance) seem to decrease through time, but also become smaller. Some researchers have noticed that grasses tend to respond to reduced water availability with reduced cell size. Therefore, we hypothesize that the reduced size of grass phytoliths observed in the Santa Cruz Formation during the MMCO is due to increasing aridity. However, because this trend of decreasing cell size was only noticed by qualitative observation, we need to quantitatively assess significant changes in cell size. To do so, I studied and imaged grass phytoliths under a microscope, categorized them by subfamily/tribe based on their shape, and measured their size. I then statistically compared the phytoliths from younger and older strata to test whether there was a change in size through time. This work will be used to predict how our current global warming event may impact plant life based on the trends of the past.

Precise spatiotemporal control over biochemical cue presentation is necessary to mimic the complex, heterogenous environments found in biological systems. Achieving this level of control within engineered microenvironments would allow for the manipulation of cell growth and differentiation, which could be utilized in tissue engineering and drug delivery. To this end, we developed a method that utilizes fusion proteins made from a novel PhotoCleavable protein linker (PhoCl) and a protein of interest (POI). This method allows for spatiotemporal control of POI release from hydrogels in response to cytocompatible violet light (λ = 405). This system is flexible, as PhoCl can be conjugated to many different POIs, including fluorescent proteins, enzymes, and growth factors, and was found to not affect protein function. Additionally, PhoCl undergoes a green-to-red transition after photocleavage, allowing for real-time tracking and quantification of POI release. As PhoCl cleaves in response to visible light, which is less damaging to cell function and has a greater tissue penetration depth than the traditionally used UV light, PhoCl fusion proteins hold promise for use in vivo. To demonstrate the feasibility of this system, PhoCl fusion proteins were formed with several fluorescent proteins (e.g., mRuby, sfGFP, mCerulean). Conjugating these fusion proteins into gels and exposing them to patterned light produced spatiotemporal localized release of proteins with micron scale resolution, which was demonstrated through fluorescent imaging of the photopatterned gels. To support the potential in vivo applications of this system, PhoCl was also used in mammalian cell studies with epidermal growth factor (EGF). These studies showed the expected increased cell growth in response to photomediated EGF release. This illustrates the potential versatility of the PhoCl system in biological applications, thus supporting the relevance of this novel system to tissue engineering and drug delivery methods.

Small insect-inspired robots have much potential in exploration and have been experiencing a wave of innovation in recent years. Small robots have promise especially in space exploration where each kilogram costs $10,000 to launch, but tiny robots tend to weigh under a gram. However, some problems persist, such as difficulty with landing after flight and hopping mechanisms wearing down after a few uses. Our work focuses on developing a hopping robot that is capable of attaching to an overhanging surface when it jumps and that has durable mechanisms to optimize the number of jumps per bot. The hooking mechanism differs from previous work, usually electrostatic patches, and instead is inspired by the hooked feet of beetles, which is lighter and does not require constant electrical power. For optimizing jumps, we are working to develop a jumping body constructed from and designed for carbon fiber rather than the previously used fiberglass. Carbon fiber has a higher strength to weight ratio and is more elastic than fiberglass, making it efficient for flight and the repetitive motion carried out by the body when bent by the onboard actuator. All designs are created using an iterative design process where parts are micromachined and assembled, then tested for desired qualities. From this, we are aiming to develop an autonomous hopper capable of completing multiple jumps and grabbing without maintenance on any part of the bot.

Mathematical knots are non-intersecting closed loops which may be tangled; links are knots that are possibly intertwined. These 3-dimensional paths often resist description, so mathematicians choose nice ways to describe them. One such way is to project them onto a plane. Even more, it is interesting to build knots in discrete ways such as placing them on tiles in a plane. In this poster we are considering hexagonal mosaic knots, knots that are projected on a plane tiled by the honeycomb hexagonal tessellation. In this way, knots can be built from a small collection of hexagonal tiles with loops. We create an interactive tool which presents hexagonal tile types, a grid on which to lay them, and options for analysis. The researcher uses a point-and-click tool to lay down a mosaic grid, and in so doing, creates an underlying data structure representing the segments contained in the mosaic. When requested, the software traverses this data structure like a linked list. In this manner, one may determine if the data structure represents a suitably connected hexagonal mosaic knot or if it contains dead ends or stray segments; that is, determine if a data structure represents a knot/link or not. This process helpfully assigns segments to their respective knots, distinguishing not only ‘over’ and ‘under’ but also ‘self’ and ‘other’. We hope to continue exploring automatic generation of information about knots from their tiled representations. Once more developed, we hope to be able to answer more questions about the knot or link represented by the data structure. We also hope to continue exploring the use of rapid, flexible feedback from prototypes in aiding exploratory research.

Latent class models are frequently used to classify observations into homogeneous albeit qualitatively different sub-groups. Typically, these models are unrestricted, meaning there is no a priori structure or restrictions on model estimates. This approach is similar to many cluster analysis approaches. The study examines modeling conclusions when an unrestricted model is applied to data generated from a highly restrictive population model through a simulation study. We expect that a researcher will conclude fewer classes than the true number specified in the population. Simulated data for this work is based on a substance use example identified in other research. The population was generated based on six classes, but with a within class error rate fixed to 5%. Preliminary analyses indicate that commonly employed model selection criteria indicate that models with fewer than six classes are preferable. This is important because most analysts using latent class models use unrestricted models with little apparent consideration to what realistic error rates may be. In research domains where smaller error rates may be plausible, restrictive models of the sort used to generate the data for this study may be worth considering.

Modifiable psychosocial and behavioral factors place youth at risk for severe and persistent pain after major surgery. Opportunity exists prior to surgery to intervene with youth and families to prepare them for surgery including helping to manage distressing cognitions and teaching non-pharmacologic coping strategies, to reduce acute pain and prevent chronic post-surgical pain. This study aims to develop and evaluate a cognitive behavioral program in reducing acute and chronic pain in youth undergoing major surgery. In the pilot study, fourteen children ages 10-18 years (M= 14.5), 71.4% female, scheduled for major spine surgery, and their parents, were enrolled into the study. Enrollment rates were excellent with 88% (14 of 16) of families approached agreeing to participate in the study, with a range of 4 to 16 weeks (M = 6.3, SD = 1.3) until surgery at the time of enrollment. Teens and their parents completed three pre- surgical modules containing surgical preparation and relaxation tips during the month preceding surgery. Participants completed three post-surgical modules during the 6 weeks following surgery containing tips for managing pain and returning back to school and activities. Each module was accessed online and followed by a coaching phone call with a trained study team member to ensure comprehension of module content. All of the participants completed all pre-surgery and post-surgery modules within the prescribed time frame. Parents and teens completed assessments at four timepoints: 1 month pre-surgery, 1 week pre-surgery, 6 weeks after surgery, 3 months after surgery. The majority of parents and children (79%) completed the study phone calls within the prescribed time period. Preliminary results indicate excellent program feasibility. Further study must be done on patient outcomes to assess efficacy of the program in a larger population.

The associations between toxic stress, adversity, and mental health are widely documented in public health, medicine, and social science research. Much of this work stems from the findings of the CDC-Kaiser Permanente Adverse Childhood Experiences (ACE) Study from the late 1990s. The results of this study showed that individuals who experienced significant childhood adversities and traumas were at a higher risk for depression and suicide attempts, health risk behaviors, and adult diseases such as cancer and heart disease (Felitti et al., 1998). This research has been invaluable in improving the health of populations who have faced such severe stress, but it is somewhat limited in that it does not acknowledge other aspects of health, such as immune function and frequency of acute illnesses. It also does not take into account adversity that occurs after childhood and adolescence. Recent studies demonstrate that toxic stress and adversity in different stages of the life-span can have negative effects on immune function. This indicates a need for more emphasis on the immune impacts of adversity in future health interventions and research, as well as a need for integration of trauma-informed practice into clinical settings. Although more research is needed to thoroughly establish the causal pathway between adversity and immune dysfunction, the studies discussed in this review demonstrate a strong correlation between these variables, thus providing justification for these interventions.

This presentation seeks to summarize a solution to helping the visually-impaired navigate new areas. While previous solutions have been relatively successful, many lacked two key features that we hope our solution addresses: being affordable and allowing customization towards those with compounding disabilities. Our solution consists of two main parts: (1) a user-interface created for Fusion 360, a popular 3D-modeling application, that is built upon an existing framework detailed in Hofmann (2018) called PARTs (Parameterized Abstractions of Reusable Things), and (2) an optimization algorithm to generate maps that are tailored for its users. Through PARTs, we developed different variations of modular pieces of map (e.g., roads, buildings, and sidewalks), which increases ease of customization. After the user specifies personal information and preferences through the PARTs UI—such as the width of their finger, their physical limitations, their understanding of braille, and their desired map features—the optimization algorithm will select the best combination of features from the PARTs database for that specific user. At the end of the process, users have a model of a tactile map in Fusion 360 which can be printed out with commercially-available 3D-printers. With 3D-printers becoming more affordable, this solution is significantly less cost prohibitive than other means of generating tactile maps, which required an initial investment upwards of a thousand dollars. Through user studies, we also test how blind users interpret these maps, which helps us guide design improvements in the future. In this presentation, we discuss the efficacy of our solution by comparing it to previous works and detail our plans to improve the system by making the PARTs user-interface more accessible and incorporating user feedback about the map itself. 

Climate change will have significant impacts on Pacific Northwest hydrology. Rising temperatures and shifts in precipitation will lead to changes in snowpack, runoff, and streamflow timing, impacts that will have implications for water and environmental resource management. The Pacific Northwest’s Green River Basin is a valuable water supply and provides habitat to several cold-water aquatic species including the threatened Puget Sound Chinook salmon, but also has a major flood risk. Streamflow in the basin is seasonally regulated for flood prevention and ecosystem health, and changes in the annual hydrologic cycle will have consequences for flood risk and ecosystem habitat. To investigate the implications of climate change on streamflow, snowpack, and stream temperatures in the Green River Basin, climate sensitivity analysis and future climate impacts are simulated using two watershed models with varying spatial and process complexity: 1) the conceptual Snow17/Sacramento Soil Moisture Accounting model (Snow17/Sac) implemented with two elevation zones and 2) the process-oriented Structure for Unifying Multiple Modeling Alternatives (SUMMA) model implemented using twelve USGS HUC-12 subareas. Stream temperature climate sensitivities are modeled using the River Basin Model (RBM) Semi-Lagrangian Stream Temperature model. Future climate change impacts on basin hydrology and stream temperatures are assessed using an ensemble of statistically downscaled climate projections from 34 Global Climate Models (GCMs) run as part of the Intergovernmental Program on Climate Change 5th Assessment Report. The future warming scenarios show moderate changes in streamflow volume, shifts in streamflow timing, and reductions in snowpack, which differ depending on the watershed model. The presentation provides key results and findings from the study, and comments on potential impacts on stream temperature and fish.

The ability of an organism to dissociate environmental cues for either safe or threatening situations is key for survival. Generalized fear is an adaptation in which behavioral responses for threatening stimuli are produced to non-threatening cues. In mice, discriminative or generalized fear responses are modeled using a fear conditioning paradigm of two shock intensities, 0.3 mA or 0.5 mA. Mice trained at 0.3 mA intensities could discriminate between safe and threatening cues, yet mice trained at a 0.5 mA intensities displayed generalized fear behavioral responses. Previously, we had identified that dopaminergic neural activity was critical for the ability to discriminate between cues when shocked at 0.3 mA. Dopamine neurons express Kv7.3 potassium channel subunits, which modulate neural activity. I hypothesized that Kv7.3 subunits on dopamine neurons would be critical to threat discrimination and mice that had undergone mutagenesis of Kv7.3 would show generalized fear discrimination. My approach used transgenic mice expressing Cre-recombinase and viral-mediated gene delivery of cre-inducible CRISPR-Cas9 plasmids targeted for the specific mutagenesis of Kv7.3. Mice underwent a three day paradigm known as fear conditioning. Baseline freezing behavior was assessed by playing two tones, A and B. This was followed by fear conditioning trials where at the end of tone A, mice received a shock of either 0.3 mA or 0.5 mA (CS+) and at the end of tone B, mice received no shock (CS-). On the third day, mice underwent a probe trial to assess final ability to discriminate between threatening and non-threatening cues. These findings could provide insights into the mechanisms underlying neurological disorders and serve as a guide for future pharmacological interventions.

Many genes are associated with microcephaly, a condition characterized by a small head size. Through exome-sequencing, we identified de novo missense mutations in an actin polymerization gene, ARPC4, in four individuals with microcephaly, mild developmental delay, and mild intellectual disability. ARPC4 is involved in actin filament formation. Actin is an essential component of the cell’s cytoskeleton that gives the cell its structure and aids in cell movement and division. The goal of this research project is to understand the molecular mechanisms that lead to the disease phenotype observed in these patients. I began by using CADD, a measurement used to predict the deleteriousness of single nucleotide variants. The mutations identified in the patients were located in highly conserved loci, indicating they might be pathogenic. To provide further evidence of the pathogenicity of the ARPC4 variants, we were interested in determining the functional effect these variants have on actin polymerization – specifically, the role of ARPC4 in this mechanism. I established fibroblast cell lines from two patients with the same ARPC4 mutation. I performed immunofluorescence staining for actin to quantify the amount of actin present in the patients and control cell lines. Preliminary data from this experiment suggests that there is greater abundance of actin filaments in the control sample compared to the patients’ cells. To observe the effect of decreased actin abundance on cell migration, I executed a scratch migration assay. The results from this study elucidate the impact of ARPC4 in actin polymerization, and establish actin deficiency as a clinically recognizable cause of microcephaly.

A person’s age is one of the greatest risk factors for many age-related diseases, such as Alzheimer’s disease, heart disease, and cancer. Developing interventions that target this common risk factor may allow us to slow down the progression of all age-associated diseases. One promising target for aging research is the mTOR (mechanistic Target of Rapamycin) signaling pathway, which is a master regulator of cell growth that allows the cell to fine tune its response to various environmental conditions. Inhibition of mTOR pathway has been shown to extend lifespan in yeasts, worms, fruit flies, and mice. In addition of being a target in aging research, the mTOR pathway is also a well-known effective target in some human cancers to prevent cancerous cells from dividing uncontrollably. We have previously developed a yeast-based system to identify mTOR inhibitors by comparing the growth of yeast strains that are differentially sensitive to mTOR inhibitors; a wild type strain, a tor1Δ mutant, and an fpr1Δ mutant. However, the system is not able to identify a few known ATP competitive inhibitors that have been shown to inhibit mTOR in human cells. This could be due to dissimilarities between yeast and human mTOR protein kinase domains. To address this issue, we are developing a humanized strain of yeast that should allow for identification of additional mTOR inhibitors that are effective in human cells. I am developing a novel hybrid gene containing the human mTOR kinase domain fused with the N-terminus of the yeast TOR2 gene. This new humanized strain will be utilized in our yeast-based assay with the goal of first detecting mTOR inhibitors known to be effective in human cells but unable to inhibit yeast mTOR. Successful completion of this goal will facilitate high-throughput screening of novel compounds that may have mTOR inhibitory and cancer fighting effects.

The nucleus is the information center of the cell, acting as a hub for DNA storage, regulation, and replication. Therefore, transport of molecules into and out of the nucleus is vital for proper biological functioning. This transport is tightly regulated via the nuclear membrane, and a collection of proteins called nuclear pore proteins that interact with molecular signals. These signals allow molecules that cannot passively diffuse through the nuclear membrane (typically greater than 60 kD) to be shuttled into or out of the nucleus via a variety of pathways. Like all biological pathways, this process can be disrupted and lead to phenotypic abnormalities. Our lab identified two siblings with biallelic variants in NUP188, a known nuclear pore protein; we identified four additional cases in three families through collaborators. Clinical features include brain abnormalities with thin corpus callosum, progressive microcephaly, severely delayed myelination; congenital cataracts; mild dysmorphic features; and hypoventilation leading to death in infancy. In order to better understand our patients’ phenotype, we are investigating nuclear import pathways as a potential mechanism of disease. Using green fluorescent protein (GFP), we can directly visualize protein localization in living cells, without the use of additional stains such as immunohistochemistry. Based on size restriction of the nuclear pore, we used a vector construct with three repeats of GFP and our nuclear localization signal (NLS). Specifically, we are investigating four main NLS pathways: Importin α+β (SV40 NLS), Kap β2 (hnRNP NLS), Importin β (CREB NLS), and no NLS. We have been able to successfully create a viral vector for each NLS. Next steps include optimizing expression in patient cell lines. This approach will allow us to quantify and visualize discrepancies between patient and control localization patterns, leading to better understanding of causes of patient phenotype and potential novel therapies.

Trigger-action platforms enable end-users to program their smart homes using simple conditional rules of the form: if condition then action. Although these rules are easy to program, subtleties in their interpretation can cause users to make errors that have consequences ranging from incorrect and undesired functionality to security and privacy violations. Based on prior work, we enumerate a set of nine error classes that users can make, and we empirically study the relationship between these classes and the interface design of eight commercially available trigger-action platforms. Particularly, we examine whether each interface prevents (e.g., via good design) or allows each class of error. Based on this analysis, we develop a framework to classify errors and extract insights that lay a foundation for the design of future trigger-action programming interfaces where certain classes of errors can be mitigated by technical means or by alerting the user to the possibility of an error. For instance, we identify that an analysis of a dataset of functionally-similar trigger-action rules could be used to predict whether certain types of error patterns are about to occur. We believe that this work is a first step towards trigger-action interface designs that significantly mitigate user error.

Augmented reality (AR) for the consumer market is gaining momentum and public attention. Besides smartphone platforms, early-stage head-mounted displays such as the Microsoft HoloLens are now publicly available. Many compelling uses of these AR technologies are multi-user: for instance, in-person collaborative tools, multiplayer gaming, and telepresence. Although multi-user AR technologies enable new forms of interaction, they also raise new security and privacy challenges, not only from untrusted applications but also from other users’ malicious or unthinking behavior. It is imperative that these challenges be addressed while the technology is still new and highly malleable. In this work, I explore emerging challenges in securing multi-user AR content sharing from user-to-user threats. I argue that supporting secure and private AR content sharing when users can augment each other’s reality requires careful consideration of AR’s tight integration with the physical world. I systematize design goals for security and functionality that an AR content sharing module should support, and I design and prototype an application-level module for the HoloLens that meets these goals. By evaluating my module against representative application case studies, I show that it meets desired security and functionality goals flexibly across a range of use cases. I further demonstrate that applications’ content sharing needs can be achieved in relatively few lines of code and with low performance overhead. I am currently converting my research prototype into an open-source toolkit so that developers can address these challenges in practice. This work opens up directions for future research on supporting developers in effectively addressing these issues in practice, including making recommendations on how these underlying paradigms should manifest in user interface design. By building foundations for secure multi-user AR content sharing, my work takes steps toward allowing AR to securely reach its full potential.

We introduce Project Sidewalk, a new web-based tool that enables online crowdworkers to remotely label pedestrian-related accessibility problems by virtually walking through city streets in Google Street View. To train, engage, and sustain users, we apply basic game design principles such as interactive onboarding, mission-based tasks, and progress dashboards. In an 18-month deployment study, 797 online users contributed 205,385 labels and audited 2,941 miles of Washington DC streets. We compare behavioral and labeling quality differences between paid crowdworkers and volunteers, investigate the effects of label type, label severity, and majority vote on accuracy, and analyze common labeling errors. To complement these findings, we report on an interview study with three key stakeholder groups (N=14) soliciting reactions to our tool and methods. Our findings demonstrate the potential of virtually auditing urban accessibility and highlight tradeoffs between scalability and quality compared to traditional approaches.

 Developmental and epileptic encephalopathies (DEEs) are an early-onset form of epilepsy characterized by intractable seizures and severe cognitive and developmental impairment. While most genetic variants that cause DEE reside in the coding regions of genes, splice-site variants can also be pathogenic. Splice-site variants are changes in the DNA close to, or on, the exon-intron boundary, which can cause aberrant splicing, resulting in exon exclusion or intron inclusion within spliced mRNA, generating a protein that is non-functional, partially functional, or aberrantly expressed. Aberrant splicing can have pathogenic consequences, but predicting which variants near splice-sites will have an effect on splicing is difficult. I am studying three potential splice-site variants in three genes associated with DEE: SYNGAP1, SCN1B, and WWOX. I used RNA extracted from fibroblasts from three DEE patients, each with one of these variants, to confirm whether the splice-site variants cause aberrant splicing and what the predicted consequences of this aberrant splicing is on the protein. I have been able to discover the effects of the variants on splicing in WWOX and SYNGAP1. In SYNGAP1, a synonymous variant at the exon-intron junction caused an exon 4 deletion, resulting in a severely truncated protein (SYNGAP1:p.Glu120Alafs*20). In WWOX, a duplication which included exon 5 resulted in a transcript with the inclusion of two copies of exon 5, leading to a frameshift mutation and predicted truncated protein (WWOX:p.His173Glyfs*13). We are still investigating the effects of the intronic variant in SCN1B, which appears to decrease expression of the gene. We are using nonsense-mediated decay inhibitors in order to better understand the mechanism through which this decreased expression occurs. This research could potentially improve the care of these patients by providing genetic evidence of the causes of DEE, which can be the basis for advancing better treatments.

Developmental and Epileptic Encephalopathies (DEEs) are a group of severe epilepsy disorders in children and infants characterized by prominent EEG (electroencephalography) abnormalities that disrupt brain function leading to cognitive decline. Identifying genetic causes of DEE is a key step to help researchers develop and personalize medical treatments for affected patients. Approximately 5% of DEE cases are caused by a copy number variation (CNV), where a region of DNA involving a disease gene has been duplicated or deleted. Historically, this type of mutation has been difficult to detect using sequence data. To address this, I have written a multi-step algorithm that analyzes smMIP (single molecule molecular inversion probe) targeted DNA resequencing data for known DEE genes to identify CNVs in patients’ DNA that are potentially disease causing. I have run this algorithm on the large collection of smMIP data for 1158 DEE patients available in the Mefford Lab and identified several potential CNVs. Among these, three CNVs ranging in size from 250,000-2,790,000 base pairs, each involving a DEE gene - GNB1, GRIA2, and UHRF1BP1L - were validated by a second method, array CGH, the current gold standard for CNV validation. To date, the validation rate of high-confidence CNV candidates is 50% or higher. Currently I am expanding the algorithm’s functionality to include the ability to selectively search for single-exon CNVs, which are as small as 500 base pairs, are more challenging to detect, have largely been missed by all CNV detection methods, but could still be pathogenic. To do this, I am leveraging the power of intersecting duplicate smMIP datasets to improve the sensitivity of single-exon CNV detection. As any disruption of a pathogenic DEE gene could be disease causing, inclusion of these smaller CNVs will increase our ability to solve DEE cases and improve patient care.

Proteins are essential to life, but many structural methods fail to capture the dynamic nature of proteins. This means researchers are left with an incomplete view of how protein function and structure relate. The Stoll lab uses electron paramagnetic resonance (EPR) to study the dynamic structure of proteins. The project I am working on is investigating the way in which the measurement conditions in EPR affect the determined protein structure. We use maltose binding protein (MBP) as a model system, since its structure has been previously well-characterized. My primary role has been to create new mutants for site-directed spin labeling, in which a radical spin label is attached to the protein. This radical is measured by placing the sample in a magnetic field and results in a probability distribution of distances. Common spin labels used in EPR, however, have many rotatable bonds, andd can cause uncertainty in the extracted distance distribution. Our project is investigating the contribution of spin labels to the EPR experiment. I use polymerase chain reaction to create new mutants of MBP by swapping a native residue with a cysteine residue in the mutants. Each mutant has one or two amino acids replaced with a cysteine. After mutating the DNA, I then transform the mutant DNA into wild type cells to grow the mutant protein and purify the protein. The spin label forms a disulfide bond with the cysteine residue in the mutant, providing an unpaired electron for measurement. By using various commonly used spin labels on many different site pairs in MBP, we hope to develop a model in which the contribution of spin labels to the probability distribution of distances is accounted for. This will ensure more accurate results in determining protein structure and will aid in structural characterization of many proteins.

Human pathogenic viruses are responsible for nearly all recent pandemic diseases. We set out to search for viral protein sequences that could be important for tissue tropism. To achieve this goal, human pathogenic viruses were classified according to the tissue they infect (pulmonary, gastrointestinal, etc.) — irrespective of whether they were enveloped or non-enveloped RNA or DNA viruses. Next, we developed a customized amino acid sequence alignment program to speed up protein-sequence comparisons and alignments in each viral category. We identified the conserved seven amino acid motif, VAIVLGG, in both Old World and New World alphaviruses. Our further analysis localized the VAIVLGG consensus sequence on the adherence spikes of the chikungunya virus (CHIKV), a well-known mosquito-borne arthrogenic member of the Old World alphaviruses which caused a recent chikungunya fever outbreak in Florida. Our further search revealed that this sequence is located within the viral region involved in its binding to the newly-discovered human CHIKV receptor. In light of the fact that several ongoing clinical trials are aimed at developing vaccines against CHIKV, it is tempting to entertain the idea that our identified VAIVLGG consensus sequence might potentially be used to serve as a single-antigen for producing a pan-vaccine effective not only against CHIKV but also the following alphaviruses: Onyong-nyong, Semiliki Forest, Ross River, Mayaro, VEEV, WEEV, EEEV, and Sindbis.

The application of quantum dots (QDs) is increasing in optical manufacture (solar cells), biological and chemical devices (cancer research). Exposure to QDs can potentially lead to a variety of adverse health effects especially for children and pregnant women. The goal of this study is to determine the toxicity of CdSe/ZnS QDs on brain development of both sexes using in vitro techniques. To determine sex-specific response, we used human neural progenitor cells (hNPC) lines derived from male (NSC-H14) and female (hNP1). An in-vitro model was established using an adverse outcome pathway (AOP) framework. We plated cells in proliferation or differentiation media for treatment to assess the morphology and biochemistry response in cells. Two QDs, differing in their surface chemical properties: carboxyl functional group – ITK and polyethylene glycol (PEG) without reactive functional group (Qtracker) were assessed. Cadmium chloride (Cd) was also tested to determine whether the toxicity of QDs is associated with ion release. The NSC-H14 and hNP1 cells were exposed to QDs of concentration from 0, 2.5, 5, 10, 20 and 40 nM on days in vitro (DIV) 0. After 24 hours, we evaluated the number of cells remaining (cell viability) with an LDH assay at each dose treatment. The results showed that exposures to ITK QDs demonstrated significant dose-dependent decreases in viability of both cell lines during the proliferative stage. Male (NSC-H14) cells were more responsive than female (hNP1) cells to the cytotoxicity of ITK. We did not observe significant dose response for Qtracker and Cd at the same dose range as ITK, either in proliferation nor differentiation stages of both male and female cell lines. Our results indicate that the coating on quantum dots may play a significant role in the exposure and toxicity of the cells, suggesting potential strategies to reduce the adverse health effects of quantum dots.

Drug addiction is a neuropsychiatric disease characterized by compulsive and uncontrolled drug use. Rodent self-administration models can represent certain aspects of substance abuse in humans. Studies have shown drug use and drug-associated cues increase dopamine transmission. Data from the Paul Phillip’s Lab demonstrated rats that escalated in their cocaine intake had a decrement in dopamine release to cues in the nucleus accumbens. Administration of Levodopa (L-DOPA), the molecular precursor to dopamine, decreased cocaine consumption to pre-escalated levels. However, we have not yet confirmed whether the impact of drug-associated stimuli and its dopamine-mediated aspects can be generalized to opioid use. Thus, the current study investigates if increased dopaminergic signaling via L-DOPA decreases consumption of fentanyl, a highly potent synthetic opioid. We tested L-DOPA’s effect in two separate behavioral assays. The first assay is a two-bottle choice paradigm in which the animal is given 3-hour access to liquid fentanyl (50μg/mL) and water. Additionally, animals were trained to self-administer fentanyl, in which rats were required to nose poke for liquid drug delivery. Preliminary data shows intraperitoneal injection of L-DOPA significantly decreases overall fentanyl consumption in both two-bottle choice (p<0.05) and in the instrumental task (p<0.05). These data imply that dopamine release is regulating opioid consumption. A second aim of the current work is to characterize drug-taking patterns in animals self-administering fentanyl orally. Permitting animals to extended access to drugs of abuse is known to induce escalation of drug intake. Utilizing this paradigm we provide six hours of liquid fentanyl access and examine intake patterns of individual animals across sessions. Future studies will utilize electrochemical detection techniques to examine subsecond changes in dopaminergic signaling during oral self-administration. Overall, this work provides evidence that dopaminergic signaling regulates fentanyl consumption and treatment with L-DOPA can stabilize and reduce drug intake.

The University of Washington (UW) has a rich history around diversification and over the past 50 years anti-affirmative educational policies have reconfigured what “achieving diversity” looks like beyond admission statistics. Effective support is critical for the underrepresented minority (URM) student who gets into the UW and faces many disadvantages that make it difficult to succeed. The UW Educational Opportunity Program (EOP) Scholars Academy was created in 1968 to facilitate the metamorphosis (transformation) of low-income, first-generation URM students into independent and successful scholars. However, what is not publicly known is why the EOP Scholars Academy support program is effective and in what ways. This study explores how the EOP’s process of curating the student metamorphosis experience impacts 1) students’ academic outcomes and 2) their sense of belonging. The chosen field of perspective in this study is Organizational Communication (OC), looking at the interaction between parts of an organization (UW’s EOP and students) and the resulting behavior as seen through student actions. Some OC concepts used in exploring students’ responses to EOP affiliation include performance, social support, motivation, sense-making, diversity, and identity. Pre-existing data of two EOP-affiliated student-groups (~165 in EOP-1 and ~165 in EOP-3) include longitudinal grade point average, retention, major acceptance, and campus resource engagement metrics over the 2015-2016 school year. The data was statistically analyzed and compared across the two EOP-affiliated student groups, where EOP-3 consists of conditionally admitted Scholars Academy students and EOP-1 consists of non-conditionally admitted students. It is hoped these findings will assist in informing improved diversification policies, program changes, and future research on URM support programs within similar public selective universities.

Establish-Maintain-Restore (EMR) is a professional development training for teachers to strengthen their relationships with their students. Previous studies have shown that the strategies presented in the training have significantly improved academically engaged time and reduced disruptive behavior among elementary and middle school students. The proposed study will examine 9th grade high school student perceptions of the appropriateness and effectiveness of the EMR strategies to improve student-teacher relationships within the school context. Additionally, this study will analyze whether there is a significant difference in these perceptions between the genders of students. It is predicted that male students will tend to perceive the EMR strategies as less effective and appropriate in improving student-teacher relationships compared to their female peers. A focus group was held to present the EMR strategies to 9th grade students at a racially/ethnically diverse high school in the Pacific Northwest. After the strategies were presented, students were asked to provide ratings and comments regarding the appropriateness and effectiveness of each individual strategy. The students were asked about the following items for each of the EMR strategies: appropriateness for school context, appropriateness for both students and teachers, and effectiveness at improving relationships with high school students. Findings from this study will offer insight for improving student-teacher relationships with consideration for the students’ genders. Research has shown that strong student-teacher relationships can serve as a protective factor against high school dropout, and this study may help provide information about culturally responsive strategies to reduce the dropout rates among students of color and male students.

With the rise of social media numerous nationally publicized incidents of large groups of people harassing a private party over the internet have taken place. A review of current research points to several possible causes. One body of research suggests certain patterns in neural activity which could be encouraging individuals to harass total strangers online - a phenomena which may be partially to blame. These patterns may be anthropological artifacts evolved to protect humans in primitive tribal groups which provide neurological rewards for actors who punish detrimental behavior in bad actors. These reward structures are now manifesting in the online environment due to its unique low-risk nearly anonymous nature and/or lack of tangible repercussions that would normally inhibit this behavior. Other researchers suggest these attacks may be a form of virtue signaling to let peers know the harasser is not like the perceived bad actor. (e.g. harassing a perceived racist signals to others that one is not racist). The issue is so new there is no strong scientific agreement in the psychological community as to what is really taking place, or in some cases even what terminology applies. Research in this topic may lead to better understanding of human machine interaction, and cyber-psychology.

Polymorphisms in the gene, FKBP5, and its resulting protein, FKBP51, are associated with stress-related disorders. Although FKBP51 inhibitors may have antidepressant-like effects, the relevant brain regions mediating this effect are still unknown. We found that FKBP51 expression is elevated in serotonin neurons of the mouse dorsal raphe nucleus (DRN) after stress, so we tested whether FKBP51 inhibition in the DRN by the novel FKBP51 antagonist, SAFit2, has antidepressant-like effects. First, we implanted guide cannulas into the DRN of wildtype mice stereotaxically, then we habituated the mice to 2.5% sucrose-containing bottles in their home cages overnight. On the following two days, the mice were stressed through repeated forced swims after receiving either SAFit2 (n=8) or a vehicle (n=7) to the DRN via the cannulas, prior to each swim session. That evening, the mice underwent a sucrose preference test to assess motivation by quantifying sucrose versus water preference using lickometers. On the next day, the mice were tested in a three-chambered social interaction test, where one chamber contained a wired cup enclosing another mouse of the same sex and the other chamber had an empty wired cup. Our results show that the SAFit2 and vehicle mice had the same immobility time during the forced swim stress, signifying that SAFit2 did not interfere with our immediate stressor. The SAFit2 mice demonstrated an increased preference for sucrose after stress compared to the vehicle mice, indicating greater motivation to consume a pleasurable liquid. However, there was no significant difference in the time spent interacting with the same sex during the social interaction test. This suggests that SAFit2 may have blocked stress-induced anhedonia by inhibiting FKBP51 activity in serotonergic neurons, as measured by the sucrose preference test. Further studies of FKBP51 inhibition in the DRN can lead to potential therapeutic treatments of neuropsychiatric disorders.

Rats produce ultrasonic vocalizations (USVs) in a range from 20-kHz to 95-kHz that vary in frequency and shape across social and motivational contexts and can correspond to the affective state of the animal. To assess these USVs accurately and efficiently, our lab created DeepSqueak, a novel machine learning software package that expedites the detection and analysis of rat USVs by using neural networks to differentiate them from noise. DeepSqueak also allows for automatic and unbiased classification of USVs into discrete categories using call parameters such as shape, frequency and duration. Prior to this unbiased categorization method, identified 14 subjective categories in 50-kHz rat vocalizations that could be manually identified by a trained experimenter. These categories have received some limited study, but the excessive labor and time needed for manual classification restricted broad adoption. We aim to use neural networks to quickly and automatically classify USVs into these categories to promote broad adoption and better our understanding of the relationship between USVs and behavior. The process of training our neural network to differentiate between vocalizations was approached in two ways. Audio files were converted to sonograms through DeepSqueak and manually labeled. Thousands of these labeled calls were then inputted as training data for the neural network. This method allowed the network to learn using a large set of labeled vocalization data. The second method is based around the manual selection of an optimal call for each subtype using DeepSqueak's "call clusters" function; the neural network was then trained around how closely vocalizations matched the optimal calls. We now plan to compare DeepSqueak's automated calls and clustering to manual scoring in order to develop the best possible system that reliably categorizes USVs, thus allowing for more specific analyses of USV categories and behavior.

Field research is an important way to understand complex ecosystems and the roles of individual wildlife species within these systems. As climate change and other human factors continue to affect our global patterns, studies must be conducted to assess the health of current populations and predict future trends. Many studies involve direct or indirect contact with the focal animals, which may impact the fitness of study animals despite efforts of researchers to minimize cost. Long-tailed Jaegers (Stercorarius longicaudus) in Denali National Park, Alaska were captured and fitted with satellite-linked GPS trackers to study migratory routes. The birds were tagged by other researchers while on their summer nesting grounds caring for eggs or recently hatched chicks. This disturbance has potential to affect the nesting success of the jaeger which is thought to already be in decline in the area. A long-term study of the nesting success of jaegers and other shore birds in DNP is being conducted to assess the suggested decline in these species. What impact did radio tagging nesting jaegers have on nesting behavior and success? I collected behavioral data in the field during a four-week period in July of 2018. With a UW grad student, I directly observed 2 breeding pairs of jaegers that had been tagged and 3 that had not. We observed the birds from over 150 meters away, recording parental feedings, chick protection, and vigilance. Preliminary analysis suggests that the two subsets of jaeger behaved differently during chick fledging. This could have impacted the way chicks were raised and the nesting success rate of tagged parents. Further analysis into the feeding rates and protective behavior is underway to determine the complete impact of radio tags on the population.

Secondary metabolite chemicals are specialized chemicals produced by plants that serve specific roles in plant survival beyond aiding in growth or development. Sometimes, the presence of these chemicals negatively impacts surrounding species, a phenomenon known as allelopathy; an example of this is the inhibition of germination of neighboring species. One common non-native species that is known to have high concentrations of leaf secondary metabolite chemicals is Plantago lanceolata (ribwort plantain). Focusing specifically on prairies ecosystem implications, this experiment aims to test the allelopathic effects of Plantago leaf secondary chemicals on the germination of native prairie species. The predicted outcome of this experiment was that increased concentrations of Plantago extract would lead to decreases in germination quantity. To accomplish this, numerous extraction concentrations (including a controlled no-extract treatment) of Plantago leaf chemicals was applied to several prairie species. These species were additionally tested in the presence of high concentrations of yarrow and lettuce extracts; yarrow is another species that contains high concentrations of secondary chemicals, while lettuce leaf material lacks substantial secondary metabolites. Prairie seeds germinated in the presence of secondary chemical extracts include yarrow, Oregon sunshine, Roemer's Fescue, Blue wildrye, and Plantago. 1,400 seeds per species were placed in petri dishes and germinated in either spring or summer growth chambers based on each species' germination requirement. Germination data were analyzed to determine the significance of germination inhibition by each leaf extract. Because Plantago is a non-native and potentially invasive species, it is important to understand the potential for native ecosystem disruption. Additionally, since yarrow and Plantago seeds were germinated in the presence of extracts from their own species, we could determine whether extracts have stronger effects on disparate species than on the species that the extract is derived from. 

Understanding how adolescents explain gratitude in peer interactions uncovers how they view their identities and social worlds during a time when they are transitioning to the responsibilities of adulthood. Earlier studies define “gratitude” as a state of appreciation, and have shown that adolescent feelings of gratitude correlate with increased well-being, academic performance, and prosocial behavior. Furthermore, our previous findings suggest adolescents have differing rationale for why they feel grateful in situations when they either enact or receive calming, angering, avenging, and reconciling intervention from their peers. The goal of this study was to ask: 1) How do adolescents explain feelings of gratitude they feel following intervention in victimization events? 2) How do rationales for feelings of gratitude vary between actor and recipient of a peer intervention? 3) How does gratitude differ when adolescents calm, amplify, avenge, or reconcile a previously victimized peer? We qualitatively coded explanations provided by 265 adolescents for emotions in each condition. Our findings showed actors felt more gratitude when calming their peers, and recipients felt more gratitude after reconciliation. Peer gratitude was predicted to be more strongly linked to a desire for security when the subject was the recipient (e.g. “I was grateful she looked out for me”), and more strongly linked to a desire to display competence when the subject was the actor (e.g. “I was grateful she took my advice”). We carried out quantitative analyses using repeated measures analysis of variance and Epistemic Network Analysis. The findings from this study contribute to understanding peer relationships, which could help educators navigate student actions that de-escalate conflicts and promote well-being in student social environments.

Computer vision models are used to help analyze biomedical images for diagnosis and treatment through looking for differences between images by a comparison to a template image. For instance, optical coherence tomography (OCT) is used to diagnose and treat retinal issues. When looking at the brain, injury, cellular uptake and characteristic features vary across regions, therefore images are often segmented into established brain regions to determine how the brain is impacted in a particular study. Current models fail to work in segmenting brain regions because each brain has variation in local microstructure, making it difficult to compare one brain to another. Furthermore, when brains are sliced, the exact location within the brain can be difficult to pinpoint, particularly in regard to depth, because the regions vary slice to slice. Therefore, my research addresses the increasing need for a method of analysis to align and compare images from brain regions across slices from a single brain, and from brain to brain. Using scikit-image analysis tools, I extracted information from cell images and videos of nanoparticles obtained in brain slices and determined trends within various regions. My program extracted cell density, shape, and death, then analyzed the uptake of nanoparticles to determine where a small segment of an image is most likely located within the brain. Iterating over the entire image generated a rough map of the regions within the brain which is refined using mapping descriptions detailed in literature. This research resulted in a systematic program that uses image analysis tools to extract features of defined brain regions. This program allows for quick, accurate and consistent analysis of regional differences of cellular features, nanoparticle distribution, toxicity, and other important measures.

The goal of this project was to determine if mitochondrial biogenesis in zebrafish cone photoreceptors is circadian and/or regulated by light. Photoreceptors use more energy in darkness compared to light, and at night the number of mitochondria in zebrafish cones increases. We hypothesized that mitochondrial biogenesis would correlate with increased energy needs and increased mitochondrial number.  Zebrafish retinas from light/dark and dark-only cohorts were collected over a 24-hour cycle. Retinas were fixed and sectioned at 20 µm for immunohistochemistry. Sections were incubated with primary antibodies against mitochondrial biogenesis genes and cytochrome oxidase and imaged with confocal microscopy. Length measurements were taken from the center of single cone mitochondrial clusters. Retinas were also analyzed by Western blotting to assess cone mitochondrial protein content. 21 genes involved in mitochondrial biogenesis were analyzed via qPCR, in addition to ratios of mitochondrial DNA (mtDNA) to nuclear DNA (nDNA). Experiments were conducted in triplicate with three biological replicates and the ΔΔCt method was used to determine relative expression.  Immunohistochemistry revealed that cone mitochondrial clusters elongate 30% following dark onset. Western blot analysis is ongoing. mRNA transcripts for two genes involved with mitochondrial biogenesis, PolG1 and TFAM, increased roughly 6-fold and 3-fold respectively in the hours leading up to dark onset; transcripts for the mitochondrial fusion factor, Mfn2, increased 3-fold just prior to light onset. Cone mitochondrial clusters enlarge at night, and this is preceded by upregulation of mitochondrial biogenesis genes. Lastly, mitochondrial fusion prior to light onset may be followed by a decrease in mtDNA number. These effects occurred independently of light exposure. Overall, these results highlight a possible mechanism in photoreceptors to increase energy production in the dark while following the circadian clock.

My research has worked to develop an automated system that utilizes techniques that will modernize pathology and reduce diagnosis times from days to hours. The current method of diagnosing cancer (histopathology) requires a tissue biopsy that is fixed with formalin for 6-72 hours, dehydrated and embedded with wax, then manually sectioned, mounted on slides, and stained for imaging. This manual process is extremely time and labor-intensive and is the reason diagnoses can take up to ten days. The preferred, and least invasive, way to obtain tissue from a patient is the core needle biopsy (CNB), which is taken by inserting a needle into a region where cancer is suspected to exist, and removing a cylindrical section of tissue. Although CNBs are rapidly becoming the standard-of-care, their small diameters make it difficult to prepare and section the tissue for use in conventional histopathology. My research project over the past year has been to develop CoreView, a device designed to handle CNBs, automatically staining and imaging their entire surface for more complete images used to diagnose cancer. We use deep ultraviolet light to image the outer 2-3 cell layers of fluorescently stained tissue in a lab-built microscope to produce sharp images that can be equivalent to standard histology images from thin sections. I used LabVIEW to develop the rotational and imaging control to image the tissue at different focal points so the biopsy surface stays in focus during rotation. Along with designing necessary components of our system, I have worked on improving processing techniques for staining fixed porcine liver to produce clearer images with high contrast between the nuclei and the cytoplasm/cell boundaries. Our collaborating pathologist has confirmed that these images are at diagnostic quality, proving that CoreView and my improved techniques for processing tissue have the opportunity to revolutionize current histopathology.

Atomic Layer Deposition (ALD) is a process whereby thin films of a material, ranging from dielectric materials to metals, are deposited onto a substrate. ALD reactions operate using two vapor phase chemical precursors that react with the substrate material sequentially one at a time, slowly forming the thin film. Because of the sequential nature of ALD, the process is self-limiting and offers exceptional control of thin film thicknesses, film composition, and high conformity on high aspect ratio features, such as trenches and sidewalls, making ALD an extremely useful process for the fabrication of semiconductor devices. The purpose of this project was to develop processes and refine process parameters for thin film deposition using an industry grade ALD machine. Thin films were deposited onto silicon substrates with etched features. The films were then examined and characterized using ellipsometry and sidewall conformity was measured using a scanning electron microscope.  This data was used to refine processes and parameters that were then employed by research staff and industry users in the fabrication of semicondctor devices.  Overall, this data can be employed by the semiconductor industry to better understand this process and utilize it to manufactor silicon devies with  greater uniformity and efficiency.

Research has shown that positive outcome expectancy (i.e., anticipated positive consequences as a result of engaging in a behavior) and positive affective responses to exercise play an important role in predicting exercise behavior as well as future exercise intentions. Unlike most research in which the valence (i.e., positive - negative) of outcome expectancy and affective responses are typically assessed through survey items whose valence is predetermined, the current study used a spontaneous word association test (WAT) to examine the subjective meaning of exercise-related outcome expectancy and mood before exercise, and how they are related to exercise intentions and behaviors. One-hundred and eleven undergraduate and graduate students (74 females; 64 undergraduate students) performed an exercise-related WAT in which they were asked to write down the first word or a short phrase that comes to mind when they thought of (a) things that might happen from exercising and (b) their mood right before exercising. Subsequently, they were instructed to rate their subjective valence (i.e., positive-negative) to each of their responses to the WAT. They also completed a series of online self-report surveys that included assessments of exercise intentions and past exercise behavior. Path analyses will be conducted to test our hypotheses that the subjective valence of their mood right before exercising is expected to be directly associated with exercise behavior whereas the subjective valence of outcome expectancy is expected to be indirectly associated with exercise behavior through exercise intentions. This study examines the potential value and usefulness of a spontaneous word association procedure to more accurately measure affective evaluations of an individual’s feelings and thoughts toward exercise behavior.

The damascene process is an additive manufacturing technique commonly used in the nanofabrication industry to produce semiconductor devices. This process utilizes deposition and patterning of successive layers to produce interconnected copper patterns separated by interlayer dielectric. The goal of this project was to implement the damascene process to develop and refine methods at the Washington Nanofabrication Facility (WNF) for manufacturing multi-layer devices. For our purposes, we constructed an integrated passive device (IPD) that contains capacitors, resistors, and inductors. We utilized basic nanofabrication tools in our damascene process including deposition, photolithography, etching, electroplating, metrology, and polishing tools. In fabricating this method at the WNF, our main objective was to produce a highly repeatable device with structural integrity. The main challenges accompanied with this involved generating a successful etch on all three layers of the IPD and optimizing polishing conditions. Cross sections of the final product were analyzed in order to demonstrate that the layout expected from the process was achieved. The procedure we developed can be applied to future multi-layer damascene processes at the WNF. Multi-layer devices are significant in the semiconductor industry as they allow for high packing density and an increased variety of circuit configurations in a compact device.

Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne New World alphavirus, causing encephalitic disease in mammals. Increased circulation of VEEV in the Americas underlines the need to characterize alphavirus replication and develop countermeasures. The VEEV genome is a single-stranded RNA of positive polarity (+ssRNA). MicroRNA (miRNA) are small, cell-specific non-coding RNAs that aid in post-transcriptional regulation of gene expression. Previous studies have demonstrated that host miRNA can affect viral replication and pathogenesis by directly binding to the viral genome. Recent work on host miRNA in related alphavirus Eastern equine encephalitis virus (EEEV) found miRNA binding sites in the EEEV 3’ non-translated region (NTR). Binding of the host miRNA enhanced pathogenesis. Prediction software miRDB identified potential miRNA binding sites in the 3’ end of VEEV genome, including one for miRNA hsa-miR-1268. In this study, the impact of miRNA interaction with its putative binding site on VEEV pathogenesis was investigated. We performed site-directed mutagenesis of VEEV strain TC-83 to engineer point mutations at the hsa-miR-1268 binding site in the 3’ end. We are currently testing the impact of these mutations on viral replication by analyzing growth kinetics of wild-type and mutant viruses in cell culture. We anticipate that a mutation disrupting the interaction between hsa-miR-1268 and the predictive binding site on the +ssRNA genome will result in the decreased ability to replicate the viral genome and subsequently infect the host. Understanding the impact of the interaction may lead to novel mechanisms to prevent RNA virus replication.

Geothermal flux, the amount of heat from the Earth’s interior that reaches the Earth’s surface, is an important boundary value used when modeling ice sheets in Antarctica and estimating future sea level rise. However, geothermal flux is difficult to measure directly. This research project used a numerical ice and heat flow model to estimate the upper bound for geothermal flux under ice domes in Antarctica. We applied this model to ice domes with identifiable Raymond arches, structures in the internal stratigraphy which form only when the ice is frozen to the bed. We estimated the geothermal flux at which an ice dome’s modeled basal temperature reaches the melting point, thus setting an upper bound, using site-specific values for the accumulation rate, surface temperature, and ice thickness. Where measured basal temperatures are known, we made more precise estimates of geothermal flux. Uncertainty values for the modeled flux values were derived by testing the uncertainty of each input value. Model estimates were compared with Martos et al. (2017) and An et al. (2015) geothermal flux estimates derived from remotely sensed data. Comparisons show that in regions such as the Siple Coast, estimates disagree significantly, while they mostly agree in the Antarctic Peninsula. The results of this project set an upper limit on geothermal flux values that can be used to support past and future geothermal flux estimates at these locations.

Mosquitoes primarily navigate using their olfactory system, and can use this system to form “memories” that influence their choice in hosts. When a mosquito encounters an odor, information is sent through the antennal lobes in the brain to the mushroom bodies, which are structures responsible for learning and memory consolidation. This odor-learning pathway is mediated by neurotransmitters like dopamine and serotonin. Recent research has shown that the mosquito Culex quinquefasciatus has extremely low levels of dopamine in the antennal lobes compared to other species, and is unable to learn to avoid odors associated with a negative response. This led us to predict that dopamine is essential for aversive learning in mosquitoes. We hypothesized that Cx. quinquefasciatus differed from other mosquitoes in learning ability because they were previously tested in the light and they are the most nocturnal of the originally tested species. To test this hypothesis, we conditioned the mosquitoes in the absence of light in an aversive learning paradigm to measure how frequently they chose to avoid the conditioned odor. An inability to learn regardless of light condition would indicate that the role of dopamine as a neuromodulator in the antennal lobes evolved partly to allow diurnal mosquitoes to avoid defensive hosts. Next, specific neurotransmitters in the antennal lobe were mapped using confocal microscopy, revealing their concentrations which may explain behavioral differences from other mosquitoes. Most mosquito species show some plasticity in host selection, which can lead to the transmission of animal diseases, like West Nile Virus, to humans. Mosquitoes are the world’s deadliest disease vector, killing over 700,000 people globally each year, so understanding how and why this adaptation occurs can help us understand the framework that underlies the spread of mosquito borne diseases and bring us one step closer to solving this global issue.

Methanol is a common pollutant in freshwater ecosystems due to its widespread use in industrial operations, fuel, antifreeze, paints, and insecticides, and being a result of the burning of garbage. As a bioindicator species, Daphnia magna health indicates changes in aquatic ecosystem health. They are an important part of the food web, eating algae, and as a food source to insects and fish. No previous studies have examined the effects of the pollutant methanol on Daphnia heart function and mortality. This experiment examined the effects of varying methanol concentrations on heart function and mortality of Daphnia magna. It was hypothesized that methanol significantly affects the heart and mortality rate of Daphnia. Fifteen experimental biospheres were used in each trial, with three jars for each of the five concentrations. The biospheres were filled with deionized water and methanol in concentrations of 0 ppm (control), 822.6 ppm, 1644.5 ppm, 3289.0 ppm, 7119 ppm. In a second trial, the concentrations were 0 ppm, 822.6 ppm, 1644.5 ppm, 205.7 ppm, and 411.3 ppm. Heart and mortality rates were observed and recorded for each trial over 4-8 days. For each jar, videos were recorded for 15 seconds each and heart rate was counted, and mortality counted every other day. Based on the survival and heart rate differences, it was concluded that as methanol concentrations increase, the heart rate of Daphnia varied but didn’t respond linearly to concentration levels. Additionally, higher concentrations of methanol negatively affect survivability, although the initial control groups had somewhat high death rates. This study highlights the negative impact of methanol pollution on Daphnia because a negative impact on Daphnia affects the whole freshwater ecosystem. Indeed, in Lake Washington, Daphnia represent a major source of nutrients for juvenile Sockeye Salmon, making Daphnia indispensable for their growth.

Astrocytes are a type of glial cells in the central nervous system, play a critical role in protecting neuronal signaling by regulating brain homeostasis, synaptic plasticity and transmission, and blood brain barrier functioning in central nervous system. Accumulating evidence has indicated that abnormal behaviors of astrocytic functions, including astrodegeneration and astrogliosis, are implicated as the primary factors contributing to a number of chronic neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). Kir4.1 is an inwardly rectifying K+ channel expressed on the projections of astrocytes, which serve important roles in the neuroprotective function of astrocytes, such as maintaining K+ homeostasis and regulating extracellular glutamate. Abnormal expression of Kir4.1 has been reported in certain neurodegenerative diseases, including Amyotrophic lateral sclerosis (ALS) and Huntington’s disease (HD), suggesting a vital role in the development of pathophysiology. However, the association between the molecular mechanism and expression of Kir4.1 and the underlying pathogenesis of AD and PD has been largely uninvestigated. In this study, we have had the critical opportunity to access human post-mortem brain tissue, provided by the University of Washington Alzheimer’s Disease Research Center, and conducted confocal microscopy studies. Through a quantitative immunofluorescense staining approach, we expect to demonstrate a distinct expression pattern of Kir4.1 in various brain regions of AD and PD post-mortem tissues when compared to control subjects. Determining the role this protein has in neurodegeneration may provide new insight into the development of therapeutic targets to ameliorate the progression of AD and PD.

Nanopore sequencing is a “third-generation” sequencing approach in which a constant electric voltage is applied across a nanoscale pore and the changes in the ionic current flow through the pore are measured as single molecules such as RNA or DNA pass through it. It is our goal to expand and adapt this sensing technology to enable single-molecule proteomics. Specifically, being able to characterize protein post-translational modifications at the single-molecule level is important for quantifying protein complexity and understanding how different protein mod-forms contribute to cellular processes such as differentiation and the progression of disease states like cancer. In this project, we modified a model protein to contain a protein kinase A phosphorylation motif with the purpose of demonstrating the ability to discriminate the modified protein from the unmodified with the Oxford Nanopore MinION, a high-throughput nanopore sequencing device. We hypothesize that the observed ionic current pattern will change upon phosphorylation and enable direct quantification of modified peptides. Ultimately, these analyses will inform us of the general ionic current signature that phosphorylated residues generate, which can then be added to our growing library of nanopore signal signatures that are informative of protein sequence and structure at the single-molecule level.

Cardiovascular disease (CVD) continues as the leading cause of death worldwide. The underlying cause of CVD is atherosclerosis, characterized by fatty plaques in the inner walls of the artery, and exacerbated by oxidative stress, inflammation and immune cells. The high-density lipoprotein (HDL)-associated enzyme paraoxonase-1 (PON1) plays a significant role in protecting against CVD. However, the mechanism of PON1’s protection is not well understood. Our laboratory and others have reported a progressive decrease of PON1 activity in several diseases. Our goal is to understand how PON1 prevents oxidative stress and its potential measurement as an early biomarker of risk of disease. Our hypothesis is that oxidative stress inhibits PON1 enzymatic activity, leading to progression of the atherosclerotic process in CVD. The objective of this research is to generate a mouse model to allow us to study the human enzyme PON1 in induced atherosclerosis in vivo.  Starting from two strains of knockout (KO) mice, we have generated the Pon1/apolipoprotein E (apoE) double KO mouse, known to be susceptible to atherosclerosis. We are now crossing this double KO mouse with Pon1 KO mice that express human PON1 (transgenic human PON1 mice, tgHuPON1). We collect ear punches for DNA extraction and blood from the saphenous vein for activity assays. We use polymerase chain reaction (PCR) genotyping methodology, which amplifies DNA, to identify mice that are KO for mouse Pon1 and apoE and that express human PON1. We run enzymatic assays to determine activity levels of the human PON1 in mice. Once we have created the tgHuPON1/apoE KO mouse, we will feed mice with an atherogenic diet, which will induce subclinical atherosclerosis. This knowledge will contribute to understanding the relationship between PON1 and CVD, and will likely generate a useful biomarker for risk of disease.      

The focus of this research is on Spanish heritage language (HL) and second language (L2) learners. An HL learner is a student who comes from a house where Spanish is spoken, but still; needs Spanish classes to master certain aspects of his/her first language. Sometimes English is also spoken at home: e.g., one parent speaks Spanish and the other English, or the student speaks Spanish with his/her parents but English with his/her siblings. On the other hand, an L2 learner is a student who is learning Spanish in a classroom setting. His/her first language may be English or any language other than Spanish. Between these two groups of students, there are important differences when it comes to learning Spanish, for example, L2 students are more knowledgeable about Spanish grammar rules and academic vocabulary. On the other hand, HL students have more fluency and much more knowledge about the culture. The focus of this research is on how the interaction between an HL and an L2 learner in a classroom impacts learning for both students. My role in this research is to transcribe the audio-recorded conversations between two L2 students and to compare these conversations with those between the same L2 students and an HL learner. I will analyze how the students collaborate and how they work to find the solution to any challenge they face that is associated with vocabulary, grammar or orthography. I hypothesize that pairing an L2 and an HL student will generate more interaction since each student offers different sources of knowledge. Pairing an L2 student with an HL student creates a diversity of ideas that I expect to increase learning. This analysis will help us to better understand how to create a more efficient learning environment, for both HL and L2 students, within mixed classrooms.

Autism Spectrum Disroder (ASD) occurs in one in every 59 children, yet the causal mechanisms remain widely unknown. Research is advancing through genetic testing as well through speculation of external environmental influences. Recent stuides have examined in greater depth gene by environment interactions and have found an impact on severity symptoms of ASD. This research follows the two-hit model of gene by enviornment effects and investigates the link of auoimmune disorders, specifically thyroid disfunction, Likely Gene Disrupting (LGD) mutations to genes related to ASD, and the relation to IQ and regression. Behavioral and cognitive data are collected using clinician-administered questionnaires and assessments. Those who carry an LGD mutation with exposure to maternal thyroid dysfunction lean towards a trend that show more severe behavioral phenotypes than those without an LGD mutation. These results spotlight the importance of gene by environment contributions in addition to mechanisms involved in the disorder. These findings may help improve future treatment and intervention for those with ASD. 

Barcoding of physical objects with molecular tags holds an advantage over traditional paper or electronic barcodes in that they are discreet, durable, and difficult to falsify. Here, we developed a DNA tagging system that labels objects to verify their authenticity and trace their origin. We chose DNA as our tagging medium due to its information storage capacity and chemical stability, allowing us to generate a wide variety of unique barcode sequences that can be read by Oxford Nanopore’s MinION sequencing device. The MinION contains an array of thousands of nanopore sensors that are capable of sequencing single strands of DNA. The nanopore sequencing process creates distinct disruptions in the ionic current through the sensors that are indicative of the DNA sequence. However, the DNA basecalling software that processes the raw ionic current is computationally expensive, making it impractical when our goal is to quickly “scan” and identify a tagged sample. Because of this, we designed our barcode sequences to generate unique current patterns that are identified using a simple classification algorithm as opposed to arduous basecalling. So far, we have synthesized and classified a set of 96 barcodes that can be indiscriminately combined to create multi-bit tags. In a given tag, each bit is defined by the presence or absence of a particular barcode, and in practice, we have assembled and read up to 16-bits. We have also explored increasing bit capacity by independently varying barcode lengths, which adds another dimension to the barcode space. We also tested the durability of our barcodes by drying them onto filter paper and sequencing them 24 hours later, proving that our barcodes could survive in a dehydrated state. Future experiments will aim to lengthen this duration and expose the barcodes to different environments, in order to better simulate intended tagging conditions.

The North American Nanohertz Observatory for Gravitational Waves (NANOGrav) uses an array of galactic millisecond pulsars to search for low frequency gravitational waves. The stability of millisecond pulsars allows their pulse time of arrival (TOA) to be used as precise clocks. Gravitational waves will produce timing delays that are are correlated across pulsars. In order to detect such correlations in TOAs, we must also understand the noise processes in the pulsar signal. Noise model selection aims to produce custom noise descriptions for each pulsar. Using NANOGrav's search code enterprise a Markov Chain Monte Carlo (MCMC) algorithm is used to search for the most favored model. A hyper model framework is used to explore across a set of models, which have different red noise and dispersion measure (interstellar medium effect) processes. The posterior odds ratio is then represented by the relative amount of time the chain spends in a model. An iterative approach is taken, where one model selection analysis is used to inform the next set of models from which to choose. The resulting noise descriptions will aid in mitigating its effects within the pulsar signals, increasing chances of gravitational wave detection.

Insect pollination is crucial to agriculture and conservation, but little is known about the ecology and evolution of floral scent, which is one of the strategies that plants use to attract pollinators. Flowers that rely on insect pollinators have floral scent compositions that attract certain types of pollinators more than others. Oenothera pallida is a plant which is pollinated by both daytime and nighttime pollinators, so examining its floral volatiles gives us an idea of what attracts the different pollinators to this flower. My research examines how floral scent emissions from Oenothera palllida differ between the day and nighttime, and how these differences in floral scent emission affect the attractiveness of the flowers to different pollinators. I extracted the floral scent from Oenothera pallida that is grown in the lab. I used Porapak traps to sample volatiles from each plant for six-hour periods in the evening and in the morning, which allowed me to see the change in composition depending on the time of day. I analyzed the floral scent samples using gas chromatography - mass spectrometry (GCMS). Then I created artificial scent blends in mineral oil that reflected the scent compositions of daytime and nighttime floral scent emissions. I exposed the hawkmoths and honeybees to the different scent compositions in a wind tunnel and observed the different responses of the two species. Finally, I determined what proportion of the moths or bees were able to locate the scent source by counting the number of individuals that flew upwind and landed on the artificial flower. 

In the last decade, a large amount of studies have been done using virtual environment (VE) because of the increased control over the sensory stimuli used and the detailed observation of the associated behavioral and sometimes neuronal responses. In this study, we placed honeybee in a VE and exposed them to visual stimulus in closed-loop. We showed that honeybees are able to fixate the stimulus regardless of the level of feedback fed to the sensors(e.g., the gain between the animal motion and the stimulus motion on the VE). Our next step is to investigate how different neuromodulators such as the octopamine and dopamine, may be important for fixation and adaptation to the different level of sensor feedback. Octopamine (OA) is key in modulates physiological process in invertebrates including honeybees. Recent studies have identified OA neurons that are critical for visual behaviors and that increase their activity during active behavioral state. To identify the effects on octopamine and dopamine (DA) on honeybee’s ability to fixate, we are injecting bees with OA, DA or their respective antagonists in a visual processing brain area. Potential results of this study will impact the fields of neuroethology, providing insights on the modularity of neural processes and the feedback between sensory and motor pathways.

For many Somali refugees in Italy, the journey from Somalia to Italian land is fueled by an overwhelming desire to seek better opportunities in education, employment, health, and lifestyle. As a country previously known for its luxurious beach resorts and affectionately named “the nation of poets,” Somalia has since dramatically shifted to a land inflicted with ongoing violence, terror, and instability. In this research, we will be exposing how the legacy of Italian colonial power has led to numerous detrimental effects on both the people and the government in Somalia. Furthermore, we will be investigating the ongoing refugee crisis in Somalia, focusing specifically on political and colonial history. Using an ethnographic approach, our research project provides insight into the harsh realities that face Somali refugee immigrant populations in Italy. Over the course of six weeks in Rome, Italy, our team has engaged in qualitative research methods in which we collected personal testimonies from current Somali refugees living in Rome through observations, interviews, and daily interactions. The results of our research will uncover the role Italy has had on the ongoing humanitarian crisis affecting the Somali diaspora.

The interactions between pollinators and plants have a strong correlation to the fitness and reproductive success of both parties involved. These interactions are responsible for most of plant reproduction by seeds and they also drive evolutionary diversification of both plant and pollinator species. Wind turbulence plays an important role in navigation by smell, which is important for many pollinators while locating flowers. Climate change may alter wind patterns, which in turn may affect the ability of pollinators to locate flowers. The goal for this project was to determine the effect of wind on pollinator success. We determined the visitation rate of pollinators at Oenothera pallida flowers in the field by analyzing infrared camera videos recorded last summer at a field site in Grant County WA. Next we ran a multiple linear regression to determine the effects of wind speed, temperature, humidity, and ozone levels on floral visitation rates. Pollinators of Oenothera pallida include the hawkmoths Hyles lineata and Manduca sp., various bee species including Andrenids, Apids, Lassioglossum sp. and Megachilids, Bembix wasps, and various flies. Wind speed is the strongest variable that affects pollinator visitation at different times of day, which implies that changing wind patterns significantly impact plant-pollinator interactions.

Building upon our rat testicular o-culture system developed to improve evaluation of chemicals and identify their potential adverse health effects on humans, we have designed in vitro mouse system to expedite such assessments. Models of in vitro cell cultures are, however, limited in their approach typically using a monoculture of single cell types. Using a 3 dimensional organotypic approach can provide a framework for evaluating systematic interactions between cells with a goal to reduce the need for in vivo assessments. We utilized a novel organotypic, in vitro model of testicular development that mirrors the development shown by in vivo studies. We used isolated testicular tissue harvested from C57BL/6 male mice on post-natal day 9 and digested into a single cell suspension. Testicular co-cultures were maintained for up to 16 days in 24 well plates. Data collections occurred at days in vitro (DIV) 3, 7, and 16. These timepoints represent “windows of potential susceptibility” for testicular development. Plates were stained with antibodies providing markers corresponding to morphological features of specific cell type; six 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, SCP3 and c-kit, and proliferation with PCNA. We used an immunofluorescence dual staining technique with Scanning Laser Image Cytometery (iCys) to quantify the proportion of cell types and to determine changes in phenotypic distribution of the cell population. Our observations in vitro demonstrated concordance of changes in Sertoli cells, Leydig cells and Germ cells throughout testicular development with similar trends in vivo. Our observation of similarities in testicular development in our 3 D in vitro experiment and in vivo studies is important and supports the current trends in minimizing the need for in vivo studies for chemical toxicological.

I am studying the connection between the criminal justice system and public school education system in America. As our current system stands, students are being punished so severely through punishment and explosion that it leads to their lack of success in completing education which leads to their involvement in the criminal justice system. My research focuses on how black students are punished disproportionately greater than their white counterparts which directly correlates to the huge population of black people making up the population of prison cells in America. This is known as the school to prison pipeline, a cycle which limits a students ability to get out the system resulting them to be incarcerated. Through my research, I am looking at disciplinary methods in public school systems and how their ineffectiveness leads to more people of color, specifically black students to eventually be removed from the school system. As of today, many of these practices have led to the continuous erasure of black students from the education system by placing them in the prison system.

Microfluidics is a field that consists of the manipulation of fluids in microchannels and chambers for a variety of biomedical applications from drug screening to the study of cell biology. Currently, the majority of microfluidic devices are made from drug-absorbent materials and manufactured using processes that are expensive, labor-intensive and time-consuming. These constraints have limited the commercialization and dissemination of microfluidic technology into healthcare markets. Digital manufacturing is a computer-based manufacturing method which integrates digital designs, automated fabrication, and device testing in order to increase fabrication efficiency. Through recent advancements in digital manufacturing technologies like 3D printing and laser cutting, and the development of non-drug absorbent resins for 3D printing, the Folch lab has been inexpensively prototyping complex 3D microfluidic platforms capable of testing the effectiveness of personalized cancer therapies that utilize multiple drug exposures. Current methods for modeling cancer lack the ability to replicate the human microenvironment in which a tumor develops, and prevent high throughput analysis of the effects of therapeutics. This need to efficiently recapitulate physiologically relevant effects of disease progression have been addressed by patient-derived tumor organoids. Composed of patient-derived cancer cells cultured in vitro, tumor organoids are a promising method for accurately modeling cancer because they serve as a representative snapshot of the types of cancer cells seen within the patient. By performing tests on tumor organoids to observe the effect of different combinatorial therapies, personalized cancer treatment regimens can be developed to most effectively treat individual patients. Combining the advantages of digital manufacturing with tumor organoids, I have been able to 3D print a microfluidic device capable of trapping and treating organoids with different combinations of drugs through the use of biocompatible, non-drug absorbent resins. This device’s functionality and manufacturability demonstrates that digital manufacturing is vital for the implementation of microfluidics into healthcare industries.

In cystic fibrosis (CF), a genetic defect in the CFTR anion channel compromises host defenses and causes chronic lung infections with organisms like Staphylococcus aureus. Our lab has been studying the effects of combining ivacaftor, a CFTR modulator which increases CFTR channel activity, with a period of intensive antibiotic treatment. We found that S. aureus lung infections generally persisted despite this aggressive treatment. However, most subjects undergoing treatment were found to be infected by different S. aureus strains one year after treatment than were present before treatment was initiated. Understanding the dynamics of strain switching provide new knowledge about the natural history of chronic CF infections, help define the effects of CFTR modulators and antibiotics, and inform new approaches that might produce infection eradication. We hypothesize that (1) strain switching is most likely to occur during the period of combined ivacaftor and antibiotic treatment, as sputum bacterial burdens were lowest during combined treatment; and that (2) strain switching is rare in the absence of combined treatment. To test this, we used a new population-based multilocus sequence typing (PopMLST) method we developed to perform strain-level genotyping on S. aureus. PopMLST uses PCR amplification and next generation sequencing of housekeeping genes from bacterial isolate pools cultured from sputum. Sequencing determines the number and relative abundance of unique sequence types present, and the data can be used to infer the number of strains present. This analysis was performed on samples obtained before treatment, during treatment with ivacaftor alone, and during combined treatment. We also examined a cohort of subjects receiving usual care. These data improve understanding of strain dynamics during CF infections and suggest new strategies to eliminate infection.

Econometrics lacks an analytical framework for estimating and discussing the impact of intersectionality on economic outcomes of groups of marginalized people (e.g., women and people of color). As a result, a rich body of literature on intersectionality is left largely unused, leading to potentially misspecified regression models. In this paper, I outline an analytical framework for estimating and discussing the impact of intersectionality on economic outcomes, such as annual wage differentials between groups of marginalized and privileged people. I construct the analytical framework using principles of intersectionality theory, such as simultaneity and multiple jeopardy. I then use the framework to construct a multiple-linear regression model to investigate the following hypothesis: Do people with more marginalized identities earn less average annual wages than people with more privileged identities in the United States, all else equal? The results indicate that there is evidence to support the hypothesis, yet more in-depth investigations are necessary to better estimate the impact of marginalized and privileged identities on average annual wages.

Quantum confined nanomaterials have become an important field of study with many applications from color displays to low-energy alternative lighting sources. Discovered in the early 1980s, these semiconducting nanocrystals continue to draw attention; their unique properties differ from their bulk counterpart’s due to a quantum confinement effect rising from their small nanometer-scale size. Indium phosphide (InP), a group III-V semiconductor, is a promising nontoxic, environmentally innocuous material. The morphology of the synthesized InP nanocrystal is commonly a quantum dot quantum-confined in all three dimensions. However, the utility of the dot in biological imaging and display applications is hindered due to reabsorption resulting from overlap in its absorption and emission properties. This dims the light of an indicator and limits efficiency in catalysis. The subject of this investigation—InP quantum rods— offers a solution to this problem, as it is quantum confined in two dimensions and exhibits bulk semiconductor characteristics in the third, separating the absorptive and emissive features and improving the photoluminescent quantum yield. My procedure involves a hot-injection method. Currently, a magic sized cluster hot-injection synthesis in N-methyl pyrrolidone at 150 °C is known to afford InP rods (Dr. Friedfeld, UW Cossairt lab). I explore multiple experiment sets that manipulate the reaction length and temperature of the synthesis, cluster identity and concentration, and the identity of the aprotic polar solvent in which the reaction takes place. I characterize all material via UV-vis spectroscopy and imaged on a transmission electron microscope. The aim of the investigation is to learn why these rods form and what reaction conditions favor their formation. In understanding how to efficiently control the distribution of InP rods v. dots using chemical tools, the usefulness of nanocrystals in nanobiotechnology and clean energy science can be improved.

Glioblastoma multiforme (GBM) is a highly aggressive variant of brain cancer that has been a focal point of chemotherapeutic development for years. However, initial drug screening using traditional in vitro culture of GBM cells frequently produces encouraging results that do not translate well to animal models and clinical application. To address this disparity, implementation of three-dimensional tumor modeling can better emulate the microenvironment that tumor cells experience in situ, improving accuracy of early in vitro screening. We developed two chitosan-based polymer blends to produce biocompatible, porous scaffolds that mimic the extracellular matrix and promote cell adhesion. Scaffold production was done in 96-well cell culture plates for high-throughput drug screening with a large sample size. These scaffolds were used to grow human GBM cell lines U-118 MG, U-87 MG and GBM6 for 14 days, confirming cell compatibility with the materials and promoting formation of tumor spheroids. The cultures were treated with the established chemotherapeutic agent temozolomide (TMZ) for 72 hours, and cells were then tested for metabolic activity using the Alamar Blue resazurin assay. We demonstrated increased resistance to chemotherapeutics in cells with this induced morphology relative to cells grown in two-dimensions for all cell lines and both scaffold compositions. Additionally, based on gene and protein expression analysis, GBM cell spheroids more strongly expressed cancer stem cell characteristics and greater malignancy. The presence of GBM resistance to chemotherapy and enhanced characteristics associated with in situ tumors indicates the potential of using chitosan-based tissue scaffolds for more accurate high-throughput screening of novel GBM treatments.

Polycystic kidney disease (PKD), commonly caused by defects in polycystin-1 or polycystin-2, results in the formation of fluid-filled cysts and progressive loss of kidney function. Our laboratory has established a cellular model for ADPKD using kidney organoids, multicellular tissue that functionally and structurally resembles the organ of interest, derived from gene-edited human pluripotent stem cells (hPSC). To address the need surrounding a cure for PKD, we have also discovered a basis for a form of treatment involving myosin. Non-muscle myosin is a protein that controls cell protrusion and adhesion; we have established that lack of adherence increases cystogenesis dramatically. We discovered blebbistatin, a non-muscle myosin (NMMII) inhibitor, is a robust inducer of cystogenesis. Our previous finding begged the question if activators of NMMII have the opposite effect and reduce cystogenesis in PKD organoids. To better understand the role of myosin, we differentiated kidney organoids from human PKD hPSCs in a 24-well plate coated with Matrigel. We proceeded with microdissecting the organoids at 3 weeks before they formed any cysts and transferred the organoids to suspension culture where they were treated with either DMSO as a control or a pharmacological myosin activator for one week. The organoids were then imaged and number of cystic organoids were quantified. The treatment using the myosin activator compound resulted in decreased cystogenesis, in terms of the size and number of cysts. Although we have yet to clarify myosin’s effect in the PKD pathway, we have identified a myosin activator as a potential inhibitor of cystogenesis. Further experimentation is to be done with other compounds such as actin activators, and proceeding with experimentation on ex vivo kidneys of mice. Our current findings suggest that the polycystin proteins positively regulate actomyosin’s contractility, therefore myosin may be an important factor for keeping kidney tubule integrity and preventing cystogenesis.

Polycystic kidney disease (PKD) affects nearly 600,000 people in the United States and it is caused by mutations in the genes that encode polycystin-1 (PC1) and polycystin-2 (PC2). These modifications are responsible for the growth of fluid-filled renal cysts that can impair kidney function over time, and lead to end stage renal disease. PC1 and PC2 have also been localized to the mitochondria, suggesting that they are responsible for regulating cellular metabolism and energy production, which can lead to mitochondrial dysfunction and increased PKD progression. Our lab uses human pluripotent stem cells (hPSCs) to generate kidney organoids that can be used to study the advancement of PKD, which contain the major proximal structures of the nephron including podocytes, proximal tubules, distal tubules, and endothelial cells. Orgnaoids that lack both PC1 and PC2 will develop cysts that can grow large enough to be seen by eye. Unfortunately, these organoids lack a collecting duct (CD) system, a crucial component of the kidney that expands greatly in PKD. To address this need, we developed a protocol to differentiate hPSCs into ureteric bud (UB) cells, the precursors of CD cells. First, we identified Dolichos biflorus agglutinin (DBA) as a key CD lineage marker in developing kidneys through immunofluorescence analysis on human kidney tissue. Then, we took undifferentiated hPSCs and investigated their ability to express DBA by treating them with a concentration gradient of small molecules known to induce kidney lineage cells. The resulting cells were stained with DBA and GATA 3, an additional, early CD marker, and we found that both markers were expressed in vitro. We will continue modifying this protocol to better study the increased metabolic rates seen in PKD, its effects in CD cells, and the mechanism behind the PC1 and PC2 pathway that leads to cyst formation.

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.

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.

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.

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.

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.

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.

 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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

 The Diabetes Community Care Ambassador (DCCA) Program represents a promising intervention for improving glycemic control in youth with type 1 diabetes (T1D) struggling with diabetes management. In this novel program, lay health workers called DCCAs supported youth with T1D with poor glycemic control (HbA1 >8.5%) and their caregivers through home visits, school visits, and phone support, and connected participants with legal support. Given the findings that youth with T1D in the DCCA Program demonstrated improved glycemic control, we carried out a follow up qualitative study to understand the salient components of the DCCA program that promoted improved diabetes self-management from the youth and caregiver participant perspectives. We conducted semi-structured exit interviews with a subset of DCCA Program participants (18 caregivers, 14 youth). Participants reported on how the DCCA was helpful in supporting the youth’s diabetes management and how DCCA support compared to care provided by the multidisciplinary diabetes care team. A qualitative content analysis was carried out and emergent themes were identified. We found that within the home environment, participants felt the DCCAs helped youth address underlying weaknesses in their diabetes management routine and provided accountability for self-care goals between visits with their diabetes provider. DCCAs also provided psychosocial support that youth and caregivers believed they did not sufficiently receive from their usual multidisciplinary diabetes care team. At school, caregivers, in particular, felt that DCCAs successfully advocated on behalf of the student’s interests to facilitate diabetes management at school and also provided diabetes education to school staff. Finally in the community setting, caregivers shared that DCCAs helped to connect them to legal and support resources and better navigate the healthcare system. Our study results highlight the value of using lay health workers in providing individualized assistance for youth with T1D in supporting diabetes management outside of the ambulatory care setting.

Patient reported outcomes (PRO) are becoming increasingly important in the follow-up of patients after cancer treatment. The specific aim of this study was to investigate the time taken and completeness of PRO questionnaires. Study subjects were identified from an institutionally approved database of patients who had undergone surgical management of esophageal cancer with curative intent (1991-2018). Patients that were alive in April 2018 were asked to complete six questionnaires, including: Digestive Symptom Questionnaire (DSQ, 23 questions); Dumping Syndrome Rating Scale (DSRS, 25 questions); SF36 (36 questions); EORTC-QLQ-C30 (30 questions); EORTC-QLQ-OG25 (25 questions); and EuroQol 5D (6 questions). Patients were offered either hard-copy (paper) or Electronic versions of the questionnaires. Electronic questionnaires compiled in RedCap were completed consecutively by patients allowing for accurate quantification of the time taken to complete each questionnaire. In total, 144 patients were asked to participate, 117 patients (81.3%) agreed to complete questionnaires, of whom 60 (51%) of the patients choose the electronic version. Completion rates for all of the questionnaires was 91% (52 patients) and 85% (51 patients) for paper and electronic versions respectively. The average age of patients choosing electronic questionnaires was 74 (range 55-96) years compared to 71 (range 53-91) years in the paper questionnaire group. On average, the 6 questionnaires, consisting of 145 questions, took 26.9 (range 10-55) minutes to complete: 7.5 minutes for DSQ, (range 1-39 min), 4.4 min for DSRS, (range: 1-19 min), 6.8 min for SF-36, (range: 3-18 min), 3.7 min for EORTC-QLQ-C30, (range: 2-8 min), 2.7 min for EORTC-QLQ-OG25, (range: 1-5 min), 1.7 min for EuroQol 5D, (range: 0-6 min). In conclusion, the high response rate in the study, indicates that it is feasible to ask patients to answer multiple PRO questionnaires after cancer treatment. Continued focus on PROs is warranted to further increase the knowledge of cancer survivorship.

Chronic postsurgical pain (CPSP) develops in 10-50% of pediatric patients after major surgery. Despite potentially severe health implications, little literature exists examining the epidemiology and mechanisms of pediatric CPSP. A barrier to progress in this area is that while definitions of CPSP exist in adults, definitions do not include impact of pain on health related quality of life, a critically important aspect of pain assessment. Consequently, the objective of this research study is to develop a clinically meaningful definition of pediatric CPSP that incorporates measures of pain intensity and quality of life, which can be standardized across clinical and research populations. The aims of the study were to (1) identify and extract common elements of current definitions used for CPSP in the existing literature, and (2) identify clinically meaningful cutpoints for CPSP based on pain and quality of life, through secondary data analysis of two clinical research studies examining pediatric post surgical pain. Literature search found that existing studies employed inconsistent definitions of CPSP, limiting our ability to develop a literature-based definition. Our dataset included 179 adolescents 10-18 years old undergoing surgery for spinal and chest wall deformities. Measures included pain intensity (Numerical Rating Scale), quality of life (PedsQL) and pain interference (Visual Analog Scale) at 4 and 12 months post-surgery. We conducted scatter plots to visually inspect the associations among pain and health outcomes. Cluster analyses of pain and health-related quality of life identified four unique cluster groups differing on level of pain and functional impairment. Next steps will include determining cutoffs for pain and quality of life based on these cluster groups, and validating the newly proposed definition in an independent sample of youth undergoing surgery. A consistent definition for CPSP which incorporates both pain intensity and functional impact of pain will help guide future research and treatment.

Uruguay’s history as a place of refuge for European Jews fleeing antisemitism during the first half of the twentieth century and the rise of global fascism has been understudied. As survivors and children of survivors are now in their 70s, 80s, and 90s, there is an urgency to record their stories. Some of these migrants fled Europe as early as the 1920s, while others arrived in Uruguay shortly after the war, surviving alone or with family members. Working with a team of student and faculty researchers who are studying the experiences of Jewish migrants now residing in the Hogar Israelita, a former orphanage and home for the aged founded in 1937 and current nursing home in Montevideo, I have translated primary and secondary documents for my non-Spanish-speaking professor as well as conducted historical research. I am helping build the photos and recordings that we collected in January into a digital project. I’ve worked to situate these individual stories within a greater history to understand how political tensions of the time period and ideology of the government affected individuals and their families. US immigration policy, which significantly restricted Jews from entry beginning in 1924, directly affected Uruguayan policy, which remained largely open to Jews until 1937. As Jewish immigrants arrived, the presence of antisemitism increased through restrictive policies and pressure from the Catholic Church, despite the government’s denial of racism and antisemitism. Study of previously recorded testimonies recorded in Spanish of Jewish immigrants, both before and after fleeing Europe, reveals the creation of organizations aimed to ease the transition of immigrants as well as women’s associations and orphanages. The newly collected testimonies of the residents of Hogar, their families, and the staff, bring additional insight and nuance into our understanding of the Holocaust, the Jewish diaspora, identity, and migration.

Sea ice, frozen ocean water, in the Arctic is declining due to climate change. This is getting more attention, since sea ice can substantially affect wildlife, ecosystems, and human society. Sea ice extent, a measure of the surface area of the ocean covered by sea ice, is used to monitor the environment. A good sea ice extent model can benefit not only studies of the Arctic but also the global economy, as many ships use the Arctic area as part of their route. There are various sea ice extent models in the science community that give good estimates of sea ice extent. However, there are instances where their predictions do not match observations. My research explores bias correction methods that help predictions to match observations and compares the performance of sea ice models after bias correction. In this analysis, I consider the performance of a sea ice model produced by the Geophysical Fluid Dynamics Laboratory using boxplots and rank histograms. This work helps show the value of bias correction. I will compare the performence of the models to identify in what month and in what location models predict well. This information will support improved prediction of the Arctic going forward. 

Skin plays an important function as a highly innervated sensory organ. This sensory function is critical to organism survival, but the skin, and its axons, are easily damaged and need to be repaired to maintain homeostasis. Zebrafish are an excellent model to study tissue repair because they regenerate tissue efficiently and share conserved skin architecture with other vertebrates. A cell type shown in previous lab experiments to contribute to skin repair is a macrophage like cell, the Langerhans Cell. I hypothesize that if Langerhans Cells are not present within zebrafish epidermis then tissue repair will be incomplete or delayed. I investigated these cells using two different methods. First, I analyzed mutations that cause a loss of function in genes required for Langerhans Cell development. Second, I used the transgenic ablation technique to inducibly kill Langerhans Cells in the skin by addition of the antibiotic metronidazole. I imaged fluorescent Langerhans Cells in the zebrafish epidermis in both of these genetic scenarios to quantify the reduction in Langerhans Cells. Following the completion of these experiments, we expect to see that a lack of Langerhans Cells will induce slower or halted recovery from damage. In the loss of function method, I expect that various mutants will not have as many Langerhans Cells and that following induced ablation, Langerhans Cells will die out when the drug is introduced and slowly recover following metronidazole removal. The key implication of this is finding more about our own biology that can lead to faster healing. In theory, if Langerhans Cells have a major effect on this process then knowing more about our own skin can help us translate this understanding to our own healing process.

Spinal cord injury is known to cause an inflammatory immune response in the central nervous system (CNS), activating local immune cells microglia and astrocytes as well as recruiting circulating macrophages. Previous studies have shown that distinct populations of macrophages can exhibit either neurotoxic or reparative effects, depending on the cytokines activating them. Injury to the CNS also results in enzymatic breakdown of extracellular matrix (ECM) molecule hyaluronic acid (HA) into lower-molecular weight glycoproteins. It is known that after injury, many of these cleaved glycoproteins from the spinal cord extracellular matrix act as damage-associated molecular patterns to modulate immune response. However, it is still unclear which facets of the inflammatory response are subject to control by HA, a key ECM component. In this study, we seek to determine whether the breakdown of HA causes proliferation and activation of microglia and astrocytes. Introducing the enzyme hyaluronidase that degrades HA to an uninjured spinal cord decreases the levels of HA in the local area. Subsequently, we used double immunohistochemistry with markers for either microglia or astrocytes in combination with a marker for cell proliferation, to analyze cell activation and proliferation after treatment with either active or heat-inactivated hyaluronidase. We expect hyase treatment to result in both increased activation and proliferation of microglia and astrocytes. The expected data would indicate that the breakdown of ECM HA leads to activation of microglia and astrocytes. Understanding these cells’ activation could lead to future treatments for spinal cord injury focused on modifying the ECM to induce beneficial rather than neurotoxic inflammation.

Cystic Fibrosis (CF) is a genetic disorder associated with chronic, polymicrobial lung infections. One of the most common treatments for these infections involves inhalation of the antibiotic Tobramycin, used to treat Pseudomonas aeruginosa infections. Tobramycin’s effect on other members of the CF respiratory microbial community is unclear. The Tobramycin inhaled powder (TIP) study assessed the effect of Tobramycin on the entire respiratory microbial community before, during and after one month of therapy and demonstrated that, on average, Staphylococcus aureus viable counts dropped during the first week of therapy before returning to pre-therapy levels. However, there was variability in the response in viable counts to antibiotics in different patients with some that did not change at all throughout the course of drug therapy and no individual clearing their S. aureus infection. The purpose of this study is to better understand why Tobramycin did not clear S. aureus in people with CF as well as determining why patients responded differently. We initially hypothesized that the infection was not cleared due to antibacterial resistance to Tobramycin. I answer this question using standard susceptibility tests on Tobramycin, Cefoxitin, Sulfamethoxazole and Levofloxacin. The use of four different antibiotics help determine if the bacteria are resistant to Tobramycin and if there is a viable alternative to Tobramycin. We anticipate that results will show a shift from susceptibility before therapy to resistance after week one due to the proportion of resistant bacteria increasing. CF lung infections can be a model for many other diseases as well and we hope that this study may provide more insight into how to treat these infections better.

Enteric diseases, or diseases of the Gastrointestinal (GI) tract, remain one of the most prevalent killers of children in sub-Saharan Africa. The most practical way to prevent such diseases is through vaccination, but antigens for enteric diseases need to be delivered directly to the GI tract to be most efficient, making vaccination difficult. Recent studies by the von Adrian group at Harvard University have found that both T and B cells are reprogrammed to home to the GI tract when they encounter retinoic acid, a metabolite of vitamin A. The King Lab at the University of Washington is working to develop a novel vaccine candidate using recently developed self-assembling protein nanoparticles, that can simultaneously package all-trans retinoic acid (ATRA) and multivalently display enteric antigens. Previous work has suggested that two cystine mutations to Cellular Retinoic Acid Binding Protein I (CRABP-I) create a disulfide bond as a result of the conformational change that CRABP-I undergoes when it binds ATRA. This disulfide bond would essentially lock ATRA into CRABP-I, reducing its dissociation constant in vivo and maintaining the gut-homing properties of the nanoparticle post-injection. In order to assess the efficacy of these cysteine mutations, I expressed two versions of CRABP-I, the wildtype protein with no cysteine residues, and a version with no cystine residues except for the two that create the disulfide bond. After establishing that these new CRABP-I mutants folded into the approximate shape of wildtype CRABP-I via circular dichroism, I designed and tested new assays that measured free thiol concentrations of each protein after binding ATRA, as well as free ATRA concentration overtime. This data will help us determine whether these two cystine mutations make a significant difference in the ATRA binding quality of CRABP-I, which could improve the immune response generated by our vaccine candidate.

Natural proteins often assemble into various complex geometric structures based on their interactions with each other. These structures can hold and transport "cargo" as well as display antigens, making them extremely useful in vaccine design. The King Lab at the University of Washington uses the way these proteins assemble to develop computational models that help them design novel self-assembling protein cages, or nanoparticles. These nanoparticles are then used to develop vaccines or treatments for diseases. Components of the designed protein cage can be modified and expressed individually before being assembled together into the nanoparticle. I am working on stabilizing one of these protein cages known as T33DN2, so it can be used towards creating a vaccine. T33DN2 is a tetrahedral cage comprised of two trimeric proteins known as T33DN2A and T33DN2B. When expressed individually through E.coli, DN2A is produced in a soluble form while DN2B is produced in a mostly insoluble form. T33DN2 is currently an unstable cage, as only the A component is expressed solubly. Soluble proteins are generally more stable and thus easier to work with than their insoluble counterparts. To increase the solubility of DN2B, I have been making mutations to specific amino acids in the DNA that produces this protein, as well as expressing and purifying this component to determine its stability.

Dementia is a neurological condition that impairs memory, cognitive functions, and the performance of daily activities. It is estimated that 5.5 million Americans suffered from dementia in 2018. Currently, the predominant method used to treat persons with dementia is through pharmacological means. However, through reviewing current research, we have found evidence to suggest that cognitive behavior therapies (CBT) may be more beneficial to patients, with the potential to reverse some symptoms of dementia. Our study aims to improve CBT through virtual environments. Virtual Reality (VR) is not merely a visual platform but an immersive environment that stimulates the brain in the same way real environments do. However, in VR we can track certain markers like head and eye movement, metrics that can be valuable in tracking the progression of the disease as well. We have developed a virtual experience that can calm and stimulate seniors while being able to track a person’s ability to perform free recall and spatial recognition through a series of memory games. This experience has the potential to have both therapeutic and diagnostic capabilities, as well as provide insight into how VR can affect memory. Over the past 6 months, our research team has worked with seniors at the Greenwood Senior Center to test different virtual reality platforms such as the Oculus Go and HTC Vive, as well as various virtual environments. Using our experience from the center our team is creating a platform tailored to fit seniors who are affected by dementia. In the near future, our team will be volunteering at a local assisted living facility to work with these seniors. This project will offer understanding of how implementing VR therapy can improve patients’ morale and cognitive capabilities, as well as exploring the use of VR as a diagnostic tool.

Efforts to engineer flying micro-robots (~50mg) are motivated by their potential advantages relative to larger robots, such as greater deployment numbers at the same cost. There are significant developments in flapping wing robots at insect-scale; however, little advancement has been made in the development of robots with ionic actuation using electrohydrodynamic (EHD) thrust. This thrust is generated through the ionization of air particles and momentum transfer of these positive ions with neutral air molecules. EHD thrusters have used collector grids and emitter wires to generate a thrust for controlled flight. In this research, we design and fabricate a 1.8 x 2.5 cm micro-thruster that weighs a total of 43 mg including the carbon fiber collector grid, four blue tempered steel emitters, and eight fiber optic glass tubes. This robot is hand-assembled using a laser fabricated external fixture. Electrodes of the robot are fabricated using a laser based system. The whole robot takes a total of 20 minutes to assemble. Emitters are supplied with a high voltage (~2.5kV) using a bundle of 51-gauge insulated copper wires. Similar wire is used for grounding the collector grid. A parametric study is carried out to optimize the physical parameters of the robot. Experiments performed in this research show that the thrust generated is larger than the weight of the robot. 

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition associated with deficits in social interaction and the presence of restricted patterns of behavior. ASD is clinically and phenotypically heterogeneous. The most recent update to the diagnostic definitions for mental disorders (DSM-5) provides additional flexibility for capturing the diverse array of phenotypes shown by diagnosed individuals. Despite categorized behavioral symptoms across core and comorbid dimensions of ASD, the neural mechanisms are unknown. Studies have shown atypical neuroanatomy and functional connectivity of the brains of individuals with ASD, suggesting a neural etiology. Here, we focus our attention on the superior temporal sulcus (STS), a region of the brain demonstrated to play a role in processing communication, social information, and theory of mind. Our research question evaluates whether neural activity in STS is affected by behavioral phenotype in children with ASD. We speculate that neural activity between individuals with ASD varies significantly more than typically developing (TD) children, who show more clustered, similar outcomes. Functional near infrared spectroscopy (fNIRS) distinguishes concentrations of oxygenated (HbO) and deoxygenated (HbR) hemoglobin in regions of cortical vasculature, signifying neurovascular coupling. This study uses HbO and HbR measured as subjects watch the events of a social scene on a monitor and analyzes ASD individuals’ deviance from average TD activity. Eye-tracking, clinical assessments, and parent questionnaires are considered to extrapolate possible correlations between ASD individuals’ variation in neural outcome and the behavioral phenotype expressed. We expect that individuals showing higher degree of neural variance from TD activity will show more severe autism behavioral phenotype. It is possible that in the search for neural mechanisms of ASD, considering behavioral factors signifying atypical variance could reveal significant differences. This exploratory analysis aims to examine the wide range of possible influential factors on neural heterogeneity within the social brain of individuals with ASD.

There is a critical lack of knowledge regarding the effects of human immunodeficiency virus (HIV) and zika virus (ZIKV) coinfection in respect to ZIKV pathogenesis, vertical transmission and current vaccine strategies. ZIKV has received global attention because of its clinical complications including congenital malformations during vertical transmission and Guillain-Barré syndrome, a neurocognitive disorder in adults. Recently, ZIKV outbreaks have occurred in tropical and subtropical regions endemic with HIV, therefore it is imperative to understand the impact HIV-ZIKV coinfection may have when moving forward with ZIKV vaccine design. Furthermore, in humans and non-human primates (NHPs) frequencies of blood monocytes increase during HIV and simian immunodeficiency virus (SIV) infection and monocytes are early targets of ZIKV infection. Therefore, we hypothesize that cells from HIV infected individuals have the capacity to harbor increased ZIKV replication and could lead to enhanced ZIKV viremia and pathogenesis. For this study, we use a NHP model to determine the impact of acute SIV infection on ZIKV pathogenesis. We determine ZIKV cellular targets in the blood and preliminary results show an increase in NHP blood monocyte within the first six weeks of SIV infection. We evaluate whether SIV infection increases the susceptibility of cells to ZIKV infection by isolating cells from SIV- and SIV+ animals, infecting them in vitro with ZIKV, and assessing viral replication by plaque assay. Our preliminary findings suggest that in vitro ZIKV replication may increase in cells from SIV+ NHP blood when compared to SIV- blood. Future studies will look at the impact of SIV infection on in vivo ZIKV replication and whether ZIKV replication is enhanced in cells from HIV-infected individuals.

This project aims to better understand the effects of removing global topography on atmospheric and oceanic circulation in numerical climate model simulations. The Community Earth System Model (CESM) was run for a hundred years under three different scenarios: the removal of all mountain ranges, the removal of the Rockies, and the removal of the Tibetan and Mongolian Plateaus. When mountains are removed it results in changes to ocean and atmospheric circulation. This begins with warmer surface temperatures where the mountains were removed (without the elevation-induced cooling) and changes in both vertical and horizontal air motion in the vicinity of the mountains (as the topographic-induced circulations are disrupted). Consequently, rainfall is altered due to changes in temperature and air motion. Our research aims to better understand how mountain ranges affect rainfall, particularly in the tropics. and how this in turn affects local climatology in tropical regions.

Many people in today’s society do not devote enough time to enjoy the food they are eating, consuming their food with their attention devoted to phones or television screens, and in some instances even finishing their food without realizing how much they have eaten. This is especially prevalent in people who regularly eat alone, falsely believing that multitasking will increase their productivity. In this design research project, we investigate the problem of people’s lack of focus while eating with the goal of using our design insights to develop technological solutions to help people be intentional, mindful, and present when they eat. Our work is grounded in the premise that mindful eating provides health benefits and is a gentle and approachable way to introduce mindfulness into people’s lives. Our design process follows the established practice of exploration, divergent ideation, and then convergence, with an added reflection component. Specifically, we first explore the problem space by gaining a deep understanding of the relevant literature on mindfulness, multitasking, and the interactions between meals and technology, followed by conducting several user interviews about the problem. These interviews are with college students and other individuals who tend to eat alone in their homes. We then use divergent thinking to ideate many possible, diverse solutions, for example, a phone application, use of smart home technology, a standalone physical object. From there, we converge on a few candidate solutions and analyze the implications—positive and negative— of each. Design reflections consider not only the design outcomes but also our design process and key points in that design process. Our work contributes to a growing body of design research concerned with Slow Design, distraction, and mindfulness.

We have built an air quality sensor to track smoke from wildfires at UW’s Manastash Ridge Observatory (MRO). The increasing number of wildfires over the last few years has raised concern that smoke may contaminate the telescope optics at MRO. Our goal is to measure the amount of smoke in the air at the site in real time. Our design consists of an Adafruit micro-controller connected to two dust sensors that connect to Wi-fi. We interviewed Edmund Seto, a professor at UW, since he has much more experience with building sensors. He suggested that we use multiple of the same device so that we could average the data or have a backup sensor if one were to stop working. Using Arduino code and Adafruit.io, we were able to code the micro-controller and connect the data to a Wifi-interface so we could watch the data come in. We are currently field testing the sensor in Seattle, but we expect to permanently install at the MRO this summer.

Cancer is increasingly a global health issue. Access to radiation therapy, the primary method of cancer treatment, is limited in low- and middle-income countries due to difficulty translating technologies in resource-limited settings. We are developing a new generation of cost effective IMRT (intensity modulated radiotherapy) devices for low- and middle-income countries. The current IMRT is performed using linear accelerators with multi-leaf collimators (MLC) which is very expensive and challenging to maintain in low- and middle-income countries. As a team, we are replacing the current technology with an alternative one using physical compensators which have lower commitments in terms of cost, overhead, and complexity. During my time working in the Imaging Lab, I have implemented all of the custom scripting protocols in a Python script (IronPython Interpreter) which is connected to the treatment planning system (RayStation - RaySearch Laboratories). Treatment planning systems are at the heart of radiation therapy systems and the key to improved patient outcomes. My script has enabled the creation of a compensator map and contour from the fluence data of the beamset. To test validity and correctness of the equations derived - I created a treatment plan based on the CT image for a head and neck cancer patient. The preliminary results of my script on this treatment plan indicate that compensators with ray lines divergent with the radiation source can be constructed for use in the treatment planning system. My contribution satisfies a key requirement of the project. A prototype of the compensator will be developed in commercial and partner sites in India, validating the script with a large number of patients.

Control of the cell-cycle is a topic of fundamental importance in cell biology. We are using the unicellular eukaryotic green alga Chlamydomonas reinhardtii to better understand how DNA damage affects transition of these cells in and out of the mitotic cell cycle. We find that UV treatment of cultures of C. reinhardtii gametes (in Go) delays re-entry of these cells into the mitotic cell cycle upon addition of nitrogen to cultures of gametes, a standard treatment which releases these cells to re-enter mitosis. Using a C. reinhardtii mutant which is unable to carry out photorepair of UV-induced DNA damage, we are characterizing the degree to which the kinetics of re-entry into mitosis depends on this very important repair system; we are thus beginning the 'parsing out' of the relative importance of the various DNA repair systems in controlling the transition from Go, a non-dividing stage, to G1,  the start of DNA replication and cell division. This will potentially provide insight into other downstream effects of UV exposure, such as mutagenesis. Our work is of a very basic nature, but with application to understanding e.g. dynamics of natural populations of microalgae in a changing global environment.

Homo naledi is a species of hominin that lived in South Africa at between 335-236 ka, around the same time that anatomically modern humans were evolving in Africa. While the lower limb of Homo naledi shares many characteristics indicative of obligate bipedality with modern humans, the upper limb shows a more primitive morphology related to climbing. The distal humerus is one of the more common bony elements found in the fossil record and its morphology directly reflects the functional requirements of the limb, making it a good place to study upper limb function and adaptation. Using 3D geometric morphometrics, we compared seven distal humeri attributed to Homo naledi with distal humeri from great apes, modern humans, Neandertals, and other extinct hominins to place H. naledi in a functional context. We conducted a principal components analysis and partial least squares analysis on anatomical landmark data to investigate variation in distal humeral shape. Preliminary results indicate that H. naledi had a distal humeral morphology broadly similar to gorillas and unlike modern humans. Our results provide new insights into the upper limb mechanics and the role of climbing in the locomotion of Homo naledi, as well as clarify their phylogenetic relationship with other hominins.

Hair cells are sensory receptors responsible for hearing and balance in the auditory and vestibular systems. These cells are surrounded by supporting cells, which are non-sensory cells similar to glia. In non-mammals, hair cells get replaced after damage through conversion of supporting cells. Recent studies have shown supporting cells can also transdifferentiate into type ll hair cells in the vestibular system of adult mice. The signals that control hair cell regeneration in mammals are poorly understood. It is known that the transcription factor Sox2 is utilized for specification of hair cells in the neurosensory domain of the otocyst. This project tests the premise that Sox2 is required in adult supporting cells for their transdifferentiation into type II hair cells after damage. We used time specific gene deletion technology, CreER-LoxP, to delete the gene encoding Sox2 in supporting cells prior to damage. The mice used include the following alleles (genetic segments): 1) the floxed Sox2, or Sox2loxP/loxP allele, which enables Sox2 deletion when Cre is active; 2) the Sox9CreERT2 allele, which targets Cre expression to supporting cells; Sox9CreERT2 is tamoxifen-dependent, so the timing of Sox2 deletion is controlled by tamoxifen injection; and 3) the Pou4f3DTR allele , which enables hair cell killing upon injection of diphtheria toxin (DT). Hair cells were identified and “typed” using several markers, including antibodies to myosin VIIa, neurofilament, and ßIII tubulin. I compared the number of regenerated hair cells of Sox2 expressing supporting cells and Sox2 negative supporting cells. Sox2 deletion in supporting cells resulted in a significantly reduced number of type ll regenerated hair cells. This result provides evidence that Sox2 is required for transdifferentiation of supporting cells. Understanding the function of Sox2 will give insight into potential downstream molecules that can become prospective targets for future research in understanding cellular regeneration in adult mice.

Metacarpal and phalangeal fractures can be treated in a variety of surgical procedures ranging from k-wire fixation, plate/screw constructs, external fixation, or intramedullary fixation. All treatments must account for normal pressure loading, stability, and maintenance of normal tendon and ligament function. Intramedullary fixation has gathered interest as it has advantages in less surgical work, the cannulated screw being guided by a wire, shorter time of operation, no interference of soft tissue, and enough stability to immediately begin range of motion rehab. The crucial question is whether there is a change in pressures from joint contact and reaction forces of the proximal interphalangeal and metacarpophalangeal joint as a result of the articulating surface area due to this procedure. The methods of this study were comparing joint contact pressures in ten fresh-frozen cadaveric hands that I prepared before and after intramedullary fixation, and developing finite element models of the fingers. These have allowed more precise results of changes in joint contact pressures as well as testing of other conditions such as changes in joint pressure when the location of the hole in the joint is changed. Grasping forces were simulated by my attaching weights to flexor and extensor tendons while a pressure sensor inside the joint recorded forces. The anticipated result of this ongoing study is that placement of an intramedullary screw in the joint articular surface will increase contact pressures throughout regions of the joint that contact the articular defect. The significance of this study is that joint replacement research in cadavers has been shown to cause a change in contact pressures, however there is no literature detailing if this is true of the proximal interphalangeal and metacarpophalangeal joint. Once a CT-based finite element analysis model is validated by cadaver testing it will be usable for deeper research of finger surgery.

Harmful radiation, such as UV photons from the sun, can damage DNA in a manner that results in cation-radical formation which leads to nucleobase loss and strand breakage. In the Frantisek Tureček research group, DNA cation-radicals were generated in the gas phase, isolated and subjected to incremental wavelengths between 210-700 nm with intent to observe their absorption action spectra that can be used to assign structures and intrinsic properties. The difficulty with these experiments is the ability to effectively communicate the experimental set-up of mass spectrometers, tunable lasers, and various other pieces of equipment in a supporting manner that delivers concise information to be understood regardless of prior knowledge in this specific field. I had the unique opportunity to take two-dimensional, over-simplified schematics and transform them into three-dimensional, professional and photorealistic images of our experimental arrangements using Siemens NX CAD modeling software.

Alzheimer’s is a progressive, age-associated, neurodegenerative disease characterized by memory loss, deterioration in thinking and reasoning skills and gradual loss of executive function. Two well-documented biochemical hallmarks associated with disease progression are the accumulation of extracellular beta-amyloid (Aβ) plaques and intracellular neurofibrillary tangles found in the brains of Alzheimer’s patients. One theory of the disease holds that aggregated proteins found in these two deposits inhibit protein degradation by the 26S proteasome, a large protein that is one of the central components of the ubiquitin-proteasome clearance system. This system, of which the proteasome is a key component, executes most of the controlled protein degradation in the cell. Importantly, impairments in proteasome function are associated with multiple neurodegenerative diseases. The overall goal of this project is to determine whether proteasome stimulators can delay toxicity associated with Aβ aggregation in a C. elegans Alzheimer’s disease model. C. elegans is a powerful model organism in biomedical research due to its ease of culturing, well-described genetics, gene homology and availability of transgenic tools. My project utilizes a C. elegans strain that expresses the full-length human amyloid beta peptide (Aβ_1-42) in body wall muscle cells. These animals become paralyzed when up-shifted to a restricted temperature due to aggregation of Aβ proteins in the muscle. To test the hypothesis that proteasome stimulators delay the progression of Alzheimer’s symptoms, I will treat animals with four drugs and measure the time of paralysis. Using a high-throughput drug screening system recently developed in our lab, I will treat animals with four proteasome stimulators or vehicle controls, in triplicate, and determine the onset of paralysis for each drug. These results will help shed light on the involvement of protein aggregation clearance in treating symptoms of Alzheimer’s in this model organism, and help inform future treatments for this and other neurodegenerative disorders.

The growing use of opioids in the United States has become a dangerous epidemic. The people most susceptible to overdosing on opioids are those who relapse after extended drug abstinence, whether forced or by choice. This study investigates the effects of heroin addiction on KCNQ channels in the basal ganglia, which plays an integral role in addiction.  More specifically, our research is focused on relapse after a prolonged period of no drug use. If the population of KCNQ channels are affected by heroin use and addiction, then these channels are a possible site for treatment to target. The drug retigabine, a KCNQ channel opener, has shown promise in reducing self-administration after abstinence by affecting dopamine levels in the striatum, a neurological center often involved in addiction. Given that dopamine release is critical in establishing and affecting addiction, retigabine is a likely candidate to diminish relapse behaviors and, therefore, reduce the occurrence of relapse-related overdoses. This study measures the effect of a global administration of retigabine. Catheters were surgically into the animals’ jugular vein to allow for self-administration of heroin with limited researcher interference. Over the course of three weeks, we ran our animals inoperant boxes for periods of self-administration following various drug availability periods and ending with forced abstinence. After two weeks of forced abstinence, the animals with high and low responding on self-administration were separated into three different treatment groups: Retigabine, XE991 — a  drug that has the opposite effects of retigabine — and a control solution (all administered intraperitoneally). Our animals then underwent one hour of continuous access self-administration where they could relapse. Behaviors such as drug intake, drug seeking, drug taking, and motivation to administer were measured across all six groups.The results from this study will provide evidence on the efficacy of retigabine in reducing relapse behavior after abstinence.

Risk taking is strongly associated with many disordered behaviors. Many studies implicate the orbitofrontal cortex (OFC) in such behaviors, though its modulation yields inconsistent results. This could be due to possible contrasting effects of intratelencephalic (IT) and pyramidal tract (PT) neurons, which have distinct morphologies and projections. Despite this, specific functionality differences are unknown. Given that 5-HT2A and D1 receptors have predominant expression in IT neurons over PT neurons, and antagonism of these receptors decreases risk-seeking, it was hypothesized that inhibition of all IT neuron activity in the OFC would also result in risk aversion. IT neurons in rats were inhibited during a risky-decision making task (RDT). To modulate IT neurons, an inhibitory designer receptor exclusively activated by designer drugs (DREADD) was injected into lateral OFC bilaterally, conjugated to CRE and FLP drivers injected into contralateral nucleus accumbens. In the full RDT, animals were presented with two levers: The “safe” lever delivered one pellet reward per press, while the “risky” lever delivered four pellets, with descending probability of reward administration (100%, 50%, 25%, 12.5%). Two test sessions were conducted whereby animals received intraperitoneal injections of clozapine-N-oxide (CNO) or a vehicle (DMSO) 30 minutes prior to task onset. Animals receiving CNO the first time received vehicle the second time. To determine if IT neurons were involved in perseverative responding, animals underwent a reversal task. They were presented with an active lever -which administered a food pellet per press -, and an inactive lever. Five consecutive responses on the active lever switched the inactive lever to the “active” lever. Results showed no significant changes in decision-making or reversal learning upon receiving CNO or vehicle. IT neuron modulation may need to be more temporally specific; future studies will focus on monitoring IT activity during decision-making paradigms to further elucidate their contributions within OFC.

Mushroom bodies are paired structures in the brains of invertebrate phyla. They are characterized by densely packed neurons that are essential for facilitating learning and memory. Previous research using anatomical observations and immunohistology on mushroom body-like structures across arthropod species supported genealogical correspondence over convergent evolution of these learning and memory centers. The data collected so far, however, lacks representation from certain taxa, namely the crustaceans. To continue gathering evidence to further support or refute genealogical correspondence of mushroom bodies, we will examine neuroanatomical features as well as the presence of proteins required for learning and memory formation in a class of crustaceans called the malacostracans. Protein kinase A catalytic subunit alpha (PKA-Cα) is one such protein that is highly conserved in amino acid sequence and in learning and memory function across insects and mammals. Its conserved nature makes it a useful indicator for mushroom body homologs across phyla as its expression is known to be enhanced in mushroom bodies. We will be utilizing antibodies raised against PKA-Cα on brains of crustaceans closely related to insects in order to reveal structures that may genealogically correspond to mushroom bodies. Evidence suggesting that mushroom bodies are linked through homology would be supported if paired brain structures of crustaceans in multiple lineages are found to resemble mushroom bodies in morphology and protein expression patterns. By identifying mushroom body-like centers across invertebrates, we are able to make a comparison of the structures in context of the sensory environments of each animal in hopes of understanding the role of mushroom bodies in the evolution of learning and memory.

Many psychiatric disorders, including substance abuse, have been linked to risky decision-making, but the mechanisms underlying these pathologies remain unclear. Cortical intratelencephalic and pyramidal tract (PT) neurons have distinct projections, morphology, and firing properties, but their role in behavioral regulation remains unknown. PT neurons have been identified in the orbitofrontal cortex (OFC), which is known to be heavily involved in the cognitive process of decision making. Based on previous studies in our lab demonstrating that inactivation of PT neurons increases reward preference, we hypothesized that PT neuron inhibition would increase risky decision-making. To test this hypothesis, rats were trained on a risky-decision task (RDT) in which they were trained to lever press for a food pellet reward. In order to target PT neurons in the OFC, CAV2-CRE virus was bilaterally injected into the pontine reticular nucleus (PnC), and an inhibitory Designer Receptor Exclusively-Activated by Designer Drugs (DREADD; DIO-hM4Di) was injected bilaterally into the OFC; this strategy allows selective expression of DREADDs in PT neurons. In the RDT, two options were presented: a “risky” choice associated with descending probability of administration (100%, 50%, 25%, and 12.5%) for delivery of four food pellets, or a “safe” lever that always delivers one food pellet. To evaluate response flexibility, rats underwent a reversal task whereby five consecutive responses on the active lever switched the “active” lever to the previously inactive one. In both tasks, rats underwent two sessions: in the test session, animals received an injection clozapine-N-oxide (CNO) to activate DREADDs, and in the control session, animals received an injection of vehicle (DMSO). Interestingly, we found that inhibiting PT neurons did not significantly alter decision-making or reversal-learning. Future studies will monitor activity of PT neurons using in vivo calcium imaging to determine the contribution of this cell population to decision-making tasks.

Manu National Park in southeastern Peru is an incredibly bio-diverse national reserve at the meeting point of the Tropical Andes and the Amazon lowland rain forest, and an important location for tropical ecology research. Cocha Cashu Biological Station is one of few research locations in the Neotropical rain forest in which mammal communities remain almost completely undisturbed by human impact, including hunting and road construction. As a result, mammal population densities and compositions accurately reflect their natural environmental state. Among these mammals are fifteen known species of primates, and as major seed dispersers they play a critical role in the stability of the ecosystem. The aim of this study was to learn more about the behaviors of eight primate species within the Cocha Cashu trail system, during September of the dry season, using quantitative and qualitative observational methods. We used the focal sampling methods to quantify the proportions of time spent on daily activities for each species, and created activity budgets from this data to compare time spent on each activity. We also collected data on troop size, social interactions, habitat, and location throughout the day in order to compare and contrast the different groups. We were correct in our prediction that most species spent the largest proportion of time moving and feeding, but varied in other activity categories such as curiosity and aggressiveness. We found that there was significant overlap in the habitats and resources used by different species, but there were notable differences in foraging behaviors, troop size, canopy level, and the time of day designated to different activities.