Eclipsing binaries (EBs) are systems in which two stars orbit and pass in front of each other as observed from Earth. They are important astrophysical tools utilized in this project to directly measure the fundamental properties of stars, such as their masses and radii. We create a sample of 35 bright, detached EB targets from the Villanova Catalogue, based on high-quality photometry from the Kepler Satellite and spectroscopy from the Apache Point Observatory Galactic Evolution Experiment (APOGEE). Here, we present mass, radius, and orbital solutions for a subset of these EBs. For each system, we extract radial velocities (RVs), the speed at which each star in the system is moving away from the observer, from the APOGEE spectra. Then, we combine the RV with Kepler light curve (LC) information to simultaneously model the system light and line-of-sight speed as a function of time. Because our model has high dimensions with 18 free parameters, we first solve for the LC and RV solutions separately, and then simultaneously solve them. We use a nonlinear least-squares optimization method to determine the best fit solution and quantify the uncertainties in model parameters running Monte Carlo Markov Chain (MCMC) simulations. The model parameters that we find will further our understanding of fundamental stellar properties and binary star orbital parameters.

Across animals, embryos can hatch in response to environmental cues. Early hatching can improve embryo survival when eggs are in danger, but may come at a cost to the larval life-stage. Thus, understanding the adaptive value of hatching plasticity requires evaluating the costs and benefits that characterize selective trade-offs. Several species of glassfrogs (Centrolenidae) can hatch as early as 7 days in response to predators, dehydration, and parental abandonment, or delay hatching to 20 days under good conditions. We measured two fitness correlates, for survival and growth, to test the adaptive value of delayed hatching in five species: Cochranella granulosa, Hyalinobatrachium fleischmanni, Hyalinobatrachium colymbiphyllum, Teratohyla pulverata, and Teratohyla spinosa. Hatchlings fall from arboreal eggs into streams and must dive to the bottom to escape predatory fish. We measured diving performance for early and late hatchlings to infer predation risk. As tadpoles cannot benefit from external food resources until they reach feeding competence, we quantified the onset of feeding and compared gut-coil development in siblings of different hatching ages. Older hatchlings dove faster and began feeding sooner after hatching than did younger individuals, suggesting that delayed hatching is advantageous for escaping predators and reducing lag-time in exotrophic-based growth of larva. This study provides insight on the selective trade-offs that favor hatching plasticity in glassfrogs.

Chronic low back pain (CLBP) poses a major public health burden, affecting 31% of the general population and 54% of older adults. Among individuals with CLBP, multisite pain increases the risk for persistent pain and can lead to physical and mental impairments. Despite this, multisite pain research is limited and little is known about its relationship with health-related quality of life (HRQoL). This study describes the effect of multisite pain on HRQoL and the association between multisite pain and falls in older adults with CLBP. We conducted a secondary analysis using the Back Pain Outcomes using Longitudinal Data (BOLD) registry. BOLD consists of 5,239 participants, ≥65 years, from three health systems, with new primary care visits for back pain. We identified 899 participants with CLBP (>2/10 pain intensity, 6 months after new visit) and assessed comorbid pain at 6 pain sites, including widespread pain. Outcomes of HRQoL (EQ-5D, scored 0-1) and falls prevalence in the past 3 weeks were evaluated 6 and 18 months after participants met the chronic pain criteria. We used linear and logistic regression models to test the relationship between number and type of pain sites with outcomes, adjusting for demographics and health characteristics. Widespread pain (b=-0.035; CI: -0.058, -0.012) and pelvic/groin pain (b=-0.027; CI: -0.050, -0.004) sites were associated with lower HRQoL. For each additional pain site, HRQoL scores decreased an average of 0.013 points (95% CI: -0.020, -0.007) and odds of a fall increased 30% (OR, 1.30; CI: 1.12, 1.51) with nearly all falls occurring in those with >1 pain site (>95%). Number of pain sites had stronger associations with decreasing HRQoL than individual pain sites. Multisite pain increased the risk for falls. Clinicians and researchers should assess multisite pain as a potential risk factor for low HRQoL and falls in older adults with CLBP.

Ocean acidification is projected to put coral reefs in a state of net dissolution by the end of the century. Coral reef ecosystems are important habitats, supporting 25% of marine biodiversity in less than 0.1% of its surface area. As humans continue to burn fossil fuels, adding CO2 to the atmosphere and oceans, local mitigation approaches become increasingly important to consider for preserving these vital ecosystems. Bubble stripping is a geoengineering approach to ocean acidification that has been modeled and tested in the laboratory as an effective means of enhancing air-sea gas exchange in coastal ecosystems. Bubbling of CO2-deplete air through the water column allows dissolved CO2 to diffuse into the bubbles and, ultimately, the atmosphere. Bubbling is strategically timed to occur at night, when organisms are respiring and CO2 is not removed by photosynthesis. By increasing the rate of air-sea gas exchange, the ocean and atmosphere equilibrate such that concentrations of CO2 do not reach the extremes that would otherwise occur in the water column. In this study, we used airstones (bubble diffusers) and a test tank to confirm the results of an earlier bubble stripping experiment. Bubbling increased pH and decreased dissolved inorganic carbon (DIC). Its effectiveness could be optimized by testing parameters like bubble size, air flow rate, and water column height. However, obtaining and expelling compressed air is an energetically expensive process, so bubble stripping would likely be useful only for stabilizing seawater chemistry in specific, small sections of reef.

Increased specialization within the forestry industry has led to the rise of a distinct industry known as forestry services. Whereas logging historically encompassed this work, a separate population increasingly participates in the remote grooming and tree planting of forest lands. Physically demanding, dangerously hazardous, and low paying, forestry services work in the Pacific Northwest predominantly employs Mexican and Central American immigrants. As an extension of my honors project at the UW School of Nursing, I examined how occupational injury among this group of workers with correlates with attitudes that workers and employers hold about their work environments. Performing a secondary analysis using survey interview data collected by the UW Pacific Northwest Agricultural Safety & Health Center, and the Northwest Forest Worker Center, I identified top risk perceptions and barriers to workplace safety as reported by workers, as well as by a set of employers and supervisors. Not only was there variation in the prevalence of worker injury between different employers, there was also variation in the perceived attitudes about workplace safety. In future research, it will be possible to link the experiences of workers with the attitudes and policies of those who employ them.

Flowering plants have coevolved with insect pollinators in a mutualistic relationship; plants provide nectar to insects and insects in turn cross pollinate flowers. Plants have employed a range of colors, scents and shapes to attract their insect pollinators. Vision, olfaction, and mechanosensation all have roles in the identification and interactions with flowers. While the roles of vision and odor sensing have dominated the literature, recent work has shown that mechanosensation plays as much a role as vision in ensuring that moths stay engaged with a moving flower. Moths use their straw-like proboscis to probe a flower, using the overall shape of the flower as well as tiny grooves in the petals to guide the insect’s mouthparts toward the nectary. Using the feeding behavior of the nocturnal hawkmoth, Manduca sexta, we ask how moths use mechanosensory information to find the nectary opening in flowers. We combine 3D printing technology--to generate different 3D flower curvatures, with micro-sensing technology--that allows us to detect the proboscis tip inside nectary, and computer vision techniques--to detect the motion of the hovering moth, to test the relationship between flower shape and efficiency in locating the nectary. We find that flower exploration depends on its 3D curvature. Moreover, over repeated trials, moths take less time to find the nectary across all curvatures suggesting that moths use tactile exploration to learn flower shape. Mechanosensation is one of many inputs used by moths in the wild to interact with their environment. In future studies we wish to explore the integration of mechanosensation with other sensory information, and the salience of each modality.

Mass shootings are becoming a common occurrence in the media. Often times, in an effort to cover mass shootings, reporters are putting out information as soon as possible. The coverage often encompasses victims, suspects, death tolls and gruesome details. That practice leaves room for victims to become statistics and leaves many questions unanswered, which may result in insensitivity. The media has a duty to report the facts to the public, but what precautions should be taken when reporting on an issue that requires the lense of ethics? In an effort to better understand the perspective of journalists, a focus group consisting of media personnel was conducted. The focus groups allowed for open conversations between media personnel about the professional requirements of reporters during field reporting and the privacy expectations of victims. The focus group consisted of four media personnel who had been in the industry for several years and came from different backgrounds. The focus group was given five guided questions and the discussion was recorded. This study hopes to open up a discussion about the ethical coverage of mass shootings. These results could yield future guidelines that pertain to the ethical coverage of mass shootings.

South Korea’s rapid industrialization and democratization led to policy reforms that allowed women to invest more heavily in their education, career, and leisure beyond the domestic sphere. Consequently, these women became active participants and consumers of the goods and services within their society, as exemplified by their consumption of media. Given that Korean women in their twenties and thirties have embraced strategies to improve their status as citizens who operate in society in ways that transcend traditional normative, restrictive spheres of action, we would expect them to explain their consumption habits in terms of how the cultural objects resonate with their own experiences. Instead, they reveal ambivalence with regards to the value of these dramas as accurate representations of Korean society. Why? I argue that the widespread consumption of Korean dramas replete with mixed messages that call into question these women’s self-fashioning aspirations can be explained as a function of their ability to detect and stand apart from the submissive qualities reflected in female characters whose behavior represents a capitulation to traditional gendered norms. Through open-ended interview questions about professional women’s viewing habits and career objectives, I demonstrate how the critical distance attendant upon drama consumption is an agentive coping mechanism beyond a passive act of acquiescence to gendered discrimination, and is premised on self-perceptions of critical acumen nurtured by their academic and vocational background. Such knowledge resulting from women’s intense focus on education derives from their perception of education as a conduit for the actualization of career aspirations, which equipped them to interrogate gendered power relations that pose challenges to their success. Critical acumen is viewed as the source of their capacity to recognize and distance themselves from popular media’s representation of gendered socio-economic inequality and the broader patriarchal discourse in Korea that perpetuates norms of women’s submissive position.

The misfolding and aggregation of free light-chains into amyloid fibrils is the hallmark of antibody light-chain (AL) amyloidosis, a fatal disease associated with the accumulation of amyloid species in tissues throughout the body, including the heart and kidneys. Current treatment options, including chemotherapy and bone marrow transplant, do not address the causes of aggregation on a molecular level. Molecular dynamics (MD) simulations were used to investigate misfolding pathways in the aggregation of two light chain monomers, Jto and Wil. These simulations showed that under amyloidogenic conditions, conversion from beta-sheet to alpha-sheet secondary structure was observed in both Jto and Wil. Misfolded conformations, obtained from the MD simulations, were used to guide the design of alpha-sheet peptides, which have been used previously to inhibit amyloid formation in diverse systems. The designed peptides were evaluated computationally by docking them against misfolded conformations of Wil, and the best performing peptide was chosen for future experimental work to explore its potential to limit aggregation.

Previous studies investigating the perception of sexual misconduct by individuals in a university setting have not examined the effects of socioeconomic status on attitudes towards sexual misconduct. While these effects were considered in a university setting, understanding male perceptions of sexual misconduct more broadly is becoming increasingly relevant as allegations against high status individuals of varying political backgrounds continue to emerge. This paper paves the way for future research as to the effects of socioeconomic status on these perceptions at a more universal level. Using a survey composed of different hypothetical scenarios, this paper examines the relationship between the socioeconomic status of a male perpetrator and the attitudes of male college respondents regarding sexual misconduct toward women. Male undergraduates at the University of Washington were recruited from different residence halls and classrooms on campus to ensure sociodemographic variation in the sample. The data supported an analysis of how perpetrator’s socioeconomic status and respondent’s socioeconomic status may separately or jointly shape perceptions of hypothetical misconduct, and whether a respondent’s beliefs about feminism influence these associations. This study expects to observe a significant impact from both the socioeconomic status of the perpatrator and the socioeconomic status of the respondent both jointly and when considered separately.

Joubert syndrome (JS) is a neurodevelopmental disorder characterized by developmental delay and a specific hindbrain malformation resulting in the “molar tooth sign” (MTS) as seen on MRI. Individuals with JS have variable intellectual disabilities, polydactyly, retinal dystrophy and cystic kidney disease. JS is classified as a ciliopathy—disorders with overlapping phenotypes affecting 1/1000 live births combined. Currently, 36 genes when mutated cause JS, and all their encoded products localize in and around the primary cilium—a cellular organelle important for signaling and human development. We recently identified the newest JS-associated gene ARMC9 and its function, like the molecular mechanism(s) underlying JS, is unknown. Our preliminary data suggest that ARMC9 is required for cilium stability by promoting post-translational modifications (PTM) of ciliary microtubules. In stably ciliated, fixed (non-living) cells, ARMC9 localizes to the ciliary base, but to understand ARMC9’s role in cilium stability, we must determine ARMC9 localization during ciliogenesis (ciliary growth). We hypothesize that ARMC9 redistributes to the ciliary tip to promote tubulin PTMs during ciliogenesis. To test this hypothesis, I am using GFP and BFP (green and blue fluorescent protein) tags to visualize ARMC9 and primary cilia respectively. I created 5HT₆-BFP, a DNA vector encoding a BFP-tagged serotonin receptor fragment called 5HT₆ which naturally localizes to cilia. Currently, I am optimizing the transfection of 5HT₆-BFP and ARMC9-GFP into control cells for live imaging. As suggested by our data, I expect to see ARMC9 at the ciliary tip during growth, then redistribution to the base once the organelle is built. Determining where ARMC9 localizes during ciliogenesis will give us additional insight into its mechanism of action and role in JS. Ultimately, this work will allow us to identify therapeutic targets to mitigate the progressive features of JS and improve the quality of life of affected individuals.

 The so-called DREAMers are the current generation of largely undocumented youth named after an unrealized piece of Congressional legislation known as the Development, Relief, and Education for Alien Minors or "DREAM" Act. These youth, many of college-age, are the source of an unrelenting voice for the advancement of immigrant, civil, and human rights throughout the United States. Their movement mirrors earlier struggles that resulted in significant social, economic, and political change; taking the form of direct-action protests and involvement with state, national, and transborder organizing campaigns through social media networks. This ethnographic research project explores the DREAMers' Movement in terms of activists' enunciations of identity, subjectivity, and civil disobedience in the context of the State of Exception created by the Trump Administration's engagement in biopolitics. I address the principal research questions: Are new radicalized political subjectivities emerging from the widely shared daily-lived experiences of precarity among the self-identified members of this movement? How does this subjectivity shape DREAMers' perceptions of and engagement with identity politics and civil disobedience in their rebellion against their status as bodies without rights? These questions were research through ethnographic methods, such as one-on-one interviews and participant-observations. Ultimately noting new forms of engagement in activism and the creation of new identities and ideologies surrounding civil disobedience, this project will provide a scholarly space for reflections on the DREAMers' Movement and its prospects for transforming national and transborder narratives of self, citizenship, and belonging in this political era.

Prevention of aquatic invasive species transmission by recreational fishing and boating is a fundamental management challenge. These activities can entrain non-native plants and animals via tangled lines, bait buckets, or hull encrustation, leading to introductions into new waterbodies. With hundreds of millions of people participating in fishing trips each year, understanding angler movement behavior can provide critical insight into the most effective locations and scales at which to apply preventative measures. Angler behavior is often inferred from infrequently and sparsely conducted surveys that provide limited spatial and temporal insight into this challenge. Here we capitalize on a big data opportunity provided by ReelSonar’s recently launched iBobber, a sonar-enabled bobber with over 3,000,000 records of fishing location, water depth, and environmental variables collected over three years. By quantifying geographic patterns of fishing activities and assessing how these patterns change seasonally, we explore angler behavior in terms of fishing frequency and distance traveled between sites, and characterize the attributes of fished ecosystems. Our study offers novel insight into spatiotemporal patterns of angler behavior and carries important implications for predicting and preventing future transmission of aquatic invasive species via recreational fishing.

Seasonal stratification of the water column likely influences food availability to mussels grown at certain depths on aquaculture lines, as well as the environmental conditions experienced by the mussels. Fatty acids are important structural molecules that reflect the diet of the organism, such that fatty acid composition provides information on how the condition of mussels grown in different environments responds to food changes. Food sources vary based on a number of environmental conditions, including water temperature and turbulence, which differ between stratified water layers. Fatty acids in aquaculture mussels grown at 1m depth were compared to those at 7m in depth in the summer and fall of 2016 to test effects of varying environmental conditions between the depth layers. The results showed significant variability in the fatty acid composition of mussels grown at different depths in the summer months, but none in the fall. The difference between depths was contingent on the season. The variability in the summer months is likely due to stratification from increased surface temperatures, which decreases mixing and nutrient supply to mussels at lower depths. Stratification is then reduced in the fall and may explain homogenization of mussel fatty acid signatures from that period. In 2017, monthly sampling at the two depths was repeated and another experiment analyzing mussel plasticity was conducted in which mussels growing at 1m and 7m depth were switched during the summer and monitored at the new depth. Fatty acid signatures of switched mussels are predicted to adjust to become consistent with signatures of mussels established at the new depth by the end of the five-month sampling period. The results of this study will demonstrate the adaptability of mussels to new feeding environments and the effects of environmental changes on mussels as variable water conditions impact their algal food sources and overall health.

Despite the large number of gametes that clams release, very few offspring survive to reproductive age and harvestable sizes. There are several ways that aquaculturists try to protect young settlers, including adding gravel on top of fine sediment. We tested whether the addition of gravel helped decrease the mortality rate from small crabs in lab experiments. We tested predation rates on juvenile manila clams, Ruditapes philippinarum by the hairy shore crab, Hemigrapsus oregonensis in different sediments. Clams were placed in tubs with no sediment (NS), fine sand (FS), or sand with gravel on top (SG). After allowing time for the clams to burrow, crabs were added to each tub and given 24 hours to consume the clams. Crabs consumed some clams in all treatments although there was high variation among individuals. Gravel addition did not reduce predation rates compared to fine sand alone, but there was a trend for more predation in no sediment than with sediment. We also tested the ability to consume small clams of different predators that live in the same sediment habitat as R. philippinarum. The worms, Nereis brandti, Paranemertes peregrina and Hemipodus borealis all showed no predation on clams within a 24-hour period. The snail, Alia also showed no predation on juvenile clams. By understanding multiple factors that lead to juvenile clam mortality, fisheries can improve upon their methods to increase harvestable populations.

Within the dimensions of temperament, effortful control (EC) is the ability to regulate urges over certain actions and adapt to the demands of an environment.  EC is salient to study for its contributions to socio-emotional development, regulations, and child adjustment. It is instrumental to further examine the role of EC as it allows the caretaker to handle the child and take actions to alleviate their undesired dilemma. In this secondary correlational study, we examined the positive association between children’s (N= 301) EC levels from kindergarten to second grade and adjustment to school, including their academic performance and peer relationship quality. Measures include reports from both parents and teachers of children’s peer relationship, effortful control, the relative level of chaos in the classroom, and children’s standardized assessment of academic achievement. We analyzed whether classroom chaos based on teacher reports modified the relations between EC and children’s adjustment. We predict that for children in low chaos classrooms, EC would correlate to stronger academic performance than for children in high chaos classrooms. For children in high chaos classrooms, we predict that EC has a stronger association to peer relationships than children in low chaos classrooms.

Antibiotic resistance is a major public health problem. For example, in people with the genetic disease cystic fibrosis, Pseudomonas aeruginosa causes chronic lung infections that resist treatment to all existing antibiotics. Gallium is a promising new antimicrobial agent that works through a novel mechanism of action. Bacterial uptake systems are unable to distinguish gallium from iron due to their nearly identical ionic radii. Once inside, bacterial gallium is thought to disrupt iron-dependent processes because Ga³⁺ cannot be reduced in physiological conditions, and iron's biological functions depend on its capacity for redox cycling. Here I sought to better understand gallium’s mechanism of action by identifying gene mutations that decrease P. aeruginosa gallium sensitivity. To accomplish this, I used transposon (Tn) mutagenesis, which transfers a genetic element to random locations on the bacterial chromosome thereby inactivating genes. Of the 295,000 mutants generated, I selected for mutants capable of growing in the presence of increased gallium compared to the parental strain. Using a procedure known as rescue cloning, a restriction digest was performed on the chromosomal DNA of these mutants to produce individual fragments. One of these DNA fragments will contain the Tn insert and chromosomal DNA flanking that insert. The Tn insert encodes resistance to gentamycin and holds the capacity to replicate as a plasmid in E. coli. I ligated the isolated fragments and transformed E. coli, selecting for gentamycin resistance. I isolated this plasmid DNA from two mutants and their Tn insertion sites (and the genes inactivated by the Tn) were identified by sequencing the DNA surrounding the Tn inserts. These genes were found to be involved in iron transport. By completing these experiments, I hope to suggest hypotheses for the roles these genes play in gallium sensitivity and to provide data useful toward guiding its development as an antibacterial agent.

Research into health disparities often focuses on minority groups, but there is a distinct lack of literature surrounding multiracial peoples' experiences in healthcare, especially with racial microaggressions. Improving our understanding of their experiences with microaggressions presents an opportunity to enhance the communication process between providers and patients. This study aims to characterize the manners in which microaggressions manifest in the healthcare setting for multiracial individuals and families. Thirty one individuals who (1) identified as multiracial (i.e., more than one race) or were part of a multiracial family and (2) who received or had a family member receive healthcare within the past 12 months shared their healthcare experiences with racism, racial bias, and racial microaggressions in an interview or focus-group setting. Using content analysis, we identified six predominant raical microaggressions: mistaken identity, mistaken relationships, fixed forms, entitled interrogator, pervasive stereotypes, and intersectionality. Multiple participants stated that although these microaggressions were similar to those they experienced in everyday life, it was fundamentally different in the healthcare setting due to the power dynamic between patients and providers. Obtaining a more nuanced understanding of how multiracial microaggressions present in healthcare allows for the identification of areas in patient-provider communication that can be improved to provide more culturally competent care, as well as encourage greater patient engagement with their own health in this setting.

36.7 million people worldwide are living with HIV/AIDS, of which almost 15 million receive antiretroviral therapy (ART). These patients require regular HIV-1 viral load (VL) tests to monitor ART effectiveness and compliance. However, the majority of affected people live in low-resource settings where disease monitoring through medical laboratory-based systems, such as nucleic acid amplification tests (NAATs), are inaccessible. There is an increasing need for accurate, affordable HIV-1 VL tests at the point-of-care (POC). We previously demonstrated the ability to leverage an electrokinetic separation and preconcentration technique, isotachophoresis (ITP), and an isothermal nucleic acid amplification method to develop a proof-of-concept POC NAAT for extraction, amplification, and detection of nucleic acids from human serum. The limit of detection (LoD) of our paper-based test was hampered by the loss of nucleic acids during ITP across the paper membrane. This work is focused on lowering the LoD of our test by improving the isotachophoretic extraction of nucleic acids from human serum. We have addressed the adsorption of nucleic acids by screening membrane types and pre-treatment methods. We have observed significant nucleic acid entanglement of DNA greater than 50,000 base pairs in length, which we can mitigate using DNA shearing techniques. We have also developed specialized ITP chemsitries for increased extraction efficiency. The completion of this work will result in more effective separation and purification of nucleic acids from human serum, ultimately leading to a reduction of target loss and improved test sensitivity. Employing the ITP extraction techniques developed in this work will aid our lab's ongoing efforts to create a POC NAAT for monitoring HIV-1 viral load.

Cancer stem cells are thought to play a role in relapses and metastasis in numerous cancers. The inability of traditional cancer therapies, such as chemotherapy, to eradicate these cancer stem cells prompted a search for small molecules that induced apoptosis in cancer stem cells. Drosophila germline stem cells can be used as a model system to emulate cancer stem cells. Upon irradiation, Drosophila germline stem cells are able to survive apoptosis through a molecular signal released by the apoptotic daughter cells via the TIE receptor. We have conducted an in vivo drug screen of 512 compounds in Drosophila melanogaster to find drugs that would disrupt this protective mechanism and induce apoptosis. In particular, Camptothecin, NSC 125197, and NSC 127458 were effective in killing germline stem cells. To test the effect of the small molecules we fed female flies the compound for 3 days, dissected and fixed the ovaries and stained for an apoptosis marker, activated caspase, and the GSC marker, adducin. We quantified the effect of the drug by analyzing the number of germline stem cells and caspase signaling on a confocal microscope. Through this system we aim to find potentially new, and more powerful anti-cancer drugs that can affect cancer stem cells. Future directions include attempting to understand the mechanism of action of these apoptotic compounds in hopes that they might be useful in the fight against cancer stem cells.

The Jasmonic Acid (JA) sensitive system is an important stress and pathogen resilience pathway in plants. Understanding the kinetics of the components of this system allows for a more rational approach to improving crop resilience than traditional breeding.  MYC transcription factors upregulate the expression of particular defense or stress response genes, and these are inhibited by JASMONATE-ZIM-DOMAIN (JAZ) proteins, which are in turn degraded in the presence of JA-Ile, the bioactive form of JA. This leads to a system whereby MYC transcription factors are only active when JA-Ile is present. The variable defenses plants are capable of mounting may be regulated by differential interactions between some of the 12 JAZ proteins and 3 relevant MYC proteins in Arabidopsis thaliana. We have used a fluorescent yeast model to characterize the differences in those interactions in order to predict changes in plant responses when particular JAZ proteins are up or down regulated. Although we have been unable to replicate the canonical direct repression of MYC transcription factors by JAZ proteins, repression was observed when the JAZ protein was fused with an Mxi1 repression domain. This allows us to determine the relative effect of each JAZ protein on MYC transcription factors. A rough model involving related Hill functions is built using this information which can be used to predict the effect on the downstream response based on the abundance of the different JAZ proteins. The model can then be verified in planta using a dCas9 transcription factor with an appropriate gRNA, and a MYC-responsive GUS gene in a transient transformation.

Necroptosis is a lytic and immunogenic form of programmed cell death (PCD), characterized by pro-inflammatory cytokine production and the release of intracellular molecules, including cell-associated antigens. This form of death occurs after RIPK3, Receptor-Interacting Protein Kinase 3, activation. RIPK3 is a cell death regulator that promotes necroptosis. Previous studies have shown that necroptotic cells can promote maturation of antigen presenting cells (APCs) and are capable of priming antigen-specific CD8+ T cell responses. Understanding the downstream immunogenic effects of necroptosis allows for implicative applications within the field of tumor immunology. Previous work has shown that necroptotic NIH-3T3 fibroblasts produce inflammatory cytokines and chemokines, contributing to their immunogenicity. To recapitulate the immunogenic nature of 3T3s, we evaluated inflammatory chemokine and cytokine production via ELISA (enzyme-linked immunosorbent assay), quantifying these productions through antibodies and color-change, from necroptotic tumor cell line supernatants, including B16.F10 melanoma and LL/2 adenocarcinoma cells. Surprisingly, our results did not show significant chemokine or cytokine production from necroptotic tumor cells, suggesting that anti-tumor effects are not from signals derived from the tumor micro-environment (TME). This suggests that other forms of signaling downstream of RIPK3 activation, such as upregulation of non-chemokine transcriptional programs, could be the source of inflammatory signal production by necroptotic tumor cells. Further actions include RNA sequencing of necroptotic cancer cell lines to differentiate global changes between apoptotic and necroptotic forms of cell death, to provide unbiased analysis of transcriptional changes. With evidence of T cell-mediated immunity and the immunogenic nature of necroptosis, induction of this form of cell death within the TME will activate anti-tumor immune responses, potentially controlling tumor growth and contributing to the field of immunotherapy.

This project aims to create a comprehensive park master plan for the transformation of the City of Westport, WA’s Pacific Ave property into a functional public park by utilizing principles of ecological restoration and community-based restoration. The City of Westport recently finalized its Comprehensive Park and Recreation Plan. Within the plan, the Pacific Ave property is zoned as a park, but is not currently used as a public park and has no intention of redevelopment by the city in the near future. The underutilized site has served many important uses throughout its history, and is located on the shore of the Elk River with a beautiful panoramic view of the bay and the mountains. The master plan is focused on research regarding site restoration with an assessment of the needs of both the community and the City of Westport. The information gathered through research and community engagement meetings will be synthesized into a master park plan for the Pacific Ave Property that will be presented to the Westport City Council in order to pursuade them to pursue funding for the project. This parcel holds historic and aesthetic value, and with restoration, it can be turned into a unique and valuable asset for both the city and the community.

Reactive oxygen species (ROS) are byproducts of photosynthesis that can damage plastid DNA (ptDNA), and 8-oxoguanine (8-oxoG) is the most common DNA lesion. Our lab previously showed that maize ptDNA damage, in general, increases during the development of non-green proplastids to green, photosynthetic chloroplasts. The objective here is to determine the amount of 8-oxoG in ptDNA during plastid development under light and dark growth conditions. DNA damage will be assessed using a semi-long qPCR procedure and the enzyme formamidopyrimidine DNA glycosylase (Fpg) which selectively removes 8-oxoG lesions. Testing of the semi-long qPCR method was performed with control DNA treated with damage-inducing UV light. After UV treatment, PCR amplification decreased, as expected for Taq DNA polymerase inhibition by bulky lesions. PCR amplification of ptDNA also decreased after UV light treatment of light-grown, dark-grown, and dark-to-light transferred seedlings. When ptDNA was extracted from plants grown in these three conditions, treatment with Fpg affected the PCR amplification, indicating removal of 8-oxoG lesions. 8-oxoG will now be assessed along the developmental gradient from proplastid to mature chloroplast. We may find more 8-oxoG lesions in mature chloroplast due to high ROS from photosynthesis than in the undeveloped proplastids, as well as more 8-oxoG in light than dark growth conditions.

Active nests at the world’s largest Magellanic penguin (Spheniscus magellanicus) colony at Punta Tombo, Argentina have declined 40% since 1987. Climate change has increased rainfall and intense storms resulting in high chick mortality. Although these large-scale weather changes are known to factor into the decline, the effect of weather patterns on the scale of individual days is uncertain. To gain insight into penguins’ daily foraging patterns throughout the annual breeding season, automatic tread scales were placed on a penguin “highway” so when a penguin crossed we could document their time and direction of crossing, weight, and RFID tag. We sought to redesign the scales to improve energy efficiency by switching to solar power and increase accuracy and durability by changing the protective covers on the devices. Most importantly, the modified scales were required to be waterproof to protect internal components from heavy rain and flooding. The batteries used to power the scales had to last 7 days before needing to be replaced. Lastly, the materials used had to withstand temperature fluctuations and be animal-proof. The new design implements solar panels to charge batteries for the scales and cable glands to prevent water ingress through sides of the scales. The updated scales are made of wood and fiberglass then encased in heat-sealable fabric and sealant for waterproofing. Prototypes were firstly tested in the lab to see if they resisted flood-like conditions. Next, we tested whether the scales performed well after being exposed to large temperature changes using temperature controlled rooms. Additional tests were performed in the field to determine whether the design modifications decreased the amount of water ingress and increased battery life. Long-term tests in the field will be important to see how the materials weather over time when faced with temperature fluctuations, flooding, and animal usage. 

Magellanic penguins (Spheniscus magellanicus) have highly variable reproductive success, and while most eggs successfully hatch, about 50% of the chicks survive to fledging. What determines which of the two chicks in a brood fledges? Typically the first chick hatches two days before its sibling, and has an early size advantage in terms of weight. We predict that larger chicks will occupy the preferred nest position, switching from the warmer position early in development to the optimal feeding position. We also expect that chicks more often found in the “better” position at these different stages will be more likely to fledge. To assess optimal nest positioning we collected weight, nest position, and fledging data on over 1,200 chicks during the 2017-18 Magellanic penguin breeding season at Punta Tombo, Argentina. We extracted data from our SQL Database using a number of SQL queries, and we will use R Studio to analyze our results. We expect to find larger chicks preferentially in the back (warmer) position of the nest early in growth for better thermoregulation, and in the front of the nest later in development since they would be closer to the adult’s head during feeding. Developmental priorities should change as the chicks begin to independently thermoregulate at around 15 days old, so we expect a transition in chick positions at this time. Chicks consistently in the preferred position should have a higher likelihood of weight gain and fledging. These findings will further our understanding of the key factors and challenges in fledging and reproductive success at our study colony at Punta Tombo, Argentina.

Although crystalline two-dimensional (2D) protein arrays are often found on the surface of archaea and bacteria where they form a protective S-layer, their potential in bionanotechnology applications remains unfulfilled. Progress in computation has recently allowed the (re)design of proteins for self-assembly into arbitrary structures. We are working with a rationally modified protein from S. typhimurium that can self-assemble into large (> 100 µm) and thin (~ 5 nm) hexagonal 2D arrays pierced by ~ 3 nm pores upon addition of divalent cations (e.g., Ca²⁺). The goal of our research is to test the ability of these arrays to organize gold nanoparticles (AuNPs) with desirable plasmonic characteristics. To this end, we stain protein arrays with the lipophilic fluorescent dye Nile Red, and analyze fluorescence microscopy images to quantify how the decoration of arrays with various concentrations of AuNPs affects the rate of photobleaching of the Nile Red fluorophore. Understanding how AuNPs bind to protein arrays could lead to further applications, such as templated growth of inorganic materials or co-assembly of enzymes and inorganic catalysts.

Familial caregivers often serve as the primary coordinator of care for children with medical complexity (CMC). However, they currently lack a central tool to organize their child’s health information from multiple fragmented information sources and support their unique information needs. The primary objective of this study was to develop a user-centered, care organization tool by incorporating the information needs and preferences of CMC caregivers. Following a user-centered design methodology, we first conducted interviews with CMC caregivers between 3/16-11/16 to understand their information needs and elicit their preferences for a care organization tool. Next, we conducted design sessions with caregivers between 8/17-12/17, which involved content categorization activities, drawing exercises, and scenario-based prototype testing. Between design sessions, we applied content analysis to interview and design session transcripts, and incorporated findings into the ongoing development of a functional prototype. We conducted interviews with 17 caregivers and design sessions with 6 caregivers. We grouped findings into two categories: design and implementation. An overarching theme of both categories was the need for customizability, as the primary purpose of the tool differed based on the caregiver’s main information needs. In terms of design, caregivers voiced a desire for both mobile and web interfaces, with a customizable home screen, containing templates to track medications, symptoms and major events, and outline communication preferences based on their child’s developmental status. In terms of implementation, caregivers were agreeable to the idea of a cloud-based tool which would provide easy access to emergency information. However, they wanted control over customizable permission settings for others to view and/or edit other content within the tool. We developed a novel, user-centered, cloud-based care organization tool for CMC families by engaging caregivers in the design process. Next steps include examining prototype usability, effectiveness, and integration with provider health records.

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!

In this economics thesis, I addressed one of the effects that the Affordable Care Act has had on US Health Care since its full implementation in 2014: supply side effects. Specifically, I answered the following question: what is the effect of the implementation of the Affordable Care Act on patient wait times in primary care offices? In order to narrow the field of research, I focused on the tier of the ACA that called for increased Medicaid expansion. Since Medicaid has not been expanded evenly in all states, it has created a robust control group for causal studies such as this. I used a difference-in-difference model and a multivariable regression to establish causality between Medicaid expansion and increased patient wait times. I used data gathered from the Current Population Surveys from 2004, 2009, 2014, and 2016, in 15 different cities around the US (some faced increased Medicaid expansion, and others did not). The dependent variable data (new patient wait times) were extracted from a 2017 Merritt Hawkins Survey which found the wait times for new patient appointments in different medical services across the 15 different cities for the four different years. The different services are as follows: cardiology, dermatology, obstetrics-gynecology, and orthodpedic surgery, and family medicine (where wait times were only measured in 2009, 2014, 2017). This thesis has been fully developed over a yearlong process of data collection and analysis. My findings highlight areas of the ACA that can be improved to accommodate the proven increased demand for health care, especially given that the supply of health care services responds slower than demand for health care, leading to longer patient wait times.

This research focuses on the mathematics of gerrymandering. Gerrymandering refers to how political parties draw district boundaries to give them better odds at receiving a majority during congressional elections. Every 10 years district boundaries in the United States are redrawn for congressional elections by the current majority party. With such change in political cartography, redrawing district boundaries not only affects who wins but also the people who live within them. Given the loosely defined criteria for redistricting, we seek to quantify the process of redrawing district lines to determine when this partisan process becomes an act of manipulation and exclusion. We will be use The Metropolis Hastings (M.H.) Algorithm to produce a random walk that has a stationary distribution that will be the probability distribution of all possible districting plans for a given U.S state. By collecting congressional maps and election results, we implemented the M.H. algorithm in python to produce sample spaces for Washington State and Iowa. We will simulate local and federal redistricting requirements using self-defined parameters which measure: compactness of districts, population division, division of counties, and minority voter populations. We simulated election results with respect to our sample districts and compared the simulated outcomes with actual district maps and their election results. This study helps to determine if current redrawn maps legitimately reflect the people they purport to represent or if they are manipulations and subversions of our democratic process.

The Internet of Things (IoT), is used to describe a network that connects objects installed with autonomous components to other objects and to computers. This has made inroads into many aspects of our lives. The application of IoT has enhanced our workplace with such technologies as RFID sensors for tracking and replenishing resources. Yet, there is limited research about the way human processes, and in particular, team processes are changed by IoT objects. Herein, we focus on sociotechnical systems theory in order to connect IoT and team processes, where IoT objects are differentiated based on functionality. We draw on the team process framework to clarify the type of task-oriented activities team members engage in overtime as they collectively complete work projects. We connect different IoT objects to team processes and propose that the synergies may enhance team efficiencies and effectiveness. As well, we provide a real-world scenario about air conditioning service that illustrates how different IoT objects may be introduced to affect the team processes that apply. Using my business discipline perspective, my research provides a IoT framework that projects can adopt to improve team efficiency and effectiveness. This research demonstrates how “smart” automation engages with service, via the aid of Internet of Things, enhances team processes, and may improve the service customer experience. From other disciplines, this research encourages information technology and hardware advancement to explore more comprehensive and utilized networks to abridge convenience created by updated tech and skills with people’s desire and satisfaction, that can be applied to any aspect of contemporary human lives.

This work seeks to address some problems faced by deaf and hard of hearing persons who work in confined or hazardous spaces. The issue they face that I am focusing on is the timely access of alerts and alarm, which are commonly provided solely through sound. Many approaches used in more general work conditions, such as flashing wall lights or another person notifying them, are heavily impeded by a confined work area. Additionally, a hazardous environment requires strict safety features regarding electronics. Any tool used must not have exposed electrical connections that could cause a spark or that it could break in such a way that could provide a source of ignition to flammable gases. Currently available bluetooth headsets and pagers do not meet these safety specifications and would be an additional piece of equipment for workers to carry. We have worked to develop a device that can clip onto existing safety equipment, conform to hazardous environment safety standards, and pair with the user’s current cell phone and radio to notify them through vibration and light patterns. We are working with people who would benefit from the device as the design improves to its signals are clear in an industrial environment and that it suits their need. Future developments include allowing the device to relay more complex messages from multiple sources.

Spinal cord injury (SCI) is a debilitating disease with few treatment options available for recovering motor function. Based on past studies using electrical stimulation of the spinal cord, we believe that long-term optogenetic spinal stimulation (OSS) may improve motor function after an SCI. We are investigating this therapeutic potential using a rat model of SCI with an implantable LED to deliver optogenetic stimulation in vivo. However, activation of the LED produces heat that could damage the surrounding tissue. I have modified these LED implants by incorporating a thermistor that tracks temperature changes during optical stimulation. Using this device, I determined how the modulation of stimulation parameters affects heat production at the site of the implant and have identified several safe parameter sets. These results will inform the parameter choices used in future studies on OSS. An optimized OSS methodology has the potential to improve the lives of those with an SCI by enhancing their capability for volitional movement.

Large data centers, such as those built by Google, Amazon, and other information technology leaders consume about 1.3% of the world’s energy, of which about 40% is used on electronics cooling [1, 2]. This amounts to 245 TWh per year, which, with the average US price of 12 cents per kWh, amounts to about $29.4 billion dollars spent per year on cooling high heat semiconductors [3, 4]. The work presented here proposes an innovative way to improve this cooling process. The proposed concept features a levitating inner rotor using fluid bearings that result in no physical contact between solid parts, eliminating friction. For the first time, precision-manufactured plastic parts are utilized to achieve both a low cost and a high reliability. The micropump is expected to last in operation for over one million hours Mean Time to Failure. This work emphasizes model-based design verification and optimization to ensure adequate performance for different form factors – so that a drop-in replacement of an air fan passive heat sink can be quickly developed for every microelectronics product. Twenty-four designs and prototypes were used in evaluation of two key criteria in order to optimize the pump’s design. Three separate herringbone geometries, square, beveled-step, and circular, of herringbone grooves were prototyped based on experimentation of optimum groove parameters. These findings helped determine the optimal layer height of 100 micron for use in the micropump design. Finally, the application of a sensorless, brushless DC motor reduces overall cost of the pump and increases efficiency due to the removal of friction.

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

Lateral flow tests are assays conducted on porous media, commonly referred to as paper, that can detect and quantify analytes in a sample. They have the potential to return results within minutes and can be used in low-resource or non-medical settings. Protein adsorption is critical in these tests because protein interaction with a media can affect the delivery of reagents or choice of blocking agents to prevent nonspecific binding. A computational model of the fluid and adsorption physics may improve the development of paper-based assays. Yet-to-be-published data from the Yager group evaluates protein adsorption based on the deposition and analysis of protein spots on paper. The computational model used is derived from Darcy’s law, commonly used to model fluid flow in porous media and to calculate volumetric flow rates. This model makes two main assumptions: the porous media is fully saturated, and there is zero outflow on the boundaries of the media. These assumptions are not applicable because the protein spot dries as a result of evaporation, creating a non-zero outflow at the surface of the paper. The saturation level in the paper will also vary therefore Darcy’s law is not an adequate representation of the paper. My project aims to develop a more accurate computational model of fluid and protein absorption dynamic by modeling protein spots on paper. I incorporated an evaporation component that will allow the use of Richards equation to model fluid flow, which applies to unsaturated conditions. This is coupled with a protein transport and adsorption component to achieve a complete model. Although literature on evaporation from sand or soil is abundant, these results cannot be directly applied to evaporation from paper. This model will aid the diagnostic community in better understanding their assays and ultimately help improve the sensitivity and specificity of their assays.

Microglia are the innate immune cells of the central nervous system that exhibit a sustained pro-inflammatory response in the Alzheimer’s disease (AD) brain. Regulation of inflammatory gene expression in microglia by microRNA miR-155 modulates transition between distinct phases of the inflammatory response. Though altered expression profiles of miR-155 is seen in other neurodegenerative disorders, the precise role of this microRNA in modulating inflammation and downstream behavioral deficits in mouse models of AD remains unknown. We hypothesize that microglia specific deletion of miR-155 will alter neuroinflammation and behavioral phenotypes in transgenic mice expressing human mutant amyloid precursor protein and presenilin 1 (APP/PS1), an AD model that exhibits Aβ pathology and memory impairments. We generated trigenic (Cx3cr1-Cre^+/-/Floxed-miR155^+/+/APP/PS1^+/-) to acutely induce microglia specific Cx3cr1 driven Cre-mediated deletion of floxed miR-155 alleles in the APP/PS1 mouse AD model. Changes in inflammatory gene and microRNA expression in microglia 6 and 9 months post miR-155 deletion were assessed by qPCR. We expect that conditional deletion of miR-155 leads to anti-inflammatory gene expression and thus improve cognitive performance. To measure anxiety, spatial memory, and spatial learning, we employ open field chambers with and without novel object recognition and T-maze assessments. Preliminary results support the hypothesis that conditional miR-155 deletion specifically in microglia alters innate immune gene expression and behavioral phenotypes in the APP/PS1 mouse model of AD, further elucidating the impact of the molecular regulators in neuroinflammation in AD.

Microglia are the resident immune cells of the CNS and are hypothesized to influence aging in the brain. Like somatic cells, microglia can be replaced by self-renewal. Recently, some studies have suggested that new microglia derive from asymmetric cell division of a progenitor population. Microglia progenitor cells have been difficult to study due to a lack of specific molecular markers of this population. However, the Garden lab has recently identified novel candidate markers. We hypothesize that in neurodegenerative disorders associated with advanced age, microglia progenitor senescence may contribute to disease pathology. To efficiently study the senescence of microglia progenitors, we turned to neonatal mixed glia cultures, in which the presence of microglia progenitors has long been inferred. In these cultures, microglia are harvested from cells floating above a monolayer culture of mixed neonatal glial cells. The size of each microglia harvest generally decreases with successive harvests. This suggests that microglia progenitors in the attached monolayer may become senescent after multiple rounds of the cell cycle, leading to stagnation in the generation of new floating microglia. We evaluated microglia progenitor senescence in neonatal mixed-glia cultures by labeling with BrdU, a thymidine analog taken up by proliferating cells and remaining in their daughters. Microglia harvested from these cultures weekly were assessed for BrdU incorporation using flow cytometry and immunofluorescent microscopy. We co-labeled floating microglia and dissociated monolayer mixed glia cultures with antibodies directed against a progenitor marker (CD133), a microglia marker (Iba1), and BrdU. The attached mixed-glia cell layer was also labeled for SA-ß-Gal, an indicator of cellular senescence. Progenitor senescence will be detected by a decrease in CD133/BrdU-positive cells and an increase in CD133/ SA-ß-Gal positive cells.

The goal of this project is to explore how Brain-Computer Interface (BCI) devices are depicted in the media, especially news media. BCI technology is not new, but it is still very much in its infancy, with few feasible embodiments usable for practical, non-medical applications. Additionally, a majority of BCIs that are (only somewhat) feasible require dangerous invasive surgical procedures. Yet in the last year, the technology has received a higher-than-average level of press coverage. Media coverage of upcoming medical technology is not a trivial issue. Substantial research has shown that positive portrayals of novel medical technology in the media can indirectly affect patient consent to undergo treatment. Consequently, we argue that it is essential that the media reports and discusses the ethical impacts of BCIs. We aim to discover whether media coverage depicts the technology realistically, discussing its shortcomings, risks associated with its use, and ethical issues related to neural implantation. We use a research software called FACTIVA to survey and analyze the depiction of BCI technology inn English-speaking media such as news publications, radio transcripts, press releases, etc. This content analysis allows us to understand mass media values and narratives in three general ways: 1) it generates evidence to demonstrate whether there is any positively-biased and over-enthusiastic depiction of BCI in mass media; 2) it sheds light on whether there is an absence of discussion of risks and ethics associated with BCI technology; and 3) it exposes unrealistic discourse, such as wide-reaching claims of the panacean nature of BCIs (i.e. transhumanist arguments, the race against artificial intelligence, etc.). In brief, this study allows us to explore whether media misrepresentations of BCI could influence the narrative about the technology in ways that may increase the risk of harms for prospective patients and their families.

At the 2017 Undergraduate Research Symposium, I presented a low-cost, automated device for influenza detection that was being developed in the Yager lab. After creating, testing, and optimizing this device, we were left with many questions. While certain components of fluid flow in paper are understood, there is much more to learn. In this device alone, three different types of paper were used to run the two-dimensional assay. Current unanswered questions include the following: how do additives affect protein deposition, rehydration, and capture? How much of a dried protein on paper can be rehydrated by a passing solution, and which paper and solution properties affect this value? How do the viscosity and complexity of our patient samples affect the quality of our results? Our overall goal is to determine how to optimize our test line and generate a better understanding for optimization of future diagnostic devices. To make progress towards this goal, my project centers on the development and characterization of a laboratory technique to quantitatively study the effects of these parameters on protein interactions with membrane surfaces and other proteins bound to those membrane surfaces. Improving our understanding of these interactions in membranes will enable better diagnostic device optimization and enable illness detection with lower amounts of infected sample – allowing for earlier detection and better disease treatment. Through the development of this testing apparatus, I have begun to address these questions.

X-ray spectroscopic techniques utilize selective x-ray absorption or fluorescence to interrogate the element-specific properties of atoms in a sample of interest, such as oxidation state, ligand identities, and bond lengths. Until recently, x-ray spectroscopic techniques have been primarily limited to large-scale synchrotron facilities employing expensive commercial crystal analyzers. This leads to high barriers to access because of high competition for synchrotron beamtime and the large cost of acquiring optics not presently possessed by the facility. Over the past several years, the Seidler lab has pioneered solutions to both these problems. First, the development of lab-scale x-ray absorption and emission spectroscopy apparatus has enabled a wide range of studies without need for the synchrotron, and second, by designing an inexpensive method for manufacturing the necessary crystal analyzers. I focus here on the second issue, improving the availability and decreasing the cost of the crystal analyzers. Crystal analyzers are at the heart of high energy resolution x-ray spectrometers. They serve the same role as a prism or grating in visible-light spectrometers, that is, they disperse x-rays into their component energies. Our work using temporary vacuum forming of silicon wafers reduces the cost of such optics from $5000 - $10,000 to only a few hundred dollars. Furthermore, the use of vacuum together with modern computer-assisted machining gives the freedom to use either the traditional spherical shape or a superior customized toroidal form, specific to each study. These advances in instrumentation will dramatically speed up analysis of materials and permit feedback on synthesis procedures, battery performance, detection of hazardous chemicals, and catalyst activity.

Periodontal disease (PDL) results from a serious infection in the gingival tissue (gum) that can eventually lead to tooth loss and jawbone damage. The disease is common with more than 3 million cases in the US per annum. Bacteria build up in plaque lead to gingivitis and periodontitis under improper oral hygiene. If left untreated, the supporting tissues of the teeth e.g., cementum and periodontal ligaments will be lost, therefore making the teeth and supporting tissues vulnerable to bacterial attack, leading to serious infections and, even, to death. Current approaches in regenerating periodontal ligaments include the use of bioactive molecules and barrier membranes for guided tissue regeneration using human stem cells. Although the utilization of such materials enhances the cell proliferation and differentiation to a degree, the absence of cementum-like tissue prevents the complete regeneration of periodontal ligaments on the tooth surface. The aim of this project is to develop a biomimetic strategy to restore cementum tissue and regenerate the periodontal ligaments using human periodontal ligament (hPDL) cells in vitro. Using peptide-guided remineralization, we created a new cementum-like mineral layer on exposed dentin. The hPDL cells are then cultured and seeded on the novel cemento-mimetic layer and induced to differentiate. The proliferation and differentiation of the hPDL cells are monitored in detail using 3-(4,5-Dimethylthiazol-2-yl)- 2,5-diphenyltetrazolium bromide (MTT) and alkaline phosphatase (ALP) assays, respectively. Our results show that the newly formed cemento-mimetic mineral layer facilitates the hPDL growth and differentiation. The method described herein offers a unique biomimetic solution to regenerate periodontal ligaments and thereby ultimately prevent tooth loss and eliminate periodontal disease. This work is supported by WA-State Life Sciences Discovery Funds, UW-School of Dentistry Spencer Funds, and Amazon-UW/CoMotion Catalyst Program.

Mutations in the Presenilin 2 gene, (PSEN2), cause early onset familial Alzheimer’s disease (FAD). PSEN2 encodes the presenilin 2 protein which forms the catalytic subunit of the gamma-secretase complex, responsible for cleaving amyloid precursor protein into fragments. One of the resulting fragments is Aβ_1-42, a major component of brain amyloid plaques and a clinical hallmark of Alzheimer’s disease. Microglia are the resident innate immune cells in the brain clearing the brain of Aß plaque and debris through phagocytosis. Without presenilin 2 protein present, levels of secreted cytokines increase implying a higher immune response, and recent data suggest that hyper-activation of an inflammation state can contribute to development of Alzheimer's disease. We hypothesized that FAD mutations can impair normal presenilin 2 protein function and therefore promote AD through dysregulation of immune function. We have developed a mouse model to study the impact of the most common FAD PSEN2 mutation, the PSEN2N141I, also known as the “Volga German” mutation. Previous experiments in the lab have shown that the absence of wild type PSEN2KO disrupts normal microglial phagocytosis of neuronal debris. My work involves measuring phagocytosis of apoptotic bodies by mouse primary neonatal microglia expressing the FAD PSEN2 mutation to determine if AD associated mutations contribute to AD through altering microglia phagocytosis behavior. Microglia from wild type mice, mice with presenilin 2 knocked out, and mice heterozygous for the human N141I mutation are collected and co-cultured with apoptotic cell bodies. Microglia and apoptotic cell bodies are membrane-labeled and FACS analysis is used to measure percent phagocytosis. My studies will further our understanding of how familial AD mutations alter the normal cellular behavior of brain immune cells and may highlight new areas in pathways appropriate for therapeutic targeting.

For many rising metropolitan cities across the United States, the implementation of a major mass-transit system is a potential means of combating unemployment by connecting citizens to jobs that might be otherwise inaccessible. However, relatively little is known about how the effects of mass-transit systems scale with population density, which may deter many cities that stand to gain from investing in such a project. This study examines the effect of population density on the impact of Commuter Rail, Light Rail, and Street-Car transit systems on unemployment rate across every metropolitan city in the United States, in order to enable more informed policy and investment decisions. In applying a difference-in-difference regression model to panel data that spans 192 cities from 1990 to 2016, it is revealed that the introduction of a mass-transit system results in a 19% average decrease in unemployment rate. In addition, it is shown that the existence of a mass-transit system reduces the effect of each percent increase of population density in driving up unemployment by 64%. This study’s findings underscore the viability and effectiveness of mass-transit infrastructure as a means of combating rising unemployment rates by providing citizens with a cheap and consistent method of connecting with a wider selection of job opportunities.

Klebsiella pneumoniae is a gram-negative bacterium that asymptomatically colonizes the intestinal and upper respiratory tract of healthy humans. It is also an opportunistic pathogen that causes bacteremia, pneumonia, urinary tract infections, and other severe infections in individuals with significant comorbidities. Klebsiella infections are often healthcare-associated and antibiotic-resistance is a major problem for treatment. A K. pneumoniae lineage known as multilocus sequence type 258 (ST258) is resistant to virtually all beta-lactam antibiotics, including the carbapenems, and many clinical isolates are also resistant to fluoroquinolones and aminoglycosides. Additionally, the capsule of ST258 confers resistance to phagocytosis by neutrophils and killing by the complement system. However, it is readily killed if phagocytosed. One possible therapeutic approach is to develop an antibody-based immunotherapy that targets the capsular polysaccharide (CPS) of ST258. As a step toward developing the tools needed for such an approach, we developed an enzyme-linked immunosorbent assay (ELISA) that can be used to detect CPS and titer CPS-specific IgG antibodies. Polystyrene ELISA plates were coated with purified ST258 CPS and then incubated with rabbit antiserum containing antibodies specific for CPS. Anti-CPS IgG was then detected with goat anti-rabbit IgG antibodies and a detection reagent. We anticipate the ELISA will be an important quantitative tool in our efforts to develop an immunotherapy that targets the CPS of K. pneumoniae.

T cell-based immunotherapy has shown immense therapeutic potential for the late-stage treatment of cancer. The synthetic ex vivo activation of T cells is a key step in manufacturing these therapies, inducing proliferation and cytotoxic functionalization of the cells before reinfusion into the patient. This is generally done with the use of artificial antigen presenting cells (aAPCs) consisting of antibodies triggering the receptor signaling necessary for activation directly conjugated to a spherical polystyrene bead. Although intended to mimic the function of antigen presenting cells (APCs) in the body, currently used aAPCs do not fully recapitulate natural size, morphology, or membrane fluidity, all of which have been demonstrated to be important determinants of activation properties. Therefore, there is a need for an activation platform that more closely mimics APCs in vivo, which could significantly improve the efficiency of T cell activation for use in cancer immunotherapies. To achieve this, we utilize cell-molded silica microparticles that retain the size and morphology of their cellular templates. The fusion of an antibody-loaded lipid bilayer to these silica microparticles results in a closer recreation of natural APCs. We have fabricated these cell-molded silica aAPCs with various cell template morphologies and lipid compositions. Using a variety of cell-based assays, we are characterizing the capacity of these aAPCs to induce T cell proliferation, cytokine release, and surface marker expression, all of which are metrics indicative of activation. If these results indicate that this platform successfully improves the efficiency of T cell activation as compared to current alternatives, this has the potential to improve the cost and scalability of these promising cancer treatments.

Ovarian cancer is the deadliest of gynecological malignancies, with approximately 70% of patients diagnosed at an advanced stage of disease. With the current standard of care, cytoreductive surgery plus chemotherapy, the relapse rate is about 70% and the 5-year survival rate is less than 50%. Innovative therapeutic interventions are greatly needed, and one promising new strategy mimics the body’s endogenous anti-cancer immune response. This immunotherapy approach uses donor T cells engineered to express a T cell receptor (TCR) that is specific for a tumor-expressed antigen. Mesothelin (MSLN) is a validated antigen target, frequently over-expressed in cancer cells compared to healthy tissues. Using the mouse ID8 ovarian tumor model, we found that T cells engineered to express a high-affinity MSLN-specific TCR can kill ovarian cancer cells. However, the T cells lose effector function over time, which correlates with increased expression of the T cell inhibitory receptors PD-1, Tim-3 and Lag-3, markers of T cell exhaustion. Signaling through inhibitory receptors is stimulated by respective ligands that we showed are present in the tumor microenvironment (TME). Blocking these “immune checkpoint” signals can improve T cell proliferation and anti-tumor function within various TMEs. By applying checkpoint blockade, we hypothesized that both donor and endogenous T cells will have prolonged longevity and increased effector function in our ovarian cancer model. In ongoing studies, ID8 ovarian tumor-bearing mice received MSLN-specific T cells plus antibodies that block PD-1, Tim-3 and Lag-3 checkpoints; T cell phenotype and function were characterized at early and late time-points. We will discuss our findings and the potential relevance of this combination immunotherapy as a clinical treatment of ovarian cancer.

Peripheral neuropathies involve the destruction of peripheral nerves, which leads to impairment of the neuromuscular junction (NMJ). This is the area where the nerve transmits information to muscle. NMJ breakdown will cause this synapse to degrade, generating symptoms such as reduced muscle contraction, respiration, and movement. The problem is that current efforts to develop treatments against peripheral neuropathies are severely dampened by having a lack of human-based models of synapses. Therefore, there is a need for a non-invasive method to explore and characterize synaptic function for future treatments. This research study offers a novel system to investigate the differences in neuromuscular junctions between healthy and disease states by utilizing induced pluripotent stem cells (iPSCs) to derive an in vitro NMJ. Procedures involving the differentiation of healthy-state iPSCs into motor neurons have been optimized. The iPSC cultures were matured until day 45 after induction towards a neural ectoderm lineage, and were analyzed using immunocytochemistry, imaging, patch-clamp electrophysiology, and flow cytometry. Differentiated neurons stained positive for neuronal marker p75, Islet-1 and choline acetyl-transferase (ChAT). Electrophysiology data showed neurons were capable of high degrees of repetitive firing sequences, while flow cytometry showed neuronal purity in culture was roughly around 97%. Human skeletal muscle myoblasts have also been differentiated into myotubes-the precursors for muscle tissue-and imaged for acetylcholine receptor clusters. The culture medium was supplemented with various additives in order to determine which medium promoted greatest acetylcholine receptor (AChR) cluster density and size. It was found that AChR clusters are more prominent and enlarged when the muscle cells are cultured with Agrin supplement. Ongoing studies are looking at combining these cell types into a novel contractility assay in order to investigate NMJ function in vitro. The establishment of this system will enable more effective applications for novel therapeutics and disease progression studies.

Stem-cell derived engineered cardiac tissues are a promising avenue for the research of heart disease, enabling disease-specific modelling and drug screening. However, their validity as a model hinges on the similarity to native cardiac tissue, both in super- and sub-cellular structure and organization. When cultured on nanopattern substrates, myocytes orient the sarcomeres along a similar axis, allowing for greater force production and higher similarity to native cardiac tissue, though the evidence of the finer details are obscured by the diffraction limit of light. Super-resolution microscopy has opened the door to the analysis of diffraction-limited biological structures, and one such recently developed super-resolution technique, Expansion Microscopy (ExM), has made this analysis more accessible. By embedding the fluorophores from an immunostained sample into an expandable hydrogel, sub-diffraction details are physically enlarged and made measurable on standard fluorescence microscopy equipment. In this work, expansion microscopy was performed on engineered cardiac tissue to evaluate the effect of the nanopattern substrate on sub-sarcomeric structure and organization. As expected, it was found that the sarcomeres were more aligned within the cardiomyocytes, and the length between the z-lines were increased when cells were cultured on the nanopattern substrate as compared to the flat substrate. In addition, the width of the Z-disks were significantly different in nanopattern cultured cardiomyocytes as compared to myocytes cultured on flat substrate. The transverse tubules, responsible for a unified action potential, were larger in diameter and better localized with the Z-line, and the myosin heads were closely localized with the actin filament. When examined with super-resolution microscopy, the engineered cardiac tissues display sub-sarcomeric organization that allows for greater and more efficient force production, further demonstrating the efficacy of nanopattern substrates in cardiac cell differentiation and maturation. Though ExM needs further validation, it has proved a powerful sample-side tool for probing diffraction limited features.

Current drug testing methods are unable to accurately predict and study the effects of drugs on human myocardial tissue. These methods are unable to accurately mimic the physiology and maturity of native cardiac tissue, and as a result, the tissues are unable to react to cardiotoxic drugs the same way that native cardiac tissue. Therefore, there is a need for physiologically accurate and mature tissue constructs in order to test clinical drugs for effectiveness, cardiotoxicity, and arrhythmic effects. To fulfill this need, we will use an electroconductive bioink containing decellularized extracellular matrix (dECM) from porcine cardiac tissue, reduced graphene oxide (rGO), and incorporated human induced-pluripotent stem cell (hiPSC)-derived cardiomyocytes to develop a more physiologically accurate cardiac tissue construct. This will result in more adequate cell maturation, and therefore, more accurate preclinical drug screening. The success of this project would lead to the development of high throughput production of biomimetic cardiac tissue models for use in accurate drug screening, along with improving the understanding of cardiac maturation.

Modern disease research utilizes two-dimensional (2D) stem-cell tissue culture models, simplified 3D engineered tissues, and animal organisms to study microenvironments and human physiology. However, in vitro platforms often oversimplify the physical tissue niche and animal models do not always accurately represent the function of human tissues. For instance, 2D tissue platforms used to study cardiac biology are limited because they cannot accurately recapitulate the pumping motion of the human heart which is responsible for the circulation or blood. Furthermore, animal models have an under-representative cardiovascular physiology making them inadequate systems for studying human cardiac biometrics. As such, we propose to develop a 3D tissue culture system that can accurately mimic the hierarchical organization of different human tissues. Using our novel flexible cell-sheet stacking technique, we can precisely stack layers of organized cell-sheets to create 3D laminar tissues. Then, these organized laminar tissues can be manipulated by the flexible scaffold into complex 3D tissue shapes using custom-made molds. For example, the human heart is helically aligned cardiac tissue throughout its structure that allows for the generation of intraluminal pressure during ventricular contraction. Inspired by the intricate architecture of human myocardium, this project aims to analyze how varying degrees of cell orientation can influence intraluminal pressure generating function. To account for the hollow and conical nature of the human heart architecture, we have designed a model for casting closed 3D hydrogel scaffolds with a hollow lumen that allows for intraluminal pressure measurements. The proposed model will allow for the determination of the optimal angle of cell alignment that produces the greatest intraluminal contraction. We will validate this platform using a contractile mouse skeletal muscle cell type. This approach can be adapted to model the organization of any contractile muscle tissue and be used to study the function and microstructure of human tissues.

The ability to recapitulate the dynamic presentation of signals in a stem cell's microenvironment remains a major hurdle in tissue engineering. By controlling cell growth and differentiation in 4 dimensions (i.e., time and 3D space) through biochemical and biomechanical cues, heterogeneous synthetic tissues could be produced that match the complexity of their native counterparts. By combining strategies in light-programmable hydrogels and recombinant protein engineering, we have demonstrated the ability to control the cellular microenvironment with a UV light mediated reaction that allows a covalent bond to form between a modified protein and the hydrogel. While covalent interactions form strong bonds, they are generally irreversible using mild, cytocompatible chemistries and pose potential temporal limitations. In addition, this technique uses UV light, which may be harmful to cells. Instead, by incorporating LOVTRAP into the photopatterning system, we introduce a greater amount of control by allowing for full reversibility using blue light. In the dark, LOV2 and Zdk1 dimerize to form a protein-protein bond with similar stability to an antibody-antigen interaction. Upon exposure to blue light, the dimer dissociates, allowing for fully reversible control over conjugation. A protein of interest can be tagged with the Zdk1 domain using recombinant protein engineering, while still maintaining its binding affinity for LOV2. LOV2 can then be conjugated throughout a hydrogel to make a light responsive protein binding material. By utilizing a light controlled dimerization event between proteins, the LOVTRAP system is fully reversible using only blue light. Thus far, I have been able to illustrate the photopatterning ability of LOVTRAP and am working towards demonstrating full reversibility. If successful, this technique could be used for tissue engineering applications that require mild treatment conditions and full dynamic control over the presentation of biochemical cues.

In mammals, daily rhythms of physiology and behavior are synchronized to a 24-hour light-dark (LD) cycle via input to the suprachiasmatic nucleus (SCN), the master circadian clock. Disruptions to the circadian system are associated with neurological and psychiatric disorders, including mood disorders like depression. These disorders are associated with symptoms such as sexual dysfunction and anhedonia, the inability to experience pleasure from activities that are typically enjoyable. Previous work has shown that rats exposed to a 22-hour LD cycle, which leads to desynchrony between neuronal oscillators in the SCN and mimics an internally desynchronized state, display behaviors indicative of these symptoms. Jet lag is a common challenge to the circadian system and, in rats, causes desynchrony between SCN neuronal oscillators. We hypothesized that desynchrony induced by jet lag could also lead to depressive symptoms. We measured sexual behavior before and after a 6-hour phase shift, simulating jet lag. Male rats were placed in an arena with a receptive female and sexual activity was quantified. We also performed a saccharin preference test where males had continuous access to water and saccharin solution. The volume drank from each bottle was measured daily; anhedonia is evident as a decrease in the preference for saccharin solution. Locomotor activity was recorded using infrared detectors, to associate behavior with the amount of time it took for males to re-entrain to the new LD cycle. Six-hour advances and delays of the LD cycle were not associated with behavioral manifestations of depression. This work, combined with previous work, provides greater insight into the consequences of circadian disruption and suggests that mental health consequences depend on the specific type of circadian misalignment. Whereas steady state misalignment induced by exposure to 22-hour LD cycles is associated with a depressive phenotype, the transient misalignment induced by jet lag is not.

TOPLESS (TPL) is a transcriptional co-repressor protein that plays a central role in the regulation of plant growth and development. In the model plant Arabidopsis thaliana, TPL acts in essential hormone response pathways, including that of auxin, a small signaling molecule. TPL acts in the auxin response pathway by binding another co-repressor from the Aux/IAA family (henceforth referred to as IAAs). In the presence of auxin, IAAs are degraded, relieving TPL repression and allowing for transcription of auxin responsive genes. Despite its central role, the molecular mechanism by which TPL confers repression is not well understood. Recent structural analyses indicate that TPL has interfaces for both homodimerization and homotetramerization. Synthetic assays have shown that TPL truncations in which the tetramerization interface has been deleted have a significant decrease in repressive function. To determine the repressive mechanisms of TPL, we created a structure-function map. We have created full-length TPL variants with point mutations at the dimerization and tetramerization interfaces, as well as serial domain deletions. We tested the repressive function of these variants in a yeast synthetic assay in which TPL represses expression of a fluorescent protein. Repressive function was then quantified from fluorescent reporter output with stronger repression corresponding to decreased fluorescence. We then validated the results of our synthetic assays in planta by expressing TPL-IAA14 variants that negatively regulate lateral root development. The repressive strength of each TPL variant will be quantified by measuring the number of lateral roots, with fewer lateral roots corresponding to increased TPL repressive strength. TPL homologs exist in many species. Defects in TPL homologues have been implicated in the causes of many cancers and developmental diseases, therefore a better understanding of the functional mechanisms of TPL will have broad implications across organisms, including humans.

This essay delves into the portrayl of fruit in Italian Baroque still life painting and its relationship to period botanical studies. By formally analyzing two seperates artists of the Baroque I hope to understand the importance of still life in scientific history. I focus my research on Caravaggio due to his cultural importance as a famous Baroque artist. In particular, the works of Caravaggio can be used as tool to understand the culture of fruit in Baroque Italy. I take a point of departure the high naturalism of Caravaggio, whose attentive depictions of fruit reflect seventeenth-century Italian domestic agriculture and import market. Botanical artist Giovanna Garzoni painted for Medici members of Florence specifically Grand Duke Ferdinando II and Grand Duchess Victoria. Garzoni provides an example of the fruit being grown in Medici botanical gardens. Medici botanical gardens are a prime example of horticultural practice within the seventeenth - century. By contrasting the depiction of the same species of fruit in Garzoni's painting Still Life of Birds and Fruit and Caravaggio's work Still Life With Fruit On a Stone Ledge, we can explore how the artists represented truth differently. Caravaggio paints from a specific subject by paying close attention to the detail of his subject in imperfections, which represent truth in specific form. This contrasts with Garzoni who a generalized truth of the species as a whole and not each individual subject. In this essay the contrast between these two artists will be explored to understand their different avenues of depicting truth in their artworks. Theatrical metaphor, sexuality, religion, and genre painting will all be employed to approach Caravaggios work. Comparitively Garzonis work will be viewed in the context of gender, class, and botanical collection.  Caravaggio and Garzonis seventeenth century still lifes explore how artists enter the discourse of scientific truth. 

Manila clams, Ruditapes philippinarum, are a widely used species in Washington shellfish aquaculture. Juveniles in particular have high mortality rates due in part to predation, but the extent of this predation is unknown. This study investigates the prey size range and preference shown by the crabs Hemigrapsus nudus, Metacarcinus gracilis, Cancer productus, and Romaleon antennarium when preying on R. philippinarum. To test if crabs prefer to prey on larger clams due to their higher food content, we placed crabs and clams together in microcosms and measured mortality rates of the clams. It was found that all crabs could eat all tested clam sizes. Cancrid crabs preferred to eat larger clams; R. antennarium ate the most clams. In contrast, H. nudus had no preference for a particular clam size. Based on these results, countermeasures against juvenile Manila predation should have a special focus on cancrid crabs, and further research on the reasons behind the trend of cancrid preference for larger juveniles should be considered. 

Corporate Social Responsibility (CSR) is when companies make an effort to improve society through their business practices. Corporate Social Responsibility is a growing topic and has been researched extensively and implemented mostly among large corporations, garnering the attention of stakeholders, sponsors, investors, and media. Researchers have conducted meta-analysis on the effects of CSR on financial performance of companies and found that though implementing CSR activities can result in an expense for the company, the overall benefits of CSR, such as increases in public support, employee satisfaction, investor’s involvement, and community engagement, far outweigh the cost. However, little is known on the impact of the size of a company and the effects of CSR and financial performance. The goal of this research is to identify, based on the size of a company, the effects of CSR on financial performance and examine whether CSR results in financial benefits. Data will be extracted from three large, three medium, and two small profit companies and analyzed following existing protocols and procedures for conducting a systematic review. For each company, I will examine its CSR report and identify studies that used more than two outcome measures (e.g., environmental sustainability, human right advocacy, empowering employees, etc.) of CSR to determine financial performance. The significance of my research is its potential to provide context-specific findings that could inform managers from small to large companies how engaging in CSR activities may be beneficial.

Augmented Reality, the superimposition of digital features into the real world environment, has already made great strides in fields such as entertainment and advertising. However, the use of compound technology that bridges reality and the digital world has yet to be implemented cogently and thoroughly into the manufacturing field. This first part of this research paper explores the range of augmented reality hardware and software interfaces in fields such as medicine, academics, entertainment and advertising through a review of other scientific studies on augmented reality. Next, this research applies these observations to the current preliminary augmented reality trends specifically in the manufacturing field. Taking into account the positive and negative cognitive effects of augmented reality systems on attention, motivation, and ease of use, this paper then further delves into the potential uses of augmented reality in manufacturing. In the next section, this paper uses its examination of augmented reality’s ability to cater the manufacturing community’s needs to evaluate the advantages of implementing augmented reality technology in conjunction with human ability to improve the manufacturing process. Finally, the last section of this paper synthesizes the ideas presented into a set of principles for augmented reality use in manufacturing, and gives real-world examples of these principles’ efficient applications.

Hydrogen sulfide (H₂S) is a gas most commonly known for its pungent scent and toxicity. However, administered in low doses, H₂S can be tolerated, and it can even facilitate the acclimation to higher doses in the nematode Caenorhabditis elegans, a model organism with relatively short generation times and extensive tools for genetic manipulation. Furthermore, H₂S could have important medical uses due to its function as a vasodilator and chemical signal in cellular signaling, such as conserving donor organs, extending the time prior to an ischemic response, and decreasing nociception in severe injuries (Miller, and Roth). Data from our lab suggest that a low dose exposure to H₂S during early stages of development forms a “bookmark” which permits the survival of the animal at high doses of H₂S during adulthood. Through a genetic screen, epigenetic factors including spr-5, set-2, swsn-4, and swsn-1 were discovered to be involved in the bookmark. The ease of bookmark formation and the short time between formation and manifestation of phenotype present a unique opportunity to dissect a complete epigenetic pathway in addition to understanding cellular responses to H₂S. Our project aims to develop tools that will help understand temporal and spatial requirements for the protein products of these bookmarking genes. To achieve this, we intend to use CRISPR to attach a tag to the endogenous loci of target genes that allows for auxin-induced degradation (AID) (Zhang, L. et al.). Our targets will include both bookmarking genes and previously identified H₂S response elements such as hif-1. Thus far, we have tested the efficiency of the tag on Green Fluorescent Protein (GFP). Presently, we are working to create the transgenic lines of nematodes that carry the AID tag alongside proteins involved in the formation or maintenance of the H₂S bookmark.

In plants, the hormone auxin plays a crucial role in the regulation of many different genes during growth, embryogenesis, differentiation, and many more developmental processes. The promoters of auxin responsive genes are bound by a transcription factor called an Auxin Response Factor (ARF), which is repressed by a protein complex consisting of a linker protein called an IAA and a corepressor known as TOPLESS (TPL). In the presence of auxin, the IAA is degraded resulting in the dissociation of TPL and subsequent activation of transcription of these auxin responsive genes. IAA20, IAA30 and IAA31 are members of a closely related sub-clade of IAAs that are known to be auxin insensitive. These genes are transcribed at low levels in nearly every cell type, yet their role in the auxin signaling network is completely unknown. I hypothesize that the auxin insensitive IAAs create an auxin concentration threshold to reduce the noise of auxin signaling output. In this model, auxin insensitive IAAs interact with all ARFs to generally increase the concentration of auxin required to elicit a transcriptional response. To test my hypothesis, I examined phenotypic changes in single, double and triple-mutants for the auxin insensitive IAAs, which I have generated via CRISPR/Cas9 mutagenesis combined with existing mutations. I am currently testing whether these mutants have quantifiable auxin-related defects in the highly stereotyped root development and arrangement of organs along the stem, or phyllotaxy. If I observe that mutants in the auxin insensitive IAAs have defects with these processes, it will suggest that these IAAs buffer noise present within the auxin signaling network. This work will enhance our understanding of how auxin coordinates transcriptional repression and how signaling noise is reduced in a multi-component molecular system.

C. elegans is a prolific model organism that is well established in the field of aging research and age-related diseases. C. elegans can be genetically manipulated to express human toxic proteins associated with neurodegenerative diseases. Its amenability to genetic screening and short lifespan make it an ideal animal model for studying the genetic basis for the neurological health-declines associated with Alzheimer’s disease (AD). Here we introduce new experimental approaches for quantifying the organism-wide impacts of nervous system specific expression of human AD-associated toxic proteins.. The pharynx in C. elegans is an oral pumping structure used in feeding. The pharyngeal nervous system, comprised of only twenty neurons, dictates the rate of pharynx pumping in the animal. Pharyngeal pumping rates have been shown to change and decay with the age of the animal, making it an ideal metric in aging research. The frequency of pharynx pumping can be measured via an electrophysiological recording of the pharynx’s contractions. We plan to use this electropharyngeogram (EPG) as a measure of neurodegeneration to compare wildtype animals with our AD-model mutants. Furthermore, the proper function of extracellular vesicles (ECVs) are thought to be important in the clearance of toxic peptides associated with AD. The only reported phenotype for ECV signaling is the differential development of the cuticle, the animal’s outer-most layer of epidermis. The cuticle’s formation can be assessed through the appearance of the worm’s alae, a set of three lateral stripes running across the animal from head to tail. The appearance of alae has been observed to be different in our AD model mutants, indicating that ECV signaling has been disrupted. Using these AD-model mutants, we aim to establish these novel phenotypes as a means to further investigate the physiological consequences of AD-associated toxic peptide expression.

Anthropogenic climate change is gradually reducing snowpack and shifting the timing and volume of streamflow in the Columbia River Basin. Mountain snowpack plays a key role in the water cycle by storing water in the winter and releasing it as snowmelt runoff in spring and summer. Snowmelt and the resulting streamflow are critical for a variety of sectors: irrigation, hydropower, flood risk management, and ecosystem services, particularly regarding salmon. There is a large network of reservoirs along the Columbia River and its tributaries that water managers use to store water from snowmelt to satisfy the needs of industries and communities. Snow can also be thought of as a reservoir, as it delays the streamflow response to a precipitation event. With anticipated increases in temperature due to a changing climate, the size of that snowpack reservoir is expected to decrease. We will analyze projections of changes in the amount of water contained within the snowpack and determine the volumetric size of the snow reservoir that will be “lost” due to a warming climate. We will compare it to existing reservoirs in the western United States. As the basis for these analyses we will use an ensemble of 160 different hydrologic projections included in the Columbia River Climate Change dataset. We will relate these changes in snowpack to changes in streamflow timing. The results of this study may help inform discussions about the need for changes to reservoir operations on the Columbia River.

Oysters support a multi-million-dollar aquaculture industry in Washington State and provide important ecosystem services in estuarine habitats. Sustaining aquaculture and restoring native oysters depends on oyster health. Food availability is a driver of oyster health that interacts with environmental effects of global climate change. These global changes may be altered by the effects of local species interactions like association with eelgrass. Measuring essential fatty acids, which are necessary for survival and physiological processes of oysters, can show the level of food availability to oysters in environments with and without eelgrass. We tested the hypothesis that eelgrass alters oyster health by growing oysters inside and outside of eelgrass at 5 sites in Washington state. We used fatty acid composition of tissue from Pacific and Olympia oysters to look at changes of assimilated food in relation to habitat and environment. We predict that eelgrass will slow water flow, resulting in a decrease in food availability and thus essential fatty acid concentration in oysters grown in eelgrass. Looking at essential fatty acids of oysters from different environments, specifically with or without eelgrass, provides a better understanding of environmental impacts on oyster health and contributes to a collaborative effort in Washington state focused on sustaining the valuable food production and ecosystem services of oysters in our ever-changing climate.

Over the past few years, the presence of smart homes has increased rapidly. Previous research has observed that people make errors in smart home programming with their mental models differing from their actual programming implementation which can cause serious security and safety concerns. The most common errors include missing half-rules and the incorrect use of conjunctions in triggers. For example, if users desire to program a rule for turning on the light when they are at home, they might program a rule such as “when I come home, turn on the lights”, forgetting to program the rule for “when I leave home, turn off the lights”. Our research focuses on reducing user errors in end-user programming by using programming by demonstration. Our hypothesis is that when users physically demonstrate a trigger-action rule, they are less likely to commit the trigger-action programming errors explained above. We compare the number and types of errors made within the IFTTT (if-this-then-that) interface that does not implement programming by demonstration and two interfaces that we built that implement programming by demonstration: a web interface and an augmented reality based interface within the Microsoft HoloLens. If our hypothesis holds true, we might observe that programming by demonstration significantly reduces programming errors in end-user programming in the case of both missing half rules and incorrect trigger conjunctions. We postulate that there might not be a difference in the case of error reduction between both the web and augmented reality interface; however, the augmented reality interface might provide for a broader range of programming by demonstration interfaces such as those related to temperature, humidity etc. Moreover, if our hypothesis holds, we might further suggest that smart home providers incorporate programming by demonstration models in their programming processes for end users within smart homes.

Development of traditional anti-cancer drug has suffered from low success rate to difficulties in engineering approaches and clinical trials. Since metastasis is the major cause of cancer death, the current trend has been shifting towards a combined therapy of traditional cancer drugs and anti-migratory therapy. Cell migration assays provide straightforward visual and efficient quantitative analysis on cell migration distance and pattern. To implement these assays, one of common approach is to apply an elastomer block and create a cell-free area into which adjacent cells can migrate without damaging the cells. Our lab’s current cell exclusion migration assay is limited by uncontrolled barrier block adhesion to the substrate surface and to the well wall due to hand cutting and placement of the block. Therefore, to improve the usability and reproducibility, an accurate migration assay is developed to integrate an approach of controlling the geometry of the barrier block and confining the cell seeding area against cell penetration under the block. Our proposed barrier block fabrication utilizes laser-cut acrylic molds, which produce barrier blocks consistently in the same geometry. The block-placement device is optimized by designing a row of handles, which allows for placement of multiple blocks into the multi-well tissue culture plate at once and adjusts their positioning and adhesion precisely. Block-controlled migration is validated using a multi-well cell migration assay with respect to its ability to consistently confine cell seeding area and efficiency of use. The success of this method enables a more efficient method of anti-migratory drug screening and in vitro migration pattern analysis.

Over 70 million people are infected by HIV and 79 million of Americans by HPV every year. Even in developed countries, these particular sexually transmitted diseases (STDs) grow at an unyieldingly steady rate. In the Chiu Group, we address this increase in infection by working on the development of a fully automated microfluidic instrument to help improve early diagnosis of HIV and HPV. While many diagnostic techniques already exist, our goal is to advance state-of-the art approaches in novel microfluidic technologies, primarily concerning the reduction of cost to run clinical samples, shortening the time required to analyze samples, and enhancing the reliability of results. We are developing our automated microfluidic instrument in two phases. The first is a preparative step in which we create high-quality microfluidic chips that help digitize thousands of nanoliter droplets in a static array of wells. In the following experimental step, we amplify target HIV/HPV sequences in these nanodroplets from patient samples through polymerase chain reaction (dPCR) and the static array format provides a direct readout through changes in fluorescence of the sample droplets.The successful implementation of the instrument together with the microfluidic chip will maintain a high level of accuracy and sensitivity as well as observe a large decrease in cost and time for diagnostics. Among the conventional diagnostic instruments available today, our development will offer a faster, cheaper, and more accessible way to diagnose HIV and HPV, and ultimately slow the rate of STD cases throughout the world.

Computational simulations of protein dynamics provide an efficient way of predicting protein behavior and are increasingly being applied to peptide and protein design. However, design tools and software focus on static structures. Incorporation of dynamics directly or through design libraries derived from dynamics simulations allows the user to focus on optimization of the native dynamics of the protein for a specific purpose. Critical libraries for design, such as side chain rotamer libraries and amino acid propensities are typically derived from static structures, which do not reflect behavior in dynamic conditions. Therefore, including rotamers and conformational propensities derived from behavior during protein simulations in molecular modeling and design software should improve the design process and outcome, particularly for peptides. Additionally, current software does not allow the user to adjust the main chain dihedral angles of the backbone according to Ramachandran plots reflecting the unique free energy landscape of each residue. The WRANGLER software was designed in order to include dynamic data to better model and design against and for dynamic systems. A number of libraries derived from dynamics simulations of all known protein folds have been incorporated. In addition, the software is interactive with a graphical interface to easily change and visualize geometries and analyze peptide/protein properties. WRANGLER was evaluated based on ability to facilitate design of several amyloid peptide aggregation inhibitors. Resulting designs were evaluated through molecular dynamics simulations for their secondary structure retention and physical properties. Control amyloid peptide aggregation inhibitors were included that have already been designed, synthesized and tested experimentally in lab. Several peptides designed in WRANGLER appear to be better than the controls by a variety of metrics. The next step is to synthesize these new designs and test them against the amyloid-beta peptide associated with Alzheimer’s Disease to see if they outperform our current compounds.
 

Obliquity, or axial tilt, is the angle rotational axis and a line perpendicular to the orbital plane. At low obliquity, Earth-like planets will tend to form permanent ice sheets at the poles, if anywhere. However, at high obliquity, the poles receive more sunlight on average than the tropics, and so ice sheets might be expected to form at the equator. We investigate the formation of such “ice-belts” under a range of orbital parameters, obliquities, and host star properties. We find there is a narrow range of semi-major axis and obliquity values that allow for such "ice-belts" to form. First, we experiment with changing the luminosity of the host star to see the effect of changing the stellar flux on ice belt formation, while keeping the relative stellar flux approximate to Earth's, as well as making the appropriate adjustment to the ice-albedo for the host star’s spectrum. Our results suggest that the more luminous the star is, the smaller (and ultimately less stable) the range of ice belt formation becomes. To fully understand the full effect the host star had on ice belt formation, we vary the orbital eccentricity, the spin-axis orientation (precession angle) and the depth of the ocean that can absorb stellar energy (mixing depth). This work suggests that it should not be typical for Earth-like worlds at high obliquity to maintain large ice sheets around main sequence stars.

During development, profound changes occur in the liver from a hematopoietic organ to a major organ for xenobiotic biotransformation. Developmental regulation of epigenetic modifiers, such as factors involved in DNA methylation and histone modifications, may modify the transcriptional output of drug-metabolizing enzymes. The goal of this study was to develop an in vitro model to recapitulate human liver development using HepaRG cells and implement this model in investigating the developmental regulation of epigenetic modifiers and drug-metabolizing enzymes. Previously, HepaRG cells were maintained in proliferative phase and were tested up to 14 days at fully differentiated stage. In this study, we collected cells during differentiation from 0 to 14 days, and isolated total RNA for RT-qPCR of epigenetic modifiers and drug-metabolizing enzymes. Among a panel of 92 epigenetic genes, there were 52 genes differentially regulated at earlier time points as compared to the fully differentiated stage. Most of these epigenetic modifiers increased during differentiation and reached a plateau either at Day 7 or Day 14; whereas the class II major histocompatibility complex transactivator (CIITA), which has an acetyltransferase domain, gradually decreased during differentiation. The adult hepatocyte marker albumin gradually increased and reached a peak at Day 7, which decreased thereafter. The mRNA of the fetal-specific drug-metabolizing enzyme cytochrome P450 3A7 (CYP3A7) was high between Day 2 and Day 3 but decreased rapidly thereafter. Conversely, CYPA3A4 mRNA was increased till Day 7, when peak mRNA levels were observed, and decreased thereafter. In conclusion, the present study is a first step in establishing a working model to investigate human liver development in vitro.

The purpose of this study was to explore the interrelationship between two major DNA repair systems--photoreactivation, with blue light as an energy source, and excision repair, which uses ATP as an energy source--of Chlamydomonas reinhardtii, a single-celled algae, by studying the in vivo efficiency of photoreactivation when the excision repair system was suppressed. Working with a mutant which was completely lacking in excision repair, we found that this strain was also deficient in photoreactivation, as compared to wild-type, at low levels of post-UV visible light treatment, measured by killing on plates. We hypothesized that the level of light intensity might have an impact on the efficiency of the photoreactivating enzyme. Using alkaline agarose gel electrophoresis analysis, we quantitatively evaluated the extent of repair of DNA damage over 24 hours under two different light intensities. We found less damage removal in the mutant under low light intensity, suggesting that a positive correlation does indeed exist between the flux of visible light used in our experiments and the amount of photoreactivation for the mutant. This correlation was not observed in the wildtype. Our work is interesting in the context of human-caused changes to Earth’s atmosphere; both photoreactivation and excision repair of DNA damage are present in virtually all organisms studied, including bacteria, fungi, plants and most animals (although not in placental mammals). With the weakening of the stratospheric ozone layer, there is the possibility of increasing solar UV flux to the surface of Earth, with possible negative downstream effects on biological systems. Understanding the functional relationship between these two DNA repair systems could provide information of fundamental importance to ecological and agricultural problems arising from increased solar UV flux to Earth.

Osteoarthritis, a disease in which the cartilage that cushions joints is lost, affects 27 million people each year. Ankle arthroplasties, or total ankle replacements —i.e., replacement of joint surfaces with artificial materials— have become the procedure of choice for many end-stage ankle arthritis (ESAA) patients. The purpose of this study is to compare foot joint kinematic differences in end-stage ankle arthritis patients pre- and postoperative to receiving a total ankle replacement. Hypotheses over the recovery period include (1) increased range of motion in joint and planar angles, (2) negative correlation between patient pain and ankle function, and (3) ankle function converging towards that of normal gait patterns. Twenty adults with ESAA scheduled for ankle arthroplasty surgery were evaluated preoperatively and at 12 and 24 months postoperatively. A validated five-segment foot model was applied to the affected limb using retro-reflective markers. The model allowed for five three-dimensional joint angles and eight planar angles to be calculated. Subjects completed follow-up surveys self-assessing function and pain preoperatively and at 3, 6, 12, and 24 months postoperatively. Results are limited as the longitudinal study is still ongoing. Thus far, mean joint rotations show increased range of motion at the ankle joint, decreased range of motion between the midfoot and forefoot, and decreased toe splay during the stance phase of gait 24 months postoperative. Correlation between patient pain and ankle function show a trend in decreasing ankle range of motion with increased patient pain, both preoperatively and 24 months postoperatively. Patient pain also significantly decreased between every survey administration time point. These findings will likely aid ESAA patients when considering ankle arthroplasty surgery, informing them about expected recovery and comparing trade-offs between pain and function. Future work includes the ongoing collection of control data for comparison.

A heritage language learner (HL) is a person who was raised in a home where a non-English language was spoken and who is to some degree bilingual, while a second language learner (L2) is someone who learned a non-English language after first acquiring English. The ways in which Spanish is acquired produces strengths and weaknesses among HLs and L2s. While L2s tend to have more knowledge with respect to Spanish grammar, metalanguage, and orthography, HLs have more fluidity and a larger vocabulary. This study aims to identify what educational environment that utilizes peer interaction between HLs and L2s would be the most effective for Spanish language acquisition. A prior research team recorded three types of peer interactions—HL-HL, HL-L2, and L2-L2—ranging from ten to fifteen minutes long. The participanting students were all part of either the HL 300 level Spanish series, or the L2 equivalent. In addition to the recordings, linguistic background questionnaires conducted at the beginning and end of the quarter surveys were completed by all participants to establish their Spanish proficiency level and their attitudes with regard to Spanish as well as Spanish classes. I have been assigned four peer interaction recordings to transcribe using Conversation Analysis notation so that I can codify and analyze the participants’ use of English within those interactions in addition to their reliance on it. I will be comparing their collaborative problem solving activities, how the students work together to solve vocabulary and grammar related challenges which will result in the acquiring of new language knowledge. Preliminary results propose that HL-L2 interaction does not produce as many instances for learning as in L2-L2 interactions. This analysis will help to create a more effective learning environment within mixed classrooms for both HL and L2 learners, which will ultimately increase professional marketability and social cohesion.

Enormous outpourings of energy blasted into space by an accreting supermassive black hole (SMBH) are known as quasars. Previously, it was believed that SMBH’s enter a quiet state, thus extinguishing the quasar, over thousand-year-timescales. Changing-look quasars (CLQs) are a recently discovered, rare type of quasar that have been observed to transition far quicker than was thought possible. These short timescales motivated researchers, including ourselves, to reconsider our understanding of accretion phenomena in quasars to better understand what is driving the unexpectedly rapid changes observed in these CLQs. It is essential to establish a larger, more comprehensive, and less biased catalog of CLQs than currently available to answer such questions; and our work emphasizes creating this catalog. Our research involves both visually comparing spectra from the Sloan Digital Sky Survey database to each other and to new Sloan observations in the interest of detecting variations that suggest the quasar has turned on or off between observations. Sierra Dodd has recently identified three extremely probable CLQ candidates, bringing us closer to an improved understanding of which key changes in spectra correspond to CLQs. Further work on our part will aim to discover additional candidates to enlarge the pool of discovered.

 Studying the ground-strike force and acceleration of male and female runners can provide information about gait and foot strike patterns and can contribute to improved running efficiency in individual runners. Researchers at Southern Methodist University have showed that the motion of two anatomically discrete components of the body’s mass sufficiently explained the vertical ground reaction force-time waveform pattern observed during human running. The anatomical differences of male and female runners lower extremities were compared biomechanically by using force and acceleration data combined with video analysis to assess gait patterns. This experiment further examines the acceleration and force created by runners, while moving through their respective biomechanical patterns, by assessing the impact force and acceleration patterns of the lower limb joints. Acceleration data was collected at the ankle, knee, and hip of the runners to better understand the overall force distribution throughout the lower limbs. Preliminary data shows force differences between sprinters and distance runners, seen at each joint in the lower limb with the largest difference occurring at the hip. When comparing males versus females the preliminary data also shows differing force patterns through the observed reference points. This data will contribute to a better understanding of the biomechanical differences in male and female gait patterns when sprinting versus running for distance, which could lead to better injury recovery. Therapeutic evaluations of injured limb could be made by looking at the forces experienced throughout each limb during injury recovery to better personalize and appraise individual rehabilitation progress.

Mixed classes are foreign language classes in which second-language (L2) learners work alongside heritage language (HL) students, who have exposure to the language at home and are bilingual to some extent. Heritage language students, while typically having a greater vocabulary and a better sense of linguistic flow, often lack the metalinguistic and mechanical knowledge of their L2 peers. These differing strengths present a potential asset for the language classroom, but a challenge for teachers, too, who need to ensure all students’ needs are being met. Therefore, mixed classes ought to be studied to address whether both heritage- and non-heritage- learners benefit, and in what ways, from working in mixed pairs. My study investigates the differences in classroom interaction between and among HL and L2 students by tracking the progress of two L2 learners across one quarter of Spanish class. I have transcribed audio data recorded in mixed-language Advanced Spanish classes which document collaborative writing tasks and include interactions between both L2-L2 and L2-HL pairs. I am analyzing these conversations for the use of English and its impact on learning, attention to language (grammar, vocabulary, or orthography) relative to natural conversational flow, self- and peer-correction, and for evidence of learning or change in students’ interactions over the quarter. By analyzing and comparing these trends, I address whether second-language students benefited most working with heritage speakers or fellow second-language learners, and whether and in what cases heritage speakers benefited from working with these students. This information will help teachers make informed decisions about collaborative learning activities in mixed classes.

Color is often a very intentional and comprehensive choice as a visual element; artists, filmmakers, designers, and animators recognize color as a tool that signficantly shifts a viewer's perception of their work. While there are universal associations of solid colors- blue for sadness, and red for love, for example, the vastness and complexity of the color wheel leaves much room for nuance between the relationship of humans and color. Color in animation makes use of this nuance, but with a more varied stylistic choice and a greater control over very specific palettes. Through the conceptualization and production of a series of short animation clips, I aim to use color as a deliberate element to evoke subtle shifts in mood, as well as further explore the relationship between animation and color psychology. I've taken inspiration from color scripting in films through the use of a specific color palette to achieve visual balance and strong story support. My work, through tradittional and digital animation methods, aims to bring color in harmony with motion and composition to create a unique visual experience. I hope for my project to contribute to the growing understanding of color as an artistic, technical, and psychological asset in the viewer's engagement in animated films.

Dental hypersensitivity (DH) is a common oral health condition in the U.S. affecting the majority of the adult population. It is caused by the exposure of dentin due to the demineralization of the protective cementum or enamel that covers the tooth surface. When the dentinal tubules are exposed, nerve fibers in the pulp or predentin are stimulated by the displacement of the fluid and report pain. The stimulus that triggers the onset of pain can be of thermal, chemical or mechanical origin. There is still no effective agent to completely resolve the patient’s discomfort with DH. Over-the-counter products are commonly advised in the management of DH while toothpastes containing strontium, oxalate or potassium salts, or fluoride are recommended with limited efficacy to reduce the sensitivity from DH. Restorative materials using composite, glass ionomer or amalgam are adapted to treat the affected area with limited success. The goal of this project has been to develop a biomimetic treatment by restoring cementum tissue using a peptide-guided remineralization approach, thereby occluding the exposed tubules with a newly formed mechanically and thermally stable mineral layer. The College of Engineering working closely with School of Dentistry-UW involves mimicking the hypersensitivity condition by removing enamel/cementum of extracted human teeth to expose underlying dentin. The samples are then treated with peptide-guided remineralization resulting in 10+ micrometer thick new layer over the damaged dentin. Our results exhibit a highly effective way to occlude the exposed dentinal tubules by a newly formed mineral layer which penetrates into the dentin tubules. The method described herein offers a unique biomimetic treatment protocol for dental hypersensitivity, which will be developed as a platform technology for effective in-clinic and over-the-counter hypersensitivity treatments. The work is supported by WA-State Life Sciences Discovery Funds, UW-School of Dentistry Spencer Funds, and Amazon-UW/CoMotion Catalyst Program.

Phytoliths are microscopic silica bodies that form in many plants. Being resistant to organic decomposition, they can be used to track plant evolution and past vegetation changes. Although they were traditionally considered as non-functional cellular by-products, recent studies suggest that phytoliths may have photonic, structural, nutritional and defensive benefits in plant growth and survival. Grasses, which are large terrestrial producers of biogenic silica, are the suitable model system for studying the adaptive significance of silica accumulation in plants. Identification of phytoliths within the plants (for studying function) and inside the sediments (for studying evolution of vegetation) have so far been limited to optical microscopy-based methods where fluorescent dyes are commonly used to increase contrast between silica bodies and plant tissue. Due to their non-specific nature, however, fluorescent dyes often accumulate in different parts of the cells and silicified tissues, causing false positives and leading to incomplete staining and difficulties to construct 3D structures. With exquisite molecular recognition and assembly properties, solid-binding peptide tags (dubbed GEPIs) are surface functionalization moieties that can be chimerized with fluorescent and utilized as material-specific probes to selectively label variety of inorganic materials at surfaces and within interfaces. Our goal is to develop peptide-based phytolith-specific fluorescent probes to identify and delineate phytolith shapes with high precision and in situ. Using phytoliths-specific peptides probes, designed and chimerized with fluorescent molecules, our goal is to incubate different grass species, and visualize them using laser-confocal microscopy. We hypothesize that the novel molecular construct enable specific detection of phytoliths in situ. The method we are developing will offer a unique solution for fast and accurate identification and 3D organization of inorganic nano- and micro-structures in tissues from living plants and in paleontological samples.