Women still represent a small percentage of the Oregon police force even 30 years after the first push for integration into the field. As increasing numbers of departments include more strategic efforts to be made to encourage women to pursue a career in the police force, it is important to recognize the difference in how male and female police officers react to crisis situations. Research has shown that policewomen are less physically aggressive which leads to fewer lethal police encounters. Building on prior research of policewomen, my results can add to the discussion to emphasize why women are less susceptible to reacting violently during crisis situations. Data will be gathered through the collection of systemic social observations and in-person interviews with policewomen. Through the lens of the hegemonic masculinity theory, the thematic results from the interviews can assess how the internalization of gender ideologies factors into the use of nonviolent tactics in the field. The goal of the proposed research is to examine these questions; (1) What is the experience of policewomen using nonviolent conflict resolution tactics in Hillsboro, Portland and Forest Grove, Oregon? (2) How do policewomen use de-escalation and nonviolent communication learned in their police training? (3) To what extent do policewomen feel the need to use their gun in a crisis situation? This research will more clearly demonstrate to police departments the increased need for the thorough training in verbal judo, de-escalation and other nonviolent communication skills in initial police training and ongoing training for male and female police officers.

Before the Brown v. Board of Education (1954) Supreme Court decision, African Americans struggled to provide adequate education for the younger generations and continuously fought for the betterment of African American education as well as integration of African American students into segregated schools. This research will investigate how school integration ushered in by the Brown decision impacted Historically Black Colleges and Universities (HBCUs) in the moments following Brown compared with students perceptions of HBCU’s today. In the present day there is much debate concerning whether or not HBCUs provide adequate education to its students. In an effort to examine how Brown may have negatively impacted HBCUs prestige and educational value, I will carefully examine historical evidence as well as data on enrollment of four public Universities: two HBCUs (Alabama A&M and Albany State University) and two schools who integrated African Americans into their school populations post Brown (The University of Alabama and the University of Georgia). The central question I seek to answer is whether the perceived prestige of HBCU’s among African Americans was impacted by integration in the post-Brown era. Ultimately, if Brown affected HBCU’s negatively and contributed to their devaluation then efforts should be made to restore the prestige and educational value of HBCUs.

Gastrulation is an early phase in the embryonic development of vertebrates during which the three germ layers differentiate. The movement of the cells during this phase, is mediated by actin structures stimulated by integrins, extracellular matrix, and ligands. Migration of the cell is activated by Rho GTPases and focal interactions with cadherin-p120 catenin interaction stabilizing cell-to-cell adhesion. To be more specific, the protein, p120 catenin, is required for the extension of the dorsal axis and normal migration of the presomitic mesoderm. This lab studies the molecules that define the pathways of cell migration and tissue migration in zebrafish embryos. Specifically, we are studying how various mutations affecting the phosphorylation state of p120 catenin family genes were produced by undergraduate students and their respective effects on the dorsal axis extension were visually observed. In this experiment, zebrafish embryos were injected with mutated mRNA and analyzed using our in situ hybridization of two probes. Somites were stained using the myoD probe while the presomitic mesoderm was stained using the papC probe. Staining the mutated mRNA, allowed the team to witness phenotypic abnormalities of the dorsal axis much more clearly. Quantifications of the stained somites and presomitic mesoderm will allow a statistical analysis on various p120 catenin mutants. Overall, this experiment provides a deeper understanding of cell migration during developmental processes.

Improving the efficiency of photosynthesis has the potential to help attain a net reduction of atmospheric carbon dioxide (CO₂). Cyanobacteria are an enticing target phylum as they contribute an estimated twenty five percent of global photosynthesis. Under ideal conditions, cyanobacteria grow and reproduce rapidly yielding numerous generations over a relatively short time span. Most research on cyanobacteria carbon fixation has been conducted under increased concentrations of CO₂. In contrast, this research investigated: 1) whether cyanobacteria subjected to CO₂-limited conditions will produce successive populations that have improved carbon fixation efficiency, 2) the viability of those adapted populations in present day atmospheric conditions, and 3) whether the survivors fix carbon at an increased rate compared to control cyanobacteria. To answer these questions, control cyanobacteria were maintained in ambient air conditions while an experimental population of cyanobacteria was developed under a range of CO₂-limited conditions. Half of the adapted populations were then returned to ambient air conditions. The rate of carbon fixation under both CO₂-limited and ambient air conditions was approximated by measuring biomass. This research could provide a laboratory-scale proof of concept for net reduction of atmospheric CO₂ by low energy biological means. This method could also eliminate the need for direct gene manipulation by capitalizing on an evolutionary process. Future experiments could replicate this study with different species of cyanobacteria to develop regionally compatible cyanobacteria with more efficient carbon fixation resulting in a net reduction of atmospheric CO₂ in an environmentally sustainable manner.

Child Sexual Abuse (CSA) and Interpersonal Violence/Domestic Violence (IPV/DV) are serious, continuing problems in our country as both forms of abuse lead to negative mental health, physical and psychological outcomes. According to the Child Maltreatment 2013 report, 679,000 children were victims of maltreatment in the year 2013 with 9% being subjected to sexual abuse.  IPV is a combination of rape, stalking and physical violence. The lifetime prevalence for IPV is 35.6% with physical violence the most prevalent form of IPV at 32.9%. My research project was to investigate what commonalities exist between the outcomes of CSA and IPV and to research the impact of CSA upon the psychological and physiological development of an individual. The main purpose of this literature review is to examine CSA and IPV/DV in determining if experiencing CSA leads to an increased vulnerability of being subjected to IPV/DV. The comprehensive literature review consisted of examining the existing research from 2008 to present day. Research suggests that CSA has a lifelong psychological and physiological impact upon an individual that lasts into adulthood. These changes affect the body’s stress response, emotional regulation, and cognitive processing. These areas are implicated in the development of outcomes due to CSA including the increased vulnerability of a CSA survivor being re-victimized through a relationship with IPV/DV. Understanding that CSA increases a person’s vulnerability to IPV/DV will allow researchers and clinicians to develop and implement interventions for CSA survivors in order to decrease the negative current and lifetime impacts. 

There has been a clear rise in diagnoses of Autism Spectrum Disorder (ASD) in recent years: it is estimated that 1 in 68 children now have ASD. Thus, there is a pressing need to detect early indicators of ASD to help create new early intervention programs with the hope of optimizing the lives of individuals with ASD. One of the most distinct features of ASD is a deficit in social skills. This study investigated infants’ social attention in relation to parental levels of ASD-like characteristics. Specifically, we measured parental levels of the Broad Autism Phenotype (BAP), which refers to an individual’s ASD-like characteristics, such as social deficits, repetitive behaviors, and social language deficits that are milder than clinically relevant symptoms. Parents were given a Broad Autism Phenotype Questionnaire (BAPQ). A high BAP score, indicating more ASD-like characteristics, was hypothesized to affect how parents engage with their children, including less flexibility with their social communication styles, which may in turn affect children’s social development. Infants were observed in a highly controlled laboratory task in which they watched social and nonsocial videos, followed by an interactive task that consisted of playing with a parent and toys. Infants’ social and non-social attention was coded from these tasks. It was hypothesized that high parental BAP scores would be related to lower levels of infants’ social attention. The results will be discussed with regard to current theories of the sources of social deficits in children with ASD. The findings from this study could help to further identify individuals at risk for later development of autism within the first year of life, allowing for early implementation of intervention programs.

Calcium is an ubiquitous and critical signaling molecule that mediates a wide range of cellular processes. Cytosolic calcium is maintained at concentrations that are orders of magnitude below both the extracellular space and intracellular organelles. Even small, sustained increases in cytosolic calcium can have harmful effects on the cell. As such, calcium homeostasis mediated in large part by the endoplasmic reticulum (ER) and mitochondria that serve to sequester calcium enable normal functioning of the cell. To examine cellular mechanisms that mediate calcium homeostasis, we are using mechanosensory hair cells of the zebrafish lateral line. Mechanosensory hair cells can be stimulated via a mechanical stimulus or drug-mediated calcium release from intracellular stores. The hair cells' abilities to easily uptake drugs and respond to physical stimuli make them an ideal tool to examine calcium homeostasis. Preliminary studies using transgenic zebrafish in which the calcium indicator GCaMP3 is targeted to the cytosol vs. the mitochondrial matrix demonstrates that stimulation of hair cells causes an immediate increase in cytosolic calcium in contrast to a gradual increase in mitochondria calcium. The question is whether the calcium in the ER is changing in response to the changes in mitochondrial and cytosolic calcium. As a first step to investigating the role of ER in calcium homeostasis, we will use gateway cloning to generate transgenic zebrafish lines in which calcium indicators are targeted to the ER. We predict that stimulation of mechanosensory hair cells will cause changes in ER calcium levels. These studies may provide valuable insight in how cells maintain health by buffering intracellular calcium levels in response to activity. 

Post-traumatic stress disorder (PTSD) is a widely known and generally understood condition, however, in pain medicine, it is often overlooked and not considered in treatments. PTSD has been shown to greatly affect mood and quality of life in the general population but has not been studied extensively in general pain medicine. Data collected from the University of Washington Center for Pain Relief’s web-based questionnaire that patients fill out prior to clinic visits was used to analyze how PTSD correlates with common components of pain such as intensity, interference with common tasks, quality of life, and substance use. PainTracker^TM is a web-based patient reported outcome tool that assesses pain treatment over time. PainTracker incorporates a variety of questions and instruments to effectively understand the various components of pain. This research illuminates the importance of PTSD in chronic pain patients and how it affects the population suffering from chronic pain. Current analysis has indicated that as PTSD severity increases, so does pain intensity, interference in daily life, mood, anxiety, and quality of life. This illustrates the importance of understanding PTSD’s role in pain and may potentially lead to more effective pain treatment by understanding the roots of pain in post-traumatic stress disorder.

Today's contemporary debate over the broken immigration system in the United States has placed politicians and policy makers at every level of government in a legal gridlock. It is estimated that 11 million undocumented immigrants reside in the U.S., and that at least a fifth of these are young people who have lived in this country since childhood. Of these 2.1 million youth nationwide, about 65,000 graduate from U.S. high schools every year and an even smaller percentage of these students go on to pursue a college education. President Obama's enactment of Deferred Action for Childhood Arrivals (DACA) in 2012 and its expansion in 2014 provided undocumented youth who meet certain criteria with deporation relief and temporary work permits, and with that a potential new outlook on their future prospects. Although there is a growing body of literature on undocumented youth's self-perceptions in American society and the challenges they face in their transition into adulthood, there is little academic work that focuses on undocumented students who have entered college environments. For this research project, I intend to capture the experiences of undocumented college students as they navigate through the university landscape. This process will include an ethnographic survey and semi-structured interviews with 18-30 undocumented university students at the University of Washington. My sampling strategy will involve contacting pro-immigrant groups, organizations, and clubs on campus to establish a pool of potential subjects in addition to snowball sampling. The results of these in-depth interviews and surveys will provide a unique insight into the lives of students and will contribute an additional narrative that will expand the body of knowledge on the subject at hand. The impact of DACA will be explored as well as its implications on undocumented students' educational trajectories and future aspirations. 

Postsurgical treatments for human malignant gliomas prove ineffective as there are high rates of tumor reoccurrence due to their elevated DNA-repair mechanisms. There is a group of human gliomas, oligodendrogliomas, that present longer survival periods of patients receiving chemotherapy and/or radiation. Certain genetic aberrations, specifically deletions of chromosome arms 1p and 19q, are associated with oligodendrogliomas that may lead to better responses to postsurgical treatment. My work addresses the hypothesis that this observed trend is due to decreased O6-alkylguanine DNA methyltransferase(MGMT) activity, which may be a result of the 1p and 19q deletions. MGMT is a known repair enzyme of DNA that contributes to tumor reoccurrence following alkylating agent based therapies. The MGMT activity is determined by estimating the number of MGMT molecules present in a homogenate through an assay developed in the Silber lab. The highly-sensitive assay exploits the reaction of an alkyl group irreversibly binding to MGMT. By incubating [3H]-labeled O6-methylguanine contained in double-stranded DNA with tumor homogenate, each MGMT molecule is covalently bound to a methyl group. The radioactivity is then counted by a liquid scintillation spectrometer. Preliminary data collected indicates that oligodendrogliomas with the deletions typically have lower amounts of MGMT activity than oligodendrogliomas without the deletion. When analyzing the clinical outcome information available, patients whose tumors have lower MGMT activity tend to follow the trend of higher responsiveness to treatment and longer periods of survival. By better understanding the DNA repair mechanisms of human malignant gliomas, new therapies can be developed that can improve the prognosis of patients.

The process of building is not permanent, but encompasses changes far beyond the initial construction. The Moore Theatre, at the corner of Second Avenue and Virginia Street in Seattle, is much more than the innovative 1907 combination of steel, brick and plaster conceived by architect E.W. Houghton and owner James A. Moore. It has evolved over the course of the past century, serving as a testament to the individuals who have owned and occupied the building, and to the changing Seattle society since it first established the city’s national cultural prominence. Many buildings as old as the Moore had their lives cut short by management that was slow to react to changing cultural tides. The Moore, in stark contrast, has continued living due to the efforts of a few individuals who were brave enough to intervene – particularly women. My research examines the architectural and programmatic changes during the reigns of the “Moore women,” Cecilia Schultz and Ida Cole, and determines the extent of their influence on continuing and shaping the life of the Moore Theatre, and, as an extension, the history of Seattle. I will investigate this by taking apart historical, first-person accounts of the women’s involvement in the form of interviews and newspaper articles, analyzing architectural documentation in the form of original and altered plans, sections, elevations, and detail drawings, and currently accessing and analyzing the building physically. I hope to discover the extent of these women’s influences on the Moore, and to draw larger conclusions about women’s roles in Seattle history and the history of historic preservation and architectural history nationwide. These results could implicate the different genders’ roles in architecture and the performing arts and how these have shaped their current ability to gain meaningful leadership in these areas.

Childhood cancer is the highest leading cause of disease-related deaths among youth between the ages of 0 and 19 in the United States. Although many children afflicted with pediatric cancer recover, research has shown that the diagnosis and treatment experience puts significant stress on children and their families. There are many family subsystems that may be at risk, including the marital relationship. Findings regarding pediatric cancer’s effect on the marriage have been mixed, and there is a need to identify factors that predict which families in particular may be at risk for poor marital adjustment. Research has indicated that how a partner responds to emotions can highly impact the quality of the marriage. The Parent Meta Emotion Philosophy (PMEP) refers to parents’ thoughts, beliefs, attitudes, and experiences regarding their emotions, as well as the emotions of their children and others. This study examines PMEP as a predictor of individual differences in marital adjustment in the context of pediatric cancer. Participants consisted of 176 families recruited as part of a larger study from two children’s hospitals in urban areas of the Northwest and Southeast United States. Caregivers completed self-report questionnaires of marital adjustment each month over the first year following diagnosis. Caregivers also participated in a meta-emotion interview, which assessed dimensions of PMEP for emotions of sadness, anger, and fear. Findings suggest that on average, marital adjustment increased over the first year after the child’s diagnosis. In addition, dimensions of PMEP were examined as predictors of trajectories of the marital relationship over the first year. Finally, we discuss and emphasize the importance of examining predictors of variability in the trajectory of marital functioning in pediatric cancer, and how to increase assessment, prevention, and intervention efforts for such at risk families.

Third-party content on websites (such as included advertisements or social media widgets) has recently become a huge topic in computer privacy and security, but few studies have examined the visual impact of third-party content on web pages. Without this information, developers of commonly used tools that interact with third-party content (such as AdBlock and Ghostery) are unable to provide users with information on which advertisers are responsible for specific pieces of content on the page, which users could then use to selectively block certain third parties responsible for undesirable content. This project, in contrast, focuses on the visual nature of different types of third-party content. To gather this information, I created a tool to detect when third-party content is inserted into web pages, allowing me to connect third-party content to DOM nodes (elements of a webpage). This correspondence allows me to collect information on the visual characteristics of elements inserted by various third parties after they have been rendered by the browser. I am able to gather information that Ghostery and AdBlock cannot collect because of their usage of network requests to identify third-party content. I use this information to survey the distribution of size and location of different third-party elements, comparing web pages from different categories and countries to uncover trends in the layout of third-party content. Preliminary results indicate that there are specific visual hotspots for third-party content, and there are a few domains that provide a disproportionate amount of visible third-party content. Other possible directions to explore with this information include improving current tools to help users make informed decisions about which third-parties to block or allow, helping developers debug their web pages, and giving the research community a deeper understanding of how third-party content affects the visual layout of web pages.

Our research at the Applied Physics Laboratory of the University of Washington seeks to develop the controlled flux technique for measuring ocean turbulence for use from a ship in the presence of rainfall. This method has been shown to be effective at determining turbulence at the surface of the ocean under rain-free conditions. However, the application under development will use the technique in the field to measure oceanic turbulence due to various types of rainfall. My objective is to determine whether or not the technique and available equipment will work in the field. A 125 W CO₂ laser operating at a wavelength of 10.6 μm (i.e. in the infrared) was assembled, tested, and aligned so that the laser beam was directed at the surface of water in a small container. The laser was pulsed so that a small patch of water was heated. A fan provided varying amounts of turbulence and an infrared imager was positioned to take images of the heated patch of water. We expect to find that the temperature of the heated water will decay more quickly for greater amounts of wind, and surface turbulence. This is important because rain also generates turbulence at the ocean surface. It is thought that the difference in turbulence as a function of rain intensity will be enough to distinguish between different amounts of ocean rainfall. Using this method at sea will give oceanographers a greater level of insight into how rainfall affects oceanic turbulence. This information can be used to improve models of upper ocean dynamics that affects large-scale ocean circulation which in turn will improve performance of global climate models. This will help scientists better predict climate events and the associated weather patterns that affect the lives of billions of people.

Previous research has shown that adolescents, age 12 to 20, seek identity or intimacy based outcomes when engaging in romantic relationships, either long term or casual. At the same time adolescents show different sets of needs (ex. coping, impressing peers, enhancing sexual feelings) when becoming sexually active. Research on dating goals and sex motives is primarily conducted with adolescents in high school; thus there is a knowledge gap regarding how different sexual motives (ex. sex for intimacy or sex to enhance one's identity) may associate with dating goals in older populations. For our research we surveyed women (n=432) in the greater Seattle area ranging from ages 21 to 30. These participants completed questionnaires that assessed their dating goals as well as their sexual relationship goals. Significant bivariate correlations indicated women who date to explore different identities are more likely to engage in sexual activity to cope with negative emotions, fit into a peer group, please a partner, and enhance their sense of self, but were not more likely to use sex to enhance sexual feelings. Additionally, dating for intimate bonds was positively correlated with engaging in sexual activity to increase intimacy and enhance sexual feelings, but was negatively correlated with using sex to fit into their peer group. Women in this age group traditionally are going through a social and personal shift into adulthood. Future studies should take a longitudinal approach to understand the shifts in women's dating and sexual preferences as they move from adolescents to adults. This information can be used to tailor interventions in relation to sexual health for this age group. 

Changes in phenology, the timing of biological events, are a commonly observed response to climate change, generally with earlier onset of life-history events in the spring. However, high-elevation grasshoppers deviate from this pattern displaying delayed maturation over the last 50 years. To better understand this apparent paradox, we experimentally explored the interactive effects of temperature and light regimes on maturation rates of Melanoplus boulderensis, a montane grasshopper inhabiting a broad elevational cline. We generally expected warmer temperatures to speed development, but this effect might be mediated by day length, which is an important phenological cue for many species. As predicted, grasshopper maturation took longer at lower temperatures. Day length affected maturation rate at low temperatures only, with short day lengths delaying maturation. Elevation of origin did not affect maturation rate. These results suggest that if climate change allows grasshopper eggs to hatch earlier in the spring when day length is short, maturation would require longer at cool, high-elevation locations as observed. Our results highlight the importance of considering all factors affected by climate change when attempting to predict the consequences of such phenomenon on organisms.

Intraspecific studies of morphology and performance are essential for understanding the factors that enable resource partitioning within ecological communities, yet these have received little attention in mammal ecomorphology. Sea otters (Enhydra lutris) is one of the few marine mammal species in which individual-level dietary specialization has been quantified and linked to competition and prey abundance, making them an ideal system to investigate the morphological basis of food resource partitioning. Here, we assess whether differences in cranial morphology and bite force predict dietary variation among sea otter populations. We use geometric morphometric analyses and two-dimensional bite force models to (1) estimate differences in cranial shape and bite force among the three sea otter subspecies groups, E. l. kenyoni, E. l. lutris and E. l. nereis, (2) evaluate the extent of sexual dimorphism in cranial morphology and bite force within subspecies, and (3) relate the variation in cranial morphology and bite force to available dietary information. Although some sexual dimorphism in cranial features exists, preliminary results do not show significant differences in bite force between subspecies or between male and female sea otters. These results suggest that resource-use variation may be linked to individual foraging behavior and not to differences in morphology in sea otters. However, unique cranial features leading to high bite forces may enable this species to have higher diet plasticity; higher bite force in sea otters allows for the consumption of a variety of hard-bodied prey items and allows for either generalized or specialized diets, depending on prey availability and competition.

Unhealthy alcohol consumption can result in alcohol-related diseases such as hypertension, cancer and depression. One of the ways in which primary care settings have helped address unhealthy alcohol use has been through a method called screening and brief intervention (SBI). Latino immigrant day laborers are at a higher risk of unhealthy alcohol use; however, they are less likely to receive SBI due to barriers in accessing health care services. Vida PURA is a culturally adapted SBI designed to address such barriers by placing Spanish speaking promotores at a worker center. We evaluated the feasibility of providing brief interventions to Latino day laborers in a community setting. Interested men completed a screening survey and, if eligible, proceeded to take a baseline survey. Participants were then randomized to the culturally adapted BI or the control group and also completed a follow-up survey two weeks and eight weeks later. The recruitment, retention, and reach measures were recorded in logs and tracking forms kept by the promotores. I evaluated the feasibility of the intervention by analyzing these logs. After 28 weeks of data collection, 118 participants have been screened, of which, 67% were eligible for the study. Baseline surveys were completed by 78 participants, 51 were randomized, and 48 received the intervention. The participant retention rate was 91% for the two-week survey and 89% for the eight-week follow-up. Findings suggest the study is feasible in regards to recruitment, retention, and reach. This analysis highlights the importance of using promotores at a worker center to provide brief interventions to Latino immigrant day laborers, a population considered to be hard to reach. Future studies should consider the use of promotores to target other hard to reach and underserved populations to address unhealthy alcohol use.

In recent years there has been much speculation about how events that occur during childhood can have a lasting impact on a child’s development. There have been many studies that attempt to look at how the impact of child stress affects different parts of development: physical development, psychological development, and social-emotional development. The purpose of this research was to observe and learn how stress affects emotional and social development and consequently impacts the child's risk for mental health issues. Although stress is a multidimensional concept and can be measured by biological responses, the presence of challenging environmental factors, and self-reports, for the purpose of this research stress was defined as the presence of adverse environmental factors. For development, I specifically observed attachment and emotional regulation. My focus on mental health was internalizing psychopathology, especially anxiety and depression. To gain a better understanding of the emotional social development of a child suffering from toxic stress, I looked at multiple studies already done that observed the effects of stress on a child’s social-emotional development. I also used conclusions drawn from experience gained while working at the Stress and Development Lab directed by Dr. Katie McLaughlin. For this approach I reviewed papers that demonstrated a connection between stress and mental health, between stress and development, and between development and mental health. I also looked for and identified factors that showed evidence of mitigating the effects of stress on mental health and development. These factors are referred to as protective factors. Identifying the aspects of development influenced by toxic stress and the mitigating factors is crucial to creating and implementing intervention techniques to promote healthy development and to decreasing the risk of internalizing psychopathology.

The position of leaves around a stem (phyllotaxy) impacts a plant’s yield, pollination conditions, and light harvesting abilities. Auxin plays a critical role in establishing phyllotaxy. Expressing sequence variants of the auxin-regulated protein IAA28 in the plant Arabidopsis thaliana led to changes in phyllotaxy, specifically in the angles between flowers along the inflorescence bolt. Normally, the IAA28 protein binds and represses AUXIN RESPONSE FACTOR (ARF) transcription factors. When auxin is present, the IAA28 protein is degraded, initiating organogenesis. I am currently using three strategies to characterize an IAA28 knockout mutant (iaa28-ko) to better understand IAA28’s role in phyllotaxy. Loss of IAA28 is reported to cause a number of phenotypes by Wang and Guo, but phyllotactic patterning has not been characterized. My first goal is to quantify phyllotaxy by using a measuring device made in the Nemhauser Lab to measure the divergence angle between siliques. I hypothesize that the divergence angles measured in iaa28-ko plants will be smaller than the wild type. My second goal is to determine the change in auxin patterning in iaa28-ko mutants by using plants expressing an auxin reporter called DR5::Venus. Because the iaa28-ko mutant is reported to have more lateral roots, and lateral root initiation requires auxin, I hypothesize a higher expression of DR5::Venus in the iaa28-ko root and inflorescence meristem than in the control. Finally, I will test the functional conservation of BIF4, the putative maize ortholog of IAA28. To determine if BIF4 is functionally similar to IAA28, I will use Agrobacterium-mediated transformation to express BIF4 in an iaa28-ko plant. I hypothesize that the BIF4 protein will fill in the role of IAA28 in the auxin pathway, rescuing the mutant. By understanding the underlying mechanisms that control the phyllotaxy of Arabidopsis, we can learn how to apply similar engineering strategies in other plants.

Dandy-Walker Malformation (DWM) is the most common cerebellar malformation in humans affecting one in every 10,000 live births. DWM is characterized by underdevelopment of the cerebellar vermis, as well as an enlarged fourth ventricle and posterior fossa. Symptoms range from intellectual disability to autism, although some patients are minimally affected. Recent research performed in our laboratory implicated deletion of a transcription factor called FOXC1 in DWM. Surprisingly, Foxc1 expression is absent in the developing cerebellum of mice. Instead, it is abundantly expressed in the meninges overlying the growing cerebellum. Therefore, we hypothesized that Foxc1-mediated meningeal signaling plays a critical role in cerebellar development. In Foxc1-/- mice, we used a combination of immunohistochemical and in vitro assays to demonstrate devastating decreases in neuronal proliferation in the cerebellar ventricular zone, concomitant with increased neuronal differentiation during crucial embryonic stages of cerebellar development. These contributed to a severe reduction of the neural progenitor pool and significantly reduced cerebellar size. Aberrant cell migration and dysmorphic radial glial cells were also detected in mutant mice. Sfd1α is a Foxc1-dependant secreted factor in the meninges that signals to Cxcr4 in the cerebellum. We demonstrated that disruption of Sdf1α-Cxcr4 signaling in Cxcr4 mutant mice phenocopied the Foxc1-/- mutant cerebellum. We conclude that interactions between head mesenchyme and the early embryonic cerebellum are crucial to the development of the cerebellum. Most recently we have extended these studies to show that the developing cerebellum in FOXC1 +/- human DWM patients largely resembles the Foxc1 and conditional Cxcr4 mouse mutant phenotypes. This suggests that key mechanisms controlling early cerebellar development are conserved between mouse and human. This also strongly argues that we have identified the key developmental pathological disruptions causing human DWM.

O6-methylguanine-DNA methyltransferase (MGMT) is the sole DNA repair activity that removes cytotoxic methyl group adducts from the O6 position of guanine. My overall hypothesis is that MGMT in human glioblastoma (GBM), a malignant brain tumor, limits tumor cell killing by chemotherapeutic methylating agents such as temozolomide. To address this hypothesis I will compare MGMT activity in GBMs with a mutated copy of the IDH1 (isocitrate dehydrogenase) gene with that in wild type tumors. IDH1 mutant GBMs differ from wild type in being much more responsive to methylating agent therapy and having longer survival. Mutant IDH1 converts isocitrate to 2-dihydroglutarate that suppresses the expression of epigenetically regulated genes. As MGMT expression is controlled epigetically by a mechanism sensitive to 2-dihydroglutarate, I hypothesize that the better clinical response of IDH1 mutant GBMs is associated with lower MGMT activity than wild type tumors. To address my secondary hypothesis, I will assay MGMT activity in homogenates of human GBM tissue with known mutation status and a complete history of the course of alkylating agent treatment. Tissue and clinical outcome data will be provided by the Neurosurgery Tumor Bank. When necessary I will determine mutation status of archived GBM tissue by an established PCR assay. Finding significantly lower MGMT activity associated with longer survival in mutant tumors will support my hypotheses. I will also examine the association of MGMT activity with survival following alkylator therapy for wild type and mutant separately to provide additional evidence of the role of MGMT as a mechanism of treatment resistance. An inverse association between tumor MGMT activity and treatment response will suggest (1) that MGMT can be used as a prognostic marker for treatment outcome and (2) that inhibition of MGMT as part of alkylator therapy may improve clinical outcome for GBM patients regardless of tumor IDH1 mutation status.
 

The Astronomy Undergraduate Engineering Group is building an attachment to improve the science capabilities of the Manastash Ridge Observatory 30 inch telescope. This attachment is an offset guider which will improve tracking capabilities allowing the telescope to stay within two arcseconds of a target star (seeing limit) for an extended period of time. The guider uses unused light from the main optical path that is reflected off with a pick-off mirror onto a detector. A rotating periscope design is used to take full advantage of all of the unused light by creating a simulated large field that the detector can use to increase the sampling area. The periscopes rotational position along this field will be driven by a high precision stepper motor for maximum control. Two linear actuators will als  o be used to check the primary focus of the telescope so that it may dynamically correct for any wandering of the focus.

Bigleaf maple, Acer macrophyllum, is an iconic species in Western Washington, but in recent years (starting in 2010), they have undergone significant dieback, marked by tree mortality, reduced and yellowing leaf growth, and crown thinning. In this study we examined potential causes behind the dieback. The Washington State Department of Natural Resources (DNR) has previously examined the plant pathogens Verticillium wilt, Xylella fastidiosa bacteria, Phytophthera spp. (a root pathogen), and Armillaria (a parasitic fungi), which are often implicated as causes of the symptoms seen in declining Bigleaf maple, and determined that none of these pathogens were significantly present in all symptomatic trees. We tested the hypothesis that climate trends such as precipitation and temperature could cause tree stress and contribute to dieback. We also analyzed the locations of 56 symptomatic trees in Western Washington, documented by DNR in 2014, to determine if spatially significant clusters existed. To analyze climate trends, we collected National Oceanic and Atmospheric Administration data from three Western Washington cities for precipitation and temperature from 2000-2015. Using data from DNR, symptoms of stand mortality and stand reduced leaf growth, as well as the 56 symptomatic tree locations were plotted in ArcMap and spatially analyzed using R. We found that climate patterns do not appear to have an effect on tree death, although spatial analysis in R found that symptomatic trees were significantly spatially clustered. There was a significant correlation between mortality and reduced leaf size with location, but no significance with regards to symptom intensity. The spatial clustering of affected trees indicates that the cause of decline could still be a biotic factor, though further specific studies will be necessary in to determine which pathogen, if any, is responsible for widespread symptoms.

Little is understood about how Supermassive black holes affect their host galaxies in terms of growth and shape. Using the Simulation Romulus25, we are able to study how galaxy properties correlate with black hole properties throughout time. The simulation is a cube with lengths of 25 Mpc on each side, which is about 75 million ly or 21000 Milky way galaxies. We look at how the properties of galaxies relate to the properties of their black holes. We present trends that distinguish star forming galaxies from quenched galaxies.

Agressive cancers are resistant to apoptosis and stem-like cancer cells may be responsible for re-growth of cancerous tumors. This inspired this search for compounds that could aid in the destruction of cancer cells with stem-like properties. Drosophila germ-line stem cells under radiative or chemotoxic stress are protected by a molecular signal from apoptotic daughter cells via the TIE receptor. Thwarting this protective signal by the introduction of a small molecule may lead to the discovery of compounds that can be effective against stem-like cancer cells. The NCI Diversity Set of 1,596 small molecules was screened by undergraduate research students, in-vivo, to find compounds that can induce apoptosis in germ-line stem cells of Drosophila melanogaster. Four compounds have been found that induce apoptosis in both the male and female germ-line stem cells at a low 5 uM concentration. Future investigations will uncover the mechanism of action and efficacy against stem-like cancer cells.

Cardiovascular disease and diabetes have been and are currently associated with obesity. Understanding the connections between obesity, lipid droplets and these diseases is crucial to ameliorating their recurrence and the six hundred thousand people that are affected yearly. The roundworm C. elegans serve as a model for genetic and physiological regulation of lipid metabolism. A previous study by our lab identified numerous proteins that localized to C. elegans lipid droplets. One of these, ldp-1 (F22F7.1) shows similarity to a mammalian lipid droplet protein called CGI-49. Because the analysis of lipid droplet quantity and localization is crucial to understanding the physiological mechanisms of fat storage, we intended to determine if knocking down the gene encoding ldp-1 had any effect on fat accumulation. To determine the phenotypic effects of knockdown of ldp-1, the study used both Nile Red and Bodipy staining, and the process of RNAi. Analysis of the staining found that neither the intensity, nor the quantity of lipid droplets was affected by the knockdown of the gene ldp-1 when compared to wild type C. elegant. Thus, ldp-1 is not required for proper fat accumulation in well-fed young adult staged C. elegans.

The current obesity epidemic catalyzed research in the area of incentive motivation, examining the role of reward mechanisms in our eating behaviors. Sugar-sweetened beverages are of particular interest as their consumption is correlated with obesity, increased energy intake, and incentive motivation. At the individual level, food choice and behavior are influenced by an array of factors, including reward, as well as explicit and implicit attitudes. Explicit preferences and even labels on food influence consumption while implicit attitudes toward stimuli also influence behavioral intentions, and are commonly examined with Greenwald and colleagues (1998) Implicit Association Test (IAT). In this study, the Personalized IAT is used, along with the Extended Personalized IAT using “I want” and “I don’t want” for responses to provide better understanding of hedonic liking and motivational wanting, respectively. The Personalized IAT is used to remove possible biases from extrapersonal associations such as influences of social norms. In this study, we combined the Personalized IAT and explicit measure questionnaires, Cohen’s (1988) Perceived Stress Scale and the Three-factor eating questionnaire (TFEQ, Stunkard & Messick, 1985) to examine the evaluation of sweetened beverages. These hypotheses indicate expected results: (1) sweetened beverages produce the same level of hedonic addictive value as natural sugar, (2) individuals with higher dietary restraint prefer sweetened beverages over non-sweetened, (3) BMI is positively correlated to both implicit liking and wanting, and (4) stress moderates the relationships between BMI and implicit liking and wanting.

Overnutrition and sleep loss are widespread problems in today’s society and major risk factors for metabolic diseases. As with overnutrition, sleep loss impairs glucose regulation, though the mechanisms underlying this effect are unclear. Hypothalamic neuroinflammation disrupts leptin and insulin functions, resulting in the promotion of obesity. Sleep loss also elicits neuroinflammation, though little research has focused on determining whether this occurs in brain regions that regulate glucose metabolism. To examine the role of neuroinflammation in insufficient sleep- and overnutrition-induced deficits in glucose regulation, adult C57BL/6J mice were subjected to one of four treatments: undisturbed sleep and standard chow (control); undisturbed sleep and high fat diet (HFD); 18 hours/day sleep fragmentation (SF) and standard chow; 18 h/d sleep fragmentation and high fat diet. After nine days of manipulation, a glucose tolerance test was conducted, and then brain tissues were obtained and processed for immunohistochemical analyses of microglial and astroglial activation in the hypothalamus and brainstem (n=6/group). Sleep fragmentation or high fat diet reduced glucose tolerance compared to the control, with the greatest deficits observed in mice subjected to both sleep fragmentation and high fat diet. Analyses of numbers of activated microglia and astrocytes will determine whether patterns of glial activation across treatments reflect changes in glucose tolerance. These findings will be important in determining the contributions of neuroinflammation to glucose tolerance within the context of chronic insufficient sleep and poor diet.

The lateral habenula (LHb) in the brain is an important regulator of midbrain dopaminergic systems that are known to be involved in the reinforcing properties of cocaine. We have previously determined that activation of LHb neurons using Designer Receptors Exclusively Activated by Designer Drug (DREADD) technology decreased cocaine-induced locomotor activity and cocaine self-administration in rats. To determine if these effects were due to disruption in motor coordination, in this study, male Long-Evans rats underwent survival surgery and were injected with hM3Dq (2 microliters), which is an activating DREADD virus bilaterally into the LHb. They then went through a training period of 2 trials per day for 5 days to master the Rotarod, a test for motor co-ordination. The Rotarod test entails a rotating wheel in which rats must balance and walk, thus testing their coordination. The amount of time they remain on the wheel is recorded with the maximum time per trail being 120 seconds. After the training period is over they are subjected to testing days where the rats are then injected with 1 or 3 mg/kg i.p. clozapine-N-oxide, which is the inert ligand that activates DREADD receptors. Twenty minutes is elapsed before they are subjected to the test. The amount of time spent on the Rotarod is again collected. Interestingly, our results demonstrated that activating the LHb produced no change in the level of motor coordination. This is interesting because with our cocaine self-administration experiments, a decrease in lever pressing is observed. Our results tell us that inhibiting the LHb has no effect on coordination and thus the decreased lever pressing expressed in the cocaine self-administration rats is in fact not due to a decrease in coordination. These results helped us rule out a possibility as to why our self-administration rats decreased their lever pressing.

Minimizing the energy consumption of wireless sensors is critical, yet a challenge for the design of wireless sensor networks (WSN). Energy is consumed in WSNs by sensing, communicating and processing. In various WSN applications, it is likely that communications are the major source of power consumption, rather than computation. Therefore, assuming that local processing is much less expensive than communicating, we focus on minimizing the number of transmissions for a distributed clustering problem in a sensor network. In our setup, each node in the network senses an environment that can be described as a mixture of Gaussians and each Gaussian component corresponds to one of the elementary conditions. For estimating the Gaussian components, we propose a distributed EM (expectation-maximization) algorithm based on stochastic approximation (DEM-SA), and we study a trade-off between local processing and communication for the distributed clustering problem. DEM-SA reduces the traffic and contention in a WSN by keeping computations and communications local and avoiding the need for cycles through the network. Simulation results are presented.

CYCLOIDEA (CYC) is a member of the TCP family of transcription factors, whose name stands for TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS.  The members of this transcription factor family are involved in regulating plant growth and cell proliferation by binding to DNA. Previous studies show that CYC has duplicated at least twice in the core eudicot angiosperms and that the CYC2 paralog is involved in controlling flower symmetry. The goal of our research was to characterize duplications of CYC in Rhododendron, with the long-term goal of seeing how these duplications affect flower symmetry. To accomplish this task, we used the R. williamsianum genome sequence to design primers specific to each paralog in order to PCR-amplify the CYC genes from four Rhododendron species, representing two subgenera (Hymenanthes, Rhododendron). Amplified products were cloned and sequenced to recover all alleles. We used our Rhododendron sequences and sequences from the conserved TCP and R domains of other species as out-groups in a Bayesian analysis to reconstruct the gene tree. From this tree, we have identified 2 main duplications in Rhododendron CYC genes as seen in other core eudicots. We also found that the CYC2 paralog has undergone at least 2 gene duplications and that the CYC1 paralog underwent one. Future research will focus on finding when CYC2 duplications occurred in rhododendrons and determining if, where, and when these CYC2 duplicates are expressed in Rhododendron flowers.

Some physiological markers, such as heart rate, may be related to the development of later intrusive memories following a distressing event. Several analogue experimental studies have found a relationship between lower heart rate and an increased number of subsequent intrusions. When looking at a trauma-exposed sample, increases in heart rate in response to a stressor were positively correlated with trait anxiety. However, the potential interplay between trait anxiety, heart rate, and subsequent intrusive memories is yet to be established. The aim of this study is to explore the relationship between heart rate and intrusions by examining how trait anxiety may mediate this relationship. We predict that there will be a strong negative correlation between heart rate during intrusive memory sequences and number of subsequent intrusions, a positive correlation between heart rate during intrusive memory sequences and trait anxiety, and that trait anxiety will mediate this relationship. We collected data from 178 undergraduate students who viewed a 10-minute video clip that has been shown to elicit distress and lead to the development of later film-related intrusive memories. Participants’ heart rates were monitored using Microsoft wrist bands, and we specifically looked at heart rate during film sequences most commonly reported as later intrusive memory content. Participants were assessed for intrusions (frequency, distress, and content) 24 hours after film viewing. Being able to identify individuals who are most likely to experience intrusions after a traumatic event can play a crucial role in treatment and prevention of post-trauma psychopathology.

Seattle’s Combined Sewer Overflow (CSO) system discharges approximately 100 million gallons of untreated sewage and storm water runoff into its waterways annually. The sewer system includes two combined waste streams: waste from sewer basins, which captures storm water runoff, and wastewater from buildings and industry. Pollutants in the effluent such as human waste, automotive by-products, pesticides, and pharmaceuticals can degrade ecosystems. To determine the impact that CSO outfalls have on Seattle’s waterways, this study tested for pollutant levels in sediment near two discharge areas: Elliott Bay and the western end of Seattle’s Ship Canal. Sediment samples were collected using a Van Veen grab, then handled and stored using sterile, inert materials to avoid contamination. Sediments were tested for heavy metals including mercury, via cold-vapor atomic absorption, and lead, via inductively coupled plasma mass spectrometry. The organic pollutants ammonia, nitrate, and phosphate were quantified via automated calorimetry. Laboratory testing for pollutants was done in accordance with EPA guidelines or standard analytical methods. Results were compared to the Washington Department of Ecology’s Sediment Management Standards. Preliminary results suggest that lead and mercury levels do not exceed the Department of Ecology’s sediment quality standards, while cadmium levels are slightly above or below recommended levels at each site. This data can be used as a baseline to help better understand the contribution of CSOs to pollution levels in these areas. More research will be necessary to determine the extent of damage to ecosystems near the outfalls.

Vascular injury causes platelets to form hemostatic plugs. Platelets are activated by high shear and collagen, and adhere and contract to protect a clot from mechanical forces. The role of collagen and the anticoagulants heparin and ASA (Acetylsalicylic Acid), which inhibit thrombin and TxA2 (Thromboxane A2) respectively, are not fully understood. Our lab has designed a microfluidic device to measure clot forces and area. Microfluidic channels with block-post sensors generate shear gradients that induce platelet adhesion. Clots grow towards the post and contract, pulling the post closer. Fluorescence microscopy allows post deflection to be analyzed with MATLAB code using Hooke's Law, and phase images monitor area. First, channels were coated with and without collagen. Then, channels were collagen-coated and blood inhibited with heparin or ASA. Blood was incubated with 15 USP (U.S. Pharmacopeia standard) heparin lithium in H2O or 0.3 mM ASA in DMSO for 20 min. Clots in uncoated channels had lower forces than in collagen-coated channels. Blood with ASA in DMSO had less platelet adhesion and contraction than in blood incubated with DMSO. Blood with heparin in H2O had lower force but higher clot area than without heparin. Reduced force of clots formed in uncoated channels relative to collagen-coated channels suggests that collagen is important in force. Inability of platelets to adhere or produce normal force with ASA indicates that TxA2 promotes platelet aggregation and force. Heparin reduced force but not platelet aggregation, thus thrombin is involved in force generation only. This clot-on-a-chip technology can shed light on the clotting process and diagnose patient clotting issues.

Eclipsing binaries are systems in which two stars orbit and pass in front of each other. They are important astrophysical tools we utilize to measure fundamental properties of stars, such as their masses, radii, and temperatures. Here, we analyzed photometric data acquired from the Kepler satellite in order to model the light as a function of time of specific eclipsing binary systems. We selected these targets from the Villanova Kepler Eclipsing Binary Catalog. For each system, we used a least-squares optimization method to determine the best fit solution between the model and the observed light curve. Our light curve model has a total of 13 parameters. They include stellar elements such as sum of radii and flux ratio, as well as orbital elements such as period and eccentricity. In addition to providing orbital solutions, our models can be used to search for the presence of additional bodies in the system, such as a third star or a circumbinary planet.

The Executive Office of the President has declared opioid misuse among youth a national epidemic owing to its prevalence and the severe associated consequences. Little research has been conducted on the types of opioid prescriptions provided to children and their family members, which are the primary source of misused opioids. Knowledge of the trends in opioid prescriptions to children and families could help us better understand the rise in misuse. Therefore, our aim was to uncover trends in the quantity, type and reason for opioid prescriptions as well as sociodemographic factors associated with opioid prescriptions to children and adolescents ages 0-17 and their families from 1996-2012. Secondary data analysis was performed on a population-based sample from the Medical Expenditures Panel Surveys (MEPS). MEPS are a set of surveys that collect data on the healthcare of a nationally representative sample of approximately 40,000 US citizens annually. We abstracted information on demographics, type of opioid prescribed, number of opioid prescriptions per participant, whether a family member received an opioid prescription, and medical diagnoses associated with opioid prescriptions. We found that while the number of opioid prescriptions to the family members of children and adolescents increased by 71% from 1996 to 2012, the portion of children and adolescents prescribed opioids remained stable at around 2.8% annually. Among children and adolescents, those who were white-non-Hispanic, older in age, and had private insurance had higher odds of being prescribed opioids. Furthermore, we found that codeine was the most commonly prescribed opioid in pediatric populations, accounting for 40% of all pediatric opioid prescriptions despite guidance from the U.S. Food & Drug Administration to limit codeine prescriptions in youth. These findings add to our understanding of opioid prescribing trends and will be important for guiding future research and clinical practice to ensure adequate, safe, and effective use of opioids.

Historically, only clinicians and researchers have been involved with decisions about what research topics to pursue, and patients have been left out of the process. This creates a gap between clinical application of research and patients’ experience. By expanding the scope of how researchers and clinicians obtain patient data to include research topic priorities, we explore how to incorporate patient perspectives better. Although there are many studies that aim to analyze patient registries, there are limited studies that attempt to elucidate the degree of the participants’ interest, or willingness to get involved in providing input on research activities. Through a study funded by the Patient-Centered Outcomes Research Institute (PCORI), we developed a two-phase approach to prioritize topics for low back pain research. In phase one, we invited participants from a patient registry of older adults with back pain , and in phase two, invited participants using Amazon Mechanical Turk (MTurk), an online crowd-sourcing platform. Participants completed an initial screening survey comprised of the Roland Morris Disability Questionnaire, a standard tool to identify individuals experiencing back pain. Those scoring 7 or higher on the RMDQ were sent a research topic prioritization survey. 1966 people completed the screening survey, and 480 qualified, of which 353 completed the prioritization survey (completion rate: 74%). Using both recruitment strategies, we had a high response rate, and participants are diverse in terms of pain, gender, and age. Responses show participants’ effort to fully answer the survey and voice their opinion, including providing additional topics that had not been identified previously.This work highlights that recruiting from a patient registry or using MTurk are both effective tools to obtain patient input, and increases the flow of information from the public/patient to the researcher, and inevitably the clinician; we expect incorporating these methods will increase patient voice in research.

After large loading events, such as earthquakes, buildings are inspected to determine the extent of damage done to the structural systems and whether it is still safe to use. These building inspections are completed mostly by observing visible damage and using engineering judgment to determine the residual strength of structural elements, or members. This approach is subjective, and accurate inspections demand a more robust approach. Non-destructive testing can be performed on structural steel that attempts to quantify a member’s strength, but these tests have marginal accuracy. Permanent instrumentation of a building can also provide data, but sensors must be powered and well maintained. An interdisciplinary team, led by Professors Dawn Lehman and Laura Lowes from the Department of Civil and Environmental Engineering and Professor AJ Boydston from the Department of Chemistry seeks to develop a polymer coating that can provide a better way to quantify strain in building members. The polymer is comprised of strain-sensitive units (mechanophores) that undergo molecular-level transformations as the polymer chains are extended. The chemical reactions provide visible outputs, such as intense changes in color and fluorescence properties. By changing the microstructure of the polymer and mechanophores, we will be able to control the threshold sensitivity and strain-dependent intensity of color changes. Once applied to a member, the polymer would effectively track the strain that the material undergoes through a change in color, which can be correlated to a residual strength. This color can be observed after earthquakes and other extreme events and allow inspectors to quickly and accurately determine structural health. Our research objectives include applying color-changing strain-responsive (mechanochromic) polymer coatings to building members and analyzing the response to applied strain. My contribution to the project is creating the metal samples and testing them after the polymer has been applied.

Body image dissatisfaction is a leading contributor to the development of eating disorders. Eating disorders have the highest mortality of all mental illnesses, are most common among females, and most often develop between ages 16 and 20. Research shows that Facebook use is associated with increased risk of eating disorders among female college students, and that appearance comparisons mediate this relationship. However, it remains unclear whether Instagram increases the risk of eating disorders among this population. Instagram is an image-based social networking platform that is more commonly used among women compared to men ages 18-29. The purpose of this pilot study is to examine the influence of Instagram use on body image perceptions among college females. Higher Instagram use is expected to be associated with an increased risk of body dissatisfaction. Female undergraduate public health majors were recruited through an email list-serve to complete an online survey. The survey asked about frequency and patterns of Instagram use. Additional questions assessed appearance comparison to peers, family members, celebrities, and models on Instagram. The survey also assessed prevalence of and appearance comparison to fitness motivation accounts on feeds. Finally, body dissatisfaction is assessed with the Body Dysmorphic Disorder (BDD) scale. Analyses include descriptive statistics for quantitative data and thematic analysis for open-ended responses. Predictive models will be created to predict BDD from Instagram use per week and per day. Results include descriptive statistics of demographic information, Instagram use, and body dysmorphic scores. Assessment of social group appearance comparison on Instagram will also be included. Additionally, open-ended responses may reveal themes in fitness motivation accounts or general Instagram use. Findings will inform relationship patterns between Instagram use and body image dissatisfaction. Future studies could determine whether Instagram should be targeted for eating disorder interventions.

Social media, as a source for social connection and information, has been shown to be a platform by which users display content related to risky health behaviors such as problem drinking. This type of content has both the potential to influence social norms and behaviors especially in populations that are greatly interacting with social media such as young adults. Snapchat, a social media application (app), is used by 77% of college students at least once a day. As an app, Snapchat allows users to display information through pictures and videos, 10 seconds or less in length, that are then erased or self-destroyed after being viewed by a recipient. This unique feature for transient content and popularity among college students positions Snapchat as a potential platform for displaying both intoxication and general alcohol references due to the lack of permanent display. In the current literature there exists a gap in understanding of alcohol displays and college student behavior in regards to Snapchat. The purpose of this study is to investigate self-reported alcohol content and displays on Snapchat among college students. Surveys will include questions related to participants’ own experience with viewing alcohol on Snapchat, their own display or lack of display of alcohol, which social media platforms they believe have the highest amount of alcohol content, and how likely friends are, if intoxicated, to post to Snapchat. Data from this study could indicate the prevalence of alcohol displays on Snapchat among college students, provide evidence for the monitoring of Snapchat use by peers and friends, as well as support a potential area for intervention.

Arrhythmias kill 300,000 people annually and effective cardiac drugs are imperative in their management. However, heavy reliance on in vivo testing results in low throughput and ineffective preclinical prediction of human response. Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are a promising cell source for highly predictive, high-throughput in vitro testing. Unfortunately, culture conditions in current hPSC-CM assays leave hPSC-CM tissues immature, making them ineffective at modeling human myocardial drug responses. Tissue culture conditions that mimic the myocardial microenvironment promote the maturation of hPSC-CMs with higher efficiency than non-mimetic conditions. Taking advantage of this, our lab's NanoMEA system successfully melds biomimetically nanopatterned substrates with microelectrode arrays (MEAs) that perform high-throughput electrophysiological analyses of in vitro tissues. However, greater maturation efficiency is necessary to improve NanoMEA screening throughput. Electrically conductive environments promote hPSC-CM maturation, and numerous electrically conductive scaffolds exist. Yet, overlaying MEA electrodes with these substrates results in noisy signals that bar automatic processing. NanoMEA nanopatterns are made of Nafion, a nanoporous polymer that does not negatively impact the recordings from underlying MEAs. Since Nafion exhibits robust self-assembly with electrically conductive reduced Graphene-Oxide (rGO) molecules, we hypothesize that Nafion-reduced Graphene-Oxide (NrGO) nanopatterns will convey the benefits of conducting surfaces without impacting signal clarity. To investigate this, NrGO-nanopatterns are fabricated and characterized using Raman Spectroscopy, transmission electron microscopy, scanning electron microscopy, and conductive atomic force microscopy. Then, hPSC-CM monolayers are cultured on NrGO nanopatterns of varying rGO content and differences in morphological and transcriptional maturation markers are assessed. Promising NrGO nanopatterns are then integrated into a multiwell MEA platform to examine their effects on signal clarity and electrophysiological hPSC-CM maturation. If effective, we anticipate that this enhancement to the NanoMEA system will enable faster development of safer drugs, reducing animal model reliance, and improving the treatment of arrhythmias.

We have obtained three epochs of observations of the nearby spiral galaxy, NGC 300, using the Chandra X-ray Observatory. Using this data, we searched for variability in the X-ray luminosity function (XLF) of NGC 300's X-ray point source population. When the entire X-ray source population was considered, the XLFs were best described by using a power law with a slope of ~0.6-0.7. However, the XLFs of intrinsically variable X-ray sources showed significant variability between observations, especially at low luminosities (< 10^37 erg/s). We created synthetic, variable X-ray sources to probe the characteristics of the X-ray point source population in NGC 300. In order to match the observations, our models required that the peak X-ray luminosity of variable sources are significantly lower than commonly assumed, which is characteristic of a mass transfer due to direct wind accretion at significantly sub-Eddington rates.

Delivering lethal doses of radiation directly to a tumor without damaging surrounding tissue has been one of the biggest challenges in radiation based cancer therapeutics. The development of Pre-targeted Radioimmunotherapy (PRIT) uses a two-step system to deliver radiation directly to targets, like cancer cells, but may be immunogenic. The overall purpose of my research is to enhance Pre-targeted Radioimmunotherapy (PRIT) for a better therapeutic outcome by producing and characterizing a bi-specific antibody to directly target radiation to cancer cells, while minimizing off-target radiation and immunogenicity concerns of traditional PRIT approaches. Initial experiments showed preferential targeting of disease sites via a biodistribution study in a leukemia (Acute Myeloid Leukemia) mouse model. Biodistribution studies involved therapeutic groups (5 mice per group) that were injected with 280 µg of 30F11-C825, (the bi-specific antibody recognizing murine CD45, a cell surface marker on most hematopoietic tissues). The negative control group mice were injected with 280 µg of CC49-C825 (a non-binding bi-specific antibody control). Mice from all groups were then injected with 5 µg of DOTAY-dextran clearing agent (to clear unbound antibody from circulation). The second step was an injection of 50 µCi of ⁹⁰Y-DOTA-biotin (radioactive injection) to mice in all groups. Mice tissue harvest was performed at 6hrs and 24hrs after ⁹⁰Y-DOTA-biotin injection. The biodistribution study showed mice treated with 30F11 bispecific antibody had greater amounts of radiation in the disease target sites [spleen=21.7±15 % injected dose pre gram of organ (%ID/g); bone marrow=10.3±3.2 %ID/g], compared to uninvolved organs [lungs=0.3±0.2 %ID/g; kidneys=0.6±0.2 %ID/g; bowel=0.6 ±0.2 %ID/g]. The next phase of my work includes a therapy study using our bi-specific antibody to treat leukemia in a mouse model, and if successful may lead to clinical trials for AML patients.
 

In the field of cognitive psychology, multiple studies have shown that humans seem able to recall a large amount of information with great detail. Thus, scientists are particularly interested in understanding the exact mechanisms by which memories are encoded in the human brain. Current models of semantic knowledge origin can be classified into two families: semantic network models and embodied cognition models. My experiment provides a way to distinguish between these two models by examining which type of interferences (semantic vs. sensorimoter) has a larger effect on semantic memory retrieval. Thirty participants were asked to perform a computer task, during which they chose the picture of an object that matched the target word from an array of objects that containd different distractors. There are three conditions, corresponding to the different types of distractor objects: unrelated distractors, sensorimotor distractors, and semantically associated distractors. Greater interference from distractors reflects greater similarity in concept representation, and thus results in slower response times. Our results show that the mean reaction time of semantically associated distractor condition is the largest. The mean reaction time of unrelated distractor (control) condition is the second largest and that of sensorimotor distractor condition is the smallest. The results support the semantic network models and indicate the facilitation of sensorimotor related objects. The results from these comparisons can not only provide us with a general idea of how the embodied cognition model and semantic network models differ from each other, but also provide us with potential applications to everyday life. First, for example, knowing the patterns from which people build concepts in mind inspires people to create memorization strategies, leading to the improvement of memorization. Second, as a growing area in cognitive psychology, embodied cognition is related to not only memory, but also emotion, perception, and language, etc.    

According to the Centers for Disease Control and Prevention, diarrheal diseases are the second leading cause of death in children under the age of 5 globally. Cryptosporidium and Giardia are two microscopic parasites that cause diarrhea, infecting both humans and animals. The current gold standard field method for collecting water samples for parasite testing (Environmental Protection Agency (EPA) 1623), is not practical for remote sample locations as it requires 10-L of water to be kept on ice during transport to testing facilities. A pilot study by the UW Center for One Health Research will implement a new water sampling system, known as Bag-Mediated Filtration System (BMFS), to look at how these parasites impact low resource communities. My goal was to determine if BMFS could be used in conjunction with EPA 1623 to give recovery rates consistent with the current EPA 1623 method. I went to 4 different locations in Washington to retrieve surface water samples using the BMFS kit. Sites were chosen based on the likelihood that there would be parasites present: sources with the possibility of animal waste and areas with turbid water. The environmental samples, along with 10 parasite-spiked laboratory samples were analyzed using the EPA method - after filtration using the bag. Parasite numbers were measured as oocysts per liter using immunofluorescence, and recovery rates of spiked samples were compared to acceptance criteria from the EPA. This study will be useful to water quality researchers working in rural or remote field sites, or areas where climate conditions make sample storage challenging.

Organic acids are crucial factors in creating the aromas and flavors in wine, each adding their own qualities and characteristics. Winemakers regularly use various forms of technology to quantitatively determine the contents of wine. Analytical tools such as enzymatic spectrophotometry, paper chromatography, and high-performance liquid chromatography offer methods to quantify chemical components including acetic, malic, lactic, tartaric, and citric acids, as well as sulfates and sulfites. Although ion chromatography (IC) has not been a widely studied method to analyze organic acid content in wine, it offers the potential to simultaneously analyze multiple ions with greater specificity and sensitivity than other approaches. This project examines the various ways that IC can be used to analyze the components of wine, allowing for further application within the wine industry. The malolactic fermentation process was tracked to measure the changes of malic and lactic acids within the wine. Sulfites and sulfates were measured as the wine was exposed to oxygen during the aeration process. The results show that IC provides greater accuracy than paper chromatography and enzymatic spectrophotometry, the most commonly used methods in wineries. This increased accuracy provides additional knowledge that allows winemakers to further understand and evaluate the chemical components in the wines that they create. This is a useful step towards making the characterization and marketing of the wines less subjective.

Amnesic shellfish poisoning is the result of eating seafood contaminated with domoic acid, produced by toxigenic diatom species from the genus Pseudo-nitzschia. In the summer of 2015, abnormally large assemblies, known as super chains, of Pseudo-nitzschia australis appeared in the massive algal bloom that swept up the Pacific Coast. This affected commercial and recreational shellfish harvesting and cost millions of dollars in shellfish sales. Due to their recent appearance, knowledge of P. australis super chains is extremely limited. Here, we investigate the prevalence of super chains in Puget Sound and along the Pacific Coast. The deep chlorophyll maximum, DCM, is a layer in the water column that is often found to contain a high volume of photosynthesizing phytoplankton.  A collection of electronic devices that measure conductivity, temperature, and depth (also called CTD) was deployed to determine DCM, from which plankton samples were collected. Scanning electron and light microscopy were used to identify P. australis species and to examine the morphology of their associated bacteria. Most surveys have been conducted during the late summer when blooms are at their peak. By conducting our survey in the late winter, we have had the opportunity to measure P. australis super chain prevalence during what is typically a less active season. Our results provide novel information of P. australis super chains and their associated bacteria during a season that has been so far neglected. In addition, our diverse sample sites in Puget Sound and along the West Coast present a systematic survey and allow us to make regional comparisons. This study lays a foundation for more comprehensive research of super chains in the future. 

 The African and Afro-Caribbean Women’s Health Study (AACWHS) focuses on perceived discrimination and stress among African and Afro-Caribbean U.S. immigrants. The overall aim of the study is to gain a better understanding of how perceived discrimination triggers a physiological response that leads to negative health effects, in the short term and over the life-course. The hypothesis is that the longer participants have lived in the United States, the more likely they are to ascribe daily hassles to discrimination, correlated to negative health effects. We are interested in collecting quantitative data from surveys utilizing scales including the Everyday Discrimination Scale and Phinney’s Multigroup Ethnic Identity Measure (1992), and biometrics to assess allostatic load. The survey will assess perceived discrimination in the form of attribution of everyday hassles, and connection to one’s own ethnic group here in the U.S. The study seeks to determine why health profiles differ between foreign-born and native-born peoples, and identify how immigrants’ appraisals of daily experiences may serve as a protective factor that mediates the impacts of discrimination on health. The data will provide a better understanding of the role that perceived discrimination plays in stress level, while examining the biological pathways that link perceived discrimination and chronic stress. Expected results include data demonstrating an increased perception of discriminatory events in relation to years spent in the U.S., and indications via biomarkers of chronic stress in adults experiencing discrimination.

Hox complex genes constitute an essential and ubiquitous component in the construction of the animal body. Despite their wide range of body plans, every member of the bilaterian clade utilizes these key genes to pattern the anteroposterior (AP) axis, with one potential exception - radial echinoderms. In addition to the possession of an adult radial body plan, Echinodermata are also mostly characterized by indirect development, beginning their lives as bilateral larvae, which undergo radical metamorphosis into a radial adult. The echinoderms, outside the sea urchin, Strongylocentrotus purpuratus, remain poorly studied, and it is unknown how classically bilateral planning mechanisms like hox are involved in patterning these very different life stages. To help begin to resolve this, we present in situ hybridization data of four hox genes present in the indirect developing bat star, Patiria miniata in its larval stages. Hox expression was observed in the posterior during the development of larval forms, similar to the expression patterns seen in other bilaterian animals. These results suggest that, despite a greatly divergent radial body plan of the adult, echinoderms use many of the same developmental mechanisms found in bilateral organisms to pattern their larval stages prior to metamorphosis.

The University of Washington's Manastash Ridge Observatory is being upgraded with a telescope auto-guiding system and a replacement camera, funded by Student Technology Fund.  The new, in-house, upgrades call for a high-level software implementation from the ground up.  Utilizing the programming language Python, we build two graphic user interfaces (GUIs) for controlling the telescope and camera independently.  With a telescope control GUI, we supply the basic features to drive the telescope, while also ushering in the controls for the auto-guider, greatly enhancing the past capability.  Meanwhile, the camera GUI handles the different camera exposure settings, camera filters, and saving of images.  We construct the GUIs using the software package wxPython in conjunction with the package TwistedPython.  In tandem, these software comprise of the bulk underlining functionality; where we use the feature set of wxPython to receive top-level client input and then talk to our hardware systems with TwistedPython to convey the user's needs.  Ultimately, the move to completely new, high-level software allows us more control than proprietary solutions allowing us to implement an intuitive end-user experience that will run on any computer towards the future.

Growing degree days (GDDs) are a commonly used method for determining plant growth patterns in agricultural settings. This technique uses daily heat values, rather than calendar-based predictions, to help estimate total amounts of seasonal growth. This study is intended to determine how GDDs correlate to the flowering phenology and growth of golden paintbrush (Castilleja levisecta), a threatened species native to Washington State. I monitored 40 newly-grown and 40 3-year-old golden paintbrush plants, with approximately half of each group containing an additional host plant. Plants of both types were evenly assigned to four different temperature treatments within the Center for Urban Horticulture (outdoors, unheated hoophouse, spring growth chamber, and greenhouse), and were constantly monitored for air temperature by dataloggers placed onto the soil of select pots. I recorded weekly measurements of the growth of each plant in terms of plant size, percent fill, and flowering times, and am relating these variables to the GDDs associated with each treatment. We also collected data from field specimens in Puget Sound in order to analyze differences in growth based on field conditions, as opposed to controlled environments. Finding relationships between growing degree days and golden paintbrush phenology will help us understand when and why it flowers, which influences how many seeds are produced at restoration sites, as well as help our understanding of its sustainability as a food source for Taylor’s checkerspot, an endangered butterfly species.

Since the mid-1990s, the Implicit Association Test (IAT) has been used in psychological experiments to measure the strength of a person’s automatic associations between concepts and attributes. The Brief IAT (BIAT) uses a procedure similar to the standard IAT, but with simplified instructions and different task structures. Unlike the standard version, the BIAT instructs subjects to focus on only two of four categories (focal categories) and respond to them with a “focal” key and to the other two categories (non-focal categories) with a “non-focal” key. By means of the BIAT, the present study examined whether race categories (represented by surnames) are associated with positive or negative valence (represented by pleasant-meaning or unpleasant-meaning words). It also correlated the BIAT’s association strengths with those obtained from the standard IAT. One hundred and ten volunteer undergraduate students from the University of Washington completed six BIATs and two standard IATs. Three of the six BIATs differed from the other three only in the identity of the fourth category (e.g., Black American versus White American names). The two standard IATs, which used the same four categories as their BIAT equivalents, also differed from each other in the identity of their fourth category. Self-report measures of race attitude were administered. D scores, an effect-size measure, were calculated to estimate the strengths of association between categories. The significance of this research lies in its potential to support the development of more valid and useful IAT methods for evaluating a person’s implicit attitudes toward socially-sensitive concepts.

It is accepted that the Amazon rainforest is a significant carbon sink. The Amazon River was only recently discovered to be a supersaturated CO₂ source, outgassing at a rate almost equivalent to that which the forest sequesters (0.5 Pg C yr-1). Since this landmark discovery, one of the principle investigations within the River Systems lab has been developing a refined understanding of the biogeochemical processes that shape the Amazon River into such a prominent CO₂ source. In situ incubations have indicated that lignin and other organic molecules unique to terrestrial flora are in fact decomposed in the water column and are potentially a significant source of CO₂ outgassing. Utilizing Mass Spectrometry we are now analyzing the presence and abundance of various lignin derivatives across spatial and temporal variables to track the fluctuating degradation rate of organic substrates. Linking the forest’s carbon sequestration to the river’s outgassing mechanisms and applying the principles to other river systems around the world is a vital step to better comprehending the complex global carbon cycle.

Current synthesis for thermoresponsive magnetic nanoparticles such as iron oxide nanoparticles coated with poly(N-isopropylacrylamide), pNIPAm, usually requires extensive surface functionalization or high temperature procedure, and the yield is very limited. Here we present a simple and reproducible approach for the synthesis of thermosensitive iron oxide nanoparticles, via coprecipitation of Fe2+ and Fe3+ ions from basic aqueous solutions at room temperature in the presence of block copolymer, poly(N-isopropylacrylamide)-block-poly(acrylic acid) with a dodecyl tail following the acrylic acid block. The polymer facilitates iron oxide nanoparticle synthesis by forming micelles via hydrophobic dodecyl tail assembly and coordinating iron oxide formation via complexation with the poly(acrylic acid) segment. The block copolymers were synthesized through reversible addition-fragmentation chain transfer polymerization. Proton NMR characterization shows incorporation of 11 acrylic acid monomeric units to pNIPAm macro chain transfer reagent with 150 degree of polymerization. The new synthesis approach is rapid, taking one hour, and can be easily purified via size exclusion chromatography. The resulting magnetic nanoparticles’ surfaces display pNIPAm, which enables particle aggregation when the solution temperature is above 34°C. The particle aggregates exhibit high magnetophoretic mobility, which results in rapid and efficient magnetic separation, ≥95% in few minutes. The particle’s hydrodynamic diameter is ca. 30 nm, characterized using dynamic light scattering. This simple method overcomes the problem of using high temperatures while maintaining reproducibility, which could make it useful for larger scale synthesis.

As concern over antibiotic resistance continues to grow, there is a critical need to discover and develop new methods of controlling and preventing bacterial infections. Essential oils derived from the peels of oranges are known to possess antimicrobial properties. Previous research has established that limonene, the principle compound present in orange oil extract, is a particularly effective antimicrobial agent that both destroys bacteria and inhibits bacterial growth. To determine whether different varieties of oranges have varying antimicrobial potency, the efficacies of oil distilled from blood, navel, and valencia oranges were compared. Oils extracted through steam distillation were diluted with methanol to concentrations ranging from 1:20 to 1:1. Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli bacteria were exposed to the oils using the disc diffusion method on TSA plates. The minimum inhibitory concentration (MIC) for each oil was determined using the agar diffusion method. Gas Chromatography Mass Spectrometry (GC-MS) was used to compare the relative concentrations of limonene present in each essential oil. A better understanding of the potency of orange oil as an antimicrobial agent could lead to development of novel drugs and products to be used to combat infection and prevent the spread of bacterial pathogens.

Airflow inside a telescope dome is crucial for the efficient collection of data. The purpose of this project is to analyze the airflow inside the dome of the 3.5 meter telescope at Apache Point Observatory. Air flow metrology was used to measure wind velocity at multiple points in the dome over several months. This data was reduced using numerical computation. With this data, analysis was performed for trends both computationally and using 3D visualization of vector flow patterns. This data will be used to improve the dome airflow by moving and replacing louvers throughout the dome. By doing so, the wind flow across the telescope light path will be optimized and the resolution of targets at this telescope will be improved.

Previous research suggests that taking gender/women’s studies classes increases positive attitudes towards feminism and gender equality. This study generalizes prior findings to the University of Washington (UW) by investigating the impact of participation in Gender, Women, and Sexuality Studies (GWSS) classes on students’ attitudes towards women, feminism, and homosexuality. Undergraduate UW students who have taken at least one GWSS class and students who have never taken such a course were surveyed to determine their attitudes toward women, feminism, and homosexuality and to assess their views toward the field of Gender, Women & Sexuality Studies. We hypothesize that students who have taken GWSS classes will have more positive attitudes of women, feminism, and homosexuality and that these findings will hold when controlling for students’ demographic variables such as gender, political ideology, and socioeconomic background.

Cell adhesion and motility are important cell processes that are necessary for embryo morphogenesis. Prevous studies have identified p120-catenin as a key player in coordinating cell movements by either stabilizing E-cadherin complexes to strengthen adhesion or activating cytoplasmic CDC42 and Rac1 GTPases to initiate motility. Most of these studies were done in-vitro using cells grown in a 2-dimensional plane. Comparatively, few studies have attempted to describe p120-catenin's function in a 3-D space. In an effort to investigate p120-catenin's function in embryos, we are co-immunoprecipitating p120-catenin from developing zebrafish embryos. We are specifically investigating how the tyrosine 228 (Y228) residue of p120-catenin mediates binding to E-cadherin. The hypothesis is that phosphorylation of Y228 causes p120-catenin to bind to E-cadherin. To test this, we are injecting zebrafish embryos with p120-catenin containing either an Y228F of Y228E mutation. If our hypothesis is correct, the Y228F mutation would prevent phosphorylation of the 228 residue and decrease affinity between E-cadherin. The Y228E mutation mimics the negative charge of phosphorylation and would instead cause p120-catenin to bind to E-cadherin. 

Loss of heterozygosity (LOH) frequently occurs in tumor cells and is associated with the expression of deleterious recessive phenotypes. However, relatively little is known of its mechanisms or the various functional/regulatory factors involved. The goal of our research is to characterize the mechanisms of LOH and identify the factors involved. One cause of LOH is homology-directed repair (HDR), which uses the homologous chromosome as a donor to repair DNA damage like DNA nicks or double stranded breaks (DSBs). In HDR, the homologous chromosome functions as a template for repairing the damaged DNA strand. In order to study the mechanisms and factors involved in LOH, we developed a novel flow-based reporter model that utilizes an endogenous gene. This model was developed by making genetic modifications in a human cancer cell line (HT1080) in such a way that would allow the detection of a LOH event. Using our flow-based reporter, we will target DNA nicks and DSBs using CRISPR/Cas9 and quantify the resulting LOH events using our flow-based reporter. We will also use siRNA knockdowns to assay other candidate factors potentially involved in the mechanisms and regulation of LOH. To simulate mutations seen in tumors, we will downregulate the expression of common tumor suppressors (BRCA1, BRCA2 and PTEN) with siRNA and determine how these factors affect LOH. When common tumor suppressors are downregulated in our model, mutations that take place are expected to follow a similar mechanism to mutations seen in tumors. Using our model in this way, we will verify which common tumor suppressors are involved in the mechanisms of LOH often seen in tumors. With a better understanding of the factors involved in LOH, prophylactic therapies can be developed to minimize occurrence of LOH and tumorigenesis.

This project is focused on the use of genetic anlysis to study population dynamics of the African lizard genus Agama. I investigate how the genetic diversity of Agama populations is correlated to geographic distance, environmental distance and phenotype. I have collected the genetic information from 90 lizard samples using a genetic sequencing technique known as ddRAD. Using this information, I employed principle component analysis to cluster individuals in groups based on genetic diversity. The relevant individuals were plotted on the map using geographic coordinates, which provides researchers insights into the spatial pattern of the relevant populations. I then test for correlations between environmental and landscape variables that are downloaded in vector form. I use a species distribution model called MAXENT to assess the relationship between landscape type and genetic distance. Depending on the results of the aforementioned tests, I will assess the correlation between phenotype and genetic diversity by measuring physical features on the Burke Museum's Agama specimens. The anticipated results show four distinct populations within Ghana that differ in genetic diversity due to a number of environmental factors. The results allow researchers to predict future changes in the habitat status of these African lizards, thus contributing to ongoing conservation efforts. 

Research on Mexican-migrants in the United States usually focuses on the 1st and 2nd generations; 1st generation being the migrant who exits their home country, and the 2nd their children born in the Unites States. Often overlooked by the complexities of the two is the 1.5 generation; migrants who were brought to the United States as children and have been socialized here. This is relevant since the 1.5 generation has increasingly become an integral and significant force in the political agenda of Mexican-migrants in the United States. In spite of their contribution to the movement for comprehensive-immigration reform, and small successes such as the Dream Act and Deferred Action for Childhood Arrivals, there are many of the 1.5 generation that didn’t, and do not, benefit from these legislative efforts, and who have returned to their home country because of these and other circumstances.This proposed research project attempts to analyze how these individuals, specifically females of the 1.5 generation, lead their lives between and across borders by asking the following questions: 1) How do young transnational Mexican women form and reform identities when moving across borders? (2) How have they learned to navigate these transformations and adapt or readapt to U.S or Mexican society? and (3) What role has culture, tradition, community, machismo and the borderlands played in their process of self-identifying? Building on theories of transnationalism, identity and Chicana-feminism, this proposed research explores the themes of immigration, gender, globalization and community through the employment of qualitative methods including semi-structured interviews, participant observation and life histories, such as testimonios, with six women on both sides of the US-Mexico border. Although this is an exploratory study it will serve to better inform our perceptions of undocumented people in the United States who lead their lives across borders.

Eating disorders (ED) such as anorexia and bulimia nervosa currently affect more than 30 million individuals in the United States. Eating disorders are linked to adverse health consequences including osteoporosis, multi-organ damage, and even death. Many studies have found a clear association between social media exposure and social comparison with idealized body figures leading to disordered eating. It remains unknown the impact that Instagram, a visually driven social media platform has on individuals already experiencing the symptoms of disordered eating. The purpose of this study is to compare the attitudes and motivations displayed on pro-ED and ED-recovery Instagram profiles, in order to understand how social media platforms can be utilized as a tool for encouraging and sustaining ED recovery. In this retrospective content analysis study, 30 public pro-ED and 30 public ED-recovery profiles were selected based on the profiles use of specific ED related hashtags. Posts within this three month period on these profiles were thematically categorized and coded based upon themes in the grounded theory tradition. Data collected from both types of profiles were comparatively analyzed. Descriptive data included the quantity of followers, comments, and likes received per post displayed on the profile. With the pro-ED and ED-recovery data, categorical and quantitative comparisons were conducted using Chi-squared tests and t-tests. Findings from this study could potentially inform ED related agencies and clinicians on how social media can be used as a tool for effective prevention, screening, and early treatment for eating related disorders.

Iron is an essential micronutrient, playing key roles in neurodevelopment and erythropoiesis. Maintaining iron sufficiency is essential for brain growth and development, particularly in preterm infants. Current guidelines for iron supplementation of these infants (2-4mg/kg/day) may not be adequate to maintain iron sufficiency. Our objective is to assess concordance of ferritin and zinc protoporphyrin-to-heme ratios (ZnPP/H) in evaluating iron sufficiency in Neonatal Intensive Care Unit patients and clinical conditions in which these values diverge, and to evaluate iron sufficiency in these infants over time. All infants who underwent paired ferritin and ZnPP/H measurements between October 2014 and October 2015 in the University of Washington Medical Center NICU were assessed. Concordance of these measures was evaluated, as were effects of iron supplementation, blood transfusion, and inflammation. 144 patients met inclusion criteria with 352 paired samples collected between day of life 9 to 114. 34% of ferritin values were at concerningly low levels, indicating severe iron deficiency. In infants with low ferritin, ZnPP/H was higher than normal 60% of the time, which shows that ferritin and ZnPP/H were overall concordant. There were 36 abnoramlly high ferritin values in 14 infants; ZnPP/H ranged variably in these infants, with 5 cases of significant discordance. Of the infants with high ferritins, half had proinflammatory states within 2 days of obtaining the ferritin value suggesting it was elevated due to inflammation. Transfusion did not affect either ferritin or ZnPP/H values. Ferritin values decreased with advancing postnatal age. Despite iron supplementation that followed AAP guidelines, infants in this cohort became more iron-deficient with advancing age. This suggests the need for more aggressive iron supplementation among critically ill infants. Either ZnPP/H or ferritin can be used to assess iron status, although elevated ferritin may reflect a proinflammatory state.

Lung diseases, including chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis, are major health concerns in older people. There is currently a paucity of drugs available that are effective in treating these conditions.  A potential drug target in the lungs is a cell type known as fibroblasts. These cells are very abundant and are essential in providing support and structure for alveolar cells, which are responsible for the vital gaseous exchange of oxygen and carbon dioxide. A drug that has been shown to target fibroblasts in the skin, and currently used in skin creams, is a tripeptide designated as GHK. The objective of this project was to see if GHK could target lung fibroblasts collected from old mice by restoring functional capacity. Lung fibroblasts were grown in culture to a monolayer and a scratch wound assay was performed to measure the rate of closure. Immediately proceeding the scratch, cells were treated with different concentrations of GHK while one received a placebo treatment. The closure rate was then measured every 24 hours for a total of 72 hours. The highest concentration treatment of GHK had a significantly faster migration rate than that of the placebo treated monolayers, suggesting that GHK enhances fibroblast migration and restores functionality to more youthful levels. These results provide the rationale for preclinical studies in mice to help determine if GHK might be a potential drug to consider for treating chronic lung diseases in the elderly.     
 

We know that climate sensitivity can vary within species, but the factors that influence which climatic variables influence population dynamics remain unclear. In this study, I am assessing whether macroclimate influences the climate sensitivity of three prominent conifer species: Pacific silver fir (Abies amabilis), mountain hemlock (Tsuga mertensiana), and Alaska yellow cedar (Callitropsis nootkatensis) on Mt. Rainier. I am analyzing tree core data from three high elevation sites. Each site is located in a distinctly different climatic area on the mountain. I am comparing standardized tree growth to climate variables (mean growing-season temperature, total growing-season precipitation, snow duration, etc.) using linear mixed effect models. This will determine how influential climate variables differ by location and by species. Gaining more insight into which climate variables have the greatest influence on growth in different areas will allow us to better predict how specific plant populations will react to ongoing climate change. Moreover, studying tree communities at high elevations is particularly important, since behavior at treeline will determine whether a species’ range expands, contracts or shifts. Range expansion of one species could lead to the crowding or elimination of another. For example, conifer range expansion on Mt. Rainier could negatively affect the alpine wildflower meadows, a major attraction for tourists. Widespread range contractions could also decrease forest density and potentially reduce the ability of those forests to sequester carbon from the atmosphere. Thus, with better predictions of tree shifts, we can make more informed management decisions for ecotourism and conservation.

Cleft lip and palate (CLP) is one of the most common birth defects and has been found to be associated with multiple dentofacial anomalies, including hypoplastic teeth, and defects of the orbicularis oris muscle. In view of this associated spectrum of anomalies, numerous studies have investigated the risk of caries development in the CLP population, with the vast majority reporting an increase in caries incidence and severity. However, the cause of the observed increase in caries is largely unknown, making it difficult to manage and significantly prevent. In the Cox lab, we have established conditionally targeted mice for the cleft gene, Irf6 (Irf6 null), by deleting the gene only in the oral epithelium after the development of the lip has been completed, thus permitting investigation of the gene’s other roles in the oral phenotypes. Therefore, these mice provide an ideal system with which to investigate the susceptibility and risk factors for caries progression in CLP population. Initial observations revealed these mice to have an array of tooth anomalies and salivary gland hypofunction. Using null and control mice, we employed an established caries induction protocol that involved infection of the oral cavity with S. mutans, a cariogenic bacterium, followed by feeding with a high-sucrose diet for eight weeks. After eight weeks, bacteria were recovered from the animals by sonication of the lower jaw in normal saline and bacterial numbers counted and the existence and severity of caries scored. The data reveal a massive increase in carious lesions in the CLP mice but not controls and this was associated with a significant increase in both total cultivable flora and the S. mutans population (5.2x105 in Irf6 null vs. 2.6 x105 wildtype mice; p value<0.001). These results may ultimately translate into more effective caries preventive approaches in patients with cleft lip and palate.

Childhood maltreatment is one of the most common adverse events in children and has been associated with a variety of negative effects on children’s social adjustment and mental well-being later in life. One explanation is that maltreated children may develop maladaptive emotion regulation skills, which mediate the pathway between maltreatment and psychopathology. Accumulating literature suggests that attachment security may be a protective factor against maladaptive emotion regulation skills in maltreated children. Prior research has investigated attachment as a mediator between childhood maltreatment and poor behavior outcomes. However, little research has examined attachment as a protective factor associated with better emotion regulation skills in maltreated children, which in turn results in better behavioral and emotional adjustment. The current study hypothesizes that, childhood maltreatment will have a less negative effect on children who are securely attached to one of their care givers, compare to those who have insecure attachment. In other words, secure attachment will serve as a protective factor for children exposed to adverse experiences, leading to better emotional and behavioral outcomes. Data from two separately collected samples of maltreated and control children (n= 221 and n= 124) are analyzed based on multiple linear regression models. We expect to find a significant difference between the effect of maltreatment on emotion regulation in high and low attachment individuals, such that children with more secure attachment are less affected by maltreatment. These findings would suggest that secure attachment may protect maltreated children from developing maladaptive emotion regulation skills which contribute to better general behavior outcomes in children.

Ammonia-oxidizing archaea and bacteria (AOA, AOB) are important contributors to soil ecosystem function, as they convert nitrogen (N) as ammonium (NH4+) into nitrate (NO3-), a more readily available form for plant uptake. This study examines the abundance of AOA and AOB in forest soils of the Pacific Northwest that have experienced wildfire 31, 7, and 5 years previously. Charcoal, a common residue of wildfire, may play a significant role in stimulating nitrification in soils, possibly by adsorbing monoterpenes that may inhibit mono-oxegynase activity in nitrifying organisms. The goal of this study was twofold. We first hypothesized that charcoal would increase the quantity and quality of AOB and/or AOA in wildfire-affected soils. To test this hypothesis, we extracted and compared DNA between burned and unburned sites using real-time quantitative polymerase chain reaction (RT-qPCR). We expect to find a greater abundance of AOA and AOB nucleotides in the burned sites indicated by qPCR, and a larger array of species indicated by DGGE analysis. Secondly, we will introduce monoterpenes (α-pinene) into soils with charcoal present, and soils void of charcoal to assess the interaction between the terpenes and charcoal surfaces. We hypothesize that the addition of terpene will readily adsorb onto charcoal surfaces. Therefore, burned soils will show reduced nitrification inhibition compared to soils without charcoal present and result in higher nitrification rates. These data will be matched with an assessment of the AOA and AOB from the burned and unburned soils, with and without the addition of charcoal in order to reach a better understanding of wildfire effects on forest soils.

Although many learners are able to learn vast amounts of vocabulary and master the grammar of another language, many learners find difficulty in mastering the sounds of another language. Korean, in particular has a set of consonants that seem strikingly similar to English speakers, which makes it arduous to tell them apart. For example, the words for 'moon' and 'mask' in Korean, pronounced [tal], both begin with a [t] but are produced slightly differently with the [t] in 'moon' unaspirated and the [t] in 'mask' aspirated (Aspiration refers to the puff of air that can accompany certain sounds like [b, p, t, d, k, g]). Research has shown the pitch of the vowel following these consonants can also serve as a reliable cue, with the vowels following aspirated sounds having a higher pitch than the vowels following the unaspirated sounds.

In this study, I examined whether training learners of Korean to recognize this cue can help them better discriminate between these consonants. In order to test this, learners were asked to take a short survey where they watched a video that explains these cues. They then were tested on their perception of these consonants by taking a matching quiz where they were asked to listen to a set of audio files to gauge any possible improvements. With this training, it was expected that learners of Korean could better segregate these consonants with better accuracy. It is hoped that this study will bring attention to the need to improve pronunciation education and pave the way towards further research in teaching learners of Korean not only how to better perceive these sounds, but also pronounce these sounds as well.
 

The McMurdo Dry Valleys in Antarctica is a cold desert with a frigid, hyperarid environment. Physical models predict that the sediments should have a net loss of water vapor, but in reality ice-cemented ground is pervasive within decimeters of the surface. Scarce, episodic snowfall is mostly lost to rapid sublimation; however, some water vapor may diffuse into the subsurface and possibly stabilize or form ground ice. This study investigates ice within a 30-m permafrost core that was collected from Beacon Valley in 2008 using a dry coring technique. The entire core is ice rich, ranging from 20-80% water content by weight and is largely composed of weathered sand with some fractured cobbles. The high ice content suggests that the ground surface inflated as the ice formed. Processes leading to the excess accumulation of ice are investigated using δ18O and δD. Potential sources of the ice include surface percolation, water vapor diffusion, and accumulation of snow into thermal contraction cracks. Subsamples of the ice-cemented core were cut from its interior, thawed, and the water was collected using a double-bottom centrifuge tube. Isotope analysis was also performed on water samples from hoarfrost collected from the abandoned core holes, snow, and glacier ice in Beacon Valley. The core’s isotope depth profiles will provide information on the origin of the ice and processes that modify it. This site serves as an analog for Mars, where excess ground ice has been confirmed at the Phoenix landing site, and will provide insight on ice accumulation there.

Blood clotting after injury requires processing of Von Willebrand Factor (VWF), a large blood protein that self-associates into long fibers which are then broken down by the enzyme ADAMTS13 into smaller fragments. These cleavage fragments self-associate after injury to stabilize clotting factors and activate platelets for clot formation. When the activity of ADAMTS13 is insufficient or inhibited, overactive clot formation leads to thrombotic thrombocytopenic purpura (TTP). VWF fiber formation can be modeled using a microfluidic device that measures the flow of platelet-free plasma through a microscopic channel. My goal is to investigate the properties of cleaved VWF fragments and how they regulate the capacity of ADAMTS13 to further cleave normal VWF. I hypothesize that the presence of cleaved VWF by ADAMTS13 will inhibit further cleavage and produce longer VWF fibers. To test this hypothesis, I will examine VWF self-association in the microfluidic channel - in the presence and absence of the cleaved VWF fragments. The addition of VWF fragments will be expected to inhibit further cleavage of VWF and increase self-association through the microfluidic channel. Understanding how cleavage products from ADAMTS13 breakdown of VWF can regulate self-association of VWF will provide critical insight into causes of TTP and developing novel treatments for patients with this disease.

Transcranial magnetic stimulation (TMS) is a method of noninvasively and reversibly influencing brain activity through the generation of brief magnetic fields. Utilizing this approach, we investigate the role of the semantic representation of objects in the dorsal portion of the premotor cortex (PMd). The ventral portion of the premotor cortex (PMv) has been known to be involved in the representation of manipulable objects, such as tools. Conversely, we provide evidence that stimulation of PMd facilitates access to foot-related objects (such as sandals or slippers) by observing decreased decision times in a categorization task when PMd is stimulated at 110% of motor threshold. Within this task, subjects are shown a category, either “object” or “animal”, and asked to select which of two options match the provided category. These findings also provide support for the notion that the human premotor cortex has a topological organization and that part of the organization of sematic knowledge for objects depends on the modality with which they are interacted.

Ankle foot orthoses (AFOs) are commonly prescribed to improve gait in individuals with cerebral palsy to stabilize gait. AFOs have also shown additional benefits in reducing the metabolic cost of walking, preventing bone deformities, and providing support during gait. The advent of the affordable 3D-printer has provided a new tool in the manufacturing of AFOs which may be able to overcome many limitations of current production methods. The purpose of this study is to improve the manufacturability and functionality of AFOs by improving AFO design and manufacturing techniques. Validation testing through the use of material testing, and multiple subject gait experiments verified the study’s results. The subjects’ lower leg was scanned with a portable 3D scanner and using this scan the AFO was form fitted to the unique shape of the subject’s foot. Parametric and non-parametric computer aided design tools were used to design the AFOs. Using a fused deposition modeling 3D printer the AFOs were fabricated using polylactide (PLA) filament. In order to adjust the stiffness of the AFO, elastic polymer bands were fabricated with polyurethane. Since a single elastic polymer band only allows for one specific AFO stiffness, multiple of elastic polymer bands might be need to be used to control the wide range of AFO stiffness. To solve this issue, the AFO was designed to have a support structure that allows for the moment arm of the elastic polymer bands to be changed, thereby adjusting to a wide range of AFO stiffness with minimum number of elastic polymer bands. Designing an open-source, 3D-printed AFO that helps rehabilitate the user could allow for low-cost, easily accessible rehabilitation devices to be common place.

Women with a history of sexual victimization experience differences in triggers for sexual arousal excitation and inhibition compared to women without a history of sexual victimization. Although most studies suggest that women experience decreased sexual arousal in the presence of negative consequences (e.g. unwanted pregnancy), recent research has found that some women actually experience increased sexual arousal.  Theory suggests that post-traumatic stress (PTS) symptoms may play a role. Studies indicate PTS symptoms may influence sexual arousal responding, resulting in decreased sexual arousal inhibition. Little research has examined this relationship; no research has investigated how PTS and sexual arousal inhibition interact among women with a history of sexual victimization.  PTS symptoms (arousal and intrusion symptoms), may potentially explain the decreased sexual arousal inhibition in the presence of negative consequences due to similar physiological factors of fear arousal and sexual arousal and the contextual commonalities (e.g. impulsivity) shared by PTS symptoms and sexual arousal.  Participants (n=17) came from a subset of a larger umbrella study. Participants were recruited via poster and advertisement (newspapers, Craigslist) from the Pacific Northwest. Inclusion criteria included being: 1) female, 2) 21-30 years old, 3) sexually interested in males (exclusive sexual interest in males not required) and 4) not pregnant. The following measures were administered: Finkelhor’s Child Sexual Abuse Measure, The PTSD Questionnaire, and the Inhibition Due to the Threat of Negative Consequences Subscale of the Sexual Inhibition and Sexual Excitation Scale. This study analyzed the effect of PTS symptoms on the relationship between SA and sexual arousal inhibition in an attempt to better understand the range of outcomes SA survivors experience. A supported hypothesis may demonstrate that those with high PTS symptoms may potentially react differently to negative consequences than those with low PTS symptoms, suggesting a potential pathway as to why this might occur.

Sea ice plays a vital role in the Arctic ecosystem and is a good indicator of climate change, so it is important to understand the physical processes that control sea ice evolution in order to get a better sense of the detrimental effects of climate change on the environment. Thus, accurate measurements of the features of ice – such as ice concentration – are needed to provide a clearer picture of how and when the ice evolves. This project aims to document and quantify ice variability from airborne imagery during the summer melting season in the Beaufort Sea. Images were taken from US Coast Guard Arctic Domain Awareness (ADA) flights in June, July, August, and October of 2014, with data collection to be continued in coming summers, including this summer, the summer of 2015. Algorithms were developed to automate the identification and quantification of features of the sea ice and open water such as ice concentration, floe size, melt pond coverage, and melt pond size. This data will be charted over time and space (latitude) to identify and analyze patterns in the evolution of Arctic sea ice. Results from this study will be useful for verifying satellite data, evaluating models, and initializing predication schemes. This information will be helpful for quantifying and analyzing the effects of climate change on the Arctic ecosystem.

High-risk human papillomavirus (HR HPV) can establish a persistent infection in epithelial cells through its ability to evade immune detection. HR HPV type E6 is an oncogenic protein that is known to downregulate the innate immune response in human keratinocytes. Previous studies have shown that NFX1-123, an endogenously expressed epithelial protein, acts as a novel binding a partner for HR HPV type 16 E6 (16E6). We examined whether or not NFX1-123 also plays a role in the repression of the innate immune response in human foreskin keratinocytes (HFKs) transduced with HR HPV type 16E6. By stimulating the immune response with Poly(I:C) or double stranded DNA in HFKs, cells with overexpressed levels of NFX1-123 (FWT), and cells with endogenous levels of NFX1-123 (LXSN), we demonstrated that stimulation occurs both at the RNA and protein levels. We found, however, that the immune response of 16E6 HFKs with overexpressed levels of NFX1-123 were more downregulated than those with endogenous levels, confirming the protein’s association with 16E6 in the repression of the innate immune response. By understanding the roles of 16E6 and NFX1-123, we will further understand how together they cause a persistent infection, which can ultimately lead to cancer.

Little is known about mammalian diversity in North America during the mid-Cretaceous (Albian-Cenomanian, 120-90 mya). This was an important interval in mammalian evolutionary history, during which metatherian (including marsupials) and eutherian (including placentals) mammals first appeared in North America and multituberculates (a now-extinct group of mammals) began to radiate. Unfortunately, our understanding of this period is poor because mid-Cretaceous mammal-bearing fossil localities are sparse in North America. Accordingly, each newly discovered specimen from this interval could provide important insights into therian and multituberculate diversity and their early stages of evolution. Recent paleontological fieldwork in the mid-Cretaceous (ca. 100 mya) Wayan Formation of eastern Idaho has led to the recovery of 30 mammalian specimens, including 15 metatherians and 13 multituberculates. These specimens, all isolated teeth, were discovered in situ and in the lab. Previous work by myself and other members of the Wilson Lab has focused on describing three metatherian species from this sample, as well as documenting a new occurrence of the genus Targheedelphys. Here, I focus on describing the multituberculates and analyzing their taxonomic diversity, as well as comparing them to those from a larger, contemporaneous sample from the Mussentuchit member of the Cedar Mountain formation of central Utah. Some of the Wayan specimens are attributed to new species and others are referred to previously known species. Current results indicate that multituberculate and metatherian diversity is approximately equal, with three species observed in each group, and each occupying close to fifty percent of the local fauna. The similarities and differences in taxonomic composition and diversity between these two localities will give us important insight about mid-Cretaceous mammalian evolution in North America. Additionally, this information fills a gap in the timeline of mammalian evolution that will further our understanding of mammal evolution through the K-Pg and onward into the Cenozoic.

College presents many challenges for students, and how students cope with these challenges can affect how well they fare academically and socially. First-generation college students (FGs: students whose parents do not have four-year degrees) face more social, academic, and financial challenges and have higher dropout rates than continuing-generation students (CGs: students with at least one parent with a four-year degree). Research has shown that when facing challenges in college, FGs are unlikely to seek university resources; however, it is not clear what FGs are doing in the face of challenge. This exploratory study uses a social and cultural-psychological lens to begin understanding how FGs respond to challenges in college. We presented 273 undergraduate students (70 FGs) with a series of vignettes describing academic, financial, and social challenges and asked students to predict how they would respond to each challenge. Initial analyses suggest that when faced with financial challenges, FGs were less likely than CGs to “seek resources they would need,” and when faced with academic and social challenges, FGs were more likely than CGs to seek social support, to distract themselves from thinking about the challenge, and to remove themselves from the situation. These findings suggest that FGs may struggle in particular when faced with financial challenges, as they do not seek the resources they need to overcome this type of challenge, perhaps because they do not have access to many financial resources. When facing academic or social challenges, rather than turning to the university, FGs may seek social support outside of the university or disengage from these situations altogether. Given that FGs tend to struggle more in college than CGs do, this research has implications for understanding how to help future FGs deal with challenges in the university.

This study aims to address the historical origins of colonial mentality in Philippine society and media, as well as identify its resulting movements of resistance. Under Spanish and American colonialism, Filipinos developed an attitude of inferiority in which they viewed Western beauty, society, and discourse as superior to that of the Philippines. This “colonial mentality” has become an intergenerational trauma that has been passed down since the 1500s. It is increasingly evident in Philippine society through media forms of television, fashion, film, and more. In terms of movements of resistance, this study will identify what they are and how they carry out their mission in a crowded society that is saturated with colonized attitudes. These movements include but are not limited to art, music, academia, and fashion that aim to return to indigenous roots and values. In defining the mentality’s contemporary presence, Philippine society will be analyzed through the lens of modern media (e.g. film, television, etc.). To identify mechanisms and movements of resistance, Filipino Americans in the Seattle area are currently being interviewed to ascertain the present state of both colonial mentality and movements towards cultural reclamation. The interviews will serve as primary accounts of colonial mentality’s present-day effects and ways to overcome it. This study aims to shed light on the little-known resistance movements that have been bubbling underneath the surface of Philippine society. This research will reveal the Filipino potential and strength that is often ignored. The people’s ability to survive amidst pressures of cultural assimilation demonstrates their centuries-old resilience. The scarce research that does exist on Filipino colonial mentality often overlooks a new atmosphere in the Philippines that is filled with self-potential and cultural reclamation.

 Clinicians in low-resource settings face several challenges when using nucleic acid amplification to diagnose disease at the point of care, because conventional methods have high costs per sample, require trained technicians, and require the use of expensive equipment which relies on grid-supplied electricity. The first step of diagnosis using nucleic acid amplification is release of amplifiable DNA from the cell. The AudioLyse is an inexpensive lysis device, which is powered by any audio device (such as a cell phone or any small mp3 player, both of which only require charging before reuse). Lysis takes just 10 minutes in a “set it and forget it” format. I show that the AudioLyse is capable of lysing methicillin-sensitive Staphylococcus aureus (MSSA). I compared the lysis of MSSA using the AudioLyse method, to lysis with the Bead Beater, a standard lysis technique. I found the AudioLyse effectively released amplifiable DNA from MSSA cells. I also tested the effects of glycerol and simulated nasal matrix, or SNM, on the lysis method’s ability to release amplifiable DNA. I found that high levels of simulated nasal matrix decreased the efficiency of amplifiable DNA release when both the bead beater and AudioLyse were used. However, we expect nasal swabs will be AudioLyse compatible, after dilution in lysis buffer. I found that the AudioLyse doesn’t perform well in releasing amplifiable DNA in viscous solutions. Glycerol was added to samples to test how the AudioLyse’s efficiency was affected. The AudioLyse displayed a statistically significant decrease in amplifiable DNA released in a 50% glycerol solution, releasing just 7.8% of the amplifiable DNA the bead beater was able to release. As of now, the AudioLyse is an efficient device in terms of releasing sufficient amplifiable DNA for disease detection, but remains limited by the viscosity of samples. Future work will include testing the AudioLyse on other genera of bacteria.

Sore throat is one of the top reasons that adults and children visit their primary physician. Group A streptococcus bacteria is a significant contributor to the prevalence of sore throat and is linked to roughly 11,300 invasive disease cases per year, with 1,800 of those leading to death in the United States alone. Lateral flow assays are a currently available rapid diagnostic of group A strep, but suffer from poor clinical sensitivity, thus requiring additional time consuming and expensive throat cultures for confirmation of negative rapid test results. The clinical sensitivity of commercial rapid immunoassays is limited by its relatively high limit of detection (LoD). The incorporation of electrokinetic techniques, such as isotachophoresis (ITP), has been shown to improve the limit of detection in surface reaction biosensors. ITP concentrates small amounts of colloidal gold-labeled target protein into a band at the interface between a fast-moving leading electrolyte (LE) and a slower trailing electrolyte (TE), which travels across a porous nitrocellulose membrane to a capture protein test line. The reaction between target and capture protein is greatly accelerated due to the high concentration of target protein in the ITP band, consequently improving test sensitivity compared to standard LF tests. Our previous work demonstrated the ability of ITP to lower the limit of detection of fluorescent proteins in comparison to a lateral flow assay. We hypothesized that previous performance enhancement from ITP in a one-site colorimetric assay could be attained in an infectious disease sandwich assay. In this work, we show that integration of ITP into a strep sandwich immunoassay, by incorporating protein extraction chemistry into the LE solution, exhibits two orders-of-magnitude LoD compared to commercial rapid lateral flow assays. We also achieved 75x improvement in analytical sensitivity.

It is known that diseases such as ADHD and nicotine addiction are linked to dysfunction in cholinergic signaling and accompanied by increased levels of impulsivity, which begs the question – is there a direct relationship between the cholinergic system and impulsive behavior? To answer that question we began by determining whether systemic administration of atropine, a muscarinic antagonist that blocks cholinergic signaling, would increase impulsive decision-making in rats. We found that it does increase impulsive decision-making, and we are currently trying to determine whether atropine’s effect can be explained by its impact on other psychological processes. For this reason, we performed an experiment to test whether administration of atropine also impacts working memory performance in rats. Specifically, we tested 8 Long Evans rats using a delayed alternation working memory task on a T-maze, which asks rats to correctly remember the location of a reward after a delay. The task consisted of 24 pairs of trials; each trial pair had a forced choice trial and a free choice trial with a 4, 8, or 16 second delay preceding the free choice trial. Once the rats displayed 80% choice accuracy over 3 consecutive days, the 3 day injection protocol began – rats were injected with either saline or atropine, retrained for 1 day, and then injected with the remaining solution on the final day (with solution order counterbalanced). Rats injected with atropine performed no differently than rats injected with saline, suggesting that atropine does not impact working memory. This supports the claim that working memory impairment is not responsible for the relationship seen between impulsive decision-making and atropine.

Monosodium titanate (MST) is an effective metal ion-exchanging material and has been used for decontaminating nuclear waste solutions. More recently, MST has been considered a candidate to exchange calcium ions in biological applications, especially for therapeutic delivery in dentistry. However, the toxicological properties of MST and MST-Ca(II) are poorly defined. Yet, it is critical for the mechanisms of toxicity to be understood to accurately assess MST as a therapeutic agent. In recent experiments, a decrease in the in vitro growth of MC3T3 osteoblasts exposed to MST or MST-Ca(II) attached to culture wells has been observed, but the cause of the inhibition is unknown. We observed (phase contrast microscopy) a tenacious affinity of the MST for the cell culture plate and the MC3T3 cells. This current study tested the hypothesis that MST limits cell growth in vitro by competing for attachment sites on culture polystyrene using L929 cells. Unlike MC3T3 osteoblasts, the growth of L929 fibroblasts was not inhibited when MST was added to cultures after cells had attached. We added MST or MST-Ca(II) (0 [control]–200 mg/L) to culture wells (n=8) 24 h prior to adding the L929 cells. The cells were then added (5000 cells/cm²) and the culture was incubated for 72 h to allow growth. Cell numbers and metabolism were estimated using a fluorescent-based assay (Cell-Titer Blue®). Statistical differences were detected using ANOVA and Tukey post-hoc tests (α=0.05). We expected that the addition of MST or MST-Ca(II) before cells will impede L929 cell growth; these experiments provided evidence that disruption of cell attachment to substrate may be one factor causing MST to inhibit cell growth in vitro. We will extend our investigation to other cells such as MC3T3 and dental pulp stem cells. 

Fear of predators may cause changes in prey species behavior with cascading impacts on the environment. When large herbivores such as deer are less sedentary, herbivory is dispersed and vegetation does not get browsed heavily in one area. As gray wolves (Canis lupus) naturally recolonize Washington state after a 70 year absence, deer behavior may shift in response to fear. Accordingly, under the hypothesis that greater movement may reduce encounters with wolves, we predicted that deer (Odocoileus spp.) would spend more time traveling in wolf-present areas compared with those from which wolves were absent. To test this prediction, we reviewed video clips recorded on deer-borne camera collars during the winters of 2013-2015 in the study areas and categorized the behavior of the deer. We compared the time deer spent traveling in wolf-present and wolf-absent areas. Our results will help us better understand the impacts of wolf recolonization on the ecosystem, including possible trophic cascades that may result from dispersed herbivory.

Mature Red alder (Alnus rubra) forests are now found in large contiguous patches which stand as legacies of past intensive management (logging, conversion to agriculture, etc.) of previously conifer-dominated forests of the Puget lowlands. King County acknowledges that a disproportionate amount of land under their ownership is comprised of mature alder forests nearing the end of their lifespan. King County is concerned with these forests’ ability to meet certain ecological, social, and economic objectives, such as providing wildlife habitat, carbon sequestration, and riparian function. In this study, we analyzed the quantity, distribution, and current conditions of these forests across three watersheds in central King County to provide landscape context. We compare the effects of alternate management approaches of varying harvest intensities on carbon uptake, and examine the distribution of forest types in riparian areas. We predicted that greater intensities of hardwood harvesting with conifer replacement will result in the highest long-term carbon uptake, while improving riparian forest function. To test our hypothesis, we used a forest vegetation dataset that was compiled by Oregon State University’s Landscape Ecology, Modeling, Mapping & Analysis Group in 2014. We combined this data with visual surveys of representative forests on King County property to classify county land into narrow forest cover types, which we then used for further modeling. We used the US Forest Service Forest Vegetation Simulator (FVS) to model forest treatments and obtain carbon storage projections. We found that coniferous forests provide greater long-term carbon benefits than short-lived hardwood forests. We support increasing conifer presence in mature hardwood forests to increase function and longevity.

The Theory of Narrative Thought (TNT) is a descriptive—as opposed to a normative—theory of decision-making, one that dispenses with those optimality criteria that governed more “rational choice” theories (e.g. Expected Utility Theory) from earlier eras. TNT strives to balance cognitive experience with brain processing subservient to a person’s higher-order, narrative decision-making process. This balancing renders TNT especially well suited for application to those decision makers who possess a wealth of cognitive experience within a choice domain (for example, Supreme Court justices adjudicating disputes between parties). The Court’s June 2015 holding extended 14th Amendment due process and equal protection rights for the first time in our nation's history to same-sex couples who desire to marry. During autumn, 2015 I collaborated with fellow students and professional consultants to my advanced Judgment and Decision making class on a project that treated the textual narrative of Justice Kennedy’s lead opinion as a case study. Our purpose was to apply Lee Roy Beach’s TNT in a novel fashion—to evaluate as “sound” or “flawed” the reasoning embedded within a US Supreme Court justice’s opinion. In particular, we applied TNT’s “narrative errors” and “undetectable errors” features, its overarching “coherence” principle and evaluated the “normative narrative” Justice Kennedy utilized as a reference point for his majority opinion judgment in the recent and momentous “same-sex” marriage case. Finally, we applied D. Kahneman’s “goals are reference points” analysis to the main narrative that the Constitution “provides liberty to all within its reach” in assessing whether Kennedy was operating at a gain or avoiding a loss in the judgment he delivered. My analysis of Justice Kennedy’s lead opinion demonstrates that nomothetic theoretical constructs within TNT have broad applicability across knowledge domains in characterizing those high level judgments that impact long-established policies, practices, and laws of a society.

This study explores the cognitive effects Bisphenol-A (BPA) has on the mature Helisoma trivolvis, a Ramshorn pond snail common in North America. BPA is a synthetic hormone used in plastics, making it ubiquitous around the world. BPA is easily leached into water and accumulates in many aquatic habitats, making this pond snail a prime candidate for research. BPA has been shown to interfere with the natural estrogen activity in the brain of pond snail embryos leading to developmental complications and premature death. This study focuses on the cognitive effects that BPA has on mature Ramshorn snails. Specifically the snail’s ability to form short-term memories in response to a negative stimulus. An operant conditioning procedure was used to assess the memory capacity of the mature snails in a range of BPA-contaminated conditions (10-800 µg/L). We raise two consecutive generations of snails both separated into five populations. Each generation had a control group containing non BPA treated water and four other groups with BPA concentrations of 10, 200, 600 and 800 µg/L solutions. Memory deficits were correlated with BPA concentrations. The results from this study add to the growing understanding of both the potential cognitive impacts of BPA as well as potential ecological consequences of BPA contamination.

Tree lines play a vital role in plant community composition in montane ecosystems. Over the past several decades, increasing annual temperatures have led to shifts in tree lines in montane environments. However, little is known about how local topography may have an effect on tree line advance. My research incorporates historical and repeat, ground based and aerial photography to assess the change of alpine tree line in a range of topographical conditions in Mount Rainier National Park over the past century. My study quantifies changes in tree cover and tree-line elevation in ridge and cove environments of the park. To track treeline change, historical and recent photographs were aligned, and areas of the photograph were broken up into polygons based on their small-scale topography. Random points were overlaid in these polygons to assess the rate of change of tree line shift. By looking at the change in tree cover in each random point relative to the polygon type, we are able to determine the amount of tree thickening that has occurred. We predicted that tree lines on sun exposed ridges will shift more quickly than those in cove environments. Snow is prevalent for longer periods of time in concave valleys limiting the amount by which the trees can shift up. Our results thus far indicate that small-scale ridge regions have the highest rate of change for tree line shift followed by cove. Subalpine meadows often occur in cove topography. Tree thickening in these regions over time may impact the wildflower populations and decrease species richness in subalpine meadows. In all, our research adds to the growing body of evidence that tree lines are moving up in elevation as well as provides the National Park Service with information about tree line influences on the plant communities of the park.

The Astronomy Undergraduate Engineering Group's (AUEG) is designing and installing a new instrument multiplexer for the 0.76m telescope at the Manastash Ridge Observatory (MRO). The multiplexer includes mechanics for the focal reducing optics, guider, filter wheel, the Student Technology Fee (STF) funded high performance photometer, as well as the STF funded spectrograph. Most of the research effort is going into the quick-change, fiber fed spectrograph that will extend our capabilities into new areas of astronomical observations. This instrument will be capable of switching between imaging and spectroscopic observations within seconds, all while maintaining an on-sky lock on the target. It will also include several resolution modes allowing for a varied ability for the user to choose between high throughput and high resolution. Through the efforts of the AUEG and the funding by the STF and MRO will once again have a full suite of high performance instrumentation with the ability to take several minute exposures, both photometrically and spectroscopically. Expected final product completion date for the instrumentation upgrades is Fall 2016.

Mass shootings are a growing public health and social policy concern in the United States. Mass shootings are defined by the Gun Violence Archive as four or more shot and/or killed in a single event, at the same general time and location, not including the shooter. Most media accounts attribute this phenomenon to lack of access to mental healthcare leading to untreated mental illness of the shooter and/or poor gun legislation leading to easy access of firearms. For this research project, I explore additional social factors which may help to determine variation in mass shooting across states. Using data from the United States Census Bureau, Uniform Crime Report, Kids Count Data Center, the Henry J Kaiser Family Foundation, and the Gun Violence Archive, I will be utilizing ordinary least squares regression to examine the role of poverty, social disorganization, gun legislation, and mental health spending to explain variation in the number of mass shootings across states during the period of 2010 to 2015. The results of these findings will provide a greater understanding of the contributors for mass shootings, further existing research, and assist policy makers in the reduction of future incidents.

Cerebral malaria (CM) is a multifactorial disease with lethal neurological complications plus increased risks of cognitive and neurological impairments making CM a leading cause of childhood neuro-disability. The malaria parasite, Plasmodium falciparum, accounts for most mortality from malaria, and primarily kills children under five in sub-Saharan Africa. Some children infected with P. falciparum go on to develop CM – a potentially lethal disease complication where red blood cells infected with parasites (iRBCs) bind to the endothelial cell wall in brain microvasculature. This process of parasite sequestration via cytoadhesion is mediated by parasite ligand, P. falciparum erythrocyte membrane protein 1 (PfEMP1) encoded by a family of 60 var genes. Requirements for maintaining binding surfaces conserved in structure and binding potential despite significant sequence diversity remain a mystery. Understanding these requirements will be critical for developing therapeutics to mitigate disease severity. A subset of PfEMP1 proteins associated with severe/cerebral malaria bind highly conserved regions of the host receptor, endothelial protein C receptor (EPCR), and inhibit binding of its natural ligand, activated protein C (APC). There are six PfEMP1 subdomains that bind EPCR (CIDRα1.1 and CIDRα1.4–1.8 domains), which share limited sequence identity among PfEMP1 variants. Our study uses computational and molecular biology tools to generate putative gain-of-function CIDRα1.3 mutants. Biophysical properties are assessed and compared across al CIDRa1.x domains to determine features that predict EPCR binders which are subsequently incorporated or removed substituting amino acid residues via cloning of PCR-mutagenized and synthesized gene fragments followed by protein expression in E. coli. Purified CIDRα1.3 mutants will be tested for their ability to bind EPCR using Bio-Layer Interferometry. This study demonstrates the potential for this approach to develop PfEMP1-derived peptides that will mimic the shape and binding potential of diverse CIDRα1 domains for use in vaccines to reduce the incidence of CM.
 

Nanoparticle delivery to specific locations within the brain requires the ability to control transport properties of the nanoparticle platform. Neurological injury or disease is not generally limited to one location or one cell type. A therapeutic or diagnostic platform must have the ability to move from the point of access in the brain to diffuse disease-related cells. Nanoparticles with no electrostatic, hydrophobic, or hydrogen bonding interactions within the brain microenvironment are classified as brain-penetrating. These brain-penetrating nanoparticles (BPN) can determine the steric limitations of nanoparticle transport within the brain microenvironment, and can characterize microrheological properties of the brain extracellular space. Therefore, adequate characterization of nanoparticle physicochemical properties in physiologically relevant solutions is critical to understanding nanoparticle behavior within the brain microenvironment. Here, we developed a methodology to assay nanoparticle size, surface charge, and polydispersity in the presence of cerebrospinal fluid (CSF), the primary medium that nanoparticles are exposed to in the brain. Typically nanoparticles are characterized in low concentration salt solutions (i.e 10mM NaCl) or in serum, which does not contain any unbound divalent ions, unlike CSF. We demonstrated that the hydrodynamic diameter measured in CSF is 10-20 nm larger than that measured in NaCl or serum, and that surface charge is more negative in CSF. In addition, we saw a decrease in nanoparticle stability in CSF compared to NaCl or serum. This methodology for characterization of nanoparticles in CSF, with comparison to literature standards, will be useful in determining critical nanoparticle physicochemical properties for brain penetration in the presence of brain microenvironment mediums like CSF.

A known carcinogen, arsenic is elevated in many areas through natural and human causes. Its persistence in the environment and toxicity at low levels impacts both human health and ecosystem integrity. In humans, arsenic has been linked to cancers of the skin, lung, and bladder. Phytoremediation is a cost-effective, eco-friendly technology that uses the natural ability of plants to remediate pollutants, such as arsenic, from contaminated soils. We are investigating whether endophytes, mutualistic microbes colonizing the internal tissues of plants, can improve this process. Endophytes have been shown to increase host-plant tolerance to a wide range of environmental stressors, and we hypothesize that arsenic-tolerant endophytes may improve the tolerance of their host plants to arsenic. Willow (Salix ssp.) are fast growing, high biomass plants, with deep roots, and have demonstrated tolerance to arsenic. In this research, eight willow varieties were screened for arsenic uptake from hydroponic solution in order to establish the best candidates for the phytoremediation of arsenic-contaminated soils. The plants were exposed to arsenic for ten days, then the dried tissues were separated (root/shoot), digested in concentrated nitric acid, and assessed for total arsenic via ICP-OES. Four species, S. scouleriana, S. discolor, S. vimanalis x S. miyabeana, and S. sachalinensis x S. miyabena accumulated the highest level of arsenic in their shoots. Because the purpose of phytoremediation is to remove pollutants from the site, ideal candidates will translocate higher proportions of arsenic into their above ground tissues. These four species will be used in further phytoremediation trials. 

Chiroptera (bats) forms the second most diverse branch of mammals, with over 1,300 species documented. Bats play important roles within the environment because they feed on a wide range of prey items, ranging from fruit, nectar, to insects and blood. One of the main drivers of species diversification in bats is the structural specialization of the cranium and jaw muscles, which allow bats to produce adequate bite forces to exploit and process different types of food. This study investigated differences in bite force and prey hardness among insectivorous free-tailed bats (Family Molossidae), and the factors explaining the breakdown and processing of their meals through physical digestion. The bite forces of seven Costa Rican molossid species were measured and compared with the degree to which insect exoskeleton was broken down in their feces. The size of the exoskeleton particles in the fecal samples gave clues as to how much bats chewed and broke down their meal, whereas the thickness of these particles was a proxy for insect hardness. We anticipate to find a clear correlation between exoskeleton particle thickness and size across species, which would support the prediction that the size and morphology of the skull and teeth have an effect on the food these bats can consume. A relationship between the thickness of the insect exoskeleton particles and bite force would indicate that each bath species is specialized to feed on certain types of insects with varying level of exoskeleton hardness. Our results will provide clues to understanding feeding behavior of free-tailed bats and the role of morphology on species ecology.

Crowdsourcing platforms provide a common market place for job seekers and requesters to work collaboratively. The existing platforms fail to address the needs of the workers and the requesters due to unjust distribution of power and insufficient information about the parties involved in a task. In platforms such as Amazon Mechanical Turk new workers struggle to find tasks, workers face rejection without adequate feedback, whereas requesters do not get high quality results in time. In this research we contribute to Daemo a collaborative project from Stanford crowd research collective. Daemo is a self-governed crowdsourcing platform that aims to improve work quality and provide equitable representation. We studied the surrounding literature about existing solutions to learn about the flaws in the current platforms. Then, we interviewed professional workers and requesters to find their needs. We envisioned ways to improve the requester experience by suggesting tagging for tasks to make the tags easier to be searched and tailored for their skills. We also proposed adding ratings to requesters profile and adding rejection rate to requester profiles. Then, we illustrated our design choices by creating prototypes to communicate and evaluate our work.

According to the Anxiety and Depression Association of America, Anxiety Disorders are the most common mental illnesses in the U.S. Currently there are about 40 million adults in the United States with anxiety disorders. People with anxiety are thought to show an attentional bias to negative events or stimuli in their environment. In our lab we have found that anxious people have larger amplitude brain activity to negative stimuli than do people who are not anxious. We did this by implementing an emotion counting and stroop task to measure the influence of anxiety affecting responses to negative stimuli. For example, participants had to count the number of negative words on the computer screen and click the correct number using a mouse; the slower the response to negative words, the higher the anxiety of the participant. In addition, several studies have found a genetic contribution to anxiety. In our lab we have done studies examining the role of the BDNF or "Brain Derived Neurotrophic Factor" in anxiety. In this study we genotyped all of the participants for the different BDNF alleles in order to determine whether a certain allele is more susceptible to anxiety. All of our participants were college students recruited right outside of our laboratory and by referrals. Among our expected results were that those with the BDNF val/val allele would demonstrate the lowest levels of anxiety, followed by val/met allele that display moderate levels, and finally the met/met allele that have the highest levels of anxiety.

Studies have been exploring the use of neurofeedback training as a treatment for Attention Deficit Hyperactivity Disorder (ADHD), although the application of neurofeedback training to healthy subjects in order to improve reading comprehension ability has not been investigated. It is important that the relationship between specific brain oscillation frequencies and cognition is broadened from the cognitively unhealthy population to the cognitively healthy population. Additionally, this research is necessary in order to expand the knowledge and use of neurofeedback training. The purpose of this study is to further understand the connection between specific brain oscillation frequencies, attention, and reading comprehension. To date, 16 typically developing college undergraduate students from the University of Washington have completed the study. Participants were assigned to either the neurofeedback-training (NFT) group or the pseudo neurofeedback training group. In the NFT group participants were trained to decrease theta (4-8 Hz) while simultaneously increasing beta (12-20 Hz). In the pseudo NFT group participants were re-played feedback which was pre-recorded from participants in the experimental group. Participants were blind to group assignment. Assessment included attention measured with the Attention Network Test (ANT), reading comprehension measured by scores on the Nelson Denny Reading Comprehension test, and EEG during eyes-open resting state before and after two sessions of NFT or pseudo-NFT. Preliminary results suggest a significant improvement in reading ability following theta-beta ratio neurofeedback training.

Oxygen transportation in red blood cells occurs via a protein called hemoglobin. When hemoglobin is either absent, flawed, or impaired, the transportation of oxygen is hindered and this is known as anemia. Due to the prevalence and dangers of anemia, our goal is to effectively measure the concentration of hemoglobin in small volumes of a patient’s blood in order to diagnose critical levels of anemia. In order to do this, we take advantage of Beer-Lambert’s Law – a physical law that states concentration scales linearly with absorbance (a measure of how much light a molecule can absorb at a given wavelength). With the use of a microfluidic device, whole blood flows through an 8 mm x 250 μm x 50 μm channel and is illuminated by a white LED. A portion of the light is then absorbed by hemoglobin and continues at a reduced intensity to a green filter to focus our measurements to the visible green spectra, because it is known that hemoglobin absorbs the most light at about 540 nm, which is in this region. We demonstrate that our devices can determine hemoglobin concentration effectively with less than 40 μL of blood and at a low cost. The immediate impact of hemoglobin measurements of small volumes is its use towards children. The long-term impact is a diagnostic point of care device to solve global needs.

Masting refers to annually variable seed production; whereby plant species release large quantities of seeds one year, followed by one or more years of significantly lower seed production. Seed masting behavior is thought to be evolutionarily favorable, a technique for survival. Two main theories exist to explain mast seeding, predator satiation and increased pollination. The purpose of this research study was to determine A) if a group of six conifer species within Mt. Rainier National Park exhibit mast seeding behavior (i.e. synchronized seed production over large areas, annual variation in seed production exceeds annual climate variation); B) Whether seed viability is greater in 'boom' years than 'bust' years (which would support wind pollination efficiency as an evolutionary driver of masting); and C) whether these patterns vary by species and/or elevation. We examined six species of conifers: Abies amabilis, Callitropsis nootkatensis, pseudotsuga menziesii, Thuja plicata, Tsuga heterophylla, and Tsuga mertensiana. Data was collected from 108 seed traps located in 18 stands at multiple elevation ranges within Mt. Rainier National Park. Seeds were sorted based on tree species, and classified as filled (viable) vs. unfilled (not viable). We then calculated mean total seed production for each stand and used correlations to assess how correlated annual seed production is across 18 stands. Next, we compared annual variation in climate within each stand, to assess whether species showed higher variation in seed production in comparison to climatic variation. Finally, we compared results for our six focal species to assess species specific similarities and differences. Understanding the mechanisms behind masting is important, as masting can control tree population demography, and influences ecosystem dynamics. Moreover, our study may provide greater understanding of the implications of climate change on masting dynamics for forests at Mt. Rainier National Park.

Affordable 3D-printing technology may improve fabrication and accessibility of orthoses for individuals with impaired movement. The goal of my research is to leverage 3D-printing to improve the design of wrist-driven orthoses (WDOs) for individuals with spinal cord injury (SCI). Specifically, I have sought to improve comfort, aesthetics, and ease-of-use of WDOs while reducing fabrication time and increasing customizability using 3D-printing. WDOs are used by individuals who can move their wrist but have little to no mobility in their fingers. Through wrist flexion and extension, this device assists in opening and closing the hand. Unfortunately, current WDOs are laborious to fabricate, uncomfortable, and have poor aesthetics. The potential of 3D-printing for orthosis fabrication was evaluated with a group of orthotists. I modeled the 3D-printed WDO using computer-aided design software and asked orthotists to assemble and rate the device and provide feedback. The average assembly time decreased from 12+ hours for traditional metal WDOs to 1.5 hours and the device received average scores of 6.6, 6.6, and 7.6 on a scale of 1-10 (1 = poor, 10 = great) for function, aesthetics, and comfort, respectively. Based upon the orthotists’ feedback, I implemented design improvements and created a fatigue tester to ensure the device’s safety for extended use. The next round of testing focused on getting feedback from individuals who have had an SCI. The device enabled participants to achieve a three-jaw chuck grasp, which they could not achieve without it, improved performance in functional tasks, and was lighter than traditional devices. The device received average scores of 6.8, 6.5, and 8 for function, aesthetics, and comfort, respectively. Participants’ feedback was used to further improve the design. Upon finalizing the device design, fabrication method, and assembly manual, editable CAD models of the WDO design will be released for open-source development and use.

Merkel cell carcinoma (MCC) is an aggressive skin cancer with a propensity for early dissemination. As little is known about this process, we sought to identify the preferential sites of initial distant metastatic MCC in order to guide imaging evaluation and clinical follow up. In this retrospective study, we analyzed the clinical and imaging records of 442 initial distant metastases from 305 MCC patients enrolled in our data and tissue repository. Initial distant metastases were defined as the first lesions detected beyond the regional lymph nodes of the primary tumor. Among 305 patients, 69% had 1 initial metastasis, 19% had 2, 9% had 3, and 3% had 4 or more. Of the 305 patients, 50% were evaluated only by radiologic and/or clinical criteria, while 50% also underwent biopsy-confirmation of MCC metastases. Of the 442 initial distant metastases, the distribution of sites was: 26% to distant lymph nodes (typically supraclavicular, retroperitoneal, or iliac), 15% to liver, 13% to skin, 13% to bone, 13% to other visceral sites, 6% to lung, 5% to pancreas, 3% to brain, 2% to kidney/adrenal gland, 2% to gonads, 1% to chest wall, and 1% to stomach. Although there were similarities in initial metastatic sites between MCC and melanoma, the brain (3%) and lung (6%) were markedly less common in MCC than in melanoma (20% and 36%, respectively), while the pancreas was more common in MCC (5%) than melanoma (<1%). Given the aggressive nature of MCC, with ~40% of patients eventually developing distant metastatic disease, these findings may facilitate improved detection and management.

Trustworthiness is an invariant characteristic that is independent of changes in emotional expressions. However, the perception of trustworthiness is highly varied and is not often accurately portrayed. As an attempt to understand what causes variations in perceived facial trustworthiness, participants were asked to rate trustworthiness of facial expressions (sad, happy, neutral) presented individually and as a single unit. Results found participants viewed happy expressions as more trustworthy, but when presented with all emotional expressions, neutral expressions were more likely to be used as an indication of trustworthiness. Overall, this study suggests neutrality is a better indicator of personality traits.

With concern about climate change increasing, assessing how plant reproductive success is impacted by increases in temperature is crucial in order to fully understand how climate change influences ecosystem structure and dynamics. This study measures how population variation and the climate of different elevations affect the capsule size and seed mass of the high-elevation plant mountain monkeyflower, Mimulus tilingii, at Mt. Rainier National Park. If climate is the primary limiting factor determining the range of M. tilingii, plants within the species’ climate range will produce the most abundant capsules and seeds whereas plants grown outside the species’ distributional range will produce smaller amounts. Sample seedlings were planted at two elevation sites: 1)  M. tilingii’s range center and 2) below M. tilingii’s range to mimic the increase in temperature due to climate change. Populations were categorized as either within-population (for crosses within the same elevation site) or between-population (for crosses between the two elevation sites) with equal amounts at both sites. This study quantifies M. tilingii’s reproductive success both in the context of the site as well as the population type, allowing for comparisons on these two levels. Results show that parent plants from the lower site produced more flowers and grew faster, indicating that plants in the lower elevation site might be more successful. These unexpected results suggest that M. tilingii may be better adapted to a warmer environment and that climate change might even be beneficial for this reason. Determining the exact impact of temperature on reproductive success is crucial not only for measuring the species’ fitness but also for understanding how these new adaptations will play an even bigger role in competition for resources among different plant species and how those new interactions will alter the ecosystem as a whole as the climate warms.

Mass incarceration has disproportionally impacted communities of color over the past 41 years. Indeed, policies that are currently operating as a result of the “War on Drugs” have created large racial disparities in drug convictions. For an example, despite research suggesting that Blacks and Whites use marijuana at similar rates, Blacks have been convicted at a higher rate. Many proponents of criminal justice reform argue that just as certain policies have led to the creation of racial disparities in drug conviction, the creation of new policies and laws might also be able to reduce or eliminate these disparities. For this research project, I use longitudinal data of all Washington State convictions between 2000 and 2015 and ordinary least squares regression analysis to examine the association between the 2012 decriminalization of marijuana in Washington State, I-502, and in drug conviction rates by race. I also include a series of controls including: year of conviction, sex, county and prior convictions to test the robustness of this association. In particular, I am interested in understanding if racial disparities in drug convictions decreased post the implementation of marijuana legalization in Washington state. My results suggest that marijuana legalization leads to decreased disparities in drug conviction rates for Blacks. The overall lower conviction rates for all types of drugs may have been produced by the lessening of police contact with Blacks in Washington State for suspicion of marijuana possession.

When a star undergoes the transition to the white dwarf stage of the stellar life cycle, an outburst of ionized gas is expelled in a planetary nebula. It is currently unknown if planets orbiting a white dwarf are able to survive this transition. However, between one fourth and one half of white dwarfs have elements in their atmospheres that are heavier than helium and will sink into the white dwarf quickly unless they are somehow being replenished. The recent detection of a disintegrating rocky planet orbiting a polluted white dwarf suggests that the source of metal pollution may be debris from these bodies. As the Sun will become a white dwarf in the distant future, our team began the search for an intact planet, which could provide a model for examining the future of our own planet and solar system. Using observations from the ARCSAT 0.5 m telescope at Apache Point Observatory, we examined fluctuations in brightness of a small sample of white dwarfs, over a period of several nights. We visually inspected the white dwarf light curves for strong dips in brightness that could indicate the transit of a planet, and promising candidates were further analyzed via Lomb-Scargle Periodograms. Most of the white dwarfs displayed periodicities in flux, but none were indicative of the presence of a planetary body. Included in our data was an eclipsing binary white dwarf system with a known periodicity that our function could not detect correctly. We have improved our search by using the Box-Least Squares method to detect weak transits instead of periodograms, but have yet to detect an intact planet orbiting a white dwarf.

The study of neonatal neuroanatomy is a complex field because of the rapid changes occurring continuously. The physical development of tissues is critical to understanding the cognitive development of behavior and learning in the neonate. These structures can be visualized and analyzed with Magnetic Resonance Imaging (MRI). The hippocampal structure in particular is vital to memory consolidation and is therefore key to understanding how newborns build upon acquired knowledge and how this affects their behavior as they grow. This strucure has been studied at many different ages with parallel work analyzing how changes in anatomy result in observable cognitive differences and developments. This study in particular has a rare cohort of scans that were taken shortly after birth. Prematurity is an especially important factor to consider here as it affects physical and behavioral growth. Here we looked at 42 premature MRI subjects and used these to build a temporal model of brain development. Our primary aims of the study are to: (1) develop a protocol for labeling the hippocampus in premature neonate scans, (2) create a growth over time model of the structure in order to automatically segment a larger number of scans and (3) observe how volume varies with behavior as projected by Bayley's Scale of Infant and Toddler Development. So far aim 1 has been achieved and current work is increasing the previous atlas size of 32 scans to 42 in order to improve automatic segmentation. The overarching goal of premature neonatal MRI segmentation is to provide further data for early diagnosis of behavior abnormalities that could develop later in the subject. Results here could produce a meaningful indicator of cognitive development through MRI analysis as well as assist in improving the accuracy of MRI automatic segmentation algorithms. 

Premature births, or births before 37 gestational weeks, are associated with structural and functional abnormalities in the brain. Magnetic Resonance Imaging (MRI) is used to examine brain injury in neonates. Previous work demonstrated correlations between neonatal cortical lobes volumes from MRI and scores on the Bayley Scales of Infant and Toddler Development-Third Edition (Bayley-III), which measures cognitive, motor, and language skills of infants. The occipital lobe is important to diagnosis of visual and neurodevelopmental delays. In this work, I examined the relationship between occipital lobe subdivision volumes and Bayley-III scores. In order to do this, I designed a parcellation or labeling protocol that divided the occipital lobe into two regions based on the calcarine sulcus, the cuneus region and the lingual region. I applied the protocol to the 32 MRI training dataset. Using this parcellation protocol, I created a spatio-temporal atlas of brain parcels, which is a time and space model of brain tissue and parcel probability estimates. This atlas was used to validate our protocol using a leave-one-out validation and to automatically parcellate the larger dataset using EM or Expectation-Maximization labeling. The dataset contained 270 T1-weighted MRI scans from premature neonates who took the Bayley-III at 18 months. Once the larger dataset was labeled, I used multi-variate linear regression, normalizing for head size, to examine the relationship between occipital lobe gray matter volumes and scores on the Bayley-III and analyzed the growth pattern of the regions of the occipital lobe. Both regions showed symmetric and exponential growth patterns. Statistically significant correlations between the lingual region of the occipital lobe and Bayley-III scores were found. This suggests that regional occipital lobe volumes are associated with developmental outcomes in premature neonates.

Ecological imbalances have manifested as environmental, social, and political concerns worldwide. Simultaneously, technology, a continued rise in urban cities, innovation, and instant gratification place a disconnect between a majority of people and the workings of nature. Much research seeks to understand the demographic and internal factors, and implicit and explicit attitudes, that attribute to environmental knowledge, attitudes, and behaviors of everyday citizens in an effort to make leaps in sustainable development. Former and recent findings illustrate the reality that positive sentiments toward the environmental movement are common, yet behavior and activism is difficult to achieve. For this research project I explore environmental knowledge, attitudes, and everyday behaviors among first year and last year University of Washington students utilizing survey research and a focus group approach. More particularly, I explore the strength and power of normative influences that develops over this traditional four-year span. Seattle, a distinguished hub of sustainable values and actions, reflects environmentally-supportive intentions and behavior among its residents, with a novel capability to inspire visitors and newcomers with its visible and verbal support. These findings will contribute to the growing understanding of environmental awareness and activism, in addition to evaluating and mapping out the power of social influence within environmental contexts.

In cells, phosphorylation of p120 catenin causes it to dissociate from cadherin transmembrane proteins, which leads to the activation of downstream pathways and cell motility. We have mutated amino acids in p120 catenin in order to locate the functions of specific sites of phosphorylation in zebrafish embryos. The phosphorylated tyrosine amino acid, Y335, in p120 catenin is a target of the phosphatase "PTP-PEST” and controls epithelial cell motility and Rho GTPase activity in colon carcinoma cells. We designed a knock-out of normal activity by mutating the tyrosine to a phenylalanine, which cannot to be phosphorylated. We also mutated Y335 in p120 catenin to a glutamic acid (E), which mimics the negatively charged phosphate. These mutants were transformed into bacterial cells and the isolated DNAs were transcribed into mRNA. We have also injected zebrafish eggs with the mRNAs to analyze the effect of these mutants on development. We have also mutated several other serine and threonine phosphorylation sites on p120 catenin including, S252, T310, and S312 to determine if the mutation to an alanine or to a glutamine will result in altered downstream activity. We have injected mRNAs with the S252A and S252E mutants into zebrafish eggs and determined that the S252E mutation rescues a knockdown of the endogenous p120 catenin, while the S252A mutation does not. The results suggest that phosphorylation of S252E is required for the migration of presomitic cells to the dorsal axis. In fibroblast cells, phosphorylation of p120 at T310 promotes adhesion junction disassociation, allowing cells to mobilize in a “treadmill” fashion. We used p120 catenin mRNAs with the mutations T310A and T310E to measure their impact on cell motility in zebrafish. These individual mutations may give insight on the downstream effects p120 catenin in cell motility, including morphological bone abnormalities and metastasizing cancer cells.

Properties governing the equations behind Newton’s Law of gravitational force and Coulomb’s Law of electrostatic force are similar—namely, both share an inverse square distance dependency, as well as a product of some property of two interacting objects multiplied by a constant. Although the relationship between these similar forces has been explored as a theoretical endeavor, experimental study of electrostatic forces as a central force in orbital mechanics has been limited due to technical challenges. As we continue to push the frontiers of space exploration and expand our knowledge of the workings of our universe, an improved understanding of the electrostatic force will become increasingly important for various applications—from predicting behaviors of motion aboard spacecraft, to creating an orrery through which to understand systems on a cosmic scale. Successful experiments conducted on earth are a crucial first step in testing ideas that can be verified in low-earth orbit and further expanded into functional models. Previous ground experiments, the first of which was published by a team at Rhodes College in 2008, have explored the orbital behaviors of interacting charged spheres. My investigation aimed to demonstrate electrostatic orbits around a non-spheroidal object under microgravity conditions using Portland State University’s Dryden Drop Tower. Footage collected via a high-speed camera was analyzed and compared with orbital predictions obtained through theoretical analysis.

The prevalence of non-medical prescription drug use has recently increased dramatically. It is estimated that 52 million Americans over the age of 12 have used prescription drugs for non-medical purposes in their lifetime. Prolonged use of benzodiazepines, and Alprazolam (Xanax) in particular, has detrimental effects ranging from physical and psychological dependence to increased risk of Alzheimer’s disease. Xanax displays are present on social media such as Twitter, a popular social networking site with approximately 320 million users. These social media displays provide novel opportunities to capture epidemiologic trends in displays about Xanax. While Xanax abuse is more common among females, it’s unclear whether and how Xanax social media displays are present across genders. The purpose of this study is to examine the different types of Xanax displays on Twitter and compare them between males and females. To identify profiles, we identified common Internet nicknames for Xanax including “Xanax”, “xan”, “zanland”, “zannies”, and “zans” and will use these as search terms on Twitter. Inclusion criteria include profiles being publicly available and the gender of the profile owner clearly being determined by the profile picture and/or pronouns used in their tweets. Profiles were excluded if the age was clearly stated under 18 years old. One hundred participants’ Twitter profiles will be analyzed. We will conduct content analysis on the profiles’ tweets for a 3 month span. The tweets will be coded into 1 of 3 categories based on content: anti-Xanax sentiment, Xanax use in reference to “blacking out”, and describing Xanax co-use with another substance. Analyses will include evaluating the proportion of Xanax-related tweets among total amount of tweets in the coding period and will be compared between males and females. Results from this study could inform gender based interventions for prescription drug use.

Epileptic encephalopathies (EEs) are devastating childhood epilepsies characterized by multiple seizure types that are usually refractory to medication. Next-generation sequencing has revealed the prominent role of de novo mutations in causing EEs with clinical diagnostic labs reporting a molecular diagnosis in as many as 24-40% of cases. Despite this significant progress, the majority of cases are unexplained. Exome sequencing, a next-generation sequencing technique, allows one to look at all the protein coding regions of an individual’s genome, offering an affordable and unbiased approach to gene discovery. Using exome sequence data for 50 trios (proband and unaffected parents), in which the child had seizure onset in the first 2 years of life, we identified 76 candidate genes, of which 37 are confirmed de novo variants through Sanger sequencing. Notably, 2 affected individuals were identified to have a de novo variant in the guanine nucleotide-binding protein (G-protein) beta1 subunit, GNB1. This was a statistically significant finding (p=0.005), and in collaboration with colleagues we have now identified 13 patients with neurodevelopmental delays with and without seizures. This previously unrecognized genetic condition is characterized by global developmental delays (13/13), hypotonia (11/13), seizures (10/13), ocular manifestations (8/13) and growth delay (6/13). These genetic findings will have immediate impact to clinicians and families when discussing diagnosis and prognosis, and hopefully guide future studies of finding effective therapies for these patients. Future work will screen for genetic variants in the candidate genes identified by exome sequencing using a targeted sequencing approach in a cohort of 600 patients with EE of unknown etiology.

Glacial erratics are rocks that have been transported and deposited by glaciers. They are typically characterized by large size and a composition that differs from the surrounding geologic features, indicating a foreign source. Determining the source of these erratics provides evidence of ice flow direction, which helps to reconstruct glacial history of a region. Our project focuses on a glacial erratic located in West Seattle at the entrance to the South Seattle College campus. Our research has two main goals. Our first goal is to determine the composition of the glacial erratic through mineral property tests and optical analysis, and use this information to identify potential origins of the rock. Our second goal is to determine if the characteristics of the sediment underlying the erratic are consistent with recent glacial transport. Using sediment samples and existing borehole data, we have constructed subsurface cross-sections showing the stratigraphy of underlying deposits. Preliminary mineralogical and composition analyses indicate that this rock is not native to the Puget Sound basin, and may have been transported from as far away as the northern San Juan Islands or Canadian Cascades. Analysis of existing borehole data and sediment sampling indicate the underlying stratigraphy includes glacial till and outwash deposits consistent with our hypothesis that the erratic was deposited during one of the recent glacial pulses. Learning more about the glacial erratics in the Puget Sound area can help confirm the path and timeline of ice sheets that covered the area thousands of years ago.

Human stool sample collection is a non-invasive method of assessing the gut microbiome. Rapid changes in microbial composition upon defecation limit the use of fresh stool for microbial community analysis. This investigation tests the effects of stool sample storage and shipment conditions on bacterial DNA quality and microbial community structure to establish and validate a methodology for stool collection in human population-based studies. The goal is to establish a protocol that minimizes bias due to shipping conditions. Fresh stool samples were collected from three participants, homogenized, and aliquoted with or without a preservative (RNALater) within 48 hours of collection. To mimic sample transport conditions, we incubated samples from three individuals under the following conditions: -80°C without RNALater, 37°C, 22°C, 4°C, -80°C -5°C, or frozen samples packed in ice left at 22°C for 48 hours. Samples were then stored at -80°C for 48 hours after which fecal DNA was extracted. We used 16S rRNA gene sequencing of the V1-V3 region (Illumina Mi-seq) to measure the community composition. Multivariate analysis was used to test the effect of sample storage and shipping regime on the microbiome. On average, the phylum level distribution was 76% Firmicutes, 20% Bacteroidetes, 3% Actinobacteria, and <1% Lentisphaerae, Tenericutes, and Actinobacteria. A perMANOVA (F=2.25, p< 0.1) showed that there was no statistically significant difference in the phyla due to temperature and handling. Regardless of treatment, samples from each individual clustered together suggesting that between individual variation exceeds any differences due to shipping regimen. Our current protocol for stool collection and preservation shows no significant loss of bacterial DNA quality, nor does it significantly affect microbial community representation and is adequate for investigations on microbiome composition, structure and activity in human studies.

Epileptic encephalopathy (EE) is an umbrella-term for a class of severe epilepsies characterized by debilitating seizures. Epileptic activity often begins in early adolescence, contributing to developmental, cognitive, and behavioral abnormalities. Identification of genetic mutations in EE-patients has implicated >50 genes, with clinical diagnostic labs reporting a molecular diagnosis in 24-40% of cases. Current EE gene discovery focuses primarily on identifying de novo mutations in genomic coding regions, which alter the amino acid sequence of the resulting protein, disrupting the protein’s function and leading to neural abnormalities. A de novo mutation is not inherited from either unaffected parent; it first occurs in an affected individual, suggesting a genetic cause for the phenotype. My research focuses on identifying novel noncoding mutations in a cohort of 167 patients with EE of unknown cause. The proportion of rare diseases caused by noncoding mutations is unknown and relatively few examples of functional noncoding causative mutations exist. My goal is to identify de novo variants in intronic and untranslated genomic regions, and also to identify synonymous variants in which the resulting amino acid is unaltered. Initially, the 167-patient cohort was screened for variants in 44 established EE genes using targeted next-generation DNA sequencing. I have filtered this data for high-quality noncoding variants, which are unreported in a healthy population. I am currently screening patients’ parents for these noncoding variants to determine the mode of inheritance. Confirmed de novo variants will be followed-up with functional studies to test their molecular consequences (via mRNA, splicing, gene expression). Determining genetic causes of EE unveils molecular mechanisms behind phenotypes, allowing for precise diagnoses, and leading to treatment of severe epilepsies based on their causes. I hope to identify causative noncoding variants in epilepsy genes to expand epigenetic analysis of EE, and contribute to a better understanding of EE genotype-phenotype relationship.

Aging leads to the loss of physiological function such as cognition, mobility, and cardiovascular performance. One possibility for this loss is an age-dependent decrease in the generation of proteins necessary to support these functions at a youthful level. Many of these protein factors are secreted into the general circulation and can be detected in the serum of blood samples, this provides the opportunity to monitor their levels at various ages. The objective of this project was to determine if serum proteins could be identified that decreased with increasing age using mice as a preclinical model of aging. Mice with a mixed genetic background, designated as CB6F1, were used because they represent a heterogeneous gene pool and a co-morbid disease pattern similar to humans. Serum was collected from 8-month and 32-month old mice (comparable to 22 and 80 human years, respectively), and tested for 200 serum proteins using a slide capture array (RayBiotech). Levels for 23 proteins, involved in supporting blood vessels, the immune response, brain cells, skin, muscle and bones, were significantly decreased in old mice compared to young mice, correlating with an increase in frailty, fatigue, heart failure, and cognitive impairment. This preliminary data suggest specific serum proteins, alone or in combination, may be useful markers for aging. This provides the rationale to investigate the ability of anti-aging drugs to restore specific protein factors to their youthful levels and monitor for any delay or reversal of age-related functional decline.

Thomas Edison argued that video must be presented at 46 frames per second (fps) for smooth motion to be perceived. Most console video games are presented at 30 fps, but new technology allows for more than 60 fps. Gamers argue about whether the increased fps affects the perception of movement within games, and whether the increase in price is worth it. In a case study, Linus showed that a console-gamer was able to correctly identify the fps only 20 percent of the time, whereas a PC-gamer who regularly played at 60 fps or faster correctly identified the fps 100 percent of the time. We predicted that in a larger sample with more clips, PC-gamers would correctly recognize video clips presented at 120 fps versus 60 fps more often than console-gamers would. A set of 10, 10-20 second screen capture video clips of an active game of Portal2 were created, and each clip was duplicated in 60 and 120 fps, resulting in 20 clips. In a sample of 10 console-gamers and 8 PC-gamers, the PC-gamers correctly recognized the 60 versus 120 fps clips (M=12.38) more often than the console-gamers (M=10.5; t=1.52, p=.08), approaching significance. On certain clips, the PC-gamers were significantly better at recognizing the fps. This small sample provided good insight into the issue of whether video gamers can detect the difference between frame rates. These results support our hypothesis and the results from Linus that PC-gamers can tell the difference between video games presented at 60 fps and 120 fps more readily than console players can. This small sample provided good insight into the issue, but future research will need to focus on objectively determined “PC-gamers” versus “console-gamers,” rather than relying on the participants to self-identify.

Retinitis Pigmentosa, a progressive neurodegenerative disease, is a significant contributor to loss of vision due to retinal degeneration. The retina is made up of light sensing cells called rods (for night vision) and cones (for day vision). In patients afflicted with this disease, there is a degeneration of rod photoreceptors over time, which leads to a decreased visual field and night blindness. At a certain point, the loss of rod cells leads to the breakdown and loss of cone cells, which are responsible for color vision. Mutations in the rod gene Rhodopsin have been linked to the development of this disease. By down regulating this defective gene, the degeneration of rods would likely be prevented. Subsequently, cone degeneration would also be prevented, limiting the loss of vision in afflicted individuals. The expression of Rhodopsin is controlled by a nuclear hormone-like receptor transcription factor called Nr2e3. In collaboration with another lab (Dr. Sheng Ding, UCSF), we have identified small drug-like molecules that can block Nr2e3, and we have called them CA88, CA95, and CA97. We predict these antagonists will lower the expression of rod genes. Wildtype mouse retinas were treated in culture with CA88, CA95, or CA97. The use of these small molecules resulted in the significant down regulation of a number of rod genes. These genes include Rhodopsin, NRL, NR2E3, and GNAT1.  Stained tissue sections further confirmed a decrease in Rhodopsin with treated retinas.  When retinal ex plants were done using mice with a P23H mutation in the Rhodopsin gene, treated retinas were found to have a significantly thicker photoreceptor layer than non-treated, indicating the ability for these compounds to prevent retinal degeneration. With a way to reliably down regulate problematic genes such as Rhodopsin, a potential avenue for treatment of humans affected by Retinitis Pigmentosa is opened.

Chronic pain is a common condition associated with psychological distress, functional impairments, and age-associated comorbidity. Preliminary studies, based on relatively small sample sizes, suggest that chronic pain contributes to telomere shortening, a widely recognized marker of cellular aging. We sought to determine this association in 7,816 community-dwelling adults ages 20 and older who participated in the 1999-2002 National Health and Nutrition Examination Survey. Consistent with previous studies, leukocyte telomere length was assessed using the quantitative polymerase chain reaction method and compared to a DNA reference standard to compute a Telomere to Single Copy Gene (T/S) ratio. Standardized, in-person interviews were used to identify chronic regional pain (CRP) and chronic widespread pain (CWP) in 784 (10.0%) and 266 (3.4%) participants, respectively. Multivariable linear regression models were used to examine telomere length according to demographic factors, health behaviors, comorbidity, and chronic pain. Older age, male sex, obesity, and less physical activity were associated with shorter telomere length (P<0.05 for all comparisons); however, there was no statistically significant association of chronic pain with telomere length. The age-adjusted mean (standard error) of T/S ratios were 1.04 (0.02), 1.03 (0.02), and 1.02 (0.02) in participants with no chronic pain, CRP, and CWP, respectively (P=0.69). In addition, chronic pain did not modify the effects of age, sex, race/ethnicity, education, or psychological distress on telomere length (P>0.10 for tests of statistical interaction). Findings from this large, nationally-representative study indicate that chronic pain does not contribute to telomere shortening, but further investigation with additional biomarkers in large studies are needed to investigate the potential impact of chronic pain on cellular aging.

The need for effective, on-demand contraceptives and protection against sexually transmitted infections is constantly increasing in our ever-growing society. We plan to contribute to this need by utilizing the barrier and drug eluting properties of a non-woven matrix of electrospun nanofibers made from the hydrophobic polymers polycaprolactone (PCL) and poly(lactic-co-glycolic acid) (PLGA). Our experiments will demonstrate that nanofiber technology can be effective as a barrier contraceptive. This fibrous network will serve as a platform to sustain the release of the hormonal contraceptive Levonorgestrel (LNG), providing a chemical barrier against unintended pregnancy. We quantify in-vitro via optical microscopy how effectively the fiber inhibits penetration by observing its interaction with sperm. To optimize the physical barrier properties of the fibers we investigate sperm penetration as a function or fiber thickness and pore size in order to obtain an optimized barrier contraceptive of the thinnest fiber and highest protection. We then look at how well the fibers sustain the release of LNG in-vitro such that the contraceptive is eluted over a span of 7 days. We will also investigate materials that can be encapsulated within the fiber barrier to expand and block the cervical os (cervix opening) for ensured protection against sperm. This system will swell to many times its original size instantaneously, providing immediate protection for the user upon insertion. Beyond contraception, we plan to further understand the capability of these materials to impede the penetration of HIV. By utilizing drug-eluting nanofibers we can produce a platform that acts not only as a contraceptive but also as a means of preventing the spread of HIV.

DNA origami is the fabrication of biochemical structures using DNA as the building material. Using base pair design principles, DNA can be synthesized to self-assemble into dynamic objects such as a piston. The resulting creations have potential applications in nanotechnology including drug delivery, enzyme immobilization, photolithography, environmental restoration, and biocompatible devices. The goal of this project was to design a nanoscale mechanical spring and determine the parameters for spring constant and size. First, a spring comprised of multiple columns of double-stranded DNA was designed and fabricated. Size measurements were taken and morphology was verified using a transmission electron microscope. To measure the force constant of this structure, the 5’ end of the first column was functionalized with a thiol group which was then bonded to a gold cantilever tip on an atomic force microscope (AFM). This construct was brought very close to a magnesium substrate and allowed to bond. Force measurements for the spring were taken via AFM by slowly retracting the cantilever from the substrate. The spring force constant was calculated from this data using Hooke’s law in order to predict the amount of work that the DNA nanospring can perform when included in a complex nanostructure. The nanostructures created in this project can be used in conjunction with other DNA origami designs in order to create increasingly complex machines on the nanoscale.

This abstract is no longer available. Please contact urp@uw.edu if you have any questions.

The Mefford lab is identifying the genetic mutations that cause early-onset epileptic encephalopathies. This is a rare class of epilepsy that is characterized by refractory seizures that often begin in infancy and carry a poor prognosis for the patient. We accomplish this by identifying de novo mutations in affected children using Sanger sequencing to compare the children’s DNA to that of their unaffected parents. This approach, however, lacks the sensitivity to detect genetic mosaicism. A mosaic mutation occurs post-fertilization and causes one’s body to contain cells with different genotypes from one another. These mutations can be difficult to identify with Sanger sequencing because they are often present at very low levels. However, recent advances in gene-sequencing technology has enabled us to detect mosaicism in patients at increasingly lower levels via deep sequencing using smMIPs (single-molecule molecular inversion probes), a technique that allows us to quantify the number of alleles assayed. Recent studies have reported that 1.7% - 10% of alleged de novo mutations were actually inherited from a mosaic parent, inspiring us to find the rate of falsely identified de novo mutations in our own research. We re-sequenced the parents in our cohort of 50 solved de novo cases using smMIPs to investigate how often the mutation had actually come from a mosaic parent. This revealed 10 parents as candidate mosaic carriers. We are still performing further testing on those parents and are adding more families to the study. Knowing the origin of a mutation is crucial for genetic counselors, and knowing whether a child’s epilepsy came from a de novo or a mosaic mutation in the parent can have huge effects on the recurrence risk of the disease. The data from this study will also help other researchers assess the accuracy of their research on disease inheritance as well.

With increasing age and as a result of mitochondrial-generated reactive oxygen species such as hydrogen peroxide, lung fibroblasts cells undergo DNA damage which is leading to a loss of function and premature ageing (senescence). The objective of this project was to assess whether the presence of the mitochondrial-specific antioxidant enzyme catalase (mCAT) could affect the levels of DNA damage and senescence in fibroblasts collected from the lungs of 24 month old mCAT mice versus control. Immunostaining of lung fibroblast cultures, using specific antibodies against markers of DNA damage/premature ageing showed, a significant decrease in DNA damage and a decrease in cell division in mCAT lung fibroblasts against control.
Aging is the most significant risk factor for developing cancer, and majority of malignant cancers that are treated in clinics, occur in older patients that are suffering from cellular senescence/aging and uncontrollable cell division, leading to cancer. Therefore, understanding the consequences of senescence may help with designing new strategies, such as anti-oxidant therapies that lead to prevention of DNA damage and age-related diseases, in the future.
 

This project consisted of examining how disability is excluded from discussion and curricula in a high school setting, in particular, when the focus is around sex education. Students, youth and even adults with physical and intellectual disabilities are not exposed to the same imperative information around sex, sexuality, and relationships that is required for healthy sexual development and intimate relationships that their non-disabled peers receive. Nor do curricula on sex education have information concerning disability specifically. I focused on analyzing issues of consent, policy and law, violence, and what ableist ideologies and stereotypes surrounding disability are imbedded in the institution of sex education. For my project I reviewed and analyzed scholarly literature, conducted interviews with educators as well as students with disabilities, utilized platforms of social media such as Twitter to gather data and information on educational resources and examined online sources on disability-centric sex education and curricula. Myths and stereotypes around disability were found to be contributing factors to the lack of discussion around sex and disability, specifically the myth that all disabled people are asexual. Additionally, because of the stigma attributed to disability, parents, educators, and health professionals felt unprepared and uncomfortable addressing anything regarding sex with youth who were disabled. I worked with the social worker and health educators at Mountlake Terrace High School to bring in a new perspective on sexuality and relationships around disability. I created and provided an introductory kit that consisted of scholarly work from my research around Disability Studies, information on how and what kind of language to use, fact sheets, and lesson plans and curriculum ideas for them to use as a starting point for implementing a more inclusive experience for disabled students.

Initially designed by Michelangelo, Santa Maria degli Angeli e Martiri is a Roman Basilica built atop the ruins of the Baths of Diocletian and represents a collaborative relationship between science and religion. The famous meridian line that extends throughout the church was constructed by Francesco Bianchini in order to validate the Gregorian calendar and more specifically, predict the date of Easter. Meridian lines are a variation of a sundial; a hole in the wall of the church that allows an image of the sun to transit the meridian line on the floor. The location of the image corresponds to a particular day of the year, calculated by Bianchini using the geometry of the hole’s placement. Additionally, a second hole in the wall allows light from the North Star to follow a pattern of ellipses at one end of the meridian line and traces the expected long-term path of the star. During a UW study abroad trip under joint-guidance of the Astronomy and Art History departments during Spring quarter 2015, students were able to take physical measurements of the meridian line. Using videos and images of noon solar transit, the accuracy of the meridian line was calculated with respect to predictive models in astronomy, with emphasis on the historical contexts of religion and art. Our inquiry includes quantitative analysis of changes in precession of Polaris, declination of the sun, and obliquity of the ecliptic, over several centuries. Ultimately, this project intends to investigate how the meridian line can provide an insight regarding the longevity and accuracy of scientific models as well as acknowledge the implications of scientific discourse on society, art, and religion.

Enzymatic pathways comprising multi-step biochemical reactions in biological cells constitute a key part of life. Biomimetic reconstruction of these metabolic pathways holds tremendous promise for developing sustainably powered devices. In biological cells, enzymatic components are kept in strict compartments or in serial networks. To mimic this complex hierarchical assembly of enzymes found in nature, a common approach is immobilizing these enzymes on the surface of porous substrates i.e., anodic aluminum oxide (AAO) membrane. However, one common limitation has been immobilization of multiple enzymes with a single type surface chemistry. As a result, these approaches have failed to provide enough capability to control spatial localizations of enzymes on AAO surfaces. Solid-binding peptides (SBPs) offer a novel solution to circumvent these problems with their exquisite recognition and long range solid-coverage properties. The ease of genetic conjugation of these short peptides with large proteins makes them an ideal candidate in utilization as molecular linkers in designing new multi-enzymatic devices. In this study, the utilization of a gold binding peptide (AuBP) as a molecular linker in combination with histidine-tag to immobilize Lactate Dehydrogenase (LDH) and Formate Dehydrogenase (FDH) enzymes on AAO based flow bioreactor was demonstrated. The efficacy of the described approach was tested by monitoring the sequential lactate and formate break down by LDH and FDH enzymes spectrophotometrically. The overall sequential catalytic conversion with greater than 90% yield was observed. Furthermore, the surface selectivity of the SBP conjugated enzymes were tested by visualizing their localization on Ni-NTA patterned gold surface using fluorescence microscopy. Cumulatively, this study highlights the utility of solid binding peptides as a molecular linker for addressable immobilization of multiple enzymes in the AAO based devices.

Danon disease, a form of cardiomyopathy, results in deficient blood flow due to the weakening of heart muscles and can lead to a shortened lifespan. In collaboration with the Song lab at the University of Colorado, we aim to better understand the differences in contractile function between healthy cardiomyocytes and those from individuals with Danon disease. The Song lab obtained primary adult cells from two control groups—healthy individuals without cardiac problems—and three diseased groups—people suffering from Danon disease. The patient cells were used to generate induced pluripotent stem cells (iPSC), from which they derived cardiomyocytes that possess genetic information of the original donor. The Sniadecki lab has the technology to make micropost substrates from polydimethylsiloxane (PDMS), using a soft lithography process. The iPSC-cardiomyocytes were seeded onto the microposts. As the cardiomyocytes contract on the microposts, each post under the cell deflects. Videos were taken at the tips of the microposts underneath the beating cells, to record the post deflection over time. A still image was taken at the bottom of the microposts in order to determine the relative deflection of each post. From the deflection of the posts, we were able to measure contractile forces produced by the iPSC-cardiomyocytes using simple beam bending theory. For this experiment, we used microposts with following dimensions: height = 4.14 μm, diameter = 1.75 μm, and center-to-center spacing of 6 μm. These dimensions gave each post a stiffness = 56 nN/μm, which was used to calculate the force. We hypothesized that the diseased cells will produce lower contractile forces than the control cells. The results produced supported our hypothesis. We hope this study contributes to the effect of Danon disease on the contractile function of cardiomyocytes. Further, this work would exemplify a methodology to investigate cardiac disease modeling and treatments.

3 million Americans and 65 million people worldwide have been diagnosed with epilepsy. In two-thirds of these patients, the causes of epilepsy, and therefore the therapeutic targets, are unknown. Recently, de novo mutations in the EEF1A2 gene, which encodes for a protein translation regulator, were found in several individuals with pediatric epilepsy and intellectual disability. In order to study how a mutation in this gene causes the neurological defects, we generated mutant eef1a2 zebrafish using the CRISPR/Cas9 method. Zebrafish models to study diseases have gained momentum due to their genetic similarity to humans, large amount of offspring in each generation, easy genetic manipulation and amenability to large-scale drug screens. Our initial in situ hybridization studies showed that eef1a2 has a limited expression pattern in the developing zebrafish that includes neurons involved in movement and escape behavior. To understand whether the mutation causes observable behavioral dysfunction or seizures, we tracked wild type (WT) zebrafish and heterozygous and homozygous mutants in various behavioral assays and genotyped tracked fish using Sanger sequencing. We are expecting that the mutants to have defect in movement and escape response. In a future study, the electrophysiology of the forebrain will be recorded to determine whether eef1a2 mutants reveal abnormal electrical discharge characteristic of a seizure. These studies with the zebrafish model will provide more insight about the EEF1A2 protein and its neurological function, and may lead to a better understanding of epilepsy etiology and the design of targeted therapeutic approaches.

For a community suffering from collective trauma, unity is vital for building community resilience, which is the capacity to withstand, recover from, and respond positively to a collective crisis. Both the Native American Tulalip community and the predominantly White Marysville community were affected by an October 2014 school shooting in which five students (3 Native American; 2 European American) died. We sought to identify factors that contribute to community resilience. We surveyed 597 employees of the Marysville School District and assessed perceptions of unity prior to and after the shooting, as well as personal experiences following the shooting (i.e., negative and positive feelings). My project focuses on the relation between people’s individual experiences and their perceptions of community unity following the shooting. I conducted a series of regression analyses predicting unity from personal experiences and found that people who had more positive feelings following the shooting perceived the communities as more united, while people who had more negative feelings perceived the community as less united. Furthermore, these relationships were magnified among people who knew at least one victim of the shooting compared to those who did not know victims. These findings suggest that in cases of collective trauma, projections of negative feelings following the event have the potential to hinder efforts to rebuild the community, whereas positive feelings may serve to aid this effort, especially among people who are closely tied to the traumatic event. These results highlight the importance of understanding how to foster positive feelings in the promotion of post-trauma healing. Given the frequency of mass violence in contemporary society, it is increasingly important to examine not only preventative measures but also understand how to promote healing for those affected by these tragedies. This work seeks to begin answering this question.

Antibiotics are present in nearly every facet of our lives including personal hygiene, medicine, food processing, and the treatment of infectious diseases. Because of this widespread exposure, antibiotic resistance occurs in dangerous pathogens around the world. Novel antibiotics are needed to combat these resistant organisms and reduce both the loss of lives and treatment costs. Most antibiotics originated in microorganisms cultured from soil, but very few novel compounds have been discovered in this environment over the last several decades. It is imperative that other environments are screened for antibiotic producing microbes. We sampled the Puget Sound, isolating and culturing bacteria from the surface. Isolated cultures were tested against reference strains of common pathogens for antibiotic potential by measuring the zones of inhibition they produced via agar diffusion. Phylogenetic analysis with 16s ribosomal RNA was used for identification of cultures with inhibitory activity. This type of analysis, especially if scaled-up, has potential to identify novel therapeutic compounds that may elude common resistance mechanisms.

Individuals with impaired finger function are commonly prescribed a wrist-driven orthosis which utilizes wrist movement to open and close the fingers. However, if the individual has weak wrist extensors and flexors in addition to weak fingers, this device becomes obsolete. While multiple prosthetic devices are available to amputees, options for orthotic devices are limited. The purpose of this research is to adapt elements of successful upper limb prostheses into an open-source orthosis made with 3D printed and off the shelf materials for an individual with unilaterally impaired hand and wrist function. We continue to draw inspiration from body-powered prostheses, where the motion of other joints, such as rotation of the elbow, is used to control artificial hand motion. Gaining hand motion through the use of this device will allow users to perform daily tasks independently and with improved performance. We first created a series of prototypes to identify task specific designs. An optimal design will utilize elbow or shoulder movement to operate a low-profile hook positioned under the palm while also stabilizing the wrist and fingers which are flaccid. Input from practitioners aided in optimizing the design and process. In order to augment design acceptance, our research included user testing and feedback. Once a design was finalized, we resized the device to fit our participant. The participant then went through a series of hand functional tests which compared their ability to complete an assortment of tasks, such as lifting and moving small blocks, with and without the device. These results as well as user feedback assisted in further improvements to the overall design of the device. After completing our design, the orthosis was made open-source to make it both accessible and low-cost, while allowing users and makers to further improve upon the device.

We are investigating adverse event (AE) reporting in clinical trials on cystic fibrosis (CF) to address whether specific approaches to coding AEs prior to un-blinding of study data is informative. While attribution standards are available in the Common Toxicity Criteria; there are no formal guidelines on how this determination should be made. The process of reporting attributions increases both time and cost of the trial although it is uncertain whether this process is accurate or valuable. This is a retrospective data repeated measures data analysis with pooled clinical trial data from four randomized controlled trials involving patients with CF. We will employ descriptive statistics to describe the overall population and demographics from individual studies who experienced at least one adverse event and summarize the adverse event rates over all and per study by individual rates. We will also employ repeated multiple variable regression techniques to describe associations of demographic and clinical characteristics with the attribution of AE’s. We hypothesize that physicians are not very good at attributing these events when the patient is on the placebo. We currently have available data on 11,974 adverse events in 785 subjects in the four randomized controlled trials. This study could have implications to how clinical trials are conducted in the United States. A future goal would be to clarify the value of attribution of adverse events in clinical trials.

The research sought to understand the mechanisms through which human glioblastoma (GBM), a highly aggressive primary brain tumor, are resistant to post-operative radio- and chemotherapy. While many new treatment protocols for GBM have been developed over the years, none have made a substantive difference in survival. As a result, the prognoses for these types of cancers remain very grim with most patients surviving for 9 to 15 months. To gain a deeper understanding of factors that promote this poor prognosis I investigated the contribution of DNA repair activities to resistance to alkylating agents and radiation that are used to treat human GBMs. One DNA repair protein of particular interest is O⁶-methylguanine-DNA methyltransferase (MGMT). MGMT's repair mechanism works by removing the cytotoxic O⁶–methylguanine DNA adducts. The use of exogenous DNA containing ³H-labelled O⁶-methyguanine allows me to approximate the amount of MGMT molecules in tumor homogenates. The assay exploits the fact that MGMT transfers a methyl group to the cysteine of the protein’s active site from the O⁶ position of guanine. I worked in lab to optimize the assay for GBM homogenates. Through this research project, I hope to establish a standardized assay that is optimal for determining the MGMT activity in homogenates of glioma tissue that can be widely implemented. To this end, I investigated the impact of assay salt concentration, the presence of tumor, incubation duration and repeated freeze-thaw cycles on homogenate MGMT activity. The suppression of the glioma MGMT DNA repair capacity can potentially help in the development of new treatment protocols, thereby improving the treatment outcomes for individuals with malignant gliomas.

How do Seattle’s urban gardens impact public health and who has access to these gardens in the midst of gentrification? This research project analyzes the public health impacts of urban gardens and their utility in the midst of gentrification in Seattle’s Central District and South Seattle neighborhoods by assessing the ways that building a collective community through gardening can produce positive health outcomes. In order to address population health in the contexts of gentrification and access to food a systematic literature review was done to assess environmental and socioeconomic impacts that gentrification has on communities’ access food and health disparities. By using an Observational method of the Central District/South Seattle and urban gardens within these communities to obtain an analysis of the social ecological model addressing the ways that individual, intrapersonal, organizational, community and policy influence heath outcomes and access to food and urban gardens within a gentrified space. The expected results of this study will provide a better understanding of gentrifications connection to health disparities and impact on food access. Additionally it will assess how urban gardens function as an important site for producing health outcomes beyond the cultivation of nutrient rich crops. Implications of this research will provide a preliminary assessment of gentrifications limit on access to food in Seattle and urban gardens utility to improve food access, health benefits and equity with the community.

Hair cells are mechanosensory receptors in the inner ear used for hearing and balance. When hair cells are damaged or die, hearing is lost or impaired. Many studies have also shown that genetic mutations affecting mitochondrial function are another cause of hearing loss. However, it is unknown which cells in the auditory system are affected. In this study, we sought to determine whether or not these deafness-causing mutations impact hair cells. To do so, we took advantage of zebrafish as a model system and studied hair cells of the lateral line. To generate mutant fish, we used the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR)/Cas system, a genome editing tool that allows for gene-specific changes to be made to DNA. If these mutations do affect hair cells, we predict to see changes in mitochondrial and hair cell function. Characterizing these mutations in zebrafish will inform our understanding of the cellular mechanisms of hearing loss.

Engineering metabolic pathways in bacteria requires regulation of cellular biology with predictable genetic control devices. Characterizing these controls is key to optimizing biochemical pathways for the sustainable production of high value chemicals. In prokaryotes, small RNA (sRNA) downregulate gene expression by antisense binding to messenger RNA (mRNA) transcripts. The relative ease of re-engineering sRNA targets by replacing its antisense targeting sequence makes sRNA an ideal candidate for implementing post-transcriptional controls in metabolic engineering. In previous work, we incorporated sRNA into metabolite-responsive RNA controllers, but in many cases did not observe the hypothesized trends in mRNA repression. However, we observed the lack of secondary structure within the antisense targeting sequence correlated with higher mRNA repression. To understand these effects and refine the functionality of our constructs, we built a range of new sRNA devices with additional sequence at the 5’ end. We targeted the sRNA to repress fluorescent protein expression, and used functional assays to measure fluorescence across a range of sRNA induction levels. We hypothesized that sRNA carrying a 5’ hairpin will result in greater repression than sRNA lacking structure at the 5’ end, and that base-pairing interactions between the 5’ sequence and the targeting sequence will lead to lower repression. This work aids in the development of rational design principles for using sRNA in RNA-based controls. By understanding the effects of sRNA structure, we will be better able to expand the post-transcriptional controls available to metabolic engineers. Ultimately, this extends our understanding of cellular biochemistry, while providing novel means by which to optimize engineered biochemical pathways.

Currently, about 90% of the world languages are endangered and many are quickly vanishing. Language Endangerment is considered one of the most urgent problems in humanities. We aim to design and develop web services on a cloud platform to process endangered language recordings and extract audio features to facilitate effective language documentation and analysis. To achieve this goal, in my project, we deployed Praat audio analysis components into a cloud-based web application. Praat is a linguistics tool that has been widely used by researchers to analyze sound samples. However, Praat is a standalone application, and does not expose any libraries or services to be used in third-party applications. We deployed Praat audio analysis components as web services in the Azure cloud platform that can be integrated into any application that supports HTTP communication. We have also designed a web UI for general users to access Praat component via web browsers. With these Praat components, users can not only view the spectrogram of a specific soundtrack but also its pitch, intensity, formant, pulse and waveform within a same screen. Users can also zoom in, zoom out or select a specific time range of a soundtrack based on individual needs. In addition, all such information can be saved or printed for future access or sharing among users. In our future work, we plan to deploy more Praat functions and other linguistics tools to our web application and further improve the efficiency and availability of our web services.

Cancer is a leading cause of mortality worldwide, and the number of new cases is projected to reach 22 million in the next two decades. Surgical resection of tissues is a standard of care for treatment of a variety of cancer patients. For the prostate, surgically removed tissues usually undergo a process of bread-loafing (cutting into 0.5-1.0 cm thickness), chemical fixation, embedding in paraffin (wax), sectioning (5-10 μm thick), staining, slide mounting and finally microscopic examination to determine whether all tumor growths have been excised. The procedure is labor-intensive, time-consuming and expensive. In addition, the majority of the prostate specimens are normal tissues that do not require detailed microscopic examination. These factors reveal the need to significantly accelerate the screening process and increase the efficient use of healthcare resources. Therefore, to reduce unnecessary processing time and costs, we proposed a fast and inexpensive imaging system to screen the surface of thick tissues for abnormality, before full histological processing. This system was designed to enable a wide imaging area and integrate deconvolution algorithms, which achieve high contrast and resolution. More specifically, the project was carried out in three phases: 1) design, construction, and optimization of a fluorescence microscope; 2) system calibration and optimization of deconvolution algorithms; and 3) system validation using fresh human tissues. The system is capable of generating a 1 x 1 cm² image in a few minutes with 4 nm resolution. Success of such a system will facilitate clinical translation and increase efficiency of histopathological procedures, which are beneficial to both patients and healthcare providers.

The rise of multidrug resistant bacteria necessitates finding alternative therapies against bacterial pathogens. Virulence in many pathogenic bacteria are predicated on their ability to communicate and act in unison. In a phenomenon known as quorum sensing (QS), a threshold mass of bacterial cells produces an amplified chemical signal that triggers the collective expression of a new phenotype, such as enhanced virulence. Therefore, inhibiting QS, without preventing cellular growth, may be a recourse against drug resistant bacteria. Marine invertebrates found in warmer waters, such as the Australian reef and Indian Ocean, have shown quorum sensing inhibitory (QSI) potential. However, most marine invertebrates in the Pacific Northwest’s Puget Sound have not previously been screened for QSI compounds. This research presents the findings for QSI sources among Puget Sound’s marine sponges and tunicates, using a bacterial reporter strain to screen for QSI activity. We used the reporter strain Chromobacterium violaceum (ATCC 12472), which uses the QS signal n-Acyl-homoserine lactone (AHL) to produce its purple pigment. QSI activity was screened for by overlaying the reporter strain with a sponge or tunicate sample. Subsequent absence of pigment in the indicator strain suggested the presence of a QSI compound. Promising compounds were then extracted and identified using analytical techniques. These results help expand the catalogue of known QSI molecules from marine sources, advancing potential therapies against existing and future antibiotic resistant pathogens.

The majority of the population living with HIV resides in African countries where the cost-effectiveness and ease of implementation of the technology is imperative. Our goal is to develop an assay that eliminates the need for expensive nucleic acid sequencing technology, to test and diagnose drug resistance by detecting variation in nucleic acid sequence of the virus. One of the missing pieces that will allow us to reach this overarching goal is to design a method for isolating the viral particles in a manner appropriate for point-of-care application. Our approach, which will contribute to the assay being developed at the same time, is to use protein G magnetic beads, which are affinity molecules, to isolate the HIV virus from plasma sample. The protein G on the magnetic beads interacts with the coat antibodies on the viral particles and facilitate their removal from plasma. We show that the protein G magnetic beads have comparable efficiency at isolating the viral particles compared to the gold standard, Qiagen extraction, without the use of strong chemical reagents and complicated instruments. Yet, further work is needed to demonstrate that the viral RNA can be extracted starting from clinical plasma specimens with a protocol applicable in point-of-care settings defined by limited use of complicated insturments and cost effectiveness of the solution. 

This research uses the SPA System (Sustainability Performance Assessment, Paun 2015) to assess sustainability performance for three natural resource-based case study companies in Asia, Europe, and the United States. The SPA System is built on the Global Reporting Initiative (GRI) framework, and consists of 91 performance measures in three categories: economic, environmental, and social. The economic dimension of sustainability concerns impacts on the economic conditions of stakeholders, and on local, national, and global levels. The environment dimension concerns impact on living and non-living natural systems, related to inputs (e.g. energy, materials, water), outputs (e.g. emissions, effluents, waste), biodiversity, transport, and environmental compliance and expenditures. The social dimension concerns the impacts on social systems within which the firm operates and includes labor practices, human rights, product responsibility, and society. The sample consisted of three case study companies from three countries: China Steel (Taiwan), Fairmount (U.S.), and Givaudan (Switzerland). Data was extracted from their annual sustainability reports. China Steel reported the highest percent of GRI indicators (97%) and had the highest mean sustainability performance (3.1). It reported more than double the indicators as compared to the other two case study companies, indicating substantially greater transparency. Fairmount, a U.S. producer of sand-based products for the energy and building construction industries, reported on the fewest percent of indicators (20%) and had the lowest sustainability performance mean (0.7). Givaudan, a Swiss company that produces flavors and fragrances, reported on 37% of the GRI indicators and had the middle mean sustainability performance. Using SPA means stakeholders can assess and compare sustainability performance among companies, thus enabling better, more informed decision making (e.g., which companies to buy from, work at, invest in, lend to).

The plant hormone auxin plays a role in nearly every aspect of plant growth and development. Auxin facilitates interactions between two protein families: the transcriptional repressor Aux/IAA family and the auxin receptor TIR1/AFB family. TIR1/AFB proteins act as the substrate recognition subunit of SCF ubiquitin ligase complexes. SCF^TIR1/AFB-auxin-Aux/IAA interactions lead to ubiquitination and degradation of Aux/IAA proteins, allowing transcription of auxin-responsive genes. Each of these protein families is comprised of many functionally distinct members, allowing auxin to drive numerous developmental responses in plants. This complex network can be decomposed and signaling dynamics of individual pairs of TIR1/AFB and fluorescently-labelled Aux/IAA proteins can be measured in a yeast synthetic system using time-lapse flow cytometry. This dynamic analysis can give insight into the behavior of developmental networks in planta. However, of the six TIR1/AFB genes in the model plant Arabidopsis thaliana, only TIR1 and AFB2 induce degradation of Aux/IAAs in yeast. We aim to engineer a variant of AFB5 that is functional in this synthetic system, as AFB5 is known to be the target of many agriculturally important herbicides, but little is known about its role in development. We hypothesize that AFB5 is non-functional in yeast because it cannot form an SCF complex with the native yeast proteins. This is potentially caused by the extended N-terminus of AFB5 or the sequence divergence within AFB5’s SCF binding domain. To test these hypotheses, several N-terminal truncations of AFB5 and chimeric AFB5 proteins with the SCF binding domain replaced by that of AFB2 or TIR1 will be individually tested for their ability to induce degradation of Aux/IAAs in yeast. Functional variants will allow identification of key AFB5-regulated Aux/IAAs and associated developmental networks. Additionally, this work will guide engineering and allow functional characterization of the remaining Arabidopsis AFB genes and AFB genes from other plant species.

Most of the tissues in our body contain adult stem cells that in theory could combat many aging phenotypes observed in human. However, these stem cells do not regenerate the tissue during aging. To understand, and in the future govern adult stem cell regenerative capacity we need to study the regulators of human adult stem cells. DPSCs are adult mesenchymal stem cells with powerful regenerative capacity that can easily be isolated from waste product, extracted wisdom teeth. Due to low cost and easy accessibility, dental pulp is a more feasible source for mesenchymal stem cells than bone marrow. DPSCs are thought to have the ability to differentiate into multiple cell lineages, and thus hold great promises in tissue regeneration. However, little is known about the molecular markers, cellular regulators, and differentiation capacity of these cells. The goal of my research project is to generate a large diversity set of DPSC to carry on a careful analysis of true common markers and differentiation capacity of these cells. At the moment I have optimized the procedures and isolated DPSCs from over 50 patients in partnership with UW dental clinic. We have now identified the molecular markers of DPSCs, and evaluated their differentiability to better understand the key criteria in the self-renewal and differentiation capacity of these cells. Western blot and flow cytometry analysis shows that most of our DPSCs have a robust expression of CD29 and CD146, both molecular markers of mesenchymal stem cells, but displaying an unexpected diversity on the levels of these markers among individuals. In differentiation tests, we also observe diversity in cartilage and adipocyte differentiation efficiency. With this unprecedented diversity set of easily accessible adult stem cells we will now identify the key components and metabolites that enhance the stemness and regenerative capacity of these adult stem cells.

Argonaute (AGO) proteins are known to function in many small RNA pathways. AGO4 (Argonaute 4), a specific Argonaute protein, is mostly used for transporting small interfering RNAs (siRNAs) in the RNA-directed DNA Methylation (RdDM) pathway in Arabidopsis thaliana. siRNAs are primarily used for RNA regulation, such degradation of mRNAs in a cell. After directing the siRNA to the appropriate DNA location, AGO4 proceeds with recruitment of Pol V and DRM2 for methylation of the DNA, resulting in silencing genes. ago4 mutants are generally more vulnerable to harsh stresses, but recent phenotypic analysis suggests they demonstrate a better survivability under cold stress. Currently, we are investigating whether COR genes are present at higher baseline levels than the non-mutants and if they play a major role in this phenotype difference. Using RNA extraction and PCR with COR78 genes, we will measure the present baseline COR78 in each plant and draw a comparison. We expect that the mutants have a higher baseline of COR78, thus allowing them to have a better survivability in colder temperatures. Although additional investigation is required, COR gene interactions have a vast network that triggers later responses that might affect cold temperature resistance.

Transformations over assembly code are common in many compilers. Such transformations are useful in applications ranging from peephole optimizations to software fault isolation. These transformations are also some of the most bug-dense compiler components. Such bugs could be eliminated by formally verifying the compiler, but state of-the-art formally verified compilers like CompCert do not support assembly-level program transformations. This paper presents Peek, a framework for expressing, verifying, and running assembly-level program transformations in CompCert. Peek contributes four new components: a lower level semantics for CompCert x86 syntax, a liveness analysis, a library for expressing and verifying peephole optimizations, and a verified peephole optimization pass built into CompCert. Each of these is accompanied by a correctness proof in Coq against realistic assumptions about the calling convention and the system memory allocator. Verifying peephole optimizations in Peek requires proving only a set of local properties, which we have proved are sufficient to ensure global transformation correctness. We have proven these local properties for 26 peephole transformations from the literature. We discuss the development of our new assembly semantics, our liveness analysis, representation of program transformations, and execution engine, describe the verification challenges of each component, and detail techniques we applied to mitigate the proof burden.