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.

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.

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.

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.

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.

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.

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.
 

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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. 

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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. 

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.

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.
 

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. 

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.

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.

 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.

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.

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. 

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.

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.

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. 

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.

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.

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. 

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.

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.

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.

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.
 

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.

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.

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.

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.

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.

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.
 

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.
 

 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.

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.

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.

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. 

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. 

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.

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.

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.

In 1996, a scandal involving members of the Congressional Asian Pacific American Caucus triggered the United States Senate to launch an investigation. In the scandal, Asian American campaign contributors were accused of funneling foreign Chinese funds in an attempt to hijack U.S. politics. The Senate investigation concluded that several Asian Americans were committing espionage by colluding with the Chinese government as political spies. This research asks how the U.S. Senate concluded that these Asian American contributors were spies. My findings suggest that the Senate’s conclusion rested not on sound inculpatory evidence but a historic racial logic of Asian Americans as politically suspect. I argue that the “model minority” stereotype centrally informed the Senate’s racial logic of Asian Americans in their investigation. In particular, the model minority stereotype celebrates the industrious work ethic of Asians while condemning political participation as a dangerous behavior. My research thus explores the informative role of the model minority stereotype in the U.S. Senate’s investigation of the 1996 CAPAC’s scandal. My findings imply that the model minority stereotype ideologically disenfranchises Asian Americans within the American polity. In effect, Asian Americans are disproportionally scrutinized in the political arena through a racial logic that casts them as foreign, suspicious, and disloyal to the polity.

In the South China Sea, has the Association of Southeast Asian Nations (ASEAN) Regional Form been effective in crisis management since its inception in 1993? If so, to what extent? It is the only current multilateral framework for potential conflict management in the South China Sea disputes particularly with regard to island settlements between China and other claimant nations including the Philippines, Vietnam, Malaysia, Brunei, and Taiwan. This research will shed light on how effective this multilateral framework has progressed since its creation in achieving its mission of resolving regional conflicts and the implications this has for US foreign policy. The research relies on current scholarship and on expert interviews. The ASEAN Regional Forum is a work-in-progress in resolving regional conflict, especially island disputes in the South China Sea. Its operating emphasis on consensus-building and the ‘ASEAN Way’ assures that both weak and powerful nations alike are involved. Yet, differences between rival nations threaten to dismantle the positive influence it has potential to wield in the region. This has strong implications for the US ‘Asia Pivot’ and the continued influence of the US in the East Asia region as the forum is valuable in articulating US interests including adherence to international law under The United Nations Convention on the Law of the Sea.

Since 1904, when the first voter-sponsored bill appeared on the ballot in Oregon, the frequency of initiatives and referenda has greatly increased, most especially over the last 40 years. While there were only 98 bills voted on nation-wide between 1960 and 1969, over 370 initiatives made it onto state ballots between 2000 and 2009. My research examines several underlying causes of this rising frequency in order to help understand trends in the increasing use of direct democracy. Previous work has focused on the increased participation by moneyed interest groups who use paid petitioners to circulate legislation; however, I am proposing a new, original theory which connects political alienation and dissatisfaction of representative democracy to increased participation in direct democracy. I have built an original dataset which will combine measures of polarization within government, public trust in Congress, and the number of initiatives and referenda throughout the multiple states in which they appear. With this dataset, I ran multivariate regressions to analyze statistical significance in the relationships between these variables. I expect to find that as political polarization in Congress increases, people will lose faith in traditional modes of representative democracy. I further hypothesize that as trust in government decreases, people are more likely to turn to modes of direct democracy to instill change in government, therefore increasing participation in the initiative and referendum process. If my hypothesis is correct, my research would serve as a tool for political scientists to use to predict the rise or fall in the political activity of voters, the implications of which could influence timing of legislation, outreach efforts, and a number of other participation-related issues.

Traditional political participation is at an unprecedented low among American youth. But while youth voter turnout is suffering, alternative forms of political participation are on the rise—namely, political consumerism, the intentional buying or abstention from buying specific products for political, social, or ethical purposes. This research seeks to understand the motivating factors behind the youth shift toward political consumerism as a means of representation. Three possible explanations were tested: First, youth choose political consumerism because they receive immediate material benefits from the products and services they buy, a feature absent from traditional participation. Second, youth choose political consumerism because of convenience; they have too many other pressing priorities to engage in more time-consuming forms of participation like voting or writing to officials. Third, youth choose political consumerism because they prefer corporate actors over political actors to enact change because the latter has failed them. In order to test these explanations, I conducted a public opinion survey, interviews with leaders in consumer advocacy, and research on the evolution of youth political participation and consumerism. The analysis finds that the second hypothesis has the most explanatory power. Youth recognize that corporate actors have significant influence on political outcomes, but usually opt for convenience when it comes to making politically-informed consumer decisions. If sufficient information about the political context of products and services is given to youth, it affects their decision-making process. A surge in political consumerism among youth can be consequently be explained by a surge in available information due to the Internet and social media platforms. The results of this research demonstrate the importance of information framing in the digital age, efforts by companies to appeal to young consumers on a political level, and the relationship between political knowledge and participation.

This research project explores disenfranchisement in America. Today, citizens living in unincorporated US territories (Guam, Northern Marianas Islands, US Virgin Islands, Puerto Rico, and American Samoa) are considered “second-class Americans,” having all other fundamental rights as mainland Americans do except federal voting rights. To help understand this phenomenon, this project examines the circumstances under which the political elite had extended suffrage or had established additional protection for minority voters since the early 1900s. Since then, women, African-Americans, 18-year olds, and citizens living in US territories have used different movement techniques and strategies to achieve suffrage, such as establishing conventions, organizing violent and nonviolent protests, and committing to quid pro quo services like serving the country in times of war. This closes in on a theory where political will—defined as the mobilization of mass movements to gain the right to vote—helps explain why Congress votes to extend suffrage to previous disenfranchised groups. This variable is operationalized by counting the number of organized events and the number of people in the group lobbying for suffrage during the year prior to a congressional vote on the floor. I hypothesized that the greater amount of political will present in a year, the more bills will be introduced in Congress. The time frame of data used in this project is from 1910-2015. This presentation can serve as a guide to explain when suffrage extension happens, and what disenfranchised groups did to get what they wanted from big government.

 Respiratory dysfunction is the leading cause of death in the acute phase of high-cervical spinal cord injuries (SCIs). While survivors of high-cervical SCIs regain some of their respiratory function, many individuals require assisted ventilation. Despite the fact that there are currently many ongoing treatments, more needs to be understood about the anatomy and physiology of the respiratory pathways in the spinal cord in order to find cures for those suffering from high-cervical SCIs. Recent rodent studies using intra-spinal micro-stimulation (ISMS) for forelimb motor recovery has shown moderate functional recovery. In this study we mapped the motor neuron pools of three muscles used in respiration along the cervical and upper thoracic spinal cord. Additionally we explored the extent to which we can activate those muscle with ISMS in spinally intact rats.

Area V4 is a cortical region that carries out intermediate visual processing along the ventral ("what") visual pathway. It integrates information about boundary and surface features from the primary visual cortex and sends signals downstream to the inferior temporal cortex, which supports complex object recognition. Neurons in area V4 have been shown to encode the boundary curvature of 2-dimensional (2D) shapes in an object-centered coordinate system. For example, a neuron may prefer a wide variety of stimuli that have a protrusion (convexity) to the upper right. Our goal is to determine whether this type of boundary representation along 2D boundaries also applies in three dimensions (3D). We also aim to determine whether the same V4 neurons that encode 2D shapes also encode 3D form, or whether there might be separate populations activated by 2D and 3D form. To address this, we created a set of images of spheres that are deformed by the addition of a dent or protrusion. We varied the pose and the direction of lighting. The images were based on wire-frame models created in Blender. We recorded responses from single neurons in the fixating macaque monkey using a novel set of 156 3D images and a set of 230 2D images have been studied in previous experiments. We found that our 3D stimulus set elicited robust differential responses from V4 neurons. Some neurons responded better to 2D shapes without surface shading, while others preferred 3D shapes. Our next steps are to determine whether responses 2D and 3D shapes can be explained with one unified model. Ultimately, we want to understand how neurons encode natural scenes, and studying responses to such parametric, naturalistic stimuli brings us closer to achieving that goal.

Hot flashes (HF) are acute vasomotor disturbances that cause facial flushing and sweating. They commonly occur in menopausal women as a result of a decreased production of estradiol from the aging ovary, which triggers an acute malfunction in the brain’s control of body temperature. However, the molecular and cellular mechanisms that generate HF are poorly understood. Recent studies suggest that super-activation of KNDy neurons in the hypothalamus, which occurs in response to either reduced levels of estradiol or artificial stimulation, can disrupt thermoregulatory centers in the brain. To test this, we are developing an optogenetic animal model for HF aimed at understanding their physiological origins and enabling preclinical testing of potential therapeutics. We have created a transgenic mouse that has a light-sensitive membrane channel (channelrhodopsin-2) inserted into KNDy neurons, which can be activated with a fiber optic probe inserted into the brain. Selective activation of KNDy neurons and the subsequent behavioral response of the animal along a thermal gradient allow us to explore the role of KNDy neurons in thermoregulation. We hypothesize that following activation of KNDy neurons, the thermoregulatory set-point for excess heat perception will be lowered, so the animal will move to a cooler place along the gradient. We have preliminary evidence to suggest that when activated with a different technology (Designer Receptor Exclusively Activated by Designer Drugs) animals do, in fact move to cooler temperatures. Testing this hypothesis is our primary objective. We believe development of an animal model for hot flashes will aid our understanding of their neurobiological basis and foster development of better and safer therapeutic options for treatment.
 

Motor behavior is the result of neural programs emerging from the Primary Motor Cortex (PMC). To generate behavioral outputs the PMC integrates exogenous and endogenous sources of variance. Electrical activity from the PMC has been effectively used to operate minimally invasive brain-machine interfaces (BMIs) that can operate prosthetic limbs to achieve basic motor outcomes such as operating a joystick.  Further development of neuroprosthetic technology will rely on a deep understanding of sources of variance to the PMC and how the PMC compensates for this. The circadian system regulates physiology and behavior within the 24-hour time frame and it represents a predictable source of endogenous variance for the generation of motor behavior. The specific pathways by which the circadian clock(s) may modulate PMC motor programs is not understood, but preliminary results from our lab show that the circadian system modulates the PMC electrical activity associated with wheel running in mice. We implanted electrocorticographic (ECoG) electrodes onto the PMC of mice and recorded electrical activity while they ran on a wheel at different circadian times. This showed that the PMC electrical signals associated with wheel-running are modulated in a predictable manner by the circadian system. I propose to replicate these experiments in mice with a malfunctioning circadian clock. I hypothesize that the canonical molecular circadian clock is essential for this modulation. To test this hypothesis, I used ECoG electrodes to record PMC electrical activity of Bmal1^-/- mice, which have no copies of the clock gene BMAL1, and their wildtype (Bmal1^+/+) littermates. This determines whether the circadian modulation of the PMC depends on an intact molecular circadian clock. Understanding the regulatory effects of the circadian system on PMC brain wave activity is crucial for the design of BMIs and their effective operation throughout the 24-hour day.

Pain catastrophizing has been associated with increased pain experience and expression in children with chronic pain. Parental catastrophizing about child pain has been associated with increased parental distress and overprotection. This study sought to understand how catastrophizing might be reflected in pain-related parent-child communication. 70 children with chronic abdominal pain and their mothers participated. Mothers and children independently completed child- and parent-report versions of the Pain Catastrophizing Scale. Dyads then conversed for 10 minutes about the child’s pain. Conversations were audio-recorded, transcribed and reduced using a linguistic analysis program. Dependent variables were the percentage of negative affect words uttered, including anxiety, sad and angry words such as worried, grief and mad, respectively. Multilevel modeling was used to estimate an Actor-Partner Interdependence Model assessing the effects of role (mother versus child) and catastrophizing on the percentage of negative affect words uttered during the conversation. Main effects of role emerged for the higher level category of negative emotion words and the subcategory of sad words (p values < .001), such that mothers uttered more of these words than did children. A main effect of catastrophizing also emerged for negative emotion words, such that those higher in catastrophizing uttered more negative emotion words than did those lower in catastrophizing, regardless of role (p < .01). The analysis for anger words was more complex, yielding role x actor and role x partner interactions (p values < .05). In essence, maternal catastrophizing was positively associated with both maternal and child anger word usage, whereas child catastrophizing was inversely associated with maternal anger word usage. Findings extend the literature on behavioral and interpersonal correlates of catastrophizing. Future research is needed to fully elucidate parent-child interactional patterns in the context of chronic pain. Findings could inform the design of cognitive-behavioral interventions aimed at reducing symptoms and disability.

Public policy for families has shifted focus to population level evidence-based parenting interventions (EBPIs). EBPIs have been proven to reduce child maltreatment and improve emotional and behavioral health in research. As a result, there has been an increase in individuals trained in EBPIs, but this has not translated into successful implementation of EBPIs in the real world. One factor in the successful implementation of EBPIs is the practitioner’s perceived self-efficacy in delivering the intervention. One EBPI with the potential to saturate at the population level is Triple P. Triple P (Positive Parenting Program) is a multi-level parenting intervention designed within a public health framework that allows individuals to deliver the intervention within the communities they reside in. In this exploratory study, we hypothesize that individuals in certain work environments will report differential levels of self-efficacy in the delivery of Triple P post training. Our sample population was comprised of individuals from five different work environments, including social services, health, education, and youth offending. They completed surveys on self-efficacy across three time points: at baseline, immediately following training, and 6-8 weeks after training. Results of the study will attempt to seek if work sector may be an influencing factor on an individual’s self-efficacy following training in delivering Triple P. This is important because the qualities of Triple P training are highly generalizable to other EBPIs, thus this study increases knowledge about the role of promoting self-efficacy when supporting successful implementation. The consideration of work environment in implementation science can be used to determine what changes should be made for conducive implementation of interventions.

“Human Libraries” are interactive, community-based events in which ordinary people gather to share information and discuss ideas face-to-face with members of the community they wouldn't typically interact with. Created in Denmark in 2000, they have since spread around the globe, reaching the U.S. in 2008. This project examines several Human Libraries that have taken place across the U.S. and tries to determine which elements are most responsible for the events’ success. Findings for this research are based on interviews with several Human Library organizers, participant observations at a Human Library event in Vancouver, B.C., and an analysis of the commonalities shared between multiple Human Library events throughout the United States. The results of this research will help Human Libraries reach their full potential by providing organizers with a strengthened set of best practices and successful case studies on which to model their own events.

Raves are a carnivalesque liminal space wherein socially constructed differences between participants such as race, class, and gender are intentionally (if imperfectly) deemphasized. This phenomenon allows for social bonds to be formed based on a perceived “common humanity.” A highly structured kinship system emerges out of this discourse and is generally based on the ideology of PLUR(R) (Peace, Love, Unity, Respect, and Responsibility). This philosophy or code of ethics emphasizes caring for others and in practice has been an internal mechanism for safety in the community whereby ravers educate and protect each other through positive social policing. The strong sense of belonging and community created within this space is often overlooked by media and therefore, public perception of this community is often based on misunderstanding and associations with illicit drug usage. In order to better inform harm reduction strategies, this study illuminates these kinship bonds and how these bonds impact safety at raves in Seattle, Washington using qualitative ethnographic methods such as interviews and participant observation. Through gathering this data of first hand experience in the rave community, systems of public safety can better tailor harm reduction strategies to be more effective.

Lost, confused, lonely, and out of place: these are sentiments felt by many transfer students as they try to acclimate to the University of Washington. Adjusting to a new institution can be a difficult process to undergo alone. For transfer students, the inability to acclimate or the delay in acclimation can result in higher levels of stress, poor academic performance, psychological instability, and unbalanced social well-being. In response to these issues, my senior project investigates how current University of Washington transfer students can help incoming transfer students acclimate to the university. Drawing on the Transfer Students United organization (the first transfer student club at the UW), I conducted surveys and focus group interviews with current UW transfer students in order to better understand their experiences acclimating to the UW and identify their specific needs as incoming transfer students. Based on the results of this research, I then proposed several social and psychological focus areas for the Transfer Students United organization to incorporate as they create resources and services for transfer students.
 

In preparation for the 2021 opening of a new light rail station, the University District community in Seattle has begun to address safety and cleanliness concerns in the alleyways around the station and in the neighborhood as a whole. This project contributes to that effort by identifying areas of particular concern and recommending steps that the community and city can take to address them. Specifically, working with the U District Partnership, a local neighborhood non-profit, I have focused on cleanliness and safety in the alleyways. I then completed a more specific analysis of two alleyways in Seattle identified as being particularly clean and safe. The findings of this analysis were combined with best practices derived from literature on neighborhood safety and used to develop several design and policy solutions for the neighborhood alleys. Finally, these solutions were applied to a single alleyway closest to the future light rail station, providing both a guide for the development of this space as well as a case study for other alley improvements in the University District.

One of the central tenants of modern urban planning is that communities and citizens should be involved in the planning process, in part so that planners can focus on problems and solutions that people care most about. However, one group that is often missing from these conversations is children, even though children often have specific needs, experiences, and ways of interacting with the built environment that are quite different from adults. To help fill this gap in planning knowledge, this project uses an age-appropriate method to uncover children’s perceptions of and experiences with the city. Specifically, this project worked with students from two local elementary schools to produce drawings of their streets and neighborhoods as they see them now, and envision them changing for the better. These drawings were then analyzed for common patterns, elements, and themes, and used to develop recommendations of child-centric items that planners can further focus on. Additionally, the maps were collected in a bound book that was provided to the children to reinforce the value of their own experiences and perceptions of the built environment, and to demonstrate to planners that children’s views of the city also matter.

In the United States today, biking is a gendered activity. Nationwide, far fewer women bike commute or ride their bikes in urban areas than men. This gap holds true even in bicycle-oriented cities such as Seattle, where the majority of people who ride their bikes in the city identify as male. This research investigates the cause of this gap and identifies steps that cities and communities can take to encourage more women to cycle. The research includes a review of the literature on bicycle commuting, with a focus on known barriers to and attitudes about bicycle commuting; in depth interviews with leaders in Seattle’s bike community; and an analysis of other American communities known for strong bike infrastructure. Findings from this research are then used to inform several policy, practice, and design recommendations aimed at closing the gender gap by increasing the number of women who regularly commute or bicycle in urban areas.
 

As a result of rapid urbanization, Lake City, a neighborhood in north Seattle, has experienced a significant shift in its demographics, local socio-political dynamics, cultural values, economic conditions, and spatial boundaries. As an effort to better represent and improve the Lake City area, residents created the Lake City Neighborhood Alliance (LCNA), a network of 28 neighborhood organizations, including multiple neighborhood associations, a parent teacher association, a food bank, and a safe-street advocacy program, among others. Such alliances are often championed by neighborhood planning advocates as an effective way to increase citizen participation, enhance community representation, and improve neighborhood conditions. However, very few studies have looked closely at the challenges and internal dynamics of such alliances. This research fills that gap by understanding the benefits and difficulties that come with a parent organization, such as the LCNA, working to improve a community through collaboration between member organizations. Through a series of in depth interviews with LCNA members and participant observations, this project uses the LCNA as a case study to explore why organizations and their representatives continue to be a part of such coalitions, and how the structure of a neighborhood alliance can influence its ability to effectively address local problems and strengthen the community overall.

Evidence suggests that today’s radio caters more to consumer behavior with more product advertising than original content. Community radio aims to change this trend by producing original content with free form product advertising. In this way broadcasting can be used to empower marginalized groups and cultivate diversity. This community-based action research supports the development of UWave Radio as a campus/community Low-Power FM station. Our research question is, “How can UWave Radio and other community low power FM radio stations best serve diversity and student voice at public universities like UW Bothell?” We approach this question using action-oriented community engaged methods that allow researchers to work with community members in building a participatory media organization. We are able to do this by researching how local community radio stations are engaging with the community. Some of the stations that we have been able to contact for interviews are Bellevue College’s KBCU, KAOS in Olympia and WWU’s KUGS. We’ve also conducted surveys from UWave Radio listeners by collecting emails at the events we host on campus. We also use focus groups in order to brainstorm and review effective strategies for outreach. Our progress to date also includes a robust student-run online radio station (http://uwave.fm), with long-range budget and business planning, an FM construction permit for 104.9 (KUWU) and approval of an 18-month extension to our construction permit while we continue to negotiate with the UW for final approval. Thus far I’ve observed how this student led organization facilitates the cultivation of diversity by amplifying a diverse body of voices as directors, managers, show hosts and listeners to the station. By making broadcast radio accessible on campus it can be used as a resource for students to express themselves in a way that also develops their appreciation for diversity.

The Odegaard Writing and Research Center (OWRC) is one of the most well-known and broadly focused writing support resources on the UW campus. Our staff of nearly 70 tutors offers about 500 bookable appointments each week; additionally, a consistent flow of unscheduled writers enter the center daily. To manage incoming traffic, two years ago, the OWRC instituted a concierge position with responsibilities that include answering general questions, assisting writers with booking appointments, notifying tutors of appointment arrivals, and conducting drop-in sessions. Still, traffic flow into the OWRC is occasionally overwhelming and concierge staff often mention the logistical challenges and frustrations inherent in the position. We decided to assess the concierge position from a design perspective, using focus groups, interviews, surveys and ethnographic observation. We wanted to know more about the nature of challenges faced by concierge staff and to identify measures that would improve our writers’ user experience. Preliminary results from this project point us to several recurring problems for which we plan to generate and test solutions iteratively. In addition to improving the experience our fellow Huskies have in the OWRC, our work may have implications for other institutions that experience high traffic flow and want to make their check-in experience more streamlined and welcoming.

This research represents the culmination of my fieldwork as an anthropologist and activist in the Seattle counter-trafficking movement.The Seattle anti-trafficking movement is experiencing a transitional moment, as it reemerges from antebellum abolitionism to transform into the standard-bearer for human rights in the 21st century. Though renovated with the human rights vernacular of modern social justice, many of the mythologies found thriving within the global discussion of modern slavery are those of antebellum characters revived and renamed. Grassroots efforts have begun to instigate a culture shift in how we view ‘our role’ as bystanders to these heinous crimes, though the methodologies utilized by counter trafficking activists and volunteers in Seattle have yet to be given serious critique. While productive, it is my observation that some of the tactics utilized by both myself and fellow activists may reflect the nature of a community and culture that demands the commodification of humanitarianism – methodologies requiring by nature the depreciation of the ideal of inalienable human rights. How does this observation help us to define the 21st century abolitionist movement? While the isms of today are often discussed as contours that define and divide us, the people that I have had the privilege of working with over the past three years have found common ground not in faith, methodologies, or even priorities; rather, it has been an earnest desire to do good in addition to merely surviving. It takes great courage to overcome the paralysis triggered by the overwhelming global horrors we are confronted with everyday. I chose here to explore this space between the rhetoric of ethics and the demands of work in the field, focusing both on the trends represented in character mythologies, and how we work to move forward within and despite them.

Since the founding of the United States, education has been used as a means to create and maintain the idea of a citizen. Classrooms are therefore always social and political spaces. Often classrooms are spaces where people are socialized into dominant ways of thinking and understanding of the world which perpetuates existing structural inequalities and systemic violence. Mainstream understandings of poverty that hold individuals responsible for their own situation fails to recognize structural causes of poverty and its relationship with the reproduction of privilege. In order to push back, it is important to begin unlearning these dominant ways of thinking about poverty and privilege. The purpose of my research was to better understand how university classrooms can be spaces where previous beliefs and social norms about poverty and privilege are affirmed or altered. I examined what role the teacher’s instructional content, class activities, and approach to learning played in that process of possible transformation for students. Specifically, I examined how these pedagogies affect pre-existing ideas about poverty, privilege, and class relations in the U.S and how people understand their own class identities and shape their. My research had two main components: 1) participant observation in a University of Washington class where themes of poverty and privilege are related to course content, during Winter Quarter 2016; and 2) several focus groups with students enrolled in the class. Through my research I found that the instructor incorporated radical pedagogies through decentering his own authority, creating lots of space for discussion, and presenting ideas and questions that challenged dominant ways of understanding. Students expressed that these methods helped build a trusting yet rigorous space that allowed them to begin a process of unlearning previous assumptions. My research therefore has implications for educators working to create spaces of unlearning in their own classrooms.
 

Pursuing undergraduate education in developed countries has become a phenomenal trend in China over the past ten years. At the University of Washington (UW), among 7299 international students in 2014, 3845 are from China and over three-fourths of them are undergraduate students. Though Chinese students have been a significantly growing student body at UW, there has not been sufficient research to comprehensively understand them. My research is to create an ethnography of undergraduate Chinese international students at the University of Washington. The ethnography centers around the challenges they have faced at the crossroad of stepping into young adulthood and adjusting to American culture; and changes they have undergone in the U.S., including those of identities, beliefs, life styles, interests, and personalities. I aim to capture characteristics unique to this Chinese generation studying abroad who were born in 1990s under one-child policy, growing up in the era of economic reform in China and globalization; and to understand the sociopolitical, economic factors in China that made this studying abroad trend possible. The ethnography also focuses on students’ values and relationships with their families as singletons and how their transnational lives change the dynamics of their original families. I conducted in-depth interviews with ten junior and senior Chinese international students with various majors and backgrounds at UW. Reoccurring themes from fieldwork, which are being further investigated, include realization of being racial and ethnic minority in the U.S., challenges of assimilating into American society, social dynamics among Chinese and American peers, restrictions of working opportunities in the U.S., non-traditional definition on filial piety, etc. This ethnography intends to promote understanding of Chinese international students at UW and shed light on the only-child generation in China.
 

Until today, the Coptic culture is seen and studied by most of its onlookers as a dead Egyptian culture of late antiquity, neglecting the fact that there are more than 20 million people who identify as Coptic and live across continents and cultures. Copts only lived in Egypt until about 60 years ago, and thus, the sudden incline in rates of migration to different countries raised concerns regarding the loss of their culture's identity(ies), and opened dialogues concerning cultural adaptation. In light of these concerns and dialogues, this study explores what it means to be Coptic in a diverse society such as the U.S. The Coptic culture is founded on Orthodox Christian beliefs that are embedded in the symbolic significance of the physical aspects of the culture (i.e music, art, etc). Dressing these religious values in the aspects of a culture is a concept in this research termed as the "immersive experience" and has also been thoroughly explored. The data needed for this study has been gathered through 35 interviews, four focus groups, full participant observation, and auto-ethnography in three specific Coptic communities: Copts in Washington DC, Seattle, and in Mallawi in Egypt. The findings of this study construct a framework of meanings that shapes how the Coptic faith is embodied in the Coptic culture and how different Copts who have settled here in the States negotiate their culturally-embodied faith with the cultures of their new homelands. The framework suggests a theoretical approach that can provide both a proper transition of faith to new homelands, and a successful way to maintain heritage. This work is not only helpful to Copts, but also to communities of similar religious structure, and communities who wish to remain unified but not uniformed with their peers across different spaces and cultures.

This research examines how three Seattle-based global health organizations produce particular perceptions of mental health in the “developing world.” The Bill and Melinda Gates Foundation, Health Alliance International, and The University of Washington Program on Global Mental Health all incorporate mental health into their work abroad in some capacity. Their programs and the way they publicize them are both methods of setting standards for the global health industry and of acquiring potential major donors. I use critical discourse theory, relational poverty theory, and critical development theory in examining these materials to determine which organizations produce what types of representations. I argue that certain representations serve to reinforce unequal power structures between those giving and receiving aid while other representations challenge these structures. Some programs and publicity for mental health interventions support the discourse of people living in the Global South as only being susceptible to mental illness after traumatic events. Other programs take a more holistic approach that acknowledges the daily burden of mental illness and challenges unequal power structures by encouraging collaboration between the organization and the communities receiving aid. Using content and discourse analysis in this research, I argue that specific key terms such as “mental health” are strategically placed in press releases and other publicly available materials to produce either a discourse of otherness or one of similarity. The types of discourses produced through these representations have real world implications as they either reinforce or challenge existing power structures.

Brand image is perhaps the most important asset to modern marketers. Some marketers have chosen to use spokescharacters (such as Pillsbury’s Pillsbury Doughboy) to represent their brand. The most successful spokescharacters encourage the development of parasocial, or one-sided, relationships with consumers. Research has begun focusing on improving our understanding of how consumers develop these relationships. This research extends previous studies by exploring possible moderators that may potentially play a role in consumers’ behaviors and attitudes towards the brand. More specifically, this research has focused on changes in consumer spokescharacter relationships when changes in spokescharacter imagery occur. To investigate, I performed an experiment with students from the Milgard School of Business as participants. Using questionnaires, respondents were first asked to answer questions regarding self-congruency with the Pillsbury Doughboy. Once these questionnaires were completed collected, respondents were then shown one of four images – the original Doughboy, a blue Doughboy, a muscular Doughboy, or a Doughgirl. Each group was exposed to only a single image. Respondents were then provided a second questionnaire with scales to evaluate opinions on the provided depiction as well as a repeated set of the original self-congruency questionnaire. For results, I expect to find that sociality and effectance motivations as well as self-congruency play roles as moderators in the impact of changes in spokescharacter imagery on the consumer spokescharacter relationship.

Mass media can play dual role in the social life: reflect or affect political and social opinion. The current migration crisis in Europe is one of the cases when mass media can reflect the people's opinion and interpret the reaction of political officials, and in some cases can influence the possible changes in immigration policies of taking in refugees. This research analyzes mass media representations of migration from the Middle East to Europe between July, 2015 and February, 2016. This period spans the terrorist attack in Paris in November 13, 2015, which my research finds is an important turning-point in the discourses about migrants, with potential implications for changes in migration patterns in the wake of high profile terrorist violence. The research examines mass media representation of the current migrants in more depth and shows that the revising of immigration policies in many cases can reflect mass media representation of migrants and social discourses about immigration. Also, the study analyzes shifts in asylum admission numbers accepted by some European countries, mostly Germany, the United Kingdom, and France before and after the Paris attack. This research uses mixed methods including quantitative method to analyze existing statistical data which can provide main data about accepted asylum applications, and qualitative content analysis to study mass media editions and to analyze representation of immigrants in mass media at different periods of time.

For many immigrants to the United States, the process of acculturation, adapting to the ideals, values, and behaviors of a new culture and balancing them with those of a culture of origin, can be mentally and emotionally challenging. One potential response to these problems is art therapy. In the west, art therapy has been used as a successful intervention for a range of mental, emotional, and social problems, however there is little research on how making and sharing art may specifically affect immigrants. This research aims to examine the effectiveness of art making and sharing as a coping mechanism for acculturation. After reviewing the literature on the impacts of immigration and the benefits of art making, I interviewed seven immigrant artists from different countries, focusing on the role that art plays in their personal acculturation process. The results of my interviews provide a deeper insight into the effectiveness of using art as an individual and community coping mechanism and suggest several lessons that recreational or community-based art programs could use to ease the difficulty of acculturation for other immigrants.

 As millionaire art collector turned excavator Theodore M. Davis’s mistress, Emma B. Andrews documented significant archaeological excavations during the so-called ‘Golden Age’ of Egyptian archaeology at the end of the 19th and beginning of the 20th centuries. Within her journals, Emma detailed annual voyages along the Nile for more than two decades, providing important contemporary insights into Egyptian society.  The goals of our Diary Project include the digitization and publication of diary content along with wide-ranging biographical and historical research. To date, student interns have transcribed all 19 volumes of the original diaries. This year we have focused on completing structural markup to prepare the texts for online publication.  Our historical research has been wide-ranging, bringing to light many contemporary images of family, friends, fellow travelers, archaeological sites and Nile travel. However, we have not yet discovered a clear photograph of Emma herself.  Although she was the daughter of a prominent Ohio family, and a nexus of archaeological and social activity in Egypt, her controversial affair with Theodore Davis may have caused her family to destroy documents and photographs after her death in 1922. Using digital tools and methodologies, our intention is to use the information we have gathered programmatically from the diaries as the basis for creating an artist’s sketch of Emma Andrews.  We have customized a generic Text Encoding Initiative (TEI) tagset to create a new ‘trait’ tag enabling us to document physical characteristics and automatically compile them in a database.  We will be incorporating similar details mined from related contemporary diaries and correspondence that reference Emma. We are completing a pictorial analysis of close family members along with further written descriptions we have identified to facilitate the recreation of our ‘invisible diarist’. Our proposal melds digital technology, traditional humanities research and an imaginative recreation of the past.

Anthropogenic emissions are projected to double atmospheric concentrations of CO₂ by the end of the century, increasing ocean acidification and fundamentally changing the marine environment. Since diatoms are responsible for ~40% of marine primary production, it is important to understand their response to variations in CO₂ concentration and how they regulate their carbon assimilation. In previous work, we identified gene clusters with differential expression under elevated CO₂ in the model diatom Thalassiosira pseudonana. One cluster of genes that was down-regulated under elevated CO₂ encodes putative carbon concentrating mechanism (CCM) proteins, which participate in control of carbon assimilation. These genes share an upstream cis-regulatory motif involved in the regulation of CCM genes in Phaeodactylum tricornutum, a distantly related diatom that uses cyclic AMP (cAMP) as the second messenger. To test whether cAMP plays a similar role in CO₂-responsive gene regulation in T. pseudonana, we grew T. pseudonana under high and low CO₂ conditions and sampled cultures prior to or following exposure to 3-isobutyl-1-methylxanthine (IBMX), which raises intracellular cAMP concentrations. We have sequenced RNA from these samples and determined differential expression of genes between treatments. Contrary to our predictions, we find that most genes in the CCM sub-cluster are significantly up-regulated following IBMX treatment under high CO₂. We also identify a number of other gene clusters that are highly responsive to the IBMX treatment, suggesting other cellular processes under cAMP control. We are supporting this research with targeted metabolomics to look for changes in the ratio of cAMP:AMP and other key compounds between treatments. This research will facilitate mechanistic insights into diatom responses to changing ocean environments, and improve our understanding of the evolution of carbon concentrating mechanisms in this group of globally significant phytoplankton.

Marine microbes drive virtually every major biogeochemical cycle in the ocean. These microbial communities consist of two major groups: primary producers, called phytoplankton, that use energy from sunlight to transform carbon dioxide into organic matter, and consumers, like heterotrophic bacteria, that degrade about half of phytoplankton-derived organic carbon. Recently, it has been recognized that certain phytoplankton and heterotrophic bacteria form intimate relationships with one another and exchange specialized metabolites. This project has focused on characterizing such relationships between phytoplankton and bacteria, particularly between diatoms (a type of phytoplankton) and bacteria that enhance or deter diatom growth. These bacterial-diatom interactions impact rates of carbon fixation and nutrient flux in the ocean, and this project aims to better characterize the types and specificity of these interactions using laboratory cultures. To observe the effects of bacteria on diatoms, laboratory studies were conducted in which diatoms were exposed to individual bacterial strains in order to examine the specific effects of each strain on each diatom. In subsequent experiments, diatoms were exposed to multiple bacterial strains simultaneously in order to examine the impacts of multi-bacteria consortia and to create a more realistic model of the environment in which diatoms are exposed to many different types of bacteria.

Fronts are dynamic regions in the ocean where contrasting water masses meet, characterized by rapid currents, sharp density gradients and high productivity. What drives the phytoplankton community structure in these regions is still not well understood, but it has been hypothesized that fronts could act as either a barrier or a blender. However, few observations exist to test this hypothesis. The Kuroshio Front off the coast of Japan, extending eastward into the North Pacific Ocean, is an important western boundary current front, known to be important for fisheries. During a cruise in October of 2009, fine-scale sampling was conducted, and diatom and dinoflagellate phytoplankton taxa were identified to the species level by microscopy. Concurrent measurements such as salinity, temperature and chlorophyll were also taken to relate the physical and biological characteristics of the sample region. My analysis has revealed that distinct water masses found in the frontal zone have significantly different phytoplankton diversity indices. Conversely, I found that the most frequently observed and most abundant species in these water masses were remarkably similar. Major differences between the water masses were driven by the diversity of rare species. I show the importance of rarity in driving diversity and highlight the disconnect between the physically distinct water masses observed and the structurally similar phytoplankton community. My results reflect the importance of lateral mixing, mingling species from distinct source regions along the front. Rare species most likely represent the least competitive constituents of those original source populations. This research suggests phytoplankton may mix into new water masses diferent than their initial environment even if the water masses themselves remain physically distinct.

For the past twenty years, scientists have attempted to learn more about the effects of pollution on coral species. However, identifying coral species in today's scientific community is more of an art than a science. For the last five years, researchers have been attempting to address this problem by comparing the skeletal structures of different coral species. Coral calcification is distinctive because it involves the formation of rapid aragonite super saturation. Aragonite is a very unusual form of calcium carbonate. It is much less thermodynamically stable than the primary form of calcium carbonate--calcite. There are two lines of thought as to why aragonite is preferentially precipitated in coral skeletons. One, the proteins secreted by the polyps within the coral create microenvironments that promote aragonite precipitation. Two, the magnesium from the surrounding ocean water interacts with the proteins in such a way that aragonite becomes the more energetically favorable precipitate. Our research examined the proteins and water involved in these calcification sites and compared them among species of coral collected from the Mo’orea Islands using Thermo Gravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC), Energy Dispersive X-Ray Spectroscopy (EDS) and Fourier Transform Infrared Spectroscopy (FT-IR). In short, we wanted to compare the magnesium, water content, and protein content/functional groups between species in the hope of finding species or site-specific trends. Our results confirmed the correlation between magnesium and protein, and discovered that the way in which corals create their exoskeleton is highly evolutionarily conserved.

Non-traditional isotopes have become increasingly important as tracers for geological and environmental processes on earth. Recently, renewed attention has been direct towards potassium (K) isotopes given the abundance of K in the earth and the potential for significant mass-dependent fractionation between ⁴¹K and ³⁹K. There is little existing research on K isotopes primarily due to analytical difficulties, however recent technological developments have made precise analysis possible. Seawater has the potential to be an excellent geostandard for K isotope geochemistry because of predicted ⁴¹K/³⁹K homogeneity through the water column, and its wide accessibility around the globe. A total of forty-seven, 30 mL samples were collected in July 2015 aboard the R/V Thomas G. Thompson on the VISIONS 2015 Expedition to Axial Seamount on the Juan de Fuca Ridge. Samples were collected from CTD (Conductivity Temperature Depth) casts as well as niskin bottles operated by the Remotely Operated Platform for Ocean Science (ROPOS). Seawater profile samples were taken at several locations from 7 m down to 2890 m. Evaluating the K isotopic composition at each depth and geographic location will determine if the K isotope composition of seawater is homogeneous and therefore if seawater may be useful as a future geostandard. If K behaves similarly to other non-traditional isotope systems, ³⁹K will preferentially be released into the hydrosphere during weathering, leaving the residual rock enriched in ⁴¹K. This behavior will be useful in constraining the process of granite weathering, and its effect on the K budget in the hydrosphere. In chemical oceanography, there is thought to be a missing sink for K, and it is theorized that clay formation, crustal fractures, or both may remove K from seawater. Determining the feasibility of seawater as a geostandard for K isotopes will further facilitate new research in these and other geochemical topics.

Due to the rise of pathogen genetic knowledge and implementation methods of diagnoses pathways for patients, an increase in access to speedy and efficacious therapies is needed. The development of inexpensive, high-performance point-of-care (POC) tests does not only improve healthcare in low resource settings, but also moves the diagnoses out of hospitals and into homes and primary care offices. Paper-based microfluidic devices help both identify and screen for pathogens by allowing for more rapid care and treatment. The multiplexed, autonomous, disposable nucleic acid amplification test devices fabricated in the Yager Laboratory performs sequential functions - sample preparation, nucleic acid amplification, and lateral flow detection – for target identification. My project aims to bridge the last two segments into a single unit by introducing a method of inhibitory competition that permits for measurable, fluorescent-based analysis of isothermal DNA amplification from dry reagents in porous media. To prove this concept, a simplified experimental model of a multi-region, paper-based nucleic acid amplification test was designed, and new interference amplification mixtures developed. The isothermal strand displacement amplification (iSDA) technique utilized in these devices incorporates a fluorescent hybridization probe that allows for the detection of the increase in amplicons using an optical detection method. By incorporating a dilution of comparable, secondary strand of DNA as an internal control, a competition for reagents is established which creates different chemical sensitivities in the amplification zones. As a result, target DNA from the pathogen is amplified against a competitive threshold in a range. In the long run, fluorescence imaging of all regions can yield a quantitative measure of the concentration of pathogens in a sample. Overall, this project tests the fundamental groundwork for a new family of optical-based, quantitative devices by testing the use of fluorescent detection for POC tests, and investigating the principle of inhibitory competition.

One third of adults from ages 20 to 44 have untreated dental caries, typically treated through irreversible fillings and root canals (Centers for Disease Control and Prevention, 2012). Current technologies require professional consultation for caries detection – an inconvenient and costly process. Our objective is creating an optical system of detecting early caries formation to be performed at home on a weekly basis via spectral imaging of the plaque on teeth. The bacterial growth in plaque and demineralization of underlying enamel is detected by optically monitoring the fluorescent byproduct of bacterial metabolism, porphyrin. By imaging teeth in blue reflectance light and red fluorescence signal, concentration and growth of plaque deposits are measured using target versus background (T/B) pixel peak values (PPV) and T/B pixel count (PC) of PPV. Repeated measurements are plotted for plaque deposits and trends. Statistical analysis and comparison of T/B ratios and PCs trending can identify the most efficient measurement for locating plaque deposits most susceptible to caries development, prompting more efficient preventative care and triggering a dental examination. This new concept was simulated in vitro using a dental training model of teeth, measured applications of red stain, image stitching software (123D, Autodesk), image analysis software (ImageJ), and a mobile phone. Red stain was applied in increasing concentration and volume to both occlusal and interproximal crevasses that would most likely be missed by brushing and flossing. At each time period, a series of 2D images were acquired to reconstruct 3D models of simulated bacterial growth and were processed using ImageJ for T/B ratios of PPVs and PCs, which were plotted against each time period. T/B ratios of PPVs produced the most consistent measure of trending of the simulated growth, R^2 values 0.77, with statistically significant differences in variance with PC ratios (f-test).

This project aims to develop a better model for testing gene therapy vectors in vitro. Gene therapy uses a modified virus to insert a functional copy of a gene into a patient’s cells, but testing new viral vectors on 2D cell culture does not accurately predict success in vivo. To address this need, I have designed a 3D-printed microfluidic device for optimized viral vector testing. Cells are cultured in 3D in one channel, while media and viral vector load can be easily adjusted in a connected channel through a gravity perfusion system. The device is currently undergoing tests for cell viability and demonstrating its utility for gene therapy applications. The primary advantage of this device is that cells cultured in 3D mature more similarly to true skeletal muscle and thus are better models for predicting the success of a viral vector in a patient. The small size and fine tune control over the cell’s environment also save time and money during testing, allowing the maximum number of options to be explored. A new, physiologically relevant model for testing viral vectors would expedite gene therapy research to help bring treatments faster to patients in need of gene replacement therapy.

College retention in the United States has been a growing concern among minority populations for decades. However, the Asian American and Pacific Islander (AAPI) population is one of the most overlooked and understudied populations in higher education because of the stereotype that all AAPIs do well in academia. To better understand the various resources needed for AAPI subpopulations, data among this diverse population needs to be disaggregated. This also suggests how resources can be improved to help these specific groups in higher education institutions. Although there have been numerous studies on specific subgroups in the AAPI community, minimal research has included Hawai'i's population in higher education. Retention rates among students from Hawai'i remain invisible. Additionally, retention rates are unclear of why and how these rates occur among students from Hawai'i. This study explored the challenges of students from Hawai'i in a predominately-white institution in relation to retention rates. From semi-structured interviews, commonalities were found from analyzing student responses that attended a public, four-year, predominately-white institution in the Pacific Northwest. This study found that student retention factors affecting college adjustment is pertinent in higher education for student persistence.

Despite recent growth in the rate of bachelor’s degree attainment for Latino/a college students, from 8 percent in 1990 to 15 percent in 2014, Latino/as remain in the lowest division least likely to earn their four year degree. Latino/a college students face many academic related barriers to obtaining a bachelor’s degree, such as prior academic college preparation, socioeconomic barriers, and cultural/social capital. This study is the examination of the cultural differences between many Latino/a home and community lives compared to the setting in a college or university. For example, many first-generation Latino/a students’ experience a setting where they rely on family and community to navigate difficulties. However, in college these aforementioned students are away from this support and may not be prepared for the challenges higher education brings. We are conducting semi-structured interviews for elaborate answers that may potentially highlight transitional ordeals. The sampling technique we are using is convenient sampling. Participants are recruited from a multicultural center “Chicano/a Latino/a center” in the Compton Union Building of Pullman, WA. The population we are targeting is first generation Latino/a college students from Washington State University in their first or last year of undergraduate career. Influenced from previous research, we are specifically examining what disparate experiences are happening when transitioning from their accustomed culture to an individualistic college campus. Our expected results are that students will be discouraged by unfamiliarity and the new challenges faced in another environment. Specifically, problem-solving skills and avoidance of challenges may differ from the collectivist and individualistic environment. We expect to find this transition to impact first-generation Latino/a college students. Our potential implication of this study is a development of a program, prior to college or in their first year to help these students become familiar with the individualistic environment.

There are significant pregnancy health disparities experienced by American Indians in the Great Plains region that are not well understood. Community-based research projects (CBRPs) are one of the best ways to understand why these disparities exist and how we can reduce them. Conducting a CBRP requires building a trusting relationship with the American Indian community and the researchers. As well as having community members and researchers work together on the project will show that we value the community members and their input just as much as our own. It will also allow us to write the findings from a community perspective not just an outsider’s perspective. Our McNair research plan is to establish a trusting CBRP collaboration with the Turtle Mountain band of Chippewa Indians focusing on institutions that will help us conduct the Healthy American Indian Pregnancy Project that is under grant consideration.

Fostering students’ motivation and interest in higher education composition classes is vital to sustain student engagement. However, short-term motivation does not necessarily determine long-term success; recent research has found that an individual’s level of grit plays a significant role in his or her long-term success (Duckworth, Peterson, Matthews, & Kelly, 2007). To investigate the role of grit in writing classrooms, we are exploring how writing instructors can foster students’ grit for a greater chance of long-term success. Because Duckworth et al. (2007) consider interest and effort to be crucial factors in grit, we chose to examine whether or not service-learning (SL) can foster students’ grit, as SL been shown to increase student engagement in the past. Using Duckworth et al.’s eight-question grit scale, this project investigated the impact of SL on the grit of students in basic writing classes at Shippensburg University in Pennsylvania, comparing three SL classes (Group 1) and two non-SL classes (Group 2). Data was analyzed using t-tests to compare the average grit scores between the groups at mid- and post-semester. Although results indicated no significant correlation between grit and SL, this study suggests that grit stems more from internal rather than external motivators. Thus, this research can potentially open up a conversation about factors and influences that affect an individual’s grit.

The present study examines low-income Latina mothers' influence on their preschool aged children's self-regulation of caloric intake. There is limited research done on the minority population in regards to parenting styles associated with children's self-regulation of eating. The research conducted is part of a larger study and analyzes the children's self-regulation and parents pressuring their children to eat as contributors to childhood obesity in terms of several procedures. The total number of participants consisted of 187 low-income Head Start Latina mothers with the exception of 2 grandmothers and their preschool children. Mothers were recruited through Head Start, a federally funded preschool program for low-income families and their children. Four procedures are used in my study, which observe children in the eating in the absence of hunger task, caregiver reports of feeding practices, observed pressure to eat during meals, and anthropometrics. It is predicted that caregivers who pressure their children to eat at the first time point will have children who show low levels of self-regulation and higher BMI's 18 months later. These results will have implications for the development of programs to address childhood obesity.

Protein synthesis is a tightly regulated cellular process important for all of life. Specific diseases such as cancer can hijack the process of protein synthesis to drive specific disease states. My research focuses on determining if the protein making factories of a cancer cell can be secifically therapeutically targeted. I have focused my studies on prostate and bladder cancer. Prostate cancer is the second leading cause of cancer death in men. A well-studied signaling pathway that is altered in prostate cancer is the PI3K-AKT-mTOR pathway. This pathway converges on and activates the apparatus necessary to start protein synthesis through a protein called the eukaryotic initiation factor 4E (eIF4E). eIF4E is an mRNA cap-binding protein which recruits another translation factor to start protein synthesis in cells. Ribavirin is an mRNA cap-mimetic that can compete with eIF4E to inhibit mRNA translation. I will present my results from a preclinical trial using Ribavirin and a mouse model of prostate cancer. In addition to my work in prostate cancer I have also initiated preclinical studies in bladder cancer. Bladder cancer is the 5^th leading cause of cancer death in men and there have been no new theurapeutics for two decades. ARID1A is an ATP-dependent chromatin modifier that is one of the most mutated genes in bladder cancer. The Hsieh lab has discovered an intimate link between ARID1A levels and mRNA translation. I hypothesize that protein synthesis machinery represents a unique vulnerability, which can be therapeutically targeted in bladder cancer. I will present data on my findings using protein synthesis inhibitors such as puromycin and an ATP-site inhibitor of mTOR in ARID1A wild-type and mutant bladder cancer cell lines. Together, my work in the Hsieh lab points to a new treatment paradigm for targeting the protein synthesis machinery in human cancers.

Intestine is responsible for the biotransformation of many orally-exposed chemicals. The nuclear receptor constitutive androstane receptor (CAR/Nr1i3) can be activated by various drugs and environmental chemicals, and in turn it is known to up-regulate the expression of many drug-processing genes (DPGs) in liver to facilitate xenobiotic biotransformation. However, relatively less is known regarding the effect of CAR on the basal and inducible expression of DPGs in various sections of intestine. To fill this critical knowledge gap, sixty-day-old wild-type and CAR-null mice were administered the CAR-ligand TCPOBOP (3mg/kg, i.p.) or vehicle once daily for 4-days. CAR-null mice had altered basal expression of many DPGs in a section-specific manner in intestine. Consistent with the liver data (Aleksunes and Klaassen, 2012), TCPOBOP up-regulated many DPGs in specific sections of small intestine in a CAR-dependent manner. In contrast, the mRNAs of certain DPGs were previously known to be up-regulated by TCPOBOP in liver but were not altered in intestine. Interestingly, many known CAR-target genes were highest expressed in colon where CAR is minimally expressed, suggesting that additional regulators are involved in regulating their expression. In conclusion, the present study has shown that CAR is critical in both maintaining the basal expression as well as the pharmacological regulation of certain DPGs in a section-specific manner of the intestine, and the CAR activation in liver and intestine produces overlapping but not identical results. Therefore, Identification of the xenobiotic responses to CAR activation in intestine is critical for further understanding the adverse drug-drug interactions for many orally-exposed chemicals.

Protein glutathionylation is a post-translational modification that can take place under mild oxidative stress. It occurs when the antioxidant glutathione (GSH) forms mixed disulfide bridges with low pKa cysteine residues on proteins. This may play a role in reversibly regulating the activity of proteins that have key cysteine residues or protecting those cysteines from further irreversible oxidation if oxidative stress worsens. GSH itself is synthesized in a two-step process, and the rate limiting step is catalyzed by glutamate-cysteine ligase (GCL), a heterodimer composed of the catalytic subunit (GCLC) and modifier subunit (GCLM). GCLM acts to increase the activity of GCLC. Thus, in the absence of GCLM, GCLC is less efficient in making GSH. We have generated Gclm null mice and these mice have liver GSH levels that are about 10% of normal, resulting in an oxidized thiol redox environment. An important question that has not been answered is whether Gclm null mice have different levels protein glutathionylation than Gclm wild-type mice. The oxidized thiol redox status of Gclm null mice is predicted to increase the level of protein glutathionylation. On the other hand, there may in fact be less protein glutathionylation in Gclm null mice because they have less GSH to begin with and there is a compensatory increase in sulfiredoxin and thioredoxin reductase expression, both of which are known to reverse glutathionylation. Using assays of protein glutathionylation, this project seeks to provide confirmation of the hypothesis that Gclm deficiency results in adaptive regulation of glutathionylation under different degrees of oxidative stress.

Endophytes are symbionts that live in the intercellular spaces of host plants. They can be fungi, bacteria, actinomycetes and/or viruses. Initial investigations indicate that endophytes provide a number of benefits that promote plant growth including, but not limited to, dinitrogen fixation, plant hormone production, nutrient acquisition, stress tolerance and increased immunological response. In exchange, they receive domicile and photosynthates. Endophytic biological and ecological services hold great potential for bioengineering and evolutionary inquiries, particularly so for sustainable agriculture. Nitrogen has historically been the nutrient limiting factor in all crop production. Bioengineering endophytic biomes capable of alleviating input demands while ameliorating soils damaged from industrial agriculture stands to offer novel solutions. This two year student-independent research is evaluating the inoculation of three fruit species, Malus domestica, Prunus avium, and Fragaria × ananassa with an endophytic consortia isolated by the UW Doty Lab. Washington is a leading state in fruit crops with over a hundred thousand hectares dedicated to production. Sweet fruit crops require heavy nitrogen inputs to yield nutritionally and economically viable fruits. Our primary objective is to investigate the effect of inoculation on the aforementioned crop physiology and fruit production. We are examining these effects through ecophysiology metrics involving rates of photosynthesis, stomatal conductance, biomass accretion, chlorophyll content, fluorescence rate, drought response, fruit sucrose content and biostatistic analysis. We hypothesize that our inoculated fruit crops will out perform controls as indicated with greater total biomass, fruit production and quality. First season preliminary results point to greater fruit biomass with higher sucrose content in Malus domestica. With crops now well established after season one, we anticipate a continued trend of improved crop total yields, higher sucrose content and greater total biomass production in all three varieties.

Developmental phenotypic plasticity can be a vital means to buffer the sudden and persistent effects of anthropogenic climate change, through facilitation of species persistence and possible facilitation of species range shifts. Integrating our understanding of plastic physiological growth mechanisms with functional traits may prove useful for interpretation of the ecological impacts of climate change. We investigated the influence of water-stress and light limitation on leaf mass per area (LMA), leaf anatomy, and leaf gas exchange of juvenile Populus tremuloides trees. Leaves that developed while water-stressed had significantly elevated LMA, due to increased leaf density from significantly higher spongy mesophyll surface area per leaf area (A_smes/A) and reduced stomatal conductance (g_s) but only marginally reduced photosynthesis (Pmax). In shade, leaves had significantly reduced LMA, due to reduced thickness, density, and combined A_mes/A, but maintained the same A_smes/A, and reduced palisade mesophyll surface area per leaf area (A_pmes/A), which was coupled with a reduction of g_s and P_max. Furthermore, water-stressed leaves had elevated intrinsic water use efficiency (WUE_i: P_max/g_s) while the shaded leaves, despite reduced g_s, maintained similar WUE_i. Our results suggest that, under water-stress and full sunlight, greater A_smes/A conferred maintenance of photosynthetic rate possibly through reduction of mesophyll resistance (r_m), at the cost of reducing expansive leaf area (and increasing density) as leaves were more dense but were 20 % the area of control leaves. In shade, suppressing A_pmes/A while maintaining A_smes/A may be a plastic strategy to increase laminar light capture, as leaves had reduced density and thickness but were still 50 % the area of control leaves . Together, in P. tremuloides saplings, these stresses induced developmental plasticity in LMA with differing plastic underlying anatomy and function; we discuss future implications specifically in the context of developmental plasticity, growth trade-offs, and the ecological impacts of climate change.

Growth promoting endophytes have been isolated from wild poplar and willow plants in Prof. Sharon Doty’s lab and have been shown to promote growth in several other plant species as broadly diverse as rice, tomato, and Douglas-fir. One of the proposed reasons for this increased growth is that endophytes living within the plant fix nitrogen from the atmosphere and exchange it for a carbon source from the plant. Nitrogen is one of the most important nutrients for plant growth and fertilizers are heavily used worldwide to provide this nitrogen. However, fertilizers are costly to produce and have significant negative impacts on the environment so the goal of our lab is to replace these fertilizers with a consortia of natural endophytes. This study seeks to determine the genes necessary for nitrogen fixation in these endophytes by using random transposon mutagenesis. Endophytes will be selected for their ability to grow on nitrogen-free medium. Then, an E. coli donor strain will transfer a plasmid containing a transposon, a segment of DNA that can transpose into the bacterial genome, with an antibiotic resistance gene to our bacteria through conjugation. The bacteria will then be screened for resistance to that antibiotic to check if the plasmid was taken up by the bacteria, allowing for transposon integration at random areas of the genome. Transposon integration will disrupt the genome of the bacteria, creating mutants. Finally, the conjugated bacteria will be screened for their inability to grow on nitrogen-free medium. Bacteria that lost their ability to grow on this medium will then be sequenced in order to determine the location of the insertion into their genome and therefore the location of genes related to nitrogen fixation. This project will also result in the creation of many mutant endophytes that have lost their ability to fix nitrogen and we will therefore be able to compare their effect on plant growth to wild-type inoculated plants.

Flowering plants exhibit diverse forms of floral symmetry that represent many independent changes throughout their evolutionary history. The selective and genetic basis to these changes has provided scientists with a complex puzzle that Darwin once referred to as an “abominable mystery.” Recent genetic studies began to uncover the genetic causes for this mystery, revealing the presence of certain genes that show correlations with this evolutionary trend. One such gene, the CYCLOIDEA (CYC) gene, has been identified as a major contributor to changes of floral symmetry. We have found this gene in the sequenced genome of Rhododendron williamsianum where it has experienced multiple duplications. The goal of my research is to identify the main duplications in one of the CYC copies (CYC2) in the Rhododendron genus. I accomplished this by using polymerase chain reactions to isolate any CYC2 copies present in two species from each of the subgenera of Rhododendron: Hymenanthes, Azaleastrum, Therorhodion, and Rhododendron. I then used cloning and sequencing to obtain the sequences of the CYC2 copies from each of the sampled species. I will conduct a phylogenetic analysis of these sequences in order to reconstruct a gene tree that will display a summary of the main CYC2 duplications that have occurred in the genus and when they emerged. Preliminary results from four species sampled thus far show that two independent duplications in CYC2 have arisen in both Hymenanthes and Rhododendron. My expanded analysis, sampling species from additional subgenera, will provide a more thorough history of this gene and its duplications throughout the genus. This will allow for more robust testing for correlation between symmetry and gene duplication in the future.

The scope of this project is to invite an expert to make a speech focused on water mismanagement and global climate change and to conduct pre-speech and post-speech surveys to explore the effects of the speech on knowledge and attitude change regarding these two issues. One common assumption among those combating climate change is that providing the public with expert knowledge on the subject will change their opinions and behaviors. This project tests whether that assumption is correct by measuring the impact of a single speech on the knowledge and attitudes of college-aged students. For the application of my research, I planned and organized the event inviting 300 students to listen to a 1-hour speech delivered live by a Senior member of the United Nations on climate change and global water issues, and conduct pre-speech and post-speech surveys that were administered to determine what effect, if any, the speech had on the students’ knowledge and attitudes about the topics. 197 pre-surveys were completed while 130 attendees were present at the event and 60 attendees completed the post-survey. The post-survey results are in the process of cross comparison with the initial pre-survey. I hypothesized that the results speech measured by the pre-surveys and post-surveys will show significant positive change in both knowledge and attitude change. The implications of my research results will be used to suggest broader implications for scientific and policy communication to a lay audience in order to continuously educate and successfully convey knowledge and information while advocating for positive change in attitude to further advance our efforts in solving the global threat of climate change and water management.

Islands are home to some of the world's most unique and rare species but often are heavily underfunded for scientific monitoring and conservation efforts. In light of a changing climate, it is important to catalogue the diverse species in island environments to estimate current distribution and abundance to establish baseline data records. Historically, smaller organisms like insects are overlooked. However, native pollinators are an integral component of ecosystem functioning and health. In summer of 2015, I surveyed a small island in the middle of the Indian Ocean off the western coast of Java, Indonesia for native bee and wasp species. Utilizing hand held GPS, insect net collection techniques, and colored bowl traps, I was able to conduct the first pollinator survey on Tinjil Island getting a glimpse of the myriad of pollinators inhabiting the area. Transition from my Indonesian field research experience, beginning in March 2016, I am now surveying the coastal meadows and endemic wildflowers of the San Juan Islands for native bee species. By photographing pollinator visitation of wildflowers in San Juan Island National Historical Park, I am contributing to the creation of a citizen scientist species identification catalogue for the region. In celebration of the National Park Service centennial, I am collaborating with a small team of regional pollinator experts to help identify native bee species of Washington's most iconic islands through a rapid 24-hour survey known as a BioBlitz (May 21-22). In addition, I share with you how you can contribute to local citizen science initiatives and entomology-based educational experiences from your own backyard.

Suction feeding is a valuable process to study since most aquatic vertebrates, which make up nearly half of all vertebrates, eat this way. Having a better understanding of this may give important insight into the evolution of vertebrates as a whole. During suction feeding the cranium elevates, causing bending in the vertebral column, resulting in a rotation of the cranium and body plane about an axis of rotation located on the vertebral column. We hypothesized that the vertebral column behaves like a flexible rod and accordingly asked if axial rotation is located more posteriorly with larger degrees of cranial elevation. Using video reconstruction of moving morphology and joint coordinate systems, which use coordinates to measure the 3D motions of bones in a anatomicaly meaningful coordinate space, we compared movement of the cranium in relation to the body in striped surfperch, largemouth bass, and Pacific staghorn sculpin. We found no significant correlation between degree of cranial elevation and location of axial rotation. However, the degree of cranial elevation and location of axial rotation varied among these species in a consistent way. These species’ unique ways of performing these movements could be related to their differences in morphologies.

The Cretaceous-Paleogene (K-Pg) mass extinction and resulting biotic recovery mark a pivotal moment in mammal evolution. The recovery period, which spanned about 1 million years from the Puercan North American Land Mammal Age (NALMA) to the Torrejonian NALMA, represents a transition from species-poor “disaster” faunas directly following the extinction event to species-rich “recovery” faunas. Though previous research has broadly studied the faunal dynamics of the early Paleogene, the exact mode and tempo of the biotic recovery has not been well examined. To investigate the ecological trends of the “disaster” to “recovery” faunal transition, specifically changes in diet, we analyzed dental evolution within the periptychid and arctocyonid “archaic ungulate” lineages over a time period that spans from the Puercan NALMA to the Torrejonian NALMA. We measured relief index (RFI), a metric that determines the ratio between the 2D and 3D area of mammal teeth, on both the “archaic ungulates” and a set of ecologically diverse extant mammals to identify the dietary ecologies of the extinct mammals. Previous research has demonstrated a correlation between RFI and diet in extant mammals; high RFI values correspond to herbivory and insectivory, while low RFI values correspond to omnivory and frugivory. Our preliminary results suggest an increase in dietary diversity and an overall decrease in RFI during the biotic recovery. This reduction in RFI reflects a trend in “archaic ungulate” dietary preference from insectivory in the Puercan NALMA to omnivory and frugivory in the Torrejonian NALMA. The results of our study will help scientists understand how ecosystems recover from catastrophic events, such as mass extinctions, on large timescales.

In order to understand the paleoecology of extinct animals, it is useful to look at extant species for comparison. Due to the shared ancestry between the modern opossum, Didelphis virginiana, and the extinct marsupialiform, Didelphodon vorax, the opossum is often used as an analog for understanding the life history of D. vorax. Didelphodon vorax, which was the largest mammal from the latest Cretaceous of North America (~66 million years ago), is thought to have had an ovivorous (egg eating) or durophagous (hard-shelled eating) diet; however, little is known about its ontogenetic patterns and ecology. Therefore, we aim to construct an age series of D. vorax to gain insight into diet changes throughout its life. A mandibular bending strength analysis investigates the level of force the mandible is capable of withstanding during biting in both dorsoventral and labiolingual directions. Additionally, we can use it to determine variation in bending strength along the body of the jaw, which allows us to further explore feeding behavior. Here, we illuminate cranial ontogenetic patterns in D. vorax by examining different development stages to determine diet variation based on mandibular strength profiles. We analyzed mandibular cross-sectional properties and applied beam theory to 15 D. virginiana and seven D. vorax specimens. Each individual used in the study resulted with a relative force greater than one, which is indicative of an adaptation toward exerting forces directly on prey, whereas a ratio less than one would indicate an adaptation toward withstanding struggling motions or transverse stresses. Finally, we find similar patterns of ontogeny for both species at different tooth positions, which supports the notion that diet changes throughout ontogeny of these marsupials. Thus, comparison of mandibular bending strength between extinct and extant mammals has the ability to gain insight into their feeding behavior and morphological adaptations.

The South Pacific Convergence Zone (SPCZ) is the most prominent rain feature of the Southern Hemisphere, but is a very understudied region. Changes in the SPCZ can affect freshwater availability to people living on the islands in the South Pacific. The satellite record shows precipitation patterns from the past 37 years; in the tropics the best way to investigate rainfall before 1979 is to examine lake sediment. We used sediment cores with age models from Barora Lake, a shallow freshwater lake in the Solomon Islands, to obtain a detailed view of past rainfall patterns. This lake’s lack of oxygen one meter below the water’s surface has left its sediment in a uniquely undisturbed state. Because of this, and a high accumulation rate, the sediment provides a record of the rainfall in the Solomon Islands over the last millennium. Lipids are well-preserved in sediment over geologic time, making them an ideal proxy for reconstructing tropical paleoclimate. The lipid dinosterol is produced primarily by a limited group of dinoflagellate microalgae and acts as a “molecular fossil”. The isotopic ratio of deuterium to hydrogen (2H/1H) found in dinosterol reflects the 2H/1H ratio in the lake water, which is dictated by changes in precipitation and evaporation. In the tropics, more rain results in 2H-depleted rain and lake water. After purifying dinosterol from the sediment with column chromatography and high-performance liquid chromatography, we found minor fluctuations in the dinosterol 2H/1H ratios, which implies a fairly stable rainfall pattern at this location during the past millennium.
 

Understanding the genetic changes by which organisms adapt to novel and extreme environments is a central goal of evolutionary biology. One mechanism that may offer a rapid path to adaptation is hybridization: the union of two genetically distinct populations or species. Hybridization may transport beneficial genetic variation from a related species or may stimulate new variation to form within genomes, such as the mobilization of transposable elements (TEs). Transposable elements are large, repetitive sequences that can independently move around the genome, and thus mediate a cascade of large-scale changes in chromosome structure, gene expression, and gene content. I am interested in studying whether TE insertions occur more frequently in hybrid species vs. parental species and identifying the types of genomic changes TE insertions facilitate in hybrids. To do this, I am using a two-part approach in the model system of budding yeast, Saccharomyces cerevisiae. First, I am performing fluctuation assays to assess the rate of transposition in S. cerevisiae, its relative Saccharomyces uvarum, and an interspecific hybrid of the two. Second, I am using sequencing to identify novel TE insertions in hybrids evolved in nutrient-limited environments. If TEs do play a role in hybrid adaptation, I would expect to map transposition events with sequencing data and identify associated chromosome rearrangements and/or gene disruptions that may confer a fitness benefit. I also hypothesize finding higher transposition rates in the S. cerevisiae x S. uvarum hybrid clones compared to the non-hybrid parental clones. In doing so, I hope to gain a deeper understanding on the genetics of hybrid adaptation, which has yet to be studied in greater detail in the field of experimental evolution.

Long intergenic non-coding RNAs (lincRNAs) have been discovered to be widespread in mammalian genomes, with thousands existing in humans alone. lincRNAs exceed 200 nucleotides in length and are capped and polyadenylated. They do not overlap with protein-coding genes, and generally exhibit poor sequence conservation across divergent species. The lincRNA cyrano, discovered in zebrafish, possesses a very highly conserved 300 nucletotide region in at least 80 species. Cyrano has also been demonstrated to be essential in embryonic development in zebrafish. Given the sequence conservation of cyrano, we hypothesized that the secondary structure of the 300 nucleotide region was conserved across divergent species. Using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) we determined the RNA structure of this 300 nucleotide conserved region in vitro in mouse, human, and zebrafish. Four structural motifs were found to be common in all of the species. To validate the integrity of these secondary structural motifs, we aim to probe the structure of the 300 nucleotide conserved region as it exists in the cell by performing SHAPE in vivo. Currently, our findings represent some of the first steps towards understanding the roles of lincRNAs and non-coding RNAs in general. The miniscule amount of information we collectively know about this vast new enigma of the genome emphasizes the need for biochemists to tackle this issue and improve the methods at our disposal. 

Pseudo-nitzschia is a diverse and cosmopolitan genus of diatoms composed of 37 species and known for its production of the neurotoxin domoic acid (DA). The phylogeny of the Pseudo-nitzschia genus is complex due to the presence of cryptic species complexes and the frequent discovery of new species. In previous phylogenetic studies, large subunits of ribosomal RNA (LSU) were used as a genetic marker to estimate how Pseudo-nitzschia species were related to one another. We sought to reevaluate the phylogeny of Pseudo-nitzschia both through recreating a LSU tree that accounts for recent discoveries made about the genus, as well as using the rbcL gene, which encodes the large subunit of the carbon fixation enzyme, ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO), in order to better understand the evolutionary relationships within the genus. Both trees provided better resolution in the branching pattern of Pseudo-nitzschia species and identified the presence of a third clade within the genus. Each clade had distinct morphological and physiological characteristics, such as cell size, frustule morphology, pigment content and DA production, which further supported the branching order. Metatranscriptomic reads obtained from four stations along a transect ranging from the Washington coast to the open ocean were placed on the rbcL tree and reflected a biogeographical distinction between the clades. The resolution provided in these phylogenies reflects the importance of continued identification and sequencing of new species. Furthermore, the phylogeny of the rbcL shows that it is an excellent marker for both phylogenic comparison as well as community profiling in the environment.

Exposure to 17a ethinyl-estradiol (EE2), an endocrine-disrupting compound found commonly in birth control and the environment, impacts both development and reproduction in fish. Although it has been established to also cause aneuploidy in those exposed, the effect of EE2 on disease resistance is not well understood. This study uses the zebrafish model to address the effect of EE2 on fish health. Embryos will have been exposed to three concentrations of EE2 (1, 10, 50 ng/L) and a vehicle control from 10-72 hrs post fertilization. At 72 hrs, embryos will have been infected with Edwardsiella ictaluri (gram negative pathogen of fish) and monitored for differential mortality. In addition, the host immune response (via induction of immune genes) is assessed on day two and three post infection using quantitative RT-PCR. Quantitative RT-PCR is a method where RNA is transcribed to cDNA using reverse transcriptase and then is then used as a template for the PCR reaction. Specifically, we will have assessed the regulation of serum amyloid A1 (SAA1-acute phase response) and the proinflammatory gene interleukin 1 b (IL1B). From previous experiments and test runs, these two genes are expected to be upregulated after the exposure to EE2 and the subsequent infection. Overall, this study addresses the hypothesis that exposure to endocrine disrupting compounds can lead to increased disease susceptibility in fish at the individual and population level.

Mosquitoes, such as Aedes aegypti, mainly rely on olfaction to find a host to feed on. By exploring mosquitoes’ olfactory learning abilities, we can increase our knowledge of how they choose their hosts. Using an olfactometer, we have conducted behavioral experiments demonstrating mosquitoes can associate a single odorant, 1-octen-3-ol, with a punishment. To further these results, we tested if mosquitoes would use their experience to guide their host feeding preferences, even when confronted with strong appetitive stimuli such as heat and potential blood meal. We found mosquitoes are indeed capable of aversive conditioning in the context of feeding. In this present project, we investigate if mosquitoes can learn the association between more complex vertebrate body odor mixtures (e.g. rat, chicken, human) and a punishment. After sampling the body odors of various vertebrates, we will aversively train mosquitoes to these odor bouquets. Mosquitoes are trained by simultaneously pairing the delivery of the host odor with a negative stimulus (mechanical shock), mimicking host defensive behavior. Upon training the mosquitoes, we test them in an olfactometer giving them the choice between the aversively trained odor bouquet and the solvent used as a control. To examine whether learning affects mosquitoes’ preference between two individual hosts, we plan to use both olfactometer and blood feeding assays. Further analysis of chemical profiles of the vertebrates species using a gas-chromatograph coupled with a mass spectrometer (GC-MS) will provide insights on the interspecific variability that may be used by mosquitoes to discriminate between individual hosts. These results help to advance knowledge of the behavior and biology of disease transmitting mosquitoes and provide interesting cues to develop efficient tools (e.g. bait) to fight them.

Nudibranchs are shell-less mollusks that live in marine environments where water movement produces variable flow forces. Having to deal with these forces has contributed to the evolution of diverse mechanisms that help organisms withstand the effects of strong currents. In this study we investigated how the distinctly shaped bodies of two nudibranchs change with the speed of the water flow. Two species of dorid nudibranchs were placed into a flume tank and exposed to low and high flow speeds. Photographs of the specimens were taken inside of the flume tank from different angles and at different flow speeds in order to analyze different features of their bodies. We found that the overall body shape for both species tested changed with increasing flow, becoming more compact. The nudibranchs seemingly acquired a body shape of a streamlined bump (half teardrop shape), which is known for its drag reducing properties. Understanding these types of interactions could help in improving the design of scientific equipment used in challenging marine environments.

Johann Sebastian Bach is widely known as the “Father of Classical Music."   Today, his compositions are held in the highest esteem by musicians in many different disciplines. During his lifetime, however, he was recognized more as a great teacher, diligent church musician and virtuoso of the organ and harpsichord. Following his death in 1750, his music lay largely forgotten until its revival with the St. Matthew Passion under Mendelssohn in 1829. My presentation will focus on J.S Bach's Art of the Fugue, his greatest composition in that genre. Written during the final decade of his life, this magnum opus consists of fourteen fugues and four canons, the fourteenth fugue being left unfinished due to his death. Each of the pieces constitutes a variation on a twelve-note fugal subject introduced in the first fugue. Bach develops this subject using various contrapuntal techniques such as augmentation, diminution, inversion, and mirroring. The first four fugues are “simple" fugues, with each entry of the subject clearly delineated. The next three are “stretto" fugues, where the subjects overlap each other. The next four are “double or triple" fugues, meaning two or three subjects are presented and developed contrapuntally. The next two fugues are “mirror" fugues, where the same subject appears twice, the second time in inversion. The last fugue, left unfinished, would have been a quadruple fugue, something unheard of in his output up to that point. I will perform Contrapunctus I,VII, and XI to highlight the different types of fugues mentioned above.

Current chemotherapies exploit the larger pore size of tumor vasculature to reach cancer cells. However, this rudimentary form of targeting offers low selectivity and carries the risk of severe systemic toxicity. In addition, chemotherapy distribution to tumors is limited by the large distance between blood vessels in tumors, increased interstitial fluid pressure, and physiological resistance by the extracellular matrix (ECM). With the goal of addressing these limitations, researchers have developed drug-bearing polymers of various sizes and architectures that selectively target tumor cells. The Pun lab previously produced a novel drug delivery polymer, the sunflower polymer, that can be utilized for anticancer drug-delivery. The sunflower polymer is a macrocyclic brush polymer that can be functionalized with a folic acid targeting ligand and an anticancer drug, doxorubicin, that is released in the acidic tumor microenvironment. In order to maximize the potential of anti-cancer drug-delivery polymers such as this, the impact of polymer size and architecture on tumor penetration must be better understood. This is because the efficacy of any anticancer drug, regardless of its mechanism of action, is limited by its ability to navigate the tumor microenvironment and reach all viable cells in a tumor. This project seeks to discover how polymer size and architecture impacts tumor penetration by using a 3D in vitro perfusion chip model of the tumor microenvironment. The model consists of microfluidic channels seeded with KB carcinoma cells and ECM, and has been optimized using model polymers of polyethylene glycol (PEG) and dextran. Tumor penetration is studied by perfusing fluorescently labelled polymers of various morphologies through the seeded microfluidic channels. The information obtained from this project could potentially be used to optimize the size and architecture of drug-delivery polymers for tumor penetration. In turn, these optimizations could present a significant contribution to the development of anticancer drug-delivery polymers.

In diagnostics, the ability to detect small quantities of molecules with high sensitivity and specificity is crucial for a quick and accurate diagnosis of the presence of target antigens. The ELISA assay, which uses fluorescence to detect the presence of target molecules, is a standard diagnostic and research method for antibody-antigen detection. However, current ELISA methods do not have fast binding kinetics at low target antigen concentrations, requiring several hours for complete results. Therefore, there is a significant need for development of a simple and inexpensive method to improve the molecular binding kinetics in ELISA assays. My hypothesis was that rotational stimulation during enzyme incubation would greatly increase the sensitivity of the assay in a much shorter amount of time. To test this hypothesis, I compared the measured fluorescence of two different types of incubations – the traditional static incubation and a rotational incubation method. I measured the fluorescence generated by each set of assays at varying enzyme concentrations to determine the limit of detection, the minimum concentration that can be detected in a sample, for each method. I also analyzed the binding kinetics of each method using time-based data of each method. It is expected that the rotational method increases the sensitivity of the assay using half the concentration of target molecules compared to that of the static method. It also significantly decreases the time required to reach a binding equilibrium state by several hours. Promising results would suggest that rotational stimulation could significantly improve the molecular binding kinetics in diagnostic assays and could be implemented in future protocols to produce a more efficient diagnostic assay procedure.

Considering the current price and competitiveness of higher education, extra-institutional programs like Advanced Placement, International Baccalaureate, and Running Start are playing an increasingly critical role in public education. Unfortunately these programs, varying in curriculum, course structure, assessment, and aptitude, are not always consistent with the learning outcomes of universities. At University of Washington, Texts and Teachers, a part of the UW in the High School Program, attempts to bridge the gap between extra-institutional college curricula and university learning outcomes by creating collaborative course design, teaching common texts, using common culminating writing portfolios for assessment, and scheduling reciprocal faculty visits to high school classrooms and high school class visits to the linked UW classrooom. In order to assess the program’s success in meeting common learning outcomes, I have designed a research project guided by program instructor Professor Gary Handwerk which evaluates student portfolios for their demonstration of writing ability relative to the UW Expository Writing Program’s learning outcomes. Using a text-response oriented scoring pathway taken from Linda Flower’s 1990 text Reading to Write, I reviewed student portfolios from ENGL 111 and from T&T classes both on and off campus, assessing three primary trait categories: organizational strategies, concept development, and critical analysis. Once scored, I tested for statistically significant differences between class setting and course level and concluded that there was no significant difference between classes. In addition, this methodology distinguished average rates at which students improve their writing ability in each setting. This research provides evidence to support the compatibility of T&T and EWP writing instruction. It thus demonstrates the success of extra-institutional college curricula operating in a context specific to the learning outcomes of a particular university.

Current drug delivery methods lack the ability to effectively deliver a drug to a targeted region and fail to escape from the endosome. The ability to gain greater control over a drug’s effective delivery would lead to an enhanced efficacy of existing drugs, decrease the amount administration sessions, and reduce the number of side effects. Nanotechnology is a means to address these issues as the unique quantum properties witnessed on this scale allow for enhanced targeting and greater control over the delivery of the targeted drug. However, biocompatibility and toxicity are concerns with many developments within nanotechnology. To address these concerns, we have designed a siRNA-aptamer chimera based on protein biosynthesized calcium phosphate (CaP) nanoparticles. This was done due to CaP’s well-known biocompatibility and biodegradability as the calcium phosphate dissolves within the endosome, therefore releasing the siRNA into the cytoplasm of the cell. Within this project, we have targeted cancer cells as a means to quantify the efficacy of our nanoparticles. Through engineering a dual-functional protein expressed in E.coli, we were capable of 1) biosynthesizing CaP nanoparticles utilizing the protein’s affinity to calcium phosphate, and 2) binding siRNA onto the designed protein for delivery, which is utilized to inhibit the translation of the targeted cancer cells. The biomineralized nanoparticles were characterized via DLS and TEM to reveal that we had synthesized uniform 100nm nanoparticles, a promising result which supports our goal of designing nanoparticles capable of establishing greater control over drug delivery. The completion of this project would entail the successful design of biocompatible nanoparticles that could be effectively used to silence cancer cells. As the protein’s affinity for a substrate can be manipulated, these siRNA-aptamer chimeras could see use with other drugs as well; effectively leading to a powerful and versatile drug delivery system.

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s Sarcoma (KS), a cancer of endothelial cell origin that commonly presents in immunocompromised individuals. While relatively rare in the United States, KS remains endemic to certain parts of Africa, where it is the most common cancer. Previous research has established that the number of peroxisomes is altered during latent KSHV infection. Peroxisomes are multifunctional cellular organelles involved in a variety of metabolic pathways important to KSHV pathogenesis. We propose to evaluate the cellular mechanism by which KSHV induces peroxisome biogenesis. I hypothesized that KSHV increases the transcription of specific regulatory genes responsible for the increase of peroxisome biogenesis. After mock and KSHV infecting cells, I evaluated gene expression of a known transcription factor, peroxisome proliferator-activated receptor alpha (PPARA), that has been shown to be responsible for peroxisome biogenesis. I used real time PCR to evaluate gene expression of the transcription factor PPARA. Our preliminary data shows that PPARA is increased, suggesting that PPARA regulates the expression of peroxisome associated genes and peroxisome biogenesis. Currently, I am evaluating if other peroxisome genes are increased, including those involved in peroxisome formation and enzyme activity. In addition, I am using small interfering RNA (siRNA) to transiently knock down PPARA. Silencing the expression of PPARA will determine its specific role in peroxisome biogenesis. I will mock and KSHV infect the cells in which PPARA is knocked down and use real time PCR to evaluate peroxisome biogenesis. In the absence of PPARA, I expect that PEX gene expression will be downregulated, which would suggest that PPARA regulates PEX genes at the gene transcription level. These results will help elucidate one of the key pathways involved in KSHV latency, and potentially contribute to the development of novel therapeutic avenues for KS treatment. 


Our research project was to design, construct, and launch a high powered rocket with the intention of pushing its velocity significantly past the speed of sound while simultaneously collecting data from which to interpret the max achieved acceleration, velocity, and altitude. The rocket's body has a three inch inner diameter made to fit the 3-inch motor casing without any extra room. This minimum diameter design reduced its weight so that less force was required to achieve higher acceleration, and it provided a smaller cross sectional area than a traditional rocket, thereby reducing the amount of drag force impeding its acceleration. Atypical of most high powered rocket designs, our rocket features a metal tipped nose cone to provide resistance to the heat caused by friction when breaking the sound barrier. At the speeds achieved, unmodified rocket fins will vibrate at extreme rates due to turbulent flow. In order to combat this destructive effect the fins were reinforced with carbon fiber to significantly stiffen them and reduce any resonant effects during flight. The payload consists of a StratoLogger SL100 Altimeter to keep track of the maximum altitude and velocities of our flights as well triggering two separate parachute deployments, achieving a safe landing while also minimizing drift time due to winds at altitude. It is our hope that our research rocket will push the boundaries of velocity and altitude achieved by a junior college rocket team as well as provide insight into ways to optimize our rocket designs to maximize future results.

A pressing issue for much of the world is finding energy resources alternative to fossil fuels. I conducted a literature review through databases such as JSTOR and ERIC that addresses fractal kinetics to describe the saccharification of lignocellulose. Lignocellulose is one of the most abundant biomass resources on earth found in plants and can be converted into a biofuel, ethanol. The process of converting lignocellulose to ethanol is similar to the process of converting starch, found in corn, into ethanol. In both processes the substrates go through saccharification, a procedure where they are broken down into glucose. The glucose is then fermented and is converted into ethanol chemicals. However, converting lignocellulose to ethanol has a very low conversion rate which inhibits the ability to use lignocellulose as a viable energy alternative. Primarily, the classical kinetics model is used to describe the saccharification of cellulose. Before the introduction of fractal geometry in the 1970s, the geometry of nature was considered too complex and irregular to describe analytically using Euclidean geometry. Since then, fractal geometry has been found to model natural phenomena. Fractal theory is important to helping scientists understand the saccharification of lignocellulose and develop models for efficient conversion in the future. With a consistent method to converting lignocellulose into a biofuel, society can move away from fossil fuels as our greatest energy source.

For over twenty years the Text Encoding Initiative (TEI) has managed and developed a set of encoding guidelines for the representation of humanities, social sciences, and linguistics -- to preserve and share -- texts in digital form. Using the Extensible Markup Language (XML) as its backbone, TEI is the generally accepted encoding model for the digital humanities. Due to XML’s extensible nature, it can often be difficult to share these files and even more problematic to make them interoperable. The goal of our project is to build a prototype Application Programming Interface (API) for TEI-XML documents that provides greater interoperability while at the same time being easy to use by an audience with backgrounds in the humanities, social sciences, and linguistics. Currently, we have produced a deliverable with two components. The first: an API that, once installed, can return multiple views of a TEI-XML file using a Uniform Resource Identifier (URI) as its query method. The second is a set of user-tested support documentation that is both easily discoverable and easliy usable by our target audience. In future iterations of our prototype we plan to include a more robust listing of return view types, the ability to support multiple TEI-XML files, and API key permissions support.

Recognizing partially occluded objects is a major challenge for even the most cutting edge computer vision systems even though humans recognize partially occluded objects effortlessly. To begin to understand the neural basis, past research studies have investigated the correlation between animal behavior and neural activity during recognition under occlusion. These studies have been done on stable occluded objects even though it is well known that stimulus motion can attract attention to objects and can facilitate segmentation of objects in clutter, for example, in breaking camouflage. We investigated whether motion of an occluded object facilitates its recognition. To address this question, we asked human subjects to report whether two stimuli were same or different by pressing keys, M or N, for match or non-match. We moved the second stimulus at different speeds behind a field of occluding dots and asked how the percent correct performance and reaction time were influenced by the speed of movement of the visual stimulus. We found that 4 of the 6 subjects we tested exhibited a decreased reaction time and increased percent correct performance with stimulus motion. To verify that this difference was not simply because motion revealed parts of objects that were previously occluded by dots, we designed a control where the occluded shape underwent random jumps as opposed to coherent motion. In this case we did not observe the benefit of motion on performance. Thus, our results support the hypothesis that motion of an occluded stimulus enhances its recognition and discriminability.

Therapsids (mammal-like reptiles) document the transition to modern mammals and are an important study tool in examining how the past informs the present. Understanding diseases today requires understanding the deep evolutionary history in our fossil ancestors. We present an instance of dental pathology in a gorganopsid therapsid (~260 million years old). Using fossil histological techniques, we examine a gorganopsian canine and preliminary results reveal abnormal mixture of dental tissue next to the functional tooth. These individual ectopically expressed teeth have preserved tissue layers such as enamel, dentine and a pulp cavity. Based off of the histological characters of our specimen as compared to modern clinical studies we hypothesized two possible diagnoses: odontoma and enamel pearls. Enamel pearls show dento-enamel pearl nodules protruding from the enamel of a functional tooth. Odontoma presents as individual teeth with their own histological packaging (i.e. dentine and enamel). These results suggest that our specimen most likely had odontoma. In modern cases, this results in excess dentinal tissue growth and un-alignment of teeth. The cause of this odontoma in modern clinical practices is a result of either trauma or rapid tooth replacement. The canine tooth of this gorgonopsid was prone to trauma since it served to pierce prey and was subjected to intense forces. Alternatively, gorgonopsids replaced their teeth continuously. This continous replacement could have gone awry resulting in this disease. This study presents the oldest possible case of cancer in the fossil record and elucidates the evolution of such pathologies. This study has relevance in dental clinical studies because understanding how diseases operate in humans requires an understanding of how they evolved in our deep evolutionary history. 

When setting up interspecies crosses between female Caenorhabditis species 29 (C.sp.29) and male Caenorhabditis nouraguensis (C.n.), the resulting progeny are all dead. However, the reciprocal cross (mating male C.sp.29 with female C.n.) still results in mostly dead progeny, but there are rare progeny that survive. These rare, surviving progeny can either be sterile or fertile. My research focuses on studying what causes the sterility of the rare offspring genetically. Thus, I set up crosses between female C.n and male C.sp.29 and collect the resulting rare offspring to genotype them. Then I characterize these offspring based on their morphology and genetic differences such as homozygous or heterozygous type inheritance at each chromosome. The worm genome consists of six chromosomes and I am currently testing chromosome I and IV. So far, fertility is associated with only maternal inheritance at chromosome I, while sterility is associated with offspring being a hybrid (heterozygous) at chromosome I. The fertile progeny are able to survive possibly due to a process called gynogenesis. Gynogenesis is when the egg is activated by the sperm but sperm’s DNA is excluded in the offspring. Some offspring exhibit a homozygous genotype at one chromosome while a heterozygous genotype at another. Therefore, if a reoccurring pattern is observed where a sterile worm has a homozygous genotype at chromosome I and a heterozygote genotype at chromosome IV, then I could hypothesize that sterility of the offspring is due to this particular pattern of inheritance. This implies that there could be more than one combination of inheritance contributing to the degree of sterility of each offspring. The main goal of the project is to investigate the complexity and the genetic requirement for sterility that is caused as result of these crosses.

Chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) is the gold standard for assaying the binding sites of chromatin-binding proteins and their modifications, such as histone tail modifications. One major limititation for this method is that it requires large amounts of starting material, therefore limiting applications in those cases where only a limited number of cells can be recovered, e.g. rare cell populations obtained directly from patients. In the last few years, great efforts have been made to develop new ChIP-seq protocols to overcome this limitation. In my lab, they have developed a method called carrier ChIP-seq (cChIP-seq). The method is based on the use of a DNA-free carrier to enhance recovery of DNA after IP. Using cChIP-seq they have been able to perform ChIP-seq on 10,000 cells for several histone tail modifications. I tested a series of modifications on the cChIP-seq protocol. The goal of my project was to develop a protocol that can be performed in one day. Currently the cChIP-seq protocol takes 3 days to be complete. This is mainly due to two overnight incubations. The first one is the immunoprecipitation, so I performed multiple trials to identity the minimum time sufficient for immunoprecitating the chromatin. The second overnight incubation is to reverse crosslink immuneprecipitated chromatin. I tested a version of the cChIP-seq protocol for native chromatin, meaning the DNA is not crosslinked. By optimizing and combining these two modifications I was able to shorten the cChIP-seq to a single day. Through my project I contributed to a larger project with the goal of scaling down the number of cells used for ChIP-seq.

Polio is on the cusp of worldwide eradication but remains endemic in Afghanistan and Pakistan. The Global Polio Eradication Initiative has implemented an environmental surveillance program to detect poliovirus (PV) in environmental samples such as sewage. Systematic environmental sampling provides supplemental data to disease-based clinical surveillance data. However, traditional PV detection methods from environmental samples, cell culture and quantitative reverse transcriptase polymerase chain reaction (RT-qPCR), are time-consuming and expensive. Development of a screening test has potential to streamline environmental surveillance of PV. Reverse transcriptase recombinase polymerase amplification (RT-RPA) is an isothermal molecular amplification technique with potential as a screening test. In this technique, virus particles are lysed to release RNA, which is converted to cDNA and amplified using enzymes. Amplified PV cDNA can then be detected through lateral flow detection. Collaborators at PATH have developed a RT-RPA protocol that has shown promise in rapid PV detection in stool samples. The aim of this research is to adapt PATH’s clinical PV RT-RPA protocol for use with environmental concentrates. Concentrates were obtained by filtering raw sewage from a Seattle wastewater treatment plant. Results of the RT-RPA test and subsequent visualization on lateral flow detection strip were compared to cell culture and RT-qPCR. We anticipate that RT-RPA will show similar PV recovery rates when compared to traditional methods and will be suitable as a rapid screening test for environmental concentrates. Future work will include designing primers to expand PV serotype detection and evaluating PV detection in environmental samples from existing sampling sites. Rapid PV detection with RT-RPA may streamline environmental surveillance methods, improve outbreak detection, and provide data for certification of polio-free status and global eradication.

Macrophages play a large part in the immune response to Mycobaterium tuberculosis (M.tb) infection, and its response to infection is modulated by pattern recognition receptors. CD43 is a receptor glycoprotein on the macrophagal surface that has been shown to be associated with differential response severity of TB. The mechanism behind CD43 involvement in the macrophage response to M.tb is still unknown. Our hypothesis is that CD43 controls M.tb growth in human macrophages by mediating pro-inflammatory modulators. We knocked out the CD43 gene in the monocytic cell line THP-1 using the gene editing system lentiviral CRISPR Cas9. Using this cell line, we investigated how the knocked-out cells were affected when infected with M.tb compared to wild-types. We did this by measuring replication of a luminescent M.tb strain. Additionally, since M.tb capsule protein CPN 60.2 is a known ligand of CD43, we used CPN 60.2 to stimulate a tumor necrosis factor (TNF) cytokine response in both wild-type and knocked-out cells. We evaluated the TNF response using an ELISA assay. We found a statistically significant higher rate of replication in the CD43 knocked-out cells compared to wild type cells, indicating that CD43 plays a significant role in the macrophage’s pathway of killing M.tb. We also found significantly lower TNF secretion in CD43 knocked-out cells when compared to wild type cells after stimulation with CPN 60.2, which shows that cytokine response to M.tb is likely modulated by CD43 as well. Taken together, these results show that CD43 is a novel receptor on the macrophage surface that modulates the innate immune response to M.tb by controlling growth and pro-inflammatory cytokines such as TNF. The next steps in this project are to explore the exact mechanisms, such as M.tb macrophagal uptake and phagosome formation, that CD43 targets to control M.tb growth to develop targeted therapies for better TB treatment.

Xenobiotic biotransformation is a vital process in the body that detoxifies various drugs, dietary factors, and environmental toxicants. This process is mediated by various drug-metabolizing enzymes in Phase-I (oxidation, reduction, and hydrolysis) and Phase-II, as well as transporters. The hepatic nuclear factor 4alpha (HNF4α) is a master regulator that transcriptionally up-regulates a wide spectrum of drug-metabolizing enzymes and transporters in liver. HNF4α also plays an important role in liver development and nutrient homeostasis. Previously, it has been shown that HNF4α can trans-activate the constitutive androstane receptor (CAR), which is a major ligand-activated xenobiotic-sensing nuclear receptor. However, very little is known about the effect of CAR activation by xenobiotics on the regulation of HNF4α in liver. In the present study, male mice at either 5-day-old neonatal age or 60-day-old adult age in wild-type, CAR-null, or humanized CAR-transgenic (hCAR-TG) genotypes were treated with vehicle (corn oil, which served as the control), or a species-appropriate CAR ligand (TCPOBOP for mouse CAR and CITCO for hCAR), once daily for 4 days. A novel truncated coding exon 9 was observed for the HNF4α transcript variant in mouse liver (RNA-Seq). Isoform-specific RT-PCR and gel electrophoresis confirmed the presence of the novel HNF4α isoform. During development, both the known and the novel isoform had increased expression with age. The mouse CAR ligand, TCPOBOP, down-regulated HNF4α in a mouse CAR-dependent manner only at mice at age 60, whereas hCAR did not appear to regulate the expression of HNF4α at any ages. In conclusion, the present study has identified a novel HNF4α transcript variant in the mouse liver, and discovered that both the known and novel isoforms were regulated by CAR in a species and age-specific manner.

Since DNA replication and transcription are concurrent in most bacteria, collisions (or conflicts) occur between these two processes. Conflicts have deleterious effects on cells, including double strand breaks and mutagenesis, especially when a gene is transcribed head-on to replication. Because conflicts increase mutagenesis specifically in genes that are oriented head-on to replication, this process may be a conserved strategy for targeted evolution. Consistent with this, a bioinformatics analysis determined that many genes in the head-on orientation are involved in stress response. We previously showed in Bacillus subtilis that the error prone translesion synthesis (TLS) polymerase YqjH is required for the asymmetric mutagenesis of genes in the two orientations and that transcription-coupled nucleotide excision repair (TC-NER) is also involved in this repair pathway. Under DNA damaging conditions, however, a different TLS polymerase, YqjW appeared to be responsible for mutational asymmetry, though TC-NER appears to still be involved. To show this, I used RecA-GFP microscopy to measure rates of replisome stalling in Wildtype, YqjW deletion mutant, and YqjW/UvrA double-deletion mutant (WT, ΔyqjW, and ΔyqjW/ΔuvrA) in B. subtilis, along with measuring these same strains' survival rates in response to two types of DNA damage. The data I generated was supported by mutation rate data generated through reversion assays done by a technician in the lab, and these data led us to propose that during conflicts in the presence of DNA damage, YqjW outcompetes YqjH to fill in gaps in DNA during TCR.

Microparticles are 0.1-1.0 μm vesicles derived from cell membranes upon cell activation, injury, or apoptosis, and are believed to aid coagulation. Due to their clinical significance, a calibration method to quantify microparticles on an upgraded flow cytometer was developed in this study. Optimal settings were previously sest on the Apogee A40 flow cytometer. However, this flow cytometer has recently been internally upgraded to a newer model, Apogee A50, making re-calibration necessary for accurate microparticle measurements. The same beads used for calibration appeared to scatter even more light on the A50 using the same settings and no longer corresponded to the desired upper limit. As a result, steps were taken to re-calibrate the optimal settings for microparticle detection. These were achieved by using polystyrene and silica beads of known sizes, antibodies with fluorescent molecules attached, and normal patient platelet rich and platelet poor plasma. Instead of using the forward scatter curve as previously done on the A40, experiments on the A50 utilized the side scatter curve due to the histogram’s appearance. After adjusting the voltages and threshold, the 1 μm microparticle cutoff corresponded with 0.4 μm polystyrene and 0.7 μm silica beads. The compensation settings (subtraction values to correct for overlap of fluorescent light signals) also differed significantly on the A50 compared to the A40. Based on these results, the Apogee A50 needs to have these newly established settings applied in order to effectively quantitate and measure microparticles.

Melioidosis, a disease caused by Burkholderia pseudomallei, is the third most fatal infectious disease in Thailand and causes morbidity and mortality in many other Southeast Asian countries. Due to fears that this bacterium could be weaponized, the US government lists this bacterium as a tier 1 select agent. Current treatments involve weeks of IV-delivered antibiotics and months of pills to prevent reoccurrence of the infection. Despite the availability of these treatments mortality can be as high as 40% in some locations. This situation calls for a more effective means of treatment to reduce loss of life, treatment time, and cost involved in fighting melioidosis. In order to develop a more efficient treatment, I created a novel delivery system to deliver large doses of antibiotics and, potentially, prophylactically load cells with therapeutic to prevent infection. I formulated nanoparticles using reversible addition-fragmentation chain transfer (RAFT) polymerization and microemulsion. The particles were first formulated using an inert monomer to test uniformity of the constructs and optimize the microemulsion procedure. Once this procedure was optimized, I added a prodrug monomer containing ciprofloxacin to the construct and the new constructs were characterized for size, shape, and the kinetics of prodrug degradation to its active form. Cytotoxicity to mammalian cells was tested with MTS assays using RAW 264.7 cells. Planktonic assays were also performed to test the efficacy of this novel delivery system to combat Burkholderia as compared to free ciprofloxacin.

Seattle’s young homeless population has long been underrepresented and misunderstood—their experiences are largely absent from public conscious. In the University District, young people often face discrimination, stereotypes, and violence rooted in negative perceptions from University of Washington students. These two groups share a history of mutual distrust and even fear. Exposure is creating a 3D interactive narrative to challenge stereotypes toward homeless youth and allow an audience of University of Washington students to step into the shoes of a young person experiencing homelessness as a way to confront misperceptions. We took a community-grounded approach to researching this marginalized group. Through volunteering with service organizations and meeting with community leaders, we have curated stories and experiences by which to design this dramatic narrative. We also draw upon existing literature on daily youth community practices as well as game design for addressing social issues. We have then developed requirements for key scenes and interactions for this narrative. For example, cell phones, which play a large role in managing young people's’ lives, will be represented in the narrative. The diversity of the community across race and gender identity will manifest as playable characters with narrative outcomes distinct to those identities. As of today, Exposure is completing a working prototype for this narrative which will then become a playable demo. Key elements of our narrative have been written and storyboarded. By exposing our audience to the youth community through this fictionalized interactive experience, we hope students will confront prevailing misperceptions of young people, develop empathy for this underrepresented community, and engage with movements addressing structural causes of homelessness. In the same way film and literature are used to communicate our lived experiences, we hope that the use of an interactive medium will be a novel and impactful approach to represent a community long neglected.

In order to successfully invade and survive within a host cell, pathogens such as the bacteria Shigella flexneri have to suppress the host cell’s immune response. To do this, Shigella flexneri inject bacterial effector proteins into the host cell that hamper the host cell’s ability to detect and respond to invasion. One such protein is IpaH4.5, a bacterial E3 ubiquitin ligase, which hijacks the host cell’s ubiquitylation machinery to transfer ubiquitin, a small signaling protein, to a substrate. Ubiquitin signaling impacts all aspects of eukaryotic cell biology. Often modification of a protein by ubiquitin serves to mark protein for destruction. IpaH4.5 targets proteins involved in the host cell’s immune response, dampening the host cell’s ability to respond to invasion by Shigella flexneri. I am investigating IpaH4.5 and its interactions with both host substrates and the host ubiquitin machinery. After sub cloning out the various domains of TbK1, a known substrate of IpaH4.5, I will perform ubiquitilation assays in order to determine which domain of TBK1 is polyubiquitilated, indicating that IpaH4.5 interacts with this domain. Then, this domain can be used for structural and mechanical analysis of IpaH4.5, such as determining how mutations in IpaH4.5 affect ubiquitilation through biochemical assays. Understanding how IpaH4.5 binds to and interacts with its substrates will increase our understanding of how Shigella flexneri dampens host immune response as well as help us better understand the mechanisms of bacterial E3 ubiquitin ligases. Since IpaH4.5 functions differently than eukaryotic E3 ubiquitin ligases, increasing our understanding of its mechanisms could allow us to use it as a target for future drug development. Finding new targets for drug development is becoming increasingly important with the spread of antibiotic resistant bacteria.

A myriad of health disparities exist among Somali refugee and immigrant children living in the United States. Child undernutrition is a prominent issue in the community that affects children at a critical point of development and can lead to negative health outcomes later in life. Recent data estimates that the percentage of underweight children in the United States is 0.5%, the rate of underweight children in Somalia is 23%, and the rate of underweight Somali refugee children living in America is as high as 22%. Field data for the Somali refugee and immigrant population was collected from October 2015 – February 2016 at the Refugee Women’s Alliance (ReWA) in South Seattle in a job readiness program. The data was used to assess possible barriers in accessing healthy food, as well as barriers in accessing services meant to combat nutritional disparities. Data was then juxtaposed with qualitative data and statistics on the social determinants of health, as well as the nutritional status and food insecurity levels, of Somali refugee and immigrant children living in Lewiston, Maine. The research shows that Somali refugee and immigrant children of King County are affected by the same social and structural barriers that led to the poor nutritional status of refugee children living in Lewiston, Maine. Furthermore, the purpose of this research is to find what factors contribute to the substandard nutritional status of Somali refugee and immigrant children in hopes to reduce the clear level of inequality present in King County.

Explosive boiling is characterized by an unstable, non-uniform liquid/vapor interface consisting of multiple gaseous lobes. Explosive boiling at microscales is a process of extreme interest in the studies of micromechanical systems and actuation due to the nearly instantaneous pace and large amounts of kinetic energy associated with the process. These characteristics that make the explosive boiling phenomenon highly attractive for certain microscale applications also hinders the study and understanding of the dynamics of the unstable liquid/vapor interface, and thus the prediction of the overall behavior of the process. The objective of my research is to overcome the challenges posed by the small temporal and spatial scales by designing and building an experimental apparatus to observe the explosive boiling phenomenon. This apparatus consists of a test chamber in which the explosive boiling of a droplet of test fluid will be controlled by the host fluid temperature gradient, and a high speed camera used to capture the process in a high level of detail. The experimental results will be compared with theoretical results acquired from direct numerical simulation to elucidate the dynamics of the liquid/vapor interface. The experimental apparatus design and preliminary imaging results are presented.

Humans have an intrinsically symbolic nature that leads individuals to seek a stronger connection to the physical world around them. At numerous archaeological sites all over the world, red ochre has been utilized as a decorative pigmentation with an evidently ritualistic and spritual purpose. For example, on the Kamchatka Peninsula in Russia, multiple Upper Paleolithic burial pits have been filled completely with red ochre, which covered the bones and related grave goods. Early hunter gatherers at the Tanginak Spring Site in Kodiak, Alaska coated their living surfaces with red ochre and archaeologists are divided about whether this paint is a byproduct of waterproofing tent seams or a purely ritual application of color to ritual spaces. In my research, I will attempt to test predictions regarding whether or not the the residents of this particular Ocean Bay 1 site were employing ochre for its abilities as a tent waterproofing agent or if its pigmentation served a purely spiritual purpose. Through experimental archaeology and an analysis of the ochre and ochre processing tools discovered at the Tanginak site, I will gather evidence to either support or disprove my hypothesis that ochre served both a practical and symbolic purpose. 

Highly controllable adhesives refers to adhesives that can be activated to attach strongly when needed but deactivated for easy and non-damaging detachment. There currently is a need to develop highly controllable adhesives that work optimally in wet environments, like those found inside the human body. Single fimH proteins, found at the tip of E. coli type 1 fimbria, form bonds with mannose that can be activated to bind strongly when pulled at high speeds, but are not activated under low speeds and as a result bind weakly. We hypothesize that thin-films composed of E. coli type 1 fimbriae can act as a nanoscale locking seatbelt, where they lock in at high speeds but not at low speeds, and that we can use mechanical force to control the adhesive behavior. Using atomic force microscopy (AFM) we tested the adhesive behavior between fimbriae thin-films and mannose covered surfaces. We observed that the force required to break the surfaces apart, as well as the number of activated bonds formed, increased the faster the surfaces were pulled away from each other. Also, by using the AFM to preload the bonds with high force, we observed that we could increase the number of activated bonds by a near 4 fold, as opposed to pulls with no preload. Inactivation after preload was also observed by allowing enough time for bonds to inactivate under no force, which decreased the bonds activated to only a 2 fold increase. These results show that these adhesive thin-films are capable of acting like a nanoscale locking seatbelt and can be controlled through mechanical force. An adhesive that can display these properties can have the potential to be incorporated into devices like pill endoscopy, giving an increased ability of controlled precise movement in fields like medical micro-robotics.

Glioblastoma multiforme (GBM) is the most common and highly malignant brain cancer diagnosed in adults. Due to its high invasiveness and difficulty of surgical removal, there is a need for novel therapeutics to treat this disease. Recent evidence suggests that cannabidiol (CBD), a non-psychoactive compound from the Cannabis plant, possesses antitumor properties in a number of cancers. However, the mechanism by which CBD acts to decrease tumor viability and proliferation is unclear. To better understand the antitumor properties of CBD, we tested this compound against standard of care chemotherapy drugs BCNU, Temozolomide, and Cisplatin in human GBM cell lines T98G, U87MG, and U251. Using the water soluble tetra-zolium salt (WST-1) reagent and bromodeoxyuridine (BrDU) assay in vitro, we assessed the dose response of CBD on GBM cell viability and proliferation, respectively. Using the same assays, we also investigated the effects of CBD in combination with standard of care chemotherapy. We found that CBD dose-dependently (IC50 = 3.1µM) suppressed viability and proliferation in all GBM cell lines tested, and that this response was more potent than standard of care chemotherapy. In addition, CBD exhibited additive effects when combined with standard of care chemotherapy in vitro. Implications for this research include development of novel cannabinoid-based cancer therapeutics.

People in agriculture commonly use pesticides to prevent insect damage on crops. One common pesticide is called acetamiprid (ACP). While this pesticide has low toxicity to mammals, there have been cases of acute toxicity from overexposure to this pesticide. In this study, we focused on pesticide handlers, people who apply pesticide to crops in the fields, from the Yakima valley and analyzed their urine samples to measure their exposure to the pesticide ACP. The primary goal of the study was to quantify urine biomarkers to ACP exposure, including the parent compound ACP, and two metabolites: acetamiprid-N-desmethyl (ACPDM) and 6-chloronicotinic acid (6-CNA). We collected urine samples from 10 pesticide handlers in the 24 hours after applying ACP in an orchard. Each person was given a liter sized sampling vial to collect each void. We collected 34 human samples in total. I identified and quantified the biomarkers in the human urine samples collected. I did this by processing the samples using Solid Phase Extraction (SPE) and then quantifying them by using high-performance liquid chromatography and tandem mass spectrometry (HPLC-MS/MS). We expected to see small amounts of each biomarker in each sample, but found relatively high concentrations of the metabolite ACPDM. The results of this study will help to improve our ability to measure urinary markers of exposure, better estimate exposure and risk to pesticide handlers, understand the kinetics of ACP in the human body, and think of means to minimize exposure to prevent acute toxicity.

Much of the topography of Eastern Washington was shaped by the recession of the Cordilleran Ice Sheet and by periodic flooding from Glacial Lake Missoula towards the end of the last ice age. The age of flooding is approximately known from Carbon-14 dates, but because the floods distributed granite boulders across much of Eastern Washington we can improve the chronology using exposure dating with cosmic-ray-produced nuclides. In this method, the build-up of Aluminum-26 and Beryllium-10, two isotopes produced in quartz by cosmic rays, indicates the length of time these boulders have been exposed. By applying this technique to selected deposits we can shed light on the age of the last floods, sources of floodwater, and how the extent of the Cordilleran Ice Sheet controlled the floodwater paths. Initial data show that the last floods through Grand Coulee occurred approximately 15,500 years ago, but younger floods passed down the Columbia Gorge until approximately 14,100 years ago. This final flood may represent breaching of the glacier-ice dam across the Columbia River, or a glacial outburst flood from a more distant source. We can distinguish these possibilities by dating glacial deposits on the Waterville Plateau and in the Okanogan Valley. One exposure age on a glacial erratic from north of the Columbia River near Brewster gives an age similar to the final flood, possibly suggesting that the flood resulted from breakup of the Columbia River ice dam. Chemical analysis and accelerator mass spectroscopy of additional samples will give us a more accurate picture of the chronology of the last of this catastrophic flooding.

In recent years, heart rate variability biofeedback (HRVB) has been used to treat a variety of illnesses and disorders such as depression, hypertension, and asthma. HRVB method includes presenting to an individual his current heart rate (HR) on the screen and teaching him to increase/decrease his HR by breathing at frequency of 0.1Hz (6 breaths/min). Such breathing will elicits high-amplitude oscillations in HR and blood pressure (BP). Such oscillations arise since baroreflex, as a closed-loop system for BP control, has resonance property (i.e., produces high-amplitude oscillations in response to 0.1Hz stimulation). The benefits of HRVB are derived from these oscillations which train reflexes and improve cardiovascular regulation the same way physical exercises improve muscle condition and regulation. The purpose of this study was to evaluate the response of the baroreflex to paced 0.1Hz emotional stimulation and how alcohol affects this response. Seventy-two subjects were randomized into three beverage groups that received an active dose of alcohol, an inactive dose of alcohol (placebo), or no alcohol. Each performed eight 5-minute tasks: two baseline tasks (before and after beverage consumption), four emotional stimulation tasks (negative, positive, alcohol, and neutral picture cues paced at 0.1Hz), paced breathing task (using a moving bar), and paced breathing task (using alcohol images). ECG, beat-to-beat blood pressure, and respiration were collected. Alcohol reduced baroreflex activity across all tasks. There was a strong positive association between the amplitude of 0.1Hz HR oscillation with baroreflex gain (activity) in both alcohol and control groups. Paced 0.1Hz breathing significantly increased baroreflex gain in the control and placebo groups, but did not change it in the alcohol group. All emotional tasks decreased baroreflex gain. Paced breathing versus breathing plus emotional stimulation tended to increase baroreflex gain more. Results showed that the application of breathing in HRVB is more effective than emotional stimulation.

Congenital heart disease is a problem with the structure of the heart that is present at birth. In the United States, about 40,000 babies are affected by this disease annually. In our lab, zebrafish are used to investigate the genetic causes of this disease. Previous research investigations from our lab have shown that two important genes that are responsible for the regulation of heart muscle are Pbx4 and Pbx2, which are homeodomain transcription factors. Pbx2 and Pbx4 are genes of interest because their roles in heart development are not completely understood. CRISPR/Cas9 method is a method that can be used to target specific DNA sequences and create modifications in the genome. We used this method to engineer different strains of zebrafish with a variety of Pbx gene alleles to determine the role of the Pbx factors in heart development. In order to figure out how the different alleles affect the Pbx genes, each of the strains were observed for phenotype. The null alleles of Pbx2 and Pbx4 were used to demonstrate that embryos lacking both of these factors have severe defects in heart muscle differentiation and outflow tract formation. Then, in-frame deletions were made in the Pbx4 gene demonstrating the importance of an alanine tract for critical functions in heart development. Next, a strain was engineered which contains a Pbx gene variant associated with congenital heart disease in humans. Crosses were set up between strains to compare the effect of each mutation. Thus, the use of genome engineering allowed us to conduct analyses of vital transcription factors involved in heart development.

A method will be presented for dating the last time sub-glacial mountains in West Antarctica were fully exposed by measuring the cosmic-ray-produced isotope ⁴¹Ca. The use of ⁴¹Ca will add a new cosmogenic isotope to the existing toolbox to improve surficial dating. The advantage of ⁴¹Ca over other isotopes is its short half-life (99,000 years), which reduces the complication of prior exposure in natural samples. To accomplish this, calcium will be extracted from Antarctic bedrock samples, converted to oxalate, and then further treated by column ion exchange to produce pure calcium, free of problematic potassium contamination. The biggest challenge will be to produce calcium hydride for measurement by accelerator mass spectrometry (AMS) to determine the ⁴¹Ca/⁴⁰Ca ratio. Current AMS capabilities allow ratio measurements in the 10-10 or 10-11 range. Measurements of the hydride should allow us to extend this down to the 10-14 level necessary for geological applications. Successful measurements in this range will open up applications such as tests for whether sub-glacial bedrock in West Antarctica was exposed to cosmic rays during the last warm interglacial climate period, approximately 120,000 years ago. Perfecting this method and making it available to others in the field can open a door into the past to determine if current global warming trends are leading us down a path similar to the last deglaciation, which raised global sea level by several meters. Though we are working on a geological and glaciological issue, the ultimate product of this research touches areas of meteorology, biology, and sociology as the Earth adjusts to increases in global temperature.

This project focused on redesigning the application and related sites for mPOWEr, a research project building a mobile post-operative wound evaluator to reduce surgical site infections. The redesign of the application’s overall aesthetic focused on improving usability and creating a more cohesive look. One of the major tasks in redesign was reimagining the patient-facing site. After brainstorming and interacting with the initial patient site, I realized the necessity of a distinct, categorized system for the website instead of a primarily single-document layout. I created basic wireframes, which turned into higher-fidelity prototypes, and eventually culminated in coding the live site. Through group critique, feedback, and continued iterations, the patient-site went through the steps of creative problem-solving to construct a cohesive identity for mPOWEr and provide compelling visuals that match the group’s purposes. After creating a new identity for the patient-facing site, similar design can be applied to the application itself, as well as other of marketing materials, to build cohesive aesthetic and distinctive design across all elements of the project.

Our project is to characterize the Caenorhabditis elegans (C. elegans) ortholog of PICK1 and we will henceforth refer to this C. elegans gene as pick-1. In other systems, PICK1 is involved with dense-core vesicle (DCV) biology and has been shown to affect the trafficking of AMPA glutamate receptors to the cell membrane, which are believed to be trafficked in a non-DCV process. DCVs are a specialized organelle in neuron and neuroendocrine cells that are loaded with, and release, several important neuromodulators. These DCV-release neuromodulators regulate a broad spectrum of biological processes such as blood glucose homeostasis, the plasticity of the nervous system, and even appetite. AMPA trafficking is crucial to signaling in the brain. Glutamate is the major transmitter of excitatory signals in the brain. Our project aims to figure out if, and how, pick-1 is affecting these processes in C. elegans. To investigate pick-1's involvement in DCV biology we tested its interaction with RIC-19 (ICA69 in mammalian systems), a protein that is known to interact with PICK1 systems. To test pick-1's interaction with AMPA receptors, we tested how PICK1 affects the localization of GLR-1 (an AMPA receptor). If PICK1 does not affect the localization of GLR-1, then we would expect to see GLR-1 not properly trafficked to the synapse. If PICK1 is involved in DCV biology, we would expect a deletion of pick-1 would create lower levels of RIC-19 in the worms. To this point, our raw data has suggested that PICK1 does not play a role in DCV biology or AMPA receptor trafficking in C. elegans.

A barrier to quality healthcare in low-resource, rural areas is the lack of surgical care, and current anesthetic delivery devices either are expensive or require resources such as electricity. The Bioengineers Without Borders have proposed a low-cost, point-of-care anesthetic vaporizer, and seek a tool to assist in designing the device. To this end, a finite element model was constructed to predict the performance of a device in different operating conditions. We have imported the prototype’s geometry into finite element multiphysics software and added a domain representing the liquid anesthetic. Conservation equations and boundary conditions for mass, momentum, and heat transfer were applied to the domains of the device and numerically solved over clinically relevant time periods. Physical properties of the liquid halothane, stainless steel, and air were approximated using literature values of similar compounds. The model is currently being validated by comparing the vaporizer’s benchtop measurements of concentration and temperature to the computational model’s prediction. Computational results indicate that a vaporizer with no external heat transfer will experience a significant temperature and concentration drop, which in turn lowers the amount of anesthetic vaporized. When validated, the model will prove useful to engineers as proposed modification may be tested computationally before production, allowing for design refinement and less chance of device failure.

Low wage (<$15 per hour) jobs are often structured in ways that expose workers to dangerous chemical and physical agents, as well as policies and practices (e.g., volatile work schedule, low job control, etc.) that may result in adverse stress-related health outcomes. These outcomes are compounded when social disparities such as race, immigration status, and gender are also present. This study will provide a comprehensive assessment of working conditions among low-wage workers and examine the relationship between work conditions, stress and health, and further, if this relationship is affected by union status. Two hundred and fifty low-wage workers from local community-based organizations and labor unions were recruited to participate. Each participant completed a survey describing his or her workplace exposures and health. A composite index of work-related psychosocial stressors was created by combining previously validated scales relating to job strain (control and demand), security, benefits, and overall satisfaction, and each worker was assigned individual scores of work-related psychosocial exposures. We described work-related stressors and health status by union status and other demographic variables. We then examined the association between stress and health, and between union status and health. We further assessed the interaction of belonging to a union and stress on health outcomes. We anticipate that these psychosocial exposures will be associated with stress-related health outcomes. Further, we anticipate that unionized low-wage workers will show less psychosocial exposures to workplace conditions and in turn, less stress-related health outcomes due to better job security, workplace empowerment, and less volatile work schedules. The study information collected from this population may also provide baseline data on which a future longitudinal study proposal can be developed to evaluate the effect of the increase in the minimum wage laws over the next few years.

Freshwater lakes are an important source of the greenhouse gas methane contributing around 6-16% of the total atmospheric methane budget. Methane oxidation in freshwater lakes is the result of different functional guilds of bacteria working together as opposed to just methanotrophs themselves. Microbial communities in methane-fed lake sediment microcosms have not only displayed a clear response to methane by methanotrophs, but also by non-methanotrophic methylotrophs. To obtain a better understanding of the interaction between methanotrophs and methylotrophs, we investigated the role of methanol as a key methane-derived carbon compound enabling stable co-culture formations between a non-methanotrophic methylotroph (Methylotenera mobilis JLW8) and a methanotroph (Methylobacter tundripaludum 31/32). Along with JLW8 wild type, we tested different mutants of Methylotenera with deletions in the methanol oxidation pathway; XoxF mutants 1170, 2048 and 48/70-9. By monitoring the populations of Methylobacter and Methylotenera in the co-cultures with the use of flow cytometry, we find evidence that methane-derived methanol is likely the growth substrate used by Methylotenera in the artificially created methane-fed microcosms. All co-cultures formed stable communities with the exception of the double mutant, which is unable to grow on methanol, indicating that methanol is the key methane-derived component in community establishment. The wild type and both single mutants established co-cultures in similar patterns resulting in somewhat equal distributions of Methylobacter and Methylotenera by the 4th week. Both single mutants, however, showed consistently higher abundances of Methylotenera in comparison to the wild type co-cultures. This data also suggests that both single mutants may be better at oxidizing methanol than the wild type although the mechanisms for this are still unclear. These results provide insight into the growing significance of methanol in facilitating the complex communities invovled in methane oxidation.

Sediment cores were recovered from Limnaea Sø and Braya Sø, closed-basin lakes in Southwestern Greenland, to reconstruct temperatures during the Holocene epoch (past ~10,000 years). The closed-basin topography makes the lakes ideal for studying changes in evaporation and precipitation, and variations in past lake conditions are recorded by authigenic carbonates in the lake sediments. The sediment cores were analyzed by x-ray, magnetic susceptibility, and bulk density to allow stratigraphic correlation between cores and to determine changes in sedimentation rate and lithology. After sectioning, a series of samples taken 20 cm apart were sent for radiocarbon dating, which placed the samples between present day and 9.5 ka (Calendar age). Due to the deposition rate (~0.1 mm/yr), these sediments were sectioned at 0.5 to 1 cm intervals to achieve ~100 year resolution. A series of samples were analyzed for total organic carbon, which provided insight into the history of vegetative changes surrounding the lakes. Samples were then prepared for δ13C and δ18O isotopic analysis on the Kiel Carbonate system/isotope ratio mass spectrometer. The δ13C and δ18O data show periods of isotopic changes, indicating either a strong change in the hydrologic regime or changes in surface air temperatures. We are analyzing these abrupt periods using novel clumped-isotope paleothermometry to determine whether the isotopic variations are a response to lake temperature variations as previous alkenone analyses indicate, or shifts in precipitation/evaporation patterns. While work from ice cores show relatively stable temperatures during the Holocene epoch, recent lake sediment records have suggested that temperatures may have been more variable than thought. If our results show no significant temperature variations, it will confirm previous interpretations based on δ18O that large shifts in the hydrologic cycle occurred. The clumped isotope paleothermometry technique will be the first of its kind applied to Greenland lake sediments to produce a temperature reconstruction.

Wildland firefighters are trained to combat forest fires by prescribed burning or wildfire suppression. Prescribed burning is a planned fire lit intentionally by firefighters to reduce fire hazard and to provide greater safety for firefighters and the public. Wildland firefighters often work on controlled burns using one of two work tasks: lighting, which consists of laying a strip of fire on the forest floor; and holding, keeping fire inside specified boundaries. It is the exposure inherent to these work tasks that our research is primarily concerned with. During these operations, firefighters are exposed to various combustion products, including fine particulate matter (PM2.5), carbon monoxide, and polycyclic aromatic hydrocarbons (PAHs). Many PAHs are carcinogens that undergo metabolism and are excreted in urine. In order to measure the PAH exposure severity, urine samples from wildland firefighters were collected before and after prescribed burn operations as well as on non-burn days. Urine samples were hydrolyzed by treatment with sulfatase and glucuronidase enzymes, and cleaned up with solid phase extraction. High performance liquid chromatography with fluorescence detection was used to analyze the samples for PAH metabolites. Our data analysis compares PAH exposure by work task, by season, and between burn and non-burn days. We anticipate that urinary concentrations of PAHs in firefighters will be higher after the prescribed fire operation compared to pre-burn levels. Findings of this research can be used to measure PAH exposure not only in wildland firefighters, but also in other occupational or residential settings where people are exposed to high concentrations of PAHs to reduce risk factors of developing cancer.

The brain's ability to learn and adapt in response to its environment lies in the plasticity of its synaptic connections. Studying these neuroadaptations is complicated by the tremendous heterogeneity of the brain. Simply isolating a portion of the brain and homogenizing it results in a preparation that includes irrelevant cell types like mitochondria and glia, as well as the specific synaptic targets under consideration. Thus, neurobiologists use synaptosome preparations, which are enriched for synaptic particles, to study synaptic proteins. These preparations are the foundation for the study of synaptic neurobiology. While these synaptosomes preps are of great use, they also have limitations in regards to specificity and purity, with non-synaptic neuronal contaminants occupying a large part of the preparation. Beyond the creation of “cleaner” preparations, it would also be desirable to isolate specific cell types or projections (eg. Thalamo-cortical vs. cortico-cortical synapses). To tackle this issue, we created the Fingr-Sare “TAG” construct, which will allow us to physically isolate synapses that express the construct with high specificity. The FINGR insert is a fibronectin intrabody that binds endogenous PSD-95 and localizes the construct to the synapse, while the “TAG” serves as a target for antibody-based magnetic sorting of glutamatergic synapses. Following transfection of neurons in culture, the construct shows correct dendritic spine localization, with the CD4 portion appearing extracellular of the synaptic membrane. We have been able to sort cells using the TAG construct, and future research will focus on isolating pure populations of “tagged” synaptosomes. Overall, the versatility of this construct could provide researchers with the opportunity to customize and pinpoint specific types synapses from the brain in the hopes of advancing future neurobiological research.
 

Due to society’s increasing energy demand and the push for technological innovation within key industries (e.g. consumer electronics and electric vehicles), major advancements in energy storage technology, specifically battery technology, are needed. While Li-ion batteries are currently regarded as one of the premier options for reusable energy storage, they are not as safe, environmentally-friendly, or cost-effective as currently researched alternatives. One promising alternative is the rechargeable Zn/MnO₂ battery which offers many benefits such as high energy density, low cost, and the ability to use non-corrosive electrolytes. In addition, the cathode material, MnO₂, can exist in a variety of crystal structures which will offer distinct pathways or mechanisms for Zn-ion transport. This project explores how the crystal structure of MnO₂ influences the electrochemical reaction mechanisms and subsequent performance of the Zn/MnO₂ battery. Three different phases of MnO₂ (α, β, and δ) were synthesized hydrothermally for use as cathode materials. Coin cells consisting of a Zn metal anode, MnO₂ cathode, and an aqueous ZnSO₄ electrolyte were then assembled and cycled to determine the charge/discharge behaviors of the batteries. Finally, the results of this project will help identify optimal cathode materials for improving the electrochemical performance of Zn/MnO₂ batteries. 

The Redbluff landslide, situated at Washington-Oregon state border, is part of the larger Bonneville landslide complex. In 1450 A.D., the Bonneville landslide dammed the Columbia River, but the river eventually breached it. In the present day, only one part of the landslide complex, namely the Redbluff landslide, is still slowly creeping into the Columbia River. It also poses a risk of damaging nearby public infrastructure. Interferometric synthetic aperture radar (InSAR) is a remote sensing technique used to measure millimeter-scale surface deformation. These satellite data are complemented by Light Detection Ranging (LiDAR), which is used to produce high-resolution topography images. Using these observations, I seek to understand how the movement of the Redbluff landslide relates to the surrounding geology and morphology. The downslope landslide movement is computed by back-projecting the line-of-sight InSAR observations onto a downslope vector, as done by previous InSAR glacier studies. ArcGIS software will be used to produce a higher-resolution model of the landslide movement. Furthermore, surface roughness will be computed as a geomorphic proxy of active movement on the slope. I expect that the InSAR surface displacement will show active movement in the regions with highest surface roughness. The InSAR and LiDAR data sets are highly complementary data sets and both help to better characterize landslide hazards along the Columbia River.

Understanding the sources and salience of gender stereotypes in society is of huge interest to social scientists as well as the broader public.  Indeed, a large body of research has been devoted to examining gender stereotypes represented in different forms of media particularly digital and print media.  A burgeoning body of research has begun to examine gender stereotypes in video games.  There are 155 million Americans who play video games and four out of five U.S. households own a device used to play video games.  Therefore, gender stereotypes portrayed in video games may be an important way in which people understand gender.  In this research project, I examine trends of female gender stereotypes in both actions and appearances in top rated PC and console games from 1996 to 2015.  I use data from a video game review aggregation website to find the top ten rated games of each year and randomly select four from each year.  I code each game on the stereotypes shown through the actions and appearances of the female characters to determine the overall trends in gender portrayals throughout the years.  This study will help us to understand how women are represented in a wide-reaching media outlet and whether video game companies are displaying more, less, or the same amount of stereotypes in their games over the years.