The question that I am researching is as follows: what is the culture of recruiting high school football players to Division-1 colleges, and how does the experience vary depending on the rating of each individual recruit? I am interested in this question because I feel there is little known about recruiting high school football players, except for what is displayed in the media. The way in which recruits are portrayed creates an image for highschool football players everywhere, and leaves them stereotyped as non-academics. I will use different research methods to pursue my question. Through interviews with teammates and former recruits of varying backgrounds I will gather first hand accounts of their experiences. Through the use of photovoice I will find images that best define what society thinks of recruits today. I anticipate that I will find players experiences with recruiting to vary greatly . I also anticipate that I will be able to show that there are many aspects of recruiting that are still unknown to the public. I hope to show how every recruit is held to a standard that the public is oblivious to, and to eliminate the stereotypes built up by pop culture.

Arsenic-contaminated groundwater poses a major environmental hazard and adversely affects the health of over 100 million people worldwide. Prolonged consumption and exposure leads to arsenicosis, which can result in skin lesions, impaired cognitive development, cancer and death. One current groundwater remediation technique involves injecting microbial nutrients (i.e. sulfate and carbon) into the subsurface of contamination sites to promote the formation of minerals (through microbial-induced reducing conditions) that either integrate arsenic into their matrix or adsorb arsenic onto their surface. However, studies have shown that post-treatment arsenic levels can increase beyond pre-treatment levels if the predominant removal mechanism is adsorption, and if sufficiently high levels of organic carbon are present to further reduce the adsorbing minerals, resulting in the re-mobilization (release) of arsenic. Therefore, it is important to determine the dominant removal process in order to develop effective long-term remediation techniques. Presently, we are working to determine the effectiveness of techniques involving induced microbial sulfate reduction through nutrient injections, which are currently being used for arsenic removal near Tacoma, WA. To simulate field conditions I pumped contaminated groundwater, extracted from the site, through sediment test columns to determine the arsenic retention capacity of the system. Once effluent and influent arsenic concentrations matched, we used the method of sequential chemicals extractions, along with μXRF and μXRS (microscale x-ray fluorescence and absorption, respectively) to determine the speciation and prevalence of the various arsenic-utilizing and -adsorbing minerals created. Next, we will pump uncontaminated groundwater through the columns to determine the post-treatment concentrations expected for this site due to re-mobilization. If our results show that the dominate removal mechanism is the incorporation arsenic into precipitates, preliminary treatment will be sufficient. However, if adsorption is the primary removal mechanism, a long-term treatment plan will need to be developed to minimize the remobilization of arsenic.

Most procedures for DNA transformation of chloroplasts involve the use of circular DNA as vectors and green leaves as the target tissue. Although such procedures are successful with some plants, they are inefficient and do not work with other plants, especially monocots. In maize, plastid DNA (ptDNA) is comprised largely of linear molecules. Furthermore, ptDNA is rapidly degraded as the cells become green. In consequence, the introduction of transgenes into maize chloroplasts has been problematic. In order to create vectors for monocot transformation, the plastid chromosome is most efficiently targeted in its natural form. Previous work suggests that the plastid chromosome is found primarily in a complex, branched linear form with defined ends. We chose one of these ends, “End 1,” which is near an origin of replication, as our target for transgene integration. We constructed vectors with the “End 1” gene sequences and a mannose-metabolizing transgene, PMI, as the selectable marker. Plastid transformation was performed by particle bombardment using gold microcarriers coated with either the circular or linear vector. The successful introduction of a transgene using the “End 1” DNA sequence indicates that the transgene integrates either by end joining of the linear vector to the linear ptDNA or by homologous strand invasion. Thus, using a linear vector with an end sequence produces optimized results when engineering monocot plastid transformants.

Possession Sound is a complex estuary system home to diverse marine life that is impacted by local anthropogenic activity such as surface point and non-point source runoff. Introduction of nutrients with runoff as well as from the Snohomish River and upwelling can lead to increase nutrient concentrations in the surface water, which can cause algal blooms. Phosphate, one of the nutrients, is known to act as a fertilizer for phytoplankton while preventing the growth of zooplankton populations (Phosphates in Water Pollution). We hypothesized that Coscinodiscus spp. will vary directly with phosphate concentrations. To test our hypothesis, we reviewed historical data collected on State of Possession Sound (SOPS) cruises collected in the fall by Ocean Research College Academy (ORCA) students. Nutrient and plankton data in October, November, and December of 2010 as well as November of 2011 were compared. We found that during plankton blooms, phosphate levels are extremely low, possibly due to increased absorption of the micronutrient for photosynthesis. Similarly, when phytoplankton populations were low, phosphate levels increased, likely because of decreased absorption. Conversely, an analysis of tides and seasonal anthropogenic activities are likely to have affected the results of our study and could lead us to further questions.

The evolution of multicellular animals required the development of epithelial tissues that function in controlling the transport of molecules from environment to organism. Collagen proteins are crucial to the formation of epithelial tissues, and are therefore critical in understanding the origins of multicellularity and Metazoan evolution. We characterized the collagen complement from the sequenced genome of the ctenophore Pleurobrachia bachei. 1) We discovered that P.bachei has 7 distinct type IV collagen genes, an expansion unseen in any organism sequenced to date. These genes show unique distribution across the genome: four were in an in-line pattern (αAand αB, αD and αE); two were found independent of other genes (αF, αG), while another two were aligned in a head-to-head fashion (αB,αC). This exceptional arrangement suggests both traditional and inverted gene duplication events in the ctenophore lineage. Ctenophore collagen intron/exon arrangements were also uniquely diverse, with a range of 14-40 exons, depending on the gene. 2) Phylogenetic analysis revealed two distinct collagen groups, the α1-like and α2-like sub-families that are common in bilaterians. Yet, gene to gene comparisons reveal a more diverse type IV collagen complement than found in chordates, including humans. 3) We found widespread expression of type IV collagen. Our findings imply that the common ancestor to all Metazoa might have contained a much more developed collagen complement than was previously appreciated. At the same time, there is extensive parallel evolution of ancestral collagens with remarkable functional specification and diversity of body plans in ctenophores.

Since gaining the right to vote, women’s influence in the political sphere has been on the rise. While voters have started to embrace women as political leaders, research done by Huddy and Terkildsen on gender stereotypes and their effects on candidates finds that female leaders are not given the same respect as male leaders when it comes to military and police issues. Their research also finds that the inverse is true; male leaders are not perceived to have the same competence as female leaders on social welfare issues such as health care and family support programs. I will investigate this question of gender issue ownership by examining the impact of gender on gubernatorial power in 50 states over ten years. I will compare the changes in state spending across policy areas. I hypothesize that, other things equal, a change in the gender of the governor will predict changes in program spending across policy areas. I expect that governors who are perceived to be more competent in a specific policy area will have a greater effect on the spending in that area and therefore that a change in gender of the governor will predict a change in spending.

Active learning generally increases student achievement, but not all instructors experience the same magnitude of gains. This variation in student achievement is likely due to differences in how active learning is implemented in the classroom as well as differences in total classroom time devoted to active learning. Although multiple tools exist for characterizing active learning in the classroom, none have been used to explain variation in student achievement. We are developing a new type of Classroom Observation Tool (COT) that characterizes how closely an instructor’s use of active learning matches the best practices suggested in education literature and can be correlated with observed variation in student exam achievement. Currently, we are using the COT to analyze 3 randomly selected classroom sessions from 27 different introductory biology instructors using archived footage. We will create a linear model that combines instructor’s COT scores with controls for variability in student ability and exam challenge between instructors to predict student exam performance. This model will allow us to identify which elements measured by the COT are most strongly correlated with variation in student performance. With this baseline data, we will be able to recommend the use of the COT to help Faculty assess the effectiveness of their instruction, thereby enhancing teaching and student learning not only within Biology education at UW, but also across all postsecondary education.

It was estimated in 2012 that over 30 million Americans watched National Football League (NFL) football each week. At the same time, over 65% of American households play computer or video games. It is no wonder then, that video games like Electronic Arts (EA) Sports’ Madden NFL has developed what could be called a cult following. Madden has produced multiple editions over the last 25 years, with the recent addition of thousands of virtual media sites dedicated to it. In the last two decades, this has allowed fans new and ever-increasing access. Does this increased access through video games like Madden NFL and the virtual media sites dedicated to them lead to the commodification of players and the perpetuation of historically entrenched stereotypes? To answer this question,  I am building off of Thomas Patrick Oates’ work in his article: New Media and the Repackaging of NFL Fandom, particularly what he refers to as “vicarious management”. Vicarious management is the “presentation of athletes as commodities to be consumed selectively and self-consciously by sports fans”. I used many of the ideas expressed by Grossman and Andrews. Throughout my research I employed the methods of participant observation, discourse analysis, photo analysis, semi-structured interviews, and surveys. The purpose of this research is to gain a better understanding of how vicarious management affects public perception and what steps can be taken to address the ways in which “authority, dominance and social inequality are constructed, sustained, [and] reproduced” through the platforms of video games and virtual media.

Proteins perform a vast array of functions within all living organisms. These functions are heavily dependent on the protein’s 3-D structure. The loss of protein structure can lead to a wide variety of problems, one being the formation of insoluble protein aggregates, which can result from cellular stress. Aggregates can inhibit proper protein function, disrupt cellular homeostasis, and are implicated in many diseases. In order to combat aggregate formation, a family of proteins exists that interact with misfolded and aggregate prone proteins (clients). This family, known as the small heat shock proteins (sHSPs), delays the formation of insoluble aggregates in the cell. Their expression and activity as molecular chaperones have been seen to increase under stress conditions. However, how sHSPs delay aggregation is not well understood. We seek to better understand binding between sHSPs and their clients. Interactions between the sHSP αB crystallin and the model client Δ131Δ (a mutant of staphylococcal nuclease) have been characterized by Nuclear Magnetic Resonance (NMR). We hope to test the observations made from this simplified system in more functionally applicable assays. sHSPs not only interact with clients, but also amongst themselves. There are ten known human sHSPs, some of which have been shown to interact with each other. While this interaction is not well understood, we do know that sHSP monomers associate non-covalently to form dimers, which in turn form higher ordered oligomers. To begin understanding these interactions, we seek to investigate whether sHSPs can exchange their monomer subunits to form heterodimers. The ability to heterodimerize would suggest an even greater diversity of oligomer structure and function. We are interested in characterizing the properties of this proposed heterodimerization. Through site directed mutagenesis, experimental based assays, and gel electrophoresis, we seek to gain a detailed description of these proteins that play such a critical role in cellular health.

Thermostability is the capacity of an organism to survive and thrive at high temperatures and is a characteristic with many biotechnological applications, such as food processing. We are seeking to understand the mechanisms of thermostability in viruses by using an RNA virus, phi-6 Cystovirus. We are evolving the phi-6 virus to become thermostable by exposing it to a target temperature of 61°C over many generations (wild type viruses grow at 25°C). In order to see if exposure to different intermediate temperatures affects the genetic pathway to thermostability, we will expose the phi-6 virus to different temperature regimes prior to reaching the target temperature. The temperature treatments are sudden, where the virus is exposed to the target temperature throughout the entire course of the experiment, moderate, where the virus is exposed to the target temperature halfway through the experiment, and gradual, where the virus is exposed to the target temperature on the final day of the experiment. The genome of phi-6 has already been characterized, which enables us to compare the genome of the evolved, thermostable phi-6 viruses to the ancestor and allows us to study the genetic basis of thermostability. In future studies, we hope to use these thermostable viruses to learn about costs and benefits of maintaining thermostability.

Homeless young people aged up to 30 encounter difficulties when looking for work. The U-District Job Co-op is a design vision that seeks to overcome these difficulties by connecting homeless youth to short-term employment opportunities. Unlike other job search websites, the U-District Job Co-op accommodates the needs of homeless young people by inviting community members to offer mini-jobs and a system of support. Mini-jobs will help homeless young people develop life-skills and work experience that may lead to long-term, permanent employment. Support is provided by employers who offer mini-jobs and feedback, and service providers who assist with the job search and application process, facilitating communication between youths and potential employers. The initial design of the U-District Job Co-op was articulated through wireframes, representations of the layout and structure of the website. Content for the wireframes was drawn from community workshops where homeless young people and other community members discussed barriers and solutions homeless youth encounter in securing work. Three sets of wireframes were developed to show the different perspectives of how a homeless young person, service provider, and employer might interact with the U-District Job Co-op. Eight homeless young people participated in co-design activities (2 participants per activity) that provided assessment of the wireframes. In the co-design activities, homeless young people responded to designer prompts by sketching information they want to present to potential employers through the U-District Job Co-op. Quantitative analysis of the co-design data mapped the number of occurrences of features presented by homeless youth to existing wireframe features. This data informs the refinement of the wireframes. Future work includes developing the U-District Job Co-op into a fully functional website based on the refined wireframes and exploratory field deployments.

Isochrysis galbana is a marine alga that produces large quantities of lipid per cell. Lipids contain extensive amounts of potential energy. Therefore, this haptophyte may be considered for use in biofuel production. The lipid body organelle—the site of neutral lipid storage—is involved in many cellular processes. To date, little is known about this organelle in I. galbana. Chloroplasts contain lipids stored within smaller structures, termed plastoglobuli. For the purpose of the study, lipid body and chloroplast isolation techniques have been developed for I. galbana.  While light intensity has shown no direct effect on I. galbana’s growth rate, we hypothesize different qualities of light will affect growth by altering cellular protein, carbohydrate and lipid content. We will culture I. galbana under red and blue wavelengths of light. Using chloroplast isolation techniques, as well as developed lipid body isolation procedures, we will analyze the lipids contained within I. galbana lipid bodies and chloroplasts when grown under different light qualities. We will also determine if these wavelengths of light induce a stress response concurrent with lipid production. Preliminary data shows that heat shock proteins 70 and 90 –proteins that maintain homeostasis within the cell—are present in I. galbana whole cell protein extracts as well as isolated lipid body proteins. Using Western blot techniques, the abundance of these stress proteins will be measured under different light conditions. These studies will provide information on growth and lipid production under different light qualities, and whether these wavelengths of light elicit a stress response in I. galbana, an alga with potential for applied biomass production.

Drilled oil is becoming increasingly expensive because it is a non-renewable resource that the planet depends on for energy and transportation. Algae may become the next source of global fuel. Chrysochromulina sp. is an ideal model for algal biofuel production because it has a high growth rate in culture, and the two lipid bodies (the organelles that store potential biofuel precursors) are easily detectable using cell biological techniques. The ability of Chrysochromulina sp. to change its lipid metabolism quickly in response to replicated environmental stress conditions is a crucial factor to better understanding its growth optimization and survival. Based on our preliminary data, this microalgae has the potential for production and commercialization of its lipid-based compounds. Guschina and Hardwood’s 2006 studies have shown that lipid production increases in algae under various environmental stress conditions, such as nitrogen limitation, salinity, or increased temperature. Thus, we have investigated the growth dynamics of Chrysochromulina sp. under the following stress conditions: increased salinity, depleted nitrate levels, depleted ammonium levels, and depleted phosphorous levels. For each of these experiments, flow cytometry was used to obtain cell counts and determine growth rate (K’). Neutral lipid content and lipid body size are essential measurements because they represent how efficiently Chrysochromulina sp. produces lipids (i.e. biofuel) and the characteristics of the different lipids being produced. Using Gas Chromatography/Mass Spectrometry (GC/MS), we have elucidated that the lipid profiles change under different growth conditions. The results attained from these studies provide relevant information about the physiology and ideal growth of lipid producing conditions of Chrysochromulina sp. Using this information, we will be able to determine the proteins involved in lipid biogenesis and apply genetic modification techniques to optimize lipid production for commercial use.

Trypanosoma cruzi is a protozoan parasite prevalent in South and Central America that causes life-long infection in humans. Approximately 30% of infected individuals develop a condition called Chagas disease which usually manifests as life-threatening cardiomyopathy or pathologies in the gastrointestinal system. Over 8 million people are believed to be infected. Unfortunately, current drugs for treating Chagas disease have low antiparasitic activity, are expensive, and are known to cause harmful side effects. As a result, research needs to focus on discovering new drug targets in Trypanosoma cruzi to lead to improved drugs. Most eukaryotic organisms synthesize sterols for essential biological functions that when manufactured incorrectly can lead to cell death. This research is investigating the effects of blocking the synthesis of ergosterol by deactivating an enzyme called sterol 14-demethylase. This enzyme catalyzes one of the intermediates of 20 steps of ergosterol synthesis. Inhibitors of sterol 14-demethylase, known as azoles, have been shown to be extremely active on T. cruzi in vitro and are now the center of research regarding anti T. cruzi drug discovery. We are developing novel azole compounds that target the sterol 14-demethylase homolog of T. cruzi to deprive the cell of its necessary sterols. However, further evidence shows that blocking sterol 14-demethylase can lead to an accumulation of sterol intermediates that are converted into toxic agents in the presence of another enzyme, ERG3 enzyme, which is normally active in a later step in the biosynthesis of ergosterol. The objective of this research project is to analyze the ERG3 homologs of T. cruzi. The putative homologs have been cloned and sequenced. No significant mutations were found. The research now is focused on engineering genetic knockouts of the ERG3 genes to test the hypothesis that the knockout parasites may be resistant to treatment with azole drugs.

One role of the state is to help foster economic growth. Financial incentives and regulations are thought to play important roles in industry location and investment decisions. Industries related to bioscience address important problems in society, from how to increase food production to how to defend against viruses. These industries are projected to see large levels of growth over the next 20 years. To explain differences in bioscience industry growth across states, I created a data series that analyzes the incentives available in each state against the impact of each of their bioscience industries. I then defined the quantitative and qualitative effects of these policies in order to show which provide the best areas for growth of bioscience firms and in-turn State economies. I expect to find that high levels of state incentives and reduced regulation directly lead to increased levels of employment, increased number of bioscience establishments, and an overall more impactful bioscience industry.

Currently, various methods of creating engineered heart muscle cell, or cardiomyocyte, patches are being researched. These cardiomyocytes patches have shown therapeutic potential for implantation over injured or killed heart tissue. Current research often focuses on deriving these cardiomyocytes from stem cells, but these stem cell-derived cardiomyocytes are often not as mature as adult cardiomyocytes. Growing these cells on patterned as opposed to flat surfaces, or substrates, also affects the maturity of the cells. This project is the development of automatic video analysis software for cardiomyocytes. This provides a method of automatically quantifying contraction strength and orientation of cardiomyocytes, therefore providing an indicator of the maturity of the analyzed cells. Furthermore, the analysis program can simultaneously measure voltage-sensitive dyes in order to provide information about calcium levels as electrical signals called action potentials travel throughout the cells. This computational analysis will be performed upon human embryonic stem cell (hESC) derived cardiomyocyte tissue, as well as primary adult cardiomyocyte tissue isolated from rat hearts, grown on both flat substrate as well as nanopatterned substrate. Primary cardiomyocyte tissue is anticipated to show greater contractility, higher levels of alignment, and faster action potential propagation than the hESC-derived cardiomyocyte tissue due to its greater maturity. Furthermore, cardiomyocytes grown onto nanopatterned substrate are expected to show greater contractility, alignment, and action potential propagation than those cells plated onto flat substrates. The program in development can be used to automatically create a quantitative measurement of cardiomyocyte maturity levels across a wide array of various experiments. Being able to use the same computational analysis on different experiments both allows for easy comparison of results as well as substantiating the resultant data. Ultimately, this project provides simple automatic quantification of certain key properties of cardiomyocytes based upon videos of their contractions.

While the current, classical, and experimental treatment for ovarian cancer focuses on destroying malignant cells, these cells are actually moving targets for therapies. The tumor “stroma” contains dominantly tumor-associated macrophages (TAMs). TAMs produce factors that support tumor growth and block immune responses against the tumor. Our strategy to eliminate TAMs is based on a new adenovirus vector that expresses suicide gene specifically in TAMs. Our adenovirus vector will transduce TAMs in cell culture and mouse tumor models. We will use a microRNA based system to avoid suicide gene expression in myeloid cells other than TAMs (such as white blood cells). To generate that system, we used mouse tumor models and isolated macrophages from blood and tumors and delineated their micoRNA expression profile using microarrays with >1,000 known microRNAs. We selected the microRNA with the highest expression level white blood cells and a low level in TAMs (mmu-miR-106a). As a negative control, we chose a microRNA that was high in TAMs (mmu-miR-210). My task was to insert 4 target sites with 100% homology to the selected microRNAs into the 3’UTR of a GFP gene, which was under the control of an EF1a promoter. The GFP expression cassette, together with a cassette containing the mCherry gene under the control of the PGK promoter, were inserted into adenovirus (Ad5/11) vectors. We demonstrated in vitro and in vivo, after intravenous injection into mice, that transduction efficiency of white blood cells and TAMs was comparable for the Ad5/11-miR106 and control vector (based on mCherry expression). However GFP expression from Ad5/11-miR106 was absent in white blood cells due to miRNA-mediated degradation of GFP mRNA. My future plans are to substitute the GFP gene with a suicide gene and to demonstrate that corresponding Ad5/11 vectors selectively kill TAMs in vivo, which in turn should slow down tumor progression.

Despite much investigation, there has been relatively little progress in the development of novel analgesic compounds to treat debilitating chronic pain conditions that affect millions of people. Inherent problems in behavioral screens to identify analgesic compounds include the use of expensive and time consuming low throughput rodent based assay as well as the use of behaviors that only measure the presence or absence of acute behavioral responses to noxious stimuli, whereas assays that measure an animal’s ability to choose between an innocuous and noxious environment overcome these setbacks. In this study, we aim to develop a high throughput two-choice thermal discrimination assay utilizing zebrafish (Danio rerio) larvae that can be used to screen for novel analgesic compounds. In order to do this, we will profile the ability of zebrafish larvae to discriminate between two temperatures. Individually arrayed 5 days post fertilization larvae will be placed in wells containing two distinct thermal zones and assayed to determine if they display a thermal preference between a testing temperature and a normal rearing temperature (28.5^oC). The testing temperature will range in one degree increments from noxious cold (10^oC) to noxious heat (38^oC). We will also test the limits of thermal preference by testing the ability of larvae to discriminate between two noxious temperatures, for example 36 vs 38^oC. To conclude if thermal preference is malleable based on the thermal environment to which larvae are acclimated, we will determine if prior incubation at a selected temperature other than 28.5^oC will alter the thermal preference of zebrafish larvae. Finally to determine if our assay may be appropriate for the use in a screen for novel analgesic compounds, we will investigate whether or not known noxious or analgesic compounds alter the thermal preference of zebrafish larvae.

Jane is blind and in need of a new wall oven for her apartment. As she shops for the new oven she discovers that almost all ovens have digital displays for showing the state of the oven, its temperature, and the time left on its timer. They also have buttons flush with the display panel for providing input. She knows from past experience that she can put Braille labels on the buttons and will eventually memorize which button does what, so input will not be a problem. However, how will she read the digital display? Through a friend she learns of a smartphone application called Appliance Reader, which can read digital displays for various appliances including some wall ovens. In order to implement the appliance reader, we have to utilize computer vision algorithms particularly those that match one image against another. The two images can be taken from different perspectives so geometric transformation needs to be inferred from the two images. Once the two images are matched properly, the digital data has to be interpreted to form what would be told to the user. The interpretation requires a machine learning algorithm because standard optical character recognition is not sufficient. A user interface suitable for blind users is needed to make the Appliance Reader practical. As a part of CSE Mobile Accessibility group, which develops smartphone application to aid handicapped people, the two of us have been developing Appliance Reader from the ground up. Under the guidance of Professor Ladner and our mentor, an Intel researcher, Bryan Russell, we have been researching and building Appliance Reader, which is a computer vision-based smartphone application.

Our study aims to determine how physiological measures of affect such as heart rate variability and galvanic skin response may be linked to other representations of emotion that arise naturally in text-based communication during online collaboration. Research in this area is important because people increasingly collaborate in a distributed manner across greater distances, and text-based communication is one of the primary means of facilitating these collaborations. The inspiration for this work comes from Aragon and Williams' (2011) paper, which introduces a complex systems model of collaborative creativity and describes ways that affect contributes to this model. In this study, we test and validate the model by using physiological measures to detect and explore the relationship between affect and creativity. Possible outcomes include correlations of creative events with physiological measures of affect and/or the occurrence of affect in chat messages.

The question that I am researching is," Does social media shape the public's perception in ways that can negatively impact the ability of college athletes to be drafted by professional teams?" I am interested in this project because I want to find out if negative social media has an influence on an athlete's chance to get drafted by professional teams and impacts their ability to achieve a top draft status. For my project, I decided to focus on the Manti Te'o girlfriend hoax, a recent case of a star athlete caught in the social media crossfire. With Manti all over the social media I was able to utilize photovoice and discourse analysis to critically examine news coverage, comments, interviews and other types of social media including facebook, twitter and instagram. I also conducted interviews with my teammates to find out how they think Manti's hoax will affect his draft stock or player earnings. A player's draft stock is determined not only by how good the player is, but how a player can sell their image. In other words, social media directly impacts a player's draft stock or how much money they could make. This work has important implications for a career of success of college athletes.

While professionals in the Information Technology (IT) industry are able to read and understand new terms by associating them with previous knowledge and current context, professionals outside of the industry struggle with unfamiliar words and acronyms in dense technical documents. In these circumstances, many people turn to online resources such as Wikipedia to define or explain terms they don’t understand. Yet, switching attention between reading an article and searching for information using various resources can increase cognitive load, thereby increasing perceived stress level and potentially reducing the effectiveness of both tasks. To address this problem, we propose the D-Jargonizer: a web-based tool that assists non-technical professionals as they read complex technical documents by allowing users to select and define technical terms with minimal distraction. We hypothesize that this tool will reduce cognitive load, perceived stress and make it more enjoyable for professionals outside of the IT field to read and comprehend technical documents. First, using a diagramming application, we will create a static prototype that imitates the proposed functionality of the D-Jargonizer. Students at the University of Washington who are unfamiliar with technical documents will be recruited to test perceived stress and enjoyment while using the prototype, as well as provide feedback about the overall user experience. Based on our initial user testing, we will develop a Google Chrome extension that allows users to select a term on a web page, searches for the term in an ontology based on Wikipedia entries and displays the definition in a text box on the page itself. Our tool will be tested again to confirm our hypothesis and verify usability. While the D-Jargonizer currently focuses on helping people understand technical documents, the basic concept could be applicable to medical or legal documents in the future.

Specialty search engines cover the web, powering everything from product lookups to niche subject material. These small systems are tasked with indexing unique information and presenting small snippets of highly consolidated information, often on a certain domain or topic. As a result, the algorithms and techniques utilized are often different than a conventional search system, which aggregates vast amounts of diverse data. There are many different techniques employed by contemporary search systems to handle wide varieties of data. These systems are tailored to handle the widest range of data out of the box to provide a turnkey system. However, for these specialty search engines, these techniques are often too broad or do not encapsulate the scope properly. Our team’s goal for the 2013 UW Research Symposium is to analyze the underlying mathematical models powering search appliances determine which algorithms have the greatest effect on the search engine’s accuracy and precision while maintaining a sufficient recall rate. Our first phase is to analyze the mathematical models and algorithms which power search appliances to determine which have the greatest impact in narrowing scope and improving precision. The second phase is to implement our predictions on production servers scraping unique datasets. This data will be processed through a multivariate regression function to determine any trends and compared against our initial predicted data. Overall, our hypothesis is that current search engine platforms do not have optimal accuracy and precision and that through the analysis of the underlying data-processing techniques, these aforementioned values will be improved.

America has become a world leader in medical research because of the achievements in research and technology made by pioneering physicians in various specialist medical fields. In America, specialist physicians have come to dominate the physician population, more than in other developed nations. For government health insurance programs such as Medicare, specialist physicians already receive substantially higher reimbursements than primary care physicians, namely because of the higher costs of running their practice, in addition to complex and risky nature of their field of medicine. Medicare calculates reimbursements based on the costs, skills and liability of a physician's practice at the same rate throughout the country. However, Medicare provides for regional adjustments of these costs through the Geographic Practice Cost Index. I hypothesize that the geographic index amplifies the difference in how much specialist physicians make compared with their primary care counterparts. As the index increases in value, the compensation gap between the two groups widens, providing additional incentives for specialists to practice in areas where the geographic index is high. Using physician population statistics and the Geographic Practice Cost Index, I ask whether the income advantage of specialty physicians where the index is high leads to an undersupply of primary care physicians compared to other areas.

Stem cell therapies for the replacement of human heart muscle tissue are an attractive solution to cardiomyocyte loss experienced by the heart. However, the successful development of these therapies will depend on the ability to image stem cell-derived cardiomyocytes in living systems. Our lab has previously reported intravital imaging techniques that enable assessment of electrical integration of stem cell-derived cardiac cells, but these require arresting of the mechanical motion of the heart with drugs like Blebbistatin. We hypothesize that a speckle interferometry phase correlation method can be used to successfully image fluorescently active stem cell-derived cardiac muscle cells engrafted in the heart, thereby yielding translational information that can then be used to motion correct electrical information gathered from the grafted cells. We will achieve this through the application of fluorescent speckles to the surface of an excised heart followed by simultaneous dual-channel acquisition of the signal from these speckles and from the fluorescently active grafted cells. Then, a phase correlation frequency analysis and normalized sinc function data interpolation will produce the local displacement in regions of interest in the heart from the speckle signal data. Neutralization of the determined displacements allows for the motion correction of the simultaneously acquired electrical data, which will eliminate the need for Blebbistatin as well as its potentially unknown and undesirable off-target effects.

In Africa, emergency humanitarian relief operations, in response to ongoing conflict and natural disasters, continue to struggle with violent, targeted attacks on humanitarian workers, aid supplies and refugees. While food aid plays an important role in addressing food shortages, previous studies suggest that food aid can contribute to the spread of civil conflicts under certain conditions. The purpose of this study is to examine the possibility that certain levels of food aid could exacerbate political violence against refugees in Africa because armed groups are likely to be motivated to prevent food aid distribution to an opponent refugee population, and to achieve material gain. To evaluate this claim, I analyze the relationship between three different types of food aid and delivery methods reported in the World Food Programme between 1988 and 1998, and data on affected refugee population by political violence against refugees in African countries. Food aid, defined as emergency food aid, programme food aid and project food aid, is delivered through direct transfer, local purchase and triangular purchase. In this study, the basic conditions of food aid consist of all commodities and all donor countries. There are fifty-three African countries that reported the amount of food aid they received, and twenty-six African countries that reported the number of refugees affected by political violence during the years of study. Based on the available data, I create several regression models that show the effects of each food aid and delivery method on rate of violence. I expect that emergency food aid and direct transfer have a strong positive correlation with violence involving refugees because they are directly delivered to targeted refugees who are at risk for insurgent attack.

Adenoviruses (Ads) are the most exhaustively researched and well-understood viral platforms for gene therapy and oncolytic virotherapy, with potential applications including the treatment of numerous inborn and acquired genetic diseases, including cancer. However, when injected into the bloodstream, Ad vectors can bind several blood coagulation factors that facilitate the transduction of hepatocytes, sequestering the virus in the liver. Although both coagulation factors VII and X bind the Ad5 hexon with very high affinity, only FX appears to play a role in mediating Ad hepatocyte transduction in vivo. To understand the discrepancy between efficacy of FVII binding to the virus and its poor capacity at supporting cell entry, we conducted structural analyses on the Ad5-FVII complex. Using high-resolution cryo-electron microscopy followed by molecular dynamics flexible fitting (MDFF) simulations, we have determined that the FVII GLA-domain sits within a surface-exposed hexon trimer depression in a different orientation than found for FX, althouth several of the same hexon residues that mediate FX binding also mediate FVII binding to hexon. Furthermore, we found that two proximal FVII molecules on the viral surface may interact via their serine protease (SP) domains, burying potential heparin sulfate proteoglycan (HSPG) receptor binding residues within the dimer interface. Several viruses with point mutations in critical residues of the hexon protein were engineered and grown. Infection assays revealed cell transduction efficacy that varied independently of the strength of the interaction between the hexon and FVII. MDFF simulations revealed an altered interface between hexon and FVII that could affect the orientation of FVII in the pocket and, thus, the efficacy of dimer formation. Since the occluded HSPG domains are crucial for cell entry, our results suggest that differing binding orientations for FX and FVII GLA domains lead to disparate quaternary structures, which ultimately determine the cell-transduction efficacy of the complex.

Fluorodeoxyuridine, FUDR, is a widely used treatment for many different types of cancer. It starves cells of deoxythymidine triphosphate, dTTP, which causes an imbalance in the deoxyribonucleotide, dNTP, pool sizes in the cell during DNA replication. We are predicting that with a lack of dTTP, the DNA polymerase sometimes will substitute an incorrect nucleotide in place of dTTP causing mutations, and we believe that this will affect the number of mutations in the mitochondrial genome. To study this, we are using combinations of FUDR and O4-ethyldeoxythymidine (O4-EtdT). This second mutagen, a modification of Thymidine, is used during the salvage pathway for the synthesis of dTTP. It can compete with dTTP and causes a loss in specificity for the DNA polymerase during further rounds of replication. We are treating colon cancer cells with combinations of these mutagens and using the random mutation capture (RMC) assay to quantify the mutations in the mitochondrial genome. The mutations are enriched with a restriction enzyme that cleaves the wild type DNA leaving only mutated DNA to be amplified using qPCR. We are then using TOPO cloning to sequence the mutations. Many believe that uracil will be used as substitute when the cell is starved of thymine because of their similar structures. However, incorporation of uracil will not result in mutagenesis, while incorporation of the other three nucleotides will. With the results from TOPO cloning, we will be able to take a closer look at this hypothesis. Further on, results will be analyzed using the Student T-Test and One Way ANOVA. So far, the data shows a change in the quantity of mutations in mitochondrial DNA when either O4-EtdT or FUDR are added. Results can help us to understand and respond to post-chemotherapy health problems that may be due to mutations in the mitochondrial genome.

Does gubernatorial leadership matter? Declining revenues associated with the great recession encourage state governments to use their limited resources more efficiently. However, elected officials will often disagree about priorities, which can make enacting necessary reforms difficult. The goal of this research is to investigate whether state variations in gubernatorial powers impact the ability of governors to respond to important challenges, such as the effects of the great recession. I study fifty states from 1960 to 2012, and ask whether unified government versus divided government, the strength of the governor’s veto power and the strength of the governor’s budget powers is related to a state’s economic performance. Controlling for other factors, I expect to find that states where governors have more veto and budget power, and where the government is unified under same party also tend to have lower unemployment rates. By improving our understanding of the relationship between governors and state economic performance, this study may also shed light on how national reforms strengthening the executive powers might impact presidential economic performance.

Chagas Disease is a tropical disease caused by the parasite Trypanosoma cruzi. An estimated 100 million people are at risk in 21 endemic countries and ~8 million persons are currently infected. Left untreated, Chagas disease can cause fatal heart rhythm abnormalities, a dilated heart, a dilated esophagus, and/or a dilated colon. The efficacy of current treatments decreases the longer the person is infected, and 40% of treated patients experience adverse reactions, demonstrating the need for new and improved drugs. A drug target has been identified in T.cruzi: the Methionyl-tRNA synthetase (MetRS). Like tRNA synthetase enzymes in other species, the T.cruzi MetRS is crucial for protein production and survival. To exploit this target in T.cruzi we developed a robust assay (Z' factor ≥ 0.5) to identify hits against the MetRS enzyme using a luminescence ATP detection method (Promega's Kinase-Glo™). Compounds that inhibit the T.cruzi MetRS enzyme will be tested for specificity by assaying the compound with the human MetRS homolog. Specific T.cruzi MetRS inhibitors will be tested for potency against intracellular T.cruzi amastigotes and cytotoxicity against mammalian cells. Compounds that are toxic to T. cruzi, not cytotoxic to mammalian cells, and have good pharmacological properties will be selected for hit--to--lead drug development. 

Imagine a world of social and gender equality- what does it look like? Can social justice be achieved through the real-world production of such an environment? While drawing and other visual art mediums are considered to be the primary communication tool to depict the imagined constructed environment, language and the written word are powerful methods of spatial description that are often overlooked. As a means of constructing an imaginary environment, or an environment that has political and emotional associations tied to it, fiction literature is an especially compelling tool for creating environments with social implications. Thus, through spatial analysis of fiction pieces by Margaret Atwood, a noted contemporary author of feminist and dystopian literature, I am examining the role of the constructed environment in issues of gender inequality within the writing. How does the built environment impact women’s role in society in the novels? Does Atwood depict a new type of environment that provides more oppurtunities for gender equality? I will be reading The Edible Woman (1969), The Handmaid’s Tale (1985), and Oryx and Crake (2003), and comparing Atwood’s language used in constructing the novels’ settings to academic writings on gendered spaces. I will also be comparing each of the novels’ commentaries on the state of women’s rights and gender equality with the historical timeline of second and third-wave feminism in North America. I expect this research to show new links between the constructed environment and feminist and architectural theory, with the aim of incorporating such knowledge into modern day architectural design that supports current efforts against gender inequality.

Local and regional public health departments in the U.S. are legally required to make their services available in languages other than English. Most health departments outsource translation of health and safety information materials (e.g. websites and flyers on vaccinations, emergency preparedness, etc.). This is costly and time-consuming and makes it impossible for health departments to translate many important documents. We designed a web-based collaborative system to enable the production of multilingual health communication materials by bilingual public health workers. Our system could reduce the cost of translation and increase access to public health information for people in the U.S. with limited English proficiency. The system is based on a workflow where a source document in English is machine-translated and then revised and corrected by humans to produce a finalized translation. We designed the system for public health professionals who are bilingual domain experts but not necessarily trained translators. We initially gathered data to inform the design of our system through interviews and focus groups with local and regional public health departments. Based on the design recommendations extracted from the data, we implemented a web-based prototype collaborative translation management system. We further refined the system through an iterative design process that included informal user testing with multilingual participants. Future work will include usability studies with public health workers and the integration of additional collaborative features.

DNA replication is vital for cell division as it produces exact copies of all chromosomes for the two daughter cells.  During S-phase of the cell cycle, DNA replication begins at specific, defined locations within a chromosome known as origins of replication.  Interestingly, some origins activate in early S-phase while others activate late.  The biological significance of this temporal control of replication is largely unknown.  In multiple species, centromeric DNA, the site of recruitment for proteins required for separation of chromosomes during mitosis, has been found to be early replicating.  The Brewer/Raghuraman lab has recently shown that centromeres in the budding yeast Saccharomyces cerevisiae promote their own early replication by advancing the activation time of their neighboring origins.  The conservation of early centromere replication coupled with the Brewer/Raghuraman lab’s recent finding suggests that early centromere replication may be important for chromosome maintenance.  We set out to determine the consequences of a late replicating centromere by artificially delaying its replication time in S. cerevisae, through replacing its nearby origins with drug resistant markers.  To enhance sensitivity of the experiment, I impaired the activity of the spindle checkpoint that monitors correct chromosome segregation.  I also constructed a control chromosome with an early replicating centromere and the same markers.  I will then compare the degree of chromosomal instability, as measured by survival on drug plates, of the control cells to those that contain a late replicating centromere.  We expect the experimental group to show an increase in the number of cells that have lost the chromosome compared to the control cells.  Even if the effect is small we will perform long-term growth experiments to analyze how the cells cope with reduced genetic stability.  The results of this study will provide a better understanding of the biological importance of the temporal replication program.

Capillary Force Lithography (CFL) is one of the novel techniques that established recently for fabricating biomimetic substratum of tissue engineering. This approach of making nano-scale scaffold allows us to fabricate complex design of polymer substrates at low-cost. One practical challenge to further application of CFL to biomedical science is biocompatibility of the materials used in CFL. Most of the materials used for CFL are only biocompatible in vitro, but not in vivo. 2-hydroxyethyl methacrylate (HEMA) is introduced as a good alternative biomaterial with exceptional biocompatibility. We recently succeeded in fabricating nano-structured pHEMA via CFL. We confirmed the structure of pHEMA nano-substrate with SEM imaging and AFM measurement. We hypothesized that biocompatibility of HEMA will enhance the cell contact with the nano-substrate, which will let cells penetrate through the grooves. Cells penetrating through the nano-grooves can benefit from increased surface area for cells to contact with polymer substrate, and allow cells to efficiently interact with glycan present on the surface to achieve more biomimetic environment.

The hypoxia-inducible factor (HIF-1) is an oxygen-dependent transcription factor that plays a crucial role in an animal’s response to changing oxygen availability. When oxygen is plentiful, HIF-1 is ubiquitinated and targeted for degradation by the von Hippel Lindau protein (VHL-1), which inactivates HIF-1. Recent studies have shown that HIF-1 stabilization through mutation of vhl-1 increases longevity in the model organism Caenorhabditis elegans. This is contrary to humans, where VHL-1 mutations cause a disease characterized by angiomas, renal carcinomas and various other tumors as a direct result of aberrant HIF-1 activation. Since nematodes are post-mitotic organisms in adulthood, constitutive activation of HIF-1 does not cause tumor formation and is able to increase lifespan. In order to better understand how HIF-1 increases longevity and to relate these findings to mammals, our project aims to find the specific genes and tissues downstream of HIF-1 that benefit worm longevity without the consequences of VHL disease. To identify these genes, we conducted an RNAi screen for genes that are necessary for HIF-1-mediated longevity. Using the results of this screen, we are creating transgenic worms that overexpress these genes under specific nematode promoters. To test for the tissue specificity of HIF-1-mediated longevity, we are stabilizing HIF-1 in different tissues using tissue specific promoters. Our initial data are promising; we have found two genes downstream of HIF-1 that when overexpressed increase nematode longevity. At least one of these genes, flavin-monooxygenase-2, is a well-conserved protein known to be involved in xenobiotic metabolism. Additionally, we have found that expressing stabilized HIF-1 in neurons is sufficient to increase nematode lifespan. Our continuing studies will identify additional target genes and tissues important for HIF-1 mediated longevity and will attempt to elucidate the mechanism by which they increase lifespan.

A quadrotor is a small air vehicle propelled by four rotors, or propellers. It is capable of vertical flight, as well as hovering and smoothly changing direction. The quadrotor is more versatile than a fixed-wing air vehicle, as it can move through environments that would limit a larger and less maneuverable vehicle. This research aims to create a successful autonomous computer-based controlling system for a quadrotor's flight. By implementing this technology, the quadrotor could move freely in environments unsafe for human flight controllers. Researchers developed and executed experiments to determine vehicle properties to improve control safety and robustness. In order to create a flight control system that will successfully maneuver the quadrotor without the use of a remote control, the quadrotor's inertia and thrust properties were ascertained. With the inertia and thrust data, controlling the quadrotor with high precision will be possible. The quadrotor's inertia was determined by measuring its rotational period using a photogate timing mechanism and a flashlight beam. Its inertia was found on three principal axes: x, y, and z. A thrust curve was determined for the quadrotor by measuring the thrust produced at each throttle setting using a force transducer. The resulting inertia and thrust properties allow for a deeper analysis of the quadrotor's abilities. In addition, an optic flow sensor will contribute to the quadrotor's flight capabilities. The sensor was calibrated and code was implemented to create communication between the sensor and a computer. When attached to the quadrotor, the sensor rapidly photographs the quadrotor's surroundings, detecting changes in altitude, rotation, and velocity. The optic flow sensor will help stabilize the quadrotor's position and allow it to maneuver away from objects in its flight path.

Sensory hair cells in our inner ear are necessary to detect sound, and hair cell death is the primary cause of hearing loss. A certain class of antibiotics, including neomycin, induces hair cell death. Understanding the mechanisms involved in preventing hair cell death may yield pharmacological advancements to protect sensory hair cells when these antibiotics are administered. Zebrafish are often used to study hair cells because fish have readily accessible hair cells on their exterior that are analogous to sensory hair cells within our inner ear. This project investigated the effects of heat shock on neomycin-induced hair cell death. Heat shock can trigger several signaling pathways known to protect cells against cellular insults. We hypothesized that applying heat shock prior to exposing the hair cells to neomycin would inhibit damage by increasing cellular defense mechanisms as seen in other organisms. The data were obtained by placing 5-day-old zebrafish in a 38 degree Celsius water bath for one hour (heat shock), followed by an hour break for recovery, and then a 30-minute incubation period in neomycin. We quantified the degree of damage to the hair cells 5 hours after neomycin treatment by scoring (ranking) hair cell clusters based on cluster size and counting the number of hair cells located in specific areas. Our results suggest that heat exposure partially inhibits neomycin-induced hair cell damage. Further research may yield insight toward pharmacological advances that prevent antibiotic-induced hair cell damage.

Duchenne muscular dystrophy (DMD), an incurable disease that causes severe morbidity and mortality, affects one in every 3600 male children in the United States. Stem cell therapy and cell replacement therapy have been utilized as possible solutions to the disease; however, there has only been limited success due to two major deficiencies: the lack of blood vessels in the regenerating tissues resulting in oxygen deficiency, and the lack of proper structural cues resulting in the disorganization and un-differentiation of the stem cells. Previous research has demonstrated the angiogenic and myogenic potentials of sphingosine-1-phosphate (S1P). Moreover, muscle tissues in human body have highly organized nanoscaled structures that guide the organization and differentiation of muscle cells. We designed nanopatterned muscle patches conjugated with S1P, and proposed if the patches would allow better cell survival, retention, and long-term functionality. We developed biodegradable S1P-conjugated nanopatterned muscle patches with capillary force lithography (CFL), chemical conjugation, and culturing of undifferentiated muscle cells in vitro. The patches’ biochemical, structural, and functional properties were characterized. We also evaluated the force generation, the long-term potential of regeneration, and the synchronization of the engrafted tissue of the patches within the limb muscle of mice. We anticipated proper vascularization of the patches and that the implanted cells would develop into differentiated, mature, and functional skeletal muscle cells due to the bio-mimicking mechanical cues provided by the nanopattterns. This project aimed to develop fully functional muscle cell patches which could be engrafted into patients with DMD and thereby treating the disease. In addition, the experiment would also improve our understanding in the response of muscle cells to topographical cues.

It is projected that in 40 years, 3.6 million individuals in the U.S. will have a limb loss and approximately 40% of them are major lower-limb amputees. Lower-limb prosthesis is needed to regain the mobility in these amputees. Many implications have been made in prosthetic feet to improve the mobility of the amputees, yet seldom investigations have done on the design of the pylon to improve the same function. This project is to design a novel elastic pylon fitted with a rigid foot to have the same, if not better, functionality to a rigid pylon with a high performance prosthetic foot. Due to the expensive cost and the limitation of the prosthetic feet, the design of elastic pylon is needed to reduce the cost of the overall prosthesis and find alternative ways to improve the mobility. The elastic pylon was modeled first using a finite element analysis program. Then, the modeled elastic pylon was manufactured, fitted with a rigid foot and compared to the rigid pylon with the high performance foot on bench testing. Ultimately, the elastic pylon will be tested on the amputees for gait analysis and the kinematics of the amputees during walking in both rigid pylon-high performance foot and elastic pylon-rigid foot and compared. The success of this project would result in a reduced cost in the prosthesis, as well as alternative ways to improve the mobility of the lower-limb amputees.

 A significant proportion of the 23 known human-specific duplicated genes are implicated in neurological processes. The Rho GTPase activating protein 11 (ARHGAP11) is one such gene that is also found in an area associated with schizophrenia, intellectual disability, and autism. We determined that the human-specific duplicated copy (ARHGAP11B) duplicated 5.3 million years ago (mya) shortly after the human-chimpanzee divergence (~ 6.5 mya). The human-specific duplicated copy is not found in all humans, and represents an incomplete version of ARHGAP11A, suggesting a potentially alternative function. The goal of my project was to identify sequence differences between A (ancestral) and B (duplicated) paralogs (i.e., genes related by duplication within the same species) and use these differences to assess gene variation and expression. By sequencing 64 different transcripts (i.e. protein coding regions) we found nine “paralog-specific variants” (or PSVs) allowing us to distinguish between A and B. We assessed the level of gene expression (how much a gene is “used”) for each paralog in human fetal brain samples and found that A was expressed approximately two times more than B. Interestingly, we found similar results from other tissue types including blood. Further, we have used these PSVs to identify potentially pathogenic mutations of ARHGAP11A from targeted large-scale sequencing data of a collection of children with intellectual disability. We are using these data to understand the function of different members of the ARHGAP11 gene family both on neurological development and potentially on the evolution of traits that make us uniquely human.

The 38mm bore ram accelerator at the University of Washington has traditionally used a light gas gun to accelerate the projectile to a desired speed before it enters the test section. The light gas gun uses helium pressurized to 6000 psi. This method is expensive, time consuming and the high pressures require the use of a specialized compressor. A new launch gun concept has been developed which uses a shock-induced ignition of hydrogen-oxygen mixtures to produce pressurized steam which is then used to launch the projectile. This new launch system produces the same or better results (i.e. muzzle velocity) as the light gas gun while being easier to operate as well as more time and energy efficient since large quantities of helium are no longer required. Performance data obtained experimentally will be compared to theoretical calculations to validate the theory used to develop the gun.

Over one sixth of the world’s population, including 60 million people in the western United States, depends on snowpack for their primary source of water. Water resource managers use snow models to help quantify the amount of water stored as snow. Many modern models explicitly quantify how various methods of energy transfer affect snow ablation but are limited by a lack of in-situ observations for some forms of energy transfer. In particular, measurements of incoming radiation (one of the dominant sources of snow melt in many climates) and snow albedo (the fraction of solar radiation reflected by snow) are scarce due to the high cost of radiometers and the difficulties of obtaining quality measurements in mountainous terrain. Sensor windows are easily covered by heavy snowfall and require frequent maintenance. In contrast, small, inexpensive temperature sensors require minimum maintenance and are far less likely to be covered by snow. Their low cost and ease of installation allow for far greater numbers of observations. Because of this, we are exploring new methods of estimating radiation and albedo by deploying groups of temperature sensors purposefully shaded in different ways. Each group has one temperature sensor shaded from all radiation, one sensor shaded from downwelling radiation, and one sensor exposed to radiation from all directions. We hope to develop a reliable, inexpensive, and accurate method for calculating radiation and snow albedo from the difference in temperature readings between each sensor. Observed radiation at each study site will be used to engineer and validate the method. One year of measurements at Tuolmne Meadows, CA has been recorded and another recent installation at Snoqualmie Pass, WA provides additional data to include in our study.

In rural Kyakitanga village of the Luweero Triangle in Central Uganda, inequalities resulting from structural violence of colonialism and the post-independence regimes of Milton Obote and Idi Amin trickle down as negative effects on the local food system, which in turn degrade the environment and peoples’ health. Locals express a desire to remedy this food insecurity through modern farming techniques. My research explores the potential role of Traditional Ecological Knowledge (TEK) in the village’s pursuit of food sovereignty and the formation of a future food system. TEK is the usually place-based intergenerational knowledge of indigenous populations about how to thrive in a mutually evolving and beneficial relationship with the environment; as an informer of subsistence methods, TEK tends to be more environmentally sustainable and socially equitable than modern farming. My methodologies included literature review of colonial and post-colonial political economic history of Uganda, current food insecurity in rural Sub-Saharan Africa, TEK in East Africa, and examples of TEK recovery in other communities. Additionally, in Summer 2013, I will conduct participant observation and a community-based participatory action research (PAR) study involving multigenerational semi-structured individual and group interviews in the village. I will collaborate with locals in the research process and share all results with Kyakitangans as a resource for pursuing food sovereignty. My research is significant because it addresses upstream issues of local autonomy, historical trauma, and ecological factors that are often neglected in public health and development discourses in the Ugandan context, which is historically dominated by verticalization and neoliberalism. As applied anthropology, my research will promote the autonomy and agency of an oppressed community, and lead to relevant broader implications for global health and development work and discourse.

Ubiquitin (Ub) is a small post-translational signaling protein with roles in DNA double stranded break (DSB) repair, apoptosis, and protein degradation.  The pathway for attaching Ub to a substrate involves sequential interactions of three enzymes: Ub activating enzymes (E1), Ub conjugating enzymes (E2), and Ub ligases (E3).  Substrate proteins can be poly-ubiquitinated and the nature of the poly-Ub chain determines the fate of the substrate.  One type of poly-Ub chains signal for a DSB repairing complex, as opposed to another type of poly-Ub chains that signal for proteasomal degradation.  RNF168 is an E3 involved in the DSB repair pathway. Whereas the E3 ligase binds its substrates, in ubiquitination mechanism it is the E2 that determines the type of Ub moieties formed. There are dozens of E2s found in the human cell; therefore, it is important to study and understand the E2:E3 pairwise interactions. Currently, the published investigations of RNF168 provide varying conclusions about RNF168’s relationship to specific E2s and with that its role in DSB repair.  In order to remove the ambiguity, I examined in vitro protein interactions between RNF168 and a library of human E2s using yeast-two hybrid experiments. The Klevit Lab has investigated the process of poly-ubiquitination with other E3s, BRCA1 and RNF8, and found involvement of different E2s at different stages of ubiquitination.  To further clarify the poly-ubiquitination mechanism of the RNF168:E2 pairs, I conducted similar activity assays to those done for BRCA1 and RNF8.  These in vitro assays consist of autoubiquitination reactions, where RNF168 itself is used as a proxy-substrate to determine different types of Ub product formation utilized with different E2s.  By yeast-two hybrid I have found that several E2s bound to RNF168. These interactions will be further confirmed and further tested with activity assays to determine the type of Ub modification by the different RNF168:E2 pairs.

My research question is: do media portrayals of female professional volleyball players affect teenage girls' perceptions of gender norms and athletics? This research directly relates to Elizabeth Daniel’s study titled, Sex Objects, Athletes, and Sexy Athletes. She explored how misrepresentations of female athletes' impacted adolescent girls and college women's self esteem. I will use methods such as: photo analysis, survey, focus groups, and interviews to conduct my research. I hypothesize that media’s emphasis on appearance and beauty of female athletes perpetrates stereotypes that can be detrimental to young girls' interpretations of athletics, specifically volleyball. This research matters because many adolescents are involved in athletics and athletics has the ability to create a positive atmosphere for young girls to build confidence. With awareness to media’s impact we can challenge and become sensitive to gender stereotypes and the ways in which young girls identify with athletics.

I am interested in how female collegiate and professional athletes portray themselves to society to avoid negative stereotypes. Female athletes are expected by society to act tough like a man when they are in the sports arena and elegant like a women when they are not. How do these women react to these expectations and how do they choose to portray themselves to avoid being put into these harmful categories? Whether they are avoiding being portrayed as overly masculine or too feminine to participate in sports, female athletes face these challenges on a day-to-day basis. I will use the methods of photovoice, interviewing, and discourse analysis to gain further insight on this topic. Sally Ross and Kimberly Shinew wrote an article titled Perspectives of Women College Athletes on Sport and Gender that relates to my research. They interviewed college softball players and gymnasts about how they felt about the different stereotypes placed upon them and if they fit the label. They discussed with the athletes what kinds of social settings they chose to embrace different images to conform to social norms. This research matters to society because female athletes should not have to constantly worry about the image that they are portraying. They should be respected for their athletic ability as well as their feminine qualities. All women are unique regardless of their participation in sports and should not be categorized into a label that is often incorrect. The pressure to act a certain way also negatively affects young girls who are aspiring to be athletes. As a society, we want young female athletes to be able to grow up comfortable in their own skin.

I was interested in exploring the relationship between women athletes and the media. I focused particularly on how women athletes are portrayed by the media. Over the years, I have noticed a big discrepancy between how men are represented within the media compared to women. Men are depicted as very masculine and are praised as great athletes, almost as if males are the only gender capable of excelling in sports. While women were depicted more as sex symbols and models. However, this contrast between men and women did not match my life experience. I was raised in a very active and athletic family; my sisters are all athletes and good at their respective sports. Having known that women are more than just sex symbols and swimsuit models, I thought it would be interesting to do some research on this topic. My research focuses on the hyper-sexualization of women in the media, and its position within sports. The question I will explore through my research is: "How much does the sexuality of women involved in sports matter to the media?" This connects to an article written by Richard Deitsch, et al., called, "Q + A Lisa Guerrero." In this article Lisa Guerrero, a female sports broadcaster, is interviewed about the role sexuality plays in sports broadcasting. To conduct my research, I used the methods of interviewing, participant observation, and discourse analysis to analyze my research question. First I interviewed two student athletes, one male and one female, to get both ends of the spectrum for my topic. I then engaged in participant observation by attending both a men's and a women's basketball game, and observed the different media messages and depictions at each game. Finally, I analyzed four different articles for the discourse analysis method. This topic is important because it sheds light on issues in the media today, like the hyper-sexualization of women. Everyone has access to the media, so it is very difficult to miss these media messages. I believe that my research will not only expose the media of their false advertisement of women athletes, but also provide the public with a new respect for women in sports.

Cortinarius is the largest genus of ectomycorrhizal fungi. Ectomycorrhizal fungi are extremely important to the function of forest ecosystems and plant communities as they form symbiotic relationships with over eighty percent of vascular plants by colonizing the feeder roots and increasing nutrient and water uptake. My research will focus on the identification and phylogenetic relationships of a subset of Cortinarius species associated with the Oregon oak in the Columbia George of southwest Washington. Identification of the species associated with Oregon oak will allow me to better understand their ecology and relationships to other Cortinarius species. I am extracting DNA from samples collected in the field over the past four years. Using PCR, the nuclear ribosomal DNA (rDNA) internal transcribed spacer region (ITS1-5.8S-ITS2) will be amplified with primers ITS1F and ITS4. DNA sequencing and analysis will be done using Finch TV and Basic Local Alignment Search Tool (BLAST) software. We expect that most of the species will be new to science, and that these analyses will provide insight into their ecology and relationships to other oak associated species in western North America and Europe.

For the Mixtecos from Oaxaca, Mexico, their native language has functioned as an indicator of “inferiority” and “backwardness” due to prevalent stigmatization and stereotypes associated with indigeneity throughout Latin America. Now as the fastest growing indigenous population in the U.S., Mixtecos are challenged with the recent proliferation of the Mixteco/Spanish/English language divide that has emerged within Mexican-American communities throughout the U.S. west coast. In the face of the more dominant Spanish and English languages, the Mixteco language has seemingly been relegated to a “useless” language in the eyes of some Mixtecos. However, this view is not shared by all, and therefore the question arises as to how discourse regarding language is shaped for the transborder Mixteco communities in the United States. By using language as an indicator of the dynamics of power and cultural celebration within Mixteco satellite communities in the U.S., I address the paradox regarding the simultaneous decrease of Mixteco speakers and the increase of discourse via subaltern public spheres promoting the revitalization of the Mixteco language. By employing a comparative discourse analysis of the dialogue within their grassroots organizations and personal narratives, I examine the agency of the Mixtecos in forming their own suitable discourse to tackle the issues they face as transnational migrants. I suggest that via their grassroots organizations, the Mixtecos are creating a new hybrid language by incorporating Mixteco with other forms of discourse in order to advocate their indigenous consciousness and cultural celebration against constant discrimination and stigmatization of their language, culture, and voice. By addressing the agency of the Mixtecos, this research will contribute to the study of indigenous migration and social movements from Latin America.

The hair cells of the inner ear are the functional sensory units of hearing and balance in the auditory and vestibular system, respectively, and are therefore a major cause of deafness and balance deficiencies when lost after damage. Unlike in reptiles, birds and fish, existing studies suggest that the mammalian sensory epithelia of the inner ear lack the ability to regenerate hair cells after such damage. Here we focus on the cristae, which are a component of the vestibular system, and are responsible for sensing angular acceleration and rotation of the head.  Previous research has suggested that Notch activity, a crucial signaling pathway necessary for patterning the sensory epithelium, continues in adult mouse cristae, suggesting the potential for regeneration after damage.  We characterized a lesion protocol for this system through the administration of the ototoxin iminodipropionitrile (IDPN) to test whether spontaneous regeneration of hair cells is present in the mammalian cristae. We used confocal microscopy to image the layers of the cristae's sensory epithelium  after immunohistochemistry staining with markers specific to hair cells.  Each cristae's hair cells were counted, and an average was obtained for cristae for each of several time points after IDPN injection. Preliminary findings show a severe reduction in total hair cell number in the mouse cristae one week after IDPN injection, and continued loss of hair cells in subsequent weeks.  While we saw no evidence of spontaneous regeneration in the mouse cristae, this lesion protocol may be used in further hair cell regeneration studies using various manipulations or drugs, such as inhibition of Notch signaling.

Mobile video communication has been popularized by applications such as Skype and Facetime, but the technology suffers from resource limitations both on the device and on the cellular network. Transmitting high quality video requires high bandwidth and battery draining processing power on mobile devices. These requirements hurt the user experience by creating high data cost, reducing call time, and limiting use to high speed networks such as WiFi. My research contributes to the MobileASL (American Sign Language) project that applies video compression to solve these issues specifically for mobile sign language communication. The deaf and hard-of-hearing community can benefit immensely from a mobile video chat application as ASL is a visual form of communication. We conducted a web study investigating sign language comprehension and intelligibility of video transmitted at four low frame rates (1, 5, 10, 15 fps) and four low bitrates (15, 30, 60, 120 kbps). The purpose was to determine how much video quality can be reduced before compromising sign language comprehension and intelligibility. The study found intelligible sign language video can be transmitted at frame rates and bitrates much lower than the current recommended standard for sign language video communication (25 fps at 100 kbps or higher) without diminishing the user experience. These findings strongly suggest that the recommended international standards are too high and can be reduced while maintaining intelligibility.

 A new non-visual method of numeric entry into a smartphone is designed, implemented, and tested. Users tap the smartphone screen with one to three fingers or swipe the screen in order to enter numbers. No buttons are used—only simple, easy-to-remember gestures. A preliminary evaluation compares the method to a standard accessible numeric keyboard with a VoiceOver-like screen reader interface. Preliminary results indicate that users can enter numbers faster and with higher accuracy when using this method. The Tapulator, a complete calculator based on this non-visual numeric entry that uses simple gestures for arithmetic operations and other calculator actions is described.

Recent studies on the influenza nucleoprotein have shown that stabilizing mutations play an important role in how the nucleoprotein has evolved. In addition, other studies have shown that stabilizing proteins are more tolerant to mutations and evolve more rapidly, and that fluctuations in mutation rate due to varying stabilities overdisperses the molecular clock. It is clear that understanding the effects that mutations have on protein stability is important to understand and predict the evolutionary process. However, the difficulties involved in purifying protein mutants and measuring their thermodynamic properties often make said procedures impractical for obtaining thermodynamic information about many different mutants of a various protein. Because of this, we look for a method to analyze the data from simpler experiments to infer the effects of mutations of protein stability. We consider an experiment where we select a protein, subject it to error prone PCR, and sequence the generated library to determine the frequency of each mutation. We then purge the library of inactive mutants and sequence the library again. From this experiment, we determine how often each mutation appeared in the stable and unstable libraries and from this we can infer the effect that each mutation has on protein stability.

I explored the ways in which the media overshadow women’s basketball and portray men’s basketball as the dominant driving force behind the game. Methods I engaged with included social mapping of men and women’s basketball games at the University of Washington, what were the demographics of the crowd, who was present and what did this tell me about who was attending the games. I observed various photographs (photo analysis) that featured in magazines, newspapers such as Sports Illustrated, who was featuring on the cover and who was featured as the ‘main star’? Another method was interviewing, I spoke with ushers at men and women’s games, I listened to their views and what they said were the main differences between the two games, and how the University presented or advertised them. On a professional level, the NBA is the driving force behind professional basketball, yet is reserved specifically for males, therefore portraying males as sporting leaders. WNBA is a separate entity and I feel if women wish to be seen playing the sport they need to be in an entirely different league and can’t be seen playing the ‘main’ sport (through the NBA). This is just one example of the divide that is driven between these two genders and people’s eyes need to be opened as to why this exists.

Aging is a degenerative process characterized by a progressive deterioration of cellular components and organelles resulting in mortality. The nematode Caenorhabditis elegans has been used extensively to study the biology of aging, and several determinants of C. elegans longevity are conserved in higher order organisms. The specific mechanisms of longevity in C. elegans have not been completely identified and many pathways are still poorly understood. Dietary restriction (DR) is one promising pro-longevity intervention, though its mechanism is poorly defined. DR, a reduction in caloric intake in the absence of malnutrition, extends lifespan in C. elegans and in a wide range of other species, including yeast, flies, mice, and primates. However this extension is highly dependent on genetic background. To investigate this, we are performing a genome-wide screen of the Vidal RNA interference (RNAi) Library, which has a catalog of 11,511 clones. By knocking down specific genes within the C. elegans genome through RNAi, we are able to observe an extension or reduction in longevity in response to DR. We have screened over 1500 genes; 61 of which are short-lived and 67 of which are long-lived. We are currently following up on our collected data by measuring the full lifespans using the RNAi clones that significantly shortened or extended lifespans in our screen. By screening such a large number of genes, the widespread effect, and hopefully mechanism, of DR will be elucidated. We hope to see genes significantly affected by DR cluster into groups with common functionality, or along the same pathway, and then follow up on those specific pathways to clarify the mechanisms underlying DR. If these pathways are conserved, research findings relating to C. elegans may be applicable to other organisms. We hope to confirm these results and further investigate the interaction between DR and other potential longevity pathways.

What factors influence the evolution of media depictions of female athletes, particularly in soccer, running and basketball? I’m going to look at factors surrounding the time period as well as the factors attributed to the changes in the athlete that could influence the way the media decides to represent them. Helene A Shugart wrote a paper, entitled She Shoots She Scores: Mediated Constructions of Contemporary Female Athletes in Coverage of the 1999 US Women’s Soccer Team, which connects to my current research in that, it explores the different ways female athletes are displayed in the media while connecting it to the ideas of the time period. There has also been research done by Vikki Krane and Michelle T. Helstein. Both authors wrote articles about how companies are shaping the public’s view of what a female athlete is and how this view affects women, both athletes and non-athletes. I will use photo voice, discourse analysis, participant observation, and social media analysis to further research this subject. Because I am researching these three very different sports, I believe my findings will all be diverse. However, I believe there will be a common need to reform the way the media represents female athletes whether its lack of media attention, a sexualized form of media attention, or reinforcing gender norms. I think my findings will be important because in further understanding the factors behind media’s representation of female athletes, we can find better ways of promoting and reshaping the public’s view of female athletics so there is more focus on the competition rather than the politics surrounding it.  

In my research I wanted to find out how women’s and men’s professional soccer in the United States is portrayed by the media which has a big influence on the popularity of the sport. The media, especially social media, is growing and expanding immensely all over the world. All of the promotion and interaction with millions of people over social media has a high potential to grow the sport and over the past couple of years soccer in America has become increasingly popular (mostly women’s soccer). In the article “The ‘Olympianization’ of Soccer in the United States,” Markovits talks about how soccer used to be a marginal sport in America and the ways in which it has gone through a huge metamorphosis, attracting many more to the game. The methods I used to conduct my research were photovoice, social media, and discourse analysis. I used photovoice to look at billboards that portrayed womens soccer in a positive way. I also used discourse analysis and photovoice to analyze different aspects of social media on certain professional womens and mens soccer players, such as their number of Twitter followers. Lastly, using discourse analysis I viewed articles promoting different upcoming mens and womens soccer games to see how they were advertised differently. My results showed that mass media is a key factor in the popularity of soccer in the United States because it has such a big influence on our lives through advertising, televised events, and personal interactions through social media. My work contributed to understanding this influence by depicting specific examples from the media that could have an impact on gaining supporters of the game.

Though the rules of chess can be learned in a day, people spend years learning the nuances of the game that can make them masters. Important strategic details often go unnoticed or are not fully understood by novice players. Tactical play refers to maneuvers that limit an opponent’s options, or present multiple problems simultaneously resulting in a tangible gain. Moves like pins, forks, and skewers all fall into tactical play. Positional play refers to maneuvers that strengthen a player’s position on the board or weaken an opponent’s. Space, or how many squares a player controls, is an aspect of positional play. We speculate that by just seeing these strategic details, novice players could play stronger games of chess. We will be designing and implementing a set of visualizations that can be overlaid onto a digital chessboard that may help novice players more quickly and meaningfully see potential patterns, threats, and opportunities in hopes of helping them play more successful games. Our application could serve as a tool for further research on the relationship between visualization and chess learning, but our focus for the remaining quarter is only to design the application through research of chess and collection of feedback from chess players of all levels, and to implement a working application that may run in a web browser. Assuming the project is a success, future work may include a within-subjects study that compared how well novice chess players fared against a consistent chess AI both with the visualizations enabled, and without based on victories, losses, total moves until the end of game, and total value of pieces lost versus pieces captured.

 Blindness is a condition that impacts people across the globe. Some of these people are born blind due to a genetic defect, while others become blind through an accident or as the result of disease. Thus dissecting the underlying molecular causes of blindness is a critical component in improving the lives of many people. To study causes of blindness, we are analyzing disease causing mutations in the model organism Danio Rerio, or zebrafish. The recessive ZVM10 mutation causes very early degeneration of both rod and cone retinal photoreceptors, causing complete blindness. To study this mutation we have determined the identity of the mutated gene. I helped in this endeavor by first determining the position of the mutation within the zebrafish genome (i.e. map the mutation). This was done by mating the ZVM10 AB fish with a polymorphic fish strain. The crossovers between the different DNAs were traced, and used to identify the area homozygous for the AB allele. By continually reducing this region we specified a small group of genes that potentially were mutated. I then helped sequence these genes. A single base pair mutation that introduces a premature stop codon was identified in the gene encoding N-ethylmaleimide-sensitive attachment protein, beta (NAPB). I am currently working on a reliable genotyping protocol based on this mutation to sort mutated from non-mutated fish. The mechanism of photoreceptor degeneration in this mutant will further be studied by examining the role of this gene in wild type cells. The identification of this mutation will permit the identification of people who are blind due to this genetic mutation, through genetic screening of the patient. Finally, if this gene is also involved in human blindness, it will become a candidate for rescuing blindness through gene therapy.

Liver transplantation is a widely performed treatment for patients with end stage liver disease. Each day, the liver transplant waiting list grows longer due to a shortage of acceptable organs. Hepatic steatosis in donor livers is an increasing problem that contributes to discarding otherwise-transplantable livers. Numerous studies and surgeries have shown that high fat content in livers correlates with poor graft function and lower patient survival. Longer waiting lists are causing transplant centers to consider moderately steatotic livers as a part of extended donor criteria. However, a method is needed to objectively quantify fat content in livers in order to select suitable organs. Many studies over the past 30 years have characterized a correlation between fat content of livers and acoustic properties such as sound speed and attenuation. This research seeks to employ an acoustic caliper device to acquire acoustic measurements that can be used to quickly, accurately, and noninvasively evaluate the fat in transplant donor livers. Sound speed and attenuation were measured by transmitting short pulses of ultrasound at frequencies from 1-10 MHz through excised pig and cow livers. Liver thicknesses were measured with a dial caliper to permit sound speed estimates, and reference measurements were taken in water to calculate the additional attenuation created by the presence of the liver. In addition, a thermocouple was used to take precise temperature measurements in liver and water, since sound speed varies with temperature. Although fat content was not quantified, sound speed and attenuation did correlate with the presence of visually observable fat. However, significant variabilities between measurements were also found with regard to the preparation of the liver samples and tissue inhomogeneities. This work has led to ideas for an improved acoustic caliper device and for testing lipid emulsions as tissue phantoms for evaluating measurement capabilities.

Leishmania, a kinetoplastid parasite, causes a wide range of diseases with asymptomatic to lethal pathologies accompanied by widespread human and animal disease, death, and economic loss. Current drugs targeting Leishmania are inadequate. Leishmania exhibits an unusual DNA modification – a glucose is added to certain thymine nucleotides – mainly in the telomeric repeat regions of the genomic DNA, but also in strand switch regions (SSRs) between polycistronic transcription units (PTUs), where transcription initiation and termination occur. This DNA modification converts about 1% of thymine (T) in the nuclear DNA to β-glucosylhydroxymethyluracil (base J). Previous studies show that J plays an important role in transcription termination, and removing J entirely causes Leishmania to die. Using episomal plasmids, it has also been shown that the primary DNA sequence is sufficient to direct J insertion and that an enzyme called JBP2 is required. My project focuses on determining the mechanism of J insertion in Leishmania by using Single Molecule Real Time (SMRT) sequencing to identify the positions of J in SSR and telomeric repeat sequences inserted into plasmids grown episomally in Leishmania, and to search for a DNA sequence motif common to J sites that may be the insertion signal for recruiting the enzymes that modify T to J. We found that the J insertion motif in both SSR and telomeric repeat sequences appears to involve a 14 basepair spacing of Thymine on opposing strands, with GC-rich sequence in between. Additional experiments will further define the J insertion motif using additional SSR sequences and mutated telomeric repeats sequences, and will address whether the insertion sequence is specific to JBP2. Furthering our understanding of the role of J in Leishmania transcription may provide new targets for disease therapies and also help explain the origins of transcription regulation in other eukaryotes.

 The performance of machine learning (ML) classification algorithms in an open-ended problem with manual labels is difficult to assess, because errors can exist both in classification and manually labeled datasets. An additional dataset of manually re-annotated data can help to differentiate classifier and manually labeled data errors; however, there is currently no effective way to visualize all three datasets simultaneously. To address this problem, we introduce a new type of visualization called a confusion diamond. The confusion diamond consists of 8 triangles, with each comparing different dimensions of all three datasets. The arrangement of the triangles complement traditional confusion matrices and utilize many of their visual properties. The confusion diamond layout allows users to pre-attentively perceive data errors as distinct from classification errors, which makes the visualization easy to use. Multiple confusion diamonds can be analyzed at once, making it useful for datasets containing multiple labels, and giving researchers the ability to quickly identify which labels have errors and how to solve them. This work presents the key design elements of the confusion diamond visualization, relevant usage scenarios, and findings from semi-structured interviews with members of a research team interested in using the confusion diamond to help them visualize ML classification performance on large social media datasets.

The Hepatitis C Virus (HCV) infects millions worldwide and is one of the leading causes for the demand of liver transplants. Currently there are various treatments that benefit particular patients but not all. The objective of this project is to develop a rapid and inexpensive sequence based assay to drive the proper drug treatment selection. Mutations in the HCV genome from a specific patient could arise spontaneously from prolonged drug therapy or could be acquired during the initial infection. By sequencing, these mutations can be detected at the amino acid level; this will allow determination of which drug treatment will not be effective. I have performed PCR on HCV lab strains that have been isolated on a plasmid and will test the same protocols on patient isolates. From these PCR products, I will be using Illumina sequencing technology to sequence the targeted drug resistant mutations and create a database. Currently, expected results will include optimized PCR protocols and preliminary sequencing. Software can then be developed and allow for clinical usage. If this assay proves to be successful, this method can be applied to various other diseases that also confer drug resistant mutations. 

Grounded in subaltern studies, a body of work that analyzes the viewpoints of those who are outside of the social, political and geographic power structure, this paper strives to illuminate the Nueva Canción, or “New Song” movement. Emerging in Latin America during the 1960s, Nueva Cancion celebrated the lives of indigenous and laboring class communities, but was largely made up of figures from positions of racial and economic privilege within the larger system. Investigating the seemingly contradictory politics of representation present, this paper discusses how the movement sought to champion disenfranchised figures, while simultaneously casting such figures as incapable of representing themselves; thus rendering them voiceless. At the center of my inquiry is Mercedes Sosa, a prominent Nueva Cancion figure of local and international recognition, who, as a woman of mixed European and indigenous ancestry, attempted to traverse the gap between the movement and its sentimentalized subject matter. By using Sosa as a focal point, this paper aims to illustrate the complex dynamics of the social and political climate in Latin America from 1960-1982, that enabled Sosa to function neither as producer or subject, but as what can be referred to as a “knowledge mover,” circulating the dominant ideology at the same time as effectively challenging it.

What does Nike expect of their athletes, and how does the behavior of athletes outside of sports affect the company's endorsement deals? I feel that this research question should be shared because I feel that it is important to know how endorsement deals affect athletes financially and culturally by having or losing these deals from companies such as Nike. I believe Nike chooses to hand out million dollar endorsements to "Hot Commodity" or "Supernatural" athletes. Nike, having a money-making mentality, exploits the use of athletes as investments in order to make money for themsleves as a company, whereas pro athletes have the motive for a reputation and fame opposed to money, seeing that they are making millions already. I have examined how Nike punishes the athletes they sponsor by stripping them of their sponsorship and consider the types of actions Nike finds intolerable off the field of play, as well as the impact that it has on the athletes. For my research, using the methods photo analysis, interviews, and also social media analysis, I examined different Nike ads, multiple articles based on Nike, and also watched documentaries on the company. I found these methods to be very effective in my study because Nike powerfully shapes the sports industry. By continuing my research, I found that Nike bases its decision on the athlete and what they have accomplished athletically, rather than the person they truly are.

It is no secret that men’s sporting events rule mainstream sports media while women’s sports seem to have less prestige. The media’s focus on men’s sporting events generally is about the talent level, or success of the team while in women’s sports there is an emphasis on the sexual appearance of the athletes as well as the performance aspect. In contemporary culture, biases and prejudices are formed through media representations and marketing of female athletes. With sports being as popular as they are, media is able to use female athletes in a way that deters the consumer from viewing her as an athlete. This leads me to my question: Does the media’s portrayal of women athletes as sexual objects rather than athletes influence their performances and thus, sexualize their accomplishments? While research, participant observation and social mapping helped gain a better understanding of the differences between male and female sports coverage and cultural involvement, an interview with a former Division 1 volleyball player was the greatest insight to how the media really portrays women athletes. After the interview it was clear to see that the media puts an enormous amount of added pressure on women to look good as well as perform at the highest level. I predict that through my research and observations there in a correlation between media coverage of sports and the stereotypes surrounding women athletes and that these stereotypes do in fact add societal pressures on the athletes.

Rhododendrons are plants native to the Northern hemisphere, comprising over 1000 species, most of which have eye-catching flowers. The native Rhododendron of the Pacific NW, R. macrophyllum, harbors a degree of DNA sequence variation exceptional for a single species. Our study focuses on RPB2d, the gene encoding the second largest subunit of RNA polymerase II. Within intron 4 of R. macrophyllum RPB2d, there exist four conserved haplotypes, which have a structured geographical distribution. (Puget Sound differs from Oregon Cascades differs from Oregon Coast.) This surprising pattern of intraspecies variation inspired my project of looking into the degree and pattern of genetic homogenization in these populations by recombination events within and near the RPB2d gene. Thus far, I have sequenced most introns throughout RPB2d and some of the non-coding region upstream. The results have shown that the intron 4 haplotypes are linked to specific variants in intron 1. However, the later introns (6-13, 13-15, and 23-24) are uncoupled from the intron 4 haplotypes and show increasing recombination. About 1 kb upstream, there is a 341 bp DNA sequence inversion in certain plants. An inversion is a segment of a chromosome that has been reattached on the same chromosome in the same location, but in the opposite direction. The inversion found in most RPB2d genes of R. macrophyllum is not found in other species or in haplotypes 1 and 4, the ones most similar to other species. The data continues to show that fewer recombination events occur in introns closer to the inversion. My research is now focused on how the inversion limits the rate of recombination. The next step will be to sample heavily from homozygous populations to see if there is a normal rate of recombination. This regulation could help explain the persistence of varied haplotypes in intron 4.

Eukaryotic genomes contain many copies of ribosomal DNA (rDNA) encoding the RNA components of ribosomes, ranging from 150 tandem repeated copies in the budding yeast Saccharomyces cerevisiae to approximately 700 copies total in diploid human cells. It is not known what dictates rDNA copy number, but we hope to gain insight by identifying genetic regulators of rDNA copy number. Recent work in the Brewer/Raghuraman lab using S. cerevisiae reveals connections between rDNA copy number and cellular processes, such as genome replication and replicative aging. These studies suggest that too few rDNA copies cannot satisfy ribosome demand and too many copies can interfere with DNA replication. Thus, certain genetic pathways must function to maintain such balance. Our preliminary survey finds that some strains with specific single gene deletions have varying rDNA copy numbers, suggesting genetic control of the flexibility of rDNA copy number. Our goal is to identify genetic regulators of rDNA copy number in a systematic genome-wide screen. I have developed a high throughput screen to look for strains with variation in rDNA copy number by measuring the size of chromosome XII, the chromosome that carries the rDNA locus. I will use this method to screen a yeast library of approximately 5000 non-essential single gene deletions. After finding and analyzing mutant strains with chromosome XII size changes, we will have a more comprehensive understanding of the cellular mechanism that controls rDNA repeat number. As rDNA repeat number is linked to replicative lifespan, we hope to uncover the common genetic pathways that regulate rDNA copy number and longevity.

Cleft lip with or without cleft palate is among the most common congenital birth defects, but its phenotypic presentation is highly variable. This variability not only impacts the clinical management of patients, but also poses many challenges for recurrence risk counseling. Population studies indicate a diversity of causative factors, including genetic and non-genetic factors. Although some genetic causes have been identified, further progress in this area will require more precise classification of subphenotypes. Numerous cleft lip/palate classification systems have been developed over the years, but there is a lack of consistency among these models. These discrepancies lead to problems regarding precision and interpretation when documenting clefts for research or treatment purposes. The Ontology of Craniofacial Development and Malformation (OCDM) project, part of the National Institute of Dental and Craniofacial Research’s FaceBase Program, aims to develop a framework of anatomical terminology to facilitate integration of diverse sources of research and clinical data, including genetic, embryological, and phenotypic information. The overarching goal is to maximize sharing of research data and promote collaboration to drive research into the causes and treatment of craniofacial disorders. To this end, we have comprehensively reviewed existing classification systems with respect to the methods of categorization of cleft types, including placement, severity, and other distinguishing features. Along with wide variation in terminology, there was also wide variation in the extent of content among systems. Each system categorized clefting differently, but none encompassed all other systems’ classifications, nor all cleft types observed in the clinic. It is predicted that integrating these systems through a common anatomical ontology will serve to facilitate standardization of cleft classifications and terminology. In addition, this foundation should enable further subclassification to ultimately benefit studies exploring relationships between causes and manifestations of orofacial clefting, as well as underpin advances in interventional therapies and surgical treatments.

It is important to see how the National Collegiate Athletic Association (NCAA) handles situations of illegal contact and improper benefits between agents and student athletes. Such situations include players being contacted before they are eligible for the draft, as well as money stipends to entice players to sign with them when they are eligible. As a result of these incidents, the NCAA’s regulations affect players' families and institutions, as well as the fans. The implications of these infractions produce institutional sanctions such as loss of scholarships, bowl bans, and the possibility of coaches getting fired. To sufficiently unveil my research, I will use discourse analysis looking at how media responds to players that have been accused of or found guilty of accepting improper benefits. I will also use qualitative interviews of other student athletes to reflect on how they have been contacted by various people to accept benefits and how they have responded. I also include my own positionality as a student-athlete to reveal how I have been approached by runners, which can be anyone who mediates interaction between a player and a booster or agent such as a friend, family, or significant other. I anticipate my research will reveal that agents have been bribing players early in their collegiate careers so that when the time comes for them to enter the NFL draft they are inclined to choose those particular agents to represent them. Through my research, I hope to inform student athletes to be more cautious before making decisions because they may be pressured when influenced by money. My research will also give insight to fans that the players they love to watch on Saturdays do not always go looking for these offers that are presented to them frequently.

Kaposi’s sarcoma-associated herpesvirus (KSHV) is a human pathogenic γ-herpes virus and is the infectious cause of Kaposi’s sarcoma (KS), primary effusion lymphoma, and plasmablastic multicentric Castleman’s disease. The KS tumor is highly vascularized and is characterized by latently infected spindle cells of endothelial origin. While in the KS tumor 1-5% of the cells are lytic and producing more virus, greater than 90% are latently infected and not producing virus. The goal of this project is to investigate whether the latent genes expressed by KSHV are sufficient to alter endothelial cells to induce angiogenesis, metabolism, and oncogenic cell signaling. We will determine if latent genes alone induce these effects or if the small percentage of lytic genes play a paracrine role. In order to do this we are cloning the entire KSHV latent locus into a gutted adenovirus expression vector that eliminates the contamination from expression of adenovirus genes. The latent locus includes the 4 genes expressed during latency and the 12 virally encoded microRNAs. The adenovirus vector expressing the latent locus will be used to infect endothelial cells and we will examine the cells expressing the KSHV latent locus for changes in factors involved in angiogenesis, metabolic pathways and oncogenic cell signaling. If the latent genes recapitulate the pathways of a KS infection, this will indicate that latent gene expression alone, without the low percentage of lytic genes in the culture, are sufficient to induce many cellular pathways induced by KSHV and are relevant for the pathogenesis of KSHV in KS tumors.

Possession Sound is located at the Snohomish River estuary system between Everett and Whidbey Island in the greater Puget Sound. Mixing between fresh and saline water occurs as a result of the river’s influence and varying tidal exchange. It was hypothesized that more plankton will be present at North Jetty, a site near the mouth of the Snohomish River compared to Buoy, a site located on the opposite side of the jetty, farther from the river. Therefore, it is expected that the plankton biodiversity of North Jetty will be greater when compared to Buoy. Plankton samples were collected at flood and ebb tide at North Jetty to observe the effects of both location and tide height on plankton biodiversity. At North Jetty, there was a wider variety of phytoplankton and zooplankton species during flood tide while ebb tide demonstrated less biodiversity in a smaller population according to data collected in February of 2013. The data from North Jetty depicts that at flood tide there is a greater influence of salt water flow moving planktonic organisms up river.  Gaining an understanding of the effect of flow on plankton in this local area will help strengthen students' understanding of the Possession Sound estuary system.

Public transit plays an important role in the daily lives of blind individuals. Unable to drive, blind commuters must rely on buses, subways, and other methods of public transportation to travel from one destination to another. Although transit schedules and even real-time arrival information are now readily available and accessible, there are still barriers to overcome. For example, a blind bus rider may find it difficult to locate a designated bus stop. Prior research has shown that, given a set of information about a bus stop, blind commuters will find their bus stop with significantly greater ease and lesser time spent. Our goal is to create a database of useful and reliable information regarding every bus stop in Seattle and make that information accessible to blind individuals. In order to collect such a vast amount of data, we have turned to crowdsourcing, a process that involves dividing work amongst a large group of workers over the Internet. By providing workers with Google StreetView images (ground-level visuals on the appearance of a location) and simple, multiple-choice questions, we hope to collect accurate information to answer questions such as “How many benches are at the bus stop?” or “In what direction is the bus stop relative to the intersection?” After acquiring a sufficient set of bus stop data, we will test the usefulness of this information to blind commuters by providing them with access to our database and analyzing their feedback. We believe that our work in this field will improve the public transit experience for blind individuals by providing them with a feeling of confidence and independence during their commute. Our work in this field may lead to further research in utilizing crowdsourcing to solve accessibility issues.

Humans are exposed to environmental toxins which can contribute to acute or chronic diseases, such as Parkinson's disease. Different people, however, have variable susceptibility to these toxins due to genetic variability within the population. In this project, we will utilize the model organism Saccharomyces cerevisiae(yeast) to investigate the molecular mechanisms of differential responses to environmental toxins that target the mitochondria. Many yeast single-gene deletion mutants will be exposed to mitochondrial toxins using a high-throughput Biosreen C instrument(combined shaker, incubator and plate reader, allowing for growth rate determination of yeast cells) and subsequently, bioinformatic methods will be exploited to identify genes involved in the response to mitochondrial stress and mechanisms of toxicity. We explored optimum concentration of different toxins for mutant yeast, expecting that different mutations will response genotype-dependently to different compounds. Identifying genotype-dependent responses to the environmental mitochondrial toxins may illuminate how mitochondria toxins contribute to disease and identify genetic factors invovled in susceptibility.

Prostate cancer is the most common type of male malignancy in the Western world. Patient death often occurs when treatments which decrease circulating levels of male reproductive hormones are no longer effective. This lethal stage is termed castration-resistant prostate cancer (CRPC). Under normal conditions, androgens function through androgen receptors (ARs) to cause AR activation. The recently identified androgen receptor splice variants (AR-Vs), which lack part or all exons coding for the AR-ligand binding domain, are believed to cause the continuous AR activation found in androgen-independent conditions such as CRPC. Ubiquitin-conjugating enzyme E2 C (UBE2C) is an oncogene expressed in many types of solid tumors and has a function of marking proteins for degradation. Uncontrolled cell growth can be caused by overexpression of UBE2C which targets proteins that serve as cell-cycle check points to be degraded. Overexpression of UBE2C is reported to be positively correlated with AR-V expression. The transcription activation of UBE2C requires chromatin-looping through a phosphorylated transcription factor, mediator of RNA polymerase II transcription subunit 1 (p-MED1). My project investigates the relationship between AR-V and p-MED1 in mediating UBE2C gene expression. We used LnCaP and M12 human prostate cancer cell lines and transfected them with AR-Vs. Expression assays were carried out to measure the UBE2C gene expression levels and the presence of p-MED1 in response to AR-V expressions. We also performed functional assays such as co-immunoprecipitation to determine the functional interplay between AR-V and p-MED1 in mediating UBE2C transcription. We hypothesized that p-MED1 is required in AR-V-directed UBE2C expression. Our data suggest that, through a distinct transcriptome, the presence of p-MED1 as a mediator is required in AR-V-directed UBE2C expression and cancer cell proliferation. The importance of AR-V, p-MED1 and their mechanisms underlying CRPC progression might provide a new therapeutic approach for targeting AR-independent CRPC.

Consolidated bioprocessing is the creation of one engineered organism that can handle a chain of chemical reactions that take a low cost feedstock, such as plant biomass, and synthesize high value products such as biofuel or medicine. This project aims to address the first stage of consolidated bioprocessing which is the digestion of the feedstock. Our design is an E. coli strain that can be in one of two states: the consumer state or the altruist state. In the consumer state, the cell carries out normal function by growing and dividing. In the altruist state, the cell produces a large payload of digestive enzymes that degrades plant biomass then lyses to release the payload to the environment where it can act. The consumer cells can then utilize the products of the digestion process to grow and divide. This system is made up of three major genetic components. The first component is a plasmid that designates whether the cell is in the consumer or the altruist state. This plasmid carries a genetic toggle switch that has two operons that produce transcription factors that co-repress each other. The second component is a plasmid that handles the production of digestive enzymes coupled with a lysis gene. Expression of this plasmid is only active if the cells are in the altruist state. The third component a genomic set of enzymes that handles the digestion of cellobiose, the product of the breakdown of cellulose. Initial results demonstrate that the engineered strain is able to grow solely on cellulose and current work focuses on the optimization of the system.