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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

 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.

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.

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.

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.

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.

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.

 

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.

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.

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.

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.

 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.

 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.

 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.

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.

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.

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.

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.

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.

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.

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.  

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

 The themes I explore in my research include the examination of population exclusion and social marginalization in car-centric communities and the resulting socioeconomic and geographic marginalization of communities due to transit structures. Accessibility to transit is a structural barrier that contributes to opportunity inequalities which further stratify marginalized populations in terms of socioeconomics. My research highlights the consequences of creating communities and systems that are car dependent without incorporating effective mass transit. Populations considered in this research include youth, elderly, socioeconomically disadvantaged, differently abled, and those in international transition such as refugees or undocumented communities.  I present an examination of such texts as Jane Jacobs' The Death and Life of Great American Cities, Edward W. Soja's Seeking Spatial Justice, and Highway Robbery edited by Bullard, Johnson, and Torres.  Using literary analysis and community feedback, I aim to illuminate the opportunity discrepancies of marginalized populations between communities with transit isolation and those with more comprehensive transit accessibility.  Spacial and social restriction due to transit isolation bars marginalized communities from having equal access to employment, health, civic, housing, and educational opportunities.

In conjunction with Sustainable Seattle, my project seeks to identify barriers to recycling and composting in Seattle in order to ultimately increase the amount of recycling and composting that takes place. My research questions attempt to address this in two parts. First, if Seattle residents participate in recycling and composting, what is preventing them from recycling and composting more? Second, what changes can be made by the government or policy makers in order to encourage more recycling and composting? To identify barriers, I have read past reports studying difficulties in implementing recycling, and also behavioral studies identifying which methods can lead to behavioral change. From this, I discerned that the ideal methodology would consist of conducting interviews of consumers and testing multiple waste infrastructure systems at Seattle Tower using different plans on each floor to determine obstructions to commercial recycling in Seattle. Next, to identify possible behavioral modifications for more renewable action, I will conduct consumer interviews as well as the Seattle Tower project, both of which are still in progress. Initial research suggests that common recycling problems for consumers are a lack of standardized labeling on packaging and products. The results of this study and recommendations about labeling will be posted on the Sustainable Seattle website, and the Seattle Tower will be given infrastructure recommendations for improved efficiency based on the results of what was most effective. Ideally the implications of this project will lead to increased recycling and composting rates in Seattle. This can lower the costs of waste disposal for the public, businesses, as well as the city. Recycling and composting is much more cost effective and environmentally responsible than hauling trash each day to a landfill, and therefore should be utilized as much as possible. 

This project was aimed at helping UW Recycling identify inefficiencies in waste disposal and provide them with information that will assist in ascertaining their optimized waste diversion rate of 70% by 2020. Having a 70% diversion rate means that the UW would be sending 70% of its waste to recycling or compost facilities instead of a landfill. In turn, this means the University has less monetary investment in waste disposal practices while simultaneously making a beneficial and a substantial reduction in its environmental footprint. We hypothesized that individuals were not properly utilizing the trash, recycle and compost bins, and that upon evaluation of these bins we would find contamination that would allow us to identity inefficiencies. To test if waste was indeed being deposited incorrectly we chose to sort and examine trash, recycling, and compost from two locations over a five week period. During this time we documented the weights of pre-defined categories of waste and observed common trends in the waste stream. This revealed that compost was the main source of contamination in both the recycling and trash bins. The average trash and recycle bin compost contamination was 72% and 36%, respectively. However, the composition of the compost container showed that 93% of the materials in the bin were indeed compostable. These results align with our initial hypotheses. Furthermore, our study allowed us to identify possible causes for this behavior and to propose a series of measures to help mitigate it. We hope to expand this work with future efforts, including: educational outreach through trash sorts, implementing programs that engage the community and further divert waste, experimenting with new bin labeling systems, using Geographic Information System for mapping of campus compost bins for better tracking, and introducing more compost bins throughout campus buildings.

Emerging from the political decline of the Islamic “Gunpowder Empires,” the Central Asian Nadir Shah assumed leadership of the former Safavid Empire before winning notable victories over his Ottoman and Mughal counterparts. In this paper, I attempt to grapple with the complex issue of Nadir Shah’s ethnic identity, which has alternately been presented as either Turkic or Persian. As such, I attempt to navigate the trend of nationalist historians to appropriate Nadir Shah into their own nation’s retroactive “national history,” relying not only on the works of such historians, but also those more removed from nationalist perspectives. Using readings spanning from the 18th century until the present day, I note the shifts in Nadir Shah’s ethnic identification across nations and time periods as well as the differing degree to which historians attempted to restrict the king’s identity to a single ethnic group. Highlighting political changes affecting Central Asia during the 18th century and their enablement of Nadir Shah’s navigation of class and race-based hierarchies, I then critique narrow national identifications of Nadir Shah and attempt to highlight nuances within the issue of pre-nation state ethnic identity. In conclusion, I assert that pre-nation-state identity may have been mutable and that Nadir Shah’s identity, rather than sitting on one side of a Turkic-Persian dichotomy, reflects a fluidity of nationality extant in 18th century Central Asia.

During the colonial period in Korea the Japanese tried to squelch Korean identity, enfolding the Korean people within their expanding empire. As Japan’s policies and actions on the peninsula became increasingly oppressive, the Western world naively accepted Japan’s benign explanations. However, not everyone disregarded the warning signs in East Asia. Thomas F. Millard, an American journalist, was struck by the Korean plight and took up the Korean cause for independence in his writings. Millard was not only immersed in the affairs of East Asia, he was passionate about what he wrote. As Japanese historians and politicians worked to distort the Korean voice so that it reflected a supposed need for and acceptance of Japanese assistance, Millard attempted to expose their deception. In response to Japanese domination, Korean nationalism rose. Koreans formed a national identity centered on their shared heritage. Identity needs both internal and external recognition. Though the Korean people never identified as Japanese, during the colonial period the rest of the world saw them as Japanese citizens, not Koreans. In 1948 the United Nations agreed that nationality was a human right. Though the Universal Declaration of Human Rights was far from being conceived in the early 1900s some people already believed in the rights that it would solidify; Millard was one of those people. He saw Japan’s actions as criminal, and he wrote about just that. As the Japanese tried to muffle Korea’s voice, Millard became a conduit for that voice. In a present-day world that still wrestles with the vestiges of imperialism, Millard’s work is a testament to the importance of listening to the multitude of voices that continue to sound around the globe.

In 1807, William Sampson is banished from Ireland for his radical cause lawyering and immigrates to America to become its first civil rights lawyer. Some have researched the practice of his critical postcolonial legal theory that culminates to America’s first constitutional victories for religious freedom and labor rights. However, few have investigated this practice in promoting racial equality, particularly in the context of scientific constructions of race. One of Sampson’s most famous trials, Almshouse v. Whistelo involves an unprecedented number of medical expert witnesses attempting to prove and disprove categories of race using physiological understandings of human development. Sampson’s cross-examinations of these expert witnesses serves as an entry point to examining the practice of his critical legal theory in the context of scientific racial categories. First, this project identifies Sampson’s critical postcolonial legal theory from his writings, particularly his Memoirs and Discourse on the Common Law. Then, it examines the practice of Sampson's legal theory in Almshouse v. Whistelo, by focusing on his cross-examination of Dr. Mitchill, a famous scientist. And finally, discusses the various books and scholarly research articles citing Whistelo that support or challenge research on human physiological development. This case is cited almost every decade after it is argued from 1832 to 1902 in many scientific texts, such as a chapter on fetal development in America’s first physiology textbook, Human Physiology by Robley Dunglison—the Father of American Physiology. Legal publications mention the humorous nature of Sampson’s cross-examination of Dr. Mitchill, a famous scientist. This project suggests that Sampson’s entertaining cross-examining plays a key role in both challenging Dr. Mitchill’s scientific constructions of race and altering physiological constructions of race in 19th century America. It adds to research on Sampson’s postcolonial legal theory and illuminates another facet of America’s first civil rights lawyer

The pancreatic islet β-cell maintains blood glucose homeostasis by releasing insulin, a process that becomes dysfunctional in type 2 diabetes mellitus. Thus, maintaining normal β-cell function is critically important and occurs through many mechanisms including interactions with the surrounding extracellular matrix (ECM). We have recently shown that the polysaccharide hyaluronan is a normal component of the islet ECM. Under normal conditions, hyaluronan exists in a high molecular weight (HMW) form (>500 kDa) which exerts anti-inflammatory effects on surrounding cells. One study has shown that HMW hyaluronan can potentiate β-cell glucose-stimulated insulin release (GSIS). Our preliminary data suggest, in diabetic islets, hyaluronan can become fragmented. Low molecular weight (LMW) hyaluronan (<10 kDa) is pro-inflammatory. Furthermore, agents that can activate the same intracellular signaling pathways as LMW hyaluronan (e.g. free fatty acids and lipopolysaccharide) have been shown to impair GSIS, suggesting LMW hyaluronan may have a similar effect. I hypothesize that HMW hyaluronan potentiates GSIS, whereas LMW hyaluronan inhibits GSIS in vitro. Rat pancreatic islet cells were cultured on plates coated with HMW hyaluronan, LMW hyaluronan, or L-ornithine (control). After 48 hours GSIS was determined by comparing insulin release under basal (low glucose) and stimulated (high glucose) conditions. Our preliminary data show that as expected HMW hyaluronan potentiates GSIS 2 fold while LMW hyaluronan decreases GSIS by 30% compared to control. Thus it appears HMW hyaluronan is beneficial for β-cell function whereas LMW hyaluronan lacks this effect. Hence, hyaluronan fragmentation in the islet under diabetic conditions may contribute to impaired β-cell function.

Pharmacogenetics is the study of how variations in a person’s DNA affect their response to drugs. It is the foundation of ‘personalized medicine’ and could one day enable drug therapies for individual patients based on genetic composition. Glucocorticoids are a group of cholesterol-based signaling molecules including endogenous hormones such as cortisol, which the body produces naturally in response to various forms of stress, and commonly prescribed anti-inflammatory drugs, which are used to treat diseases ranging from asthma and cancer to autoimmune disorders and psoriasis. For a glucocorticoid to produce its physiologic effects in any cell of the body, it must first bind to the glucocorticoid receptor (GR) and translocate with the GR to the cell nucleus. Both of these biologic processes are dependent on the molecular chaperone protein hsp90. A necessary first step in glucocorticoid-based pharmacogenetics research is better understanding the genetic variation associated with alterations in endogenous cortisol signaling. Our goal was to identify correlations between individuals’ variations in endogenous cortisol signaling and underlying genetic variability. Salivary cortisol (CORT) concentrations were measured in healthy volunteers (n=66) before and after CORT stimulation to determine variability in circulating CORT levels and CORT response. Statistical analysis revealed that inter-participant CORT variability in concentration or percent change was not exclusively correlated to participant demographics, health history, or GR single nucleotide polymorphisms (SNPs). Interestingly, nuclear localization of hsp90 correlated with an elevated pre-stimulus CORT concentration and a decreased post-activity CORT concentration. To investigate the observed CORT response and hsp90 localization association further, coding regions of the hsp90 gene were sequenced to identify possible genetic linkages. Eight hsp90 SNPs were detected, four previously unreported. All participants expressed between two and five of these SNPs. These data demonstrate inter-participant differences in CORT response, nuclear hsp90 concentrations, and GR/hsp90-associated SNPs are readily detected and potentially interrelated.

Abnormal perinatal environment, commonly manifested as low birth weight, has been associated with birth defects as well as chronic disease. In particular, studies have shown low birth weight to have a deleterious association with type II diabetes, hyperlipidemia, hypertension, cardiovascular disease, renal disease, and renal failure. Of specific interest are the mechanistic details concerning low birth weight subjects’ altered excretion. Maternal low protein diet (LPD) during gestation and lactation results in offspring with significantly lower birth weight. Using the maternal LPD rat model, we determined renal excretion of select endogenous compounds by collecting blood and urine at various times of age. Clearance of creatinine and uric acid are indicators of glomerular filtration rate and reabsorption, respectively. High Performance Liquid Chromatography assays were used to simultaneously quantify creatinine and uric acid in the urine and in the blood of the rat. It was found that creatinine clearance and uric acid clearance decreased in LPD rats in an age-dependent and sex-specific fashion. Specifically, there were observed significant decreases in both creatinine clearance and uric acid clearance in LPD male offspring at both age’s day 90 and day 120 old. No differences were observed in both creatinine clearance and uric acid clearance in LPD female offspring until age day 120 old indicating an age-dependent programming of females as opposed to males. The results strongly correlate with decreased and altered excretion observed in low birth weight subjects and suggest that perinatal LPD has a long-term programming of renal excretion. These findings could partially explicate the underlying mechanisms that lead to higher incidence of renal disease/dysfunction in perinatally growth restricted subjects. Furthermore, altered renal function could affect the renal handling of therapeutic agents and thus affecting the overall treatment outcomes in low birth weight subjects.

Obesity is a major cause of health-related problems in the developed world and recently studies have demonstrated a link between environmental factors and obesity. 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47) is one toxic chemical used as a flame-retardant in consumer products. BDE-47 contaminants are commonly found in dust, air, and soil and their accumulation in the food chain contributes to significant levels found in humans, particularly children. Recent studies have linked BDE-47 to a range of toxic impacts, including disruption of insulin signaling. The objective of this study is to investigate the in vivo effects of BDE-47 in hepatic metabolism. We hypothesize that the drug will cause increased cell injury, inflammation and accumulation of fat within the liver (hepatic steatosis) and will have significant effects on individuals predisposed to disruption in insulin signaling. In order to disrupt insulin signaling in vivo, we have generated mouse models with liver-specific deletion of Tsc1 and Pten, negative regulators of mTORC1 and Akt respectively. Both of these complexes play critical roles in the cell cycle and insulin metabolism within the liver. Cohorts of Tsc1-/-, Pten-/-, and control mice were exposed to BDE-47 or placebo for six weeks within their first 10-12 weeks of life. During exposure, the mice were tested for insulin sensitivity and glucose tolerance. Liver tissue was also tested for several markers of hepatic insulin signaling post-mortem. Differences in impacts on these genetic mutants could indicate if the BDE-47 targets the Akt or mTOR cascades differently and if those predisposed to aberrations in insulin signaling may be more sensitive to the toxic effects of BDE-47. This study will determine if a significant interaction between the environmental influence of BDE-47 and the genetic deregulation of insulin signaling occurs, which could have deleterious implications for the use of these compounds in consumer products in the future.

Pathologic enlargement of the esophagus, termed megaesophagus, results in a failure to complete peristalsis leading to vomiting, severe weight loss and potential death. Megaesophagus is characterized in a number of disease states including parasitic (Chaga’s disease), autoimmune (myasthenia gravis), and neuromuscular (muscular dystrophies), however, a detailed cellular and mechanistic understanding is lacking. To address this deficit, we performed a comprehensive examination of the onset, pathology and cellular composition of megaesophagus in the mouse model of Duchenne muscular dystrophy (DMD). DMD affects ~1/3500 male births and is a catastrophic and ultimately fatal muscle wasting disease resulting from a mutation in the gene encoding the integral skeletal muscle protein dystrophin. Although poorly defined in human DMD patients, megaesophagus is documented in canine and mouse models of DMD. Advancements in DMD therapies has increased patient lifespan and underscored a need to assess the impact of the disease in a range of organ systems, including the esophagus. We find that older dystrophic mice can develop severe megaesophagus, but that the timing of onset depends on the nature of dystrophin expression in muscle and non-muscle tissues and the genetic background of the mice. Further studies are in progress to delineate the precise dystrophin expression pattern in different cell types of the esophagus that contribute to pathology. Work presented here will be essential for future work aimed at identifying new therapeutic targets for DMD.

 Flying organisms achieve flight stability by employing a multitude of control surfaces, most notably the wings. However, airframe deformations, such as abdominal motions in the hawk moth Manduca sexta, have recently been shown to play a significant role in stabilizing flight. In my research I have studied the control potential of abdominal deflections using a closed-loop flight arena. Tethered moths controlled the velocity of a projected black bar with their abdominal angle. Image velocity varied according to the difference between the abdominal angle and the set point (relative to the average abdominal angle), scaled by a gain factor. Experimental trials were performed for a ten-fold range of gains at three different set points and consisted of 60s periods during which the moths attempted to stabilize the drifting bar. The moths were capable of stabilizing the image for all experimental conditions, with the highest average performance (50%) occurring at the medium gain and the set point corresponding to the average abdominal angle. Poor performance (<50%) during low gain trials was characterized by steady state error, likely the result of the relatively low image velocities. For high gain trials, the decreased performance (<35%) was characterized by large abdominal oscillations. These results support an active and plastic role for the abdomen in flight control, but also tested the limits of the abdominal control circuit. To continue exploring the role of the abdominal motion I have been working on performing EMG recordings from the abdominal muscles during free flight. For this research the virtual arena serves as a controlled environment to collect preliminary data and to refine the experimental procedure and animal preparation. Finally, I will present my work developing a biometric controller for the Parrot AR.Drone quadrotor. This project utilized a Kinect and custom software to control the quadrotor with body postures.

Mirror self-recognition (MSR), the test of whether or not an animal can identify their own reflection, is one of the highest markers of animal intelligence. To assess this capability, a mark test is conducted. Through this method, the only animals that have reliably displayed self-recognition are humans, magpies, dolphins, and four species of primates. A recent study on magpies showed that this avian species passed a mark test and was capable of MSR. Building on their research, we looked at MSR in parrots (Psittaciformes) of varying species to determine if they too were capable of self-recognition. Our test was done on an individual level. Our test subjects come from varied backgrounds with different life histories, and therefore mark test results within each species differ. In our experiment we exposed 24 parrots to reflective mirror surfaces, and analyzed how their behavior towards the mirror changed over time. After the birds grew accustomed to the mirror, we conducted a mark test. We anticipate that individual birds capable of self-recognition will pass this test because of their high brain-to-body ratio and social predispositions, which are signs of a high intelligence level. If our research shows that Psittaciformes are capable of MSR, they will become only the second avian order ever to pass this test and this would put them on the same intelligence level as mammals.

Visual-Motor processing provides a mechanism for animals to translate visual cues into useful information for locomotion. My research aims to investigate this mechanism by analyzing the responses made by fruit flies to certain visual stimuli. I accomplish this by first tracking and quantifying fruit fly locomotion when two flies are present. By quantifying this behavior I can create a behavioral map of fly responses in relation to other fruit flies. I can then replace one of the flies with a cylindrical, fly-sized magnet that is readily controlled by me. This step is important because by controlling the magnet it is possible to reproduce large amounts of a specific behavior, instead of watching two flies interacting randomly and waiting for relevant interactions. It also will allow me to investigate the affects of object speed and angle of approach and create a behavioral map of the fly's locomotor response. Once this is accomplished it will then be possible to test fruit fly responses to visual stimuli presented on an LED screen surrounding the fly and to measure brain activity in the flies while these stimuli are displayed. Ultimately we hope to identify the neurons that are responsible for visual-motor processing and how they accomplish the transition from visual input to locomotor response.

The figure of the mala or “bad woman” is present in much of Ancient Greek and Latin literature. In this context, being a mala means being a woman who participates in the process where an older woman advises a younger woman about how to profit from men who will pay to sleep with her. The mala assumes many different forms from the lena (madam) and the puella (girl) of Roman love elegy to the ἑταίρα (courtesan) of Lucian’s Dialogues of the Courtesans and is also present in Roman comedy. Although, mala is a Latin word, Lucian’s work provides examples of the same type of “bad women” who advise other women how to profit from their lovers. Despite the fact that the mala is one of the most pervasive characters in classical literature, my research project is one of the first to look specifically at the figure of the mala as a distinct character type across several literary genres. The characteristics of the mala that are present in all of these genres highlight the fact that this character is an important vehicle for expressing cultural anxieties surrounding women. I am most interested in defining the characteristics of the mala in these different literary contexts and genres, and documenting the ways in which the language of power and control is used with malae. Above all, power characterizes the mala. She has power over men, language, and worst of all, she has the power to transform other girls into malae through her teaching. In this paper, I will define the characteristics of the mala and document the ways in which the language of power and control is used with malae in Plautus’ Casina; the elegies of Propertius, Tibullus, and Ovid; and Lucian’s Dialogues of the Courtesans.

Virgil utilizes descriptions of and comparisons to various animals in The Aeneid, which may represent how contemporary Romans and the ancient world in general viewed the wildness and domestication of animals. Animals are ridden in battle and interpreted as omens; possessed as property and feared as predators; emulated as models and admired for beauty. Animals of all sorts appear across the landscape of the text and inside the imagination of the reader. The interplay between domestic animals and wild beasts in this epic poem highlights how Romans thought of themselves: beastly comparisons are used to demonstrate viciousness and courage in battle, and domestic animals are used as tools to appease the gods (in sacrifice) and as a way of showing human dominance. Dangerous animals remind humans (and Romans) of their place and size in the world, while domestic animals help enforce the social hierarchy and define humanity. However, the wildness of the beasts highlights the negative space behind “humanity” as well. When wildness is necessary in man’s definition of “self”, one must ask: what is the purpose of conquering (in some cases, even destroying) wildness, how is this utilized in literature, and what does it mean in ancient times or today? Exploring the animals of The Aeneid helps to define not only Virgil’s textual landscape and the world of ancient Rome, but in fact our own humanity and the role of wildness in it.

Emma B. Andrews' diaries give insight into the lives of archeologists working in Egypt’s Valley of the Kings at the turn of the last century. Due to her association with the archeologist Theodore Davis, Andrews had a unique opportunity to see the excavations in the Valley of the Kings firsthand during her travels between 1889 and 1913. Though these diaries provide valuable cultural, social and archeological perspectives on this period of Egyptian history, they have gone largely unnoticed by the academic community, and this project intends to make these works available as invaluable for academia. In order to bridge a gap in the publishing world, the NEH-funded Newbook Digital Texts project provides a unique environment for the multi-media publication of texts, transcriptions, translations, and annotation of works that are not compatible with traditional publishing or available large-project digital platforms. Newbook Digital Texts’ collaborative nature enables individual projects to inexpensively adapt to the project, providing opportunities for individuals to publish academic works with less expense and hassle. It also enables people to access important texts and resources more easily. As undergraduate researchers, we have the opportunity to work with these primary texts, learning useful digital humanities skills. At the beginning of the process, we learned how to create a structured transcription, allowing us to auto-tag the text. During this process, we have been able to complete a structural analysis of the text. We all worked with XML formatting, creating name lists, and doing content tagging within the text. Additionally, we completed independent research for inclusion in the project’s Wikipedia. Upon reading through the diaries and editing them, our project recognized important links to other excavators and research done in the Valley of the Kings, and we believe the diaries will fill gaps within academia in this field.

Among writers both ancient and contemporary there is great interest in magic and wonder --- thaumata, thelxis, and cognates in the Greek. From the shining gods of the Homeric epics, through the second-century collection of spells known as the Papyri Magicae Graecae, down past the the occultism of Yeats, to the popularity of the Harry Potter series today, the western literary tradition has long been held fascinated by the imaginative power of such factors. Beyond popular culture, today's wealth of scholarly articles, anthologies, and monographs on the study of magic attests to a lively academic discussion around magic's cultural import. This paper aims to participate in that perennial discussion. Although it can be traced back to Platonic philosophy, it has become something of a commonplace that stories themselves work magical effects. This paper seeks to unpack the claims about narrative magic through a literary analysis of its representative deployment in selected works of Classical Antiquity. The Greek Magical Papyri are my main source for the internal terminology of magic, as it was employed in the Imperial period. For language scrutinizing magic, external to the practice itself, and for the fictional representation of both registers, I primarily examine two particularly important oeuvres: those of Lucian of Samosata, in Greek, and Apuleius, in Latin. Lucian's Philopseudes and Alethe Diegemata are key examples of fantastic stories, containing as they do the first versions of the ``Sorcerer's Apprentice'' and the ``Voyage to the Moon'' tales, respectively. Equally significant, Apuleius' Metamorphoses tells a series of magical accounts in a well-wrought masterpiece of early novelistic prose. Furthermore, both these authors are careful and clever, expressing within their texts a self-awareness of the narratological process itself. Outside these decisive thaumata, further comparative examples will be brought to bear as tangental explorations of storytelling's magical properties.

Despite the growing interest in studies of gender and sexuality, little has been published about the figure of Attis since the initial monographs almost three decades ago. Not only does this figure, who was imported into Rome from Asia Minor during the Republican period, represent an important instance of gender ambiguity and nonconformity living in the heart of Roman society, but these issues play out in an incredibly vivid way on the body of Attis. Because of a fit of madness and grief induced by his lover in retaliation for his perceived infidelity, Attis commits suicide by castrating himself. Therefore, the choice made by artisans working in central Italy (Latium and Campania) to obscure Attis’ genitals through his characteristic and unique garment gives insight into distinctly Roman concerns with the integrity of the male body and how to construct the masculine gender. By analyzing one class of the sculptural representations of Attis that combine aspects of both masculine and feminine iconographies of dress and selectively obscure Attis’ genitals, I will demonstrate that these representations were produced under specific social conditions that differed from those in the Hellenistic world and in the periphery of the Roman Empire. In so doing, I hope to rescue Attis from what I feel are oversimplified and typologically driven analyses that obscure the active dialogue between these figures and Roman notions and representations of masculinity. In the process, I also wish to raise questions about other less valorized male bodies that place their owners into liminal gender categories: the hermaphrodite, the androgyne and the eunuch, with the hope of engendering future discussion about alternative masculinities in Rome.

Mobile devices have become ubiquitous in today’s society, yet their role in artistic practice is often relegated to documentation, communication, and play. I have spent the last quarter as the TA for Media, Time, and Technology, a course designed to explore the use of mobile devices in contemporary arts research and practice. Student assignments ranged from concrete conceptual exercises to thought experiments designed to explore and develop idealized future works. My research draws on my experiences in this class as well as the development of my own artistic practice, focusing not only on emerging technologies but also the exploration and reconceptualization of historical works of art. Through the marriage of technological exploration and historical interrogation I hope to develop a personal practice that is grounded in the rich lineage of art yet always looking forward.

NSFW (“Not Safe For Work”) is an acronym used to indicate that a website, a picture, or a link contains inappropriate (usually pornographic) content. One could say that all of 4chan.org is NSFW. 4chan is an imageboard where communication takes place in the form of pictures and images posted by anonymous users and deleted minutes after they appear online. This anonymity and ephemerality of communication unleashes levels of racism, sexism, homophobia, and general malevolence unseen in Social Web communities like Facebook. However, 4chan operates with virtually no advertisement (or profit-motive) while Facebook is now a publicly traded corporation, with a mandate to generate revenue for its stockholders by monetizing its assets, which happen to be the words, pictures, jokes, and plans of its more than 1 billion users. Discourses surrounding the Social Web speak in terms of “openness,” “connectivity,” and “transparency,” promising a more civil online community. However, these trends make personal data and communication susceptible to appropriation by capital. How has 4chan remained a largely non-commodified space in the midst of the corporate colonization of the Social Web, and what do we make of its sociopathic ethos? I studied the community and signifying practices of 4chan's random board /b/, finding that although the fundamental anonymity and ephemerality of communication on the board free up participants to be racist, sexist, homophobic, and generally malevolent to degrees unseen in the Social web, these same conditions create a space for truly free speech (in both the monetary and behavioral sense), creating a novel mode of signification and a space for subversive political consciousness in the process.

Death has been a phenomena that has been dealt with in varying ways throughout human history. How we deal with physical death online, specifically through Facebook, has proved to be an insightful challenge to the current digital age. The use of Facebook as the link between the living and the dead highlights the level at which we appropriate our Facebook profiles as extensions of our physical body due to the desire for reinvention associated with death. While only a few studies exist directly related to death on Facebook, they expose communities of mourners interacting with each other and the deceased on a surprisingly horizontal level, and contacting the dead without necessitating time restraints or religious/spiritual intermediaries. Traditional death rituals usually have temporal limits on liminal periods of mourning, divided between private and public time, but Facebook offers us unlimited access to memories of the deceased. The choice to mourn communally and virtually problematizes not only our personal relationships with the deceased, but also the legal ownership of our feelings and sentiments. The final element of death on Facebook examined in this paper is the spiritual space that deceased profiles occupy. For the secular and religious, these profiles give a virtually physical body to what might traditionally be called a spirit, which challenges the finality and permanence of death. In studying the posts and stories that decorate the profile walls of the deceased, it is clear that this virtual aspect of ourselves has very real elements, and it is exactly this questioning of reality that death demands of us in the first place. 

Building a reference library of life on earth is an enormous task of paramount importance given the current threatened state of species across the planet. Collecting DNA barcodes - essentially genetic fingerprints - for every species on the planet has been proposed as a means of rapid species identification. In 2004, the Barcode of Life Database (BOLD) was initiated and is compiling DNA barcodes for every species using a small fraction of the genome called the, "CO1" gene. Unfortunately, the universal primers used to sequence the CO1 gene have a low success rate at producing DNA sequences for amphibians, and a relatively high error rate for species identification. My research investigates the success and accuracy of new amphibian-specific CO1 primers in comparison to an alternative DNA barcode, 16s rRNA, which is widely used in amphibian systematics and taxonomy, but is presently not accepted by the DNA barcoding community. I analyze and compare both CO1 and 16s genes for their utility as DNA barcodes by building phylogenetic trees using maximum likelihood and Bayesian inference to quantify their species identification accuracy. In collaboration with the UW Burke Museum of Natural History and Culture, I sequenced DNA for 162 frogs (representing 22 species) collected from the rainforest in Southern Ghana. The sub-Saharan rainforests of West Africa host a high number of endemic amphibian species. However, increasing habitat threat are heavily impacting species in these forest, and an estimated one third of amphibians are considered threatened. All DNA sequences obtained for this study are being submitted to the BOLD and GenBank databases and are linked to voucher specimens at the UW Burke Museum, which will inform future biodiversity studies, assist monitoring, and aid conservation efforts.

Fatty acids (FA) are commonly used as biomarkers to infer contributions of different basal energy sources to consumers. However, modification, catabolism, and storage of dietary FA are poorly understood for most animals. Controlled feeding experiments are critically needed to determine the appropriate use of FA as dietary tracers. We conducted two such experiments with juvenile isopods to investigate their use as a model organism for FA signature analysis in a direct herbivore. Newly hatched Idotea wosnesenskii were raised for 10 weeks on five different macroalgal diets at two different temperatures. Broods were raised from hatching on a single food source. Highest growth rates were on Ulva spp., fresh Nereocystis luetkeana, and aged N. luetkeana. Animals grew significantly slower on diets with chemical (Fucus distichus) and structural (Mazzaella splendens) anti-herbivore defenses. Temperature did not substantially affect growth rates. Preliminary analyses indicate that FA in Idotea tissues reflect those of their diets, and that FA driving the patterns include common biomarkers for the algae consumed. Juvenile Idotea are a promising model organism for FA trophic ecology because they generally thrive in a laboratory setting and can be hatched and quickly grown on a variety of diets.

Drift algal material is expected to play a significant trophic role in ecosystems adjacent to kelp beds. The contribution of drift algae to the overall nutritional state of various invertebrates can be assessed using phenotypic traits such as gonad index (larger gonad mass with better nutrition) and for sea urchins, jaw diameter (larger jaws with inconsistent food supplies). In this study, we collected green urchins (Strongylocentrotus droebachiensis) within kelp beds (5m depth) in the shallow subtidal photic environment (SSPE) and outside of kelp beds in nearby deep subtidal environments (DSE; 100m depth) during spring and winter seasons. SSPE and DSE sampling stations were less than 1 km apart. In the initial spring analyses, urchins in the DSE had significantly larger gonads but also larger jaws than SSPE animals. Winter gonad indices showed a reverse pattern, in which SSPE urchins had larger gonad indices, but still had smaller jaw indices than the DSE urchins; gonads in all urchins on this sampling date were much larger than those in the previous spring. These results suggest that food supplies may vary among seasons, especially in deep habitats, where the subsidy of algal material exported from shallow water may be inconsistent; the jaws from DSE urchins concur with this hypothesis. Gut content analyses from winter samples will be used to evaluate the types of foods available to deep vs. shallow-water animals.

Since neuronal morphology is linked to neuronal function, the nervous system goes to great lengths to ensure that neurons achieve their proper shape, and failure to do so is associated with many cognitive disorders. However, the precise regulatory mechanisms underlying the coordinated expression of certain genes in a given cell type, at the right amount, and at the exact developmental time is one of the longstanding questions in developmental biology. MicroRNA biogenesis is a common mechanism by which cells regulate gene expression, often by “tuning” levels of target gene products, allowing for fine regulation of protein levels over a broad dynamic range. From a genetic screen for mutations in fruit flies that affect dendrite morphology in sensory neurons, we identified a novel Dicer-1 allele that causes stereotyped dendrite defects, including deregulated growth and defects in dendrite self-avoidance. Dicer-1 encodes a type III RNA endonuclease that is required for processing many types of small regulatory RNAs, including microRNAs. Time-lapse imaging and quantitative analysis of the dendrite patterning in Dicer-1 mutant sensory neurons reveals that there is a significant increase in the number and overall length of dendrite branches as well as an increase in dendrite-dendrite crossing-over, especially at late stages of larval development. Interestingly, mutation in a gene (pasha) that functions upstream of Dicer-1 to process a subset of miRNAs recapitulates the exuberant branching, but not the dendrite crossing phenotype of Dicer-1 mutants. We hypothesize that different classes of miRNAs regulate dendrite branching and dendrite self-avoidance and we plan to use microarray analysis of Dicer-1 and pasha mutants to identify the pathways regulated by these different classes of miRNAs.

Ischemic preconditioning (IPC) is a robust neuroprotective phenomenon in which a brief ischemic exposure increases resistance to the injurious effects of subsequent prolonged ischemia. Characterizing the cellular and molecular mechanisms of IPC is an active area of investigation in stroke research. Microglia are the resident immune cells of the central nervous system and are the primary cell type responsible for post-stroke neuroinflammation in the brain. Several lines of evidence support a role for microglia in IPC. Previous research from the Weinstein laboratory has demonstrated using ex vivo flow cytometry that IPC induces a robust increase in the number of microglia/macrophages that can be identified and sorted from the preconditioned (ipsilateral) cortex. However, it is uncertain if this increase reflects a true change in cell number (due to proliferation or migration) or if it reflects a novel characteristic of the preconditioned microglia to better survive the enzymatic and mechanical tissue digestion that precedes the flow cytometry processing. In order to address this question, we are carrying out quantitative immunofluorescent microscopy on tissue sections from preconditioned or naïve mouse brains that have been stained with a fluorochrome-conjugated antibody (anti-Iba1) specific for identifying microglia/macrophages. My contribution to this work will include tissue preparation and sectioning, antibody staining, microscopy image capture and cell quantification using custom calibrated image analysis software. Answering this initial yet fundamental question will be an important starting point for additional investigations into the function and phenotype of microglia/macrophages in the preconditioned brain and may shed light new light on the mechanism of IPC.

During embryonic neural development mouse hindbrains exhibit spontaneous depolarizations that propagate from cell to cell across the tissue in waves. There is a discrete, anatomically identifiable population of cells responsible for generating these waves: the cells of the initiation zone (InZ). Spontaneous waves of activity have been shown to affect neuronal migration, pathfinding, and differentiation, among other developmental sequences. Spontaneous depolarizing events, in general, allow passage of ions into and out of the cell; of developmental importance are calcium ions, which are involved with regulating gene expression. During critical windows of development these calcium fluxes help to determine the adult fate of a neuron. The spontaneous and variable nature of the propagating neuronal events makes them difficult to manipulate experimentally. Were these propagating events able to be elicited experimentally and discretely that would provide both a vehicle for further study and an indication of what properties of the initiator population allows the cells to generate propagating events. I have used a combination of several techniques, including calcium-dye imaging, whole-cell patch clamp, and extracellular electrical stimulation, to probe the details of the cells’ activity. These experiments have identified separate populations of cells that are capable of initiating propagating waves, both spontaneously and elicited by external electrical stimulation. One population includes the previously identified cells of the InZ, and another population exists at the isthmus between the midbrain and hindbrain. Cells in these populations respond differentially to a variety of electrical stimuli. Within each of these initiator populations may exist single, highly-networked neurons capable of initiating propagating electrical activity evoked by intracellular stimulation, which is the subject of further investigation.

Once subjected to an extractive history of British colonial and Indian national imperatives and ignored by development institutions, the mountainous region of Kumaon, Uttarakhand now thrives in its current development trends. Given that developers and donors disregarded the region while much of the rest of India prospered, it seems incongruous that the region should now be succeeding in its own development. This project asks why the isolated and “underdeveloped” region of Kumaon that was “left behind” by mainstream development and has only recently emerged is now able to succeed in its own grassroots development. My thesis posits an answer grounded in the notions of agency and identity politics in regional social movements and development vision. I examine the interdependency between the environment and social and historical processes, which informs my analysis of local development strategy regarding regional preferences for grass use in livelihood practices. The analysis employs data collected through qualitative, ethnographic interview processes and participant observation in the field. Supplementing the primary data with literature on identity assertion as a response to colonial and neocolonial processes, I argue that Kumaon has thrived and created significant agricultural development, notwithstanding the lack of outside aid, because development there is inextricably linked to regional movements for social change. These social movements have distinguished Kumaon from national trends of development and have led to the emergence of a conservationist and rights-oriented regional identity, which has helped form a particular vision for Kumaoni development focused on the environmental rights of the people.

Rio de Janeiro is infamous for violence. In the city’s large, informal shantytowns known as favelas, violent drug gangs rule with impunity while a corrupt and murderous police force contributes to distrust of formal government. With Rio scheduled to host the World Cup in 2014 and the Olympics in 2016, pressure to tame the favelas and reduce violent crime is high. Facing the need to try something new, in 2008 Rio’s leadership introduced an innovative, community-oriented policing program known as UPP in an attempt to “pacify” the favelas. The program represents a paradigm shift in policing methods, focused on breaking down the adversarial relationships between favela residents and police and encouraging community involvement and integration. It has shown impressive progress: in favelas that have received UPPs, murder rates have fallen to nearly zero. However, much remains to be done--the UPPs are an expensive fraction of the police force, and skeptics worry that if the UPP’s leave, all progress will be lost. The challenge, then, and the focus of this Task Force, is to ensure that the favelas are integrated and supported in a way that preserves the progress that has been made and fosters permanent change. Each of the 11 chapters within this Task Force presents policy recommendations prepared for the Public Security Secretary of Rio de Janeiro José Beltrame, and as such, are tailored to his position and responsibilities. Subjects include reforms within the police force, such as improvements in police training, organization, and working conditions, as well as policies intended to promote integration of the favelas into the formal city, including methods to improve education and access to healthcare, implementing programs to target at-risk youth, and providing economic opportunities for favela residents.

Since the international ban on the ivory trade in 1989, environmental science has been constructed as a ‘value-neutral’ and ‘objective’ realm in which elephant conservation is expressed as a universal reality. However, preservationist formulations of environmental science have been privileged over their utilitarian counterparts, precluding many Southern African countries from employing science-based arguments in favor of sustainable ivory harvesting. Concurrently, the relatively recent global transition from consuming elephant bodies to consuming elephant imageries has facilitated the production of a wildlife-based international tourism market, as well as reinforced the belief in delineated conservation areas. In this context, transfrontier conservation areas (TFCAs) have gained traction as a means of simultaneously restoring historic elephant ranges and promoting regional tourism to benefit African elephants and economies alike. As a result, environmental science as a political tool has been utilized to produce elephants as either regional or global resources, silencing local and national claims to elephant populations and related management. In the process, placed-based frustrations for local communities associated with problematic elephant populations and related human-wildlife conflict have been subsumed under the importance of the regional environment and national economic development. To explore science’s role in framing and understanding environmental problems, I analyze how scientific concepts such as biodiversity and the precautionary principle are utilized in international conservation policy and the elephant management debate, with particular emphasis on Botswana. I aim to show that science is neither ‘objective’ nor ‘neutral’ but instead is a field with international politics that recommend vastly different philosophical and ethical ways of understanding humanity’s role in the environment.

This paper challenges the Kantian account of autonomous moral decision-making. Kant’s definition of autonomy, I argue, is excessively narrow and does not place sufficient importance on the contextual factors which one encounters when attempting to act as an ethical agent in the empirical realm. An intersectional view of autonomous moral decision-making such as that put forth by Meyers takes these considerations more fully into account. By way of an exemplification illustrating a "real-world" scenario, I show how an application of Kant’s definition generates seemingly irresolvable conflicts. Then, through utilization of an intersectional definition of autonomy, I demonstrate how this alternative moral reasoning system allows for a more holistic understanding of individuals and the multiplicity of factors which shape and influence their situations and choices.

Intentionality is defined as the characteristic of having thoughts that represent and refer to things in the world. While some current research suggests apes can be said to have intentionality, traditionally intentionality is a hallmark of being human. How do we come to know that an intelligent organism or system is intentional? In this presentation I will argue that an artificial system that can be described as having the same computational and algorithmic levels as a human system has the same intelligence and is plausibly intentional. This is because if the qualities we attribute intentionality towards in a human system are programmed in an artificial system, we would attribute intentionality to an artificial system in the same way we would to a human system. So, we should consider the artificial system plausibly intentional. To explain how this works I will discuss David Marr’s tri-level hypothesis and Turing’s ideas about intelligence and intentionality to show that an artificial system that has the same intelligence as a human system also has intentionality. I will then show how under the Physical Symbol System Hypothesis attributing intentionality may be another intelligent behavior we can computationally model.

Combining wildlife tracking skills with motion-sensitive cameras, environmental anthropology students can provide practical results for stakeholders who are seeking to provide sustainable solutions to human-wildlife intersections and inform land management decisions. In 2010, the Learn and Serve Environmental Anthropology Field (LEAF) School at Edmonds & Everett Community Colleges partnered with Snohomish County Public Works to monitor a wildlife passage: a 4’x4’ box culvert installed in a new road alignment in Granite Falls, WA. The passage connects a five-acre wetland, a mitigation site for the County, with a larger wetland complex associated with the floodplains of the South Fork of the Stillaguamish River, designated critical habitat for Puget Sound Chinook Salmon (Oncorhynchus tshawytscha) and Coastal-Puget Sound Bull Trout (Salvelinus confluentus). Research results show the culvert being utilized by targeted low-mobility species and Columbian Black-tailed Deer (Odocoileus hemionus columbianus), who was thought to be too large to access the passage. July 2011 photos show the first does with their fawns using the passage to cross between the wetland and the riparian corridor. Summer 2012 data shows the return of the does as well as two adolescent bucks accessing the passage. Two years of data appear to show the black-tailed deer are willing to adapt to and use this size of culvert. Through the application of a service-learning strategy students are investigating the effectiveness of the structure and considering whether current land use issues may compromise the long term viability of the wildlife corridor. This research sets the stage for continued citizen science and community outreach projects in Granite Falls. These citizen-science projects become even more critical as populations push into the rural areas of the Pacific Northwest.

The successful growth of a plant is dependent on many variables, such as location, extent of available resources, competition by other plants, and reproductive success; what if there was a way a plant could almost guarantee survival and success? Many invasive species have found ways to be very successful; Alliaria petiolata (garlic mustard) has developed allelopathy, which can decrease surrounding plants germination rates and ability to grow. In my experiment I will attempt to determine if different populations of garlic mustard have variations in allelopathic strength. At least ten samples of garlic mustard from three different locations throughout Seattle will be grown, along with ten control lettuce plants. The three sites for this experiment are Seola Park, Woodland Park, and the University of Washington. Throughout the experiment I will try to figure out if the lettuce seeds germination rate and growth abilities are affected as a result of the garlic mustard. I will plant lettuce seeds in with garlic mustard and analyze the germination rates compared to the control samples, and at the end of my experiment I will harvest the lettuce and garlic mustard samples, and they will be biomassed. The data collected will be analyzed for significant results. My hypothesis for this experiment is that the sites in which the garlic mustard has been present the longest will have the greatest negative effect on the lettuce plants; but, because I don't know how long each population has been established I believe the Seola Park location, because it had the largest garlic mustard population, will have the largest effect on the lettuce.

The Clean Water Act (CWA) divides water pollution into two categories based on source: point sources (discernible end of pipe discharges), or nonpoint sources (diffuse runoff including agricultural nutrients/sediments). But federal regulatory provisions for the enforcement of water pollution control are made only for the point source pollutants. The primary reason for the resulting voluntary basis of federal nonpoint source pollution laws is the inherent land use controls required to regulate landowner practice. Authority to regulate land use is traditionally left to State governments in the American federalist division of powers, and consequently nonpoint source pollution control has also been delegated to State authority in the CWA. The federal government only addresses nonpoint water pollution through planning provisions which incentivize State programs and landowner compliance with federal funds. The CWA can be used as a case study for the statutory limits of federal authority to regulate land use in order to reveal the political culture driving this federalist division which preserves agricultural landowner property rights. Furthermore, an internship at the Environmental Protection Agency (EPA) provided unique insight into the consequent regulatory limitations of the nonpoint source distinction, but also into the internal regulatory culture which mirrored the same federalist land regulation issue, highlighting similar underlying cultural choices. At the EPA there is still some discretion for State program funding along a spectrum of regulatory or assistive approaches to agricultural environmental policy. Therefore, the federalist boundaries for nonpoint pollution control can be compared in statute (CWA) and administrative practice (EPA) to juxtapose the cultural drivers for policy. Both cases reflect an established political culture of property rights that is sacred in the history of federal agricultural policy.

While writing the first quarter of a Gothic fantasy novel titled Deathwatch, I also carried out analytical research examining Romantic Gothic themes appearing in my creative text. I was largely unfamiliar with Gothic literature while planning this novel and these themes appeared naturally in my text from the start as a clear example of intertextuality. However, in order to gain a better understanding of the tradition I was referencing and use it effectively as a framework, I began researching features of Romantic Gothic literature. Key to Romantic Gothic literature is its villain-hero model of the outcast who is unable to determine whether his alienation is his own fault or the fault of the larger world. This model in turn leads to the Gothic features of doubles and the dangerous lover, both of which allow the hero frightening insight through physical confrontation with his own self. By identifying these literary themes in both Mary Shelley’s Frankenstein and my own work over the course of my research, I was able to better understand and deepen my own intertextual framework. As a result, during Deathwatch’s writing process, I was able to both reference and alter these unique features of the Gothic genre in a knowledgeable way, significantly enriching the quality of my own text.

As Korea is becoming internationally noticed due to its technology and pop culture, it is becoming more important for the rest of the world to understand its culture. One promising route to a deeper understanding of culture is through the study of its children's literature as an early medium that educates and socializes children into the native culture by exposing them to social norms present within the texts. Translating Korean children's literature into English requires a sophisticated but enlightening balancing act: a balance between the two languages often referred to as having "mirror image structures," a balance between the author's story and covert cultural messages, and a balance between the translator's literal and liberal approaches. To contribute to the cultural understanding, this project aims to experiment with various ways of balancing, in an effort to maximally retain cultural imagery and voices of the characters in each story, while conveying the sense and sounding elegant in translated work. The focus is on translating at least five different speech styles in Korean into what is structurally one in English. This project aims to contribute towards finding the best method in conveying the author's message both precisely while maintaining botha aesthetic and cultural values within the text for non-Korean readers.

This project strives to address the surprisingly high rates of eating disorders (ED) in southern Italy. Determinants for ED in southern Italy are characterized by perfectionist tendencies and parental criticism, rather than the low self-esteem and body image problems most often associated with ED. The high prevalence of ED and unique composition of symptoms and psychological determinants among southern Italian women point to a compelling paradox: Given the widely supported theory that the development of eating disorders in a population may be ascribed not only to media-stimulated body image concerns but also to processes of modernization and industrialization, why do women in southern Italy, which has not conformed to or successfully undergone these processes, exhibit relatively high rates of eating disorders? This thesis argues that ED in southern Italy is a symptom of transgenerational transmission of trauma related to collective regional fear of the end of WWII and loss of the precarious economic certainty of the Allied occupation. This fear and eventual loss could not be openly mourned because of its conflict with the Resistance and liberation myths that sustain WWII memory in the popular national narrative. To substantiate this claim, I will further propose that both culture-specific ED pathologies and acclaimed films represent ciphered articulations of the psychically “indigestible” nature of this conflict. I will analyze selected films of acclaimed southern Italian directors: Ettore Scola’s La famiglia, Giuseppe Tornatore’s Cinema Paradiso, Francesco Rosi’s Tre fratelli, and Mario Martone’s L’amore molesto. Each film is analyzed anasemically—that is, completely wthin the bounds of its auditory, visual, and cinematographic language—before connecting it to historical and social contexts.

Statistical designs are a way to layout experiments before conducting your experiment. A well-chosen experimental design allows one to get more information out of the experiment. Regular fractional factorial designs are types of experimental designs that are used for studying effects of two or more constraints simultaneously, but leave large gaps in run size. Run sizes are the amount of experiments an experimenter has to conduct. Non-regular fractional factorial designs can be constructed for every run size that is a multiple of four, which allows run size flexibility and economy. My research focuses on construction of optimal designs of size 32 runs using graphic processing unit (GPU) technology. I have been working on creating a design table of non-regular fractional factorial of size 32 runs. Creating design tables make it possible for engineers and scientist to plan experiments for any combination of runs and number of variables to be studied.

White-nose Syndrome (WNS) is a wildlife disease caused by the pathogenic fungus Geomyces destructans that has resulted in the mass mortalities of North American cave bats. One clinical sign of WNS is wing necrosis.  Geomyces destructans may secrete proteases that degrade tissue, thus reducing wing strength and elasticity. We isolated Geomyces destructans extracellular enzymes from an in vitro system and applied enzyme solution to bat wing tissue. The toughness, strength, and elasticity of tissues was assessed with tensile testing. Protease activity was assessed with SDS-PAGE and peptide mass fingerprinting by MALDI-TOF MS. Protein profiles generated by SDS-PAGE indicate higher solubilized protein in treated samples. Major bands were identified as integumentary proteins by MS. Tensile testing did not detect damage, but Geomyces destructans proteases may cleave host integument.

Geomyces destructans is a psychrophilic (cold-loving) fungus that causes cutaneous infections in cave dwelling bats and high mortality in North American populations. Geomyces pannorum is a closely related psychrotrophic (cold-tolerant) species that is a rare skin pathogen of vertebrates. Cold-adapted organisms adjust lipid synthesis to lower membrane viscosity and thus survive unfavorable habitats. Lipid profiles, or lipid class composition, may partially explain ecological niche and G. destructans pathogenicity to bats. Additionally, profiles are species specific and may be utilized to differentiate closely related species and detect disease. We incubated Geomyces at 5°, 8°, 15°, 18°, and 22° C and isolated fungal lipid content. Broad lipid classes were determined to be primarily sterols, free fatty acyls (FFAs), and triacylglycerides (TAGs). Geomyces destructans produced higher proportions of unsaturated 18 carbon TAGs than G. pannorum. Geomyces produced more 18:3 (18 carbon, 3 double bonds) TAGs at five degrees than at higher temperatures. Geomyces destructans made higher proportions of TAGs at its growth limits, suggesting alterations in lipid synthesis to decrease cellular toxicity and reproductive effort. Furthermore, these results indicate Geomyces alter lipid structure to survive cold temperatures by increasing lipid unsaturation. Future studies should focus on temperature optima of enzymes involved in TAG synthesis and disruption of lipogenic metabolic processes. Lipid profiles among multiple Geomyces species should be further investigated as a method of disease detection.

President Obama’s recent inaugural speech included the call for equal rights for members of the GLBT community. Among the issues transgender people especially face are access restrictions to transition related health care. This project examines the implications for transgendered people in terms of access to gender-confirming surgical procedures and how this affects their quality of life. The sites of this study were the United States and Germany, two countries using the same parameters to determine if a person suffers from Gender Identity Dysphoria, the clinical diagnosis required to undergo gender-confirming procedures. In the U.S. these procedures are widely not covered because they are labeled elective or cosmetic. German law on the other hand mandates full health insurance coverage as surgery is considered a necessary and effective treatment of a clinically established condition. This project uses quantitative data collected with questionnaires and qualitative data in the form of life history interviews. It compares the results of the National Transgender Discrimination Study (n=6,540) with responses to the same questionnaire by transgender Germans (n=88). Findings indicate that access to transition related care via health insurance improves the mental and physical well-being of individuals whereas access limited due to lack of coverage can be detrimental. Life histories provided by five individuals, three Americans and two Germans, evaluated in open and closed coding according to the Grounded Theory approach, also indicate lower rates of depression and drug use in people after gender-confirming procedures. Yet due to the small size of the German sample these findings may not be representative. Furthermore, even though gender-confirming procedures are effective, they should not be understood as mandatory for everyone diagnosed with Gender Identity Dysphoria.

Tribal communities often lack access to high-quality healthcare, prevention programs, cancer education, cancer screening tests, and cancer clinical trials. As a result, American Indians and Alaska Natives experience the worst cancer-related disparities and the poorest survival rates of all racial and ethnic groups in the U.S. Comic books have long been used as an educational tool to improve public health. In 2008, the Native Comic Book Project was launched as a youth-focused community education project of Native People for Cancer Control, a Community Network Program Center funded by the National Cancer Institute. The purpose of this ongoing project is to use comic book creation as a way to educate Native youth about cancer, especially methods of cancer prevention. Along with basic art skills, participants learn about traditional foods and wellness, non-ceremonial tobacco use, human papillomavirus, and obesity prevention. Modeled after Dr. Michael Bitz’s Comic Book Project, the Native Comic Book Project has been adapted for both urban and reservation-based youth by incorporating Native storytelling and traditional values. Its ultimate goal is to promote healthy decision-making for Native youth and their communities. We are currently conducting a formal evaluation of this project by using pre- and post-intervention assessments to measure knowledge, habits, and decision-making among youth participants regarding tobacco use, healthy eating, exercise, and human papillomavirus. The Native Comic Book Project has been implemented at 10 sites and has enrolled 55 participants. Data will be fully analyzed in Summer 2013.  Future planned activities for research and education include developing more youth-oriented health interventions.

College students (usually between the ages of 18 and 24) are in a transitional period in their lives in which they are expected to adapt to many overwhelming and sudden changes. Mental health problems that college students experience most commonly arise from extreme academic, relationship, financial, and psychosocial strains. Despite these high rates of stressors and mental health problems, these same college students demonstrate a persistently low level of perceived need for help and actual service utilization which leads to non-treatment seeking behaviors. This study examined common barriers that prevent college students from seeking mental health treatment by using standardized measures. Two hundred and fifty college students in the Psychology Subject Pool (PSP) at the University of Washington volunteered to participate in the study which was conducted by using online survey software. Information collected included past/current mental disorder diagnoses and mental health treatment, duration of the treatment, and knowledge of on-campus resources (e.g., Counseling Center, Hall Health). Further, participants answered seven questionnaires about attitudes toward, barriers to, and fear of treatment, in addition to participants’ ambivalence concerning emotional expressiveness. The results are primarily descriptive in nature and focused on exploring common barriers, attitudes, and issues that interfere with reaching out to and receiving mental health treatment. By identifying the barriers we hope to bring the target consumer audience closer to effective treatments via distributing our findings to local counseling centers. We also examined how demographic variables relate to college students’ attitudes toward mental health treatment which will help local universities and colleges to tailor advertising efforts with greater specificity to ensure that college students in need of mental health services are aware of and engaged in available services.

Immigrant farmworkers have been an integral part of Eastern Washington communities for decades. Their health and well-being are essential for the health of our communities. But for many farmworkers, health care access is unavailable or limited by a lack of insurance, health providers, discrimination, and social marginalization, making it difficult to assess their health status and burden of disease. A lack of basic information about farmworker health complicates the decision-making of state and local officials, physicians, and other advocates dedicated to improving farmworker health. In partnership with the Migrant Clinicians Network and the Pacific Northwest University of Health Sciences, I used community-based research techniques to design a farmworker public health study which could provide the necessary data to inform policies to improve farmworker health. Our survey research was designed to assess the serious injuries, diseases and causes of death among farmworkers and their families.

Bathsheba, the Queen of Sheba, and Jezebel are the three queens presented in the Bible who are known most widely today.  These three figures are not the only important female leaders mentioned in the Bible: there are stories of numerous other women who stood near the heart of political power.  I argue that the Bible presents four archetypes of women in power.  The first is the Israelite women in an Israelite king’s court.  This woman will rarely speak in the text and, when she does, it is only to show her obedience to God’s will.  The second archetype is the Israelite women in a foreign king’s court.  They serve an instrument of God’s will within the foreign courts that they inhabit.  Their presence near the foreign power brings blessings and wealth to the Israelites in their adopted kingdom, at the expense of its native subjects.  The third group is the foreign women in the court of an Israelite king.  These women are viewed as dangerous.  They are nearly always portrayed as acting contrary to the interests of the kingdom and they also frequently accused of drawing the king away from God in some sense.  The fourth and final group is the foreign women of a foreign king’s court.  They represent God’s power to act even outside the boundaries of Israel, often acting as witnesses to God’s punishment or the instrument through which God acts to carry out his plans for Israel.  A study of these women, through a careful reading of the Bible, will give us a better understanding of how the biblical authors conceived of female power – whether that of queens or other positions of political power.

Between 2001- 2003 there has been a surge in an ancient yet taboo tradition of bacchabazi in Afghanistan; baccha meaning “child “and bazi meaning “gaming” with a connotative meaning of “boys for play”. This is a significant concern because the act of bacchabazi is one that focuses on the sexual exploitation of young poverty-stricken Afghan boys for the sole purpose of elevating the statuses of their owners, mainly high ranking ex-military officers. By engaging in research of bacchabazi I intend to find answers surrounding why the act of bacchabazi has increased and what the triggers are, that permit it to flourish? The objective of my research is to look at the factors involved in this practice, including aspects of class, socioeconomic status, and conflict areas. The method I am going to use is a feminist discourse analysis of media artifacts current and historical ones. This will include newspapers foreign and domestic, blogs, academic texts, and documentaries reported by researchers within the field of child exploitation in Afghanistan, specifically focused around bacchabazi. This analysis will be done through a lens of transnational feminism while supplementing theories of colonization and post-colonization. Since the theoretical context is colonization and post-colonization, my research will fit into existing related scholarship and contribute to the field because there is not a substantial amount of research currently being published. Since my data is still accumulating I do not have solidified results but rather, informed opinions that would infer recommendations for the young men affected. Some proposed findings/recommendations include: education for the young men with the purpose of identifying the ramifications of being selected/recruited as a bacchabazi, support in way of agency for the young men, and an increased awareness among local jurisdiction in regards to not criminalizing the actions forced upon the young men.

Patient centered health care requires that individuals be linked to a team of care providers responsible for guiding them through the full range of health and preventive services. This research addresses the considerations and lays the foundation for understanding how to incorporate patient characteristics when creating patient panels to match the needs of patients and the skill sets of their health care providers. We illustrate how a strategic plan can be developed with varying combinations of care provider team composition. This strategic plan enables clinics to hire staff with the appropriate skill set to meet patient demand for health care. By examining a representative data set, patients will be pooled according to a minimal set of attributes, such as age, gender, and medical conditions, in order to model the mix of patient attributes within a panel. Using probabilistic distributions, an estimate of total workload for each care-giving panel is established. Different combinations of preferences and panel mix amongst the medical professionals are analyzed with respect to the objectives of meeting patient demand while matching patient preferences with physician capabilities and preferences.

Force-feedback (haptic) displays are becoming increasingly common in consumer technology. Perceptual thresholds for haptic interaction are important for determining how much force output is required from a haptic display to provide detectable feedback to the user. In this presentation, I will talk about an experiment measuring force perceptual thresholds for single and multi-finger interaction with haptic targets. Using the UW Multi-Finger Haptic Display, subjects feel two targets on a virtual surface. One target produces center-attractive force when in contact with the subject’s finger while the other produces no force. A thresholding algorithm presents the subject a new set of haptic targets with a smaller maximum force after correctly selecting the force-producing target twice. Eventually the subject can no longer detect a target and the max force is adjusted upward. This type of forced-choice algorithm causes the threshold force to converge to where the user successfully detects the stimulus 71% of the time. In this experiment, three new methods of presenting time-correlated haptic feedback to the subject were tested. Statistical analysis shows significantly lower minimum force thresholds for multi-finger methods providing time-correlated feedback (mean thresholds of 22.94, 21.75, 22.13 mN) when compared to the single finger and multi-finger spatially correlated methods (29.24 and 33.37 mN respectively). These results suggest a neural summation effect when haptic targets are arranged to provide time-correlated stimulation to multiple fingers at once.

The process flow in clinical laboratories resembles that in a traditional manufacturing setting, but there are distinct differences between the former and the latter which make it difficult to directly reflect the essential functions of a clinical laboratory in a simulation model. Creating a simulation model enables us to analyze and determine the impact on key metrics such as turnaround time and utilization rates when we change the physical configuration of the laboratory and vary the input parameters of the model. We have adapted the object-oriented nature of SIMIO, a program commonly used in a manufacturing setting, to create a discrete-event simulation modeling language for clinical laboratories reflecting the technical knowledge of experts from the clinical laboratory domain. We organized critical aspects of the clinical laboratory into class hierarchies to clearly delineate their functions and relationships. We then developed specific modules using the class hierarchies to represent the unique behavior of instruments, equipment and processes in a clinical laboratory. Using these modules, we created a simulation model of the clinical laboratory. The domain-specific modules we have formulated provide clinical laboratory experts with a customized tool to understand and improve their own system from a modeling perspective.

In this project, we explore conditions that are critical for de novo evolution of cooperation and altruism in a bacterial system. Previous theoretical work has shown that there is a competitive advantage to defection and selfishness, but the ubiquity of cooperation in nature suggests that cooperation may be adaptive. Here, we aim to uncover environments and genetic conditions that actually promote greater cooperation. We use an engineered cooperative strain of Escherichia coli. Through a bistable genetic switch, single cells have the capability to be either a producer cell that makes the cellulase enzyme to break down cellulose, or a consumer cell that eats the byproducts of cellulose breakdown. Our first aim is to characterize the social dynamics of this synthetic system and determine if a social dilemma is in fact occurring—i.e., is there a cost to producing cellulase, and can cheaters that do not produce cellulase displace the cooperators that do? Our second aim is to evolve the system over many generations and analyze how it changes. Uncovering the conditions favoring higher cooperation (e.g., greater production of cellulase) provides insight into how cooperation can evolve and how populations circumvent social dilemmas. We hope to use evolution as a tool to tune the synthetic genetic circuit for maximal cellulose breakdown. On a broader scale, these conditions that favor cooperation may have practical applications in waste degradation and biofuel production.

 Affecting nearly 1% of the human population, von Willebrand Disease (VWD) is the most prevalent inherited bleeding disorder worldwide.  VWD is caused by impaired platelet adhesion due to low plasma von Willebrand Factor (VWF) concentration, or dysfunction.  The largest plasma glycoprotein, VWF's function is to mediate attachment of platelets to the exposed collagen on blood vessel walls at sites of injury.  This interaction is sensitive to changes in flow forces or shear stress.  To facilitate the study of VWF, the Thomas Lab is developing a single-molecule force measurement platform called magnetic tweezers; a tool capable of performing multiple single-bond force measurements in parallel.  To use magnetic tweezers, VWF protein domains of interest are adsorbed to a glass surface on one end, and to a magnetic bead on the other.  Electromagnets are then placed above the slide, applying an upward force to the VWF domains.  The design and optimization of the VWF domain tethers is the focus of this research project.  At present, a tethering scheme is being tested that utilizes the strength and longevity of the biotin-streptavidin non-covalent bond and the fimH lectin domain to mannose interaction.  An alternative tethering scheme employing histidine tags instead of fimH is also being explored.  While both types of tethers have been expressed successfully, tested in the magnetic tweezers, and shown to bind beads to the surface under force, recent data has shown that non-specific adhesion between protein-functionalized magnetic beads and the coverslip is an issue.  Using immunoassays such as ELISA and the Western Blot, tether designs will be optimized using magnetic tweezers.  With the capability to more accurately mimic physiologic conditions than immunoassays alone, coupled with the intrinsic ability to multiplex, the quantity and quality of data that could be acquired is impressive.

New DNA sequencing technologies have increased the throughput of sequencing by several orders of magnitude, reaching upwards of 50 GB of data per day on a single instrument. However, advancing our understanding of how genetic variation impacts human health and disease depends on studies that survey very large numbers of individuals, and as such may only be economical by analyzing specific subsets of the genome. This is complicated by the fact that traditional methods of preparing DNA samples for sequencing do not allow selection for such candidate genes. One solution is the use of “capture by circularization” by molecular inversion probes (MIPs). MIPs allow dozens of genes to be targeted and amplified simultaneously; however, individual MIPs suffer from notoriously variable performance relative to one another, which results in uneven coverage of target regions. Prior work highlighted the potential for statistical analysis to improve MIP design and selection, inviting further testing. After performing a large scale sequencing run using an unbiased set of 12,000 MIPs, logistic regression was used to build a model capable of scoring MIPs prior to synthesis. New design software incorporating this model into the selection process was developed and tested by designing MIPs to over 60 new genes. Analysis of the resulting sequence data demonstrated the successful in silico identification of challenging genomic regions and a reduction in the number of gaps in coverage, which should support the use of MIPs in future large scale studies.

The warmest climatic event of the last 34 million years occurred during the middle Miocene, culminating in the Middle Miocene Climatic Optimum, (MMCO; 17-15 Ma) which was a period of substantial warming. The climate change likely affected plant community composition as grasses spread across North America, but because plant macrofossils from the MMCO in North America are rare, the response of vegetation to this warm interval is poorly understood. We combine analysis of plant silica (phytolith) assemblages and study of stable carbon isotopes from the same paleosols to document vegetation changes during the MMCO in southwestern Montana. Phytolith assemblage analysis provides information about vegetation structure, as well as the composition of grass communities, whereas isotopic data allows determination of the proportion C3 and C4 plants. The site near Drummond, Montana, has previously produced Barstovian-aged mammals and is productive for phytoliths. Our results show that grass silica short cells, diagnostic of grasses, in particular C3 pooid grasses, dominate assemblages (up to 75%). The remainder of the assemblages is made up of phytoliths typical of forest indicators, including palms, woody and herbaceous dicotyledons, and conifers. This suggests a fairly open habitat, with grass communities dominated by C3 grasses. Preliminary stable carbon isotope data are consistent with the phytolith results, indicating dominantly C3 plants (90% or above) in the samples. Lateral and vertical sampling from the site shows very little variation in phytolith composition, indicating low spatial and temporal variability.

Recent reports have shown that metabolic signatures are highly characteristic for a cell and may act as a leading cause for cell fate changes. In particular, we have shown that during development from naïve to primed embryonic stem cells, the cells undergo a dramatic transition from metabolically bivalent to highly glycolytic. However, this state of inert mitochondria rapidly changes to highly potent mitochondria during further differentiation. It is not yet understood how and why the pluripotent cells enter the highly glycolytic, metabolically cancer-like (Warburg effect) stage and how a differentiating cell leaves this stage. We have now performed metabolomics profiling of naïve and primed pluripotent cells using mass spectrometry. Interestingly, primed cells accumulate the tryptophan degradation product kynurenine. Kynurenine (KY) can act as a ligand for the transcription factor AHR. In cancer cells AHR activation by KY incudes growth while in surrounding T-cells KY based AHR activation will inhibit T-regulatory cells. My hypothesis is that kynurenine is a key metabolite in determining stem cell stage and in helping protect the primed stage embryo against the mother's immune cells. I will now test this hypothesis by analyzing the levels of the key KY metabolism enzymes by qPCR. My prediction is that the tryptophan degrading enzyme IDO1 will be unregulated in the primed stem cells. To test whether kynurenine can change the state of naïve stem cells, I will add different concentrations of kynurenine to the stem cell media and test potential cell fate changes. Since primed ESC-like metabolism is also observed in cancer cells, it is of great interest to understand how the cellular transitions in and out of this metabolic state are controlled during normal development. These studies will shed light on the function and regulation of metabolism during normal and disease developments.

Miller syndrome is a rare autosomal recessive disorder resulting from mutations in the DHODH gene. DHODH encodes the enzyme dihydroorotate dehydrogenase, which is involved in de novo pyrimidine biosynthesis. Clinical characteristics of Miller syndrome include craniofacial abnormalities, coloboma of the eyelids, cleft palate, and missing postaxial digits on the hands and feet. To broaden the spectrum of causal mutations, DNA samples obtained from two unrelated affected probands were Sanger sequenced to screen for mutations in DHOHD. In family 1, the affected individual was a compound heterozygote for a mutation in one of the canonical splice bases of intron 6-7 (c.820+1G>A), and a missense mutation in exon 8 (c.C1036T, p.R346W). DNA samples obtained from both parents of the affected proband were screened using Sanger sequencing and each parent was found to be heterozygous for one of the DHODH mutations. The c.C1036T mutation has been reported now in three families with Miller syndrome and functional studies have demonstrated a reduction of DHODH activity by 40%-70% in yeast with this mutation. No pathogenic mutations in DHODH were found in family 2. The next steps we will take include whole genome sequencing of the proband and parents in family 2 to determine if there are mutations in other genes that cause Miller syndrome. Our results mark the first report of a splice site mutation in a patient with Miller syndrome and further expand the spectrum of causative mutations in DHODH.

The nuclear transport pathway performs the fundamental function of moving cargo between the cytoplasm and nucleus in all eukaryotes. Nuclear transport is carried out through a highly conserved mechanism across all eukaryotes. Yet, in Drosophila, several components of the nuclear transport apparatus, including importins, evolve rapidly under positive selection. Genetic conflict with selfish elements has been suggested as a possible cause for this pattern of rapid evolution. Here, we present a comprehensive phylogenomic analysis of importin gene evolution in Drosophila. Importins are adapter molecules that directly mediate the transport of cargo into the nucleus. Our analysis reveals a recurrent pattern of gain and loss of importin paralogs across independent lineages of Drosophila. Interestingly, we discovered that almost all new copies of importins have acquired a testes-specific expression pattern since their birth through gene duplication. This pattern of repeated gains of testes-specific copies of importins suggests a function in suppressing genetic conflicts such as segregation distortion in the male germline. Segregation distorters such as SD in Drosophila melanogaster act by impairing nuclear transport in the testes. We are currently performing functional tests for the hypothesis that an increased dosage of these testes-specific importins may serve a role in suppressing segregation distortion in the male germline by restoring nuclear transport during spermatogenesis.

Speciation is the process by which one species becomes two species that can no longer interbreed. A common hypothesis is that infertility between closely related species is due to the rapid evolution of DNA double-strand-break (DSB) hotspots that are active in meiosis. DNA DSBs play an important role in meiosis by initiating recombination after chromosome replication and can be repaired as crossovers. During DNA DSB repair, the broken strand of a homologue invades and repairs its break with the strand of the aligned homologue by matching complementary nucleotides. The repair can result in a heteroduplex which refers to a mismatch, such as adenine paired with cytosine. Heteroduplex rejection occurs when the cell’s recombination machinery rejects recombination at sites where heteroduplex forms, and it is known to require the msh2 gene. We hypothesize that heteroduplex rejection inhibits DSB repair in interspecies hybrids and can result in infertility and thereby the isolation of species. Schizosaccharomyces kambucha and Schizosaccharomyces pombe are two very closely related fission yeast species that are 99.5% identical at the DNA sequence level. Despite their similar genetic makeup, we found that their hybrids show decreased fertility and decreased recombination frequencies. We are testing whether inhibiting heteroduplex rejection will increase the fertility and recombination rates of the fission yeast hybrids. For this experiment, we have created msh2Δ Schizosaccharomyces pombe and Schizosaccharomyces kambucha mutants that cannot do heteroduplex rejection so the cells should go through DNA DSB repair even if there are mismatches. We expect to see an increase in fertility and recombination in the msh2Δ hybrids. This research may be extended further to explain speciation in other organisms or unexplained infertility between human couples.

It is well known that mammals contain several types of phospholipase A2. The cytosolic phospholipases A2 (cPLA2s) are one type, and are composed of six enzymes: cPLA2alpha, cPLA2beta, cPLA2gamma, cPLA2delta, cPLA2epsilon, and cPLA2zeta. There has been significant interest in the cPLA2alpha isoform because of the enzyme's 10 fold preference for the hydrolysis at the sn-2 position of the glycerol backbone in phospholipids, resulting in the liberation of arachidonic acid. Arachidonic acid serves as a precursor for several highly regulated inflammatory mediators that play an important role in asthma, atherosclerosis, and arthritis. To address these problems, inhibitors that target cPLA2alpha have been developed to serve as anti-inflammatory therapeutics. Wyeth pharmaceuticals has released a class of indole inhibitors that inhibit cPLA2zeta at <10 nM IC50. However, a recent study has shown that in cPLA2alpha-/-stimulated lung fibroblasts arachidonic acid production is lessened but still present. cPLA2zeta has been identified as the other enzyme involved in the release of arachidonic acid. To further our limited understanding of cPLA2zeta's role in the inflammatory process, we are developing selective and potent inhibitors of the cPLA2zeta isoform. Our synthetic strategy is to modify the scaffold of Wyeth's cPLA2alpha inhibitor. Analysis of the structure-activity relationships and 3D molecular modeling has revealed 4 different places on the scaffold to introduce substitutions. To date, we have generated and assayed a panel of inhibitors. These inhibitors display low nanomolar potency, but have only minimal selectivity for cPLA2zeta. Thus, our main focus is to increase the selectivity of our inhibitors towards cPLA2zeta in order to further our understanding of cPLA2zeta's role in arachidonic acid production.

Ethosuximide is a succinimide anticonvulsant used in the clinical treatment of petit mal epileptic seizures in humans. Although its exact mechanism is not fully elucidated, it is believed to inhibit T-type calcium channels. In addition to its medical use, ethosuximide has been found to increase lifespan in the model organism, the nematode C. elegans. Nematodes exhibit lifespan extension when treated with ethosuximide at concentrations below a toxic threshold. While the published experimental results on ethosuximide-treated nematodes are promising, we have discovered that ethosuximide breaks down in the presence of 254 nm ultra-violet (UV) light, forming a toxic by-product. This change in ethosuximide that results in toxicity is specifically caused by irradiation, not heat. Acute exposure of C. elegans to ethosuximide treated with UV light results in death at lower dosages compared to nematodes treated with the control, native compound. UV-treated ethosuximide toxicity is independent of chemosensation (i.e. the sensing of chemical stimuli) as evidenced by the fact that chemosensory mutants do not show enhanced resistance to the UV-treated drug. Some human patients taking ethosuximide experience a butterfly rash under the eyes following exposure to sunlight. We speculate that this rash may be indicative of a similar mechanism of UV-induced cytotoxicity occurring in these patients. Taken together, these studies will help explicate the mechanism of toxicity resulting from exposure of ethosuximide to UV light, as well as the mechanism of action of native ethosuximide.

 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 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.

Leigh syndrome is a clinically defined collection of diseases comprised of multiple genetic defects related to mitochondrial function. This syndrome results in early death in children typically due to respiratory failure as a consequence of progressive neuropathy, and currently no viable treatment options exist. Leigh syndrome can result from mutations in several different mitochondrial genes, one of which encodes the NDUFS4 subunit of complex I in the mitochondrial electron transport chain. As the NDUFS4 knockout mice phenocopy human patients with Leigh syndrome remarkably well, this model was utilized for the purpose of this study. Dietary restriction (DR) was identified as a possible treatment for mitochondrial deficiencies through a yeast genetic screen, which found that mitochondrial gene mutants generally received a robust lifespan benefit from DR. Thus, the primary focus of our research is to determine the efficacy of rapamycin (a DR mimetic) as an intervention in the NDUFS4 -/- mitochondrial disease mouse model. Rapamycin functions as a DR mimetic through its inhibition of the mechanistic target of rapamycin (mTOR) signaling pathway, which is responsible for modulating a variety of metabolic and cellular processes. Our model suggests that the increased NADH/NAD ratio resulting from a complex I deficiency in these knockout mice is sensed as energy abundance and results in systemic metabolic derailment. We propose that inhibiting mTOR signaling addresses this defect by altering intracellular energy sensing and modifying metabolic status. In order to test the efficacy of rapamycin treatment, NDUFS4 -/- mice were treated with daily injections of rapamycin or vehicle. Lifespan data for each treatment and additional assays for health related parameters were conducted to determine the response to the treatment regime. Investigating Leigh syndrome in this context will allow us to better understand the underlying mechanisms of pathogenesis, and directly test novel interventions aimed at attenuating this disease.

The purpose of the double slit experiment is to observe the wave-particle duality of light. When a steady stream of photons hits a double slit, the resulting interference pattern is a clear indicator of the wave nature of light. However, if at a given time only a few photons hit the double slit and the signal is recorded over time, one can observe both the particle and wave nature of light: individual particles (particle nature) are recorded over time while their sum will eventually produce the familiar interference pattern (wave nature). The experimental setup uses light filters to reduce the intensity of a laser beam to just a trickle of photons. These photons, after passing through a double slit, slowly produce an interference pattern on a detector. The detector is a digital video recorder set up to record photon hits. The video frames are superimposed to show the production of an interference pattern over time. The double slit experiment has been done numerous times and in different forms. The experiment conducted here does not produce, but confirm previous results using a new experimental setup. The challenge will be to successfully show the wave-particle duality of light with readily available equipment to allow for a straightforward demonstration to future students. The enormous historical importance of the double slit experiment lies in the fact that it is at the heart of quantum mechanics, a field of physics viewed as challenging yet vitally important to the future of human technological advancements.

This investigation focused on the unique electrical behavior of exfoliated graphene; planar sheets of carbon atoms stripped from bulk graphite flakes. Specifically, the doping effect from self-assembled monolayers (SAMs) on the graphene surface was examined. Previous research has found that certain peptide SAMs are capable of influencing the electrical nature of graphene as both n-type and p-type dopants. This phenomenon can likely aid in development of biosensing and “lab on a chip” technologies. Graphene prepared by the scotch tape method was exposed to chemical solutions of tyrosine (Y) and phenylalanine (F) amino acids. These results are compared with the behavior of similarly deposited GrBP5, a peptide sequence selected for its high binding affinity to graphite. To measure the conductivity and current-voltage profile of graphene doped with each material, graphene field effect transistors (g-FETs) were fabricated on a silicon oxide substrate. Previous research has confirmed GrBP5 is a p-type dopant (electron acceptor). Data collected in this investigation suggests that the tyrosine binding group of GrBP5 is likely the electron acceptor, based on its highly similar doping effect. This p-type nature may be due to the aromatic functional group of tyrosine and would be recommended for future investigation. Furthermore, phenylalanine was found to be an n-type dopant, exhibiting a lower magnitude of doping despite its chemical similarity to tyrosine. By understanding the role of specific amino acids in peptide SAMs for g-FET applications, a large range of peptides may be integrated into this technology, leading eventually to novel biosensing devices.

β-Ga2O3 is a transparent conducting oxide that is well suited to ultraviolet (UV) photovoltaics. One application possibility is as a UV energy harvesting device in space, where UV light is much more abundant than solar. Because of the anisotropy of β-Ga2O3, spectroscopic measurements for a full range of polarization with respect to angles of orientation were taken to obtain optical constants. These measurements were made for both single crystal and thin film samples. As expected, the optical constants vary depending on both the sample type and the orientation of the sample. From these data a model was built that is able to identify the orientation of the single crystal samples. The next step is to build a model that will be used to determine thin film thickness of β-Ga2O3 deposited by our group on different known substrates.

Merkel Cell Carcinoma (MCC) is a rare, aggressive, neuroendocrine cancer of the skin. The disease is associated with a virus and is strongly linked to immune system function. Disease-specific mortality is >40% and few effective treatments are available for advanced disease. MCC metastases are typically treated by chemotherapy and/or radiation therapy (RT) delivered over >20 sessions. These options are usually successful at shrinking the targeted lesions, but these effects are often short-lived and/or associated with significant side effects. Mouse model data suggest that RT delivered in a single dose is more effective in promoting tumor immunity and that subsequent RT fractions suppress the function of lymphocytes that are recruited to the tumor. Therefore, we explored the use of single dose RT for MCC metastases. 28 patients with a total of 78 tumors were treated with a single dose of RT between 2010-2013. 86% of treated tumors showed a response that persisted for over 6 months. Overall, 45% of treated tumors had a complete radiological/clinical response and an additional 41% had partial responses (>50% reduction in size). These results are encouraging and show that single-dose RT is an effective palliative strategy with minimal side effects.

Neutralizing antibodies, which prevent entry of the HIV virus into a host cell by binding to the HIV envelope and neutralizing the biological effects of the virus, is an important focus of HIV vaccine design. It is hypothesized that these neutralizing antibodies may protect against initial infection from HIV if they are elicited by vaccination and are thus present at the time of virus exposure. The high rate of HIV mutation results in an enormous number of HIV variants circulating in the human population. Thus, an effective neutralizing antibody-based vaccine must be broad and potent. In order to understand how to create factors that elicit broadly neutralizing antibodies (bNAbs), it is important to identify and map regions of the viral envelope important for recognition by bNAbs. The best way to map the molecular basis is to identify two closely related variants that are or are not susceptible to neutralization by a certain virus and identify the regions that differ between the two variants. PGT128- is a HIV-1 monoclonal antibody that has been identified as having a broad neutralizing activity that would be desirable for a vaccine to elicit. Our lab previously found that longitudinal viruses from a HIV-1 infected patient, QA255, across 560 days post infection (dpi) display increasing ability to be neutralized by PGT128. PGT128 recognition has recently been found to depend on residue N332 of the V3 envelope region of HIV. As this residue is intact in QA255 viruses over time, there are additional determinants of sensitivity to PGT128. We found that chimeric sequences containing 560 dpi DNA in the V1-C3 region of the HIV envelope sequence show more sensitivity to PGT128 compared to chimeric sequences from earlier time points. This result suggests that amino acids in the V1-C3 region are important for PGT128 sensitivity.

A critical problem in the treatment of addiction is the tendency of addicted individuals to relapse to drugs-seeking with as many as 90% of addicts relapsing to use within one year. Exposure to stress is an important factor that precipitates relapse, though the exact mechanism is yet unknown. The Lateral Habenula (LHb) and the Rostromedial Tegmental Nucleus (RMTg), nuclei in the dorsal diencephalon, have recently become brain regions of interest in addiction research. Both regions have been shown to be important regulators of the midbrain dopaminergic systems, which are involved in relapse to cocaine seeking. However, very little is known about the precise role of these nuclei in stress-induced cocaine relapse. In our initial experiments, male, Long-Evans rats were handled for 3 days, and then injected with cocaine (10mg/kg) or exposed to intermittent footshock. Preliminary results demonstrate an increase in the expression of cFos, an early-detection transcription factor and marker for neuronal activity, in both the LHb and RMTg upon acute exposure to cocaine or foot shock. Studies are currently underway to determine the role of the LHb, and LHb projections to the RMTg on stress-induced cocaine reinstatement using the DREADD (Designer Receptors Exclusively Activated by Designer Drugs) technology in a rat self-administration reinstatement model.

The goal of this study was to obtain an age of the marine Quillayute Formation by correlating fossils from other similar rocks in Washington and Oregon. The Quillayute Formation, located along the outer coast of the Olympic Peninsula, Washington, consists of fossiliferous marine sandstones and siltstones, and its age has been controversial. Obtaining the correct date will allow for further understanding of the geologic history of the Olympic Peninsula, especially the rates of tectonic uplift and determining the climate at time of deposition. The Quillayute Formation has 37 identified species of fossil gastropods and bivalves. These fauna have been compared with those of the geographically and temporally closest units, the Quinault Formation (Washington) and the Empire Formations (Oregon). The Quinault Formation is Early Pliocene in age (3.6-5.3 million years), based on benthic foraminiferal biostratigraphy. The age of Empire Formation is Late Miocene (5.3-11 million years), determined by magnetostratigraphy and diatom biostratigraphy. To obtain the age of the Quillayute rocks, a comparison of age ranges of each of the correlative species was made. Results of this identified 15 species from the Quillayute Formation that also occur in the Empire Formation, and are apparently restricted to the Miocene. Six species are in common with the fauna of the Quinault Formations and those are still-living taxa.

Neurons are specialized cells that receive and relay information throughout an organism, and the compartment that inputs the signal has multi-complex structures known as dendrites. The form of the dendrite is tightly regulated to neuron function; therefore, any abnormality that alters the structure of the dendritic arbor can lead to severe defects in neuronal function. However, the mechanisms of how dendrites develop and maintain their arborization are poorly understood. From a forward genetic screen for mutant alleles with progressive defects on dendrite patterning we identified one mutant allele that leads to a complete loss of terminal dendrites. We mapped this allele to a small genetic interval, and using complementation tests and DNA sequence analysis we identified Acsl (Acyl-CoA synthetase long-chain) as the gene affected by this mutation. Interestingly, Ascl is also associated with human X-linked mental retardation (XMR), but to date the role that Ascl plays in dendrite development has not been investigated. Here we report the phenotypic analysis of the Acsl mutant, effects of Acsl knock down in neurons, and our plans for functional analysis of Acsl in dendrite development.

Stroke is one of the leading causes of death in the United States; however, due to the apoptotic death of neuronal cells from lack of oxygenated blood, prognosis and recovery is not always favorable even if the event is survived. Our laboratory focuses on finding therapeutic agents that show neuroprotective qualities in cerebral ischemic events. The compounds we have focused on in this study are progesterone and its metabolite allopregnanolone. Previous studies have shown that both compounds have neuroprotective qualities in vitro and that progesterone administration in vivo suppresses inflammatory response and subsequent edema. Our hypothesis is that both progesterone and allopregnanolone would show neuroprotective, as well as neurogenic, qualities in vivo. This is tested through a mouse stroke model using progesterone receptor knockout mice and wild type mice, both being subjected to a middle cerebral artery occlusion. Groups are treated with different compounds or control. The brains are then perfused after 11 or 28 days, fixed, and sliced to be put through immunohistochemistry, where cells are identified by certain neurogenic markers (bromodeoxyuridine incorporation and doublecortin labeling). Slides are finally analyzed through confocal microscopy to look for these markers in certain areas such as the hippocampus, striatum, and lateral cortex. Finally, positively labeled cells are counted in both the ipsilateral (stroked) and contralateral hemispheres. Data are currently being analyzed for 11 day post-ischemic mice. We anticipate an increase in the number of bromodeoxyuridine and doublecortin labeled cells in mice subjected to progesterone and allopregnanolone, and we also expect this to be more dramatic in the ipsilateral side due to new cell migration to the injury site. Hopefully, these results will allow for a greater push in implementing progesterone and allopregnanolone in clinical use for the recovery of ischemic stroke.

For thermoelectric (TE) applications, oxides possess certain advantages over conventional intermetallics, including excellent high-temperature stability, low toxicity, and a complex structure, which aids in lowering the thermal conductivity. Recently, it has been found that SrxBa1-xNb2O6 (SBN) holds potential for use in high-temperature TE applications (e.g., waste heat recovery). In our work, a solution combustion synthesis (SCS) process was devised to fabricate SBN with a range of Sr:Ba ratios in order to ascertain an ideal SBN composition for optimum TE behavior. The SCS method, which is highly amenable to mass production, allowed for good control of the SBN stoichiometry, and the as-processed powders were found to possess good single phase purity. Powders processed with different SBN compositions were subject to conventional sintering followed by reduction. The TE properties of each SBN composition were then tested and compared. Preliminary results of our acquired data suggest a decrease in the thermal conductivity as the Ba content is increased, likely due to the larger mass of Ba when compared to Sr. From the obtained results, an ideal SBN composition was determined having the optimal TE performance. Field assisted sintering (FAST) was then employed to processed SBN powder having the optimum composition, and the TE properties of the SBN from both conventional sintering and FAST were compared.

Superior spatial abilities in Autism Spectrum Disorder (ASD) are popularly associated with savant behaviors, and have been demonstrated in previous studies including tests of spatial intelligence. Our study examines participant's performance on a classical mental rotation task, which provides an objective measure of spatial ability. We seek to demonstrate how differences in reaction time (RT) and brain responses of adults with ASD differ from controls in this task. Previous research in typical individuals demonstrates that as the degree of rotation increases, participants are slower to make orientation decisions. These RT measures suggest individuals mentally rotate a second image to a reference image in order to make a decision. Our study tested age and IQ matched ASD and typical controls in a task that required a decision about the orientation of images of block alphabet letters. Participants were asked to decide whether the second of two images was identical to or a mirror of the first image. Images were presented at one of four angles. Dense array electroencephalography (EEG) and RT were recorded. Thirty-five male adults (17 in ASD, 18 in control) participated. RT, IQ, angle of images, and accuracy were variables for behavioral analysis. EEG data was analyzed in the time/frequency domain using open source and in-house software. EEG and RT measures from each trial of the task were compared based on subject group, types of images (normal or mirrored), and angle of images. Our analysis extends to include investigating brain activity prior to the pressing of the response key (the time that participants are making a decision). No general advantage in mean RT was seen in ASD group, however, high performance IQ (PIQ) participants in ASD group performed faster over the course of the experiment. This suggests high PIQ autistics may learn faster in this particular task.

Cervical spinal injury can result in a loss of function in the hands and arms. Restoration of hand and arm function is nearly 5-fold more important to patients than restoration of other functions. A major difficulty in restoring function lies in overcoming the formation of perineuronal nets (PNNs) and the accumulation of chondroitin sulfate proteoglycans (CSPGs), which contribute to the scar around the lesion site. The disruption of CSPGs in both the scar and PNNs is possible with Chondroitinase ABC (ChABC), and more chronically, through the use of a novel intracellular sigma peptide (ISP). The inhibition of CSPGs allows for axonal regeneration, which may be guided through the use of intraspinal microstimulation (ISMS). Preliminary results shows that the combination of these approaches act synergistically, leading to much greater recovery than through ChABC and ISMS alone. Functional recovery is assessed through a series of behavioral tests, including a trained forelimb reaching task and the Irvine, Beatties & Bresnahan test (IBB). These behavioral tasks are designed to measure attributes that are important for upper limb rehabiliation, such as spasticity, ability to grasp, movement in the wrist and digits, and plantar contact. If successful, this treatment may be used to rewire spinal circuits around a lesion and restore function below the site of the lesion.

Research in our lab has demonstrated that stimulation of the spinal cord may enhance rehabilitation and restoration of forelimb function after spinal cord injury. Building on previous experiments, the goal of this project is to see how the combination of Chondroitinase (a treatment of enzymes) and spinal stimulation could promote the recovery of forelimb function in rats with chronic spinal cord injury. We trained animals on a skilled forelimb reaching task and determined their dominant hand. Once trained to proficiency, animals received a contusion injury to the lateral aspect of the 4th and 5th cervical segments resulting in paresis of their dominant forelimb. Animals were then randomly assigned to groups receiving stimulation, Chase treatment, or the combination of the two treatments. We are conducting a battery of forelimb functional tests, including skilled forelimb reaching, each week for the duration of the study in order to record their progress and observe their improvement using the injured forelimb. It is the anticipated result that the addition of Chonroitinase during rehabilitation will result in an increase of the formation of synapses in circuits bypassing the lesion, which may be investigated using neuroanatomical tracing techniques. If successful, our results can be utilized in human medicine to improve the healing of a spinal cord-related injury and promote rehabilitation.

What cultural norms do the Rat City Rollergirls challenge and what are the implications of creating these new norms? Women and sports have by and large been at odds in America because of societal pressures and cultural norms that hyper-sexualize athletic women and undervalue their athletic achievements. Conversely, many women who challenge this are considered unwomanly and become unjustly labelled as a “beast” and often times their sexual identity becomes questioned. I will be exploring how women, specifically the all female roller derby league, the Rat City Rollergirls are challenging and creating new cultural norms by employing research methodologies such as, photo analysis, discourse analysis, ethnographies, and observations in order to answer these inquiries. It is important to study these cultural norms to elucidate a seemingly complicated and elusive societal bias towards women athletes and identify the root causes, what types of actions or behaviors continue the standard cultural norms, and how action can be taken to further challenge these long standing biases. To properly answer this inquiry I examined my own positionality regarding sports to uncover any hidden biases and then used this insight to remain open minded and unbiased while conducting further research. By analyzing the social media surrounding the Rat City Rollergirls I will be able to answer, in part, much of this inquiry. Using the Seattle Times’ online database I will deconstruct the hidden associations and meanings behind the pictures that I analyze. Furthermore, I will analyze the discourse used within these articles, as well as other social media sites, such as online forums, to see if my results are congruous with the dominant cultural norms regarding women in sport within America. The Rat City Rollergirls are challenging and changing these norms in new and exciting ways through the use of naming strategies, imagery, and events.

Chemostats are a continuous culture system in which cells are grown in a tightly controlled, chemically constant environment where culture density is constrained by limiting specific nutrients. Unlike batch cultures, the selective pressure imposed in a chemostat is constant. This has made them a desirable tool for evolution and competition experiments. Traditionally, chemostat experiments with S. cerevisiae have been constrained due to the limited number of cultures that can be run at once. In order to solve this problem our team is working with a new culturing system that allows 64 chemostats to be run simultaneously. In our experiment we evolved 96 biological replicates of haploid MATa yeast cells under either constant sulfur, phosphate, or glucose limiting environments for 300 generations. We are now using a variety of techniques including array-comparative genomic hybridization and whole genome sequencing of evolved populations to characterize mutations that have been selected for during the course of these evolution experiments. These techniques have revealed that amplification of genes that code for nutrient transporters are a common mutation that occur in the evolved populations over the course of the experiments. Therefore, we will also be experimenting with strains that have the most common amplified genes knocked-out in the hopes of identifying alternative pathways for nutrient-limited fitness increases. Changes in the genome can be correlated to changes in relative fitness, which we assayed through competition with a green fluorescent protein (GFP) expressing ancestral strain every 50 generations. Ultimately it is our hope that higher replicate number will better reveal the spectrum of genes important for adaptive growth in specific nutrient-limited environments.

Dendrites are branched extensions of the cell body of a neuron that act to receive and process synaptic or sensory inputs. The elaborate branching pattern of the dendrite is a hallmark of neural type, and has a considerable impact in determining what signals a neuron receives, and how these signals are integrated. Alterations of dendrite morphology can lead to abnormalities in neuron function--dendritic defects are associated with neurological disorders such as Ret syndrome, Fragile-X syndrome, and Down syndrome, and in many cases the dendrite pathologies are progressive. Therefore we set out to identify mutations that result in progressive defects in dendrite growth and stability with the hope that the genes affected by these mutations and the processes in which they regulate will provide new insight into human disease. A series of complementation tests using chromosomal deficiencies, as well as meiotic mapping have been used to map one such mutant (cc215) to a small chromosomal interval. In addition, we have performed a non-complementation screen to determine other alleles that affect the same gene mutated in cc215. Complementation tests and sequence analysis are currently being performed to classify the gene affected by this allelic series, which will allow us to investigate the underlying cause(s) of the dendrite defects in the mutants.

For my research, I was interested in the growing popularity of belly dancing in the United States, with a focus on misconceptions, stigmas, stereotypes, and the benefits that have attracted women (and some men who take classes and perform) to belly dance. I  researched these ideas that contribute to and surround belly dancing because of my personal experience as a local Seattle Belly Dancer. I was interested in both the reasons for the increase of interest and the stereotypes that need debunking. My question is: why have cultural perceptions of belly dancing shifted from a stereotype of sexualized dance to one of female empowerment and growing popularity? In order to answer this question I used participant observations, discourse analysis, photovoice and articles from both the media and scholarly. Rachel Kraus’s article titled “We are not Strippers: How Belly Dancers Manage a (Soft) Stigmatized Serious Leisure Activity” was useful in quoting and comparing her research on the stigma’s of belly dancers. From my research I found female empowerment about their bodies to be one of the core reasons for the growing popularity and also found stigma’s of the dance form being for male entertainment, which is a fallacy. The research  helped me become more aware of my community and its complexities.

Social media has had a history of creating facades of cultures, and this is especially true in the scope of sports. My question then is what is the effect of social media’s portrayal of Pacific Islander athletes on the cultural image of Pacific Islander students? For many higher education campuses, Pacific Islander (PI) student populations are vastly underrepresented in the general population spectrum. Yet there exists on sports teams a vast overrepresentation of Pacific Islanders, especially in football. The issue then is the effect this has on the image of Pacific Islanders, where we are seen as either "savage" or "barbaric" but rarely academic. My research will address this issue and see if the underlying misperception stems from social media. I will also analyze the effect this portrayal has on PI student athletes. The methods I chose to analyze the issue are interviews of PI athletes, photovoice and social media analysis. Through photovoice I will contrast how social media interprets the image of PI’s as and how PIs themselves view their cultural heritage. From these methods I anticipate a qualitative understanding of how social media has propagated a false image of PI culture to the general public. Then I hope to address how we as a society can oppose this image through more accurate education of PI culture.

MicroRNAs (miRNAs) are crucial regulators of gene expression in plants and animals and play a critical role in many biological processes, including nervous system development. From our previous study of Drosophila melanogaster peripheral sensory neurons, we found that miRNA bantam is both necessary and sufficient in epithelial cells to initiate an epithelia-derived signaling pathway that regulates dendrite growth. Using miRNA sensors, which report the location on miRNA activity, we found that bantam activity is developmentally regulated in epithelial cells. We hypothesize that this developmental regulation of bantam activity is the result of transcriptional regulation of bantam, and we aim to investigate this using bantam transcriptional reporters. To this end, we are developing bantam transcriptional reporter constructs in which the bantam transcript has been replaced by different reporter genes, such as GFP or Luciferase, while preserving the cis-regulatory landscape. We will use these reporters to monitor bantam transcript levels over developmental  time and, pending the outcome of these studies, we will use the reporters to identify trans-acting factors that regulate bantam transcription.

Ultrasound (US) and microbubbles (MBs), as tools for gene transfection, have promising implications for gene therapy. Through permeation, US facilitates the diffusion of a gene or drug from the capillaries into the cell. Binding of the gene or drug to the MBs can further enhance the delivery efficiency to the cell, and when exposed to US, the MBs cavitate, allowing the gene to diffuse into its target destination. Optimal US parameters (intensity, exposure time, central frequency) and MB characteristics (concentration, size, distribution, stability) are interdependent with regards to transfection and cavitation optimization, and thus the optimization of each individual parameter is important. Preliminary data has indicated that the optimal intensity and exposure time for US is 2 W/cm² for 3 minutes. However, optimizing US frequency has not been widely explored. The goal of this project is to investigate the effect of US frequency on MB cavitation, with both pure MBs and DNA-bound MBs . In order to do this, the following areas have been completed or are in the process of being completed. 1. A method has been designed to isolate home-made MBs by size; 2. A novel set-up to record the interaction of the US with the MBs with a hydrophone has been created and tested. The signals must be collected and processed with a written MATLAB program; 3. The results must be applied to in vitro US transfection with MBs of human embryonic kidney 293 (HEK 293) cells to demonstrate the effect of frequency on transfection results. By expanding research in US-mediated gene therapy with MBs, it is the hope that one day this method will be advanced towards clinical application as a means of non-invasive, localized, and efficient gene delivery.

DNA replication faces many obstacles as the genome is duplicated in all organisms. These obstacles include breaks in the DNA, tightly bound proteins as well as transcription. The encounters between replication and roadblocks can lead to replication stalling and genomic instability. To deal with replication conflicts, cells have mechanisms that act at regions of conflicts and help resolve them. Our lab is interested in these factors and in understanding how replication conflicts are dealt with in our model organism, Bacillus subtilis. Because Translesion Synthesis (TLS) polymerases are thought to act at certain stalled replication forks, in the context of DNA damage, we hypothesize that they play a more generalized role in resolving many different replication conflicts including those that are due to breaks. To determine if this is the case, we generated a deletion mutant of the yqjH gene. We have characterized this strain by specifically looking at its phenotypes under DNA damaging conditions. We are now looking to see if YqjH has any role in replication conflicts, both in terms of the severity of stalling and replisome stability, in B. subtilis.

Those who have studied genetics have a keen understanding of the fact that incredibly small changes can have tremendous, and often tragic, consequences. In patients with Fragile X Syndrome (FXS), a repeating sequence of genetic information (CGG) in an X chromosomal region is repeated more often than in the general population. This results in a spectrum of conditions including intellectual disability, anxiety, and physical features that deviate from the norm. About one fifth of people who have FXS also have seizures; the underlying cause of seizures in this fraction of FXS individuals is unknown. We hypothesize that FXS individuals who have seizures will have specific genetic variants –duplications and deletions of genetic information –that are not seen in FXS individuals without seizures. The experimental group is composed of DNA samples of FXS patients with seizures, while the control group will be composed of DNA samples of FXS patients without seizures. In order to find genetic variants, I utilize a genomic technique called array-comparative genomic hybridization (array-CGH). In array-CGH, DNA samples are tagged with fluorescent dyes to contrast patient DNA (tagged with pink dye) from control DNA (tagged with blue dye). The ultimate product of this technique is a quantitative representation of any differences between patient and control DNA, which can be processed and analyzed by computer software. By comparing the genomes of these patients, we will determine if there are common genetic variants across the experimental group that are distinct from the control group. If such variants are found, the next step is to associate specific genes with the subset. Establishing an association between a gene and the FXS and seizure phenotype is essential because it deepens our understanding of the condition and provides a foundation for future therapeutic treatments.

Autism is a disorder characterized by deficits in social and communication skills and repetitive behaviors. Fifty-two percent of the children with autism are treated with medication for some of the common co-morbid behaviors – e.g., anxiety, aggression, and hyperactivity. However, only 49-69% of these children respond positively to the medication, and about 18-26% of these children experience side effects such as insomnia, sedation, and increased appetite. An extensive series of trial-and-error might be needed for a patient, which could be time-consuming and stressful for both the patient and parents. A reliable method is needed to predict the effectiveness of the pharmacological treatment. This study used electroencephalography (EEG) to detect early changes in the brain that we cannot yet observe in behavior. Children who are diagnosed with autism and starting a medication (e.g. stimulant, antidepressant, or atypical antipsychotics) participated in this study. EEG was recorded while the subjects participated in a social processing task, a resting task, and the Go-NoGo inhibition task. The participant’s caregiver completed three questionnaires: Child and Adolescent Symptom Inventory, Aberrant Behavior Checklist, and Social Communication Questionnaire. This project analyzed the subject’s change in EEG and behavioral data over three different time points (T1= before, T2= one week after, T3= one month after the start of medication). Multiple aspects of each individual’s EEG signal were examined by comparing the difference from T1-T2 and T1-T3 against the null hypotheses of no change (or comparing change to 0). The goal of this project is to search changes in the EEG signal that is related to positive (or negative) behavioral changes in this population. This study will provide an important first step for understanding changes in the brain in response to medications, which may provide useful information to professionals during the process of choosing the most effective medication for children with autism.

I am interested in the dynamics of injury in sports culture. Are there social consequences of injury for athletes undergoing treatment? If so, what are these social repercussions? In the culture of sports, athletes are many times expected to perform above a reasonable level. Mistakes, failure, and imperfection in sports are not accepted or supported. Injury is categorized as imperfection in our culture surrounding sports despite it being something that most individuals face at some point in their career. I expect there to be substantial social consequences for injured athletes. In a study looking at collegiate athletes who suffered a severe injury called "Transitioning out of Sport: the Phycosocial Effects of Collegiate Athletes' Career-Ending Injuries", positive and negative social consequences were found to be incredibly influential in the lives of the athletes involved in the research (Stoltenburg et al, 2011). My research methods include interviews, discourse analysis, and archival support. This subject is important because if there are negative consequences, coaches and advisers to athletes can be aware of these factors and emphasize the importance of pushing athletes to invest in multiple interests. More effort may be needed to create environments and systems that support injured athletes. Whether this research draws awareness and slowly changes social discourse on injury within an athletic arena, or initiates action and forms foundations for structures such as support groups for injured athletes, I believe it will implement positive change.

The PIRL genes are a family of nine genes discovered during the sequencing of the Arabidopsis thaliana genome, the first fully-sequenced plant genome. PIRLs are a previously uncharacterized class of plant leucine-rich repeat (LRR) proteins that are hypothesized to be important to plant development. As part of an ongoing systematic study to gain insight into PIRL functions, I examined Arabidopsis plants engineered to overexpress the PIRL9 gene. Plants containing an extra copy of PIRL9 designed to drive overexpression of the gene were identified and observed as they grew. Abnormal leaves were observed in most of these plants and stunted growth was quantified through measurements of leaf length and width, as well as primary stem height. Using qPCR, the amount of PIRL9 mRNA present in the different plants was quantified and linked to previous plant measurements. Data showed a correlation between severely stunted plant growth and overexpression of the PIRL9 gene. Significance of these results for PIRL9 function will be discussed, but further genetic and phenotypic analysis is needed to confirm and assess the effects of PIRL9 overexpression. 

The purpose of this study is to investigate the effects of different pollutant sources in Sinclair and Dyes Inlets, both located in Puget Sound, Washington. Puget Sound is a fjord-like waterway extending from Olympia, Washington to the Canadian border. Sinclair Inlet and Dyes Inlet are connected by the Port Washington Waterway near Bremerton in Kitsap County, Washington. Bremerton is the home of Puget Sound Naval Shipyard. This naval base is a Superfund site that discharged large amounts of industrial pollution into Sinclair Inlet. In comparison, agricultural and residential pollution are deposited in Dyes Inlet from streams surrounding the perimeter of the inlet. This study aimed to analyze foraminiferal assemblages to determine if environmental changes through pollution and other factors have affected the health of the Bremerton area marine ecosystems. Foraminifera are shelled single-celled marine microorganisms that react to environmental stresses, thus they act as good indicators of environmental change. Foraminifera were collected from a total of 21 samples provided by the Washington State Department of Ecology from 1998-2009. Thirteen of these samples were taken from Dyes Inlet and 8 were taken from Sinclair Inlet. This study focused on examining the density and diversity of foraminifera from 1998-2009. Our results show that Dyes Inlet contains a low diversity of foraminifera with 7 different species found. However, 2 samples did not contain any foraminifera and several samples from more recent years only contained one species. In Sinclair Inlet, 15 species were identified in total, but diversity was nearly cut in half over the time period studied. The dominant species in both inlets was Elphidium hannai. By comparing foraminiferal assemblages from our locations with samples from less anthropogenically impacted locations in the Puget Sound, we can begin to analyze the potential effects of different types of pollution on the health of Puget Sound.

Foraminifera are a diverse and extensive group of marine shelled protists that are found all over the world, including Puget Sound. Because foraminifera are relatively abundant, short-lived and susceptible to environmental change, they have the potential to be inexpensive and effective environmental monitoring tools for local estuaries. Since Puget Sound exploits its water ways for industrial profit, foraminifera could prove to be useful tools for environmental monitoring. Thus it is surprising that, to date, no one has ever catalogued and observed foraminifera in the Sound to search for any changes in structure, abundance or diversity that could indicate a change in the environment. In fact Puget Sound is the only industrialized waterway that has not done this. The purpose of this project is to assemble an atlas of the foraminifera found in Puget Sound, from Bellingham Bay to south Sound. This atlas contains photographs, and in-depth descriptions of each foraminifera species. A catalogue such as this is a useful tool because it helps to better understand the foraminifera of Puget Sound and furthers the understanding of the organisms and their ecosystem.  This atlas can also be used as a quick and easy reference to compare any changes discovered among foraminifera and their communities. Ultimately, the complete atlas will be submitted to Paleontologica Electronica for publication.

Ubiquitin is a protein modifier that is essential for many eukaryotic cellular processes. Attachment of ubiquitin to substrate proteins (ubiquitination) occurs in a three-step cascade that involves a ubiquitin activase, ubiquitin conjugase, and ubiquitin ligase; it is the ligase that targets substrate proteins. One challenge for the ubiquitin field is identification of substrate cohorts for ubiquitin ligases. Although ubiquitination only occurs naturally in eukaryotic organisms, we previously demonstrated that it is possible to reconstitute the ubiqutination cascade in E. coli, allowing for analysis of ubiquitination outside of its natural environment. Our project consists of the construction of a protein complementation assay, using two fragments of dihydrofolate reductase (DHFR) to detect the ubiquitination of proteins in E. coli, outside of the natural eukaryotic environment of ubiquitin. To perform the assay, I transformed all of the essential components of the ubiquitination pathway, including individual fragments of DHFR fused to ubiquitin and a substrate protein of interest, into E. coli cells. The assay tests for the covalent attachment of ubiquitin to the substrate protein through growth on selective medium, which is possible only through the combination of the separated fragments of DHFR. After construction and transformation of vectors using a known yeast ubiquitin ligase and substrate partner, I have found that ubiquitin fused to a fragment of DHFR functionally attaches to other proteins via a known ubiquitin ligase. Transformation of entire cDNA libraries into the bacterial cell in place of a ubiquitin ligase will allow for high throughput screening of ligases with homologous function as well as discovery of new ubiquitin ligase substrates. As no functional screening mechanisms presently exist, our system to efficiently screen for ubiquitin ligases and substrates provides a novel tool to address a significant challenge faced by the ubiquitin field.

The basic functional unit of the nervous system is the neuron, which contains two highly specialized compartments, the axon and dendrite. Dendrites received synaptic/sensory inputs, and the dendrite arborization pattern has a profound influence on the type and number of inputs a dendrite can receive. We are studying dendrite patterning in the Drosophila peripheral nervous system (PNS), with a particular focus on the role that non-neuronal signals play in shaping dendrite development. In the Drosophila PNS, sensory neurons grow on top of a monolayer of epithelial cells, which provide instructive cues to shape dendrite patterning. To date, there are plenty of tools available to genetically label and manipulate neurons, but few tools are available for genetic manipulation of epithelial cells. My goal is to design a reporter construct that will specifically label and facilitate targeted expression of transgenes in epithelial cells. To this end, I am assembling a modular plasmid construct which contains a minimal promoter, an enhancer sequence which we have found to be sufficient to direct epithelial expression, and the coding sequence of green fluorescent protein or other genes of interest. After assembling the construct, I will use germline transformation to generate transgenic flies and test the efficacy of the construct. If successful, this will represent the first epithelia-specific transcriptional reporter, and will provide a template for assembly of additional tools for studying dendrite-epithelia interactions.

I am interested in how new developments and understandings of degenerative brain disease in football players have influenced discourse and policy surrounding risk. A recent explosion of information regarding the long-term dangers of cranial trauma in contact sports has flooded the public conscience. The question I want to address is: has this new information impacted the way that risk is discussed and understood among football players, coaches, and fans? I will look at a combination of print and social media, conduct interviews, and use discourse, positionality, and archival research methods to understand the issue. Through these methods I hope to find that new developments and understandings of degenerative brain disease have cultivated discussion and promoted more stringent testing and policy towards cranial trauma in football players. At both the collegiate and professional level football is part of a multi-billion dollar industry; therefore, the serious, long-term health effects of the sport are discussed within a highly politicized, mediatized, and emotional arena. It is my hope that this research will illuminate these underlying issues, provide clarity, and enrich the discussion of risk in football.

The media impacts sports in many ways by reporting stories as a way to distract an athlete. There are many stories in the sports industry where the media attacks an athlete and their personal life through outlandish stories. Some examples of this are how many athletes are targeted through their girlfriends. Manti Te’o and his hoax girlfriend, AJ McCarron’s girlfriend during the BCS national title game, Tiger Woods’ affair and Hope Solo and Jeramy Steven’s domestic abuse are some stories that the media has focused much of their attention on. Most importantly, how does the media shape cultural norms about significant others of athletes? I will be looking at popular culture and media to analyze what impact media has on an athlete’s relationship. From my personal experience I believe that the media propagates stories exponentially out of proportion. To challenge my hypothesis I will use the methods of photo voice, interview and discourse analysis of pop culture. An article written by Paul Husselbee and Kevin Stein shows an analysis of Tiger Woods’ scandal breaking down what exactly happened during his affair. This article focused on what was going on during trials and the aftermath. ESPN and other sports broadcasting companies made his affair a worldwide issue. Most media articles are written to get more people to tune into the story rather than laying out the complete truth. This research is important because people follow media and believe everything that is being broadcasted without looking at the fine print and details. I believe I will find that the media has a significant impact on fans when they view athletes. If more people realize there is more to a story than what is being shown, then stories would not be so extreme.

It has been hypothesized that effective treatment of neurodegenerative diseases, such as Huntington’s Disease and Alzheimer’s, may be possible through the manipulation of neural stem cells to divide and replenish afflicted neuronal cell populations. A crucial component of this treatment would be the creation of a vehicle for the efficient delivery of stimulating genetic material into target cells. Prospective virus-based vectors accomplish this by making use of a recombinant virus and its natural ability for gene transfer. These viral vectors, while inherently effective, have significant safety issues with the possibility of eliciting harmful immune responses. Peptide-based copolymers are a promising non-viral alternative for delivery systems. While safer, these synthetic vectors have thus far proven less efficient. One problem is lack of consistent cell membrane penetration, preventing the therapeutics from reaching areas within the cell where they would come into effect. Our laboratory has recently incorporating the membrane-lytic peptide melittin (a molecule derived from bee venom) into our base DNA-binding peptide-based polymers. The melittin-functionalized materials were shown to increase gene delivery efficiency by at least 10-fold compared to control materials both in vitro and by injection into mouse brain. This current study seeks to develop a multifunctional delivery system by incorporating the neuronal-targeting peptide “Tet1,” for specialized treatment of neurodegenerative diseases. Previous work showed that conjugation of Tet1 to control polymers results in increased transfer specificity to neuronal cells in vivo. Potentially, Tet1 and melittin can synergize to further improve gene delivery to the central nervous system.

Cardiovascular disease is an epidemic, prevailing as the leading cause of death worldwide. One consequence of cardiovascular disease is a myocardial infarction (MI), or heart attack. An MI is caused by a blockage in the coronary arteries which cuts off the blood supply to a portion of the heart wall, forming nonfunctioning scar tissue. We are aiming to improve heart recovery post-MI by replacing scar tissue with functioning cardiac tissue through a cell engraftment therapy. Cardiac cell engraftment is difficult because cardiac cells die quickly due to lack of vascularization of the graft. We believe that by promoting vessel growth in grafts, we will improve therapeutic cardiac cell survival for better heart function during recovery. To study the coronary network’s ability to vascularize cell grafts, we inject skeletal muscle cells, which survive better than cardiac cells, into the heart wall post-MI. We observed vessel development in mice 14 days after MI and engraftment, and compared it to vessel development at other time points to better understand how the coronaries can vascularize cell grafts. To characterize the graft vasculature, I used histology to mark vessels and quantify vessel growth in the graft. My results shows that the coronary vasculature is able to expand and vascularize newly implanted tissue grafts post-MI. I detected capillaries as well as smooth muscle coated vessels in the graft suggesting vascular remodeling has occurred by 14 days post MI. My work establishes a baseline comparison for future research that will identify factors to increase the vascularization of graft tissue. We hope that promoting vessel growth will improve cell therapy methods for heart recovery to become applicable to clinical practice in the future.

Until recently, little research has been done on C-S bond formation in transition-metal catalyzed transformations compared to other carbon-heteroatom bonds such as C-N, C-O, and C-P. As sulfur-based coupling partners (thiol and disulfide for example) tend to poison transition-metal catalysts, development of C-S bond formation has been slow. However, a recent nickel-catalyzed system shed new light on this difficult transformation. In this context, C-H functionalization is a sustainable and straightforward approach to sulfur-containing heteroaromatic production. C-H activation is a process whereby a carbon-hydrogen bond is cleaved, thereby allowing the exposed carbon atom to form new bonds. Thus, in order to expand the above research of C-S bond formation toward development of short synthesis for fused thiophene systems, focus was placed on a palladium catalyzed cascade-type reaction system. C-H activation reactions can and have been manipulated to work in a cascade-type fashion. By combining cascade-type methodology with the reduced environmental impact of C-H activation, these fused thiophenes can be synthesized cleanly and efficiently. The test substrates in this work are O,O-diethyl S-phenyl phosphorothioate and 4,4,5,5-tetramethyl-2-(thiophen-2-yl)-1,3,2-dioxaborolane. Both substrates were chosen because they contain sulfur, thereby aiding the C-H activation process. By effecting a C-H activation with a palladium catalyst at one of the ortho carbons of the phenyl ring with the boronic ester of the thiophene, the first C-C bond will be formed. In the time immediately after this first transformation, the now-changed palladium complex is able to insert into the S-P bond of the phenyl-based compound. This step sets up the second reaction, whereby the phosphorothioate directing group is cleaved along the S-P bond and the resulting thiol is coupled to a carbon atom to close the ring. This molecule is known as benzo[b]thieno[2,3-d]thiophene.

 As human development continues to encroach on wild places, wetland bird species lose vital nesting habitats.  To combat that loss, many cities nationwide create urban wetlands, in part to protect or replace lost habitat; it is unknown how effective this effort is.  Previous Canadian studies identified four wetland bird species that do not generally nest in urban wetlands in Eastern Canada: American Coots (Fulica americana), Pied-billed Grebes (Podilymbus podiceps), American Bitterns (Botaurus lentiginosus), and Virginia Rails (Rallus limicola).  This project will compare four urban wetlands with four rural wetlands in King and Snohomish Counties to see if the four species show any nesting preference between urban and rural wetlands.  In addition, the project will investigate if those target species that nest in both urban and rural areas exhibit greater habituation to human presence in urban areas.  I will visit each of the eight wetlands weekly during the morning or early evening and note the presence of courtship or nest-building activity and the number of individuals of each species exhibiting those behaviors.  Using a laser distance device, I will measure the distance between the birds or their nest and the closest human access point to determine relative habituation.  If urban wetlands birds are more habituated to humans, they will nest, on average, more closely to human access points than their counterparts in the rural wetlands.  If urban wetlands are effective as nesting habitat, then mated pairs of the target species will utilize them, demonstrating that small created wetlands can serve as a buffer to habitat loss for wetland birds.

In this study, we attempt to gain a better understanding of how poly(3-hexylthiophene) (P3HT) nanowires self assemble in solution. P3HT is used as the primary p-type donor in conjunction with phenyl-C61-butyric acid methyl ester (PCBM) in bulk heterojunction polymer solar cells. During self assembly, individual P3HT chains begin to kink after about 40 monomer units into an S-like shape. These S-shaped chains interact with one another via pi-pi interactions and form nanowires with widths typically between 20 and 70 nm and heights between 3 and 5 nm. In an attempt to improve device efficiency, we would like to exhibit greater control over the size of the nanowires. Controlling the morphology of the nanowires would allow us to improve the efficiency of the device. Thus, we demonstrate a method to create self-assembled nanowires from 12.5, 16, and 28 kDa molecular weight P3HT. P3HT solutions were made with a concentration of 1 mg of polymer to 2 mL of solvent (anisole and chloroform in a 4:1 ratio). These solutions were then heated at 80°C and thoroughly mixed for 16 h. After mixing, the solution is removed from heat and allowed to self-assemble for several days. Finally, the solution is then spin coated onto a silicon dioxide coated silica substrate. The samples were analyzed using atomic force microscopy to provide detailed information about the surface coverage, width, and height of the nanowires.

Three distinctly different beach environments can be observed at Owen Beach in Tacoma, Washington; a natural beach environment, a partially modified beach environment and a fully engineered beach environment. Each part of the beach has a unique morphology and profile. This study was designed to analyze these differences and determine the effects, if any, that the anthropogenic modifications have on the slope, change in elevation and sediment characteristics along this beach over the course of a year. The beach slope and change in elevation were measured monthly starting May 2012 at three points along the beach face from each type of environment using a tape measure and Brunton compass. Sediment samples were taken from the same points and measured using a Particle Size Analyzer or grain size chart. Sketches were made of the beach profile that include tide line, landscape, data points, sediment deposition, high tide line, and modifications. Preliminary analyses of data shows that the anthropogenic modifications have a direct effect on the morphology and profile of the beach. The fully modified portion has been more static than the other two parts with larger particles and less change in slope. The modified portion has smaller particles along its shore and its slope has been more dynamic than the fully engineered portion of the beach. The natural portion of the beach is the most dynamic with much smaller particles along its shore and a larger change in slope throughout the year. It is important to study the effect that human engineering has on natural beach environments so that we can fully assess its impact on and applicability for managing coastlines for residential, commercial and recreational use in our communities.

Imidacloprid (IMI) may be a viable alternative to carbaryl for controlling burrowing shrimp (Neotropea californiensis) that destabilize sediments resulting in poor survival and low yields of the commercially harvested Pacific oyster (Crassostrea gigas). Previous laboratory tests indicate the shrimp are overtly affected (immobile, cannot burrow) when exposed to IMI concentrations in sediment pore water, but are not killed. These results contrast sharply with observed efficacy in the field, i.e. mortality 72-96 hours post application and subsequent reductions in burrow counts. Understanding the factors governing efficacy in the field may improve control. We exposed 10 adult female shrimp that had burrowed within native sandy sediment to IMI (Nuprid® 2F) for 96 hours simulating the theoretical maximum pore water concentration (146 ppb) associated with an application of 0.5 lbs active ingredient [ai] per acre. We compared the response of the shrimp to that of an equal number of negative controls, and five shrimp in a comparable pore water-only exposure, and five in clean seawater. Behavior was monitored daily and water quality was measured at the end of the test. As expected, all shrimp in the water-only IMI exposures were overtly affected, but survived. Eighty percent of the shrimp exposed to IMI within their burrows died, whereas 90 percent of the negative controls survived. Dissolved oxygen (% saturation) varied among treatments (clean seawater: 51-69.6%; seawater + IMI: 42.4-57.4%; clean sediment surface water [alive]: 4.1-20.1%, [dead]: 3.4%; sediment + IMI surface water [alive]: 5.4, 57.9%, [dead]: 4.2-65.4%). Results suggest the shrimp can tolerate very low dissolved oxygen within sediment without IMI, but their sensitivity to IMI increases due to factors associated with their impaired ability to move water within the sediment.

Solar energy is arguably the most promising source of renewable energy because it is thought to be both the cleanest and most abundant source. There are several types of solar cells including organic, inorganic, and hybrid organic-inorganic solar cells. While inorganic solar cells have high efficiencies, good charge carrier mobilities, and relatively long charge carrier times, their expensive production and materials competition with the microelectronics industry has kept their prices high. Organic solar cells are solution processable, applicable to flexible substrates, and have the promise of being relatively cheap to produce. However, their relatively low charge carrier mobilities and short exciton diffusion lengths prevent them from being used as an alternative to inorganic solar cells. Hybrid organic-inorganic solar cells have been introduced as a substitute to both organic and inorganic solar cells in order to overcome the short-comings of each. Inorganic semiconductors are used in hybrid photovoltaics as the acceptor in the solar cell due to the ease of changing the size and shape, and therefore the bandgap, of these semiconductors, which allows them to contribute to the photocurrent of the cell while enhancing the conductivity. This project addresses the synthesis of cadmium selenide (CdSe) nanotetrapods, which may facilitate control of direction of electron motion in the active layer of the cell. The reaction time, growth temperature, ligand type, and monomer concentration were used to control the synthesis, and the effects of each variable on the size and shape of the tetrapods were studied via transmission electron microscopy (TEM).

Organic electronics is a growing area of research that investigates the properties and applications of conjugated polymers and conductive small molecules. Devices made from organic electronic materials can be flexible, inexpensive to process, and have lower weight compared to inorganic devices. Prominent synthetic techniques for conjugated polymers, including the Suzuki reaction, Heck reaction, and Kumada coupling, utilize a palladium or nickel complex as the catalyst. When the reaction completes, organometallic molecules and metal nanoparticles remain stuck in the polymer, decreasing the efficiency of resulting devices by acting as charge trappers or photo quenchers. The potential commercial success of organic electronics is highly dependent on their efficiency, and so the impurities need to be removed. A palladium-catalyzed model Suzuki coupling reaction of bromobenzene and phenylboronic acid was analyzed by 31P-NMR both before and after the post-synthetic addition of thiuram disulfide (TMTD). Pd(PPh₃)₂Br₂ dibromide was present in the solution prior to the post-synthetic disulfide addition, but not after. When TMTD or diphenyl disulfide were added directly to metal catalyst in chloroform, the resulting product precipitated out; the solubility of the product was different from the reactants. The change in solubility indicates that disulfide molecules can behave as metal scavenger for residual palladium or nickel catalyst. In order to restore the performance of organic polymers, scavenger molecules are used post-synthesis. This additional step isolates palladium or nickel atoms and changes their solubility, allowing them to be separated from the polymer. The performance of disulfide-based metal scavengers added to catalyst-metal-contaminated conjugated polymers is discussed.

I am interested in understanding how the impact of media portrayals on African American quarterbacks. I chose to look at the discourse used by sports analysts and spectators. Through social media and main stream sports news outlets, I began to gain an understanding of: how sports analysts and writers describe Black and White quarterbacks and how they differ? Hundley and Billings directly link this line of analysis in their article, "A Content Analysis of Racial Representations of NBA Athletes on Sports Illustrated Magazine Covers". Additionally, I looked at the research of Andrew Billings and Eugenio Mercurio in the differences of how White and Black players are characterized in terms of intelligence and athletic ability. I chose to use discourse, social media, and popular cultural analysis to answer my question. The importance and relevance of this work lies in the disproportionate perceptions created through hegemonic forces. The naturalization of these stereotypes discredits African American athletes’ achievement and may have residual effects on personal identity.

Organic Photovoltaics (OPVs) provide a potentially cheap and clean option to harvest energy from the largest source of energy available - the sun - however they are still fairly inefficient when compared to inorganic photovoltaics. Attaching fluorine to the polymer backbone has been shown as an effective way to increase the open circuit voltage (Voc) and power conversion efficiency of the devices by lowering the highest occupied molecular orbital of the polymer. However, the impacts of fluorine attachments on the other properties of active layer, like morphology under different processing conditions and electrical properties, have not been fully studied. Knowing this information will help the future designs and processing of donor-acceptor polymers for OPV application. In this project, three structurally identical polymers, with zero, one, and two fluorine attachments (named P0F, P1F, and P2F) were studied. The morphological impact of fluorine attachments are studied by varying the ratio of PCBM (a widely used and promising acceptor) and these three polymers as well as the solvents used when processing through atomic for microscope (AFM). Hole features were found on the surface of the thin film. The density of and depth of the holes were found to correlate to the number of fluorine attachments and processing condition respectively. Future works are being done to investigate the reasoning behind the device efficiency with the attachment of fluorine and differentiating whether this is due to these physical morphologies or bandgap manipulation being the primary contributor to a higher efficiency. The influence of fluorine on the dielectric constant of the thin film and operation of OPVs will also be studied. 

A major obstacle in the efficient delivery of genes using non-viral vectors is sequestration and subsequent degradation of the vector in the endosomal/lysosomal trafficking pathway. While incorporation of membrane-lytic peptides into gene delivery vectors has been shown to increase transgene expression by disrupting the endosomal vesicles, non-specific membrane-disruption caused by these modified vectors leads to significantly increased toxicity. One approach to mitigating this increased toxicity is to mask the membrane-lytic peptides inside a pH-responsive micellar core that destabilizes during vesicle acidification in the endosomal/lysosomal pathway, revealing the membrane-lytic segments only when internalized. Incorporating pH-responsive imidazole elements in the hydrophobic micelle core which become charged under acidifying conditions can disrupt the micellar structure by electrostatic repulsion, leading to display of the active peptide, membrane lysis, and increased DNA delivery to the cytoplasm. After synthesis of the pH-responsive motif a panel of representative DNA delivery polymers will be evaluated for pH-responsiveness, transfection efficiency, and cytotoxicity.

We  present an extension of the Astronomy Department’s curriculum for visually impaired junior high  school students. Our lesson plans are a complementary addition to  Noreen Grice's Braille and large print  readings. These lessons satisfy the Washington State Essential Academic Learning Requirements (EALR's) for junior high school students, the level at which students are introduced to astronomy. We  present here a sample of new material that covers the composition, formation and evolution of the Sun.   Our lessons include activities, audio tracks, 3D models, and online links to advanced topics. We outline additional curricula that we are actively  developing, such as biographies of visually impaired astronomers and topics including the formation and evolution of the Solar System's terrestrial planets.  We will test our curricula during this coming school year, as we did in  2007, at the Washington State  School for the Blind,  with the  expectation  of deeply  strengthening the  students' understanding of the  evolution of the Sun beyond what is available in their textbooks.  Ultimately, this curricula will be distributed and utilized throughout the United States as part of the on-going national and international efforts  to promote astronomy for those who are visually impaired.  We conclude with a description of our  role in building and testing additional educational tools.

The export of signals is a vital aspect of bacterial communication with its environment and it was recently found that Gram-negative bacteria can send signals directly to neighboring bacteria via the type VI secretion system (T6SS). The bacterial T6SS translocates antibacterial toxins into neighboring bacterial cells and provides a means for bacteria to compete in their environment. Bacteria can also target their own cells with the T6SS but are protected against self-intoxication by cognate immunity proteins that inactivate their partner toxins. For example, one T6-exported toxin found in Pseudomonas aeruginosa, Tse1, degrades the cell wall of the recipient cell. The cell wall provides structural support for bacteria, and degradation of this protective layer by Tse1 causes the target cell to lyse. P. aeruginosa is immune to this toxicity, however, because an immunity protein, Tsi1, in the cell wall layer of P. aeruginosa binds and inhibits T6-exported Tse1. Our lab has found that Tse1 and Tsi1 are members of a large superfamily of type VI amidase effector-immunity widely found in Gram-negative bacteria, suggesting that these T6 toxin-immunity pairs may play a major role in influencing the structure of polymicrobial communities in general. Because of the large influence the T6SS can have on polymicrobial environments, I predict the T6-toxin-immunity system could also be utilized as an antimicrobial strategy. My aim is to engineer a novel Tse1–Tsi1 toxin–immunity pair that escapes rescue by immunity proteins in naturally occurring bacteria, thus giving the engineered P. aeruginosa strain the ability to outcompete the natural wild-type strain. To do this I will use a structure-based approach in conjunction with a genetic directed evolution strategy to identify and mutate Tse1 and Tsi1 residues that play an important role in Tsi1–Tse1 recognition and inhibition.

The Moon does not have a dipolar magnetic field, like that of the Earth. Instead, the Lunar surface has areas of magnetized crust called magnetic anomalies. Many of these magnetic anomalies are coincident with features called lunar swirls - regions with high-albedo or high-reflectance material. As many of these lunar swirls often appear in the same location as areas of relatively intense magnetic fields, one of the leading hypotheses explaining the formation of the lunar swirls is that the surface is shielded from the surface darkening solar wind by the magnetic anomalies. We seek to further understand the connection between the visual high albedo and the magnetic anomalies by creating three-dimensional models of the magnetic fields and particle deflection around well-known lunar swirls. We do this through the use of a three-dimensional particle tracking program. The particle tracking program simulates solar wind interacting with the magnetic field and determines the final location of the solar wind particles on the surface of the Moon. This work focuses on the results for simulations of the Mare Ingenii swirl region. Preliminary results show that the particles are in fact deflected, and as expected the smaller electrons are more highly deflected. Better understanding of the origin of the Lunar swirls not only allows us to gain insight into the process of space weathering and magnetic shielding but can also offer clues for methods to mitigate the harmful effects of solar wind and particle radiation during human space travel and at lunar or Martian human colonies.

Colloidal zinc oxide nanocrystals (NCs) become charged with electrons upon reduction with decamethylcobaltocene. Understanding this redox chemistry can further develop research on quantum dot sensitized solar cells and other various applications of NCs. The goal of my project is to determine whether this electron transfer can be characterized by an equilibrium constant K_eq, and if so, to see which variables in the reaction affect the K_eq. Two models were tested: (1) in which the concentration of NCs would affect the K_eq, and another (2) in which it would not. Using data from optical titrations, I found that the K_eq is affected by NC concentration and is therefore better described by model (1). Similarly, other variables are currently being tested in order to refine a working model that can accurately describe the reaction of NCs with reductants. The contribution of a simple model for these charge transfer processes can be applied to various areas.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by broad social and cognitive impairments and the presence of stereotyped, repetitive behaviors. Our research examined the hypothesis that impairments in neural signal routing in ASD underpin behavioral symptoms. Specifically, we investigated structural and functional differences in the basal ganglia (BG), a group of subcortical nuclei that regulate signals to frontal cortex. The BG is known to regulate movements, balance, and posture and their abnormal development has been related to motor impairments in ASD. It is necessary to extend these investigations, as previous research did not account for the relation between BG structure and function, or the role of the BG in complex cognitive tasks. In the current experiment, anatomical tracings of two of the key input stations of the BG (the caudate and putamen) were generated for 31 individuals, including 14 with ASD and 17 controls. To determine whether the size of the BG nuclei correlated with their functional influence over cortical regions, we correlated our volumetric measures with indices of effective connectivity, measured using dynamic causal modeling analyses of an fMRI data set. Our results indicated that across all individuals, there were reliable negative correlations between the size of the BG and its modulation of synchronization between several cortical regions. This finding was particularly evident in the individuals with ASD. However, inconsistent with previous investigations, between groups t-tests showed that there were no significant differences in absolute BG volume between groups. Future analyses will account for total brain volume to see whether absolute value or relative value of the BG account for differences in network-level signal routing properties in individuals with ASD. We will also correlate these findings with behavioral measures to establish its relevance for the symptoms of ASD.

Quantitative mass spectrometry (MS)-based proteomics is a powerful approach to measure relative expression changes across thousands of proteins in a complex mixture. Commonly, stable isotopes like ¹³C and ¹⁵N are incorporated into proteins and peptides by metabolic labeling (ML) or chemical labeling (CL) to produce “heavy” labeled forms. Mixtures of light and heavy peptides can be identified and quantified by MS. In ML, proteins are labeled in vivo by growing cells with isotope labeled metabolic precursors, while peptides are chemically labeled in vitro in CL. These two labeling approaches have distinct workflows and their own strengths and limitations. In a typical proteomics experiment, complex mixtures of peptides are separated on reversed phase liquid chromatography (LC) and sampled in real-time by the mass spectrometer for peptide identification and quantification. We propose to analyze mixtures of chemically and metabolically labeled peptides in single LC-MS runs, comparing each method’s quantitative accuracy and precision, and other factors, such as analytical losses from sample processing without errors introduced by stochastic sampling. We compare stable isotope labeling by amino acids in cell culture (SILAC) and reductive dimethylation CL by mixing equal amounts of peptides from each approach.Preliminary results indicate minimal differences between ML and CL in quantifying proteins (median of >2 peptide ratios). With individual peptides, however, CL showed 13% larger variance than the ML. We observed signal losses in CL samples compared to ML samples, and fewer quantified peptides and proteins in CL (6005 peptides, 897 proteins) than in ML (7448 peptides, 1059 proteins). We attribute the differences to the extra labeling step in CL, and will perform further analyses with ratio mixtures of heavy and light labeled peptides to clarify the source of variance. Our comparison of CL and ML will guide future optimization and applications of both quantitative proteomics labeling methods.

In aquariums and zoos across the world marine mammals are among the most popular exhibits. Caretakers strive to provide the least stressful and natural environments for the animals. Analysis of (steroid) hormones in excrement has proven to be an effective, non-invasive method. It allows animal keepers to monitor physiological health associated with reproduction and the stress response in captive animals. Prolactin (PRL) is a non-steroidal, non-tropic peptide hormone most commonly associated with milk production in nursing females. However, it has a multitude of normal physiological functions such as: regulation of the immune system, osmotic balance, angiogenesis, an indicator of parental care (in both males and females), sexual maturity in males, and near-term pregnancy in females. Chronically high or low levels of PRL have been associated with a number of ailments. For instance, impotence reduces the secretion of estrogens and testosterone. To date, no studies have been documented on prolactin PRL levels in captive northern fur seals, (Callorhinus ursinus), harbor seals (Phoca vitulina), or sea otters (Enhydra lutris). Using an enzyme-immunoassay (EIA) kit, previously tested only in human and elephant serum analysis, we investigated PRL levels of several samples collected from captive marine mammals (Northern fur seal blood serum, harbor seal saliva, and sea otter urine/fecal samples). Due to the helical structure of PRL, fecal samples were not expected to survive intact after transit through the digestive tract; therefore, were not expected to produce positive results. Here we report preliminary results of the EIA PRL assay on several different types of samples, as well as several longitudinal samples from the same individual, to show significant changes in this hormone over time. If detectable in urine, fecal matter, and/or saliva, this assay could prove to be a useful non-invasive method for determining health in captive marine mammals.

M dwarf stars are classified by their small radii and relatively cool surface temperatures. Their internal structures are known to be almost entirely convective, and this extreme convection causes a tangling of the stars' magnetic field lines. Upon realignment of the magnetic field lines, an incredible amount of energy is released from the star in what is called a flare. This research project is an ongoing observation of the flare activity on the M dwarf stars GJ1243 and GJ1245. Two months of flare activity was observed using the flux measurements made by NASA's Kepler telescope. The frequency, duration and types of flares were recorded and analyzed with the aid of the computer program "Flares by Eye." It has been observed that most flares have short rise times and long decay times, the intensities of which seem to follow a power law. Continued research on this topic will help us learn more about the physics behind the ignition of these stellar explosions, how the flares decay, and how the stars become less active as they age.

In the past few years, there have been some prominent sexual assault scandals in American sports, such as the Pennsylvania State University football and Duke University lacrosse scandals, as well as a variety of lesser known cases. I am interested in how the mainstream and alternative media depict sexual assault in sports, and what values and social norms are revealed by these depictions. Do media portrayals of sexual assault in sports change depending on the race, gender, and age of the victim and perpetrator? I predict that these portrayals will follow common racial and gender discourses in America by vilifying black men accused of sexual assault more than white men, and minimizing or normalizing the rape of adult women. The rape of children, especially young boys, is more shocking and therefore elicits a stronger media response. I will investigate this question through discourse analysis of news articles, news websites, and blogs, and through analyzing the images that accompany the articles and blogs. My research will be linked to the feminist concept of rape culture. It will also build upon work such as the article Innocent Until Proven Innocent, a discourse analysis of the Duke lacrosse rape scandal written by David J. Leonard. In his analysis, he concludes that after the accusation of upper class white male athletes by a black woman, the mainstream media framed the case as showing unfair prejudice against white men and unfair credibility given to the black woman’s story just because of her race. By analyzing portrayals of sexual assault in sports, I hope to shed light upon cultural assumptions, values, and stereotypes that surround sexual assault in sports, and in the United States in general.

Cardiovascular disease is the leading cause of death worldwide, and current treatments for heart failure are limited to slowing the disease progression or transplanting a donor heart. One potential approach to restore heart function is to transplant human embryonic stem cell-derived cardiomyocytes (hESC-CMs). An independent and similarly promising approach is to overexpress the enzyme ribonucleotide reductase (RR), the enzyme responsible for the production of the small molecule deoxy-ATP, which has been previously shown to improve contractility and diffuse between cardiomyocytes via gap junctions. We hypothesize that by overexpressing RR in hESC-CMs and then transplanting the latter into infarcted hearts, we will improve global cardiac function by increasing dATP content throughout the myocardium. To begin testing this hypothesis, I will test the efficacy of an RR adenovirus in hESC-CMs in vitro using quantitative PCR and immunostaining, and I will then correlate the subsequent improvement in fractional shortening following in vivo transplantation to the amount of successfully engrafted cells. To date, I have successfully developed an immunofluorescence staining protocol for RR. I am currently working on designing an immunohistochemistry protocol to identify graft tissue and stain for RR and GFP and localize RR in relation to the infarct. After confirming the protocol, I plan to apply it to the fixed rat heart slices to assist in the proof of concept of the transplantation of hESC-CMs overexpressing RR as a novel therapeutic method.

MML 53 is a system of young stars which, in 2010, was discovered to be an eclipsing binary. A detailed analysis of the brightness changes and velocity variations of an eclipsing binary provides precise measurements of the masses, radii, temperatures, and luminosities of two stars with the same age and chemical composition. Thus, eclipsing binary stars are extremely important astronomical systems that are used to test our understanding of the structure and evolution of stars. Despite their importance, young eclipsing binaries, like MML 53, are rare. We applied the PHOEBE (Physics of Eclipsing Binaries) software to the observed multi-wavelength time series photometry data of MML 53 to derive precise values for the combined radii of the two stars, the effective temperature of the secondary star, and reasonable locations for the starspots on both the primary and secondary stars. Using a Markov chain Monte Carlo analysis (eMCMC Hammer) we ran over 60000 PHOEBE models which has allowed us to explore correlations between various parameters and derive realistic uncertainties on the final fundamental properties of these two young stars.  

With any particle physics experiment, precision is paramount. In experiments with electromagnetic shields, the inherent magnetic field noise from the shield itself can impede the accuracy of high precision experiments. For this research project I designed a model of an electromagnetic shield to find the magnetic field noise of the shield; the results of which can be used to increase the precision of a particle physics experiment being conducted at the University of Washington, searching for a potential source of time reversal symmetry by looking for a permanent electric dipole moment of a specific isotope of mercury (the existence of which would suggest a source of CP-violation). The cylindrical electromagnetic shield was modeled in the finite element analysis application, COMSOL Mulitphysics. The model is initially configured with a single magnetic dipole arranged on the axis of symmetry of the magnetic shield. The accuracy of the model is then compared to an analytic solution found by S.-K. Lee and M. V. Romalis at Princeton University. After refining the model to reflect the analytic solution, the number and orientation of magnetic dipoles is changed, producing the first, second and third derivatives of the magnetic field noise of the shield being used. Accounting for the magnetic field noise will increase the sensitivity of the experiment being conducted.

Malaria is a parasitic infection due to Protozoa Plasmodium. This is a severe global disease with 250 million annual cases leading to 1-2 million deaths. The most virulent, P. falciparum, is responsible for severe clinical malaria and death. An array of anti-malarial treatments exist today, however parasites evolve continuously to develop resistance even to the newest frontline anti-malarial drugs. Previous studies in the Rathod laboratory have demonstrated that drug resistance can be generated in the lab and that some drugs can be utilized to characterize Accelerated Resistance to Multiple Drugs (ARMD) parasites, such as the laboratory strain Dd2, and non-ARMD parasites, such as the laboratory strain HB3. In the current study, we are using a cyclopropyl carboxamide (GSK 2645947) to select for resistant parasites. Cyclopropyl carboxamides are a chemically novel class of antimalarial agents identified recently and they prevent the growth of P. falciparum in the early trophozoite stages of the erythrocytic Plasmodium cycle. This project focuses on determining the conditions for the development of resistance against GSK 2645947 with Dd2 and HB3 by conducting a series of selection experiments utilizing different concentrations of GSK 2645947 and starting parasites populations. Unlike previous conditions which indicate that the Dd2 strain acquires resistance at a significantly higher frequency than the HB3 stain; the data from this study suggests that both Dd2 and HB3 strains respond similarly to GSK 2645947. Through this study, we can further understand the behavior of resistant P. falciparum parasites. 

Experimental studies have suggested that pain and dyspnea (shortness of breath) may involve the same affective experience. This association has not been explored in large community samples. We analyzed data from Cohort 12 of the Medicare Health Outcomes Survey, which measured subjective health status in 275,000 Medicare Managed Care recipients in 2010 and 2012. Dyspnea was defined by aggregating three questions (shortness of breath at rest, while walking one block, and while climbing stairs). Pain was measured by a question about how much pain interfered with normal work inside and outside the home during the last month. Both measures were dichotomized as high and low / none. We produced descriptive statistics to characterize the overlap of pain and dyspnea at baseline. We created regression models to measure the strength of the association of pain with dyspnea, adjusting for age, sex, race, education, and three potential medical causes of dyspnea (CHF, obesity and asthma). We estimated the likelihood of dyspnea and pain co-occurring at the two measurement points two years apart. 22.2% of participants without dyspnea had pain and 69.9% of those with dyspnea had pain. In an adjusted regression model, participants with dyspnea were 8.3 times more likely to have pain than those without dyspnea. Pain was strongly associated with the onset and the persistence of dyspnea. In this large sample of Medicare recipients, pain and dyspnea were very strongly associated, to the degree that they may represent different facets of the same experience. These results confirm experimental studies about the affective experience of both symptoms. These findings might help clinicians to appreciate better how patients experience pain and dyspnea. Additional research is needed to understand the exact mechanisms by which pain and dyspnea co-occur, and other risk factors for them.

In this paper I will do a cross-cultural comparison of attitudes towards chess in the United States and Uzbekistan to answer the question: “is chess a sport or a game and how does this vary in the U.S. and Uzbekistan?” Chess is considered as an official sport in Uzbekistan, where chess players are considered athletes. Therefore they go through physical evaluation and drug tests before participating in upper level tournaments. Meanwhile the U.S.’s view on chess commonly assigns it a status of a game, not a sport. This attitude comes from a popular belief that sport can only be a challenging physical activity, nothing less. This evidence shows that popular culture dictates the way we view sports and activities. The media impacts what categories we assign them, the amount of coverage of the topic, or in case of chess, lack thereof, and stereotypes about chess and people who play chess competitively. Through my positionality, analysis of media coverage, participant observation, and interviews I will examine the differences in cultural attitudes towards chess in both countries. The outcome of the research will shed some light on the understanding of cultural differences and values put on human activities in the time of massive globalization. As a result the data produced and analyzed through the research will be helpful in creating new types of activities related to chess and intellectual engagement for school kids that will in turn transform certain views on sports.

I am interested in discovering the effects of tough love motivation fed from coaches to athletes. I view "tough love" motivation as an expression used by one person (i.e. coach) to treat another person (i.e. athlete) harshly, with the underlying intent to benefit this person (i.e. athlete) in the long run. For my research, I will primarily focus on the mainstream college sports of men's basketball and football. I wonder to what extent tough love motivation from coach to athlete effects an athlete's performance, and what are the resulting repercussions for their coach-athlete relationship as well as for the athlete's future? To supplement my research, I relate to recent research conducted by Renata Baric and Valentin Bucik, entitled Motivational Differences in Athletes Trained by Coaches of Different Motivational and Leadership Profiles (2009). In investigating my research question, I will use the following anthropological methods: photovoice, discourse analysis, and interviewing. By my results, I intend to uncover the impact of tough love motivation in college level sports. I assume its effects are not only lasting but also detrimental for an athlete's performance and future. Depending upon my results, I hope to provide college coaches (present-day and future) with the encouragement to adjust their coaching profiles, if need be. Finally, I envision my research will serve as a resource for coaches to refer to, in their effort to shape, mend, and/or strengthen coach-athlete relationship(s), and consequently, in refining their athletes' performances not only in the game but also in their futures.

Accessibility to sports is not equitable to all groups of people. Individuals living in low economic and homeless communities do not have the same opportunities to sports, as those of a higher socioeconomic standing. This disparity can reinforce negative stereotypes because children especially will follow the expectations set for them. Having inequitable accessibility to sports is a concern of physical health, for sports promotes exercise. What are the economic barriers in accessibility to sports in the lower economic population? The methods I will use to conduct my research are interviewing, discourse analysis, and social mapping. I will interview members of these communities to learn about their accessibility to sports, as well as attitudes revolving around sports. I will also analyze the overall discourse around homeless and low socioeconomic populations. The method of social mapping will help to illustrate the physical accessibility to sports for these groups of people. The anticipated results will demonstrate how economic barriers such as, the cost of housing, are too great of an impediment to overcome. The populations of higher economic standings are often not aware of the extensive economic barriers. It is important to raise awareness about the inequality to accessibility, for everyone should have equitable opportunity to basic recreation. By creating awareness of sports inaccessbility, I hope to ultimately bring about change on a governmental level. This is a health disparity that demands attention. 

I am interested in examining the importance and values that super sports fans hold towards their favorite teams through the cultural and linguistic norms that are created and reproduced through social media outlets. Cultural and linguistic norms are the commonalities found within the actions, behaviors, and language tendencies of a particular group of people. For the purpose of this research, I will be looking specifically at the Seattle Seahawks “12th Man,” a group of football fanatics that consider themselves to be the Seahawks’ most loyal supporters. Fan cultures can be difficult to understand if you are not part of one, and are often devalued. Research done by Harrington Lee and presented in the article "A Life Course Perspective on Fandom,” discusses the concepts of fandom and how these identities evolve throughout the course of one’s life and are influenced by many factors (i.e. family, location, media, etc.). Social media outlets such as online forums, blogs, internet memes, Facebook, and Twitter have become a large part of the super sports fan communities and how they interact and communicate with each other, as well as how they are perceived by outsiders. While using these social media outlets as my main method of research, I will also be utilizing photovoice (analyzing photographs that portray the community and have symbolic meaning) and discourse analysis (words and language used in media that shape identity). This research is meaningful because sports fans around the world hold a great amount of passion, dedication, pride, and emotional attachment to their teams, and the influence this has made among their identities and cultures outside of sports is essential to note. The super fan culture is important to every “12th Man” and it will be interesting to see how social media continues to perpetuate these norms within the community.

Currently, one of the main challenges is the development of new technologies for the storage of energy. Hence, there exists a particular interest for a low-cost, safe, rechargeable battery with high capacity, voltage and rate capability. My project consists of developing a better understanding of the charge-discharge cycles and the factors constraining the electrochemical performance of the active material within a lithium-ion battery. Electrode efficiency depends highly on the active materials used. The chemical composition of the cathode material is one of the keys to optimize the performance of these batteries where three metal salts (Co, Ni & Mn) are combined under the following formula: (1-z) Li [Li_(1⁄3)Mn_(2⁄3) ] O₂ - (z) Li [Mn_(0.5-y)Ni_(0.5-y)Co_(2y)] O_2. Each metal has major downsides such as high cost, toxicity or reversibility loss, but they also offer high capacity or stability. In order to maximize the performance of the cell, an optimized battery must comprise a particular percentage of each metal. Under the supervision of Carolina Vinado, we have successfully synthetized several lithium-ion rechargeable coin cells which are currently being tested for reliability. For our first batch, we used an equivalent amount of cobalt and nickel, assigning the values of 0.4 and 1.6 for z and y respectively. The resultant formula is shown: Li_1.20Mn_0.54Ni_0.13Co_0.13O_2. The next phase of the project involves the modification of the cathode’s chemical composition for testing and future analysis. In addition, we are planning to analyze the surface of the cathode using Transmission Electron Microscopy (TEM). This facilitates the examination of the interface morphology, which after various charge/discharge cycles may develop defects on its surface. It is essential to understand these surface anomalies as they critically affect the battery’s ability to perform effectively.

The research question for my poster project will be, "Do media portrayals of the financial hardships NBA players endure impact youth who aspire to play at that level?" The thesis to go with the above research question will be that the media’s tendency to glorify materialism plays a direct role in not only influencing lavish spending among current NBA players, but also contributing to the prevalence in the cycle of former NBA players experiencing financial stress by sending a similar message to future NBA players. For the hypothesis of my research, I referred to the financial case study of Allen Iverson to make the prediction that expenses coming from taxes, supporting family members, child support, divorce, and lavish spending habits are the common factors that apply to the reported 60% of NBA players that struggle financially within five years after their professional basketball career is over. As means of conducting the research, the arguments presented by Todd Kendall’s Journal of Sports Economics were used to explain why it is prevalent for superstar athletes to struggle financially during or after their professional athletic careers. To list some of the common factors that often leads to NBA players filing for bankruptcy, the episode “Broke” from ESPN’s 30 for 30 series were also used as references. My third research method used were the discourse analysis from interviews of elite basketball players in both high school and college levels as means of determining whether or not these amateur athletes have been affected by the media's portrayals of professional basketball players. The findings from my research brought implications to the idea that the media plays a role in contributing to the apparent cycle of NBA players encountering financial struggles by glorifying materialism and affluence to these players from a young age.

Nanoimprint lithography (NIL) has become a widely used technique in fabricating nanoparticles using a top-down approach with several advantages over bottom-up chemical methods, including being able to precisely control particle shape, size, structure, and composition. Using NIL, synthetic antiferromagnetic (SAF) nanoparticles can be fabricated using multilayer deposition techniques, imprinting, liftoff, and particle release into water with limited defects. The particles can also be coated with a functional polymer so that they can be used in a number of drug delivery systems. However, common NIL techniques often make it difficult to add functional coatings to the particles after the particles are released in water. Deposition methods for different layers, as well as using silicon molds that introduce defects and irregularity in particle size are other pitfalls that can be corrected using a new approach. The nanoparticles (~300 nm diameter) were homogeneously patterned using a mold to etch disk-shaped nanoparticles on a silicon substrate with layers of titanium and magnetite deposited on its surface via magnetron sputtering to contribute to the antiferromagnetic properties of the particles.  The fabrication process is extensive and utilizes many clean room processes, including nanoimprinting, dry etching, undercutting, multilayer deposition, liftoff, and polymer coating, though polymerization was not explored in this study.  Following, release techniques were used to produce a monodisperse and homogeneously-sized sample of high moment, multilayer particles in water with high saturation magnetization and low toxicity. Final results to determine the effectiveness of the particles were determined by studying the magnetic properties of the nanoparticle solution sample in the presence of an external magnetic field. With antiferromagnetic and useful imaging properties, functional biomagnetics could become a highly useful material system. Future work in this field includes biofunctionalizing the particles to modify in-solution behavior and implementing them into various biomedical systems, depending on how small the particles can be made using NIL.

Poly(3-hexylthiophene) (P3HT) and 6,6-phenyl-C60 butyric acid methyl ester (PCBM) are model materials used to study and understand the performance of polymer solar cells. A critical design parameter in improving device performance is the structural morphology of the active layer. Traditional processing of organic solar cells involves the deposition of a P3HT/PCBM composite film from a common solvent and then post-processing treatments (i.e. annealing) to influence the extent of phase segregation and improve the percolation of electron and hole transport pathways throughout the film volume. Therefore, the electronic properties of the resulting solar cells are inherently tied to how the film is processed (e.g. choice of solvent, annealing temperature, film thickness). While process optimization has led to improvements in laboratory performance, it is challenging to extend the same principles to improve the performance of large scale roll-to-roll processes because deposition conditions vary significantly. Increasingly, researchers recognize the need for methods that decouple film processing from active layer structure and device performance. My research involves the synthesis of P3HT/PCBM composite nanoparticles (CNPs) in aqueous dispersion as a means to circumvent the dependence of active layer structure on the specific mode of deposition of the P3HT/PCBM film. I have synthesized CNPs with variable content of P3HT/PCBM and different preparation procedures while also controlling particle size. The characterization of these particles focuses on spectroscopy, small angle X-ray scattering (SAXS), dynamic light scattering and the performance evaluation of devices produced with CNP active layers. This project will tie device performance to CNP structure regardless of active layer processing, and assist in identifying CNPs with optimized morphology without the need for annealing or post-processing.

Botulinum neurotoxin type A (BoNT/A) has been extensively used in human masticatory muscles for cosmetic reduction of large masseter muscles, relaxing the muscles and reducing pain in temporomandibular joint and muscle disorders, and decreasing loading on the mandible. Multiple applications of BoNT/A over time is a clinically routine practice to reach the treatment goal. However, it is unknown how the muscle responds to multiple neuromuscular blockages by BoNT/A, and whether or not the injected muscle shows functional recovery differently after each application. This study was designed to answer these questions. Adult New Zealand rabbits were injected 3 times either with BoNT/A (n=13) or saline (n=5) in one masseter at week 0, 12, and 24. Non-invasive surface electromyography (EMG) of bilateral masseter muscles was recorded during natural mastication 1 week before the first injection and every two weeks thereafter up to week 35. Jaw movement was video-taped and synchronized with EMG recording for identifying the chewing side. Body weight was tracked weekly to examine the effect of BoNT/A on general health. From each of these recordings, 15-20 consecutive chewing cycles from each chewing side were sampled and analyzed for chewing cycle length, muscle mean and integral activity, and durations. The preliminary results indicate that the recovery patterns of the 11-12 weeks after each BoNT/A injection differed significantly, and both the chewing frequency and muscle activity 11 weeks after the 3rd injection (week 35) were close to those of saline animals and the baseline recorded before injection. These findings provide new information about the consequences of multiple applications of BoNT/A on masticatory muscles, and may lead to the better understanding and use of BoNT/A in clinical dentistry.

CO₂ separation from flue gases constitutes to nearly 40% of the CO₂ emission in the United States. Developments resulting from this work address factors key to increasing the transport properties in polymer membrane systems. In particular, this work explores method to engineer porous structure to enhance the selectivity of polymeric membrane. The polymer system of interest in this study is poly(l-trimethylsilyl-1-propyne) (PTMSP), a glassy polymer of extraordinary high free volume compared to conventional polymers. It is “reverse-selective” for CO₂ separation from flue gases such as nitrogen or hydrogen, i.e., transports CO₂ gas faster in respect to lighter flue gases. Based on prior studies that showed that enhanced transport properties for PTMSP if constrained to thin films, here we present our data for PTMSP if constrained in nanoporous functionalized anopore alumina oxides (AAO) “sieve” membranes. Impregnation was achieved via vacuum solution impregnation. The overall CO₂ permeability of impregnated membranes was found to be ~80,000 Barrer, which is almost two times higher than that of bulk PTMSP membranes. Selectivities of CO₂/Helium and CO₂/Nitrogen in impregnated membranes were found to be ~7.0 and 9.0, respectively; these are also noticeably higher than the corresponding selectivities of 6.0 and 6.6 found in bulk membranes. Furthermore, we investigated the temporal stability of these membranes that are notorious for their fast aging in the form of ultrathin films. The origin for physical aging is the collapse of the free volume. A two week aging study of PTMSP revealed a significantly slowed down physical aging process if confined in nanoporous AAO by about a factor of 20 over thin films. The exposure to the radial constraint within the pores helped stabilize the free volume and reduce the occurrence of free volume collapse.

Organisms can develop normally and thrive in dynamic environments. The interplay between the environment and the biomechanics of morphogenesis can help us understand how development operates in a changing world. Effects of salinity on blastula expansion in the sand dollar Dendraster excentricus were used to investigate interactions among the environment, development, and mechanics. Salinity fluctuations, which are common in Dendraster's habitat, affect embryonic cell size. The hyaline layer, an extracellular matrix layer closely associated with the outside of the blastula, is hypothesized to resist blastula expansion. Four models describing how the hyaline layer responds to blastula expansion were compared. In three models the hyaline resists expansion as either an elastic, plastic, or viscous layer. In these models, salinity-driven changes in cell size were predicted to cause changes in the ratio of blastocoel volume to cell volume. In a fourth model, the hyaline is a perfectly accommodating layer that allows the embryo to expand freely as cells divide in a single layer. In this model, salinity changes were predicted not to affect the blastocoel-to-cell-volume ratio. To test these hypotheses, Dendraster embryos were placed in either 25‰ or 32‰ seawater wells and switched to wells of either the same or the other salinity. In a second experiment, Dendraster embryos were raised in 32‰ seawater until the 16-cell stage, at which point a subset of embryos were moved to 25‰ seawater for one cleavage stage and then moved back to 32‰ for the duration of the experiment. In both experiments blastocoel-to-cell-volume ratios were not affected by the salinity treatment. These results suggest that the hyaline layer does not resist blastula expansion in Dendraster, thereby maintaining a constant blastocoel-to-cell-volume ratio.

Triadic eye gaze, a form of coordinated attention, is defined as an infants’ eye gaze shifts between another person, and an outside object or person. The current study examined whether 9-month-olds’ triadic eye gaze influences language learning; we specifically asked whether infants who engage in more episodes of triadic eye gaze show increased phoneme learning in a foreign language. The current project was conducted as part of a larger research endeavor, the Interactive Exposure study, which examined infant language learning in the context of peer social interactions. In the Interactive Exposure study, infants were exposed to a foreign language, Mandarin Chinese, through individual and peer language exposure sessions. In 12 sessions over four weeks the infants watched video clips of Mandarin Chinese. Infants activated the 20-second video clips by touching the screen. Infants in individual exposure sessions were in the room with only the touchscreen and their caregiver whereas peer exposure sessions consisted of two infants and two caregivers. Following exposure, infants’ discrimination of the Mandarin Chinese phonemes was tested via Conditioned Head Turn procedure and an ERP task. Fifteen 9-month-old participants from the peer language exposure sessions were selected for the current analysis of triadic eye gaze patterns. Using ELAN coding software, infants’ eye gaze was coded for looks to their own caregiver, other caregiver, other infant, and screen. Next, episodes of triadic eye gaze were identified for eye gaze patterns that consisted of looks between the other infant, caregiver, other caregiver and screen (e,g,, other infant – TV – other infant). Although coding and analysis are currently underway, we predict that infants who engage in more episodes of triadic eye gaze will show increased phoneme learning. If our prediction is accurate, this finding will indicate that language learning requires complex social interactions, such as triadic patterns of attention.  

Being the target of a positive stereotype (e.g., “women are nurturing”) can elicit many negative effects. The current study investigates the influence of positive stereotypes on women’s math performance and their identification with science, technology, engineering, and math (STEM) fields. In the present study, some women were the target of a positive stereotype before being asked to take a math test. Women who were positively stereotyped did not differ in their math performance compared to women who were not the target of a positive stereotype. However, positively stereotyped women felt that it was less important for them to do well in math than women who were not the target of a positive stereotype. These results suggest that positive stereotypes may lead women to identify less with STEM fields, an important predictor of success or retention in a field, and may be a factor in perpetuating gender disparities.

We are studying the roles of the p120-catenin protein in zebrafish development. p120-Catenin has a critical role in adhesion and migration by associating with E-cadherins and small, Rho family GTPases. The regulatory domain of p120-catenin contains 8 tyrosine and 8 serine or threonine residues that can be phosphorylated. To date, the function of these phosphorylation sites has been controversial. In cell cultures there is evidence that phosphorylation of 6 serine sites cause adhesions to recover quicker as well as form stronger connections. Some studies, however, claim that phosphorylation of these serine residues has no effect on adhesion. Tyrosine phosphorylation has been associated with nascent adhesions suggesting its role in adhesion formation, while its presence in carcinoma cell lines implies a role in cell motility. By selectively blocking phosphorylation at these 16 residues we hope determine the roles for the phosphorylation of serine and tyrosine residues in adhesion and migration of cells during embryogenesis. We mutated mouse p120-catenins at tyrosine residue 228 to phenylalanine, and at serine residues 252 and 268/288 to alanine via site-directed PCR mutagenesis. We inserted the DNA into PCS2+ vectors containing the fluorescent protein mcherry, and translated the mutant DNA into mRNA. We injected one-cell zebrafish embryos with an antisense morpholino RNA, complimentary to a splice-site region of endogenous zebrafish p120-catenin. Injections of this morpholino effectively knockdown the expression of newly translated p120-catenin mRNAs, and inhibit normal somite formation and axis extension during development. Co-injection of a wild-type mouse p120-catenin mRNA with the morpholino showed nearly normal development. Preliminary data suggests that co-injection of Y228F p120-catenin mRNA with the antisense morpholino RNA also produces nearly normal phenotypes. We will be testing the localization and function of the other mutated p120-catenins. This research could have important implications in development, treatment of some cancer types, and wound healing.
 

Since the introduction of DNA testing in 1989, post-conviction DNA testing has exonerated over 300 individuals in the United States who were wrongly convicted (Innocence Project, 2013). Evaluations of these cases have revealed that the single greatest contributor to these errors has been mistaken eyewitness identification (Garrett, 2011). Recommendations proposed to improve eyewitness decision-making in identification procedures include the use of unbiased instructions, the “appearance change instruction” (ACI; reminding the witness that the perpetrator may look different now than s/he did during the crime), and sequential presentation of lineup members. Past research on unbiased instructions and sequential presentation has shown that these procedures encourage more conservative decision processes which lead to fewer false identifications, but also fewer correct identifications. In contrast, recent research in our lab has indicated that the ACI appears to have the opposite effect; the instruction generates more liberal choices that lead to more correct, but also false identifications. Given the effects of these recommended procedures, the present research examines the relative influence of these three procedures on witness decisions in photographic lineups. A 2 (unbiased instructions: yes/no) x 2 (ACI: yes/no) x 2 (lineup presentation: simultaneous/sequential) between-subjects factorial design was used. Participants (N=121) viewed photographs of individuals and later had their memory tested with both target-present and target-absent photoarrays. Preliminary analyses indicate that, as expected, sequential presentation resulted in more conservative decision-making whereas the ACI produced less conservative decisions. There was no effect of unbiased instructions on decisions. This poster will present complete results on all participant data in relation to the main effects of and interactions amongst the ACI, unbiased instructions, and sequential presentation on witness’ decisions. These results will provide further information regarding the use of the ACI and its’ relative contribution to improving the collection of eyewitness evidence.

Bone tissue healing is problematic for more than a fifth of fractures, bone defects, massive bone loss, and osteoporosis and requires regeneration or implantation of bone. The introduction of a therapeutic bone strategy in the body elicits the foreign body immune response which is characterized by the inflammatory cell recruitment and subsequent encapsulation of the foreign material by fibrotic tissue. The formation of the fibrotic tissue is generated by a process in which macrophages adhere to the foreign material and fuse to generate multi-nucleated cells called foreign body giant cells (FBGCs). FBGCs effectively separate the foreign material from surrounding tissue resulting in sustained inflammation and reduced efficiency. This response, known specifically as the chronic inflammatory response, represents a very challenging complication for biomaterial fabrication in tissue engineering applications. Very recently, preliminary evidence has indicated that an optimal pore size exists in porous scaffolds that upon implantation result in the regeneration of a variety of tissues. Simultaneously incident findings in vivo have indicated that differentiated macrophage may have greater plasticity than previously accredited, and may transdifferentiate into various cell types. These advances may aid clinical treatments for bone repair by facilitating bone growth and avoiding stem-cell therapy controversies. The aim of the project was to design a porous scaffold to promote efficient bone tissue regeneration by enabling macrophage transdifferentiation. The proposed biomaterial synthesizes new information on optimal scaffold pore size and macrophage plasticity in conjunction with a well-studied osteoinductive cue, to both control the human body immune response and facilitate bone growth. The approach thus far has entailed an in vitro analysis of macrophage morphology and structural fabrication of the biomaterial.

Atmospheric carbon dioxide, the primary greenhouse gas associated with climate change, has been rising steadily since the beginning of the industrial era. Most C3 plants are likely to benefit from higher concentrations of CO₂ which is the substrate of photosynthesis. However, with more carbon dioxide available to photosynthesize, the growth of plants is often limited by other resources: notably, nitrogen. Recent research with specific strains of endophytes, bacterial or fungal organisms living within plants, shows positive symbiosis to supply the needed nitrogen to the host plants in elevated carbon dioxide scenarios. In this study, medium grain M206 rice (Oryza sativa) was inoculated with 9 strains of endophytes from native poplar (Populus trichocarpa) and willow (Salix sitchensis). The inoculated rice and uninoculated control were then put in CO₂ enrichment chambers to replicate current atmospheric and future elevated levels of carbon dioxide. I hypothesize that 1) the endophytes will give the rice plants an advantage in both ambient and elevated chambers when compared to the control because of the biologically fixed nitrogen the endophytes will provide, and 2) this advantage will be more pronounced in elevated CO₂ than in ambient CO₂. Tests concerning photosynthetic capacity, water use efficiency, and overall biomass will be used to determine significant differences. If conclusive, endophytes may be a means to capitalize on the benefits of increasing atmospheric CO₂ while curbing the negative impacts of excessive nitrogen fertilizer use by modern cropping systems on climate change.

With the proliferation of autoimmune diseases and cancer it is of increasing importance to discover new ways to utilize nanoparticles as carriers for the delivery of therapeutic agents. To achieve this aim, the trafficking of nanoparticles within dendritic cells must be better understood. When cells uptake foreign material, an innate immune response is triggered through the activation of pattern recognition receptors such as toll-like receptor 9 (TLR9). TLR9 ligands follow one of two pathways when introduced into a cell - one trafficking through early endosomes, the other through late endosomes. This research analyzes the intracellular trafficking of TLR9 ligands through the image analysis of dendritic cells. Using an imaging software, ImageJ, it is possible to plot the relative intensities of fluorescently labeled polystyrene nanoparticles coated with TLR9 ligands CpG 2216 or CpG 1826 as well as late endosomal markers Rab7 or LAMP2. By analyzing the co-localization of these intensity profiles, it can be determined if there is recruitment of the late endosomal marker to the endocytic vesicle of the nanoparticle. The recruitment analysis confirms which intracellular pathway is taken by these nanoparticles. A statistical analysis of a large sample size of nanoparticles will be performed. This research will shed light on how nanoparticles can be used as drug carriers by supplying critical information about the intracellular fate of nanoparticles coated with TLR9 ligands.

Extensive green roofs provide environmental, economic, and aesthetic benefits. Some benefits include: improvement of storm water management, conservation of energy, mitigation of urban heat island effects, reduction of noise and air pollution, provision and enhancement of habitat for urban biodiversity and sequestration of carbon. However, although green roofs may reduce the volume and velocity of storm water runoff, studies have shown that the quality of green roof runoff is decreased from higher levels of water-soluble nitrates and phosphorus being leached from fertilizers present in green roof substrate. Biochar, a by-product of the pyrolysis of organic materials thermally decomposed to produce energy, has proven to provide multiple environmental benefits including the reduction of pollutants from fertilizers, increased water-holding capacity, and potential carbon sink capabilities. This project will evaluate the impact biochar has on the quality of runoff leached from green roof soils, as well as water-retention abilities. Two different types of 7% (v/v) biochar, added to a green roof soil mix currently used in a permanent installation at the University of Washington, will be tested. 5 cm deep green roof trays with and without biochar will be planted with common green roof species: Allium cernuum (nodding onion), Festuca glauca (blue fescue), and Anaphalis margaritacea (western pearly everlasting), and unplanted trays with and without biochar will also be tested as controls. Controlled “rainfall” events will be conducted on the green roof trays, and runoff will be collected and analyzed for nutrient content and electrical conductivity. An appropriate substrate composition is essential to reap the full environmental benefits that extensive green roofs could provide. Amending green roof soils with biochar may be the key to improving storm water runoff quality and potentially mitigating a future source of water pollution.

In today’s world of globalization and expanding corporations, it is crucial that leaders act ethically to avoid the scandals, fraud, and financial collapses whose vibrations resonate internationally. Our research is guided by a desire to discover more successful strategies to teach ethics to business professionals and students. Unethical behavior spans an extensive range, all of which is financially costly for a company. Drawing from Ironic Thought Processing Theory, we hypothesize people will commit counterintentional errors when under a mental load, such as stress, fear, and distraction. In application to ethics, we hypothesize that participants directed not to think about ethics will consequently engage in less unethical behavior. Our hypothesis was tested with a sample of undergraduate business students, who were randomly assigned to one of three conditions. In the first two conditions, participants read passages about ethical principles, but one was instructed to reflect upon the ethics they read, whereas the other group was instructed not to consider ethical principles they read. Our third condition served as a control group, who read a similar length, yet irrelevant news article. Participants then attempted to complete 10 unsolvable math problems, requiring them to add impossible sets of numbers to 15, and report if they could successfully solve problems for extra cash payment. Results show that students who read about ethics, but are instructed not to think about it, engage in less unethical behavior when compared to the other conditions. Our study has broad implications. First, it is an application of the Ironic Thought Processing Theory in a new domain, widening its theoretical application. Second, our research will provide preliminary evidence to aid administrators to better structure business ethics curriculum.

Thermoelectric materials have the ability of converting wasted heat into electricity. The energy conversion efficiency of thermoelectric materials is determined by its figure of merit- ZT. The equation of figure of merit is ZT = S2T/ρκ, where S is the thermopower, T is the absolute temperature, ρ is the electrical resistivity, and κ is the thermal conducivity. Currently, existing homogeneous bulk thermoelectric materials have the highest ZT, at around 1.5. This project consists of designing high efficiency hierarchical thermoelectric composites with a ZT value greater than 2 by using energy filtering at interfaces to block the low-energy charge carriers, and, thus, increase the average energy transported per charge carrier. This results in an increase in thermopower(S) and, hence, an increase in power factor of ZT. Using solution-based solvothermal chemistry, which allows for control of the dimensions and morphologies of the nanoparticles through variations of the reaction parameters, we prepared low-dimensional thermoelectric nanobulk Bi2Te3. The surfactant-free scalable synthesis of Bi2Te3 provides quick and bottom-up synthesis with 90% yield. After these chemical processes, a dry nanoparticle sample will be consolidated by Spark Plasma Sintering, and turn into a pellet. The lowest sintering temperature determination will benefit to define the processing limitation in the further nanocomposite design. More comparison of the electronic transport properties measurements in bulk and nano Bi2Te3 will be carried out later. If the high-yield synthesis with doping capability can be achieved; also, if the processing limitation is known, it has high potential to achieve thermoelectric material with ZT higher than 2.

Although every cell in the human body has nearly the same DNA sequence, there are many different cell types performing different functions; for example, lymphoblast cells which differentiate into white blood cells or endothelial cells which provide a lining throughout the human vascular system. But cells do not always function as they should, for example, overproduction of white blood cells can be caused by lymphoblastic leukemia, a type of cancer. I intend to use data on the sensitivity of parts of the genome to deoxyribonuclease (DNase) digestion to explain the differences in cell behavior. Regions of the genome structure that are hypersensitive to DNase have already been shown to affect gene expression. I want to determine if portions of the genome which are mildly sensitive, or mesosensitive, to DNase play a role in cell differentiation. My hypothesis is that DNase can identify large scale regions, on the order of thousands of base pairs, that harbor cell type specific genes. I used Segway, software which uses a dynamic Bayesian network, to segment the genome based on DNase sensitivity data into regions of low sensitivity, mesosensitivity, and hypersensitivity on six different cell types. From my segmentations I removed the hypersensitive regions from considerations, and compared the low and mesosensitive regions to gene expression data. I found that regions Segway labels mesosensitive had higher levels of expression than low sensitivity regions. I expect to find that many of the regions responsible for cell type specific behavior are mesosensitive. If this is the case, I hope the results will be robust enough such that anyone with access to DNase data can determine what genes are active in a population of cells, enabling them to better predict the behavior of the cells. In furthering our understanding of gene regulation, we may better understand diseases such as leukemia.

Although eyewitness testimony is a critical element in criminal investigation, decades of research have demonstrated the fallibility of eyewitness memory. Among the reforms proposed to minimize eyewitness errors is the recommendation that investigators instruct eyewitnesses that “individuals depicted in lineup photos may not appear exactly as they did on the date of the incident”. Although expectations were that this appearance change instruction (ACI) would enhance the quality of the eyewitness decision, recent research suggests that the instruction may actually result in more mistaken identifications. Two theories were proposed to account for this finding.  The first suggests that the increase in mistaken identifications caused by the ACI is a result of witnesses mental transforming the individuals in the lineup to imagine what they would look like if they were more similar to the perpetrator.  The second theory proposes that the increased mistaken identifications are a product of witnesses simply becoming more willing to choose someone from the lineup as a result of being told that the true perpetrator may not look the same as their memory. The present study was designed to test the first hypothesis using a novel secondary recognition task paradigm. Relying on data collected from 120 college students, we evaluated whether the ACI encouraged witnesses to engage in a “mental transformation” of the lineup members when viewing a lineup. Part 1 of the study involved showing participants photographs of individuals and then testing their memory for those individuals with simultaneous lineups. In Part 2, witness’s memory for the lineup members themselves was tested. Overall, results did not support the “mental transformation” hypothesis.  However, given that participants performed at chance levels in the Part 2 task, it is possible that the null results are due to task difficulty.

Palladium is a part of the Platinum Group Metals (PGM), and is highly used as a catalyst in many applications such as in an automobile’s catalytic converter. It has also been successfully used for hydrogen gas sensing devices. Employing low-cost, efficient means to synthesize palladium nanowhiskers in the lab has been the focus of my research thus far. Hydrothermal synthesis and dislocation mechanisms have been used for the growth of palladium nanowhiskers using a palladium (II) chloride charge. The hydrothermal synthesis involved chemical reactions as well as thermal reactions in the growth of the nanowhiskers. In the dislocation mechanism, the growth of the whiskers is the result of the thermal decomposition of palladium chloride to palladium plus chlorine gas. Scanning electron micrographs from the first four runs of the hydrothermal synthesis showed little to no nanowhiskers. The first run of the dislocation mechanism grown samples is currently awaiting characterization. Future work for my research involves many more dislocation mechanism growths of the palladium nanowhiskers, as well as an attempt to use electrochemical deposition as a third technique in producing these whiskers. The application of these nanowhiskers in hydrogen gas sensing is based on the change in the conductance of the whiskers upon absorption of hydrogen. This allows for highly sensitive sensors to be made.

Synapses, the connections between neurons, are not constant in strength but instead are plastic, adjusting due to various biophysical rules. While various types of plasticity have been identified, the interaction of different plasticity rules in a network of neurons in not well understood. We consider the behavior of two experimentally observed forms of synaptic plasticity, homeostatic and spike time dependent plasticity (STDP), and seek to exploit these rules to tune a model neural network towards a state in which activity throughout the network maintains dependence on its inputs. Our network consists of firing neurons arranged in layers connected in a sparse, feed-forward manner. Reliable propagation of layer-wide firing rates without all neurons firing together (synchrony) is required to achieve graded transmission of input rates, that is, signal transmission. Plasticity is introduced to our network through mathematical learning rules. One of our learning rules, STDP strengthens causal linkages by increasing or decreasing synaptic weights depending on the timing of pre- and postsynaptic activity. STDP by itself is often unstable, causing synaptic weights to grow without bound. We therefore attempt to stabilize STDP with a homeostatic rule, adjusting the weights of all of a neuron’s incoming synapses in order to achieve some intrinsic firing rate. While current literature has focused primarily on the behavior of these rules in single neurons or in rate-based systems, we examine the interactions between these rules in a spiking, stochastic system with dynamic inputs, and their effectiveness in tuning such a network towards reliable rate propagation. Our hope is to shed light on the development of cortical networks able to perform successful computation.

Nitrogen (N) is an essential element of life that organisms need to make DNA and proteins. Unlike other essential elements such as phosphorous, nitrogen takes many different forms (NH₄⁺, N₂O, NO, NO₂^-, NO₃,  N₂) which are constantly cycling in the recently revised oceanic nitrogen cycle. One group in the Archaeal domain of life, ammonium-oxidizing Archaea (AOA), has recently been discovered to be a key player in the oceanic nitrogen cycle. In this cycle, Archaea oxidize ammonium (NH₄⁺) into nitrite (NO₂^-) in a process called nitrification. We hypothesized that different abiotic factors such as copper, light, and temperature regulate the physiology and depth distribution of the AOA. To test our hypothesis, we conducted ¹⁵NH₄⁺-oxidation experiments in July 2012 aboard the R/V Clifford A. Barnes in Hood Canal, Washington. Samples of seawater were filled in bottles, spiked with ¹⁵NH₄⁺, and incubated for 10 hours. We measured the oxidation of the ¹⁵N isotope using mass spectrometry, and compared the rates for control treatments to rates for treatments amended by copper (Cu), light, and other factors. ¹⁵NH₄⁺-oxidation rates were consistently low at the surface, increased until 30-40 m, and decreased to 115 m depth. Our experiments clearly showed light inhibition of ¹⁵NH₄⁺-oxidation, but the data did not clearly determine whether sunlight-produced peroxides inhibited AOA. Copper additions in Cu-deplete regions increased nitrification, possibly because the key enzyme in ammonium oxidation (amoA) is Cu-dependent. TETA, a chelator that binds Cu, did not show any effect when added during incubations. All together our results suggest that Archaea are Cu-limited, but may store Cu in small amounts. This project is part of a larger interdisciplinary effort to understand the oceanic microbes and the impacts they have on biodiversity and greenhouse gases such as N₂O and CO₂. Future studies in 2013 will extend these experiments to the open ocean.