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.

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

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.

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

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.

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.

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.

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.

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.

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

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.

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.

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.

 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.

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.

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

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.

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.

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

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

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.

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.

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

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.

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.

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.

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.  

 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.

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.

 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.

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

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

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

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

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

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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

 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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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

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.

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

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.

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.

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

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.

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.

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

 The 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.

On October 29th, 2012, King County Metro of Washington State implemented a set of congestion reduction policies, including the elimination of the Ride Free Area (RFA) in downtown Seattle, which was once an area in which any individual could ride a Metro bus without charge. The elimination of such a service stands to have a disproportionate impact on low-income and homeless individuals as many once used the RFA to reach social service agencies clustered in the downtown area and will now have to pay to reach those destinations. This research works to understand how different groups in the city have reacted and adapted to the end of the RFA (including activists, social service agencies, bus drivers, and low-income or no-income individuals) in order to theorize around (im)mobilities of homelessness in the city. I draw on qualitative interviews, participant observation, and archival research in order to build an inductive, exploratory analysis of how homeless individuals are adapting to this policy implementation. In doing so, I call attention to the need for further research on the intersections of homelessness, mobility studies, and public transportation policy in human geography.

The national government is relying increasingly on faith-based organizations for poverty relief, and especially to address homelessness. Some faith-based organizations are criticized for only addressing poverty’s symptoms and perpetuating stereotypes about spiritual, ethical, mental, and moral shortcomings of the impoverished. How can these organizations instead create spaces in which traditional assumptions about homelessness and community are disrupted, and new bonds of solidarity are created between people of different socio-economic classes? I seek to answer this question by focusing on how volunteers express and act upon their faith in the context of progressive faith-based organizations. I will conduct participant observation in two Seattle Christian faith-based organizations addressing homelessness in the Aurora area. I will also conduct interviews with volunteers and organization directors in order to examine how the theological foundations of these organizations may help volunteers become more invested in and involved with the entirety of their neighborhood community. This project will reveal how small-scale, faith-based work addressing homelessness can impact the communities in which they operate by shifting perceptions of poverty through cross-class exposure and an engagement with spirituality.

Current scholarship on geographies of encounter posits that situated encounters with difference, or bodies that represent difference, can create openings for new subjectivites, shifts in personal politics and new understandings of individual agency. This paper considers the possibilities of such encounters with difference in the context of the Real Change Cross-Class Advocacy Listening Circles. Listening Circles are community conversations that bring together individuals of different class backgrounds to reflect on questions of class and economic inequality. These conversations reach across class boundaries and differences to establish an open and respectful cross-class dialogue, one which is based on personal connection, empathy and understanding. Through interviews, participant observation and auto-ethnography, I investigate the Listening Circles as situated encounters with difference, where story-telling and shared experience actively (re)interpret and challenge the socio-political divisions which maintain class boundaries in everyday life. I consider how this model for disrupting class divisions in and through our everyday interactions might be applied to further the advocacy work of  organizations like Real Change in cultivating critical, caring and empowered social justice actors.

Due to the increasingly publicized socioeconomic disparities in coffee production, there is a high consumer demand for ethical bean sourcing. My research pertains to the transparency and functionality of Social Responsibility Initiatives (SRIs) within the coffee commodity chain, and their effects on power distribution. In particular, I investigate the SRIs of three Seattle based coffee companies: a multi‐national corporation, a medium‐sized coffee roaster and café, and a small local café. I analyze the incentives and drawbacks of these initiatives through semi‐structured interviews with employees, as well as how the initiatives influence business decisions and situate power distribution along the commodity chain. In addition, I conduct participant observation while volunteering on a Honduran coffee farm in order to understand the relationship producers have with their coffee. Using SRIs as a lens to political and socioeconomic factors that influence interaction within the coffee industry, I conclude with suggestions for ways in which a more equitable distribution of power may benefit coffee producers and increase transparency in SRIs.

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 research analyzes interviews and census data to explore the varying ethical perceptions of water use in Oman. For many populations living in the hyper-arid Arabian Peninsula, cultural and religious values have always required that people strictly limit their water use. Today after one generation of intense urbanization, Omanis still maintain these values of conservation, however they have also come to glorify water-intensive, urban lifestyles. Given this apparent contradiction, why has “development” been able to frame urban water use so positively, while contradictory perceptions of ethical water use remain intact? I argue that people do not change their water usage based on actual scarcity or ability to consume, but rather based on the symbolism that their surrounding community attaches to their resource use. In urban and rural Oman competing symbols have been introduced that support two very different water ethics. To reduce cognitive dissonance, Omanis compartmentalize each ethic in relation to different community settings and go through a process of switching their ethical codes when traveling between the countryside and urban centers. For much of the Middle East and other regions around the world, water scarcity is increasing dramatically, while urbanization and population expansion has produced increasing demand. Understanding how peoples’ perceptions of water are formed will be essential for policymakers as many regions of the world are beginning to face extreme water shortages and related socio-economic crises.

Biosolids are the treated sludge from wastewater treatment. Despite many scientific studies and tests that prove the environmental benefits and sustainable features of biosolids applications, there still exists ignorance, hesitation and aversion to utilizing recycled biosolids in society. In 2012, King County launched “Loop,” the county’s biosolids product brand. Loop was launched to increase awareness and foster positive perception toward biosolids recycling and its application. In this project, I developed a survey to assess public perception and knowledge on biosolids and their land applications (e.g. compost, fertilizer, etc.). The survey questionnaire has been developed using authoritative surveys that have been conducted previously with similar purposes as references. In addition, I pretested the survey to ascertain how well the questionnaire works. Pretesting and administering the questionnaire to a small sample of students can validate the survey. My target audience is the general public, but for the purpose of this project using a sample of students was more than sufficient. Preliminary results from the pretests identified problems in formatting or confusing language in the questionnaire. These pretested survey questions can potentially be utilized in future studies, such as in acquiring baseline data to analyze how much influence “Loop” branding has on public knowledge and perception of biosolids in King County.

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.

Urban farming is on the rise, not only in cities across the United States, but also around the world. From backyard gardens to large-scale community projects, people are returning to the land. This research explores the causal agents and impacts of this movement in Seattle, while also exploring why the expansion of community gardens and large-scale urban farming efforts have failed to progress as rapidly in Seattle’s sister city of Tacoma. An in-depth comparison will focus on the South Park area of Seattle and the Hilltop area of Tacoma. While much has been written about the ways in which urban agriculture has benefitted Seattle through its community gardens and large-scale urban farms, very little exists about why the same movements have not flourished in Tacoma. This project will employ a range of ethnographic methods, such as participant observation, in-depth interviews, and archival investigation into city policies and historical records. The data gathered will be used to explore the multiple and complex factors that influence—both positively and negatively—community based urban agriculture (CBUA) in the study areas.

In Washington State, the number of incarcerated individuals has nearly tripled in the past three decades, and almost half of all current inmates are repeat offenders. At the same time, in response to recent budget cuts, the Washington State Department of Corrections (WADOC) closed two correctional facilities, decreased their staff, and cut funding for offender rehabilitation programs. This problem is not unique to the state of Washington. The United States has the highest incarceration rate of any country- about 1 in every 100 citizens are currently behind bars- and bloated correctional facilities throughout the nation are feeling the impact of the economic recession. Now more than ever, it is apparent that we need to seek new, innovative approaches to imprisonment and rehabilitation. This study examines the potential of prison gardening projects to help address this need. I focus on the Sustainability in Prisons Project (SPP) in Washington, but include evidence from similar projects happening throughout America and abroad. My methods include first-hand observations of SPP’s gardening activities at Cedar Creek Corrections Center, interviews with program directors, and a literature review of comparable case studies and existing science on the benefits of human-nature interactions. I find that prison gardening projects in correctional facilities offer financial benefits to the state, shrink the environmental footprints of facilities, and create positive experiences for the staff and inmates. I conclude with a discussion on these benefits, including possible areas for further development of gardening programs in prisons and suggestions for future research.

How we discard speaks volumes about how we consume, which in turn speaks loudly about how we live and interact with the material world around us. Food waste is a special category of what we discard. It expresses our innermost beliefs and boundaries about aesthetics, health, and hygiene. Food scavengers, or pepenadores as they are known in Mexico, refer to the urban poor who pick through garbage in search of fresh produce either to consume on their own or to sell. My research begins with the basic question: what does it mean to be a food scavenger in Mexico City? Specifically, it examines the relationships negotiated between waste, want, and worth in the context of the food scavenging economy at an organic dumpster at Mexico City’s Central de Abastos – currently the world’s largest wholesale food market. What do the pepenadores know about valuing food that we do not know? What unseen and unsung roles do they perform in the urban food distribution network today? Employing anthropological methods of participant-observation, my research hopes to lay the groundwork for further qualitative analyses of the capital-scarce, labor-rich livelihoods of the pepenadores in Mexico City. Given that scavenging is often shorthand for marginal status, understanding this informal economy can assist in destigmatizing the work and its actors. Furthermore, this research aims to better illuminate our relationships with time, people, and food through its study of the pepenadores as a unique, entrepreneurial, urban class of ‘hunters and gatherers’.

Whether colonizers encouraged the growth of religion or attempted to stamp it out, they played a pivotal role in formation of religious movements within regions under their control. During the Russian colonial rule of Central Asia, a group of intellectuals began a modernist Islamist movement called Jadidism. This movement formed in response to the founders’ belief that Central Asian society was backward and primitive, as well as, in opposition of Russian colonial rule. Though Central Asia did not have a printing press prior to the Russian colonization, the printing press arrived with the Russians and enabled the Jadids to spread their ideas. Yet the low literacy rates within Central Asia caused the Jadids to push for educational reform. My research focuses on the influence of Russian and then Soviet rule on the Jadidist movement. Furthermore, it discusses the Jadids’ influence on education at the beginning of the twentieth century until today. I conducted my research by reading and analyzing texts on the issue and piecing together the information within a field which has been largely ignored by academia. My project attempts to draw attention to the gaps in the knowledge surrounding the Jadidist movement and its significance for the current education systems in Central Asia.

In the early seventeenth century, French Catholic missionaries arrived in the region of New France now known as Quebec intending to make Christians out of the Amerindian population. Over the next century and a half, the missionaries proceeded to build schools and hospitals and to establish their orders in the colony. Two of the Catholic orders that sent members were the Jesuits and the Ursulines. Both orders concerned themselves with the education and conversion of the Amerindians, mostly the Huron tribe. Through their missionary activities, they formed a nascent community of individuals with shared beliefs and purposes. A number of factors, including their geographic location, their connections to their founding orders back in France, and the particular social environment surrounding them caused the Jesuits and Ursulines to live and work differently from their counterparts in France. These differences caused the missionary community to develop a distinct identity. Using The Jesuit Relations and Allied Documents and the correspondence of Ursuline Mother Superior Marie de l’Incarnation, this research project examines the distinct identity missionary communities in New France developed. These sources record the daily activities of the Jesuits and the Ursulines in New France, while also revealing how individuals of each religious order understood their collective mission, which was characterized by interaction and cooperation between the orders. More universally, this project sheds light on how individuals form new communities and the way identities, even institutional identities, adapt to new environments.

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.

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

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.

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.

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.

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.

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.

Hot flashes affect 75% of menopausal women, leaving them with recurring flushing, sweating, skin blotching, and occasional anxiety, palpitations, and sleep disturbances. 20% of those affected describe the symptoms as “intolerable,” and current treatment methods carry too many side effects or are insufficiently effective. We propose the drug nalfurafine to prevent these symptoms. Nalfurafine has the distinct clinical advantage of being taken orally and targeting κ-opiod receptors outside of the blood-brain barrier, leading to minimal side effects. κ-opiod receptors decrease the activity of Kiss1 neurons, and we believe kappa agonists such as nalfurafine inhibit the Kiss1 neuron activity we hold responsible for hot flashes. To test this hypothesis, we injected nalfurafine in mice and collected blood and brain samples, expecting reduced levels of specific hormones and proteins associated with Kiss1 neuronal activity. Analysis of data collected in this study is ongoing. If our hypothesis is incorrect, we will have a new understanding of how κ-opiod receptors regulate Kiss1 neuronal activity. However, if we find evidence that nalfurafine inhibits Kiss1 neuronal activity, it may alleviate hot flashes in women, thereby providing rationale for clinical studies and potentially leading to a therapy that would improve quality of life for millions of women.

The most common rheumatological disorder found in children is juvenile idiopathic arthritis (JIA), a disabling disease of unknown etiology and with no cure to date. Previous studies have suggested autoantibodies of adult rheumatoid arthritis (RA) cross-react with oral pathogens, suggesting that oral infection could trigger arthritis. Severe gingivitis, an inflammatory disease of the gums, is present in 50-100% of adolescents, and may exhibit this same interaction with JIA. Costimulatory molecules on antigen presenting cells are induced during an inflammatory response to regulate T lymphocytes. Specifically, programmed death ligand-1 (PD-L1) known to be expressed during infection, is also highly upregulated in JIA. To test the hypothesis that PD-L1 expression is induced by oral pathogens associated with gingivitis, peripheral blood cells were isolated from JIA patients and healthy children. Gingivitis was scored by oral examination. PD-L1 expression was assayed on myeloid DCs and monocytes by flow cytometry. Preliminary data on a subset of subjects (n=7) showed a higher percentage of monocytes with PD-L1 in JIA patients compared to controls; however JIA patients had a lower density of PD-L1 per cell. There was no association between extent of gingivitis and PD-L1 expression. The results of this study could contribute to a new field of JIA therapy targeted at costimulatory molecules and oral hygiene.

 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.

Hawkmoths, Manduca sexta, feed mainly during early morning and late evening in low light conditions by hovering and tracking moving flowers. The variable lighting conditions in which the hawkmoths feed in nature allow for the perfect setting to examine how visual signal acquisition can affect the performance of motor controlled tasks. By varying the luminance levels, it could result in a change in the amount of time it takes for hawkmoths to react to visual stimuli. In other words, motion-sensing tasks, like tracking a moving flower while feeding, may vary with the background sensory environment. We tested our hypothesis with freely flying moths feeding from a robotically actuated artificial flower at a low luminance level of .3 lux and a high luminance level of 300 lux. Because the flower motion was composed of the superposition of multiple sine waves (0.2-20 Hz), we were able to examine how moths responded at different frequency levels, making it possible to reconstruct a performance pattern. The flower's movement was done in both the vertical and horizontal axes. By calculating the coherence at each frequency, gain, and phase delay, we discovered that moths reliably track at frequencies exceeding 5 Hz. As predicted, we perceived much larger processing delays from the moth's response to the flower's movement at lower luminance levels than higher. This processing delay corresponds to moths being able to perceive and react to visual stimuli 16ms faster at high luminance levels than low luminance levels. At low luminance levels, moths actually overcorrected by overshooting the flower's position at peak tracking frequencies (1-2Hz), possibly due to longer integration delays. Future experiments involve integrating two degrees of freedom by combining multiple axes. Background sensory environment significantly alters the performance of an ecologically-relevant tracking behavior as predicted from sensory neurophysiological mechanisms.

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.

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.

The JMS Diaries is a collection of 16 original diaries and 30 transcriptions of original diaries written by Joseph Mathia Svoboda, an employee with the Lynch Brothers’ Tigris and Euphrates Steam Navigation Company. He wrote his daily accounts of life on the Euphrates rivers between 1862 and 1908. The diaries give us insight into the everyday life of people in Iraq during the later half of the 19th Century. These diaries offer valuable cultural, social and anthropological perspectives about Iraq during this period and are invaluable to academia as primary source documents. The NEH-funded Newbook Digital Texts in the Humanities project works to transform such valuable primary source documents into digital texts in order to make them more accessible to scholars. In order to further this academic resource development, the project has been licensed with the Library of Congress as an independent publishing house. In this way, the Newbook project offers a collaborative environment in which individual projects can be inexpensively adapted, providing opportunities for individuals to publish academic works with less expense and inconvenience. It also enables scholars and the general public to access important texts and resources more easily. As undergraduate researchers, we work with these primary texts learning both research and digital archiving skills. We work through a five phase process consisting of transcribing, editing, analyzing, encoding and formatting each text. Each phase offers us a different challenge and requires a different skill set. Over the quarter our work varies from the physical transcriptions of the diaries to creating Perl scripted programs and using XML to markup and digitize the texts. Since beginning the project in September 2012, we have completed two diaries consisting of 400 pages each, and continue to work toward advancing this evolving, ongoing repository of primary source documents.

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.

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.

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.

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.

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.

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.

Internet pornography is a cultural and generational phenomenon. A majority of the academic studies involving pornography tend to focus on the physical and psychological responses to pornography. From a Communication perspective, Internet pornography provides an interesting area of study as both a form of media and a topic of discourse. This study analyzes textual user responses to Internet pornography via comment sections on the popular pornographic website Pornhub.com. Eight classifications of comments were developed to include comments of Praise, Self-Promotion, Self-Description, Fantasy, Advertising, Asking/ Answering, Critique, and Miscellaneous content. Publicly available user profiles were also coded in complement to their respective comments. Profiles yielded user reported Age, Sex, Sexual Orientation, Relationship Status, and more. Through classification and close textual analysis, this study attempts to understand how and why users “talk back” to their porn.

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. 

The progression and development of Singapore as an independent country has been a topic that draws in mixed reactions amongst the local and international community. As remarkable as Singapore’s economic growth has been, the avenues for political expression are limited. The goal of my project is to understand how the Singaporean public uses social media to voice their political opinions when significant restrictions and censorship are in place. Unlike in past decades, the rise of social media has allowed for a new outlet of voice in political opinions. I will examine closely if people can be empowered to voice their political opinions with social media tools. I will record two Skype interviews per age group with Singaporeans ageing from teens, twenties and fifties and using a wide range of online responses on selected social media sites such as Facebook and Twitter. This will allow me to draw the connections between the political voices of Singaporeans and social media. I want to compare the responses I get over different generations to examine whether the rise of social media change people’s attitude towards their political expression. Furthermore, I want to extensively look at the responses the people I interview and their reactions toward the comments made within social media sites. This would allow me to understand whether social media sites would be a platform to share and extent their views or an outlet to vent that otherwise serves no “actual” empowerment of their political views.

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.

The North American river otter, Lontra canadensis, population is widely distributed throughout the Northern Hemisphere, but has become increasingly rare in some areas due to anthropogenic effects. L. canadensis feeds primarily on shallow-water fish. Research has shown that L. canadensis feeds on crustaceans, insects, and birds. Feces are deposited in communal latrine sites along with scented mucilaginous material to mark territory. Foundational research was conducted between October 2012 and March 2013 in the Snohomish River Estuary to uncover the population distribution, predominant food sources, and presence of protozoa contaminants near Jetty Island at Everett, WA. Remote camera deployment recorded two individuals frequenting one of the latrine sites centrally located on Jetty Island, however, there have been no cameras deployed on North Jetty. Protozoan presence was not observed in preliminary samples. Thirty percent of collected samples are predominately fish scales and bones, while the remaining samples are crustaceans. Fifty-three percent of otoliths analyzed were Sebastes sp., which has been endangered since 2010. This research will help further understanding of the apex predator's behavior and predator-prey relationship in the estuarine system.

 In the desert Southwest, predation and monsoon thunderstorms are determinants of aquatic invertebrate communities. Recent research has focused on the potential of non-native species, like bullfrogs (Rana catesbeiana), to change communities into which they are introduced. Bullfrogs were introduced into Arizona in the mid-1900s and have established widespread populations that predate on and compete with native fauna. In an effort to control bullfrog populations, state and federal agencies have focused on the eradication of bullfrogs in Southeast Arizona – a biodiversity hotspot with many endemic species. Although the effects of bullfrogs on vertebrate species are documented, how and whether bullfrogs alter aquatic invertebrate communities remains uncertain. We examined how the effects of bullfrogs compare to the seasonal effects of the monsoon in influencing invertebrate communities. The objectives of this study were to 1) examine and quantify the effects of bullfrogs on aquatic invertebrate communities by comparing ponds with and without bullfrogs; 2) determine the effect of monsoonal seasonality by sampling invertebrate communities during the early- and late-monsoon, and 3) observe the interaction of bullfrogs and monsoonal seasonality to explore the relative importance of these two factors in shaping aquatic invertebrate communities. We hypothesized a lower invertebrate abundance and richness in ponds with bullfrogs. We expected to see taxonomic differences in community composition based on body size, dispersal ability, habitat use, feeding group, and defense. We anticipated smaller invertebrates and a higher number of defended invertebrates in ponds with bullfrogs. Finally, we expected that the relative abundance of high dispersing insects would increase in late monsoon samples. Preliminary analyses suggest that invertebrate abundance and richness is negatively related to the number of bullfrogs present at a pond. By studying the effects of bullfrogs on aquatic invertebrate communities, we can begin to understand and quantify the impact of this heavily managed non-native predator.

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.

Ongoing neurogenesis in the adult brain is a fundamental process of neural plasticity. The songbird is an established model for studying neuroprotection, neurogenesis, and neuronal turnover due to dramatic plastic changes in morphology and function in the nuclei that control avian song production. HVC, a region of the brain that times the production of song, doubles in size at the beginning of the breeding season, largely as a result of an increase in new neuron incorporation. In the nonbreeding season the song control circuit rapidly regresses in size. Within 7 days HVC regresses to non-breeding condition volume, and neuron number decreases by around 25% (> 68,000 neurons) via neuronal apoptosis. We tested the hypothesis that regression of HVC via neuronal apoptosis upon transition into nonbreeding conditions is tightly linked to proliferation of neural stem cells (NSC) in the nearby ventricular zone and changes in singing behavior. We also asked whether new neurons recently incorporated into the song control system were retained or lost through transition into non-breeding conditions. We rapidly transitioned birds from breeding to nonbreeding conditions and measured neuronal death and survival, NSC proliferation, and song behavior over a time-course of 28 days. We found that some but not all neurons incorporated into HVC during the previous breeding season persist at least 28 days into the nonbreeding season, suggesting that both new and mature neurons must undergo apoptosis during transition into nonbreeding conditions. Interestingly, we found that proliferation in the VZ was tightly linked to the amount of cell death occurring within HVC. We also quantified song degradation following rapid transition into nonbreeding conditions and correlated the observed changes in behavior to the cellular changes occurring within HVC. These findings demonstrate a relationship between cell death and neural stem cell proliferation.

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 early development, spontaneous waves of electrical activity propagate across many structures in the central nervous system. These waves are believed to regulate neuronal migration, physiological maturation, and synaptic connectivity. In the developing mouse cerebral cortex such waves manifest as increases in intracellular calcium and bursts of actions potentials that occur simultaneously in the majority of neurons in the cortex. We have developed a microfluidic multi-electrode array for use in the study of these waves of activity. This array records extracellular signals from twelve 50 micron microfluidic apertures that can also be used for focal electrical or chemical stimulation. The array is transparent and is compatible with simultaneous fluorescent imaging of intracellular calcium signals at single-cell resolution. We have used this array to study propagation patterns and mechanisms of cortical waves in postnatal (P) day 1 to day 5 brain slices. Waves initiate in the ventral (piriform) cortex and are detected by the array sequentially at each of the apertures placed along the ventral-dorsal axis of the slice, and by simultaneous calcium imaging as the spread of a fluorescence signal along the same propagation axis. The calcium signals outlast the electrical events by several seconds. We used a power spectral density analysis to identify the unique frequency components of different types of cortical waves. The signals from the dorsal regions show a prominent low-frequency oscillation late in the signal that is not present in ventral initiator regions. We have also used this device to study the contributions of the neurotransmitter GABA to network development by investigating a transgenic mouse missing the primary enzyme that creates GABA. Use of this device will lead to a greater understanding of the development of neural networks in the mouse cortex.

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.

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.

The Arctic is receving global attention as climate change transforms the region. With increased interest in natural resources and sovereignty issues, the security discourse in the Arctic is also changing. This Taskforce report seeks to understand Arctic security as the capacity for communities and states to build sustainable and resilient systems and to assert a representative voice, in arenas of diplomacy and negotiating power. The Taskforce group spent one week in Quebec City and Ottawa, Canada gathering research with scholars, government officials, and Inuit leaders. This report combines relevant literature with these engagements to understand the evolution of Arctic security. Aspects of security discussed include: the Northwest Passage, devolution of resources, Quebec’s Arctic policy, tourism, food security, biodiversity, homelessness, education, the Arctic Council, and China’s role in the Arctic. Each chapter provides specific policy options that together form a model for building capacity for communities.

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.

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.

Evaluation of the current Israeli-Palestinian conflict by analysis through a historical framework, centered on the events and ideologies of the anti-apartheid movement in South Africa in the early 1990’s, provides a template for enhancing human rights efforts in the present-day Middle Eastern crisis. Comparison of this conflict against a successful internal political shift to promote peace presents the foundation for research in which the synergistic combination of knowledge gained through human rights coursework applies to a current humanitarian dilemma. The cooperative relationship between theories of international studies, historical analysis, and political structural components will help contribute to the ongoing dialogue about the paradigm shift in Israeli-Palestinian relations that is so urgently needed. Methodology for this research relies heavily on the historical framework of the grassroots movement to overthrow the apartheid system in South Africa. Theories of international and national conflicts from coursework in the Jackson School of International Studies, as well as firsthand accounts of the state of affairs in the Middle East gathered through field research in sociology, contextualize the problem within a larger historical and analytical picture. The implications of this research therefore centers on human rights promotion and enhancement with regards to a modern-day conflict. This critical investigation allows for active understanding rather than passive scholarly observance of a deadly and drawn-out battle for land, identity, freedom, and dignity.

Secular institutions responsible for decision-making are often required to make moral decision that affect groups that live by other moral and cultural rules than their own. For instance, human rights and development organizations have worked to eliminate Female Genital Mutilation, seen as harmful and oppressive by these organizations, but as an important cultural practice in some parts of Africa. The law-makers involved in Obama Care required that employers to provide employees insurance coverage for contraceptives, even though some religious organizations believe contraception to be a sin. To understand these conflicts, I propose that these decision-making bodies must be seen as entities with moral and cultural traditions of their own which must be taken into consideration. Hence, decisions made can be seen as two groups of people with different ethics and cultural practices—one of which proposes to act on or control the other. The situations I research are those where there is no ethical common ground between the two (or more) parties on a specific issue, and where the issue cannot be side-stepped by non-action, but requires a decision. In such cases, a third ethic, an ethic of decision-making must be used. For institutions that will eschew coercion, there are a number of ethics that can be employed: an important one, both because of its scope and its claim to universality, is the United Nation’s Universal Declaration of Human Rights (UDHR) which, as its original drafters intended, was free of a metaethical stance, intending only to declare the most basic rights necessary for insuring human dignity and freedom. Universal human rights is an important ethical framework for secular decision-making in cases where the moral stances of the two parties cannot be reconciled.

In her letters to Descartes, Princess Elizabeth of Bohemia asks a question that many modern philosophers have tried to answer: "Given that the soul of a human being is only a thinking substance, how can it affect the bodily spirits, in order to bring about voluntary action?" Here Elizabeth questions the very nature of the relationship between mind and body. It is not easily understood or explained how a nonphysical substance can affect or be affected by a physical substance in order to create both sensations and voluntary movement. Through the attempts to find solutions to this problem, it becomes clear that the true problem lies in Descartes' separation of the nonphysical mind and the physical body within the idea of a person. Drawing from Spinoza, Locke, and Hobbes, I argue that mind and body are simply two ways of understanding a single, indivisible human being.

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.

Mikhail Bakhtin’s concept of dialogics, emphasizing open-endedness and multi-referentiality, has emerged as a central construct for analyzing how literary texts are read. Rather than reducing terms into singularities, dialogics allows for multiplicity and simultaneity. In film, a dialogic structure is an equally impactful format that has the power to problematize a narrative. Through my research and an exemplification of theory, I will demonstrate that the development of multi-referential and dialogic narrative structure is both ethical and activist: encouraging conversation and thoughtful consideration of multiple positions simultaneously instead of monolithic acceptance of a single, dominant narrative. The ambiguity introduced by the dialogic structure challenges the traditionally held binaries and dichotomies which govern so much ethical discourse. The rational subject operating within a system which places conceptual priority on a-priori knowledge and deemphasizes particularized knowledge is oppositional to feminist ethics which prioritize the personal over the a-priori rational, reclaiming those traits held as traditionally feminine as the sphere of ethics. These two systems mutually reinforce a binary dialectic and generate a contextual/non-contextual, emotional/rational, female/male dichotomy. I argue the works of Nussbaum and Kant (exemplars of these philosophies) serve to generate false dichotomies. A dialogic discourse allows for formation of the self endowed with such qualities as allow marrying context to ratiocination without placing undue priority on one over the other, generating a conception of self which is intersectional and better able to work within ethical constructs in the real world without falling back on restrictive definitions of normativity which cannot extend to reality. Dialogics does not propose a new dialectic, thereby reinforcing this dichotomy, but rather generates a polyphony of foci and meanings, allowing for a nuance and simultaneity of discourses permitting one to fully negotiate the complexities of ambiguous situations without the impulse toward reduction which often threatens to accompany resolution.

 Contemporary theorists are still coming to terms with Michel Foucault's conception of power structures and how those relate to biopower, the State's control over its subjects. My research focuses on what Michel de Certeau calls heterology (logic of the Other) present within these structures. I use the theoretical work of Certeau to examine heterology and tactics (everyday ways of "making do") as well as Bruno Latour's framework of Actor Network Theory to chart the movement of actors within the structure. Latour also explains the "mediation" that happens, where the actor itself is changed through the process of action. It is this mediation, as part of an actor-network, that I will use to describe the photographs of Abu Ghraib, detailing the complex assemblage of military personnel, detainees, and even the non-human agency of the cameras themselves. I explore the contextual "framing" of the photography through a close reading of a number of the photographs released, an examination of their material reproduction through various news media (news outlets, Government publications, and the internet), and their reception in both American and British cultures and Iraqi culture. In addition, I use a number of secondary sources, such as the documentary film Standard Operating Procedures and the White House press release, to understand how the production and reproduction of these photographs might serve political reasons, either complicit with or subversive to the motives of State structures of power. Preliminary results suggest that the actor networks at Abu Ghraib engaged in politically subversive behavior through an intuitive combination of competing ideologies that norms of the State could not fully capture. The "framing" of the photographs both ideologically and culturally served to portray messages that the American Government, at the time of the photographs' release, could not have anticipated or intended.

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.

Metallothionein (MT) is produced by benthic invertebrates in response to metal pollution, and as such provides a valuable tool for monitoring metal contamination impacts in Puget Sound. In this study, we explored the degree of correlation between MT in benthic invertebrates and metal contamination both in the field and in the lab. Seven stations were sampled, including five in Commencement Bay, an industrial harbor, and two control sites near the less impacted Nisqually delta. MT concentrations in collective samples of benthic worms were analyzed and compared with metal concentrations (Cd, Cu, Pb, and Zn) found in sediments to determine the benthic response to metal stress in situ. In addition, sediments were collected from all stations and used in a lab validation study exposing clean polychaete worms, Alitta virens (formerly Nereis virens), to metals in the sediments for 21 days in order to determine how the proteins develop in a controlled environment absent of normal adaptive responses. Both the collective sample of worms and Alitta virens were analyzed for MT concentrations using a published spectrophotometric method. Results indicated that average MT concentrations for in situ worms and metals concentrations Cu, Pb, and Zn at the Point Defiance station were higher than other stations. This is suggestive of a relationship between metals in the sediment and MT in the worms, although in some cases, the pattern is complicated by the bioavailability of metals as reflected with grain size. Quantifying MT allows for measurement of the bioavailability of metals, which can be difficult to quantify in other ways, such as directly sampling sediments. The use of MT in marine worms as a bioindicator of metal stress may be beneficial in monitoring the health of Puget Sound.

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.

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.

More than a millennia after the earliest-known version was committed to text, fairy tales continue to occupy our bookshelves and airwaves. The current popularity of fairy tale-based television programs such as Grimm and Once Upon a Time offer continued proof that the appeal of these tales is not lost on 21st century audiences. Beginning with the rise of fairy tales in the ancient cultures of China and India, this paper will follow their journey through Asia, long before these tales reached their traditionally recognized European birthplace. In this examination of the multicultural variations of a single tale—the Cinderella story—we begin to understand just how these stories have evolved. By means of textual analysis, I will examine the familiar French literary version (Perrault) of Cinderella using V. Propp’s morphology of “function” and character, and semiotic theories advanced by Scholes (1982) and Berger (2000). I will then apply this structure to three television adaptations of the Cinderella story: the 1957 live-television broadcast of Rodgers and Hammerstein’s Cinderella, the 2006 pilot episode of ABC’s Ugly Betty, and—adding a global aspect—the 2007 Mexican production of La Fea más Bella. Likewise, I will examine the ways that the Cinderella tale has retained its relevance as it crossed cultures—a literary example of globalization through cultural flow—and how the sharing of its ideas has contributed to its historical persistence.

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.

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.

Methylotrophic bacteria have long been recognized for their metabolism of reduced single carbon (C₁) compounds. Their potential for biotechnology and the occurrence of C₁ metabolism in all organisms signify their importance on an industrial and fundamental scale. Currently, mechanisms used by methylotrophs to regulate and reset their metabolic network in response to perturbations are not well understood. Previous studies suggest abrupt shifts in nucleotide levels drastically affect growth. This project will examine how nucleotide ratios correlate with carbon flux in Methylobacterium extorquens AM1. Once C₁ compounds undergo serial oxidation to formate, carbon flux is partitioned for further oxidation or assimilation. Two reactions involved in C₁ oxidation are known to generate reducing power: (1) the dehydrogenation of methylene-dH₄MPT into methenyl-dH₄MPT catalyzed by MtdA or MtdB and (2) the oxidation of formate into CO₂ catalyzed by Fdh1 or Fdh2. Genetic studies demonstrated differential phenotypes in which mtdB fdh1 grew similarly to wild type while mtdB fdh2 grew worse relative to the mtdB mutant strain. One possible explanation is a global decrease in NADH production offsets the delicate balance of intracellular nucleotides required for an already reducing power-limited mode of growth. To explore this hypothesis, I will conduct experiments to: (1) quantify the levels of NADP⁺, NADPH, NAD⁺, and NADH in WT, mtdB, mtdB fdh1, and mtdB fdh2 and (2) manipulate nucleotide ratios with overexpression and deletion of the pntAB and udhA genes. These genes encode for membrane bound (PntAB) and soluble (UdhA) transhydrogenases capable of interconverting between NADPH and NADH. Since mechanisms exist in other bacteria to alter nucleotides pools to meet metabolic demands, a similar mechanism can be predicted to operate in M. extorquens AM1. Success in this project will lead to better understanding of how cells balance reducing power and energy for oxidation and growth, ultimately leading to improved biotechnological utilization.

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.

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.

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.

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.

Male circumcision has been found to lower the risk of heterosexual transmission of HIV infection in men by up to 60%. In efforts led by the Ministry of Health and Child Welfare in Zimbabwe in upscaling male circumcision, the new Prepex™ device, a double plastic ring that necrotizes the foreskin, has been suggested in resource poor settings as an alternative to surgical methods of circumcision. For a comparison of the Prepex™ device vs. surgical methods psychosocial behavioral interviewing and clinical safety testing was conducted on a group of men in Zimbabwe (N=240) at three intervals: immediately prior to the procedure, and at two weeks and three months following the procedure. This provided a measure of the clinical safety of both methods as well as the effects on daily living, sexual relations, and perceptions regarding the procedure. In both study arms positive attitudes increased throughout the trial, with satisfaction of 'very' or 'extremely' satisfied with the procedure at 95% in the surgical group and 88% in the device group. Other than pain being slightly more of an issue in the device group there were few differences among expectations, perceptions, and experiences between the two groups. This study suggests that the switch from surgical methods to Prepex ™ device will not change the psychosocial barriers limiting the current male circumcision programs in Zimbabwe.

Ecofeminism is a movement which shows how the marginalization and subjugation of women by men parallels the domination and exploitation of nature by human beings. Interdisciplinary at its inception, ecofeminism draws from a wide range of fields including philosophy, ecology, english, and gender studies. Sometimes though, the values of these different fields conflict with one another in ways that question whether some theories can (or should) be put into practice. Queer ecocriticism, pioneered by Timothy Morton, is one such theory. Queer ecocriticism attempts to fuse ecological criticism with queer theory to challenge essentialist views of women and nature in existing environmentalisms. In Queer Ecology, Morton suggests that subjects only appear to fit neatly into stable categories like “women,” “humans,” and “nature” because we fail to perceive them on larger timescales. The best approach to environmentalism, he argues, is one which contemplates “ecology's unfathomable” and “almost unbearable” intimacies—that is, one which recognizes our world as a cacophony of interrelated, messy, and untotalizable “strange strangers” rather than a mere collection of discrete beings who can be categorized. What this “contemplation” means in practice, however, is unclear. Moreover, queer ecology appears difficult to reconcile with environmental activism, which often organizes strategically under essentialist labels like "women" or “human beings” to protect "nature." So what is the interdisciplinary-conscious ecofeminist to do? Drawing from the work of ecofeminists Sherry Ortner and Val Plumwood, queer theorists, and environmental activists, my project investigates ways in which ecofeminist activism might incorporate queer ecocritical theory into practice. If it’s true that, as Morton says, ecofeminism “is grounded on binary difference and [is] thus unhelpful for the kinds of difference multiplication that is queer theory’s brilliance,” activism informed by queer ecocriticism might be able to achieve its aims without relying on problematic, essentialist views of women and nature.

Digital inclusion is the ability of individuals and groups to access and use information and communication technologies (ICT). Vulnerable populations that experience barriers to ICT include low-income families, residents of rural communities, seniors, disabled citizens, at-risk youth, immigrants, refugees, and people of color. Despite its thriving agricultural industry, the Yakima Valley in South Central Washington is designated as an economically distressed area with low wages, significant unemployment, and high poverty levels. The area's agricultural emphasis attracts a large population of migrant workers who are generally perceived to be information poor, meaning they face major challenges with finding and using greatly needed everyday information. Little research in ICT access for migrant populations exists because differences in language, culture, and other factors make migrant workers and their youth a difficult population to study. This research involves reviewing literature on the information ecosystem of the Yakima Valley, interviewing relevant school district administrators of Educational School District 105 in South Central Washington, and evaluating current educational technology access strategies within the region. Five to ten administrators from ESD 105 are interviewed in a semi-structured fashion for their insight into the current ICT landscape of their schools. All conversations are recorded, transcribed, and coded to transform qualitative data into a standardized format for interpreting recurrent concepts. By way of grounded theory, this research paints a clearer picture of current digital inclusion efforts towards migrant youth and provides transferable recommendations as to how they can better participate in today’s digital economy.

In The Left Hand of Darkness by Ursula LeGuin, the humans inhabiting the planet “Winter” are genderless, and through the monthly phase called “kemmer” choose to develop either male or female sexual reproductive organs. With one equal gender either member of a relationship can choose pregnancy, and “no one is quite so thoroughly ‘tied down’ here as women, elsewhere, are likely to be- psychologically or physically.” Since there is lack of gender subjugation on Winter, nature is not regarded as being connected to the womanly tasks of nurture and reproduction as it is here on earth. Nature is not viewed as an “other” and is instead an active part of a human ecology rather than something to abuse or command. In similar regard: “Winter is an inimical world; its punishment for doing things wrong is sure and prompt: death from cold or death from hunger.” On Winter humans better survive by working with Nature and not against it. Reading this novel as an ecofeminist text involves uncovering details regarding the relationship between feminism and ecology. Viewing the planet Winter as a utopian example of the absence of dualistic genders provides a fascinating scope into what the impact of a non-gendered society has on its environment: a planet where humans advance slowly and cautiously with respect for their natural world. This project examines the comparison between this model and that of ours on Earth. Winter’s slow technological development is accented by its low level of significant cultural change, whereas on Earth technology develops rapidly as culture blends, infuses, and diversifies. From this example I find that dualistic gender, or the lack thereof, greatly impacts not only the behaviors of a society, but determines its rate and quality of technology, egalitarianism, and ecology.

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.

This project examines new visual representations for spatial and temporal work tasks in the commercial flight deck. Utilizing integrated map and timeline views, we are exploring an alternative design concept for programming and replanning flight routes with the flight management system. In the current design of the flight management systems, pilots must manage a set of input devices and paper printed flight plans to program the flight route using numeric way points and time markers. Rerouting due to weather or inflight emergencies requires verbal coordination with air traffic control and the flight company. A new integrated interaction design approach to these interface operations could potentially lower the cognitive overhead required for these workflows and provide pilots with a better contextual understanding of their situation. When provided with clear information on the context of the plane and status of the mission, pilots can make better decisions during replanning and emergency scenarios. The presented research applies a human-centered design approach to the commercial flight deck and flight information displays that supports the interactions between pilots and the aircraft. Extensive video prototyping examines new directions for possible flight plan representations.

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.

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.

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.

 This research discusses the investigations of a research project regarding the likelihood of adoption of particular mobile payment platforms by University of Washington students. Mobile payments have been around for several years now, but users have been slow to adopt the technology. Recently, companies are beginning to invest in this technology despite its previously slow growth. College students are also usually at the forefront of technology adoption, but this has not been the case with mobile payments. This research project details our investigational study of determining which type of mobile payments platforms UW students are most likely to adopt and will continue as follows: First, we discuss background information to define some key terms, concepts and technologies. Next, we detail the methods that we used to find the answer to our research question. These methods included research methods often used for usability research including focus groups and surveys. We report on the findings from our investigation at the end of our research paper. Given the data and analysis of our research, our findings have the potential to inform both consumers but most importantly mobile payment providers.

 Our capstone project discusses a redefinition of a social bar experience. Opening and closing tabs at bars is stressful, time consuming and frustrating. Today, the process to order a drink at a bar is tedious: wait in line, order a drink, then hand a bartender a credit card to open a tab. Stand in the same line for each subsequent drink as well as to close the tab. This process is time-consuming and detracting from a customer’s bar experience. With the imminent rollout of mobile payments as a ubiquitous brick-and-mortar payment method, we identified an opportunity to utilize mobile payments technology to develop an elegant solution to order drinks at a bar. One of our goals is to eliminate as much friction from the experience as possible, which will allow users to better enjoy their drinks with their friends. The service will handle ordering, paying and tipping for menu items, as well as offer additional value-added features that are only possible when customers order and pay for drinks from a mobile device. While we will focus on the bar scenario, our technology platform will be applicable to several other verticals including restaurants and stadium venues. By employing the user-centered design process supplemented with usability research, we seek to create a solution that redefines the bar experience.

Everist Genomics reports, "If ~20% of Americans currently diagnosed with hypertension reduced their systolic blood pressure by 12.5 points it would reduce heart disease risk by 21%, stroke risk by 37%, and risk of death from heart disease or stroke by 25%, and generate >$75 billion in annual cost savings for healthcare payers and employers." Current procedure for health monitoring requires that patient be monitored by an in hospital or out-patient basis. Monitoring the daily variations involved with everyday activity can produce a more complete and exacting type of diagnosis and prognosis for health care professionals, as well as providing important information to the health compromised, regular, or health conscience individual. Real Time Health Monitoring System (RTHMS) is a conceptual idea that would benefit people of all ages and health categories. The interface would be worn against the skin and reports encrypted real time health information to a secure on-line database through a cellular data network. The user would have administrative abilities to personal health records and has the only authority to grant access to suitable parties. Depending on the application, monitoring scenarios could include detecting patterns in pre-seizure activity, and monitoring of blood chemistry and distribution of medication. Real time monitoring may give physicians information for earlier diagnoses prior to the onset of illness. Patients suffering from addiction difficulties may be presented with the monitoring option as a way to avoid incarceration and remain productive. The concept is sound, the finance required for implementation is tricky, but could be done creatively through mass markets and stylized design. The benefits that could be achieved by the Real Time Health Monitoring System are obvious and realized through the saving of time and money in the treatment of health issues, and also could provide significant health safeguards and embellishments for the individual as well as an individual’s interactions with society.

While timely and specific diagnosis can enable optimal treatment of patients, modern-day diagnostics are not optimized for the needs of low-resource settings due to: 1) low sensitivity, 2) slowness in providing results, and 3) dependence on electricity, chemical reagents, and trained clinicians, at a high cost. The result is frequent poor diagnosis, which can increase the rate of negative health outcomes such as patient mortality and evolution of drug resistant pathogens. There is therefore a pressing need for diagnostics that are sensitive, accurate, rapid, and inexpensive. The field of synthetic biology holds much promise in this area due to the ease and affordability of genomic re-engineering and replicating of single-cell organism like Escherichia coli and Saccharomyces cerevisiae. To address this need and opportunity, we have engineered a prototype detector in E. coli that utilizes two DNA-based modules to sense a low concentration of target analyte and produce a large output response. Module 1 detects small concentrations of target analyte by switching cells from an ON to OFF state and Module 2 significantly amplifies an output signal by enabling ON cells to grow rapidly. By seeding these cells in an environment with a non-detector strain that grows faster than OFF cells but slower than ON cells, we hope to demonstrate that this genetic logic enables a detector strain that conditionally and significantly takes over the population after detection event. This approach holds much promise for a multiplexed diagnostic, as different strains of detector cells sensing a specific pathogenic marker could be co-cultured, with the result that only the cells that detect a target analyte grow. As a cell that is a diagnostic could be easily replicated and simple to use, this approach could be extremely feasible for a low-resource setting.

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.

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.

 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.

Bacterial antibiotic resistance is a rapidly growing concern for global health care. Typically, clinical antibiotics work by targeting essential pathways involved in bacterial metabolism or growth while leaving host cells unaffected. There are three basic mechanisms of bacterial resistance: (1) bacteria can chemically modify the antibiotic to a non- toxic form, (2) pump the antibiotic out of the cell, or (3) modify the enzyme or pathway targeted by the antibiotic. The second two mechanisms can be thought of as being selfish, as the mechanism doesn't directly help the community on a macroscale. However, the first mechanism helps the whole community, thus it can be thought of as cooperative. We hypothesize that the class of resistance mechanism, i.e. cooperative or selfish, is the primary factor that determines the geometry of colony morphology surrounding an antibiotic source. To test this hypothesis, we computationally simulated the diffusion of antibiotic on a plate inoculated with bacteria that express a cooperative resistance mechanism. Using insights gained from these simulations, we also experimentally explored this phenomena by imaging the growth of resistant E. coli cells in the presence of various antibiotics. In my talk I will discuss the results from the simulation and the experimental stage, as well as the current state of the analysis.

Prior to about 650 million years ago, the Earth's surface is believed to have completely frozen and thawed multiple times, each frozen period lasting for millions of years. The term "Snowball Earth" describes the runaway effect of ice expanding equatorward, with its brightly reflecting surface causing reduced absorption of sunlight, increased cooling, and further ice expansion. We used Global Climates Models to better understand the conditions necessary for other planets to be trapped in a Snowball state. We modeled planets that are Earth-like but with ocean-only surfaces. Our object is to investigate and further define the inner edge of the habitable zone - the theoretical region around a star where liquid water can exist on the surface. Our research has big implications for habitability, as liquid water is required for life to exist as we know it. The obliquity of a planet is also very important, as it controls the relative proportion of sunlight received at each latitude. Even within our own solar system there is a wide range. The Earth is tilted 23 degrees, Uranus 97, and Venus 177. We present results for an ensemble of planets with differing obliquities to demonstrate its effects. Furthermore, we also present results for planets around G-type stars, like our Sun, and M-type stars, also known as red dwarfs. Red dwarfs are by far the most common type of star in the Milky Way Galaxy. It is easier to detect orbiting extrasolar planets around M-stars. M-stars tend to have a relatively high abundance of Earth-sized and smaller planets, which are more likely to be rocky - a necessary condition for habitability. The effect of an M star’s solar spectrum on a planet’s energy balance is significantly different than a G star’s, which changes the location of the habitable zone. Our model study provides exciting new insights into the differing dynamics.

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.

In seeking to put future climate change in context, researchers have used past glacier fluctuations as a proxy for temperature. While an undeniable correlation exists between a warming climate and shrinking glaciers over long time-scales, it has also been shown that the interannual climate variability that occurs in a constant climate can drive large-scale glacier fluctuations. In other words, there is a classic statistical problem of identifying a signal-to-noise ratio. This study seeks to establish how large a change in glacier length needs to be in order to be considered statistically significant. Physically, this study asks how far a glacier must recede, and how quickly, before one can say with confidence that a trend exists. Two glacier models, one linear and one dynamic, based on the geometry and weather patterns of Mt. Baker glaciers in Washington State, USA, are randomly forced in a constant climate and the resulting time series are used for statistical analysis. The statistical significance of a trend depends in large part on constraining the effective degrees of freedom contained in a glacier record. A glacier is a large block of ice and thus has more inertial resistance to change than the weather that forces it. Glacial flow is therefore an integration of multiple years of previous climate forcings. This memory of previous years means the change in glacier length one year does not represent independent information about the current climate; a glacier can lengthen even if the temperature warms for a period. We present several methods for correcting for this effect, and evaluate the power of two standard trend tests for detecting whether a given glacier trend should be attributed to climate change.

Due to its global position, the Cotopaxi Nation Park (CNP) area in the Ecuadorian Tropical Andes is expected to experience a large temperature increase of 4° - 7° C during this century due to global warming, affecting approximately 200,000 people, especially regarding water scarcity and environmental degradation. Land use and land cover changes in relationship to climate change are being analyzed using four remote sensing images of the area from 1987, 1999, 2007, and 2009 using a geographic information system (GIS) framework. We are analyzing the recession of glaciers in Mount Cotopaxi, an active volcano with an elevation of 5897 meters above sea level, and changes in highland grasslands (i.e. the paramo ecosystem), which are the two primary water sources for the region. Our analysis will allow us to determine rates of change and estimate future scenarios to help local officials plan for more efficient land and water use. In addition, we are performing statistical analyses on weather data obtained from two weather stations in the area located at different elevations to determine changes in temperature, soil moisture, rainfall, and relative humidity. These data, in conjunction with information gained from the remote sensing images and GIS, will help us answer our research question regarding the effects of climate change on water resources, land use, and land cover in CNP.

Cells process an enormous amount of information from their environment and translate this information into phenotypic behaviour that will dictate critical biologic activities. To do this, cells must collect, store, and respond to information both inside and outside the cell. This information is stored in the chemical composition of its cytoplasm, and these conditions will regulate complex biochemical pathways that relay the information from the cell’s exterior to the effector proteins that modulate behaviour. These pathways, known as signal transduction pathways, are largely regulated by phosphorylation. Protein kinases are the class of enzymes responsible catalyzing the phosphorylation of intermediary signaling enzymes (resulting in their activation), and thus, stimulate the transduction of an external stimulus to intracellular machinery. As cellular conditions change, protein kinases sensitive to these conditions will modulate their activity through a change in shape (conformation). Research shows that disregulating signaling pathways through aberrant kinase activity can lead to grievous disease, making them good drug targets for cancer treatments and other conditions. Selective pressure has lead to the 500+ kinases in the proteome to adopt well-conserved active and inactive conformations, making it difficult to understand how nature can distinguish between them. Due to low abundance of kinases, quantitative analysis of kinase conformations is difficult with existing methodology. To this end, we have developed a catch-and-release system that allows us to enrich and quantitatively distinguish between kinases of specific conformations. This project will focus on the development trifunctional probe that serves as a chemical handle to enrich kinases in the novel system. The new catch-and-release system employs improvements over existing biotin-steptavidin systems by taking advantage of bio-orthogonal chemistry and specific elution conditions that increase signal-to-noise ratios. Our probe marks significant progress towards a panel of probes that will profile kinases for diagnostic means and drug target identification.

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.

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.

The reversible phosphorylation of proteins mediates a wide range of biological processes that range from signal transduction cascades to regulation of protein abundance. However, little is known about the mechanisms and evolution of phosphorylation networks. Despite the extraordinary advances in genome sequencing of many yeast species, evolutionary studies on the phosphoproteome of yeast species have been limited to the experimental analysis of phosphorylation in one species and theoretical analysis of the conservation of phospho-acceptor residues with other species. To properly study the evolutionary conservation phosphorylation in yeast, we are utilizing mass spectrometry to study and compare the phosphoproteome of 21 species of yeast, including representative species from each clade of the yeast phylogenetic tree. Most of these species have not been studied before by proteomics. This high-throughput phosphoproteomic study on the yeast species will contribute to the construction of phosphoproteome datasets, which can be exploited for comparative analysis of phosphorylation between the species. One of main aims is to identify phosphorylation sites that show a high degree of conservation across the 21 species of yeast. These highly conserved phosphorylation sites likely regulate the same functions across the different species, and these functions can be further studied and correlated to our understanding of the mechanistics of phosphorylation in key biological processes, as well as the diseases that occur when the signaling pathways that involve these sites are defective. The second aim of this project is to study the correlation between the conservation of the phosphoproteome with the conservation of the genome and transcriptome, which will expand our understanding of the evolution of phenotypic diversity. Finally, the large-scale dataset of the proteomes and phosphoproteomes holds a great potential for other types of computational analysis, and also serves as a foundational reference for future experiments.

Genes crucial for cell differentiation have been shown to change position within the nucleus at the appropriate stages of development. For example, it's been shown that the beta-globin locus moves from the periphery to the interior as transcription increases. The nuclear periphery is considered a repressive compartment, where silenced genes are located. Expression of Pax5, which encodes for the B-cell lineage-specific activator protein (BSAP), is vital for the commitment to the B-cell lineage and development. However, Pax5 is repressed during the differentiation of B-cells into plasma cells. In this study, we used fluorescence in-situ hybridization (FISH), to look at the position of the Pax5 locus at various stages of B-cell differentiation in order to determine if Pax5 position is correlated with its expression. We then performed RNA/DNA FISH to visualize the actively transcribing allele position. 

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.

Tubes are the foundation for many organs in all animals. Although tube formation is critical for development, relatively little is known about how cells coordinate their behaviors to form tubes. To investigate this process, we are studying the development of the dorsal appendages (DAs), two respiratory structures that are formed in Drosophila ovaries and protrude from the fly egg. We use a genetic approach to disrupt gene function, then study cell behaviors during tube formation. Previously, our lab showed that trimeric G proteins play a role in DA formation. Trimeric G proteins act as signal transducers and Gα, one subunit of the trimeric G-protein complex, is responsible for signal specificity. Although in situ hybridization showed that six of seven Drosophila Gαs are expressed in the ovary, functional studies demonstrated that Gα12 was most important. RNAi against Gα12 in a subset of DA-forming cells resulted in 90% of egg chambers exhibiting abnormal DAs. We hypothesize that concertina and its partial duplicate CG40005, the genes coding for Gα12, work together in DA-forming cells to coordinate cell behaviors. To test this hypothesis, we generated null mutations in cta and CG40005. We induced random deletions in the DNA via irradiation and screened for loss of a visible marker carried on a transposon near cta. Through complementation tests, we showed that 22 deletions extended into cta, or the neighboring essential gene, light. Although the genomic region contains many repeated sequences, I developed PCR tests and found 18 deletions disrupting cta, CG40005, and light, and one deleting only CG40005. Finally, rescue studies using large BAC clones generated by the P[acman] project will let us examine cell behaviors during DA formation in the absence of cta and CG40005. Since DA formation resembles neural-tube formation in vertebrates, our studies will give insight into tube-forming processes in other animals.

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.

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.

In an effort to study evolution and mechanisms of adaptation, seven populations of S. cerevisiae were cultivated in chemostat under nutrient limitation. Whole genome sequencing and Single Nucleotide Polymorphisms (SNPs) analysis were performed on clones isolated at 200 generations. I sought to test the effect of each mutation on the cellular fitness thus to characterize beneficial and passengers mutations. By combining PCR and Sanger sequencing, I confirmed five mutations (4 SNPs, one indel) detected by whole genome sequencing on one clone. Using backcross-mating techniques with the ancestral strains, I was able to isolate each mutation and test their individual fitness. I found that 4 of the mutations are passenger mutations that do not impact the fitness of the cells. One of the mutations, a non-synonymous change in SGF73 leading to the truncation of the protein, increased the competitive fitness by 24%. Mutations leading to the truncation of SGF73 were also found in three other independent clones. The presence of similar mutations in four independent populations suggests that the loss of the protein is an important process of adaptation to sulfate limitation. I am now studying the dynamic and the spread of this mutation in the population over 200 generations. SGF73 is the human ortholog of ataxin-7 of the SAGA complex associated with spinocerebellar ataxia diseases and our findings may be important to study the role of this protein in the development of human disease.

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.

Organisms have evolved specific mechanisms to respond to molecular and environmental stress. These stress-response pathways are evolutionarily conserved and can modify lifespan in model organisms, making them popular targets of aging research. Using the nematode Caenorhabditis elegans (C. elegans), we have found the loss of important genes in stress-response pathways can cause a phenomenon called age-related vulval integrity defects (Avid). Worms with Avid show a small protrusion near their vulva that can eventually lead to expulsion of the intestine and premature death. While many labs have noted this phenotype, it is unknown if Avid is a natural part of C. elegans aging or if genetic and environmental factors induce this phenotype. Because of this, there is confusion as to whether worms with Avid should be censored in aging experiments. The goal of our project is to determine the mechanism of Avid and whether it is part of normal worm aging. Our initial work has identified several conditions and genetic pathways important for Avid, including temperature, food availability, the hypoxic response pathway, the oxidative stress response pathway, and the protein assembly pathway. We have also identified that the reproductive period of the C. elegans lifecycle is influential on Avid frequency, despite the phenotype occurring post-reproductively. We are currently testing the hypothesis that Avid is caused by secretions from the bacteria worms eat that influence nematode physiology and lead to Avid. We hypothesize that the pathways that influence Avid frequency do so by altering the digestion of bacteria in the intestine or by modifying the worm’s immune response. To test our hypothesis we measured the quantity of bacteria ingested and digested by various worm strains at different temperatures and tested whether bacterial metabolites can cause Avid. We intend to combine our results and develop a more complete model of Avid.

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

Fandango is a centuries old community based musical tradition from Veracruz, Mexico dating from the first half of the XVIII century. With Indigenous, African, and European influences, this tradition takes place around a tarima, a wooden platform where mostly women improvise foot percussion as a group, involving each other and engaging the community in a musical dialogue. The intent of this research is to explore the tarima as a space of female empowerment and communal decolonial praxis. This research uses as its primary method the collection of oral histories from women participants in the fandango tradition in the U.S and Mexico. Considering the community building nature of Fandango and the tarima as an important space for women, it is anticipated that the results of this research will reflect the empowerment women and communities have found through this practice. Moreover, this research focuses on the collection of personal narratives that support this argument to further explore their implications for resistance and healing in response to gender, institutional and social opression. My interest in theorizing and writing about these oral histories is to elicit examples and create community for other women and individuals who might want to explore community-based arts as a mode of healing and resistance. This research is an important part of a longer project that explores and proposes community-based arts as tools for recovery from trauma and violence prevention for individuals and communities at large. This research will also open the door for other scholars in the field to consider alternative ways of responding to trauma.

Every aspect of nature is governed by the laws of physics. These laws include the basic principle of the center of gravity which is defined as a point in an object’s body at which the total net torque due to gravity equals zero. Understanding and applying this basic principle is crucial for dancers if they are to be successful movers. Yet the popular form of dance known as breaking seems to defy the laws of physics, particularly static equilibrium – a state where an object will not rotate unless an external force is applied because the center of gravity is located above an object’s base of support. Many breakers are able to perform gravity defying movements as they invert their bodies and hold various poses known as “freezes.” Using a series of cameras and a three-dimensional (3D) modeling program, I am able to locate the center of gravity in individual breakers and reveal that their movements do not violate the laws of physics. Using the information collected from this research, I can then propose and create new possibilities for freezes based on the concepts of static equilibrium. This research will be a stepping stone for further biomechanical researches in breaking and other forms of dance. Similar experimental techniques can be used to analyze more complex principles such as dynamic equilibrium – balance while in motion.

As theater artists, we must research the human experience through the work of playwrights and group collaboration; because our work dabbles heavily into art, our research is very different from that of an engineering student. Instead of taking a microscope to a petri dish, we take a microscope to the human experience, the rehearsal process acting as our catalyst. We must constantly ask ourselves, why is live theater relevant today? Why is our work important and necessary? Here on campus at the UW, the Undergraduate Theater Society operates as a completely student run production company that has been performing on campus for the past fifteen years, currently in the middle of our sixteenth season. All work is student directed, acted, designed and produced bringing together undergraduates who share a love and passion for creating theater and art. Upon selecting a season, consisting of five shows, each director is unique in their rehearsal process, each is welcome to create their regiment for their actors to follow. For example, Ben Philips, director of UTS' current show, Cyrano, has utilized a diverse array of rehearsal techniques to support his actors; ranging from the Laban effects, to animal behavior exploration to the Linklater Vowel Laddar. The physical demands of the rehearsal process emphasized the importance of "doing" on stage as opposed to "acting" on stage, a concept eternally exploring by undergrads. The final production in the current season The 39th Steps, directed by senior Andrew Pritzkau, will draw heavily the work of Alfred Hitchcock, allowing this stage adaption to be continuously influenced by his films. Through these various techniques, the Undergraduate Theater Society seeks to research the human experience through collaborative and exploratory work. In a theater artist's life, especially that of a student, a production is an opportunity to further our education through pratical application. This is our research.

It may be uncommon to associate Christianity with spoken word poetry (poetry that is recited aloud, usually involving a dynamic, theatrical, and urban feel) and dance (esp. street dance). However, several young artists are using urban art forms as a means of cultivating and sharing their faith. This project explored the relationship between the Christian faith and spoken word poetry and dance via the ethnographic research process. Questions that guided my research included: How can the faith and art forms be used together as impactful forms of outreach? Why is poetry and dance valuable to the church? How can Christian poets and dancers successfully engage their audience? The ethnography consisted of interviews and public observations of eight Christian spoken word poets and dancers in addition to reflections on the researcher’s own performance practice. As ethnography is described to be an “encounter of differences”, I have come across new findings that revealed my own biases about how Christianity and the two art forms intersect. Even as an insider to Christian spoken word poetry/dance, my views have been challenged, deepened, and broadened by this work. For instance, I have gained a greater understanding for certain ways a Christian performing artist can be successful in outreach by: 1) clearly conveying how the faith has enabled their own life changes 2) "being real" in sharing important, yet difficult aspects of one's life to others 3) performing with excellence and 4) reaching out to the audience offstage. In this presentation, I will strive to acknowledge and represent the many different findings I have come across in seeking to develop a more comprehensive and evolving understanding of the relationship between the Christian faith and spoken word poetry/dance.

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.

Annually, an estimation of 1.7 million people in the U.S suffer from traumatic brain injury (TBI), in which 50,000 people dies and another 85,000 people survive with long term disabilities. Moreover, TBI is reported to be the most common combat-related injury and accounts for 25% of combat casualties. CT and MRI are the current diagnostic tools for TBI, but due to their bulky size and complicated interpretation procedures, prevalent implementation of the devices is limited in undeveloped areas and near the battle field. Consequently, a size deployable diagnostic tool that is able to present quantitative evaluation of TBI is needed. The purpose of the project is to optimize an ultrasound elastography machine for detection and classification of mild and moderate TBI based on the theory that abnormal brain elasticity will be observed in presence of hemorrhage and edema. The goal was achieved in three steps: post-processing and stiffness maps were first generated in MATLAB for breast phantom to test and ensure the feasibility of coding, then data collected from moderate TBI rat brains were fed into the code with modified parameters to generate brain elasticity maps highlighting areas of damage, finally elasticity maps were be constructed for mild TBI rats. All the brains were imaged in alginate of same impedance. The quantified elasticity values in moderate and mild TBI brains allow classification of injury levels; the accuracy of constructed images will be ensured by comparisons between TBI, control and histology results. Successfully optimized ultrasound elastography machine displays quantitative analysis of brain elasticity which simplifies diagnostic procedures. Furthermore, implementation of the device in hospitals and battle fields enables early TBI detection, which will potentially reduce TBI-related deaths, lower TBI-related treatment costs and greatly enhance residents’ life quality.

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.

Lignin serves as the natural glue that holds plant fibers together. It constitutes roughly 15 to 30 percent of cellulosic biomass weight. Lignin is the second most abundant natural polymer on earth. Despite lignin’s ample availability across the globe, it has largely been discarded as waste or burned as low value fuel; especially in the pulp and paper industry. Lignocellulosic biomass based biorefineries typically involve substantial capital cost with many negative externalities such as biomass and crude oil price fluctuation as well as changes in government policies (tax deduction, government-backed loans, subsidies, etc.). Therefore, producing added value fuels and chemicals from lignin, the major biomass pretreatment by-product, via commercially viable routes is essential to increase the profitability and the sustainability of these biorefineries. One of the leading biorefinery developers based in Colorado, ZeaChem, is currently investigating the possibility of producing hydrogen gas for their ethanol production by gasifying lignin residues. This research project focuses on modeling the lignin gasification process (using Aspen Plus, a commercial process simulation software) and determining the techno economic feasibility of producing hydrogen from lignin residues. The research approach is explained and some of the research findings - including the hydrogen gas yield, overall mechanical energy and heat consumption, optimum operating conditions, and capital cost - is presented.

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.

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.

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.

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).

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.

Public parklands provide a space for recreation and ecosystem protection. However, managing parks for these traits can be a challenge as the two activities are often in conflict. The aim of this study is to explore the trade-offs between ecosystem protection and recreation in public parks through a case study of Fay Bainbridge Park (FBP) on Bainbridge Island, Washington. Bainbridge Island Metro Park & Recreation District (BIMPRD) with guidance from Washington Sea Grant (WSG) proposed the addition of three boardwalks at FBP with the intention of providing beach access and reducing trampling. For this study, I worked with WSG and BIMPRD to survey park visitors. The survey focused on participants’ use of FBP, their current understanding of the local ecosystem, and their feelings toward the addition of beach boardwalks, specifically impacts of boardwalks on beach ecology, aesthetics, and accessibility. In order to place this study in the context of public park management, I conducted a literature review of related case studies. The survey results revealed patterns concerning park use, prior ecological knowledge, and feelings toward the addition of boardwalks at FBP. This study will help inform BIMPRD and WSG on infrastructure decisions and the development of educational signage. More broadly, this work contributes to the larger body of information concerning appropriate public parkland management that maximizes value to visitors without compromising the health of park ecosystems.

Traumatic brain injury (TBI) is a common injury sustained by soldiers and requires immediate and sensitive brain imaging in order to diagnose the extent of damage. Currently, conventional methods of brain imaging such as computed tomography and magnetic resonance imaging are not field-deployable and immediately available on the battlefield. Tissue pulsatility imaging (TPI) is a technique that measures the natural pulsatile motion of tissue as a result of blood flow. Preliminary brain tissue samples of mice with TBI observed under widefield microscopy have shown increased mitochondrial accumulation at the site of injury relative to comparable sites in the hemisphere contralateral to injury, suggesting that TBI disrupts normal mitochondrial migration patterns. It is hypothesized that biological responses such as this, as well as the development of hemorrhage and edema, cause a change in brain tissue pulsatilities of TBI animals that can be detected by TPI. In this project, TPI by ultrasound will be used to image the brains of mice with acute and chronic (24-hour) TBI to determine whether this method of ultrasound imaging has the potential to be used for initial detection of TBI. Animal trials with both bilateral and hemispheric cranial windows will be used to study TPI patterns in the brains of these mice. Among the issues we will address include the effects of the skull on image resolution. Subsequent data analysis and device parameter adjustment should increase the resolution of images in order to optimize a design for an ultrasound device based on imaging tissue pulsatility that can accurately detect TBI and may eventually serve as a field-deployable brain imaging device. 

Traumatic brain injury (TBI) is a major issue in warzones and it is often misdiagnosed and therefore mistreated in the field due to unavailability of accurate imaging technologies and subjectivity of motor response tests. Soldiers who experience TBI and are not properly treated often deal with severe mental, physical, and emotional consequences for their remaining lifetime. As such, there is a need for a field-deployable modality for the detection of TBI. Proposed here is the use of ultrasound vibro-acoustography for detection, which has been shown to measure differences in mechanical properties of materials using intense focused ultrasound (iFU) to vibrate the material and record the acoustic emissions. I am working to quantify the emission differences of healthy and damaged tissue through in vivo rat testing.  By optimizing ultrasound parameters and experimental protocol, my work will support the end-goal design an affordable and portable device for TBI detection away from modern medical centers.

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.

All plants contribute to the productivity and biomass of an ecosystem. With generalized formulas we have gained an understanding of these fundamental processes, however, to understand the precise contribution of a particular plant species more accurate and specific equations are required. Through the dissection and fine-scale measurements of individual plants, allometric equations relating detailed plant structure to easily measurable quantities (i.e., stem diameter) can be developed. Because of their relative small stature and relatively small contribution to total ecosystem biomass, little is known about the exact biomass and productivity of shrubs. Yet, diverse angiosperm shrubs in western forests can have a disproportionately large impact on the ecosystem in terms of providing a food source for wildlife and fuel for low-intensity fires. Field measurements and samples were collected from 41 individual plants of Cornus sericea L. [Cornaceae] (red osier dogwood) in Yosemite National Park, California, USA. In the lab I processed the field data and calculated a number of allometric equations, including cambial surface area, wood mass, bark mass, and foliage mass in relation to basal diameter and diameter at breast height. This dataset will generate a foundation for future research helping scientists more accurately determine carbon stocks, carbon sequestration rates, fuel loads, and other changing trends. The collection of more comprehensive and scientifically accurate data will also help improve land management policies in an era of projected climate change.

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.

The control of infectious diseases in low-resource settings continues to be impacted by the limited availability of low-cost, easy to use diagnostics. However, even in developing nations, smart phones are common and can be used as “instruments” to control diagnostic devices. My senior capstone project aims to use a smart phone to input a sound wave into a microfluidic card and measure a sound wave coming out of the card to determine whether an analyte—the chemical that indicates whether a person is infected—is present in the sample. This is done by creating a network of fluid channels that can be modeled as an electrical circuit containing the fluidic equivalent of resistors, inductors, and capacitors (RLC circuit). When the sound wave is input to the system, it causes the fluid to oscillate and has a resonant frequency that is dependent on the characteristics of the system (the resistance, inductance, and capacitance). The goal is to cause a change in the fluid resistance, fluid inductance, or fluid capacitance through a chemical reaction (e.g. the creation of a bubble would change the capacitance or a change in viscosity would change the resistance). This change in a characteristic shifts the resonant frequency of the fluid circuit, allowing the presence of the analyte to be recognized. This project seeks to integrate a means of detection (like a microphone) into the diagnostic card to measure the analyte-dependent resonant frequency. This card would then be used as the platform for a measurement of blood clotting. Completion of this project would take the system one step closer to bringing simple and effective diagnostic platforms to developing nations.

Traumatic brain injury (TBI) is injury to the brain caused by external trauma. Approximately 1.7 million cases of traumatic brain injury are reported every year in the US, and contributing to an estimated 30.5% of injury related deaths. TBI is currently treated by managing symptoms, present treatment methods are incapable of reversing the damage done by the initial trauma. Gene therapy is a promising method of treatment for TBI; by transfecting cells such as neural stem or progenitor cells (NSCs and NPCs respectively) in the brain with plasmids which induce differentiation and migration damage to neurons can be alleviated or even reversed. This projects aims to develop and optimize a protocol which utilizes non-viral transfection vectors in conjunction with ultrasound to efficaciously target and transfect neural progenitor cells (NPC), i.e. cells capable of differentiation into neurons. By transfecting NPCs with plasmids which cause differentiation and/ or migration NPCs can be induced to become new neurons and migrate to areas of neuronal injury caused by traumatic brain injury. In this manner some of the dead and dying neurons might be replaced and the initial trauma mitigated. This is a novel method of treatment both in its use of non-viral vectors capable of targeting NPCs in conjunction with ultrasound mediated increase in transfection efficiency and in its potential for reversing the initial damage seen in TBI; something that no current method of treatment is capable of.

Ultrasonic neuromodulation is the process of stimulating different neural pathways in the brain through the use of transcranially delivered ultrasound in order to induce clinically relevant emotional, cognitive, physical or behavioral reactions. My research goal is to find out if it is possible to add anatomical specificity to current neuromodulation practice through the use of modulated focused ultrasound (mFU), where 'modulated' refers to adding complex temporal structure to the waveform to optimize neuromodulation. Since mFU has a small focus relative to the brain, the acoustic power from the ultrasound can be moved within the brain; previous experiments have used unfocused ultrasound which sends ultrasound through the entire brain. We hypothesize that we can map varying physical reactions through stimulation of different parts of the brain, with initial emphasis on the motor cortex because stimulation there produces readily observable results. With lightly anesthetized mice as our subjects, and always delivering ultrasound through the skin and skull, we began neuromodulation with unfocused transducers to transmit our ultrasound. This critical step was done to determine the optimal intensity, waveform shape and carrier frequency of ultrasound that created robust, observable effects. Next we translated these ultrasound parameters to our mFU transducer. The current stage of the process includes moving through different parts of each hemisphere and recording the associated motor response such as leg movements and tail flicks. We have already seen a change in activity between activating the front, middle, and rear regions of the brain, as well as dosing effects. Going forward, we intend to see if we could produce varied motor movements with greater spatial resolution using our focused ultrasound across a predefined grid atop the brain. Further studies will also change the applied stimulation intensity. Clinical implications for neuromodulation research include retraining brain function after injury and improving current therapeutics.