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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

“It is useless to consider the house except as a part of a community owing to the interaction of these on each other.” This was the opening sentence to the Doorn Manifesto written by Team 10, a collective of architects in the 1950’s who discussed the future of modern architecture and the modern city. My research begins with delving into Team 10’s theories on urbanism and Aldo van Eyck’s writings on the architect’s role on modernization and the relationship between a house and a city. With those theories as the driving force of my research, I delve into the development of housing projects as architectural responses to political and social impacts and modernization. I begin with the rise of housing projects in Algeria and Morocco as colonialism has made Northern Africa the experimentation grounds of new architectural types that differ from the traditional casbah and impoverished bidonvilles. From there, I move to France and investigate the banlieue as a reaction to post-war migration into the city and how the architecture has fallen to the banlieue’s socio-economic image. Using Team 10’s utopian ideals, I address the successes and failures of the housing projects up to this point and examine how architecture can act as a solution instead of a reaction to urbanization and modernization.

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.

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.

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.

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.

 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.

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. 

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.

 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.

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.

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.

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.

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.

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.

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.

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.

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

Xanthan gum (XG), a biopolymer excreted by bacterium Xanthomanoas campestris, is used in pharmaceuticals, cosmetics, agricultural products, food products, industrial products, and is used in enhance oil recovery processes because of its properties as a thickening agent, dispersion agent, and stabilizer of emulsions and suspensions.  Locust bean gum (LBG), a polymer extracted from the seeds of the carob tree (Ceratonia siliqua), is of interest in the biopharmaceutical field as a medium for oral drug delivery.  With the addition of nanoparticles, the material properties of the polymer solutions can be significantly altered.   Understanding of polymer-particle interactions and their impact on the material response to shear through rheological measurements is necessary for targeted design of material properties for specific applications. Flow and oscillatory testing was performed on XG and LBG solutions with and without the addition of silica dioxide (SiO₂) nanoparticles.  Under constant shear, XG solution shows a shear thinning behavior typical of weak gels.  With the addition of nanoparticles, the shear thinning behavior of XG is still present but at an overall higher viscosity.  LBG shows shear thinning behavior with a Newtonian region at lower shear rates.  The addition of nanoparticles to solution shows a region of shear thickening at lower shear rates and shear thinning behavior at higher shears at a considerable higher overall viscosity than the LBG solution without nanoparticles.  When strain is held constand with increasing frequencies, the storage (G') and elastic (G'') modulus show that XG has a tendency of more elastic behavior than LBG.  The addition of nanoparticles results in more viscous solutions with a higher elastic response.  LBG behavior is mroe  heavily impacted by the addition of SiO₂ nanoparticles than XG.

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

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

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.

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.

 Passage of Eocene slab windows beneath the Pacific Northwest is documented by plate motion reconstructions as well as the on-land geologic record. The earliest known record of this process is the 55-44 Ma Basalt of Summit Creek (BSC), a steeply dipping 1600 m section of subaerial lavas exposed southeast of Mount Rainier. These tholeiitic basalts erupted in an arc setting (as evidenced by underlying tuffs) but display a mix of MORB and OIB traits and have isotopic signatures of a depleted mantle source. In chemical and isotopic composition BSC lavas overlap with the voluminous Crescent Formation basalts on the Olympic Peninsula, which are of similar age but located ~100 km farther west. A few BSC samples display arc traits (e.g., HFSE depletions); we suggest these may record interaction between ascending asthenospheric mantle / melts and a mantle wedge previously modified by subduction processes. Compositional diversity among BSC lavas appears to reflect both fractional crystallization and source heterogeneity. Modeling with MELTS (Ghiroso and Sack, 1995) indicates that differentiation dominated by removal of clinopyroxene and plagioclase took place at mid crustal depths (P = 5 kbar) and that the parent magma had <0.2 wt. % water. However, this process cannot account for all incompatible element data, which appear to require multiple parent magmas. The Eocene was a critical juncture in Pacific Northwest tectonics. Subduction, slab window magmatisim, terrane accretion and mantle plume activity were all ongoing at this time. Increased understanding of the petrology BSC will contribute to our overall knowledge of the evolution of the western margin of North America.

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.

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.

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.

Autism is a developmental disability characterized by social deficits, communication deficits, and repetitive behaviors. Previous research has shown that having an older sibling with autism is a significant risk marker for a younger infant sibling developing ASD. The Early Connections study investigated the developmental trajectory of infants, looking for early markers that may predict whether or not ASD will be developed later on in toddlerhood. The two subject groups were identified as follows: high-risk (infants with an older sibling with ASD) and low-risk (infants that do not have any family history with ASD). Both groups were tracked longitudinally from 6 to 24 months at 6-month intervals. The Communication and Symbolic Behavior Scales Developmental Profile (CSBS DP), an assessment tool for early communication in infants and toddlers, was administered to both groups at 12 and 18 months. Each infant was videotaped during the CSBS DP administration and those videos were coded offline by trained undergraduate coders. Coding is still in progress. Using the CSBS DP, previous studies have shown that delayed word, sound, and language development are consistent markers for ASD. Therefore, we expect infants from the high-risk group to have lower CSBS DP scores in word and sound acquisition domains when compared to the low risk-group. A better understanding of early deficits in the core elements of language development will provide researchers with clearer insight on early identifiable signs of ASD. Targeted intervention in language acquisition may help children at high risk for ASD overcome potential communication deficits earlier on in development, thereby improving future prognosis.

To be infected with human immunodeficiency virus (HIV) is to face a lifelong battle. Even with the combined force of multiple antiretroviral drugs to target different phases of the HIV life cycle, one cannot eliminate human immunodeficiency virus (HIV) from the body. This is due to persistence of virus reservoirs, compartments, or sanctuaries. Reservoirs are tissue sites characterized by collection of virus over time: viral populations show low divergence from the founder virus and high diversity between each other. Compartments are tissues with limited gene flow: they are pockets of virus with limited entry and exit. Sanctuaries are tissues that resist penetration of antiretroviral drugs: they can set up the conditions for reservoirs or compartments. To understand how and where these sites of persistent infection endure in the body even during antiretroviral therapy (ART), we are conducting a systematic characterization of possible sites in the infected host. We are studying viral populations present in biopsy-derived gut-associated lymphoid tissues (GALT) and other autopsy-derived tissues of patients who died while on antiretroviral therapy (ART). Viral populations are sampled from tissues using molecular lab techniques (including polymerase chain reaction and Sanger sequencing) and analyzed using phylogenetic trees and computational programs that measure diversity, divergence, and clustering. Our study addresses two main aims: (1) to find the tissue sites in the host critical in maintaining latent HIV infection during suppressive ART and (2) to find tissue sites critical in supporting continued viral replication and the emergence of pathogenic phenotypes during ART by characterizing sites as reservoirs, compartments, or drug sanctuaries. Hopefully our research will help to direct future methods of HIV treatment by allowing researchers and clinicians to better understand how and where virus persists in the body.

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

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.

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

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

Autism Spectrum Disorder (ASD) is characterized by deficits in communication, social skills, and repetitive behaviors. Understanding the risk factors in early childhood that lead to the diagnosis of autism is an important area of research. Specifically, researchers are trying to understand how communication development differs in children who go on to develop autism in comparison to those that do not. Previous research has shown that 18.7% of infants, who have at least one older sibling with ASD, develop autism. In this current study, two groups of infants between the ages of six and twenty-four months were tracked longitudinally: high-risk infants who have an older sibling with ASD and low risk infants who have no family history of ASD. The Communication and Symbolic Behavior Scales (CSBS) protocol was used to identify various communication modes used by each infant at 12 and 18 months of age. The videotaped interactions between the infant, clinician, and parent were coded offline by a group of trained undergraduates. The following communicative acts were defined and coded: (1) behavior regulation: the infant’s attempt to control some behavior of an individual around him/her; (2): social interaction: the infant’s ability to bring attention to him/herself; and (3) joint attention: the infant’s ability to bring attention to an object. Our aim is to explore differences between rates of communicative acts in high risk and low risk infants at 12 months of age. Previous research suggests that children with ASD are less likely to draw the attention of others to objects or events. We hypothesize that high risk infants will display significantly lower rates of communication acts in all three domains when compared to their low risk peers. This study will contribute to a better understanding of possible deficits in early communication in this high-risk population, leading to earlier intervention opportunities.

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

Autism Spectrum Disorders (ASD) are characterized by atypical social development, decreased verbal and non-verbal communication, and repetitive behaviors. Retrospective studies of children with autism suggest an association between pregnant mothers’ use of certain medications and the occurrence of ASD diagnoses in their children. Other findings have also determined a relationship between an infant’s cognitive development and maternal mental health. In addition to maternal variables influencing development, infants may be at genetic risk based on sibling status: specifically, infants with siblings who have been diagnosed with ASD are at high-risk for also developing ASD. Using data from the Early Connections study – a longitudinal study of high-risk infant siblings compared to low-risk infants, we examined whether maternal variables resulted in added risk for poor child outcomes in the high-risk group. Information about family history of medical and psychiatric diagnoses, mother’s medication use during pregnancy, pregnancy complications, and other details pertaining to the mother’s delivery history were compiled for three groups: infants who develop autism (high risk, n=13, low risk, n=1); high risk infants who do not develop autism (n=32); and low risk infants who do not develop autism (n=42). Data analysis is ongoing. This study will examine the role of prenatal and postnatal effects in infant development in a high-risk sample. It is expected that mothers of high-risk infants will exhibit more medical and psychiatric conditions.The results of this study could aid in medical care for families who have a child with autism and are considering care options during a later pregnancy.

Event related potentials (ERP) are electrophysiological responses of the brain measured during an electroencephalogram (EEG). The Mismatch Negativity (MMN) is an ERP component that occurs as a result of the brain detecting a deviant sound among a sequence of standards. It is represented by a negative peak in the fronto-central region of the scalp with latency 100-250 ms after onset of the abnormal stimulus. Previous studies have shown that the MMN is reduced in children with autism spectrum disorders (ASD) relative to typically developing children. It has been suggested that this indicates atypical automatic auditory processing in ASD. Other research has found abnormal MMN activity in schizophrenia patients as well. These studies have found an association between MMN activity and test measures of social function in individuals with schizophrenia. It has been theorized that impairment in auditory detection present in schizophrenia (as evidenced by a reduced MMN) may have downstream effects on certain facets of social cognition. No known work has yet been done to assess the same association in ASD. This study investigated the relationship of the MMN with social skills in individuals with ASD. In this study, EEG was recorded from children and adolescents with and without autism while they listened to auditory stimuli consisting of a standard sound ("ba") and deviant sounds ("da," "bi") to elicit an MMN. Parents reported on children’s social adaptive behavior in the Vineland assessment. The aims of this study are to (1) replicate previous findings that individuals with ASD have a reduced MMN relative to typically developing individuals, and (2) explore the relationship between the MMN and social behavior in children with ASD and typical development, as measured in the Vineland. A strong association may shed light on the sensory involvement in typical social functioning.

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

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

Titanium Oxide (TiO₂) nanotubes, nanowires, and coreshell structures have the potential to be implemented in new unique devices. TiO₂ has a variety of gas-sensing, photovoltaic, and semiconductor properties. TiO₂ has multiple forms such as TiO₂(B) and anatase, which could be surface modified. These forms are synthesized depending on the hydrothermal treatment. The ultimate goal was to create a thin film, out of nanowires, for a top contact field effect transistor. For an efficient top contract, the film must be homogeneous and be composed of one or two layers of nanowire. The creation of nanowires started with anatase or p25 combined with a 10 M NaOH solution that underwent a hydrothermal process for 48 hours. With two autoclaves, two reactions can be done simultaneously. Keeping one reaction constant as control, the other autoclave had its parameters slightly modified. The modifications in thermal ramp rate, solution molarity, hydrothermal duration, and amount of starting material, helped understand the titante nanostructures and growth mechanism. 170°F was the established temperature where nanotubes started turning into nanowires while 200°F was the control. There were several treatments, post-hydrothermal, to acquire TiO₂(B). An ion-exchange transformed Na₂Ti₃O₇ into H₂Ti₃O₇ then calcination produced TiO₂-B. With these materials, several methods, such as spin-coating and drop-casting, were tested to create a thin film.  For a consistent film, the nanowires must be uniform and the fabrication process reproducable. 

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.

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.

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

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.

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

Two strains of Botryococcus braunii algae were grown in three different sets of conditions to compare growth characteristics and lipid production. One species, UTEX LB 572, was a Race A Botryococcus braunii from the culture collection of the University of Texas in Austin. The second species, AC 762, was a Race B Botryococcus braunii from the culture collection of the University of Caen, France. UTEX 572 was found to produce two hydrocarbon chain lengths of C:16 and C:18 in a 2:3 ratio respectively. The AC 762 was found to produce hydrocarbons called botryococcenes of chain lengths between C:30 and C:36. The lipid chain lengths of both strains were evaluated by mass spectrometry. The UTEX 572 lipid content was quantified by analytical spectrometry after direct transesterification of the lipid content to biodiesel. The AC 762 lipid content was quantified by a photospectrometry technique developed by UC Berkeley researchers Eroglu and Melis (1985). Cells of both species were harvested during exponential growth phase from 400 mL of growth media and then freeze dried and analyzed gravimetrically. Nine flasks of each species were grown with 3000 lux average light intensity on a 12h:12h light:dark cycle at room temperature averaging 22° C. Three flasks of each species were grown with 1.5% CO2 in BG-11 media, three flasks of each species were grown in BG-11 media with air only and three control flasks were grown in respective carrier medias as those used in the algae collection of origin. Knowledge of the rates at which AC 762 and UTEX 572 produce hydrocarbons as well as the specific lengths and proportions of those hydrocarbons contributes to data needed for comparison of economic considerations in industrial applications.

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.

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

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

The purpose of this study is to determine fundamental structure-solvent-property relationships in organic photovoltaic polymers (OPV’s), with the overarching goal of increasing the efficiency of OPV’s. A typical silicon-based photovoltaic plant outputs approximately 88,000 m2 of photovoltaic cells each year- about the size of 16 football fields. On the other hand, an organic photovoltaic printer will produce the same area in up to 10 hours. OPV’s are incredibly fast, cheap, and easy to produce relative to their inorganic counterparts, but fall short within the realm of efficiency; the 10% efficiency of OPV’s can hardly rival the ~40% efficiency of inorganic photovoltaic technology. If the efficiency of OPV’s can be increased, this will have a drastic impact on the competitive marketability of photovoltaic technology. This project aims at developing computational models to study the role of solvents in the self-assembly of polythiophenes during the printing process. These models are generated in GROMACS, a program that uses classical forces such as Coulombic or Van Der Waals forces, to predict how molecules will behave with time. This is problematic, however, for OPV’s, as key interactions occur on the quantum level, and new classical force fields, which are computationally very efficient, need to be altered in order to accurately calculate these interactions. A force field is being developed and refined by comparing our computational results with experimental results from the Pozzo Research Group within the Department of Chemical Engineering. Once these results are reliably consistent with each other, we can begin running simulations and gathering data regarding how OPV’s assemble in various environments. In particular, this poster explains a systematic methodology I have developed to use the GROMACS program to perform molecular dynamics (MD) simulations of single chain OPV’s in various solvents as well as simulations of bulk OPV’s in the melt state.

Currently, the United States faces an impending energy crisis. To ensure energy security, conversion of biomass to small molecules for use in fuels or chemical processes must become more energy efficient. However, a major hurdle to raising productivity is the robust structure of biomass and subsequent resistance to breakdown. In the past ten years, experiments have shown “ionic liquids,” a special group of solvents, dissolve biomass. Unfortunately, these experiments are not guided by molecular scale design principles hindering this promising research. This project focuses on providing the fundamental knowledge to guide and explain the phenomenon by using molecular dynamics (MD) to study the interaction of cellulose and other parts of biomass as a function of solvent environment. This new perspective requires simulated MD in combination with an enhanced sampling method. Enhanced sampling, in this case umbrella sampling, involves applying artificial forces on atoms to cause rare events that would not normally occur on the time scale of molecular scale simulations. Examples of rare events that are challenging to directly observe in MD simulation include chemical reactions, protein folding and unfolding and binding and unbinding of polymers. This work focuses on binding and unbinding events of biomass polymers. To cause the binding and unbinding events, umbrella sampling uses a force similar to a spring to hold a variable like dihedral angles and number of hydrogen bonds constant. Umbrella sampling is a versatile technique and is used on a wide variety of variables but this work uses it to vary the position of the dimer with respect to the cellulose surface. By varying position, the interaction energy is calculated. The interaction energy will give a deeper insight into the mechanism of dissolving biomass while providing a profounder understanding of the fairly new materials, ionic liquids.

Individuals with autism spectrum disorder (ASD) demonstrate impairment in communicating with others and responding to social cues appropriately. These impairments may extend to family members. The Broader Autism Phenotype (BAP) refers to relatives of individuals with ASD who exhibit impairments similar to those with ASD. BAP suggests that some traits of ASD may be inherited separately and exist in individuals without ASD. Social language impairment is consistently observed in individuals with ASD. Twins are useful in studying the genetic components of a disorder, because they share 50% (dizygotic) or 100% (monozygotic) of their genes. This study examined the presence of BAP traits in disconcordant twin pairs (where only one twin has an ASD diagnosis) compared to twin pairs with typical development. twins aged 7 to 30 years completed a 15-20 minute conversation with an experimenter, which was later coded for pragmatic (social) language abilities using the Pragmatic Language Scale (PRS). In the PRS, coders blind to diagnosis, rated individuals on skills such as eye contact, intonation, facial expression and reciprocity of conversation. First, analyses compared pragmatic language in three groups: (1) the twin with ASD, (2) the unaffected twin of the child with ASD, and (3) an age and gender matched typical twin with no family history of ASD. We expected that pragmatic language was most impaired in the ASD group compared to the typical group, with the unaffected twin showing intermediacy performance, suggesting that pragmatics are part of the broader phenotype. Next, we compared the relationship of symptom severity in the twin with ASD and the level of pragmatic language in their unaffected sibling. This study will provide insight as to whether pragmatic language skills are a part of the broader autism phenotype and the degree to which they are related to familial autism symptoms.

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

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

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

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

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

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

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

This project seeks to better understand climate change corollary to the migration of the Intertropical Convergence Zone (ITCZ) in the tropical Pacific from the Little Ice Age (~AD 1400-1850) to the present using hydrogen isotopes as a proxy for climate change. During this time, the ITCZ is hypothesized to have reached its most southern location, the consequences of which were evident on a global scale. However, more research is needed to further investigate this hypothesis. Specifically, this study examines hydrogen isotope ratios of the source specific lipids Taraxerol and Dinosterol from Lake Escondido, Isabela Island, Galapagos. Lipids were solvent-extracted from sections of the cores, separated through silica gel columns, and the ratio of Deuterium and Hydrogen (δD) of specific lipids was quantified using a Gas Chromatograph-Isotope Ratio Mass Spectrometer. The combined fluxes of both terrestrially and aquatically sourced δD ratios over time provide a proxy for climate change through the present. Due to the widespread effects of the ITCZ on global hydrology, understanding its movement, and what triggers migration, can provide insight into future climate scenarios.

Aerospace vehicles, such as reusable spacecraft and hypersonic flight vehicles, require materials that can both provide high thermal resistance and high mechanical strength. Thermal insulation is required to protect the vehicle interior including occupants from the high heat of reentry and mechanical strength is required to withstand the variety of loads including the forces experienced during launch. In general, it is difficult to meet both these requirements at a high level since the normal way to increase thermal resistance of porous ceramics is to increase the porosity but this reduces strength. We are currently developing and investigating anisotropic porous ceramics that have the potential to optimally meet both these requirements. We are making the anisotropic porous ceramics from through a route called polymer derived ceramics (PDCs). The class of PDC’s that is being investigated is siloxanes, which decompose at high temperatures (~800^oC) into a SiOC ceramic. These materials have excellent high temperature resistance including creep and low thermal conductivity. Polymethylphenylsilsesquioxane (Waker H44) is first cross-linked and milled into a fine powder. The powder is then pyrolyzed to a SiOC ceramic that is then milled into a fine ceramic powder. A water-based slurry is made and poured into a mold that sits on a cold copper rod that is cooled in a liquid nitrogen bath. This causes ice crystals to form in the slurry which grow perpendicular to the copper rod. The frozen component is then freeze dried, causing the ice to sublime leaving a highly anisotropic porous structure. The thermal and mechanical properties will be measured in the longitudinal and transverse directions and the properties of these anisotropic porous microstructures will be compared to those of isotropic porous ceramics of similar porosity.

Silicon microring resonator biosensors utilize nanoscale light confinement to detect biomolecules in a real-time and label-free manner with high sensitivity. Detecting the presence of antibodies that bind human tissue and blood antigens is crucial in transplant and transfusion medicine, as mismatched products can impact the clinical outcome of the recipient. The focus of the current research is to improve data analysis methods to perform serologic analysis of human plasma using a silicon photonic chip. Microring resonator chips were prepared by physisorption of streptavidin followed by functionalization with biotin-conjugated histo-blood group antigens. Testing was performed using undiluted human plasma to detect histo-blood group antibodies on the functionalized chip surface. A secondary enhancement step using an anti-immunoglobulin antibody enabled the quantification of the surface bound antibodies. Data analysis was performed using on-chip positive and negative controls, and kinetic analysis was accomplished using association models. The quantitative determination of antibody binding profiles with a model antibody system is discussed to show how these devices can ascertain kinetic behavior. Positive determination of plasma antibody content is shown, proving these devices can be used in this application at current clinical standards. These devices are suited for clinical translation and with proper quantitative models and testing they could surpass current clinical methods.

The neurotransmitter dopamine is a key component of the limbic sysem, which plays a critical role in emotional processing, learning and memory, and reward processing.  Disruptions in dopamine synthesis, release, and reuptake underlie many neurological disorders, learning deficits, and diseases.  Previous work from our lab established the importance of the glutamatergic NMDA (N-methyl-D-aspartate) receptor in maintaining normal phasic activity in dopamine neurons of the ventral tegmental area (VTA) and showed that mutations of this receptor cause deficits in fear-related learning, highlighting the importance of dopamine in fear-related learning.  In this project we use in-vivo electrophysiology to record from dopamine neurons of the VTA during Pavlovian fear conditioning.  The paradigm consists of two types of trials where one cue (CS+) is paired with a mild footshock (0.3mA, 0.5 sec), while the other trials utilize a cue (CS-) which predicts the absence of a footshock.  Our preliminary data show plastic differences in neuronal activity patterns across training days associated with both conditioned and unconditioned stimuli, where initially there is increased activity in response to the fearful stimulus, but across days of conditioning, this response shifts to being associated with the conditioned stimulus.

Contemporary US society has in many ways written off self-mutilation, the deliberate damage or modification of one’s body tissue without intention of suicide, as a pathological act whose roots lie in mental illness and destruction beyond any sort of rationality. Often, self-mutilation is linked to suicidal behavior, but even when it isn’t it bears a transgressive nature and is frequently met with repulsion. In order to understand and examine the effects of the transgression of self-mutilation on individuals and larger communities, I took into account some ways in which individuals in specifically religious contexts have been marginalized by these practices. Parts of the Lakota Sun dance involving self-mutilation were banned in the US between the years 1895-1978 and the Modern Primitives, a group that emerged in the late 1960s and 70s seeking to reclaim self-mutilating religious rituals were met with extreme ostracism. In my research I explored spiritual self-mutilation as a vehicle for connection to something beyond an individual’s bodily limits, examined the physical and psychological capacities humans have to endure intense physical sensation, and looked at the implications of the process of physical healing as a powerful and direct metaphor for spiritual healing. Taking all of these into consideration, with the help of the narrative of the Modern Primitives, I sought to understand the way in which, for many individuals, the brutal destruction and modification of skin and flesh becomes an act of creation, of reconstruction and life-affirmation. If we allow ourselves to reconsider our cultural taboos surrounding self-mutilation in a religious context, we begin to see that there may be a stronger, deeper connection between spiritual self-mutilation and pathological self-harm than we can realize, without taking a closer look at the roots of both.

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

One of the major intracellular barriers to non-viral gene delivery is degradation through the endosomal/lysosomal pathway. To overcome this barrier, pH-sensitive polymers that swell in acidic pH and ultimately disrupt the endosome can be designed to escape these compartments. Previously, the Pun lab developed HPMA-oligolysine copolymers that have transfection efficiencies approaching that of polyethylenimine (PEI), the gold standard for transfection. In order to increase the copolymers’ transfection efficiency, oligohistidines were incorporated into the copolymer in both statistical and block architectures to impart pH-sensitivity. Transfection studies with these two copolymers showed that statistical incorporation of oligohistidine increased transfection efficiency, while block incorporation did not increase transfection efficiency. To determine if structure-function differences affected cellular uptake and endosomal buffering, we performed uptake inhibitor and endocytic buffering inhibitor studies. Through these studies, we found that both copolymer geometries preferred non-clathrin coated caveolae uptake pathways, and that they differed in endosomal buffering capabilities. The statistical copolymer showed increased endosomal buffering capacity, which was consistent with the overall higher transfection efficiency of the statistical copolymers over the block copolymers. From these two studies, we are better able to understand the relationship between structure and function in gene delivery using polymers.

The swell shark, Cephaloscyllium ventriosum, is one of the most popular sharks in public aquaria on the west coast of the United States, but very little is known about the early growth and development of this species. Swell sharks, members of the catshark family Scyliorhinidae, are small oviparous sharks that lay semi-translucent egg cases which they attach to rocks and seaweed during egg laying. Limited data on post-hatch growth exists for this shark, but there is essentially no data available on the early growth and gestation time of this shark within the egg case. The goal of this study was to determine the gestation period and early growth of the Swell shark. The gestation time of 10 egg cases and the post-hatch growth rates of 39 swell sharks were recorded over a 23-month period. Juvenile swell sharks were reared from egg cases deposited in laboratory aquaria during July 1990 by eight female swell sharks previously caught off Santa Barbara Island, California. Mean gestation time for the eggs (n = 10) maintained at 13.5-17.5° C with a constant photoperiod (12 hrs light, 12 hrs dark) was 264.4 + 18.106 SD days. Newly hatched sharks had a mean total length (TL) of 15.3 + 0.7 cm SD (n= 42) and had a mean weight of 15.0 + 1.4 g SD (n= 27). The average percent growth of sharks approximately one year old (n=21) was 38.74 + 7.66 % SD. The gestation time of C. ventriosum is significantly longer than that of a similar catshark, Hemiscyllium osellatum, which has a gestation period of just 140.3 ± 4.6 days. However, TL at hatching was very similar to this species and the average neonate length of H. osellatum was 16.5 ± 0.5cm and average weight was 19.9 ± 2.1 g.

Protein phosphorylation is a common regulatory mechanism carried out by the cell, as adding a phosphate group to a particular protein can switch its activity on or off.  Signaling pathways employ this control method to instigate series of phosphorylation events that elicit a particular cell response.  Our research involves extracting and characterizing the phosphoproteome, or the cell’s entire set of expressed phosphorylated proteins, in both yeast and mammalian cell models.  To generate lists of phosphoproteins present in these cell models, we use mass spectrometry, an analytic technique that produces characteristic spectra for individual phosphopeptides that are then matched to a library of known protein spectra through the use of computer algorithms.  In our preliminary results, we have generated large-scale data sets identifying thousands of phosphorylated proteins present in each species and cell type.  The goal of the first project, the yeast study, is to determine the degree of evolutionary conservation in phosphorylation events across 19 yeast species to learn about the basic principles of phosphoregulation.  The conservation of phosphorylation can also give insight into phosphorylation events in other species evolutionarily related to yeast, such as humans.  The second project, the mammalian cell study, examines the phosphoproteome of different breast cancer cell types in order to identify common phosphorylated proteins, from which we can deduce a molecular signature for breast cancer.  This signature can be used in future studies to design a universal protein inhibitor drug as an alternative anti-cancer therapy.  Additionally, by identifying the phosphoproteins exclusive to each cell type, we can uniquely characterize specific types of breast cancer.  Knowledge of the proteins active in one type of breast cancer may facilitate development of inhibitor drugs as a form of personalized medicine.

The mechanisms that enable bacteria to be metabolically active at subzero temperatures are of considerable interest to studies of polar microbial ecology, astrobiology, climate and cryopreservation. The true nature of these mechanisms in marine bacteria remains elusive. Previously, protein synthesis within the sea ice bacterium Colwellia psychrerythraea str. 34H has been observed down to -20°C (and possibly lower) after being flash frozen with liquid nitrogen (Junge et al 2006). Here we report on the results of a long-term study of subzero metabolic activity, growth and protein expression of 34H cells not impeded by possible flash-freezing artifacts. 3H-Leucine- and Thymidine incorporation in addition to shotgun proteomics techniques were applied to 34H cultures incubated for up to 8 weeks at -1, -5, -10, -15, -20, and -196°C. Protein synthesis rates were found to be significantly higher without flash-freezing, in particular as temperatures dropped below -5°C. Furthermore, maximum protein synthesis and growth rates were observed at -1°C and -5°C. Evidence for growth cessation with continued protein synthesis at -10°C, and possibly below -10°C, were also obtained. Triplicate detailed proteomic profiling using tandem mass spectrometry are in progress and will help elucidate specific metabolic pathways that are selectively turned on or upregulated in order to facilitate the observed metabolic activities and growth at subzero temperatures. These combined efforts contribute to solving the critical puzzle concerning the establishment and maintenance of life in saline ice formations as well as provide valuable insight into low temperature cell physiology and adaptations for life in ice with significance to sea-ice ecology and seasonal transitions.

Hypoxia is the term used in aquatic systems to describe low concentrations of dissolved oxygen (i.e. ≤ 2 mg O2¬/ml). Over the past 30 years, the intensity and duration of hypoxia has increased worldwide, with notable examples in the Gulf of Mexico, Chesapeake Bay, and Hood Canal, WA. Increased nutrient pollution from anthropogenic sources like agricultural fertilizers and raw sewage is contributing to the increased phenomenon of intense hypoxia in aquatic systems. Low dissolved oxygen is not only a major stressor to fishes, but may also be responsible for dramatic ecosystem shifts with respect to energy flows through the food chain. Zooplankton communities, an important energy source for fishes, were analyzed in Hood Canal, WA in relation to summer hypoxia. Zooplankton abundance, taxonomic composition, biomass, and length distributions were compared between areas of Hood Canal that experienced moderate versus intense hypoxia at the beginning and end of the summer hypoxia season. The goal of the project is to track differences in zooplankton composition between the two sites, with intense hypoxia relating to a shift towards smaller types of zooplankton and more gelatinous organisms relative to the site with moderate hypoxia. The size of zooplankton will potentially affect the efficiency of energy transfer between zooplankton and fishes, with larger zooplankton transferring more energy relative to smaller zooplankton. Gelatinous organisms like jellyfish, siphonophores, and ctenophores generally have lower oxygen requirements and few predators. Thus, an increase in these organisms is a ‘trophic dead end,’ shunting energy that may otherwise contribute towards fish growth. Analyzing trophic changes in Hood Canal in response to hypoxia will provide insight into major ecosystem changes occurring as a result of anthropogenic perturbations.

The evolution of multicellularity is one of the most important yet least understood biological phenomena. What selective pressures drive this major evolutionary transition? To address this question, we use a theoretical approach to model the spatial properties of cell groups in a simulation entitled Tree-Multicellularity (TreeMu). In TreeMu a simple multicellular organism is represented as a graph, with nodes representing cells, and edges representing physical connections between cells. Like cells, nodes carry intrinsic attributes, such as reproduction, mutation and death rates; these dictate life processes and define an individual's fitness. Like multicellular groups, graphs have similar properties that emerge from individual contributions. When a node dies it splits the graph in two, analogous to group level reproduction. We explore how the evolution of a node's death rate affects multicellular growth. In the simulation we implement an evolutionary algorithm that selects for 'multicellular' graphs of large sizes by removing small groups from the population. Preliminary data supports a tradeoff between group size and reproduction. TreeMu provides a computational framework to explore the dynamics of multicellular evolution.

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

Ramsey Theory is an intricate field of pure mathematics, but it also has applications in computer science, where graphs are commonlu used as data structures. Every pair of "forbidden" graphs has a Ramsey number, which indicates when one of those graphs must occur. A Ramsey number for a pair of forbidden graphs is the smallest number of points R for which every edge-coloring of the complete graph on R points includes one of the forbidden graphs in its respective color. In this paper we use two original methods to find and prove new Ramsey number formulas for certain tadpole graphs based upon known Ramsey number formulas for arbitrary cycle graphs.  A tadpole graph Qn,t is formed by connecting one end of a path graph on t points (called the “tail”) to a cycle of size n (called the “head”). A pan graph Qn is defined as a tadpole graph with t=1. We first use an intuitive counting method to prove exact Ramsey number formulas for all “near-diagonal” pan graphs, i.e. those pairs of pan graphs where the maximum cycle size of the pair is no more than 5/2 times the minimum cycle size. Then, we demonstrate a number-theoretic method to find exact Ramsey numbers for arbitrarily far-from-diagonal tadpole pairs with arbitrarily long tails. However, the second method requires that the tadpoles meet number-theoretic constraints (rather than size constraints). For example, in the diagonal cases, n-1 must be relatively prime to n+t, where either n-1 has an odd order (mod n+t) or the additive inverse of n-1 has an even index relative to n-1 (mod n+t). These “scattered” on- and off-diagonal results provide upper bounds on the Ramsey numbers for other tadpole pairs that fail to meet the number-theoretic constraints.

The mining industry is extremely controversial. Resource extraction holds many negative environmental effects in addition to an overwhelming amount of economic benefits. Weighing these benefits often puts industry in conflict with the public, with governments forced to mediate the mining licensing process. Public participation is the means to ensure that the people's interests are voiced in order to limit the monopoly of power corporations would otherwise hold. The report provides an in-depth analysis of the two countries' dissimilar mining licensing processes, inspects the amount of public participation involved in those processes, and finally demonstrates findings through specific case studies relevant to each countries' licensing system. Through this comparison it becomes clear that the presence of the public participation is not enough to ensure that people's voices are heard.

Colonization in the 16th century permitted the creation of borderlands of indigenous groups in Mexico. As Mestizos became the majority in the country, indigenous groups rested in a borderland of injustice and inequality. To this day, indigenous groups still live in the struggle for justice. My aim is to research Los Triquis from San Juan Copala, Oaxaca and explore the realities surrounding the conflict that is taking place there; especially the implications in shaping Triqui identities around this conflict. Though various scholars have examined the paramilitary conflict in San Juan Copala, Triquis along with a study of their identify formation have been left out of the picture of the conflict. I intend to focus on the direct consequences on the individual rather than on the nature of the conflict itself through analyzing interviews with experts on the conflict and videos with first-hand accounts by Triquis who have escaped such violence. Since 1988, rising Triqui paramilitary groups allegedly helping Triqui people in San Juan Copala against injustices from the government, have created a paramilitary conflict. The resulting violence has led to the displacement of thousands of Triquis, who find it impossible to return home as they are attacked by their own people once they try. The particularity of this conflict is the government’s hidden involvement and it has affected every age and gender group in San Juan Copala thus changing the dynamics of interaction.

During the Pinochet dictatorship in Chile (1973-1990), attempts to exclude leftist-oriented thinkers resulted in the exile of over one million Chileans from their homeland. In what was perceived to be a temporary absence, Chilean exiles faced unusual dilemmas while waiting for democracy and normalcy to return to Chile. This period of uncertainty was especially pronounced for those exiles arriving in the U.S., a nation that contributed to destabilizing the socialist government and securing the military coup in Chile. This research seeks to examine the ways national identities or concepts of the homeland emerge in testimonies and cultural productions of these exiles. Primary sources include: testimonies of exiles, essays, short film, as well as the 9/11 Collective- a group of exiles responding to the shared date of national tragedy in the U.S. and Chile. Theoretical concepts surrounding diaspora, exile, identity, and memory provide an analytical lens to better understand the fluidity of nation, home, and identity in the self-representations of Chilean exiles in the U.S. This research highlights the permanent impacts that power dynamics impose on identity processes, as well as the role of culture to overcome these obstacles. I conclude with suggestions for possible avenues to both complicate and contribute to conversations surrounding the ongoing identity negotiations for Chilean exiles in the U.S.

The levantamientos of 1990 and ’92 in Ecuador demonstrate the incredible ability of indigenous political organizations to present local concerns at the national level. After 500 years of resistance and oppression, the government was forced into serious political negotiations. I hope to add to an ongoing conversation regarding indigenous political organization in Latin America by studying the specific case of Ecuadorian indigenous peoples of the Oriente, and the construction of political voice in response to government policy, the actions of private companies, and the involvement of international lending organizations that led to years of unfettered, destructive practices of extraction and colonization in the last half of the 20th century. Through an analysis of documentary film, academic writing, and media coverage, this project looks to show that this struggle has been wrought with contradictions and unintended consequences and characterized by a high level of coordination at the local and national level. Emphasizing contradictions in the construction of political voice is appropriate in a discussion of political representation of historically marginalized or excluded peoples, who more than ever occupy an uncertain borderland space. I think it is crucial to understand that, in the construction of indigenous political voice, contradictions reinforce the borderlands they seek to escape, or the dominant power structures.

The infamous dictator Augusto Pinochet came to power through a bloody coup on September 11, 1973 and drastically changed the face of the Chilean government. His regime instituted strict policies of neoliberalism that led to the privatization of the university system. Forty years after the coup, many of these policies remain in place, untouched and accepted as the reasons behind Chile as the ‘economic miracle’ of South America. However, tensions under these neoliberal policies, specifically in the university system, fomented a recent eruption of political activism in May of 2011. Why is it that Chile, one of the most economically ‘successful’ countries in South America and the ‘pride’ of the IMF and World Bank models, is seeing the rise of a powerful student movement against neoliberal legacies? My research juxtaposes the master narrative of Chile as a ‘model country’, in terms of hegemonic modernity, against the experiences of the Chilean university students who have fought to challenge it. I argue that the catalyst behind the student movement can be in part explained by the legacies of Pinochet’s repression and the political struggles of past generations. This contradictory temporal space forms a ‘generational borderland’. These generational ruptures combined with the legacies of repression, have led to the emergence of new forms of innovative and marketable protest, cultivated longevity for the movement through the mistrust of politicians, and inspired a reinvigoration of the Communist Party of Chile.

The purpose of my research is to examine the impact of an Afro-centric prototype (ACP) on target populations utilizing Community-Based Education (CBE). I define an Afro-Centric Prototype as a distinctively positive symbol that frames black people with an affirming perspective that promotes a constructive self-image. I characterize CBE as instruction occurring outside typical school facilities, and instead in community centers, bookstores, libraries, faith centers, etc., commonly accessible to the public. ACPs can exist as a person, object, or geographical region, and is communicated through language that results in black student confidence building and impacting non-black students in a similar manner. The ACP in my research is St. Maurice, a black General of the Holy Roman Empire that originated from the Nubian Kingdom of Africa. My non-profit organization, The Good Pharaoh Foundation was in the land of St. Maurice in 2011. My discoveries in Africa pointed to extensive evidence of this ACP’s impact on western civilization, culture, and society. Maurice is venerated amongst the early Kings of Europe and all Popes of the Church. Present-day leaders such as Colin Powell have been inducted into the order of St. Maurice. His influence on European and African culture are both fascinating, and world-impacting. I will hold a series of ACP lectures on St. Maurice and compare the resulting impact on black students occurring in CBEs to classical school classrooms. I will also investigate if the CBE sessions create a demand for additional research, activities, and publications that further promote the Afro-Centric prototype of St. Maurice. I hypothesize that positive learning experiences will occur in the CBEs indicating a need for allocation of further resources in CBE environments.

From a young age, every child in Singapore is taught that the surest way to succeed in life is to have academic success. Education is seen as a way to secure your bread and butter as it leads to a well-paying job, which then allows you to afford a comfortable lifestyle. Of course, few would argue against education being one of the most important things in a person’s development. But when the stakes for being the smartest in your class are so high, the education system inevitably becomes a rat race for the highest numbers and the best scores. There is an “overbearing focus on grades and paper qualifications are elevated to unholy heights and worshipped,” and this pressure gives birth to a generation of Singaporeans who are risk-averse, lack the motivation to think critically, and don’t have the drive to innovate. The Singaporean education system is touted as a meritocratic one that allows students the freedom to climb the social ladder provided that they are hardworking enough to achieve the grades to advance. A meritocratic system seems fair as grades and paper qualifications don’t lie, but this encourages a tunnel-vision approach to education, ignoring the many aspects of education which cannot be measured by numbers. Is meritocracy at fault, then, for creating a generation of humanistic robots? I will examine and critique the current educational system in place by highlighting its faults and advantages, as well as by drawing contrasts with the systems in other countries. I hope to propose a way to reform Singapore’s education system for the better, to one that is more holistic, aiming to produce a generation of creative and motivated thinkers, which will help Singapore progress even further into the 21st Century.

One of the most universal problems faced by persons with transtibial amputations is volume fluctuation of their residual limb. Since the shape and size of a prosthetic socket stays the same, fluctuations in limb volume affect the fit of a socket. For example, if a prosthesis is too tight; pressure spots, skin irritation, and muscle atrophy can occur. Conversely, a loose prosthesis creates gait instability and compromises the comfort of a patient’s prosthetic. Prosthetic socks of different materials and thicknesses are worn to compensate for the changes in volume and manage the discomfort created by daily and monthly volume changes. Properly fitting a residual limb to a socket is further confounded since the industry standard measurement of sock thickness is Ply, a non-linear unit of measurement. Our research examines how absolute thickness and material properties of prosthetic socks change with regular use. We measured the thickness and compression response of new out-of-box socks at three distinct points while in a donned condition. Measurement locations corresponded to area traditionally related to high interface stresses. Thickness and compression response were measured by a custom instrument. Participants walked for two hours while wearing a new sock, after which thickness was measured again in all three locations. Afterwards, volunteers took the socks home, along with a activity monitor, for regular use and returned every two days for one week, and then weekly for a month to re-assess sock thickness and response. The compression response after two hours of walking was used to validate cyclic testing conducting on an Instron material testing machine. Thickness response over long periods of normal use was used to characterize sock fatigue. We hope our study will help practitioners create more accurate volume management recommendations for their patients with a new understanding of the sock stiffness and durability.

The field of tissue engineering is becoming increasingly aware of the role that the extracellular matrix (ECM) plays in driving cellular structure and function, especially in highly anisotropic skeletal muscle. Skeletal muscle is a cell dense tissue composed of bundles of aligned myotubes responsible for lateral contraction. Replication of this organization is critical for engineering physiologically-relevant tissue constructs. The fibrous nature of the ECM has led us to the use of bio-inspired topographical line patterns on the nanoscale. We employ UV-assisted capillary force lithography to generate polyurethane-based substrates which stimulate cell elongation and alignment. By incorporating glycidyl methacrylate into our substrates, we present a novel method for engrafting a brush polymer coating of the temperature responsive polymer p(N-isopropylacrylamide) (NIPAAm) onto nano-topographically defined substrates. Seeded with C2C12 mouse skeletal myoblasts, these substrates allow for the harvest of intact cell sheets without the use of enzymes. Using a gelatin coated plunger, these cell sheets are stacked to form tri-layer thick tissue constructs. This study explores the effects of a 3D microenvironment on mature myotube formation and the ability of our NIPAAm-based system to control myotube dimension in 3D by altering nanotopography dimension as well as layer number and the timing of differentiation, contributing to the understanding of the 3D microenvironment in regulating the skeletal muscle cell niche. In addition to paving the way for clinically-significant cell-based therapies, this work may prove vital to the development of advanced in vitro drug screening platforms for patients suffering from muscular dystrophy.

Matthew G. Lewis' Gothic novel The Monk (1796) has often been read as a representation of England's disapprobative response to the violence and chaos of the French Revolution.  The novel's subtle treatment of paranoia, which was a common theme during the Reign of Terror, and clear defilement of the virtuous feminine icon of ancient European government indicates a strong ambivalence toward revolutionary sentiment.  It is perhaps a result of its proximity to the events of the French Revolution that its location within the latter years of the Age of Enlightenment is often overlooked.  During the Enlightenment, reliance upon God as a source of meaning had dissipated in favor of understanding humanity through itself. I will argue that The Monk's depiction of intensely oppressive, Godless religious societies suggests the consequences of this shift.  Without a connection to the sacred, humanity spirals toward damnation; the extremes of unconscious desire are inseparable from the individual and activate supernatural forces within the novel.  Lewis creates a scene akin to that of Original Sin in the Book of Genesis, wherein the consequences of succumbing to temptation are not only inevitable but inescapable: the fall of humankind is unavoidable, and God's absence renders redemption impossible.  Ultimately, the novel offers a reconstruction of the Biblical parable in a way that expresses ambivalence about a secularized, post-Enlightenment world from which events like those of the French Revolution can only be expected.

Many have demonstrated that Edmund Burke and other male writers contributed to, if not constructed, a gender binary in which males perpetually subdue and dominate the feminine. For instance, in A Vindication of the Rights of Men, Mary Wollstonecraft deconstructs passages from Edmund Burke's Reflections on the French Revolution, demonstrating that his ideal world is one in which sublime, masculine authority usurps the rights of women. For Wollstonecraft, Burke's efforts to counter revolutionary ideas are of no benefit to women. While these readings are certainly valid, some scholars have expressed the concern that in limiting our understanding of masculinity to its being a fixed institution determined to maintain power over women, we are grossly over-simplifying individual as well as collective masculine experience(s). Thus, I hope for this project to contribute to a more complex portrait of masculinity particularly in the late 18th century. Limiting my discussion to Burke's Reflections and Thomas Paine's Common Sense, I argue that however much these two literary works convey opposing ideologies, elements of their rhetorical strategy reveals that both writers understood that the success of their arguments largely depended on how effectively they controlled the semantic value of manliness. In order to provoke revolution, Paine seeks to assure his readers that engaging in revolution is an indisputable reflection of manhood. But unlike Paine, Burke wrote in order to prevent revolution. In the Reflections, Burke argues that the failure to sustain the pre-established order would result in the failure to retain masculinity. Ultimately, that Paine and Burke fought to control the meaning of manhood suggests masculinity was a loosely defined social institution--one consisting of males who lived in perpetual fear of losing, or failing to perform their masculinity; who were ever in need of affirmation that they were, indeed, men.

The idea of poetry as a literary practice that is concerned with its own ontology has developed through the device of the ars poetica poem—poetry about poetry. Beginning with Horace’s ancient treatise Ars Poetica, published in c. 18 BCE, poets throughout history have sought to explain the nature of their craft through the medium of their craft. In the past century, ars poetica poems have morphed into examples of metalanguage, in which the poems work as vehicles to carry the defining characteristics of poetry itself. In order to track the movement of metalanguage, I examine the progression of the ars poetica poem from the Classical era to the Enlightenment to Modern twentieth and twenty-first century works. My research traces and analyzes the trajectory of poetic modes that discuss language itself. Shifts from didactic to introspective to aesthetic have marked the rhetorical turn of ars poetica, thus exemplifying how poetry as heightened language creates the need for metalanguage. In poetry more than any other literature, each component element is significant, so the elements of a poem inevitably turn in on itself. Ars poetica poems demonstrate how images, rhetoric, narrative, and linguistic mechanisms can all be self-referential. The presence of metalanguage in poetry suggests that the types of poetic knowledge—sensory, emotional, and imaginative—are more than externally meaning-making about “aesthetic” and “ethic” subjects, but that they are intrinsically expressing the nature and value of poetic theory.

Like their Victorian forebears, Modernist authors have always placed keen emphasis on women’s hair, often presenting their luscious locks in vivid and scrupulous detail. Aldous Huxley's Crome Yellow (1920) uses hair as a tool of social commentary and trope of the fairytale epic to challenge and even reverse traditional Victorian gender roles and sexuality norms. The tension between the private and public self is also explored; what Modernist women could not say aloud, they expressed through the style, color and length of their hair. Crome Yellow constantly alludes to the hair of the female protagonists Jenny Mullion and Mary Bracegirdle, yet the intentions behind the loaded descriptions of their physical appearance are left up in the air. The characterization of an infamous Fallen Woman and modern flapper girl allows distinctions to be made between the Victorian and Modernist eras that determine the emergence of new gender ideals. This paper will use a close reading of Crome Yellow and Freudian theories on sexuality to explore the multifaceted significance of hair in the Victorian era so we may fully appreciate the past’s influence on modernist eras. A woman’s hair became a phallic image used to engender fear in men, which posits a move towards gender equality and the emergence of the suffragette. Hair was no longer just a physical attribute but a body politic that reflected changes taking place in modernist British society of the entre deux guerres period.

 From the fillers that give body to ordinary paper to the antacids that relieve indigestion, calcium carbonate suspensions play an important role in our day-to-day lives. It is often desirable to work with slurries that contain the highest possible fraction of solids. The goal of this research has been to investigate ways to improve the flow of high solids dispersions of calcium carbonate through the use of of rheology modifiers. These are chemicals which, when added in small amounts, allow the dense slurries to flow as easily and smoothly as possible. Improving flow characteristics of high solids dispersions has a huge potential for reducing the amount of energy needed for various processes, such as pumping, coating and de-watering. One very promising modifier has been found to be sodium polyacrylate . Both traditional and new products, like nano-sized calcium carbonate particles, have shown significant improvements using this modifier. In this research, the rheological properties such as the viscosity function and the yield stress are determined as functions of additive amount, volume fraction of solids, and pH of the aqueous dispersion medium. All of these have been shown to important parameters in achieving optimum performance.

Gas sensors are widely used in daily life and industry. An important application of gas sensing is the monitoring of environmental factors affecting health, such as the concentration of carbon monoxide, in populated areas. However, most conventional gas sensors are powered by batteries, which need periodic replacement. The goal of this project is to integrate a Wireless Ambient Radio Power (WARP) energy harvesting platform with a new class of amperometric electrochemical gas sensors, provided by KWJ Engineering, Inc, to create novel battery-free gas sensor nodes. The WARP sensing platform, developed in Dr. Joshua Smith’s group, utilizes ambient radio frequency (RF) energy from common sources such as cellular towers and TV broadcast stations, which provide a reliable and pervasive 24-hour power source. The gas sensors manufactured by KWJ Engineering possess the advantages of low power, low cost, high sensitivity, and high selectivity. Particularly, the low power requirements of the gas sensors make it possible for them to be powered by the RF energy harvested by the WARP platform. Currently the potentiostat circuit needed to properly bias the gas sensor and acquire the gas concentration is being developed. The gas sensor circuitry will be integrated with the WARP platform to produce the battery-free RF-powered gas sensor nodes, followed by system optimization for reliable and efficient operations. With such gas sensor nodes, long-lived wireless sensor networks with zero maintenance cost could be deployed in continuous toxic gas monitoring applications, including air quality monitoring in cities and process control in industry.

Titanium dioxide (TiO₂) displays a variety of interesting properties and has been intensely investigated for applications in environmental cleanup, photocatalysis, dye-sensitized solar cells, and semiconductor fabrication among others. However, the underlying mechanisms which govern TiO₂ chemistry are not well understood. Here, the tendency for reduced TiO₂ nanoparticles to donate stored electrons to other reagents is being characterized. The reduced ("charged") nanoparticles are made by UV irradiation which excites an electron from the valence band to the higher energy conduction band of the TiO₂ nanoparticles. In the absence of oxygen and other oxidants, the charged TiO₂ nanoparticles are stable and can be easily monitored by their absorption of visible light and blue color. We are exploring the chemical reactions of the charged particles. If the optical spectrum changes after the addition of other reagents, that is an indication that the nanoparticles are reducing the reagents. Removal of the electrons from the nanoparticles has been previously accomplished using aqueous Cu²⁺, but not Zn²⁺ or Mn²⁺. I am repeating this result and extending it to other metal ions such as Cr³⁺ in order to estimate the standard reduction potential of the charged particles. In addition, I am studying optically and via NMR whether dimethyl sulfoxide (DMSO) is reduced to dimethyl sulfide by charged TiO₂ nanoparticles. Because one-electron reduction of DMSO results in extremely unfavorable intermediates we are probing whether the reaction by charged TiO₂ occurs by the direct transfer of two electrons from the TiO₂ nanoparticles to the DMSO. These studies will provide valuable insight into the electronic chemistry of TiO₂ and will aid in the application of TiO₂ to other systems which require the transfer of multiple electrons.

Electrophoretic displays, such as the Kindle®, currently employ electrostatic effects in apolar media to create a paper-like display. In an electrophoretic display, images are comprised of black and white pixels generated by applying an electric field to reposition charged pigment particles. The optimization of this technology is limited due to the incomplete knowledge of the mechanism(s) by which particles acquire charge in these systems. My project explores the charging behavior of carbon black pigments dispersed in apolar media. Previous studies of mineral oxide particles have provided support for the theory of an acid-base charging mechanism for particles dispersed in apolar media with various charge stabilizing surfactants. My current work looks at the possible extension of the theory of an acid-base charging mechanism to carbon black pigments in apolar systems. I have investigated the charging behavior of four different carbon black pigments by measuring the electrophoretic mobility of each pigment dispersed in solutions of heptane, and a charge stabilizing surfactant at varying weight percentages. Three surfactants were used for charge stabilization: Aerosol OT, SPAN 80 and OLOA 11000. Aerosol OT is a neutral surfactant in water, whereas SPAN 80 is acidic and OLOA 11000 is basic. The surface characteristics of each carbon black pigment were studied by Inverse Gas Chromatography (IGC) and X-ray Photoelectron Spectroscopy (XPS). The preliminary findings of my investigation show the sign of the charge for the carbon black pigments to be dependent on the charge stabilizing surfactant used.

Serotonin (5-HT) is implicated in numerous emotional behaviors, including depression and anxiety. One form of serotonin receptors is the 5-HT_1B autoreceptor, which is involved in regulating 5-HT transmission and uptake. 5-HT_1B autoreceptors are located on serotonergic neurons and are pharmacologically indistinguishable from 5-HT_1B heteroreceptors located on non-serotonergic neurons. Distinguishing between activation of the two receptor types is important as they have different functions. A novel strategy to accomplish this is to use an engineered receptor to mimic the 5-HT_1B autoreceptor using a modified DREADD receptor (Designer Receptor Exclusively Activated by a Designer Drug). The DREADD-1B receptor will mimic the 5-HT_1B autoreceptor function with pharmacological specificity. The DREADD-1B receptor is G_i/o-coupled G-protein coupled receptor that is activated by the selective ligand clozapine-N-oxide. When G_i/o-coupled GPCRs are activated, decreases in intracellular adenylyl cyclase and, subsequently, cAMP levels are measured. It is expected that when the DREADD-1B receptor is activated, a decrease in cAMP levels will be observed. To verify this, I created a stable DREADD-1B cell line and will use transient transfections of a luciferase plasmid to measure cAMP levels via proportional luminescence using luciferin. Optimizing the conditions for receptor activation and observing sufficient decreases in cAMP levels will confirm the general functionality of the receptor. If there are large variations in the downstream biochemistry between the DREADD-1B receptor and the 5-HT_1B autoreceptor, using the DREADD-1B receptor as a surrogate for the 5-HT_1B autoreceptor could have profound effects on behavioral data obtained in other projects. Creating and characterizing the DREADD-1B receptor in an in vitro setting will provide valuable information and tools for future projects involving the 5-HT_1B autoreceptor and this novel tool.

Dravet syndrome (DS), also known as severe myoclonic epilepsy of infancy (SMEI), is a rare genetic form of epilepsy, caused by a mutation in the neuronal voltage-gated sodium channel, NaV1.1, encoded by the SCN1A gene. This form of epilepsy is characterized by febrile seizures at infancy that often change with age into afebrile seizures, which include generalized tonic-clonic and myoclonic seizures. In most cases, DS is a debilitating disorder that renders patients with decreased cognitive function and impaired development. To study this disorder, a mouse model of DS, with heterozygous deletion of the SCN1A gene (Scn1a +/-), was developed, demonstrating a phenocopy of the DS condition, with similar seizure patterns and atypical behaviors. In vitro work in the model demonstrates selective loss of sodium current and excitability in hippocampal GABAergic interneurons. However, it remains unknown if similar changes in neocortical GABAergic interneuron excitability occur. We hypothesize that fast spiking neocortical interneurons are responsible for control of cortical excitability via GABAergic inhibition and that reduced excitability of fast spiking interneurons associated with heterozygous loss of NaV1.1 contributes to hyperexcitability and seizures. To explore this hypothesis, we will compare neocortical interneuron excitability measured from single action potential parameters and repetitive action potential firing patterns in unaffected wild type mice and the DS mouse model, using pre-existing single-cell recordings. Excitability will be determined from the peak amplitude, width at half height, threshold for single action potentials, and from total number of action potentials in induced neuronal spike trains. If this hypothesis is correct, we expect that there will be atypical action potentials and firing patterns showing reduced excitability. This experiment will provide more insight into DS epilepsy and better therapeutic targets for the disorder.

The primary cilium is a sensory organelle found on most cells. In the brain, most or all neurons contain a single primary cilium, yet its function is not entirely understood. Ciliopathies are defined as a group of disorders physiologically characterized by malformation or dysfunction of primary cilia, which in turn result in a variety of symptoms including cognitive deficits, retinal blindness, situs inversus and polydactyly. The serotonin 6 receptor (5-HT6) is the only 5-HT receptor that localizes to neuronal primary cilia, and previous research has implemented the receptor in learning, memory, and drug addiction. Our experiment will investigate the link between neuronal primary cilia and 5-HT6 in an attempt to better understand the significance of this unique localization. Using an immortalized line of rat adrenal cells (PC12), we will express the 5-HT6 receptor using viral vectors, and then pharmacologically manipulate the activity of the receptors with either an agonist (WAY 399885) or an antagonist (SB 208466). We will first stain the cells using immunohistochemistry, then image using florescence microscopy, and lastly quantify the morphological change in primary cilia length. We expect to see a shortening of primary cilium in response to the introduction of an antagonist, and an increase in length with an agonist. Since the 5-HT6 receptor has been shown to be homologous between rats and humans, a practical application of this research could eventually result in a pharmaceutical solutions to some of the cognitive symptoms associated with ciliopathies like congenital cerebellar ataxia or Joubert syndrome.

The use of a fluorometer as a proxy for cell counting is a common method to track phytoplankton culture growth. A fluorometer works by emitting a beam of light, which excites the electrons in chlorophyll a, causing it to emit residual light. The fluorometer then measures the intensity and wavelength of that light. This information helps identify the relative abundance of cells present without giving a direct cell count. When conducting experiments involving the growth rate of photosynthetic cells it would be more beneficial to know the direct cell count as opposed to relative chlorophyll abundance because it is possible they may not correlate exactly as cells have the ability to adjust the ratio of chlorophyll in response to differences in light used in culturing. The marine picocyanobacteria, comprised of the genera Prochlorococcus and Synechococcus, are the most abundant photosynthetic organisms on Earth. I will culture five strains of picocyanobacteria in batch cultures using artificial seawater media in varying light and temperature conditions. I will measure the relative fluorescence of the chlorophyll a in the cultures at regular intervals throughout the growth cycle of the batch cultures. At the same time I will also measure the cell abundance using the flow cytometer. The flow cytometer will individually count and characterize the cells by chlorophyll fluorescence, accessory pigments, and cell size. My hypothesis is that the fluorescence based proxy of cell abundance measured by the fluorometer will highly correlate with the cell count from the flow cytometer, but that exact cell counts will vary under different culturing conditions. My results will be able to provide scientists who use the fluorometer as a proxy for growth a better understanding of the actual number of photosynthetic cells growing in each tube.

Francisella noatunensis is an emerging fish pathogen that causes disease and mortality for several economically important fish including tilapia and Atlantic cod. The Francisella Pathogenicity Island (FPI) is a region of the genome known to govern virulence for the genus. PdpA is one of the genes found in the FPI that has been implicated in the ability of Francisella tularensis, the human pathogen, to replicate in infected phagocytes. A recent study by our laboratory using zebrafish as a model host indicated that pdpA is important for the ability of F. noatunensis to cause mortality in infected zebrafish—thus the functional role of the pdpA protein appears to be conserved for the genus. Our goal is to compare the innate immune response of zebrafish during infection with either wild type or pdpA knockout strains of F. noatunensis to determine if the host immune response is altered. To accomplish this, we are monitoring the expression of key proinflammatory genes (IL1B and TNFA) using quantitative RTPCR during acute Francisella infection in zebrafish. The results from this study will provide additional information about the potential use of the F. noatunensis pdpA knockouts as live vaccine candidates for fish.

Administration of Anti-Retroviral Therapy (ART) slows disease progression and reduces HIV-1 viremia to near undetectable levels. Poor adherence or withdrawal of therapy often results in rapid rebound of viremia with the potential for the establishment of drug resistant variants. HIV is known to establish latency in long-lived central memory T-cells (CM) and is often referred to as “the reservoir”. However, we now understand that there is both latent and actively replicating HIV-1 that comprises reservoir sites. Using sequence information and computational tools we can define reservoirs as cells or tissues harboring HIV-1 with genotypic features of reduced temporal structure, high diversity within the population, and low divergence from their most recent common ancestor (MRCA). This is because reservoirs are populated with virus seeded at both early and late periods of infection. If a reservoir is established in a site with reduced drug penetrance, “drug-sanctuaries”, continued viral replication and diversification could occur. This may result in the accumulation of drug resistant variants that lead to therapy failure. Here we hypothesize that tissue and cellular sites with phenotypes reflective of reservoirs may also be drug restricted providing a boundary for unrestricted viral replication. To test this hypothesis we sequenced single genome template derived amplicons (SGA) of env and pol regions of HIV-1. Presented is data from the autopsy of subject S104. S104 presented with multi-drug resistant genotypes in all tissues sampled. Bioinformatical analysis measuring viral genetic diversity within and divergence from the MRCA of the viral population of S104 demonstrated reservoir phenotypes in tissue virus isolated from lung. We continue to expand our characterization of reservoirs and compartments to clearly define sites that must be targeted to eradicate HIV-1 in the host.

My project explores the stereoscopic technique to express Mt. Rainier in 3D images for the first time.  By extending the camera distances to fabricate the vision of a giant, the mountain and its surrounding terrian is experienced disembodied, yet familiar. This effort represents a 3-year culmination of art-practice with the stereoscopic-3D video medium. Experiments with projection surfaces, short film, video-installation art, and computing have placed me as a leader in the field at the University. Stereo-3D's rise and fall in popularity and its function in popular culture is easily visible, but my research places it in the Fine Arts context in an attempt to embed 3D video in a tradition of visual poetics and technique.

Ai WeiWei, a contemporary Chinese artist and self-described "dissident," is the first to admit that political activism forms the basis of his aesthetic. In an artist’s statement, from a recent exhibition at the Hirshhorn Museum in Washington, DC, Ai plainly stated: “I’ve always believed it is essential for contemporary artists to question established assumptions and challenge beliefs.” The majority of Ai’s installations at the Hirshhorn function as a platform for his renegade agenda, and his piece He Xie is no exception. The striking collection of ceramic river crabs, in various shades of red and brown, is invested with manifest symbolism. However, a deeper investigation of the work reveals a latent significance, not readily gleaned from a limited investigation of its formal elements. In order to adequately engage with Ai’s work, one must look beyond the surface and trace the installation back to its historical origins and cultural conditions. To draw out his strategic use of symbolism, I analyze Ai’s installation according to German art historian Erwin Panofsky's iconographical approach. Panofsky begins with the simplest translation of visual forms and works his way toward a more nuanced historical and culturally relevant perspective. In short, Panofsky’s three-pronged methodological approach allows me to demonstrate the complexity of Ai’s He Xie. In this presentation, I discuss the conceptual stimulus behind Ai's sprawling display of porcelain delicacies, exploring its political significance and identifying a larger metaphysical trend in the artist's career.

When looked at in chronological order, it is impossible to deny that the work of Francisco Goya (1746-1828) underwent a major shift in style, palette, medium and content in the middle of his life. Past scholars have pointed out that there are multiple reasons for this shift, including Goya's increased involvement in the turbulent politics of eighteenth century Spain and his fascincation with the aging process that only increased with his own age. Another frequently cited cause is the onset of deafness that the artist suffered after a near fatal illness in 1792 at the age of forty six. The relationship between his deafness and his new found forms of expression has been explored by scholars in a variety of fields. In my research on the topic, I have gathered information from otology and neuroscience periodicals and placed them alongside art history and biographical information, blurring the line between the art and science of Goya. Along with these unusual sources, I will be taking a different approach in terms of my visual analysis of Goya's work. Most scholars resort to analyzing his most famous paintings to point out the differences between his early and late style, such as his royal portraits and "Saturn Devouring his Children" (1819-1823). I have decided to use three of his seven known self-portraits instead: "Self Portrait 1" (1773), the frontispiece for "Los Caprichos" (1798), and "Self-Portrait with Dr. Arrietta" (1820). I chose to examine these self-portraits because Goya created them at three pivotal points in his life and they reflect the artist's self-image at the time. Goya was very self-aware of his position in the universe and his extraordinary knack for creating truthful depictions allow his self-portraits to freeze him in time for us to dissect hundreds of years later.

 The field of kinetic and interactive sculpture has been the focus of my research. Capturing the subtleties of movement in structures, experimenting with materials, and creating a slow, organic shifting of materials that functions as an open system in a modular kinetic sculpture which coexists with other elements in a space as an installation is the focus for my investigation of movement, fluidity, and flux as it relates to memory, shared experience and secrets. The central sculptural element in this installation uses modularity as a metaphor for this. Incorporating bones on the floor of the gallery along with a sound element tie together this experience as I explore the creation process of a whole and integrated installation. The next part of my research will incorporate the movement mechanisms more seamlessly as I will replace visible motors with nitinol muscle wire.

Breast cancer tumors are classified within different subtypes based on the expression of three types of cell surface receptor proteins.  These proteins connect the extracellular environment with cellular activities via signaling pathways.  To elicit cell responses, signaling pathways employ protein phosphorylation as a regulatory mechanism, as adding a phosphate group to a particular protein can switch its activity on or off.  However, normal signaling can go awry if mutations in signaling proteins lead the cell to believe its components are always phosphorylated and active.  Consequently, the entire signaling pathway functions abnormally, which can lead to uncontrolled cell growth characteristic of cancer.  Given its potential role as a molecular mechanism of disease, our research focuses on obtaining a global view of the phosphoproteome, or the cell’s entire set of expressed, phosphorylated proteins, of 10 breast cancer cell lines.  To generate lists of phosphoproteins present in these cell lines, we are concurrently extracting and analyzing cell line phosphopeptide samples via mass spectrometry, an analytic technique that produces characteristic spectra for individual phosphopeptides that are then matched to a library of known protein spectra through the use of computer algorithms.  In our preliminary results, we have generated large-scale data sets identifying thousands of phosphorylated proteins present in two cell lines and generated side-by-side comparisons of the proteins expressed in each line.   By identifying common phosphorylated proteins across all of the cell lines, our goal is to deduce a molecular signature for breast cancer.  This signature can be used in future studies to design a universal protein inhibitor drug as an alternative anti-cancer therapy.   By identifying the phosphoproteins exclusive to each cell type, we can uniquely characterize specific proteins active in one type of breast cancer which may facilitate development of inhibitor drugs as a form of personalized medicine.

Earmark spending has proven to be a popular political tool for members of Congress because it allows them to claim credit for a concrete economic benefit for their districts. I ask whether expectations of political benefits similarly influence large-scale stimulus spending allocations and, more importantly, whether these allocations have political benefits for the incumbent president. This research project examines the link between federal spending and shifts in election outcomes. It asks whether spending in the stimulus package of 2009 substantively influenced President Obama’s share of the popular vote in 2012. Other things equal, did competitive regions of the nation receive disproportionately more spending, and was that spending associated with increased vote shares for the incumbent president between 2008 and 2012? To answer these questions I examine government spending and popular vote shares in over 3,000 counties from 2008 to 2012. I also control for underlying social and economic issues by county, such as foreclosure and unemployment rates. Finally, I control for other political influences on stimulus spending, including whether certain counties had representatives in powerful congressional roles. Overall, this study will promote understanding of the political implications of large-scale federal spending. It will also shed light on the political dynamics of “swing counties” and whether stimulus spending is a useful political tool for winning these counties.

Around 650 health services professionals in the Washington State Department of Corrections provided care for over 24,000 inmates in the last year, and the number of people being housed in correctional facilities is on the rise. Discourse abounds regarding the necessity and adequacy of health care provided to this growing population in the US, yet the bulk of this discourse applies a biomedical lens. This exploratory study employs qualitative methods to examine the role of the health care provider in the prison environment in an effort to understand the factors within the correctional system that influence the provision of health care in prisons. Through participant observation, in-depth interviews, and cognitive mapping, this study aims to shed light on the interactions among the medical staff, correctional staff, and inmates. All research is conducted at a single Washington state prison. Interviews are conducted with around 10 health care professionals who volunteered to be interviewed; field notes are taken during the course of interviews and observations; and diagrams expressing inmates' perceptions of the process of receiving care are collected. For analysis, open coding is performed to identify significant themes in the data, and closed coding is performed to explore the themes more deeply and make connections among them. An understanding of how these major players in correctional health care perceive health care and perceive each other has the potential to help increase the effectiveness of care.

My research details how the austerity measures enacted at the federal, state and county levels have impacted women's reproductive healthcare in Washington State since 2008. This project examines how public-private partnerships have emerged in response to widening disparities and cutbacks in women's reproductive healthcare access and provisioning. Through a case study of an NGO dedicated to enhancing women's access to reproductive health care, I demonstrate that new models of public health provisioning are emerging to fill the void left by the neoliberal rollback of state sponsored public health programs. In order to examine the ways in which austerity measures have impacted women's access to reproductive healthcare services in Washington State, I engaged in archival analysis of State budget documents detailing cutbacks/shifts in public health funding for the past five years. Additionally, I interviewed employees of the Washington Department of Health (DOH) and King County Public Health (KCPH) about the impact of funding decreases on their service provision programs. After establishing this broad landscape of state disinvestment, I moved into an examination of my case study organization and the ways in which shifts in funding structures for public health have facilitated the creation of new models of health governance.

Perineuronal nets (PNNs) are a matrix of proteins that surround nerve cells and reinforce the most often used synaptic connections between neurons, essentially hard-wiring neural connections made as a child into permanent pathways that respond to specific stimuli. By dissolving these PNNs, we recreate the plasticity characteristic of a young developing brain, granting us the ability to rewire the brain with respect to any stimulus. In this study, we are looking at PNNs within the vestibular system – the sensory system that, under natural conditions, is primarily responsible for maintaining images on the fovea during movement. Hair cells within the semicircular canals of the vestibular system register head accelerations and then send reflex signals through vestibular afferent nerve endings to extra-ocular eye muscles that drive eye movements. This vestibular ocular reflex aids the maintenance of stability of images on the retina. As a therapy for vestibular loss, our lab has developed a vestibular prosthesis that electrically stimulates the afferent nerve endings of the vestibular system, thereby simulating natural vestibular response to movement. This electrical stimulation, however, spreads to untargeted as well as targeted vestibular afferents and cause inaccurate eye movements as a result. By dissolving the PNNs in the vestibular nuclei and then allowing them to regrow during a period of adaptation, we hope to suppress inappropriate eye movements in response to our prosthesis’ electrical stimulation. If our lab can prove that electrically elicited eye-movements become more accurate after the dissolving and guided re-growing of PNNs, we can show that it is possible to restore plasticity to the brain and shape its neural connections through controlled electrical stimulation to the target system. By extension, such results will ascertain if it is possible to use this method to re-wire a physiological system to accept prosthetic stimulation in place of a non-functioning system.

The vestibular system is responsible for maintaining stable vision and posture by interpreting accelerations of the head in various planes. Impaired function of this system can cause debilitating vertigo, as seen in Meniere ’s disease. Our lab has developed a prosthesis that aims to counteract these deleterious pathologies through electrical stimulation, and our research is directed towards improving the effectiveness of this device. In order to stabilize gaze, the vestibular system must incorporate demands from several neural inputs, many of which are dependent on direction of the line of sight. Additionally, the effectiveness of electrical stimulation may be altered by the background activity of the activated neural pathways, which vary with orbital eye positions. Therefore, in this study, I am focusing on the dependency of stimulation-evoked eye velocities on initial position of the eye. I have collected data from two Rhesus Macaques by stimulating the right lateral, posterior, and superior semicircular canals at different eye positions. My data shows linearly graded velocities depending on stimulus amplitude, so it is clear that eye position must be taken into account when evaluating eye velocities. Speculation into the cause of this phenomenon will help to better customize our implant’s effectiveness according to the physiology of the patient in consideration.

What is a “straight” spine? What do people mean when they refer to a straight spine in a dance class? Are they talking about a lengthened spine, which can represent a well-supported postural alignment? Unfortunately, an instructor’s improper use of language can often lead to a student’s misinterpretation, resulting in injuries and life-long alignment problems including less efficient and dangerous movement patterns. Posture and alignment are an important part of every dance class, as they instruct not only how dancers carry themselves, but also how they prepare for and react to movement, however, verbal postural cues vary widely, and have differing amounts of success in achieving a healthy postural alignment in students. By observing classes of multiple levels, styles and ages I have gathered information regarding the language used by dance instructors to describe posture in the classroom. This research, combined with information from dance literature, and clinical language used by physical therapists has allowed me to determine that some verbal cues are more effective than others in eliciting a healthy supported spine in the classroom.

Among the library of plays known as “classics” within Japanese theatre, few compare in longevity, versatility, and uniqueness to Kanadehon Chushingura. This work weaves the tale of 47 loyal retainers enacting revenge on behalf of their deceased leader by murdering the man responsible for his death. The play draws on themes of loyalty, trust, and righteousness. First debuted in 1748, this story has been adapted hundreds of times into multiple artistic mediums, including kabuki and bunraku theater, woodblock prints, and film. However, unlike most literary classics of the Western World, Chushingura’s compelling plot was drawn directly from current events. Through the examination of primary and secondary sources, as well as through close reading of Kanadehon Chushingura, I have traced the transition of Chushingura from fact to folktale. This research begins with the actual bloody events that inspired the story. I later explore the event’s changes and adaptations for the purpose of both suiting its consumption by the merchant class in Edo period Japan, and to evade censorship by the shoganate government. My research concludes by following Chushingura into its role within contemporary entertainment. I hope to accurately chronicle the metamorphosis from historical event to contemporary folktale and thus invite others to examine the origins of what they may consider familiar. Doing so will result in a more accurate catalog of our cultural origins for both current and future generations.

In the urban centers of Senegal, graffiti artists work to deconstruct the memories of the former French colonial apparatus by refurbishing public spaces with new and sacred meaning.  These artists belong to the Muridiyya Sufi tariqa, an order of Islamic mystics, and the basis of their art is reimagining the only known photograph of the order's enigmatic founder, Cheikh Bamba.  This photograph, taken by French authorities while Bamba was under house arrest in 1913, has been used as the matrix image for subsequent representations of the Cheikh.  This paper will explore the efforts of those contemporary Murid artists who adorn the city walls of Senegal with Bamba's likeness, relating their endeavors to the writings of social critic Walter Benjamin and cultural theorist Stuart Hall.  For the Muridiyya, images of Bamba function as transmitters of his baraka, his divine blessings.  As a receptacle of this baraka, public space is transformed in a process that I will compare to the Muridiyya's appropriation of land controlled by the French during the tariqa's formative years: members of the order, the Murids, had initially emigrated into certain areas based upon the proximity to Bamba, and his presence invested the space with new meaning.  The settled land became part of the larger Daar-al-Murid, or the House of the Muridiyya, considered sacred and conceptually separate from other spaces in which Bamba's baraka could not be felt.  Around this space, a communal identity for the Muridiyya was formed, an identity culturally and religiously autonomic.  Drawing on the theoretical bases of Benjamin and Hall, concerning respectively the dissemination of images and the circulation of culture, this research will examine the development of a distinct visual culture, highlighting how imagery can reshape and invest public space with new meaning.

A vast amount of research exists in the field of education psychology concerning topics such as brain-based learning, teacher-directed versus student-centered learning, the impact of social and individual factors on the learning experience, and more. Despite this wealth of information, there is often a striking disconnection between the current educational research and the actual experience of students in the classroom. Undergraduate classes, modeled on teaching practices that have been the norm for decades, are often out of sync with contemporary research addressing the scientific and social realities of the learning process. An exception to this phenomenon is observable in dance technique classes in the University of Washington Dance Program. Dance instructors at the UW implement many education theories successfully in their classes, and students reap the positive benefits of these teaching techniques. In order to better understand the teaching methods at work in these learning environments, I conducted observations of UW dance classes and interviewed dance students. Through my research, I have identified key factors that combine to create a classroom environment conducive to learning theory application in everyday teaching. Although the physicality of dance sets it apart from most academic classes, I argue that these same factors could be replicated and utilized in academic classes with similar success. This research is a critical step towards closing the gap between what we know to be effective education theories (and related teaching techniques) and the reality of student experience in many academic classrooms.

Wnt signaling is known to be critical for proper embryonic development in most animals studied to date. But key evolutionary questions on the origin and evolution of this pathway in the metazoan common ancestor are still unresolved. Recently, the genome of Pleurobrachia bachei, a member of the early branching metazoan linage ctenophora, has been sequenced. Insights into the function of the Wnt pathway in P. bachei will provide information on early evolution of this key pathway. Three Wnt ligand genes were identified in P. bachei and cloned for in situ hybridization. These genes showed expression in the combs, tentacles, mouth, ciliated grooves and polar fields of the adult P. bachei. In a genomic search for other members of the canonical Wnt pathway, components of the destruction complex and antagonists were incomplete or missing from the genome. High levels of Wnt expression in the adult P. bachei indicates that Wnt could also be playing a role in signaling in the adult.

In typical ascidian development, a tailed larva hatches, swims, becomes competent, and then responds to settlement cues, that initiates metamorphosis. Metamorphosis triggers apoptosis, which is required for tail loss. At this time, the notochord is lost as the tail reabsorbs and the juvenile settles to a substrate. In the ascidian family Molgulidae, species have evolved tailless larval development at least four times independently from a tailed ancestor. We hypothesized that a heterochrony in metamorphosis is responsible for the evolution of tail loss in the tailless ascidian larvae. We show that there is early expression of metamorphosis genes in Molgulidae, including genes involved in the Mannose Binding Lectin (MBL) Complement pathway of innate immunity. We hypothesize that the maturation of the immune system early in tailless larvae could be a progression to competency and trigger to metamorphosis. Jeffery (2002) showed programmed cell death happens in cells that form a tail early in development. We further hypothesize that a heterochrony in metamorphosis promotes the early activation of programmed cell death in the tailless ascidian larvae. Using next generation sequencing techniques, we sequenced transcriptomes of a tailed and tailless species and their hybrid through development. We examined genes that have been shown to be expressed during metamorphosis in other ascidians and saw earlier expression of genes critical for metamorphosis in both species. Our ultimate goal is to elucidate the ascidian molecular trigger for metamorphosis and uncover whether heterochrony of metamorphosis leads to tailless ascidians.

Darwinian natural selection produces an organism that is adapted to its environment, an organism whose traits (phenotype) are tuned in critical ways to its habitat. If organisms and their phenotypes are so finely tuned to their environment, how can they deal with changes to that environment? One strategy is to evolve the ability to change phenotype in response to a change in the environment, or phenotypic plasticity. Theory predicts phenotypic plasticity to be adaptive when (1) organisms experience different environments either spatially or temporally and (2) different environments favor different phenotypes. In some cases, changes may be accompanied by cues that provide reliable information about future selection. Previous studies modeling adaptive plasticity suggest plasticity to be favored when the environmental cue always predicts the correct selection and not when the environmental cue is unreliable. We experimentally tested theoretical predictions about the de novo evolution of adaptive phenotypic plasticity with a clustering phenotype of baker's yeast by selecting alternately for large or small clusters. Selection for size was cued by alternate forms of growth media and this cue was either a reliable predictor of future selection or an unreliable predictor. After a preliminary run of the experiment, we have found indications of an emergent plastic response in one of our replicates from the reliable cue treatment. This provides a biological example that is consistent with accepted theoretical predictions.

Corals are important marine animals that provide significant habitats for thousands of marine teleost and invertebrate species, natural barriers to protect coastal communities, and sources of income for people in more than 100 countries around the world. Despite their vital importance, however, little is known about their taxonomy. Currently, they are classified based on their calcium-based skeleton morphology and coloration, which often causes problems because of high phenotypic variability within species. Thus, I used DNA sequencing in my research to identify species of the genus Lobophyllia from the Indo-Pacific Ocean. Specifically, I tested whether color morphs from different areas in Indonesia actually represent different species or mere color variations. For that purpose, I conducted PCR amplification of the mitochondrial DNA cytochrome oxidase gene and two nuclear genes in 42 colonies of 14 color morphs of Lobophyllia sp. The PCR products were sequenced in both directions at the High Throughput Sequencing Center of the University of Washington, and phylogenetic trees including known species were used to determine the species identities. I expected that color morphs would be genetically differentiated and therefore might represent different species. Regardless of the outcome, this project has helped to understand the biodiversity in coral reefs better, and is also useful to identify appropriate units for coral management and conservation.

Exoplanets are planets outside our solar system, and the current explosion in exoplanet discoveries is revolutionizing our understanding of the potential for extraterrestrial life. This prolific era of detections has stemmed largely from the unprecedented observing capabilities of NASA's Kepler Space Telescope. The Kepler Spacecraft collects high precision time-series photometric data on a fixed group of approximately 160,000 stars. The data are represented by temporal lightcurves (i.e. brightness vs. time) that can be used to detect transiting exoplanets, the topic of our research. Transits are events where an orbiting planet partially eclipses its host star, casting a small shadow on the telescope. To detect transit signals, we rely on the Quasi-Periodic Automated Transit Search Algorithm (QATS). As an automated tool, QATS provides a crucial means to reduce the Kepler dataset to a manageable size. However, since the algorithm is sensitive to stellar variability, eclipsing binary stars, and systematic artifacts of the spacecraft, additional analysis is required to separate true detections from false positives. Determining the best way to do this is the present focus of our work. Concurrently, we are exploring the potential for QATS not only to determine orbital period, but also to constrain transit depth and duration (properties related to the size of the exoplanet and to the density of the stellar host). While this increases the complexity of the QATS algorithm and the amount of output to manage, it provides greater potential for a fully automated transit search process with results that are more descriptive of the exoplanet systems detected.

The presence of fungal symbionts residing in the root tissue of plants is a well-documented occurrence, yet questions regarding the identification and comparison of fungal partners in mycorrhizal relationships have been largely unanswered. Ericoid mycorrhizae, an example of a mycorrhizal relationship, are found in host plants within the order Ericales. Ericales, which contains such familiar species as persimmon, blueberry and Rhododendron, are able to persist in edaphic conditions due to their fungal symbionts. These symbionts form hyphal coils inside plant cell membranes, and thereby exchange crucial nutrients with the host plant. This project aims to evaluate the specificity between fungal communities and their host Rhododendron species, with the expectation that differing communities may exist, even in closely related hosts. Using known techniques to extract fungal DNA from the root systems of Rhododendron species in varying conditions and proximity, this DNA is then used to generate species based communities within specific Rhododendron hosts. By using type-cultures and genomic sequencing, comparisons of the presence or absence of fungal species within host roots can be made. This will shed light on infection intensity, and specificity between roots and fungal symbionts. Anticipated results of high levels of specificity between host plant and fungus could prompt questions regarding the importance of fungal symbionts in genus Rhododendron, especially with regards to the speciation between individual host plants.

This study explores mass media as a means of reducing intergroup prejudice. The theoretical impetus for this study was contact theory, the idea that interaction with individual members of outgroups can reduce prejudice toward the group as a whole. The field has recently expanded to include non-interpersonal types of contact, including parasocial contact, and contemporary research points to parasocial effects comparable to and even wider reaching than those from interpersonal contact. Evidence of prejudice reduction through use of imagined contact scenarios and stories about ingroup members in contact situations sparked my interesting in entertainment as a potential vehicle for prejudice reduction through mediated contact, a topic which surprisingly little research has examined. Synthesizing the literature on mass media cultivation effects in the field of communication, and perspectives in social psychological research, I examine mediated parasocial contact’s potential application in situations in which geographic limitations or active cognitive filtering in prejudiced individuals act as a barrier to contact. I theorize that parasocial contact via mass media can be a viable alternative to interpersonal contact in these situations because it affords ease of exposure with one media artifact potentially viewed by millions, and it has the potential to subvert cognitive resistance to contact if put in the format of entertainment: viewers don’t expect the message to be strategically crafted to influence them. Parasocial contact appears to be mediated by cognitive change (stereotype alteration) which could have a far more lasting effect on prejudiced behavior and beliefs than the affective change observed from interpersonal contact. This might prove an advantage of parasocial contact over even feasible interpersonal contact. The focus of the present study is theoretical understanding, with the ultimate goal of designing an experiment to explore the impact and potential mediators of parasocial contact via entertainment media on prejudice reduction.

Early medical philosophers describe psychiatric illnesses as natural, biologically bound entities with clear definitions. However, other thinkers have begun to trace the source of these definitions to a more political root. I argue that the very language we use to diagnosis, define, and treat mental illnesses is influenced by the social and political climate, and that this language has been creating an increasing number of borders within the spectrum of human experience since the introduction of the DSM (the primary mental health diagnostic tool in the U.S.) in 1952. Using discourse analysis as a tool to examine the four editions of the DSM, I will discuss how the change in language of the last 60 years has followed political and social movements of the times. In particular, an investigation into the changing language describing and defining gender and sexuality disorders will uncover these changes. Psychiatry has been using particular language to create and negotiate the line between “normal” and “abnormal” since the origin of the field. Individuals labeled using this fluctuating language have to negotiate all the legal, social, political and cultural consequences of this line, and understanding the origins of these borders will shed some light on the human experience behind them.

Approximately 54 million Americans have some form of cognitive or physical disability. This minority status crosses lines of age, gender, race, ethnicity, sexuality, and socioeconomic status. We are all subject to becoming disabled, should we experience illness, an accident, genetic difference, or the effects of aging. Despite such large prevalence, we are faced with limited and stereotypical images of disability as a problem that should ideally be fixed or eliminated. Such a view is the medical model, which contrasts with a more inclusive view of disability, the social model. The social model holds that being disabled is a neutral form of human difference. Problems come from the lack of accessibility for disabled individuals in a society built predominantly for people without disabilities. My project uses the social model framework; first, I will analyze representations of disability in contemporary media. This uncovers marginalizing portrayals of disability that manifest in television today, such as pitying attitudes, “supercrip” depictions, and disability as a burden. Second, I will use focus group methods to examine perceptions of disability among UW students with and without disabilities. I will ask students to interpret various media portrayals of disability and examine salient patterns among their responses. I hypothesize that students will tend toward stereotypical generalizations consistent with the medical model of disability. I predict these results will demonstrate a need for students to develop skills for critical media consumption. With the results of this project, we can identify points for intervention and reframing of harmful stereotypes about disability.

Asian Americans respond negatively to being the target of a positive stereotype (e.g., Asians are smart) even though these stereotypes are often attempts at praising their group. The current work focuses on how targets’ responses to positive stereotypes depend on the race of the stereotyper. Asian and Asian American participants imagined an interaction with a White classmate or an Asian classmate who stated a positive stereotype of their group or stated no stereotype. Results showed that participants responded more positively when the stereotyper was Asian compared to when the stereotype was White. Participants did not respond differently to White and Asian classmates who stated no stereotype, suggesting that it is positive stereotypes which lead to different responses based on who says them. These results show that group membership is an important consideration when thinking about stereotypes.

Since the French and Spanish occupation of Hispaniola and specifically the US occupation from 1915-1934, Dominicans and Haitians have lived in a borderlands of blackness. However, these imaginary boundaries have been entwined with the African American response to the US occupation in Haiti. There have been many studies on the relationship between Dominicans and Haitians, but few have complicated how the relationship of African Americans living in Hispaniola played a fundamental role in shaping the multiple dimensions of blackness. By drawing upon Antonio Gramsci's theory of cultural hegemony, Stuart Hall's concept of cultural identity and diasporas in the Caribbean, in conjunction with Michael Omi and Howard Winant's work on racial formation in the United States, my research aims to draw the connections between these three groups and determine how these understandings have transformed preexisting definitions of blackness on the island. This paper is significant for comprehending the complexity of Dominican and Haitian identity, as well as locating the mechanisms of Western power, privilege and discourse. My research contributes to scholarship on the cultural production of blackness and race in the Caribbean and the United States.

Ceftaroline fosamil, otherwise known by the name ceftaroline (trade name Teflaro) is a cephalosporin antibiotic indicated for the use against MRSA skin and soft tissue infection and bacterial pneumonia. Though approved by the FDA, the drug is thought to be safe and thought to be well tolerated, however, our team has found it to cause neutropenia in patients. Neutropenia is defined as the abnormally low number of neutrophils, which seems to be present in some patients during and after taking ceftaroline. It is our objective in this study to determine the incidence of neutropenia among patients using ceftaroline. The drug has been approved for more than a year but the post marketing experience has been limited. We have seen two cases of agranulocytosis, which has led us to conduct this study. The study will be conducted in the Tri Cities, which is comprised of Kennewick, Pasco, and Richland. The Tri Cities has a diverse population of 193,000 individuals and there are three major medical facilities: the Kadlec Regional Medical Center, Lourdes Medical Center and the Kennewick General Hospital. The study will determine the incidence of neutropenia among patients receiving ceftaroline. We also hope to describe the side effects of the drug, and track patients’ health over the course of a 7 month period by reviewing patients' charts and through phone interviews. All patients that are included in the study received ceftaroline from August 2011 to March 2012. The patients’ data will be secured from hospital records from the three local hospitals. Our hope is to find a link between usage of ceftaroline and incidence in neutropenia in patients.

Pseudomonas aeruginosa can cause chronic and latent infections within many human diseases especially those related to immunocompromised individuals such as cystic fibrosis. This species also engages in a density dependent communication known as quorum sensing, which can often increase the species' virulence through the production of extracellular products such as proteases and components for the production of biofilms. Quorum sensing is a highly conserved process in nature yet quite interestingly we find that cystic fibrosis lungs provide a unique environment for the profileration of quorum sensing mutants (LasR mutants) as opposed to free living forms of the species elsewhere in the general environment. I am working to characterize 100 environmental isolates of Pseudomonas aeruginosa to test the hypothesis that quorum sensing mutants are infrequent within free living populations of the bacteria and to this point, I have not conclusively found an environmental mutant. Any information will in turn help us understand more about the selective pressures leading to the emergence of LasR mutants in the cystic fibrosis lung and consequently the therapeutic significance or insignificance of targeting quorum sensing in cystic fibrosis chronic infections.

Mosquitoes are the principle disease vector of malaria, yellow fever, and dengue fever, which are responsible for more than a million deaths worldwide annually. This makes controlling transmission a global health priority, and underscores the importance of understanding their behavior. Although it is known that olfaction is the main sensory modality mosquitoes use to select prey, many behavioral patterns, such as changing prey preferences, suggest that associative learning has a role in mosquito behavior. Previous research has established mosquito’s affinity for human scent and characterized their olfactory receptors, but little is known about the neural substrates and molecular underpinnings that modulate olfactory learning. To gain insight into the importance of olfactory learning, I have been introducing controlled perturbations into the larval mosquito nervous system and assaying their behavior using a classical conditioning model. This is achieved through genetic manipulation and injection of drugs with known targets. Initially, I have focused on the role of dopaminergic neurons, because they are known regulators of associative learning in other species. To this end, I have developed microinjection techniques that allow for delivery of silencing RNAs (siRNAs) to knockdown dopamine receptor expression. Using this approach, I have found that Dopamine receptor deficient animals, as well as those injected with Dopamine antagonists, are unable to learn like their untreated counterparts. Knockdown animals suffer a much higher mortality rate in survival experiments that test their ability to avoid predation, underscoring the importance of these receptors in vivo. Currently, we are using cell biological approaches to visualize the relevant neurons. Together these data show that larval mosquitoes are able to learn within days of hatching, and that dopamine plays a crucial role in facilitating aversive learning. In addition to clarifying the mechanistic basis for olfactory learning, these findings may ultimately enhance the development of vector control strategies.

There are a variety of air pollutants that can adversely impact health, including diesel exhaust from vehicles and other sources. In the Duwamish River valley of Seattle, WA, there are many sources of air pollution that emit diesel exhaust. Based on concerns of local residents, the overall objective of the Diesel Exhaust Exposure in the Duwamish Study, or DEEDS, was to measure exhaust levels throughout two Duwamish River valley neighborhoods: South Park and Georgetown. I assisted in nearly all spects of this pilot study which included the deployment of nitrogen oxides (NOx) air samplers to nine sites throughout the two neighborhoods to perform passive sampling over a ten day period in the summer. During NOx sampling, fine and ultrafine particle measurements were also collected for ten minutes at each of the nine sites using direct reading instruments and a mobile setup. These pilot study results collected from this preliminary assessment were used to optimize location selection for measurement of NOx, NO2, 1-nitropyrene, light absorbing carbon, and fine particulate matter during the DEEDS sampling campaigns taking place over the past year.

How did the Indian English novel function within the Indian independence movement? Literature illuminates unique narratives not necessarily communicated by other forms of print media like newspapers and history books, and these stories exert a very different kind of influence. In the particular instance of Indian English novels around the time that India gained independence from Britain, literature established power through its inherent cultural capital, its role in imagining nations, and its critical abilities. These novels embodied traits of both the colonized and the colonizer, allowing them to occupy a position of notable political and cultural influence. Drawing on theories on literature and nationalism, this study employs close readings of novels by Rabindranath Tagore and Mulk Raj Anand within the context of historically evident politics and cultural phenomena of the time period to explain the role Indian English novels played in revolutionizing India. An understanding of the factors enabling the novel’s influence will illuminate how India’s independence was imagined and realized. Situating Indian English novels of the Indian independence movement in their historical and social context may yield further understanding to the way historical events played out and reveal more of literature’s effect on the societies in which it is produced.

Cooperation occurs in the natural world between molecules, cells, individuals, and communities. In cooperative systems, both cooperating partners benefit from each other. To discover how cooperative systems evolved from its incipient state, we utilized an engineered system called CoSMO (Cooperation that is Synthetic and Mutually Obligatory) as a model for incipient cooperation. CoSMO consists of two non-mating yeast strains that are reliant on the other’s metabolite. CoSMO requires a minimum total cell density in order to be viable, i.e. able to grow from low to high cell density in the absence of supplemented metabolites. Evolved CoSMO cocultures are viable at significantly lower starting cell densities compared to their ancestors. What changes facilitated this increase in the system’s viability? We hypothesize that there will be changes in the yeast’s genome that accounts for this change in viability. To address this, we will perform genome-wide re-sequencing on evolved isolates to identify relevant mutations that contribute to increased system viability in evolved CoSMO. Specifically, we will extract genomic DNA of evolved cooperators at early and late time points during their evolution. We anticipate that there will be mutations in the genomic sequences of these strains. We will then compare these genomic sequences to their ancestral sequence and couple the identified mutations with phenotypic changes such as increased affinity for metabolite and starvation tolerance. We will perform similar analysis on replicate lines to elucidate the diversity in evolutionary trajectories of incipient cooperative systems. Through this, we hope to learn how an incipient cooperative system could evolve to an improved state.

Chemical modifications to histones, such as acetylation, phosphorylation, methylation and SUMOlyation, play a major role in dictating gene expression by changing the structure of chromatin. In particular, the modification of histone H4 by SUMO (called SUMOylation) was reported to be associated with gene repression. However, preliminary results from our lab show that the structure of SUMOylated chromatin resembles transcriptionally active, rather than silent chromatin. In order to comprehend how SUMO achieves gene silencing, biochemical studies with nucleosomes containing uniformly and site-specifically SUMOylated histones are necessary. Here we present a synthetic strategy to produce histone H4 modified by SUMO at Lysine 12. This strategy requires two native chemical ligation reactions. The first is between two fragments of H4- one synthetic and one recombinant. The second is a ligation between the SUMO-3 isoform and H4. In order to achieve the ligation of SUMO-3 to the side-chain of Lys in H4, we have developed a new ligation auxiliary. The synthesis of this auxiliary will be presented along with its application toward the total synthesis of SUMOylated histone H4. By understanding how SUMO-H4 controls gene function we hope to identify novel means to change cellular processes that result in diseases such as cancer.

Despite considerable effort, immune correlates of protection against HIV have not been identified, therefore making a successful vaccine challenging. In other words, since we have no examples of a successful immune response against HIV, we are unable to mimic that in a vaccine. One aim of the Overbaugh Lab is to identify immune correlates of protection by studying individuals who have mounted an immune response against HIV and who are at risk of superinfection, which is a second infection of HIV after the initial infection. My project is to clone a library of autologous HIV envelope genes from superinfected individuals whose immune responses we’re interested in studying, isolating both initial and superinfecting variants. These clones I generate will be tested for functionality (infectivity), used to produce target viruses in neutralization assays that measure the neutralizing antibody response in patient plasma, and used in assays measuring non-neutralizing antibody functions. Cloning patient envelope sequences involves isolating viral RNA from patient plasma and reverse transcribing it into DNA. After a polymerase chain reaction (PCR) to amplify the target envelope DNA sequence, I then ligate it into a mammalian expression vector. Sequencing analysis of the clones we obtain from each sample enables us to ensure that viral variants from the initial and second infection events are represented so that we can measure immune responses against both. After working with three patients, I have successfully obtained 11 initial and superinfecting variants from one patient, which produced 10 replicating viruses. From the next two patients, I cloned nine variants from each. Performing the functionality assay is in progress for these patients, as well as the neutralization assay. Currently, the assay to measure non-neutralizing antibody response is under optimization.

The host seeking behavior of disease-vector mosquitoes may be impacted by olfactory and visual learning. By enabling mosquitoes to better find bloodhosts, this behavior may allow mosquitoes to remain longer in the environment, transmitting diseases to more organisms. Recent work has shown that mosquitoes respond to Pavlovian conditioning that pairs visual and olfactory cues with an unconditioned stimulus. However, the function and relative importance of each sensory system has not yet been explored. We investigated both subjects using adult and larval Aedes aegypti. Firstly, we conducted appetitive conditioning experiments on Aedes adults. We found that adults were able to learn associations between novel odors and blood-feeding: they recruited to the conditioned odor consistently and significantly more than the odorless location choice. In contrast, naïve animals showed no innate preference to these odors. Secondly, we conducted aversive conditioning experiments on Aedes larvae. We compared the learning capabilities of wild-type specimens and specimens molecularly (RNAi) or chemically altered (receptor antagonists) to decrease response to dopamine, a critical neuromodulator involved in the aversive learning pathway. Our assays included a conditioned stimulus of indole and multiple unconditioned aversive stimuli (e.g., salt, bitter tastants). We found that wild-type Aedes exhibited a consistent behavioral change after conditioning, whereas transgenic or pharmacologically altered Aedes larvae did not. Finally, we analyzed threat-sensitive larval learning. We tested larval mortality in treatments containing a natural predator (a dragonfly nymph). We found improved survivorship in trained control-injected larvae versus dopamine antagonist injected larva. This is consistent with our data that lowering dopamine sensitivity alters an important pathway in the Aedes larvae olfactory systems to learn and recognize threats. These experiments suggest that both appetitive and aversive learning may be important to mosquito behavior. Our data also supports the conclusion that learning in mosquitoes is at least in part mediated by dopamine.

Quantum dots are nanoparticles with several applications including cellular imaging and drug delivery. Because of quantum confinement, their ability to fluoresce under ultraviolet light is size dependent. However, quantum confinement not only plays a role in emissive properties, but is also a factor in the absorbance spectrum of quantum dots. As a result, there is not a simple relationship between the concentration of quantum dots and optical density. It is the goal of this project to craft a new approach in accurately measuring the concentration of quantum dots in solution. We have determined a correction factor relating response units as measured by surface plasmon resonance (SPR) to values of refractive index. With this, we further use SPR in conjunction with analytical ultracentrifugation (AUC) to determine the concentration dependence of the refractive index, dn/dc, for TOPO-PMAT quantum dots. The measurement of dn/dc for the quantum dots allows us to use an interferometric determination of their total fringe increment observed by AUC synthetic boundary to measure the concentration of quantum dots in solution. We have estimated a dn/dc for 565 TOPO-PMAT CdSe quantum dots. In addition, we have used AUC to show that total fringe increments scale with concentration. Furthermore, we have estimated mass extinction coefficients for all wavelengths at which absorbance is observed for these quantum dost. This allows for UV-vis determination of concentration. Our results indicate that our strategy holds promise for providing a new method for measuring the concentration of quantum dots in solution.

Proper patient-provider communication (PPC) regarding choices available to patients and management of diabetes-specific care can lead to better patient outcomes. Our pilot study describes the specific demographic and clinical characteristics associated with PPC in families with children who have type 1 diabetes (T1D). Thirty-four caregivers of youth with T1D ages 2-18 were recruited for a study describing quality of care (QOC) measures, specifically PPC and quality of diabetes-specific education. Parent-report of patient quality of life (QOL), via a standardized assessment, was also collected. Clinical measures including insulin regimen and current glycosylated hemoglobin (A1c) was recorded from the medical record. Descriptive statistics, including Pearson and Spearman correlation coefficients, chi-squared tests and one-way analyses of variance tests were used to explore differences between demographic and clinical variables with QOC. Thus far, 34 caregivers have completed enrollment. On a scale of 4-16, with higher scores reflecting better PPC, the mean was 13.8 +/- 2.6 (range 8-16), indicating relatively high PPC overall. When asked to indicate whether 7 diabetes-specific topics (i.e., what to do for a low or high blood sugar) have been addressed, 23/34 (67.6%) reported all 7 as being discussed (mean = 6.6 +/- 0.7; range 5-7). Among clinical variables (QOL, A1c, and insulin regimen), QOL associated with PPC (r=.42, p=.01). For quality of diabetes education, income was the only demographic variable associated (families with higher income were more likely to report maximum education scores; chi-squared = 9.48, p=.05). No clinical variables were associated with diabetes education scores. Initial results from this pilot study indicate high levels of quality of care in this population. Certain demographic indicators, such as income, did affect quality of care indicators. Quality of life was also an important correlate with PPC, which suggests adequate communication plays a role in patient outcomes.

The late Oligocene (~23-28 million years ago) Blakeley Formation of Puget Sound has received multiple interpretations over the past century, ranging from a coastal embayment to a submarine fan. The formation is exposed along an uplifted terrace just south of the Seattle fault zone, in a discontinuous east-west band across Puget Sound. At Alki Point, the formation appears as an asymmetrical northeast plunging anticline and is characterized by fossiliferous siliciclastic siltstone and mudstone, typically in units several meters thick. These fine-grained units are interbedded with limestone in the lower part of our measured section and with sandstone in the upper part. Deposits of reworked volcanic ash and pumice are scattered throughout the section as well. The overall lithology and paleontology of the section suggests that the Blakeley Formation at Alki Point was deposited in a continental shelf environment. Sandstone beds in the upper section are broadly consistent with distal storm deposits, indicating a relatively shallow depth (< 100m). Finer sediment size and the absence of storm deposits in the lower section suggests deposition in somewhat deeper waters, perhaps in a middle to outer shelf environment. Some siltstone beds contain fossil bivalve shells, calcareous concretions, and infilled burrows, which are characteristic of cold methane seep ecosystems. The presence of reworked tephra, possible volcanic flood deposits, plant debris, and the general immaturity of sediment at Alki Point indicate that sediment was probably supplied by a river draining an active, ancestral Cascade volcano. Based upon the abundance of volcanic material in the sediments, it is also likely that the volcano was nearer the open coast than current Cascade volcanoes are. A possible modern analog for the Blakeley Formation of Alki Point might be the eastern Japan-island arc, where rivers deposit sediments from nearby volcanoes onto the continental shelf.

Biosolids applications can increase heavy metals in soils, which may impact seedling survival in managed forests. Western white pine (Pinus monticola) seedlings, planted in a biosolids-treated site at Pack Forest in the lower foothills of the Washington Cascades, have experienced heavy mortality which has prevented reforestation of the site even after 30 years of replanting. The purpose of this study was to determine whether these seedlings are exhibiting metals stress. Soil and foliar metal content was measured using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Phytochelatins and glutathione, compounds that are induced by metals stress and serve as bioindicators of metals stress, were measured in freshly emerged needles using high performance liquid chromatography (HPLC). Soil metals, at 16 ppm for cadmium, 293.5 ppm for copper, 585 ppm for zinc, and 509.5 ppm for lead, were substantially elevated at this site compared to comparable untreated sites, and furthermore, these were significantly higher than at other biosolids-treated sites. Foliar cadmium was 2.6 ppm, copper was 10 ppm, zinc was 177 ppm, and lead was undetectable; of these, all but lead was significantly elevated in seedlings growing in the biosolids-treated site compared to control seedlings. While phytochelatins and glutathione measurements are not yet complete, based on preliminary results it appears that seedlings are producing elevated levels of these compounds. The elevated foliar metals, in particular the highly toxic cadmium, suggest that these seedlings are experiencing metals stress. Further analysis of phytochelatins levels in seedlings in this biosolids-treated site may help to explain why these seedlings are experiencing such high mortality rates.

Auxin is the plant hormone, guiding phototropism, gravitropism, cell elongation, cell division, cell determination, and a host of other processes. Plant cells respond to auxin by turning on certain genes. When auxin enters the cell, it binds to a receptor protein; this receptor then binds to a repressor protein which typically prevents expression of auxin genes. This interaction triggers repressor breakdown and gene expression. We are investigating auxin-induced interactions between the receptor and repressor proteins (IAA’s). In our model plant, Arabidopsis, there are 29 IAA repressor proteins and 6 receptor proteins. Some combinations of repressors and receptors are known to result in differential degradation of the repressor; other interactions do not seem to lead to degradation. Our data suggests that receptors AFB4 and AFB5 cannot degrade repressors. This could be because AFB4/5 do not interact with the repressors (hypothesis 1) or because their interaction with the repressors does not trigger degradation (hypothesis 2). We are testing these hypotheses by examining repressor/receptor interactions in Arabidopsis proteins expressed in budding yeast cells. To address hypothesis 1, we are using a yeast two- hybrid assay to investigate the strength of interaction between several IAA repressors and the AFB4/5 receptors in the presence of auxin. To address hypothesis 2, we will determine whether IAA: AFB interactions identified at the yeast two-hybrid assay lead to repressor degradation. We have tagged the IAAs with yellow florescent protein and will co-express them with AFB4/5 in yeast. Flow cytometry will be used to measure changes in florescence levels upon addition of auxin. The next step will be to confirm these findings in plants. Understanding the variation in auxin repressor/receptor interactions brings us a step closer to understanding how auxin drives so many different plant behaviors and responses.

Because African immigrants are often lumped into the same category as African Americans, there has been very little research conducted on the health outcomes of African immigrants. This has resulted in an ideology of promoting preventative medicine versus treatment.  This study, based on self-reported information, will ask the question: what are the differences in susceptibility to hypertension and other cardiovascular disease-related risk factors among different African immigrant groups in the Pacific Northwest, specifically those from Somalia, Nigeria, and Ethiopia. The hypothesis of this study is that Ethiopian and Nigerian immigrants are at a lower risk of hypertension and other cardiovascular diseases as compared with Somali immigrants because of differences among their country of origin's health care systems. To be able to answer this question, I examined and evaluated the recent historical backgrounds of these three countries by conducting literature review. I also used surveys to collect data and critically analyzed and grouped the responses according to key words and comment phrases to test the correlation of the responses to the main research topic. I expect that the results will paint a mixed picture about African immigrants’ health outcomes, specifically rates of hypertension and cardiovascular disease, as region of origin confers major health effects on immigrants. This research will shed light on the differences among African immigrant groups separate from the African American population.

According to the CDC, diabetes mellitus affected 11.3% of US residents over 20 years of age and 26.9% of those over 65 in 2011. Because this disease can lead to severe health complications, patients with diabetes are over-represented in healthcare settings. A person with diabetes must incorporate disease management into every aspect of his or her life, remaining constantly vigilant and accommodating continual lifestyle modifications. Despite the daily challenges that confront these individuals, healthcare providers often practice without fully understanding the impact this diagnosis has on a patient’s life. As a result, patients may experience negative attitudes from healthcare workers that make them feel objectified and stigmatized, ultimately leading to poor health outcomes. Studies have shown that health simulation experiences, in which a person experiences the reality of a disease or condition, can be powerful tools for influencing the perceptions of healthcare workers. However, little is known about how these programs impact the perceptions of nurses who work closely with patients to manage chronic conditions such as diabetes. The purpose of this research study is to explore and describe the perceptions of nurses after completion of the Diabetes Reality Experience, an educational program in which they live for several days as though they have diabetes by incorporating monitoring, treatment, and prevention measures into their daily life. Evaluations and reflections written by participants will be qualitatively analyzed and interpreted to identify themes related to how the simulation experience influenced their insight and attitudes. This research has the potential to contribute to our understanding of how nurses and other healthcare workers can be better prepared to work sensitively with patients who have complex chronic conditions.

Horseradish peroxidase (HRP) is part of a family of heme-containing metalloenzymes that reduce the O-O bond of peroxides while oxidizing a wide variety of substrates; in the case of HRP, hydrogen peroxide is reduced to water. In the presence of an oxidant and the absence of a substrate to oxidize, hydrogen peroxide coordinates to the iron cofactor of HRP, forming a ferric-hydroperoxide intermediate known as Compound 0, and subsequent O-O bond cleavage releases water and a very oxidizing ferryl-oxo porphyrin radical cation intermediate, known as Compound I. The goal of this project is to probe the potential reversibility of Compound I formation, a step traditionally thought to be irreversible. A key experiment will react HRP with unlabeled H₂O₂ in ¹⁸O-labeled water, and determine whether mixed-labeled H₂O₂ is formed. The presence of mixed-labeled H₂O₂ indicates that there is reversibility of the O-O bond cleavage that forms Compound I and its existence will be determined by addition of a water soluble phosphine that is too bulky to fit into the active site of HRP. In this case, the phosphine cannot be oxidized by Compound I, but can readily react with free hydrogen peroxide in solution to give the corresponding phosphine oxide. ³¹P-NMR will be used to determine whether the phosphine oxide is labeled because the NMR shifts of ¹⁶OPR3 and ¹⁸OPR3 are distinct. If this reaction proves to be reversible, this knowledge could then be used to describe other enzymes that catalyze oxidations with similar intermediates. This would not only be important to enzymatic systems, but possibly catalytic chemical processes.

Greenhouse gases absorb Infrared (IR) light at specific frequencies; some of these gases are CO2, CH4, O3, and H2O. Research has shown that trapping of light by these gases leads to warming climate conditions. For my research, I will be improving upon a lab that is designed to teach students about the greenhouse effect. This lab is a part of the general chemistry curriculum at UW Bothell. The purpose of the Lab in Bothell CHEM 142 is to show students the greenhouse effect using the FTIR. To improve this lab, I had to determine a way to provide students with a step by step process that would help them understand what greenhouse gases do, and how they work at a chemical level. My work consisted of repeating the experiment many times to determine what was working and what was not, and then I had to provide a solution to fix what was not working. This entire lab was done with a Fournier Transform Infrared (FTIR). This experiment is done as a laboratory to help students understand the chemistry behind greenhouse gasses. The hope behind improving this lab for undergraduates is not only furthering their knowledge of chemistry, but also deepening their understanding of the greenhouse effect and how humans impact it.

 With an international focus on limiting greenhouse gas production, advancements in biomass conversion are needed. Conversion of biomass into more convenient fuels can lead to carbon neutrality. Biomass has the potential to be converted to transportation fuels after undergoing oxygen-free thermochemical decomposition, known as fast pyrolysis, and upgrading in a Fluid Catalytic Cracking reactor. Wood, one form of biomass, is largely made up of cellulose, hemicellulose and lignin. Lignin is comprised of polymers constructed of p-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol monomers. In the present project, pyrolysis of these monomers will be modeled using phenol, guaiacol and syringol, respectively. Individual monomers and mixtures of monomers will be pyrolyzed using a Pyroprobe and the bio-oil contents will be quantified by gas chromatography-mass spectroscopy. It is expected that when combinations are pyrolyzed, the bio-oil production will be suppressed due to secondary reactions of each monomers’ product. As combinations of these monomers are characterized, pyrolyzed lignin can be characterized. Eventually, all aspects of pyrolyzed wood will be characterized and optimum conditions for pyrolysis of woody biomass can be assessed, thus yielding the highest quality bio-oil.

In the next 50 years, global population in urban areas will double; mass transit systems are one area where both policymakers and planners have the ability to ameliorate potential negative environmental and social impacts of urbanization. Research in the United States has found that socioeconomic status (SES) is related inversely with physical access to employment and public services, partially due to underlying inequalities in spatial distribution of housing and transportation. Thus, mass transportation projects that provide mobility across neighborhood SES boundaries have the potential to positively impact the quality of life and future opportunities for billions of urban dwellers by improving inequalities of access to important urban areas. Examining the case of Seattle, Washington, I investigate how inequalities are addressed by the public transportation planning process and how SES is linked with differing levels of transit service. Interviews with individuals involved in transit planning explore transit characteristics unique to Seattle, steps taken to address inequity in the planning and design stages of transit provision, and broader factors that impact building and maintaining equitable transit services. A complementary GIS-based examination of the relationship between SES and the level of access granted by public transit to other areas of the city is performed. SES is measured using census and property value data, while transit access is measured using a novel network-based, parcel-level approach. Preliminary findings indicate that a significant tension exists between maximizing ridership and providing similar mobility to neighborhoods of differing SES; this problem is poorly addressed by methods currently used for incorporating equity in transit design and further aggravated by overlapping jurisdictions of power and systemic funding uncertainty. Informed by these results, I present both new techniques for evaluating mobility granted by transit in relation to spatial equity and a discussion of challenges to providing equitable public transit beyond measurement.

A century of fire suppression has led to higher tree densities, higher basal area, and increased abundance of shade-tolerant Abies concolor and Calocedrus decurrens in the lower montane forests of Yosemite National Park. Although fire was reintroduced to these systems over forty years ago, the effects of fire on forest structure and radial tree growth are still not well understood. This study compares live tree and snag basal area and density, seedling establishment, and radial growth patterns at four 0.1 ha plots in A. concolor-dominated stands of similar climatic water balance. Two sites had burned at different levels of low-severity fire in 2005, and two sites had not burned since the onset of fire suppression. On average, unburned plots had three times the tree density and 2.6 times more trees with DBH between 2.5 cm and 30.0 cm than burned plots. Burned plots had a mean seedling density 3.8 times greater than unburned plots. Low-severity fire also appeared to affect radial growth patterns as both burned plots showed decreased growth relative to the control plots for two years immediately post-fire. However, only burned plot 1, which burned at a higher severity than burned plot 2, showed increased growth relative to control plots 3 to 5 years post-fire. This study has implications pertaining to frequent fire forests of the West. 

Orbital spectroscopy provides evidence for the presence of liquid water throughout the history of Mars through analysis of the surface composition. In order to determine surface mineralogy, we use remotely sensed visible/near-infrared spectroscopic data from the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) on board the Mars Reconnaissance Orbiter. We identify minerals by their unique absorptions at specific wavelengths through the examination of CRISM surface reflectance data across 438 wavelengths from 1.0 to 3.9 microns. Spectral datasets like CRISM contain large volumes of data and each spectrum usually covers an area that contains several unique compositions, or spectral endmembers. Factor analysis uses a set of mixed spectra to derive a set of orthogonal eigenvectors and associated eigenvalues. Although physically meaningless, the eigenvectors and eigenvalues can then be used to estimate the number of components present in a mixed system. Target transformation is used to reconstruct endmember spectra using a linear combination of the set of eigenvectors, even if those pure endmembers do not exist in the original data. In practice, the target transformation test is simply a least squares fit of the significant eigenvectors to laboratory spectra. If a laboratory spectrum can be closely matched, then it is a possible endmember present in the system. This methodology can also be used to remove noise and significantly improve the quality of CRISM data. We tested our methodology using CRISM data containing evidence for the presence of carbonates. Target transformation clearly confirmed the presence of Mg-rich carbonates and phyllosilicates in Nili Fossae, a series of extensional faults. We are automating this technique and applying this methodology to test for a variety of minerals across the entire planet. Ultimately, by applying our data analysis technique to the global CRISM dataset, we will have a more detailed understanding of surface composition and aqueous processes on Mars.

Income inequality and level of education affects countries across the world. Within the last few years, Thailand’s income inequality seems to have worsened, as is seen from many political conflicts created from the significant gap between the rich and poor.  From the World Bank Poverty Analysis, there has been a dramatic decline of poverty in Thailand since early 1960’s.   However, the decline in poverty was not uniform across regions of the country; poverty is more concentrated in the rural areas.   Therefore, the increase in inequality was also not uniform across the country; the wider income differentials between households in different locations accounted for the increase in overall income inequality.  This means educational attainment plays an important role for labor to make a transition from the old sector to the new sector, and thus is one of the determined factors for income inequality.  In this paper, I will examine the impact of education and skills owned by individual on wage and income distribution of Thailand.  First, I will explain about the previous research on the relationship between education, skills, and wage. Then, I will explain about the data set and the methodology that will be used. Lastly, I will present and explain the result using Mincer's wage regression analysis and give the conclusion.

 Washington State is home to many diverse prairie ecosystems, which have severely been degraded or converted to agriculture/farmland. Due to the impact over the last several decades, it is crucial to research Washington’s native prairie ecosystems and work towards preservation, conservation, and restoration of these areas. There are many ongoing projects on these prairies, in efforts to gain more knowledge about the growth, development, and interactions of rare prairie species. It is very important to determine underground processes because these processes could affect the long-term success of restoration. I compared microbial metabolism and nitrogen mineralization among three restoration treatments: burning, herbicide, or solarization, at Glacial Heritage Preserve in Olympia, WA. Plots were seeded with a diverse mix of native prairie species 2, 3, or 4 years before this study. The goal of the project is to determine if soil processes differ among plots, and if it is a result of treatment or year seeded. Soil samples were collected from replicates of each treatment plot from each year, and extracted and inoculated into Biolog Ecoplates^TM. The amount of Nitrogen available for mineralization was also measured. Preliminary results display that there is some difference between treatments and years, and available Nitrogen varies greatly among treatment plots. The results of each experiment are being further investigated.

The pro-apoptotic (cell death inducing) peptide (KLAKLAK)2 (“KLA”) has been recently investigated for tumor killing applications. To increase the efficacy of the peptide, our group has added additional charged amino acids to increase cellular uptake (Gly-Lys-Arg-Lys-(KLAKLAK)2) (“GKRK-KLA”) and synthesized a polymeric construct of this peptide and HPMA (N-(2-hydroxypropyl)methacrylamide) (“p(HPMA-co-GKRK/KLA”). Preliminary studies have shown an increase in cell death per KLA unit in the modified constructs over the unmodified KLA construct. However, the mechanisms of cellular internalization and subcellular distribution of the peptide is unknown. Recently, we showed using fluorescence microscopy that the KLA constructs do not colocalize with mitochondria, the organelle that was believed to be affected. In this work, we applied radiolabeling and organelle separation techniques to investigate the mechanisms behind cellular uptake and subcellular trafficking over time of both the KLA peptide and our modified designs. These insights will allow us to design better materials to increase the efficacy of KLA peptide delivery.

Youth with mental health problems face many challenges not faced by youth that do not have mental health difficulties. Many of these young people drop out of school, do not have stable housing, have lower rates of access to employment and there are few services that address their needs. As part of the Pathways Transition Training Collaborative of the Pathways to Positive Futures Research and Training Center, we wanted to know what services are available for young people aged 14-30 with mental health needs within the Portland metropolitan area. We conducted face to face interviews with seven targeted key informants who provided information about mental health programs for young people in the transition years, and we also did internet research on the programs and emailed/called the programs with questions. Of the 38 programs researched, only fourteen reported that they accepted Oregon Health Plan (OLP). There were few programs that provided employment services (n = 4), healthcare (n = 2), and food (n = 1). There were not many programs that were culturally specific (n = 5). The data showed that there are few programs in the Portland area that meet the needs of young people in the transition years that have mental health difficulties. Through the process of research it became very apparent that there needs to be a network of communication between the programs, so they may better serve this population.

 Transition-metal ions promote a wide range of vital enzymatic biological and chemical processes involving dioxygen (O₂), including photosynthetic H₂O splitting, biosynthesis of neurotransmitters, and DNA replication and repair. These are some of the most fundamental processes of life, and yet they are also some of the most poorly understood. A complete grasp of how these processes function at the chemical level is therefore of critical importance to our development of technology that improves our lives and the world around us. For example, understanding how to efficiently oxidize H₂O to O₂ is essential to the development of renewable solar fuels and fuel cells. The challenge for research lies in that these transition-metal containing enzymes are inherently difficult to probe by traditional spectroscopy methods because of their structural complexity. The difficulty in characterizing these species and their reactions, coupled with their importance in the natural world, has made them a subject of intense research across all scientific disciplines. The Kovacs research group studies the structure and reactivity of these transition-metal containing enzymes, or metalloenzymes. Our research method involves modeling a metal ion’s local environment with a ligand scaffold and implementing changes to these so-called biomimetic models that may elucidate how reactivity corresponds with various structural and electronic modifications. Spectroscopy is more diagnostic in these simpler models because the complex proteins that obscure the active site in the actual enzyme are not incorporated into the model. By comparing similarities in reactivity between the biomimetic model and the actual enzyme, we may help elucidate properties and chemistry of the enzyme itself. Preliminary work has been undertaken with a novel series of thiolate ligated, coordinatively unsaturated Co(II) complexes; the reactivity of these complexes with O₂ and O₂^- is currently being probed.

Expression of glycans or carbohydrate antigens on mucosal surfaces is known to influence interactions between the host and bacteria. Variation in the expression of a single glycosyltransferase B4galnt2 is associated with significant shifts in the composition of the intestinal microbiota of mice (Staubach F, ISME, 2012). Glycosyltransferases are a class of enzymes that transport and assemble glycans. Preliminary studies of a mouse Salmonella model has found a significant association between Salmonellosis and expression of B4galnt2. In this project we will test the hypothesis that Salmonella spp. show preferential binding to the B4galnt2 β 1-4 GalNac sugar, which is commonly expressed by human intestinal epithelial cells (Mohlke et al., Cell 1999). We have adapted an in vitro method from Ruiz-Palacios et al. (JBC, 2003) to study this question, which utilizes Chinese hamster ovary (CHO) cell genetically engineered to express specific glycans to assay bacterial binding. Cells will be grown toconfluency in chamber slides then they are they are fixed and blocked. Clinical Salmonella enterica isolates will be grown in culture tubes overnight. Diluted bacteria will then be directly applied to the CHO Cells in the chamber slides and incubated together. After incubation the slides will be fixed and stained with a fluorescein isothiocyanate (FITC) conjugated anti Salmonella antibody. Stained slides are examined under a fluorescent microscope to quantify the number of bacteria bound to CHO-B4galnt2 cells vs. control CHO cells. Increased numbers of bacteria binding to the CHO-B4galnt2 cells compared to the control CHO cells would support a role for the B4galnt2 β 1-4 GalNac in host-Salmonella interactions. If no significant difference in binding is seen by this method, we will also test the hypothesis by doing introducing shear in a modified dot blot binding assay using mucus from B4galnt2 (+/+) and (-/-) mice to investigate Salmonella spp. differential adherence.

American students regularly get advised to “follow your passion” in choosing a career. However, people's passions are often shaped by what is considered appropriate for their gender. Could encouraging students to follow their passion inadvertently perpetuate gendered career choices? The present work examines how the cultural ideal to follow your passion may maintain gender imbalance in stereotypically masculine or feminine careers. In the current study, some participants were randomly assigned to write about what it means to “follow one’s passion” before writing about their career plans. We hypothesized that women who wrote about following their passions would report more feminine career plans compared to women who did not. Similarly, we predicted that men who wrote about following their passions would report more masculine career plans compared to men who did not. The American cultural ideal to “follow one’s passion” may help reinforce the gender makeup of career fields, contributing to the underrepresentation of women in certain fields like science.

 Personalized medicine aims to improve patient outcome by tailoring cancer treatment to individuals based on the specific molecular makeup of tumors. This approach is showing particular promise in the treatment of gliomas, the most common type of primary brain cancer. The DNA repair protein O⁶-methylguanine-DNA methyltransferase (MGMT) removes O⁶-alkylguanine adducts from DNA produced by the therapeutic methylating agent temozolomide (TMZ). In glioblastoma multiforme (GBM) tumors, low levels or lack of MGMT activity is correlated with longer progression free survival (PFS) following TMZ treatment and other alkylating chemotherapy. However, in oligodendorgiomas and oligoastrocytomas the effect of MGMT activity on tumor resistance has not been established. Better clinical outcome is associated with 1p and 19q loss of heterozygosity (LOH), which occurs in an appreciable fraction of oligodendrogliomas. Other studies associate these deletions with CpG methylation of the MGMT promoter, an epigenetic indicator of low MGMT activity. However, there have been no studies linking MGMT activity to chromosomal deletion, and 1p/19q LOH is associated with better clinical outcome regardless of therapy, suggesting that other mechanisms may also be responsible for prolonged survival. To clarify the unknown role of MGMT in these tumors, we tested the hypothesis that 1p/19q LOH accompanies low MGMT activity by: [1] assaying MGMT activity by measuring the extent of transfer of tritium-labeled methyl groups at the O6 position of guanine to MGMT in substrate DNA extracts of deleted and non-deleted tumors; [2] assessing promoter CpG methylation status using methylation specific PCR; and [3] examining the correlation of MGMT activity to TMZ treatment response using a Cox regression analysis. This approach should help to clarify the relationship of MGMT activity and 1p/19q LOH.

The project I worked on was part of a larger project in which we examined the activity of O6-methylguanine-DNA methyltransferase activity, CpG promoter methylation, and progression-free survival following alkylating agent therapy in glioblastoma and anaplastic glioma brain tumors. For my part in the research I performed standard biochemical assays to quantify O6-methyalguanine-DNA methyltransferase (MGMT) in extracts of glioblastoma (GBM) and anaplastic glioma (AG) tumor samples from adult patients operated on with consent at the University of Washington Medical Center between 1991 and 2008. MGMT is a DNA repair protein that excises methyl adducts from the O6 position of guanine residues. Chemotherapy and other alkylating agents such as methylating triazene derivative temozolomide (TMZ) are responsible for methylating DNA, or damaging the DNA and thus destory the tumor cell. There has been poor prognosis for GBM due to the intrinsic resistance mechanisms in the MGMT that limit the efficacy of TMZ and other alkylators. GBM and other gliomas display a wide range of MGMT activity and thus the question for research was whether the amount of MGMT in tumors correlated with progression-free survival following alkylator-based chemotherapy. Overall the data strongly supported that MGMT activity in GBM and AG tissue mediates resistance to alkylator therapy.

Atherosclerotic cardiovascular disease is the leading cause of death in North America.  Hepatic lipase (HL) a liver enzyme that hydrolyzes lipoprotein triglyceride, plays a critical role in lipid metabolism and may influence the development of atherosclerosis.  Hepatic lipase may serve dual roles in the development of atherosclerosis: 1) HL may be pro-atherogenic by converting low-density lipoprotein (LDL) to small-dense LDL, causing build up of cholesterol in arteries. 2) HL may be anti-atherogenic by increasing the cholesterol-poor form of high-density lipoprotein (HDL) that removes cholesterol from the arteries, decreasing build up of cholesterol in arteries.  Previous studies have reported that elevated levels of human hepatic lipase (hHL) reduce the development of atherosclerosis.  However, those studies were done in transgenic mouse models with supra-physiologic levels of hHL and may not accurately reflect the role of physiologic levels of HL on atherosclerosis.  Therefore, we created a physiologic model of hHL expression to analyze the role of hHL in the development of atherosclerosis.  This “humanized” mouse model expresses hHL at physiologic levels in the liver.  We hypothesize that physiologic levels of HL will reduce the development of atherosclerosis compared to mice lacking HL.  To test this hypothesis we bred the transgenic hHL mice onto a low-density lipoprotein receptor knock out background (which is an established model for atherosclerosis).  Littermates with and without the hHL transgene were fed a high-fat, cholesterol enriched (“Western”) diet to accelerate atherosclerosis development, after which the aortas were harvested, dissected longitudinally, and pinned to expose the inner aortic walls for visualization.  Cholesterol buildup was stained and the ratios of atherosclerotic accumulation to total aortic surface area were quantitatively measured via Adobe Photoshop.  Results from this study will clarify the contribution of hHL to atherosclerosis development.  Ultimately, our results will guide the development of new treatments to prevent and treat atherosclerosis.

A replicative lifespan (RLS) screen in yeast (Saccharomyces cerevisiae) was recently performed in the Kaeberlein lab to determine how different mutants respond to caloric restriction (CR). The results of this screen indicated that many mutants lacking genes encoding proteins related to mitochondrial function were rescued to wild-type lifespan by CR. The beneficial effects of CR in both yeast and mammals are mediated by reduced signaling through the mechanistic target of rapamycin (mTOR) pathway and can be mimicked by the drug rapamycin, a specific inhibitor of mTOR. Based on the findings from the yeast screen, we decided to investigate the effects of rapamycin on mitochondrial disease in a mammal. Leigh syndrome is clinically defined as a collection of genetically heterogeneous human mitochondrial diseases. These diseases result from mutations in genes encoding mitochondrial proteins and are characterized by progressive neurological degeneration resulting in early childhood mortality. To test rapamycin as a therapeutic intervention for Leigh syndrome, we are using a mouse line carrying a heterozygous loss of the electron transport chain complex I subunit Ndufs4, a direct homolog of the human NDUFS4 gene whose mutation causes Leigh syndrome. Mice homozygous for loss of NDUFS4 provide a robust phenocopy of the human disease, including neurological degeneration and early life mortality. Our results so far show that rapamycin dramatically increases lifespan and rescues the Ndufs4-/- mice for several health-related parameters, such as general mobility, visual ability, and grip strength. We are working towards determining the mechanistic basis for these effects, and we hypothesize that they may result from a metabolic shift toward increase fat metabolism in the liver. Understanding how rapamycin rescues Leigh Syndrome mice has clear translational implications, as rapamycin derivatives are FDA approved and patients with Leigh syndrome and other human mitochondrial diseases currently have limited treatment options.

This research examines the cultural climate that existed in Seattle’s Central District and on Jackson St. in the 1940’s-1960’s and the music produced at the time, jazz music. I examine Seattle’s changing laws (like racial restrictive housing covenants and prohibition), newer freedoms in the Black community (like desegregation), the influence of the Great Migration, and changing national attitudes toward racism and equality. I parallel those changes with evolutions in the styles of jazz produced throughout this period, and the social, political and economic landscape becomes evident in the music, to the extent that the way jazz sounded at a certain time reflected the social, political and economic atmosphere. I look at these issues through the lens of Floyd Standifer, a well-known Seattle trumpet player, who began his career in the 1940’s and was active in the Seattle jazz community until his death in 2007. Standifer witnessed some of the most radical changes in the socio-political landscape of Seattle throughout the ‘40’s through ‘60’s that I examine. The malleability he demonstrated in his music is testament to the changing social climate, population increases in the Black community, new freedoms, and the changing desires of community members and music venue patrons. In the shift from “rags” to jazz to rock ‘n’ roll, I demonstrate how jazz can be seen as political and reflects how music lies at the heart of the African American resistance to oppression during this period.

The low educational attainment of students of Mexican origin in the United States is a growing concern. Research identifies parental involvement (PI) as an important asset to student success and defines it as parents’ active participation in their children’s education at home and at school. Little research addresses the ways Mexican parents help their children during their K-12 education and college-going process, however. To address this gap, this research attempts to understand Mexican parents’ involvement and other factors first year Mexican-American college students perceived as important in shaping their educational success. Semi-structured interviews were conducted with 17-college freshman that identified themselves as Mexican, first-generation, low-income, and migrant/seasonal farmworker background. Based on students’ responses, Mexican parents provide deliberate exposure to agriculture work in order to direct their children towards an educational path. They also provided emotional support and encouragement to their children. Findings indicate that Mexican parents are involved in their children’s education, but in a different form than described by the initial models and definitions of parental involvement. Based on these findings, a new model of parental involvement can be created – one that recognizes Mexican parents’ contributions and guides schools to better work with parents in their efforts to increase the proportion of Mexican origin students going to college.

Despite recent sweeping advances in DNA sequencing technology, whole genome sequencing remains impractical as a routine medical service. Nevertheless, recent work suggests that rare genetic mutations may play large roles in modulating disease progression. More affordable targeted DNA sequencing is currently necessary to study variants of low frequency in the human population and attain sufficient statistical power to link these variants with specific disease phenotypes. Previous studies have demonstrated the effectiveness of a capture by circularization approach using molecular inversion probes (MIPs) whereby thousands of individual sites in the genome can be captured simultaneously for DNA sequencing. Yet, non-uniformity across large numbers of targeted sites persists as a major barrier to more widespread adoption. In this work, we show that statistical analysis of past MIP sequencing runs readily informs modifications to the process of probe design and selection. Additionally, logistic regression on carefully selected MIP features enhances in silico identification of ineffective probes that leave gaps in sequence coverage. Richer data sets from MIP sequencing runs representing a broader range of MIP characteristics and interactions may offer further guidance in perfecting the design of MIPs, achieving greater uniformity across targeted sites and ultimately lowering the cost of sequencing.

As Seattle's light rail system expands, one branch is being designed to cross the I-90 floating bridge in order to connect downtown to Redmond. The challenges associated with designing a rail system over a floating bridge are significant. Traditional train rail systems are not built to accommodate the wide range of movements undergone by a floating bridge but Parsons Brinckerhoff have designed a new kind of rail called CESURA that will allow this new branch of Link light rail to exist. I have been helping to construct and test a full-scale replica of part of the CESURA system and my personal research has focused on the specific stiffnesses of the rubber fasteners which hold the rails to the rest of the system. These stiffnesses are very difficult to determine without a specialized test to isolate their properties. A hydraulic actuator was used to provide loads that would either rotate or linearly translate a rail that was secured by a single fastener. Various instruments were calibrated and placed throughout the system in order to monitor the fastener's behavior in response to different loadings. The newly discovered fastener properties will improve computer models of CESURA and allow Parsons Brinckerhoff to more accurately understand how the entire system behaves. Armed with this new knowledge Parsons Brinckerhoff will be better prepared for their next test in Pueblo, CO with an actual Link light rail train running over the full CESURA system.

Proton radiation therapy is an emerging modality for the treatment of cancer. Clinical use of protons is growing around the world because of their favorable energy deposition patterns in tissues, but many unknowns remain in terms of the radiobiology of proton radiotherapy. Therefore, more preclinical research is needed. To this end the UWMC is developing a first-of-its kind experimental proton beam specifically designed for preclinical laboratory studies. The goal of this experiment is to compare biological endpoints of DNA damage and repair to radiation dose deposition patterns of the proton beam. As the proton beam passes through tissues it loses energy exponentially. At the end of its track it reaches very high levels of linear energy transfer, LET, i.e. – the energy deposited per unit length. We hypothesize that cells within high-LET regions of the beam are subject to more DNA damage. A549 lung cancer cells were grown to confluence in chamber slides, irradiated with protons or ¹³⁷Cs gamma rays (control), and fixed in methanol at 0, 15, 30, 60, 120, and 1440 minutes post-irradiation. DNA double-strand breaks were indirectly measured by immunohistochemical staining for γH2AX, a histone protein modified at sites of double strand breaks. The resulting biodosimetric assay will provide valuable information concerning DNA damage as a function of varying LET. Future work will extend the results to an in vivo model of mouse brain tissue with the goal of analyzing normal tissue toxicity in high-LET regions of the proton beam. This research has implications for current cancer treatment planning by, for example, avoiding proton beams directed at an organ at risk, or correcting normal tissue toxicity tolerances currently accepted by the academic community.

The fact that hydrogen isotope deuterium/protium (D/H) ratios in algal lipids co-vary with their surrounding water D/H ratios is well established. Paleoclimatologists have taken advantage of this relationship in their compound-specific D/H analyses, but little is known about the individual environmental parameters, such as temperature, salinity, light levels, and nutrient concentrations that influence D/H fractionation, or the state of unequal isotope composition. Laboratory experiments conducted with batch cultured green algae, Eudorina unicocca and Volvox aureus, grown at temperatures of 15°C and 25°C suggest that there is increased fractionation with increased temperature. The work presented here aims to elucidate the magnitude of D/H fractionation in a natural population of algae where temperature is the primary environmental variable. To test this relationship, surface water was sampled from Lake Washington once a month for one year, with a surface temperature range from ~8°C in February to ~24°C in August. Phytoplankton were filtered from the water and lipids are extracted and analyzed by gas-chromatography isotope ratio mass spectrometry (GC-IRMS) to determine the extent of D/H fractionation. We found that there was a positive correlation between temperature and D/H fractionation, in which fractionation increased with increasing temperature. The results from this research, as well as the results of similar experiments with other environmental parameters, will give paleoclimatologists accurate modern-day calibrations to apply to the analysis of lipids extracted from sediment cores in order to reveal climatic variations for the past.

Over the past decade, measurements of hydrogen isotopes of lipid biomarkers, in particular leaf waxes, have been used to reconstruct past climate change. This method is appealing because lipids are well preserved in sediment and their hydrogen isotope ratio is primarily controlled by the hydrogen isotope ratio of their source water, which itself is controlled by factors such as precipitation amount and temperature. However, it has been shown that the isotopic difference between source water and lipids is distinctive among different plant species. In particular, it has been shown that salinity strongly affects the hydrogen isotope ratio of lipids produced by mangroves, but the mechanism that controls this relationship is unknown. Plants, including mangroves, take in water mainly from surrounding source water, but the deuterium to hydrogen ratio within the plant may be impacted by differences in transpiration rate, photosynthetic rate and respiratory water production. The photosynthetic rate (mol CO2 m-2s-1), internal carbon, (μmol CO2/ mol air) and conductance (mol H2O m-2s-1) of three species of mangrove, Rhizophora apiculata, Avicennia germinans, and Xylocarpus granatum, were measured at six different salinities from 5 to 30 ppt. The date, time, and leaf number were also recorded as additional measurements. Determining whether salinity, time of day and/or differences among species affects photosynthetic rate, internal carbon, and conductance is important in comparing the biosynthetic pathways of the three species of mangroves. It will allow us to investigate the cause of increased deuterium discrimination in mangroves at high salinity.

The unique geography and ice dynamics of the West Antarctic Ice Sheet (WAIS) are believed to make it susceptible to instability and rapid collapse. Predictions of WAIS stability in a warming world rely heavily on ice sheet model simulations; one drawback is that ground truth for these models comes from the last ice age, when the climate was colder. Geologic evidence of ice sheet behavior during warm interglacial periods is currently hidden beneath the Antarctic and Greenland ice sheets. We expect WAIS to have been thinner and less extensive under warmer conditions, and we ultimately plan to determine its past extent with cosmic ray exposure dating of subglacial bedrock. As a prelude to subglacial sampling, during January-February 2013 we collected samples from elevation transects of exposed granitic bedrock at three WAIS nunatak sites: the Pirrit Hills, Nash Hills, and Whitmore Mountains. We also conducted radar reconnaissance surveys to evaluate potential sites for future subglacial rock sampling, which will extend the transects beneath the ice sheet. We have separated out the quartz and potassium feldspar content of our samples for measurement of cosmogenic beryllium-10/aluminum-26, and chlorine-36 respectively. We are using the results of these analyses to determine the history of exposure and ice cover in the past 1-2 million years at each sampled elevation. Based on field observations, we expect our samples to show evidence of prolonged exposure, suggesting that presently subglacial surfaces were also exposed in the past. Ultimately our work will determine whether rock surfaces beneath the WAIS have ever been exposed to cosmic rays, providing clear evidence for or against a thinner ice sheet in the past. Such data will be useful in tuning ice sheet model conditions and establishing WAIS vulnerability to collapse, which is crucial to forecasting future sea level change.

During the last ice age the Missoula Floods – huge cataclysmic floods caused by failure of the glacier dam that impounded Lake Missoula, a massive ephemeral meltwater lake – spilled across eastern Washington in periods of a few days. Repeated floods transformed the Eastern Washington landscape, eroding coulees and re-working the resulting sediment into extensive sand, gravel, and boulder deposits. Although widely studied, debate persists over the number and timing of the floods. Flooding is known to have spanned a period of several thousand years; this is constrained by several areas of research including radiocarbon dates, dated volcanic ashes, and examination of the interbedding of Missoula Flood deposits with those of the 18,000 yr BP Bonneville Flood on the Snake River. To further constrain the chronology of flooding, we plan to measure the cosmic ray produced isotope Beryllium-10 in granitic quartz from boulder deposits near Ephrata, and at Priest Rapids on the Columbia River. Concentrations of Be-10, accumulated since the boulders were deposited, will allow us to determine their exposure ages. So far, we have collected several samples from the Ephrata boulder fan and from the Priest Rapids deposit. We have sampled high-standing, water-polished boulders to avoid the effects of past sediment cover and post-depositional erosion, both of which can lead to erroneous age estimates. We have crushed the samples and separated quartz in preparation for Be-10 analysis. After further purification, the quartz will be dissolved for extraction and isotopic analysis of Beryllium. We expect results of this work to better constrain the relative timing of the deposits at Ephrata and Priest Rapids, and the age of the floods that produced them, the last to pass through the Grand Coulee and Sentinel Gap, respectively.  

Observations suggest that the intracluster medium in galaxy clusters is strongly influenced by supermassive black holes residing in cluster centers. We investigate the consequences a black hole can have on the thermodynamics of the gas in galaxy clusters by comparing the properties of a simulated galaxy cluster without black holes to X-ray observations of real clusters, which have black holes. For our data we used Python to manipulate a cosmological simulation made with ChaNGa, a code capable of simulating gravity, thermodynamics, and other things. Our cluster simulation includes gravity, hydrodynamics, gas cooling, star formation, and stellar feedback in a fully cosmological setting. However, this simulation lacks black hole formation, growth, and feedback, allowing us to pinpoint the effects of these processes on the cluster by comparing to observations. In our investigation, we found only minor differences in the density, temperature, and pressures of the gas between the observed and simulated galaxy clusters in the cluster outskirts. However, we found significant deviations between the simulation and observations near the cluster centers, where a large spike in star formation is present in the simulated cluster, not seen in the observations. Our results suggest that black hole formation and feedback in galaxy clusters most strongly affect the cluster in the central regions, where it can significantly decrease star formation by heating the gas.

One of the functions of the vestibular system is to engage neural reflexes, which ensures the stabilization of a visual image during head movements. This is accomplished through the stimulation of vestibular hair cells, which respond to accelerations, and then produce compensatory eye movements opposing head motion. This called the vestibulo-ocular reflex (VOR). Hair cell loss results in vestibular deficits, and for these individuals, this loss of function is debilitating and results in vertigo and decreased visual acuity. To address these deficits, the Phillips lab has developed a vestibular prosthesis, which aims to use electrical stimulation to restore function by artificially activating individual branches of the vestibular nerve. However, it is not known precisely how the system changes after hair cell loss; this may have implications for the effectiveness of the prosthesis in treating vestibular loss. To explore this, we examined the interaction between the electrical activity and residual vestibular activity after vestibular loss. We first introduced a vestibular deficit in a rhesus macaque through successive gentamicin injections into the middle ear to destroy vestibular hair cells, and measured VOR responses to verify the progressive vestibular loss. Next, we recorded eye velocities in response to electrical stimulation to characterize changes in the efficacy of stimulation, thus providing insight into the prosthetic mechanism. Finally, modulated electrical stimulation was provided during rotation of the rhesus macaque to test the efficacy of the prosthesis in restoring VOR in conjunction with residual vestibular activity. Characterizing prosthetic function during increasing vestibular deficit is important in determining the mechanism of stimulation, the physiological responses succeeding hair cell loss, and ultimately a model for the prosthetic efficacy for human patients.

My research uses ethnographic methods to examine personal histories and subsistence strategies of health workers in Sierra Leone. The project is designed to ‘study up’ (Nadar 1969), that is, to use ethnography as a tool to understand the macro- political, social, and economic context of people’s day-to-day experiences. I look to understand the impacts of Sierra Leone’s post-conflict economic restructurings on the quality of life, employment distribution, and clinical practices of healthcare providers. My project includes a preparatory stage at the University of Washington and, subsequently, six weeks field research in Sierra Leone. My work particularly considers Sierra Leone’s debt-relationship to International Financial Institutions (IFIs), such as the International Monetary Foundation (IMF) and World Bank. Loans issued by IFIs stipulate shifts in governmental spending and regulation that, in terms of healthcare services, translate to reduced funding for governmental healthcare services, the development of a private healthcare sector, and use of NGOs to funnel aid money into the nation. These shifts, inspired by neoliberal market fundamentalism, result in fewer jobs and lower wages for health workers, as well as a discordant healthcare system fractured between NGO, private, and government services. Globally, anthropologists have worked to document the collateral damage to health from neoliberal economics. However, there is a dearth of ethnographic work explicitly considering economic restructuring’s effects on health in Sierra Leone. Health workers are integral to health services and their stories incisively reflect the toll of neoliberal economic agendas on health. My research adds to the anthropological evidence that these agendas are systematically denying people health services and undermining health in developing countries.

Auxin is one of the most important plant hormones that regulates almost every developmental process during plant life cycle. Auxin response factors (ARFs), are DNA-binding transcription factors that regulate auxin-mediated transcription by activation or repression. In Arabidopsis, ARFs are encoded by a family of 28 genes, and each member is thought to play a central role in various auxin-mediated developmental processes. ARF2 has shown to be a transcriptional repressor. Nemhauser lab uses Arabidopsis seedling hypocotyl, the embryonic stem, as a model to study growth. Loss of ARF2 alters hypocotyl growth in Arabidopsis seedlings. arf2-9 is a single point mutation in DNA-binding domain that results in loss of ARF2 function. I have analyzed the hypocotyl growth in arf2-9 mutant in presence and absence of exogenously applied auxin. The results indicate that arf2-9 exhibits longer hypocotyl in comparison with wild type seedlings not only in control untreated condition but also in response to auxin application. This data suggests that ARF2 is a negative regulator of hypocotyl elongation. To investigate the mechanisms how ARF2 regulates hypocotyl growth and elongation, I have crossed arf2-9 mutant with a reporter line P_PKS4::GUS that marks actively growing hypocotyl region. I have used dCAP genotyping method for arf2-9 single point mutation and Basta resistance selection for P_PKS4::GUS transgene to isolate double homozygous arf2-9 X P_PKS4::GUS plants. My hypothesis is that long hypocotyl in arf2-9 is a consequence of indeterminate growth. Given that, my prediction is that GUS staining pattern of P_PKS4::GUS will be different in arf2-9 genetic background compared to the original line. This includes possibility of having GUS staining in different regions of hypocotyl or extended staining pattern over the time when in wild type background P_PKS4::GUS marker is no longer active. Those differences will help us understand the function of ARF2 better.

 In Perlmutter lab’s ongoing study, a combination of activity-based motor training and EMG-triggered electrical spinal stimulation is used as therapeutic intervention for rats with spinal cord injuries (SCI). In addition to the reach training being a form of physical therapy, electromyogram (EMG) electrodes are implemented into rat’s impaired arm and on the spinal cord area that receives related motor commands from the brain. By detecting electrical potentials produced by the skeletal muscle, the electrodes then carry out electrical stimulation on the spinal cord. In response to repetitive and consistent transmission from a presynaptic neuron to a postsynaptic neuron, the connection between two neurons is reinforced as a result of Hebbian “plasticity” or the ability to strengthen or create new synaptic connections with the associated neurons. Although preliminary data suggested greater functional recovery in this novel intervention, many rats did not recover fully. This may be due to discrepancies in the timing between the EMG and the descending command arrival in the spinal cord, preventing optimal timing of the electrical spinal stimulation. In my proposed experiment, I hypothesize that triggering the electrical stimulation from the source of the descending motor commands, the brain, rather than from residual muscle activity will enable better synchronization of the stimulation, hence optimizing the intervention. Instead of EMG electrodes, electrocorticographic (ECoG) electrodes that are designed to detect brain electrical activity will be implanted on the surface of the brain. During the 12-week intervention along with the reaching exercise, a device called the Neurochip will record and trigger the stimulation of spinal cord. The ECoG technique may provide a less noisy signal by recording directly from the brain and enable a better estimate of the occurrence of spinal stimulation, thus maximizing the therapeutic potential of the intervention.

Alcohol is the only abusive substance from which withdrawal symptoms can be fatal. As such, the recovery processes from alcohol abuse are mentally, physically, and spiritually challenging. When alcoholics begin to move through the recovery process, they initiate a critical transition phase that shapes their identity as an alcoholic and as a human being within society. This study seeks to better understand how the recovery process transforms the identities of alcoholics. Furthermore, this research investigates how recovery alters the relationships between alcoholics and their communities. Through participant observation and interviews, this study examines the narratives of healthcare professionals, treatment facility employees, community members, family members, and alcoholics. Data from these groups were collected from individuals, treatment facilities, and Alcoholics Anonymous (AA) and affiliated meetings in order to provide a holistic perspective on how alcoholics move through the recovery process. This research expands our understanding of the effects of alcoholism as a social phenomenon by incorporating the perspectives of recovering alcoholics into the discourse while preserving individual anonymity. By providing a comprehensive conceptualization of alcoholism, this work has the potential to provide a framework for new modes of treatment that not only give alcoholics the agency to make a positive recovery, but also change the way society perceives the family disease of alcoholism.

Our 800,000-year climate record is dependent primarily on data obtained from ice cores. Analyzing and dating the ice, gas, and sediment in these cores allows us to construct a remarkably accurate historical record of Earth's climate and atmosphere. However, the dating and chronology of the ice record is not as exact as we would like it to be, especially deeper in the ice. Our ability to date ice cores with accuracy depends on our understanding the evolution of glacial firn, fallen snow that gradually compacts into ice. Researchers have developed many different models of firn evolution. The aim of this project is to run these models against each other under the same boundary conditions, so that we may compare their responses and determine the strengths of each model. Participants have submitted their model output and our results have been returned to them. A second inter-comparison will be organized to address issues brought up by our initial results. These comparisons will improve future efforts in firn-modeling, ultimately leading to a better understanding of our climate record.

Waves carry a significant amount of energy, but this energy has not been thoroughly explored for human use. There are a myriad of different ways to harness this energy. One very promising method is through the vertical oscillation of a buoy as waves pass beneath it. The Applied Physics Lab (APL) has teamed up with Oscilla Power to test an APL buoy design paired with an Oscilla power generator. This pairing has been tested over a matter of months on Lake Washington, just off of Sand Point. The buoy itself is anchored to the bottom of the lake by three anchors, and a weight consisting of two railroad wheels hangs in the water column beneath the buoy. The Oscilla Power energy-generating device attaches mid-line above the hanging weight. There are a number of data acquisition devices onboard measuring the motion of the buoy via accelerometers, the loading on the tether, and electrical output of the Oscilla Power device. The results of this test show a relation between wave height and power output via tether loading, verifying the buoy design. Optimal power output coincides with optimal wave heights and frequencies, and the results of this test and subsequent data analysis reveal these values. This information is crucial to the design of future moorings for wave energy conversion devices. This work may be scaled up to provide power to open ocean research buoys, extending the battery life of these devices. If these tests are promising, additional uses for this energy on a larger scale could be explored.

The distribution of temperature and precipitation on our planet (i.e. our climate), affects plant growth, animal habitats, and the livability of Earth's varied regions. In order to predict future climate we need to know about our past climate. This is important to better understand how temperature and weather conditions change when the radiative forcing (e.g. CO2 greenhouse effect) on our atmosphere increases. The best way to predict these changes is researching past radiative forcing increases and how these events impacted Earth’s climate. Some details of our past climate are discovered by analyzing polar ice and the gas bubbles trapped within. Firn is fallen snow that compacts and eventually turns into glacial ice. During this process gas can move relatively freely throughout the firn. When the firn densifies enough to block the air passageways, young gases are trapped in significantly older ice. This work is building a web-based community firn densification model that allows the user to accurately determine the difference between the age of a gas sample and the age of the ice surrounding it. Our transient model determines this delta age more accurately than current steady-state models by accounting for changing conditions as the firn turns into ice, instead of assuming conditions remain static throughout the firn evolution. This model is open-source, and written using the Python programming language, along with the NumPy library, allowing the model to be free and usable by anyone. Because the model is modular, users can easily change it to fit specific conditions or to incorporate different physical processes. Our goal is to provide a model that is simple to use, freely available, and helpful for developing a more accurate understanding of our past climate.

In natural environments, animals seeking resources face potential perils associated with foraging behavior, namely predation. Thus, animals must balance their needs with risks by utilizing adaptive behavioral strategies. One such strategy is hypothesized to be provided by the fear system through adapting foraging behavior in the presence of environmental threats. The advent of new molecular biological techniques such as Designer Receptors Exclusively Activated by Designer Drugs (DREADD) and optogenetics has provided novel approaches to investigating the amygdala’s modulating role in fear behavior. DREADDs are based on the G-protein coupled receptor pathways in which the receptors are activated by systemic injections of clozapine-N-oxide to stimulate or inhibit neurons initially and affect a host of downstream cellular signaling pathways that results in changes to cell function. Optogenetics uses receptors that immediately open in response to certain wavelengths of light to allow the passage of relevant ions in order to activate or inhibit the cells. The current project utilizes these targeted approaches to remotely activate or inhibit the basolateral amygdala and the central amygdala. The animal's ability of fear learning will be assessed using the Pavlovian fear conditioning paradigm. The effect of activating or inhibiting the amygdala in a semi-naturalistic setting will be evaluated using the Robogator paradigm. After habituation and training, rats will be placed in the chamber in which a predatory presence, known as a Robogator, will surge and snap when the animals attempt to grab a food pellet. The analyzed behavioral results in control animals and experimental DREADD and optogenetic animals can be compared to affirm the use of DREADD and optogenetic in behavioral research while providing new information as to how different groups of neurons and their connectivity in the amygdala affect fear behavior.

Pareiasaurs were a group of herbivorous reptiles that lived during the Middle to Late Permian (~265–252 mya) in what is modern day Europe, Asia, and Africa. Fieldwork in the Moradi Formation of Niger has produced three scapulocoracoids of the pareiasaur Bunostegos akokanensis, two of which were identified to taxon by associated skull material, with the third not found in association with a skull. The considerable size disparity and slight morphological variation among the scapulocoracoids suggest that they are from different ontogenetic stages ranging from juvenile to adult. This variation permits the first description of ontogenetic change in the scapulocoracoid in pareiasaurs. An increase in overall size is associated with morphological change in each region of the scapulocoracoid, including the expansion of the anterior coracoid, the reduction of the posterior coracoid, increased robustness of the scapula, increased depth of the glenoid fossa, and a higher angle of the acromion process. To analyze these trends, precise measurements were taken from important physical landmarks in order to quantify ontogenetic shape change. Following a description of the morphology and ontogeny, an analysis of phylogenetic relationships will be conducted based on morphological characters, comparing Bunostegos to other pareiasaurs and their closest relatives. This research will further understanding of ontogenetic change in pareiasaurs, but more importantly, it will form the basis for further hypotheses regarding function, locomotion, and ecology in this important group of Permian reptiles.

Stress can have a major impact on the cognitive functions of the brain in both humans and animals. One of the possible areas affected is the hippocampus, a structure known to be important in consolidation of short and long-term declarative memory and spatial memory. Previous studies have shown that stress can reduce long-term potentiation, impair spatial memory, and affect the firing rate of location-specific place cells in rats. This study aims to investigate the effects of temporary hippocampus impairment during stress on risky foraging behaviors in rats using APV, an NMDA receptor antagonist that inhibits the synaptic plasticity of local neurons at the site of injection. Rats were trained to retrieve food pellets from a simulated foraging environment and return to a safe nest, and APV infusions were then made via implanted cannulas into the rats’ hippocampus 30 min prior to stress. Foraging behavior in the presence of a robot predator was assessed in comparison to control rats infused with artificial cerebrospinal fluid. Hippocampal dysfunction is hypothesized to contribute to faulty contextual fear conditioning and memory formation, thus rats with an impaired hippocampus may exhibit excessive, contextually-inappropriate fear behavior in the presence of an artificial predator. The results of this study may help us understand the affects of stress and its role in the behaviors of individuals with post-traumatic stress disorder.

It is well documented that low levels of antibiotics are present in both surface water sources and in soil near industrial, large-scale farms. However, very little work has been done exploring the selective pressure for the evolution of resistance at these sub-inhibitory antibiotic concentrations. It is our concern that mutations acquired in a low antibiotic environment may be “potentiating:” that is, the presence of these first mutations opens more mutational paths after a shift to a high antibiotic environment. The converse may also be true in terms of “dooming” mutations that close off evolutionary paths in the new environment. Here we aim to investigate the prevalence of potentiating and dooming mutations and to understand their role in adaptive evolution. We study these phenomena by performing evolution experiments with Escherichia coli grown in a permissive environment (low drug concentration) followed later by a sudden shift to a new environment that imposes a strong selective pressure (high drug concentration). Here the permissive environment serves to generate mutational diversity and the harsh selective environment serves to assess the evolutionary potential of mutant isolates relative to their wild type ancestor. This will increase our knowledge of the evolution of antibiotic resistance and as well as the unintended but potentially dangerous effects of long term selection in the presence of low levels of antibiotics.

UVC is ultraviolet light in the wavelengths 280 – 100nm. UVC’s germicidal ability has been employed to prevent forward contamination, or the contamination of a pure planetary body with terrestrial organisms. Scientists have used UVC to sterilize equipment on land and water, but the effective dose of UV needed to prevent contamination when probing a pure ice environment is still unknown. In order to safely explore pure icy environments, data of bacterial response to UVC in ice are needed. To create these data, we first irradiated Escherichia coli in water as there is a known decimation curve for this experiment, which serves to standardize our irradiation set up and techniques. After matching the decimation curve of Escherichia coli of previous UV sterilization experiments, we will then proceed to irradiate bacteria in ice. In addition to irradiating commonly tested bacteria such as Escherichia coli and Bacillus subtilus, we will also irradiate samples of glacial isolates that would be more likely contaminants in an icy environment. Each sample of bacteria will be assessed before and after radiation using the Most Probable Number technique, or MPN. The MPN method uses serial dilutions of a sample bacterial culture until no colony forming bacteria are present to determine the concentration of bacteria present in the original sample. From our irradiations, we will create curves of UV dose versus survival of bacteria that will allow future equipment used in the exploration of pure icy environments to employ the correct dosage of UVC light to minimize forward contamination.

Pulsed plasma thrusters are a modular electric propulsion technology with extensive flight heritage. Flight-ready PPTs are tailored to a specific mission based on the power and mass budget of a mission. The lower bound for both parameters is far less than competing electric propulsion (EP) technologies, such as Arcjets and Hall Thrusters, which makes them desirable as spacecraft size decreases. The variable components of PPTs are typically electrode geometry, capacitor size, spark plug geometry, and fuel feeding system, but rarely if ever does a space mission select an unusual fuel. Teflon is used almost exclusively, and PPT fuel research is effectively stagnant. This investigation has concluded that alternative fuels are indeed significant. The sulfur PPT (SPPT) is inspired by natural sulfur plasmas in the Jovian magnetosphere. Thrust stand tests over the course of six months have demonstrated clearly that the specific thrust (thrust per unit power) is three times higher than in a corresponding test using a Teflon PPT of the same electrode geometry. Both pure sulfur and a sulfur-epoxy binder have been considered, and show the same specific thrust within error of the experiment. Pure sulfur will outgas in space, and may not be suitable for long missions, but the sulfur-epoxy fuel could potentially solve this problem. Additionally, an insulated semi-conductive bismuth sulfide compound shows similar thrust characteristics to the Teflon fuel, albeit at a lower exhaust velocity. This investigation is ongoing, with a parallel application project performing the SPPT experiment on a high-altitude balloon airship. This mission will demonstrate systems control, test the SPPT in a non-laboratory environment, build flight heritage, and represent and important advancement in PPT applications.

Deficiencies of monoamine neurotransmitters including serotonin, norepinephrine, and/or dopamine have been associated with many CNS diseases including depression, schizophrenia, ADHD, autism, Parkinson’s disease, and Tourette syndrome. The intensity and duration of monoamine signaling is mainly determined by the clearance of the released transmitters through uptake1 and uptake2 transporters. The recently discovered uptake2 transporters including the plasma membrane monoamine transporter (PMAT) and organic cation tansporter3 (OCT3) have been less studied partly due to the lack of specific inhibitors. Recently, inhibition of PMAT and/or OCT3 has been proposed as a strategy for the development of antidepressant drugs with improved efficacy and faster onset of actions. The goal of this project is to characterize specific chemical inhibitors for PMAT and OCT3. Previously, 10-40 small molecule inhibitors for PMAT and OCT3 were identified from high throughput screening. We will choose two to three inhibitors for PMAT and OCT3 obtained from the initial screen and further analyze their potency, specificity and mechanism of inhibition towards PMAT and OCT3. We first will determine their inhibition potencies (IC50) towards PMAT and OCT3 using radiotracer uptake assays in cell lines stably expressing these transporters. Preliminary data showed that two compounds inhibited OCT3 with IC50 values of 1.97 ± 0.766 and 2.86 ± 0.532 µM. One compound inhibited PMAT with an IC50 value of 2.15 ± 0.537 µM. Further studies will be performed to determine the specificity and mechanism of inhibition for these inhibitors. The proposed studies may lead to novel, highly specific and potent PMAT and OCT3 inhibitors that could be further evaluated and developed in preclinical models for the treatment of depression and other monoamine-related diseases.

In the 20th century, mathematicians attempted to reduce mathematics to a set of axioms. One of the properties that David Hilbert, a famous mathematician, postulated was decidability. This refers to an algorithm that can determine whether or not another algorithm in the same system is actually computable. In his 1939 paper, Alan Turing proves decidability cannot occur in formal mathematical systems. Turing used an unconventional way to prove his argument—the Turing Machine. The machine is a theoretical computational device. This abstract device has revolutionized the way we think of computing and computers among other fields. It consists of four parts: a head that reads symbols, an infinite tape that stores inputs and outputs, a state register that holds the current state (or state of mind if you prefer), and a table that describes how the machine transitions from state to state. Turing machines can compute anything that is computable. Computability equates to being able to describe how to obtain the solution of some function with an algorithm. This abstract idea is interdisciplinary; which makes it a great educational tool. We have built a working Turing machine out of LEGOS. To both extend and improve functionality, we have added various components. These components cross over to other fields of study making the project great for students of various education paths to reproduce in a team setting. Our hope is that others can use our work and further devolop it. Besides providing a concrete example of an abstract idea,  building the Turing machine allows us to reaffirm findings.  It is in the spirit of scientific descovery to reproduce work. This research project allows us to follow in the foot steps of intellectual giants.

Chitin is the second most abundant polysaccharide extracted from the cuticles of insects and crustaceans. Chitin is known for its biocompatibility and superior mechanical strength. Silk fibroin is produced by the Bombyx mori silkworm and is known for its biocompatibility and superior toughness. Composites of chitin and silk fibroin would possess each biomaterial's unmatched mechanical strength and toughness, making them ideal candidates for biomedical applications requiring such mechanical properties. Here, squid pen β-chitin and Bombyx mori silkworm cocoon silk were blended in Hexafluoroisopropanol (HFIP) solution in specified ratios to synthesize the nanocomposites. As a result, chitin/silk hybrid nanocomposite thin films were produced to test the mechanical properties. Studies of both X-Ray Diffraction (XRD) and Fourier Transform-Infrared (FTIR) Spectroscopy revealed a successful effective interaction between the chitin nanofibers and the silk proteins matrix, which was most likely caused by hydrogen bonding. Results of the self-assembled chitin nanofibers embedded in the silk matrix showed a noticeable enhancement in mechanical properties. The tensile strength, flexibility, and toughness of the biomaterial nanocomposites were enhanced compared to just pure chitin or pure silk fibroin. Due to the improvement in mechanical properties, these chitin/silk engineered nanocomposites can be utilized in biomedical applications such as hybrid scaffolds for bone tissue engineering or microneedles to serve as a new methodology for drug delivery systems.

There are currently an estimated 350 million people worldwide chronically infected with the Hepatitis B virus (HBV). These individuals, over the course of their life, are at an increased risk of developing liver cancer. While antiviral drugs can suppress HBV replication, latent HBV viruses, lying dormant but still potent in the hosts’ cells, so far have proven difficult to eradicate. Homing endonucleases (HE), enzymes that recognize long DNA sequences and induce DNA double strand breaks, could be a means to target and inactivate latent HBV. In particular, we aim to modify the recognition site of the WT I-GzeII homing endonuclease specific to the HBV genome and introduce DNA double-strand breaks. By exploiting the error prone nature of non-homologous end joining, the cellular process to repair double-strand breaks, these modified HEs will have a mutagenic effect on target sequences. Repeated HE activity will eventually cripple the replicative ability of latent viruses. To selectively modify the structure of homing endonucleases, a variant library of the I-GzeII gene is generated with randomized bases corresponding to the amino acid residues that interact with the DNA substrate. Variants that encoded for active HEs with the appropriate recognition site are selected for by In Vitro Compartmentalization (IVC). The selected variants will then be run through bacterial selection and in vitro cleavage assays to further select for structurally stable variants that function in vitro. The final step is to test the HE product on an in vitro HBV cell line. Through our research, we hope to prove that the target of I-GzeII recognition sites can be effectively altered and that latent viruses can be targeted and inactivated through mutagenesis by homing endonucleases. Hopefully, our research will be the first step to a more permanent cure for HBV infections and help to reduce incidences of liver cancer.

Thirty-four million people worldwide currently live with HIV-1. Despite the availability of highly-active antiretroviral therapy (HAART) which may prolong the lifespan of HIV patients, HAART does not target the latent viral reservoir in infected cells, enabling viral rebound in the absence of treatment. Introducing genetically-engineered DNA cutting enzymes (endonucleases) into HIV-infected cells may disrupt the integrated provirus. The site-specific DNA cutting activity of these endonucleases operating in conjunction with cellular error-prone DNA repair mechanisms may result in sustained damage to the integrated viral genome and prevent the virus from replicating. We are investigating 3 classes of engineered endonucleases: homing endonucleases (HEs), zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENS). While the large DNA-binding domains of these endonucleases allow for customization to a desired target sequence, delivering these enzymes to a cell (vectorization) poses a challenge. TALENS in particular require a DNA coding sequence beyond the capacity of many viral vectors. As such, a method of co-transduction must be pursued, whereby two halves of the endonuclease coding sequence are delivered by separate viral vectors and coordinately expressed in the HIV-infected cell. My project aims to determine the optimal multiplicity of infection (MOI) for co-transducing HIV-infected cells using adeno-associated virus (AAV) vectors. I have determined AAV-1 to be the optimal serotype of AAV for infecting SupT1 cells, a cell line used as a model for HIV-infected T-cells. I have constructed two sets of AAV-1 viral vectors to express either Green Fluorescent Protein (GFP) or a red fluorescent protein (mCherry) as surrogates for endonuclease genes and infected SupT1 cells with both sets of vectors at variable MOIs, using flow cytometry to determine the rate of co-transduction. Through this method, I have successfully co-transduced cells with two AAV-1 viral vectors. These results may have applications in future HIV research and clinical therapy.

The nematode Caenorhabditis elegans is a powerful model for the analysis of the conserved mechanisms that modulate healthy aging, from organismal to molecular levels. As animals age, tissues deteriorate at different rates. It has been shown previously in the Kaeberlein lab that deletion of the hypoxia-inducible factor, HIF-1, extended lifespan of worms at high temperature (25°C), but did not do so at low temperature (15°C). Accordingly, it was speculated that at low temperature, worms were not as healthy. At low temperature, we noticed an abnormal vulva phenotype and called it age-related vulva integrity defect (Avid). As worms age, their vulvae protrude and rupture, causing internal organs such as the intestine to erupt out of their bodies. Through investigation, we realized that animals lacking oocytes tend to show more Avid phenotype, compared with the animals that produce enough oocyte. It has been shown before that at 15°C worms produce around 300 fertilized and unfertilized oocytes, while at 25°C this number increases to 400. My preliminary results suggest that germline is involved in the progress of Avid. I studied animals with germline defects and observed 100% Avid phenotype in germless mutants. Avid is a sign of healthspan as animals age, and decline in germline fecundity due to aging can induce Avid. Healthspan is defined as the period of life spent in relatively good health, and maintenance of healthspan is an important component of aging. Our data indicate that Avid can be used as a measurement tool of the age-related healthspan of worms.

Understanding the complex signaling pathways that lead to tumor formation is essential for developing methods the diagnosis, prognosis and treatment of cancer. As the proteins implicated in these pathways are often overexpressed or constitutively activated, the technology for detecting these proteins is necessary for this area of research. Recently, studies have suggested the importance of subcellular localization of these proteins in diagnosing cancer subtype and survival rate. However, the current analytical methods for detecting specific proteins do not provide enough spatial or quantitative information for single-molecule resolution. Quantum dots are nano-sized fluorescent crystals that can label single molecules and be more accurately quantified than fluorescent dye, which is currently used. Quantum dot labeling technology offers the high spatial and temporal resolution that is needed to study the localization of cancer-relevant proteins. We studied the correlation of the protein Akt, which has previously been suggested to preferentially localize in the nucleus or cytoplasm depending on the breast cancer subtype. We used a combination of quantum dot labeling and cellular compartment staining on a breast cancer cell line, and stimulated with insulin to activate Akt for varying amounts of time. Cells were imaged via fluorescent microscopy and the localization of proteins was conducted through MATLAB. Our results showed increased activation of Akt in the stimulated cells over non-stimulated cells, as measured with our quantum dot probe. We also showed an insulin stimulation-dependent localization of Akt. This project suggests that quantum dots can effectively label Akt in breast cancer cell lines at a high spatial and temporal resolution and offer a new platform for studying the mechanisms of cancer signaling proteins.

Pancreatic cancer is the fourth most common cause of cancer-related deaths in the United States. The overall survival rate is low because current therapies are ineffective. However there is growing research that High-Intensity Focused Ultrasound (HIFU) can be used to significantly improve current therapies for treating pancreatic cancer. HIFU works by accumulating ultrasound waves (i.e. energy), which generates heat causing tissue damage (i.e. hyperthermia). The thermal damage caused is measured by using thermal dose. Thermal dose describes the temperature the tissue is treated at and how long that treatment occurs. The theory of thermal dose has been tied to hyperthermia of cancer cells since at least the 1980s and there is a lot of strong mathematical background behind the time-temperature relationship. However with the rapid development of clinical hyperthermia for cancer therapy there is a need for accuracy when it comes to predicting thermal dose. My research focuses on whether or not equivalent thermal doses actually mean equivalent cell death (with cell types Panc-1 and MIA PaCa) and if this can be translated into a clinical setting where higher acoustic power can be used (i.e. using higher energy with HIFU to get lower time of treatment). I simulate HIFU by treating pancreatic cancer cells in water baths at equivalent thermal doses and measure cell survival with spectroscopy. My initial results suggest that the thermal dose relationship is accurate in relating amounts of cell death. An early conclusion from this is that thermal dose can be used to provide better calculations in a clinical setting and help evaluate data. Patients may even be able to experience shorter treatment times through using higher acoustic power with HIFU resulting in a more comfortable experience.