Ocean acidification resulting from increased partial pressure of carbon dioxide (pCO₂) in seawater (due to increased atmospheric CO₂ levels) lowers seawater pH. Declining seawater pH dissolves shells and increases mortality of many shellfish. The risk of losing oysters is discouraging not only because of their influence on biodiversity, but also because of the economic importance to the shellfish industry. By studying the optimal growth conditions, the Friedman lab has been able to look at whether it would be feasible to grow Pacific oysters under present day or elevated pCO₂. To do this we raised groups of oysters in either high or low pCO2 levels and observed their mortality and overall growth. We have found that the oysters raised in the highest pCO₂ levels as well as those whose parents were raised in low pCO2 levels but were themselves raised in high levels had the highest mortality, while the oysters in the lower pCO₂ had lower mortality.

Ion thrusters have a wide range of applications because of the small amount of fuel needed in order to make large delta-V maneuvers. One possible ion thruster concept is for use in the upper Martian atmosphere which is comprised of mainly CO_2. At lower orbits where the atmosphere is still faintly present, an ion thruster could be used to provide constant thrust, and keep a low orbiting satellite in this orbit for an extended duration without the satellite falling due to the drag caused by the upper Martian atmosphere. The research being presented is on an air breathing low mars orbit electrostatic ion thruster concept that uses trace amounts of CO_2 in the upper Martian atmosphere as the plasma fuel source. Our team has designed, built and tested an ion thruster testing this concept. The ion thruster has a cylindrical chamber with an inner chamber diameter of 4.8 inches. The plasma is created by ionizing CO_2 gas with emitted electrons from a tungsten filament cathode in a 12 inch diameter vacuum chamber. A two screen electrostatic grid is used to control the plasma and accelerate ions in order to produce thrust. The ion beam is neutralized using another tungsten filament cathode. Four separate power supplies were used in order to create the plasma, supply voltage to the electrostatic grids, neutralize the ion beam, and create the axial magnetic field that controls the electrons inside the thruster. The high velocity ions that are generated by the thruster are emitted in a controlled fashion that then produces thrust. This thrust was calculated by using the measured power going to the neutralizer cathode, and the particle exhaust velocity. The exhaust velocity was calculated from the separation between grids, and the potential difference applied across the grids.

Landscape immersion, commonly accepted as best practice for zoo exhibit design, often fails to provide meaningful moments between visitor and animal that can trigger an empathetic connection. With many zoos seeking to further their conservation mission, exhibits must push the boundaries of immersion design and provide opportunities for cognitive and affective stimulation for visitors. Exhibits that provide visitors with both an intellectual and an emotional connection to the animal increase the desire to learn more about the species and its habitat and, in turn, foster a reverence for the natural world that can lead to a more environmentally conscious shift in behavior. In analyzing research on conservation psychology and visitor motivations, I found zoos create and support a social context surrounding the interaction with nature. Offering multiple ways for visitors to engage simultaneously with each other and the exhibit improves the social quality of the visit, increases connection to the animals, and concern for their wellbeing. In conversations with designers and curators, I found animal wellbeing, visitor experience, and animal husbandry are essential components to exhibit design. Each offer opportunities that enable an empathetic connection that can increase desire to care for animals at the zoo, and as a consequence, for the species and the broader ecosystem in which those animals live. Finally, I visited three case studies that demonstrate a progressive immersive design approach: the Woodland Park Zoo Humboldt Penguin exhibit, the Arizona Desert Museum Desert Loop Trail, and the Bronx Zoo Madagascar! exhibit. I found that these exhibits contained cultural and ecological narratives that highlighted impacts people have on those particular ecosystems. The immersive nature and compelling narrative of these exhibits prompts individuals to reconsider their role in environmental problems and conservation action, and see themselves as part of the solution.

Paleoclimate data suggest that anomalously cold conditions across the Northern Hemisphere (NH) and a southward shift of the Intertropical Convergence Zone (ITCZ), a major feature of the tropical atmosphere, occurred during the Little Ice Age (LIA) ~ 1350 – 1850 AD. The purpose of this research is to identify whether these climate changes are simulated by the latest Coupled Model Intercomparison Project (CMIP5) General Circulation Models, and whether they can be attributed to changes in solar irradiance, volcanic aerosols, and greenhouse gas concentrations. In each model, two types of runs are analyzed: pre-industrial control runs and last millennium runs. The pre-industrial control runs are 1,000-year runs with external forcings held at 1850 AD levels and the last millennium runs are 1,000-year runs with external forcings that change over time in accordance with paleoclimate records. While anomalous global cooling occurs during the LIA in all models, little agreement exists on the magnitude of the cooling and the changes in interhemispheric temperature gradient. In addition, changes in the position of the ITCZ are small and vary widely between models. We perform an energy budget analysis using the approximate partial radiative perturbation method to further investigate the LIA temperature and the ITCZ changes. Volcanic aerosol forcing and surface albedo feedbacks appear to be the main drivers of global cooling during the LIA, while the contribution from changes in solar irradiance is small. Changes in the position of the ITCZ are well correlated with changes in cross-equatorial atmospheric heat transport, as expected from theory.

The lab I am involved with investigates the molecular events of neuromodulation, a form of neuronal chemical signaling that determines behavior, emotions, learning and memory. Neuromodulators are carried and released by dense core vesicles, a type of cellular vesicle which little is known about. Dr. Ailion's lab has performed genetic screens for C. elegans mutants that have altered dense core vesicle secretion and has isolated many unique mutants. During my time in Dr. Ailion's lab I focused on genetically mapping two of these mutants which were given the names yak90 and yak91. With yak90, I used a well-established mapping method where my mutant strain was crossed to marker strains which contained alleles causing obvious deformities on each chromosome. Generations later, I examined their offspring and was able to pinpoint one mutant phenotype that was not segregating according to Mendelian ratios, indicating linkage to chromosome IV. When a candidate gene was found near the linkage site, I did a complementation test and confirmed that yak90 contains a mutation in an already characterized gene, unc-31. With yak91, a new method was tested using a marker strain that contains alleles for multiple fluorescent tags instead of body deformities. This was necessary because yak91's mutation causes it to be "egl", or distended with mature eggs, and it was difficult to tell it apart from one of the marker phenotypes. The cross with the new strain was a success and after examining the progeny, linkage was found on chromosome IV. Another complementation test was performed, and yak91 was found to contain a mutation in ric-8. Total loss-of-function mutations in ric-8 are lethal so yak91 must contain a splice site or point mutation that significantly alters the function of the protein product. Both genes I identified play important roles in neuromodulation. 

The past 40 years has seen extraordinary growth amongst the Latino population in Washington State. Our study asks why the population of Latinos is increasing and what is driving the migration of Latinos to Washington State. After analyzing data from the U.S. Census from 1970-2010, we revealed that in the last decade the Latino population has risen in some Washington counties as much as 300%. Although the information from these government sources account for the general Latino population, the Latinos who are undocumented in the United States are more difficult to track. In lieu of these numbers we were able to access non-traditional data through a Seattle-based Latino organization that works with this specific population and confirmed the continued growth. Furthermore, the overall increase in the Latino population has seen the most dramatic rise in three Western Washington counties: King, Pierce, and Snohomish. Other data sources such as the Washington State Department of Financial Management and the U.S. Bureau of Economics revealed that since the 1970’s, industries such as construction and hospitality services in King County, port labor in Pierce County, and farming in Snohomish County were attracting this population. In addition to labor opportunities, we believe that the increase of Latinos in these counties can be attributed to the absence of restrictive immigration legislation such as laws set in place in states like Alabama and Arizona. Moreover, Washington’s liberal social tendencies and geographic location deflects much of the anti-immigrant sentiment that makes news headlines in states along the U.S. – Mexico border. According to a Pew Research study, by 2020 Latinos in the United States will account for approximately 19% of the population – a number that is likely to increase in Washington State and continually change the population, economic, and social landscapes.

According to dual process models of alcohol use, both explicit (controlled/reflective) process and implicit (automatic/reflexive) cognitions are important predictors of alcohol-related problems. These models also suggest that there are certain types of people for whom implicit processes may be more influential – e.g., people who are more impulsive. Based on these theories, this study seeks to examine whether impulsivity influences the strength of the relationship between implicit drinking identity (cognitions about the self and drinking) and alcohol-related problems. 506 college students completed the Drinking Identity Implicit Association Test, the Impulsivity Subscale of the Substance Use Risks Profile Scale, and the Rutgers Alcohol Problem Index. As hypothesized, both impulsivity and drinking identity scores were significantly and positively correlated with alcohol-related problems. Moderation was also supported: drinking identity was more predictive of alcohol-related problems for those reporting higher impulsivity rather than lower impulsivity. These results are consistent with theories that suggest that implicit cognitions should be better predictors for individuals with higher levels of impulsivity. This suggests that targeting implicit drinking identity might be helpful in reducing alcohol-related problems, especially for those individuals with higher levels of impulsivity. In addition, targeting impulsivity may also help reduce alcohol-related problems.

Cocaine and other drugs of abuse have destroyed the lives of many individuals as those who take such drugs struggle with the powerful vice of addiction. Such drugs have been shown to cause changes in the brain, specifically in the cortex and the striatum, which has been linked to the manifestation and maintenance of addiction. Within the striatum there exists cell populations of neurons, which vary in their outputs to the brain and are regulated by glutamate inputs from the cortex. The involvement of these individual cell populations in addiction, including how they are regulated by cortical glutamate, is not yet fully understood. In order to investigate this issue, I collect data in and run rat behavior experiments with rats that have been treated with viral vectors, which temporarily decrease neuron activity in specific cell populations when activated by specific ligands. After the behavioral data has been collected I process the tissues by slicing the brains and stain them with techniques such as immunohistochemistry. Then I determine if the vectors were actually present in the expected cells due to their fluorescence after immunohistochemistry procedures. In some of the work that I have done with Kerry Kerstetter we have found that decreasing activity in cortical glutamate projections to the striatum resulted in an increase in motivation for cocaine. A better understanding of the intricate pathways involved in drug motivation will allow for better treatment and care for those suffering from addiction. Our hope is to provide more information on such pathways to help progress the development of future treatments for victims of addiction.

Vascular calcification greatly increases risk for heart disease, the leading cause of death in patients with diabetes and chronic kidney disease. Vascular calcification is an active process attributed to vascular smooth muscle cell (VSMC) mineralization. The sodium-dependent phosphate cotransporter, PiT-1, mediates VSMC calcification. The mechanisms by which PiT-1 causes calcification may include cellular matrix degradation, apoptosis, calcium phosphate vesicle release, and changes in gene expression. Of these mechanisms, my research focuses on the poorly understood signaling pathway by which PiT-1 induces VSMC calcification through up-regulating osteogenic (bone-forming) and chondrogenic (cartilage-forming) genes and down-regulating smooth muscle genes. These changes in gene expression make VSMCs more readily calcified in elevated phosphate. Recent literature suggests that VSMCs respond to elevated phosphate through PiT-1 with a novel cell signaling mechanism independent of phosphate uptake. My project concentrates on understanding the function of the PiT-1 protein's intracellular domain, which currently has no known function. I hypothesize that this section of PiT-1 is responsible for signaling in response to elevated phosphate, triggering a phosphorylation cascade that activates osteogenic transcription factors, such as Runx2, which initiate this osteogenic conversion. I am working toward integrating the gene for the intracellular domain of PiT-1 into the vascular smooth muscle cell genome to overexpress the truncated protein in cells. From my hypothesis that PiT-1 has a role in cell signaling, I predict that the overexpression of the intracellular domain of PiT-1 will reduce VSMC calcification by competing with the wild type PiT-1 protein for binding to proteins in the activation pathway, and inhibiting the signaling process. If my data support this hypothesis, I may engineer the intracellular domain of PiT-1 for therapeutic purposes.

Staphylococcus aureus is a Gram-positive bacterium that colonizes the nose and skin and causes a variety of infections in humans. The acquisition of resistance to many first line antibiotics has made S. aureus increasingly difficult to treat. Previous studies have shown that an S. aureus enzyme called nitric oxide synthase (NOS) is necessary for both colonization and infection in animal models. The goal of the present study is to determine the role of NOS in staphylococcal physiology. We treated the S. aureus strain COL and an isogenic mutant strain lacking NOS with several redox-active compounds including menadione, paraquat, and pyocyanin. The minimal inhibitory concentration (MIC) of each agent was measured in liquid culture. A NOS mutant was substantially more sensitive than wild-type S. aureus to menadione, and menadione-resistance was restored by treatment with exogenous nitric oxide. In contrast, NOS mutant and wild-type strains were equally sensitive to paraquat. As both menadione and paraquat are redox cycling reagents that generate superoxide radicals, this observation suggests that the menadione-sensitivity of the NOS mutant is unrelated to superoxide. The NOS mutant also appears sensitive to pyocyanin, which blocks the electron transport chain. We hypothesize that nitric oxide regulates electron flow through the electron transport chain, most likely by inhibiting terminal oxidases. Further studies will investigate the effect of electron transport inhibitors that target NADH-dehydrogenase (rotenone) or the F₀F₁-ATPase (DCCD), and the effect of mutations that impair cytochrome assembly or the regulation of redox metabolism, in wild-type or NOS mutant bacteria. ATP and NAD/NADH levels will be monitored in parallel to determine effects on energy generation and redox balance. These studies will reveal how endogenously generated nitric oxide maintains redox homeostasis in bacteria and may lead to novel strategies to treat or prevent S. aureus infections. 

Autism spectrum disorders (ASD) are neurodevelopmental disorders with symptoms related to social communication and repetitive behavior. One aspect of social communication that is particularly challenging for children with ASD is pragmatic language including the ability to clearly convey narrative information to others. Narrative language, such as story telling, is a type of pragmatic ability that utilizes cognitive-linguistic planning and coordination of information. The first objective of our study is to compare the narrative language abilities of typically developing children to children with ASD. Our second objective is to test the relation between narrative abilities and severity of symptoms within the group with ASD. Seventy-five 6 to 11 year old children with idiopathic ASD or typical development participated. Groups matched in age, IQ, and sex ratio. Narrative language samples were extracted from a longer diagnostic interview, the Autism Diagnostic Observation Schedule (ADOS). Scoring of narrative language skills was based on the coding system developed by Reilly and colleagues. Symptoms were assessed via the ADOS, the Autism Diagnostic Interview-Revised, Social Responsiveness Scale-2, and Repetitive Behavior Scale-Revised. We expect to find a lower level of narrative ability in the group with ASD, given previous reports of pragmatic errors , misinterpretation of key events, and dysfluencies among children with ASD. For the second objective, we predict that there will be a correlation between the narrative level and social symptoms, such that better narrative ability relates to fewer symptoms. In the repetitive domain, we expect to see more repetitive behaviors with relation to lower level of narrative ability by looking at dysfluent speech, which entails repetitions and self-corrections. Our results may lead to future studies regarding narrative ability in speech interventions towards children with ASD. 

Oxygen (O₂) is essential for aerobic organisms to complete development. However, genetic mechanisms exist to promote development and avoid damage under low oxygen conditions. Elucidating how these mechanisms regulate development is important for understanding diseases, such as ischemia and tumor formation, which have a hypoxic component. We are studying the hypoxic response in Caenorhabditis elegans, a genetically tractable organism that uses simple diffusion for gas exchange with the environment. Previous research has suggested that at 5000ppm O₂, loss-of-function mutations in either the transcription factor hif-1, or an AMP-activated protein kinase (AMPK) subunit aak-2, prematurely arrest development. Given that these two mutants have similar phenotypic responses in severe hypoxia, we hypothesized that aak-2 and hif-1 act in the same genetic pathway to coordinate developmental arrest in hypoxia. To test this, we pharmacologically activated AMPK and performed epistasis analysis with genetic mutations. We found that activating AMPK by treatment with Metformin in a hif-1 mutant was not sufficient to sustain reproductive activity in 5000 ppm O₂. We also generated a strain that constitutively expresses HIF-1 in an aak-2 mutant background and found no difference in developmental arrest from aak-2 mutant animals with wild-type HIF-1 activity. We conclude that aak-2 and hif-1 act in distinct genetic pathways to promote development in hypoxia. Our results suggest that C. elegans has multiple, redundant pathways that coordinate development in hypoxic conditions.

Poliovirus (PV) remains endemic in three countries and is responsible for sporadic outbreaks in several others. Clinical surveillance for acute flaccid paralysis (AFP) is the gold standard for PV surveillance. However, as few as 1 in 100 to 1 in 1000 PV infections will develop AFP, particularly in well-vaccinated populations. Environmental surveillance of wastewater using a bag-mediated filtration system is currently being investigated to detect sub-clinical circulation of poliovirus. However, the filter samples will be collected remotely and evaluated centrally, which requires a shipping period. During this shipping period, bacterial and fungal growth may degrade PV on the filter surface. Inhibition of fungal and bacterial growth is necessary to ensure PV survival on filters during transit from field collection to the processing lab. Shipping on icepacks at 4°C is costly, thus finding an alternative is ideal. Preservative agents were investigated as an alternative to reduce microbial growth while not affecting PV recovery from its performance methods. Preservatives investigated included sodium azide, calcium propionate, o-phenylphenol, and sodium benzoate. Preservative solution or PBS control was pumped into the positively charged Virocap filter and eluted with beef extract, pH 9.50. After 1.5 hours, the eluate was pumped out, pH adjusted, and dosed with 10^2 PFU/mL PV1. Filters were run in duplicate and samples were plated on BGMK cells for enumeration by plaque assay. 0.0195% sodium azide eluate had a 64% recovery when compared to PV expressed in the PBS control eluate. 0.1% calcium propionate had a 102% recovery, 2% sodium benzoate had a 101% recovery, and 0.02% o-phenylphenol had a 111.1% recovery. Sodium azide is not recommended as a good preservative for PV due to low recovery, but 0.1% calcium propionate, 2% sodium benzoate, and 0.02% o-phenylphenol should be investigated further for PV preservation and recovery in wastewater over time.

Tuberculosis (TB), an infectious disease caused by the bacterium Mycobacterium tuberculosis (Mtb), kills nearly 2 million people a year and is a major cause of morbidity and mortality worldwide. The increasing prevalence of multi-drug resistant (MDR) strains that fail to respond to all currently available drugs underscores the critical need for new therapeutic strategies. DNA topoisomerases (topos) are a class of enzymes responsible for maintaining the correct topological state of DNA molecules by modulating the degree of supercoiling through the breakage and reforming of covalent phosphodiester bonds in the DNA backbone. With the precedent-setting success of several anticancer and antibacterial drugs that target topos, focus in TB research has increasingly turned to these enzymes as new potential targets for chemotherapy. In this study, we isolated Mtb topoisomerase type IA (MtbTOPA), a subclass that only acts on single-stranded DNA (ssDNA), as our target of interest. At least one type IA topo activity must be present in every organism for resolving topological obstacles that require ssDNA cleavage, and fortuitously, Mtb happens to only encode one type IA, further validating MtbTOPA as a high-value drug target. We have cloned, expressed, and isolated highly purified recombinant MtbTOPA protein for enzymatic studies and work is currently underway to solve its crystal structure to aid in target-based approaches to drug development. In efforts to develop a high-throughput screen (HTS) for identification of small molecule inhibitors of MtbTOPA, we have collaborated with the Global Alliance for TB Drug Development (GATB) and leading structural genomics centers to gain access to large compound libraries as well as to accelerate the drug discovery process. We adopted a HTS method based on fluorescence resonance energy-transfer (FRET) and requisite MtbTOPA mutants were designed. It is our hope that the HTS will identify several hits that can be developed into novel TB drugs.

There is a wide-spread belief among professionals and parents that raising children with Autism Spectrum Disorders (ASD) in bilingual households will be detrimental to their language development. Although some early studies reported an association between bilingualism and cognitive deficits, more recent studies have called these findings into question. Furthermore, the few studies of ASD and bilingualism also support potential benefits. Children with ASD from multilingual households have been shown to demonstrate increased gesturing and sociability. Our study proposes to directly investigate the relationship between bilingual environment, social ability, and language ability in toddlers with ASD. We hypothesize that toddlers with ASD who grow up in a bilingual environment will exhibit greater social ability and increased language ability compared to toddlers with ASD from monolingual households. Thirty-eight, 12-24 month-old toddlers from the UW Autism Center who were part of a larger, multisite study were categorized based on their mother’s language ability: bilingual (BL; 18) and monolingual (ML; 20). Language measures included the MacArthur-Bates Communicative Development Inventory, Communication subscale of the Vineland Adaptive Behavior Scales (VABS-II), and Expressive and Receptive Language subscales from the Mullen Scales of Early Learning. Social skills measures included the VABS-II Socialization subscale and a measure of joint attention. We will use two sample t-tests to compare social skills and language skills between the two experimental groups. This research will provide some of the first direct evidence regarding the impact of a bilingual language environment on the early social and language abilities of very young children with ASD. We hope to raise awareness towards the need for evidence-based approaches to guide professional and parents of young children with ASD.

Solar power is an increasingly significant resource as we look to move from fossil fuels to a cheap and sustainable source of energy. Solar cells can be manufactured using organic semiconductors by using cheap roll-to-roll printing techniques, however, the efficiency of such organic photovoltaic (OPV) devices is currently too low for cost-effective implementation. These devices utilize a built-in electric field, resulting from the difference in potential energy between the device’s electrodes, to collect photogenerated charges at the electrodes as current. Fine-tuning of the electrode energy levels also dictates the amount of voltage that can be generated by the device. As a result, the ability to chemically alter the electrode energy levels can greatly influence the overall power output of the solar cell. Phosphonic acid self-assembled monolayers (SAMs) are molecules that can be chemically attached to a variety of electrode interfaces and have been shown to alter the energy levels of certain electrodes. I am investigating the effect that attaching SAMs to the zinc oxide surface of an OPV electrode will have on both the built-in voltage and power conversion efficiency of an OPV cell. In order to test the hypothesis that the SAMs can affect OPV performance, I have fabricated solar cells with SAMs in order to compare them with solar cells without SAMs. Experiments that measure the built-in voltage of the device and investigate the lifetime of photogenerated charges will help to clarify the specific role that the SAMs play in affecting OPV device performance. If this hypothesis is correct, we have the potential to achieve higher power conversion efficiency than what is currently reported in these devices and this may lead to a greater emphasis towards understanding the role of interfaces in developing sustainable solar technology.

Domestic violence, defined here as violent or aggressive behavior from one intimate partner to another, is one of the prime contributors of female homicides, known as femicide. Between 2005-2013, over 1042 women were reported murdered in Italy, increasing from 84 to 134 victims per year. My research analyzes women inequality in Italy by focusing on how domestic violence and femicide have been interpreted and portrayed to the Italian public. I pose the following question: In what ways have literature and media sources portrayed or helped raise awareness on women’s rights issues in Italy, specifically regarding domestic violence and femicide? This research is salient because most research focuses solely on developing countries, but when it comes to women’s rights, all countries including Italy are affected. In order to explore the relationship between intimate partner violence and femicide, I use synthesis and comparison of Michael Johnson’s Typology of Domestic Violence with other literature and social media. First, I analyze how literature and media sources portray domestic violence and femicide to the Italian public. Second, I compare my findings with Johnson’s interpretation of intimate partner violence. Third, I combine all said sources to formulate my own interpretation of domestic violence and femicide. Much of this research has been conducted in Italy and from Italian sources; therefore, most of the literature is translated into English. I hypothesize that cultural acceptance of gender inequality in Italy has contributed to domestic violence becoming a major factor in femicide. I anticipate that my research will help raise international awareness of femicide and domestic violence issues in Italy, and that the results will provide assistance in decreasing violence against women. I also seek to provide an alternate perspective of domestic violence, which I hope will lead to future research into the policy implications of my work.

The prevalence of HIV cases in the African born national population versus the African American or national population in general is notably high. In Washington state, there are approximately four times more HIV cases for the foreign born black male versus the African American black male along with about eleven times more HIV cases for the foreign born black female compared to the African American female counterpart. Stigma can impact medication adherence, quality of treatment and undiagnosed contributing mental disorders that, when treated, can improve one’s HIV status. However, little is known about how HIV stigma impacts the treatment and intervention outcomes for the African-born population. My lab as well as my individual role in this research project aims to analyze the nature of HIV stigma among this population, which will provide fundamentals of an intervention that is most ideal for African born population. We conducted semi-structured qualitative interviews with African born patients receiving treatment at Harborview Medical Center Madison HIV Clinic and those receiving social service at BABES YWCA network, and then I as the primary coder analyzed the data through ATLAS.ti, analytic software. Preliminary results indicate that stress due to community paranoia and disturbances due to family history of HIV are common obstacles faced by this population. These findings have important implications for focusing on treatment and other interventions for this understudied population.

Youth in the U.S. juvenile justice system are faced with various physical and mental health disparities, such as sexually transmitted diseases, and mental illness. Youth are at elevated levels of risk of contracting chlamydia and gonorrhea. People under 25 years old make up 15% to 30% of HIV cases (Morris, et al., 2006). It has also been found that many externalizing disorders such as attention-deficit/hyper-activity disorder, conduct disorder, and oppositional defiant disorder are also associated with delinquency (Wareham & Boots, 2012). Given these health disparities, it is essential that consistent health care be readily available and accessible to this high-risk population. However, many communities do not have efficient resources to identify possible factors that hinder the consistency of health and mental health care for adjudicated youth. The current research project focuses on risk factors preventing continuity of health care (both physical and mental) among youth in the King County Juvenile Justice system. Through analyzing and coding over twenty qualitative interviews, risk factors preventing youth’s access to care are identified. The study explores how factors such as lack of knowledge on how to navigate the medical system and youth’s rights to independently access care, create unique barriers for youth seeking and receiving care. As a result of these obstacles, many high-risk youth receive much of their primary care while in detention facilities. Based on analyzing the interviews and a literature review on programs fostering access to health care among adults, I will propose a model to promote continuity of care among this high-risk youth population.

Colicins are a family of antimicrobial toxins that are produced by E. coli. The colicin gene is carried on a small circular DNA molecule, called a plasmid, along with a gene encoding an immunity protein. The immunity protein binds and neutralizes the antimicrobial colicin in a highly specific manner. Bacteria lacking the plasmid (and thus lacking immunity) are killed by the colicin. The immunity and the colicin are mutually dependent on one another, creating a system that seems unable to evolve. If either changes then they will no longer fit together, which in this system would result in the death of the cell by its own colicin. However, evidence shows that there are many different pairs of colicin and immunity proteins that share common ancestors, suggesting that diversification has occurred. How is this diversity possible if the system seems evolutionarily trapped? Our research looks at the idea of promiscuous protein intermediates. Under this hypothesis, the immunity changes first so that it can bind both its original colicin as well as another distinct colicin protein, we then attempted to recreate this possible evolution pathway in lab by evolving our own colicin-immunity pair. Using directed evolution we first evolved a “broadened” immunity protein then a matching colicin through error-prone PCR, which created a diverse collection of mutated colicins. Then we screened for matching colicin-immunity pairs. In pursuit of our novel protein, we generated and screened over 6000 colicins and have successfully isolated two potential novel colicin proteins.Through sequencing analysis, we know that the two potential novel colicin genes each have two nonsynonymous mutations.

Atmospheric particles and gases play a large role in Earth’s climate and have negative impacts on human health. Currently, there are air quality standards for the mass concentration of particles less than 2.5 micrometers in diameter, PM_2.5. However, there are no standards for ultrafine particles, i.e. those smaller than 0.1 micrometers, even though studies have shown that ultrafines can cause negative respiratory health effects. The mass and number concentrations of ultrafines, and therefore their sources and concentrations, are not well characterized. We report measurements of ultrafine particle concentration and size distributions in Port Angeles, Washington made using a Scanning Mobility Particle Sizer (SMPS). We used the observed diurnal cycle and seasonal variations in ultrafine particle abundance to gain insights into the primary sources in this region, including traffic, wood smoke from residential heating, and shipping, among others. By analyzing data from the SMPS together with wind direction and speed, we assessed the potential contribution of specific point sources, such as the new biomass cogeneration facility or specific roadways. We conclude with a discussion of the current site location and implications for a forthcoming study in nearby Port Townsend.

 The vast majority of current protein-based drugs involve binding a therapeutic target with an exogenous molecule that neutralizes or blocks its function. A major drawback of this approach necessitates a stoichiometric number of binding sites be administered to the patient, resulting in many caveats such as high dosage, stability, and immunogenicity. Enzymes represent an underexplored avenue for protein therapeutics with vastly enhanced potency. Proteases are essential and ubiquitous enzymes that catalyze peptide bond cleavage. While there are multiple therapies available derived from naturally occurring proteases, currently there are no novel, engineered protease therapeutics. In this work, we seek to establish a highly specific and processive protease system with traits desirable for use as a protein therapy, such as high solubility and thermostability. For this purpose, we have chosen to engineer the small ubiquitin-like modifier (SUMO) protease. The target of this protease, SUMO, is a small protein important for cell cycle regulation in eukaryotes. The mechanism for SUMOylation is analogous to the ubiquitin regulation system; these small proteins are adducted to other molecules and serve as signals for degradation or cellular localization. Removal of these tags is essential to the regulatory process, and is mediated by the highly specific SUMO protease. This inherent specificity makes the SUMO protease an ideal engineering platform. Here, we take the first steps toward unlocking the therapeutic potential of the SUMO protease by enhancing the stability and solubility of the yeast homologue. To accomplish this, we re-engineered surface residues with the Rosetta software suite. Furthermore, we have developed a novel Förster resonance energy transfer assay to allow us to monitor protease activity in real time. In addition to laying a foundation for the creation of highly selective therapeutic proteases, our work has immediate implications for the production and purification of recombinant protein in a laboratory setting.

In liver transplantation, increased overall fat content in donor livers causes poor graft function and lower patient survival post-transplant. Longer waiting lists combined with a shortage of organs has resulted in transplant surgeons considering moderately steatotic livers as a part of extended donor criteria. Clinically, the fatty infiltration is diagnosed by the lipid droplet size. Macrovesicular steatosis refers to large droplets or vesicles that distort the nucleus, while microvesicular steatosis refers to droplets equal to or less than the size of the hepatic cell nucleus. While macrovesicular steatosis negatively impacts graft function, livers with microvesicular steatosis result in patient outcomes that are almost the same as that of nonsteatotic livers. Therefore, a method to quantify the amount and droplet size of hepatic steatosis can be an innovative tool for transplant surgeons. In our previous studies, sound speed and attenuation correlated with the presence of visually observable fat. However, significant variabilities were discovered in the attenuation. The next step in this research involves exploring the effect of lipid droplet size on attenuation, using an attenuation spectroscopy method developed in colloid science research. If the total fat content is known, mixture rules based on a volume average of the fat and non-fat components can be used to estimate the intrinsic attenuation at a given frequency. Beyond this estimate, excess attenuation attributable to interactions between fat and non-fat phases of the mixture can be estimated using a coupled-phase model. Here, we quantitatively evaluate the excess attenuation caused by small lipid droplets by comparing attenuation measurements of well-characterized dairy products with model predictions. Results confirm that sub-micron sized lipid droplets produce a measurable amount of excess attenuation at 1 MHz. These results suggest that analogous measurements may be made in quantifying the amount of microvesicular steatosis present in livers with known overall fat percentage.

The brain effortlessly carries out the daunting task of visual perception by utilizing millions of neurons to process various aspects of the visual scene. The systematic arrangement of these cells across the primary visual cortex (V1) can be described by a set of superimposed maps that convey the orientation, scale, location and eye of origin of the image features that best excite the neurons. Current theory suggests these maps are arranged such that all combinations of stimulus parameters are covered equally and continuously in local regions across the visual cortex. This idea is appealing because it corresponds to the intuition that we should be able to see the features of a simple shape equally well at any rotation and at a variety of distances, and it is important because it places a constraint on the architecture of the cortex. To examine whether this constraint fits with other known anatomical and physiological measurements, we have conducted computer simulations to measure the evenness of coverage in large-scale, biologically plausible models of V1. We presented a large combination of visual stimuli to the model and computed a coverage metric, c', defined in the literature as the standard deviation divided by the mean of cortical activity across all stimuli. Taken together, c' and the associated map of neuronal activity in stimulus space reveal the coverage uniformity of map variable combinations. We found that our original models had a striking imbalance in activity across spatial scale, which counterintuitively arose from the assumption of a uniform change in neuronal receptive field (RF) size across the visual cortex. In these models, there were equal numbers of neurons with small and large RFs. Based on our observations, we are developing an improved model that uses a nonlinear distribution of RF sizes in an attempt to preserve uniform coverage.

Understanding how the brain processes information using neural circuits remains a challenging task. For example, although neurons in the mammalian visual cortex are known to be specialized for processing particular visual features, such as motion, color or depth, little progress has been made on elucidating the underlying circuit diagrams. To address this problem, we have developed a system with a Java-based user interface that can apply optimization strategies to rapidly test competing models against large amounts of neurophysiological data, parallelizing the computational load across a cluster of workstations, to uncover plausible circuit models. In order to demonstrate the effectiveness of this system, we are applying it to understand the function of motion-sensitive neurons in the primate visual cortex. These neurons are direction selective (DS), meaning that they respond well to a visual stimulus moving in one direction but not in others. Previous studies demonstrated that this response also changes with stimulus speed: as the visual world moves faster, the neurons appear to operate on a shorter timescale. Current mathematical models for DS neurons, which are based on filters that change position linearly with time, predict the response to some stimuli but do not account for the ability of the neuronal response to adapt to changes in speed. We hypothesize that a model using a filter that changes position nonlinearly with time will better explain the experimental data. To discover this filter, we are building several candidate models and will apply our optimization system to test their performance against our own experimental data. We will test these nonlinear filter models against an alternative that uses multiple linear filters, each tuned for a different velocity. If our approach can improve upon current models for DS neurons, it may offer neuroscientists a powerful tool for revealing neural circuits that underlie visual perception.

Our lab has recently developed computational methods for designing cage-like protein nanomaterials built through the self-assembly of multiple copies of two distinct protein components. This new technology holds great promise for a wide range of applications including targeted drug delivery, vaccine design, and biofuels. Moving towards these real-world applications, one desired but as of yet unrealized feature of our current designs is the ability to produce each protein component independently of one another and then trigger assembly by mixing the purified components in vitro. Obtaining this level of control over the assembly process requires that the individual protein components are stable and soluble in the absence of their designed binding partner. This property is not explicitly considered in our current design protocol. Here we present work aimed at addressing this problem by implementing a new step into our design protocol wherein we redesign the amino acid sequences of the proteins to increase the net positive charge on the surface of one protein subunit and the net negative charge on the surface of the other subunit. This supercharging approach should improve solubility by disfavoring aggregation between identical subunits of individually purified components while favoring the interactions between distinct subunits required for nanocage formation. To supercharge the proteins, we use the molecular modeling software package Rosetta to determine positions on the surface of each protein that are predicted to tolerate mutations to either positively or negatively charged residues. This information is used to automatically generate initial designs, which we then manually inspect and refine.

Castilleja levisecta (CALE; golden paintbrush) is endemic to the Pacific Northwest prairies and is an endangered plant. Recovering this species requires an understanding of its seed production and dormancy. As a hemiparasite, CALE can acquire resources from host plants by forming connections with them. I am trying to find out whether host identity can affect the number of seeds per capsule by, for example, altering pollinator visitation. My research focused on the effects of two known hosts of CALE, Festuca roemeri and Eriophyllum lanatum. CALE were grown without a host or with one of these two hosts. Two pods were harvested from each of twelve CALE per host treatment, for a total of 72 capsules. Each pod was evaluated by counting the seeds inside and weighing the components of seed and chaff separately. With these data I determined fecundity and density of the seeds. To date my research indicates CALE may be benefited by Eriophyllum lanatum as these plants have greater fecundity than the no host treatment. Festuca roemeri had no major effect on CALE when compared to individuals grown without a host. This research indicates that hosts can affect reproduction by CALE, reinforcing the importance of considering host identity when recovering this species. Variation in seed dormancy among sites and/or years can affect the success of recovery efforts. I conducted germination testing on 8 accessions of CALE by putting seeds onto petri plates on moist filter paper, exposing them to cold moist stratification, and monitoring germination. I am interested in whether different populations of CALE may differ in their need for stratification. To date my research indicates population is important for how dormant CALE is and when CALE will germinate. The factors affecting dormancy and seed production in CALE are important for reintroduction and management of this endangered species.

This exploratory study investigates levels of stress among informal caregivers of cancer patients and the amount and kinds of social support they received while providing care. Previous research indicates that informal caregivers, defined here as family members or friends providing care to loved ones, often times experience extended periods of stress that can be reduced with increased social support. Social support includes the instrumental, informational, appraisal, and emotional forms of assistance caregivers provide. The aim of this study is twofold: to examine why previous social support services at a care facility in the Pacific Northwest had fluctuating participation rates, and to find strategies to strengthen social support for caregivers through understanding the levels of stress and support they experienced. I hypothesize that fluctuation was due to a lack of knowledge of support services and receiving support outside of the agency. I use a mixed methods design with a quantitative survey and a qualitative focus group component. Participants are given surveys inquiring information about the levels of stress they experience in their daily lives and the amount of support received from others. The focus group consists of guiding questions including open-ended questions about their experiences with caregiving, levels of stress, coping methods, forms of social support, observations on health changes, and perceptions of supportive services. I expect to find that caregivers receiving social support from family and friends will report experiencing less stress compared to caregivers that primarily receive social support from healthcare professionals. Overall, this study provides a deeper understanding of the extent to which caregivers feel social support and highlights barriers to social support service use at an organizational level. These findings have implications for existing knowledge on caregiver support and increases the knowledge base of stress and support of informal caregivers.

Children’s oral narratives can give clinical insight into their language abilities. Often, clinicians use narrative performance as a screening tool for diagnosis of language impairment. Hoffman (2009) found that finding a proportion of utterances that contain semantic or syntactic errors ([RESTRICTED] utterances) is an efficient and effective tool for differentiating between narratives produced by children with typical development and those with specific language impairment (SLI). Using a group of 48 age-matched pairs of 8-10 year old children, Hoffman (2009) found that this tool differentiated between the groups. Post-hoc analysis found that this tool accurately identified those with SLI when using a diagnostic criterion of 14% and higher proportion of [RESTRICTED] utterances, correctly classifying 85% of her sample. Confirmation of these findings is necessary if this tool is to be developed for clinical use. This investigation attempts to replicate Hoffman’s 2009 findings with an existing set of narratives elicited using similar methods. Narratives from 16 age-matched pairs of 8-9 year old children, half with known language impairment identified by an interdisciplinary team assessment, half from children with typical development, will be segmented and coded using methods described in Hoffman 2009. The two independent coders will be blind to diagnosis, age and gender. Proportion of [RESTRICTED] utterances will be calculated for each transcript. We hypothesize that the groups will differ in the proportion of [RESTRICTED] utterances and that Hoffman’s 2009 diagnostic criterion will accurately identify children with and without language impairment. We anticipate reliable results that are similar to Hoffman’s (2009), within a reasonable margin, given the small group size. Replication would indicate that this method has the potential to be an efficient and effective clinical screening tool that warrants further development. Future research would need to confirm generalizability with larger, randomized groups

Traumatic Brain Injury (TBI) is an issue that seriously affects people of all ages; older adults with TBI have the highest rates of hospitalization and death. Additionally the overall recovery is significantly poorer than a younger person with a similar TBI. With normal aging, there is a reduction in the number of white blood cells (WBCs). However, in certain chronic diseases with an inflammatory component that are more common with older age, such as diabetes, there may be an ongoing activation of available WBCs which could affect viability in response to injury. This investigation used data from an ongoing parent study of the immune response following TBI in order to examine the number of and viability of peripheral blood mononuclear cells (PBMCs) within 24 hours of TBI in both older and younger adults as well as non-injured controls (N=133). Older age was defined as 55 and older for the purposes of this study. Whole blood was collected and processed for plasma and WBCs from subjects using Ficoll technique (separation of blood components). Cells were manually counted and viability of cells was determined using the trypan blue method (type of stain to observe cells). Data analysis is underway. Descriptive statistics were performed along with ANOVA to assess for group differences in cell count and viability. Time from blood draw to processing will be used as a covariate. The results of this study will enable us to determine if lower cell counts or cell viability differ by age and injury status. This will provide support for or refute the hypothesis that the immune response following injury is different in older adults which could impact patient outcomes. By understanding this relationship, we can implement clinical changes to potentially help change the immune response and improve the outcomes older adults experience post injury.

As the NFL was going into a lockout in 2011, linebacker Ray Lewis made the controversial statement that crime rates would rise if the NFL season was lost. Mr. Lewis said, "There's too many people that live through us," and that without football teams to follow, those people would turn to crime. At the time, there were many arguments provided on both sides of the issue, but no empirical research was done. Studies have shown that professional athletes commit more crimes during a lockout; and that children with access to sports programs are less likely to grow up committing crimes; but no one has ever tested the claim that a professional sports team has an effect on the crime rate in the area in which it is based. My experience living in a Seahawks-enamored Seattle in 2013 has motivated me to take Mr. Lewis's assertion one step further and investigate whether the success of a pro sports team can raise or lower the crime rate in its city. I look at more than just the relationship between winning percentage and change in crime rate (note that I cannot compare nominal crime rates, due to the varying base levels of crime in metro areas as diverse as New York and Denver). Other measures I investigate are margin of victory or closeness of playoff race, as perhaps a more dramatic season gives the fans more to live vicariously through. Despite some relationship between winning percentage and playoff success of a team and the city's crime rate, I can't show a significant enough correlation to conclusively say that the NFL influences the rate of crime. While this doesn't have any direct implications on the NFL or on policy makers, I believe that my results are enough to encourage further study of the issue.

Biomarkers capable of diagnosing and tracking the progression of Parkinson’s disease (PD) are urgently needed. Saliva has been explored as an alternative to a more traditional sample source such as cerebral spinal fluid (CSF), which involves painful and invasive collection processes, and blood. Indeed, PD patients typically have dysfunction of salivary production, indicating that the disease involves this organ system. In order to increase sample availability, many protocols use cotton or plastic to stimulate saliva production. However, this raises the question of how these materials affect salivary protein composition, specifically in regards to proteins of interest as biomarkers. In order to explore these effects I incubated various materials potentially capable of stimulating increased saliva production in saliva samples and measured the concentration of alpha-synuclein (α-syn), a protein believed to be important in PD pathogenesis and a possible biomarker, and total protein. By comparing the concentrations of α-syn, total protein, and the α-syn:total protein ratio between the various material groups and control (no material) groups I am able to determine whether the materials increased, decreased, or had no effect on protein concentration. It was hypothesized that all tested materials would decrease both α-syn and total protein concentrations by some degree due to protein attraction to the materials. The results of this study contribute to a clearer basis for salivary biomarker studies involving induction techniques, facilitating collection techniques in a clinical setting, particularly in older patients with decreased saliva production.

Endocrine disrupting compounds (EDCs) present in wastewater treatment plant (WWTP) effluents are a significant water quality issue. EDCs have been demonstrated to have adverse effects on aquatic life at extremely low concentrations. The synthetic estrogen, 17α-ethinylestradiol (EE2), is a particularly potent EDC of concern in WWTP effluents. Biological degradation is a critical mechanism for EDC removal in WWTPs. The goal of this research was to isolate and identify bacteria capable of degrading EE2 with an eventual goal of using the bacteria to improve WWTPs’ removal efficiencies. The experiments started with enrichments established in pH-buffered mineral salts media containing 1000 µg/L EE2 as the only added carbon and energy source, which were originally inoculated with activated sludge obtained from a local WWTP. Vitamin solutions were added to overcome loss of EE2 degradation abilities that were seen in earlier isolation attempts, and the new enrichments were monitored weekly for EE2 concentration using High-Performance Liquid Chromatograph with UV detection (HPLC-UV). Of the eight enrichments, three were found to degrade EE2 to below 200 µg/L within 54 days, as opposed to 120 days in the other enrichments. These were transferred to fresh media to reduce inactive bacteria concentrations through dilution and were monitored for degradation. Two of the three were transferred again after 78 days to fresh media and monitored for continued degradation. Transfer of the liquid cultures to solid media is currently underway to allow selection to single colony isolated cultures that can be assessed for their EE2 degradation abilities. This work is a promising advancement in the isolation of an EE2 degrader that will have a positive impact in bioaugmentation for the removal of EDCs from WWTP effluents.

We researched how animals in Pacific Island legends vary from island to island, and the cultural significance of these animals. This research question directly relates to the readings we have done in Pacific Island Legends and Research is Ceremony. Pacific Island Legends has showed us a variety of stories from various areas of the pacific islands. Shawn Wilson’s book Research is Ceremony shows us the importance of using culture when teaching students. We used the methods of legend analysis, interviews, participant observation, and discourse analysis. We hypothesized that we will find patterns of animals used in the legends. Our research matters because legends are important for character building in children. Legends are important to bring to the classroom because they help people build relationships not just with people, but also with all of their surroundings.

Developed in the mid-1990s, the Implicit Association Test (IAT) has been used in psychological experiments to measure the strength of a person’s automatic associations between concepts and attributes. IAT measures are shown to predict people’s behavior more accurately than do parallel self-report measures in socially sensitive domains such as race and age attitudes. The Brief IAT (BIAT) uses a similar procedure to the standard IAT, but with simplified instructions and different task structures. Unlike the standard version, the BIAT instructs subjects to respond in each trial with a “focal” key to only two of four categories (focal categories) that they are told to focus on and with a “nonfocal” key to the other two categories (nonfocal categories). The present research examines whether the BIAT has the ability to identify whether categories are associated with positive or negative valence (positive or negative attributes of a person, object, or event). It also seeks to compare the BIAT’s association strengths with those obtained from the standard IAT. One hundred voluntary undergraduate students from the University of Washington completed two BIATs that differed only in the identity of one of their categories. The same subjects were also administered two parallel standard IATs with the same categories. D scores, an effect-size measure, were calculated using data from the BIATs and standard IATs to estimate the strengths of association between pairs of categories. Through their task structures, the BIATs are expected to identify more precisely than the standard IATs can the valence association of each category. Each BIAT’s association strengths are also expected to approximate those obtained from the corresponding standard IAT. The significance of this research lies in its potential to support the development of more valid and useful IAT methods for determining a person’s unconscious attitudes toward individual objects and concepts.

The First World War (1914-1918) introduced the world to the horrors of warfare on an industrial scale. But it also gave rise to the one of the most dynamic and active anti-war movements of the 20th century. This research explores the activities of the local Pacific Northwest anti-war movement during World War I. National resistance to the militarist and imperialist policies of the United States peaked during the war period, and the Seattle anti-war movement provides a fascinating case study of how socialists, anarchists, labor unions and pacifists organized a robust anti-war movement. Using a wide variety of contemporary local newspapers, letters, activist memoirs and labor union meeting minutes, this study weaves together the story of Seattle’s radical and pacifist organizations during the First World War. This study finds that despite aggressive persecution from the Federal government, conservative labor unions and pro-war business interests, the Seattle anti-war coalition continued to offer active and radical resistance to militarist policies up until the end of the war.

Von Willebrand factor (VWF) is a multimeric blood glycoprotein involved in the process blood clotting. Its primary function is to be an adhesive proteins that platelets can bind to a wound site. In the Sniadecki lab, VWF is used as a matrix protein for capturing platelets under shear flow in a microfluidic device for blood coagulation studies. Currently, VWF is purchased from a company and coated on the surface of the microchannels. High molecular weight VWF has a higher ability to form a clot, while low molecular weight VWF has a lower ability. Since the VWF comes from a commercial source, the purity of its molecular weight weight is unknown. The goal of my project is to improve the VWF coating by purifying VWF from Enzyme Research. We hypothesized that low molecular weight VWF does not support clot formation and that high molecular weight VWF will show more clot formation than the control vWF in the microfluidic device. My research efforts have been to purify VWF using the fractionation gel filtration technique developed by Professor Dominic Chung’s lab at the Puget Sound Blood Center. The gel filtration technique can isolate the vWF according to size. Gel filtration was done using a 10x10 Sephacryl 500 Column. After the filtration process, vWF of different molecular weights are then applied primarily to the surface of PDMS so that platelets can bind to them under fast flow, in order to measure forces of platelet clotting. We found that there is a link between the molecular weight of the vWF and the rate of clot formation. Low molecular weight vWF does not support clot formation and that high molecular weight vWF will show more clot formation than the control vWF.

Imidacloprid (IMI) may be a viable alternative to carbaryl for controlling burrowing shrimp (Neotropea californiensis) that destabilize sediments resulting in poor survival and low yields of the commercially harvested Pacific oyster (Crassostrea gigas). Previous laboratory tests indicate the shrimp are overtly affected (immobile, cannot burrow) when exposed to IMI in sediment pore water, but are not killed. These results contrast sharply with observed efficacy in the field, i.e. mortality 72-96 h post application and subsequent reductions in burrow counts. Understanding the factors governing efficacy in the field may improve control. We exposed 11 adult female shrimp that had burrowed within 30 cm of native sandy sediment to each of four concentrations of IMI (Nuprid® 2F) for 96 h: 6, 30, and 150 ppb active ingredient. We compared the response of these shrimp to that of 10 negative controls. Surface water (10 cm) was exchanged with clean seawater (salinity=30 ppt) 6 h post dose and then twice daily simulating tidal exchanges. Behavior and water quality were monitored once daily. All shrimp in the IMI exposures were overtly affected and mortality was dose dependent: 0 ppb (0%), 6 ppb (9%), 30 ppb (27%) and 150 ppb (82%). The LC50 was 51 ppb (95% CI=24-146 ppb). Mortality at 150 ppb occurred 30-54 h post dose; mortality at lower concentrations occurred between 54-78 h. Shrimp that survived the highest doses were closest to the surface when immobilized where dissolved oxygen (DO, % saturation) was greatest. Immobilized shrimp were unable to maintain their burrows, the burrows subsequently collapsed, separating them from the DO within the surface water, resulting in asphyxiation. Results suggest the shrimp can tolerate very low dissolved oxygen within sediment without IMI, but their sensitivity to IMI increases due to factors associated with their impaired ability to maintain burrow integrity and circulate water.

Aphasia, a language disorder typically resulting from neurological damage such as a stroke, impacts an individual’s ability to use language, but is generally thought to leave broader cognitive skills intact. Some evidence, however, suggests that this may not be the case. In particular, Silkes (2010) asked participants with and without aphasia to complete a task that used language-based stimuli but did not require language processing. Surprisingly, most individuals with aphasia performed worse on this task than typical adults. It is possible that these findings reflect unexpected differences in broader aspects of cognitive processing, such as memory or attention. Therefore, to better understand these previous results, this study investigates differences between adults with and without aphasia in rapid perception of language vs. non-language stimuli on a computer screen. Participants include 11 typical adults and 5 individuals with aphasia seen over 1-2 two-hour sessions. Participants press computer keys to indicate whether a white rectangle, in each trial, is blank or contains linguistic or non-linguistic characters. The rectangles are masked, meaning that they are hidden among strings of letters and symbols. They are presented at various exposure durations on a computer screen, making them progressively more difficult to see as exposure duration decreases. Data collected reflect the shortest exposure duration at which participants reliably distinguish between filled and empty rectangles in each of three conditions (word, non-word, or non-linguistic filler). Comparing these thresholds between conditions lets us explore the relative role of language processing vs. other cognitive skills in this task, and how this may differ between adults with and without aphasia. If individuals with aphasia show different patterns of performance than typical adults, this will expand our understanding of the underlying processes that are impaired in aphasia. Ultimately, better understanding of these processes will lead to better treatment of this language disorder.

 The development of new medications is critical for treating disease and extending life. Approximately 40-60% of drugs target a specific type of membrane protein termed G-Protein Coupled Receptors (GPCRs), which permit cells to communicate with each other (by binding neurotransmitters) and regulate body physiology. The Hague lab studies the molecular mechanism of drugs targeting these receptors. Specifically, they examine a small, yet important structural portion of the receptor - the PDZ binding motif - which acts a protein-protein interaction site. Interestingly, of the ~800 different GPCRs in the body, 30 have this PDZ binding motif, including those activated by the neurotransmitter 5-hydroxytryptamine (5-HT), which is commonly known as serotonin. Serotonin regulates many key CNS processes including mood, sleep, and appetite. Current 5-HT medications that are on the market are used to treat depression, generalized anxiety disorder, and social phobia. Two common antidepressants that affect serotonin GPCRs are Selective Serotonin Reuptake Inhibitors, or SSRIs, and Monoamine Oxidase Inhibitors, or MAOIs. My goal was to examine the necessity of the PDZ binding motif for 5-HT serotonin receptor function in human cells. To do this, HEK293 cells expressing the wild-type 5HT receptor (WT) or mutated 5-HT receptor missing the PDZ binding motif (ΔPDZ) were subjected to diagnostic assays including: microscopy, protein biochemical analysis, proteomics, and cellular signaling. In summary, the data suggest the PDZ-binding motif is not essential for 5-HT serotonin receptor function in HEK293 cells, although further experiments are necessary to solidify this conclusion.

The mammalian cortex is composed of excitatory and inhibitory interneurons which regulate the firing of action potentials in the brain. Excitatory neurons increase the likelihood of an action potential in other cells while inhibitory neurons decrease this probability. Excitatory transmission develops first, resulting in electrical activity in the form of waves, which are important in the formation of neuronal circuit formation until the development of inhibition shuts down this spontaneous activity. While excitatory and inhibitory neurons are born in different locations in the brain, those that are born on the same day of development migrate and find each other in the same cortical layer. Excitatory neurons originate in the dorsal ventricles and migrate radially towards the plial surface. Inhibitory cells originate from the medial ganglionic eminence and migrate tangentially to the cortex where they then migrate radially to find their correct cortical layer. This project explores the idea that spontaneous electrical activity helps drive this organization. Tbr1 is a transcription factor shown to be important in neuronal layer finding. By using a Tbr1 KO (knockout) mouse, we show the disorganization of the neocortex compared to normal mice by quantifying the fraction of radially oriented interneurons versus non-radially oriented interneurons. Further, we examine the implication that waves and asynchronous electrical activity play a role in layer finding of excitatory and inhibitory neurons, as demonstrated by the differences in activity between Tbr1 knockout mice and controls.

Synthetic biology aims to engineer biological systems that perform complex tasks such as producing therapeutics and biofuels. Synthetic gene networks are developed that interact with an organism’s native genome to modify its behavior, and the design of synthetic gene networks is guided by computational models. However, the ability of computational models to accurately predict gene network behavior is limited by a poor understanding of how individual network components operate; and this often results in repeated rounds of experimental refinement. This work aims to improve the predictive power of computational models by characterizing the function of promoter sequences. We developed methods to easily detect intracellular RNA levels with high accuracy using an RNA-based fluorescence reporter. The method is used to quantitatively measure RNA synthesis rates in E. coli. This technique may be used to enable high-throughput characterization of DNA promoter sequences for use in synthetic biology applications.

 The development of drugs is essential for human health. Approximately 40-60% of all currently prescribed drugs target a specific type of membrane protein called a G-protein coupled receptor (GPCR). In the human body, the binding of a neurotransmitter or hormones to a GPCR transmits signals across the membrane to bring about an intracellular response, which ultimately permits cells to communicate with each other and regulate body physiology. The Hague lab studies the molecular mechanism of drugs targeting GPCRs. Currently, we are investigating an important structural portion of certain GPCRs called the PDZ binding motif, which is a site for protein-protein interactions. My role in the lab focuses on the somatostatin (SST) receptor subfamily, which regulates the endocrine system and neurotransmission by inhibiting the release of secondary hormones produced in the gastrointestinal tract and pituitary gland. A drug that targets SST receptors is octreotide. This drug inhibits growth hormone and insulin release, and is FDA approved for the treatment of growth-hormone producing tumors and GI tract disorders. Interestingly, all five SST GPCRs contain this PDZ-binding motif, and my research examined the importance of this motif using a variety of biochemistry techniques that quantified the expression, localization, signaling, and protein-protein interaction network. I created SST receptor mutants lacking the PDZ-binding motif using polymerase chain reaction and then transfected the SST mutants into human cells. These novel clones were subjected to plasma membrane assays, confocal microscopy, and mass spectrometry analysis. I found that removing the PDZ-binding motif had minor impact on overall receptor function, but more studies are necessary to determine the role of the PDZ-binding motif for SST receptor function. Our ultimate goal is to identify novel PDZ-interacting proteins for GPCRs, and then disrupt or enhance this interaction with novel small molecules to treat disease.

Disfluent speech has typically been regarded as noise in spoken language processing: aspects of speech that should be ignored in order to automatically detect and understand the intended meaning of spoken language. However, it has also been suggested that disfluencies provide information about a speaker's cognitive processes and efforts to manage the discussion. Most work on disfluencies has investigated very controlled scenarios or conversational speech. In our work, we are studying high-stakes debates, including Supreme Court oral arguments and congressional hearings on the financial crisis, in addition to informal conversations among strangers and family members. By studying disfluent speech in both high and low stress situations, we can better understand the impact of stress on disfluency rates. We use text alignment techniques to understand the relationship between the perceived mistakes and correction. We subdivide and partition disfluencies into categories by classifying inserted, deleted, and substituted words according to their semantic similarity; thus, making correlations between social context and disfluency rate more evident in addition to providing a better interpretation of speaker opinions. Preliminary results show that lawyers have a tendency to model their speech patterns off of the justices they are speaking to, but not vice versa. That is, lawyers tend to be more disfluent when the justices are speaking disfluently, which indicates that disfluent speech reflects social context. Thus, we hope to develop ways to automatically detect and understand deeper meaning in spoken language, such as defensiveness and strength of opinions, through our study of disfluent speech.

Cochlear implants are electronic devices surgically implanted into the inner ear to restore hearing in those with severe or profound hearing loss. A signal processing strategy in the device’s computer interprets the input sound and sends information to the nerves of the inner ear. Mandarin Chinese, spoken by 900 million people, is a tonal language that consists of four tones, each conveying different meaning. Unfortunately, cochlear implant users who speak Mandarin have difficulty perceiving tonal changes in speech with current signal processing strategies. Improving tone perception in Mandarin-speaking cochlear implant users is an ongoing topic of signal processing research. However, if English speakers’ Mandarin tone identification can be used to evaluate signal processing strategies, a pilot study could begin with English-speaking cochlear implant users, who are easier to recruit in the US. The purpose of this study is to test the validity of using native English speakers to evaluate Mandarin tone perception with novel processing strategies. Using a Mandarin tone perception test, we evaluated the ability of English-speaking subjects to categorize spoken tones into the four Mandarin tones – rising, falling, flat, or falling then rising. Ten normal-hearing English speakers were able to correctly identify tones, on average, 88% of the time and three subjects with cochlear implants achieved 61% correct identification on average. Two processing strategies were evaluated on the normal hearing listeners using acoustic simulations of cochlear implant signal processing: CIS, a common clinically-used program, and HSSE, a novel program developed at UW. HSSE was shown to significantly improve perception of tones in normal hearing subjects (p<0.001). These results suggest the possibility of evaluating novel sound processing strategies for tonal languages using English-speaking cochlear implant listeners as test subjects.

This study examines the effects of administering hydrogen sulfide (H2S) to ancient plant species to examine the organisms’ response to the stress. While sulfur is an essential macronutrient required by several organisms for growth and productivity, there are many toxic variants of the element that have detrimental effects and produce physiological stress. It is speculated that the accumulation of H2S, a lethal gas, may have existed as a major contributing factor in past mass extinction events, where the environment was fairly anoxic with fluctuating temperatures. The potential of this toxic variant to exist as an environmental stressor suggests that certain organisms may have adapted to survive these periods of mass extinctions. It is hypothesized that due to the abundant presence of hydrogen sulfide in the past, ancient land plants may have an adaptive advantage that allowed them to survive and thrive. In the study, species of bryophytes, specifically Hypnum and Dicranum are exposed to specific concentrations of aqueous H2S over a 7 day period and measured for their photosynthetic capacity at timed intervals using a FluorCam. Studying the effects of this toxic gas on ancient plants is imperative to our understanding of sulfur’s varying biological roles, and provides insight on the evolutionary phenotypic variations amongst plants and stress responses in order to survive mass extinctions. Current results indicate that bryophytes are able to tolerate significant quantities of the toxic substance and show resilience through increased photosynthetic capacity over a period of exposure, indicating a genetic and phenotypic legacy response. The results also imply that H2S may have the potential to act as a plant regulator due to its diffusive properties and influence in minute quantities.

Protection of old buildings is one of the tools for reinforcing well-being of our communities and ensuring their sustainable development. Today, older built stock is challenged by demands for rapid urban growth and modernization, and so are challenged cultural identities of our neighborhoods. Preservation of historic urban fabric is necessary as transformations and growth occur. The question this project seeks to answer is how can we secure balance between protecting authentic character and ensuring economic vitality in historic urban cores? The primary methods are assessment of historic properties in the Old Town Neighborhood of Redmond and research of effective placemaking solutions among downtown revitalization case studies. The final report features a set of design suggestions regarding the public realm within Old Town's Historic Core and is meant to help preserve, promote, and celebrate the neighborhood. This project is a part of a planning process intended to develop architectural design standards for Redmond’s Historic Core.

Transforming growth factor-beta (TGF-β) signaling in smooth muscle cells (SMC) contributes to normal vascular development but may also play a significant role in the progression of aortic disease. Accordingly, TGF-β signaling is emerging as a therapeutic target, with strategies to block TGF-β signaling proposed as a means of preventing human aortic disease, including aortic aneurysms and dissections. However, because TGF-β signaling contributes to normal vascular development, blockade of TGF-β signaling could be harmful. We hypothesized that elimination of TGF-β signaling in aortic SMC of adult mice would cause aortic disease. We used inducible Cre-lox recombination technology to knock out Tgfbr2 in adult murine SMC. Tgfbr2 encodes TGF-β receptor II, believed to be essential for all TGF-β signaling. Mice were euthanized 4-14 weeks after SMC Tgfbr2 knockout, and effects of Tgfbr2 knockout (compared to control mice) were assessed by gross observation of aortas as well as sectioning and staining of aortic tissue. We found intramural hematomas, penetrating aortic ulcers, aortic dissection, and aortic dilation as well as significant thickening of the medial wall and adventitia in the knockout mice. Our data strongly suggest that loss of TGF-β signaling in SMC has a negative effect on aortic health and support a cautious approach in pursuing blockade of TGF-β signaling as a therapeutic strategy.

Communication is prevalent and necessary in all social animals. It determines outcomes of competition for mates and food resources, and also allows for social organization. A wide range of communication strategies are used across the animal kingdom, but for primates - one of the most social groups in the animal kingdom -there are three main strategies for communication: auditory, visual, and olfactory. For my study, I focused on the question of how group size affects amount of communication within a group. I hypothesized that with larger group size comes a need for more direct communication, in order to maintain cohesion in a group with many individuals. Therefore, I predicted that a larger group would result in more complex vocalization usage in a primate which relies largely on vocalizations to communicate. Using the genus Eulemur as a study system, I investigated if vocalization complexity is related to social group size. Eulemur rubiventer and Eulemur rufifrons are an ideal system for this work, because they share similar habitats and predation risk, and are closely related, but differ in their social group size. I studied the species for a month in the primary forest of Ranomafana National Park, Madagascar, following and watching individual animals and continuously documenting their behaviors and vocalizations. I also used a microphone to record vocalizations to get better data on the different types of calls. I found that the species with larger groups (E. rufifrons) called 88% more often than the small grouped animals (E. rubiventer), and consistently used 4 more calls than the smaller grouped species. This preliminary evidence suggests that increased vocalization frequency and use of different calls are associated with higher sociality. I postulate that this increase in vocalization usage complexity is necessary to maintain cohesion in a large social group.

Substance use in adolescence is a serious societal problem that results in a variety of severe negative consequences for youth. There is a growing body of research that examines substance use, consequences, and psychological dysregulation, but little that examines all three variables together. In order to understand reasons for why adolescent substance users continue to use despite negative consequences, the current study examined the relationship between substance use, consequences, and psychological dysregulation, with psychological dysregulation as a potential mediator between substance use and consequences. The participants were 123 adolescent substance users. Participants completed assessments to measure criteria such as substance-use quantity, substance-use related consequences, and psychological dysregulation, which was further broken down into affective dysregulation, behavioral dysregulation, and cognitive dysregulation. Alcohol-quantity at intake was found to be a significant predictor of consequences, with psychological dysregulation as a significant mediator in the relationship. Marijuana-quantity at intake was not found to be a significant predictor of consequences, but when psychological dysregulation was added as a second predictor variable, it was found to significantly predict consequences. Additionally, alcohol-quantity at intake was significantly correlated with behavioral dysregulation through the aspects of impulsivity, inattention, hyperactivity, and aggression; affective dysregulation through the aspects of emotional reactivity and irritability; and cognitive dyregulation through the aspect of cognitive flexibility. These findings suggest that psychological dysregulation influences how substance users perceive their consequences, and that substance users are more likely to experience psychological dysregulation as a result of use. The results of this study indicate that psychological dysregulation plays an important role in why substance users continue to use despite consequences, and reveals one potential mechanism through which substance users interpret their consequences. Through further investigation, these findings have important societal implications and provide a basis to alter the methodology and theory behind the treatment of substance use disorders.

‘Aigarchaeota’ is a candidate phylum of Archaea known only by 16S rRNA gene fragments from cultivation-independent microbial surveys and a single composite genome from Candidatus ‘Caldiarchaeum subterraneum’, an inhabitant of a subterranean gold mine in Japan. Gene sequences reported in various publications were found almost exclusively in geothermal settings, but a comprehensive assessment has not yet been performed. The purpose of this study was: (i) to rigorously define the phylum; (ii) to gain insight into the phylogenetic and potential taxonomic structure of the phylum; (iii) to assess the distribution of ‘Aigarchaeota’; and (iv) to design ‘Aigarchaeota’-specific 16S rRNA gene primers. Public databases were mined for 16S rRNA gene sequences related to known ‘Aigarchaeota’ and a combination of approaches were used to rigorously define the phylogenetic boundaries of the phylum and compile a neighbor-joining and maximum likelihood phylogenetic tree. Primer template gene sequences were aligned in ClustalW in order to locate regions that are suitable for targeting genus-level groups. ‘Aigarchaeota’-specific primers for the polymerase chain reaction (PCR) amplification of 16S rRNA genes were designed using sequence alignments and reviewed using the Ribosomal Database Project Probe Match tool. The analyses supported the proposed relationship between ‘Aigarchaeota’, Thaumarchaeota, Crenarchaeota, and Korarchaeota in the so-called ‘TACK’ superphylum, and identified ~300 16S rRNA genes and gene fragments affiliated with ‘Aigarchaeota’, including those recovered from terrestrial geothermal systems on several continents and marine geothermal and subsurface samples. ‘Aigarchaeota’ belonged to at least three family- to order-level groups and at least 13 genus-level groups which are represented in the resulting phylogenetic tree. All genus-level groups were recovered from geographically distant locations, suggesting a global distribution. The primers will be used to determine the presence and abundance of ‘Aigarchaeota’ in a wide variety of samples from terrestrial geothermal systems in the U.S. and Asia using quantitative real-time PCR.

Low resource clinicians face several challenges in diagnosing disease at the point of care. One of the way diseases can be diagnosed is by DNA amplification, but first amplifiable DNA must be released from the cell. Staphylococcus Epidermidis is a bacterium that is very difficult to lyse. I examined three methods of S. Epidermidis cell lysis that are feasible to use in low resource settings by measuring the amount of amplifiable DNA recovered from the lysed cells. The three methods used were: a Bead Beating machine, the Omnilyse, and a boiling water bath. A bead beater is a mechanical method of lysing cells requiring electricity. An Omnilyse is a battery operated portable machine with glass beads to lyse the cells. The boiling water bath used was a beaker on a hot plate. All of these methods have comparable cost per samples value, and can be operated with relatively simple training. I used three to five intervals of time during which the S. Epidermidis cells underwent the different lysis techniques: 30, 60, 90, 120, and 360 seconds. I found the Omnilyse outperformed the bead beater and hot bath. It was 31.23 percent more efficient at extracting amplifiable DNA, making it the best of the options tested for point of care diagnosis. Future expansion of experiments could include testing the lysis methods with different bacteria to determine if the efficiency of recovery of amplifiable DNA is comparable to S. Epidermidis' efficiency.

In the San Juan Islands, drift macrophytes from shallow waters represent a significant spatial subsidy provided to the subtidal zone. This organic matter is a potential food source for deep dwelling herbivores like the red urchin Strongylocentrotus franciscanus. Little is known about how urchins capture and use drift material. A racetrack flume was used to examine the capture of drift macrophytes of various species and size by S. franciscanus. No species-specific selectivity was found, but urchins caught 100% of small macrophyte pieces. A significant decrease in capture efficiency was noted as drift algal size was increased, probably due to the urchins’ inability to fight current drag acting on pieces with larger surface area. This suggests that drift macrophytes could be the main food source for deep dwelling urchins where available, potentially explaining how herbivores subsist at dysphotic depths. 

As the population of older adults in the United States grows, more ways are being explored to encourage an active lifestyle and promote healthy living. Many malls and other sites across the country have established walking programs that provide people ways to get exercise and fulfill social needs. The purpose of this study is to explore quantitatively the numbers and types of people who participate in these programs as well as to describe the physical environment in mall and non-mall settings with walking programs. This study will make use of a modified SOPARC tool, a tool originally designed for assessing park and recreation areas. The tool will be used to capture information on walkers’ observed sex, approximate age, ethnicity, activity level and usage of mobility aids. Information will be collected about the external and internal conditions at the walking sites including information on accessibility, safety and features of interest to the walker. Results will include data gathered at 10 mall and five non-mall sites in five states. It is hoped that the results of this study will show what types of people are using these programs as well as features that are common among the various sites. To date, one mall audit has been conducted. Of 39 walkers observed over 15 minutes, 61% of walkers were male, 77% were older adults, and 74% were of observed Caucasian ethnicity. This site also played special music for the walkers and has an information kiosk where walkers can sign in and record their miles walked. Challenges to older walkers include uneven walking surfaces from the transit stop and small writing on the mall wayfinding map. It is hoped the study will provide a basis to help tailor walking programs to target certain populations and ideas for optimal walking settings to inform a best practices guide for existing and new walking programs.    

The purpose of our research is to better understand older adults’ perceptions about fall detection devices. When an older adult experiences a fall, the results can be dramatically life altering or even fatal compared to an individual in a different age group. This led us to question what views older adults have about existing measures in place to monitor and analyze falls, such as fall detection devices or other technologies, as well as what demographic factors may influence these views. Using data from a parent study, we are currently in the process of analyzing focus group transcripts to compare perceptions of older adults from high and low socio-economic status using qualitative descriptive methods. We are analyzing transcripts for common themes that may lead to the identification of areas for further study. By studying older adults’ perceptions of fall detection devices, we hope to gain a better understanding of their needs and preferences when it comes to such devices. We hope exploring and understanding demographic or other factors that affect these perceptions may lead to more open conversations on falls, and thus better our ability to customize fall detection devices and their features, and fall prevention plans for older adults.

Older adults who participate in regular physical activity have better emotional health, as well as reduced mortality and morbidity, compared to older adults who do not participate. Mall walking programs are an existing form of low-cost physical activity for older adults that provide level walking surfaces, security, and other amenities like benches and restrooms. Although some mall walking programs have existed for decades, there is scant evidence supporting this easily accessible form of regular physical activity for older adults. The purpose of this study is to identify and describe actual and perceived costs of existing programs in mall and non-mall locations, such as arenas. As part of a larger study, structured interviews have taken place at ten mall and five non-mall locations in five different states. Mall managers, mall walker program leaders, and program participants have been interviewed over a six-week period. All interviews have been transcribed and coded for anonymity. Cost-related themes from the transcripts have been extracted and added to those identified from an already completed literature review. The data set is being analyzed using the Strauss and Corbin model of grounded theory to identify themes and categories with the intent of developing cost-structure models that reflect successful programs. Themes identified include shared program costs between the site and a hospital, regular blood-pressure testing, and retail stores offering discounted coffee for participants. By identifying best fiscal practices and cost-related variations that encourage the diversity of participants, future efforts may be directed at developing a cost calculator to help programs identify and track their costs. This component may help in establishing low or neutral-cost programs and therefore increase the accessibility of physical exercise to a wider range of older adults. 

Müller glia are the predominant glial cell types in the retina that play a critical role in development and neuronal support. In adult mammalian retinas Müller glia are mitotically quiescent. However in other organisms, such as zebrafish, the Müller glia re-enter the cell cycle, proliferate and differentiate into new neurons upon retinal damage to replace lost ones. The goal of this study was to promote Müller glial proliferation and regenerate neurons in the adult mammalian retina. p27 is a tumor suppressor and plays a role in controlling cell proliferation. To test if the loss of p27 promotes Müller glial proliferation in adult retinas, we have generated Müller glia-specific p27 knockout mouse. Using tamoxifen-inducible, CreER/lox system to control timing of p27 deletion in Müller glia our Western blot data shows that daily injections of tamoxifen for four days efficiently eliminated p27 expression in adult Müller glia. When p27 expression is lost, adult Müller glia appeared to proliferate. Our data suggest that p27 plays a role in keeping adult Müller glia from re-entering the cell cycle. The controlled re-differentiation of Müller glia and proliferation into new neurons could be used to cure diseases involving retinal damage or degeneration like macular degeneration.

 Breast cancer is the most common type of cancer in women, and 40,996 women died of cancer in 2010. I am working with Dr. Keryn Reding from the School of Nursing on examining estrogen DNA adducts (EDA) for their clinical utility as a biomarker for breast cancer. EDA is formed when estrone or estrodial are oxidized to form quinones. These compounds then attach to DNA, causing mutations that lead to cancerous cell growth. The EDA are then excised and released into the blood stream and excreted through urine. I will analyze urine samples in a triple quadrupole mass spectrometer in order to see if the ratio of EDA to parent estrogens is higher in women with breast cancer than women who did not develop breast cancer. My analysis will investigate the inter-variability of EDA in premenopausal and postmenopausal women to see if this biomarker can be accurate and reliable for women of all ages. We expect results to show that premenopausal women will have less EDA due to their younger age and lower risk of developing breast cancer. By May when I present at the URP, I will have results from the mass spectrometer and I will use the McNemar's test for statistical significance. We are investigating a hypothesis that a high EDA ratio will be associated with breast cancer risk, and thus the EDA ratio may have clinical applications for breast cancer prevention and screening. Because it is a non-invasive method of measuring the risk of developing breast cancer, it could be an ideal complement to current screening approaches, such as mammograms or biopsies.

It is known that exercise improves cancer survival, however, there is an unknown molecular link between physical activity and cancer occurrence. The purpose of this study was to determine the feasibility of studying biologic mechanisms related to exercise and cancer survival in the LIVESTRONG YMCA program. Eligible subjects were males and females who were diagnosed with prostate or breast cancer in the last three years, between 35-80 years of age, willing to provide urine samples at four time points, and enrollment in the 12-week LIVESTRONG YMCA program. Through a partnership with the University of Washington (UW) Mass Spectrometry Center and the UW Office of Nursing Research, two specific biomarkers were analyzed from the urine specimens. One of these markers is Estrogen DNA Adduct (EDA), an estrogen metabolite that binds to DNA and creates an increased potential of DNA mutation and cancer development. The other is 8-OH-dG, a biomarker related to oxidation. To determine the feasibility, we administered questionnaires to better determine patient satisfaction and calculate the percentage of participation and retention. One questionnaire surveyed the acceptability of our biospecimen collection procedures to participants, anticipated acceptability of additional biospecimen collection (blood and tissue samples) for future projects, and willingness to have a DEXA scan (for compensation). In order to determine the feasibility of conducting the study on a larger scale, we evaluated the percentage of participants enrolled out of those recruited, percentage of participants who provided urine samples out of those enrolled, and the percentage of participants who completed the program. Continuing to invest in our therapeutic, diagnostic and genetic understanding of cancer means that in the future, patients will have options based on scientific evidence.

A major focus of breast cancer research has involved the catechol estrogen pathway. Estrogen DNA Adduct (EDA) is a novel biomarker that is hypothesized to play a role in initiating breast cancer. Pilot studies have shown elevated levels of EDA in women at high risk for breast cancer and with breast cancer. The overall purpose of this project was to determine whether the EDA biomarker has potential for clinical use for breast cancer prevention. The first step toward this goal was to examine the extent to which the biomarker varies over time in the same individual. The specific aim was to determine whether the variation between urine samples taken at two points in time is significantly different from samples taken at a single point in time. We utilized a convenience sample from the DEEM (Diet, Exercise and Estrogen Metabolites) study of 6 urine samples from 3 women at 2 separate clinic visits, conducted 3 months apart. Triple quadrupole mass spectrometry was used to process 37 estrogen metabolites in the urine samples. The fragmentation pattern of each metabolite was analyzed and compared to a panel of known estrogen metabolites in which the elution times were known. The correlation coefficient between the 2 clinical visits was 0.49. The results from this analysis indicate moderate correlation between 2 time points. We will await the results from the larger study to decide whether a one point in time urine collection is adequate for the overall project. The implications of the overall project are important because determining breast cancer risk from urine samples would be a sensitive and non-invasive method that could allow healthcare providers to better target the women that should receive careful monitoring, testing, and interventions.

The Muon g-2 experiment hopes to test the difference between the experimental and theoretical values of the anomalous magnetic moment of the muon (g-2) out to a greater statistical precision than has been previously accomplished. Such a discovery would provide strong evidence of new physics such as dark photons, supersymmetry, or possibly something not yet considered. During the experiment, muons are injected into a large superconducting ring. A muon decays to an electron and the electron curls to the inside of the storage ring and strikes an array of lead fluoride crystals. When an electron hits a crystal, it produces light that is proportional in intensity to the energy of the electron. The energy and the time of its arrival help to indicate the direction of the spin which is used in the calculation of g-2. My research investigates how light is propagated and distributed in these crystals and how different reflective or absorptive wrappings affect this distribution. I measure light yield and pulse width, which correspond to two different extremes of wrapping material. For maximum light yield, I use a special reflective white paper called Millipore, while shorter pulse widths are achieved using an absorptive black Tedlar paper. I have developed a 2x2 array of crystals coupled to light sensitive photomultiplier tubes. This setup, which is configured for easy switching of the wrapping material, captures cosmic ray muons that hit the surface of the earth. Capturing these muons simulates the conditions of the experiment. I analyze the resulting data by fitting the pulses and extracting the functional form of the light distribution. The results of this research will ultimately contribute to the development of more complete theories of the fundamental building blocks of the universe.

Diverse lines of evidence indicate that humans have come to dominate many environmental and climate systems across the globe, prompting some researchers to declare the present part of a new geologic age known as the “Anthropocene.” Since plants form the base of many biological ecosystems (including those to which people belong) and agriculture alone covers approximately forty percent of land surface, studying how humans appropriate Earth’s plant production allows us to explore one of the most significant ways people have come to dominate Earth systems. Previous work has mapped the global distribution of plant growth supporting humans but failed to fully link this production to specific populations. To understand these connections, we begin by tracing global agricultural and forest production through a simplified representation of the global economy (containing about sixty million economic flows). To do this, we use global economic data collected by the Global Trade Analysis Project, enabling us to connect fields and forests with the often distant human populations whose lives they eventually support. Our model accounts for indirect plant consumption (for example, factory products require plant consumption by laborers) as well as plant materials people consume directly. Mapping these results and transforming them through Geographic Information Systems (software which can visually and computationally manipulate the results in diverse ways) allows us to describe major intersecting processes of globalization linking distant peoples and lands. For us to respond effectively to the increased human domination of Earth systems, improving our understanding of these socioecological relationships will be critical.

Proteins perform a vast array of functions within all living organisms. These functions are heavily dependent on the protein’s 3-D structure. Cellular stress can result in the loss of protein structure and can lead to a wide variety of problems, one being the formation of insoluble protein aggregates. Aggregates can inhibit proper protein function, disrupt cellular homeostasis, and are implicated in many diseases. There exists a family of proteins, known as the Small Heat Shock Proteins (sHSPs), which are thought to combat aggregate formation. They interact with misfolded and aggregate-prone proteins (clients) to delay the formation of insoluble aggregates. How sHSPs delay aggregation is not well understood. I seek to characterize interactions between sHSPs and their clients. A binding interaction between the sHSP αB crystallin and the model client Δ131Δ (a mutant of staphylococcal nuclease) has previously been characterized by NMR. My goal is to confirm this interaction and look for additional interactions between these two proteins through chemical cross-linking. Chemical cross-linking is a process that links two proteins that interact. One can use this method to detect which surfaces of proteins are involved in a protein-protein interaction. The chemical cross-linker I am using is incorporated as an unnatural amino acid (p-benzoyl-L-phenylalanine, or BpA) into the sHSP αB crystallin. Upon exposure to UV light, BpA can covalently cross-link to another protein if it comes into close contact with it. This approach can allow us to explore how sHSPs interact with the client Δ131Δ. By gaining an understanding of this specific sHSP-client interaction, I hope to provide insight into general mechanisms of how sHSPs interact with clients, a process that plays a critical role in cellular health.

In my research, I am studying what composes the identity of a city, how we can perceive a city differently from another city. In architecture studios, we learn how to design for human experiences - what it would be like to be in the spaces that we design. To design for a complete sequence of experience, I first need to understand how people experience, see and read spaces they occupy, understand their process of passive and active perceiving and sensing. The urban city is a good place to study this because it has its duration and complexity. Experiencing a city is an open ended continuous process. What you see at a certain moment at a certain time represents a snap shot of many conflicts happening in a city. To experience is to perceive. It requires both immediate sensation and memory of past experience. What people perceive is identity. The identity of a city is shaped by the physical built environments, and the identities and activities of people in these environments. Action and interaction are important because identity does not mean anything until there is interaction between differences and conflicts. I am studying the identity that defines a city from other cities; how people perceive, act and interact with the built environments, and with each other; and also how the city shapes their action and interaction through the built environments. Looking at films gives a better sense of these actions and interactions because they are visually presented. I use films to look at urbanism, the portrait of city, the life within city, and the vision of city. Using the city of Seattle as an example, I will document my own experience through this urban environment, and also observe how other people act and interact in public spaces in this city.

The development of simple and affordable diagnostics is critical to the diagnosis, monitoring, and management of disease. Nucleic acid amplification has become the gold standard for many diagnostic applications due to its high sensitivity, specificity, and low limit of detection. Fluorescent dyes typically detect the success of amplification, but require expensive optical equipment including lasers and filters. A cheap and visually distinctive method for detecting nucleic acid amplification will simplify and lower the cost of molecular diagnostics. This research project aims to develop a simple colorimetric reaction for detection of loop-mediated isothermal amplification (LAMP) reactions. LAMP produces large amounts of pyrophosphate by-product during amplification. Pyrophosphate complexes many metals and can displace dyes bound to metals in solution to create color changes. Our goal is to identify a set of chemicals consisting of colored dye and metal ions that will present an unambiguous color change denoting success (or lack thereof) of amplification. Using knowledge of metal-ligand formation constants, we have determined a group of metal-dye complexes that may be viable candidates for detection and are currently testing them in the laboratory. One example is indigo carmine dye. In the presence of pyrophosphate, the dye stays blue (a positive test), while the lack of pyrophosphate will turn the dye clear (a negative test). We are in the process of fully understanding the chemistry of this reaction and further optimizing the process to improve its viability. Exploration of other metal-dye complexes, as well as continuing investigation of the literature, will be conducted to improve the present results. This colorimetric reaction has the potential to simplify and lower the cost of DNA detection.

Climate change is a crucial factor that affects plant physiology, population dynamics and geographic ranges. Little is known about the effects of changing climate on conifer morphology, whether their key morphological structures have the ability to change in response to environmental differences and what the impact of these changes mean for future ecological population dynamics. Are morphological and physiological traits locally adapted within a species or do they acclimatize to specific environmental conditions? Two studies were conducted to test 1) whether morphological structures of conifers differ between source populations when transplanted across an elevation gradient and 2) whether photosynthetic levels under a light treatment differ between source populations. Tsuga mertensiana seedlings from three study sites, varying from high to low elevation on Mt. Rainier, were each transplanted across and beyond the species' elevation range. For the first study, measurements of shoot to root ratio, specific leaf area (SLA) (m²/g) and leaf mass vs. stem mass were calculated. We expect our results to show that as elevation increases, SLA and shoot to root ratio decrease, however overall values are smaller for trees at higher elevation. This indicates that within a single species, trees from distinctive ecotypes are inherently different morphologically, even though all seedlings have the ability to acclimate to changes in elevation. The second study manipulates light as a single variable and addresses whether the driving force of morphological and physiological characteristics are due to light levels at different elevations or whether T. mertensiana seedlings at different ecotypes are genetically different physiologically.

Autism spectrum disorder (ASD) is a neurodevelopmental syndrome characterized by impairment in social interaction and restricted/repetitive behaviors. Perinatal complications, which occur at the time of birth, have been associated with the presence of ASD, including low birth weight, planned caesarian section, and umbilical cord problems. Though these complications and their link to autism have been heavily researched, the variability of perinatal complications has yet to be compared to the genetic diversity within ASD as a disorder. Due to recent advances in genome science, several dozen autism susceptibility genes have been identified that account for 10-20% of ASD cases. The goal of this study is to analyze both prevalence and type of birth complications in a large genotyped sample as a function of co-occurring genetic abnormalities. Using medical history data collected from a population of over 2000 genotyped families, we will determine the prevalence of perinatal complications within the presence or absence of genetic mutation. Autism severity will be examined as a function of presence of perinatal complications and presence of genetic mutations. Results from this study could serve as a starting point to further evaluate the potential shared etiology of autism and birth complications, as well as other potential genetic links among common co-occurring disorders such as gastrointestinal illnesses and epilepsy.

Autism Spectrum Disorders (ASDs) are genetically heterogeneous neurodevelopmental disorders largely characterized by impairments in social interaction. Many with ASD face other comorbidities, including sleep problems. Prevalence of sleep problems in those with ASD are significantly greater than typically developing children and range widely from difficulties falling asleep to parasomnias. Although many studies investigate the link between sleep and autism, none have considered variability in sleep differences as a function of the genetic variability of the disorder. The underlying assumption for this project is that behavioral variability, such as differences in sleep problems, observed in ASD is a function of the genetic variability in ASD. Chi square analysis was conducted using data collected about sleep problems in a medical history interview from a large, well characterized and genotyped sample of children with ASD to determine the prevalence of sleep problems in ASD as a function of genetic subtype. Those individuals with similar, recurring gene mutations were further examined in order to view whether sleep problems (both pervasiveness and type of sleep issue) may be a specific phenotype related to that gene mutation. Using ANOVA, gender differences in sleep presentation were also examined.  Results from this study may serve as a starting point to evaluate other wide ranging comorbidities, such as gastrointestinal illnesses, as a function of the genetic differences present in those with ASD.

 Snailfishes of the genus Careproctus are known to deposit egg masses inside the gill cavity of lithodid crabs. Identification of the species responsible has been inconclusive due to the difficulty associated with identifying snailfish eggs or larvae to species. DNA samples were collected from egg masses found in crabs both in the commercial golden king crab (Lithoides aequispinus) fishery and during survey work conducted by the Alaska Fishery Science Center. Egg masses were found in both golden king crabs and scarlet king crabs (L. couesi). Cytochrome Oxidase I (COI) was amplified from egg mass samples and sequenced. Comparison of COI sequences from eggs with COI sequences from positively identified adult vouchers yielded identification of 75 egg masses to species: 38, 29, 7, and 1 egg masses were identified as Careproctus rastrinus, C. colletti, C. furcellus, and C. simus, respectively. Egg masses were determined to contain eggs from only one species. These results are the first positive identification of the snailfish species responsible for laying egg masses in crabs. Identification of species involved may be useful in further attempts to classify the nature of this relationship between snailfishes and crabs.

 The purpose of this study is to determine structure-solvent property relationships in organic photovoltaic polymers, with the overarching goal of increasing the efficiency of organic solar cells (OPVs). OPVs are of great interest due to their flexibility, low environmental impact, and modest cost. Additionally, OPVs can be dissolved in organic solvents and printed using roll-to-roll, high-throughput processing – a feature that lends them a large advantage in the photovoltaic industry. Unfortunately, OPVs fall short within the realm of efficiency; the ~10% efficiency of OPVs can hardly rival the ~40% efficiency of inorganic photovoltaic technology. Improving the efficiency of OPVs is an important obstacle in producing low-area, economically viable solar cells. This project aims to use computational models to study the role of organic solvents in mediating the self-assembly of polythiophenes, a commonly studied class of OPV polymers. These models are generated in GROMACS, a program that uses an empirical potential energy function for the polymer, solvent, and polymer-solvent interactions to predict the molecule’s time-dependent behavior with classical molecular dynamics. In particular, these simulations can predict how physical properties such as the free energy of the polymers change as the torsional angles between monomers are varied throughout the simulation. Moreover, changes in the preferred conformations of the polymer are primarily signified by the lowest free-energy states. If we do discover changes in the preferred conformations of the polymer, simulations can be used to test whether these changes are predominantly due to the solvent or the structure of the polymer. This yields information about the equilibrium and self-assembly of the polymer, which can eventually improve the efficiency of OPVs by allowing more control over the polymer nanostructure during high throughput manufacturing processes such as roll-to-roll printing.

Cochlear implants (CI) are neural prostheses that provide individuals with profound hearing loss the ability to hear through artificial electrical stimulation to the inner ear. Despite the relative success of cochlear implants in providing speech in quiet settings, listening to complex signals such as music or speech in background noise is still difficult. Spectral resolution, the ability to extract frequency information from a signal, is important for interpreting complex signals, and this ability is impaired in CI users. In this study we compared two measures of spectral resolution: a pitch discrimination task and vowel identification. An individual’s ability to identify vowels depends on how well they can distinguish characteristic concentrations of energy at specific frequencies. Pitch discrimination is the ability to perceive small directional changes of sound frequencies between two pitches, and like vowel identification, relies heavily on one’s ability to discern frequency information. In this study we tested the pitch discrimination ability of CI users through the Clinical Assessment of Music Perception (CAMP) test (Kang et al., 2009), where participants were presented two tones 1-12 semitones apart and asked to identify the higher of the two. We then compared performance on the pitch perception test to the CI users’ scores on a vowel identification test, which included a closed set of ten vowel stimuli presented by a male or female speaker. Since spectral resolution is integral to both tasks, we expect to find that CI users with low scores on vowel identification also perform poorly on the pitch discrimination task. By understanding pitch and vowel perception we might inform the development of new signal processing that can optimize the transmission of music to cochlear implant listeners.

Polymeric micelles are nanoscopic structures constructed with amphiphilic diblock copolymers constructed with hydrophobic and hydrophillic portions that spontaneously form micelles in solution. Small hydrophobic molecules, such as cancer drugs taxol and doxorubicin, can be encapsulated in the micelle, which effectively serves as a nanovehicle for drug delivery. Here, we will develop a diblock copolymer integrating polyurethane-based self-immolative polymers (SIPs). SIPs are polymers that sequentially disassemble into their building blocks once the disassembly process is initiated by a triggering event at the trigger head group. By using SIPs, the polymers that make up the micelle are designed to depolymerize which we hope to increase the efficacy of payload release and remove the ability for micelle reformation. For this project, the micelle and all parts of the system will be synthesized from the bottom-up; optimizing the molecular weight of the diblock for micelle formation, investigating the kinetics of depolymerization and thermal trigger activation, and examining the stability of the micelle.

Sulfate-reducing bacteria are widespread and live in many environments. Some sulfate reducers are capable of growing in a mutualistic relationship with methanogens. In nature, diverse sulfate-reducing bacteria have repeatedly evolved into obligate mutualists. We want to study how this evolution occurred by using a model system for evolution in the lab between a sulfate reducer, Desulfovibrio vulgaris, and a methanogen, Methanococcus maripaludis. After allowing these two organisms to evolve for 1000 generations in an environment that forces their cooperation, 12 out of 22 D. vulgaris populations lost the ability to reduce sulfate (sulfate-minus genotypes). We want to test whether the ratio of sulfate-minus relative to sulfate-plus (a genotype still able to grow on sulfate) genotypes in coculture affects the fitness benefit of the sulfate-minus genotypes. To do this, a sulfate-minus and plus D. vulgaris were placed together and their relative abundance in coculture was tracked over time. The experiment will tell us if some genotypes have the ability to take over when they are rare. To track these changes, we are using a method called FREQ-Seq. FREQ-Seq is an inexpensive way of analyzing the frequency of certain genes or other DNA sequences in a mixed population over time. We can use this method to understand how these populations of D. vulgaris evolved. I originally predicted there would be a higher sulfate-minus to plus ratio at the end of the competition compared to the initial ratio. D. vulgaris is an interesting model organism for studying the evolution of obligate sulfate-reducer/methanogen mutualisms because it can live either alone as a sulfate-reducer or together with other organisms in a syntrophic relationship. The data we collected can help us better understand the mechanisms of natural selection that cause sulfate reducing populations to become obligate mutualists.

Mutualistic Relationships are critical for the stability of ecosystems but their mechanisms are poorly understood. Local adaptation is an indication of how specialized the organisms are to their mutualistic partner. Most experiments that study locally adapted species focus on host-parasite and trophic interactions, however, we focus on two species, Desulfovibrio vulgaris and Methanococcus maripaludis, existing in a mutualistic relationship. We used 6 independently evolved populations. The individual species in the co-evolved populations were separated and paired with a partner from a different evolved population to see if they grew faster with the partner they evolved with. We tested for local adaptation by frequently measuring the optical density of the cocultures. The OD measurements were used to calculate growth curves. The growth curves were compared to determine if the co-cultures were locally adapted. Our results indicated that neither species was locally adapted.

Current methods for staging chronic kidney disease are deficient because they lack specificity and sensitivity. Two potential renal biomarkers, cinnamoylglycine (CG) and hippuric acid (HA) are dietary metabolites cleared by the kidneys. These two compounds are potentially more sensitive indicators of kidney function because they are shown to require active secretion into the ultrafiltrate by the renal tubules. The purpose of this project was to develop and validate a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for determining the concentration of CG and HA in serum for use in future clinical research studies. Samples were prepared by precipitating serum proteins with acidified acetonitrile followed by phospholipid removal using solid phase extraction. Compound separation was achieved with ultra-high performance liquid chromatography utilizing a reverse-phase T3 column with a gradient mobile phase. Detection and quantification were accomplished by isotope dilution-tandem mass spectrometry operated in positive electrospray mode. The transitions monitored were 206.04>131.04m/z and 181.03>105.01m/z for CG and HA respectively. The lower limit of quantification (20% CV) for this multiplexed assay was established at 0.028 ng/mL and 1.2 ng/mL for CG and HA, respectively. Linearity studies achieved an r² value >0.97 for both analytes. The mean analytical recovery was 62% for CG and 64% for HA. The following studies used concentrations of CG and HA at 44.67 ng/mL and 7063.05 ng/mL respectively: intra-assay imprecision (CV, n=20) was 5.05% and 4.36%, inter-assay imprecision (CV, n=20) was 11.90% and 5.89%, and total error was 12.92% and 7.33% for CG and HA, respectively. This LC-MS/MS method demonstrates good performance and excellent analytical specificity for detecting and quantifying CG and HA in serum. The next phase is to implement this method into a clinical research study and explore these analytes as improved biomarkers for staging chronic kidney disease.

Chronic allograft injury has replaced acute rejection as the leading cause of renal graft failure following transplantation. Graft failure is of special importance to pediatric patients since they typically require multiple grafts in their lifetime and therefore will benefit from graft life extension (Smith et al, 2010). A relationship has been demonstrated between subclinical Cytomegalovirus (CMV) and subclinical Epstein Barr Virus (EBV) and chronic allograft injury previously. This relationship could lead to insight into the mechanism of chronic allograft injury. To characterize the relationship between subclinical infection and chronic allograft injury we measured T-cell specific response to subclinical CMV and EBV infections. A panel measuring three aspects of T-cell response: activation, memory, and cytokine response, was proposed and validated. T-cell response was quantified using flow cytometry on stimulated whole blood samples from study participants in an intracellular cytokine staining assay. Analysis of T-cell activation, memory, and cytokine production was done using a Boolean gating strategy on FlowJo software. Twenty-six patients are currently enrolled, with whole blood samples being collected every six months over the course of twenty-four months. We are in the process of banking, processing, and analyzing the samples. After all of the patient samples have been analyzed for T-cell memory, activation, and cytokine production, we will quantify the relationship between T-cell response and subclinical viremia. This data will be compiled in conjunction with the GFR, kidney biopsies, and CMV/EBV PCR data to create a longitudinal history, allowing us to understand how CMV and EBV viremia contributes to chronic allograft injury.

The ubiquity of computing devices such as smartphones and wearable devices has given users access to technology at all times. However, user interactions with these devices are often cumbersome. Interacting with these computing devices is of increasing importance and minimizing their negative cognitive effects is critical to usage of these devices in order to allow users to focus on the task they are trying to accomplish, not the technologies they are using to accomplish them. I evaluated how people currently interact with computing devices such as the smartphone, wearable devices, and computers, and how these technologies try to solve computing inputs in order to minimize the negative cognitive effects of user interactions. I achieved this by identifying how users interact with computing devices and how those interactions translate to actions and outputs. I also used literature reviews to understand how people currently interact with computing devices and examined current research on cognitive impacts of human-device interactions. Analyzing how users of these existing devices interact with them informed interaction design decisions for the second part of my study. Using insights gained from this research, I designed and prototyped a wearable technology (WT) that extends the input capability of computing devices to simplify user interactions. The aim of the WT is to provide an easy and intuitive way to send instructions to a device. It uses Bluetooth to communicate with devices and transmit input and outputs between the user and their devices. Computing has become increasingly mobile. It serves as a way to augment life without the confines of space such as with the desktop computer. My research will help to elevate the mobility of computing and inform how we interact with computing devices as they become more ubiquitous.

The purpose of this research is the development of a precisely electroplated set of vacuum capacitor electrodes for inclusion in the MAJORANA Demonstrator (MJD) - the first stage of the MAJORANA project. Funded by the Department of Energy the MAJORANA program is part of an international effort to study neutrinos, dark matter, and axions led by the UW Center for Experimental Nuclear Physics and Astrophysics (CENPA). The project focus is on making the capacitors with a physical dimension tolerance (<2 microns) that is far less than what can be obtained via machining or other comparable methods of manufacturing. The desired capacitors are made using high-aspect ratio patterns in silicon as an electroplating mold. Silicon wafers are coated with an electroplating seed layer and then bonded to each other using thermcompression wafer bonding. Thermocompression bonding is a technique used to bond wafers by applying heat and force simultaneously. Following bonding, the wafers are patterned, using a photolithography process and Deep Reactive Ion Etching (DRIE), to form the mold cavaties. Photolithography is a multiple step process that includes application and patterning of a light-sensitive material called photoresist. Next, bottom-up copper electroplating is performed until excess deposit of copper called over-plating is achieved. The over-plated structures are polished back to establish dimensional uniformity. The final step is releasing the electroplated structures via a blanket DRIE process. Successful completion of this research project will allow assembly of MJD which in turn will be used to search for neutrinoless double-beta decay – one of the rarest forms of radioactive deacy. This project will also be a primer for more industry-focused capabilities for the Washington Nanofabrication Facility (WNF) with eventual development of through-silicon vias (TSVs) for research applications and a potential foundry process for precision part creation without the limitations of machining.

Mitochondria are essential organelles in eukaryotic cells and are most commonly known for their prominent role in energy production. In addition, mitochondria are involved in other important cellular processes such as lipid biosynthesis and apoptotic cell death. Mitochondria also have dynamic properties including fusion, division, and movement, which are all essential to maintain mitochondrial function. Given the plethora of essential cellular activities that require mitochondrial function, it is not surprising that defects in mitochondrial function are implicated in many different human diseases and disorders including diabetes and myopathies. Mitochondrial movement is important for the distribution of mitochondria, which is important in all cells, but especially important for asymmetric cells such as neurons. Transport is also required for mitochondrial fusion – the two organelles must move close enough to each other to fuse. Mitochondrial fusion in particular is required to maintain mitochondrial DNA and therefore, mitochondrial function. We are interested in the mechanism of mitochondrial movement and the connection between mitochondrial fusion and transport. Mitochondria move on microtubules using a complex of proteins. Miro 1 and Miro 2 are anchored to the mitochondrial outer membrane and interact with two adaptor proteins, TRAK1 and TRAK2. The TRAK proteins also interact with Kinesin, which binds to the microtubules and mediates microtubule-directed movement. Understanding the assembly and regulation of this complex and the stoichiometry of its components will provide insights into the mechanism of microtubule-directed mitochondrial movement. Our goal is to clone TRAK1 and TRAK2 complementary DNA (cDNA) into expression vectors for protein production in Escherichia coli cells and then to develop a purification protocol for TRAK1 and TRAK2. This will facilitate biochemical analysis of the mitochondrial motility complex.

The vertebrate body forms through a process called embryogenesis. In my research, I focused on the establishment of body length during embryogenesis of the model organism zebrafish (Danio rerio). Under normal conditions, the cells of the developing body intercalate towards the back, or dorsal side, of the embryo, and extend longitudinally to grow the body axis. One observed defect in this process blocks cell intercalation, thus leading to underdeveloped bodies, which is known as a convergent extension phenotype. In my research, I studied the role of Microtubule-Associated Serine/Threonine kinase-Like (MASTL) RNA in body axis formation. Because of a known role for MASTL in regulating chromosome segregation, I hypothesized that overexpression of MASTL would interfere with normal cell function and lead to a convergent extension phenotype with a shortened body axis in the developing zebrafish embryo. To test this hypothesis, I injected embryos with different concentrations of RNA and allowed them to develop. Overexpression of MASTL shortened body lengths at all but the lowest concentration of RNA. I then chose a low but effective concentration of MASTL RNA, injected embryos and quantified embryo length. Finally, I performed RNA in situ hybridizations, a process by which labeled probes are used to localize specific RNA transcripts in embryos. Using a variety of labeled probes, I found in addition to shortened body length, the distribution of the prospective spinal cord cells and muscle cells were abnormal in MASTL-injected embryos. The results of these experiments clearly show that overexpression of MASTL leads to a convergent extension phenotype. To continue this research, I will look at whether or not MASTL affects body length formation through Protein Phosphatase 2a, a known target of MASTL. The results of my research will lead to a better understanding of the role MASTL in cell intercalation and vertebrate body elongation.

Deadly and leaving patients with little time to live, pancreatic cancer is the third largest cause of deaths due to cancer in the US. Early detection and research of the disease beyond current capabilities are crucial and could be achieved by imaging fully intact pancreatic tissue core biopsies (TCBs) in three-dimensions (3D). Hence, The Human Photonics Laboratory is developing a microfluidic device to process fully intact TCBs (L=0.5-2.0 cm, d=200-1200 µm) in an all-in-one approach. Simultaneously, the device transports the TCB towards a 3D imaging platform for the end goal of enhancing cancer diagnosis. To achieve this goal, each step must be fit and performed in the small device. Typically, microfluidic devices are microfabricated with rectangular cross-sectional channels and used with no larger than cells or cell slurries, but never TCBs. To prepare TCBs for a pathologist in a microfluidic device, transportation is done in curved, circular cross-sectioned channels (CCCs)—both of which have never been achieved before this project. The channels’ cross-sections are circular to produce an intuitive Poiseuille flow profile. TCBs require a smooth directional change due to larger length and diameter of a TCB. Therefore, curved channels are necessary for direction changes and an optimized device footprint. Traditional microfabrication methods are not practical due to the time and precision required for mircofabricatation of a smooth CCC. Therefore, a new simplified method to fabricate microfluidic devices was developed to allow for CCCs and transport availability for TCBs. This new method allows for microfluidic devices containing CCCs to be fabricated in less than one hour and can provide channels that curve in 3D. Transportation of TCBs through CCCs is demonstrated for planar and multi-dimensional direction changes. Minimized channel lengths required to successfully change a TCB’s direction by 90 and 180 degrees were determined to reduce the microfluidic device’s footprint.

Protein homeostasis encompasses the creation, maintenance, and degradation of proteins, and it is essential for organisms to function properly. Yet, environmental stressors can disrupt protein homeostasis, which can lead to protein aggregation. Protein aggregation has been linked to serious aging diseases such as Huntington’s, Parkinson’s, and Alzheimer’s disease. In order to gain a better understanding of the pathways important for maintaining and disrupting protein homeostasis, we subject Caenorhabditis elegans to various environmental stressors that disrupt protein homeostasis. We have found that specific concentrations of hypoxia, or low oxygen conditions, induce an increased amount of protein aggregates in C. elegans compared to animals in room air, suggesting defects in protein homeostasis. In addition, the AMP-activated protein kinase (AMPK) seems to be crucial for allowing the formation of aggregates in hypoxia. AMPK mutants that are placed in hypoxia show a decrease in protein aggregation compared to wild-type animals. Furthermore, another environmental stressor, heat shock, also affects protein homeostasis. Heat shocking C. elegans prior to the hypoxic exposure, decreases the amount of aggregates compared to worms that did not experience heat shock. However, unlike hypoxia-induced protein aggregation, heat shock does not seem to require the presence of functional AMPK in order to influence protein aggregation.

Proton-coupled electron transfer (PCET) occurs in a variety of oxidation/reduction reactions. This thermodynamically-coupled transfer of an electron (e–) and a proton (H⁺) is important for many reactions, including catalysis and energy generation, and may occur through different mechanisms. Zinc oxide (ZnO) nanoparticles are useful for studying factors that influence the rates of PCET reactions in at metal-oxide surfaces. The ZnO nanoparticles used in this research have been well characterized and, as a colloidal solution, can be treated as molecule-like reactants in experiments. The ZnO nanoparticles described in these experiments are capped with dodecylamine (DDA), and then dispersed into air-free toluene, an aprotic solvent. The use of an aprotic solvent is important to ensure that the e–/H⁺ are transferred from the nanoparticle. When these nanoparticle solutions are irradiated with above-bandgap radiation, an electron is excited into the conduction band. This leaves a hole in the valence band that, from previously demonstrated research, is immediately quenched by EtOH left over from synthesis; EtOH provides both an electron and a proton, keeping the nanoparticle neutral. When the reduced and protonated ZnO nanoparticles are reacted with 2,4,6-tri-tert-butylphenoxyl (^tBu₃ArO·), an electron and a proton are transferred from the reduced ZnO nanoparticle to the ^tBu₃ArO·, yielding the corresponding phenol, ^tBu₃ArOH. The kinetics of this reaction are monitored using laser flash photolysis. The rates of PCET are affected by the reduction potentials and the pKa of the reactants. The reduction potentials of the nanoparticles may be tuned by changing the particle size. Initial results also show the concentration of the capping group affects the rate of PCET. We are investigating how these factors, reduction potential and capping group concentration, influence the rate of PCET from reduced and protonated ZnO nanoparticles.

Dyslexia is a complex disorder that interferes with a person's ability to read and spell with no consensus as to what causes it. The typical person processes language in the left hemisphere and is either right or left handed while very few people have ambidextrous tendencies. Our hypotheses are two-fold. First, that competition between the brain's two hemispheres underlies dyslexia. Second, that this competition is evident in cortical activation during reading tasks as well as performance speeds during hand motor tasks. To test our hypotheses, we collected data from 52 adult participants (19 with dyslexia, 33 controls) who underwent electroencephalography (EEG) measures during a word reading task and also performed an alternating keytapping task.To investigate Hypothesis 1 (lack of lateralization is associated with dyslexia), we categorized our participants' EEG data according to typically vs atypically lateralized language activation patterns. Higher than expected numbers of adults with dyslexia in the atypical hemisphere activation group would be consistent with our hypothesis. To investigate Hypothesis 2 (correlations between the two modalities), we calculated a relative lateralization score for each of these task types and tested the correlation between these two scores for significance. Evidence of correlations between these two measures would yield higher than expected numbers of participants with dyslexia in the ambidextrous group as well. Evidence for both of our hypotheses will provide important insights into the biological underpinnings of dyslexia, pointing to disorganized brain circuitry in affected individuals. 

Carbon dioxide (CO₂) is a greenhouse gas that traps radiation in the Earth’s atmosphere. Increasing levels of CO₂ in the atmosphere can lead to a warming of the Earth’s surface and can affect a number of processes that affect climate patterns. Terrestrial ecosystems contain 3 times more carbon than the atmosphere, and each year forests release more than 10 times the amount of CO₂ to the atmosphere through soil respiration than fossil fuel emissions. Although these large natural soil respiration fluxes tend to be balanced by fixation of atmospheric CO₂ through photosynthesis, the carbon balance of forests under future climate is still unknown. In order for scientists to better model the role of forests under future climate change, an improved understanding of the amount of carbon that is allocated and stored in different components of forest ecosystems is needed.This project aims to provide a more thorough understanding of whole-plant carbon allocation in temperate forests. While trees may allocate up to 50% of their photosynthetically fixed carbon belowground, carbon allocation belowground has been historically overlooked. In particular, very few studies have quantified the amount of carbon allocated to mycorrhizal fungi – the symbiotic fungi found on tree roots that provide the plant with water and nutrients in return for sugars (carbon). We employed three distinct methods (including new isotopic techniques) to quantify carbon allocation to mycorrhizal fungi across a range of New Hampshire forest types. Preliminary results show that in nutrient poor conifer forests, mycorrhizal fungi may receive as much as 30% of the total plant carbon. This is one of the first studies that will quantify carbon allocation to mycorrhizal fungi under a range of natural forests.

Fanconi anemia (FA) is a genetically inherited disease that frequently results in bone marrow failure, a high prevalence of leukemia, and solid tumors of the head and neck that are associated with genomic instability. Abnormal chromosome configurations produced in FA cells, called radials, are diagnostic of the disease. The mechanism of radial formation is not fully understood. However, they can be induced to form by exposure of cells to agents that promote a type of DNA damage called interstrand crosslinks (ICLs), covalently bonded DNA strands caused by exposure to ICL inducing agents such as those used in chemotherapy or endogenously produced metabolic byproducts. Radials can occur spontaneously in the cells of FA patients, therefore, understanding the formation of radials, as well as their fate during the cell cycle, may help in designing effective therapies to counteract the genomic instability. The current aim is to investigate radial formation and cell recovery afterwards through careful examination and identification of structural abnormalities in chromosomes that may be a result of prior radial formation. To carry out this goal, a population study will be performed using the primary PD20 (FANCD2) cell line. Mitomycin C (MMC) will be used to induce ICLs and cells will be harvested with paired controls at multiple time points following damage. Cells will be analyzed using classical G-banding for the presence of structural and numerical chromosome abnormalities. A significant increase in chromosome abnormalities structurally consistent with radials that have gone through mitosis is expected to be observed during analysis.

Language models characterize the probability of a sequence of words for use in a variety of natural language processing applications, including automatic speech recognition. Web text is a key source of data for developing the language models used in such systems because of its sheer volume, and the fact that much of it is freely available to the public. However, web text varies broadly in genre, depending on purpose, audience, formality, and other characteristics. For example, the difference between the formal exposition of a Wikipedia article and the informal banter between two Twitter users. When using web text to train language models for conversational speech recognition in particular, it is important to find text that resembles that speaking style. When training a language model using various web text sources, we use a measure of worth called perplexity. By selecting web text that matches the conversational style of speech, the language model perplexity improves, which generally leads to higher accuracy speech recognition. I work on selecting text taken from Twitter. This involves research on what kinds of Twitter searches will result in tweets containing useful text, as well as how to identify Twitter users who post useful text.

The United States spends 16% of its GDP on Healthcare, but it still has the most, inefficient, and fragmented system of care in the world. This project strives to assess the current health care system’s shortcomings, and at the same time, show the effectiveness of the health care reform, which is the original version of Obama’s Affordable Care Act that Massachusetts (MA) enacted in 2006. By addressing the government’s core regulation, the “three legged stools” of reform in MA respectively, the three policies and their effectiveness will also be analyzed at both the state level and comparing the state and the nation as a whole, since the system of ACA resembles MA’s reform closely. By comparing various properties of MA to the U.S. as a whole, such as comparing population’s income distribution, proportion of people with different levels of education background, health care expenditure from various income individual or families, poverty rate, etc., we can see whether the national application of health care reform will be successful as it is in Massachusetts. The result is that the prediction of expanding the MA health care reform national wide may not lead to as impressive changes as MA’s due to vastly different variables. Also since it is now mandatory for people to be covered by health insurance, the government may put itself into a position of long-term deficit by paying premiums for the “poor”, which will end up with higher budget deficit. Though “three legged stools” effectively implemented at the state’s level, it conceals more potential risk and obstacles in the States with a much larger scale, and may end up with less effective result with much more diverse populations.

Proteins that share similar 3D structures, or folds, can be grouped together into fold families, and evidence suggests that there may be common folding mechanisms that exist within these fold families. Finding these common folding mechanisms will shed light on the way in which folding is determined among proteins, which is a major question in biochemistry. Here I investigate the dynamics and unfolding pathways of 18 members selected from the sixth most populated fold family, the SH3-like barrel domain. The SH3-like barrel fold is an all-beta fold, constructed of beta strands only. Using molecular dynamic simulations at high temperatures, the unfolding pathways, including the characterization of transition states, can be studied for each of these proteins. A broad analysis of native and non-native contacts and secondary structure content will allow common folding patterns to be determined across the fold family. It is anticipated that a hierarchical loss of contacts between the beta-strand of the fold, with those between the turns being maintained longer will be observed. Here I report an initial analysis of the unfolding of these 18 members of the SH3-like barrel fold family and present the observed commonalities, as well as variances across the pathways.

Esophageal adenocarcinoma (EAC) is a type of cancer with the most rapidly increasing incidence rate in developed nations. EAC occurs as a result of the metaplasia-dysplasia-adenocarcinoma sequence initiated by Barrett’s esophagus. In this sequence of events, patients develop Barrett’s esophagus, wherein the acidic damage of gastroesophageal reflux disease (GERD) causes the esophageal epithelium to take on an intestinal epithelium phenotype. This metaplasia can then progress to Barrett’s esophagus with either low-grade or high-grade dysplasia. Patients that develop high-grade dysplasia (HGD) are at great risk for esophageal adenocarcinoma, and hence there is a need for higher specificity in the labeling of pre-cancerous tissues for endoscopic detection. Current imaging of dysplastic lesions is done through traditional endoscopy with the use of contrast agents for differential staining. However, current contrast agents have a low signal-to-noise ratio (SNR), and dysplastic lesions are often missed. Therefore, for early detection of esophageal adenocarcinoma, we are creating a contrast agent that increases SNR via fluorophore-labeled peptides that bind specifically to tissues with high-grade dysplasia. Peptides are ideal as targeting ligands as they can bind specifically to surface proteins on dysplastic cells and increase the likelihood of clinicians obtaining biopsies of pre-cancerous tissue. In the past year, we have isolated potential peptide sequences that bind immortalized cells lines generated from dysplastic tissues. A bacteriophage library was subjected to subtractive whole cell panning for isolation of phage expressing HGD-binding peptide sequences. The phages were added in vitro to cultured cell lines of normal esophageal tissue and non-dysplastic Barrett’s esophageal tissue to eliminate those that were not selective for dysplasia. After subtractive whole cell panning, left over phage were sequenced to determine the peptide sequences on them. Future work includes binding studies using flow cytometry to demonstrate that fluorophore-labeled peptides bind preferentially to dysplastic cell lines independent of the bacteriophage.

The lateral habenula (LHb), is an important regulator of midbrain dopaminergic systems that are known to be involved in cocaine reinforcement. The LHb exerts an inhibitory effect on dopaminergic neurons in the ventral tegmental area (VTA), though interestingly LHb-VTA projections are known to be glutamatergic (excitatory). The rostromedial tegmental nucleus (RMTg), a recently identified GABAergic (inhibitory) nucleus, that receives direct excitatory inputs from the LHb, has been proposed to be the source of this inhibition of the VTA. Here, firstly, we injected rats with anterograde TAMRA-Lys-Dextan and retrograde FluoSphere tracers in the LHb and RMTg, respectively and demonstrated that the LHb indeed projects to both the VTA and RMTg. Secondly, since the RMTg has no known anatomical boundaries, we gauged the anatomical location of the RMTg using expression of the transcription factor cFos, a marker of neural activation in response to cocaine. A significant increase in cFos expression was found in rats injected with cocaine (10 mg/kg i.p). Finally, we utilized the Designer Receptor Activated Exclusively by Designer Drug (DREADD) technology, to investigate the role of modulating the activity of the LHb on cocaine-self administration. Rats were implanted with jugular venous catheters and trained to self-administer cocaine (0.75 mg/kg/infusion). We found that DREADD-mediated transient silencing of the LHb through the activation of inhibitory G-protein-coupled signaling pathway with clozapine-N-oxide increases cocaine self-administration. In contrast, activation of the excitatory G-protein-coupled signaling pathway decreases self-administration on a progressive ratio schedule. We further show that inactivation of LHb inputs to VTA neurons have no effect on cocaine self-administration. We now propose to investigate the role of LHb projections to the RMTg using a dual-virus strategy using a combination of Cre-dependent DREADD’s and canine adenovirus expressing Cre (that gets transported retrogradely) to specifically target the LHb to RMTg projections for DREADD-mediated modulation on self-administration.

Dental caries is the breakdown of tooth enamel that causes cavities and is the most common chronic disease in children and adolescents between the ages of 6 and 19 years. Therefore, much work is being done to combat caries. We believe that the scanning fiber endoscope (SFE) developed in our lab can be used to improve the detection of early caries in children. The SFE is a small flexible probe that scans low-powered RGB laser light. It performs high-contrast high-resolution imaging and dual laser fluorescence spectroscopy with 405- and 532-nm laser excitation on both in vitro and in vivo teeth. My project focuses on the development of a calibration standard to use with the SFE in an upcoming clinical trial to be conducted at the UW Center for Pediatric Dentistry. A photostable calibration standard was created to match the fluorescence pattern of dental enamel. Spectral measurements of the standard will be taken before and after collecting data from patients' teeth with the SFE to monitor the instrument's behavior. This will allow us to account for drift in measurements and ensure that we can draw accurate conclusions from our data. 

Carboxylic acids are ubiquitous in chemistry and used in a variety of industrial applications, ranging from polymer precursors to food preservatives. Modern routes to synthesize these compounds often involve specialized equipment, harsh conditions, and potentially toxic reagents. An alternative synthetic route is the aldehyde-water shift reaction, in which an aldehyde is oxidized by water to form a carboxylic acid and molecular hydrogen. The use of water as both solvent and reagent could potentially reduce the impact of aldehyde oxidation on the environment, especially when compared to the routes . A series of iridium-, rhodium-, and ruthenium-based complexes have been synthesized and investigated for activity in catalyzing this reaction. Using ¹H NMR (proton nuclear magnetic resonance) and GC-FID (gas chromatography) to analyze reaction products, we have observed many of the catalysts to disproportionate aldehydes to alcohols and carboxylic acids in competition with the desired dehydrogenative oxidation to carboxylic acids. Mechanistic studies and catalyst optimization for dihydrogen production are presented.

It has been hypothesized that there is a correlation between the flexibility of amino acids in a protein and their conservation. Inflexible residues tend to be structurally important and thus less tolerant of change. By this theory, mutations at these positions are expected to typically be deleterious. The Dynameomics project is an ongoing effort by the Daggett Research Group to characterize protein folding space through molecular dynamics simulations of representatives of all known protein structures or folds. The representative domains are organized such that the lowest rank fold (rank 1) represents the highest populated fold – with each subsequent rank representing fewer structures. We have used a novel software module to calculate residue flexibility directly from the relevant molecular dynamics simulation files. The resulting data were used to test the hypothesized correlation between conservation and flexibility. Analysis of the entire dataset showed that hydrophobic residues and Cysteine were relatively conserved on average. Hydrophobic residues are generally found in the less flexible core of the protein while Cysteine residues form highly inflexible disulfide bonds. Thus, residues expected to be inflexible were conserved on average – providing support for the tested hypothesis, with the caveat that the standard deviations were large. To avoid these large variations, analysis of individual proteins was needed. Calculated correlation coefficients allowed for the quantification of how well each simulated structure agreed with the hypothesis. Work is now being done to characterize the difference between the various ranks of Dynameomics in terms of this conservation-flexibility relationship. We anticipate that a better understanding of evolution at the amino acid level of proteins will help us to better predict the impact of mutation. Combining this information with rotamer information can allow for the creation of tools useful in the field of protein design and engineering.

Proteins are functionally dependent on their 3-D structure. Many proteins share similar structural folds arising from either convergent evolution or a common ancestor. Understanding a protein’s folding pathway is a fundamental problem of biochemistry. The Daggett Lab created the Consensus Domain Dictionary to categorize common 3-D protein folds, termed fold families, based on various arrangements of secondary protein structure. Evidence suggests there may be common mechanisms in the folding and unfolding of members of a fold family. Here, we look for such characteristic mechanisms within 14 members of the Ubiquitin-like family, the 8th most commonly found protein fold. These proteins have a common core structure with sequence identities ranging from approximately 25% to 85%. Using Molecular Dynamics simulations to model the proteins denaturing at 498K, we compare transition states in the unfolding pathway, various atom-atom contact data, and the alpha-helical content amongst protein fold family members to analytically determine the existence of family-specific folding mechanisms. We anticipate that the early pathway will revolve around helix-turn-helix rotations or splays, sequential alpha-helical melting, and spatial separation of the four main beta sheets.

Calbindin D9k is a calcium binding protein that contains a helix-loop-helix motif, called EF-Hand. Members of the EF-Hand family are involved in calcium uptake and regulation of functions within the neuroendocrine and muscular systems. As calcium is involved in many cellular processes, such as muscle contraction and nucleotide metabolism, the function of these calcium-binding proteins is of great biological significance. Nuclear magnetic resonance spectroscopy (NMR) can provide a measure of protein dynamics, such as order parameters, that describe the residue-level mobility of a protein, including that of the backbone amide groups. These order parameters are often translated into conformational entropies, enabling an assessment of the entropic changes associated with unfolding or binding events. NMR studies that probe the stability and cooperative binding of calbindin D9k provide evidence that a temperature dependence of order parameters can identify regions of the protein that exhibit linear or nonlinear stability as a function of temperature. I will use molecular dynamics simulations to characterize the dynamics of Calbindin D9k and provide atomic level detail of the protein’s temperature dependent behavior over a temperature range of 3 to 63 Celsius. I will be comparing order parameters calculated from the simulations with experimentally derived order parameters for both the calcium loaded and unloaded states to determine the effects the calcium ions have on protein stability and conformation. Residues instrumental in calcium binding and structural stability are expected to exhibit smaller reductions in order parameters while non-structural regions should exhibit larger and more erratic reductions through increasing temperature. This study will further our knowledge of the dynamics of calcium binding proteins and offer an estimation of the free energy contribution that conformational entropy provides ligand binding. It may also be possible to extend these results to other calcium binding proteins known to act in disease and calcium deficiencies.

This research traces the origins of electron density fluctuations in the HIT-SI experiment. HIT-SI is a magnetic confinement experiment that uses two helicity injectors to initialize and sustain current in the confinement region. Densities of 1-10e19 m^-3 with density fluctuations related to the injector frequency are measured with an FIR interferometer. After spheromak formation, injector currents flow in the direction of toroidal current in the confinement volume. Peaks in the density fluctuations are seen when the injector current passes through the beam path of the interferometer. These observations are consistent with particle motion in the direction of injector current as expected by anti-dynamo action in this region. Furthermore, we have observed fluctuations that indicate that the injector current displaces the confined current. Calculating the toroidal current centroid from surface magnetic probe measurements as a function of time provides further testing of this model. Understanding density fluctuations allows a more complete description of the physics of current drive in HIT-SI.

The inequalities and marginalization of people with disabilities is an issue with global scope. Environmental influences and socially derived assumptions shape the way disability is defined and experienced cross-culturally. Statistics shed light on significant disparities throughout various countries. According to United Nations Enable (2006), 10% of people in the world have some type of disability. Of this entire population of people with disabilities, 80% live in developing countries. Further, out of the estimated 200 countries in the world, only 45 have disability-specific laws such as anti- discrimination. In this research, I examined the driving factors behind this disparity through a cross-cultural comparison of disability advocacy efforts. In particular, I looked to countries that have experienced shifts in policy that directly influenced people with disabilities. I identified disability advocacy taking place in South Africa in a post-apartheid context, Ukraine in a post-soviet context, and the US in post-ADA context (Americans with Disabilities Act). Through rhetorical/discourse analysis of the imagery and language used on nongovernmental groups’ websites, I examined how shifting power dynamics have situated people with disabilities in South Africa, Ukraine, and the US and how these patterns manifested in online communications.

This study analyzes the color complex which is defined as psychological fixation about color and features that lead African-Americans to discriminate against each other. There is a lack of dialogue around how history has turned African-American women to focus towards hurting each other through colorism - skin color biases. This research asks how issues of colorism within the African-American community lead to concerns of self-acceptance and perception of beauty among young African-American women. I expect to find evidence of the effects of the color complex and determine how young Black women perceive beauty in order to frame their identity. The findings will fill a gap in existing research by challenging the work of earlier researchers, who have looked at the existence of colorism among African-American women today and look farther into how this issue has been and is affecting their perception of beauty in relation to the acceptance of themselves. 

Autophagy is the process in which eukaryotic cells selectively degrade proteins and organelles. Autophagy has been well documented in organisms ranging from yeast to mammalian cells, with demonstrated roles in response to starvation, aging, and stress. However, there has not been an effective method for measuring autophagy in C. elegans, despite C. elegans being a popular model organism for the study of disease and aging. We refined an assay that uses double-fluorescent protein tagged Atg-8/Lgg-1 to measure autophagy in both yeast as well as C. elegans. This assay reports an increase in autophagy in response to starvation in both model organisms. We then applied this to the study of nematodes containing a mutation in Rheb, an important protein in the upstream signaling cascade that regulates autophagy. Autophagy is damped by signaling through the TORC1 pathway. A mutagenesis screen revealed two different worm mutants (ENU9 and ENU10) which are predicted to hyper-activate TORC1 signaling. Using the aforementioned assay we found that ENU9 and 10 mutants have dramatically reduced levels of autophagy. This work has implications for further research in Alzheimer’s, Parkinson’s and related diseases associated with ageing and proteostasis.

Antibiotic resistance is a challenging problem in the realm of human health today. As a fundamental evolutionary phenomenon, it provides an excellent system to test adaptive evolutionary theories in a short amount of time. Thus, I explored the rise of antibiotic resistance in two evolution experiments with Escherichia coli. In the first, I asked how differences in genetic background affect the rate of adaptation to a new environment. To address this question, I generated 19 unique antibiotic resistant mutants by evolving E. coli in an environment with low drug concentration, and then exposed thousands of populations of each isolate to a high concentration environment measuring the proportion of populations that survived. Since survival in the high-drug environment requires acquisition of a new beneficial mutation, I hypothesized that high mutant survivorship indicated an isolate with more mutational options available in the high drug environment (we call this “potentiation”). Isolates with low survivorship would have fewer available mutational options (we call this “doom”). Interestingly enough, some observed differences may be due to a phenomenon known as sign genetic epistasis – when mutations have different effects in combination than individually. Preliminary data suggests a few strong cases for potentiation. I also investigated the effect of an initial resistance mutation on the consequent adaptations in a no drug concentration environment. To study this, I generated 23 unique mutants of E. coli and tracked how fitness and drug resistance changed over time in 2,200 populations. Both of these experiments help illuminate the role of historical contingency in evolution, the idea that an initial mutation may dictate an organism’s future mutational trajectory (available mutational options). Therefore, understanding both the effect of initial mutations and the underlying mechanisms of mutation acquisition is necessary in order to combat the emergence of resistant bacteria, a current human health concern.

For the first time we are able to non-invasively measure levels of a molecule that indicates the ageing and disease state of an individual. This molecule called nictotinamide adenine dinucleotide (NAD) and its other forms (NAD, NAD+, NADH) are related to aging and muscle function. High levels of the form NADH is found in individuals with disease and old age while high levels of NAD+ is found in active and younger individuals. Through exercise on elderly subjects we show that ageing effects on muscle can be reversed and levels of NAD+ and NADH can be restored to those found in adults. The form NAD+ is an index of mitochondrial capacity for making energy. With aging the oxidative capacity of the mitochondria declines, the amount of mitochondria declines and the levels of NAD+ declines. Through exercise training this effect can be reversed to yield higher muscle capacity in elderly. Our measurements were made on a 1.5 Tesla Magnet. We acquired Phosphorus spectra on the FDI (First Dorsal Interosseous) muscle and analyzed the data using software called jMRUI. From the Phosphorous spectra we are able to extract and analyze the NAD+ and NADH peaks.

Rumination has been linked to the onset and development of depression and anxiety. Rumination is a process of repetitive negative feelings and thoughts associated with an upsetting event or situation. In this study, I investigate whether rumination explains the relationship between different types of environmental adversity and symptoms of depression and anxiety in teens. Specifically, does rumination explain the association of trauma exposure, poverty, and race/ethnicity related with the onset of depression or anxiety? Data come from a sample of 168 adolescents recruited from the community in Boston and Cambridge, MA. To examine mediation I examined four sets of models testing the following relationships: 1) the association between each measure of environmental adversity and depression/anxiety, 2) the association between each measure of environmental adversity and rumination, 3) the association between rumination and depression/anxiety, and 4) a final model that included the adversity variables as well as rumination to see the attenuation in associations of adversity with depression and anxiety once rumination was added to the model. The findings suggest that, 1) child abuse was associated with elevations in depression and anxiety symptoms, and community violence was associated with depressive symptoms and marginally with anxiety symptoms; 2) child abuse was associated with higher engagement in rumination; higher income-to-needs ratio was also related to greater rumination; 3) higher degrees of rumination predicted both depression and anxiety symptoms; and 4) the association between child abuse and depressive symptoms was reduced by 24.5% after accounting for rumination, and the association between child abuse and anxiety symptoms was reduced by 39.8% after accounting for rumination. These findings fill the void in the literature regarding mechanisms linking different types of environmental stressors to the onset of depression and anxiety. This is important for development of interventions for preventing mental illness.

Marine debris is a prevalent form of environmental pollution in which man-made products are released into oceans and waterways. Debris objects pose a variety of concerns, including entanglement and ingestion by wildlife, toxicity, and introduction of invasive species (biofouling). The Coastal Observation and Seabird Survey Team (COASST), a citizen science program at UW, is currently developing a marine debris monitoring protocol. The protocol calls for field surveys documenting basic site characteristics and attributes of debris objects. Seventeen attributes were chosen as indicators of potential harm to wildlife (e.g. loop presence and bite marks), invasive species threat (biofouling), and debris movement patterns in the ocean (e.g. size, material). Our team analyzed images from a database of over 5,000 marine debris photos collected by COASST at over 200 beach sites in the Pacific Northwest and Alaska. We utilized an iterative approach with two students independently assigning attribute states (e.g. color: black, bite marks: yes) to debris objects from 900 randomly selected photos. We compared results to understand likely sources of human error. Initially, we found that color, malleability, geometric shape, material, intactness, and weathering were attributes that posed the greatest challenges – where surveyor disagreement (error rates) exceeded 15%, with some approaching 50%. After three rounds of result analysis and attribute definition refinement only 5 of the 17 attributes had error rates exceeding 15% (range 16-30%), reducing the likely error volunteers will make. The resultant standardized attribute definitions and state assignment protocol will provide a means of collecting reliable (i.e. low error) baseline abundance and distribution marine debris data as well as risk assessment based on specific attributes of use for further research, conservation endeavors, and resource management.

Conifers are an important part of the forest industry and are extensively planted for timber production. However, high crop yield demands and increasing environmentally stressful conditions such as heat, drought, and water salinity have caused an increase in the use of chemical fertilizers and water, which can be expensive and unsustainable. A possible alternative to fertilizers is the use of nitrogen fixing endophytes. Endophytes are bacteria or fungi that live within a plant, establishing a mutualistic relationship in which they can provide growth stimulation through production of growth hormones, nitrogen fixation, enhanced nutrient uptake, and protection from potential pathogenic colonizers. Prior studies have demonstrated that the use of fungal and nitrogen fixing endophytes significantly increases growth in many crop plants grown in the presence of abiotic stresses. In this study I have inoculated Douglas Fir seedlings with various strains of nitrogen fixing endophytes. Because confirmation of inoculation is essential, some of these endophytes were marked with a fluorescent marker (GFP) to confirm inoculation using fluorescent microscopy. Once inoculation was confirmed, conifers were grown in nitrogen-free or nitrogen-low soils and solutions to compare growth and measure nitrogen levels in plant tissues between inoculated and uninoculated conifers. If these endophytes prove to be beneficial for increasing conifer growth, they could be used as a sustainable alternative to chemical fertilizers and in turn, aid in the mitigation of climate change on forestry ecosystems and the environment.

In addition to having massive environmental and public health impacts, the livestock sector of the farming industry raises important ethical questions about the humane treatment of workers and animals. One response to the industrialized animal food system has been a push to eat ethically sourced meat from family farms. In theory, this allows the consumer to trace back their food to the source, interact with the people handling their food, and support a more humane treatment of animals. Eating locally sourced meat is a part of the larger “local food movement”, or campaign to eat foods from within 400 miles. However, there has been backlash against the local food movement, with critics arguing that the movement itself has its own set of problems. This study aimed to achieve two goals. First, I critically examined the local meat movement to determine whether or not I believed “local” food was a viable solution to the problems that exist within industrial agriculture. Second, I aimed to raise public awareness about family-farmed meat and the broader local food movement. To accomplish this task, I conducted interviews and reviewed the current literature about food issues. I interviewed chefs from local restaurants that serve family-farmed meat to gain a better understanding of their motivations. I also read primary literature, magazine articles, newspaper articles, and books related to the local food movement. I concluded that the local food movement, in addition to “local meat”, offers many benefits that industrial agriculture does not. However, as pointed out by many critics, the movement does not fully address the wide array of environmental, economic, and ethical concerns within the agriculture industry. To summarize my conclusions and raise awareness about the subject, I created a booklet about local food. The problems in the food industry will not be solved overnight and the first step is to generate an educated public that is willing to make necessary changes.

 This project presents the development of a new process flow in the Washington Nanofabrication Facility to create a magnetically neutral Nuclear Magnetic Resonance (NMR) test device for use at the Department of Energy (DOE) Pacific Northwest National Labs (PNNL). At PNNL, within the Environmental Molecular Sciences Laboratory, the devices are used to characterize environmental contaminants, like radioactive isotopes, using NMR spectroscopy. The devices being developed are to be superior in uniformity and layering a stack of thick copper sandwich with a precisely deposited aluminum layer. The project includes computer-aided design (CAD) and fabrication of a precision mask set for fine resolution that limits irregularities in the test structure that could adversely impact the NMR measurement. The fabrication process starts with an electroplating seed, photolithography, and thick electroplating of copper. Following plating, chemical mechanical polishing is performed to yield an atomically smooth surface. After this, a precision thickness aluminum layer, that cannot be conventionally electroplated, is deposited and patterned via a lift-off process. This project will also be a primer for more industry-focused capabilities for the WNF with eventual development of through-silicon vias (TSVs) for research applications.

The world’s future energy needs will almost certainly require extensive use of renewable sources of energy. Organic photovoltaics are a particularly lucrative source of energy due to their cheap materials and ease of production compared to inorganic solar cells. However, organic photovoltaics (OPVs) currently suffer several drawbacks: they have an efficiency of, at most, around 10% and they are unstable – they may begin to degrade within five to seven years. This project aims to alleviate these defects by gaining a greater understanding of the chemical interaction between interfaces within the solar cell. This project is a comprehensive study of the interactions between phenyl-C₆₁-butyric acid methyl ester (PCBM) and calcium. PCBM is an extensively researched molecule which acts as an electron acceptor in OPV devices. PCBM is typically paired with an electron donor such as poly-(3-hexylthiophene) in a working device, and calcium has energetic properties which allow for very good electron transfer at the cathode of such a device. We use adsorption micro-calorimetry under ultra-high vacuum conditions to study the reaction at the interface between calcium and PCBM, and surface analytical techniques to determine growth modes and chemical binding of calcium and PCBM. These experiments will elucidate the mechanisms of interface formation of this understudied but important OPV system.

Computer face recognition and identification is an important problem with numerous applications in intelligent user interfaces, security, and accessibility. For example, identification of faces can be used for access to restricted areas, authentication without keyboards, and personalized interfaces. Traditional algorithms that solve this problem identify faces individually or use co-occurrence information for a given set of people (For example, person X is often photographed with person Y). However, such systems have many errors, and cannot generalize well to people the system has not seen together previously. In contrast, humans are much better at this because we have "common sense." We can look at a photograph and recognize that people tend to photograph with family, friends, and co-workers. We can further guess why the photograph (birthday, conference) was taken, and even where (person's house, a certain park). This abstract knowledge is very difficult for computer algorithms to learn because there are not sets of these "rules" available explicitly. In our work, we tackle this problem using structured relational graphs like Freebase, a large online graph of billions of facts about the world. Given many specific examples of people who are in photographs together and data about those photographs, we can see what connects these people on graphs like Freebase, and generalize to the "common sense" rules that are notoriously difficult to learn. Then, given a new image and possible candidates for identification of people in it, we can compute the most likely set of correct identifications. We can also hypothesize unknown faces to our existing faces. This allows us to learn, on-the-fly, a new recognizer for that specific person. Finally, by knowing relationships behind photograph subjects, we can discover and generate useful contextual information about the photograph, such as location and possible reason for the photograph. Broadly, this means that computer systems can more accurately identify meaning behind photographs; a problem that has been historically hard for computers to accomplish.

Barth Syndrome is a rare X-linked genetic disorder that can cause cardiac myopathy, muscle weakness, fatigue, immune dysfunction, and childhood mortality. Like many such diseases, Barth Syndrome is the product of a mutation encoding for a single protein, Tafazzin, a phospholipid-lysophospholipidtransacylase found primarily in cardiac and skeletal muscle, where it plays an integral role in modifying cardiolipin, a component of the mitochondria, or energy production organelles of the body. When Tafazzin, and consequently the modified form of cardiolipin are absent, the function of the mitochondrialelectron transport chain, the primary pathway by which the body converts food into useable energy, is reduced. We hope to rescue defective cardiolipin modification through Tafazzin protein therapy and learn more about tafazzin structure and function. To this end we used X-Ray Crystallography to obtain a three-dimensional electron density map corresponding to the diffraction pattern of the protein, based on the distance and angle between each atom. The determination of structural properties illuminated binding sites and chemical interactions in both functional and mutant Tafazzin. This was supplemented by the synthesis of enzymatically active and stable human and mouse Tafazzin using E. coli (BL21(DE3)pLysS). Overexpression of Tafazzin results in relatively pure inclusion bodies which we we isolated through protein metal affinity chromatography. We produced several protein coding variants of Tafazzin in order to study the enzymatic activity of different mutants. Understanding of structure-activity relationships in Tafazzin will direct future work in Barth Syndrome treatment by facilitating  in vivo studies of Tafazzin protein delivery.

Entamoeba histolytica is a water-born pathogen that is estimated to cause 100,000 deaths annually in developing countries. The disease is prevalent especially in tropical areas with poor sanitary conditions, and is treatable with appropriate antimicrobial medication. Therefore, detection of the pathogen is vital in diagnosis. We developed a sensitive electrochemical assay utilizing novel yeast-scFv detection probes targeted at E. histolytica parasite antigens in stool samples. I have previously tested the assay in solution (buffer and stool dilution) with several antigens and proved sensitivity. This project is a stability study of the assay assembled on the electrodes. I tested factors including temperature, pH, humidity, pressure, and light sensitivity to determine the optimal conditions for long-term storage and transport, as well as the limit that one factor can be pushed while maintaining sensitivity. The significance of this project is to maximize the assay’s shelf life and thus to minimize the cost of manufacture and transportation of the assembled product. Consequently, it will benefit clinicians and patients in poor countries where the disease is prevalent, as a broader population of people around the globe.

We examined the impacts of fire on herbaceous community composition within the Abies lasiocarpa (subalpine fir) vegetation zone in the northern Cascade Range of Washington, USA. We used plant functional groups, classified based on growth form, to investigate how the ecological role and physiological niches of plants in burned and unburned subalpine parkland may differ, and how the pre-fire setting (closed forest, open forest, alpine woodland, krumholtz, alpine treeless vegetation) interacts with the severity of fire to affect the abundance of plant functional groups. We addressed these questions using field data collected in 2012, 17 years after the Butte Creek fire. We sampled 68 plots in the subalpine parkland ecotone, within or near the burn perimeter, in sites ranging from closed forest to treeless alpine vegetation (1800 m to 2250 m asl). We found significantly more cushion plants in unburned sites than burned sites. Sites that burned with high and very high severity had significantly more graminoids, herbaceous perennials, and tall shrubs. Likewise, closed forest and open forests had significantly more graminoids in burned than unburned areas. Although high intra-site variability and a lack of pre-fire data limit our inferences, our results support the hypothesis that fire influences the composition and function of herbaceous alpine and subalpine vegetation. Climate change may increase area burned and frequency of fire in high-elevation ecosystems, so our results serve as a starting point for future inquiry into the effects of fire on herbaceous vegetation in subalpine parkland.

As mobile touch screen devices become increasingly ubiquitous, they are also becoming more accessible to the visually impaired. Someone who is blind traditionally enters text on his or her phone by using a screen reader and the default keyboard layout. However, this method is slow and it is difficult to correct mistakes as one is typing. We developed Perkinput, a nonvisual text entry method that uses the 6-bit Braille character encoding. In Perkinput, instead of relying on the device’s voice over system to announce each letter that is pressed, this input is based solely on the Braille keyboard. The user simultaneously presses down with his or her fingers that correspond to the dots for the character in Braille he or she wanted to enter. Once entered, the text can be sent in a text message, an email, or simply copied to the clipboard for later use in other applications. Results have shown that the Perkinput method is more than twice as fast as using the default keyboard layout for the blind. I have implemented this method into an iOS application that is currently deployed on the iTunes Store. I have instrumented this application in order to gain insight into how people are using the program outside of a lab setting. This will help us improve Perkinput and make it more accessible to the blind community. Perkinput aims to make text entry easier and efficient for people who cannot look at their screen.

Cognitive rehabilitation has been shown to be effective on cancer survivors after cancer treatment. Some evidence suggests that older adults may be more adversely impacted by chemotherapy. The purpose of this study was to examine whether age may be a moderating factor on cognitive rehabilitation effectiveness among cancer survivors. Participants were survivors 6 months or more post active treatment, and were randomly assigned to an immediate treatment group (treatment) or a wait list (control). A battery of cognitive tests and questionnaires, both computerized and by hand, were given before and after a seven-week group-based memory skills intervention, which was specifically designed to improve memory and thinking abilities. 45 subjects completed all measures and were divided by age into “middle age” (21-60 yrs.; N=23) with mean age of 51.3 years and “older adults” (60+ yrs.; N=22) with a mean age of 67.1 years. Results indicated that both middle age and older adults improved over time for immediate and delayed verbal recall (list learning task) (p < .05). Significant improvement for sustained attention (digit symbol) (p < .05) and working memory (digit span) (p < .05), however, was observed in the middle age group only.There was a significant interaction effect of F (1,43) = 5.83 for the digit span total, with only the middle age group showing an improvement. Our results suggest that there was some difference in improvement of cognitive thinking and memory between the two age groups. Although both groups improved on measures of verbal memory only the younger adults improved on measures of attention. Our results may help guide future cognitive rehabilitation programs to target specific areas of cognition that may be more likely to respond to treatment. This will help patients have a more accurate expectation for cognitive rehabilitation goals.

Cardiac arrest is a serious and often life-threatening event that can result in devastating outcomes. Targeted temperature management, or TTM, is a treatment utilized after cardiac arrest which improves patient outcomes. Determining the best treatment temperature and combination of sedative and paralytic medications, whose purpose is to slow the brain’s metabolism and maintain brain tissue oxygenation, will improve this beneficial treatment for future patients. The purpose of this study was to compare the time to ‘reawakening’, defined as the patient following commands, between post-cardiac arrest patients who received different combinations of paralytic and sedative medications and who were treated at 33°C or 36°C during TTM. Time to ‘reawakening’ after TTM is a critical factor in this patient population in terms of each patient's prognosis. The sub-aims of this study were to determine if time to ‘reawakening’ was influenced by: 1) cooling patients to the target temperature of only 36°C, and 2) the patient’s temperature when signs of shivering occurred during the TTM protocol. We were interested in studying these two aims because cooling patients to the target temperature of 36 degrees is expected to decrease the incidence of shivering and therefore less sedative and paralytic will be needed. Additionally, knowing what patient temperatures increase the incidence of shivering will better direct the dosing and timing of medications. Data for this study was retrieved through a retrospective chart review of 200 patients who received TTM treatment at Harborview Medical Center. Once we determine which treatment temperature and medication protocol results in the fastest reawakening and least amount of shivering, the results may influence future TTM protocols and could influence the care that future post-cardiac arrest patients receive. TTM could change in a way which ensures patients have the best possible outcomes after experiencing a traumatic event like cardiac arrest.

The process of directing auditory attention was first analyzed by Colin Cherry in 1953 and classically dubbed “the cocktail party problem”, referring to how an individual is able to follow one conversation at a noisy gathering. In this project I will explore how eye-gaze position may direct auditory attention and thus affect detection thresholds of sounds in noise. Behavioral studies researching this issue have shown that it is easier to segregate a target sound when it comes from a different location than the masking noise, a phenomenon known as the masking level difference (MLD). This can be observed as the improvement in detection threshold of a tone in noise when they are separated versus when they are collocated. However, these past studies did not control for eye gaze. Recent electrophysiological studies have found that the inferior colliculus, a critical auditory midbrain nucleus, shows visual and oculomotor responses. The behavioral significance of these interactions to human listeners is not yet well understood, but suggests that the oculomotor system may be able to modulate auditory processing. My project focuses on eye-gaze and the MLD. I will test whether subjects have better detection thresholds when their eye-gaze is directed towards the location of the tone versus towards the location of the noise. The experiment is generally laid out in two blocks. During the first block of trials, the subject will have visual primers directing eye-gaze; in the second block, auditory primers that do not direct eye-gaze will be used. Control trials that give uninformative visual and auditory cues will also be tested. I have promising preliminary data shows that trials using informative auditory cues can improve thresholds over trials with uninformative auditory cues. However, the more noteworthy result this study looks for is the possibility of yet another improvement when eye-gaze is brought into play.

As we move our energy production and consumption economy towards a cleaner, “green” energy paradigm, it has become clear that research into solar energy harvesting is of real world significance. While fundamentally challenging, the capture and storage of solar energy into chemical bonds, such as hydrogen, can be envisioned as a large scale energy solution. In nature, the champion of solar water splitting for energy production and storage is Photosystem I and II (PS I and II). After a photon absorption event, the manganese oxygen evolving center (OEC) in PS II increases its reductive capacity enough to oxidize water into its oxygen and hydrogen constituents. Following the water oxidation reaction, the manganese oxidation state returns to the original to further oxidize additional water molecules. In practice however, it is incredibly difficult to create a regenerative OEC mimic, as high valent Mn is not usually stable. Therefore, our focus is to develop and explore materials which mimic the PS I and II solar water splitting reaction. α-Fe2O3 has shown great promise for the solar water oxidation half reaction. Upon photo-excitation, electrons are collected at the back contact leaving the surface of α-Fe2O3 in an oxidized state, providing a driving force for water oxidation. Additionally, upon introduction of certain catalysts, we can increase the oxidative capacity of α-Fe2O3, and thus improve the overall solar-to-hydrogen efficiency. So far, we’ve observed a significant enhancement in the oxidative efficiency with the use of a certain cobalt catalysts, and we are investigating the use of other metal centered catalysts including: nickel, iridium, silicon, tin, iron, niobium, and titanium. Ideally, we’d like to see these other metal centered catalysts demonstrate a greater increase in solar-to-hydrogen efficiency than our cobalt catalysts. We hope to, one day, apply this technology towards increasing the efficiency of solar powered fuel cells.

All organisms require the pyridine nucleotides NAD(P)(H) to perform various cellular functions, but their role in methylotrophy is not well understood. Methylotrophic organisms are able to use organic substrates without carbon-carbon as a sole source of energy and carbon. In metabolism, pyridine nucleotides provide reducing power for the cell to perform redox reactions in catabolic and anabolic processes. In contrast to energy-limited modes of growth, methylotrophy is predicted to be reducing power-limited as the oxidation of methanol or methylamine is coupled to phosphorylation of ATP and energy production. Furthermore, internal concentrations of NAD(P)(H) are predicted to be saturating so the balance between catabolic and anabolic charge ratios may be of greater importance than the relative concentrations. Consistent with these predictions, fluctuations in NADPH levels are observed during as an immediate response when the facultative methylotroph Methylobacterium extorquens AM1 is transitioned from multi- to single-carbon substrates. Known mechanisms to recycle pyridine nucleotides include the decoupling of NAD(P)H using NAD(P) kinases/phosphatases or transhydrogenases and the use of enzymes with dual specificity or isoenzymes. We propose a transhydrogenation cycle between the EMC and PHB pathway to be an important mechanism to maintain redox homeostasis in M. extorquens AM1. To demonstrate this, I will use select OMIC approaches to analyze wild-type strains during succinate to methanol transitions and compare wild type to an mtdB mutant, a strain without a functional methylene-H₄MPT dehydrogenase B (MtdB). In this mutant, the assimilatory blocks on methanol and methylamine are presumably due to the disruption of a key pyridine-nucleotide producing step. These results will provide increased understanding of the mechanisms used to balance production with consumption of redox equivalents and re-distribute carbon flux in M. extorquens AM1. Insight from this work has implications for engineering methylotrophs for biotechnological applications including the production of biofuels and value-added chemicals.

Macrophage have roles in promoting and resolving inflammatory responses in the lung, and they do this in part by their ability to polarize into M1 or M2 cells depending on environmental signals. Lipopolysaccharide (LPS), a microbial initiator of inflammation, activates macrophages to the M1 polarized state, which drives the inflammatory response. M2 cells, which can be induced by cytokines IL4 and IL13, are involved in promoting wound repair responses and are considered reparative cells. Macrophages maintain their plasticity, and in vivo, pulmonary macrophages switch from M1 to M2 states during pneumonia resolution. In this project, we sought to determine the functional consequences of this macrophage repolarization using an in vitro model. We hypothesized that repolarization of LPS-treated macrophages (M1 cells) to M2 cells would alter their responsiveness to further LPS challenge. We cultured bone-marrow derived macrophages from mice. We exposed the macrophages sequentially to LPS, IL4 and IL13 or media alone, and then rechallenged with LPS. We harvested cells for RNA for analysis of gene expression of M1 and M2 markers using qRT-PCR. We found that repolarization of macrophages toward M2 states potentiated the immunoparalysis seen in LPS-treated macrophages. These results suggest that M2 cells may dampen macrophage inflammatory gene expression to promote resolution of inflammation but may also contribute to increased susceptibility to recurrent infection.

Cells and organisms must adapt to a variety of conditions to ensure survival. These adaptations have led to the evolution of a set of genetic stress response pathways, many of which have co-evolved to affect longevity. One of these pathways is the hypoxic response pathway, which is important for the response to diminished oxygen and is controlled primarily by the hypoxia inducible factor-1 (HIF-1). HIF-1 is a highly conserved transcription factor whose stabilization promotes increased lifespan and healthspan in C. elegans. Despite HIF-1 being highly conserved, similar stabilization of HIF-1 in humans leads to von Hippel-Lindau (VHL) syndrome, a disease characterized by increased tumor formation. Although the effects of global activation of the hypoxic response are well-documented, the tissue specificity and important downstream targets necessary for benefits or disease remain largely uncharacterized. My project focuses on the proteins downstream of HIF-1 that act to affect health and longevity. Work in our lab shows that multiple genes downstream of HIF-1 in C. elegans are sufficient to increase worm longevity when overexpressed in the absence of HIF-1 stabilization. One of these downstream genes that modulate worm aging is flavin-containing monooxygenase 2 (FMO-2). FMO-2 is a phase 1 xenobiotic metabolizing enzyme that may also play a role in protein homeostasis. We have found that the expression of FMO-2 either ubiquitously or in the intestine and head excretory glands of C. elegans increases lifespan and healthspan. My project involves further characterizing the FMO-2 protein by testing its role in resistance to stress and improving healthspan. In addition, I am contributing to epistasis experiments to determine whether FMO-2 acts in any other aging-related pathways. In characterizing FMO-2 in this way, my project seeks to better understand this protein in the context of health and longevity.

In spite of rapid advances in detection and treatment, cancer remains one of the most deadly diseases, killing over 1500 Americans each day. The ability of cancer cells to metastasize is the driving force behind the high mortality. For this reason, early detection and improved treatment technologies are crucial to enhance the survival rate of patients. The progression of cancer pathology begins with the accumulation of DNA mutation that transforms a normal cell into a proliferating tumor cell. This unregulated cell growth is governed by disruption in reactive oxygen species, iron homeostasis, and up-regulation of ribonucelotide reductase. Studies show chelators have significant antiproliferative properties reducing tumor growth through iron chelation. Unfortunately, they also bind to iron in normal cells, therefore, there is a great need to develop chelators that bind specifically to iron in cancer cells to prevent cell proliferation. Our study focuses on the design of a new class of site-directed iron chelators using gold nanoparticles (AuNPs) as targeted molecular carriers. These AuNPs are capped with thiolate ligands that are modified using EDC/NHS coupling chemistry for attachment of chelators and targeting moieties that recognize cancer cell surfaces. We will present the synthesis strategy and characterization methods used for confirming the presence of chelators on the AuNP surface. These methods include ultraviolet-visible, fluorescence, infrared, and dynamic light scattering spectroscopies. Metal binding studies demonstrating iron uptake will also be presented.

Tuberculosis is the second-leading cause of death due to a single pathogen, Mycobacterium tuberculosis (Mtb), with an estimated two billion people currently infected. Drug-resistant strains have emerged that are unmanageable even with combination drug therapies. Therefore, the development of novel drugs aimed at previously untargeted biochemical pathways in Mtb is of utmost importance. Among potential candidates is a newly identified proteasomal degradation pathway termed pupylation. In this system, proteins in Mtb damaged by the reactive oxygen and nitrogen species of the host’s immune response are tagged with the small prokaryotic ubiquitin-like protein (Pup) and shuttled to the 20S proteasome for degradation. Pup-mediated degradation allows Mtb to recycle key cellular components and remain virulent. Our interest is to study the two key enzymes required for pupylation: the proteasome accessory factor A (PafA) and the deamidase of Pup (Dop), which is also involved in the reverse pathway known as depupylation where Pup is removed from the substrate. Our interest is to characterize the mechanisms and substrate scopes of both Dop and PafA to facilitate the design of novel inhibitors. We synthesized and employed a model fluorescent probe that mimics the site of pupylation on a target protein to study the rates of the pupylation and depupylation enzymatic reactions. Since the Pup-probe conjugate is a substrate for Dop we also studied depupylation. We anticipated Dop to be the faster enzyme since it had fewer substrates to bind than PafA and our studies have revealed that Dop is much faster. Though the purpose of depupylation is currently unclear, our investigation has determined the relative kinetics of these opposing enzymatic pathways. The quicker kinetics of depupylation indicates pupylation of proteins also serves as a post-translational regulator rather than existing exclusively for degradative purposes.

Arsenic (As) is a human toxin and carcinogen that can be ingested by drinking contaminated groundwater or by eating crops that are irrigated with contaminated water. In the past decade, studies have shown that arsenic contamination poses a threat to global public health. Despite the health risks, few countries regulate the arsenic content of food. With this research project, my mentor and I hope to obtain information that will be valuable for the formation of appropriate regulations about arsenic content in rice. We have chosen rice because it is a staple of the diet in Bangladesh, which is currently experiencing an epidemic of arsenic poisoning. Specifically, we are studying how the diffusion of dissolved oxygen into the root-zone of rice plants affects arsenic accumulation in rice grains. We have been able to visualize these concentrations in real time using two-dimensional optical oxygen sensors (optodes) placed on the root zone. We have also measured the concentration of arsenic in the rice grains. Oxygen oxidizes dissolved iron(II) into solid-phase iron (III), which can scavenge arsenic out of solution and reduce plant exposure to arsenic. Twelve rice plants were studied, half grown in ambient temperatures and half in elevated temperatures to simulate a warmer climate. We chose to grow half the plants in elevated temperatures because many of the world’s rice producing regions are projected to experience warmer climates in the futures. Our data have provided valuable information about how dissolved oxygen concentrations near the roots of rice plants change temporally and spatially. Additionally, we've found that when grown in elevated soil temperatures, rice plants grow larger and have proportionately larger root systems. These larger plants require more water, and thus pull more arsenic from the soil porewater toward their root system, which ultimately results in greater uptake of arsenic and accumulation of arsenic in plant tissues.

Understanding how people communicate during disasters is important for creating systems to support this communication. Twitter is commonly used to broadcast information from the ground and to organize support during times of need. During the 2010 Gulf Oil Spill, Twitter was utilized for spreading information, sharing firsthand observations, and to voice concern about the situation. Through building a series of classifiers to detect emotion and sentiment, the distribution of emotion during the Gulf Oil Spill can be analyzed and its propagation compared against released information and corresponding events. I contribute a series of emotion classifiers trained from 4,000 tweets with preliminary results of accuracy between 51% and 70%. These classifiers are used to analyze the emotional impact of events, such as Obama’s Oval Office Address. A broader implication of this project includes analysis of other disaster datasets through utilizing our open-source visualization and classifiers.

 Although we normally place the academic, institutional gallery or museum exhibition space in a separate domain from the virtual space social sites like Facebook, Tumblr, and Pinterest provide, I argue that the motivations that determine our uses of both spaces are the same. Using the writings of theorists such as Foucault and Baudrillard, and the history of Cabinets of Curiosities, I look critically at the creation of online profiles (primarily related to Facebook, but also found in other popular social sites) and traditional exhibitions spaces (for instance, the galleries of the Museum of Modern Art). I examine the logic of categorization and the intended impact this will have on viewers, comparing the nature of collecting and the curatorial impulse to display, showing that ideas surrounding collection function in both spaces. Through this I illustrate that a curatorial impulse is present in each, revolving around some sense of identity, although there are clear differences in ability to create context and exhibition time frames among other things. This will demonstrate that such spaces provide similar outlets for engrained human behaviors that mediate our interaction with and understanding of not only culture, but social interactions and even personal identity. In effect, I show that these spaces are much more closely related than they have previously been given credit for, and that certain social networking sites might even be the next logical stage in the continual development and progression of our understanding of collecting and exhibiting.

The world is filled with gendered images that shape and echo society’s ideas on what is feminine, reinforce the ideologies about how a woman should look and act, and are hidden under the guise of humor. This humor shames women who step out of their place, and encourages them to step back into the gender “box” defined by the culture industry. In the modern, mediated world, this plays out in advertising as well as “humorous” pictures, called Internet memes, which are shared by individuals on social media websites. The term meme first appeared in “The Selfish Gene” by Richard Dawkins in 1976. He defines a meme as “small cultural unites analogous to genes, which spread from person to person by imitation” (as cited in Shifman, 2009, p. 1). An Internet meme, therefore, is an idea that spreads (or “goes viral”) through imitation in cyberspace. To understand how women are invited into certain feminine subjectivities, this paper performs a semiotic analysis of memes related to gender “codes” that define what is feminine through the use of humor. Building off the work of Erving Goffman(1969, 1979), Sut Jhally (2009) defines the traits (passive, childlike, and submissive) that are commonly associated with being feminine, and argues that these traits are considered subordinate to masculine traits. The Internet memes examined in this paper are selected from popular social media websites and deal with body image, behavior, dress, and a woman’s “place.” The role of advertising in society has been discussed extensively; however, there is less discussion of the role of Internet memes related to gender. This presentation fills that gap and brings to the conversation a view on a form of ideological reinforcement that is unique and increasingly widespread.

Four displaced ethnic groups populate Kyakitanga village in central Uganda. The community collaborates with small NGOs and local ministries to address conditions of “underdevelopment” and at a August 2012 workshop, participants expressed a priority of increasing community wisdom concerning “modern” food production. In a place-based subsistence community, such wisdom may be framed as Traditional Ecological Knowledge (TEK). This research explores Kyakitangan TEK as it already exists, aims to identify the local food sovereignty development model, and the implications of that model for social equity and environmental sustainability. These questions were explored through a participatory action research study involving local-led grand tours, object-and-walking probe interviews, alternative talking circles, and pile sorts. Findings indicate Kyakitangans possess tremendous TEK concerning foraging, agriculture, and pastoralism. This TEK is tied to ethnicity, as different foodways function as survival strategies specific to each group’s ancestral history and environment. Contrary to the 2012 workshop’s “modernist” atmosphere, Kyakitangans actually advocate a development model utilizing knowledge and resources already existent within the community. Implications pose questions about how ethnic groups collaborate moving forward since different foodways entail different land-shaping impacts and the livelihoods of each group are linked to each other. These dynamics are contextualized in the region’s political economic and cultural history, because the question of food insecurity is a by-product of peoples’ physical separation from native lands. This is exacerbated by structural violence and historical trauma of post-independence regimes and neoliberal globalization. Open-endedness in methodology allowed for the surfacing of important issues surrounding gender and reproductive control. Overall, the Kyakitangan context presents alternative models of development which privilege local knowledge. This type of model in broader development discourse is currently marginal, co-opted, or nonexistent.

Japan appears to be one of the most gender-segregated countries remaining in the developed world, and as such, appears to the Western eye to be a society built on gender difference. This segregation is reinforced by several elements of Japanese society, two of which being the gendered nature of the Japanese language and roles men and women are pressured to play in society, by society itself.   It would be tempting to describe these roles as 'traditional', but these 'traditional roles' are actually practices that came in with the process of modernization. Despite this, Japanese society contains elements that work against the overarching binary narrative of gender. Gender non-conforming people are visible and, to a certain degree, frequent within Japan’s social landscape. On the surface, this would give Japan an appearance of duality; of rigidness and flexibility when it comes to gender identity. Perhaps the most extreme example of a gender non-conforming person is a transgendered person. If we consider the lives of transgendered people in Japan, does Japan prove to be as accepting of such people as it appears?  These questions are explored by reading scholarly research by both Western and Japanese scholars, first-hand narrations found online via the buzzing world of social networking and video sharing services, and documentary films centered on modern-day Japan.  What I hope to reveal in my research is a complex web of gender representations, performance, and cultural tolerance/intolerance within what remains a very rigid social structure.

Equality Mainstreaming and Intersectionality are concepts that are subject to different kinds of interpretations and are often adopted to a certain extend in public policy all over the world. Equality mainstreaming refers to the widespread incorporation of ant-discrimination into public policy. Intersectionality refers to the concept that personhood is not a monolithic experience of gender, race or another factor, but rather a combination of all these factors that affect an individual’s experience. My research focuses on the incorporation of these concepts into Brazilian public policy. Brazil is a country that is still struggling with various kinds of discrimination, namely racism and sexism, but the creation of Ministries and government agencies dedicated to fighting discrimination have ushered in innovating legislation. Through a discourse analysis of government materials, primarily public policy briefs, task forces, interviews of the Ministers involved in these public polices and informative pamphlets about public policies, I was able to distinguish between explicit and implicit discourses within Brazilian equality oriented public policy. Explicitly the Brazilian government articulates an all-encompassing equality movement. However I have encountered implicit discourses that show that gender and race concerns are at the forefront of equality oriented policies and the concept of intersectionality almost exclusively represents Afro-Brazilian women. Although this detracts attention from other vulnerable populations, Brazil’s unique history of discrimination against Afro-Brazilians and women calls for this increased consideration.

  This paper asks how weaving and traditional clothing are used as a means of resistance within the Maya Movement of Guatemala. Although historical evidence and cultural traditions confirm the use of backstrap looms before the arrival of the Spanish, the use of traditional clothing and weaving techniques are often maligned as vestiges of colonial repression and backwardness by the dominant Ladino culture of Guatemala. Those who choose to wear traditional Mayan clothing face discrimination, stereotyping, and hostility. Mayan clothing denotes the sex, age, marital status, regional affiliation, and village of origin of the wearer through the use of different weaving techniques, designs, style, and color. As a result of their inability to find work or navigate through the Ladino culture outside of their communities, most Mayan men have adopted Western style clothing. As such, women have been tasked with sustaining the culture within their communities through the art of weaving and the clothing it produces. The weavers are able to incorporate their cultural history and ideas into the cloth they create. Weaving, clothing, and Mayan identity cannot be easily separated. Due to the high visibility, traditional meaning, and customizable nature of Mayan weaving, clothing has been adapted by Mayan resistance movements as a means of cultural resistance. I argue that weaving and traditional clothing are being used by the Maya Movement to inspire pride and connection with traditional culture as a means to reassert Mayan heritage within Guatemala. Not only has the popularity and use of traditional Mayan clothing grown in recent years, but the meanings and traditions continue to grow and change along with the culture. Research for this paper is based on a mix of primary and secondary sources including scholarly analyses of Mayan resistance movements, history of weaving techniques and clothing, blogs, international newspaper articles, and documentaries.

This project explores a grassroots organic food movement in Chengdu, China through a case study of an organic co-op in Anlong Village in the outskirts of the city. Due to its small size and inadequacy of official organic certification standards, the Anlong farmers refer to their produce “ecological” vegetables, as opposed to “organic” vegetables. Since the farms converted to “ecological” production in 2006, small, but growing number of Chengdu urbanites has turned to Anlong farms for a source of healthy and fresh organic produce while other affluent urban consumers enjoy organic products at metropolitan supermarkets. Given that the produce of these farms in Anlong is not officially certified, and given the fact that the cost of the produce is still on par with certified organic produce, why are they gaining popularity among urban customers who could easily buy similar produce at a shopping center nearby? Based on analyses of semi-structured interviews I conducted with Anlong farmers and customers and field observation, I argue that the consumption of Anlong products carries significance that extends beyond actual processes of production to suggest a symbolic purity untainted by the government association. In China, due to a series of reports on counterfeit food labels and the limited success of government regulations on food industry, government certified labels hardly evince moral attributes of organic foods, but generate negative interpretations. Anlong’s produce absent an official label shuns such suspicion and validates honest values that the organic agriculture elicits. 

Incidents of violence against women in Italy have been consistently on the rise for the past decade. Only this past summer did the Italian government ratify a Council of Europe treaty making violence against women illegal. Yet, prior to this past decade, Italy has had a history of women’s rights activism and feminism that reached its peak in the 1970s and 1980s. During the peak of the women’s rights movement in Italy, women succeeded in passing divorce law and overturning laws that forced them to marry their rapists, in addition to eliminating sentencing statutes that penalized murderers with no more than three years imprisonment if their victims were deemed to be adulteresses. Yet, the great strides of the 1970s toward Italian gender equality have slowed exponentially in the 40 years since. My research is seeking to understand what has hindered the Italian women’s movement in the last forty years and if these hindrances are connected to the increase in violence against women and sexism within the country. I draw on qualitative interviews with Italian women, scholarly essays and books on Italian feminism, media, government and the Italian women’s movement, as well as autoethnography from my own study abroad programs in Italy. I consider how the cultural traditions and the autocratic media mogul and former Prime Minister Silvio Berlusconi have encumbered the movement for Italian women’s rights in Italy. My project attempts to draw attention to the disparities in the rights and treatment of Italian women from the late half of the 20th century to today.

“Permaculture” refers to a design approach for creating resilient and integrated systems using principles and tools grounded in ecology. Permaculture design is usually applied to agriculture and food production, but recent permaculture-based projects in economics, urban planning, and governance have emerged as alternative applications of this design approach. However, there are few examples of applying permaculture to education systems; a gap in the general knowledge of the permaculture community and the field of education reform that I hope to help fill. This study examines how the ecological principles demonstrated in permaculture design can be used to address the problems that standardization has produced in K-12 public education in the United States. Standardization has emerged as the dominant approach of education reform, most visibly manifested in No Child Left Behind and the Common Core State Standards initiative (U.S. Department of Education, National Governors Association). However, as recent research has shown, standardization as a paradigm in education causes more harm than good for students, teachers, and schools (Robinson, Ken). Through research in educational philosophy, curriculum and instruction, development and learning, and systems theory, I justify how permaculture design principles can be applied to educational systems. From this I develop an original synthesis of education theory and permaculture principles as an alternative to standardization. My argument is presented in a three-part paper: a review of the critiques of standardization as a dominant paradigm for education; explanation of the twelve permaculture principles in the context of education; and a demonstration of applying these principles in the re-imagining of American schooling.

 When students study abroad, some find it harder than others to integrate within the culture of their host country. Scholars have created models mapping students’ process of acculturation over time. A stage of crisis, or “culture shock,” is identified as a fundamental phase of the abroad experience. This study investigates four elements influencing students’ ability to overcome this crisis stage: students’ interaction with the host community, confidence using the host language, previous experience traveling abroad, and the disparity between students’ home and host culture. This study aims to determine the role communication plays in the navigation of the crisis phase; I do so specifically by examining these four elements, and how the connection between these factors and student adjustment manifests. Past studies have flagged these elements as major predictors of a students’ achieved assimilation while abroad. This study aims to determine if and how a connection exists between these factors and students’ cultural adjustment. The qualitative method of semi-structured interviews was used to collect responses via Skype from four students in Quito, Ecuador and four students in Rome, Italy during their Winter quarter abroad. The eight students' narratives provide insight on the modern impact of the four key elements on intercultural development—and an understanding of why: why some students overcome the crisis phase and achieve healthy cultural adjustment while others remain culturally stagnant for the entirety of their exchange.

In cultures where children have regular contact with same aged peers during the first years of life, peer sociability plays a fundamental role at early stages. Currently, the only social emotional skills children are exposed to are those that they learn alongside academic learning. Additional social emotional skills are often not taught. These skills include social awareness, self-awareness, dealing with ambiguous situations, adapting to social situations, managing stress, and learning how to learn (Lindsay, 2013). It is especially challenging for English language learners (ELL), who have the additional task of learning multiple ways of communication, including both language and cultural rules. Research on social emotional learning has shown that when children are able to deal with, manage, and maneuver the social and emotional landscapes of their lives, their capacities to learn and function socially on all levels improve (Lindsay, 2013). This study seeks to compare the social emotional outcomes for ELL students with their native English-speaking peers in classroom settings. The study includes literature review and data analysis on data collected by Second Step Study researchers at the College of Education from approximately 5,000 children across 40 schools in 5 districts. One of the teacher-reported measurements used in the study is the Devereux Student Strengths Assessment (DESSA), a behavioral rating scale that measures skills associated with social-emotional competence, resilience, and academic success. The other teacher-reported measurement is the Strengths and Difficulties Questionnaire (SDQ), a behavioral screening questionnaire which measures children’s strengths and difficulties related to behavioral characteristics. Results from the measures will be compared between native English speakers and ELL students. The aim of this study is to increase teachers’ awareness of the importance of social emotional development of English language learners.

What began as a practical question for our large, interdisciplinary organization has taken on scholarly weight given active debate in the literature regarding professionalization of peer/student writing tutors -- as studies on beneficial tutoring outcomes turn away from difficult-to-assess outcomes for writers toward outcomes for tutors. What this literature says about professionalization, however, seemed troubling in that it is predicated on the assumption that tutors will necessarily go on to be educators -- patently untrue for this interdisciplinary group of student employees. Existing concepts of professionalism are also (troublingly) opposed to our center’s non-expert, collaborative approach to tutoring. Our team currently investigates two questions: (1) How might our tutors’ actual professional objectives/career paths differ from those imagined for them?  (2) How might tutors’ sense of appropriate professional practice diverge from other visions of professionalism in the context our non-directive center? Phase I of this investigation involved interviews with 50+ active tutors using a standard form we developed; tutors described both short-term goals for tutoring practice and longer-term career goals. Phase II will involve capstone interviews asking graduating tutors to report on specific experiences of professional development (transferable skills). In interviews to-date, tutors openly identified widely-varied short-term and long-term goals. Contradicting existing scholarship, we found that even tutors uninterested in writing-instruction-related careers articulated complex connections between their tutoring work and their future careers. Further challenging commonplace assumptions, interviewees articulated tutoring goals aligned in sophisticated ways with this writing center’s approach, suggesting that thoughtful tutor professionalization need not involve training in more expert, directive tutoring practice but instead can be flexibly self-directed in alignment with tutors’ own professional goals. Our methods and findings have important implications for those interested in: employee motivation and deep learning; grounded planning and programming that avoid administrative assumptions; richer professional development for students across fields.

The world faces mounting environmental problems and environmentally-minded citizens are necessary to help find solutions. Education is a critical component in shaping future citizens who think globally and act locally. However, the current system of education often disconnects concepts and ideas from geographic locations. The purpose of this study was to investigate the impact of place-based lesson plans on student learning, and to explore whether or not place-based examples help to stimulate environmental stewardship and engagement in school and local issues. To this end, I conducted qualitative interviews with local high school science teachers and performed a meta-analysis of current literature about place-based education and methods for environmental education. In addition to this research, I developed several place-based biology lesson plans for Alaskan high schools. The results thus far support the idea that place-based examples are effective tools for teaching science, and do in fact help facilitate student engagement in the classroom. Through the process of creating the lesson plans, I found that a real life example contextualized the lessons and gave them greater meaning. The use of place-based examples within science education has the potential to stimulate a connection between students and local environments. It is essential that today’s students, as future citizens and decision makers, have an established connection with the environment to prepare them for creating positive change in the world.

Are attempts by the United States to improve student educational outcomes by increasing classroom spending worth the effort? How successful have these efforts been in improving the outcomes of public school students? Using data from 2002 to 2010, which includes expenditures allocated to classroom costs per pupil and averaged freshmen graduation rates, I investigate the impact of increased federal spending on students, more specifically on expenditures allocated directly to classroom spending as opposed to administrative and operations expenditures. Major classroom costs include teacher salaries, supplies, special education programs, textbooks, and other various minor costs. After controlling for factors that may influence educational outcomes such as parental educational attainment, years of teacher experience, and teacher-to-pupil ratios in the classroom, my results show that when a higher percentage of a state’s expenditures on education are spent on costs directly related to the classroom, students succeed at a higher rate as measured by graduation rates.

The research I have conducted focused on evaluating the effect and performance of various types of ferromagnetic material on Radio Frequency isolation. RF isolation is crucial for the optimal delivery and operation of wireless energy transfer to electronic devices ranging from consumer electronics to implanted medical devices. The material was tested in a typical configuration of implanted parts for the Free-Range Resonant Electrical Energy Delivery project. The configuration was then tested for weight, cost, size, Coil Q factor and efficiency over distance. The various ferromagnetic materials were then compared with each other and to various control setups. The results show that in comparison to the control setups, all of the ferromagnetic materials performed better with respects to efficiency over distance. Further evaluation of efficiency and size determined that ferromagnetic materials IRLG5 and IBF10 had the best efficiencies and coil Q factor. Depending on whether an application requires a lower cost/ higher production or smaller size/weight, either ferromagnetic material IRLG5 or IBF10 will be chosen for use. The research has profound implications on the development of more efficient and stable wirelessly powered electronics such as tablets, smart watches, cell phones, etc. For example, ferromagnetic material can be used to isolate radio frequency signals emanating from a wireless receive coil from the metal housing of a cell phone/tablet or in ensuring that the implanted circuitry controlling a neuro-prosthetic is not disrupted by RF noise.

Myopia, or nearsightedness, is the only cause among the top five causes of blindness in the world that remains completely untreatable and has reached epidemic proportions. Characterized by a thin choroid layer and increased axial eye length, myopia develops when the eye continues to grow so that images of objects seen in the distance become in focus in front of the retina rather than at the retina itself. This study aims to find a means to prevent the progression of myopia from its onset during early childhood, and help the eye return to a length closer to emmetropia, a process in which the eye stops growing when objects are in maximal focus at most distances. Specifically, we developed and tested a prototype blurry lens (eye glasses) to see if it could serve as a potential means to decrease the axial length of the eye, increase the thickness of the choroid layer, and ultimately help prevent the progression of myopia. Subjects were required to wear glasses in which the left eye was UV irradiated with a blurry pattern and the right eye served as a self-regulated control. The choroid layer was measured in pre and post-treatment sessions using OCT (optical coherence tomography) imaging of the retina and choroid via a Rowland RETImap OCT machine and standard regression analyses. Results show a significant increase in the choroidal thickness and decrease in the axial length of the left eye compared to the control and baseline measurements, along with a change in retinal morphology. Our study suggests that the eye experiences signals that modulate its axial length in response to myopic stress. Thus, the blurred lenses were an effective means to prevent the progression of myopia because they brought about similar changes in axial length and choroidal thickness changes as seen in emmetropic conditions.

Supplementation with “good bacteria” (probiotics) has been promoted for various health conditions. Marketing and over-the-counter (OTC) access has also led to increased availability of these agents. Safety of probiotic supplementation for individuals with weakened immune systems, such as bone marrow transplant (BMT) recipients, is unknown. Since these patients are at increased risk for developing bloodstream infections (bacteremia), we sought to evaluate the incidence and outcome of bacteremia due to organisms common to OTC probiotic supplements in a cohort of BMT recipients. We reviewed all blood culture results from BMT recipients transplanted at the Fred Hutchinson Cancer Research Center in Seattle, WA between 2002-2011. Patients with at least one positive blood culture for common probiotic organisms (Lactobacillus species, Bifidobacterium species, or Streptococcus thermophilus) within one-year post-BMT were considered cases for this study. Patients with evidence of pre-transplant bacteremia from these agents were excluded. Data were collected from center databases, which contain archived laboratory data, patient demographics, and clinical summaries. We found that a total of 18/3799 (0.47%) BMT recipients developed bacteremia with Lactobacillus species within one-year post-HCT; no events with Bifidobacterium or S. thermophilus were identified. Positive blood cultures for Lactobacillus species occurred at a median of 84 days post-transplant (IQR: 34, 127), but the majority (n=12 [67%]) occurred within the first 100-days. The overall incidence rate of Lactobacillus bacteremia was 1.54 cases per 100,000 patient-days, but the highest incidence occurred during the first 100-days post-transplant (3.31 cases per 100,000 patient-days). Incidence did not deviate significantly by year of transplant. Most patients had a singular positive blood culture (n=17 [94%]); one patient developed prolonged bacteremia (30 days). No Lactobacillus-attributed mortality was observed during follow-up. We concluded that organisms frequently incorporated in available OTC probiotic supplements are infrequent causes of bacteremia after BMT. Studies evaluating the use of probiotics among these high-risk patients are needed.

Traumatic injuries can often lead to massive blood loss. When a patient’s mean blood pressure (MAP) drops due to bleeding, the standard protocol is to administer intravenous fluids with the goal of restoring normal blood pressure. However, increasing blood pressure may also increase the rate of bleeding, causing even more overall blood loss. There is no current evidence to show that MAP correlates directly to the velocity of blood exiting a wound. We hypothesize that a direct relationship exists between blood pressure and velocity of bleeding. We test this hypothesis using direct ultrasound imaging of a bleeding artery in a swine model of trauma. N=8 anesthetized pigs underwent bleeding from a femoral artery punch wound and were simultaneously given intravenous fluids to increase blood pressure and cardiac output. Ultrasound measurements of blood flow velocity from a femoral artery punch wound were taken at regular intervals. We found that MAP did not correlate with the bleeding velocity at the wound (R=0.27. p=0.068). However, cardiac output was significantly correlated with bleeding velocity (R=0.37, p=0.012). MAP and cardiac output were then stratified into normal or low categories based on their median values for the entire group. Average bleeding velocity was not different when MAP was low compared to when it was normal (normal=255.7 cm/s vs. 221.8 cm/s, p=0.18). However, bleeding velocity was significantly decreased when cardiac output was low vs. normal (normal=253.6 cm/s vs. 196.1 cm/s, p=0.01).This data does not support our hypothesis of a direct relationship between MAP and wound bleeding velocity. Alternatively, cardiac output as a measurement of blood flow, rather than pressure, may better reflect bleeding after injury and may be a more-useful guide for fluid resuscitation during active bleeding.

Lead zirconate titanate (PZT) is a piezoelectric material commonly used in sensors and actuators. The goal of this project is to formulate a process of producing PZT nanoparticles to be imbedded in a polymer ink that could be used in a 3D printer. The particles must be small enough to make a homogenous colloidal ink that will not obstruct the printer nozzle. My project analyzes the synthesis procedure in detail and how it can affect the piezoelectric properties and morphology of the product. Hydrothermal synthesis was performed at 200 degrees Celsius to control particle size, agglomeration, and chemistry of the PZT particles. It was found that the previous method of synthesis produced particles on the order of 1 to 3 microns in size. In order to reduce particle size below 1 micron I have proposed to reduce time spent growing the particles at elevated temperatures.

Although patients diagnosed with pulmonary hypertension (PHTN) are at a higher risk for postoperative complications, studies to date have not distinguished whether this applies equally to all PHTN patients, nor have they determined the severity of postoperative complications should they occur. Pre-operative screenings take place in the form of echocardiograms (ECHO), which are accurate but rather expensive. This study, one of the largest pulmonary hypertension studies to date, is headed by Dr. Gail Van Norman, director of the Pre-Anesthesia Clinic at the University of Washington Medical Center (UWMC). We look to explore the correlation between the severity of pre-existing pulmonary hypertension and post-operative complications. This study additionally explores the correlation between metabolic equivalences (METS) and PHTN, which could yield a new, more cost-effective method of screening for the disease.
As research interns on this project, we abstract data from the medical records of eligible patients at UWMC. We focus on patients who have undergone surgery with moderate to severe PHTN, and collect pre-op and post-op data using hospital affiliated databases. Patients with these specific conditions are believed to have <4 METS and are at an elevated risk for post-operative complications. Should these hypotheses be proven correct, the results of this study will benefit both patients and providers, reducing the cost of screening, as well as improving patient care by allowing doctors to better manage the disease in the peri- and postoperative settings, reducing both complication and mortality rates.
 

Childhood caries, also known as tooth decay, is on the rise worldwide and has increased the demand for portable technologies that can quickly and accurately detect and diagnose early stage carious lesions. These lesions, if identified at an early stage, can be reversed with remineralization treatments, education, and improvements in home care. A multi-modal optical prototype was previously developed at the University of Washington’s Human Photonics Laboratory for the detection and diagnosis of early occlusal caries demineralization in vivo. The device uses a 405-nm laser as an illumination source to obtain high-resolution images that can better guide the operator to identify a suspicious enamel region. When the suspicious region is located, the device can be switched to perform dual laser fluorescence spectroscopy using 405-nm and 532-nm laser excitations generating an auto-fluorescence (AF) ratio with the main goal of diagnosing the start of early caries. Recent research had the device test in vivo on 7 children’s teeth with clinically diagnosed carious, non-cavitated lesions. Using the 405-nm scanned light source, lesion depth was visually estimated by the clinician. Within a month, the clinician assessed the maximum drill depth after the tooth had been drilled and the spectroscopic data acquired. The researcher and clinicians were masked from previous measurements in a blinded study protocol. Using the drill depth as the gold standard, the researcher assessed the preliminary results of the 7 patients to see if the severity or depth of the lesion could be compared quantitatively by using the device. Preliminary results indicate that the quantitative AF spectrum of a tooth correlates with the severity of demineralization as assessed by the clinician after drilling.

Mall walking provides a safe environment for older adults to engage in physical activity and participate in a social community. Walking has many health benefits, a few of the benefits include reducing the risk of falls, reducing falls, increasing quality of life, increasing cardiac function, a low cost activity, and increasing mobility. However, there is limited data on mall walking as an activity and the benefits it provides for older adults. The purpose of this study is to understand the benefits of mall walking from the perspective of mall walking leaders and mall walking participants. The results of this study will be used to create an Evidence-informed Mall Walking Program Resource Guide which will be used to help start potential programs and to benefit programs already in place. I will utilize a structured interview guide created by the research team and conduct phone or in-person interviews with three mall or non-mall walking leaders and three mall or non-mall walking participants in the Seattle area. The interview guide includes items about how participants learned about the mall walking program, what they like and dislike about mall walking, transportation to and from the mall, how long they have been a part of this walking community, what makes this community successful, and the age and ethnic diversity of the mall walkers. To date, I have completed three interviews of mall walking participants and one interview of a mall program leader. From these interviews I learned mall walking is a great health promoting activity enjoyed by older adults. Participants and leaders alike have found a social community and are able to engage physically, mentally, and psychosocially while walking. By the time of the poster presentation I will have additional data to present on two other mall walking participants and three mall walking leaders.

Pollination is often facilitated by insects and animals guided to flowers by a mixture of volatile compounds: the components of floral scent. As an attractive cue for pollinators, scent emission may be highly regulated so that its release coincides with the activity of its preferred pollinator. This relationship is particuarly evident in the release of benzenoid volatiles by Petunia, through which it attracts its pollinator, the nocturnal hawk moth (Sphingidae). Though Petunia release volatile benzenoid compounds nocturnally through a process mediated by the circadian clock, the molecular mechanisms responsible remain uncharacterised. We hypothesise that the transcription of the ODORANT1 (ODO1) gene in Petunia, which encodes a key transcription factor involved in regulation of volatile benzenoid synthesis, is regulated by an ortholog of the highly conserved Arabidopsis core-clock genes - CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)/LATE ELONGATED HYPOCOTYL (LHY) - in Petunia. To investigate this potential association, we have characterised the Petunia ortholog of LHY (PhLHY) and will look to analyse its influence on volatile benzenoid production. We aim to understand the interaction between the PhLHY protein and ODO1, and will investigate the intracellular localisation of PhLHY as well as the tissue specific expression of ODO1. We anticipate that PhLHY will influence the rhythmic oscillation of the circadian clock, as well as influence the synthesis and emission of floral volatiles by directly regulating ODO1. In elucidating the mechanisms by which the circadian clock control scent emission, we will likely be able to generate floral varieties that display significant chronological shifts in their daily scent emmision regimes. 

The plant genus Thalictrum (meadow-rues) contains numerous shifts in ploidy number, ranging from diploid (2x) in the earliest diverging species to 24x in recently derived species. Polyploidy can result from a whole genome duplication event within an individual (autopolyploidy) or following a hybridization event (allopolyploidy). The rates and evolutionary consequences of these two mechanisms of polyploidy are currently under debate, and I am therefore attempting to estimate their relative roles within this genus using a phylogenetic approach. The current Thalictrum phylogeny relies on chloroplast DNA and nuclear ribosomal regions, which tend to underestimate the role of hybridization due to maternal inheritance and concerted evolution patterns, respectively. I am using single-copy nuclear genes to uncover potential hybridization signals in Thalictrum’s evolutionary history. This information will be used to compare the relative numbers of autopolyploids and allopolyploids in the genus. I hypothesize that allopolyploidy played a larger role in shaping the diversity of this genus, due to its potential for differential survival and reproduction as a consequence of immediate, novel gene expression in hybrid progeny. Furthermore, this analysis will estimate the hybrid origins of particular alleles within a species. In the future, this information will be applied to questions on the evolution of genes involved in flower development after whole genome duplications.

In the model organism Arabidopsis thaliana, the B-class genes of flower development are responsible for proper formation of petals and stamens in a flower. Studies in Thalictrum thalictroides, a representative of the sister lineage to all other eudicots provides insight into the ancestral function of the B-class genes. Unlike Arabidopsis, the flowers of T. thalictroides lack petals, and yet the sepals are large and colored similar to petals. Here, we investigate the function of B-class proteins in T. thalictroides through the study of the horticultural mutant known as ‘Betty Blake.’ The ‘Betty Blake’ mutant phenotype consists of many non-petaloid (green) sepals and carpels but no stamens. We have previously shown reduced expression of most B class genes in ‘Betty Blake’, yet we were not able to find any meaningful mutations in these loci. Therefore, we hypothesize that an upstream regulator of the B-class genes may be mutated in ‘Betty Blake’. UNUSUAL FLORAL ORGAN (UFO) is a known upstream regulator of the B-class genes and is therefore a logical candidate. We hypothesize that the UFO mutation is the cause of the B class phenotype in ‘Betty Blake.’ The investigation of B-class function in this non-core eudicot has provided us with insight into the evolution of gene regulatory networks affecting ectopic petaloidy and stamen identity that we will continue to pursue in future experiments.

Stickseed (Hackelia) is a genus of plants comprised of about forty species distributed primarily across the dry forests and mountains of interior western North America. This study seeks to build an evolutionary tree of Hackelia using DNA sequences from both the chloroplast and nuclear genomes. Preliminary analyses suggest possible conclusions regarding their geographic history and the evolution of their fruit characteristics. While it is currently unclear where the genus started, it appears there were two major migrations; one started in Washington and moved southward into Mexico, while another started in the Midwest and traveled southwest into California, Mexico, and Peru. Consequently, California is a diversity hotspot for this genus. Hackelia, like the rest of its family, has a fruit that divides into four nutlets at maturity. However, Hackelia is unique from other genera; it possesses elaborate prickles on its nutlets. These prickles can be described using two physical traits: whether the prickles along the border of the nutlet (marginal prickles) fuse to form a cup-like border, and if there additional prickles between the marginal prickles (intramarginal prickles). Our results suggest that ancestral species had nutlets with a cup-like border of marginal prickles and obvious intramarginal prickles. Most species of the genus have since lost the cup-like border, resulting in free marginal prickles. On the other hand, while most species have retained their intramarginal prickles, at least three lineages spread across the tree have lost them. This study will help us understand how plants have diversified in western North America, as well as how physical traits can be evolutionarily variable or conservative. 

Every plant needs Nitrogen to grow. Nitrogen is usually given through synthetic fertilizer which is expensive and causes a lot of environmental problems. Synthetic fertilizer is bad for the envieronment not only it need a lot of fossil fuel to make the high temperature and pressure condition for Nitrogen reaction, but also excess Fertilizer will bring blooming algae to the surround ponds, which will make the organism in the water die out because lack of Oxygen since the sunshine cannot get through algae and help underwater plants to photosynthesis. Since previous research in the lab showed that endophytes isolated from Willow and Poplar trees can promote growth of crops such as pepper, tomatoes, and sweet corn under low nitrogen conditions, we hope that Endophyte can reduce or completely substitute synthetic fertilizer of other commercial plants, such as corn. Endophytes (microbes living inside plants) can produce phytohormones and provide fixed nitrogen for plants. My research focuses on corn, a bioenergy crop species typically grown with large inputs of fertilizer. I screened ten commercial varieties of corn and compared the growth of endophyte inoculated plants with the uninoculated controls, in low nitrogen soil. In one variety of corn there was increased biomass in the inoculated plants compared to the controls. Currently I am testing which isolate is responsible for the plant growth promotion. These findings will have a great impact on commercial production of corn in a sustainable way.

 The first floral mutations ever documented, double flowers have been prized for centuries for their beauty. The double mutant variants ‘Shoaf’s Double’ and ‘Cameo’ are found in Thalictrum thalictroides, a member of the buttercup family. The purpose of this research is to determine the genetic mutation underlying this desirable phenotype. We predicted that a mutation in a C-class floral organ identity gene would cause the homeotic transformation (conversion of one organ type to another) of stamens and carpels to petalloid sepals in this species. C-class genes are also involved in floral determinacy, the termination of floral organ growth, which is why double flowers appear to have a second flower nested inside the first. As expected, the expression of the C-class gene ThtAG1 was greatly reduced in our mutants. Finding no changes in the coding region from wild type, we further investigated the entire genomic locus, where we found evidence of the action of a transposable element in both mutants. In ‘Shoaf’s Double’ a Mutator Like Element (MuLE) has inserted itself into a regulatory intron of TthAG1, disrupting its function. In ‘Cameo’ a ‘footprint’ at the exact same place in the sequence indicates that the same element may have jumped out, deleting a section of the intron. We hypothesize that the double phenotype in ‘Cameo’ is likely due to the accumulation of mutations before the MuLE jumped out. Since the MuLE’s transposase is expressed in ‘Shoaf’s Double’ (but not in wildtype), these results illustrate the rare case of an autonomous transposable element underlying a regulatory mutation that results in a visible phenotype. We hope that our work will provide insight into the genetic basis for the double phenotype of popular commercial flowers such as roses, camellias and carnations.

Pollination syndrome refers to suites of floral traits that influence biotic or abiotic vectors transporting pollen from one flower to another. These traits typically include flower color, position, shape, size, scent and reward. Scent is a major component of pollination syndrome, as the volatile organic compounds (VOCs) that compose “scent” often attract pollinators or deter predators. The genus Thalictrum in the Ranunculaceae (buttercup family) includes both insect- and wind-pollinated species, enabling comparisons of the role of scent in floral diversification among recently diverged taxa with distinct pollination syndromes. To characterize floral scent, we identified and compared the bouquet of VOCs emitted by insect- and wind-pollination species, as well as by floral vs. vegetative tissue. Scent was collected from tissue samples by traps in a filtered air system, then eluted and analyzed with gas chromatography mass spectrometry. Quantitation and emission rate were calculated to generate floral bouquets. Electroantennograms were performed on selected compounds to examine pollinator response. Focusing on eleven species representative of the two pollination syndromes and spanning the Thalictrum phylogeny, we identified ten key compounds of which five are deterrents against herbivory, two are pollinator attractants, and three have unknown functions. Given that these scent profiles consist primarily of defensive rather than attractive compounds, we hypothesize that repeated transitions from insect- to wind-pollination in Thalictrum may be due to the breakdown of an ancestrally weak insect pollination syndrome. Moreover, scent bouquets appear to follow phylogenetic patterns more so than pollination mode. The variation in distribution of VOCs across species in a phylogenetic framework allows us to test evolutionary patterns of compound co-option during evolution.

 For thousands of years, the Chengdu Plain in Sichuan, China has been characterized by the linpan settlement pattern, a system where the family compound is located amongst the lands they farm as well as thickets of bamboo and trees, creating a patchwork of farmland and human life across the Plain. A recent Chinese government program entitled “A New Socialist Countryside” threatens this unique pattern through nationwide reconsolidation of rural households into concentrated villages. This style of living undoubtedly places a new ecological strain on the Chengdu Plain, an effect believed to be more serious due to the concentration of environmental pollutants compared to the former dispersed pattern of waste flows. I sampled water in an area with both new and old settlement patterns, measuring the levels of nitrates, phosphates, ammonia and chemical oxygen demand. Through a comparative study of the results, initial findings point towards supporting the hypothesis that consolidated housing is more ecologically harmful than the linpan. The consolidation of the Chengdu Plain presents the exciting opportunity to capture and record the effects of modernization within rural farmland.

 Cultivation of annual species of goosefoot (Chenopodium/Amaranthus spp.) for food was practiced by the ethnographic Southern Paiute groups in southern Utah (Kelly 1932-1934, Fowler 1995). Yet our understanding of the archaeological use of these plants in the northern Colorado Plateau is limited. This study documents use of these important species over time and examines evidence for Chenopodium berlandieri management at North Creek Shelter (NCS), an archaeological site in the Escalante river valley of southern Utah. NCS contains a rich macrobotanical sequence spanning the early Holocene to Proto-historic times, of which Chenopodium spp. fruits and seeds form the largest dietary component. Here preliminary results are presented on the use of Chenopodium spp. by examining 1) change in Chenopodium spp. abundance throughout the Holocene archaeological record and 2) concurrent morphological changes in the fruit margins and/or seed coats of C. berlandieri. To my knowledge, this is the first attempt to evaluate archaeological evidence for management of Chenopodium spp. in the northern Colorado Plateau. Findings of this study provide a local history of Chenopodium spp. use and an archaeological context for ethnographic data on wild plant horticulture in the region.

The U.S. food system has been de-localized from decades of industrialization and globalization. There have been many environmental and social repercussions, including loss of farmland, devaluing of farmers, loss of food sovereignty, and a consumer disconnect. How can we support a strong local food economy and shorten the distance from farm to table? Organizations and agencies play a key role in facilitating the increasingly popular local food movement in the Puget Sound region. The purpose of this project was to analyze the capacity and affinity of each group, and investigate how a communication network could lead to greater success. My internship with American Farmland Trust researched these groups and organized them based on focal area. This served as a preliminary effort to map the overarching shared goals of the movement. Supplemental research was conducted through an extensive review of published literature and interviews. The results suggest that defining the “center” of the movement through a formal communication network and regional planning will increase overall success. Additionally, there are severe gaps in the local food supply chain and excessive emphasis in other areas that could be reallocated to better serve the broader community. A local food system with strong coverage from farm to table is imperative for the future of sustainability and food security in the region, and similar efforts elsewhere could serve to strengthen food systems nationwide.

Wetlands provide critical habitat and ecosystem services in high-elevation semiarid environments such as Yellowstone National Park. Climate change is shifting patterns of precipitation and consequently the hydrological regimes of wetlands. To better understand the influence of precipitation on wetland hydrology, I used high-resolution remote sensing data to compare changes in wetland area to local precipitation patterns. Wetlands are expected to shrink in drought years relative to normal precipitation years. Initially, wetland areas were delineated with RADAR (Radio Detection And Ranging) and aerial photographs through object-based image analysis – using spatial and spectral information to analyze images. Then, wetland pixels were extracted from Landsat satellite imagery over several years of normal and drought conditions. Finally, wetland area was matched against local precipitation data. Based on previous methods and similar analyses, the wetlands were expected to have variable and local hydrological patterns. By identifying wetlands that are vulnerable to climatic change, park managers can best identify wetlands that need attention for conservation. RADAR, as a widely available dataset, can also be used across a broader scope than other actively sensed data. Expanding the applications of RADAR-based wetland delineation across a wider area will reveal further nuances of RADAR’s potential for ecological research and management.

Urban restoration is a burgeoning movement in our increasingly urbanized but ecologically degraded living places. The success of an urban restoration project is usually measured against only ecological principles, such as complex vegetation structure, increasing biodiversity, and improved ecosystem services. The narrow set of performance criteria ignores social factors contributing to successful urban restoration practice, which potentially hinders further improvements on urban restoration projects. The study aims to examine impacts of participants’ cultural awareness and availability of long-term stewardship resources, as two examples of social factors on the outcome of urban restoration projects and also to create representative social indicators that can be adopted in urban restoration evaluations. To understand these two social variables, I conducted surveys on restoration volunteers and interviews with project managers/volunteer coordinators of local restoration groups, as well as extensive literature reviews. My internship as the volunteer coordinator for the Kincaid Ravine restoration project also provided first-hand experience working with volunteers on urban forest restoration. Findings suggest that two factors of urban ecological restoration projects selected can affect the outcome of restoration projects through various means therefore need to be incorporated into restoration evaluations. My research serves as a case study of two specific social factors; further research on the impacts of other social variables on the outcome of urban restoration projects is required. Moreover, it lays the ground for further efforts in developing social indicators to evaluate urban restoration practice, which is a necessary step towards promoting comprehensive urban ecological restoration.

The influence of environmental oxygen level on the development and histological characteristics of mammalian bones has only recently begun to be explored by the biological sciences. By utilizing bone histology as the methodology, this research works to identify and analyze the influence of environmental atmospheric hypoxia on the characteristics of the microstructure of mammalian femora. This study focuses on wild caught animals of the order Lagomorpha and the family Sciuridae, provided by the Burke Museum of Natural History. Data was collected on bone wall thickness and a wide variety of mechanical properties in order observe any possible patterns and trends as the amount of oxygen in the environment decreases. The comparison is intra-species, and each animal is collected from a discrete elevational point and compared to animals from higher or lower discrete elevations. By using paleontological preparation methods we can strengthen our ability to make assumptions through evolutionary history and into the fossil record. The implications of this research are possible inferences about the universal effects of elevation, and as a proxy, oxygen level, on the growth and mechanical properties of mammalian bone. Because oxygen is believed to be a macroevolutionary pressure, identifying the physical manifestations of oxygen’s influence within bones would further our broad level understanding of how an organism’s habitat and environment influences the mammalian body.

Through the design and implementation of a 2-credit focus group course, my project investigates how theory can be used to understand the impacts of body dissatisfaction. Widely recognized in research as a "normative discontent" for women and a growing number of men, body image dissatisfaction impacts individuals and communities on a daily basis. While many programs and organizations work to improve body image, I have found a lack of theory and criticism of current discourses within body-positive campaigns.Because of this, the goal of these focus groups is to inspire activism and change in the way that society views different bodies through a theoretical lens. The discussion-based, peer-facilitated group of 8-12 students discusses bodies in various contexts: feminism, biopolitics, normalization, medicalization, identity, oppression politics, and sociocultural norms. The results of these focus groups included awareness of the issue of body dissatisfaction and individual activism projects that challenge social, cultural, and political norms surrounding bodies.This project demonstrates an effective way of bringing issues of bodies, identity, and oppression to the community sphere to promote understanding and activism.

Women with a history of sexual victimization often have higher rates of alcohol consumption and sexual risk-taking than women with no history of sexual victimization. One explanation proposed for these associations is the self-medication hypothesis which says that women with sexual victimization histories engage in drinking and risky sexual behavior to cope with distress or to increase positive affect. Although popular wisdom and research studies link alcohol and sexual risk-taking, sexual assault victims often experience difficulty with sexual intimacy. Specific motives to consume alcohol in order to cope with or further enhance sexual behaviors have not been examined. Further, it is not known how a history of sexual assault would impact sex-related drinking motives and whether these motives would mediate the association between sexual assault history and both alcohol consumption and risky sexual behavior. We are currently in the process of recruiting undergraduate women through the University of Washington Psychology Department’s Online Subject Participation Pool. Women are asked to complete a forty-five minute online survey about their drinking patterns, history of sexual experiences and sexual assault, and endorsements of sex-related drinking motives. Data collection will be complete at the end of winter quarter, after which we will conduct mediation analyses using bootstrapping to test our hypotheses that sex-related drinking motives will mediate the relationship between a history of sexual victimization and both alcohol consumption and sexual risk-taking. We expect that these motives will partially mediate the relationships between a history of sexual victimization and both alcohol consumption and sexual risk-taking. Results will help inform effective interventions tailored toward survivors of sexual assault.

Our objective was to further explore the facial feedback hypothesis. This theory, that facial movements (efference) can influence one’s emotional experience, has historically been studied using either positive or negative stimuli. We used neutral stimuli to see if facial efference is affective in influencing emotion in the absence of stimuli that prompt an emotional response. Participants were randomly assigned to one of three conditions created by holding a chopstick – forced smile (chopstick between teeth), forced frown (chopstick between lips), or neutral (chopstick in nondominant hand). Participants were then shown 5 neutral images, each for 6 seconds, via PowerPoint. They then rated the images on 11-point Likert scales, from 0 (extreme sadness) to 10 (extreme happiness), indicating what emotion the image was expressing. Results showed no statistically significant difference between those whose facial expressions were manipulated into smiles and those who had neutral or frowning facial expressions. A deeper understanding of the relationship between facial expressions and emotions could alter the way in which we explore treatments for both mental and physical health conditions.

Despite a narrowing performance gap between women and men in Science, Technology, Engineering, and Math (STEM) in the U.S., women continue to be less likely to pursue degrees or careers in these fields. One potential explanation for this enduring gap may be tied to gender roles, or beliefs about the proper way women and men should behave. Women and men who violate these gender roles are often considered deviants and encounter social backlash. We proposed that women who choose careers in STEM are perceived to deviate from gender norms more than those who simply do well in STEM fields. In the current study, female and male students rated how typical and desirable it is for women to perform well in math and to choose a math-related career. Similar questions were asked about English, a contrasting field not dominated by men. We predicted participants would believe that it is less desirable and less typical for women to choose math-related careers than for women to perform well in math. We did not expect this pattern to appear for English-related career choice and performance in English. Interventions designed to increase women’s participation in STEM fields, therefore, may need to shift from addressing performance to addressing pressures imposed upon women to forsake STEM careers.

In the United States, eating disorders affect nearly 10% of the population and have the highest mortality rate of any mental illness. Among at-risk populations, female athletes involved in aesthetic sports, including dance, are the most likely to develop an eating disorder. High incidence and widespread prevalence of eating disorders among dancers is often interpreted as a desire to craft a body required to achieve peak artistic and athletic performance. Previously conducted studies on numerous populations of dancers reveal that body dissatisfaction, heightened sensory awareness, and trained perfectionism are contributing factors to eating disorder development. Despite commonalities between varying explanatory models of illness, the spectrum of theories pertaining to eating disorder etiology does not adequately represent the lived experiences of the primary investigators and insufficiently addresses the relationship between embodied identity and aesthetic sport. This pilot research project seeks to challenge the assumption that eating disorders among dancers manifest to maintain a performance-enhancing physique and aims to identify when and how dance can destabilize the identity of certain dancers. Drawing from data generated through an analysis of autobiographical narratives, this research seeks to generate a new theory to comprehensively explain the high prevalence of eating disorders among dancers. This theory will serve as the grounding framework for an extension of this project in which each primary investigator continues research to develop and answer a more pointed question that bridges gaps in existing literature. 

Recent longitudinal studies show a trend of declining emotional health paired with an increased demand for counseling services among college students. It has been proposed that this population faces difficulties in regulating emotions, especially in the face of challenges that are new and unique to them. In the clinical field, mindfulness practice is gaining evidence as a way to increase individuals' self-awareness, acceptance and present moment attention – qualities that have robust evidence of being beneficial for the effective regulation of emotions. The rationale of this research is that mindfulness practice could potentially increase the capacity for allowing painful emotional experiences and thus reduce maladaptive automatic responses to stressors (i.e. denying or suppressing negative emotions). The main aim of this study is to explore whether Dialectical Behavior Therapy (DBT) mindfulness skills, which are six distinct skills designed to cultivate the different components of mindfulness in everyday life, can be efficacious at reducing difficulties in emotion regulation and increasing mindfulness in a non-clinical population of college students. In addition, since few studies have evaluated the feasibility and acceptability of mindfulness-based interventions in college settings, this study fills in the gap by evaluating feasibility and acceptability using specified, testable criteria, and by exploring an alternative method of instruction: using audio recordings of DBT mindfulness practice. The study design is a between-subjects randomized controlled trial comparing an intervention group which will receive a two-week mindfulness training, with a non-intervention group which will not receive the intervention. The hypotheses of this study are that the intervention will be 1) efficacious at increasing mindfulness, 2) reducing anxiety and 3) decreasing emotion dysregulation, will be 4) acceptable in terms of participant retention and opinion toward the intervention, and 5) feasible in terms of adequate participant recruitment and compliance to the intervention protocol.

Women make up only 25% of employees in the technology industry (e.g., computer science careers, information technology, etc.). One possible explanation for this disparity is that hiring decisions are made based off cultural fit, or the perception of similarities between employers and job candidates. The current research investigates whether perceptions of cultural fit are determined in part by the design of workplace environments, and, as a result, whether stereotypical computer science (CS) environments might influence hiring decisions and contribute to the gender disparities in the technology industry. In our study, undergraduates were asked to imagine that they were hiring a job candidate for a technology company. Participants read a description of either a non-stereotypical (e.g., art posters on the wall, etc.) or stereotypical (e.g., Star Trek posters, computer parts, science fiction posters, etc.) CS workplace, and then read the resume of either a male or female job candidate. Participants then answered questions measuring perceived candidate fit into the company environment and hiring intention. We predict that participants who viewed the non-stereotypical CS workplace environment will be more likely to hire the female job candidate than participants who viewed the stereotypical environment. This work would suggest that the design of company environments can prevent non-traditional candidates from being hired, and that encouraging companies to create inclusive, non-stereotypical environments may reduce gender disparities in the technology industry.

The diaries kept by Emma B. Andrews are an undervalued resource for learning about Egyptian culture, history and many turn of the century discoveries. Andrews (1837-1922) was the mistress of Theodore Davis, an archeologist responsible for the excavations in the Valley of the Kings. Andrews accompanied Davis on his trips and kept records of her life in Egypt. Her diaries provide readers with valuable insights into the social, cultural and scientific climate during her years in Egypt. However, these first-hand accounts have gone virtually unnoticed for years. Now, at the University of Washington, undergraduate students have the unique opportunity of working with the Andrews diaries to prepare them for online publication through the Newbook Digital Texts Project. The project allows for inexpensive publication of materials with less difficulty than traditional publication methods. Students work to translate, transcribe, edit and tag large amounts of texts in order to make them universally available on the web. Students researching the diaries have a variety of tasks to complete before the diaries will be ready for publication. During our presentation, we will focus on the process by which we are compiling these writings, which include: transcribing the diaries to an electronic textual format which must be completed and edited twice for accuracy; running the transcriptions through an auto-tagging program to create an online format for the texts; converting the auto-tagged version into XML format and adding new content, including historical research on people mentioned in the diaries; as well as how we hope this will change research in this area in the future. Undergraduates working on The Emma B. Andrews Diary Project are passionate about and committed to making this valuable resource available to the world with the hope that it will become a more widely recognized in the world of academia.

 The JMS Diaries is a collection of 16 original diaries and 30 transcriptions of Joseph Mathia Svoboda's original diaries. As an employee of the Lynch Brothers’ Tigris and Euphrates Steam Navigation Company, Svoboda wrote daily accounts of life on the Euphrates River between 1862 and 1908. These diaries give us insight into valuable cultural and social perspectives about Iraq during the late 19th Century. The NEH-funded Newbook Digital Texts in the Humanities project works to transform such valuable primary source documents into digital texts, making them easily accessible to scholars and the general public. As undergraduate researchers, we work with these primary texts to gain both research and digital archiving skills. Our editorial team works through a five phase process consisting of transcribing, editing, analyzing, encoding and formatting each text. First, we transcribe the texts from the original handwritten documents to plain text digital form, editing and proofreading them. We format the transcriptions in a standardized way for our work-flow manager to then apply a program, written by our technology team, which converts this format into XML-TEI markup (tags). XML (Extensible Markup Language) is a human and machine readable markup language used for encoding documents, which we use in a form standardized by TEI, the Text Encoding Initiative. We convert these to HTML (HyperText Markup Language) for web display and to LaTeX typesetting language for printing. Our history team extracts information from the texts thus produced to write our project "wiki" (the Svobodapedia. Svobodapedia serves as the basic annotation source for the final text, which is made available to readers on our website and as a print-on-demand book. Since beginning the project in September 2012, we have completed two diaries consisting of 400 pages each, and continue to work toward advancing this evolving, ongoing repository of primary source documents.

Translation is a tricky business, especially when concerning religious texts. The problem of effectively communicating a culture's ingrained beliefs to another through a different language has potentially important implications for the original audience. An excellent example of this is the Septuagint, the Ancient Greek translation of the Old Testament Hebrew scriptures. My project focuses on the Greek version of the Hebrew Leviticus, a book which contains vital information about the Hebrew religion and sacrificial procedures. I examined the translation via a verse-by-verse, word-by-word comparison between the Greek and Hebrew versions, in particular noting the translator's accuracy, grammar, and communication of important Hebrew sacrificial terminologies and ideas into the Greek. By such a comparison and investigation of the translator's word usages, it is possible to reconstruct how the original non-Hebrew speaking audience understood and interpreted this text. The significance of this reconstruction lies in the fact that early Christianity used the Septuagint, including Leviticus, as a supportive foundation for its beliefs.

From 1996 until 2012, the rate of cesarean section in the United States has increased almost 63 percent from 797,119 to 1,296,070, reaching an all-time high of 32.9 percent of births at present. Starting in 2009, the American College of Obstetricians and Gynecologists has published guidelines for inducing labor and performing maternal-requested cesarean deliveries. Since 2007 the rate of “home-births” surged, increasing by almost 50 percent to over 35,000 now. Various media such as Ricki Lake’s popular documentary, The Business of Being Born, have questioned the current birthing system in the United States. They call for a return to “traditional” methods of infant delivery, or delivery primarily by midwife. The result is polarization between modern obstetrics and midwifery. Each faction is quick to place blame. This paper refocuses the discussion away from the usual statistical evidence of quantitative recordkeeping and concentrates on the anecdotal and proprietary experiences of ancient medical writers, drawing from often forgotten historical sources. With these in mind, I argue for a more holistic and nuanced approach to determining the correct course of action, bearing in mind the often competing interests of preserving and reducing historically low maternal and infant mortality rates against cultural and traditional concepts and identifiers. To do this I present a brief history of ancient gynecology and obstetrics, offer details into ancient dystocia (difficult labor) and its “remedies” (including embryotomy), and discuss the effect of innovation on dystocia. Finally, I reveal that birth is a far more complicated event than either traditionalists or western medicine recognize or willingly concede, reducing it to either a natural process or a pathological one, respectively.

In recent years, multi-cultural education has become commonplace in policy making and public discourse. While policy makers, educators, parents and community members surely make an earnest effort to seek out and implement standards and practices which fairly address multiple cultures, many children and young adults remain faced with intense challenges in the form of curriculum and social pressure. This study sought to better understand how students in a South Seattle refugee community negotiate identity and achievement while engaged in this American public education system. It also attempts to explore how and why certain aspects of social fabric are maintained and others dismissed in favor of mainstream American culture and the ways which these interact with this system. The common view of multi-cultural education is based on supplementing otherwise standardized curriculum and the creation of certain types of spaces. This process of supplementing pre-existing curriculum is problematic because it leads to the exclusion of increasing numbers of students from both the public education system and future socioeconomic advancement in the United States. While this system deeply affects the lives of children, young adults, parents and community, these issues remain underexplored. Therefore, this study engaged participants from South Seattle’s Yesler Terrace neighborhood to explore these concerns using ethnographic data collected based on a “mosaic approach”, including one-on-one and group participant led interviews, photo-voice, social mapping and participant observation. Using these methods, this study explored two sites within this neighborhood. The first is an after school tutoring program run by Catholic Community Services at the Yesler Terrace Community Center which pairs students one on one with tutors for help outside of the classroom. The second is a first grade classroom at a neighboring elementary school. This study has found that the complexities faced by young people in the United States education system are incredibly individualized experiences. One of the primary goals of this research is to emphasize the importance of these individual experiences over those understood through collective sets of data. It is hoped that this study may open doors for further exploring the lives of individuals in order to better serve them in the public education system. Simultaneously, this study focuses on the anthropological process and the relationships that arise from it, the various roles of anthropologists and the impacts of research.

Maps and their borders, established by states or social norms, are multidimensional tools that play an important role in the way individuals interact with each other and with the space around them. While many borders are meticulously defined and heavily guarded, others are invisible and fluid. For this research I examined the municipal border that runs through the rural community of San Antonio in Madriz, Nicaragua and the problems it presented for the development organization Amigos de las Américas while working in San Antonio during the summer of 2013. For Amigos personnel without prior experience in San Antonio, there was much confusion around the existence and meaning of a border that appeared to be acknowledged only at certain times. I conducted ethnographic research from June – August 2013, observing, interacting with and interviewing community members and Amigos personnel. Based on field notes and recorded interviews, I posit that the border in San Antonio, while known to inhabitants, was silenced by inhabitants and thus made invisible and unknowable to outsiders unfamiliar with San Antonio’s specific history. This silencing of political borders in public performances of belonging such as everyday speech and interactions, I hypothesize, is the result of painful community memories from the most recent civil war in Nicaragua (approximately 1975-1990) whose content does not fit within the nationalist, Sandinista narrative.

North and South Korea have grown increasingly distant culturally, economically, and ideologically since the division of the Korean peninsula in 1948. Although the 1953 armistice agreement ended the Korean War, North-South tensions have persisted. Yet, North Korea often takes on a dual role in the South Korean national imaginary as not just a threat, but also a lost family member. This project asks why the desire for unification, which might have made sense after the Korean war but has become more difficult to achieve, continues to resonate in South Korea such that there is a fixation on unification as the one true solution to North-South tensions. My hypothesis posits an answer in two parts. First, unification is fixated on because national division represents the continuation of a historical pattern demonstrated by Korea’s internal response to the fall of the Ming dynasty, the colonization of Korea by Japan, and the Korean war. In each case, a traumatic event triggered an anxiety over political legitimacy. I examine how the internal response to each crisis was to remove any member of the nation, construed as family, who threatened the legitimacy of the state, to suggest that unification as a continuation of this pattern symbolizes the reconciliation of this divided family. Second, unification continues to resonate because it perpetuates the problem it attempts to resolve -- that is, unification itself reminds of this historical process wherein North Korea continues to be both family and enemy. To this end, I examine recent South Korean television dramas related to unification: first, to observe how the internal response to threats to Korean legitimacy exhibited by Korea in the historical pattern I have outlined constitutes a repeated narrative trope, and second, to analyze the tension between portrayals of North Koreans as both family and enemy in these dramas.

 I will argue that youth homelessness and society are intertwined existences and that we should move beyond narratives of blame and silence in order to find a more unconditional compassion for homeless youths. I will draw from my experiences volunteering at ROOTS Young Adult Shelter over the past three and one-half years, as well as from interviews conducted there during Summer 2013. The material gathered with be analyzed through Timothy Pachirat's (2013) "politics of invisibility" and Donna Haraway's (2007) "becoming with." The narrative we use to structure our opinions of homeless youths, what I call the personal agency narrative, attributes their situations to their laziness, addictiveness, and/or generally disagreeable behavior. However, an examination of the encounter with the homeless youth, which informs the personal agency narrative, reveals that the economic, political, and cultural contexts of youth homelessness, as well as the personal experiences (before and after becoming homeless) of homeless youths are left invisible. This, I believe, is a microcosmic analog to the broader pattern of dealing with youth homelessness as a society, within which we find a conditional compassion--we only are able to empathize with certain homeless youths-- which is tied to the personal agency narrative. I will argue that we should move beyond this conditionality, recognizing the multiple ties that bind society to youth homelessness, and vice versa, to see that society is in a state of becoming with youth homelessness. We therefore have a responsibility to youth homelessness.

My experience on a short term medical mission trip to Guatemala in 2010 left me with an uneasiness. In the face of the experience itself, much post-trip discourse has been centered largely on its value as social capital. The goal of my research is to begin to unravel the complex emotions that take place both at the site of contact in the third-world host country and after returning home. In the face of the ubiquity of short term mission trips, their increasing necessity for professional and educational development, and the vast amount of development literature, this emotional ambiguity is left out. I plan to unpack and illuminate this internal conflict as a way to understand the dual nature of its effects. As an overall objective, I hope that this project invites further discussion about short term volunteer programs and their complexities. Additionally, my research questions ask what evidence of this duality in their own experiences there might be in personal accounts of returnees. Additionally, I plan to address the source, context, and representation of this ambiguity, if it does in fact exist for others, as well. My methods consist of revisiting my experience through an autoethnography and collecting data from the trip. I also include personal narratives from several returned volunteers willing to share their experiences, as well as reviewing much of the academic literature about short term trips. I plan to present emergent broad themes and possible significance for others preparing to go on a short term volunteer trip. These themes include mixed feelings about the trip in the form of a duality, the manner in which relationships formed in the contact zone might affect personal beliefs about the work being done on the trip, and the ambiguity of short term mission trips in terms of their helpfulness or harm.

In the past decade, the importance of the kisspeptin system in reproductive development and its pivotal role in the regulation of the reproductive endocrine axis has become clear. The kisspeptin system has roles in the onset of puberty, the control and regulation of sex steroid production, and regulation of fertility and reproductive function. However, the exact functions of the fish kisspeptin system are not well understood, especially their potential local roles in the gonads. Thus, the goal of my study was to characterize the expression of the kisspeptin genes (kiss1, kiss2, and the receptors kiss1ra and kiss1rb) in the marine teleost Anoplopoma fimbria (sablefish), and explore their possible gonadal functions during sex differentiation (i.e. the formation of the ovaries versus testes) and subsequent gonadal development. Using several molecular techniques, including standard, semi-quantitative, and quantitative PCR, and in situ hybridization (ISH), I revealed that kiss2 and kiss1rb are the most highly expressed of the sablefish kisspeptin genes and both show sexually dimorphic expression in the gonads. Specifically, kiss2 shows significant increases in gonadal expression during ovarian development and the receptor, kiss1rb, exhibits a similar expression profile. Localization of these mRNAs within the sablefish ovary by ISH demonstrated that they are both highly expressed in the cytoplasm of oocytes. Thus, my results suggest that Kiss1rb is the putative receptor for Kiss2 and that Kiss2 plays a role locally in ovarian development, but not sex differentiation. In the future studies, I hope to determine the specific function of the gonadal kisspeptins. If kisspeptins do have a role in early ovarian development, this system could be important to future studies on reproductive dysfunction that occurs in captive female sablefish and some other fishes.

River-dwelling organisms inhabit ecosystems characterized by an assortment of habitats that vary in their nutrient availability, temperature, flow, food resources, and risk to predation. Specific habitats rarely offer the optimal conditions for all of these variables so mobile organisms typically use habitat combinations that offer complementary risks and benefits. I hypothesize that tributary junctions within river networks are particularly profitable for fish because they offer complementary resources across small spatial scales. To test this hypothesis, I conducted snorkel surveys during the heat of the day around nine tributaries divided equally among three spatial segments in a river system in Idaho. Each river segment displayed a varying degree of historically active wildfires and provides a mosaic of heterogeneity in riparian cover and nutrient inputs. Fish were counted downstream and upstream of tributary junctions to obtain a total density per stream reach area. Nitrogen and phosphorous concentrations of incoming tributary water were measured as a proxy of primary productivity in each environment. I also measured water temperature at tributary junctions to quantify potential temperature gradients for fish to use as a thermal refuge. My preliminary results suggest that fish tend to aggregate at the junctions of tributaries that are different in temperature and nutrient status from the main stem. As climate changes, it is important to understand how river networks provide prosperous options for fish. My work will hopefully contribute to efforts designed to prioritize river habitats for protection and restoration.

Variation in river flow results in the expansion and contraction of the main channel, off-channel habitat, and the physical connections between these components. Hence, rivers are characterized by a mosaic of habitat conditions that shift across space and time. Here, we explore how a stream-dwelling fish integrates across spatial and temporal shifts in the availability of thermal and trophic resources. Across multiple years of variable flow, juvenile coho salmon (Oncorhynchus kisutch) have been observed feeding on an ephemeral food source in the cold main channel at night; returning to warm off-channel habitat during the day where their ability to metabolize large meals is greater. We hypothesize that an analogous tracking strategy is used to take advantage of in-situ prey and a shifting distribution of thermally optimal habitat within a single season. During the early summer in southwest Alaska, high lake levels flood the lower reaches of a third-order stream. As summer progresses, lake levels subside and the spatial distribution of thermal resources and connectivity of habitats within the stream is reduced. Preliminary analysis shows that juvenile coho prey heavily on stoneflies, which are concentrated in the cold main channel. Using snorkel surveys, PIT tagging, and gastric lavage, we will monitor changes in the spatial distribution and diet composition of fish over the course of a day and a season. We will compare these observations with changes in the distribution of warm habitat – recorded by i-button temperature loggers – to assess the ability of coho to integrate across shifts in resource availability. We aim to document the frequency of resource tracking in juvenile coho during this early summer period. The results have implications for understanding the importance of environmental complexity to endangered salmon populations and associated species in systems where humans have homogenized floodplains.

 North American river otter (Lontra canadensis) populations are difficult to assess by means such as live-capture; however, non-invasive fecal sampling has become a viable way to assess many aspects of river otter ecology including diet and genetics. L. canadensis uses specific locations called latrines to regularly defecate and scent mark. Fecal samples collected from latrine sites can be used for DNA analysis to distinguish unique individuals and evaluate genetic diversity in a population. Within Possession Sound, minimal research on the abundance and diversity of L. canadensis has been conducted. In fall of 2012, students at the Ocean Research College Academy (ORCA) became the first to study the species in this area. As of fall 2013, two latrine sites of L. canadensis in Possession Sound have been monitored using motion-sensing camera traps. Weekly checks for fresh scat and anal jellies are performed, with 153 samples collected so far. Diet is assessed by identifying prey remains present in feces. Currently, 27 scat samples have gone through DNA extraction, and Polymerase Chain Reaction (PCR) will be performed in the near future using the primers RIO-05, RIO-10, LUT-701, and LUT-801. DNA analysis results will provide information about population size, which is difficult to estimate using camera footage. It is expected that DNA analysis will identify a relatively small number of individuals, as the maximum number of otters simultaneously captured on camera footage is seven. With a small population size, we also expect some amount of genetic interrelatedness in the individuals identified through DNA analysis.

The marine pelagic zone extends from the open ocean basins to the continental shelves. It is a habitat for commercially important wild fish stocks and lesser known deep sea species. Both are crucial to oceanic ecosystems but poorly understood on an ecological level. Current fishery models are specific to harvested species and fail to capture the historical population collapses that occur periodically. The California sardine fishery collapse in 1949 instigated the formation of the California Cooperative Fisheries Investigations (CalCOFI), a coalition of organizations that conducts oceanographic cruises in the Southern California Current. The resulting 65 year time series of hydrographic and fish larva data represents an opportunity to observe and analyze the interactions between different fish species and their environment. This study uses first principles and the CalCOFI data to construct spatially averaged time-dependent population models parametrized for the environmental variables of temperature and dissolved oxygen. These models show bifurcations where variations in environmental parameters lead to extreme fluctuations in larval populations. In the current climate these critical parameter values are only reached under the influence of periodic events such as the Pacific Decadal Oscillation. Future climate projections indicate that environmental parameters will reach critical values over seasonal cycles. This may lead to long term changes in fish species distributions and the structure of globally important ecosystems. These considerations underscore the importance of continued observations and modeling research in the world’s oceans. Both are necessary to understand historical fishery collapses and to prepare for changes in the future climate.

Lontra canadensis, more commonly known as the North American river otter, is a resident in many riparian and coastal ecosystems across the continent. The behaviors of mainland populations – the inhabitants of freshwater lakes and rivers – have been well documented and studied over the years. The impact of tides on coastal and estuarine populations, however, is still largely unknown. Therefore in 2012, members of the Ocean Research College Academy, a dual enrollment program run through Everett Community College, began studying otters in Possession Sound. Preliminary diet analysis of scats retrieved from local latrine sites revealed target prey consisting of mostly saltwater species. Due to the high metabolic rate of otters necessitating large daily food intake and prey availability in estuaries being driven by tidal cycles, it was then hypothesized a correlation existed between tides and the presence of otters in the sound. Specifically, it was predicted otters would be present at high salinity tides when the water chemistry could sustain their prey species. To test this, game cameras were installed at latrine sites on Jetty Island and the Hat Island ferry dock in Everett, Washington. Visits by otters were documented and time stamped, with corresponding tide stages and heights recorded. The majority of visitations occurred at tide heights above 4 feet (81% of visits) with considerably fewer camera captures during low salinity tides. Further research is currently being done into the possible impacts of other local factors on river otter behavior, including spring-neap tidal cycles and river discharge.

Athol Fugard’s play Sizwe Bansi is Dead explores significant racial influences in culture. Fugard writes about the apartheid that controlled South Africa beginning in 1948. The play debuted in 1972 in Cape Town, South Africa. Two years later, it premiered in London, winning “The London Theatre Critics Award” for “Best Play of 1974”. This was quite a win for a piece of work that stemmed from improvisation. Although the narrative topic is that of a “black” issue, the majority of the audience that witnessed the work was white. Now, it is even more fathomable that most of the audience members were middle to upper class white majority. This might have changed the projective interpretive communities that the author and director originally had in mind. In this paper, I propose examining evidence, such as reviews and historical content regarding Sizwe Bansi is Dead to help fully understand which interpretive communities were involved. I will be taking a phenomenological approach: analyzing the audience's interpretation of the play, and answering the question “How are we creating social change?” I also intend on researching other works by the author, to prove that Sizwe Bansi is Dead was not his only attempt at bringing clarity to the terrible events that occurred under the apartheid. By discovering which groups were involved, it will help us gain a deeper understanding for the play, and allow us to gauge the audience’s take on the performance. Did audience members really exit the theatre with a deeper knowledge and sympathy for what happened under the apartheid? Did knowledge of the apartheid change how we see the world? How can we relate the apartheid to other elements of our history, such as the horrific tragedy known as the Holocaust? And finally, can art help our society sympathize and avoid future “apartheids”?

Vaslav Nijinsky, a dance prodigy and the star of Serge Diaghilev’s company Ballets Russes, shocked Europe when his groundbreaking work Le Sacre du Printemps ("The Rite of Spring") premiered in 1913. Choreographed to Igor Stravinsky's musical composition of the same name, Sacre caused a near-riot at its premiere in Paris at the Théâtre des Champs-Élysées and received only six performances. Sacre is an iconic work with enduring legacy even today. Stravinsky's music appears in pop culture phenomena like Disney's Fantasia, and prominent figures in the dance world continue to restage their own versions of Le Sacre to audiences worldwide, but Nijinsky's original steps have not survived. Nobody knows exactly what the original dance looked like. So why do choreographers keep constructing their own versions of Sacre? To answer this question, I researched four different modern versions of the dance: the Joffrey Ballet and Millicent Hodson's 1987 reconstruction of Nijinsky’s original choreography, Pina Bausch's Rite of Spring, Molissa Fenley's State of Darkness, and Jürg Koch's Rite of Spring, which premiered at the University of Washington last winter. I analyzed the sweeping themes apparent in each dance, regardless of the varied choreography, and compared them with what remains of Nijinsky's original ballet and artistic vision. Through interviews, historical archival research, and my own physical embodiment of aspects of each dance, I am making an effort to piece together Sacre's impact and continued allure, positing the history of Le Sacre as anything but a straight line.

Athol Fugard is regarded as one of the most prominent playwrights of South Africa; in a time of racial tensions and political dismay he brought to the stage the turmoil facing the peoples of South Africa. His play, Sizwe Banzi is Dead, is a stark play addressing the real life issues of race and tensions between the Western and African ideology, and basic survival in an the apartheid world. What his play fails to address is any significant way is the plight of women struggling with similar issues. Within the play only four women are ever mentioned, Styles homemaker wife, only mentioned in passing reference, Banzi’s wife a lonely helpless homemaker, Buntu’s radical wife and a friendly woman peddling oranges to the drunken men. None of these women are given any depth of humanity in the play and are merely used as objects to reinforce or detract from the masculinity of the men involved. I assert that in a world were being a “man” is determined by having a wife and children as Styles father claims, there must be a societal predisposition to the value of women. However, if we follow the plays view of women they seem almost disposable or at least interchangeable. But the women of South Africa at the time were not all passive flowers in the apartheid world. During this time period the Federation of South African Women was created and was politically active in attempting to stop the many changes in apartheid. In my essay I examine the stereotypes of women mentioned in the play, compare those to the realities of women in South Africa at the time and consider the negative repercussions of a play in which women are on the sideline. In the grand scheme of history what is the cost when we forget to include the women?

The 2007-2009 financial crisis and subsequent recession has brought the looming unsustainable debt and deficits of the United States to the forefront of the minds of people everywhere.  This paper will delve into the puzzle of why neither dominant political party has been able to take the large legislative action needed to implement the recommendations of four well regarded institutions (Office of Management and Budget, The Federal Reserve, the Simpson-Bowles Commission, and the Domenici-Rivlin Debt Reduction Task Force) in light of their general consensus regarding goals that need be met in order to avoid a budget/currency crisis.  I ask the question: Why has the Congress of the United States failed to enact the large scale budgetary reforms necessary to bring the US debt/deficit in line with the recommendations?  My hypothesis is that there is some threshold of power balance that must be achieved over the opposing political party to achieve a strong enough majority in order to pass legislation that makes large program or budgetary changes.  I will investigate legislation before the floor of the House and Senate in the areas of Social Security, and Medicare.  First, I discuss the various recommendations regarding the debt and deficit.  Second, I review the literature regarding theories of legislative gridlock.  Third, I research and analyze the passage or failure of bills before the House and Senate floor in terms of size of the legislative change in budget and program, as well as compare this to the party balance of power present.  Finally, I speculate as to what would be necessary for Congress to pass the large budget/programmatic changes recommended.  Having done so, it is our hope that we can provide policy makers and constituents with a deeper understanding of the debt/deficit problem that the country faces.

If there is one point of consensus in this era of divided and dysfunctional government, it is the U.S. Constitution. However, some scholars attribute institutional paralysis in government to the founding document, such as a Senate with equal representation of states. If this is the case, then improving government will require reforming the Constitution. Whether the American public supports reform will be influenced by preexisting attitudes towards the document. These split on how the Constitution should be interpreted; some support a “living” document and others prefer preserving the original content. To see with which Americans agree, I model public support towards the Constitution based on government job performance from responses to Time Magazine survey from 2011. I find that people who are more dissatisfied with the government’s handling of its jobs are neither more nor less likely to support constitutional reform. This suggests that Americans do not agree with the institutional explanation and are unlikely to support reform based on poor government job performance.

The Hashemite Kingdom of Jordan is currently working to develop a domestic nuclear power capability, to which they are entitled under the Nuclear Non-Proliferation Agreement that they signed in 1970. Jordan’s economy is rapidly expanding and their current path of importing energy is costly and unsustainable. While nuclear politics in the Middle East are complicated, and efforts to build nuclear power plants that do not produce weapons are viewed with suspicion by the world, Jordan generally occupies a favorable view among the Western world, following decades of security cooperation with the United States and their signing of the 1994 peace treaty with neighboring Israel. However, Jordan’s bold advances have been led by a strict monarchy that has been criticized for not representing the people. Furthermore, regional conflict has led to an enormous refugee influx which now makes up the majority of the population. Political upheavals in the region has made others worried if the country has enough stability to insure that nuclear infrastructure always remains in trusted hands. My research includes extensive firsthand experience from a semester in Amman, where I surveyed Jordanians, both inside and outside the nuclear profession, regarding their opinions of progressing nuclear energy in the country, taking into account the regional challenges. The rapid change in Jordan’s demographics and in the security situation of it’s neighbors makes it necessary to constantly reexamine this country. Given the overwhelming focus of Western attention towards hostile regimes, such as Iran, and their nuclear ambitions, this research covers an often overlooked area of global nuclear development.

The Occupy Movement represented the American contingent of the populist uprisings of Spain and Egypt. It adeptly deployed popular, personalized political involvement with mobilization of networking tools and crowd tactics to create the ubiquitous meme “We Are The 99%”. The emerging, novel form of protest embodied by Occupy suggests the possible trajectory of contemporary social movements but it has been criticized for failing to assert demands and institute changes. The divergence with traditional social movements who make claims on the state extends to the realm of rights. This raises the question of whether the absence of rights-talk reflects a broader ‘exhaustion of rights.’ To investigate this claim I drew on activists’ accounts as well as academics studying the mechanisms behind movement formation and development. I sought to establish a framework to understand activist’s choices to reject demands and whether this logic was consciously extended to rights. I also incorporated academic works to understand and situate the movement in the neoliberal state to which the movement was, in part, a response. I found that activists were limited by the movement’s internal structure created out of a desire to instantiate horizontality, the absence of leadership, and inclusivity, broad participation, that were crucial to its legitimacy. More importantly, the perceived dominance of neoliberalism made activists wary of institutionalizing or making demands on a system that disproportionately favored the 1%. Consequences of the neoliberal project have intensified the critique of rights, leaving rights-talk perilous or powerless for activists. This view of rights delimits rights to state-claims and ignores their unintended and potentially transformative capacities. Consequently, although rights existed within the movement, they were not extant in broader discussions, missing an opportunity to seize upon the platform created by the movement to contextualize novel rights claims giving them political salience.

Glutamate within the nucleus accumbens (NAc) regulates the development of psychomotor sensitization, a model of addiction. Two prominent sources of glutamate are the prefrontal cortex (PFC) and thalamus neurons projecting to the NAc, and previous studies have shown these two regions contribute to amphetamine sensitization. We developed a combinatorial viral-mediated gene transfer technique to alter intracellular signaling cascades and neuron activity in either PFC or thalamic neurons projecting to NAc. We hypothesized that both PFC and thalamic glutamatergic projection neurons would regulate sensitization in a similar manner. Rats received bilateral injections of a retrogradely transported canine adenovirus expressing cre-recombinase into the NAc and an adenoassociated virus expressing Gi/o-Designer Receptors Exclusively Activated by Designer Drugs (hM4Di-DREADD) in either PFC or thalamus. This allowed for transient reduction in activity of specifically PFC or thalamic neurons projecting to NAc. I gave rats 4 injections of amphetamine or saline, and I then recorded locomotor activity and stereotypies. My results indicate that decreasing the activity of PFC projections to NAc enhanced amphetamine sensitization, whereas decreasing activity of the thalamic projections to the NAc blocked sensitization. These results suggest that PFC and thalamic glutamatergic input to the NAc differentially regulate amphetamine sensitization. It is possible that the projections from the PFC to NAc may preferentially affect the indirect pathway medium spiny neurons, whereas the thalamus projection to NAc would affect the direct pathway medium spiny neurons. Future studies will begin to address this possibility.

Bilinguals outperform monolinguals in tasks measuring executive functions; particularly, in tasks that measure inhibition and flexible behavior (e.g., task-switching), all of which require increased top-down control. One interpretation of this advantage in performance is that bilinguals may approach tasks in a top-down (goal-driven) manner, and given improved performance in certain tasks, top-down control is typically viewed as beneficial. Only one study has investigated the possibility that increased top-down control may result in a cost in terms of the influence on bottom-up (automatic, non-goal-driven) processing. To further explore the potential cost of top-down control on bottom-up processing, this experiment investigated patterns of semantic priming in 50 monolinguals and 50 early bilinguals across three experiments in which the amount of top-down control required varied systematically. If bottom-up processes are impaired as a function of top-down control strategies, we hypothesized that bilingual individuals, who recruit more top-down processes, will exhibit fewer baseline semantic priming effects, and that all participants will exhibit less semantic priming as the top-down requirements of the tasks increase. The lexical decision task was used in isolation to measure baseline differences in automatic, semantic priming between monolinguals and bilinguals. An additional, task-switching paradigm, in which participants either performed a lexical decision task or decided whether the first letter of a word was between A-L or M-Z was created to engender a more top-down approach. Finally, a dual task in which participants identified changes in auditory tones while making lexical decisions, was used to attempt to decrease any top-down influence on the lexical decision task. Preliminary analysis of the data suggests that priming did not change as a function of task or language group. I will discuss the implications of this research for understanding individual differences in executive functioning.

The retina contains a dense web of photoreceptors, interneurons, and retinal ganglion cells. Although much work has been done on interactions between homologous photoreceptors, little has been done to characterize interactions between the two different types of photoreceptor cells: rods and cones. Electrophysiological recordings done in the Rieke lab found that selective activation of rod cells inhibited the response of long wavelength cones within a subsequent time window. The goal of my work was to probe whether this intercellular retinal phenomenon is robust enough so as to actually be perceptible by human observers in psychophysical trials. Using a dual monitor haploscope setup, I was able to present rod or cone isolating visual stimuli with different time offsets to subjects, who then performed a “brightness” matching task. Indeed, my results identified a perceptual suppression of cone mediated signals with a strength and latency comparable to that observed in electrophysiological recordings. This work contributes to our understanding of the neural circuitry underlying vision, particularly under mesopic or moderately dark light levels.

While language delay and speech impairment in individuals with Autism Spectrum Disorders (ASD) have been widely investigated, few studies have analyzed the role that non-verbal forms of communication, such as gestures, may play in augmenting impaired speech in individuals with ASD. One system that has been heavily studied, which has the potential to enhance or inhibit communication, is the Mirror Neuron System (MNS). While the MNS could serve to augment speech, the dysfunction of this system could prove detrimental to those who already possess impaired language skills. If the MNS were to be equally affected by ASD, individuals with this disorder would be unable to compensate for impairments in verbal communication with non-verbal forms of interaction. Although reduced activity in MNS areas in ASD individuals has been identified, the implications of this dysfunction remain unclear. In order to identify if the dysfunction of the MNS impairs non-verbal forms of communication, we recorded 16 typically developing (TD) adolescents and 13 ASD adolescents as they played a game of charades. We utilized charades that were not associated with speech centers, but instead have been shown to rely heavily on an intact MNS and motor cortex to mimic the action. This allowed us to identify whether reduced activation of mirror neurons impacts neural centers that serve to augment language through nonverbal means. Using video footage, two blind coders scored the quality of gestures based upon a 0-8 point scale that was unique to each gesture. Our preliminary results suggest that adolescents with ASD do not have significantly lower scores of functional gesture quality compared to TD individuals. One possible implication of these data is that other regions of the brain may compensate for MNS dysfunction and, importantly, may serve as potential therapeutic targets for strategic interventions to minimize the language impairments associated ASD.

Songbirds are a model organism of interest to neurobiologists as they are one of a few groups of organisms that display sensorimotor vocal learning, akin to that of humans. Once learned, birdsong is highly stereotyped and while slightly variable, has not been thought to vary systematically from instance to instance. However, biological processes separate from learning mediate the qualities of a bird’s song. It is well known that the amount of singing varies throughout the day with the light cycle, but is not well understood how the acoustics of birdsong vary with light. Recent work has shown that pitch and loudness vary in a consistent manner throughout the day, rising through the morning and early afternoon and falling through the afternoon and evening. Whether these changes in song depend on an internal circadian rhythm or external light cues remains unknown. My project focuses on determining whether finch song is endogenously driven by an internal clock. I collected song data from zebra finches housed under typical light patterns (14 hours of light, 10 hours of dark) and constant light conditions. The fundamental frequency of a sample syllable was analyzed for each bout of singing and then plotted across the span of weeks. Preliminary results suggest that birds under constant light conditions take a few days to unentrain from the light cycle, then sing throughout each 24-hour day, with FF fluctuation around a baseline frequency. I hypothesize that if birdsong acoustics vary according to a circadian cycle, FF fluctuations that occur during constant light conditions are part of a regular pattern that is regulated by an internal clock. Finding that finch song is circadian has implications for understanding how a clock might connect to song system nuclei and demonstrating how complex motor behavior and learning can be influenced by time of day.

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. One mutant allele, Acsl (Acyl-CoA synthetase long-chain), leads to a complete loss of terminal dendrites, which carries a two amino acid change that renders the gene product non-functional. Interestingly, Acsl is also associated with human X-linked mental retardation (XMR). However, to date, little is known about the signaling pathway that may be involved in this unique function of Acsl in neurons. As such, we conducted a modifier screen, which serves to identify functional modulators with genetic interaction of Acsl in maintenance of terminal dendrites. Here we report our results of funcional signaling (and/or) regulatory genes from this screen. We also conducted comparative GC/MS of the lipid profiles in both whole larval body and brains to identify the specific lipid species being affected by acsl mutation. In return, this will reveal to us more about the function and signaling pathway of Acsl in maintenance of terminal dendrites. Results from this project will lead to a greater understanding of dendrite abnormalities in neuronal development and of neurodegenerative disorders.

The study aimed to compare and contrast mother-child and father-child attachment relationships and their associations with children’s emotion regulation. It was hypothesized that both mother-child and father-child attachments would be related to regulation at school and at home. Participants were 111 children (n= 78 girls, 38 boys, 10 to 14 years of age). Children completed a questionnaire and interview measures of attachment for their mothers and fathers. Teachers completed a measure of Frustration Tolerance and mothers completed a questionnaire to assess the child’s coping strategies. Effects varied across measures of attachment. On the questionnaire measure, attachment to mothers was more consistently related to emotion regulation than attachment to fathers, but on the interview measure, attachments to both parents were equally related to emotion regulation. These results indicate that children’s attachments to their fathers are as important to the study of their emotion regulation as their attachment to mothers.

There is a noticable lack of research done in epistemology with regards to the role of the passions (or emotions). Epistemology asks questions about what knowledge is and how we come by acquiring knowledge. Due to these types of questions, the focus is put on reason and justification. However, there is also an aspect of normativity: what methodology ought one to use in order to acquire knowledge? Given recent findings in experimental psychology, it is odd that an examination of the passions' role in normativity is less prominent in epistemology. My presentation is about my recent research into the role passions play in questions about knowledge acquisition and more specifically the normative aspects of knowledge acquisition. My primary way of doing this is not solely a review of experimental psychology literature, but also an examination of the 18th Century philosopher David Hume's work on the passions and normativity. I will show how an accurate interpetation of Hume's work is relevant to epistemological issues, and how his work can inform contemporary debates around normativity more generally. 

The 2010 annual freshmen survey from UCLA found that incoming freshmen self-report as having lower levels of mental health then previous freshmen over the past 25 years. Lower levels of mental health have been found in research to correlate with higher levels of stress. If students have high levels of stress and ineffective coping skills this may negatively affect their performance. To understand how school stress, coping, and performance interact with each other, college freshmen from a mid sized university in the rocky mountain region were asked to complete a stress inventory, a coping inventory, and a demographic survey. Results showed that stress and coping are significantly positively correlated, specifically emotion coping was significantly correlated with stress. Regression analysis showed that stress accounted for over a quarter of the variance in GPA when controlling for gender. These results suggest that stress may change a student’s performance, and that freshmen may only know how to cope with stress in an emotional way.

There has been growing scholarly attention to the fact that most global health projects/research are disproportionately focused on specific locales resulting in temporary restricted interventions. This approach is, in some significant sense a 'betrayal' of the very idea of global health. This study asks how Seattle's various global health institutions and organizations approach Global health in Kenya. I hypothesize that most global health projects promote the production of inequity, unequal and uncaring exchanges between donor institutions and the recipients. I analyze the socio-historical, economic and political histories and ties between Kenya and global health institutions in Seattle drawing on political-economy analysis and feminist care ethical analysis. I also thematically code and analyze ethnographic interviews to investigate the relationship between the responses and the main research topic. I expect to find that global health projects may not necessarily achieve their intended goals because they do not fully consider the four phases of care, which involve attentiveness, responsibility, competence and responsiveness. Understanding the factors influencing the production of unequal and uncaring exchanges in global health is essential as it will impact how global health projects should be conducted.

Most living systems have complex bacterial communities (microbiomes) associated with them that are essential to the host's wellbeing. Microbiomes provide their host with nutrients, protection against pathogens and stress, and influence host immunity. Microbiomes can consist of hundreds of different bacterial species making them difficult to study. However, the algal species Chrysochromulina sp. (referred to as P3) has a small microbiome consisting of less than 10 species, making it a prime candidate for studying interactions between a host and its microbiome. Chrysochromulina sp. is also of interest as a source of biofuels since it produces a variety of fatty acids, and it belongs to an algal taxa that plays a major role in global carbon sequestration. I hypothesize that the microbiome of P3 allows P3 to withstand periods of stress. I tested this by growing P3 and an axenic (bacteria-free) culture known as P5.5 in high salt medium, a known stressor, and determined cell counts by flow cytrometry and bacterial colony counts by culturing. I found the P3 grew better than P5.5, indicating the bacteria help the alga survive high salt conditions. We cultured and identified 8 different bacterial species associated with P3 by sequencing the 16S rDNA, which encodes ribosomal RNA and is unique to each species. Next I will determine which bacterial species protect P3 from high salt. I will further determine the protective role of the microbiome by growing P3 and P5.5 under other stress conditions (e.g. low nitrogen, low pH, low light, and temperature shifts) to understand how the microbiome protects Chrysochromulina sp. during periods of environmental challenge. This will allow insight into how to optimize Chrysochomulina sp. growth for biofuel production and the effects of global warming on this alga.

Possession Sound as a part of the larger Puget Sound is located between the Whidbey and Snohomish county shoreline. This location has significant influence from both freshwater and nutrient inflow from the Snohomish River as well as saline water resulting from tidal exchange. Students at the Ocean Research College Academy (ORCA), an early college program at Everett Community College, have been conducting baseline estuarine monitoring since 2007. The Washington State Department of Ecology has been aerially monitoring phytoplankton blooms and maintains a long-term collection of nutrient data throughout Puget Sound. According to this data set there has been a nutrient shift that is hypothesized to impact diatom abundance. This project combines the ORCA data set of plankton levels and nutrient concentrations to see if a similar shift is occurring in Possession Sound. Additionally, temperature variation is analyzed. Two hypotheses combine to identify special and temporal distribution of nutrients and plankton abundance. First, when silicate levels decline, diatomaceous phytoplankton are limited by this reduction. Second, the deep water location further from the river will have less variation in temperature, less nutrient availability and subsequently less phytoplankton abundance and diversity. The location nearest to the mouth of the Snohomish Riveris predicted to experience dramatic temperature variation and higher seasonal nutrient levels. The conclusions from this work will influence future plankton enumeration protocols at ORCA.

 The ocean is the largest and arguably the most important ecosystem on the planet. Within the ocean a successful and widespread group of algae, the diatoms, are major contributors to the global carbon cycle with primary production rates rivaling the terrestrial rainforests. Yet in many areas of the open ocean, low concentrations of bioavailable iron limit the growth and photosynthesis of diatoms and other phytoplankton. Marine phytoplankton have evolved several adaptive strategies to compensate for the scarcity of this metal. Here we present a comparative analysis of the molecular repertoire utilized by diatoms to respond to variable iron concentrations. Utilizing sequence data from over 75 diatom transcriptomes, we have identified homologues for key iron metabolism genes. We are using this data in conjunction with environmental metatranscriptomes to map the distribution of these genes in the environment. Here we will demonstrate a selection of our findings. We show that the gene coding for ferritin, the iron storage protein, is expressed in ancient and derived diatom groups and forms a monophyletic clade, sharing a common ancestor with marine cyanobacteria. Several species of diatoms co-express two unique ferritin paralogs, and these show differential transcription in the environment. We also show widespread constitutive expression of the electron transfer protein flavodoxin, which substitutes iron-using ferredoxin under iron limitation. Iron responsive Clade II flavodoxin is expressed by members of coastal and off-shore diatom assemblies. We are now able to examine these and other iron-related genes with a higher taxonomic resolution and utilize them as environmental biomarkers.

Pseudo-nitzschia is a cosmopolitan genus of marine diatoms known for its production of the neurotoxin domoic acid (DA) and resultant harmful algal blooms. The production of DA varies across species; of approximately 37 defined Pseudo-nitzschia species, at least 14 have produced DA in laboratory studies. Previous work based on ribosomal RNA sequences suggested the genus Pseudo-nitzschia could be divided into two major clades, or groups made up of an ancestor and its descendants. With the discovery of new species and identification of cryptic species complexes, the structure of these clades has eroded. We sought to integrate phylogeny, morphology and physiology of Pseudo-nitzschia, by re-examining their phylogeny, using both ribosomal LSU sequences and the rbcL gene, which encodes the large subunit of the carbon fixation enzyme, ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO). Trees based on rbcL sequences provided higher resolution to resolve the branching orders of Pseudo-nitzschia species. By mapping physiological characteristics such as cell size, frustule morphology, pigment content and DA production onto the tree we can interpret the evolutionary history of these features and species distributions in the context of our presumed clades.

In the marine environment, hypoxia is defined as: a level of dissolved oxygen (DO) that has fallen below 2.0 mg O₂/L. This level is approximately 20% of a system that is at oxygen saturation. Should the DO reach 0% it is described as “anoxic”. Due to anthropogenic influences, incidences of hypoxia and anoxia in coastal marine environments are increasing globally. In Hood Canal, a sub-estuary of Puget Sound, Washington, research is underway to define and quantify the effects of hypoxia on zooplankton distribution and community structure. One copepod, Calanus pacificus, is considered to be a keystone species in this community due to its prominence in the food chain. My research has been to determine the physiological tolerances of Calanus to dissolved oxygen then compare with data from samples taken in Hood Canal to determine whether there is evidence that Calanus avoids areas with low DO. To identify oxygen tolerances, DO in seawater was manipulated in the laboratory by bubbling with N₂ gas, then 24-hr survival of copepods was tested at several DO levels. In the field, Calanus abundance was estimated from depth-stratified plankton samples taken during day and night, in regions and at depths, of high and low DO. Laboratory experiments showed that Calanus were adversely affected by low DO with a sharp decrease in survival from 87% survival at 1.44 mg O₂/L to 13% at 0.96 mg O₂/L. My research relates these findings to distributions observed in the field data. Substantial decreases in Calanus populations due to increased hypoxia in Hood Canal could cause large changes in the food web. Further research into Calanus’ behavioral reactions to these conditions could help understand, and even predict these changes.

Through their use of fertilizer, humans have critically impacted the nitrogen cycle, which must be understood in terms of addition and loss. This research focused on one aspect of the nitrogen cycle; the loss of nitrogen from the ocean that occurs in suboxic waters. Nitrogen is added to the ocean reservoir through river inputs, nitrogen fixation, and deposition from the air. Nitrogen losses ultimately strip nitrogen out of the ocean through annamox and denitrification. Oxygen minimum zones (OMZs) are responsible for 50% of oceanic nitrogen loss. One of the 3 largest OMZs where anammox (ANerobic AMMonium Oxidation), and denitrification occurs is in the Eastern Tropic South Pacific (ETSP) where I utilized a new method of targeted proteomics. I quantified the abundance of four enzymes key in the loss of nitrogen from the oceans. N2O reductase catalyzes the critical step of denitrification. Hydrazine hydrolase & hydroxylamine oxidoreductase are two enzymes necessary for the anammox reaction and cytochrome c nitrite reductase (nrfA), an enzyme specific to the DNRA pathway (where DNRA stands for Dissimilatory Nitrate Reduction to Ammonium). My overarching question was “Are there trends in the abundances of the enzymes over space within the ETSP?” I collected samples during the summer of 2013 on the R/V Nathaniel Palmer. Tryptic (a proteoenzyme that cleaves peptide chains after specific amino acids) digest of the samples were injected on a Liquid Chromatography Mass spectrometry and quantified. The data are being analyzed for spatial trends, focusing on a near shore to distant from shore transect. Of the 26 samples analyzed, 15 had detectable anammox proteins, and 6 had detectable denitrification proteins. None of the proteins for DNRA gave usable data. I will discuss quantities and correlations of enzymes over space within the ETSP and connect it to the local and global nitrogen budget.

Half of all carbon fixation on the planet is performed by phytoplankton, making these photosynthetic marine microbes essential to the global carbon cycle. It is therefore critical that we understand the factors affecting phytoplankton dynamics to predict the responses of the communities to future climate changes. While we have learned a great deal about phytoplankton growth, little is known about the factors that influence phytoplankton mortality. Studies that have focused on phytoplankton mortality rates have relied on incubations in a bottle, a labor-intensive approach that is limited in its broad-scale applicability. Our approach utilizes SeaFlow, a novel flow cytometer that can continuously measure the abundance and size distribution of phytoplankton in situ, from which cell division rates and net population loss rates are estimated using a size-structured population model. This approach essentially eliminates the bottle effects and allows for greater spatial and temporal resolution. Our goal is to monitor cell growth and loss processes of cryptophyte Rhodomonas prey populations during a bloom of a dinoflagellate predator in the Columbia River estuary, using SeaFlow. We first estimated cell growth of the cryptophyte during a time course experiment in the lab to validate our model. We then monitored the dynamics of cryptophyte populations in the Columbia River estuary, and have found that cell growth and loss processes varied widely during tidal cycles. Our findings shed new light into the biological and physical interactions that drive the dynamics of cryptophyte populations in the Columbia River estuary, and our approach will be able to be applied to previously gathered field data.

The cosmopolitan pennate diatom Pseudo-nitzschia is notable for production of the neurotoxin domoic acid. Recently, a virus was isolated on Pseudo-nitzschia multiseries that has a broad host range, infecting many genera of diatoms. This is contrary to previous reports of very specific host ranges amongst diatom viruses, and suggests a nested infection network whereby specialist viruses infect only the most permissive hosts, while generalist viruses can also infect hosts that are well-defended. To explore the infection patterns of Pseudo-nitzschia and its viruses, new Pseudo-nitzschia strains were isolated monthly at a coastal and estuarine location in the Pacific Northwest for one year. Over 100 new strains of Pseudo-nitzschia were identified by sequencing the ITS region. These new strains are then challenged with environmental viral communities that were sampled at each location concurrently. To date, 28 of 47 strains tested are susceptible to infection by at least one viral community. Three strains are lysed by the majority of viral communities, suggesting we have identified permissive hosts. This analysis will continue until all currently isolated strains are challenged. Seasonally, May and July contained viruses that infected the widest range of strains, suggesting either high concentration of generalist viruses in those months, or high concentration of both specialist and generalists together. Understanding the seasonal structure of these infection networks will inform future virus isolation attempts and provide insight into a key component of these diatom-virus interactions.

Colonization is often associated with exploitation of local laborers. However, the degree to which physical activity in local populations changes following colonization depends upon the policies of the colonizers, and the technology that is locally available. This research tests the null hypothesis that levels of physical activity, as evidenced by osteoarthritis in human skeletons, remained constant at Epidamnus, Albania during Greek and Roman colonial occupation (620-100BC). To test this hypothesis, 80 skeletons from Epidamnus were examined for evidence of osteoarthritis, and scored according to international standardized protocols. Of these 80 individuals, 27 were adults that showed sufficient preservation for analysis of osteoarthritis. Results indicate that osteoarthritis was more pronounced in all joint surfaces during the Greek than the Roman period (shoulder, elbow, wrist, hip, knee, ankle, cervical vertebra, and temporomandibular joint), with the exception of the thoracic and lumbar vertebrae. Chi-square indicates that this pattern is statistically significant in the shoulder (p=0.02) and ankle (p=0.003), and approaches significance in the elbow (p=0.09), wrist (p=0.06), and temporomandibular joint (p=0.06). These results do not support the null hypothesis of no change from the Greek to the Roman period. Historical documents indicate that Greek colonization resulted in increased dependence on agriculture and largely replaced nomadic pastoralism in local Illyrians. The Romans then introduced new technologies to increase agricultural efficiency. The emerging pattern indicates that the introduction of new, sophisticated technology made life easier for Illyrians during the Roman period. However, the impacts of small sample size are also considered.

 Depictions of Our Lady of Refuge of Sinners, or La Refugiana, were among the most popular religious images produced in viceregal Mexico since the early eighteenth-century, especially in areas north of Mexico City. Although the iconography of these images did not change, the artists who produced these works adopted a variety of styles—classical, Baroque and even popular folk. It is safe to assume that there is nothing arbitrary about the production of religious devotional images; these objects surely must adhere to specific concepts of theological decorum while, at the same time, meet the religious and devotional needs of the public. By examining an array of early nineteenth-century Mexican retablos of La Refugiana, I will attempt to explain the reasons behind these distinct formal approaches and how they may have been tailored to fit the civic, theological and apotropaic needs of an ethnically diverse population. My research will closely examine how images were produced in viceregal Mexico. Additionally, I will consider how stylistic variety may have been the result of innovation, experimentation or creative competition in reaction to European models. To this aim, I will also explore the hybridization between old and New World artistic traditions, the didactic use of images by the mendicant orders, the use of religious images in private versus public devotional use, as well as the political climate of the time. While my final research paper will not discuss all of these elements in great detail, they will be useful to gain a better understanding of why images of La Refugiana manifested such a wide variety of styles and place them within a much more decisive cultural context.

In many ways, our contemporary understanding of the Modern Civil Rights Movement, and its associated successes and failures, has been severely limited through socio-historical and political machinations to collapse and periodize it. Rather than situating it within or connecting it to the broader historical continuum and highlighting the rich multiplicity of forms of struggle and survival, the simplistic narratives we receive through media (and other forms of cultural production) are ones of heroes and villains—of near-infallible visionaries and separatist and corrupt radicals, one that highlights the contributions of the few at the expense of the many. Two such groups whose historical agency and significance suffer from such undertakings are the Black Panther and the Young Lords Parties. It can be said that both groups have suffered not from a crisis of denotation, but one of connotation—referring specifically to the ways in which their collective contributions have been socially diminished as they are instead associated with fear, needless violence, corruption, militancy and relegated to the margins. Thus my research asks: how did these groups function as powerful symbols of transformation during Modern Civil Rights Movement? To what end? How and why were individuals within these groups and even the organizations themselves framed as threats to the social order and how would their objectification exacerbate their struggles for equality? I seek to uncover through a careful examination of foundational documents, news articles and other print media, interviews, and film, how socially produced marginalization enabled a multiplicity of violence against them (and their associated communities) and also illuminate some of the associated contemporary consequences.

Humans and other primates have been in contact for the entirety of our evolution and our relationships have been complex and ever changing. Many cultures hold a position of dominance, exploitation, or power over other primates. This often results in turning them into the "Other," which allows humans to use them as they see fit. This research examines the ways in which humans relate to and perceive other primates to understand how these relationships are associated with varied human uses of them. Expanding upon the current research in ethnoprimatology, which examines the human-other primate interface, my work studies the relationships and perceptions that develop in the context of captivity. I investigate these relationships in a biomedical research facility, a zoo, and an animal sanctuary. I use observation, participant observation, semi-structured interviews, and discourse and artifact analysis to determine the human perception(s) of other primates. Qualitative data analysis will be used to discern and interpret similarities, differences, and patterns. What I expect to find from this study is that humans treat other primates as "Others" and assign them a lower status in order to justify their varied uses. This study will help us to understand our hierarchical relationships with other primates, how they allow for exploitation, entertainment, or conservation values, and what this teaches us about the construction of "human nature".

My research explores the means by which identities of “non-white” Habesha (Ethiopian and Eritrean) immigrants are negotiated through the use of media, community spaces, collectivism, and activism. As “black” immigrant subjects who do not have a longstanding historical past in the United States, Habesha face the challenges of having to re-construct and negotiate their identities within binary, black/white, American racial landscapes. To explore the ways in which ethnic-based collectivism and activism challenge stereotypical portrayals of Habeshaness and blackness which are typically cemented through media, I focus on unpacking mediated representations of Hana Alemu Williams, her death, trial, and subsequent support from the Ethiopian Community of Seattle (ECS). In short, Hana Alemu Williams was an Ethiopian child who died in 2011 from abuse, severe malnutrition, and cruelty at the hands of her white adoptive family in Sedro-Woolley Washington. Through close readings of mediated texts: news paper articles, television news broadcastings, blogs, and interviews of people from the ECS who were used as news “experts”, I will critically analyze the moments in which Habesha immigrants challenge narratives of race and identity in the American context. I hypothesize that Habesha immigrants sometimes assimilate into American constructions of race while at other moments creating counter-narratives of hybridity or exclusive ethnic-based identities like Habeshaness, or maintaining purely national identities as Ethiopian and Eritrean immigrants, in an effort to defer perceived racial stereotypes and oppression that arise with identifying as simply black or African American. Furthermore, I discuss potential steps that can be taken by Ethiopian and Eritrean immigrant communities to address these harmful and limited understandings of race and racism in America. This research enriches the existing academic literature by creating a more nuanced understanding of the Seattle Habesha community’s racial discourses in their efforts to re-imagine Habesha identities.

Microbial growth can be monitored by changes in the optical density of a culture. In the past, these measurements were generally made by hand, one at a time at regular intervals, in order to produce a growth curve. Currently no such device is suitable for monitoring the growth of fastidious anaerobes. This presented problems for both efficiency and resolution of experiments requiring analysis of multiple cell lines and different growth conditions. For growth periods greater than a work day, researchers needed to take alternating shifts in order to capture data. This is a very tedious process which is draining on the tester. The result of such a worker demand was infrequent measurements to make the minimal curve, resulting in inherent tester bias. Naturally, the desire to automate the process arose. I began development on the ROGR system began in order to implement a microcontroller operated test setup using LEDs and phototransistors to replace the manual measurements made with a spectrophotometer. Previous work has shown that LEDs of these wavelengths do not interfere with cell growth. As this is an ongoing experiment, it is imperative that the method used to measure growth does not change the testing environment. For example, the anaerobic cultures have long been incubated with constant shaking with the culture tubes oriented in a horizontal plane, but measurements were made in the upright position in order to create an accurate reading. The ROGR is a multi-disciplinary project that addresses these project needs. The electronic design ensures system isolation and achieves high precision and dynamic range. Design also ensures mechanical stability, reducing error in LED phototransistor pairs readout originating from changes in their physical orientation. Presently the system is undergoing the physical implementation phase with its circuitry at a working state. This reproducable system will allow for data colection across multiple teams to be connected with confidence of small error.

Low intensity non-thermal non-ionizing electromagnetic fields (EMF) in the ranges of extremely-low to low frequency (< 200 kHz) have been shown to kill cancer cells in various studies. The external electromagnetic field cannot be concentrated to focus enough energy in the tumor site to be effective. We are designing an EMF-emitting microchip that can easily be surgically implanted into a tumor. The microchip emits electromagnetic fields when it is activated by an ‘activator’ outside of the body. Since the chip is in close proximity to cancer cells within the tumor, the cells would be exposed to a very high local field to achieve cytotoxic effect. A prototype of microchip (cylindrical, ~12 mm in length, ~2 mm in diameter) will be tested with Molt-4 cells (human leukemia). Molt-4 cells will be incubated for 24 hours at 37^oC in a humid atmosphere of 5% CO₂/and 95% air. After initial cell count, one ml of cells each will be put in four microfuge tubes. A microchip will be placed in two of the tubes. Two tubes (one containing a microchip and other not) will be exposed using an activator. The other two (with and without microchip) will be sham exposed, i.e., they will be subjected to the same experiment procedures as the ‘exposed’ samples except that the activator will not be turned on. During exposure, cells will be maintained in a water bath at 37^oC. Viable cell count will be performed at 1, 24 and 48 hours after exposure. Our preliminary results using the above-mentioned protocol are encouraging. We anticipate to show that a microchip can be used to kill cancer cells and produce data to proceed to in vivo (experiment within a living organism) study.

Sexually transmitted infections are a major health concern, both in the developing and developed world. Despite the fact that vaccines have been developed and are under development for many STIs, there is currently no efficient method of topical delivery for these vaccines. The barrier posed by the vaginal epithelium and the difficultly of achieving intracellular delivery hinder their ability to elicit immunity. The optimal topical drug delivery system would ideally transport vaccines through the epithelium and into immune system cells. There is a naturally-occurring pathway in the vaginal epithelium in which the FcRn receptor, which is present on epithelial cell surfaces, binds and bidirectionally translocates IgG antibodies across the epithelium. We hypothesize that a nanoparticle decorated with IgG could be transported by the same mechanism. Loading the nanoparticle with the desired vaccine would then enable delivery to cells populating the vaginal submucosal tissue, providing the topical delivery that is desired. Several methods of conjugating fluorescent polystyrene nanoparticles to IgG have been investigated. I have selected two methods to pursue. The first of these is a passive adsorption method, in which the antibody was allowed to stick to the nanoparticle surface through hydrophobic interactions. The second of these employed commonly used (thiol-maleimide) conjugation chemistry. Now that these methods have been identified as potentially viable, I will assay them to determine if the IgG protein can still bind FcRn while conjugated to the nanoparticle. If this yields positive results, I will move on to animal models to determine the biodistribution of the particles. This will allow me to see if the IgG modification has increased the particles’ ability to reach immune system tissues. If this project’s aim is successful, it may become as useful system for the delivery of vaccines against a variety of diseases.

There is 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 there are currently antiviral drugs that can suppress HBV replication, latent HBV so far has proven difficult to eradicate. Homing endonucleases, enzymes that recognize long DNA sequences and induce DNA double strand breaks, could be a means by which latent HBV is targeted and inactivated. In particular, we aim to modify the recognition site of the wild type I-GzeII homing endonuclease (HE) into a HBV specific DNA targeting enzyme that will recognize specific sequences in the HBV genome and introduce double-strand DNA breaks. By exploiting the error prone nature of non-homologous end joining, the process cells undergo to repair double-strand breaks, these modified HEs will have a mutagenic effect on target sequences in the HBV genome. Repeated HE activity will eventually cripple the replicative ability of the latent virus. To selectively modify the structure of homing endonucleases, the amino acid residues that interact with the DNA substrate are identified and randomized. A library of variant forms of I-GzeII is generated. Variants that encoded for active forms with the appropriate HBV specific recognition site are selected for by in vitro compartmentalization. After several rounds of selection, bacterial selection assays and in vitro cleavage assays using a reporter cell line will be utilized to select for structurally stable variants that functions in vitro. The final step is to test the HE product on an in vitro HBV cell line. Through our research, we hope to produce a proof of concept that latent viruses can be targeted and inactivated through mutagenesis by homing endonucleases and that specificity and target of the enzyme can be modified and assessed through this protocol.

As our understanding of the genetic basis for the pathophysiology of many diseases has broadened, gene therapy, which is the delivery of genetic material into cells in order to supplement or alter defective genes, is being explored as a potential treatment option. Despite its promise, no gene therapies have been approved for clinical use due to the lack of safe and effective vectors. There are many obstacles that must be overcome in order to successfully transfect a cell with exogenous DNA. First, the vector-DNA complex must navigate through the extracellular environment and be uptaken into the target cell. Then, the genetic material must achieve endosomal escape, be released from the complex, and then translocate into the nucleus where it can be transcribed and translated into functional or therapeutic proteins. In the Pun Lab, we previously synthesized a block-statistical copolymer comprised of different hydrophilic and hydrophobic segments aimed at providing a plethora of functionalities to the formed polyplexes. Due to this polymer’s unique architecture, it exhibits transfection efficiencies higher than branched polyethyleneimine, the gold standard for nonviral gene delivery, but still fails to reach the same level of transfection efficiency as seen with viral vectors. In this project, two additional modifications will be made to the copolymer and a library of well-defined polyplexes with varying formulations and structures will be synthesized and evaluated in vitro and in vivo. These modifications, guanidinylation and conjugation of a targeting peptide, aim to increase uptake into cells through electrostatic interactions and increase localization to the target cell type. From these studies, the ideal method to incorporate both modifications into one system to improve transfection efficiency and the structure-function effects on transfection efficiency will be evaluated.

Current medical diagnostic gold standard, the Enzyme-Linked Immune-Sorbent Assay (ELISA), requires additional labels and amplification to determine the existence of interested molecules. Such process is extremely time consuming and expensive, and thus a fast and low-cost alternative is in demand. Our project aims to develop a rapid and affordable diagnostic biosensor platform that can be administered in the Point-Of-Care (POC) setting. In our silicon photonic sensor chip, we exploit a unique aspect of light when it is confined into a waveguide much smaller than its own wavelength. Since different molecules have different refraction index, the portion of light travels outside the waveguide, called evanescent field, is capable of sensing molecules binding on the sensor surface. While the design and fabrication of these biosensing devices can be done quickly and affordably, characterizing and experimenting the devices remains challenging because of the complexity of testing submicron-scale components. Chips require careful alignment of the optical I/O fibers with micron-tolerances. Microfluidics must be integrated to deliver reagents to specific regions of the chip. Real-time processing of optical spectra is needed to facilitate user operation. Hence we have customized a low-cost test bench to perform experiments and characterizations on the silicon photonic biosensors. I have designed the software, which employs industrial standard Model-View-Controller (MVC) architecture, for instruments integration, experiments orchestration as well as data acquisition and analysis. This software has greatly enhanced the efficiency of the biosensor platform development and future improvement is foreseeable because of the ongoing progress of full automation of experiment preparation. I have characterized multiple sensor devices through optical data acquisition, analysis, model fitting and key parameters’ estimation this software provides. Characterization results show great promise on the sensing capability of the platform and we will soon proceed to biomolecules (e.g. protein), and even cell (e.g. cancer cell) sensing.

The Elwha is a small mountainous river that discharges into the Strait of Juan de Fuca, and is the location of largest dam removal project in U.S. history. Millions of cubic meters of fine-grained sediment that have been trapped for a century are expected to be delivered to the nearshore in the two to five years following the complete removal of the dams. Strong influxes of suspended sediment into the Strait associated with large discharge events provide a unique opportunity to gain a better understanding of the surface plume and how it transports sediment. This study used filtration, optical backscatter data, and grain size analysis to find concentration and grain size distribution of suspended sediment in the subaerial delta channels and surface plume. Since the project began, suspended sediment in the river and its surface plume has increased by two orders of magnitude. Sediment concentration increased seaward in the western distributary channel, and the highest concentrations of suspended sediment in the surface plume occurred immediately outside of the delta and decreased rapidly away from the river’s mouth. Large amounts of sand found suspended in the western channel suggest further seaward expansion of the sandy delta.

Low oxygen concentrations in oceans exist at mid-latitudes where water circulation occurs sluggishly, causing oxygen minimum zones (OMZ’s) to form. Recent trends suggest that OMZ’s are expanding, which could decrease biodiversity, disrupt food chains, and alter seafood industries. The low oxygen content causes OMZ’s to host denitrification, a process in which organisms use nitrate rather than oxygen in cellular respiration. Understanding these rates of denitrification will allow us to predict the consequences of climate change on nutrient cycling and ocean productivity. Autonomous floats with chemical sensors are currently being designed to quantify the rates of denitrification. To ensure that future oxygen measurements will be highly accurate, I calibrated the oxygen sensor using the Winkler method, a chemical procedure. A new amperometric titration Winkler kit was used on the R/V Oceanus to analyze saltwater and freshwater samples near the Columbia River. The data showed that as the temperature and salinity of the samples increased, oxygen content decreased. These samples had oxygen concentrations in the range of 2.4 to 6.0 mL O₂/L H₂O with approximately 1% precision. For optimization of oxygen measurements in OMZ’s, past publications suggested diluting chemicals as well as adding sodium azide. I conducted a dilution experiment involving the Winkler titrant, sodium thiosulfate. OMZ water was created in the lab by adding sucrose to seawater and measuring the oxygen content with an optode, which reported around 2% O₂ saturation. This sample was analyzed using Winkler chemicals with a tenth of the baseline concentration. However, this experiment was limited by the titration system parameters and significant data could not be collected. Revision of the system programming is necessary to finish the experiment. Additionally, further research with the sodium azide modification will increase the accuracy of oxygen measurements in OMZ's and therefore greatly advance the calibration of the oxygen sensor.

One of the main areas of focus in computational geology is how to quantitatively assess the nature of geomorphic features, in particular those that cannot be directly observed, such as the seafloor. An expert may know what a feature is simply by looking at it, and will be able to expound on why the feature is what it is, but there are relatively few features for which a rigid, quantitative criteria exists, one that will define, without subjectivity, why a feature is this and not that. This project aims to develop such a criteria for the submarine features known as debris slumps, where large amounts of the seafloor along a ridge detach from the surrounding area and slowly move downwards, creating a large block of loose material. Using sonar data of a debris slump off of Samoa, several techniques are used to determine precisely where the slump begins and ends. These techniques include analysis of sediment distribution, geostatiscal models of changing depths, and analysis of slope, hill aspect, and other models of geologic change. Combining all of these results produces a distinct profile of what that debris slump quantitatively looks like. This profile can then be validated by comparing it to the profile the same suite of metrics produces for an area that is not part of a debris slump. The difference between the two profiles shows that a different set of processes are shaping each area of the seafloor, and the slump was created in a different way than the surrounding seafloor. Profiles of this nature allow marine geomorphologists, geologists, and remote sensing experts to quickly determine the identity of objects on the seafloor, and be able to assess the impact they will have on the surrounding region.

The San Juan Channel links the Strait of Georgia and the Strait of Juan de Fuca, and is dominated by an estuarine flow regime. The goal of this study was to characterize the physical water properties of the San Juan Channel for autumn 2013 including the Fraser River signal in the northern channel, the oceanic signal in the south and how tides and winds affect the expression of these signals within the San Juan Channel. Finer temporal resolution data provided by the Friday Harbor Lab weather station was used to investigate how tides and winds affect the freshwater signal in the northern channel. During fall 2013, the Pelagic Ecosystem Function Research Apprenticeship sampled a 5-station transect along the San Juan Channel. A CTD was deployed and temperature, salinity, and density data were collected. From these data, channel structure could be deduced, and contour plots were created to help extrapolate the trends. Water and air temperature decreased throughout the autumn season. Short-term channel salinity and density structure was modulated by tides and winds. Density stratification was highest at South Station and North Station stratification was greatest when the freshwater signal was strongest. The depth of the pycnocline at South Station was not correlated to tidal height. However, when data points were separated by tidal cycle, there was a correlation between neap tide’s pycnocline depth and tidal height. Also, finer temporal resolution analysis of the northern channel salinity structure revealed that there is extensive within channel variation, and that salinity is regulated by tidal phase and cycle, as well as winds. The temperature, salinity and density structure patterns presented within this study, strengthen our understanding of their physical drivers within the San Juan Channel.

Thrust faults are a type of fault where the hanging wall is thrust on top of the foot wall. In some situations, such faults cause another thrust fault to occur in the same area, but facing the opposite direction. These are called back-thrust faults. In the Seattle Fault Zone, an area which spans from the Kitsap Peninsula through Lake Sammamish and is about 8km wide, there are three main thrust faults and five back-thrust faults. However, the expression of these faulting features on the seafloor may be masked by on-going sedimentation processes. This study focuses on an area off the East coast of Bainbridge Island in Elliot Bay near Seattle, Washington. The use of ship-based SONAR (SOund Navigation and Ranging), which produces an acoustic signal and determines depth based upon the two-way travel time of sound, was used to create bathymetric surfaces. The survey was conducted by following navigational track lines which span the survey the area in parallel lines. During the survey, acoustic signal was received by multiple beams at various angles from the center of the ship. A high-resolution multi-beam sonar survey was conducted over this area of uncertainty in fault locations. Post-processing of these data generated a three-dimensional seafloor map, or surface. The excursion was used to amplify changes in bathymetry in hopes of discovering evidence of faulting. While the locations of the back-thrust faults were not indicated on the created surface, some abnormal surface features were located along a proposed main thrust fault. These features could solidify the location of the main thrust as well as indicate recent movement along the fault.