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.

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.

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.

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. 

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.

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.

 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 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.

 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.

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.

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.

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.

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.

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.

 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.

 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.

Internet resources provide an abundance of information about diabetes, mostly without any quality control. Providing resources to patients can be challenging for student and new graduate nurses due to the vast amount of potential websites. We were seeking new ways on how student and new graduate nurses can assess the value of patient websites focused on diabetes. The aims of this study were: 1) to identify the most frequently accessed diabetes websites by (N=142) undergraduate nursing students; 2) to evaluate the data based on quality criteria to see which websites provided the most complete information, and 3) to make website recommendations for patients with diabetes in regards to disease recognition, treatment, safety, and lifestyle choices. This secondary quantitative analysis was conducted with de-identified data from a class assignment at the UW School of Nursing. Websites were accessed a total of (N=399) times. Each website was evaluated for 12 categories with a quality score of 0-9 for each category. A score of 0-3 meant minimal, 4-6 moderate, and 7-9 meant complete information for that category. For each category we took the mean score of all individuals who evaluated that website to determine its strength. After identifying duplicates, a total of (N=53) websites were identified. Based on the highest quality scores, the top 10 websites were four governmental, four non-governmental and two commercial. Of these, the most complete website was diabetes.org with a mean rating of 89.3 out of a possible score of 108. The next two contenders were kidshealth.org and niddk.nih.gov with mean scores of 77.1 and 74.9 respectively. Educating nursing students and new graduates about the value of safety and quality of information on the web will enable them to better inform patients and families. More research is needed if this type of education makes a difference in patient outcomes.

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 Farnsworth-type IEC reactor was once considered to behave as a point source of neutrons with reference to the spherical central accelerating grid. This was assumed because the deuteron-deuteron fusion reaction is inherently spherically symmetric (isotropic), and current theory suggested that the vast majority of fusion events were occurring in the deepest region of the potential well (the accelerating grid, which is also the geometric center of the reactor). However, anecdotal evidence has suggested that isotropy may not be empirically accurate. Our main objective was to conclusively test the assumption by measuring deviations from uniformity in the neutron flux. To measure this we used three different types of detector: CR39 plastic, BTI bubble detectors and He-3 dosimeters. We exposed the CR39 slides to fast neutrons (2.45 MeV) at a fluence of 10^6 n/cm^2, and they indicated apparent anisotropy (p-value of .0035) with higher flux at the front and rear of the machine. The BTI bubble detectors and He-3 tubes also corroborated a higher neutron density at those sites. We then hypothesized that beam loading on the front and rear conflats by the plasma "jets" emanating from the central cathode could be responsible. Measurements with paired He-3 tubes after blocking the jets with quartz glass showed the apparent anisotropy reduced by 38% on average (p << .001). This quantitative confirmation of anisotropy, and the significant (but not sole) role that beam-target fusion plays therein, represents an important shift in the understanding of the Farnsworth-type reactor, which could have important implications in plasma physics and the development of fusion energy.

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.

Acute myeloid leukemia (AML) is a type of blood cancer. This disease is treated by chemotherapy and bone marrow transplantation, but mortality rates remain high and new therapies are needed. Because gene expression in AML differs from person to person, it is possible that personalized therapies can be designed by understanding how gene expression predicts drug sensitivity. Previous studies tested the sensitivity of 14 human AML cell lines and 30 primary patient samples to 160 chemotherapy drugs, and utilized computational approaches to identify genes that are correlated with the sensitivity to specific drugs. In my project, I am evaluating several of these predictions by silencing gene expression in AML cell lines with a tool called short hairpin RNA (shRNA), which is used to bind and degrade the expression products of genes called messenger RNA (mRNA). I will then test the ability of drugs to inhibit growth in cells that have undergone gene silencing versus control cells that have not undergone gene silencing. If we successfully validate these gene expression-drug sensitivity relationships, they could lead to personalized clinical treatment approaches in AML.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

Gas chromatography - mass spectrometry (GC-MS) is a widely used analytical technique for separating and identifying volatile and semi-volatile compounds in complex mixtures. It is beneficial to research ways of increasing sample throughput (i.e. decreasing analysis time) while not losing any chemical information. This study investigates the change in volatile chemicals (odors) that are emitted from banana peels in varying stages of ripeness. The headspace of banana peels was first analyzed using Solid Phase Micro-Extraction (SPME) with a standard gas chromatograph and a quadrupole mass spectrometer (qMS). For demonstrating a viable platform for increased sample throughput, the samples were then analyzed on a LTM (Low Thermal Mass GC) coupled to a Time-of-Flight mass spectrometer. The banana peel analyses on the LTM-TOFMS decreases the run time by tenfold when compared with the traditional GC-qMS. A new data analysis program developed by the Synovec Lab is used to visualize the data and identify compounds.

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.

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. 

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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. 

 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.

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.

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.

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.

Age-related cardiac pathologies are currently endemic in most developed nations and account for a large number of premature deaths and huge medical expenditures. Although lifestyle-associated risk factors have frequently been correlated with risk of cardiac impairment, it is also clear that aging impairs heart function even in the absence of these risk factors. Caloric restriction (CR) is known to extend lifespan and offset age-related impairment in diastolic function in murine models. Rapamycin is a CR mimetic that also extends lifespan (when given throughout life) and is protective in models of cardiac hypertrophy and failure. However, the potential role of Rapamycin for treatment of impaired heart function in aging has not been established. To determine the effect of short-term Rapamycin treatment on cardiac aging, we monitored cardiac function in 25 months old C57BL6/CR mice fed for 10 weeks with a control diet or a diet containing 14ppm encapsulated Rapamycin. Analysis by tissue dropper imaging showed improvement in diastolic function in the treatment group as early as 4 weeks. Normalized heart weights were also lower in the treatment group compared to old control mice, suggesting that short-term sub-acute Rapamycin treatment can reverse cardiac aging and regress age-related cardiac hypertrophy. Proteomic analysis showed increased stability (half-life) of the cardiac global proteome, increased abundance of mitochondrial proteins, and decreased oxidative damage of proteins in the treatment group. Further analysis revealed metabolic remodeling in the glycolytic and TCA pathways that improve energy metabolism and cardiac function in 10 weeks Rapamycin treated mice. Data from murine models offer potent approaches that may be replicable in humans and may prove effective in management of cardiac and perhaps other age-related ailments. In this project, we both assist in preparing the control and treatment diets, mice handling, imaging preparation, tissues harvesting, data analysis, and experimental design for future experiments.

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.

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.

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.

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.

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. 

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.

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.

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.

Food is a sort of cultural capital; it tells a story of the history and people of a region, directly bound to their cultural identity. In Martinique, for example, to eat is to become uniquely acquainted with Martinican culture - including the inherent problems in the sustainability of the island's food web and the attainability of a Martinican “Creole” identity. Despite its status as an overseas department of France, the island’s society sees itself not as French, but as uniquely Creole, in opposition to “Frenchness”. The food web reflects this social struggle for national identity, and shows how Martinicans have built an identity, independent of Frenchness, that they seek to hold on to through traditional food practices. It shows how the ways of eating and the ways of thinking of oneself as Martinican are mired in ambiguity, since one cannot be Creole, without having a “Frenchness” about them. Through the exoticization of Martinican cuisine, especially with tourism websites boasting the island’s unique spices and foodways, Martinicans have a chance to preserve parts of their culture, including methods of production, communal food roles, and linguistics. This thesis outlines the history of Martinican cuisine, first showing what must be preserved, and why. I then discuss the dangers inherent in the food web, including lack of sustainability as a part of Martinican reliance on the “colonizer”, pesticide use, and overconsumption. Last, I outline the strengths of Martinican foodways, and the ways in which Martinicans are working to overcome the challenges of eating in their own country. With the fear of losing their identity, Martinicans are seizing and demonstrating their Creoleness, especially through food, as a unique identity in an increasingly globalized world. Their cuisine tells that story.

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.

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.

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.

“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.

As a senior undergraduate at the University of Washington, I have personally seen, along with many of my peers, many students drift in the endless forest of knowledge at the university. They become frustrated because they cannot conceive of how to integrate and apply the knowledge they acquire into their daily lives. I hypothesize that this bewilderment comes from not knowing when or how to synthesize and apply the knowledge we have obtained in classes and losing awareness of its purpose. Many educational researchers argue that mentoring is one solution for it. It is often considered a program to advance a mentee's values, skills, knowledge, and understanding. This research project used observation and survey methodologies to analyze two models of mentoring relationships: mosaic mentoring theory and collaborative mentoring theory. In mosaic mentoring theory, pre-existing common interests and strengths of peers generate interaction among themselves which extend to nurture those interests. In collaborative mentoring, individuals unite through developmental learning relationships under the goal of education that supersedes individual interests. This research identifies and evaluates the factors that make such relationships effective for both career and personal development of college students. I anticipate my preliminary results will confirm the mentoring theory such that collaborative and mosaic mentoring relationships help students to advance their psychosocial and career functions. Both models help students in determining their "life calling" through their studies and skill development.

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.

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.

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. 

 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.

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.

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.

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.

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.

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.

 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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

 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.

The Pacific Northwest is a dialect region thus far largely understudied by linguists. Also, the Japanese-American community in the American Pacific Northwest, although a minority population, has been a salient part of the region’s history since the late 1800s. This study both draws on recent prior linguistic research and examines the speech of two second-generation, Seattle-born Japanese-American sisters in order to answer the following questions: First, do these two sisters express differently their experiences with each the Japanese, Pacific Northwest, and Japanese-American communities? And second, to what extent do Japanese-American speakers and Caucasian-American speakers similarly articulate the vowels in words such as "bag" /æ/ and "beg" /ԑ/? A conversational interview, a reading passage task, and a word list reading task were recorded for both sisters. This interview, in which both sisters participated, was transcribed and tagged for metalinguistic themes. Tokens of both vowels were taken from the individually recorded reading tasks for each sister and were measured in Praat for the formant frequencies of F1 and F2. The trends revealed in plots of each sister’s formant data are linked to the connectedness of each sister to the Pacific Northwest community. Through these collective data, this study seeks to show two things: that perceived negative experiences with a culture to which a person has ties are correlated with increased expression of disconnectedness from that culture; and that perceived positive experiences with a culture to which a person has ties are correlated with increased expression of connectedness with that culture. Finally, by drawing on recent prior research of Caucasian speech patterns in the Pacific Northwest and comparing it to the Japanese-American data in this study, this study seeks to show that Japanese-American speakers and Caucasian-American speakers show similarity in the articulation of the vowels /æ/ and /ԑ/.

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.

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.

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.

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.

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.

 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.

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.

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.

Slavery is commonly conceptualized as a limited form of chattel slavery that existed in the pre-Emancipation antebellum South. However, the 13th Amendment that abolished slavery also includes a clause that permits enslavement as an "appropriate punishment for a crime”. It is through this lens that I examine the disproportionate rise of racialized incarceration, and the subsequent privatization and profiteering that has exploded in recent years, as a form of contemporary slavery. Using an analysis of immigrant detention on the US-Mexico border, I argue that our immigration system acts as a form of racial control and neoslavery, and that such a conclusion necessitates a radical restructuring of national dependence on criminalization and enslavement.

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.

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 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.

This 2014 Jackson School Task Force project focuses on the renewal of a European Grand Security Strategy, which emphasizes the necessity of regional prioritization, global engagement, and internal capacity. In depth analysis of current EU policy instruments and previous engagement acts as a point of departure - culminating in strategic policy recommendations which advocate for comprehensive engagement, regionalization of cooperation, and regionally segmented, thematically driven policy packages to comprehensively address instability in Europe's 'neighborhood(s)'. The overall Grand Strategy is divided regionally; our task was to update the European Union’s security policy towards the Middle East and North Africa (MENA). The focus of this report was to examine the level of efficiency and strategic calculation within the EU's approach to the broader region. It is argued here that although economic integration between Europe and its extended neighborhood has been successful, its political influence in the region is in decline as a result of its shortcomings in crisis management and political reform. As a result, the probability of intensified instability in the MENA presents Europe's most pressing security concern. Our findings conclude that the European Neighborhood Policy (ENP) framework would function more effectively if the task of economic integration is confined to the ENP; while other components - crisis management, political reform, and civil society engagement - are removed from its agenda and reorganized into a broader MENA regional policy package. This strategic remapping of the EU's MENA neighborhood - to include the Gulf States, and Iran -would allow Europe to more comprehensively and holistically address the region’s common security concerns. Provided in this paper are clear strategic priorities for the EU and the means to operationalize them despite the ambiguity of an emerging multipolar global order.

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.

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.

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. 

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.

The purpose of this study was to research if people that witness another person depicting himself/herself to be in pain would induce a positive mood in the viewer. The study examined the induction of positive moods in people viewing a video depicting a person expressing discomfort or pain. Forty-five undergraduate students were recruited from the undergraduate student population of the Introduction to Psychology course at Bemidji State University. Students completed the Mood Assessment Scale to measure their current mood and then proceeded to one of two conditions. One condition viewed an America's Funniest Home Videos (AFV) video clip of people experiencing pain (n = 24) and the other condition read a collection of the Velten positive mood statements (n = 21). At the conclusion of each condition, students again completed the Mood Assessment Scale. An independent t-test was used to measure the different changes in mood induced by the Velten mood statements and the AFV video clip. Significant results were found for both the Velten Mood and AFV video condition. Results of this study indicate that observing a person who is experiencing pain induces a positive mood in the observer.

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.

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.

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.

 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.

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.

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.

 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.

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.

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.

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.

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 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.

From 1951 to 1981, the Canadian weathership program collected nearly continuous wind and wave observations at Station Papa, a common reference site in the North Pacific. The length of this time series makes it a valuable tool in determining long-term trends and statistics of North Pacific wind and waves. Due to the uncertain quality and poor documentation of the data, extensive cross-referencing and quality control of disparate data sources was performed, leading to the development of a single, high-quality dataset. To verify the accuracy and consistency of the weathership measurements, histograms of wind speed, wave height, and wave period were compared with those from modern wave buoy measurements at Station Papa, taken since 2010. While the wind measurements aligned well with the newer data, the wave observations showed notable biases. These biases are likely due to the outdated method of visually observing waves from the weatherships. A time-series model with an annual oscillation and autoregressive component was fit to the wind measurements. Such a model accurately represents both the seasonal weather cycle and short-term storm pattern at Station Papa. In addition, it was found that the wind and wave statistics were significantly correlated on interannual timescales with the El Niño Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO). Quantifying the impacts of these trends has practical implications for predicting future changes in wind and wave climate.

 The population of surfers has grown rapidly over the past 50 years and the surfing industry has expanded with it. The surfing industry was calculated in 2005 to be worth $7 billion annually and has grown since then. With this increase in popularity the ‘perfect’ surf spots around the world have become overcrowed (Scarfe, 2009). Hence there is a desire for Artificial Surf reefs (ASR) that take into account coastal, ecological and surf enhancement. In order to build successful Artificial Surf Reefs (ASR) there are many parameters that need to be taken into consideration. Three important ones are breaking wave height, wave peel angle and underlying bathymetry. Combining these three parameters produces a simple ranking system for the Surfablilty of both the wave and the location. I collected data at 3 different locations in the southern hemisphere each with a different ranking to allow a good range in data (New Zealand; Te Arai & Shipwreck bay, Tahiti; Vairao). Data was collected on underlying bathymetry, wave height and wave peel angle. I hypothesized that there was a relationship between bathymetry and the surfability of waves specifically; a sharper change in bathymetry into shallower water depth regions would produce a higher ranked wave.  Wave height mesurements were collected using pressure sensors located at the seabed, for peel angle video recordings were analyzed. For bathymetry I surved each location using a depth sounder and single beam transducer.

---still working on results

The source and fate of hazardous material released into rivers and estuaries is critically important to protecting environmental health, especially in highly industrialized areas such as the Puget Sound. This study focuses on determining the legacy of heavy metal distribution (Pb-Cu-Zn-As) from a demolished ASARCO smelter site in north Everett, WA near the mouth of the Snohomish River. The Snohomish is a complex riverine system with many potential point and non-point sources of contaminants. This site is the target of remedial actions under the Model Toxics Control Act cleanup regulation developed by the Washington Department of Ecology due to widespread As and Pb contamination in the early 1900’s. Previous studies showed a correlation between heavy metal concentrations in benthic sediment of Possession Sound and proximity to industrial sites near the mouth of the Snohomish River. If the source is the ASARCO smelter, we should be able to trace Pb contamination downstream from the site. No data are available from within the river to constrain the specific sources of anthropogenic metals. In our study, we use Pb isotope variability between natural and anthropogenic Pb to establish the extent of dispersion of contaminants derived from ASARCO. The sample suite we collected consists of: three one-meter-long river-bottom sediment cores collected 1) near the mouth of the Snohomish River, 2) near the ASARCO site, and 3) up river to compare natural baseline values with near site and downriver sites; and 4) slag samples to serve as reference isotopic signature of ASARCO Pb. Purification of Pb from the samples is complete, and the isotopic analyses of the Pb are in progress utilizing an inductively coupled plasma mass spectrometer under the advisory of Dr. Bruce Nelson at the University of Washington. This research will identify spatial and temporal relationships among fluvial processes and Pb deposition.

Bushmeat poaching -- and subsequent consumption -- presents the foremost threat to wildlife conservation in East Africa. To assess its social, ecological and economic magnitude, I interviewed a representative sample of the local population in the Lake Manyara area of northern Tanzania. Illegal poaching was evaluated based on 16 structured interviews of poachers from distinct hunting groups. Both availability and consumption of bushmeat were evaluated based on 185 structured interviews of ethnically diverse local households. Some 38 percent of households admitted to consuming bushmeat on a semi-regular basis. Conservative interpretations of numbers of wildlife species poached show rapid depletion due to illegal hunting. Swift implementation of capacity-building programs must occur to provide poachers with alternative income sources and ensure more caution in factors influencing consumption, education programs emphasizing the importance of conservation for groups with high consumption levels, and strategic enforcement patrols in Community Areas frequented by poachers.

As intertidal communities face predicted increases in temperature and hydrodynamic disturbances due to climate change, organisms may find it necessary to reallocate energy among normal physiological processes for survival. Specifically, mussels must distribute energy among processes such as attachment, shell growth, metabolism, and reproduction, all of which may be influenced by seasonality and other natural environmental fluctuations (temperature, pCO2, etc.). Examining energy distributions is the first step in predicting responses to environmental change. In the present study, we investigated the energetic cost of byssus production for the intertidal mussel Mytilus trossulus. After performing an initial pilot study to establish methods for manipulating byssus production by controlling how often the mussels had to replenish byssal threads (ie. daily, weekly, never), we exposed collected mussels to each treatment in triplicate for a four-week period. We then assessed the energetic cost associated with byssus production in relation to energy allocated to other processes such as growth and development. For all measures (length, width, height, shell mass, etc.), forcing the mussel to produce more byssus resulted in a decrease in growth rate; this was significant for length and shell mass. For this study, activities for making longer shells were first to be forfeited as mussels were manipulated into manufacturing greater amounts of byssus during a season where developing reproductive structures were of highest priority. This research identifies byssus production as a major energetic constraint in mussels, which play an important role both economically through aquaculture as well as in intertidal marine ecosystems. As these globally marketed shellfish are placing more amounts of energy towards byssus production, less energy is available for growth. Coupled with modeling predictions, this information could be useful for aquaculture practices as well as understanding physical changes mussels undergo in response predicted climate change.

The value of property, especially in an urban environment, is extremely high, yet personal vehicles are given tremendous reign over great swathes of this land. In the historic Belltown area, wide automobile corridors cut through the neighborhood. This vehicle dominated landscape poses safety risks to pedestrians and bicyclists alike while catering to large, single occupancy vehicles. In order to create a safer and more equitable streetscape, certain factors must be taken into consideration. These include reducing parking abundance, restructuring parking prices, correctly allocating road space, and implementing human scale design changes. Through the analysis of the finances of parking, and looking at case study cities, an understanding of better parking management and streetscape design will be formed. I anticipate that the reduction of parking spaces and driving lanes, as well as the introduction of market-rate pricing for parking, will result in less congestion and accidents, will not negatively impact local commerce, and will result in a more inviting streetscape for all users. Furthermore, the fundamental issue of parking is not one that affects the Belltown neighborhood exclusively, but is an issue that persists throughout Seattle and other urban spaces. The core findings of this project may be analyzed and applied to other environments.

The Society for Ecological Restoration, University of Washington Student Chapter (SER-UW), has for the past several years been restoring a forested site near the North Campus Residence Halls. After years of hard work clearing the area of invasive species, SER-UW has begun an effort to share the site and their ideas of habitat and biodiversity revitalization with the community at the University of Washington. The big question for the group now is, can we turn the restored forest into a community space for use and recreation? As the Design Intern for the group, I am utilizing my background as a Landscape Architecture student to create a design that will activate "new" space, as it was inaccessible prior to invasive species removal, and allow for an exciting interaction with, and interpretation of, a Northwest Forest experience. I have performed as a mediator for SER UW, to turn their ideas and desires for the site into design. I set to work discovering how to establish the site as an interpreted and useable site for the community. I developed drawings, diagrams, a prototype sign, and a site plan, then held a work shop with SER UW to discuss the preliminary design. From there, and through a meeting with the Campus Landscape Architect, I created a fourteen page report including details and guidelines of the site design. The design focuses on programs of community gathering and art, as well as elements implemented to influence interaction with the site. Through our design, SER UW will create a legacy at the Whitman Walk Restoration Site. The site will be sustainable from the active involvement and care of the Whitman Walk through students who grow to appreciate the site and find a sense of belonging there. Whitman Walk will grow a greater understanding of the significance of ecology in its visitors for many years to come.

This study examines the uses and needs of Third Avenue, in downtown Seattle, from Stewart Street to University Street in pursuit of possible solutions to the area’s historically bad reputation and general misuse. Using two sociological theories, Collective Efficacy and Broken Windows Theory, we examine how the social and physical attributes of Third Avenue contribute to crime and social disorder, and exacerbate the negative reputation of the area. Drawing from direct observations, interviews with key stakeholders and analysis of existing crime and transit data, we propose the main social issues of Seattle’s downtown arise from three meta themes. First, we identify four distinct user groups and discuss how the disproportionate presence of these groups impacts public perception and experience of the area. Next, we bring attention to the significant gap between the perception and reality of crime on the street; a gap that is not present when analyzing social disorder. Third, we highlight physical attributes of Third Avenue incongruent with a positive experience and inhibiting the use of existing amenities. Ultimately, we recommend improvements to both physical and social attributes to increase social engagement and decrease disorder.

Compound I is the intermediate responsible for substrate oxidation in the catalytic cycles of a variety of heme-containing metalloenzymes, such as peroxidases, oxygenases, and importantly, cytochrome P450s. Cytochrome P450s, through compound I, oxidize approximately 75% of foreign substances that enter the body, such as pharmaceuticals and chemicals from the environment, so there is an interest in the mechanism by which this reaction occurs. The goal of this project is to probe the potential reversibility of Compound I formation, a step traditionally thought to be irreversible. Due to its stability and availability, horseradish peroxidase (HRP) was used as the model enzyme. In the case of HRP, hydrogen peroxide is reduced to water at the heme cofactor, while oxidizing a variety of substrates. In the presence of an oxidant and the absence of a substrate to oxidize, hydrogen peroxide coordinates to the iron of the heme, the O-O bond is cleaved, which forms water and compound I. A key experiment reacts HRP with unlabeled H₂O₂ in ¹⁸O-labeled water, and determines whether mixed-labled H₂O₂ is formed. The presence of mixed-labeled H₂O₂ indicates that there is reversibility of the O-O bond cleavage that forms compound I. The existence of mixed-labeled H₂O₂ is ascertained by first removing HRP by filtration, leaving the H₂O₂ in the filtrate. This is followed by the addition of a water soluble phosphine. In this case, the phosphine cannot be oxidized by Compound I, but can readily react with free hydrogen peroxide in solution to give the corresponding phosphine oxide. Mass spectroscopy is used to determine whether the phosphine oxide has incorporated the ¹⁸O label. Results show that when the experiment is performed in the presence of ¹⁸OH₂, there was no observable increase in the intensity of a peak corresponding to ¹⁸O-phosphine oxide, so reversibility of Compound I formation was not confirmed.

We describe an exo-selective cyclization of enantioenriched allenols to form cyclic ethers containing an α-tetrasubstituted stereocenter. Cyclic ethers bearing α-tetrasubstituted stereocenter are present in acetogenins, macrodiolides, ionophores, and lignans. These natural products have been found to have anti-fugal, anti-tumor, and/or antibiotic properties. However, an asymmetric catalytic synthesis of α-tertrasubstituted cyclic ethers remains a major synthetic challenge. Our method works with as little as 0.02 mol % of a gold catalyst for the exo-selective cyclization of enantioenriched allenols, and proceeds with excellent chirality transfer, and high functional group compatibility.

Solar technology is a potential way to help meet the growing demand for clean, renewable energy. Hybrid composites of inorganic quantum dots, with organic semiconducting polymers, offer a potential means of producing low-cost, solution-processable photovoltaics. Photovoltaics can convert sunlight directly into electricity to capture solar energy. The synthesis of quantum dots typically involves the use of large surfactant molecules to facilitate particle growth and solubility. These native ligands act as electrical insulators that impede charge transport in photovoltaic devices. Therefore, it is necessary to exchange these large ligands with small molecules to achieve efficient charge carrier photogeneration and transport. In this research, we examine bulk heterojunction blends of low band gap PbS quantum dots with the conjugated polymer poly((4,8-bis(octyloxy)benzo(1,2-b:4,5-b')dithiophene-2,6-diyl)(2-((dodecyloxy)carbonyl)thieno(3,4-b)thiophenediyl)) (PTB1) treated with different ligands including halide ions and organic crosslinkers. By using photoinduced absorption and transient photovoltage techniques, we study the long-lived charge generation dynamics and recombination kinetics of our devices. We find that the ligand treatments exhibiting higher device performance correlate to longer carrier recombination lifetimes in both spectroscopic and photovoltaic device measurements.

The pancreatic islet β-cell secretes insulin in response to nutrients such as glucose. In type 2 diabetes, insulin secretion by β-cells is impaired, causing hyperglycemia. Our group investigates this impairment, with the goal of identifying and understanding the underlying mechanisms. Pancreatic islets contain an extensive capillary network, including endothelial cells, which produce soluble factors that may modulate β-cell function. Specifically, our group has shown that media from islet endothelial cells cultured under control conditions (5.5 mM glucose) and subsequently incubated with islets enhances insulin secretion from those islets. In contrast, media from islet endothelial cells cultured in diabetic conditions (high glucose; 25 mM) shows no effect on insulin secretion. Thus, we hypothesize that islet endothelial cells normally secrete paracrine factor(s) – signaling molecules produced by one cell that cause particular reactions in nearby cells – that enhance glucose-stimulated insulin release but that in diabetes, production of these paracrine factor(s) is reduced. The goal of this project is to identify one or more of these paracrine factors. We cultured islet endothelial cells under control and diabetic conditions. mRNA was extracted and sent for whole transcriptome analysis (RNA-Seq), creating an expression profile showing the expression amplitude for each gene. Analysis of RNA-Seq data revealed patterns of differential gene expression between control and diabetic samples. Changes in expression for genes of interest identified by RNA-Seq are being verified by quantitative real time PCR (qPCR). Subsequent protein analysis via ELISA or western blot will confirm the RNA-Seq and qPCR data. Viral vectors or siRNA will be used to either overexpress or silence respectively the gene(s) of interest in islet endothelial cells. Media will be collected from these cells and used on islets to determine its effect on glucose-stimulated insulin release. This project should reveal novel mechanisms by which islet endothelial cells influence insulin release.

The fossils of the Cabbage Patch beds of western Montana record over five million years of mammalian evolution leading up to and across the Oligocene-Miocene boundary (23 million years ago [Ma]). This boundary marks the advent of many modern mammalian families. This evolutionary event may have been driven by the climatic and environmental changes of the time. Prior studies of these deposits have identified three faunal divisions occurring chronologically within the beds. To test whether faunal change was correlated with climatic or environmental change in our study area, we quantified the number of mammalian families and their relative abundance in the two oldest divisions of the Cabbage Patch beds (28-25 Ma), and compared this record with the record of habitat change and fossil preservation biases. A preliminary analysis of 495 microfossil specimens from five well-sampled different rock layers in these two divisions shows no change in the number of families throughout the time span; however, temporal shifts in relative abundances of families likely reflect differences in habitat and fossil preservation. Despite potential preservational biases, turnover in mammalian taxa occurs between the older and the younger layers. For example, mouse-deer, interpreted as forest specialists, are very abundant in the oldest layers but absent in the younger layers suggesting their local extinction. Conversely, gophers, native to more open, drier habitats, occur in the younger layers but are absent from the older ones. Together, these data provide circumstantial evidence of changing environments in our study area. These preliminary findings increase our understanding of habitat change and preservation bias in the two oldest divisions of the Cabbage Patch beds. We are currently improving the taxonomic resolution (from family to genus level) of our dataset to provide a more detailed view of changes in regional mammalian diversity during this critical interval in mammalian evolution.

Existing polymeric delivery systems rely heavily on non-covalent interactions between chains in order to provide reduced carrier toxicity and polymer clearance. A major side effect of this strategy is premature particle destabilization making them impractical for human treatment. Attempts to resolve this issue has included the creation of single molecule scaffolds but have suffered from a complex synthesis and inefficient degradation rates. In order to overcome these issues the design of a single molecule radical addition-fragmentation chain transfer (RAFT) polymerized system was undertaken which included a polyethylene glycol (PEG) stealth cornea and multifunctional brush architecture. PEG corneas are essential through their proven ability to increase biocompatibility. Therefore the design of polymerization conditions of a novel PEG macromonomer (Mn ~ 950Da) (O950) were conducted and resulted in the creation of polymers with a polydispersity index (PDI, a metric for determining the uniformity of a molecular size distribution) sub 1.1 at 80% conversion with lauryl methacrylate, a hydrophobic stabilizing monomer, across a degree of polymerization (DP, number of monomer repeats per polymer) from 25-100. The developed synthesis conditions were then adapted for conjugation functionalities to additional RAFT agents through a degradable ester bond. Further polymerizations were carried out from the added RAFT agents with a positively charged amine monomer to increase polymer solubility, producing a 34 armed brush polymer with a PDI of approximately 1.2 at 70% conversion. Further alterations added a pH responsive functionality for endosomal escape. Light scattering was employed to determine the particle size followed by hemolysis studies to determine the pH responsiveness. The result was a synthesis technique that allows the facile creation of multifunctionalized polymer multi-brush with accurate PDI and DP, a feat not seen throughout the literature.

Early intervention programs for infants and toddlers with developmental delays and disabilities have emerged as a result of Part C (formerly Part H) of the Individuals with Disabilities Education Act (IDEA) beginning in 1987. Ample research supports intervening early while the brain has a high degree of plasticity, especially before age 3. Kindering is the largest early intervention center in Washington State, providing 1,600 infants and toddlers with comprehensive services in 2013. The purpose of the current research was to analyze the developmental growth rate for children enrolled in the early intervention program at Kindering. This longitudinal study utilized test scores from the Assessment, Evaluation, and Programming System (AEPS), which includes 6 different skill areas: cognitive, social, social-communication, adaptive, fine motor, and gross motor. Using bivariate and multivariate analysis to examine the growth trajectories of 641 children ages 0-3, we expected to find that Kindering's comprehensive model improves children’s development over time. Results were further analyzed by various demographic factors including ethnicity, income, and gender. Multivariate analysis was also used to examine whether growth rate was dependent on the age that the child entered the program, expecting to see that those who entered at a younger age will have a greater growth trajectory. We anticipate that these results will enhance the existing research about the effectiveness of early intervention, and demonstrate Kindering as a persuasive program model that can be replicated in existing and new centers. This study also has the potential to inform policy and funding decisions for early intervention.

Parent engagement has been found to have direct implications in the academic success of students. Knowing the ways that parents are or are not engaged is vital to developing ways to improve parent engagement. Additionally, it is important to reveal the ways in which parent engagement is defined in current school settings. Increasingly, school, and community based organizations are in need of understanding how well they are doing in engaging parents. To help us understand ways to assess parent engagement, this study examines parent engagement measures found in literature from 1993 to the present with a focus on its representation in urban communities. Specifically, we examine how equitable and traditional forms of parent engagement are or are not represented in the constructs used to measure parent engagement in urban settings. We synthesized literature into Excel templates and then coded using MAXQDA software. This allows us to analyze the data and more easily view patterns, differences, and commonalities among the literature. Using our coding database, we found preliminary results that indicate that parent engagement studies of urban school settings were more frequent in comparison to suburban, rural, or mixed school settings. We found that within the urban setting, when studying parent-engagement behaviors, over fifty percent of the time the behaviors studied were home-based. These findings suggest that the quantitative measures and studies of parent involvement over the last twenty years largely reflect the traditional approaches that qualitative studies have found to be inhibiting, particularly for the participation of non-dominant parents such as minorities or parents from low-income background in school-based or community-based parent engagement. These findings suggest the need to examine beyond the scope of traditional measures in order to begin to understand the potential of equitable parent, school, and community collaboration for improving student learning and success.

Localized surface plasmon resonances (LSPRs) can be described as oscillations of large electron densities. Traditionally observed in metals, LSPRs have recently been observed in semiconductors, and have gained more attention because of their tunability over a wide range of energies. Additionally, semiconductor LSPRs could offer a cheaper alternative to plasmonic applications. Here, we aim to observe the effect of band-gap engineering on LSPRs in zinc oxide semiconductor nanocrystals by incorporating Cd^{2 +} and Mg^{2 +} ions into zinc oxide host lattices. Cd^{2 +} -and Mg^{2 +} -doped zinc oxides of different molar dopant ratios are synthesized via base-initiated hydrolysis and air-free hot injection synthesis. The size and structure of the nanocrystals are characterized via transmission electron microscope (TEM), absorption and photoluminescence. The molar dopant ratios of the samples are determined analytically via inductively coupled plasma atomic emission spectroscopy. In order to observe LSPRs in semiconductors, conduction-band electrons are added to the semiconductor nanocrystals via photochemical reduction to give them metallic-like properties. The number of electrons accumulated can be measured by titrating the samples with mild oxidants such as decamethylferrocenium. The LSPRs in the zinc oxide nanocrystals are studied by electron paramagnetic resonance spectroscopy (EPR) and infrared (IR) spectroscopies. In combination with absorption and photoluminescence, EPR is used to measure the conduction-band, valence-band and overall band-gap energies. Using IR spectroscopy, we study how these energies influence the LSPR energies.

A crucial segment of sustainable jet fuel production is the fermentation of lignocellulosic-based sugars to acetic acid. Biomass from non-food sources such as wood, switch grass, and waste materials can be fractionated into their raw sugar components (glucose, xylose, mannose, arabinose, and galactose). These sugars can later be fermented to acetic acid, reduced to ethanol, dehydrated to ethylene, then oligomerized and hydrogenated to produce jet fuel. Moorella thermoacetica is an obligate anaerobe that exclusively ferments sugars to acetic acid. Thus far, fermentation using M. thermoacetica has been achieved with synthetic glucose and xylose. It is essential to investigate the fermentation of all five sugars in order to validate lignocellulosic biomass as a feedstock for this process. In this work five synthetic sugars were fermented in flasks at 58°C without pH adjustment. Samples were taken every 4 to 6 hours over a period of 48 hours and were analyzed offline by high performance liquid chromatography (HPLC). The trend of sugar consumption shows that M. thermoacetica has a substrate preference of xylose over glucose, and glucose over other sugars. The sugar consumption was 100% for xylose, 98% for glucose, and 30 - 40% for the rest of the sugars. Successful five sugar fermentation suggests a concrete potential to upscale the bioconversion process and build a feasible market for jet fuel produced from lignocellulosic biomass.

The Miocene epoch represents a hotbed of cetacean evolution; during the epoch, whales underwent a large radiation of morphological forms and ecological specialization. The superfamily Platanistoidea experienced high diversity, especially during the Miocene, with 47 extinct and extant species currently known to science. However, of these 47 species, the Ganges River Dolphin is the sole extant member of this once large clade. Here in Washington State, the University of Washington Burke Museum (UWBM) specimen 87105 is a probable representative of the Platanistoidea in the Pacific Northwest. The specimen consists of the posterior third of the skull, along with some non-diagnostic ribs and vertebrae. It is tentatively a member of the Squalodelphidae, and shares morphological similarities, namely thickened supraorbital bosses, with other members of the Platanistoidea, such as the Platanistids found in the Astoria formation in Oregon and in the Calvert Cliffs formation in Maryland. This project's goal is to describe UWBM 87105, and place it as either a member of the Squalodelphidae or the Platanistidae.  Research into the distinguishing synapomorphies of the Platanistoidea and its families is ongoing; from these synapomorphies, I am deriving a character matrix for UWBM 87105. UWBM 87105's place within the whale phylogeny will expand what we know about the cetaceans present in the Pacific Northwest during the Miocene. In addition, studying this specimen will shed light on the diversity of the Platanistoidea, diversity that is no longer present in the oceans today.

Two-methoxyestradiol (2ME or 2ME2) is a highly water insoluble metabolite of estrogen, which possesses antiangiogenic activity and can upregulate death receptor 5 and interferon-signalling pathway, exhibiting anticancer effects. It is practically water insoluble and drug crystals milled to nano-size are evaluated in humans without success to date. While 2ME can inhibit tumor growth, its insolubility (<1ug/ml) may relate to low oral bioavailability. Some studies used vehicles to improve bioavailability. To address insolubility and improve antitumor activity, we evaluated 2ME’s ability to be incorporated into lipid nanoparticles (LNPs) that have been shown to be safe and to provide some tumor cell selectivity. To do so, we investigated different lipid compositions in their abilities to incorporate water-insoluble 2ME. The drug-lipid particles were made with solvent evaporation and hydration method. The free 2ME was removed to determine the degree of drug incorporation into LNP. Drug concentrations were determined with a high-performance chromatography (HPLC) assay. The LNP particle diameter was measured by photon correlation spectroscopy. Among tested lipid compositions, DSPC and DSPE-PEG2000 mixture provided about 80% drug incorporation at drug-to-lipid mole ratio of 1:6. The diameters of the 2ME-LNPs were 47.2±7.2nm. The anti-cancer activity was evaluated in two cell lines, MDA-MB-231 and A549. The 50% effective drug concentration to inhibit cell growth or EC50 of 2ME in MDA-MB-231 breast cancer cells were 0.83µM and 32.4µM for free and LNP respectively. For lung cancer A5492 cells, EC50 was recorded at 2.13 and 3.35 µM respectively for free vs. LNP formulation. These results demonstrated that (1) lipid incorporation overcomes 2ME water insolubility and (2) the drug-lipid particles provide high (~80%) incorporation efficiency thus likely reducing the overall cost, (3) a stable lipid-drug formulation that can be easily scaled and (4) the antitumor cell potency may vary with different cancer cells.

Methylotrophs are bacteria that utilize one-carbon compounds like methane, methanol or methylamine for growth, and play an important role in the carbon cycling of aquatic ecosystems. In particular, bacterial communities investigated in Lake Washington have proven the significance of methylotrophs in methane and methanol rich environments. From these communities, individual strains of bacteria are cultivated, and their genomes are sequenced. Genomic sequencing enables taxonomic classification, which differentiates these novel strains into different classes. By cultivating these strains on selective media and observing their properties under various conditions, these novel strains can be classified further by their phenotypes. Additionally, the phylogenetic relationships between these strains rely on the analysis of their shared proteins. Through the study of an array of alpha- and betaproteobacteria, we can track the divergence of each of these strains in their key methylotrophy metabolic pathways. These subtle gene differences are a testament to the metabolic variety and ingenuity of these bacteria. Phenotypic differences among these strains also imply the variety of roles each organism has within their community and alludes to partnerships between these bacteria in their natural environment.

Recent experimental observations of draining colloid-laden liquid films show stepwise film thinning, as opposed to continuous thinning that occurs in films without colloid particles. The steps are also shown to propagate at a rate that depends on the diameter of the film. In this project, a mathematical model of a thin liquid film containing colloidal particles is derived from the laws of fluid dynamics in a cylindrical coordinate system. The particles in the film give rise to an oscillatory component of the disjoining pressure that is absent in particle free films. Solutions of the model show that a uniform film is unstable to layering. The overall goal of the work is to predict the stepwise thinning behavior seen in experiments, and to understand the physical reasons behind this and other observed film behaviors.

Biological systems coordinate themselves through cues such as ion currents and membrane electric potentials. This communication utilizing membrane proteins such as membrane receptors, channels, and pumps allows biological systems to form hierarchies of control over their systems that have yet to be achieved in conventional electronic systems. Integrating such biological components with nanoelectronics could allow exciting new developments in the field of biomimetic energy conversion. However, this approach requires the seamless incorporation of biological structures into electronics. In order to use membrane proteins, they must be integrated with a lipid bilayer which is essential to create a cell membrane mimicking environment. Lipid bilayers have previously been integrated on solid substrates for electrophysiological measurements and the construction of organic-inorganic hybrid devices, but have yet to be formed on PdH_x. In this work, we build the foundation towards harnessing this biology-based method of control by forming a lipid bilayer composed of DPhPC/DPhPE/PI/Cholesterol on PdH_x contacts. The formation and deposition of electrochemically robust liposomes on a PdH_x surface was confirmed using dynamic light scattering (DLS) measurements, atomic force microscopy (AFM), and resistance measurements with a PdH_x proton field effect transistor (H⁺-FET). Vesicle formation was proven through DLS by determining size of the lipid structures in aqueous solutions. These vesicles were then deposited onto a PdH_x contact and formed solid-supported bilayers on PdH_x surfaces by the process of spontaneous vesicle adsorption and rupture as confirmed by AFM. Finally, the electrical stability of the bi-lipid membrane was characterized through electrical measurements with an H⁺-FET, confirming minimal H⁺ leakage across the bilayer. Future work includes embedding an ion pumping membrane protein, bacteriorhodopsin, into the bi-lipid membrane to enable electrochemical gating of the PdH_x H⁺-FET through optical or other environmental cues for biomimetic energy conversion.

The brain is the most powerful computer in existence, possessing roughly 100 billion neurons with one-quadrillion synapse connections between them. Mimicking the synapse of a neuron could lead to increasing processing power, a better understanding of brain functions, or enhanced biomedical device integration. We have previously demonstrated proton-conducting devices with synaptic behaviors utilizing protons as charge carriers in a palladium source-drain system. Altering the design of these devices to become more useful to the biomedical field would be highly advantageous. Due to nature’s naturally curved geometry, we aim to develop flexible devices capable of matching these parameters for biomedical integrations. Flexible devices allow a much broader scope of applications, including health sensors on the human body that might require soft or curved morphologies. The mechanical engineering and processing conditions to create flexible devices is currently being investigated. I propose starting device fabrication with a pre-strained substrate. When palladium is deposited on this substrate, it will compress and exhibit wave-like patterning upon the release of the substrate’s strain. This is critical to the device flexibility, as previous palladium tension tests showed a high fracture rate. With a pre-induced compression in the palladium, tension would result in a more relaxed state and limit fracture in the devices to allow flexibility. Future works involve determining buckling strains for various palladium thicknesses to obtain wave-like patterns of compression, determining a suitable substrate material, and comparison of electrical properties to our current palladium devices.

Cancer diagnostic immunoassays are widely used for the detection of disease in vitro, but low antigen concentrations may not be detected in an early stage or confused for baseline noise, leading to false negative or positive diagnoses. Poly(carboxybetaine methacrylate) (PCB) is a zwitterionic polymer that strongly resists biofouling while allowing simple functionalization and effective bioconjugation to proteins. Coating this polymer on iron oxide nanoparticles via a DOPA attachment group allows for easy antibody immobilization, to realize low nonspecific binding and high signal-to-noise ratio in one platform. Methods for nanoparticle construction include synthesis of MNPs (magnetic nanoparticles) coated with PCB-DOPA and PCB-DOPA2. The coated particles are functionalized with FITC-BSA and FITC-streptavidin using EDC/NHS chemistry to optimize conjugation parameters. A model antibody (ALCAM antibody) is then conjugated to test the platform’s sensitivity for immunoassays. The functionalized nanoparticles are characterized with Dynamic Light Scattering (DLS), fluorescence spectroscopy, flow cytometry, and Surface Plasmon Resonance (SPR). Control groups with bare beads, functionalized beads with no polymer coating, or no functionalization are also processed in the experiment to compare with experimental groups. In preliminary tests, the functionalized magnetic nanoparticles have a high level of immobilization of each tested protein or antibody (FITC-BSA, FITC-streptavidin, and ALCAM antibody). In the plasma stability test, the PCB-coated and beads show low nonspecific binding even with high levels of functionalization. The experimental immunoassay can detect a low concentration of the ALCAM cancer biomarker in bovine serum, with less baseline noise than a commercial immunoassay (Luminex MagPlex®). The functionalized magnetic nanoparticles have a low detection limit to an early-stage cancer biomarker and a high signal-to-noise ratio due to reduced nonspecific binding. This platform could be extended to many clinical immunoassays in which either false negative or false positive diagnostic readings are problem.

The distinctive pigment pattern of the adult zebrafish Danio rerio is formed by stripes made up of black pigment cells called melanophores. Melanophores are the homologue of human melanocytes, which can give rise to deadly melanomas; understanding the signals that regulate the differentiation and proliferation of these cells may be key in treating cancer. Previous work in our lab demonstrated that thyroid hormone (TH) plays an important role in limiting the number of melanophores that appear during development. I wanted to know if TH was also required to maintain appropriate numbers of melanophores after the adult pigment pattern had formed. TH is produced by thyroid follicles, and if the thyroid follicles are ablated, fish cannot produce TH. I used a line of transgenic zebrafish to ablate the thyroid at adult stages to determine if this had any effect on melanophore numbers. Indeed, after several months with no TH these thyroid ablated adults showed an increase in the number of melanophores, demonstrating that TH does play a role in inhibiting proliferation of adult melanophores.

The increasing rate of suicidality and death by suicide among military service members has gained considerable attention from the Department of Defense (DOD), members of Congress, and the civilian populace as military suicide rates have surpassed suicides in the general population. Although suicide prevention has become a national research priority, it has been difficult to identify specific and modifiable risk factors contributing to the rise of military suicides. Previous research suggests that both victims and perpetrators of bullying are at greater risk for suicide, but the prevalence of bullying and its impact on suicidal ideation and behaviors within military populations in unknown. The current study will explore the relationship between bullying and suicidal behaviors among military service members using baseline data from a multisite DOD-funded suicide prevention study. Participants include 125 active duty Soldiers and Marines who have engaged in recent suicidal behavior and/or reported current suicidal ideation. As part of a larger clinical interview, participants were asked about suicidal thoughts and behaviors and experiences of bullying in the military workplace. Regression analyses will be conducted to assess whether bullying constitutes a risk factor for increased suicidality. We predict that greater instances of bullying within the military context will be associated with higher rates of suicidal ideation and increased suicide attempts. To our knowledge, this is the first study to examine bullying and suicidality among U.S. active duty service members. A better understanding of this risk factor may contribute to more effective suicide assessment and prevention strategies in the military.

A species distribution model can be used to assess the effects of climate change, the impact of invasive species, and the effects of resource management decisions, however, obtaining data for a remote and rugged areas like National Parks often takes considerable resources. Luckily, our study site, Mt. Rainier National Park, has around 1.5 million visitors every year, many of which upload images of the landscape to photo sharing websites like Flickr. Each photo has a geolocation tag and a timestamp of when the photo was taken, revealing a species’ location and phenology at a given time and place. Using this data from photo sharing websites, we are developing models to predict the spatial distributions of five montane wildflowers that are located on Mt. Rainier: Arctic lupine, magenta paintbrush, American bistort, western pasqueflower, and Sitka valerian. Species distribution models are frequently used to understand the relation between environmental variables and a species range. Using environmental data from Mt. Rainier, we will be able to predict the current habitat of these five species and make predictions of how the species range will change under various climate change scenarios. Additionally, due the relative ease of accumulating data, we plan to adjust our geographic focus to other national parks where species distribution predictions could improve resource management and conservation decisions.

Chitosan and alginate are widely used natural polymeric biomaterials that are biocompatible, biodegradable, and non-toxic. Chitosan is cationic as well as hydrophobic in nature whereas alginate is anionic and hydrophilic in nature. Ionic interaction between the amine and carboxyl group causes the formation of polyelectrolyte complex in the scaffold and thus enhancing the mechanical properties of the scaffold. Mechanical properties of the scaffolds are dependent on the fabrication process, cross-linking process, and sterilization process. Similarly, porosity plays a crucial role in determining the mechanical strength of the scaffold which relates to the lyophilization process and molecular weight of the polymer used. Chitosan-Alginate (CA) scaffolds are prepared by mixing equal wt% amounts of each polymer and due to chitosan's hydrophobic nature, acetic acid was added. The solution was mixed using a Thinky mixer at 2000 rpm for five minutes. After obtaining a homogeneous mixture, pH was tested and solution  casted into desired well plates. The solution was then refrigerated at 4 degree Celsius for 12 h at 20 degree Celsius overnight, and lyophilized for 24 hours. Scaffolds were then cross-linked with 70% CaCl2, and sterilized with Phosphate-buffered saline (PBS). Scanning electron microscope (SEM) is used in to image pore morphology of the scaffold. High mechanical strength and porous structure is presented in pore size ranges of 100-500 micrometers which is required for bone tissue engineering. Mechanical strength of the scaffold is obtained by performing compressive test. Samples are compressed at 4.00 mm/min using micro-tensile tester with 1N load cell. Dry samples were found to have a young's modulus (YM) of 1-2 MPa, whereas wet samples were found to have a YM of 1-2 KPa.  CA scaffolds were found to be mechanically strong with good porosity which was directly impacted by fabrication process. Mechanically strong CA scaffolds with proper porosity were achieved with the fabrication process used. Further work will allow an optimization of CA scaffolds for specific applications and cell lines.  

From the moment of the first cellular divisions in an embryo, a suite of genes are responsible in ensuring the proper developmental progression of an organism to adulthood. The primary tool used in identifying these genes and their biological function, is a forward genetic mutant screen. Previous mutant screens have revealed many genes required for early embryonic developmental processes, such as the critical bicoid gene in fruit flies (Drosophila). However, many critical genes, particularly those involved in regulating post-embryonic development, remain undiscovered. To identify novel genes and pathways required to execute development during post-embryonic stages, we have undertaken an ongoing forward genetic mutant screen in the model organism zebrafish (Danio rerio). We used the mutagen N-ethyl-N-nitrosourea (ENU) to randomly induce mutations in the genome. I am now screening the third generation progeny of the mutagenized individuals, specifically searching for larval arrest mutants that fail to develop adult traits. By mapping and cloning the affected genes, we hope to identify genetic factors required for vertebrate development. I have so far found one developmental arrest mutant, which I have named nikabrik. Nikabrik arrests development and growth after two weeks, and presumably lacks some gene product required for further development. I am now working towards mapping and cloning nikabrik to identify the underlying mutagenized gene. Identification of the nikabrik gene may provide valuable insight into what factors are required for larval development in zebrafish, and other vertebrates including humans.

The 21st century has seen the emergence and re-emergence of novel infectious diseases. Following in the footsteps of its communicable predecessors, the recent emergence in Saudi Arabia of a SARS-like novel coronavirus, or Middle East respiratory syndrome (MERS-CoV), since 2012 has weaved narratives of globally interdependent economic, political, and social intimacies. I will examine the contrasting narratives that reflect investigations and responses to this novel threat from Middle Eastern, European, and North American media networks, the WHO, the global biomedical community, and the Saudi Arabian Ministry of Health through several intersecting discourses: intellectual property rights and viral sovereignty; the deliberation on the taxonomy of the novel coronavirus; and geopolitical differences in information sharing and biosecurity in the context of emergent 21st century epidemics. Using Priscilla Wald’s concept of outbreak narratives and the imaginative hold of myths as a framework, I will explore how the stories on the global effort to investigate and respond to the MERS outbreaks continue to be revealed, repackaged, and transformed as experts around the world scramble to uncover its epidemiological pathways. I argue that the consideration of these counter-narratives are critical for rethinking underlying, potentially harmful, factors beyond dominant epidemiological and biomedical discourses surrounding the MERS epidemics. Such considerations may serve as a microcosm for biopolitical barriers in the response to past, present, and future emergent diseases. These counter-narratives should be regarded in light of uncertainties that still cloud the etiology and transmission of the virus which has since infected 243 people and claimed 93 lives in 11 countries in Europe, the Middle East, and Southeast Asia.

The physiological mechanism of light-induced leaf expansion may begin with the capture of blue light by the photoreceptor phototropin. This process is responsible for growth of the plant which influences photosynthetic ability and overall productivity. Our goal was to determine whether phototropin has an affect on expansion and if so, what phototropin's role in growth is. In this study, we grew Arabidopsis thaliana WT (wild type), phot1, phot2, and phot1/2 mutants in pots in a growth chamber under continuous light. Each plant's fifth leaf was photographed every day and measured with ImageJ to obtain growth rates. This experiment was run three times. The results show that phot1 mutants do not significantly differ from WT, phot2 mutants had a similar growth rate to WT but continued growing at a fast rate for a day longer, and phot1/2 had a much slower growth rate than WT. A second experiment was done using the same growth conditions, but using only WT, phot2, and phot1/2. On the sixth day after its appearance, the fifth leaf was removed from each plant and floated in a 5 millimolar solution of KCl for 24 hours. These leaves were photographed before and after to obtain their growth rates and the results were consistent with the first experiment which used intact leaves. The second experiment demonstrates that there is a phot-mediated mechanism contained within the leaf which influences growth. Knowing the cellular mechanism regulating leaf growth rate may help to understand how environmental stresses such as drought reduce plant productivity. Our next step will be to determine the mechanism which is causing the difference between the rates. First, we will look at anatomy of the leaves to determine if cell expansion or division is most affected by phototropin.

Mycobacterium tuberculosis (MTB) infection remains a major global health problem but the human immune response to this bacteria has yet to be fully understood. A challenge for vaccine development is the lack of an immunological correlate of protection from MTB. We hypothesize that studying adults that were highly exposed to MTB but failed to convert their tuberculin skin tests might help us understand protective immunity to MTB. We infected monocytes in-vitro with MTB and looked for unique gene expression signatures. We discovered that Ras-responsive binding protein 1 (RREB1) was suppressed in persistently skin test negative subjects when compared to skin test positive controls. Using the human monocytic cell line, THP-1, we are studying how in-vitro stimulation with IFN-γ, Toll-like receptor ligands, and bacteria change expression of RREB1. These studies will contribute to our understanding of the role of RREB1 in MTB pathogenesis.

Interest in renewable energy resources has increased in recent years due to the rising demand and dwindling supply of fossil fuels. While inorganic materials, such as silicon, have traditionally dominated the solar energy market, the use of organic photovoltaics (OPVs) has grown more popular due to their potential to be low cost, light weight, and their ability to comply with flexible substrates. Poly(3-hexylthiophene) (P3HT) is a polymer that readily self-assembles into nanowires under proper conditions, resulting in nanowire domain sizes that are on the order of the exciton diffusion length. Directing polymer self-assembly provides an opportunity to control the structure property relationships of OPVs and can greatly improve charge transport within the active layer. The regioregularity of a polymer is a measure of the uniformity of its geometric isomers. Because individual P3HT chains begin to kink into S-like shapes during self-assembly, a correlation between the P3HT regioregularity and the frequency of resulting nanowire defects is expected. In an attempt to understand the process of self-assembly, we would like to determine if these defects are incorporated into the nanowires during self-assembly, or if they are excluded from their crystalline domains. To investigate this, P3HT nanowires were made from solutions of anisole and chloroform in varying ratios, heated at 70 °C and thoroughly mixed for 24 hours, then removed from heat and allowed to self-assemble for at least three days. These solutions were then filtered to separate the nanowires from the decanted solution, and analyzed separately. A variety of characterization methods were used to study the presence of nanowire defects as well as their effects, including nuclear magnetic resonance spectroscopy, gel permeation chromatography, differential scanning calorimetry, atomic force microscopy, and matrix-assisted laser desorption/ionization spectroscopy.

Solar energy is arguably the most promising source of renewable energy because it is thought to be both the cleanest and most abundant source. Several types of photovoltaics are now available, including inorganic, organic, and hybrid organic-inorganic. While inorganic photovoltaics have high efficiencies, good charge carrier mobilities, and relatively long charge carrier times, their widespread implementation has suffered from expensive production and materials competition with the microelectronics industry. Organic photovoltaics are solution processable and applicable to flexible substrates; however, their output has been hindered by their low charge carrier mobilities and short exciton diffusion lengths. Hybrid organic-inorganic photovoltaics have been introduced in an attempt to overcome the shortcomings of both organic and inorganic photovoltaics. Inorganic semiconductors are used in hybrid photovoltaics as the electron acceptor due to the ease of changing their size and shape, and therefore the bandgap, of these materials, which allows them to contribute to the photocurrent of the cell while being solution processable and potentially enhancing the conductivity. Conjugated polymers are used as electron donors due to their large absorption cross-section and solution processability. This project addresses the synthesis of hybrid cadmium selenide (CdSe) nanotetrapods, which we believe will facilitate control of the direction of electron motion in the active layer of the cell. Amines are needed for CdSe tetrapod functionalization with semiconducting polymers according to our reaction scheme. Tetrapods tend to convert into quantum dots because dots are thermodynamically favorable; our approach to have kinetic control, and thus have the tetrapods retain their shape, has involved synthesizing the tetrapods with amines as ligands. The reaction time, growth temperature, ligand type, and monomer concentration are used to control the synthesis, and the effects of each variable on the size and shape of the tetrapods will be studied via transmission electron microscopy (TEM).

Transcranial ultrasound can alter brain function transiently and nondestructively, offering a new tool to study brain function and inform future therapies. Previous research on neuromodulation implemented pulsed low frequency (250–700 kHz) ultrasound with spatial peak temporal average intensities (ISPTA) of 0.1–10 W/cm2. That work used transducers that either insonified relatively large volumes of mouse brain (several mL) with relatively low frequency ultrasound and produced bilateral motor responses, or relatively small volumes of brain (on the order of 0.06 mL) with relatively high frequency ultrasound that produced unilateral motor responses. Our work seeks to increase anatomical specificity to neuromodulation with modulated focused ultrasound (mFU). Here, ‘modulated’ means modifying a focused 2-MHz carrier signal dynamically with a 500-kHz signal as in vibro-acoustography, thereby creating a low frequency, but small volume (approximately 0.015 mL) source of neuromodulation. Application of transcranial mFU to lightly anesthetized mice produced various motor movements with high spatial selectivity (on the order of 1 mm) that scaled with the temporal average ultrasound intensity. Alone, mFU and focused ultrasound (FUS) each induced motor activity, including unilateral motions, though anatomical location and type of motion varied. Of interest is the exploration of potential research and clinical applications for targeted, transcranial neuromodulation created by modulated focused ultrasound, especially mFU’s ability to produce compact sources of ultrasound at the very low frequencies (10–100s of Hertz) that are commensurate with the natural frequencies of the brain. Currently, I am working to incorporate mFU with electroencephalography (EEG) to aid researchers and clinicians in localizing neural activity. Theoretically, the vibro-acoustography paradigm allows a small volume of neural tissue to be tagged with a specific difference frequency; EEG will determine the origin of this signal.

Background: Chronically homeless individuals with alcohol dependence experience serious alcohol-related consequences (Collins et al., 2012; Hwang, Wilkins, Tjepkema, O’Campo, & Dunn, 2009). It is therefore important to identify ways to reduce alcohol-related harm, such as the use of safer drinking strategies. No studies to date have explored this topic among chronically homeless individuals with alcohol dependence. Aims: This study aimed to document participants’ endorsement of safer drinking strategies over the course of a longitudinal pilot study of a combined pharmacobehavioral intervention to reduce alcohol-related harm (Collins et al., 2013). Methods: Participants (N=31; 12.9% women) were currently or formerly chronically homeless individuals with alcohol dependence. Participants’ use of safer drinking strategies was elicited using a list of safer drinking strategies and open-ended questions (e.g., “What strategies on this list might you be willing to try over the next week?”). A qualitative methodology called conventional content analysis was used to explore, categorize and document safer drinking strategies used by this population. The safer drinking strategies that participants chose to try were recorded for weeks 0 and 8. Results: At week 0, strategies that buffered the physical effects of alcohol represented the most highly endorsed category (51.1%), such as eating more often. The next most endorsed category was altering the manner of drinking (36.17%), for example spacing drinks. The final category represented reducing alcohol use (12.76%), such as drinking to avoid withdrawal. Discussion: Preliminary findings indicate that chronically homeless individuals are interested in using safer drinking strategies to reduce harm associated with their drinking. They also indicate that the most relevant ways to reduce harm for this population might be to help individuals buffer the effects of alcohol and alter their manner of drinking.

For the past year, we have researched the contributions made by Guy Shearman Peterkin, an early pioneer urologist living in Seattle in the early 20th century. Our research focused on the life of Peterkin himself as well as his numerous scientific publications to understand his place in not only Seattle history, but the history of urology as a specialty field of medicine. We spent two quarters scouring the archives of the King County Medical located in the First Hill neighborhood to find references and publications relating to Peterkin. We also spent time in Special Collections here at UW collecting additional primary resources. We also utilized UW’s microfilm collections to search through old articles from the Seattle Times and other newspapers. The Department of Bioethics and Humanities owns a large collection of antique medical instruments. One of those exhibits is a presentation prepared by Peterkin circa 1920, “Mechanics in Developing the Cystoscope” that inspired this research to begin with. Peterkin was a pillar in Seattle society for his involvement in the King County Medical Society, the Washington State Medical Association, the American Urological Association and other professional groups. He wrote extensively on the relationship between urology and psychoanalysis of venereal diseases (i.e syphilis) with special emphasis on scientific and ethical standards. Peterkin’s legacy is overshadowed by his dramatic death in which he shot and killed his son and himself in a case of what he believed to be a mercy killing.

An efficient and environmentally benign means of creating semiconducting polymers is necessary for the commercialization of organic electronics. Furthermore, it is crucial that as much control as possible be exerted over the polymerization process. To these ends, two polymerization methods are useful – C-H activation and living polymerization. First, C-H activation is a collection of synthetic techniques where C-H bonds undergo direct catalytic alteration to yield new homo- or heteroatom linkages. Whereas organometallic reagents were traditionally used to achieve these results, C-H activation allows for shorter syntheses utilizing less-hazardous reagents and broader functional group compatibility. Living polymerization is a form of addition polymerization and in our case, the number of chains is constant during the reaction and dependent on the catalyst-to-monomer ratio. This allows for much narrower mass distributions of the desired polymer and more consistent growth. To achieve this, benzoxazole-based monomers containing a C-O electrophile are to be reacted in the presence of a zero-valent nickel species with electron-rich phosphine ligands. By increasing the electron density on the metal center, we aim to facilitate a “ring-walking” mechanism at higher temperatures than previously thought possible. Monomer synthesis and polymerization results are detailed.

Research indicates that alcohol consumption and sexual victimization history, separately, are related to women’s increased unprotected sex risk. An additional question is whether partner relationship potential (i.e., likelihood of having a romantic relationship) interacts with victimization history and alcohol consumption in their association with risky sexual behavior. Participants were 436 female heavy episodic drinkers, aged 21-30, at elevated risk for sexually transmitted infections. They completed background questionnaires that assessed sexual victimization and an alcohol administration protocol (control or BAC=.10). Next, they projected themselves into a hypothetical sexual scenario, which manipulated relationship potential (high or low) with the man in the story. Following the scenario, participants listed their reasons for and against having sex, knowing no condom was available, and rated the strength of these reasons on a 1 (not at all strong) to 7 (extremely strong) scale. We computed two difference scores. First, the number of reasons listed against having sex was subtracted from the number of reasons listed for sex. Second, the strength of the reasons against having sex was subtracted from the strength of the reasons for having sex. Higher scores indicated that women listed more reasons for having sex than against and perceived reasons for having sex were stronger than reasons against, respectively. We regressed both outcomes on sexual victimization severity, alcohol dose, relationship potential, and all interactions. Analyses indicated a significant 3-way interaction for reason strength, but not number of reasons listed. For women with high victimization severity who received alcohol, relationship potential was positively associated with stronger reasons for having sex, which is likely indicative of greater sexual risk. Results have implications for risk prevention programs and suggest the importance of providing risk information for women with victimization histories who consume alcohol prior to sexual encounters and perceive high relationship potential in their sexual partner.

Acute myeloid leukemia (AML) is a heterogeneous clonal disorder of hematopoietic progenitor cells, also known as “blasts,” that fail to both differentiate normally and properly respond to normal proliferation regulators. The consequences include possible organ infiltration as well as impairment of normal blood cell production that can result in fatal infection or bleeding. Retention of leukemia cells within the bone marrow microenvironment enables survival from chemotherapy treatment. This retention is largely mediated by surface membrane receptors, such as the chemokine receptor CXCR4. CXCR4 facilitates cellular migration towards high concentrations of the stromal derived cell factor CXCL12 (SDF-1), a chemokine that is released from bone marrow stromal cells. A CXCR4 small molecule inhibitor, plerixafor, has been shown to improve response to chemotherapy treatment in murine leukemia models, by disrupting interactions with the microenvironment, releasing leukemia cells into the bloodstream, and conferring sensitivity to chemotherapy. Our objective was to assess the functionality of an anti-CXCR4 antibody, BMS-936564, to similarly enhance chemotherapy cytotoxicity. We assayed CXCR4 expression by the leukemia blasts and stem cells, observed the time course of mobilization of leukemic blasts and stem cells, and examined the induction of programmed cell death (apoptosis) in patient samples through analysis for Annexin V expression. Mobilization of leukemia blasts and stem cells was monitored by flow cytometry. We found a significant correlation between CXCR4 expression by leukemic blasts and patient response to therapy, with high CXCR4 expression (≥20%) linked to complete remission (p<0.05). It is intuitive that the antibody to CXCR4 would require CXCR4 to be expressed by blasts. These data provide a method to predict outcomes for patients undergoing combination treatment with anti-CXCR4 antibody and chemotherapy. Our ultimate objective is to overcome adhesion mediated chemotherapy resistance in order to improve outcomes for patients with AML.

Most treatment programs for alcohol dependence have prioritized abstinence from substances as the primary treatment goal. However, abstinence-based goals are not always considered desirable or effective by more severely affected populations, such as chronically homeless people with alcohol dependence. Because these individuals comprise a multimorbid and high-utilizing population, they are in need of more focused research attention to elucidate their preferred treatment goals. The aim of this secondary study was therefore to qualitatively and quantitatively document participant-generated treatment goals. Participants were currently or formerly chronically homeless individuals (N=31) with alcohol dependence who were participating in a pharmacobehavioral pilot of extended-release naltrexone and harm-reduction counseling. During the week 0 assessment, study interventionists elicited participants’ treatment goals and recorded them on an open-ended grid. Progress and achievement of goals was confirmed via self-report and recorded by study interventionists at the week 8 follow-up. Conventional content analysis was performed to classify participant-generated treatment goals at weeks 0 and 8. Representation of the three top categories remained stable over the course of the treatment. In the order of their frequency they included drinking-specific goals, quality-of-life goals and health-related goals. Quantitative analyses indicated participants generated an increasing number of goals over the course of treatment; however, the proportions of goals achieved and made progress towards did not increase significantly. Findings confirm hypotheses that participants can independently generate and achieve treatment goals toward alcohol harm reduction and quality-of-life improvement. Larger RCTs are necessary to confirm the role of harm-reduction treatment in helping individuals achieve these goals.

This paper exanimates how the contribution of education to individual’s earning changes under economic recession. Previous economists have established the Employer Learning Model, which demonstrates that the relation between education and earning is strong at the start of one’s career but weakened through time. This paper compares this relation between education and earning during recession and non-recession periods. The study is based on the cross-sectional data from National Longitudinal Surveys that include comprehensive information about individuals’ working and educational experience. The study applies a difference in means test that builds upon a regression of individual’s education, ability (estimated by AFQT score) and years of working experience on earning. By comparing the difference in causal effects between recession and non-recession periods, this paper shows that under recession the impact of education on earning is weaker at the beginning of one’s career and diminishes faster through time. The result suggests that in economic downturn, the signal factors such as years of schooling, race and gender have less impact on individuals’ earnings. Individual’s true ability is revealed faster too. One of explanations of this result that the paper discussed is that under recession, firms have more incentives to observe employee’s productivity actively and efficiently both before and after hiring. Other inferences of the result are also included in the paper.

This was a study of the prevalence of post stroke fatigue in stroke survivors who participated in the larger Living Well With Stroke study in the Puget Sound area of Washington. Post stroke fatigue can delay progress of physical therapy, and interfere with activities of daily living. Within four months of a stroke, the Living Well With Stroke team approached people who had been hospitalized with a stroke to screen for eligibility to be part of the study. Questions were asked that screened for depression and fatigue. Using SPSS (Statistical Package used for Statistical analysis) we have examined screening data of the 414 patients from the larger study. We have examined the correlation of fatigue to the presence of depression, age, gender, type of stroke, severity of stroke and other variables that are in the literature. Based on existing literature, we anticipate that the presence and severity of fatigue will be correlated with age, gender, severity of stroke, depression, as well as socio-economic status. Using SPSS, data has been interpreted by the use graphs, and tables to best show the correlation between post stroke fatigue and the demographics I have just listed previously. By understanding these correlations, treatment options could be better improved or be tailored specifically to these patients.

Hypertrophic cardiomyopathy (HCM) is a heritable disease in which the heart undergoes pathological remodeling and thickening, leading to sudden cardiac death, especially in young adults. I am investigating how modifications to myofilament proteins, which are responsible for muscle contractions, contribute to HCM functional characteristics. My goal is to determine how the P82S mutation of cardiac troponin I (cTnI) alters the dynamic properties of cardiac troponin (cTn), such as the Ca²⁺ binding affinity to cTn and interactions between cardiac troponin C and cTnI (C-I interaction), as well as the overall effect of P82S on muscle activation and relaxation. I am testing the hypothesis that the C-I interaction serves as a critical point in contractile regulation, regulating systolic performance at basal activity and particularly during β-adrenergic stimulation. During β-adrenergic stimulation, the cardiac-specific N-terminus of cTnI is phosphorylated by protein kinase A (PKA), and the shifting protein conformation results in a cascade of conformational changes in regulatory proteins that promote myosin unbinding from actin, accelerating relaxation rates in cardiac muscle. This work combines state-of-the-art protein biochemistry, myofibril & cellular mechanics/kinetics and multi-scale computational modeling to study the behavior of P82S-cTnI with wild type (WT) cTnI. For each, recombinant troponin complexes containing WT-cTnI, P82S-cTnI, non-phosphorylatable cTnI (S23/24A), and phosphomimetic cTnI (S23/24D) are studied and compared. Initial results from the WT-cTnI variants show that with respect to the WT-cTnI, the S23/24A and S23/24D mutated troponin have decreased Ca²⁺ sensitivity to cTn, as well as the C-I affinity. Accompanying experiments are currently being done on the P82S variants. A better understanding of how protein structure and function is altered by mutations will bring the HAMM Lab closer to developing approaches to mitigate the impact of HCM-related mutations.

Methods and devices used for pressure measurement are extremely varied and typically do not offer the ability to operate accurately when subjected to pressure values outside of the standard operating range. Typical methods and devices used for pressure measurement at low levels of stress, such as those exerted by biological cells, are prohibitively expensive with quite complex manufacturing processes. This research focused on characterizing a device constructed of carbon nanotubes, paper, and polydimethylsiloxane (PDMS), for use as a pressure sensing smart skin with exceptional sensitivity. The geometry and quantum mechanical properties of carbon nanotubes make them highly sensitive to strain. The effects of various factors such as temperature, tension, and environmental air pressure on the electrical resistance of the device were recorded over time to determine its response to its ambient surroundings. Thermal fluctuation, vacuum chamber, mechanical deflection, and control tests were carried out on the sensor to identify its gauge factor and tendency towards hysteresis. The effectiveness of spin- and dip-coating at forming a suitable PDMS layer was investigated. Tests with no PDMS on the sensor were also run. The sensors resistance is directly affected by vacuum pressure and temperature. Increasing the thickness of the PDMS layer reduces the sensitivity to temperature. By characterizing the sensors behavior at various temperatures and pressures, a calibration algorithm is recommended in order to isolate the effect that strain has on the sensors resistance. This easily manufactured, nanostructured sensor for measuring pressure at very low values is an effective tool for research in many fields due to its scalability and ease of use.

Muscle contraction results from interactions between thick and thin-filament proteins within the sarcomere of a muscle cell. The movement of tropomyosin (Tm) over actin on the thin filament exposes myosin binding sites and is a fundamental step in the regulation of muscle contraction. Single amino acid substitutions in Tm and regulatory mechanisms such as Tm phosphorylation can greatly impact muscle function. Tm monomers link end to end over actin, so shifting of one Tm monomer to expose myosin binding sites may cause strain in neighboring monomers via end-to-end interactions, resulting in cooperative behavior. The flexibility of Tm may play a role in modulating the strain induced in neighboring monomers, thus we chose to assess the flexibility of phosphorylation-mimicking and clinically relevant Tm mutants that are known to affect contractile function. We produced and purified recombinant Tm in E. Coli and imaged it using rotary-shadowed electron microscopy. The flexibility of single molecules was determined by skeletonizing Tm to determine its persistence length, a quantity from statistical mechanics that describes the curvature of rod-like objects. Skeletonization and analysis were performed manually and with a novel automated image analysis program. Molecular dynamics simulations were also performed with the clinically relevant Tm mutant to determine structural mechanisms that could lead to the altered contractile function observed in muscle containing mutant Tm. Preliminary results show decreased flexibility near the region of phosphorylation in phosphomimetic Tm compared to wildtype Tm. This result is expected because Tm phosphorylation has been shown to increase cooperative behavior and the phosphorylation site is located in the middle of the overlapping region of each Tm monomer.

Education for sustainability is "learning that links knowledge, inquiry, and action to help students build a healthy future for their communities and the planet." Teaching sustainability is a crucial component of a healthy future society and a catalyst for change in behavior. While state and national standards are in place, the search for effective ways to teach K-12 sustainability education is constant. Project-based and place-based learning are effective methods of teaching sustainability and impacting behavior. This type of learning encourages collaboration, exploration of individual curiosities, and appreciation of the local community, leading to an eventual recognition of the global impacts of individual actions. Using a school-wide vermicomposting project at Sacajawea Elementary School in Maple Leaf as case study, the benefits and limitations of project-based learning to teach sustainability will be evaluated. Vermicomposting is the process of using worms to compost organic waste into a nutrient-rich soil supplement. The installation of a school worm bin serves as a learning tool for two classes of fourth and fifth graders. An initial open response survey was given to students to assess knowledge and environmental attitudes. The compost created is used in a plant growth experiment that caters to state science standards, and a school food waste audit serves to connect individual actions with localized effects. Students experience the direct effects of their behavior through hands-on engagement with the worm bin and issues of food waste. Preliminary results show that the students are empowered to make a positive impact in their school and community. Widespread application of the project will be assessed.

Distal Arthrogryposis (DA) is an umbrella term for non progressive congenital skeletal muscle defect characterized by abnormal contractures of the limbs and the face. It occurs in 1 in every 3,000 live births and is inherited in an autosomal dominant manner. Currently, there are no treatments for the disease, and the patients usually go through regular physical therapy throughout their lifetime. Severe cases require surgical intervention and amputation. One of the more common syndromes is DA 2B, or Sheldon Hall syndrome, which is caused by mutations in two genes, TNNI2 and TNNT3. I am particularly interested in studying the R63H mutation that impacts the fast skeletal troponin T (TNNT 3) subunit. The troponin subunits are critical in regulating the interaction between actin and myosin myofilaments. Mutations in the TnT can alter the way the troponin subunit interacts with the tropomyosin and have large impacts on overall muscle mechanics. I hypothesize that this mutation increases the contractility and tension in mutated proteins. To verify the hypothesis, I will compare the wildtype to the mutated version of TNNT 3 by putting a fluorescent tag on the proteins and observe the differences in calcium sensitivity, ATPase, and maximum filamented actin velocity in a sliding filament assay known as the in vitro motility assay (IVM) to piece together information about how the mutation impacts the overall muscle mechanics. My project seeks to gather information about the mechanics of the mutated muscles. Putting all of the data together will enable me to identify causes in the mechanics behind abnormal contractions. Also, it will allow me to make connections between the genotype and the phenotype of the disease to better understand it on a molecular level, and thus open up doors for therapies.

Across the United States, there is a paucity of data about food insecurity among university students. For this project, we are defining food insecurity as a lack of access to nutritious food and reduced intake due to reduced income or household demand. Currently, UWT does not know if there is an issue with food insecurity among students nor the reasons if insecurity does exist. This research used mixed methods which included a catalyst survey of the entire UWT student body to document the prevalence of food insecurity. The second method is a community mapping about food resources near UWT. Various types of food resources exist; however, we hypothesize that there are few affordable meal resources within a 10-minute walking distance of the UWT neighborhood causing barriers to accessibility. We defined a meal as hearty and filling food providing enough energy, strength, and nutrients to sustain through short periods of time (1-3 hours), an entrée (consisting of more than one food group) and beverage ranging from $6.00 - $8.00. We analyzed data to create user-friendly tools such as maps, databases, and websites for the UWT student population to access affordable food resources. By doing this research, our hope is to generate awareness of the need for more food resources and provide resource information for affordable food within the UWT community. UWT is projected to grow to 7,000 students by 2020; therefore, the availability of affordable food resources will impact the academic performance of the University of Washington Tacoma students. Each UWT student’s journey to success can be supported by the availability of affordable food resources that impacts their health (mind, body, spirit); as a result, students will not have this barrier in achieving their potential and UWT will successfully meet its mission and values.

Rachel Jeantel served as the key witness for the prosecution in the well-publicized trial of George Zimmerman, who was acquitted of charges of manslaughter after the death of Jeantel’s friend, Trayvon Martin. Media coverage was highly critical of Rachel Jeantel’s testimonies, and made claims about the intelligibility of her speech and her supposed inability to adjust her speech patterns based on her audience –none of which were supported by an actual linguistic analysis. This project is a detailed linguistic analysis of Rachel Jeantel’s speech in order to critique and evaluate the claims made in media coverage during the trial. This project explores the possible effects that her underbite and multilingual status may have on her speech. This linguistic investigation includes an acoustic analysis of Jeantel’s speech in samples from her interview with Piers Morgan. By referencing relevant theoretical knowledge from existing linguistic investigations on African American English (AAE), Haitian Creole (HC), and Dominican Spanish (DS), we compared Jeantel’s vowels and deletion of plural and possessive marker “s” in the recordings with expected features of those dialects. Using this knowledge, coupled with a review of similar research on individuals with underbites, we present a more complete analysis of the factors that influence her speech and evaluate claims the media made about her. The scrutiny Jeantel was subjected to highlights the many ways in which language, race, and class are intermixed in present-day American culture. We hope that by presenting an analysis of Jeantel’s speech, we have helped inform this conversation.

This report summarizes a method for constructing a Seebeck coefficient tester, the basics behind its operation as well as analyzation of SrxBa1-xNb2O6. Thermoelectric oxides have a very promising and bright future for waste heat recovery, and it is the aim of this project to learn more about them and develop some new materials. The goal of this project is to be able to analyze the Seebeck coefficient of materials at very high temperatures. Current technology is only around 1000 K, and the goal of this project is to be able to measure the Seebeck coefficient of materials to be around 1300 C. The tester is being constructed using our own designs, and a LabView program was created to enable the measurement and operation of the instrument. The setup is fairly straightforward using a 4 point probe test to measure the voltage and temperature difference. For these tests we are using R-type thermocouples instead of the usual K-type thermocouples, as it can handle the very high temperature that is desired. Through developement of a high temperature Seebeck tester there will be greater possibilities in the future for use of various thermoelectric materials.  This report summarizes mainly on constructing the tester to make it fully operational then beginning to obtain measurements, and finally the process of gathering necessary data for accurate measurements.

Macrophages of our immune system can be broadly classified as pro-inflammatory M1 or anti-inflammatory M2 macrophages. Imbalance in the ratio of these two phenotypes has been associated with various chronic diseases, suggesting that targeting drugs to specific populations of macrophages may achieve therapeutic benefit. Phage display is one method of identifying peptides that can be used for targeting cell populations. In whole-cell peptide phage display, a library of bacteriophage, in which individual phage display a unique peptide sequence on a coat protein, is applied to target cells. Phages that preferentially bind target cells are isolated, and their peptide sequences can then be obtained by DNA sequencing. Targeting M1 macrophages has possible applications in treating arthritis, diabetes, and atherosclerosis. Recently, we identified a novel phage-bound peptide sequence (hM1pep), using phage display, that exhibited selective binding to M1 macrophages. I synthesized the peptide form of hM1pep and evaluated its selectivity of M1 macrophage binding in vitro using flow cytometry; however hM1pep showed insignificant binding. Tumor-associated macrophages (TAMs), a type of M2 macrophage, have been shown to facilitate tumor growth and are associated with decreased survival of cancer patients. Previously, we identified a peptide that preferentially bound to TAMs in mice. We demonstrated that peptide-mediated TAM elimination improved survival in mice, suggesting that an analogous strategy in humans could be a potential cancer therapy adjuvant. In this work, I attempted to identify human M1 and M2 macrophage binding peptides by panning against human M1 and M2 macrophages, while using M2 and M1 macrophages as a subtractive panning step, respectively. Targeting M2 macrophages has potential uses in treating diseases associated with increased tissue levels of M2 macrophages, including cancer, fibrosis, and asthma.

Micro RNAs (miRNAs) control translation of certain proteins through degradation of the messenger RNA which code for these proteins. These non coding RNAs are often up-regulated in many forms of cancer and can inhibit the expression of tumor suppressor proteins. The goal of this project is to engineer a protein which can bind to and inhibit the biogenesis of a miRNA-21, which is overexpressed in many cancers. Previous reports have shown that the RNA recognition domain (RRM) of human splicing factor Fox-1 protein has high affinity and specificity for the UGCAUG sequence. We are engineering this RRM to target the stem-loop sequence of precursor miRNA-21. Amino acid site changes were introduced into Fox-1 to generate a protein which will inhibit production of the oncogenic miRNA-21 in cancer cells. This project involves the application of various methods in biochemistry, including PCR site-directed mutagenesis, cell transfection, DNA cloning, protein expression and purification, RNA transcription and purification as well as gel electrophoresis assays and 3-Dimensional structural analyses of protein and RNA through nuclear magnetic resonance studies. Currently, a stable protein has been expressed and the precursor species of miRNA-21 is being prepared to characterize its interaction with the engineered protein biochemically, biophysically and structurally.

Pericytes are mesenchymal cells that are attached to peritubular capillaries. The activation and differentiation of progenitor pericytes to myofibroblasts leads to matrix deposition, renal scarring, and is a major contributing factor leading to chronic kidney disease after injury. Connective tissue growth factor (CTGF) plays an important role in fibrogenesis by promoting the production and secretion of extracellular matrix components. The goal of this project is to dissect the contribution of CTGF/Wnt signaling pathways in pericytes during the development of kidney fibrosis and to examine the effect of using the canonical Wnt extracellular regulator Dickkopf related protein-1 (DKK-1) on CTGF/Wnt signaling. In-vitro signaling studies on purified kidney pericytes, migration assays, and immunological staining were used to characterize the roles of DKK-1 and CTGF in the regulation of renal fibrosis. Results show that CTGF induces Wnt/β-catenin signaling in pericytes. DKK-1 inhibits CTGF induced fibrotic gene activation, changes the morphology, and the capability of migration of kidney pericytes through JNK MAP kinase, and canonical WNT independent pathway.

Women in the US are at risk for sexually transmitted infections (STIs) including HIV/AIDS when they engage in sexual risk behaviors (SRB), especially failure to use a condom during sexual intercourse. Women face unique pressures when the decision whether or not to have protected sex is made, and deal with these pressures using a variety of coping strategies. This ongoing study is designed to investigate the hypothesis that women who use coping strategies based on avoidance (e.g., escaping, forgetting, ignoring stressors) in their everyday lives are more likely to have sex without a condom. The study also examines the hypothesis that women who generally use coping strategies based on problem solving (e.g., confronting, planning for, and working to resolve stressors) are less likely to have sex without a condom. We recruited women from the University of Washington Psychology Department’s Online Subjects Pool. Data have been collected from 327 women during fall 2013 and winter 2014 quarters. Participants completed an online survey including a measure of coping strategies (i.e., Coping Strategy Indicator), read a hypothetical sexual scenario, and responded to questions about their intentions to engage in unprotected sex. Data were analyzed using linear regressions and we predicted a relationship between coping strategies and intention to use a condom. We predicted that those who reported using more avoidance coping strategies would be more likely to have unprotected sex, and those who reported using more problem solving coping strategies would be less likely to have unprotected sex. If a relationship between coping strategy and failure to use a condom is established, then interventions focused on teaching new coping strategies could be implemented to help decrease sexual risk behaviors and increase women’s sexual health.

The somatic mutation theory of aging states that aging is the result of accumulated DNA mutations in somatic cells, which lead to loss of physiological integrity through tissue and organ level dysfunction. In mouse model systems, decreases in lifespan through high mutation rates have been documented by creating mutator phenotypes in these organisms. Mutator phenotypes are marked by increased cellular mutation rates, and are known drivers of tumor development in human cancers. Mutator-driven adaptations occur in natural microbial populations. Mutators represent a unique opportunity to test the somatic mutation accumulation theory of aging due to their sustained high mutation rates. Nutritional status, particularly carbohydrate metabolism, influences lifespan in numerous organisms. In yeast, which preferentially ferments glucose to ethanol before switching to respiratory metabolism upon glucose depletion, the induction of respiratory metabolism is associated with increased lifespan. This study examines the effects of high mutation rate on yeast replicative lifespan and whether induction of respiratory metabolism is sufficient to change lifespan in organisms with increased mutation load. To do this, yeast defective for DNA replication proofreading, mismatch repair, and base-excision repair were grown under dietary restriction (reduced glucose) and in the presence of non-fermentable carbon sources. Then, mutation rates and replicative lifespan were assayed. Our results show that increased mutation rates correlate with decreased lifespan in strong mutators and that this decrease in lifespan can be partially suppressed through growth on limited glucose and non-fermentable media. These findings suggest that the metabolic state of the cell modulates the severity of mutator phenotypes, which has important implications for the role that mutators play in carcinogenesis.

Luminescent solar concentrators (LSCs) are solar energy harvesting devices that promise to revolutionize the next generation of solar energy by separating the task of sunlight absorption from power generation. These devices use phosphors that absorb sunlight and wave-guide reemitted light to photovoltaics (PVs) to generate electricity. One promising class of phosphors is that of doped semiconducting nanocrystals (known as quantum dots) due to their intense absorption and minimal reabsorption of dopant-emitted light. In these materials the semiconductor quantum dot absorbs sunlight and transfers the energy to an emissive dopant to prevent efficiency loss by reabsorption. CdSe quantum dots are well known for their intense absorption across the visible spectrum, and doping with Ytterbium would enable their emission to be used in LSCs. Moreover, the Yb³⁺ ions emit at an energy that is nearly perfectly matched with the bandgap of a silicon PV cell, boosting its efficiency. The focus of my research is the synthesis of Yb³⁺-doped CdSe. Ytterbium is incompatible with the tetrahedral CdSe lattice with respect to its larger oxidation state and coordination preference, and introducing it as a dopant is a challenge that has yet to be solved by the chemistry field. While employing air-free Schlenck techniques, I am modifying the doping methods that have proven successful in the synthesis of other Gamelin Group materials, including a process we recently developed called nanocrystal diffusion doping. Success can be measured by detecting quantum dot sensitized ytterbium luminescence. The goal is that this approach will lead to a repeatable procedure by which to synthesize stable Yb³⁺-doped CdSe for novel characterizations as well as for eventual application in a new generation of solar devices.

As scientific studies have been focusing on generating alternative renewable energy sources, attention has been drawn to the need to store energy from the sun. One strategy is to develop catalysts capable of producing the energy-dense molecule hydrogen from the reduction of water. This kind of solar fuels system would allow for on-demand release of the energy that is stored in the chemical bonds of hydrogen through environmentally benign, carbon-free combustion. We are interested in the potential of catalyzing proton reduction with cobalt in a diimine-dioximato ligand framework. Previous studies on cobalt diglyoxime complexes have demonstrated the viability of such catalysts for proton reduction. Our research is focused on synthesizing bimetallic complexes using the same framework and studying the effect of another metal center on catalytic activity. Our entry into this chemistry relies on the initial synthesis of a doubly-deprotonated diimine dioximate complex of cobalt as a starting material, which can be considered as a “metalloligand”. The physical and electronic properties of this cobalt metalloligand and its multimetallic derivatives are studied by X-ray crystallography, 1H- and 13C-NMR, UV-visible spectroscopy, and cyclic voltammetry.

The diaries kept by Emma B. Andrews are an undervalued resource for learning about Egyptian culture and 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 yearly 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. The Emma B. Andrews Diary Project aims to increase the availability of this source with the hope that it will become more widely recognized in the academic world. 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 text 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. First, transcriptions of the diaries to an electronic textual format must be completed and edited twice for accuracy. Next, the diary transcriptions are run through an auto-tagging program to create an online format for the texts. The diaries are then converted into XML format and new content is added to them, including historical research on people mentioned in the diaries. Undergraduates working on this project are passionate and committed about making this valuable resource available to the world in a way it has never been before.

During the Late Cretaceous (100 to 66 million years ago), most mammals were relatively small (< 200 g) and occupied very few ecological niches. Didelphodon vorax was the largest mammal of that time period (~1.7 kg). Thus, study of Didelphodon vorax is key to understanding the range of mammal evolution during the Late Cretaceous. Although a significant amount of research has been conducted on this species, it has exclusively focused on cranial elements, specifically dentition and rare skull fragments. From these elements, researchers have hypothesized Didelphodon had a semiaquatic habit and bulbous premolars for a shell-crushing diet. However, a major limitation of these hypotheses is that they have not been tested with postcranial data. I describe parts of a disarticulated but associated partial skull and skeleton of Didelphodon vorax. The fossils were excavated from a locality called Marshoupial in the Late Cretaceous-age Hell Creek Formation in McCone County, Montana. Specifically, I compared the morphology and dimensions of the hands and feet to those of extant marsupials (e.g., Didelphis virginiana). I have determined that the hand and foot elements preserved at the Marshoupial locality include two distal metacarpals, one distal metatarsal, one complete proximal phalanx (digit III or IV), one distal phalanx, one proximal phalanx (digit II or V), and three intermediate phalanges. From these elements, I infer the locomotion, habitat, and body size of Didelphodon vorax to better understand the ecology of this species. In preliminary observations, Didelphodon vorax is larger than Didelphis virginiana (1.9–6.0 kg) and the shape of its distal phalanx (ungual flexor protruding anteriorly, broad profile in dorsal view) resembles that of aquatic extant mammals. If this interpretation of Didelphodon vorax is confirmed, it would suggest some Late Cretaceous mammals were more ecologically diverse than previously thought.

 Beryllium Oxide is a ceramic material most notably used in the electronics industry due to its outstanding thermal conductivity. Because of this property it is also of interest for use as an insulator under high density plasma exposure. Post exposure the beryllium samples undergo a very specific series of characterization steps. Samples are subject to optical microscopy, in an attempt to identify noticeable surface changes when compared to a control sample. Specific spots show maximum exposure, and are further investigated via XPS. X-ray Photoelectron Spectroscopy shows chemical changes in regions of maximum exposure. Specific depth profiling is utilized to identify possible Deuterium migration, lanthanide exposure, and oxidation effects. XPS is critical for providing detail of the depth of deuterium exposure throughout the material, along with possible deuterium implantation within the crystal lattice of the existing beryllium oxide. X-ray Diffraction comparison between irradiated and control samples shows lattice expansion and residual strain throughout the material. This is a crucial discovery when comparing the impact of the residual strain to the maximum tensile stress. Peak broadening shown on the 2ϴ XRD plot identifies the extent of intergranular strain left by possible deuterium implantation into the beryllium oxide crystal lattice identified through XPS. Thermal conductivity of irradiated samples is tested to ensure that the most redeeming quality of the material is consistent post exposure.

Adolescent obesity is a growing epidemic and has tripled in the past 20 years in the United States. This is a major public health concern as we are now observing numerous health conditions commonly associated with adult obesity in the adolescent population. The goal of our study is to determine how total sleep time (TST) affects body composition, activity level, and nutrition in adolescents. Our study population consists of 100 healthy 13-17 year old adolescents. We are currently collecting and will analyze data from sleep/hunger/satiety diaries and questionnaires, a watch that records daytime/nighttime activity, 24-hour diet recalls, serum metabolic markers, appetite regulating hormones, salivary cortisol, an air displacement device, and questionnaires that assess lifestyle factors. We anticipate our results will demonstrate differences between sleep-deprived adolescents with age, BMI, sex matched control adolescents in diet, food cravings, physical/sedentary activity, and appetite regulation. Further, we anticipate our results will demonstrate an inverse correlation between TST and body composition. The intent of this study is to provide preliminary information to suggest a need for further research in this area. We hope to apply this scientific understanding to the development and testing of innovative interventions to improve sleep and decrease adolescent obesity and metabolic risk.

Cerebellar pathology has been associated with cognitive and affective deficits and cerebellar dysfunction may play a role in schizophrenia and autism spectrum disorder. Understanding how cerebellar abnormalities contribute to characteristic features of psychiatric disorders may pave the way to creating better therapies. One cerebellar output region, the lateral dentate nucleus (LDN), is associated with cognitive and affective roles in behavior. This region has reciprocal connections with the limbic system, where dopaminergic neurotransmission has been linked with psychiatric disorders. Cells expressing dopamine receptor-1 (D1R) can be found in the LDN, but their function is unknown. To determine whether D1R-expressing neurons in the LDN modulate cognitive, affective, and/or social behavior we used a pharmacogenetic approach in mice. Specifically, we conditionally expressed a yellow-florescent-protein--tagged HM4Di, the inhibitory DREADD Receptor (designer receptors exclusively activated by designer drugs) or green florescent protein (GFP) in D1R-expressing cells of the LDN by injecting mice expressing Cre recombinase, an enzyme used for precise gene expression manipulation, under control of the endogenous D1R gene (Drd1a^Cre/+) with conditional viral vectors. Systemic injection of the DREADD-specific ligand, Clozapine-N-Oxide (CNO), reversibly inhibits HM4Di-expressing cells allowing us to test their function in behavior. In the experiments I performed, in the presence of CNO, Drd1a^Cre/+; DNC-HM4 mice showed improved motor performance, decreased prepulse inhibition of acoustic startle reflex (a reflexive jolt triggered by sound), increased anxiety-like behavior in an elevated plus maze, reduced cognitive performance in a spatial navigation memory task, and impaired differentiation of novel and familiar mice compared to controls. No significant differences were seen between groups in an instrumental conditioning experiment, a measure of motivation for food reward. D1R-expressing neurons in the LDN influence specific cognitive, affective, and social behaviors. Alterations in dopaminoceptive neurons within specific cerebellar nuclei may play important roles in the etiology of symptoms of mental illness.

Over 25,000 undergraduates at the University of Washington register for courses each quarter using an online system. This project attempts to improve the university’s registration mechanism through theoretical and empirical analysis. Registering for college courses is an instance of the multiunit assignment problem, where heterogeneous agents are assigned combinations of different goods, in this case seats in courses. In addition to college course allocation, multiunit assignment has applications in industries ranging from aerospace (airstrip scheduling) to human resources (job shifts). Standard criteria for evaluating assignment mechanisms are efficiency, or whether there are any changes that can be made to students' allocations which leave some people better off and nobody worse off; strategyproofness, or whether students can get a better result if they lie about their preferences; and fairness, or how evenly the mechanism distributes the courses. We use simulations and theoretical analysis to evaluate the UW mechanism’s performance based on these criteria. We compare it to several prominent multiunit assignment mechanisms and provide recommendations regarding potential improvements to the university’s registration system.

Grackles are gregarious blackbirds (Icteridae) native to the New World. Our research focuses on the genetic structuring and biogeography of two sister species: the Boat-tailed Grackle (Quiscalus major), and the Great-tailed Grackle (Quiscalus mexicanus), the latter consisting of western and eastern clades. We constructed a molecular phylogeny using ND2 mitochondrial sequences that suggest the Great-tailed Grackle is paraphyletic with respect to the Boat-tailed Grackle. In other words, the Great-tailed Grackle species as currently recognized includes some, but not all, of the descendants of its most recent common ancestor. Phylogeographic analysis of the same genetic data suggests that eastern and western populations of Great-tailed Grackles are currently interbreeding freely, while Boat-tailed Grackles remain reproductively, morphologically, and ecologically isolated, despite their more recent split from the eastern Great-tailed Grackle clade.

The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are difficult to distinguish using morphological or vocal characters. The Northwestern Crow is considered ecologically distinct, occupying only coastal and shoreline habitats from Central Washington, north through much of coastal Alaska. The more widely distributed American Crow occurs throughout greater North America, including Pacific coastal habitats north to Central Washington, potentially overlapping and hybridizing with Northwestern Crow in this region. Until now, no comprehensive genetic analysis has been performed to examine crows in this potential zone of overlap. This study examines Pacific Northwest Corvus species distributions with minimal spanning networks and phylogenetic analyses via the mitochondrial DNA ND2 gene. Mitochondrial DNA is inherited maternally and does not recombine giving a minimally distorted view of an individual's ancestry. Our data show that the Northwestern Crow occurs from Alaska to Southern British Columbia, and not in central Puget Sound or along the southern coast of Washington. The American Crow occurs throughout the continental U.S. and comes into contact with the Northwestern Crow in southern B.C. Further analysis is required to reveal the possible extent of this contact zone north of Vancouver and/or into northern Washington. A better understanding of this overlap zone will allow science to update natural history species distributions and further explore the effects of human impact on biogeography.

As global forests decline, conservation policy is becoming increasingly important. Though some progress to improve forest conservation policy has been made, there is much room for refinement. With this, a myriad of conservation methods are being created and used which seek to halt high levels of deforestation. A case study was conducted in the Manu-Tambopata (MAT) biological corridor in Madre de Dios, Peru which includes a diverse mix of resources such as intact forests, secondary forests, and gold deposits, in addition to agriculture, and logging industries. To identify leverage points, places in a system where small interventions can result in large system changes, local landowners and miners were surveyed on land-user demographics, current and future land-use practices, and preferences for conservation policies. The factors that mitigate these leverage points in practice had to be explored and evaluated. The findings on leverage point identification and influencing factors were then applied to the specific region of the case study in the proposed MAT corridor to help improve forest conservation policies and programs aiming to improve conservation designs. The survey-data shows the majority of both miners and farmers partake in some form of conservation and even more are interested in receiving external support to improve their conservation practices. There is a clear preference for technical support among farmers and conservation jobs among miners. This case study demonstrates the strength of field surveys in order to understand local conditions and plausible policy options, as well as the need to design policy instruments based on local conditions. My role in the research project includes survey-data compilation and analysis. Additionally, I am coauthoring the research paper and have written the results section, as well as participated in full copy editing and figure development.

The ability to learn and perform complex motor skills varies with the time of day. One complex motor skill that oscillates daily is song produced by songbirds. The study of song is particularly useful for understanding mechanisms driving the learning of vocalizations and the cellular and morphological changes that accompany changes in song production rate and quality. In one such songbird, Gambel’s White-crowned Sparrow (Zonotrichia leucophrys gambelii), the production of song and the underlying neural circuit that controls this song change dramatically between breeding and nonbreeding seasons. We sought to determine whether song also changed on a daily time scale. We analyzed song production rate, spectral features, and stereotypy of more than 1500 songs produced over the course of two consecutive days by sparrows maintained in breeding conditions. We identified daily patterns in song rate, frequency, entropy, power, and energy of breeding song within both individual birds and pooled bird data. The demonstration of daily oscillations in song rate and spectral features song supports both descriptions of ‘the dawn chorus’ and growing evidence on the modulation of the song control circuit by the internal circadian clock. Having shown daily changes in song production in white-crowned sparrows, we can now begin to study the relationship between song production, cellular changes like neuronal birth and death that occur within the song circuit, and the endogenous circadian clock.

The thermoacoustic effect provides many benefits compared to current cooling methods. The process can achieve stable and reliable cooling without the use of refrigerants or environmentally hazardous chemicals. Strontium Barium Niobate (SBN) is a relaxer ferroelectric ceramic material that exhibits piezoelectric properties due to its tetragonal tungsten-bronze crystal structure.  A piezoelectric is a material that when subjected to mechanical deformation, undergoes polarization which creates electricity and vice verse.  The purpose of this project was to identify piezoelectric properties of SBN, and utilize an SBN piezo crystal for fine-tuned sound generation in a thermoacoustic cooler. In order to achieve this, understanding the physical phenomena behind thermoacoustic cooling and building a prototype thermoacoustic cooler were first accomplished. From there, identifying the piezoelectric characteristics of SBN and construction of a miniaturized model was initiated. Comparisons were made between the macroscopic and miniature models to determine device properties and characteristics. Device miniaturization reveals a variety of challenges that were previously unobserved in the macroscopic device. A cooling effect was observed and a temperature gradient was achieved in both the macroscopic and miniaturized prototypes. However, the efficiency factor of the micro device was highly correlated to the device geometry and construction. Ultimately, the goal of this project was to achieve thermoacoustic cooling on the micro scale which can only be achieved by understanding the nanostructure and the relationship between grain size and domain polarization mechanisms. Piezoelectrics provide an excellent avenue to achieve this goal due to their high overall efficiency of converting lattice distortions into electrical energy, high curie temperature, their idealized frequency response time and their relative environmental stability.

Diatoms are an important taxon of phytoplankton that contribute to both freshwater and marine ecosystem function. For example, marine diatoms are responsible for about 14% of global primary production. My research is focused on determining the ability of these algae to regulate the production of chlorophyll a- the core pigment component of photosynthetic complexes. The enzyme light-dependent NADPH protochlorophyllide oxidoreductase (POR) is a key regulator of chlorophyll synthesis. Whereas most organisms have just one POR enzyme, diatoms have two (POR1 and POR2). The goals of this project are to understand how these enzymes are metabolically different from one another in: (a.) their enzymology and (b.) their regulation at the transcriptional and posttranslational levels. To this end, plasmids were constructed encoding the cDNAs of the por genes, adding N-terminal histidine tags to assist in affinity purification. E. coli, transformed with these plasmids, was induced to express the proteins; harvested, and lysed. Recovered POR1 and POR2 proteins were purified from the lysate by affinity chromatography. Antibodies raised against these proteins were used in Western blot protein identification and quantitation of the targeted proteins. Preliminary experiments demonstrate good affinity of generated antibodies for POR proteins, and indicate that POR 2 may be post-transcriptionally truncated. Developing an understanding of chlorophyll metabolism in diatoms has not only ecological implication, but also could prove important in commercial aspects of biofuel development- increasingly important issues driven by changing ocean conditions and the critical need for generating alternative fuel sources. Determining the properties of these enzymes and their regulation is just one step towards understanding the successful productivity of diatoms. Further studies may be required to determine if there are additional regulatory pathways and enzymes that are critical in photosynthetic production.

Emulsions of oil droplets decorated with gold nanoparticles can be used to enhance contrast in ultrasound and photoacoustic imaging. Plasmon resonance in the gold nanoparticles enables absorption of near infra-red (NIR) light, which can penetrate two to three centimeters below the skin in the human body. Upon irradiation with a NIR laser, oil droplets with a shell of gold nanoparticles will heat and vaporize as the gold absorbs the light. The vaporization of the oil creates a microbubble, providing contrast enhancement in imaging as well as a mechanical pressure wave which could be used to deliver mechanical forces inside the body. If the gold nanoparticles are functionalized with ligands that are designed to target specific areas or threats inside the body, the process could also be used to deliver targeted therapy. Emulsions are thermodynamically unstable and will coalesce over time without external stabilization. We utilize gold nanoparticle surfactants to stabilize the oil-water interface. We investigated a charge based stabilization of perfluorohexane emulsions with cationic gold nanoparticles. Size is characterized by Dynamic Light Scattering (DLS). Successful adsorption of the cationic gold nanoparticles to the oil-water interface is represented by zeta potential, which approximates surface charge. Emulsions of oil have a negative surface charge and the presence of cationic gold at the interface will result in a positive charge. Ultra-Violet Visible Spectroscopy (UV-Vis) is used to measure the NIR absorbance of the emulsions, which should be maximized to enable rapid heating of the gold nanoparticles and subsequent oil vaporization. Stability over time is determined by changes in the DLS and UV-Vis curves. The results of the investigation are analyzed in terms of size, stability, and NIR absorbance in order to determine the potential effectiveness of a charge based stabilization mechanism in creating plasmonic emulsions for contrast agents and therapeutics.

Plasmonic nanoparticles (NPs) have been reported to improve the performance of organic solar energy harvesting devices. Gold (Au) and silver (Ag) are two of the more commonly researched plasmonic nanoparticles. The plasmonic effect occurs when incident light induces a fluctuation of electron clouds within a metal. This phenomenon resonates at a specific wavelength depending on NP size, geometry and the dielectric constants of the metal and medium. Previous publications have shown that inclusion of combined Ag and Au NPs increases light absorption and can enhance the power conversion efficiency by 20 percent. This study evaluates the effect of varying concentration of Ag and Au NPs on power conversion efficiencies within a bulk heterojunction (BHJ) organic solar cell, and examines the mechanisms behind the enhancement. Lumerical FDTD Solutions was used to model scattering and plasmonic resonance in OPV devices with different combinations of 40 nm Ag and Au NPs within the PEDOT:PSS charge transport layer. Light enhancement and absorption was modeled as a function of wavelength and spatial arrangement. The results indicated that the absorption profile for the mixed NP device was dominated by the contribution of the Ag NPs, which prompted the investigation into the ideal NP concentrations/ratios. OPV devices were constructed on an ITO substrate with a PTB7:PC70BM active layer. Power conversion efficiencies were determined experimentally as a function of open-circuit voltage, short-circuit current density, and fill factor. Device morphologies were evaluated using atomic force microscopy (AFM). The absorption profiles of the devices were measured using UV-Vis spectroscopy. The optimal concentrations of Ag and Au NPs were determined. Future research on this topic should focus on optimizing particle geometry, ligands, and dielectric NP coatings.

 In 2009, the World Health Organization declared swine flu to be the first global flu pandemic in 40 years as a result of the outbreak of cases in Mexico. Although the mortality rate of the disease was lower than predicted, the narrative constructed around the disease offers important takeaways regarding how an outbreak is perceived and what groups become associated as disease carriers. Incorporating knowledge of Mexican-American relations, past and present, in the analysis of the media coverage broadens the understanding regarding the roles that racism and xenophobia play in responses to swine flu. However, the U.S media’s blaming of Mexico, especially when connecting to issues of immigration and borders, draw attention away from American culpability in the H1N1 experience. Using my digital medium as a holding space and synthesis for different thought provoking articles, imagery, and videos about this subject will allow the audience to understand the systematic conditions that influence the spread of diseases like H1N1. For example, by unpacking the capitalist economic imperatives of NAFTA (North American Free Trade Agreement), a policy signed off by Canada, the US, and Mexico to create the world's largest free trade area, I examine how its neoliberal policies encouraged transnational corporations to open up industrial pig factories and its impacts on the environment, human health, labor practices, animal welfare, and immigration. I argue that these factors are symptoms of a “NAFTA Flu”, which shaped unequal disease development conditions and unequal access to treatment in Mexico, a perspective that anti-Mexican media ignore. Therefore, critiquing the U.S media framings of the outbreak undermines the stigmatization and blaming of the specific populations in traditional outbreak narratives.

 The HIV epidemic in Southern Africa is one of the most persistent threats to global well-being, representing over twenty-five percent of global AIDS infections. As such, an increasing emphasis has been placed on developing cures or vaccines and deploying treatments for HIV. This global effort has been stymied at every turn by resource shortages, opportunistic infections and cultural and political barriers. But as South African poet Roshila Nair remarks: "we are beginning to learn / how to make everything / out of nothing again." My research reads an anthology of poems and short stories titled "Nobody Ever Said AIDS" and attempts to uncover a space of possibility for representing HIV, which is a prerequisite to fighting it, or at the very least living with it. I use the work of Homi Bhabha, Julia Kristeva, Eve Kosofsky Sedgwick, and others to show how culture represents itself through place (inhabited space) and imagined futures. I also read comparative surveys of historical and contemporary migrant mine laborers to suggest that neocolonial ideology has foreclosed a space for imagining a future in such precarity. I hope to suggest that questions of representing, fighting, and living with HIV are also always questions of culture, and that therefore developing a cultural imaginary of and response to HIV is essential to the longer-term human objective of “becoming with” HIV as a species. This cultural imaginary includes not only semiotic resources (that is, language with multiple possible meanings), but also the capacity to understand futures, and to transform spatial locales into inhabitable place.

How was U.S. immigration policy shaped by the 2009 Swine Flu outbreak? My project will explore the relationship between immigration policy, xenophobia, and Swine Flu. The uproar in the US stemming from the 2009 Swine Flu (H1N1) outbreak revealed a racialized narrative that targeted and stigmatized Mexican immigrants. Rising xenophobic sentiments were exploited to further the cause of anti-immigrant groups and to justify immigration limits. For example, xenophobia was so prominent that some citizens blindly advocated for the closing of the U.S. - Mexican border without considering the economic effect of such an action. As part of this project I will explore xenophobia itself as an outbreak linked to the Swine Flu outbreak. How did this xenophobia outbreak infiltrate the U.S.? Were U.S. immigration policy makers susceptible to xenophobia? Were they “infected” by the xenophobic outbreak? Is xenophobic sentiment evident in immigration policy? I will draw on empirical data (like immigration statistics and public opinion polls), analyze rhetoric used in immigration debates, and explore media representations, to reveal the connections between Swine Flu and U.S. Immigration policy. I argue that Swine Flu, and the xenophobic discourses surrounding it, had a profound effect on contemporary immigration narratives.

When animals (humans among them) mourn, they honor the emotional bonds that make social living both desirable and possible.  Ebola, one of the most virulent primate diseases, wreaks havoc within this sociality, bringing death and triggering isolation.  Here I examine spaces of mourning - instances when mourning does or might occur - in the context of Ebola to explore how we can protect social connection in the face of disease.  Previous Ebola narratives have often portrayed mourning as an obstacle to public health.  Journalists and academics have largely ignored how isolating people from dying loved ones and depriving families of traditional mourning rituals affects the grieving process or how forcing people to quell grief as they exterminate Ebola-infected lab monkeys affects humans.  Only recently have scholars begun to explore difficulties Ebola survivors face grappling with grief amid stigma-induced isolation.  Here, I explore what it means to reread outbreak narratives in light of theories of mourning.  Drawing upon Judith Butler's concepts of grievability and precarious life, I challenge narratives touting extermination as the sole means of stopping Ebola from crossing species.  Together, these accounts highlight the shared vulnerability and capacity for social suffering uniting humans with other primates.  Through this work I explore how recognizing the significance of relationships within and between species vulnerable to Ebola might change human responses to this disease.  If we embrace this approach for Ebola, it opens new possibilities for handling other infectious diseases and for deciding which lives (among individuals of all species) count as grievable.

The purpose of this research is to investigate hidden health narratives on campus regarding the use of tobacco products to contextualize the legitimacy of smoke-free and tobacco-free university initiatives. This academic endeavor will also reveal the structural and institutionalized violence of the tobacco industry which targets marginalized communities to entice the uptake of regular smoking habits. An analysis of biopolitical power, structural violence, and social theory will help to reveal the hidden narratives of these populations, twice-targeted by the social stigmatization of tobacco use and the manipulative advertising of the tobacco industry. By exposing, analyzing, and deconstructing patterns of profit-driven tobacco marketing directed at student demographics, it is possible to examine geographies of blame regarding tobacco use, impact of tobacco use on non-smoking populations, and the misleading agendas behind the dominant narratives of tobacco industry advertising. By identifying and bringing to light these messages, it is possible to legitimize the anti-smoking and anti-tobacco movements happening at the University of Washington, and U.S. universities at large, with a critical analysis of the health risks involved.

This paper analyzes the juxtaposing narratives between various documents and media portrayals from mining corporations, the Peruvian government, and the affected indigenous populations, focusing on how many of the more dominant narratives can often be misleading in reflecting the serious health effects from mining. Peru’s mining industry significantly influences the health of surrounding indigenous communities due to high levels of air and water pollution. Unfortunately, there is not a great deal of sincere concern for the wellbeing of these communities from either the corporations exploiting their land or the Peruvian government. Despite their efforts to express their suffering through protests, indigenous communities have seen few results. The mining industry and its detrimental health effects are often overlooked, and therefore many of these dominant corporate narratives and our own capitalist desires are all that we have to shape our understanding of how mining industries operate in other countries, such as Peru. However, the subaltern counter-narratives from indigenous populations concerning their health and rights can more accurately shape our understanding of the severity of these health effects caused by the mining industry.

Large chromosomal amplicons and deletions or copy number variation (CNV) are found in many different cancers. However, the inheritance, stability, and fixation of these amplicons and deletions within a population are widely debated and poorly understood. In an effort to better understand how the stability of this large chromosomal rearrangement, I analyzed the stability of a large segmental amplification in the yeast S. cerevisiae. This amplification is commonly observed in clones evolved under sulfate-limited conditions and contains the sulfate transporter SUL1. This amplification is an important adaptive strategy used by the cells to improve their ability to extract the limited supply of sulfate available in the media. High copy number of this gene confers a competitive fitness advantage over other clones that have only one copy of the gene. We used a GFP marker integrated next to SUL1 to differentiate green clones, which contain a single copy of the SUL1 gene, from “super green” clones that have multiple copies of the gene. A super green evolved clone was grown in steady state growth vessels for ~30 generations in media that is non-selective for adaptation and our selective media as a control. I monitored the population using flow cytometry and quantitative PCR to find clones that have lost the amplification. These green clones were isolated using flow sorting and then had their genome sequenced to look at the scar that was left behind. This tells us how efficiently the cells can remove amplifications without causing detrimental effects to their fitness.

Our research study focused on the adolescents that are living with chronic health conditions that encounter barriers to dental care during the transition from child-centered dental care to adult-centered dental care. My part of the qualitative study focused on dental transitions for adolescents with chronic conditions from the perspective of dentists. We conducted semi-structured interviews with a total of 13 dentists (7 pediatric dentists and 6 general dentists). I coded the interview transcripts and analyzed the interviews using NVivo. My main findings from the dentist-reported transition barriers included 1) the type of insurance e.g. Medicaid, 2) the lack of providers to treat individuals with chronic health conditions and 3) disturbance in the patient’s routine and comfort-level that may result from transitions. The proposed recommendations that I found from the providers were open communication between pediatric and general dentists, raising awareness amongst providers about this special population, and additional clinical training for general dentists to treat patients with chronic health conditions to facilitate dental transitions. The findings from my part of the study suggests that in order to improve dental transitions for adolescents with chronic health conditions, adult dental care for Medicaid must be covered nationwide. This will increase the likelihood that adolescents will be able to access dental care in young adulthood. Changes in the dental school curriculum, including additional training on how to treat patients with chronic health conditions, will help to improve dentists’ comfort in treating medically compromised patients.

American Indians and Alaska Natives suffer disproportionately from end-stage renal disease. For those with chronic kidney disease, transplantation may be the most effective treatment option. However, Native people do not donate organs at a rate that is commensurate with the need in the population. We developed a semi-structured, 10-question interview guide and used it to facilitate interviews with American Indians on their experiences with community activities to promote awareness of organ and tissue donation. Our nine key informants were project partners at Tribal Colleges and Universities and other tribal leaders. According to our informants, successful strategies to promote donation awareness included community engagement and active listening. Challenges included cultural beliefs and fear of discussing organ donation and death. However, community perceptions of living donation were positive, and key informants felt that living donation should be emphasized in future efforts. More education on organ and tissue donation is needed in Native communities. Information on living donation should be included in future educational efforts as part of the strategy to reduce donor shortages.

It has been shown that the chemical nor-binaltorphimine (norBNI) inactivates the k-opioid receptor (KOR) for days or weeks in vivo, and also results in downstream activation of c-Jun N-terminal kinase (JNK). If JNK is blocked in vivo by SP610025 or by knocking out the JNK1 gene, norBNI inactivates the KOR for just hours. We hypothesize that there is a JNK mediated inactivation of the KOR. To further investigate this, I will create constructs that will allow us to study the interactions of JNK and arrestin, two proteins that are involved in the transduction of KOR signaling. I aim to express a version of each JNK1 splice variant tagged with luciferase and arrestin3 tagged with Venus in human embryonic kidney (HEK293) cells that have been transfected with rat KOR. Venus and luciferase are two bioluminescent molecules that emit different wavelengths of light depending on their distance from one another. After treating these cells with norBNI, I can dtermine the level of their interaction by using a bioluminescence resonance energy transfer (BRET) assay. These experiments will provide useful data in determining the extent of the interactions between JNK1 and arrestin3. This data will help us understand the protein cascade that results in the deactivation of the KOR, and if certain drugs activate certain splice variants. Understanding this pathway has implications in creating analgesics with smaller potential for abuse and addiction, and creating pharmaceuticals that could help with stress related depression and addiction relapse.

In the Hague Lab we study a class of proteins called G-protein coupled receptors (GPCR's). GPCR's are seven-pass transmembrane proteins that are involved in cell signaling. One GPCR we study is called alpha-1D adrenergic receptor. Adrenergic receptors bind the endogenous catecholamines adrenaline and noradrenaline. An important functional role of the alpha-1D GPCR in the body is to regulate blood pressure by affecting blood vessel diameter.  Our lab recently discovered that the alpha-1D adrenergic receptor's relatively long N-terminal domain is cleaved in human cells. We are currently elucidating the specific cleavage site - which we suspect is a GL matrix metalloprotease domain - and the physiological purpose of the cleavage. Over the last few months we have narrowed down the region of cleavage to approximately 15 amino acids. We also have a working theory that the N-terminal cleavage of the protein allows for better cell surface localization. We are currently examining how the cleavage event effects the signaling characteristics of the protein.

Of the many types of devastating spinal cord injuries, incomplete injuries of the cervical spinal cord are the most common among patients. For these individuals, the highest treatment priority is restoration of hand and arm function; much more important than any other symptom of paralysis. The goal of our project is to restore hand and arm function by recording movement intention in the brain and using it in real time to control spinal cord stimulation. We use single unit activity encoding movement intention in the rat motor cortex, and intra-spinal microstimulation (ISMS) for movement induction. ISMS may be superior to direct muscle stimulation (FES), since it causes little fatigue and a more natural recruitment of motor pools. ISMS in the cervical and lumbar regions of the spinal cord can also be utilized to produce a wide array of functional limb movements. By using rats that I have trained to perform a lever-pressing task, I can quantify the functional relevance of movements evoked by varying ISMS parameters. By combining both recorded cortical data and ISMS, we have created a brain-machine spinal interface (BMSI). This BMSI can deliver brain-controlled, functionally useful stimulation directly to the spinal cord and caudal to a contusion injury in order to restore some movements to the animal’s injured forelimb. Our long-term goal is to translate this device to a clinical setting, where it could be used to restore hand and arm function to patients with complete spinal cord injuries.

The human brain is rapidly growing during the last trimester and there is evidence that premature birth is related to adverse neurological events. Magnetic resonance (MR) imaging of premature neonates and subsequent automated segmentation allows us to quantify subtle disruptions in cortical growth and folding in large population based studies. We use an age-specific automated tissue segmentation technique combined with an age-specific parcellation scheme to study regional patterns of tissue growth in a large study of brain development in premature neonates. We aimed to investigate the additional information provided by regional analysis of MR scans when determining risks for delayed neurocognitive outcomes. Our image analysis framework incorporates a spatiotemporal reference atlas that covers the age range of 27.43 to 46.43 gestational weeks (GW), and consisted of manually segmented brain tissues and 8 hemispheric lobe regions. The tissue atlas was used to automatically segment all 269 MR scans, age range from 27.29 to 47.00 GW, using a hybrid framework that combines an age-specific atlas-based EM segmentation with a patch-based prior. This tissue segmentation was then used to re-align the subject anatomy with an age-specific tissue template and the region parcellation of each subject was carried out by template probability propagation into the subject anatomy from the spatiotemporal parcellation model. Multiple linear regression models of the parcellation volumes, divided into gray matter and white matter tissues, showed a significant correlation between regional volume and Bayley’s Scale of Infant and Toddler Development scores, beyond gestational age at birth. Parietal and occipital lobes were clear markers for language and motor abilities, while the temporal lobe volumes were correlated with cognitive abilities. These findings support a more anatomically-specific analysis of brain structure after premature birth and may provide the possibility of earlier and more specific clinical diagnostics and timely developmental interventions.

In order to communicate, patients with total loss of muscle control including eye movement can rely on brain computer interfaces (BCI) that utilize evoked related potentials (ERP) which are voltage deflection of the brain following stimulus presentation recorded using EEG. Typically, ERP spellers rely on visual input. However, due to the auditory system's acute ability to selectively attend an auditory stream in what's known as the "cocktail effect", new speller paradigms that aid listeners' ability to selectively attend may increase the maximum bitrate of communication. The focus of this project was to create a unique auditory ERP-based speller that allows users to successfully use tone, spatial location, and informational cues to aid in auditory streaming while still increasing the total amount of selections of auditory streams. The research project can be separated into two phases: 1) a proof of concept psychophysics experiment assessing users ability to discriminate different auditory cues used in an auditory BCI environment and 2) an application of psychophysics findings from the previous phase to an online analysis of bitrate using EEG recording which will be conducted in the summer of 2014. This presentation will focus on analyzing and applying the experimental findings from the first phase to explore how can we modify parameters of the experiment design to maximize the bitrate (i.e. either through maximizing the ERP response amplitude, improving accuracy, lowering trial time, etc.). This project offers future possibilities for auditory systems to help not only improve the ease of use and practicality for the community of individuals who rely on speller systems but in other areas for the BCI community as a whole.

The balance between neuronal birth and death is a fundamental process of adult neural plasticity that mediates the maintenance and production of behavior. Aberration in this balance often coincides with neurodegenerative diseases including Parkinson’s, chronic depression, and stroke. Songbirds are an excellent model for exploring the dynamics of neuronal turnover, i.e. the balance between neuronal birth and death, and its effects on behavior, as seasonal production of song is under the control of a well-defined plastic neural circuit. This circuit includes the song control nucleus HVC (proper name) and its target, the robust nucleus of the arcopallium. Seasonal plasticity of HVC in Gambel’s white-crowned sparrows (Zonotrichia leucophrys gambelli) involves pronounced changes in neuron number; HVC neuron number changes 25% (>68,000 neurons) between breeding and nonbreeding seasons. The dramatic differences in neuron number between breeding and nonbreeding conditions suggest that dynamics between neuronal birth and death also differ between seasons. To determine if there are seasonal differences in neuronal turnover, I labeled two cohorts of new HVC neurons separated by one, two, and four months with two thymidine analogs, BrdU and Edu, in both breeding and nonbreeding condition birds. I determined turnover rate by quantifying the number of new neurons from each cohort that were present in HVC at the different intervals. Preliminary data indicates that in breeding birds more new neurons belonged to the first cohort, whereas in nonbreeding birds more new neurons belonged to the second cohort. The replacement of first cohort neurons by the second cohort neurons increases with time in non-breeding birds. This suggests that testosterone in breeding birds promotes survival of the first wave of new neurons entering HVC. This study demonstrates that the seasonal changes in HVC neuron number results from a dynamic shifting balance between neuronal birth and death.

Current research seeks to be able to produce detailed data through simulation for comparisons of the material budgets of individual layers, sub-layers, and components of different inner detector geometries for implementation in future ATLAS upgrades at the Large Hadron Collider (LHC). ATLAS, A Toroidal LHC Apparatus, is a particle detection experiment located at the LHC in Geneva, Switzerland. The inner tracker, a constituent ATLAS system, records the presence of particles at discrete points in space and time allowing for the reconstruction of the particles' trajectories; material budget is a measure of the energy loss of particles as they pass through the tracker. Upgrades and replacements of the current inner tracker will allow the detector to continue to function at optimal efficiency and collect more data at higher energies in the future. Present work involves simulating the performance of different geometries in order to reduce the overall material budget, thereby increasing low momentum resolution. Software is used to model the passage of non-interacting particles through the detector, recording the angle of their trajectories and the amount of matter through which each particle passes. These quantities can then be plotted against each other and compared for different geometries. Data for a forthcoming addition to the innermost section of the inner tracker and a proposed future replacement of the entire innermost layer have been produced at this time. Confirmation of a reduction in material budget for future upgrades is expected. This project will allow optimal specifications to be determined for the reduction of material budgets for future changes to the inner tracker.

In order to process large amounts of physical events and filter the interesting events worth investigating, a good detector must have a sophisticated Data Acquisition (DAQ) system. In an effort to improve and study its tasks in much detail, an identical DAQ system for the ATLAS Pixel Detector has been established in the lab environment. This flexible environment allows us to conduct various experiments for the current and future development of the Pixel DAQ System. Currently, the necessary hardware and software have been set up. Then the system will be connected to the Pixel Readout Driver, which is part of the current generation of the Pixel DAQ System to test its data acquisition performance. In the future, the system will test DAQ performance of the IBLROD, which is the new generation of the Pixel DAQ System. Also, a new data path firmware that is currently under development will be implemented in the system to evaluate its data processing performance.

In order to increase the accuracy of particle detectors, new sensors and digital acquisition systems must be developed. With the power of reconfigurable digital logic, an acquisition system has been created using a simple and fast architecture in order to test T3MAPS, a prototype sensor for the ATLAS detector. The firmware design of the system is modular to allow for iterative improvements over time and future changes to the sensor. Currently the systems first iteration is being tested using oscilloscopes, and then the system will be connected to T3MAPS for more advanced function tests. In the future the firmware will be ported to multiple platforms with additional functions to allow time over threshold test to be conducted on T3MAPS. T3MAPS is new sensor designed to detect high-energy particles generated by particle accelerators. The ATLAS detector is one of many particle detectors at the Large Hadron Collider, a particle accelerator run by CERN. The firmware for this system is written in a hardware description language, Verilog. This language is used to describe digital designs as a programming language, enabling reconfigurable digital circuits. This offers a vast level of flexibility. As nobody has tried to implement an acquisition system for T3MAPS, great care must be taken to insure that the signal to the sensor is correct and electrically clean. This is verified using a logic analyzer and an oscilloscope to insure the signal meets the specifications required. After signal verification, testing will be conducted on T3MAPS itself using the verified design. Tests will progress from simple configuration of the sensor to full pixel by pixel scans of the chip. Results from these tests will be analyzed to compare the speed and accuracy of this system vs. the existing manual methods.

The goal of this study is to search for a pseudo scalar Higgs boson. The recently discovered Higgs boson is only the simplest way to explain the generation of particle masses. It is possible to make a simple extension to the Standard Model by adding a second complex Higgs doublet which gives a rise to five Higgs bosons. A Monte Carlo simulation for the production of the A Higgs and its decay to two leptons and two b quarks was created. The simulation is used to fine tune an algorithm for distinguishing between the signal from this decay and background signals generated from other decay channels.It uses MadGraph, Pythia and Delphes for the different stages of simulation. The simulation data is compared against data available from ATLAS simulations. The study has shown how changes in parameters of the search algorithm lead to increase of the level of both signal and background. The expected results include better filtering of the signal from the background by analysis of the jet structure and increased sensitivity for higher masses of the A Higgs when using boosted jets in the analysis. The results of the study provide possiblities for creating a more complete model of the fundamentals of the physical world and practical ideas about how to analyze the data from the Large Hadron Colider in CERN.

 By developing an efficient and generalized framework, data from test beam experiments can be analyzed in an effort to improve silicon detector technologies for use in the Large Hadron Collider (LHC). Before a prototype sensor can be used in the LHC, a test beam is run to collect performance data. Charged particles emitted from a beam are recorded as they pass through the sensor. This data is analyzed to measure how efficient the sensor is at detecting these particles. By modifying a generalized framework for specific applications, analysis can be used for different types of sensors. Current efforts are focused on measuring the edge efficiency of slim edge 3D silicon sensors. Once this work is completed, the framework will be adapted for use on new sensors requiring their own specific analysis.

The Carbon IV emission line in quasar spectra is well-known to show systematic shifting toward smaller wavelengths often attributed winds flowing off the accretion discs along the line of sight. We investigate variability in the shift of the C IV line in two ways, using spectra observed multiple times: through correlation of the shift with changes in the intensity of the rest of the quasar, as well as through the effects of this variability on host supermassive black hole mass estimates. Our results show weak to no correlation between changes in the shift with quasar light flux between observations, potentially indicating near-constant outflow speeds. We additionally investigate biases in existing SMBH mass estimates by comparing our multiple-observation estimated masses with masses derived from single observations. Our results indicate that the previously observed correlation between C IV shift and SMBH mass can be empirically corrected thanks to the lack of variability in C IV shifts, leading to less biased SMBH masses. This will help pave the way for much more accurate methods of calculating masses for extremely distant black holes, and helps constrain physical structure models of active galaxies.