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

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

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

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.

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

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.

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.

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

Spontaneous neural activity (SA) during brain development has been implicated in processes ranging from regulation of gene expression to development of neural networks that ready organisms for post-natal life. Though SA is a well-known phenomenon, the mechanisms and developmental processes mediating its behavior are not well understood. This research aims to elucidate some of these processes. Preliminary findings have focused on defining dopamine’s (DA) and serotonin’s (5-HT) role in spontaneous activity in the developing mouse brainstem. It has been shown using transgenic mice expressing markers for proteins that interact with DA or 5-HT that SA propagates through regions containing these markers. I am now expanding this work by performing calcium imaging and confocal microscopy along with whole cell patch clamp in these transgenic mice to characterize SA in regions where the markers are highly concentrated. In addition, I have been working with a colleague from the Phillip’s lab, using voltammetry to try and record the extracellular release of DA. These experiments will establish whether 5-HT cells act as drivers for SA and if such activity can trigger DA release. The implications of this research are multifaceted. Primarily, it will expand on the anatomy and physiology of the developing dopaminergic and serotonergic pathways in the mouse brain. Second, its findings may shed light on pathogenesis of certain disorders involving these pathways by contributing to the understanding of how SA mediates their development.

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

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.

 I studied whether Chinook parr can tell the difference between full and half siblings based on their olfactory senses. 800 total parr were tested with four different female parents and the same male parent using a Y-maze device that allowed them to ‘choose’ the smell they preferred during the months of March and April 2014. The hypothesized results are that full siblings are recognized over half-siblings. If Chinook prefer their siblings over their non-siblings they are more likely to have a higher survival rate and lower predation rates because they will be less likely to be aggressive and cannibalistic, and more likely to school with these siblings

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

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.

Acute viral respiratory infections are responsible for much of the infectious disease in the world. Of the known respiratory viruses, influenza is probably the most dangerous. In addition to the relative lack of knowledge on how influenza produces systemic symptoms, little is known about how it affects the central nervous system (CNS) and subsequent recovery outcomes. Following an acute viral infection, the body undergoes a state of acute stress response (APR). APR is a complex array of physiological responses that leads to changes in behavior and body temperature, anorexia, immobility, sleepiness, and malaise. Anecdotal and personal experience suggests that sleep becomes more prolonged while one is battling influenza infection. Following an infection, cytokines and other inflammatory regulators affect sleep and body temperature caused by influenza. Cytokines are signaling molecules that are generally involved in the immune response following trauma or infection. IL1β, a focus of this study, is a particular cytokine that has been extensively studied for its involvement in physiological sleep regulation in normal healthy organisms and in those subjected to an immune challenge. IL1β alters the sleep profile post-infection by enhancing non-eye rapid movement sleep (NREMS). Such increase in NREM sleep has been demonstrated to increase the probability of survival due to microbial challenge in rabbits. I will focus on the involvement of IL1β and its receptor (ILR1) in influenza-induced NREMS APR responses. A transgenic mouse strain that selectively expresses IL1β receptors on neuronal cells in the brain will be used for this study. I hypothesize that ILR1 on neuronal cells in the brain is necessary for the virus-induced APR following an infection. Whether more sleep (specifically NREMS) promotes, as enhanced by IL1β, and less sleep impairs, recovery from infection remains to be determined.

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.

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.

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.

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

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.

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

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

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.

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.

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

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

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.

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.

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.

 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.

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 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.

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

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.

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.

Ion mobility mass spectrometry is a powerful technique for analyzing proteins and protein complexes in the gas phase. Ions are generated using nanoelectrospray ionization from aqueous, buffered solutions containing the protein or protein complex of interest. The resulting ions are native-like; their structures have low, narrow charge-state distributions and resemble those in the condensed-phase. There is an interest in probing different charge states of protein and protein complexes. High charge-state distributions of proteins and protein complexes, for example, can be seen after addition of ‘supercharging’ reagents, e.g., sulfolane or m-nitrobenzyl alcohol, to the electrospray buffer. Several mechanisms have been proposed to explain the mechanism of supercharging. Here, we used ion mobility mass spectrometry to probe the charge-state distributions and collision cross sections of a large set of native-like protein and protein complex ions, with masses ranging from 6–468 kDa, generated from solutions containing 1% m-nitrobenzyl alcohol. We determined the extent of supercharging by calculating the percent increase in highest charge state observed between supercharged and non-supercharged cations. We observed a large range of percent increases in highest charge state but in general, there is evidence that small proteins (<100 kDa) exhibited a greater increase than larger proteins in these experiments. Upon comparison of these results to those for ions generated from sulfolane-containing solutions, we found that the maximum extent of supercharging observed with m-nitrobenzyl alcohol was less than that observed when sulfolane was used. The most supercharged cations generated with m-nitrobenzyl alcohol had up to a 96% increase in collision cross section compared to ions generated without supercharging agents, but the differences in collision cross sections with and without supercharging were less than 2% for large protein complexes (> 100 kDa). These results suggest that ions supercharged using m-nitrobenzyl alcohol may retain their structures better than those supercharged using sulfolane.

Local health departments (LHDs) often do not routinely collect the type of data that can be used to conduct research and provide quality evidence-based feedback to inform public health policies and practice. To address the gap in evidence, we used new data from the Multi-Network Public Health Practice and Outcome Variation Examination (MPROVE) Study and explored processes for consolidating and presenting data for the usefulness of public health leaders’ development of policies, procedures, and services. The data from this study reflects the details of services provided by 35 LHDs across Washington State. In our research, we linked LHD data with data from existing sources and will present visual representations of the data for use by LHD leaders in examining variations and change in public health service provision. Services offered by the county were compared to other counties, trends in services across the state were analyzed, and health outcomes were compared to services provided on a county-by-county level. We specifically focused on public health service data relating to obesity, immunizations, and oral health. Through these comparisons we hope to identify further questions and gain insight on a variety of public health factors and their relation to LHD services provided. Through this process we hope to better understand how best to present data that helps LHD leaders (1) improve evidence-based public health policy; (2) modify procedures and services; (3) stimulate more effective and widespread data collection by LHDs; and (4) further improve the quality of research on public health department services.

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.

There has been a lot of interest in fermentation processes utilizing monomeric sugars in lignocellulosic biomass to acetic acid product: a key precursor for many industrial applications such as the production of jet fuel.  The selected microorganism for this study is Moorella thermoacetica (Clostridium thermoaceticum). This strain is a thermophilic obligate anaerobe and can homoferment glucose and xylose to acetic acid using CO₂ as an electron acceptor at temperatures between 55-60°C and pH 6.5-6.8.  This study investigates the production of acetic acid by this homoacetogen from a 1:1 mixture of glucose and xylose, the two major monomeric sugars in lingnocellulosic biomass. The research is a necessary step to further study of fermenting a sugar model of lignocellulosic hydrolysates and hydrolysates. Additionally it facilitates application of Raman spectroscopy as quantitative measurements in real-time during fermentation.  This is unlike the traditional way of using High performance liquid chromatography (HPLC) which is used in this study. Compared with current analytical techniques, Raman Spectroscopy (RS) allows analytes in samples to be measured simultaneously. Utilization of xylose and glucose as the main sugars for producing lignocellulosic acetic acid proves useful as a foundation for building industrial applications such as jet fuel through bioconversion of lignocellulosic biomass.

During spermatogenesis in animals, the developing male germ cell undergoes dramatic changes in nuclear morphology. This transformation of round spermatid nuclei into condensed nuclei of mature sperm is accompanied by loss of histones and enrichment of several sperm-specific chromosomal proteins. To date, the function of only a few sperm-specific chromosomal proteins has been studied. We are using the fruit fly, Drosophila melanogaster, to investigate the function of a protein that is encoded by the CG14835 gene. The protein is interesting because it is small, highly enriched in positively charged amino acids and it contains a small region of similarity to other known sperm-specific chromosomal proteins. To test for the possible requirement of CG14835 for spermatogenesis and male fertility, we are generating mutations by imprecisely excising a transposable element that resides within the gene. Currently, we are molecularly analyzing independent excision lines to identify gene deletions. The phenotype of males deleted for the CG14835 should reveal whether the protein plays a role in sperm chromatin remodeling, sperm success during fertilization, or the maintenance of paternal chromosomes in the early embryo. Overall, these studies should contribute to our understanding of the possible roles that sperm-specific chromosomal proteins play in sperm function.

Most bacterial infections are initiated when binding to receptors on the tissue surface via bacterial adhesive proteins. After adhesion, they form biofilms and become more resistant to the immune system and antibiotics. A novel approach to preventing infection is the use of anti-adhesive agents that inhibits bacterial adhesion to host tissues and thus blocks the infectious process. Therefore, understanding bacterial adhesion and physiology under different conditions is essential for the development of anti-adhesive drug therapies. This project involves studying the effects of pulsatile flow on Escherichia coli adhesion and testing the hypothesis that flow pulsatility enhances bacterial adhesion because bacteria are adapted to in vivo pulsatile flows caused by intestinal peristalsis, swallowing saliva, or beating of the heart. I used a programmable syringe pump to produce a pulsatile laminar flow composed of a low shear (e.g. 0.1 Pascal) and high shear (e.g. 1 Pascal) in a parallel plate flow chamber. The frequency and amplitude of this pulsatile flow was in the physiological range. Through a microscope with a digital camera, I recorded the number of E. coli that bound to the bottom plate of the flow chamber coated with the model receptor mannan. The preliminary results demonstrated that E. coli accumulation after 5 minutes under pulsatile flow was not significantly different from that under steady low shear but accumulation was more stationary with pulsatile flow. However, the difference in accumulation became significant when comparing with the steady high shear. These data suggest that E. coli initiate adhesion at low shear and they firmly maintain binding at high shear. Future work will require the adhesion assays of wide range of bacteria under various pulsatile flow conditions. This research will help us understand the bacterial physiology and advance the development of anti-adhesive drug therapies.

Currently, there is a huge waste of natural gas being vented or flared off all over the world resulting in large amounts of lost energy while the demand for liquid fuel continues to rise. This loss of energy can be reduced through the use of methanotrophs to converts natural gas to liquid fuel, also known as biological gas-to-liquid fuel conversion. This project is broken down into three areas: Strain Improvement, Process Optimization, and Recovery. My portion of the project is to help gather base-line fermentation data for the purpose of strain improvement. The ultimate goal of this project is to develop efficient fermentation process for the production of high lipid biomass. The methanotrophic bacteria strain is Methylomicrobium buryatense (5GB1). Each fermentation run is done in a 1L bioreactor (fermentor). Different mixed gases are used for each fermentation run. Optical density is used to monitor bacterial growth, and the produced gas is analyzed using a Gas Chromotography System. The different conditions tested are oxygen limited, methane limited, and methanol with a control set up of unlimited growth. Unlimited growth is found to have the fastest growth rate with a doubling time of 3 hours. Oxygen limited and lethane limited have a slower growth rate when compared to unlimited growth, which follows the expected bacteria behavior under limiting conditions. Methanol causes the bacteria to go through a longer phase of lag time and has a slower doubling time compared to unlimited growth as well. After testing the growth rates under these conditions, the produced biomass is tested for the amount of lipids in the cells. The final results are then compared to find the optimal intersection between lipid biomass production and bacteria growth rate.

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.

Currently there is extensive interest in the health of honeybee colonies, both in the United States, and worldwide. A healthy and functioning agricultural system requires honeybees, and bees in turn, require nutritious, diverse forage that includes both nectar and pollen. This study involved analyzing the pollen collected by honeybee colonies maintained on the campus of Edmonds Community College, and matching that with pollen collected directly from local plants. We isolated pollen from honey collected and stored by the bees and also collected pollen directly from cells in the hive. In order to identify the different pollen species, the pollen was chemically extracted and acetolyzed to remove sugars and waxes. The treated pollen was then stained, slide-mounted and viewed by light microscopy. These pollen samples were compared to samples of pollen that were collected directly from local plants as well as to existing pollen databases. Preliminary analysis revealed the presence of pollen from brassica, salvia, and trifolium. We were unable to identify some of the extracted pollen species. During the coming foraging season we will expand our database of locally-collected pollen and will generate a local pollen identification key. This will allow us to conclusively identify all of the pollen found in the hives. Results of this study will help us track what the bees are eating and will inform decisions about what best to plant to insure healthy colonies.

The increasing rates of drug-resistant bacterial infections is a concern to the healthcare system globally. Anti-adhesive therapy has emerged as a possible alternative therapy, focusing on preventing biofilm formation that is associated with increased drug resistance and disease. The study of anti-adhesive therapy is underway, but the basic transport mechanisms are still unclear. Adhesion depends on the bacterial concentration near the surface, as these bacteria are closest to any adhesive present. Flow chambers are commonly used to study bacterial adhesion and mechanics, but the relative concentration distribution within the chamber is often overlooked. Bacterial concentration without adhesion was found to depend on time – the concentration rises until reaching a peak level. After reaching an equilibrium level, the concentration deviates from the inflow concentration differently at separate locations along the chamber. Measured at three separate points, the peak concentration is highest towards the end of the flow chamber. Bacterial concentration remains space and time dependent without any adhesive protein in the chamber. With adhesion however, the concentration differs across the entire adhesive surface, and also dramatically over a small area near the inflow where adhesion first begins. Bacterial concentration of spotted and even surfaces will be affected by these settling and transport mechanisms - using different adhesives along the chamber increases this variability. Researching anti-adhesive therapy and dynamic adhesion requires the analysis of adhesion strength to different glycans, compounds on the outside of proteins, under different flow rates. The adhesion to each glycan can then be measured relatively and compared. Our data suggests that this data could be severely impacted by the placement of these glycans, in addition to the strength of their adhesion, a factor that has not been previously considered.

FLOWERING LOCUS T (FT) is a highly conserved protein in plants which promotes flowering by influencing the differentiation of shoot apex meristem cells from vegetative to floral identity. CONSTANS (CO) is a protein involved in sensing photoperiodic cues and promoting FT expression. Arabidopsis thaliana express a single evening peak of FT when placed under long-day and constant temperature conditions. Under natural conditions, temperature fluctuates throughout the course of a day. In order to determine if experimental conditions of constant temperature accurately describe flowering time mechanisms in nature, wild type Arabidopsis thaliana plants were grown outside during the long days around the summer solstice of 2013. Real Time qPCR analysis of FT mRNA expression levels in 14-day-old plants over the course of 3 days revealed a morning peak of FT absent under long-day constant temperature conditions – in addition to the evening peak of FT present under long-day, constant temperature conditions. To determine what factors might induce this morning peak, Arabidopsis thaliana were grown in two sets of environmental chambers. Both sets simulated average outdoor temperature conditions over the week of original tissue collection. One set simulated average outdoor light intensity conditions over the same period, while the other used constant light intensity. Real Time qPCR analysis of plants grown under these conditions revealed that the simulation of outdoor temperature conditions is sufficient in producing the morning peak of FT. Different mutants of genes associated with flowering time were then grown under simulated temperature conditions to determine what genes might be involved in the induction of the morning peak of FT. By looking at the different expression profiles of FT and CO, we seek to determine what genes are involved in the induction of this morning FT peak.

Targeted Tutoring is a program designed by our writing center to support English language learners in reading- and writing-intensive courses. The program was first piloted in 2010-2011 in response to students’ requests and to provide a space to encourage peer conversation. Targeted Tutoring is currently offered for courses in departments including English, Philosophy, International Studies, and Political Science. In Targeted Tutoring, three to five students meet for weekly sessions in which the tutor facilitates peer discussion. Group tutoring sessions are qualitatively different from the Center’s usual one-to-one sessions and tutors need to learn and apply new skills. This project is designed to further develop training for tutors, investigate effective models of group tutoring strategies, and explore what the differences and similarities are in skills useful in one-to-one sessions vs. those useful in group discussions. This research will be conducted by observing group sessions, crafting transcripts of successful group interactions in these sessions, and interviewing tutors and students to discover which strategies are effective. The project will be presented in a poster format that will include the models, guides, and strategies found to be most useful for tutor training and group facilitation. These results have significance for all those interested in peer education models and more effective small-group, discussion-based learning.

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.

Placental mammals (Eutheria) are one of the most ecologically diverse and dominant groups of terrestrial vertebrates alive today. However, prior to the Cretaceous-Paleogene (K-Pg) mass extinction event 66 million years ago (m.y.), two groups of mammals known as multituberculates and metatherians (group including marsupials) were far more successful in terms of number of species (species richness) and relative abundance. Substantial paleontological research has been conducted on the recovery of mammals immediately after the K-Pg mass extinction and their major diversification 5-10 million years later, but relatively little is known about the transition from recovery to diversification in the intervening interval. Recent research suggests that ca. 65 to 64.8 m.y. the placental radiation began, but whether this is an artifact of sampling or a meaningful evolutionary trend remains somewhat unclear. Here, I add to our knowledge of this important interval in mammalian evolution by describing and analyzing a new sample of fossils from the upper Tullock Formation of northeastern Montana, USA. The data set consists of over 70 isolated fossil teeth from the Horsethief Canyon 1 Locality, nearly doubling the size of the previously known sample. I identified each specimen to at least family level based on morphology and dimensions. Using the resulting identifications, I quantified the species richness and relative abundance of the major mammal groups: Multituberculata, Metatheria, “archaic ungulates,” Primates, “insectivorans,” Triisodontidae, Creodonta, Taeniodonta, and Pantodonta. Species richness was greatest for “archaic ungulates,” with more than 10 species, and lowest for metatherians, with 0 species. Primates had a relative abundance of ~55%, “archaic ungulates” ~27%, Multituberculates ~16%, and “insectivorans” ~1.6%. These results corroborate previous research implicating this time period as the beginning of placental radiation and takeover, and help illuminate patterns of decline and diversification during this critical chapter in mammalian history.

Modern frogs and toads (Anura) are environmentally sensitive vertebrates that are often viewed as bellwether taxa for the modern biodiversity crisis. As such, one would expect that they did not fare well in the Cretaceous-Paleogene (K-Pg) mass extinction event (ca. 66 million years ago) that killed off the non-avian dinosaurs. However, relative to other taxa, little is known about Late Cretaceous and early Paleogene anurans or how they fared in the K-Pg event. I have documented temporal changes in anuran diversity leading up to and across the K-Pg boundary, based on the vertebrate microfossil assemblages in the Hell Creek and Tullock formations in Garfield County, Montana. These geologic formations span approximately the last two million years of the Cretaceous and the first one million years of the Paleogene. I have identified known anuran species and distinct morphotypes, which likely represent unnamed species, from more than 200 isolated fossil anuran jaws and hip bones. Initial results, based on maxillae, show an increase in anuran species richness from 9 morphospecies in the lower Hell Creek Formation to 17 morphospecies in the middle of the formation. Then, species richness drops before the K-Pg boundary down to 9 morphotypes in the upper Hell Creek Formation. Anuran fossils are relatively scarce after the K-Pg boundary: the lower middle Tullock Formation includes one species that locally survived the mass extinction and one apparent immigrant taxon. Later in the middle Tullock Formation, I document only one unnamed immigrant taxon. These results parallel pre-K-Pg declines in some vertebrate taxa (e.g., mammals) from this study area but contrast with the high survivorship of more fully aquatic lissamphibians (e.g., salamanders). I hypothesize that the high levels of extinction suffered by anurans at the K-Pg boundary may be due to the greater vulnerability of their more terrestrial life habit.  My research aims to bring a greater understanding to the timing and mechanisims of one of the most important events in the history of terrestrial life (the K-Pg mass extinction), and possibly give insite into the current biodiversity crisis effecting extant amphibians.

At the Cretaceous-Paleogene (K-Pg) boundary, approximately 66 million years ago, a major mass extinction event eliminated up to 75% of all species on the planet. Considerable debate surrounds the cause of this extinction. Was the extraterrestrial bolide impact at the K-Pg boundary the sole cause? Or were ecosystems already deteriorating prior to the impact? In non-marine ecosystems, dinosaurs (except birds), lizards, metatherian mammals, and sharks and rays (Chondrichthyes) suffered the greatest levels of extinction. Chondrichthyans have received little research attention relative to other taxonomic groups. Here, I investigated the fossil record of freshwater chondrichthyans through the Hell Creek Formation in eastern Montana. The formation is ~90 meters thick, divided into lower, upper and middle parts, and spans the last two million years of the Cretaceous. I examined 12 vertebrate microfossil assemblages through the section, identifying teeth, dermal denticles, and vertebrae of freshwater sharks and rays to the genus level. I used this dataset to estimate generic richness and relative abundance trends leading up to the K-Pg boundary. My richness results show that one genus of ray occurs through the entire section. From the lower to middle parts of the section, sharks increase from one to five genera and then drop back down to one genus in the upper part of the section. This pattern temporally correlates with a minor rise and fall, respectively, in sea level of the Western Interior Seaway. Alternatively, this pattern may reflect differences in sampling intensity and site availability through the Hell Creek Formation. I will test the latter hypothesis using rarefaction analysis, which compensates for differences in sampling intensity. Results will help me determine whether these trends are a true glimpse into the shifting biogeographic ranges of non-marine cartilaginous fish communities of the latest Cretaceous or an artifact of variable sampling through the section.

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.

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.

The Mesozoic Era (250–66 million years ago) was a significant interval in Earth’s history when the supercontinent Pangaea broke apart into the continents we know today, allowing continental biotas to evolve independently from one another. Throughout this era, vertebrates diversified into many of the major groups known today. Although there has been much research on the vertebrate fauna of this era from many parts of the world, the Mesozoic vertebrate fossil record of Africa is still poorly known. In 2008, a team of paleontologists from the University of California, Berkeley, the University of Washington, and the University of Utah collected large volumes of fossiliferous sediment (~1,000 lbs) from a Late Jurassic locality (Jema-5) near Addis Ababa in Ethiopia. Our team of undergraduates has begun to process, sort, and identify vertebrate microfossils from these fossiliferous sediment samples. We are in the preliminary stages of our project, but previous workers have recorded a diversity of cartilaginous and bony fish, such as hybodont sharks, guitarfish (Rhinobatos), lungfish (Asioceratodus tiguidensis), and primitive ray-finned fish (Lepidotes, Pycnodus) from nearby localities. Other aquatic vertebrates and terrestrial vertebrates have also been identified from this area, including pleurodiran and cryptodiran turtles, crocodyliforms, ornithiscian and theropod dinosaurs, and primitive mammals. We aim to (1) develop a faunal list from this locality; (2) add to our understanding of vertebrate diversity in Ethiopia during the Late Jurassic; (3) better constrain the age of the fossil locality within the latter half of the Mesozoic; and (4) shed light on vertebrate evolution from a critical area and time in Earth’s history.

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.

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).

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.

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.

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.

Circadian rhythms are daily biological processes regulated by circadian clocks, endogenous 24-hr biological clocks. Our master circadian clock, located within the suprachiasmatic nucleus (SCN) in the brain, modulates the activity of circadian oscillators in peripheral organs, including the adrenal gland. While the circadian rhythm in glucocorticoid hormone production correlates with adrenal clock gene expression, the molecular mechanisms of adrenal circadian clock regulation require further investigation. Since the transcription factor phosphorylated cAMP response element binding (pCREB) protein is involved in the regulation of the clock gene PER1 in the SCN, we hypothesize that similar pathways to those found in the SCN control clock gene expression and circadian hormone production in the adrenal. Previous results from our laboratory display that the phase of PER1 circadian expression, in cultured adrenal tissue, can be shifted by drug treatments that increase cyclic adenosine monophosphate (cAMP) levels. Since increases in cAMP lead to CREB phosphorylation, we propose that pCREB ultimately regulates adrenal expression of PER1 in vivo. We measured adrenal pCREB levels in rats housed under constant laboratory conditions and sacrificed 11 hours after starting their subjective day (circadian time 11, CT11) or 11 hours after starting their subjective night (CT23), equivalent time points of peak and trough cAMP levels in the SCN respectively. Immunohistochemical detection of pCREB showed significantly higher number of cells expressing pCREB in the adrenal medulla at CT11 than at CT23. Elevated expression of pCREB before the onset of nocturnal activity in rats is consistent with the predicted peak of glucocorticoid levels. Currently we are investigating the presence of pCREB in the adrenal cortex. Exploring the relationship between pCREB and PER1 expression in the adrenal, and the role of pCREB in phase shifting the adrenal clock, may help elucidating how the master circadian clock relays circadian time to the adrenal gland.

For centuries, mankind has used adhesives as a means of joining materials together. A simple technology, adhesives bond materials, distribute stress, and improve flexibility. In nature, the organic-inorganice composite material nacre features very thin organic interlayers that serve as an ahdesive to hold together single platelets in a "brick and mortar" composite microstructure. This project addresses whether varying the thickness of nacre-like adhesive layers influences the mechanical properties of the composite. Typical standardized tensile tests listed in the American Society for Testing and  Materials (ASTM) will be modified to simulate nacre's structure. Our approach is to linearize the loading path, by performing the double lap shear configuration suggested in ASTM D3528 on a Shimadzu tensile tester. A digital microscope is used to focus on the interactions at the interfaces, while the Scanning Electron Microscope (SEM) focuses on the fibril formation in the adhesive. The adherends we will use are glass, bonded together with varying adhesive thicknesses and placed in the Shimadzu's metal grips for testing. The results display lap shear strengths as a function of lap length with constant lap width. By plotting lap shear versus lap length over adherend thickness (L/t),  we can compare the lap shear performances for the varying thicknesses. If the bond width is held constant it is expectd the bond area decrease with decreasing L/t so shear strength increases as a function of decreasing lap area. The use of transparent glass slides determines if the fracture patterns in bending would spread energy over a larger volume depending on the thickness of the adhesive. The effect of varying the adhesive thickness within the material is discussed as a function of the material's ability to transfer the load over a larger volume more readily during bending, and thereby control the energy dissipation. 

Community health clinics and health centers provide extensive primary health services to thousands of patients in Washington State every year. Increasing numbers of these patients have chronic and acute conditions that require specialty care or follow-up care that are not available within these health clinics or centers. This research project will examine the challenges these clinics experience in making the specialty care referrals not available in their clinic. Understanding the challenges associated with specialty care referrals could help create solutions, and a more effective and efficient health care system. Our research project involves a three phase system for research. Phase one involves data collection through one-on-one semi-structured (IRB approved) interviews with clinic managers and referral coordinators from ~35 clinics across Washington State regarding challenges, perspectives and solutions for specialty care referrals. Phase two and three will include analysis of interview data, transcribing, and coding. We anticipate phase three to produce conclusive data for our study. From phase one of the study, I can predict that anticipated results will indeed be conclusive, and consistent throughout our sample and complement our hypotheses. Exploratory observations have so far shown a consistency with thematic issues in specialty care referrals across Washington State. By providing a better understanding of the challenges, issues, and perspectives regarding specialty care referrals in community health care clinics, we can better inform both public and private agencies as well as policy makers of solutions to issues which directly or indirectly affect everyone.

The study of naturally occurring materials for use in every-day applications can result in innovative advancements in current technologies. Nacreous shell structure (nacre) is one such material. This nacre is a composite of ceramic in a tiny, organic, viscoelastic matrix meaning it exhibits time-dependent viscous and elastic behavior. This allows the normally brittle ceramic to be crack tolerant rather than to show high fracture toughness. Other complex composites have been shown to retain much of their strength after cracking, and this means high levels of energy dissipation. Because other structures with many thin organic layers have large damping abilities, it was suspected that nacre would also show such damping, but these damping abilities have not been tested. We hope to gain a better understanding of the damping effects of nacre by looking at tan (δ) through Dynamic Mechanical Analysis (DMA). Tan (δ) is a measure of energy dissipation by damping. A high amount of energy dissipation would have practical applications in creating safer buildings in the case of an earthquake. The viscoelastic matrix that allows for a crack tolerant material could allow for buildings to retain some of their structural integrity while people safely evacuate the building. As viscoelastic components are not typically used in structural ceramic composites, this could provide the basis for a new class of industrial composite materials.

This study investigated the effects of environmental pollution in Elliott Bay, central Puget Sound, by analyzing the microscopic biota collected from the sediment-water interface, in summer 1998 and 2007. The focus was on Foraminifera, single-cell microorganisms with shells made of calcium carbon or agglutinated sediment.  Many Foraminifera are sensitive to changes in the physical parameters of their environment and thus, they can be good indicators of pollution. Elliott Bay is surrounded by the city of Seattle with its large maritime industrial presence. City development and economic growth near Elliott Bay led to a focus on environmental concerns. On the southern shoreline of the Bay there are many heavy industries and Federal Superfund sites that had discharged large amounts of industrial pollution from the Duwamish River and Elliott Bay. In our study, sediment samples collected by the Washington State Department of Ecology were processed and the assemblage of Foraminifera species were obtained from  each of 16 samples. The species composition, species richness and density (number of individuals per sample) for each sample were analyzed.  Using this data, comparisons were made between those samples collected in 1998 and those collected from exactly the same sites in 2007. The results show that there are 12 different species found in the Bay, and the assemblages are dominated by the species Elphidiella hannai, Haplophragmoides planissimum, and the pollution-tolerant Eggerella advena. Large population of Eggerella advena in Elliott Bay, and the exclusion of other less tolerant species, indicates a physically stressed environment. By comparing foraminiferal assemblages from Elliott Bay with samples from less anthropogenically impacted locations within the Puget Sound, we can assess the degree of environmental damage to Elliott Bay.

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.

Premature infants are at high risk for heat loss due to immature development. For these infants heat loss immediately following birth may be significant and transport from birthing area to the neonatal intensive care unit (NICU) further contributes to heat loss. The purpose of this study is to examine heat loss during transport from birthing area to the NICU. We accomplish this by gathering environmental temperature data as well information on types of transport and interventions used. This is a quantitative quality improvement study that is dealing with collection of observational and measured data. “Temperature collection data sheets” are filled out by nursing staff for NICU admissions that go through the Infant Stabilization Room (ISR). This sheet incorporates general background information about the infant (birth date, time, and gestation), the temperature of the infant in the ISR, the interventions used in the ISR and during transport and the temperature of the infant upon admission to the NICU. Environmental data are gathered using a QUESTemp 34 thermal monitor to record ambient and evaporative temperatures as well as relative humidity in the ISR and along the transport path to the NICU. These data are being analyzed using simple descriptive statistics to identify trends. This study will provide support for Evidence Based Practice that leads to recommendations for specific thermoregulation interventions and environmental set up of the NICU to better prevent and control hypothermia in premature infants.

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.

To address the growing international attention on the high rates of obesity in the Pacific Islands, this project examines the discursive patterns that play a role in both fueling and quelling the outbreak of obesity among the Samoan population. I will provide a historical account of the diet and lifestyle during the pre- and post-colonialism periods in American Samoa. I am especially interested in tracing the racialization of food and the differences in perceiving food. I draw on theorist Michel Foucault’s interpretation of biopower in  to further illuminate the narratives that perpetuate the issues of power inequality, colonialism and the racialization of obesity towards the Samoan people, and what exactly defines “health” and “wellness”. The sources of these narratives are extracted from everday popular media, news articles, and even film or artwork. The project also uncovers the various counter narratives from Samoan Americans in the local Seattle community as well as Pacific Island authors and educators to shed light on work counteracting obesity in the community, the significance of cultural preservation and indigenizing health and incorporating de-colonial movements. This leads into the movement towards individualized risk management awhile not losing sight of community and relationship. The implications of this analysis lead us to consider the correlation between discourse and body governance in the context of a growing global health and food industry.

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.

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.

 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.

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.

Genetic conflict ensues between two parties that have an antagonistic relationship, where fitness gains in one party necessitate fitness losses in the other. As a result, there is constant selective pressure on both parties to maintain evolutionary dominance. One such conflict may exist internally between the mitochondrial and nuclear genome. This arises from the difference in DNA inheritance patterns between the two parties. Nuclear DNA is transmitted maternally and paternally in Mendelian fashion whereas mitochondrial DNA is only transmitted maternally, leaving males as an evolutionary dead end for mitochondrial DNA. This suggests that male-harming mutations could arise and fixate in mitochondrial DNA as long as those mutations are beneficial or neutral to female fitness. One way for males to counteract such mutations is for the nuclear DNA to evolve suppressors of these mutations. This conflict may not commonly exist in nature because males with mutant mitochondria would appear wild-type if their nuclear genomes contain suppressors of these mutations. To reveal if a conflict exists, we took an experimental evolution approach, using Drosophila melanogaster, to break the coevolution of mitochondrial DNA and Nuclear DNA and allow mitochondrial DNA to evolve on its own. After 34 generations, we performed a variety of assays and sequence analysis to identify any mitochondrial male harming mutations. We isolated a single mutation and an associated fertility decrease in males. We are currently trying to identify if any suppressors of this mutation exist in nuclear DNA of other strains of melanogaster by introducing the nuclear genome of these strains into a male with the mutation. We predict that if such nuclear genomes exist, then the fertility of mutant males should be restored when this nuclear genome is introduced. This study will provide an evolutionary insight into disease and defects of males associated with mitochondrial mutations.

Childhood Apraxia of Speech (CAS) is a rare, severe, persistent pediatric motor speech disorder of largely unknown genetic cause that affects the ability to acquire intelligible speech and coordinate the volitional production of sounds by sequencing muscle movements for the production of words. Developmental Dyslexia is a common and specific childhood learning disorder defined as a significant impairment in reading ability that cannot be explained by deficits in intelligence, learning opportunity, motivation, or sensory acuity. Various dyslexia studies suggest that slowed global processing speed, especially when sequential modes are involved, may be a brain-based endophenotype of dyslexia under genetic control. Impaired sequential processing, hence, may be a biomarker shared by CAS and Developmental Dyslexia. Our group recently identified a de novo heterozygous deletion of a single gene in a proband with severe CAS, raising the question whether similar deletions are causal in other cases as well. Here we report a genome-wide Single-Nucleotide Polymorphism (SNP) and CNV findings in a cohort of 20 affected individuals in nine multigenerational families with well-characterized CAS and six unrelated individuals with Developmental Dyslexia. All participants met clinical research criteria for CAS as part of a larger study on familial motor speech sound disorder or Developmental Dyslexia. The genome-wide copy-number variation study of the selected individuals was completed using the Illumina HumanOmniExpress-24 BeadChips and Human Exome BeadChips. Analysis of the SNP content and CNV for overlapping variations across the genomes of these affected individuals give us insight into genomic regions associated with the clinical phenotype of sequential processing deficit in multiple domains.

 Antibodies play a key role in imaging, diagnostics and therapeutics. Antibodies are large molecules, often proteins, produced by our immune system that recognize and bind to specific targets. This project focuses on creating antibody-like recognition proteins that can be triggered to bind and release on command. We propose to create this activatable protein by mutating key regions on an existing protein that would act as a scaffold for the new switchable binding protein. FimH, found on the end of bacteria fimbria, is an ideal protein scaffold because it can be triggered to have an allosteric conformational change that affects binding affinity. To fully explore the different mutation possibilities, we propose to randomize 3 complementary determining region (CDR) loops that are crucial in binding to FimH’s original target. This “library” of proteins will then be expressed on bacteria, filtered to remove improperly folded proteins and screened against targets of interest in order to search for unique binders. The display library size is significant in our work because a larger library increases the probability that there could be more unique binders found while screening the library. We have created a display library of 1.07x10⁵ variants of CDR loop 2 randomized. I have focused on maintaining the diversity of the expressed library by optimizing the library transformation rates while randomizing CDR loops 1 and 3. Through this work, I have found an optimum ratio of cells to library DNA that will express a sufficient sample of the library at an affordable cost. We predict that this technology could improve the specificity of diagnostics and imaging by exacting control through triggering binding and unbinding of targets in these systems.

Serpentinization, a geological process that occurs in many settings on Earth, generally involves the reaction of olivine, a mineral component of ultramafic, basaltic rocks, with water. The products of serpentinization reactions, including serpentine, carbonates, talc, and saponite, are mineralogical signatures which indicate geochemical environments and processes that are hospitable to microbial life. On Earth, these processes have been shown to sustain dense microbial communities. The identification of serpentine in particular uniquely indicates that serpentinization reactions have occurred. Therefore, the identification of the mineral serpentine on Mars has significant astrobiological implications. Previous studies have identified serpentine in three geologic settings on Mars using near-infrared spectral data collected by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) on board the Mars Reconnaissance Orbiter. Minerals are identified by their unique absorptions at specific wavelengths through the examination of CRISM surface reflectance data across 438 wavelengths from 1.0-3.9 microns. Unfortunately, spectral datasets like CRISM contain large volumes of data and each spectrum usually covers an area that contains several unique compositions, or spectral endmembers. Here, we have adapted and applied factor analysis techniques to CRISM data to confirm the previous detections of serpentine and search for new identifications in regions containing olivine-rich basalts. Our methods, factor analysis and target transformation, are more sensitive to subtle, characteristic absorptions as in the spectrum of serpentine than traditional analysis techniques and are a set of methodologies that allow for rapid and automated analysis of large spectral datasets. These methods can be used globally to both identify the number of individual components and test for the presence of and isolate individual endmembers from mixed spectral data. Ultimately, by applying this technique to the global CRISM dataset, we will have a more detailed understanding of aqueous processes like serpentinization on Mars.

Physical limitations have forced computer hardware designers into providing multiple processors rather than faster ones. To take advantage of this, software engineers must structure their programs in a parallel fashion. Separately, programming languages with commands similar to those of hardware, known as "systems languages", have long been criticized for their lack of safety. This means that programs written in these languages are easily incorrect and difficult to reason about. Rust, a new systems language from Mozilla, seeks to address both parallelism and safety by using modern language concepts. To those ends, Rust’s concurrency primitive is the task, which can be thought of as a lightweight thread that does not share memory with any other task. Message passing is used between these tasks in order to coordinate their work. While this primitive is sophisticated and suited to parallelism, the development community has expressed a desire for an Actor library. At a high level, the Actor model is a concurrent object-oriented programming model, where each Actor maintains state and takes actions based on the messages they receive from other Actors. In this investigation, the suitability of the Rust language for an Actor library is evaluated by writing and refining an implementation. It is expected that the implementation will be backed by the task primitive and its associated structures. Various criteria will be evaluated throughout development, including overall throughput, library overhead, and ease of use. The success of the Actor model within the Rust language would continue its goal of bringing straightforward parallelism and safety to the systems language space.

Underground structures are important in civil infrastructure in modern urban areas to address the growing need for space. They are used in a wide range of engineering applications including building foundations, underground transportation systems, and underground storage facilities. These shallow structures typically require soil excavation from the ground surface. Thus, stability of the excavated ground is a major challenge in the design and construction processes. Bracing approaches have been implemented in the current state-of-practice to ensure the safety of the excavation. One common “Braced Excavation” system involves vertical retaining walls on both sides of the excavated ground held in place using horizontal internal struts. These struts are designed using Peck’s method of pressure distribution envelopes, which considers the strength of the material (i.e. soil and steel) and soil lateral pressures. However, due to uncertainties involved in the material properties and estimation of the soil pressure, the design internal strut loads tend to be higher than the internal strut loads seen in real-world situations. The objective of the research was to compare the induced internal forces on the laterally resisting struts in a braced excavation system found by using Peck’s Method, and measured internal strut loads using centrifuge physical modeling. A target prototype braced excavation system was defined and designed based on Pecks method of pressure distribution envelopes. Then, a scaled physical model was constructed and employed to simulate the prototype system in a geotechnical centrifuge. The insight gained through this project will be valuable in performance-based design engineering of underground structures. In addition, it will provide a comparative assessment of the efficiency of the design procedures, which eventually will lead to lower factors of safety.

Philosophy research and teaching pedagogy are usually approached, in much of Western academia, through a method focused on rational, explicit argument. However, many other fields privilege the role of emotion in decision making and suggest that non-argumentative methods, such as stories, discussion, or implicit argument more closely represent our natural cognitive processes. This alternate approach has important implications for the field of philosophy that are worth exploring further. My research seeks to address several questions: How might stories, discussion, and implicit argument represent our everyday cognitive processes more accurately than rational, explicit argument? Why might doing philosophy without arguments be important? When, conversely, might a focus on rational, explicit argument (which brings clarity in form, a shared method among different philosophical communities, and rigorous writing and critical-thinking skills) be the better choice? What kinds of questions are best addressed by what means? These questions will be examined by a combination of methods: 1) literature review (focusing on Feyerabend’s arguments against strict, methodological rules; Bicchieri’s research on norms and beliefs; and data from neurobiological studies on the role of emotion in decision-making), 2) contrastive analysis of personal experience using different approaches to philosophy in different contexts (during interactions with children in Philosophy for Children programs; and by employing non-directive tutoring strategies in writing center tutoring practices), and 3) non-structured interviews with other participants in these educational programs. Preliminary findings suggest that non-argumentative methods of doing philosophy can be more effective in promoting social and personal change. Presentation participants will be invited to explore the question of what should be the implications of these findings for philosophy research and teaching pedagogy.

Tumor necrosis factor (TNF) is a key host factor in tuberculosis (TB). In the zebrafish model for TB, excess TNF triggers necrosis of infected macrophages which leads to exuberant extracellular bacterial growth and host susceptibility. In infected macrophages, excess TNF induces production of reactive oxygen species (ROS) which activate two death pathways one of which involves the mitochondrial transition pore, and the other leads to ceramide production and lysosomal permeabilization. In exploring the events downstream of ceramide production we found that the pro-apoptotic factor Bax is required for macrophage necrosis in excess TNF conditions. Bax has been well-characterized for its role during apoptosis, but this result suggested that Bax might also play a role in necrosis. To determine if this was the case, we engineered Bax mutants that lack its different functional domains. We studied the ability of each mutant protein to regulate apoptosis and necrosis in the zebrafish and found the BH3 domain, which is required for Bax oligomerization during apoptosis, not to be required for necrosis under excess TNF conditions. Rather, an C-terminal transmembrane helix was found to be required for necrosis. These findings demonstrate that the pro-apoptotic factor Bax also regulates necrosis but through a distinct functional domain. Since excess TNF-mediated necrosis has been implicated in human TB pathogenesis, this understanding of how Bax regulates necrosis may guide host-derived therapies.

Aging research depends on the use of model organisms to test hypotheses about the biological mechanisms common to many organisms. One commonly used model organism is the roundworm Caenorhabditis elegans. Unlike homeothermic mammals, C. elegans are poikilotherms, and as a result of a variable internal temperature, they also exhibit variable longevity based on the ambient temperature. Under standard laboratory conditions, C. elegans are commonly grown in incubators ranging between 15°C and 25°C, and lifespan varies inversely with temperature; worms live longer at colder temperatures. Our recent data show that the relationship between temperature and aging has a genetic component. By measuring the lifespan of worm strains with mutations in genes found in established aging pathways, we have identified mutations that have opposing effects on lifespan at different temperatures. For example, utilizing lifespan assays I have conducted, we have found worm strains that live longer than controls at high or low temperature, but not both, as well as strains that are short-lived at specific temperatures. These experiments suggest there may be overlapping but distinct mechanisms driving aging at different temperatures, and we are developing hypotheses to explain the temperature-dependent mechanisms of aging. Thus far, our data are consistent with the hypothesis that genes that contribute to protein homeostasis promote longevity at higher temperatures, whereas genes that limit effects of toxic compounds (both internally and externally produced) promote longevity at low temperatures. Understanding the temperature-dependent mechanisms of aging in C. elegans will advance the aging research field by extending knowledge on a widely used model organism and by testing how the mechanisms of aging and disease may be conserved in homeotherms. We hope our results will suggest how and why many genetic longevity pathways are conserved from worms to mammals despite drastically different life histories.

Tyrosinemia Type II is a genetic disorder caused by a mutation in the enzyme tyrosine aminotransferase (TAT), which leads to an elevated level of tyrosine in the blood. If untreated, individuals with tyrosinemia develop life-threatening clinical symptoms that include an increased tendency to bleed, damage to the nervous system, damage to the eyes, and organ failure. Unexpectedly, mutation of TAT in the nematode Caenorhabditis elegans results in animals that are long lived in comparison with wild-type (WT) worms. This study aims to elucidate the cellular mechanism and workings of TAT in the mitochondria, its role in the pathology of the disease, and its possible links with aging in C. elegans. Thus far, we have developed a simple method to measure the CO2 output of the worms and shown that the TAT mutant’s metabolism is about 50% compared to WT. This significant decrease in CO2 output was matched comparable to a strain deficient for mitochondrial Cytochrome C Oxidase, which served as a positive control. Cytochrome C Oxidase, or Electron Transport Chain Complex IV, is one of the three complexes that create the proton gradient inside the mitochondrial matrix upon accepting electrons. Notably, mutation of the gene acting downstream to TAT in the tyrosine degradation pathway, which causes Tyrosinemia Type III in people, or any other mutation in tyrosine metabolism that we have tested, causes no significant change in CO2 output of C. elegans. Furthermore, through our preliminary metabolomics assay we have identified three metabolites that are accumulated to extremely high levels in comparison to positive and negative controls. The future steps will include determining whether these metabolites play a direct role in the effects of TAT mutation on mitochondrial function and aging.

The current approach for FDA drug approval requires an exorbitant amount of time and money, often spent in pre-clinical animal studies, and has a high late-stage failure rate.  This is partly due to the fact that pharmaceutical companies develop drugs to treat the average patient with any given disease.  A personalized medicine approach would increase the effectiveness of a new drug for each patient and decrease the need for animal testing.  Induced pluripotent stem cells (iPSCs) are becoming the next-generation tool to study disease and discover new drugs.  Patient-specific somatic cells are reprogrammed to a stem-like state, and then differentiated in culture into the cell type most likely to manifest features of a particular disease.  High-throughput drug screens can be designed to find new compounds that can correct the disease defect in the culture dish.  Using this technology, we extracted somatic cells from the urine of patients with autistic syndrome disorder (ASD).  In addition to their cognitive deficiencies, these young patients suffer from chronic and debilitating constipation, which profoundly impacts their quality of life.  This lack of gut motility is suspected to be caused by a defect in enteric neuron function.  Our hypothesis is that the same synaptic malfunction causing cognitive deficits in ASD children also causes the enteric neuron defect.  Preliminary data also suggests that neural crest cells - an intermediate cell type in the enteric neuron lineage - can be generated using a combination of growth factors.  Therefore, I am conducting growth factor dose-response experiments on iPSCs to optimize neural crest cell differentiation.  I will phenotype the resultant cells via immunocytochemistry and qPCR analysis.  If successful, this project will lead to the discovery of new compounds able to relieve ASD patients of their constipation and further validate iPSCs as a tool for disease modeling and drug discovery.

Cardiomyocytes are the optimum cell source to model and study heart diseases and to screen drugs for cardiotoxicity in vitro. Cardiomyocytes differentiated in vitro from human pluripotent stem cells, however, are structurally and functionally immature. It is necessary to accurately recapitulate the behaviors of cells in the native myocardium for pathogenesis and drug-screening assays. Therefore, before the application of human pluripotent stem cells-derived cardiomyocytes (hPSC-CMs), we must address their maturation state. Physical cues presented to neonatal rat cardiomyocytes in a specific scale matching their native microenvironmental niche have been shown to profoundly regulate their structure and function, as characterized by elongated anisotropic morphology, well-organized contractile machinery, and faster action potential propagation. It is unknown, however, whether the same nanotopographical cues would have a similar positive influence on the maturation of hPSC-CMs. In this study, we tested the hypothesis that anisotropic nanopatterned substrates would enhance the maturation of hPSC-CMs, resulting in cardiomyocytes more suitable for in vitro cardiac tissue engineering applications. To test this hypothesis, we seeded hPSC-CMs differentiated from the matrix sandwich method on nanopatterns of various dimensions and compared their maturation with hPSC-CMs cultured on traditional flat substrates. To characterize maturation, the structural and functional phenotypes of hPSC-CMs were analyzed from their morphology/alignment, calcium handling properties, and gene expression. It was anticipated that, similar to neonatal rat ventricular cardiomyocytes, hPSC-CMs would exhibit a size-dependent change in their structure and function and that there would be an optimal substrate dimension size resulting in the most mature hPSC-CMs. The experimental result could yield a hPSC-CMs culturing protocol for deriving mature human cardiomyocytes for future drug screening assays and heart disease modeling. After optimizing substrate dimensionality, other culturing aspects such as chemical and mechanical cues and their temporal introduction to cells can be tested to further enhance the maturation of hPSC-CMs.

Gene therapy for monogenic diseases is undergoing an exciting resurgence in the last few years. Patients with hereditary blindness, blood cancers and hemophilia have been cured with minimal to non-existent long-term side effects. Our lab has been studying X-linked myotubular myopathy—a rare disease of young boys that causes profound weakness in all skeletal muscles including the diaphragm. An adeno-associated viral (AAV) vector gene therapy has been proposed to treat the X-linked muscle degenerative disease. However, the viral dose required is in excess of 10^13 viral particles per kilogram. The goal of this proposed project is to find ways to manipulate muscle cells to increase virus uptake and enhance activity of the muscle protein expression. Artificially induced mechanical stretch and contraction have been shown to stimulate intracellular signaling and gene expression. Thus, we hypothesize that preconditioning muscle cells by in vitro stretching will increase both virus uptake and gene expression. This study aims to test the influence of mechanical stretch on muscles cells treated with the AAV mediated gene therapy by inducing stretching motions with the FlexCell machine before vector treatment. The FlexCell produces cellular stretching through regulated fluctuations in air pressure. Skeletal myocytes were cultured on a clathrin coated bioflex plate and underwent cycles of equibiaxial cyclical stretch for a set time period. Cell cultures were then treated with the proposed myotubular myopathy AAV vector therapy. Transgene expression was compared using immunofluorescence between cultures that underwent mechanical stretch and cultures that did not to determine the effects of stretch in virus uptake and transgene expression. Increases in both will enable future attempts of gene therapy in animals or humans to use lower doses, which should be accompanied with lower toxicity and fewer and less severe adverse side effects.

The Rieske iron-sulfur protein (Rip1) is a nuclear encoded protein that assembles into the cytochrome bc1 complex of the electron transport chain in budding yeast, Saccharomyces cerevisiae. The iron-sulfur cluster bound by this protein facilitates the flow of electrons during cellular respiration in the inner membrane of the mitochondrial matrix. In the nematode worm, Caenorhabditis elegans, a mutation in a conserved residue of the Rieske iron-sulfur protein has been found that delays development and extends the lifespan of this organism. Mutagenesis experiments from our laboratory have identified suppressors of this C. elegans developmental phenotype that are due to secondary mutations in conserved residues within a flexible hinge region of the Rieske iron-sulfur protein. The primary mutation and secondary suppressing mutations were introduced to the yeast Rip1 gene through site directed PCR mutagenesis. Transgenic yeast have been created expressing the mutant forms of Rip1 homologous to those identified in C. elegans. The next stages of my project will entail the characterization of these mutations in yeast. I plan to assay the replicative lifespan, growth rate, respiratory efficiency, as well as sensitivity to variance in temperature, reactive oxygen species and carbon source in an effort to understand how this mutant’s lifespan extension fits into the larger picture of known aging pathways. The extrapolation of the mechanisms found in these model organisms serve as the basis for understanding our own complex aging process.

Living Independently for an elderly person is very important.  No one wants to live in a nursing home, but living alone can be dangerous for some people with health problems. I am creating a prototype of a free app that is aimed at serving elderly people who live by themselves, especially those that have medical conditions. Once the app is downloaded, the user will be asked several important questions such as: if they have a Microsoft Health Vault, medical history, medication being taken, allergies to medicine, blood type, personal contact(s), residence, secondary personal telephone numbers (optional feature), Independent Living email address, and voice activated password.  The app allows the phone to be sensitive to shock set to a sensitivity level determined by the user to detect incidents such as a fall. It can also be voice activated using the voice activated password or manually activated by a press of a button. The user will also be able to set a predetermined amount of time to deactivate a distress signal to authorities in case of accidental activation. The app will also be capable of using the phone’s GPS capabilities to help authorities locate the person, if available. If a distress signal is not terminated, the app will notify predetermined personal contacts and 911 that Police, Fire, and Medical needs to be dispatched to the person’s location and the app will provide necessary details to adequately aid the individual. The app will be a free alternative to more expensive medical alert systems.

Over the last four decades, marine community composition has changed in the San Juan Archipelago, showing a density decline in the scleractinian (hard skeleton) solitary cup coral Balanophyllia elegans. Determining predictors of B. elegans abundance, distribution, and size is important for ecological research in the eastern Pacific Ocean because changes observed over time could be an indication of realized impact from climate change and ocean acidification on calcifying organisms. Though reef corals are heavily studied, little is known about temperate, solitary corals. We studied B. elegans in the San Juan Islands in transect photos from 2008-2011 at 11 sites. At two of the sites, we analyzed photos to determine the distributions of size and abundance at 3-27 m depth. At all of the sites, we evaluated the effect of flow rate on coral size and population density by grouping the data from depths between 15-21m at the 11 sites into 4 categories of flow: low flow, medium flow, high flow, and very high flow. We used multiple statistical tests, including the Gaussian General Linear Model and the Poisson General Linear Model, with ANOVA to analyze the data. We found that the distributions of B. elegans vary by site, depth, and year. The results tell us that each site is unique. Even though some of these sites are separated by mere meters, characterized by the same flow rates, and evaluated on equivalent slopes, they appear to differ enough to create measurable variance. The patterns we found will need to be explained by researching these sites longer and adding additional site variables, such as pH. Fluctuations in pH, potentially caused by changes in rates of upwelling in the northern Pacific Ocean, could cause short term trends of increasing population size of calcifying organisms when pH is higher, but significantly reduced populations when pH is lowered by increased upwelling.

Social science research has long been interested in determining what motivates individuals to regularly attend church with previous studies examining primarily individual (e.g., gender, religious beliefs), and contextual factors (e.g., fit with church, availability of church groups). Recent research has begun to investigate the influence of one’s family life such as attendance of children’s weekend activities and the influence of one’s professional life such as the extent to which the church endorses work values. A thorough understanding of church attendance will arise from taking into consideration the interplay among one’s family and professional lives. We hypothesized that individuals who experience high conflict between their work duties and family responsibilities (i.e., low work-life balance) will be less likely to attend church as they may seek to achieve balance by reducing their commitments. More importantly, we sought to identify variables that may attenuate this relationship; that is, we wanted to determine what might motivate individuals to regularly attend church despite perceived work-family conflict. To that effect, we proposed multiple moderating variables including the extent to which (1) one’s neighbors and coworkers attend church, (2) church provides a social support system, and (3) church attendance is perceived as satisfying basic needs. To test our hypotheses, we administered an online survey using Amazon MTurk to 200 working adults. Stepwise hierarchical regression analyses will be used to test our main effect and moderating hypotheses. We believe our research has critical implications for research and practice alike. We had hoped to better understand church attendance by adding work-life balance as a predictor while simultaneously offering nuance in identifying multiple moderators. Churches may benefit from our research by being able to develop retention mechanisms that may counteract a drop in church attendance due to increased pressures on individuals to maintain a sustainable work-life balance.

Previous research on young adults shows a negative relationship in college-aged students between alcohol-related behaviors and religiosity, giving evidence that religiosity acts as a protective barrier. Verifying that religiosity acts as protective behavior allows for a clearer understanding of possible strong deterrents towards risky alcohol-related behavior. To date no study has investigated religiosity and alcohol use in both the U.S. and Sweden, an international sample that is predominantly Christian and non-religious. The present analyses aims to compare the U.S. and Sweden in religious affiliation and alcohol use. Participants completed a baseline online survey as part of a larger trial that assessed risk behavior in adolescents. In the present analyses, the severity of alcohol use was measured with the 10-item Alcohol Use Disorders Identification Test, alcohol related negative consequences was measured with the 18-item Young Adult Alcohol Problems Screening Test, and frequency of religious practices was measured with one-item. We predict a negative relationship between alcohol use and alcohol related negative consequences and religion. Regression analyses were run assessing the contribution religious affiliation has on alcohol use related problems. Analyses revealed a significant main effect of religious affiliation on AUDIT and YAAPST, such that religious affiliation was related to lower alcohol use severity and related negative consequences. This further establishes religiosity as a possible protective measure to alcohol related behaviors. Thus, religious affiliation may prevent alcohol use in adolescents. One limitation is how narrowly we tested religiosity. Future research might include investigation of religious groups such as “youth groups” or religious service attendance and alcohol use to activities holding similar properties to religious groups and behaviors.

Simian immunodeficiency viruses (SIVs) naturally infect over 40 species of African primates. From these SIV strains, only two have crossed to humans giving rise to HIV-1 and HIV-2 which have now infected over 40 million people worldwide leading to several million AIDS-related deaths per year. The goal of this project is to understand what determines the ability of the SIVs to cross between hosts and to evaluate the risk of future SIV cross-species transmissions to humans. To efficiently transmit between species, an SIV needs to be able to overcome the multiple immunological barriers imposed by a new host or rapidly adapt to gain this ability. Several of these barriers are encoded by the antiviral proteins that limit virus replication and thus constitute an innate immunological response against lentiviral infection. In this study, we studied the evolution and adaptation of SIVs during cross-species transmission by identifying the amino acid mutations that the viral protein, Vif, needs to undergo to antagonize the human antiviral protein APOBEC3G (A3G). Since, A3G has been described as one of the major barriers for cross-species transmission its degradation by the virus might facilitate SIV transmission to humans. In order to identify the adaptive mutations required to gain anti-human A3G activity, a virus encoding for an HIV-1 backbone and a SIV Vif protein was serially passaged in a human CD4+T cell line expressing human A3G. Preliminary data suggests that in short-term infection the virus is not able to overcome human A3G. We will continue to passage the virus to determine whether or not viral replication is rescued which would indicate that Vif acquired resistance to A3G. The acquired resistance then will be mapped to specific amino acid mutations through sequencing. To test the anti-human A3G activity of these mutations, molecular clones of the virus containing the mutations will be generated using site-directed mutagenesis and tested in specific A3G degradation assays.

A plane tiling is a countable family of closed topological disks T = {T₁, T₂, …} that cover the Euclidean plane E² without gaps or overlaps. There are 14 known types of convex pentagons that allow tilings of the plane, but it is unknown if this list is complete. The last new convex pentagon tiling was discovered in 1985. An i-block B is a patch of i pentagons in a tiling T by identical convex pentagons such that T consists of copies of B, the tiling formed by B is symmetrical, and i is the minimum number of pentagons for which the patch B exists. Any repeated (periodic) tiling by convex pentagons is necessarily equivalent to an i-block tiling (i-block transitive) for some i. If all pentagons that allow a tiling of the plane admit at least one periodic tiling, then the class of pentagons admitting i-block transitive tilings would represent all possible pentagons that allow tilings of the plane. Combinatorial methods establish limits on the properties of vertices and edges in i-block tilings. The results allow an ordered listing of all possible i-block transitive tilings by convex pentagons. This listing, known as an enumeration, might uncover a new tiling of the plane by convex pentagons. An algorithm is being written to automate the process of enumerating the i-block transitive tilings. If a finite limit can be placed on i, it will be possible to exhaustively complete the list of pentagons that can tile the plane -- a mathematical problem that was started in 1918 by German mathematician Karl Reinhardt and remains unsolved today.

Washington State, in response to the recent return of grey wolves, implemented a management plan that includes the monetary compensation of ranchers who lose livestock to confirmed wolf predation. Our research looks into the reasons why many Washington State ranchers refuse to participate in these compensation programs, helping us better understand the social attitudes towards wolves and their management within the state. We were able to assess the views of Washington State ranchers through numerous key informant interviews and focus groups, followed by transcription and coding. We analyzed correlations between views on compensation and other attributes to increase our understanding of shortcomings of the compensation program. Our results allow us to assess the overall effectiveness of the wolf compensation program in Washington. Through the study of stakeholder views of the current compensation program, we are able to focus future efforts on a more widely socially accepted wolf management program in the state of Washington.

The prevalence of smartphones has dramatically increased over the last several years, and with this comes an unparalleled medium for data collection. Smartphones are constantly transmitting data, and with an approximated 56% of American adults owning a smartphone, we now have a data medium that encompasses the majority of the population. One of the most valuable data that we can obtain through this medium is location data. By measuring the signal strength of a smartphone from a number external access points, we can collect accurate, real-time location data about a given user. This system has wide spread applications, whether it is being used academically for research purposes to measure travel patterns of users, or commercially to develop automated systems for building control. However, there is yet an easily accessible way to utilize the valuable information that surrounds us. Inexpensive, readily available hardware and software can be configured to develop a system that can be used to harness this data, and successfully doing so offers many opportunities. This can be done by using wireless adapters as access points, and calculating the location with triangulation with multiple nodes.

We are interested in identifying the spectrum of mutations that arise when performing the same evolution experiment many times. We have previously grown 32 replicates of haploid yeast cells in continuous cultures under constant sulfur limiting environments for 300 generations. Mutants with increased fitness will increase in prevalence and can be characterized using an array of comparative genomic hybridization (aCGH) or next generation sequencing (NGS). To date we have used aCGH on a subset of our evolutions, and in 16/16 cultures, found amplification of SUL1, a high affinity sulfate ion transporter gene used by the cells to aid in increasing import of sulfate. We are also interested in identifying alternative means for adaptation in this environment and have evolved a a strain in which we'd knocked out SUL1 (sul1Δ). With this background, we observed SUL2 amplification in 4/4 cases in the absence of SUL1. A second focus of our work is to track changes in fitness as specific mutations arise. To assay fitness, we periodically compete an evolving culture against a Green Fluorescent Protein (GFP) expressing ancestral strain of yeast. This work has shown that the dynamics of adaptation of wt and sul1Δ yeast differ, which suggests very different fitness landscapes during the evolution for these two genotypes. Collectively these data show that SUL1 amplification is a first target of evolutionary selection and that in its absence, amplification of SUL2 becomes the primary means for adaptation in constant sulfate limitation.

 Sleep is essential for survival, yet its function remains unknown. In our society, sleep deprivation and disruption of sleep architecture, namely the temporal structure of rapid eye movement (REM) and non-REM sleep stages—are common. Sleep deprivation impairs memory consolidation dependent on the hippocampus region of the brain. We hypothesize that disruption of sleep architecture in the absence of sleep deprivation impairs hippocampus-dependent memory. Our laboratory developed a rat model in which sleep architecture is predictably disrupted without the confounding effects of sleep deprivation, and without genetic, pharmacological or surgical manipulations. Exposure to an artificially short light-dark (LD) cycle (22 hours) produces two circadian rhythms within the same animal. In this “forced desynchrony” protocol, animals cycle between “aligned” days, during which the two oscillations are in phase and sleep architecture is similar to that of 24-hour LD cycle control animals, and “misaligned” days, during which oscillations are out of phase and sleep architecture is disrupted. Previous results indicated that rats trained in a contextual fear-conditioning hippocampus-dependent memory task during misaligned days show impaired memory consolidation. Because memory consolidation was measured as “freezing”, the animal’s immobility in the fearful context, we asked whether memory consolidation would also be impaired in a hippocampus-dependent task requiring active spatial navigation (the Morris water maze or MWM). We trained aligned, misaligned and control animals to swim to a hidden escape platform within a pool containing visual cues. After removing the platform, we tested memory consolidation by measuring latency to reach the original platform location along with other parameters. Our analysis showed that while circadian forced desynchrony associated with sleep-stage architecture disruption may impact memory acquisition in the MWM task, it does not appear to impair long-term memory consolidation. We conclude that normal sleep architecture may be critical for some hippocampus-dependent memory tasks but not others.

 Bacteria are encased by a cell wall made of peptidoglycan (PG). This macromolecular structure is essential for viability and defines the specific shape of each bacterium. Helicobacter pylori (H. pylori) is a helical-shaped, bacterial pathogen estimated to infect half of the worldwide population. It has long been postulated that H. pylori’s unique cell shape plays an important role in its pathogenesis; however, a longstanding question in the field has been how this helical cell shape is generated. My project focuses on studying essential genes involved in PG synthesis. The goal of my project is to determine whether the PG synthesis machinery overlaps with that which is responsible for cell shape. H. pylori displays efficient natural competence, meaning that it is able to take up extracellular DNA from its environment and recombine it into the genome (a process called transformation). I will introduce mutated copies of the essential gene by transformation at a second chromosomal locus making it possible to knockout the native copy if the mutated copy retains at least partial function. To date I have developed a plasmid vector that can direct integration at a unique position on the chromosome and shown that expression of cell wall synthesis genes of interest from this locus alone confers normal cell growth and cell shape. I have been working on increasing the transformation efficiency of my plasmid vector into H. pylori to generate a large number of mutants. While most of these mutants will have the helical phenotype associated with wild-type H. pylori, I expect a portion of these mutants to have interesting shape phenotypes. These studies will begin to address how PG synthases contribute helical cell morphology and provide a platform to study other essential processes in H. pylori.

The type VI secretion system (T6SS) is a molecular export pathway that is widely conserved in Gram-negative bacteria. It mediates interbacterial competition by translocating antibacterial effector proteins from the donor bacterial cell to a neighboring bacterial cell in a contact-dependent manner. The T6 amidase effectors (Taes) are a superfamily of lytic enzymes that degrade the bacterial cell wall by cleaving amide bonds in the peptidoglycan (PG) layer. Taes also have cognate T6 amidase immunity proteins (Tais), which prevent intraspecies intoxication by binding and inhibiting Taes in the periplasm. We hypothesize that this pathway can be exploited for an antibacterial strategy. Specifically, we aim to engineer a P. aeruginosa strain that harbors a novel Tae/Tai pair that can escape recognition by native Tai proteins and predict that this strain will be able to outcompete its wild-type counterpart through the T6 pathway. Towards this end, our group previously generated a mutant library of Tae from P. aeruginosa and screened for variants that escape inhibition by Tai (Tsi1) in E. coli. I am currently experimentally validating several potential escape variants (Tae*) identified by this screen by testing Tae* toxicity in the presence of Tai1 in an in vitro bacterial lysis assay. I will also measure potential changes in in vitro Tai1-binding affinity by isothermal titration calorimetry (ITC).

Recently King County Metro has announced plans to cut 17% of its transit service due to a $75 million deficit. Assuming that no sufficient transportation financing package is developed, Metro will have to proceed with these cuts by the end of this year. Taking this as a case study, this project develops and compares different transportation network models for optimizing equity and efficiency in the distribution of bus service in King County. Extending upon previous work, this project aims to produce a new model for optimizing decision-making and critique current methodologies for equitably allocating public transit resources. The research question is: How can we develop a transportation model in which route cuts and reductions will be designed to minimize the impact on equity and efficiency of service? An origin-destination network model will be produced using ArcGIS software and Python scripting to analyze spatially aggregated need for transit within King County. Data include 2012 ridership statistics from Metro as well as transit corridor data. Also, demographic data for identifying and locating marginalized populations will be obtained from King County census blockgroups. I predict that results will show that no self-purported objective transit network model is truly unbiased with respect to the different demographic groups it impacts.

The mammalian Target of Rapamycin (mTOR) is a protein kinase that integrates signaling from growth factors and nutrient availability to regulate metabolism and cell growth. Reducing mTOR signaling with rapamycin extends lifespan in several model organisms such as yeast, flies, and mice, and rescues virtually all symptoms in a mouse model of Leigh syndrome, a neurodegenerative disorder that causes loss of motor function and early death. Previous observations from our laboratory suggest that rapamycin induces changes in the metabolism of mice modeling Leigh syndrome, favoring fatty and amino acid catabolism over glycolysis. We believe this shift in metabolism is, at least in part, responsible for the beneficial effects of rapamycin in normative aging. In order to test this hypothesis, we are examining the effects of daily rapamycin injections in 4, 12, and 22 months old mice. We performed baseline measurements of serum metabolites, forelimb strength, voluntary running, gait and balance, body composition, blood glucose, and hemoglobin A1c, and are currently administering 8mg/kg of rapamycin daily via intra-peritoneal injections for 60 days. During this period we are monitoring body weight and food intake daily, as well as blood glucose every 15 days. At the end of this period we will measure body composition, gait and balance, forelimb strength, and voluntary running again, while maintaining the mice under treatment with rapamycin for an additional 30 days. Finally, we will sacrifice the mice and analyze serum, liver, brain, adipose, and other tissues for the activation of metabolic pathways, metabolite composition, and signs of pathology. We expect rapamycin to improve most parameters studied and profoundly alter the metabolic profile of mice at all three ages. These results will ultimately allow us to investigate how modulating metabolic pathways can increase healthspan in mice and provide insight on how to promote healthy aging in humans.

America welcomes people from all over the world, enriching the country with a diverse range of cuisines. Unfortunately, Americans also have some of the highest rates of obesity in the world. We are interested in whether this diversity in cuisines might be contributing to the obesity epidemic. Specifically, our study examined whether having diverse options of ethnic cuisines influences people’s decisions to eat out. We hypothesized that people will be more likely to eat out if they were given diverse options of ethnic cuisines. Psychology students (N = 330) were asked to imagine they were moving to a new city and viewed a map that either had a diverse option of ethnic cuisines (2 Mexican, 2 Italian, 2 Chinese, and 2 American), only Chinese food, or only American food. Participants then indicated the number of times they would eat out in a week and how much they wanted to try all of the restaurants. Participants who were given diverse options of ethnic cuisines were more likely to report they would eat out and want to try all of the restaurants than participants who were given a limited option of ethnic cuisines. Thus, the results from this study support our hypothesis that having diverse cuisine options causes people to eat out more. Future research should examine whether diverse options lead to weight gain because of this greater desire to eat out.

Leprosy, also known as Hansen’s disease, is a deteriorative skin condition caused by chronic infections of the bacteria Mycobacterium leprae and Mycobacterium lepromatosis. Leprosy was once believed to be highly contagious, so patients with leprosy were quarantined and isolated to prevent further contamination within the population. In Korea, patients with leprosy were quarantined on Sorok Island where some patients received treatment for leprosy with the antibiotic, 4,4'-diaminodiphenylsulfone (DDS). Data collected on patients receiving DDS indicated that the average lifespans of the patients were longer than the average lifespans of the general Korean population suggesting that DDS may impact aging. Consistent with this idea, DDS has been reported to extend lifespan in the nematode Caenorhabditis elegans. We have confirmed these results in C. elegans, and the goal of this project is to identify the specific mechanisms and pathways through which DDS is able to extend lifespan. Our unpublished data support the model that one of the mechanisms underlying DDS’s effect on aging in C. elegans is activation of AMP- activated protein kinase (AMPK). We are currently working to understand how DDS activates AMPK, as well as the interaction between DDS and other known longevity pathways in C. elegans, such as dietary restriction and the hypoxic response. I am analyzing the mechanisms through which DDS affects aging by performing lifespan analysis on C. elegans and its mutants. By analyzing the effects of DDS on aging, we can get a better understanding of the mechanisms that control aging to eventually comprehend the pathways through which certain aging diseases, like Alzheimer's act.

As a sculptor I work both figuratively and abstractly in a variety of styles ranging from installations to life-size figures and large sculptural vessels. Human anatomy is my starting point for exploration. Clay is the principal material for my work or a primary element of the fabrication process. I bring a diverse background of artistic training to my practice, but working in ceramic sculpture is where I find that my hands, vision, and voice come together with the greatest harmony. There is a one-to-one relationship between my hands and the clay as I manipulate it into the form of a body or organ. In its raw state the clay acts, feels, and even looks much like living tissue. These forms develop from diagrams, drawings, and photos, but most importantly from an intuitive sense of touch and sense memory. As human beings we are flawed and messy, and I strive to instill a sense of that vulnerability in my work. The surfaces and forms evoke a sense of duration, damage, decay, and the tenuousness of life. These themes stem from my interest in working with body imagery in a socio-political context, allowing me as a woman and an artist, to reclaim the female body from a historical position of subjugation and objectification. It is not my desire to limit the viewers’ interpretation. Instead I seek to question how we view the human body, relate to our anatomy, and consider our physical connection to the social structures we create around us. The content of my work originates from a visceral place, translated through a tactile process, and balanced by formal and aesthetic decisions.

Mitochondria, the energy producing organelles in eukaryotic cells, play a critical role in cell metabolism and regulation. Interestingly, mitochondrial dysfunction promotes lifespan extension in Caenorhabditis elegans. One proposed mechanism is that the induction of mitochondrial unfolded protein response (UPR^mt) increases the expression of mitochondrial chaperones, nuclear-encoded enzymes that assist in folding of misfolded or aggregated proteins, to maintain mitochondrial protein homeostasis. In an effort to elucidate genes involved in the UPR^mt pathway, we performed a genome-wide RNAi screen in transgenic animals expressing mitochondrial chaperone GFP reporter hsp-6_pr::gfp. Unexpectedly, we found that knockdown of genes involved in the pentose phosphate pathway (PPP) activates hsp-6_pr::gfp expression. The PPP is a metabolic shunt off of glycolysis that produces NADPH, a reducing equivalent used for glutathione reduction and lipid metabolism, and ribose 5-phosphate for nucleotide synthesis. In addition, knockdown of transaldolase, a gene in the reductive phase of the PPP, increases the lifespan of C. elegans. Through lifespan epistasis analysis, we found that transaldolase deficiency promotes longevity by a mechanism that is genetically distinct from known longevity factors such as the insulin-like/IGF-1 target (DAF-16), the hypoxia inducible factor-1 (HIF-1), AMP kinase (AAK-2), the UPR^mt transcription factor (ATFS-1), or the germline signaling (GLP-1). This suggests that the PPP inhibition promotes longevity through an uncharacterized pathway that may respond to mitochondrial dysfunction. In addition, we found that transaldolase knockdown alters expression of fatty acid desaturase, an enzyme that oxidizes fatty acid chains. We hypothesize that dysregulation of lipid metabolism by inhibition of the PPP may cause a defect in mitochondrial lipid composition, which may increase mitochondrial proteotoxic stress, inducing the UPR^mt. Understanding the genetics behind the UPR^mt and the PPP’s role in aging has enormous benefits to human health as both the PPP and mitochondrial dysfunction are highly correlated with many age-related diseases including cancer and neurodegenerative diseases.

This project examines the role of gender inequality in HIV/AIDS and how this inequality perpetuates the susceptibility of women to contract the virus. Focusing on Ghana and Brazil, I explore how culture and society shape an imbalance that potentially increases risks to women in becoming sick through analysis of the relationship between social determinants of health, risk factors and vulnerability. I argue that preventative measures intended to fight against HIV/AIDS have failed to consider the social circumstances that place women at greater risk than men. In my analysis, I draw on and interpret Michel Foucault’s concept of biopolitics using feministic critique and gendered perspectives. I reference anecdotes from Stephanie Nolen’s “28: Stories of AIDS in Africa” to present personalized perspectives of the painfully multifaceted reality of the HIV/AIDS outbreak, while Silvana Paternostro’s personal accounts of sexual culture in Brazil in “In the Land of God and Man: Confronting Sexual Culture in Latin America,” serve as a framework for my examination of gendered social constructs in Brazil. I examine gender relations and the dynamic of marital relationships that often disproportionately allow the male greater power over the female, and how a male dominant ideology is reinforced by politics, culture and social norm. Distinguishing between gender and sex, I look at how gender inequality, the inequality of opportunities and power that follow being a certain sex, may expose mothers, daughters, sisters, and other women at risk in ways we may not have imagined.

 The mitochondria are cell organelles that perform important cellular functions such as energy production, regulation of the cell cycle, and cell death. Therefore, proper mitochondrial function is critical for healthy aging of an organism. Paradoxically, attenuation of mitochondrial function in the nematode worm Caenorhabditis elegans has been observed to extend lifespan. It has been proposed that induction of the mitochondrial unfolded protein response (UPRmt) is responsible for this enhanced longevity. The UPRmt is a response to proteotoxic stress in the mitochondria that results in induction of nuclear-encoded mitochondrial chaperones, proteins that stabilize and fold misfolded and aggregated proteins. However, the mechanism(s) by which proteotoxic stress is recognized in the mitochondria and signaled to the nucleus, resulting in the UPRmt response, remain largely unknown. To further understand the UPRmt pathway, we carried out a genome-wide RNAi screen to search for RNAi clones that specifically reduce UPRmt signaling under conditions of mitochondrial stress. To do this, we used a mutation in the electron transport chain (ETC) gene isp-1 to cause constitutive activation of the UPRmt GFP reporter, hsp-6p::gfp and screened for RNAi clones that reduced GFP fluorescence. We expect that positive hits in our screen will target signaling components of the UPRmt. In total, we identified approximately 60 RNAi clones that reduce the UPRmt response in isp-1(qm150) worms. Currently, we are re-testing positive hits after sequence validation and determining if the targeted genes specifically signal the UPRmt or non-specifically affect expression of GFP reporters. Once we identify genes that are specific to the UPRmt, we plan to test the role of these genes in mitochondrial function and lifespan. A better understanding of the UPRmt pathway could provide significant insight into mitochondrial biology, which impacts healthy aging and several age-related diseases.

Tuberculosis (TB) is a bacterial infection that leads to 3 million deaths per year worldwide. Proper control of TB requires the ability of patrolling macrophages to detect, engulf and destroy invading bacteria and it is currently understood that macrophages play a key role in responding to early Mycobacterial infection. A forward genetic screen using the zebrafish larval model for host determinants of immunity to the bacterium Mycobacterium marinum found a hypersusceptible mutant that contains a nonsense mutation in the mTor (mechanistic target of rapamycin) gene. mTor has been shown in other systems to be crucial to protein synthesis, cell growth, and survival. Currently, our work has shown that mTor mutant fish have fewer macrophages and neutrophils than their wild type siblings. We have also shown that mTor mutants display hypersusceptibility to M. marinum infection, with bacteria displaying exuberant extracellular growth in the fish.. Treatment of fish with Rapamycin, an mTor inhibitor, phenocopies the macrophage deficiency and hypersusceptibility observed in the mutant. We hypothesized that hypersusceptibility to M. marinum in mTor mutant zebrafish is primarily due to the deficiency of macrophage immune cells. To test this hypothesis, we depleted macrophages in wild-type and mutant fish using lipoclodronate. Preliminary data has shown that without macrophages, mTor mutants still exhibit increased infection burden compared to wild type siblings also treated with lipoclodronate. This data provides us with exciting new avenues to continue searching for the cause of mTor’s hypersusceptibility. We are pursuing mTor’s role in neutrophil and cytokine induction as additional explanations for the mTor mutant hypersusceptibility phenotype. This research will help define the innate immune response to Mycobacterial infection and clarify the respective functions of mTor in host immunity.

Ocean circulation is a complex and important component of the marine environment. By understanding the dynamics of ocean circulation, including upwelling, one may be able to accurately predict future ocean conditions. Using hindcast output from a Pacific Northwest (PNW) circulation model developed by Parker MacCready and Neil Banas, relationships between wind stress and coastal upwelling in the PNW were examined. Wind stress was analyzed using several different indices, and then these indices were correlated with biogeochemical water properties throughout the coastal domain of the model. Examinations were focused on which indices were most correlated with which water properties and how these correlation patterns varied spatially. Differences in correlation were found for coastal Oregon, the mouth of the Columbia River, and coastal Washington/Canada near the Juan de Fuca Canyon. These findings indicate that different wind patterns are needed to provide biologically favorable conditions in different areas of the PNW, and they help increase the accuracy of upwelling predictions throughout the PNW. The variability in optimal wind conditions point to differences in biogeochemical properties in the coastal PNW that have important implications for U.S. west coast fisheries.

Parkinson’s Disease (PD) is the second most common neurodegenerative disorder in the world, affecting nearly 7 million people globally and more than 1 million people in the U.S. Symptoms of PD typically include tremors, rigidity, postural instability and slowness of movement. These motor control deficiencies can be attributed to a decrease in the expression of the neurotransmitter dopamine and the loss of many dopaminergic neurons in the substantia nigra of the brain. To study PD a mouse model is used in which C57BL/6 mice are administered 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). MPTP is a neurotoxin that inhibits complex I activity in the mitochondrial electron transport chain. Mice treated with MPTP exhibit PD-like symptoms, including the loss of dopamine producing neurons and physical motor control deficiencies analogous to PD. Specifically, we are interested in utilizing the MPTP mouse model to understand a mechanism by which the drug rapamycin might prevent or treat symptoms of PD. Rapamycin inhibits signaling of the mechanistic target of rapamycin (mTOR) pathway, which is a key regulator of many functions, including cell growth, cell proliferation, cell motility, cell survival, protein synthesis, and transcription. Previous research by our lab has shown that rapamycin dramatically attenuates disease progression in a mouse model of mitochondrial complex I deficiency. Because PD patients also exhibit defects in complex I, we believe that rapamycin may alleviate Parkinson’s disease progression by a mechanism similar to the effects we have seen. Currently we are administering high doses of encapsulated rapamycin in mouse diet during the three weeks prior to MPTP exposure. The expression of PD-like biomarkers in rapamycin fed mice will be measured through immunohistochemistry and western blot assays and compared to a control fed group. We hypothesize that pre-treatment with high doses of rapamycin in the diet will have robustly beneficial effects in MPTP mice.

 The Gram negative, opportunistically pathogenic Gammaproteobacterium Pseudomonas aeruginosa has a propensity to form biofilms. Biofilms are surface associated or aggregated bacterial communities, embedded in a self-derived, extracellular matrix (EPS). One major component of the P. aeruginosa biofilm EPS is the polysaccharide Psl. Psl plays a structural and protective role in P. aeruginosa biofilms by mediating attachment to abiotic surfaces and mammalian cells, conferring protection from components of the host immune response and a variety of antimicrobials, as well as promoting cell-cell adhesion. More recently, Psl has also been shown to function as a cell-cell signaling molecule that activates two diguanylate cyclases through an unknown mechanism, which results in an increase in intracellular levels of c-di-GMP. The secondary messenger c-di-GMP is central to the P. aeruginosa virulence regulatory network, and promotes biofilm formation, in part, by inducing the production of EPS components, including Psl. Thus, presence of environmental Psl appears to act as a feed-forward signaling molecule that enhances biofilm formation. In order to further understand this function, this investigation will employ mini-Tn5 mutagenesis to define the signal transduction pathway(s) responsible for activating the diguanylate cyclases through a novel feed-forward mechanism of Psl-dependent signaling in P. aeruginosa.

The blood-stage of infection with the parasite Plasmodium induces clinical malaria. Murine infection with Plasmodium chabaudi provides a physiologically relevant model of the immune response to infection. Blood-stage parasites express Merozoite-Surface Protein (MSP) 1, which undergoes a series of proteolytic cleavage events. The remaining c-terminal MSP1-19 region is necessary for erythrocyte endocytosis and serves as an immunogenic target. Control of parasitemia and resolution of clinical malaria has been shown to be T cell dependent, both through secretion of signaling molecules and through activation of B cells. To understand how T cell populations develop in a manner specific to the parasite and the contribution they make to the overall immune response, we have developed a novel system to identify MSP1-19-specific CD4+ T cells using a peptide: major histocompatibility class II (pMHCII) tetramer of our own design and magnetic bead-based enrichment techniques. Enriched fractions are stained with fluorescent antibodies against phenotypic surface markers and analyzed by flow cytometry to identify previously described CD4+ cellular subsets. T follicular helper (Tfh) cells that are required for B cell antibody production are formed around day 8 post-infection near the peak of parasitemia. Surprisingly, the number of Tfh cells decreases between days 12-15 post-infection and begins to return by day 20, persisting during chronic, low-level infection. We hypothesize that Tfh cell death is driven by high levels of antigen presentation by B cells. To address this hypothesis, we will assess markers of cell death in both TCR signaling reporters and various transgenic mice that lack important CD4+ T cell signaling molecules. Characterization of T cell depletion could elucidate mechanisms of immune evasion critical to parasite survival and persistence of infection, possibly implicating new therapeutic targets.

There are a variety of problems in the current refugee regime, however the recommendations provided in this report will focus on three primary themes. The first, which we have labeled Solidarity, refers to the cooperation present in the refugee regime through international, national and local levels. Secondly, access to information, which includes information about access to refugee status and amenities, will be addressed. Lastly the issue of documentation will be presented for it is important for the consolidation of status, rights and privileges of refugees. These themes will address concerns for various populations of refugee and forced migrants in particular urban refugees, camp refugees and forced migrants not protected under the UNHCR refugee regime. In order to cover all of these issues, we have divided our Task Force into sub-sections titled Access to Protection, Livelihood and Vulnerable Populations. Access to protection will address the process in which forced migrants gain access to host nations and refugee status. Livelihood will address access to important daily life issues such as healthcare, education and labor force participation. Vulnerable populations will focus on categories of forced migrants that are not protected by the UNHCR refugee regime. The information for this report will come mainly from sources such as the UNHCR, reports from NGOs, and government documents. This report also relies heavily on news sources as this topic is continually changing.

Aging is associated with increasing degrees of drifts in gene expression, thought to be epigenetic in origin. The resulting variegated gene expression would have the potential to lead to a loss of proliferative homeostasis, resulting in multifocal tissue atrophies and hyperplasias. Because of enhanced rates of DNA replication, the latter could lead to neoplasms via mutations in oncogenes and tumor suppressor genes. As an initial test of this hypothesis, I immunostained leiomyomas (a benign uterine tumor)of six patients for nuclear proteins, including p53, sirt 1, Cdk4 (Cyclin-dependent kinase 4) and p16/Ink4a (CDKN2A), and examined the degrees of variegated gene expression at the three sites: cells within benign leiomyomas of the uterus and of smooth muscle immediately contiguous to and distal to these lesions. The preliminary results showed that the majority of specimens gave results consistent with the hypothesis of clonal expansions derived from precursor populations of cells with more extensive variegation. There were several exceptional results, however, perhaps related to technical issues. These pilot studies encourage additional studies, including the use of alternative methodologies for the detection of neutral mutations associated with the predicted clonal expansions. In addition, these studies may provide new prospectives for diagnostic approaches to tumor formation in uterine.

Trapped ion quantum computing uses trapped ions to represent information not only as 0s and 1s as in a classical computer, but also as a superposition of 0s and 1s. This provides many benefits over traditional computing, such as enhanced encryption and more efficient factorization of prime numbers. In our implementation, one of the first steps to trapping barium ions to use a qubits, the quantum equivalent of classical bits. We use a 791 nm laser to ionize barium-137, making further operations possible. In normal operations, the frequency of this laser can fluctuate unpredictably, making it unsuitable for ionization. To combat this problem, I designed and built an optical cavity to stabilize the laser. By arranging two mirrors so that the light interferes with itself, only a limited range of frequencies are allowed to pass through. First, a spacer with a low coefficient of thermal expansion keeps the mirrors at a fixed distance, while an analog circuit regulates the temperature of the spacer to insulate it from swings in ambient temperature. A second analog circuit then monitors the light coming out of the cavity and feeds back to the laser, allowing the user to lock onto a specific frequency. This locking system provides a low cost, yet effective method of stabilizing a laser  and will be easy to implement again, with other lasers. More generally, this shows how an ion trap can be improved with the relatively simple laser locking method used here.

One goal of aging research is to identify genes that modulate aging, in order to eventually develop therapies that delay the onset of age-associated diseases. In particular, genes that control mitochondrial function appear to play an important role in aging. Although severe mitochondrial dysfunction causes childhood diseases such as Leigh syndrome, there is growing evidence that moderate mitochondrial stress can extend lifespan in yeast, worms, fruit flies, and even mice. In the nematode Caenorhabditis elegans, a long-lived mitochondrial mutant called isp-1(qm150) has a defect in the Rieske iron-sulfur protein. The Rieske iron–sulfur protein is a primary electron acceptor located in complex III of the mitochondrial electron transportation chain. Complete RNAi knockdown of isp-1 results in larval arrest, while partial knockdown extends lifespan, further supporting the idea that milder forms of mitochondrial stress can increase lifespan while severe mitochondrial stress is detrimental. We are conducting a mutagenesis screen to identify genetic suppressors of the larval developmental arrest induced by isp-1(RNAi). Through exposure to EMS/ENU mutagen, wild-type worms will have random mutations generated throughout their genomes. These mutants will then be screened for the ability to develop on isp-1(RNAi) . We speculate the novel suppressor mutations from the screen may affect proteins that interact with ISP-1 or cause mutations that bypass the need for ISP-1 in the mitochondria. Identification of such suppressors will help to clarify the mechanisms linking mutation of isp-1 to development and aging. The isp-1 gene and its function in the electron transport chain are conserved in humans. Therefore these studies may be relevant for human aging and disease.

One of the goals of modern longevity research is to find pharmacological means to increase lifespan and/or healthspan without deleterious physiological effects. Berberine is a yellow, bitter-tasting natural alkaloid with a long history in Eastern Asian medicinal use in treatments of a variety of age-associated diseases and infections. In human cell culture models, berberine treatment increases AMPK activity, resulting in delayed senescence through inhibition of the mTOR/S6 pathway. Here, we use the budding yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans to investigate the effects of berberine on healthspan and lifespan. For the yeast S. cerevisiae, growth rates of haploid and diploid yeast cells, as well as chronological (a measure of population viability through time) and replicative (a measure of mitotic potential) yeast aging paradigms were assayed in the presence of concentrations of berberine ranging from 0.1 - 100.0 ng/uL. For C. elegans, organismal lifespan as well as various healthspan measures are being analyzed. Currently, we have found that concentrations of berberine greater than 10 ng/uL in haploids are sufficient to inhibit cell growth and lower concentrations (0.1-10 ng/uL) result in increased yeast viability when shifted to respiratory metabolism, a means of extending lifespan in yeast. Our lifespan studies are ongoing. Our experiments will provide valuable insights into the role of this long-used medicinal substance on cell aging and health using two important longevity models.

The discipline of Pathology has an enormous scope and students are constantly challenged to determine which topics are essential for clinical patient care and for the National Medical Board exams. There is a significant gap between the material presented in pathology textbooks and the material outlined in medical board review books. In addition, much of the practical knowledge that is most useful for medical students and physicians falls in between this gap. To address this need, we created PocketPath, a web-based modular teaching system, to help students and physicians consume Pathology material more efficiently. PocketPath is designed in an easy to read format that delivers an optimal amount of high yield pathology content, which includes USMLE Step 1 Board Review-style questions and important research papers. Using student surveys, interviews and web usage data, we determined how students consumed PocketPath’s content and improved their pathology test scores. Initial data suggests that PocketPath may replace lecture time, promote active learning, and potentially change the way students prepare for Board exams.

 Widespread use of tetracyclines in marine and fresh water aquaculture has resulted in tetracycline resistant (Tcr) bacteria in these environments. Previously, 15 of 25 Tcr Chilean bacteria were shown to carry seven different tet genes. The tet(A) was the most commonly identified gene [n=6]. In the present study, we reexamined nine bacteria that were previously negative for the 22 tet genes tested using PCR assays for the identification of tet(W), tet(X), and tet(39). Three of the isolates’ genera designation differed between phenotypic and 16S sequencing identification. The 16S identifications were used in the current study. Six (67%) of the isolates including 3 Acinetobacter spp., 1 Pseudomonas spp., 1 Psychrobacter spp., and 1 Corynebacterium spp. carried the tet(39) gene. None of the isolates carried either tet(W) or tet(X) genes. In the present study, 6 of the isolates carried the tet(39) gene making it as common as the tet(A) in the original study. Of the 4 genera identified 3 [Pseudomonas, Psychrobacter, and Corynebacterium] represented new genera not previously identified as carrying the tet(39) gene. We are currently testing the strains for their ability to transfer tet(39) by conjugation and/or transformation. The tet(39) gene was first identified in Acinetobacter spp. from freshwater trout farms, sewage and human clinical samples from Europe between 1986-1997. Since then the tet(39) gene has been identified in fish farms in Thailand, a polluted river in Nigeria and clinical samples in the US. This study shows that the tet(39) gene has been present in bacteria from Chilean fish farms since 1999. The tet(39) gene has wider host range in water associated bacteria than previously recognized and should be considered when examining Tcr water bacteria in the future. The current study illustrates that aquaculture contaminates the local environment into surrounding soils and water sources with antibiotic resistant bacteria and genes.

Aging is a degenerative process characterized by progressive deterioration of cellular components resulting in mortality. The nematode Caenorhabditis elegans has been used extensively to study the biology of aging, and several determinants of C. elegans longevity are conserved in mammals. The specific mechanisms of longevity in C. elegans have not been completely identified, and many pathways are poorly understood. Dietary restriction (DR) is one promising pro-longevity intervention, though its mechanism is still poorly defined. DR, a reduction in caloric intake in absence of malnutrition, extends lifespan in C. elegans and in a wide range of other species including yeast, flies, mice, and primates. To investigate the genetic determinants of the response to DR, we are performing a genome-wide screen using the Vidal RNA-interference (RNAi) Library, which contains 11,511 unique RNAi clones. The C. elegans are fed E. coli that express dsDNA that, when ingested, form ribonucleic-protein complexes that bind to and facilitate cleavage of target mRNAs; effectively preventing expression of specific genes. By knocking down specific genes within the C. elegans genome through RNAi, we are able to observe extension or reduction in longevity in response to DR. We have screened over 8,143 RNAi clones; 71 of which reduce lifespan under DR conditions and 85 of which increase lifespan. We are currently following up on our data by verifying the effect of these RNAi clones on lifespan under both control and DR conditions. We hope to verify how significantly these genes are affected by DR and follow up on those specific pathways to further investigate the interaction between DR and other potential longevity pathways. These findings will provide insight into fundamental mechanisms of aging and may facilitate the development of therapies to delay the onset and progression of age-related diseases in people. 

Products of silicate mineral dissolution play important roles in geochemical cycles and biologic processes including secondary mineral precipitation and microbial and plant growth, respectively. Understanding the mechanisms and stoichiometry of silicate weathering are therefore important in relating weathering rates to global ion budget. In abiotic systems, silicate dissolution often begins as a non-stoichiometric reaction dependent on solution pH. In acidic versus alkaline solutions, forsterite leaches cations and silica, respectively, resulting in a surface enriched with the counter ion. Microbes are, however, ubiquitous in water-rock systems where active silicate weathering occurs. Recent evidence shows a dramatic increase in forsterite (Mg₂SiO₄) dissolution rate that correlates with the presence of dormant bacterial endospores. The mechanisms driving enhanced dissolution in the presence of a complex organic surface and its effect on mineral surface chemistry is unknown. We investigate the effects of Bacillus subtilis endospore enhanced dissolution on the surface chemistry of forsterite grains using Attenuated Total Reflectance- Fourier Transform Infra-red (ATR-FTIR) spectroscopy. ATR-FTIR is a technique that measures mid (MIR) to far (FIR) infrared absorption of a sample over a shallow penetration depth. Forsterite (Fo₉₀, Mg_1.8Fe_0.2SiO₄) powder was incubated with B. subtilis endospores for 40-80 days at pH ~ 7.5 under oxidizing conditions. We compare MIR and FIR ATR-FTIR spectra of un-reacted forsterite, abiotically reacted controls, and biotically weathered forsterite to determine how the surface has changed from the weathering processes. MIR and FIR ATR-FTIR spectral scans of forsterite grains incubated with endospores display peak shifts relative to the controls. Small amounts of Fe(II) present in the forsterite likely precipitated as iron oxide coatings on the mineral and endospore surfaces. Variations in FIR peaks may indicate the presence of iron oxides. Results from this research will advance our understanding of how bacterial surfaces affect chemical weathering in the environment.

The Kaeberlein laboratory uses the budding yeast Saccharomyces cerevisiae as a model organism in the study of aging. S. cerevisiae is a serviceable model organism for this task because its lifespan is relatively short and simple to assess. Furthermore, many genetic tools are available to study the effect of individual genes on lifespan. Two experimental paradigms have been extensively used to quantify lifespan in yeast: chronological and replicative. In the chronological lifespan model, cells are maintained in a non-dividing state and viability is determined over time by assessing the ability of cells to re-enter the cell cycle upon exposure to growth promoting conditions. In the replicative lifespan (RLS) model, mitotically active cells are incubated until they divide and produce newly budded daughter cells, which are then micro-dissected away from their mother cells and counted. This process is repeated until daughter cells are no longer produced by the mother cell, and the total number of daughters produced prior to irreversible cell cycle arrest is quantified. After analyzing numerous strains of S. cerevisiae, many different genes and environmental conditions that modulate replicative lifespan have been identified. Importantly, many longevity modifiers identified in yeast have been found to be conserved in higher eukaryotes.

Fire damage is a stressor that plants have evolved around (to varying degrees) for thousands of years, and is known to induce a signaling/repair pathway that is not fully understood. Illuminating the transcriptional regulatory mechanisms of this pathway could not only give us insight into a basic biological system that is applicable to all forms of life that experience aging, cancer, and disease, it could also provide us with information about plant-specific fire resistance and healing that could be utilized to fortify our crops in a warming world. This study explores possible interactions between histone acetyltransferase (HAT) proteins produced by HAC1 and RNA synthesis enzyme RNA Polymerase II (RNAPII) in Arabidopsis thaliana plants damaged by fire. HAT proteins upregulate gene expression by chemically loosening histones (tightly-wound "spools" of DNA) and exposing coding regions to increased transcription, and RNAPII regulates overall transcription by recruiting and manipulating numerous factors of RNA transcription and synthesis, but current understanding of complementarity or antagonism between HAC1 and RNAPII remains tenuous at best, especially in plants. In this experiment, I either exposed both Arabidopsis thaliana mutants (deficient in functional HAC1) and their non-mutated counterparts (containing normal HAC1) to flame wounds, or left them alone, and then collected non-burned leaf samples twenty minutes later. Because gene expression can be measured by quantifying proteins, I used Western Blotting to detect levels of RNAPII in an attempt to elucidate any interaction between these two transcriptional regulators. My preliminary results suggest that less RNAPII is produced when plants are burned, but that the HAC1 gene is not necessary for the regulation of RNAPII after burning, though replications are necessary to confirm this.

Adolescence through emerging adulthood is a peak period for risk taking and impulsivity matched with a significant increase in emotional reactivity. This increase in stress response makes those in this age group vulnerable to psychopathology and act more impulsively. One way to diminish this is using an effective mean of coping. Mindfulness meditation has been found to increase attentional control, cognitive control, and executive function, and these increases may reduce the tendency toward impulsive action when distressed. This current study will be comparing focused breathing –a component of mindfulness meditation– to rumination and unfocused attention to investigate whether focused breathing is an effective strategy for reducing impulsive tendencies. Using an expected n = 40 undergraduate students, we will test whether focused breathing produces reductions in impulsiveness and reward sensitivity following a stress induction, compared to a neutral or a rumination condition.

Traumatic Brain Injury (TBI) is a leading cause of mortality and permanent neurological disability. Microglial activation and inflammation contribute to the onset and progression of TBI-induced pathology. In this study we aimed to identify the factors that activate brain inflammatory pathways in the early responses to TBI, and the mechanisms by which inflammation is sustained during the late stages of pathology. We have previously demonstrated that the microglial expressed receptor, CX3CR1, regulates microglia activity. We have also shown that lack of CX3CR1 leads to deficits in cognitive function and synaptic plasticity. Here we hypothesized that the loss of the CX3CR1 receptor - and consequently, the loss of normal microglia function - would increase pathologic conditions in the brain after TBI and cause measurable defects in behavioral and cognitive abilities. To this end, three month old male CX3CR1 wild type and CX3CR1 knockout mice were subjected to a mild TBI (0.5mm depth) using a controlled cortical impact (CCI) animal model. Control mice (sham operations) received the same anesthesia and craniotomy, but were not subjected to CCI. All animals were humanely euthanized and transcardially perfused at fifteen and thirty days following TBI. I specifically participated in assisting TBI surgeries, behavioral testing, transcardial perfusions, brain sectioning, and immunohistochemistry. Our results indicate that lack of CX3CR1 at early time points protects neuromotor function, reduces cell death, and is associated with expression of microglia that have an anti-inflammatory phenotype. However, the long term effect of CX3CR1 receptor loss following TBI induces neuronal cell death, as well as neurobehavioral and cognitive deficits, which are associated with an increase in expression of microglia that have a proinflammatory phenotype. These results point to the presence of CX3CR1 in the early stages following a TBI as essential in slowing the progression of the neuropathology. In conclusion, CX3CR1, the fractalkine signaling receptor, plays a central role in regulating neuroinflammation after a TBI.

Recent developments in research on Human Papillomavirus (HPV) have allowed for an increase of strategies that prevent the onset of cervical cancer within communities of little economic privilege. This project will compare preventative measures taken in India and those currently called for within the U.S., primarily examining how cultural and economic limitations are taken into consideration. As a “space of negation and the socially dead, produced by expropriations and alienations in and outside European nation-states” necropolis or low and middle income countries have historically been perceived as a necessity in order to maintain the priorities set by biopolis. However, organizations such as PATH are beginning to look into more cooperative methods. I will analyze the onset of preventative practices that promote self sufficiency in a format that maintains economic functionality and decreases potential dependency for aid. One significant limitation however is that western corporations still hold much of the control regarding economic leeway of vaccination use and price on a global scale. In this project I explore alternative methods that advocate information as an alternative or supplemental method for prevention. This project will continue by examining how circumstances in low economic environments are taken into consideration through efforts of vaccination or treatment. This includes the incorporation of cultural awareness, provision of knowledge and communication within the community, and how this leads to a stronger awareness of what limitations remain.

This analysis discusses changes over time at the Gua Talimbue site, excavated in 2013 by Sue O’Conner, Ben Marwick, Tim Maloney, Emma St. Pierre and Rose Whitau in South-East Sulawesi, Indonesia. Sulawesi, formerly known as Celebes, is one of the four Greater Sunda Islands and is considered the largest island in Wallacea. This area was a major stepping stone for the migration of peoples into Island Southeast Asia and what is now modern Australia, and understandng shifts in occupation here can shed light on human movement patterns throughout the globe approximately 18,000 years ago and onward. The research has examine the changes through time with consideration to geoarchaeological and lithic samples taken from the Talimbue site, with a specific focus on shifts in human behavior, site formation, and the environment of the site over time. Geoarchaeological testing of the site includes pH and electrical conductivity testing, loss on ignition, magnetic susceptibility, color and particle size distributions. Lithic analysis is focused on the change in distribution, size, mass and type throughout the occupation of Talimbue, first occupied by humans 18,000 years ago and continuously inhabited until recent times. Preliminary results have identified an environmental shift at the Pleistocene-Holocene transition, approximately 12,000 to 8,000 years ago, which affected occupation and has implications for the decreased complexities seen in lithics analysis. The purpose of this research is to understand human impact on environmental processes, as well as identify occupation and technological trends within the context of Sulawesi and beyond. 

Public health concern in the U.S and across the world regarding the impact of environmental hazards on human health is becoming more evident as we develop tools to see disparities in exposure and health outcome. Pollutants in the air and water can have lifelong consequences for the quality of lives of many people. Therefore, our toxicology laboratory is examining the result of pesticide exposure and toxicity in children, and how it may cause harm to normal development. Our research centers on studying exposure using blood, urine, and oral buccal samples obtained as part of a Children’s Health study on Yakima Valley. We have determined blood pesticide, urinary metabolite concentrations, cholinesterase activity, paraoxonase activity, and genome wide variation in 200 families. We have analyzed buccal samples from farmworker and non-farmworker families that were collected during different pesticide spray seasons. We are studying these buccal swab samples of children and their parents to identify bacteria present within them. We are utilizing targeted 16S ribosomal polymerase chain reaction (PCR) to determine the phylogenetic composition of the microbiome in saliva samples. The microbiome refers to the vast colonization of microbes within the body. There are more bacterial cells in our bodies than human cells even though they are only about 10% of the total mass. We hope to find a difference in microbe composition and metabolism for samples from agricultural seasons (pesticide use and non-spray seasons), and for child and adult samples. We have already analyzed pilot samples and found consistent results. Recently, we have begun PCR-based analysis and sequencing the remainder of the cohort buccal samples to characterize the diversity of oral microbiomes. If a link is found between the microbiome, pesticides, metabolic traits, and host genotype then we can more fully describe risk and metabolic biomarkers for exposed populations. 

We present preliminary results of an analysis of sedimentary deposits from Malakunanja II, a rock shelter and archaeological site located in Arnhem Land, Australia. Malakunanja II is the oldest known site of human occupation in Australia. Previous dating of the site has shown the first human occupation to have occurred at approximately 50,000 years BP (Roberts RG, Jones R and Smith MA 1990). Presented here are the results of laser particle size, color and magnetic susceptibility analyses on sediments taken from deposits at the site during the 2012 excavation. These analyses will serve to further the understanding of site formation processes, environmental changes and human behavior at the site.

Gradiometer is a powerful instrument for detecting the underground condition. It works by measuring the gradient of the magnetic field so no physical contact is needed. For this reason, gradiometer is usually employed by archaeologists to figure out the condition of buried sites when excavation is not necessary (sometimes not allowed). We wrote a manual about how to use the instrument to collect, analyse, and interpret data in very detail.Considering the quality of the survey result will be affected by factors like the distance between the object to the sensors, the amount of the object, the material of the object, and the operation of the instrument, we did a series of control variable test at the Denny Yard, UW campus. Our purpose is to explore how those factors can affect the survey result, and find ways to improve the result in the real archaeological survey.According to our result, the most important factor is distance, which suggests we can get a better result by shortening the distance between the sensors and the ground. And the amount of the object has a positive relation to the strength of the signal, according to that we can estimate our result before a survey. Whether a kind of material can be detected depends on its magnetic contrast to the soil as well as the factors mentioned above. With this study, we can know when and how should we apply gradiometers into archaeological study.

The purpose of this project is to develop and refine a technique for taking photographs to be included in an atlas of the foraminifera of Puget Sound. Foraminifera are shelled single-celled organisms that live at the sediment/water interface in marine environments. Their sensitivity to environmental conditions makes them useful in monitoring ecosystems on the sea floor. The atlas will contain photographs and detailed descriptions of each foraminifera species. Despite their importance as an environmental monitoring tool, foraminifera have never been comprehensively studied in Puget Sound. This catalogue will become a useful tool for future workers in research and environmental monitoring. Key to this atlas is the inclusion of clear, accurate photographs of each species of foraminifera. Scanning Electron Micrographs yield excellent images, but these often do not portray the organism as it is viewed through a light microscope. Thus, the inclusion of photomicrographs is essential. Photography becomes quite technical when dealing with objects of a microscopic scale while still trying to produce a clear image with depth of field. With the Puget Sound Foram Project we work with specimens that can be as small as a tenth of a millimeter in size, so producing a high quality publishable picture takes time and a specialized technique. Using a light microscope, each specimen has to be photographed several times, focusing at a different depth each time. Once all of the layers have been captured, the pictures are then synchronized and edited in such a way that we get one final image that has both clarity and depth of field. In addition, each specimen must be photographed from two or more angles to illustrate critical features. Photography for research purposes can be a complicated and lengthy process but is essential for not only supplementing data but conveying vital information.

Self-regulation plays a significant role in an individual’s behavior and has been linked to various psychopathologies. The Behavioral Inhibition System (BIS) and the Behavioral Activation System (BAS) are two biopsychological systems that are hypothesized to affect approach and avoidance-motivated behaviors. The BIS/BAS systems provide one framework that can explain the self-regulatory mechanism. In addition, studies have found that mindfulness-based therapies can improve one’s self-regulation by increasing consciousness and awareness; however, there has been relatively little research on the effects of mindfulness training on the BIS/BAS systems. We recruited 17 youths aged 15-19 from a juvenile correction facility who are expected to possess extreme BIS/BAS levels, and placed them in a 6-week mindfulness-based intervention. We collected self-reported data on mindfulness and BIS/BAS level before and after the intervention. Using paired t-tests, we will test whether BIS/BAS and Mindfulness changed from baseline to a 1 month followup assessment.

This study aimed to analyze benthic foraminiferal assemblages to determine if environmental changes from pollution and other factors have affected the health of the Bremerton area marine ecosystems. Foraminifera are shelled, single-celled microorganisms that can act as good indicators of environmental change. Sinclair and Dyes Inlets border Bremerton and are connected by the Port Washington Waterway in Kitsap County, Washington. Bremerton is the home of Puget Sound Naval Shipyard and is listed as a federal Superfund site due to accumulations of industrial pollution. Additionally, agricultural and residential pollutants have been released into Dyes Inlet from local streams. Foraminifera were collected from 40 sediment samples provided by the Washington State Department of Ecology from 1998-2012. Samples were analyzed for foraminiferal species composition, diversity, and density (number of inidividuals/gram sediment). Results show 22 species were found, however most samples had low diversities and densities. Ten samples contained no foraminifera. In addition, numerous euhedral gypsum crystals were found in 13 samples in both inlets. Gypsum is a calcium sulfate mineral, and occurrences of subaquatic gypsum crystals in non-evaporitic settings are unusual. Samples with gypsum showed either lower foraminiferal densities or no foraminifera present. Sulfur isotope analysis of the crystals indicates they formed in a sulfate-reducing environment. The comparitively high Total Organic Carbon (TOC) values in gypsym-containing samples suggests that decomposition of organic material may lead to this sulfate-reduction. Additionally, significant dissolution observed in the calcium carbonate shells of many foraminifera indicates pH values of the sediment were low. This can also result from the degradation of organic matter. Thus, foramiferal assemblages within Sinclair and Dyes Inlets are responding markedly to conditions in sediments, establishing the efficacy of using foraminifera as a tool for monitoring benthic ecosystems in Puget Sound.

Patients with Alzheimer’s disease experience progressive loss of memory and thinking skills, gradual declines in the ability to carry out simple tasks and, in severe cases, full blown dementia. The brains of patients with Alzheimer’s accumulate extracellular plaques of a family of beta amyloid peptides (strings of amino acids cleaved from a larger protein called Amyloid Precursor Protein) in multiple regions of the cerebral cortex resulting in losses of synapses and neurons. Given the fact that beta amyloid peptides have been evolutionarily conserved, our group became interested in the potential normative roles of these peptides. Observations by a member of the Martin lab led to the hypothesis that small concentrations of beta amyloid may have a proliferative effect on cells. My project explores this idea with experiments that compare the proliferative effects of various members of the beta amyloid family and dose-response experiments that determine optimal concentrations for proliferative effects. In my experiments, various concentrations of beta amyloid 1-40 (and, as controls, comparable levels of a scrambled beta amyloid peptide 40-1) are added to a standard culture medium along with 10% embryonic serum (serum without detectible levels of beta amyloid peptides) and established required growth factors. The cells’ division rates within those two week periods are determined for individual clones though crystal violet staining. From these initial experiments, we have concluded that cells are indeed able to divide more rapidly in media that has beta amyloid 1-40 present and that further attempts to determine optimal concentrations should focus within the range of 1-10 nM and above 10 nM to the point at which we anticipate evidence of toxicity. Future experiments will probe changes in gene expression resulting from treatment with optimal concentrations of beta amyloid for the enhancement of cell proliferation.

Burkholderia thailandensis uses acyl homoserine lactones (AHLs) as quorum sensing (QS) signals. Broadly, QS is a communication system that, at high cell densities, allows bacteria to coordinate group activities. Recent work from our lab has shown that in B. thailandensis, QS controls contact dependent growth inhibition (CDI). CDI is an intraspecies bacterial competition system  where CDI-proficient bacteria (CDI+) contain a three-protein system of CdiA, CdiB and CdiI. CdiA is a toxic protein displayed by CdiB, and CdiI neutralizes the toxic activity of CdiA. We predict that QS-control of CDI is a means of eliminating QS mutants from the population. B. thailandensis has three QS-systems; QS-1, QS-2 and QS-3, which each comprise of a specific transcription factor and a cognate AHL signal synthase that produces a specific AHL. A B. thailandensis mutant in all three synthase genes (btaI1-3) is defective at growth, inhibiting a cdiAIB mutant. However, we do not know the specific contribution of each AHL signal synthase. Thus, we sought to test the CDI activity of synthase mutants against cdiAIB mutants within a competition. We compared the starting and ending ratios of the different strains tested in each competition. Preliminary results have demonstrated that the btaI1-3 mutant is CDI defective, relative to wild type. However, signal synthase mutants are not defective at CDI. QS is required for WT levels of CDI. Additionally, we are investigating the dynamics of how CDI controls the growth advantage of QS mutants. A btaR1 mutant has a growth advantage when co-cultured with wild type in liquid but not during growth on a solid surface, which allows for CDI to occur. Thus, we are evaluating if CDI is responsible for restraining the growth advantage of the btaR1 mutant during growth on a solid surface.

“Fetal alcohol spectrum disorders” (FASD) are considered to be the leading preventable cause of mental retardation. Among this spectrum Fetal Alcohol Syndrome (FAS) represents the most extreme consequence of maternal alcohol consumption and as such associated facial dysmorphologies and neurological defects have been heavily investigated. In this project, our lab is interested in assessing the extent craniofacial development is affected due to chronic paternal and pre-conception maternal alcohol consumption using a mouse model. For the paternal exposure project, male mice were first bred with normal females as control and then given a 10% ethanol water solution for six weeks, which covers a full cycle of spermatogenesis in mice, and mated with normal females again as experimental compare. For the pre-conception exposure project, female mice are divided into three groups given different solutions respectively, four days a week for ten weeks: 10% ethanol water exposure, calorie-matched sucrose solution, and water. Upon completion of exposure, they were bred with normal males. When litters are at 60 days of age, the craniofacial phenotype of the specimens will be assessed using high-resolution microCT and their shape differences will be statistically assessed using a set of landmark and geometric morphometric methods (GMM). By the time of the Symposium, we expect to complete the image acquisition of the control group, as well as some of the initial GMM analysis. We will also be able to report differences in litter size, birth weight, and growth rate of litters between groups in both projects. As a whole, we expect to see subtle but significant differences in craniofacial development between mice that are born to fathers or mothers consuming alcohol and their controls. From there, the leading mechanism and degrees of alteration of craniofacial development can be related to the effects of chronic alcohol exposure in humans.

X-linked Myotubular myopathy (XLMTM) is a congenital myopathy caused by mutations in the myotubularin (MTM1) gene. Clinical symptoms of the disease including muscle weakness, respiratory failure, and hypotonia. XLMTM is caused by deficiency of the protein myotubularin necessary for normal muscle excitation-contraction. Dogs harboring a canine MTM1 gene model the disease and provide valuable insight due to phenotype similarities with patients. Affected dogs exhibit muscular atrophy, weakness, and stilted gait. A neuromuscular assessment score was developed to measure neurologic impairment in affected dogs. My project involved validation of this previously tested neurological assay by an independent observer. I was the independent observer who reviewed and scored neurological examination forms. I also reviewed and scored videotaped examinations and conducted statistical analyses looking at the correlation of the results within groups of dogs and between groups of dogs. Intra- and inter-reliability were performed by another observer and myself and wild type (n=6) and affected dogs (n=4) were scored. Prior to beginning the study, I received training on the assessment scoring system, including how to perform and analyze clinical tests. The intra-reliability test involved repeated examinations of wild type dogs and generated a consistent score in 88% (46/52) of exams based on interpretation of written neurological examinations and 100% (9/9) of exams based on scoring videotaped examinations at two time-points. The inter-reliability tests generated a consistent score in 54/71 examinations (76%) based on scoring of pre-recorded neurological exams and generated a consistent score in 12/15 cases (80%) based on scoring video-taped exams. The two observers scored dogs within 1 point in 68/71 (96%) of cases based on written notes of the neurological examination and within 1 point in 15/15 (100%) of videotaped examinations. Together, these data support the reliability of the neurological assessment score in XLMTM dogs.

Duchenne muscular dystrophy (DMD), is a degenerative disease caused by a recessive X-chromosome mutation, resulting in lack of the protein dystrophin. Affected males experience profound muscular weakness in childhood and by adolescence the heart and respiratory muscles are affected. The Golden Retriever muscular dystrophy (GRMD) dog model displays phenotypes analogous to patients and is considered the premier preclinical model. We evaluated changes in limb function by assessing gait in GRMD (n=3), wildtype (n=2), and in GRMD dogs injected with an adeno-associated virus carrying a dystrophin replacement gene in a single limb (n=3). Dogs were walked at a self-selected pace along an instrumented carpet to measure gait parameters. The average velocity over time of non-injected GRMD dogs was 60.39% of wildtype. Treated dogs displayed slightly increased velocities (67.17% of normal). By the final timepoint, velocity in all groups was comparable. The average paw pressure of the non-injected GRMD group increased 8.05%, while the average paw pressure for the wildtype decreased by 12.75%. The ratio of mean paw pressure for untreated GRMD: wildtype increases from 0.819 to 1.014 over time. We therefore determined that paw pressure might be a sensitive indicator of a treatment effect. To estimate the minimum sample size required for future studies, a power of analysis was performed. Results indicate that n=14 is required to detect differences between groups with a confidence level of 5% and power of 80%. Given that human patients suffer multiple symptoms of muscular weakness analogous to the dogs, including reduced limb function, changes in treated GRMD dogs as measured through gait analysis may evaluate the efficacy of the gene therapy as treatment for DMD. Human patients suffer multiple symptoms from muscular weakness (non-ambulatory, cardiac impairment, etc). Future studies hope to transition treatment to human patients to improve ambulation and increase quality of life.

College student drinking continues to be a concern due to high consumption rates and negative consequences associated with excess use. Both male and female students are at risk for heavy alcohol use and related consequences. Symptoms of depression are also reported frequently amongst college students, particularly female students who tend to be at higher risk than males for depression. Evidence suggests that depressive symptoms are often correlated with increased alcohol use. Alcohol consumption has also been related to perceived social norms of peer drinking, i.e. the perceived amount of drinking that other students and peers typically engage in. Injunctive norms, which refer to perceived approval or disapproval of a behavior by other students, may be highly regarded by students as important for decisions regarding their own behavior. Furthermore, it is hypothesized that this relationship may shift with an increase in depressive symptomology in females. Injunctive norms-indicating approval from others-have been linked to increased alcohol use in this population. Prior research also suggests that female drinking tends to be more strongly correlated with typical same-sex student alcohol injunctive norms more than their male counterparts. Thus the proposed study examines the moderating role of depressive symptoms and gender on the relationship between injunctive norms and alcohol use in college-age students. The goal of this study is to further understand the nature of the relationship between injunctive norms and alcohol use, and whether depressive symptoms enhance risk from injunctive norms in females more than males.

The toll-like receptor (TLR) proteins are expressed on cells of the innate immune system and recognize structural motifs present on microbial pathogens. Recognition of pathogens by TLRs activates an intracellular signaling cascade and activation of NF-kB, a transcription factor that is critical for expression of inflammatory mediators. Previous studies from our laboratory have shown that single nucleotide variations present in human TLR1 lead to altered expression of TLR1 and are associated with increased risk of death in patients with sepsis. We tested the hypothesis that variations of mouse Tlr1 which correspond to common human variants would result in comparable changes in TLR1 activity. We used site-directed mutagenesis to introduce coding variations in the Tlr1 cDNA. After transfecting the variants into cultured human cells, we stimulated them with Pam3CSK4, a triacylated lipoprotein known to be recognized by the TLR1/TLR2 complex. We then used a bioluminescent luciferase reporter system to measure the levels of NF-kB transcriptional activity. Tlr1 with an Ile allele at position 605 showed increased activity relative to a Leu allele, and the Tlr1 with a Ser allele at position 605 showed increased activity compared to Leu, but to a lesser degree than the Ile allele. Tlr1 with a Ser allele at position 251 showed increased activity compared to Asn, but elucidating its specific effect will require further investigation. These results indicate that variations in the transmembrane domain of mouse TLR1 result in alterations in function comparable to that of human variants in the same region. These findings suggest that mouse models may be used to study TLR1 variants’ effect on the immune response in humans. This could lead to a better understanding of the mechanisms leading to poor clinical outcomes for patients with sepsis and other inflammatory diseases.

Recent evidence has indicated that immune activation in mucosal surfaces is a critical determinant of HIV infection risk. HVTN914 Trial aims to quantitate immune activation in foreskin, blood and rectosigmoid mucosa from HIV-negative, uncircumcised men who have sex with men and who are at high risk for HIV acquisition. RNA of high quality and quantity must be isolated to quantitate rare immune transcripts present in these tissues. I isolated RNA from human foreskin, colon, rectum and blood samples to evaluate the RNA yield and quality. Results indicated that 91% of the samples met the required quality and quantity standards for future tests and could therefore be assessed by Reverse Transcription Polymerase Chain Reaction (RT-PCR). I then amplified an endogenous control mRNA to determine if expression of an endogenous control would be different among isolations. The blood samples amplified twice as rapidly as the other tissue types, indicating normalization to the endogenous control would be required. Our data suggests one possible cause for differential amplification is the increased phenol residue in the tissue isolations compared to blood, which can reduce reverse transcription or polymerase activity.

This project examines the ethical and social frames which facilitate environmental conditions that fuel the rampage of tuberculosis in India. Three key components of the basic biomedical outbreak narrative that are often overlooked will be brought forth to attention: the tuberculosis outbreak as more than just a bacterial spread, social constructs which shape the bacteria’s accessibility to victims, and socioeconomic determinants of treatment (and lack thereof). India accounts for approximately one-fifth of global tuberculosis occurrences, and with over 2 million cases in the country, tuberculosis is a continuously growing health concern, posing a major threat to the well-being of the population. Due to India's developing health care system, pollution, and poverty, these conditions amplify the ease of transmissibility and rate of infection. As treatment regimens are abandoned due to social stigma, medical side effects, and overwhelming price tags, the bacterium which causes TB (mycobacterium tuberculosis), tends to mutate and become drug-resistant to varying degrees; increasing the difficulty of containment and scientific development of effective medicines. Furthermore, the capitalist structure of the pharmaceutical industry contributes to the financial challenges which prevent the eradication of tuberculosis. Drawing on the theory of biopolitics while using sources of statistical information and analytical discourse,  my presentation seeks to explore various properties of the disease and discover how the complex interconnectedness of these underlying issues attribute to forms of structural violence, perpetuating the growth of tuberculosis in India.

Vitamin D is an essential hormone in the body that helps regulate calcium and phosphate homeostasis. The effects of vitamin D in the body depend on dietary intake, sun exposure, and the ability of the body tissues to convert vitamin D into biologically inactive and active forms. One of the metabolic processes involves the sulfation of 25-hydroxyvitamin D₃ [25(OH)D₃], a form of the hormone that is a major circulating vitamin D metabolite in humans and can be excreted into the bile to affect the function of intestinal epithelial cells. In this research experience, I studied the relative efficiency of the 25(OH)D₃ sulfation reaction by liver sulfotransferase enzyme (SULT2A1) and the effects of the sulfate metabolite on intestinal epithelial cell gene expression. Using purified SULT2A1 and pooled human liver cytosol, I helped to determine the rate of the sulfation reaction over various 25(OH)D₃ concentrations. The Michaelis-Menten equation was used to determine kinetic parameters, which established the efficiency of 25(OH)D₃ sulfation. In order to determine which enzymes are regulated by 25(OH)D₃-sulfate, I tested the effects of 25(OH)D₃-sulfate on the expression of different gene targets in human intestinal cell systems. LS180 cells were used as a human cell model in order to examine how changes in concentration of phosphate solution and 25(OH)D₃-sulfate affect the enzyme gene expression in the cells. The experiments consisted of LS180 in various concentrations of phosphate and 25(OH)D₃-sulfate solutions. The cells were incubated, and lysed to isolate their RNA. Then, the RNA was converted into DNA to be retrieved via a PCR machine, which amplified the difference in relative mRNA expression among different enzymes. This study is expected to provide in vitro evidence that 25(OH)D₃–sulfate plays an important role in regulation of intestinal gene expression, which contributes to optimization of individualized drug therapies using vitamin D.

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