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.

Stimulation of rod photoreceptors has been shown to change the perception of hues seen for bright stimuli surrounded by black. It has also been shown that when the surround is made bright, the stimuli appear dark, and yellow becomes brown. Few aspects of these dark colors have been studied. Past research explains the existence of four unique hues (red, green, blue, and yellow) organized into two dimensions of opponent-color pairs. These unique hues are perceived to be pure colors, without influence from any other colors occurring in their composition. An individual’s perceptual “unique hue” is defined by equilibrium for red or green (a blue-yellow balance) and for blue or yellow (a red-green balance). Rod hue biases occur under dark-adapted conditions when rod signals strengthen one direction of the balance of a unique hue over the other. Observers adjusted the color of 2-4°-diameter disks presented 7° away from visual fixation, in the presence of either an all-black surround alone or a black surround with a white ring around the disk. Rod influence was measured as the difference in color settings for the same stimuli measured either after complete dark adaptation (maximizes rod influence) or after cones, but not rods, have recovered from a bleaching light (minimizes rod influence). Prior studies have shown that for bright stimuli, rods create a green bias for yellow, a red bias for blue, and a blue bias for both green and red. We find that the bright ring darkens the test stimuli, changes yellow to brown, and reverses the rod influence to become a red shift. Results for the other 3 test colors are pending. These results suggest that the weighting of signals from both cones and rods differs for the neural pathways underlying perception of bright vs. dark stimuli.

Pro-Eating Disorder (ED) movements include Pro-Ana and Pro-Mia, decentralized online movements which aim to support those with eating disorders such as Anorexia and Bulimia to attain and maintain extreme weight loss. Eating disorders (EDs) are known to become part of patients’ identity, yet stigma against EDs discourages patients from displaying this identity in everyday social interaction. ED patients are also known to have impoverished in-person social networks. Pro-ED activity has been examined on other social media sites; however, Twitter is a popular and novel social media site on which to investigate this activity. The social structure of Twitter may allow Pro-ED Twitter profiles (Handles) to express their ED identity and gain social capital in the form of other Twitter Handles who follow Pro-ED Handles' tweets, called Followers. Because ED displays are stigmatizing, Followers are expected to share an interest in weight loss. This study investigates if Twitter is a social space for Pro-ED Handles to express an ED identity through tweets (micro-expressions of 140 characters or less) and if their social ties on Twitter are made with other Handles interested in weight loss. Using the Twitter Applied Programming Interface for all data collection, a sample of Pro-ED Handles is selected from Twitter for their use of a Pro-ED keyword in a tweet. Next, Pro-ED Handles’ tweets are qualitatively coded for ED references to determine the relative frequency of ED related tweets. A random sample of Pro-ED Handles’ Followers is then qualitatively coded to determine the proportion of which reference weight loss in their basic profile information. While ED social expression and connection on Twitter may be a source of social support for Pro-ED Twitter Handles and their Followers, it also has the potential to reinforce deleterious attitudes, intentions and behaviors.

 In the last decade, and especially since the 2013 Supreme Court Ruling on Shelby County, AL v. Holder, there has been amplified discussion of voter access policies- particularly those potentially restrictive in nature. Much of this discussion has been centered on the supposed need for photo identification, shortened registration and voting periods, and the efficacy of absentee ballots. The discussion of these policies is in direct contrast to the movement to expand voting rights of the 1990s and largely anecdotal in nature. Never the less, many states have considered or adopted more restrictive policies. Using Census data, this paper will utilize regression analysis to examine the effect of voter ID requirements, limited registration and voting periods, and absentee-only balloting on turnout rates by state across race, age, and income groups in General Elections from 1992-2012. Researchers undergoing similar types of analysis have found the policies in question to have non-appreciable or no effects on total turnout rates, but have neglected to consider potential disparate impacts upon certain groups. In addition to considering such impacts, this paper will also examine factors that lead states to consider restrictive policies, such as rising minority populations or swing-state status. Research into voting practices has obvious policy implications and is particularly relevant as we approach the 2016 Presidential election.

The role jellyfish play in marine food webs is not fully understood. We investigated whether the trophic level of lion’s mane jellyfish varies with size, month, and type of tissue sampled in an individual. To investigate these questions, we used stable isotope analyses to trace the values of 13C and 15N. We found that isotopes do not change with size or month, and the effect of tissue type is unclear.

 Waste water and run-off from hospitals, sewage treatment plants, and homes discharge human byproducts to aquatic systems all over the world. These anthropogenic byproducts range from toxic compounds and personal care product chemicals to biological and genetic waste. When examining the microbial component of these byproducts, biomarkers such as antibiotic resistance genes can be identified by genetic techniques. Extended spectrum beta-lactam (ESBL) antibiotics are valuable in treating bacterial infections, and increased multi-ESBL resistance by carbapenemase-producing Enterobacteriaceae has been detected in waste water. The Klebsiella pneumoniae carbapenemase (KPC) enzyme was identified approximately 20 years ago and the resistance gene has spread to 37 states in the US. Discovered in 2008, NDM-1 is a member of metallo-beta-lactamase family revealed in K. pneumoniae and Escherichia coli, and found world-wide. Moreover, ESBL resistance genes, such as KPC and NDM-1, have been shown to move to environmental bacteria, most likely by horizontal transfer. Given the recent discovery of NDM-1 and national spread of KPC, we wished to assess for the presence of KPC and NDM-1 in nearshore pelagic waters of Puget Sound. DNA for examination was isolated from filtered seawater collected in six of the seven oceanographic basins of Puget Sound, including areas near waste water treatment plant outfalls. Analysis via quantitative PCR for KPC and NDM-1 were performed using positive controls of meropenem- and cefotaxime-resistant strains of K. pneumoniae bearing KPC or NDM-1 as assay standards. Results for these resistance markers were compared to companion analyses for human-origin and bovine-origin fecal markers, water quality parameters, and potential sources. These results can provide insight into additional stressors introduced into Puget Sound by human activities.

 “Trojan” asteroids, or asteroids trapped in stable gravitational positions preceding and trailing a planet in its orbit, accompany almost every planet of our solar system. These hunks of rock were captured into their current locations in the early stages of our solar system’s formation, and their presence hints at the dynamical history of bodies orbiting the Sun. However, we have no reason to assume that our own planets are alone in possessing Trojan asteroids. The Kepler Space Telescope mission, launched in 2009, has been instrumental in the recent search for exoplanets (planets orbiting stars other than the Sun). It identifies these planets from a tell-tale dip in starlight when a planet passes in front of its host star. It has identified thousands of new worlds to date. However, no studies have yet been made attempting to detect Trojan asteroids accompanying these exoplanets from the Kepler photometry data. We expect to be able to detect these asteroids using statistical model fitting to the Kepler data, similarly to how exoplanets themselves are detected. By fitting a model based on the properties of the particular exoplanet to the photometry data, it is possible to deduce the presence of Trojan asteroids and their properties. However, if we are unable to detect these Trojan asteroids, we will be able to set limiting constraints on the presence of asteroids in exoplanetary systems. Observations of these Trojan asteroids, or the lack thereof, would give insight to the evolution and migration models of these systems. These results will ultimately lead to a better understanding on how planetary systems form, through which processes they migrate, and how they compare to our own solar system.

We want to understand whether or not the underlying magnetic activity of a star plays a role in the "parking" of a planet as it migrates inward. Magnetic activity of a planet's host star is one among a bevy of factors that inform planetary migration, and may imprint itself on the final orbital location of a planet. In this framework, less active stars allow planets to reside nearer to them than their more active counterparts, which "brake" planets' inward migration sooner. NASA's Kepler mission collected an ideal data set to address this question. It detected thousands of extrasolar planets from the periodic dimming of their host stars as the planet crossed the face of the star. By using the data collected from the mission, we are initially attempting to find a relationship between the mass of the host star and the current location of its nearest planet. We employ stellar mass as a proxy for stellar activity for this preliminary treatment. We can infer some level of stellar activity from the mass of the star, but we plan further investigation to determine the extent of this relationship and how it may change over time. We will look at the brightness variations of the stars in the Kepler sample, over short and long timescales, in order to infer stellar activity in a more robust fashion. Then, we will jointly examine where the closest orbiting planet resides around this sample of stars. We will establish how this parking distance relates to stellar type and stellar activity. We aim to untangle the role of magnetic activity from the other factors determining planetary architecture. 

Novel cancer therapies using genetically engineered T-cells are currently undergoing clinical trials at research institutions such as Fred Hutchinson Cancer Research Center (FHCRC). The cell-based cancer therapies involve introducing novel genes into a patient’s T cells to express high-affinity tumor targeting receptors called chimeric antigen receptors (CARs). Several tumor associated molecules (tumor antigens) have already been identified and are targetable by CARs, such as CD19, which is expressed in B-cell lymphomas and leukemia. The manufacture of these patient specific CAR T-cell therapies can be very costly requiring a considerable amount of time and labor as well as raw materials that are both expensive and limited in their availability. The overall objective of the process development group at FHCRC is to improve the manufacturability and commercial potential of the CAR T-cells while maintaining their effectiveness in killing the intended targets. The goal of this work focuses on optimizing the cell culture conditions in which the T-cells are grown and, specifically, characterizing the role of glucose and human serum on process performance. Experiments were initiated by first stimulating T-cell growth using anti-CD3/CD28 antibody coated microbeads followed by lentivirus transduction to express a high affinity CD19 CAR. The cells were cultured using a range of glucose and human serum concentrations while monitoring cell growth rate and viability using a hemocytometer. The phenotype distribution of the T-cell populations was also followed using a flow cytometer. Finally, T-cell target killing was assessed using a chromium release method whereby the expanded T-cells were co-culturing with CD19 positive B-cells that were primed to release intracellular Cr51 when killed. A strong positive correlation between the concentrations of both human serum and glucose on the growth rates of the T-cells was observed. Interestingly, increased glucose concentrations also correlated with decreased T-cell target cytotoxicity. Additional work is required to fully characterize and understand the role of glucose and the other culture conditions on the T-cell expansion process and their resulting target killing activity.

The aesthetic benefits of tooth whitening have led to a recent increase in the popularity of whitening procedures. Current procedures effectively whiten teeth, but do so through the use of peroxides that cause negative side-effects. These side-effects include decreased hardness and strength of tooth enamel as well as an increase in tooth sensitivity. An alternative to peroxide bleaching that holds promise in whitening teeth involves the application of agents that promote the deposition of white mineral layers on the tooth surface. One such agent is a mineralization directing peptide (MDP) derived from amelogenin, a major protein responsible for enamel development. Previous studies have shown that the application of MDP to tooth root surface yields the formation of a mineral layer with strong, functional mechanical integrity. In this project, MDP is studied for its ability to whiten the tooth enamel surface by promoting the formation of a new mineral layer. Treatment of tooth enamel with MDP could serve as a healthy alternative to current whitening procedures. To verify the mineralization capabilities of MDP, kinetics of mineralization in a Ca2+/PO43- solution was measured through a light absorpotion method. Extracted human teeth were then sectioned and etched with phosphoric acid gel for 2 minutes and coated with MDP. The tooth samples were then rinsed with DI H2O and placed in a KH2PO4-CaCl2*2H2O solution for 18 hours at 37°C. Following this step, samples were rinsed with DI H2O and observed via SEM to characterize mineral formation. Future research will be carried out to formulate an MDP product in which viscosity is optimized for spread of the product and mineralization kinetics. Upon completion of this research we will be able to identify formulations of MDP products that form mineral layers on teeth and can be used for widespread dental care.

Glacial advances and retreats are largely responsible for the current landscape of the Puget Lowland. Of interest to this study was a period of glacial retreat 15-60 thousand years ago. Nonglacial sediments deposited during this time, known as the Olympia Beds, are discontinuous throughout the South-Central Puget Sound region. Here we attempt to correlate between discontinuous outcrops of Olympia Beds based on mineralogy. Sediment samples were taken from outcrops along the SW shore of Commencement Bay and analyzed using X-ray powder defraction (XRD) to determine whether or not the mineral assemblages of each outcrop were of the same origin. The mineral groupings consistent within the sampling area included quartz, muscovite, plagioclase feldspar species (andesine and albite), or potassium feldspar species (sanidine). This implies similar provenance for all outcrops and is consistent with deposition during the same episode of glacial retreat. These data were collected in support of an anisotropy of magnetic susceptibility (AMS) study. Mineral assemblage information coupled with AMS can provide a glimpse of past streamflow conditions within the Olympia beds, suggesting a broadly N-S pattern of streamflow. The combined mineralogical and magnetic results suggest a way forward for mapping streamflow in the Puget Sound region during glacial retreats, eventually leading us toward a better understanding of present-day glacial retreat. 

During mammalian central nervous system development, waves of spontaneous synchronous activity (SSA) are a widespread developmental phenomenon, serving to regulate neuronal migration, physiological maturation, and synaptic connectivity. In the neonatal mouse cortex, these waves of electrical activity involve a vast number of neurons firing bursts of action potentials simultaneously and producing transient increases in intracellular calcium, which can be imaged using calcium-fluorescent dyes. The Moody lab has previously determined that waves of SSA are initiated by a pacemaker in the ventral piriform cortex and are dependent on GABAergic transmission. Since developmental problems may arise when waves fail to occur during the proper developmental time period, it is crucial to determine exactly how waves are initiated. In order to gain insight into how waves are generated, I estimated key network and cellular parameters that define developing cortical networks using past experimental data. I then built a computational model of GABAergic neurons that simulates wave initiation and propagation, implementing the previously estimated parameters. By matching the simulated wave propagation frequency to those determined by experimental data, I estimated the parameter space of cell connectivity, a free parameter of the model. Finally, I am validating the model by gathering data that estimates synaptic connectivity via patch clamp experiments. This knowledge will ultimately help elucidate the pacemaking function of GABAergic cells that generate waves of SSA by characterizing intrinsic physiological properties and synaptic connectivity.

With ~34 million people infected with human immunodeficiency virus (HIV), researchers are actively trying to decipher the evasive nature of the virus--primarily its high mutation rate that allows it to escape immune recognition. We are thus analyzing evolutionary distances between viral DNA sequences and applying them to other aspects of HIV pathogenesis such as the highly variable course of infection. There is typically an initial short period of flu-like symptoms as the virus begins to destroy CD4+ T-cells, which are crucial to the immune system, then seroconversion, when the body produces cytotoxic T-lymphocytes that suppress and stabilize viral levels, and virus-specific antibodies. An asymptomatic period that varies greatly in length then follows. However, viral levels eventually increase again and T-cell levels drop and/or the immune system can no longer control opportunistic infections, the patient is diagnosed with Acquired Immunodeficiency Syndrome (AIDS). However, the majority of research focuses on HIV-infected men, despite intriguing evidence suggesting that there are gender-specific differences in the progression to AIDS. In this comprehensive longitudinal study of HIV-1 in eight different women, we are investigating the patterns of viral genetic diversity and divergence, from the time of seroconversion to the development of AIDS or until disease progression was halted by antiretroviral drugs. We amplified the conserved group specific antigen (gag) gene and the variable envelope gene (env) of various time points of each infected woman by performing Multiplex Polymerase Chain Reactions. Sequencher and Geneious programs were used to determine and align the DNA sequences after they were sent out for Sanger sequencing. We will investigate the patterns of diversity and divergence over the time course of an infection in each patient using phylogenetic trees of their DNA sequences. Results from this work will be presented, as well as a comparison to similar measures from men.

 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.

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.

 The human retina is a complex, post-mitotic tissue where the visual process is initiated. More specifically, it begins when photoreceptor cells absorb light. When these photoreceptors are lost due to damage or disease, irreversible loss of vision results. One potential therapy is cell transplantation of newly generated photoreceptors to replace these lost cells. Regardless of where these stem cells are derived from a common obstacle faced is the proper integration of the transplanted cells with the surrounding native cells. Here we investigate wheat germ agglutinin (WGA) as a potential tool to detect proper integration of photoreceptors by exploiting WGA’s known capacity to serve as a transsynaptic tracer among integrated neurons. Recombinant adeno-associated viruses (rAAVs) were generated encoding WGA conjugated to red flourescent proteins (DsRed) under either a ubiquitous (CMV) or photoreceptor specific (IRBP) promoter.The rAAV genomes also contained another fluorescent protein (GFP) to identify infected cells. Negative controls for transsynaptic movement (where WGA is absent) were included. These rAAVs were delivered via subretinal injections in 2-3 months old mice. The murine eyes were then harvested after 4 days, 2 weeks, and 3 weeks post injection and examined for red florescence, indicating transsynaptic movement. In an attempt to increase transsynaptic signaling, mice were housed in constant darkness and compared to their light-adapted controls. We have been able to show modest WGA-dependent transsynaptic signaling from the infected photoreceptors to their second- and third-ordered neurons (bipolars and ganglion cells, respectively). These transsynaptic signals appear to occur from robust cellular expression of WGA and were not affected by the housing conditions for the mice. These results support an accumulation requirement for transsynaptic movement. Further investigation into enhancing the WGA expression in photoreceptors are needed so that it could become a more powerful tool to examine the integration capacities of transplanted cells for future transplantation studies.

Bottom water hypoxia is a feature of many coastal embayments and fjords in the Salish Sea. Ongoing research in Bellingham Bay (Bellingham, WA USA) by Northwest Indian College and Western Washington University has identified a seasonally recurring area of low dissolved oxygen near the center of the bay. Similar to other regions of the Salish Sea, hypoxia in Bellingham Bay may be a naturally occurring phenomenon, yet the extent of eutrophication and anthropogenic nutrient loading’s influence on patterns of hypoxia is poorly understood. The present study has continued an established monitoring program documenting the range, duration and severity of hypoxia in Bellingham Bay, while adding an experimental component investigating factors that regulate respiration of heterotrophic bacterioplankton. Profiles of water column parameters and sample collection were performed on six regularly scheduled cruises. Dissolved oxygen concentrations below the hypoxic threshold were observed in bottom waters in the center of Bellingham Bay for most of the summer, although the layer of hypoxic water appeared to migrate upwards into the water column in late July. Manipulative experiments were conducted on collected water samples to investigate effects of temperature and organic carbon on water column respiration. These experiments revealed that temperature had a negligible effect on water column respiration, while organic carbon stimulated oxygen consumption and was thus identified as a possible limiting factor. The study’s findings broaden our knowledge of factors regulating oxygen dynamics in coastal embayments of the Salish Sea and provide further insight into the potential effects of anthropogenic stressors and climate change on Salish Sea water quality.

Circannual rhythms, such as the cycling between breeding and nonbreeding seasons, provide critical timing information for organisms’ major life history events including reproduction cycles, courtship, and migratory restlessness, among other physiological and behavioral changes. Photoperiods are particularly useful indicators of seasonal change because of their consistent nature, which allows organisms to predict and prepare for the onset of the short breeding season. The growth and regression of the neural circuits that control the seasonal production of song in Gamble’s white-crowned sparrow (Zonotrichia leucophrys gambelii) are one such example of the ability of photoperiods to time changes in brain morphology, organismal physiology, and behavior. As sparrows transition into breeding conditions, testosterone levels increase, driving an increase in the volume and neuron number of one song nucleus HVC (proper name) and an increase in song production rate and stereotypy. These seasonal changes can be replicated in a laboratory environment through strict light, temperature, and hormone regimes. However, variability in HVC volume and neuron number, testosterone levels, and song production of sparrows during the replicated breeding and nonbreeding seasons has been observed. The endogenous seasonal rhythm has been observed to persist in constant laboratory conditions across taxa, and thus may persist in white-crowned sparrows as well. We tested whether endogenous seasonal rhythms may contribute to the observed variability between individuals. By examining the persistence of an endogenous seasonal rhythm the measurement of several morphological and physiological traits associated with breeding seasons in sparrows maintained throughout the year in controlled laboratory nonbreeding conditions was collected. Finding seasonal-like differences in morphology and physiology of birds housed in constant nonbreeding conditions would suggest the need for additional experimental controls in future studies of songbirds in order to prevent variability due to endogenous seasonal rhythms.

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.

Approximately one in eight women will develop breast cancer in their lifetime. One key aspect of searching for the cure for breast cancer is to understand the metastasis of breast cancer cells, or the movement of cancer cells from one organ of origin to a distal site. In addition, the recent identification of subpopulations of cancer cells that have stem cell-like properties, termed cancer stem cells, point to a very important area of study in order to eradicate breast cancer in the body. Breast cancer cells with high cell surface protein CD44 and low cell surface protein CD24 levels are known cancer stem cells. In this study, we first validated and then employed an in vitro scratch assay to track the migration of breast cancer cells. A micrometer pipette tip was used to create a gap in a monolayer of breast cancer cells that had been stimulated with different Toll-like receptor (TLR) ligands and other controls. The gap width was measured over 24-hour time points to determine the rate of cell migration. These ligands were tested at varying concentrations and in both soluble and particle-encapsulated form. To differentiate the effect of cell migration from proliferation on gap width measurements, the rate of proliferation of the breast cancer cells after stimulation with TLR ligands was analyzed. Our results suggest that TLR ligands slow the migration of the cancer cells to varying degrees with particle encapsulated Poly(I:C) being the most effective. In addition, our experiments suggest that Poly(I:C) loaded in particles slows the migration of CD44+/CD24- BT-20 cells, known cancer stem cells. Overall, this research will allow for a better understanding of the migratory effects of various TLR ligands and, hopefully, aid in the research of breast cancer metastasis, especially the metastasis of breast cancer stem cells.

 Self-affirmation, including value affirmation, interventions help people to view identity threats in a larger context, which makes these threats psychologically less significant. It also gives people spaces to focus on other tasks as well as improve their performance on tasks. Some previous studies have demonstrated self-affirmation can help students to enhance their academic performance in both short and long time periods. Building upon the findings of previous studies, this project seeks to expand on self-affirmation interventions in educational settings. We hypothesize that self-affirmation can make individuals more persistent (less likely to give up) on difficult tasks in short time periods. Additionally, we hypothesize that the effect will be strongest for international students, who may be engaging in substantial identity formation in their new educational environment. To test our hypotheses, we will set up an experiment examining the effect of values affirmation on students’ persistence on a math test. Participants, from a local community college, will be randomly assigned into two groups: the experimental group who will complete the self-affirmation intervention writing task, and a control group who will complete a placebo writing task. After participants complete the writing task, they will begin a specially designed math test with seemingly easy but unsolvable questions. All participants will be free to leave (give up) at any time during the test, and their time spent on the test will be recorded. We expect the experimental group (self-affirmation intervention) will persist longer compared to the control group (placebo writing). Within the experiment group, international students are expected to persist even longer compared to the local students.

During zebrafish gastrulation, presumptive mesodermal cells internalize beneath the ectodermal cells and migrate toward the dorsal axis to form the notochord and the presomitic mesoderm. Our research focuses on how p120 catenin is involved in the pathways of cell adhesion and migration during zebrafish morphogenesis. p120 catenin is a regulatory molecule which has dual functions. The first is to stabilize cell-cell adhesion by binding to the intracellular and juxtamembrane region of cadherins at the cell membrane which form adherens junctions with other cells within a tissue, holding them together. The second role of p120 catenin is to function upstream of CDC42 and Rac1 GTPases in the cytosol to initiate cell motility by stimulating the formation of lamellipodia and filopodia. Both functions are greatly regulated by p120 catenin phosphorylation. The hypothesis is that tyrosine phosphorylation in p120 catenin mediates its binding to cadherins while serine/threonine phosphorylation leads to activation of CDC42 and Rac1 and thus, cell migration. Our general approach is to apply immunoprecipitation of embryo lysates to determine which proteins interact with p120 catenin when it is phosphorylated on tyrosine or serine/threonine residues. Next we will inject mutated forms of p120 catenin into the embryos and determine how that changes protein interactions. So far, we have been testing different mammalian commercial antibodies on normal embryo lysates to determine which ones work with zebrafish. This research could have important implications on treatments of some cancers and wound healing. 

Over half of the world’s population lives in urban areas. With that percentage increasing each year, enormous stress is put on the ecological health of freshwater lakes. Moreover, the urban poor are reliant on these resources for recreation and nutrition, while at the same time their health is increasingly threatened by harmful algal blooms caused by cultural eutrophication. Basic water quality monitoring data is sparse for many small lakes in Washington, despite heavy use by the public. Data collected on urban lakes using standard water quality tests are key to understanding how lakes across the country affected by anthropogenic pollution can be restored for public use. This study uses basic water quality monitoring data to determine trophic status of Wapato Lake in Tacoma, Washington. The lake has historic problems with toxic algae blooms, a result of anthropogenic nutrient input. Water samples were collected at various depths using a Niskin bottle for determination of total phosphorus and to visually identify important plankton species, both toxic and beneficial. Other water quality parameters were measured in situ, including Secchi depth and vertical profiles of temperature, specific conductivity, dissolved oxygen, pH, and chlorophyll using a multiparameter water quality probe (HydroLab MS5 or Quanta). Aquatic birds were also counted each visit, as waterfowl were shown to contribute significant nutrients to the lake in a previous study. This year-long study is still in progress. Preliminary results indicate Wapato Lake is a non-stratified lake due to shallow depth, and a very productive lake, with Secchi depth between 1.25 and 2 meters for the duration of the study. In comparison with previous years, data show an increase in maximum total phosphorus concentrations, unchanged productivity as measured by Secchi depth, and a dramatic decrease in waterfowl present around the lake. Recommendations for improvements in water quality will be presented.

For years, politicians have claimed that elementary reading scores can predict prison populations, despite a lack of credible evidence. Although the existing criminal justice literature does draw a connection between higher educational attainment and lower crime rates, this relationship has not been widely examined at the elementary level. Do early reading scores actually predict future incarceration rates? Using 4th grade reading scores and prison admission rates, I examine this question through linear regression. Controlling for other factors that could influence educational outcomes and prison entrance, such as socioeconomic status and harsher sentencing laws, I find that lower average reading scores at the fourth grade level are predictive of future prison admissions. 

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.

Infection occurs in about 30% of patients with stroke and is associated with worse outcomes. Data suggest that certain antibiotics used to treat post-stroke infection may be neurotoxic (fluoroquinolones) and others may be neuroprotective (β-lactams). We are studying the outcome of rats who are subjected to ischemic stroke then pulmonary infection. Rats are treated with either ceftiofur (β-lactam class), enrofloxacin (fluoroquinolone class) or normal saline and outcome determined by a series of behavioral tests administered over the ensuing four weeks. The behaviour tests include the rat's ability to stay atop a rotating drum (rotarod), ability to retain their footing while walking on a grated surface (foot fault test), and tendency to turn in circles (neurological score). Outcome of rats treated with enrofloxacin and ceftiofur will be compared to the outcome of rats treated with normal saline. Outcome that is better than in saline treated rats would suggest the antibiotic is neuroprotective, while outcome worse than in saline treated animals would suggest that the antibiotic is neurotoxic. The results of the study could have immediate and direct applications to clinical care as it could influence the antibiotic choice in patients who develop post-stroke infection.

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).

Specialty polymer optical fiber requires incredibly tight diameter control of ~ 1 um to minimize signal attenuation. Temperature profiles within cylindrical furnaces used to bring about necking of preforms to be drawn into fiber cause the formation of convective oscillating cells. The resulting variations in heat flux into the preform likewise cause oscillations in the fiber exit diameter. For preforms of sufficient diameter, matching a prescribed temperature profile within the necking region of the furnace leads to fiber diameter oscillations of predictable amplitude and frequency. The necessary temperature profile and the extent to which this affect can be achieved varies with the geometry of the inside of the furnace; namely, preform shape and diameter. To maintain ease of manufacturability, accommodating various preform diameters is necessary. By drawing fiber under temperature profiles described above, it is hoped that coupling these well-understood and reproducible oscillations with a PID feedback controller using draw speed to regulate exit diameter and tuned to these specific oscillations, we will attain diameter control within 1 um for the ideal case of a large 1” diameter preform. Preforms of varying diameters will be drawn under ideal temperature profiles, with the fiber diameter recorded. When steady oscillations are achieved, a PID controller tuned to their amplitude and frequency will be turned on, and the diameter response will be observed. Earlier work indicated that the process is highly sensitive to temperature and draw speed, and previous attempts to achieve 1 um diameter control using only PID feedback or temperature profile regulation proved inadequate. This work will determine if a combined approach advantageous, and provide insight into the more challenging control problems associated with specialty fiber preforms of smaller diameter. If achievable, this would allow inexpensive production of advanced graded-index fiber.

Ischemic preconditioning (IPC) is the neuroprotective phenomenon in which a brief ischemic episode induces genetic reprogramming of affected brain cells, causing physiological changes that minimize cell death from subsequent, sustained ischemic insult. We hope to characterize the cellular and molecular mechanisms of IPC. Our lab previously has shown that IPC is dependent on Toll-Like Receptor 4 (TLR4) and involves the production of interferon stimulated genes (ISGs) in microglia. Following ischemia, damaged neurons release endogenous TLR4 agonists called damage-associated molecular patterns (DAMPS), which induce interferon (IFN) release by microglia. The IFNs initiate a biochemical signaling cascade that activates transcription factors which bind to the interferon-stimulated response element (ISRE), promoting ISG transcription which alters the immunological function and phenotype of microglia, mediating neuroprotection. My project is to confirm the cell signaling mechanism by which hypoxic/hypoglycemic (H/H) conditions induce ISG expression in vitro. To accomplish this, I am using a reporter assay to detect ISRE activation with luciferase protein expression, looking specifically at the effects of H/H experimental stimulations on ISRE activity in microglia from the N9 cell line. I am first optimizing a transfection protocol using green fluorescent protein (GFP) as a reporter. I will use the optimized protocol for experiments, transfecting microglia with DNA encoding the luceriferase enzyme linked to the ISRE promoter, then incubating the cells under H/H conditions, and finally using a plate reader to quantify fluorescence. We anticipate that H/H stimulation will result in increased luminescence in wild-type microglia, and we would interpret these results as indicating that ISG expression in H/H-stimulated microglia is mechanistically due to transcriptional activation at ISRE sites. Identifying the genetic actors in IPC will reveal intracellular targets for pharmaceuticals that can mimic this neuroprotection. We can then administer these medications pre-emptively to patients at risk for stroke or emergently to acute stroke patients.

Why does the United States continue to pursue and support failed counternarcotics efforts in Latin America? What are the incentives, and who are the beneficiaries, in the foreign War on Drugs? Using the theory of the Iron Triangle relationship between Congress, industry, and bureaucracy, this paper investigates the union between private defense contractors and legislative decision-making in regards to military funds appropriations under Plan Colombia (2000) and the Mérida Initiative (2008). Although the multivariate regression model used to test my hypothesis showed no statistical significance between the number of defense contractors in a Congressional district and a Congress member's vote, it did illuminate other factors that influence legislative decision-making - specifically campaign contributions by the aerospace industry and representative ideology.

Currently, kinases are thought to function primarily in signal transduction cascades by phosphorylating target proteins. Based on emerging evidence, a novel role for kinases is promising: direct kinase binding of DNA and chromatin. To analyze the role of kinases in the nucleus and investigate whether direct kinase binding of DNA or chromatin takes place, I will generate genome-wide histone phosphorylation and kinase localization maps for multiple kinases in human embryonic stem cells. We first verified the presence of specific kinases in the nucleus of H1 human embryonic stem cells using mass spectroscopy. To visualize protein presence in the nucleus, I stained whole cells and whole nuclei using immunofluorescence. I then studied specific kinase-chromatin interactions and histone phosphorylation sites using ChIP-seq (chromatin immunoprecipitation coupled with high-throughput sequencing). Sequencing data are expected to show genomic locations where direct kinase binding of DNA and chromatin occurs. We predict we will see kinases present at promoter and enhancer elements, as phosphorylation of proteins in the complexes that bind these elements or the surrounding nucleosomes may be important for gene regulation.

Essential tremor (ET) is a very common and problematic tremor disorder that affects over five million people worldwide. It is not a harmful or fatal disease, but because it can greatly impact the quality of life of older adults. Treatment for essential tremor varies depending upon the level of magnitude of the tremor, and high levels of magnitude could possibly prompt usage of deep brain stimulation (DBS). A device that could collect data could also double as a control for deep brain stimulation in more severe cases of ET. It is because of this reason that a diagnosing wrist device is being developed. Most cases of ET involve tremor in the upper limbs, and so a wrist-mounted or upper-arm-region device would be most logical. My goal was to successfully have a piece of hardware capable of graphing simulated (or actual) tremor in real time into a figure in the program MATLAB. The hardware consists of an inertial measurement unit (IMU) and an Arduino microcontroller hooked up to the computer. Wireless capabilities were also planned in the hardware of the final prototype. This device was proposed to be integrated into fabric of some type and fastened somewhere on the human arm for testing. The prototype developed is a glove with the externally attached sensors and microcontroller, and I was responsible for designing, testing and iterating plans of this device, as well as coding in Arduino and MATLAB to collect and graph data from the device in real time.

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.

The surface of Mars is dominated by wind-blown processes and sediment deposits. Dune fields are especially ubiquitous on the surface and record important information about atmospheric circulation patterns, chemical and mechanical weathering, and sediment deposition. Therefore, dune fields are crucial in an understanding of Martian properties such as surface processes, past and present climates, and geologic history. This research investigates the thermophysical properties of sediments composing equatorial dune fields using data from the Thermal Emission Imaging System (THEMIS) on board the Mars Odyssey spacecraft. These data are accessed through JMARS, a geospatial information system developed by Arizona State University. The data are then used with other tools, including Hugh Kieffer’s KRC model, to derive the apparent thermal inertia of the fields. These thermal inertia estimates are the primary way of studying the grains for this research. A material’s temperature response during a diurnal, or daily, cycle can be used to approximate thermal inertia and subsequently be converted to an estimated sediment size. A variety of sizes is expected to be found within the dune fields. Grain size is an important characteristic that can indicate sediment source (local or regional), wind speed, and weathering history, ultimately leading to a better understanding of the surface and climate of Mars. Future research will focus on locating sediment sources and defining textural maturity for Martian sediments, which includes grain size and rounding. It will also focus on identifying inactive dunes, which may preserve historical climate indicators.

The mutualistic metabolic relationships, called syntrophic relationships, between sulfur-reducing bacteria and methane-producing Archaea are responsible for a large part of the global methane cycle. However, the genetic adaptations and regulatory pathways of mutualism are poorly understood, due in part to the difficulty associated with directly observing the behavioral and metabolic interactions of these microbes. To better understand mutualistic adaptations of syntrophic organisms, the bacterium Desulfovibrio vulgaris and the archeaon Methanococcus maripaludis were grown in co-cultures over a period of 1000 generations and their gene expression analyzed. In anaerobic conditions, the metabolic byproducts of one fuels the growth of the other, and vice versa. During lactate fermentation, the growth rate of D. vulgaris is dependent on the level of hydrogen in the ambient environment. M. maripaludis consumes hydrogen to reduce carbon dioxide and produce methane. This relationship between D. vulgaris and M. maripaludis, although syntrophic, is experimentally imposed, and ensures that neither species in the study begins with naturally-derived adaptations. Elucidating the exact mechanisms these microorganisms use to react to stress and adapt to their environment is a fundamental part not only of understanding the mechanisms behind evolution, but also of how interacting populations of microorganisms may be better suited to survive stressful environmental conditions such as global climate change.

Microglia, the brain’s primary immune response cells, can be activated by inflammatory stimuli causing neuroinflammation that can lead to neurodegeneration. It is possible to follow the course of inflammation by monitoring the positron emission tomography (PET) imaging signal of the translocator protein 18 kDa (TSPO), known to be up-regulated under inflammatory conditions, paired with a specific radioligand. Astrocytes, glial cells not involved in immune response, contribute to these PET signals as they also express TSPO, and by assessing the degree of cellular enrichment and TSPO expression in sorted populations of astrocytes and microglia by RT-PCR, the magnitude of their contribution can be measured. Immunostaining combined with a Scatchard analysis of TSPO will reveal the relative number of binding sites and expression in microglia and astrocytes which will determine if TSPO PET imaging is a viable biomarker for specifically microglia inflammation and thus a live, in-vivo tool for monitoring true neuroinflammation.

Borderline Personality Disorder (BPD) has long been misunderstood and stigmatized. Some of the misunderstanding is whether the perceived permanence or severity of the disorder differs between men and women and between the young and elderly. This study seeks to examine the stigmatization associated with BPD diagnosis, asking do people believe that BPD is an untreatable mental illness? There is evidence that the media and mental health community perpetuate stigmas attached to the Borderline diagnosis (Aviram, Brodsky & Stanley, 2006). The goal of this research was to examine people’s attitudes towards BPD patients. College students living in Washington 18-50 years of age were recruited to provide data through an online survey. Participants read one of four vignettes about the life of a patient with BPD; the patient was identified either as a man or woman in his/her 20’s or 60’s. Participants then answered questions regarding their attitudes toward the patient. A 2x2 ANOVA was used to analyze the data. It was hypothesized that there would be main effects for both gender and age with women and older adults rated as less likely to recover and more culpable. It was also hypothesized that there would be an interaction effect in which elderly women are thought to have the poorest likelihood of recovery. Potentially, the results could be used to increase awareness of age and sex stigmatization of BPD patients.

Our perception of the color of an object is strongly affected by the other nearby stimuli, i.e., the object’s context. A yellow stimulus changes to brown when surrounded by bright stimuli; this change comes with a shift of red-green balance where more red light is needed to produce balanced brown and more green light is needed for balanced yellow. However, the perceptual or physiological nature of these effects and their relation to other brightness and color context effects remain poorly understood. Our project explores aspects of the spatial and temporal dependence of both the induction of brown and the accompanying red-green shift. Our study measures: (a) the threshold of brown by adjusting the luminance of a test stimulus to find the light level that appeared pure brown and (b) the red-green balance of brown or yellow stimuli by varying the red and green lights creating the stimulus. For both measures, the test stimulus is a foveally-fixated 2° diameter disk; subjects are presented with a flashing (30 or 1000 ms) stimulus, surrounded by full-screen black or single concentric wide white ring that is either contiguous with the test or has a gap ranging from 0.25° to 3.0° in width between the stimulus and the ring. We investigate spatial influence by varying gap width and temporal influence by varying stimulus duration. Based on studies of brightness perception, we predict that brown will be stronger when bright context features are near the test stimulus and the test duration is shorter. In any case, the results will help us to understand the perceptual and physiological mechanisms underlying the induction of brown and the accompanying shift of red-green balance.

The results of Na-cyclamate (Na-c) experience generalize for a variety of sweeteners: taste sensitivities for the monosaccharides glucose (pyranose) and fructose (furanose), and the disaccharide maltose (pyranose), are significantly increased, while increased sensitivity for the disaccharide sucrose (furanose) approaches significance. Sensitivities for the structurally different sweeteners Na-c and sucralose also are increased, but D-tryptophan (D-tryp) and monosodium glutamate sensitivities are decreased (Kennedy et al., 2013). Human psychophysics and animal neurophysiology data suggest that the changes involve peripheral mechanisms, in or before the receptor cells. (Faurion et al., 2002; Hassan et al., 2006; Gonzalez et al, 2009). Here we tested both the general hypothesis that the receptor subunit hT1R3 plays a modulatory role in experience-induced changes of taste sensitivity and a sub-hypothesis that Na-c experience affects responses to amino acids and peptides differently than responses to sugars and other sweeteners. Subjects rinsed their tongues with 4mM Na-cyclamate or distilled water for 10 sec once a day for 10 days. On day 11 or 12, they tasted a concentration series of aspartame, each concentration paired with water, and indicated which of each pair was “the sweetener.” Subjects treated with Na-c made fewer correct identifications than those treated with water (p= 0.03, Logistic Regression), and thus showed decreased aspartame sensitivity. Together with the overall generalization results, these data support the hypothesis that Na-c interaction with hT1R3 leads to modulation of the whole receptor response and thus to experience-induced changes in perceptual sensitivity. These data also support a difference in the mechanism for experience-induced changes of sensitivities for amino acids and peptides.

The brainstem's important role in the motor and sensory systems makes it a vital structure for studying pediatric development. However, the developing brain's rapid growth presents significant challenges when studying preterm infants. We investigated the regional differences of the brainstem between healthy and developmental delayed preterm infants. A spatiotemporal atlas was constructed from 28 training subject magnetic resonance (MR) scans and their brainstem manual tissue segmentations (whole brainstem) and parcellations (midbrain, pons, medulla) to capture a wide range of growth over time. The brainstem in all 269 MR scans in our database was automatically segmented using an age-specific template derived from the tissue-atlas training data to initiate an atlas-based Expectation-Maximization framework. We used tissue segmentations to re-register the age-specific tissue maps and derive an accurate non-rigid transformation from the atlas into the space of the subject scan. Template propagation was used to place an age-specific brainstem parcellation from the atlas into the space of the subject MRI. Multiple linear regression analysis was performed to model the relationship between regional brainstem volume calculated from the automated parcellations and specific Bayley Scales of Infant and Toddler development-Third Edition (BSID-III) cognitive, language, and motor composite scores at 18 months of age. We covaried with post-menstrual age at scan, age at birth, gender, and with and without supratentorial volume. Significant association existed for all brainstem volumes except for the pons and all BSID-III scores near birth age (mean=32.7+/-3.2 weeks) while there was nearly no significance for the same models in children near full-term age (mean=40.6+/-2.7 weeks). This supports the hypothesis that smaller total brainstem, midbrain, and medulla volumes measured shortly after preterm birth may be useful as a biomarker to predict poor developmental outcome at 18 months of age, while measurements later (near full term age) may be less useful as brain volume recovers.

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.

Seasonal hypoxia in Hood Canal, initiated by eutrophication, is a persistent condition that can overtax marine organisms and potentially affect the marine food web. While many organisms cannot survive in hypoxic areas for an extended time and may display stress or avoidance, low metabolic jellyfish could exploit such conditions to their advantage and proliferate. The health of Hood Canal and surrounding Puget Sound fisheries require detailed quantitative analyses to determine if jellyfish populations pose a threat to the balance of these unique ecosystems. During 2012 and 2013, zooplankton samples were collected monthly through June to October using 200 micron nets from four stations representing the greatest range of dissolved oxygen levels in Hood Canal: Union, Hoodsport, Duckabush, and Dabob. After preservation, samples were cataloged by identification, counts, and measurements using a dissecting microscope. Currently, nineteen genus/species have been identified in the classes Scyphozoa and Hydrozoa and in the phylum Ctenophora. Dominant species include the ambush predator hydromedusa Aglantha digitale and the siphonophore Muggiaea atlantica. Seasonal changes showed significant increases in densities of M. atlantica from 2012-2013 during July through August. Seasonal and interannual distributions of community structures will be further explored alongside environmental conditions to identify patterns and changes in the functional diversity of Hood Canal’s jellyfish and to infer their ecological impacts.

Molecular hydrogen is an important component of star and galaxy formation, but, unfortunately, is difficult to observe and measure directly. Neutral chlorine, however, is easier to detect and can be used to trace molecular hydrogen, because ionized chlorine rapidly reacts with molecular hydrogen and becomes neutral. While it is well established that there is a relationship between neutral chlorine and molecular hydrogen, there has been little research done using modern observations to determine the specifics of this relationship and to apply it to distant absorption systems. By comparing the amounts of molecular hydrogen and neutral chlorine (as well as atomic hydrogen and ionized chlorine) along the sightlines of various stars in the Milky Way, we hope to produce a more accurate chemical model of the interstellar clouds that contain these gases and to improve on the method for using chlorine to determine the molecular content of distant galaxies. At this stage in our research, we have discovered that the fraction of hydrogen in molecular form in the dense cores of these interstellar gas clouds is significantly larger than the ratio used in current chemical models. Also, while previous research has found that the slope of the correlation between neutral chlorine and molecular hydrogen is near one, our research, which includes a wider variety of sight lines, is revealing that this slope is actually significantly smaller. As we continue with our research, our next goal will be to repeat the process we have used on Milky Way stars on stars in the Large and Small Magellanic Clouds and to see if our findings close to home hold true as we move farther away.

Kaposi’s sarcoma-associated herpesvirus (KSHV), is the infectious agent that causes Kaposi’s sarcoma (KS)—a tumor that is the most prevalent cancer found in untreated HIV-infected individuals worldwide. KSHV establishes predominantly latent infection both in cells in vitro, as well as in KS tumors. KSHV, like all viruses, lacks an independent metabolism, and it has been shown to dramatically alter host cellular metabolism, particularly in carbon utilization pathways. Similar to cancer cells, latent KSHV-infected cells require increases in the most abundant carbon sources, glucose and glutamine for survival. However, it is still unknown how glutamine is utilized during latent KSHV infection. Glutathione (GSH) is the most abundant antioxidant in eukaryotic cells. GSH is essential for cell survival because it functions to stabilize reactive oxygen species (ROS), which are deleterious to the cell. I hypothesized that latent KSHV-infected cells require glutamine to produce GSH and to stabilize ROS in infected cells. KSHV-infected cells have been shown to be under chronic oxidative stress, and increased levels of GSH could explain how latent KSHV-infected cells inactivate excess ROS to avoid cell death. To test my hypothesis, I will determine the abundance of GSH in uninfected samples compared to that of KSHV-infected samples. I will use a fluorescent GSH detection reagent and measure GSH absorbance through a spectrophotometer or flow cytometry. Secondly, to determine if glutamine is the necessary precursor for GSH production, I will compare GSH levels between KSHV-infected samples in the presence of all carbon sources and KSHV-infected samples starved of glutamine. If glutamine is the required carbon source, I expect to see decreased GSH levels in KSHV-infected cells in the absence of glutamine. This finding could reveal important drug targets for future strategies to inhibit and treat latent-KSHV infection and ultimately KS tumors.

The demand for efficient and sustainable agricultural crop growth has increased with growing world populations. Water and nitrogen are essential, but often limiting, factors for plant growth; understanding nutrient and water relations within a whole-plant system is important for larger-scale planning. Recent research has shown that bacterial endophytes, microorganisms living symbiotically within plants, may alleviate resource limitations by fixing supplemental nitrogen from the atmosphere. This dinitrogen is allocated to the plant in exchange for photosynthetically fixed carbon, altering source-sink relationships within the plant system. The change in substrate flow may also affect water movement in the plant by shifting osmotic potential. The purpose of this study is to investigate the effects of bacterial endophytes on: 1) partitioning of photosynthetically fixed carbon within the whole plant, and 2) leaf water potential. Sunflowers (Helianthus annuus) will be inoculated with WP5 (Rahnella sp.), a bacterial endophyte strain isolated from native poplar (Populus trichocarpa), and grown in a controlled environment. I will use ¹³CO₂ pulse labeling on one mature leaf of each plant (from both inoculated and control groups); plant tissues from the entire plant will then be analyzed for labeled δ¹³C content. Water potential will be measured using a pressure chamber and psychrometer. Measurements of nitrogen content, photosynthetic capacity, and biomass will also be performed. My hypothesis is that in the inoculated plants, carbon will be allocated locally to endophytes in the target leaf, subsequently decreasing osmotic potential in the apoplastic cellular spaces. Gaining a more detailed understanding of endophyte-plant relationships can have profound impacts on agricultural practices and inform resource management.

Matters of safety and vulnerability in the public sphere have dominated much of the discourse in both everyday queer media and scholarship in queer geography, as lesbian, gay, bisexual, transgender and queer (LGBTQ) individuals continue to face often violent discrimination in public spaces. This project, while acknowledging the difficulty other researchers have discovered in defining what and where queer space is, addresses a gap within queer geography. Little research has been done to analyze the contradiction that lies in the conceptualization many individuals have of “queer spaces” as sites of safety and sites of increased vulnerability. Therefore this research seeks to explore how is safety conceptualized for queer individuals in spaces identified as queer or heterosexual and examine how these different conceptualizations affect how spaces are identified and sexualized. Personalized maps are used to deconstruct a static geography of sexualized space in Seattle and qualitative interviews with LGBTQ-identified Seattle residents are coded and thematically analyzed for patterns of how a subjective geography of un/safe is constructed by queer individuals. This research highlights the importance of lived experiences in how space is categorized and perceived, as well as the complicated relationship between the socio-cultural environment and individual identities in creating these perceptions.

The treatment of cancer with proton beams makes use of beams’ favorable dose profile, which allows for the delivery of more energy to a targeted tumor than to surrounding healthy tissue. Recent investments into proton therapy centers have spurred interest in developing laboratory tools to support preclinical proton beam research. A crucial portion of this work is the accurate determination of parameters which describe these beams by comparing models to experimental results, so that the beams can then be accurately replicated in research simulations. Modeling of the research beams was done with TOPAS, (Tool for Particle Simulation) a program which incorporates the popular Monte Carlo simulation toolkit Geant4. Characterization of two beams at different energies was to be done by matching dose profiles of experimental data with those resulting from the simulation software. Experimental measurements were taken with a parallel plate ion chamber. Parameters to be determined by simulation were precise base energy, beam energy spread, and beam angular spread. Simulations with different combinations of parameter values were run and accurate values for these parameters were determined by distance-to-curve metric minimization. The energy of the low energy beam was found to be 28.9 MeV with an energy spread of 1.5% and an angular spread of 0.003 radians. These values for the high energy beam were found to be 50.0 MeV, 1.25%, and 0.022 radians. The results of this process have given an insight into the effects of each simulation parameter on beam profiles, as well as provide a procedure for determining beam parameters in the future. This work will allow any future research simulation to accurately match the results of experimental measurements were they do be done using these beams.

Leigh Syndrome (LS) is a common pediatric mitochondrial disease comprised of many biochemically distinct but symptomatically similar disorders, and affects approximately 1 in 40,000 children. We are currently studying what is considered classical Leigh Syndrome by using a mouse model with a homozygous loss of the Ndufs4 gene, which encodes an essential subunit of Complex I in the mitochondrial electron transport chain, and thus results in energetic defects. Animals lacking Ndufs4 (Ndufs4KO mice) display progressive neurodegeneration, ataxia, and respiratory failure that leads to death. Selective inactivation of Ndufs4 in neurons and glia leads to manifestation of a disease phenotype indistinguishable from Ndufs4KO mice. Accordingly, lesions in the brainstem and cerebellum are common in human LS patients. However, the neuronal cell types susceptible to the disease are unknown. Thus, to determine the role of certain neuronal types in disease progression, we used the Cre-Lox system to inactivate Ndufs4 in glutamatergic, cholinergic, and GABAergic neurons. Glutamate, acetylcholine, and GABA are three primary neurotransmitters which define specific subsets of neurons widely present in the brain. So far, it appears that inactivation of Ndufs4 in cholinergic and GABAergic neurons does not yield a disease phenotype comparable to that of a full-body Ndufs4 knockout, as they are indistinguishable from wild-type mice. Inactivation of Ndufs4 in glutamatergic neurons, however, appears to yield a mouse with a significantly shortened lifespan that is statistically indistinguishable from the full-body Ndufs4KO mouse.  

This project will use historical and contemporary photographs to test the hypothesis that the average size of salmon has noticeably declined over the last two hundred years in the Salish Sea. Native Americans and early settlers described the population of salmon species in this area with metaphors such as, “you could walk across a river on their backs,” but quantitative measurements began long after human impacts had diminished their populations. The sizes and populations that we record today are drastically smaller than they once were. Salmonids that once weighed over one hundred pounds now weigh closer to twenty pounds, on average. It is believed that human impacts are to blame for the decline of these salmon species. Shifting baselines is the idea that the benchmark of fish size has shifted over the years. We are building upon the research of author Loren McClenachan, whose work was published in Conservation Biology (June, 2009) documenting the reduction of large fish in the Florida Keys. We will be using her methods of reviewing and collecting copies of historical photos to document the considerable decline in size of Pacific Northwest salmonids over time. This research is especially significant because it is the first application of McClenachan's methods to the Salish Sea. By acknowledging former baselines of size and population, we can improve our attempts at restoring our water ways and salmonid habitats.

Forests in the Appalachian Mountains are downwind from coal-fired power plants and other industrial sources in the Midwest, thus forests are exposed to relatively high concentrations of metal pollutants. Despite heightened public concern and tighter regulations to reduce anthropogenic pollutants, spruce-fir forests in the Appalachian Mountains are declining. In previous work at our study site, elevated phytochelatins were correlated with red spruce (Picea rubens) forest decline by altitude. Phytochelatins are metal-binding peptides synthesized from glutathione, from the precursor cysteine. Phytochelatins provide a sensitive and direct indication of metals stress at the cellular level. Metal analysis in soils can reflect historical metals deposition, while lichens can reflect recent deposition. In previous research, we studied metal stress and phytochelatin production in P. rubens from six mountains in the Appalachian Mountains. We found that patterns of foliar uptake and PC production are complex, but appear consistent with induction by Zn and Cd in organic soil. Our current purpose was to collect data along an elevational gradient on Whiteface Mountain, New York to supplement the east-west transect data collected previously and to characterize mycorrhizal fungus communities on sapling and mature tree roots. In recent work, we i) explored elevation patterns in the dominance of mycorrhizal species using PCR, DNA sequencing, and BLAST search; ii) measured Cd, Cu, Hg, Pb, and Zn in organic soil, mineral soil and metals uptake in P. rubens foliage and lichens; and iii) assessed P. rubens phytochelatin, glutathione, and cysteine production in order to monitor ongoing changes in red spruce response to metals deposition. While there was a consistent trend of increasing Pb and Zn with elevation in mineral soils, reflecting historic deposition patterns, there was no evidence for any systematic variation in metals content of foliage with elevation. Phytochelatin and mycorrhizal analyses are ongoing.

While therapeutic cancer models offer potential for novel drug discovery and personalized medicine, current models seldom yield clinically-useful measures of drug efficacy because the physiology of tumor microenvironment is not accurately mimicked or fail to produce data in time to inform the best possible treatment. Thus, we have developed an approach that integrates live tumor slice culture with a 96-well plate-based microfluidic device that allows for the exposure of intact tumor slices to large numbers of drugs. The device integrates a porous membrane that allows for organotypic culture of tissue slices and contains open fluidic channels beneath the culture membrane (membrane acts as a roof) in which drugs can be delivered in parallel microfluidic streams through the membrane to the tissue slices. The addition of a 96-well plate creates a user-friendly interface in which reagents can be added with a standard pipette. Considering current advances in 3-D printing technology, we have used 3-D computer aided design (CAD) software to design a version of the proposed microfluidic device that can be printed using stereolithography, an additive manufacturing process where a photosensitive resin is solidified using a high resolution laser. This will allow us to assess the viability of this approach for the fabrication of complex microfluidic devices, and we are able to take advantage of the three dimensional design space to create a network of channels that exist on multiple planes. With this microfluidic platform, there is the potential to test up to 80 different drug compounds within an intact tumor tissue, which will ultimately be beneficial for cancer patients. 

Random fractal patterns exhibit an overwhelming distribution throughout the natural world, from the smallest scale we can see, to the most universal scales we can imagine, and appear to affect everything in between. In order to explore some small-scale examples of this, we used high voltage to burn surface tracking patterns into various media, then analyzed the fractal dimension of some of the better samples. Next, we theoretically modeled radial diffusion-limited aggregation clusters (DLA) and a linear dielectric breakdown model by computer simulations, and analyzed the Hausdorff dimensionality of those, as well. Similar to previous experiments by Kim and Roh, and Niemeyer et. al., the experimentally and physically modeled results agreed in their dimensionality. This comparative analysis model implies a method of non-destructive analysis for a broad spectrum of insulating materials. These processes could help engineers design more robust dielectric components or safer airplanes, help geologists better understand fault-fracture spreading and aid in earthquake prediction, or enable atmospheric scientists to study elusive lightning structures known as sprites.

 At typical interstellar distances, the separation between a moon and its planet is too small to resolve; the separate spectra of the two objects combine and appear like one object. At most wavelengths the planet will outshine its moon, heavily skewing the center of light towards the planet. However at certain wavelengths a moon may outshine its planet, skewing that center of light towards the moon instead. Spectro-astrometric methods would find exomoons by detecting a shift in the center of light at a moon-dominated wavelength versus a planet-dominated wavelength. Once a moon is detected, tracking the motion of the center of light would also provide information about the masses and separation of the moon and planet. This research project is examining two systems: the Moon around the Earth, and an Earth-like moon around a warm Jupiter. Modeled spectra of the three objects were then used to model the detection of the two types of systems at a distance of 10 parsecs. For the Earth-Moon system, the strongest Moon dominated wavelength was found to be 2.83 microns. For the Jovian-Earth system, the strongest Earth dominated wavelength was found to be 2.44 microns. Further work will explore the signal to noise ratios and thus determine how large of a telescope is necessary to feasibly use this technique in the future.

Neurological outcomes for premature infants with cerebellar hemorrhages are poor, but the mechanisms of injury are not understood. We hypothesize that the addition of blood to cerebellar slices would decrease external granule layer (EGL) proliferation and impair migration of cells leading to developmental disruption. Our objective is to develop a slice culture model for understanding the effects of cerebellar hemorrhage on cerebellum development. Postnatal day six mice were decapitated and trunk blood obtained using a heparinized syringe. Whole brains were removed and 200 µm thick sagittal cerebellar slices were obtained using a Vibratome. Slices were placed on a cell culture insert with serum containing media. Trunk blood (4µL) was applied directly to treatment slices. Slices are incubated for 48 hours. Media samples were collected for lactate dehydrogenase (LDH) assays. BrdU was added 24 or 2 hours before fixation. Slices were fixed in 4% paraformaldehyde overnight. Immunohistochemistry for calbindin, BrdU, GFAP, PCNA was performed. Slices were processed with LacZ and Nissl staining. Images were taken on a confocal microscope and analyzed for EGL cell counts and thickness. LDH, a marker of cell death, increased in the media of blood-exposed slices than control slices for 4, 24, and 48 hours. Blood-exposed slices have thinner EGL (control 141 versus 120 µm blood-exposed). Bergmann glia were more disorganized after blood exposure and lacked the radial appearance of control slices. Purkinje cell arborization was decreased after blood exposure. Cell proliferation was lower in blood-exposed slices than in control slices (control 77 versus 26 blood-exposed for PCNA; control 80 versus 55 blood-exposed for BrdU). In conclusion, the addition of blood to neonatal mouse cerebellum slice cultures decreased proliferation of cells in the EGL after 48 hours. Additional experiments are underway to better characterize the mechanism of action.

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.

We study silica microspheres assembled into a single packed layer, in particular, using acoustic vibrations to assist the assembly process. This single layer of spheres will be used in microsphere-based metamaterial photoacoustic experiments. By adding acoustic waves to the assembly method, it is expected that the microspheres will pack with fewer defects than traditional methods. The wedge-shaped cell self-assembly method is used to form the crystals. Water containing microspheres is left to dry between two angled glass slides. When the liquid solution between the slides evaporates, capillary forces pull the microspheres toward the water line where they will closely pack together. Our research combines this technique with acoustic vibration of the fluid generated from a loudspeaker. An experimental setup was designed with the speaker placed close to the slides, generating white noise at different frequencies and decibel levels. This sound will theoretically shake the spheres as the water evaporates and improve particle ordering. Understanding the dynamics of this material could potentially lead to their use in items such as signal processing devices, protective coatings and armors, and biosensors.

Sleep apnea is a common syndrome where a person has an irregular breath rate only during sleep, making it difficult to be detected and diagnosed. Yet, in the U.S. about two percent of children are affected by this syndrome and thus at risk of some health issues. There are some prevalent breath detection products on the market but they remain inaccessible due to the undesired prices and limited range of detection. In the breath detection project I was participating in, we intended to detect the breath rate by wireless technology, e.g. home-based WiFi. Our design would ease the cost of production by zero assembly and installation of the hardware components and would achieve the detection for anywhere inside a house (whole-home detection) by wireless signal transmissions in line-of-sight, none-line-of-sight, and through-the-wall scenarios. The detection system broadcasts the wireless signals in a home environment, receives the reflected signals from the targeted person, and then computes the frequency of the target’s breathing over a period of detection. We expected that frequency plots would be uniform for a normal person but irregular for a patient with sleep apnea. One practical implication of performing such frequency analysis in the whole-home environment is that children’s health monitoring can still happen without parental interference.

During neurological development, waves of spontaneous activity propagate through structures in the central nervous system including the hindbrain, retina, hippocampus, and midbrain. The presence of waves of activity is essential for proper maturation of these structures and aids in cell path-finding, the establishment of synaptic connections, and the expression of mature firing properties of neurons. These waves initiate at pacemaker sites and electrical stimulation of those sites can produce waves comparable to those initiated spontaneously. In our research, we compare the excitability of the hippocampus to that of a known pacemaker site in the ventral cortex and a non-pacemaker site in the dorsal cortex. To do this, we use blunt glass electrodes to electrically stimulate a mouse brain slice preparation at P3 or P4 and determine the threshold of electrical stimulation that is necessary to evoke a wave of activity at various sites in the cortex. We have found that the threshold of the dorsal cortex is higher than that of the ventral cortex—a known pacemaker region—or that of the hippocampus. The hippocampus is a common initiation site for seizure activity. So, the finding that the hippocampus and pacemaker sites are similarly excitable may aid in developing a better understanding of temporal lobe epilepsy.

Prenatal Cocaine Exposure (PCE) can cause movement disorders and developmental problems in affected children. Statistic from Substance Abuse and Mental Health Services Administration stated that over 4% of pregnant women in the United States use illicit drugs, and up to 1% of pregnant women use cocaine. Investigations in the Bamford Lab have shown that PCE causes long-lasting abnormalities in corticostriatal activity. By using slice preparation techniques and Marianas imaging system, we quantify GABA interneuron density within the striatum in 30 and 60-day-old mice that are exposed to cocaine in utero. Lhx6-GFP BAC transgenic mice are used as they express enhanced green fluorescent protein (GFP) in the GABA interneurons which makes imaging analysis more precise and accurate. From our findings, we have found that there is a decreased population of GABA neurons in the striatum than wild type mice. PCE inhibits the tangential migration of GABA interneurons, which results in a reduction of GABAergic neurons within the striatum. The decreased GABA neurons may contribute to the structural and functional deficits in the exposed offsprings. This research will also help future studies to investigate changes in GABA interneuron complementing in the prenatal period, apoptosis, and changes in dendritic spine density in hopes for better understanding of the mechanisms and effects of prenatal drugs use.

Due to rapid mutation of the Hemagglutinin (HA) antigen, the current influenza vaccine only induces strain specific protection, requiring people to get vaccinated yearly. Hemagglutinin is the main glycoprotein on the surface of the influenza virus and consists of two main components, the variable head and the conserved stem. Previous studies have shown that vaccination with the conserved stem region of the HA antigen induces the production of broadly neutralizing antibodies, which are able to neutralize a broad spectrum of influenza sub-types. Therefore we designed a vaccine regimen in order to increase the effectiveness of our current DNA vaccination delivered by a gene gun to induce antibodies against the stem. We hypothesized that priming mice with the conserved stem region of the HA antigen followed by a boost with the full-length HA would lead to an increase in antibodies against the stem and the production of broadly neutralizing antibodies. Groups of mice were primed with either the conserved stem or the full-length HA and were boosted 6 weeks later with either full-length HA or the conserved stem. Two weeks after the boost, the mice were challenged with a lethal dose of a homologous or heterologous strain of influenza. Weight loss was monitored and blood was collected throughout the experiment. Neutralization and binding antibody assays were performed in order to compare the relative ability of each immunization regimen to induce antibodies against the HA head vs. stem.

UVC is ultraviolet light in the wavelengths 280 – 100nm. UVC’s germicidal ability has been employed to prevent forward contamination or the contamination of a pure planetary body with terrestrial organisms. Scientists have used UVC to sterilize equipment on land and water, but the effective dose of UV needed to prevent contamination when probing a pure ice environment is still unknown. In order to safely explore pure icy environments, data of bacterial response to UVC in ice are needed. To create these data, we began by irradiating Escherichia coli in liquid. Because there is a known decimation curve for this experiment, it served to standardize our irradiation set up and techniques. After obtaining a replicable decimation curve of Escherichia coli, we proceeded to irradiate a variety of psychrophilic, or cold-loving, bacteria in liquid. The psychrophilic bacteria tested were isolated from glacial ice samples and are therefore a better representation of possible contaminant in an icy environment. After establishing decimation curves for these bacteria in liquid, we began irradiating the same psychrophilic bacteria in thin ice samples. For both liquid and ice experiments, each sample of bacteria is assessed before and after irradiation using the Most Probable Number technique, or MPN. The MPN method uses serial dilutions of a sample bacterial culture until no colony forming bacteria are present to determine the concentration of bacteria present in the original sample. From our irradiations we will create curves of UV dose versus survival of bacteria in ice that will allow future equipment used in the exploration of pure ice environments to employ the correct dosage of UVC light to minimize forward contamination.

The budding yeast, Saccharomyces cerevisiae is a single-celled eukaryote that provides many advantages for use as a model organism, including the ease of genetic and environmental manipulation. The replicative lifespan assay is a commonly used method for quantifying the lifespan of yeast by measuring the number of times an individual mother cell can divide. My laboratory has found that yeast lacking genes encoding subunits of the vacuolar ATPase (V-ATPase) have an extremely short replicative lifespan. The V-ATPase is a multisubunit protein complex that pumps protons across membranes and acidifies intracellular organelles, such as the lysosome-like vacuole in yeast. Lysosomes are organelles in eukaryotic cells containing digestive enzymes that break down and digest macromolecules and waste products. Yeast provides an ideal model for the study of disruption of the V-ATPase as they are able to survive loss of this complex, which is essential in most other eukaryotes. Vma21 is a protein required for the assembly of the V0 subunit of the V-ATPase. I have observed that vma21 mutants are short-lived, have a respiratory growth defect, and are sensitive to low iron levels. My experimental model demonstrates that supplemental iron and antioxidants, such as sodium ascorbate (vitamin C), dramatically increase the shortened lifespan of vma21 mutants. Supplemental iron also rescues the respiratory defect of vma21 mutants. My data supports a model where loss of V-ATPase function results in disrupted iron homeostasis leading to loss of mitochondrial function and shortened lifepsan, which can be rescued by supplemental iron and antioxidants.

Wildfires that affect homes on the edge of the wildland urban interface (WUI) are becoming of increasing interest to homeowners, government agencies, and scientists. Some of the reasons for this elevated attention include: the substantial growth of home development of these areas in recent years, the buildup of fuels due to fire exclusion over the past 100 years, and the lack of fuel treatments in forested lands that transition to these at-risk home developments. The state of Washington has one of the fastest growing WUI in the nation. The Chumstick watershed near Leavenworth, WA is one such example of a wildland urban interface in fire-prone forests of Eastern Washington. This research project is investigating the 2013 Eagle Fire, which occurred in the Chumstick watershed and is seeking to determine how residents perceive the risk of fire to their homes and property, have taken any steps taken to prepare for wildfire, and view of current federal land management in areas adjacent to these residents. Fifty surveys will be sent to two groups of residents in order to compare and contrast differences in the readiness and opinions. One group will entail those whose property was directly affected by the Eagle Fire this past summer and the other will be landowners adjacent to current fuel treatments on Federal lands. This research has been aided by a partnership with the Chumstick Wildfire Stewardship Coalition; a local NGO whose goal is to promote a fire adapted community in the region by working directly with landowners and local politicians. The results from the questionnaire will aid in increasing the knowledge of how people manage their land in the WUI, perceptions of risk, and how they view current federal natural resources management in the area.

CT and MR imaging are widely used for the staging of a newly diagnosed H&N cancer, where treatment decision highly depends on imaging findings. Currently, there is no data regarding whether or not the TNM staging is routinely incorporated into radiology reports. We conducted a national survey to determine whether radiologists routinely address the staging, in particular regards to T (primary), and N (nodal). In addition, we explored the barriers to and perceived values of the reporting incorporating TNM staging among radiologists. A total 199 responses were submitted within a week (25.4% response rate). Over 60% of the responders were at an academic practice, having more than 8 years of experience. 73% of the responders were subspecialized in H&N radiology. Only 26% stated that they routinely assigned TNM staging in radiology reports. The most common barriers were a) unable to remember the staging classification (58%), b) afraid of inaccuracy (57%), followed by c) time consuming (46%), and d) not required (37%). All responders who assign TNM staging indicated that the reasons for such practice are a) believe in added values (31%) and b) help treatment decision (26%). 75% indicated they measure a primary tumor in three dimensions. Approximately half (49%) of the responders thought that incorporating TNM staging is important, 33% were neutral, and 17% thought it was not important.

 Acute myeloid leukemia (AML) is a blood cancer characterized by the failure of differentiation of white blood cells to their progeny (myeloid differentiation). MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression by targeting messenger RNAs (mRNAs) for degradation or translational repression. In cancer, miRNA expression is altered and these changes contribute to impaired differentiation. In previous work we examined over 600 miRNAs to establish which miRNAs could promote differentiation or limit growth of AML cells. This work identified that miR-150 expression induces myeloid differentiation and that miR-150 expression is decreased in many AML patients. Because transcription factors are important regulators of myeloid differentiation, we examined the transcriptional regulation of miR-150 in hematopoietic cells to determine how miR-150 expression is decreased. We identified the minimal promoter region of miR-150 using luciferase reporter assays in THP-1 (AML) and K562 (chronic myeloid leukemia) cell lines. We identified DNA binding sites for the Krüppel-like factor (KLF) family of transcription factors as necessary for miR-150 promoter activity using site-directed DNA mutagenesis of the luciferase reporters. The current study aims to identify which KLF isoforms regulate miR-150 expression. We cloned KLFs 2, 3, 4, 5, 6, 7, 9, and 10 into lentiviral expression vectors. KLF2 and KLF4 overexpression increases miR-150 expression as measured by luciferase assays and quantitative PCR in THP-1 and K562 cells. Furthermore, we confirmed published results that KLF2 and KLF4 promote myeloid differentiation of THP-1 cells using flow cytometry and gene expression studies. Previous studies have determined that KLF2 and KLF4 expression are decreased in AML cells. This loss contributes to pathogenesis; however how miRNAs contribute remains unknown. Consequently, determining how miR-150, KLF2, and KLF4 promote differentiation will provide insight as to how loss of KLFs contributes to leukemia and how we may use miRNAs to overcome block in differentiation therapeutically.

Liquid bipropellant rockets have numerous benefits in performance and safety compared to other chemical rockets, yet their propellants are often too toxic and difficult to handle for most researchers to utilize. Additionally, these rockets are often complex in design, increasing their cost and further discouraging their use. This research project is intended to help find a solution to these challenges by designing and testing a rocket engine that uses safer, environmentally-friendly propellants and a simplified injection design. A prototype rocket has been built and is in the process of being tested on a static test stand. Multiple propellant combinations are being researched to retrieve data on combustion temperature, combustion stability, and specific impulse (thrust per unit mass flow of propellant). The results will be used to determine which propellant combination is the most promising candidate for further research, eventually leading to a design for a simple liquid bipropellant engine for use by universities.

 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.

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.

Eutrophication, an excess of nutrients from anthropogenic sources, can lead to a range of environmental problems including hypoxia and loss of biodiversity. This study, a collaboration between University of Washington Tacoma and the Pacific Shellfish Institute, examined the potential of using mussel cultivation as a mitigation tool in eutrophic waters. Mussels are filter feeding bivalves that have the ability to remove nitrogen and other nutrients from the water through bioextraction. Artificial habitats similar to what is used in mussel farming were created in Budd Inlet Olympia, WA and in the Thea Foss Waterway Tacoma, WA to collect naturally occurring sets by the native bay mussel Mytilus trossulus. The purpose of this study is to determine the viability of mussels as a tool for remediation in Puget Sound by monitoring their growth, biomass and nutrient content. We are examining how various factors such as location, depth, time of deployment, and season affect a range of parameters, in order to create a set of best practices for future mitigation work. Next steps include the composting of resulting biomass, and analysis for pollution uptake within the mussels.

Ferrofluids are colloidal suspensions composed of iron based (Fe) particles with a diameter roughly 10 nanometers (nm) or less; these particles are dispersed in a carrier fluid containing a surfactant to prevent agglomeration. This fluid has the inherent ferromagnetic qualities of the metal particles, specifically the high magnetic permeability, and the very high thermal motion spin of a suspension fluid, resulting in a paramagnetic fluid attracted to applied magnetic fields. Since ferrofluids are influenced by applied magnetic fields, the particles are susceptible to increased friction as the relative particle velocity is reduced, thus causing an artificial increase in the viscosity which can be controlled through the strength of the magnetic field. Because of the refractive qualities and friction/flow control of ferrofluids, the specific viscosity measurements of fluids can be obtained through laser analysis. I present direct experimental verifications of Shliomis’ theory of ferrofluid magnetoviscosity using both gravimetric capillary viscometry and laser-pumped birefringent relaxation time.

Polymerases epsilon and delta are responsible for replicating the leading and lagging strands of DNA, respectively. Accurate DNA replication occurs through Watson-Crick base pairing catalyzed by the enzymes’ polymerase domains, and also through the action of the polymerases’ exonuclease (proofreading) domains. The exonuclease domain of polymerase epsilon (POLE) has recently been reported to be mutated in ~4% of sporadic colorectal cancers and is associated with a high frequency of clonal base substitutions throughout the tumor genome. We hypothesize that the extent of mutational heterogeneity within a tumor will be predictive of the likelihood of resistance to any given chemotherapeutic agent and that the mutational heterogeneity due to mutations in POLE may also allow us to clinically stratify patents.The ultimate goal of the project is to identify POLE mutations in a tumor tissue, if applicable, and to find the quantity of mutations to compare with normal tissue and tumor tissue without POLE. I will utilize the newly developed Duplex Sequencing methodology to identify mutations that are present in a small number of cells within a tumor. By independently tagging and sequencing each of the two strands of individual DNA duplexes, this approach greatly reduces the number of errors. As the two strands of DNA are complementary, true mutations should be found at the same position in both strands. I will first identify tumors carrying somatic POLE mutations and use Duplex Sequencing to quantify the subclonal mutational load. My research team and I expect that the extent of mutational heterogeneity will be greatly increased in tumors bearing POLE mutations due to its impairment of proofreading capacity. For the symposium, we hope to present the quantity of sequencing errors in each of the tissues listed above or at least explain the process if we fail to collect the results in time.

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.

The Missoula Floods were a series of cataclysmic floods resulting from glacial lake drainage during the last ice age. The floodwaters from Glacial Lake Missoula sculpted and transformed the Eastern Washington landscape, eroding the coulees and depositing huge quantities of sand, gravel, and boulders throughout the Columbia Basin. Flooding spanned a period of several thousand years, as indicated by several radiocarbon dates, interbedding of the flood deposits with those of the Bonneville Flood on the Snake River, and stratigraphic position of the deposits in relation to dated volcanic ashes. To improve the existing chronology, we are dating a number of Missoula Flood deposits and related glacial erratic boulders using cosmic-ray produced isotopes. We have measured concentrations of the radioactive isotope Beryllium-10, which have accumulated since final deposition in granite flood boulder samples from Ephrata, Priest Rapids, and Babcock Bench. Results are pending from analysis of several minimally eroded samples from the Waterville Plateau and Pateros. We plan to sample more glacial erratic boulders from atop Steamboat Rock to confirm that the calculated ages of the flood boulders are consistent with the glacial history of the Okanogan Lobe of the Cordilleran Ice Sheet, which controlled possible paths open to floodwaters.

In a country with constantly changing demographics - the non-Hispanic whites are predicted to lose their majority by 2043 (US News, 2013) - the world of academia has remained somewhat stagnant: in 2009, women made up 43% of full-time faculty while 75.5% were white, and in 2005, faculty of color makeup 17% of the total full-time faculty (Department of Education, 2009). Using data from the Faculty Network and Workload Study, which was collected in 2011 and is comprised of 766 faculty from a large Mid-West University in the United States, my research examines differences in the perceived fairness of tenure/promotion decisions and service assignment rotations in order to get a better understanding of the varying experiences within academia across race and gender. Findings show that under-represented groups (women and nonwhite faculty) perceive less fairness compared to white men. Some, but not all, of these differences are explained by network size (measured by the number of faculty in the department who the respondent identified as a friend or the number of other faculty members who identified the respondent as a friend), perceptions of the effectiveness of institutional policies, and workloads for service and teaching.

How has the lumber industry’s use of sawmills on Commencement Bay of Tacoma changed the physical and chemical environment? By exploring this question I had analyzed the use of sawmills near Commencement Bay made in the mid 1850’s and its consequences that had contributed to the present pollution and future conditions of the bay. The decisions made by lumber industrialists in the 1850’s to use sawmills near the bay had created environmental changes by creating organic pollution to Commencement Bay. Using Sanborn maps and the United States Geological Survey (USGS) topography to notice the geographical differences of the earliest recordings to the present contributing to environmental changes. In order to test the hypothesis of the ecological changes by the lumber industry’s use of sawmills near Commencement Bay, historical documents and images were analyzed to compare the geographical changes of the land before and after the lumberyards sawmills were built. The chemical changes to the waters of Commencement bay as a result of the sawmills were analyzed using scientific research articles and the Environmental Protection Agency database. In the study conducted in 2006 by Joel K. Elliott and colleagues sawdust sediments are feeding the bacteria and therefore the bacteria are producing high levels of sulfur content into the water creating chemical changes and bacterial mats in Commencement Bay. The researched results show tangible evidence of one of the factors that contributed to the changing environment of Commencement Bay. The new knowledge gained is that the connections of how the sawmills effected not only the physical environment of Commencement Bay but the chemical as well. In conclusion the sawmills had contributed to the changing geographical and chemical component of commencement bay. The ecological changes can be seen in the present and restoration work being conducted to restore it closer to its original state.

This project – an ongoing collaboration between the Emerging Capacities of Mass Participation (emCOMP) and Social Media (SoMe) Laboratories at UW – investigated the spread of misinformation during the Boston Marathon Bombings over Twitter, ultimately leveraging social media in crisis situations for communication, news reporting, and aid coordination efforts. Thus far we classified six rumors within the roughly twenty million tweet dataset, isolated several temporal “signatures” representative of certain kinds of rumors, and identified tweet characteristics (URLs and location data, for instance) associated with either misinformation or correction. We then further investigated the role of URLs and domains in the spread of misinformation, postulating that outside sources play a significant role in the development of temporal signatures. Finally, using a combination of rumor classification and machine learning, we began to create an application that automatically identifies misinformation in real time as it spreads.

Although highly-skilled women (with a bachelor's degree or above) currently migrate at a rate twice as men worldwide, women's experiences in these migration patterns, especially to the U.S., have been largely neglected in the literature. Research on the feminization of "brain drain" conducted in other countries, however, have displayed how women's gender identities can radically change from the sending to the receiving country, usually resulting in greater gender inequality within both the public and private spheres. Paradoxically, while highly-skilled Latin American women come to the U.S. in the largest numbers, no research to date has documented these women's perspectives within the context of this international movement. Thus, this project aims to explore the ways in which Mexican and Caribbean highly-skilled migrant women (re)formulate their gender identities in the workplace and household as a result of their relocation to the U.S. and, more specifically, to the greater Seattle area. The methods employed include semi-structured, in-depth interviews with 10-15 highly-skilled migrant women recruited through a standard socio-scientific snowball sample. It is anticipated that, much like the findings in previous studies on other demographic groups, the shifting social, economic, and cultural realities between the U.S. and these women's home countries have significantly impacted their gender identities; in other words, leading them to perform less productive labor and to adhere to more traditional feminine roles. This work will contribute to filling the knowledge gap on highly-skilled Latin American women within feminist migration studies, and may be used to inform policy surrounding skilled migration from the region.

The Large Synoptic Survey Telescope (LSST) will carry out an unprecedented imaging survey of half the sky. With about 1000 observations over a 10-year period, these data will enable faint time-domain astronomy. The measured properties of newly discovered and known astrometric and photometric transients will be publicly reported within 60 sec. Several hundred million variable objects will be detected and due to this large number their fast classification, that is a prerequisite for timely follow up with other facilities, will have to be undertaken using machine learning methods. Before selecting a subset of the most interesting variable objects for follow up observations, known types of variable stars, which will dominate the sample, will have to be efficiently recognized and classified. This project assesses the extent to which machine learning methods are able to recognize known classes of variable stars, and how this performance scales with the number of data points. A sample of 7,000 variable stars, manually classified by domain experts, served as our training sample. This dataset, collected by the LINEAR survey, contains all the major types of variable stars and has sufficiently precise and well-sampled observations for a detailed light curve analysis. Fourier series expansions allowed us to quantify these light curves, and asses various classification methods in the subsequent best-fit Fourier coefficient space. We explored this space using Support Vector Machines, K-nearest neighbor classifier and decision tree methods, and compared the performance of these methods via their Receiver Operating Characteristic curves.

Brasília, the capital of Brazil, was constructed primarily by a migrant labor force in the late 1950s. Brasília was intended to be a modernist utopia meant to transform Brazilian society for the better. The capital, which was planned for a maximum population of 500,000, now has nearly 2.8 million inhabitants. This growth can be attributed to consistently high rates of internal migration from Brazil’s rural areas. Over 80% of the Brazilian population now lives in urban areas of the country, compared to less than 40% at the time of Brasília’s construction in the 1950s. This influx of migrants has led to severe shortages in suitable housing, leading to a steady rise in the number of slums and squatter settlements across the country. While much research has been done on the impact of internal migration in Brazil’s two largest cities, São Paulo and Rio de Janeiro, comparatively little research has been done on Brasília. Through statistical and spatial analysis of Brazilian census data and with the help of geographic information systems software, this project builds a historical profile of internal migration to Brasília and examines changes in internal migration flows since the late 1950s. Additionally I analyze the spatial distribution of the migrant population around the metropolitan area of Brasília with an examination of the descriptive spatial statistics of the population in addition to an analysis of the residential segregation of both short-term (living in Brasília less than ten years) and long-term (more than ten years) migrants. Preliminary results suggest that, since the original construction of Brasília, internal migrants have consistently and overwhelmingly originated from states in Brazil’s impoverished northeast region and have usually settled in the outlying satellite cities of the Brasília metropolitan area.

While it is acknowledged that individuals of intersecting marginalized identities experience compounded prejudices, most of the research on intersecting identities has focused on the intersections of gender and race. In two studies, we seek to explore the intersection of weight and race on perceptions of American identity. This study builds on previous research findings that Asian Americans are perceived as less American than people of any other racial group. Furthermore, because Americans are stereotyped as overweight, we hypothesized that heavier Asian Americans would be perceived as more American and less likely to be in the US illegally than their thinner counterparts. Photos of Asian American and White American men were edited to create heavier and thinner versions of each man. University of Washington students viewed either a heavier or thinner version of one of the men and assessed his American identity and perceived documentation status. The heavier Asian American men were perceived as more American and less likely to be in the US without documentation than thinner versions of the same men. Weight did not influence perceptions of White men’s American identity or documentation status. These studies demonstrate that Asian Americans who gain weight may surprisingly be buffered from prejudice directed at those who are perceived as less American.

 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.

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.

Shortly after 9/11, the United States was faced with responding to an act of war by a non-state actor. On September 18th, 2001 Congress passed S.J.Res.23, the 2001 Authorization for the Use of Military Force (AUMF). After thirteen years of conflict, this seemingly perpetual state of war has proven to be counterproductive to the U.S. goal of defeating violent extremist ideologies both at home and abroad. What is needed is a paradigm shift in the way the U.S. fights terrorism. The end of this conflict will look like the adoption of a different counterterrorism strategy. This Task Force proposes an alternative approach to combating terrorism that does not rely on a continuous military strategy, which has come under much legal and ethical scrutiny both domestically and internationally. The initial topic of this project was the authorization for the use of military force (AUMF) and the use of drones as a weapon of war. After the research was underway, this project incorporated the legality of our current strategies, ethics, consequences, and alternatives to fighting extremist ideologies. This was a project of both basic academic research as well as applied research. We used government primary source documents (reports, hearings, bills, etc.), academic books, and scholarly journals. The project culminated in a 185-page analytic report and policy recommendations. The overarching recommendation of the report is that the U.S. needs to change its current counterrorism strategy. If it does not, it risks perpetuating the current conflict, creating new enemies, and establishing a dangerous legal and ethical precedent worldwide.

Exoplanets are planets outside our solar system. The discovery and characterization of exoplanet systems informs us of the types of worlds found in nature and whether they might support life. There have been an unprecedented number of exoplanet detections in recent years spurred in large part by the advanced observing capabilities of NASA’s Kepler Space Telescope. The Kepler Spacecraft continuously monitors a large, fixed set of stars and collects time series photometric data that are unparalleled in both quantity and precision. Plots of stellar brightness against time called lightcurves are the canonical representation of Kepler data. The goal of our research is to detect exoplanets from the characteristic features they produce in these lightcurves known as transits. A transit occurs when an orbiting planet partially eclipses its stellar host, reducing the brightness observed by the telescope and recorded in the lightcurve. To detect transits, we use the Quasi-Periodic Automated Transit Search Algorithm (QATS). As an automated tool, QATS is instrumental in reducing the effective size of the Kepler dataset. However, QATS is sensitive to variability of the target star and to systematic artifacts of the telescope just as it is to transits. Thus optimal detection efficiency requires removal of all non-transit signals prior to applying the algorithm. Determining the best way to do this is the present focus of our work because it bounds our ability to detect planets whose size, composition, and orbital parameters are conducive to life.

This project aims to develop an assay, using Illumina sequencing technology, that is more sensitive than current methods at detecting CXCR4-using HIV variants within a viral population. CCR5 and CXCR4 are co-receptors that can be used by HIV to gain entry into host cells. Whether or not a patient has CXCR4-using HIV variants determines the suitability of certain therapeutic drugs. For example, the drug Maraviroc may only select for these variants, without satisfactorily lowering the total viral load. Being able to detect low levels of CXCR4-using variants within a patient's viral population could therefore prove very useful, by providing information that helps guide patient treatment.

Calcium carbonate deposits precipitate in ocean sediments when biochemically-produced bicarbonate ions react with calcium ions in seawater. Bicarbonate is the product of a reaction that consumes methane derived from thermal and biological degradation of organic matter. In areas of the Washington margin where tectonic activity squeezes water and entrained methane up through the subseafloor sediments, methane flux is very high. During a research cruise on the Washington margin in August 2013, we discovered a field of unusually large carbonate deposits at a depth of approximately 1000 meters in close association with active methane seeps. As previous studies of carbonates in this area have been limited to dredge sampling, our study will be the first to utilize sonar mapping and in-situ photos acquired with remotely operated vehicle (ROV) Jason. In order to address questions regarding the spatial extent and formation of these carbonates, we will 1) assemble photomosaics from the ROV photos, 2) process multichannel seismic data to assess whether the methane driving the formation of our carbonates was transported though the sediments via linear faults, single vents, or diffuse venting, and 3) create a large-scale sonar map using both bathymetric and acoustic backscatter data of the area. Multichannel seismic data reveals faults and other subseafloor structures through interpretation of reflected seismic waves that travel through the sediment. Acoustic backscatter data provides us with an image of the seafloor through interpretations of reflected sonar waves. We are also attempting to date the growth of the carbonates by testing embedded mineral grains for the presence of volcanic ash from the Mazama volcanic eruption that occurred 6000+ years ago. With these four datasets, we anticipate gaining an understanding of how these carbonates formed and over what time scale, ultimately contributing to the growing geological knowledge of the Washington margin.

Hemophilia, a common genetically inherited blood disorder, is currently treated by infusion of clotting factors. However, protein infusion poses disadvantages due to high cost, pain on patient, and sometimes immune responses against infused proteins. In recent years, gene delivery using viral vectors has been developed as a promising alternative strategy for treating inherited diseases. Among the viral vectors, adeno-associated virus (AAV) is favorably studied due to its non-pathogenicity and persistence; however, the uptake of AAV by host cells can be inhibited by neutralizing antibodies (NAb) against vectors, and heparin, a molecule that competes with AAV for endocytosis. This project explores if sonoporation can help overcome these barriers and enhance AAV-mediated gene delivery. Therapeutic ultrasound and microbubbles can induce the formation of transient pores in the cell membrane to enhance the cellular uptake of gene carrier vectors. Our in vitro transfection experiments in 293T cells revealed that using ultrasound and microbubbles has potential to enhance the transduction efficiency of AAV by overcoming inhibition by NAb and heparin. Additional in vivo experiments will be performed to study the relationship between endocytosis and ultrasound-microbubble induced sonoporation. Ultimately, we hope to apply our understanding of this relationship to develop an ultrasound-facilitated method to achieve non-invasive, localized, and efficient AAV-mediated gene delivery for treating inherited diseases.

Defect characterization of a completed solar cell is an important and often tricky step of improving the efficiency of photovoltaic devices. There are many well documented and useful techniques that already exist for doing this. Examples of more prominent techniques include photocurrent vs voltage (JV) and External Quantum Efficiency (EQE) measurements. In general however when preforming these measurements the cell is taken to be homogenous over the area of the cell. Cells tend to be more and less efficient in certain regions however. Laser Beam Induced Current (LBIC) is a method where a local photocurrent is generated in the cell with a laser beam. Using this method of local excitation a high density LBIC map can be generated to give insight into the non-homogenous features of the cell by taking a large number of LBIC measurements and recording the XY position that each point was taken at. Depending on the wavelength of laser used to generate the LBIC map different layers of the cell may also be probed. LBIC can be used to figure out what layers, where in fabrication, and possible after-fabrication damages that lead to drops in efficiency in certain regions of the cell. This knowledge can be applied in future fabrications to increase the overall efficiency of the cell.

Pathways by which bacteria interact likely have a large effect on the bacterial communities that are present in the lungs of cystic fibrosis (CF) patients. CF is a genetic disorder that leads to an inability to clear out viscous secretions in the lungs, allowing bacteria to thrive. Pseudomonas aeruginosa (P. aeruginosa) is one of the most detrimental opportunistic pathogens infecting CF patients. The genome of P. aeruginosa encodes the type VI secretion system (T6SS), a toxin delivery system widely found in Gram-negative bacteria. P. aeruginosa outcompetes other organisms using the T6SS. Interestingly, P. aeruginosa targets more efficiently when the other organism has an active T6SS as well, suggesting that P. aeruginosa has a mechanism for sensing the activity of the T6SS in other organisms. The goal of this project is to find if this phenomenon is unique only to P. aeruginosa and whether it is dependent on the organism it is targeting. Another laboratory found that the threonine phosphorylation pathway (TPP), which is known to regulate the T6SS activity in P. aeruginosa, is required for T6SS-sensing. The TPP is only found in a subset of organisms with a T6SS, and I am characterizing which of these organisms exhibit this neighbor sensing behaviour. I hypothesize that this phenomenon is found in the group of organisms that have a TPP. Burkholderia cenocepacia, another bacterial species with a T6SS, is lacking the TPP, and I have found that it does not have T6SS-sensing ability. This suggests that not all T6SS positive organisms exhibit the sensing phenomenon. Additionally, I am investigating whether P. aeruginosa T6SS-sensing occurs with all recipient species. Since the T6SS is conserved among many Gram-negative bacteria, it is important to determine how widespread T6SS-sensing is, ultimately allowing us to better understand targeting among microbes in CF and other polymicrobial infections.

Race is generally talked about as discrete categories, such as “Black” or “White,” despite the growing multiracial population that challenges this notion of discrete racial categories. In a recent study, twice as many people categorized Obama as “Black” rather than “Multiracial” despite his multiracial heritage. However, categorization may be less distinct for age. As age changes over time, people may perceive age as existing on a continuum. Do people implicitly perceive age less categorically than race? To test this we digitally morphed a young face into an old face to create seven faces that systematically varied in degree of age, so as to depict a person who ages over time. Similarly we digitally morphed a characteristically black face into a characteristically white face to create seven faces that varied in degree of racially characteristic traits, as a spectrum of seven faces for race. Participants completed an implicit categorization task for both race and age, wherein people quickly identified if one of seven faces randomly presented was “the same as the last face.” We examined confusion patterns participants had for these faces as indicators of implicit categorization processes. If participants confused faces in the middle of the spectrum less than on either end of the spectrum, we inferred that there is a two-category representation for that spectrum of faces, with the category boundary lying between the two faces being least confused. Contrastedly, when all seven faces were confused at similar rates, we inferred that there was a less categorical, more continuous representation of the faces. We predicted that participants would implicitly perceive age less categorically than race. By determining how we perceive different social categories, this research is a first step in understanding how perceptions of social categories influences our behavior towards others.

Many vertebrate species are dependent on sensory input for normal brain development during what is known as the critical period during young life. Depriving sensory input during the critical period results in an increase of neuron death. Microglia are immune cells that have been shown to be closely associated with neurons and facilitate synapse trimming and other phage like behavior in response to cell damage and death. We hypothesize that inducing deafness in young mice will trigger neuron death and thus activate an immune response by the microglia. The present study was a comparative analysis of microglia activation in the anteroventral cochlear nucleus after induced deafness between neonatal and adult mice. We used a unique mouse model of deafness wherein the human diphtheria toxin receptor (DTR) was inserted behind a sensory hair cell specific promoter (Pou4f3). Both wild-type (WT) littermates and transgenic mice (DTR mice) were given injections of diphtheria toxin, either as neonates or adults resulting in complete deafness by 2 days post injection. Brainstem tissue was collected at several time points post-injection and fluorescent immunohistochemistry techniques were used to visualize microglia and neurons. Microglia were counted and microglia morphology was analyzed. There was a significant amount of neuron loss seen in the neonatally injected DTR mice compared to adult DTR mice and wild-type groups. Microglia increased in number in the neonatally injected DTR mice when compared to WT mice. There was also an increase in the number of microglia in the neonatal-injected mice compared to adult-injected DTR mice. The microglia in the neonatal injected mice also showed morphological changes transforming from a highly ramified cell shape to a rounder more amoeboid cell associated with microglia activation. These results suggest a role for microglia in determining the critical period of neuronal survival in the cochlear nucleus.

HIV-1 positive patients on antiretroviral therapy (ART) who agreed to donate their bodies to science are the sampling population for this study. All patients had low or undetectable virus levels in the blood at or near time of death. DNA was extracted from each of the patient tissues and then using nested PCR, envelope and polymerase genes from single viral templates were amplified and the sequences determined. We used this data to determine whether any tissues harbored virus reservoir- or compartment-like qualities. This is the study of patient HV00103 who had been treated ART for the last 4.5 years of his life and had a viral load of less than 50 cps/ml, indicating successful suppression of virus. Despite this control, he died of multiple organ failure. We found that large intestine seemed to exhibit reservoir like properties but more samples would need to be examined before any conclusive claims can be made. We also found that 80% of his HIV-infected cells were derived from the proliferation of a single cell, as evidenced by the identical viral sequences found throughout his tissues. This represents the most extreme example to date that infected cell proliferation is an important contributor to the persisting population of infected cells under ART.

Economic inequality in the US is the most unequal amongst all advanced economies in the world- and it is larger than we often perceive. In 2013 President Obama declared economic inequality as the “defining challenge of our time.” The problem now is that this “defining challenge” is growing. Currently, the top 1% own about 40% of the entire wealth in the US while the bottom 80% own about 8%. But who is influenced more by significant changes in the economy? Do the rich continue to grow richer even during periods of economic decline? With data collected from the Federal Reserve Survey of Consumer Finances, I compare the impact of the Great Recession on changes in wealth for different socioeconomic levels. I find that on average, individuals with lower incomes at the start of the recession saw greater declines in their wealth than individuals higher income, but the more assets individuals had, the more adversely the recession affected them.

Auxin is a major plant hormone, guiding phototropism, gravitropism, cell elongation, cell division, cell determination, and a host of other processes. One of the main mechanisms through which auxin acts is by triggering the expression of auxin-related genes. Under high auxin conditions auxin will act as molecular glue bringing together a co-receptor complex that consists of a repressor protein and a receptor protein. This triggers the ubiquitination and breakdown of the repressor protein allowing for the expression of auxin genes. Under low auxin conditions the repressor persists and auxin genes are blocked. In our model plant, Arabidopsis, there are 29 IAA (Indole Acetic Acid) repressor proteins and 6 receptor proteins. Previous works shows that degradation rates between IAA’s vary widely and that rate-motif sequences outside of the degron (the minimum region of the IAA required for degradation) accelerate or decelerate auxin-mediated degradation. The work presented here tested the hypothesis that the rate of repressor degradation is linked to the binding strength between the repressor and the receptor. A yeast-two-hybrid (Y2H) assay was used to test the binding strength between the TIR1 receptor and truncations and mutations of the IAA1 and IAA28 repressors. Combined with degradation rate data collected through flow cytometry, the Y2H data shows that mutations in the rate motif region of the IAA that change the degradation rate do not change the binding strength between the two proteins. This suggests that the rate motifs do not affect the strength of the IAA:TIR1 interaction and instead affect another aspect of the interaction.

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.

Research has shown that among alcohol dependent individuals, there is a positive correlation between stress and alcohol craving and that coping motives for drinking are associated with increased alcohol consumption and related problems. However, the relationship between drinking motives, stress, and alcohol cravings has not been investigated in undergraduates. We hypothesize that the more stress people report feeling and the more they endorse drinking to cope, the more they will crave alcohol and experience more alcohol-related problems. Participants (N=506; ages 18-20 and 1st or 2nd-year undergraduates) completed a web-based survey as a part of a larger study. Measures included self-report assessments of stress, coping motives for drinking, alcohol craving, and alcohol-related problems. Both coping motives and stress were significantly and positively related to alcohol related problems. Inconsistent with our hypotheses, stress was a better predictor of alcohol-related problems in people who reported lower (versus higher) coping motives. Coping motives were positively related to craving, but stress was not. Finally, coping motives and stress did not interact to predict alcohol craving. Thus, results were not as expected. These findings suggest that coping motives and stress do not interact to predict alcohol cravings or alcohol-related problems in first and second year undergraduates. Sample differences may account for these unexpected results –for example, nearly half of our sample did not drink alcohol in the last three months. Similarly, those in our sample who do drink may not drink as much, may not have drank for as many years, and/or may not have experienced the same level of negative consequences as published studies of alcohol dependent individuals.

 Previously, details on the angular diameter, age, reddening, and distance from the sun have been published for 60 open star clusters. This previous research mentioned the metallicity of these clusters, but no results were published with metallicity values. According to the Big Bang theory, the early universe contained mainly Hydrogen with small amounts of Helium. For heavier elements to form, fusion inside a stellar core must take place. When these stars die they then expel heavier elements, called ‘metals’ by astronomers, into space. These metals will then be present for the next generation of stars that forms. Therefore, if astronomers can derive the metallicity of a star they can figure out the relative age of that star. The University of Washington League of Astronomers club research group wrote a proposal to observe at the Dominion Astrophysical Observatory (DAO) in Victoria, Canada and received eight nights of time on DAO's 1.8 m telescope. We have obtained images of many of the target clusters using Strömgren filters. Observations using these filters will allow us to calculate the metallicity of stars within each of our target clusters. Ultimately, by determining the metallicity of a range of open star clusters within the plane of the Milky Way, we can help constrain the galaxy's metallicity gradient which gives us a better understanding of galactic formation and chemical evolution models.

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.

While better social support can lead to positive outcomes for caregivers of youth with chronic disease, less is known about the specific types of social support used, and what may drive caregiver preferences for these types of support. Our pilot study describes the type of social support used in 46 caregivers of youth with type 1 diabetes who were recently diagnosed (diagnosed longer than 6 months but less than 24 months) at Seattle Children’s Hospital. Interested caregivers signed informed consent and completed a social support survey. Categories of support included: in-person support group options, internet-based support, or a friend/family member with diabetes. In addition, they were asked to rank their top 3 sources of support. Of the 46 caregivers enrolled, 9 (20%) reported using in-person support groups. Caregivers who used in-person groups reported an average satisfaction score of 3.6/4.0. Of those who did not use in-person groups, the most frequently cited reasons included: I don’t know of any available groups (41%), too far (35%) and I have too much else going on (22%). Use of the internet-based support groups such as Facebook was reported by 23 (53%). The average satisfaction score for these was 3.5. Use of friends/family with diabetes for support was used by 19 (41%) with a satisfaction score of 3.7. In summary, internet-based support was the most widely used amongst the types of social support while the use of friends/family ranked the highest amongst the types of social support. All types of support seemed to be satisfactory. When asked to rank their types of support used, the top-cited sources of support were: local and national diabetes organization support (54.2%), family (37.0%) and Seattle Children’s (21.7%). Efforts should be made to better publicize sources of support as many reported not knowing about their availability.

These days many people use more than one computer. Students use computers at home, at the library, in class and more and they’re all different. We found it annoying how each computer we use has different settings than the one we are comfortable with. Our group wants to create a product that allows users to access any computer and have the exact same settings, software, placement of shortcuts, hotkeys, languages, browsing history, etc., as the one they use at home. Any change they make on any computer, as long as they are on their account, will have the same changes on any other computer they use when they log into the same account. With this product, even if their computer at home breaks down or does not work anymore, they can easily go onto another computer with their account and still have everything just the way it was on their own computer. We plan to do this somehow through cloud computing. We are still researching how this could be done and what others have done that are similar to what we are trying to accomplish. When we are done we want whole computer settings accessible through the internet on any computer for ease of use.

The purpose of this research is to propose architectural models and modeling guidelines of Device-to-Device (D2D) systems using LTE-A cellular network which has diverse and heterogeneous subsystems. Since a D2D system consists of four subsystems - Content, Platform, Network, and Terminal (CPNT), it is not easy for a D2D project participant to understand a legacy D2D system. For example, think of a mobile game app at a Google Store (Content) using Android operating system (Platform) on a Samsung mobile phone (Terminal) by using T-Mobile LET-A cellular network and its billing system (Network). Stakeholders of each subsystem need to understand both their own and others views. For this purpose, we select a legacy D2D mobile system and apply a re-documentation methodology called 5W1H Re-Doc to the system. The architectural model of each subsystem is used to help communications among the D2D project participants - D2D system will be much easier and efficient to understand. In addition, the guidelines of architecture modeling will help the participants to share high level abstractions of the D2D system.

My research uses the Italian state to address the consequences that historic regionalism have on political performance. I examine the effects of historic regional identities that have led to a political climate wherein regional schisms hinder Italy’s political performance by limiting political efficiency and democracy. Using historical comparative research methods I evaluated a variety of archival data and secondary sources from various historical accounts to quantify the existence of regional disparities. Then I examined Italy’s modern state performance via two qualities: efficiency and democracy. Political efficiency and democracy are important factors in measuring political performance as they relate to state effectiveness and popular representation. Strong regional identities and disparities are correlated to a lack of political efficiency and democracy in the case of Italy. The Italian case study is then contextualized, as I compare the historical rates of regionalism and contemporary political performance in a handful of other Western European states. With further research regarding the relationship between regionalism and political performance, broader conclusions may be made about present and future state performance by examining historic regional divergences.

Clonal evolution is a key feature of cancer progression and relapse. As cancers progress they accumulate large numbers of mutations. Some of these mutations are present in all of cells (clonal mutations) and drive the malignant progress. We will ask if there are other mutations that are present in only a subset of cells within tumors; as the environment changes during therapy these could become new driver mutations and could be the source of resistance to therapy. The subclones with the best evolutionary fitness will, in time, come to dominate the cancer cell population. Studying the number and identity of subclonal mutations may help us to predict whether or not a tumor has potential resistance to different drugs. Our hypothesis is that the large amount of subclonal mutations within a cancer will increase the overall fitness of the tumor, by providing a greater diversity from which new phenotypes can arise. We will modify the newly developed sequencing methodology, termed Duplex Sequencing, to identify specific subclonal mutations present in colorectal cancers. By adding a barcoded, partially non-complementary adapters to both ends of an individual DNA molecules which allow mutations in both strands of a DNA duplex to be identified, this approach greatly reduces sequencing errors. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors result in mutations in only one strand and can thus be identified as technical error. We believe that most colorectal cancers will have a complex subclonal structure and may show clusters of subclonal variants, including subclonal driver mutations. Furthermore, presence of a subclonal driver mutation may be an independent risk factor for disease progression. Our study will thus uncover patterns of mutational evolution in colorectal cancer, providing insights into its stepwise clonal evolution.

Magnetohydrodynamic (MHD) propulsion uses water, electricity and magnets to create thrust.  The importance of MHD drives is that they require no moving parts, allowing for less energy loss due to friction as well as silent propulsion.  The MHD engine works by creating thrust when an electric current is run through a liquid or plasma in the presence of a magnetic field.  The interaction between the electrons in the medium and the electric field draws water in one end and expels it out the other, creating thrust.  Our project seeks to optimize the thrust of a MHD system in a saltwater solution so it is a viable replacement engine for a water craft.  We present here our design of a novel closed-circuit MHD-engine testing apparatus that allows for real-time varying of magnetic field strength and engine geometry in order to achieve optimal thrust configurations for a given MHD engine design.

The system developed uses sensor feedback to control vehicle window position with the built in power window system. Sensors are placed in strategic locations to allow the system to monitor both window position and to detect rain. When rain has been sensed, the windows will automatically close to protect the interior of the car. While closing, a feedback loop monitors for blockages in the window to ensure there are no obstructions present. When an obstruction has been found the window will reverse direction to free it. System control is managed by an Arduino UNO microcontroller platform. The rain sensor is a digital output resistive controlled sensor while the window position sensor is a toggle switch digital output sensor. Window obstruction are sensed by a current sensor placed in series with the window motor. The Arduino is continually testing the feedback signals provided by the various sensors and when the conditions to close have been detected, the Arduino sends control signals to the MOSFET H-Bridge controlling the window regulator. While closing, motor current is fed back to the Arduino to monitor for blockages which present as an over current. The H-Bridge MOSFET allows for bi-directional motor control, giving the Arduino the ability to open the window when a blockage has been detected by reversing the motor terminal polarity, thus adding to system safety. Utilizing sensors and a microcontroller, a control system has been shown to effectively regulate vehicle position based on precipitation level. Multiple feedback sensors allow for effective rain detection, window position and blockage detection. This provides the microcontroller with robust detection abilities to appropriately control window positions and increase safety by detecting blockages. Motor control through an H-Bridge configuration gives bi-directional control, further increasing system flexibility and safety.

Chronic graft-versus-host disease (cGVHD) is a frequent complication of bone marrow and hematopoietic stem cell transplants and one of the leading causes of death in patients who receive such treatments. cGVHD arises as a consequence of incompatibilities between the donor and host immune systems, including disparites between donor and host major histocompatibility antigens (mHA). Donor CD8 T cells, which are responsible for distinguishing self and non-self tissue, contribute to cGVHD development through recognition of mismatched mHA and MHC (major histocompatibility complex, a protein responsible for recognition of foreign antigens in the body) molecules. This results in subsequent destruction of host tissue and cGVHD onset. In the female-to-male transplant environment, an immune response to certain peptide fragments derived from the Y chromosomes, called H-Y antigens, correlates with an increased risk and severity of cGVHD. Less is known, however, about the nature of the T cell receptor (TCR) repertoire responsible for the reaction to H-Y antigens. This project examines the TCR repertoire of cells reactive to an H-Y antigen derived from the Y-chromosomal protein KDM5D, an antigen known to increase the risk of cGVHD. Cells were cultured in the presence of peptide, sorted to generate monoclonal cell lines, and Sanger sequenced in order to determine the exact nucleotide sequence responsible for TCR expression in order to catalog TCR sequences and look for patterns in the CD8 response to KDM5D. Five separate CD8 cell lines have been successfully established, of which one’s TCR genes have been sequenced. While still in progress, the work completed thus far on this project demonstrates the viability of the methods used; alternative strategies may yield more comprehensive results faster. Completion of this and similar projects promises to inform new efforts in the diagnosis and management of cGVHD.

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.

Understanding the relationship between student engagement and academic motivation is important when considering the experience of undergraduate students. We hypothesized that the more students engaged with the university, the more motivated they would be. Participants were invited via class appeals and Facebook posts to complete an online survey on SurveyMonkey. Eighty-three participants fully completed the National Survey for Student Engagement (NSSE), the Academic Motivation Scale (Wabash University, 2009), and demographic questions (major, gender, cumulative GPA, year in school, and graduation date). Regression analyses showed four subfactors of engagement to be significantly related to motivation. The first three subfactors fall under the NSSE’s theme “Academic Challenge,” while student-faculty interaction falls under the theme “Experiences with Faculty.” Thus, those who were engaged academically and with professors were more academically motivated. The findings may have implications for how universities engage and retain students, and the effectiveness of programs used to motivate students academically.

High school students doing college-level coursework by participating in specialized programs, such as Running Start, can be put under large amounts of stress. It was hypothesized that as stress increases, health will, in turn, decrease and that there is a significant correlation between perceived stress levels and health. Surveys were designed for voluntary participants to report stress, health, and overall well-being through a series of questions where the participants ranked their levels on a Likert scale. The surveys were implemented 6 times throughout the quarter to help identify trends in perceptions of stress as the quarter progresses with correlations to changes in lifestyle, sense of self, and overall health. However, this data set is limited. Because of the relatively small population size studied within a limited period of time, one restriction was identifying specific stress factors for each individual. Whether or not this kind of stress is harmful to teenagers undergoing rigorous course loads is not yet clear.

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.

Theoretical descriptions of nature often depend on perturbative approaches that seldom extend beyond linearized approximations, and this translates to a large body of our understanding of physical systems ranging from cosmology, to nonequilibrium chemical processes, to aerospace control systems being only poorly understood. Our research focuses on the question of the extent to which computational simulations of nonlinear systems is experimentally verifiable. Here we use a quantitative measure of computational vs. experimental agreement called the horizon time and demonstrate its use through direct comparison of theoretical, computational and experimental modes of analysis using a damped, coupled physical pendulum apparatus, and specially developed data acquisition and analysis software. We find that a strong sensitivity of initial conditions, shown in the Lyapunov exponents, causes a rapid divergence between nearby trajectories within a tolerance range for experimentally observed motion which limits the horizon time to between 0.9 and 4.3 seconds before our trajectories can no longer be distinguished. By creating our own modified horizon time definition for use in a characteristic state space of known dimensions, we can only predict up to 1.3 seconds of motion before the trajectories cannot be distinguished. This small temporal resolution severely limits how effectively our theory can function as a description of experimental motion.

This study tests environmental field samples for markers of chemical contamination to show how pollution has affected our environment. EPA regulatory methods for inorganics, volatiles, and semi-volatiles were performed on environmental field samples in order to designate contamination. Methods include several stages of analysis. Inorganic methods were used to monitor sites of storm water runoff to ensure no pollutants are leaking into the environment. These include conductivity, turbidity, and total suspended solids analyses. Volatile methods were performed to ensure no gasoline leaked from various underground gas storage tanks. Finally, semi-volatile procedures were conducted to ensure no oil contamination has affected the environment from oil spills or leaking oil on pavements. Results were positive for chemical compounds that leaked into the environment and therefore caused contamination; including BTEX, a common compound found in gasoline, 8270, common compounds found in oil spills, and turbidity. Based on these results, sites have either been shut-down or marked for clean-up by the EPA. These projects can vary from ecological restoration to satisfying regulations for the clean-up of abandoned military installations. For instance, a military site may leave behind an unknown drum of waste and therefore needs it tested for compounds before disposal. The purpose of this research was to gain insight on the methods used for these types of environmental clean-ups. Further investigation of this topic can include how the implications of CO2 emissions are affecting the ozone and how nitrates leaking into the environment are affecting native fish populations.

Giant low surface brightness galaxies (GLSB) are a class of spiral galaxies with larger and fainter disks than typical spirals. Previous theoretical work suggests that their formation history is distinct from that of normal spiral galaxies. Two main theoretical models for GLSB formation have been proposed. One possibility is that they begin as ordinary spirals and undergo a face-on impact with a small satellite, creating a compression wave (i.e., a collisional ring) which excites star formation throughout the neutral hydrogen disk and results in a large, faint stellar disk. A competing possibility is that GLSBs begin as elliptical galaxies or normal spirals and acquire disks through tidal disruption and accretion of a satellite galaxy. Preliminary investigation of these objects has shown that they possess bulges which are morphologically and photometrically similar to typical elliptical galaxies, suggesting that the GLSB disks could be the remnants of a satellite accretion event. Using the Apache Point Observatory, we have obtained longslit spectra of the central bulges of two GLSBs, Malin 2 and UGC 6614. Combining these data with spatially resolved spectra of the disks taken at the McDonald Observatory allows us to compare the disk and bulge kinematics and distinguish between the possible formation scenarios. Our analysis reveals that disk and bulge kinematics are closely correlated in both targets, which is consistent with both possibilities but may favor the collisional ring galaxy scenario.

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.

Our understanding of our own galaxy and those at great distances hinges on how well we can model the complex processes by which stars form and evolve. The best laboratories in which to test our predictions are star clusters - groups of stars which by assumption formed at the same time. The nearby Andromeda galaxy (M31) is a fantastic source of clusters with similar chemical properties to our galaxy, at a variety of ages, and close enough to be resolved into individual bright stars by space telescopes. However, distinguishing cluster members from other field stars is a difficult problem. We have developed a method to assign a cluster membership probability to a given star by comparison with the density profile and properties of the cluster. We apply this method to a sample of well-characterized clusters observed by the Panchromatic Hubble Andromeda Treasury (PHAT) program, which has provided Hubble-based photometry of unprecedented depth in the M31 disk. As a first application, we study a subset of clusters associated with evolved stars that are known to be Cepheid variables - a class of pulsating supergiant star to which stellar models can provide a precise age. We demonstrate the accuracy of the method and characterize this newly identified population of M31 cluster Cepheids. We extend this method to the entire PHAT cluster sample, seeking to establish cluster membership of bright supergiant, horizontal branch, and AGB stars therein. The unprecedented size and quality of this sample of M31 clusters will allow us to test existing models of these important stages of stellar evolution.

Until the launch of NASA’s Kepler mission in 2009, the existence of rocky, Earth-like planets orbiting stars other than our Sun was uncertain. In the 5 years since its launch, the mission identified a wellspring of thousands of planets. We now know that planets around other stars are the rule, rather than the exception. One of the most interesting and surprising discoveries emergent from Kepler is that planets are not most common around Sun-like stars. Rather, they reside most often around small stars known as M dwarfs. These stars are cool, with effective stellar temperatures of 2000-4000 K, and are significantly smaller than our sun. Despite their diminutive stature, they are also the common stars in the universe, and the hardest to characterize. We understand the planets orbiting these stars only as a well as we understand the stars themselves. To this end, for our project we seek to refine our knowledge of the temperatures and radii of a select group of M dwarf host stars of interesting exoplanets identified with the Kepler Space Telescope. We employ dozens of near-infrared spectra gathered at the 3.5 meter telescope at Apache Point Observatory in New Mexico to study these planet hosts. We will leverage features in the near-infrared portion of these stars' spectra to understand their physical properties. The radius and temperature of the star will then tell us more about the possibly terrestrial planets they are hosting, and whether they reside in their stars’ habitable zones.

On a day-to-day basis, animals are faced with many decisions concerning survival. Among such decisions, animals must sometimes choose between a small, immediately available reward and a larger delayed reward. When both the large and small rewards are available immediately, animals across species consistently select the large reward. However, as the delay to the large reward increases, their preference for the large reward decreases, suggesting that the value of the large reward is ‘discounted’ by the delay preceding it. While this phenomenon, called delay discounting, has been well characterized behaviorally, less is known about the neural mechanisms that underlie the behavior. Specifically, the role of the central cholinergic system has only just begun to be explored. A recent rodent study demonstrated that systemic administration of muscarinic acetylcholine receptor antagonists (scopolamine and atropine) caused animals to exhibit reduced preference for the large, delayed reward-increased discounting behavior. While that result suggests the cholinergic system is important for normal delay discounting, it doesn’t pinpoint essential cholinergic sources. Therefore, in this study, we were interested in determining the necessity of a major cholinergic center providing output of acetylcholine to the cortex, the nucleus basalis magnocellularis (nbm), to normal delay discounting behavior in rats. To test this, rats were surgically implanted with bilateral cannula targeting the nbm prior to training in a delayed discounting task. The task consisted of a series of choices between a small reward available immediately and a large reward available after some delay (systematically increased throughout the session). Once stable performance was achieved, we injected a mixture of GABA_A (musicmol) and GABA_B (baclofen) agonists in order to reversibly inactivate the nbm. Preliminary results show that inactivation of the nbm increases delay discounting behavior and suggests that the nbm and its cholinergic output are necessary for normal discounting behavior.

 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 Elwha River dam removal project is the largest such project carried out in the U.S., and offers a unique opportunity to study the effects of a sudden sediment flux from the river to the coastal environment. A huge amount of new littoral sediment has accumulated at the river mouth since the start of dam removal in 2011; however, it is unknown whether it will migrate eastward and accrete on the chronically eroding beaches, and on what timescales this will occur. In this study, grain-size data and beach elevation profiles were collected along three shore-perpendicular transects east of the river mouth in early March, and again for three consecutive days in mid-April, with the goal of observing short-term changes. Physical sediment samples were collected for grain-size analysis and CobbleCam autocorrelation was used to obtain mean grain size from digital photographs. Beach profiles were constructed for these periods of spring tides and large waves. Results indicate that the upper foreshore of the transect farthest from the river mouth (Line 198) lost 0.38 m of elevation between the two study periods, and the lower foreshore gained 0.41 m elevation. In addition, slope breaks on all transects migrated in the off-shore direction, and foreshore sediments coarsened, both temporally (during the three-day April sampling period) and spatially (down the foreshore). These results demonstrate that daily changes can occur on the Elwha beaches. This study adds to our understanding of how new sediments will influence this region, and possibly of mixed grain-size beach dynamics in general.

Light of a single wavelength looks yellow on a black background and looks brown on a white background. Through simultaneous color contrast and context, adding white stimuli to a black background can also induce brownness in the test light. Along with this change from yellow to brown is a shift in the proportion of red and green lights needed to produce balanced brown compared to balanced yellow. These perceptual changes reveal differences in neural processing for bright vs. dark colors. The purpose of this study is to discover how the amount and spatial distribution of white light influences both the strength of brown and the red-green balance of a test stimulus. It is hypothesized that the larger the area of white and the closer the white is to the test, the stronger the effects will be. To measure these effects, observers make red/green balance settings for the yellow/brown test stimuli and set the test stimulus to the highest luminance level at which it appears purely brown. To test the hypothesis, I varied the spatial dimensions of two types of stimuli surrounding a 2°-diameter test disk on a black background: thin rings consisted of a 0.1° white ring surrounding the test at distances from 0° to 0.75°; and segmented rings consisted of a 5° diameter ring split into 2, 4 and 8 segments with different ratios of white:black, at 1° or 0.25° away from the test stimulus. Preliminary results indicate that the strength of brown and shift in red/green balance are influenced primarily by the total amount of surrounding white and not by the proximity of the thin rings, nor the number of white segments. These results improve our understanding of the perceptual and neural processing of brown in a complex environment.

Street signs, traffic lights, and maps are the predominant navigational cues in society, each being inherently visual. When navigating through pedestrian areas that only provide these cues, people with visual impairments can experience disability. This study proposes the design of a drone for navigation, or NavDrone, a pocket-size, pilotless, and autonomous aircraft that will provide visual description of navigational cues. By creating access to visual information in the environment, the proposed NavDrone can assist people with visual impairments in navigating unfamiliar areas. The NavDrone can be used in place of or in addition to common navigation aids, such as guide dogs and white canes. We conducted a study using Value-Sensitive Design methodology, a technique that incorporates the analysis of human values throughout the design process. The purpose of this study was to investigate how the NavDrone can support the human values of autonomy, access, and safety by providing GPS navigation, auditory feedback and control, visual descriptions, and fine-grained obstacle detection. We conducted a stakeholder analysis and considered the values at stake for users and bystanders of a NavDrone in a public place. We conducted a survey with visually impaired stakeholders to gain an understanding of the value tensions that might arise when relying on a NavDrone to navigate in an unfamiliar public place. In our survey, we prompted stakeholders to reflect on a value scenario and to describe the types of information and strategies that they would use to navigate in an unfamiliar environment. We analyzed the data to find themes and underlying values that informed the technical specifications for the design of a NavDrone. Finally, we reflected on how the values of autonomy, access, and safety are implicated in the design of a NavDrone and how they might be implicated in other assistive drones for people who experience disability.

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.

As renewable energy constitutes a greater portion of the generation fleet, so does the importance of modeling uncertainty as part of integration studies. In pursuit of optimal system operations, it is important to capture not only the definitive behavior of power plants but also the risks associated with system wide interactions. Load forecasting is an area of renewable energy integration studies that is often neglected, chiefly because of a lack of available data. In this research, the dependence of load forecast errors on external predictor variables such as temperature, day type, and time of day was examined. The analysis was utilized to create statistically relevant instances of sequential load forecasts with only a time series of historic, measured load available. The creation of such load forecasts relies on Bayesian techniques for informing and updating the model, thus providing a basis for networked and adaptive load forecast models in future operational applications.

After removing the Elwha dam, sediments were exposed which pose a challenge for revegetation, due to lack of nutrients and organic matter. Ectomycorrhizal fungi (EMF) are known to facilitate uptake of nutrients and water and therefore effective colonization of seedlings would be expected to promote seedling establishment, survival and growth. Seedlings were planted in nursery potting soil mixed with local forest soil, compared to potting soil alone, to determine whether this practice will promote colonization and diversity of EMF on Abies grandis (grand fir) and Pseudotsuga menziesii (Douglas-fir) seedlings before outplanting at the Elwha restoration site. EMF species will be identified by examining morphology and then, for each morphotype, DNA extraction, PCR using ITS-1F and ITS-4 primers, and sequence analysis will be used to compare sequences to published fungal sequences using the BLAST algorithm. While molecular analyses are not yet complete, preliminary analysis of morphotypes revealed a consistent trend of increased diversity due to inoculation, based on an increased number of unique morphotypes per seedling, from 3.8 to 4.5 for grand fir, which was not significant, and from 4.2 to 5.6 for Douglas-fir, which was weakly significant (2 tailed t-test, p=0.093). This suggests that pre-inoculation with forest soil may promote colonization and therefore aid in restoration efforts.

A major public health aim is to effectively intervene with college students who are irresponsibly using alcohol. Defensiveness is a response that is often associated with this kind of behavior change intervention, and evidence suggests that mitigating a student’s defensiveness during this process can help increase the effectiveness of the alcohol intervention. This is a notion that is of great interest to university administrators, however it remains unclear how to best approach such students in order to minimize their defensiveness. In addition, it is also unknown with what accuracy students perceive the intentions of the alcohol intervention process, which is another factor that may contribute to their defensiveness towards an intervention. The purpose of this study was to investigate two factors that may contribute to a student's defensiveness towards the intervention process: the way in which they are approached when they violate alcohol policy on campus, and how accurately they understand alcohol policy and the consequences associated with violating it. Twenty five University of Washington students were interviewed to collect this qualitative data. Participants’ quantity and frequency of alcohol use over 28 days was also collected in order to observe if levels of alcohol consumption was related to different opinions on the topics of interest. Content analysis was used for identifying themes present in participants' interview responses, while participants' alcohol use data was analyzed with descriptive statistics. 

We analyzed therapists' skill at delivering Cognitive Behavioral Therapy (CBT) before and after receiving an evidence based statewide training and consultation program called CBT-Plus. Specifically, we observed how therapists' attitudes toward general evidence based practice (EBP) prior to the training affected their performance--operationalized as their score on a mock therapy session (role play)-- throughout the study. People's attitudes can have a direct impact on all types and aspects of performance. Examining this relationship in CBT-Plus will allow us to address the topic of attitude in future training practices and improve the implementation process of the treatment. Therapists who started the training with a negative attitude performed overall lower on the role plays than therapists who started with a more positive attitude. These therapists also show less improvement in skill over time. A more positive attitude towards the treatment prior to training leads to higher skill due to higher commitment to training practices. To compare the therapists based on attitude, we sorted them into low, medium, or high attitude groups based from infromation from baseline questionaires. For each group, we collected their role play scores across three different time points (before, right after, and six months after training). We compared the groups for any significant differences in overall performance scores and improvement. If personal ideas and attitudes surrounding EBP are shown to have an effect on performance when providing treatment, more attention should be given to improving therapists' perception of CBT-Plus through education. 

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.

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.

A prosthetic liner is a sleeve that wraps around the residual limb of an amputee and couples the limb to a prosthetic socket.  The inner surface is an elastomeric gel that is in contact with the skin, and the outer surface is a fabric support.  Lower limb amputees must support their body weight on tissues which were not suited for high stresses, and the liner plays an important role in how ambulatory loads are distributed.  Quantitative data on the properties of liners is limited, so a clinical prosthetist's knowledge is confined to insight gained during practical experience.  The goal of this project is to create an online tool, the Prosthetic Liner Assistant (PLA), which will provide engineering data in a clinically accessible format.  Twenty new and ten used liners from six manufacturers were tested.  The material properties of the liners were quantified using six different material tests that measured the compressive elasticity, bulk elasticity, shear elasticity, tensile elasticity, coefficient of friction, and thermal conductivity.  Across all liners, gel material determined the shear elasticity and coefficient of friction, while the fabric backing had a strong influence over the tensile elasticity.  The gel and fabric backing contributed more equally to the free compression response of the liners.  As liners aged, the gels became softer while the fabrics became stiffer.  This was seen in decreased shear and compressive elasticity, and an increased tensile elasticity.  The PLA is published online at www.LinerAssist.org.  Differences between liners can be unclear, but the Prosthetic Liner Assistant will potentially allow a better fit for patients by quantifying the physical properties of liners, providing evidence for prosthetists to improve the quality of patient care.

With the increasing application of electromyography (EMG) sensor systems (method to measure electric potential generated during muscle contraction) in automation and robotics control, investigations on an effective user-interface are essential. My goal is to investigate solutions that enable valid communications between users and a system under complex sensor behaviors. If a user is unable to complete a motion or to continuously generate the proper control signal, the interface detects the desired signal and reproduces the intended result. There are two components in this research: (i) finding the behaviors of EMG signal, which determines the way users interact with the system, and (ii) adjusting or approximating the output to an ideal signal through visual feedback. To address the first task, I have processed the EMG sensor signal by implementing an analog and digital filter system to achieve a reliable EMG signal. Towards this, I created a LabView program to generate a signal of a desired function (e.g. Asin(ωt+φ)), by detecting the magnitude, frequency, and phase information of the input signal. Currently, my signal generation program works with a sinusoidal waveform in the presence of noise. However, physical EMG signals are not perfect sinusoidal waves. Using my program, the interface between the human-generated EMG signal and the computer generated result can be explored, with the goal of using EMG signals to control the computer generated signals. This will be accomplished by modifying the detection algorithm developed for the sinusoidal inputs.

Glucose and glutamine are primary carbon sources for cells to produce biomolecules and energy. Increased aerobic glycolysis, de novo fatty acid synthesis (FAS), and glutaminolysis are hallmarks of cancer cell metabolism and many tumors are dependent upon these for their survival. Likewise, virally infected cells also have considerably altered metabolic requirements. Our lab studies Kaposi’s Sarcoma Herpes Virus (KSHV), the etiologic agent of Kaposi’s Sarcoma (KS). KS is the most common tumor found in AIDS patients. Previous work from our lab showed that latent KSHV infected endothelial cells also require increased aerobic glycolysis and FAS. Our lab also published a global metabolic analysis of latent KSHV infection, revealing that latent KSHV infection also induces increased glutamine levels. Exogenous glutamine is metabolized through Glutaminolysis; glutamine is converted to glutamate and alpha-ketoglurarate (αKG) through two key enzymes, glutaminase (GLS) and glutamate dehydrogenase (GDH). Further, αKG can enter the tricarboxylic acid cycle (TCA) and support ATP production. Cancer cells utilize glutamine to replenish the TCA cycle when glucose is primarily used to produce lactate and fatty acids. Preliminary data shows that exogenous glutamine is required for latent KSHV infection through starving infected endothelial cells of glutamine. While glutamine starvation does not reduce viability of mock-infected endothelial cells, the absence of glutamine leads to significant cell death in KSHV infected cells. I hypothesize that glutamine is required during latent KSHV infection to replenish the TCA cycle. To study this, I inhibited glutaminolysis using a compound called BPTES, an inhibitor of GLS. Inhibiting glutaminolysis also leads to significant cell death of KSHV infected cells. This data indicates that glutamine is required during latent KSHV infection to replenish the TCA cycle. In the future I will add back TCA cycle intermediates to rescue cell death. Through our metabolomics studies of latent KSHV infection, we are identifying potential targets for KS therapy.

Beta-phase gallium oxide (β-Ga2O3) is a transparent conducting oxide that is well suited to ultraviolet photovoltaics. An interesting feature of single crystal β-Ga2O3 is that channels form in the b-direction that exhibit higher charge mobility than the a- and c-directions. We confirmed this uniaxial anisotropy using ellipsometry, indicating that the optical constants in the a- and c-direction are comparable to each other and differ from the b-direction. We then produced a device by depositing a transparent palladium layer as the top contact and a titanium/palladium layer as the back contact on the single crystal. Current-voltage measurements were taken in both the a- and b-directions under bias and over a range of incident photon energies to determine the effectiveness of this design as a photodetector. The next step is to construct the same device using polycrystalline thin film β-Ga2O3.

For many practitioners within the field of dentistry, providing local anesthesia that is both effective and comfortable for the patient is a challenging art that requires great skill and the right product. Nonetheless, unsuccessful local anesthesia can oftentimes leave the patient in discomfort and the administrator waiting periods of time before a local anesthetic effects appears. Addressing these complications, this review of past and present literature examines reasons for which traditional local anesthetic products and techniques within dentistry can fail and assesses possible solutions to these failures. Findings suggest that some anesthetic agents may be less effective than others with respect to onset time, duration, and relative strength. Products with lower concentrations, fat solubility, and proportions of HCl and vasoconstrictor (e.g epinephrine), tend to produce slower, weaker, and shorter-lived effects. In addition to ineffective anesthetic agents, local anesthesia in dentistry can also fail by means of anatomical and technical intricacies such as the impermeability of the dense cortical bone in the mandible (lower jaw), and the inability of administrators to successfully perform nerve blocks such as the inferior alveolar nerve block (IANB). In assessing these failures, the results of this literature review support the use of bupivacaine with HCl and 100:000 epinephrine for a quick, strong, and long lasting effect, as well as the use of intraosseous anesthesia, a technique that delivers the local anesthetic solution directly into the cortical bone, as an effective primary anesthetic technique for procedures involving one to two teeth. Compared to traditional local anesthesia injection techniques, recent studies accredit intraosseous anesthesia with high success rates, easy administration, fast onset times, strong effects, and significant patient comfort. When performing local anesthesia in dentistry, patient comfort during and after administration is imperative. The results of this study indicate that intraosseous anesthesia attains this objective. 

Previous literature has illustrated that Asian culture emphasizes interdependence, family assistance, and fulfillment of social roles, while mainstream American culture emphasizes independence, individual choice, and autonomy. Do bicultural Asian-Americans face conflict when their interdependent and independent value systems directly collide? The present study examined the psychological consequences of simultaneously holding both interdependent (family values) and independent (autonomy) cultural considerations for bicultural Asian-Americans, as compared to monocultural European-Americans. Participants (N=121 European Americans, N=70 Asian-Americans) were presented with vignettes that required them to choose between family values and the self as a way of measuring conflict between incongruent cultural values. As predicted, Asian-Americans were more distressed when making the decision to go against the family as compared to European-Americans, suggesting that they do identify with Asian values. However, Asian-Americans felt equally distressed as European-Americans when deciding to go against the self for the family, suggesting that they have also adopted American values. The differences in how bad they felt were partially explained by interdependent and independent self-construals, and attitudes about respecting family. Our results suggest one source of distress and conflict, which Asian-American youth are particularly susceptible to when it comes to decision-making, as well as some of the factors that explain that discomfort and psychological distress.

Asians have been one of the fastest-growing populations to immigrate to America for over a century. As a marginalized minority, they still face a variety of problems, including, but not limited to, dehumanizing stereotypes, questioning of citizenship, and alienation from social expectations. Studies on ethnic populations have divulged Asian American and other minority experiences, focusing on what it means to be discriminated against. In discrimination against Asian Americans, certain stereotypes can easily be misinterpreted as positive, painting Asians as ideal students, laborers, or spouses. However, such stereotypes are too incorrect to be useful, in that they put unreasonable ideals and expectations on Asians, meanwhile glossing over the realities of anti-Asian racism. American colleges and universities have taken measures of varying degree to address and better accommodate minority groups. Even with universities implementing diversity pedagogies and equal opportunity policies, problems with racism and alienation for Asian Americans may remain salient. If Asian American college students experience racism, are there common themes of discrimination that come up when they talk about their racial experiences? Additionally, are these stereotypes and themes shared amongst ethnic groups? This qualitative research takes an ethnographic approach by interviewing Asian American college students about their experience as self-identified Asian Americans. These interviews are transcribed and coded, by highlighting themes consistent with those found in past literature, including common stereotypes and degrees of racism severity. Ascription to the popular stereotypes, including the “model minority” and “perpetual foreigner” stereotypes, are predictably a commonplace occurrence throughout the lives of Asian American students, while degrees to which the racism occurs – from aversive to more overt actions – may vary amongst individuals. This ethnography is inspired by the need to further address experiences of discrimination within Asian American populations, in order to better define their place in the racism literature.

MicroRNAs are a group of highly conserved non-coding RNAs that play critical roles in regulating networks of genes. MicroRNAs bind to target mRNAs and can inhibit translation and/or facilitate degradation. One of these miRNAs, microRNA-21, plays an important role in kidney disease as it has been shown to increase in animal models of disease. Recent studies have shown that microRNA-21 promotes interstitial kidney disease with fibrosis by silencing metabolic pathways and by promoting reactive oxygen species formation. Mice with microRNA-21 deletion show a decrease in kidney fibrosis.

Our hypothesis is that cells isolated from microRNA-21 knock out mice will have decreased expression of cytokines associated with fibrosis. I will look at the expression of reactive oxygen species by live imaging of cells where microRNA-21 has been blocked. Then I will use quantitative polymerase chain reaction and Western blots to analyze protein levels for known molecules associated with fibrosis and inflammation. We expect to see that cells treated with anti-microRNA-21 have a reduction in reactive oxygen species, leading to less fibrosis and inflammation. Blocking microRNA-21 is a potential new therapy to combat kidney disease.

Our design project is to create a robot with mapping, navigation, and computer vision to find a target object within an enclosed area. By using ultrasound sensors to define the area, the robot is able to map and autonomously navigate itself towards the target object. Initially, the robot uses walls in order to define the enclosure’s limits, once these limits are found the robot creates logs of information detailing the history of where it has already been. By logging the location history of the robot the speed of the search and mapping is optimized. The mechanics of the robot’s mobility depends on several subsystems. Using hall sensors in the wheel wells of the robot, we are able to measure the degree of rotation of the robot and the distance that it travels. Using the measurements from the hall sensors, we are able to navigate the robot to target destinations and avoid obstacles detected on the sensors. The rotation direction of the wheels will be controlled using H-bridges to switch the hot and ground inputs to the motors, allowing directional functionality. The image detection portion of the robot utilizes a camera and the image recognition software openCV to identify the target object using key features from reference images that are uploaded to the onboard computer. The camera is mounted on a pan-tilt bracket with a height adjustable neck in order to give it a 180 degree vertical and horizontal range of motion and the ability to look on elevated surfaces. Once the target object is identified using the on-board camera, the robot creates a map with an indicator for where the item was found.

Hair cells (HCs) are the sensory cells of both the hearing and balance systems. HCs that die due to trauma or certain drugs are completely replaced in non-mammalian animals but replacement is extremely limited in mammals, including humans, causing permanent loss of hearing and/or balance function. In the balance system, HCs reside in five sensory organs in the inner ear and respond to changes of head and body position for balance regulation. HCs in the non-mammalian balance system undergo cell “turnover,” a process by which cells naturally die and are replaced. To investigate whether turnover occurs in a mammalian model, I studied utricles, one of the five balance organs, of adult mice. Utricles were immuno-labeled with antibodies to several cell markers, and I collected images of them using confocal microscopy. I observed that actin rich rings, called phagosomes, are prevalent in mouse utricles. These phagosomes seem to be engulfing HCs and likely belong to supporting cells, which surround HCs, instead of macrophage cells that professionally clear dying cells throughout the body. Some phagosomes have HCs inside of them, but most appear empty. This suggests phagosomes target dying HCs or HCs destined to die, and then clear the HCs from the sensory organ. I also observed that many phagosomes have actin rich spikes that may aid in finding the targeted HCs to be removed. These findings suggest that HC death occurs in normal mammalian utricles, which was not previously thought to happen. Because HC numbers remain unchanged in adult mouse utricles, this suggests that new HCs could be added during adulthood. I am currently looking for evidence of HC addition in adult mice. If HC turnover occurs, then the mechanisms responsible can be characterized and potentially manipulated to grow HCs back after damage in human hearing and balance systems.

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.

The Advanced Propulsion Lab from the Earth & Space Sciences Department has developed a Pulsed Plasma Thruster (PPT) which utilizes a propulsion system ideal for operating in a low pressure and high altitude environment. In order to test the PPT, a high-altitude flight will be carried out at the end of May 2014. The structure housing the thruster is a zeppelin-type aircraft composed of two lifting balloons, a primary zeppelin balloon, and a supporting frame. There are several constraints that need to be fulfilled by the aircraft. The zeppelin frame needs to be strong and durable enough to support the thruster, while still light enough to fulfill the weight compliance from the FAA. In addition, the zeppelin needs to be able to raise the payload above the jet stream to an altitude of approximately 70,000 feet and maintain that height once reached. To achieve this, the structure uses two 800-g high altitude latex balloons with 150 cubic feet of helium providing the lifting force. Once the optimal height is reached, the two balloons will be separated from the main structure through the uses of NiChrome wire and the primary balloon will take over, providing neutral buoyancy at the desired location in order to accurately measure the thrust of the PPT. The main core of zeppelin is currently being fabricated in house using mylar as the primary material for the balloon and carbon fiber rod for the supporting frame by our team. Current calculations estimate the size of the zeppelin to be 45 feet horizontally with a 4.5 feet radius. There are several issues the zeppelin is currently facing such as the fragility of the material used, the expansion of the helium at high altitude, the weight of the payload, and the sheer size of the aircraft. We are currently testing various materials and structural designs that will house the payload in order to develop a lightweight and aerodynamic aircraft that will address these issues. 

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.

The focus of this research is on p120 catenin, an essential protein in the development of vertebrate embryos. p120 catenin is associated with the regulation of cell migration during development, which includes cells migrating towards the dorsal axis. The mesodermal cells that migrate towards the dorsal axis will become the notochord and somites. We hypothesize that p120 catenin regulates this movement through its association with cadherins, and its activation of the actin cytoskeleton. p120 catenin binds the cytoplasmic tail of E-cadherin to stabilizes and strengthen adhesion and in the cytosol regulates small Rho GTPases to mediate actin dynamics. The regulatory domain of p120 catenin contains tyrosine and serine/threonine residues that are phosphorylated. We are modifying these sites to amino acid residues that lack the ability to be phosphorylated, phenylalanine or alanine, or are constitutively charged, glutamic acid. A splice site antisense morpholino injected into single celled zebrafish embryos knocks down the expression p120 catenin proteins, which can then be rescued by co-injection of wild-type p120 catenin mRNA. The modified p120 catenin mRNAs are co-injected with splice site RNA morpholino and the embryos’ development is then compared to those embryos that were rescued with wild-type p120 catenin. Thus we are studying the phosphorylation sites essential in the cell migration process. Data from the tyrosine 228 to non-charged phenylalanine mutation rescues the normal phenotype. This suggests phosphorylation of the tyrosine at the 228 site is not required for cell motility. Whether serines 268 and 288 are required for cellular motility is not yet clear. Other phosphorylation sites are currently being studied for their roles in cell adhesion and migration. This research is significant for developmental biology as well as cancer biology and wound healing.

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.

Cleft lip with or without cleft palate is a common birth defect with wide etiological and phenotypic variability, stemming from diverse genetic and environmental factors. Many classification systems have been developed to aid in documentation, diagnosis, and management of clefting. Recent efforts under the Ontology of Craniofacial Development and Malformation (OCDM) project, though the National Institute of Dental and Craniofacial Research’s FaceBase Program, have been aimed toward data pooling and integrating these different fields into a unified anatomical ontology to facilitate diverse research into craniofacial disorders. However, researchers, geneticists, clinicians, surgeons, and other specialists often interpret cleft features differently and utilize classification systems best geared toward their areas of focus. In order to facilitate integration of clinical and research studies that use different classification systems, it is first necessary to identify and consolidate inconsistencies among systems. We have comprehensively reviewed existing classification systems and tested their abilities to subclassify clefts of the lip, and have found several discrepancies and contradictions between and among systems. Variations in terminology, anatomical precision, and depth of detail among every system may result in an inability to accurately compare studies using different systems. Although the scope of an individual classification system can be sufficient for a specific goal or research outcome, it is becoming more appreciated that in order to continue advancements in preventing and treating clefts, it is necessary to encourage cross-institutional collaboration. Ultimately, our work is a key first step in creating an integrated, standardized framework to better understand orofacial clefting.

The protein that I am interested in, TOPLESS (TPL), is in a class of co-repressors that is conserved across eukaryotes. A protein is classified as a co-repressor if it cannot bind to DNA itself, but is recruited by a DNA-binding protein (typically a transcription factor) to repress the expression of a specific gene. Although we know that in the model plant, Arabidopsis thaliana, the TPL mutant phenotype does not have a normally developed top half (giving the protein its name) it is not clear how TPL confers repression. Research on Tup1, the yeast homolog of TPL, suggests several possible mechanisms: TPL could physically block key interactions, recruit other repressive proteins, or cause changes in the DNA to prevent gene expression. My research aims to test the hypothesis that TPL recruits a partner protein to induce repression. To test this hypothesis I have been using a yeast two-hybrid assay. This assay works by splitting a transcription factor that activates a reporter gene into two pieces. One of the pieces is fused to TPL and the other is fused to a protein I believe interacts with TPL. If they interact, then together they will form a functional transcription factor and activate reporter gene expression. In this case, I have been using histidine as the reporter gene. I can determine if histidine is being produced by growing the yeast on an agar plate that lacks that key amino acid, so only the yeast that have interacting proteins can synthesize it on its own. The yeast containing proteins that interact form colonies, while yeast containing proteins that do not interact will fail to grow. This experiment will allow me to better understand an important mechanism that is not only present in plants, but is present in many other organisms.

According to the most universally used scale for measuring psychological distress, the Holms and Rahe Readjustment Scale, becoming a widow holds top rank for the most taxing life-event. Unless specifically defined otherwise, it is generally understood that the term ‘widow’ refers to a heterosexual female. Consequently, few studies highlight the psychological distress of self-identified lesbian widows, and even fewer examine resiliency. Resiliency is the capacity to recover from difficulties, where individuals use their personal skillsets to reengage themselves within their environment. To our knowledge, no current research directly compares features of both lesbian and heterosexual widow resiliency within the same qualitative analysis. We seek to understand key features and possible differences in resiliency between self-identified lesbian and self-identified heterosexual widows. To measure resiliency, ten lesbian and ten heterosexual widows, over 45 years of age, who have been widowed for a minimum of one year will comprise our research sample. We will conduct voluntary, in person, one-on-one, tape-recorded interviews. We will analyze interview data through the constant comparative analysis method. Expected results include emergent themes related to resiliency (i.e., perception of available support systems and/or effectiveness of support systems, if any). By the day of our Symposium presentation, we will have completed our pilot report, which will include at least one interview. Our intention is to learn what types of support best aid resiliency among widows, and whether these support systems are readily accessible to lesbian widows in mainstream heterosexist U.S. society. Participants in this research will give us an understanding of the underlying attitudes and social dynamics that influence resiliency in this context, helping us identify the conceptual framework needed to best aid resiliency among lesbian and heterosexual widowed populations. This study contributes to a broader effort to explore new ways of strengthening psychological wellbeing of the lesbian population.

The frequency of paternal mitochondrial inheritance in humans has yet to be established. However, previous studies have indicated that such inheritance either never occurs or is very rare. Whole-genome sequences (WGS) of human trios provide a new technology to test the hypothesis that paternal mitochondrial inheritance occurs, and if so, to estimate the frequency. Population genetics and genetic diagnosis may benefit from accurate estimates of paternal mitochondrial inheritance. We test inheritance in several hundred trios by comparing the mitochondrial genomes (mtDNA) in mother-father-child trios. Paternal inheritance would be deduced if the father and child mtDNA matched, but the mother and child mtDNA did not. Although paternal inheritance is unlikely to be seen with our limited dataset, we demonstrate analysis of WGS to be effective for exploring mitochondrial inheritance in humans.

Extradyadic involvement (EDI) refers to romantic intimacies outside of a primary marital or dating dyad. Despite their youth, a considerable number of young adults have engaged in EDI based on data drawn from U.S. samples (Wiederman & Hurd, 1999). In cases of unmarried dating couples, EDI may harm young adults’ emotional and physical health as well as represent risks for infidelity issues in later marriage (Maddox Shaw, Rhoades, Allen, Stanley, & Markman, 2013). With a purpose of providing suggestions to strengthen young adults’ dating relationships and to evaluate potential risks of EDI, the current study examines 3 predictors of EDI inclination in college romantic relationships including: 1) adult attachment type, 2) relationship satisfaction, and 3) the quality of alternatives. A total number of 100 participants recruited from a local community college completed a demographic questionnaire, the Dyadic Adjustment Scale (Spanier, 1976), and the Experience in Close Relationship Scale-Short form (Wei, Russell, Mallinckrodt, & Vogel, 2007) which measure relationship satisfaction and adult attachment type respectively. To evaluate the role quality of alternatives plays in EDI inclination, participants also answered questions about a vignette designed to help them imagine an EDI situation. A hierarchical regression was used to analyze the data. Consistent with previous findings, adult attachment types of either high anxiety or avoidance were hypothesized to predict higher EDI inclination. Lower relationship satisfaction was expected to predict EDI desires. Moreover, quality of alternatives was hypothesized to show the most significant predictive value of inclination of extradyadic physical intimacy among the three factors.

In humans, the Fucosyltransferase-1 (FUT1) gene encodes for a glycosyltransferase enzyme responsible for the assembly of the H sugar, which serves as substrate for A and B glycans of the ABO carbohydrate blood group antigens. In mice, the gene is primarily expressed in mucosal epithelium. Helicobacter pylori, a pathogen associated with stomach ulcers and lymphoma in humans, has been shown to use ABO related structures as receptors, and observations have been made that higher incidence of stomach ulcers occur within blood group O than any other blood group. In this study we hypothesize that mice in a spontaneously Helicobacter positive colony that do not express Fut1 (Fut1-/-) would show differences in Helicobacter spp. as compared to mice that are Fut1 sufficient (Fut1+/+). This was investigated by performing a polymerase chain reaction (PCR) on DNA collected from fecal pellets of mice that were wild type, heterozygous, and knockout for the Fut1 gene, using Helicobacter genus specific primers to amplify the 16s rRNA gene. PCR products were cloned and sequenced using a Sanger (fluorescence based) capillary sequencing method. Sequences were identified using NCBI’s nucleotide database to assign Helicobacter species. Both semi-quantitative PCR and sequencing results show the (Fut1) gene is associated with differences in Helicobacter genus abundance and species colonization in mice. These data support expression of this blood group antigen participates in Helicobacter spp. colonization in gastrointestinal tissues.

The purpose of this research is to propose an architecture re-documentation driven white-box penetration testing methodology for a mobile application. Security of the application is very critical issue especially when the application controls money and resources, and any security violation can result in significant money loss. To ensure security of the mobile application, testers must perform several kinds of penetration tests. We focus on white-box testing which is one of the penetration tests to discover a vulnerable point by examining internal process generating output with a given input. In order to perform the white-box testing, every tester has to have the same understanding of the application. Moreover, as the number of the testers increases, the total time to understand the source code also linearly increases. However, the total time spent to understand the source code could be significantly reduced with documentations of the application. In this case, several testers re-document the given application source code with the documents representing both dynamic and static views of the application, and other testers are easily able to understand how the application is constructed and working by observing the documents. We used UML, 5W1H Re-Doc, and a CASE tool to re-document an application, then applied the STRIDE threat classification defined by Microsoft to the documents to propose countermeasures. This approach has three benefits: Firstly, testers would get better understanding of the mobile application. Secondly, sharing the documents with other testers will help the testers understand the application faster which will lead to reduction of the time cost. Lastly, when the similar issue is re-visited in the future, the testers could save time to understand the application using the document.

Education has been understood as the gateway to a better life for many years, yet the view that it is a basic human right is a more recent conception. The Universal Declaration of Human Rights states, in its article 26: “Everyone has the right to education”. It is clear, based on this right, that global educational reform is a necessity in order to better the living conditions of all world citizens, a view that is supported by many people and organizations including UNESCO and NESRI. In this paper we will examine the roots of the educational system in America and compare it to other world nations in order to progress the national discussion surrounding a human right to education. Recently, with the surge of violence in the Middle East and a renewed concern for women's rights, the political implications of the “right to education” became more visible. It is no secret that the US has issues within its education system and national statistics presented by the NCES portray the current system’s failures by way of the children. The statistics reveal a deeper root problem: a disjunction between Americans’ beliefs that education is important and the concept of education as a fundamental human right. The national discussion surrounding this issue has been weak at best, and the outcome is a continuous dropout rate and children with limited options. What shall be the foundation of the educational system in the US? Based on the study of different conceptions of educational rights, and a focus on drop-out rates and their consequences in America, we will propose that a “human right to education” can be a new and powerful base for a national discussion. The results of this argument will have direct impact on the United States but will also have broader implications worldwide.  

It is often forgotten students are learning to build a better future. As a group of students, we are looking to create a form of innovative technology that provides a learning experience through two of the most important learning methods: visual and kinesthetic. To provide hands on learning experience, we have created the Dynamic Mathematical Display (DMD). The DMD is a device with pins placed within a three by three grid. The pins are 10 cm long, 3.5 cm wide, and each controlled by individual motors and slide potentiometers. The dynamic movement of each pin is measured by the potentiometer's linear resistance, which is monitored electronically by a computer program. That program will engage the pin to move to a given point projected from 3D graph. The main purpose of the DMD project is to create a morphing table that will allow a user to visualize complicated 3D graphs with all their components such as depths and peaks. These components will be represented by red, green, and blue light emitting diodes (RGB LEDs), which are attached to each pin. The LED's are programmed to provide color based on the physical location of the pin at the time according to the projected graph. Both instructors and students will have the option to manipulate the brightness and color of the LEDs. While the pins provide kinesthetic information to a graph, the LEDs provide additional visual information similar to a topographic map, enhancing the learning experience of a student by presenting more realistic and information-rich representations of physical models. 

Homosexual adoption in the United States is at the hands of state laws. In states where the laws do not specify whether or not this form of adoption is allowed, the decisions on the matter tend to rest in the hands of judges. This research then investigates what accounts for differences in gay adoption rates after adjusting for differences in laws. In addition to laws, there are various components of state society that impact gay adoption rates, including, culture, economics, and politics. While each one could have a substantial impact on homosexual adoption rates, political climate may be especially impactful. For example, a state that has more conservative judges will have lower rates of adoption than a majority of liberal judges. Using a state-level data set constructed from multiple state and private sources, I use multivariate linear regression models to examine the role of culture, politics, and economics in gay adoption rates. In these models, cultural climate is measured by hate crime prevalence and religiosity, economic climate is measured by education level and rate of urbanization, and political climate is measured by social movement prevalence and the proportion of conservative judges. The research will convey the importance of societal factors outside of the law that have an impact on homosexual adoption rates. This research can serve to inform policies and other government interventions that can be made to account for the factors that influence adoption success.

The goal of my research is to  find an efficient drug delivery system to kill brain cancer cells by considering that some hydrogels change their viscosity dramatically at different temperatures (called thermosensitive). The whole project is regarded as “rocket”system, with a drug-loaded device that delivers content into the right place as a rocket and the drug  inside as an astronaut. The innovative idea of the project is that the drug-loaded system has the capability to be liquid-like at low temperature while becoming gel at body temperature, making it easy to produce and inject into tumor tissue to concentrate the effect at the tumor site. To find a stable, biocompatible and biodegradable material to be drug-loaded, we tested the in vitro stability and drug-release during 1hr, 24hr and 96hr incubation of various polymer gels including PEG-chitosan, alginate, and methyl cellulose. We then studied the drug delivery system with brain cancer cells in vitro and monitored the migration of the cancer cells towards the gel.

Biofuels are a promising means towards the goal of creating cleaner and more sustainable energy sources, but current biofuels are hampered by incompatibility with current infrastructure and difficulties with using food crops for production. This project addresses these problems with a novel approach to consolidated bioprocessing: genetically engineering a synthetic organism to digest low cost feedstock and produce alkanes, the main constituent of diesel fuel, which can serve as a drop in replacement to traditional petroleum. One challenge of consolidated bioprocessing is that cellulose, the primary feedstock, is far too large for bacteria cells to digest, so engineered strains must be able to break down the cellulose extracellularly. To alleviate this problem, the Klavins lab has implemented a cellular “division of labor” in E. coli which serves to generate specialized cell states: the consumer state and the altruist state. In the consumer state, the cell consumes nutrients and proliferates; in the altruist state, the cells produce large quantities of cellulase and a lysis protein to release the enzyme payload to the culture environment. Cellulase hydrolyzes cellulose into cellobiose, a molecule small enough to be imported and digested by both consumer and altruist cells. This project is focused on the addition of two key genes, previously shown to produce alkanes, into the “division of labor” strain. We extracted these genes using PCR and integrated them into the cellulolytic “division of labor” strain with Gibson assembly. We then identified and quantified alkane output using GCMS (gas chromatography / mass spectroscopy). We also tested the growth dynamics of our strains using cellulose as its sole carbon source through time-lapse cell counts. The results of this project can invite opportunities for industrial scale-up and can lead the way in producing other relevant high value biochemicals such as drugs, chemical intermediates, or other fine chemicals.