Tuning the gene expression of biomolecular pathways is an area of intense interest and value to synthetic biologists. Through the use of a mixture controlled turbidostat (MCT), we have been able to streamline, and in many cases enable the processes involved in this area of study. A turbidostat is a continuous culture bioreactor that maintains constant culture volume and cell density while diluting with fresh media to keep cells in an exponential growth phase. With the addition of mixture control, the turbidostat can vary the chemical environment within the culture vessel without altering cell density levels. Tuning gene expression in Escherichia coli is a simple matter when using a MCT. Currently, an area of global interest is the industrial production of butanol with E. coli. The first step towards this is enabling E. coli to live in rich butanol environments. Because butanol is naturally toxic to E. coli, an increase in gene expressions of the biomolecular pathways responsible for detoxification of butanol is required. By placing laboratory grade E. coli into our MCT, the concentration of butanol can be increased over time while the cell density remains constant. This will allow fitness increasing mutations within the biomolecular pathways responsible for detoxification of butanol to prevail over many generations, with the hope of eventually converging to a final population of E. coli that subsists in highly concentrated butanol environments. Through increasing E. coli’s resistance to butanol, we hope to illustrate the usefulness of MCTs in tuning gene expression of biomolecular pathways.

As young people between the ages of 16 and 24 become more engaged in their communities, they begin to seek out ways to contribute to volunteer activities. As this occurs, young people often need to track their service efforts, and organizations need to regularly reach out to volunteers and validate their participation. Despite advancements in web technology, paper logs that are prone to becoming unorganized or misplaced are still used by people and organizations as the primary method for keeping track of volunteering records. Such was the case for our nonprofit client, the University of Washington Foundation. To improve this situation, we first conducted a literature review on attitudes and behavior around volunteering. We then designed an online survey that was filled out by 64 qualifying respondents, and conducted 20 in-person interviews with students from local Seattle Public Schools and the University of Washington. Results suggested that young people consider (1) organization, (2) history tracking, and (3) event coordination as important qualities in helping to better manage their volunteering efforts. Building on those findings, we sought to create a web application called vTracker that allows volunteers to centralize their records in an online database for better safekeeping, verification, and retrieval. vTracker’s design and implementation process included the creation of wireframe diagrams, user interface design specifications, and a functional prototype. According to feedback from students and our client organization that tested our prototype, vTracker provides a convenient way for volunteers to set personal service goals and have their volunteer hours validated by participating organizations; similarly, organizations can share volunteer opportunities, confirm volunteer profile records, and recommend the work of their volunteers. Eventually, the Student Philanthropy Education Program of the University of Washington Foundation will adopt the web application as an active record-keeping tool because vTracker effectively streamlines their volunteer management process.

RNA Polymerase V is a DNA-dependent RNA polymerase involved in RNA-directed DNA methylation (RdDM) (Matzke M et al 2007). RdDM is required for transcriptional silencing of intergenic regions, repetitive DNA, and transposons genome-wide. Arabidopsis polV mutants show increased developmental instability and aberrant root hairs. We hypothesize these phenotypes are the result of alterations in transcriptional silencing and we predict changes in transcriptional silencing are due to altered chromatin accessibility. To asses chromatin accessibility in polV mutant plants we will use a technique called DNaseI-seq that chops up chromatin with a restriction enzyme. This technique allows us to measure which regions of the genome are highly accessible to transcriptional machinery and which are not. Currently, I am developing transgenic plant strains as well as quality control assays to improve DNaseI-seq feasibility in polV mutant plants.  Thus the knowledge will enhance our understanding of developmental instabilities in Arabidopsis and plants in general.
 

Alcohol use continues to be a widespread and serious problem among college students. In recent years, the posting of alcohol-related content on social media such as Facebook has become an increasing concern. However, little research has evaluated the link between alcohol content on Facebook and students’ actual alcohol use. Recent findings suggest that the prevalence of alcohol-related content on an individual’s Facebook wall may be predictive of alcohol-related problems. We expected that the more students posted about alcohol, and the more their friends posted about alcohol, the more likely it was that students would report more actual drinking, more alcohol-related problems, and higher perceptions of how much others drink. A sample of 1148 undergraduate students (657 women, 403 men) completed a web-based survey that included measures of their Facebook use, their typical drinking behavior, their alcohol-related problems, and their perceptions of typical student drinking norms. Data were analyzed using generalized linear modeling. Results were consistent with hypotheses. After controlling for gender and number of Facebook friends, both participants’ postings about alcohol and their friends’ postings about alcohol were significantly associated with greater drinking, more alcohol-related problems, and higher drinking norms. Thus, the alcohol-related content that students post and that their friends post on Facebook is related to real-life drinking behavior and may be an important risk factor for predicting hazardous drinking. Future research should focus on the implications that students’ alcohol-related Facebook content may have on potential screening for treatment and research purposes, as well as on Facebook itself as a potential platform for treatment interventions.

Imidacloprid (IMI) may be a viable alternative to carbaryl for controlling burrowing shrimp that destabilize sediments, resulting in poor survival and low yields of Pacific oysters. However, efficacy varies among substrates and laboratory tests indicate the shrimp are relatively insensitive to IMI (24-h LC50's > 12,000 ppb active ingredient [ai]) and 10x greater than those in sediment pore water following application of 4x the desired application rate. These results contrast sharply with observed efficacy in the field, with significant mortality occurring 72-96 h post application in sandy substrate at 0.5 lbs ai/ac. Reasons are not known, but an understanding of the factors governing efficacy in the field may improve control within muddy substrates and those with eelgrass. We exposed adult N. californiensis in seawater to IMI (Nuprid® 2F) simulating concentrations reported in sandy substrate following application of 0.5 lbs ai per acre. Concentrations were the means from a pore-water fate curve: 0-6 h = 150 ppb ai, 6-24 h (24), 24-48 h (10), 48-72 h (6), and 72-96 h (4.3) plus negative controls with 10 shrimp at each time interval (5 IMI, 5 controls), a loading of 0.31 L/g, and water exchanges at the end of each time period. Water quality and overt effects were monitored. At the end of each exposure, the ability of shrimp to burrow in sandy substrate was evaluated. All IMI-exposed shrimp survived, were overtly affected, and none burrowed. In contrast, all controls appeared normal and 96% exhibited burrowing behavior. Results suggest applications of IMI (0.5 lbs ai/ac) will not directly kill shrimp, exposed shrimp may not be able to maintain their burrows, and death may result from burrow collapse. Factors that maintain burrow integrity (mud/organic matter, eelgrass roots) may explain differences in observed efficacy. Laboratory tests with shrimp exposed to IMI within burrows are needed.

Why are urban forests not replacing themselves?  For example, recent surveys demonstrate that adult trees are dying faster than new saplings are recruiting in Seattle (Washington), implying that the health of local coniferous forests is in decline.  Extensive resources are spent planting trees to combat this problem, but the underlying causes of this "lost generation" of trees remains unknown.  We investigate factors limiting seedling establishment of native conifers (Thuja plicata, Tsuga heterophylla) in Seattle, and use results to suggest strategies resource managers can use to address the "lost generation" problem.  We examine the effect of removing non-native English Ivy (Hedera helix) and adding mulch to understand what is limiting conifer regeneration, and to explore possible management techniques for improving growth and survival of transplanted seedlings.  We measured survival, general health (visually assessed), and height as response variables to the two treatments.  As of yet, no studies have empirically tested both of these factors.  We observed the highest transplant survival rates in areas where mulch was added, for both focal species.  Surviving transplants in the mulch treatment were also healthier than the transplants with no mulch added.  Ivy presence did not affect health or survival of either species, but it did affect growth of Tsuga heterophylla.  Treatments affected growth of the two species differently.  Growth of Thuja plicata was not affected by either treatment.  For Tsuga heterophylla, however, growth was highest in the ivy-removed treatment, but was not significantly affected by the presence of mulch.  Our results suggest that seedling survival is limited by a lack of mulch and that competition with invasive understory plants may limit growth for some species.  Our recommendations for park management are therefore that restoration transplants should be paired with mulch addition, as well as Hedera helix removal for Tsuga heterophylla, to maximize survival and growth.

The formation of amyloid ß (Aß) plaques, resulting from the inappropriate aggregation of the protein beta-amyloid, is a major pathology associated with Alzheimer's disease (AD). One potential therapy for Alzheimer's disease is to reduce cerebral Aß plaque deposition through stem cell therapies. We hypothesize that myeloablative therapy, using lethal irradiation, as well as non-myeloablative bone marrow transplantation, using non-lethal irradiation, will result in a reduction in Aß plaque accumulation in the cerebrum. To test the therapeutic potential of myeloablative and non-myeloablative bone marrow transplantation, we transplanted bone marrow into either lethally irradiated AD (APPswePSIdeltae9) mouse model recipients (myeloablative therapy) or non-lethally irradiated AD mouse model recipients (non-myeloablative therapy). The number of plaques present and the total plaque area are quantified using ImageJ software. Initial immunofluorescence quantification has shown that non-myeloablative bone marrow transplantation reduces total Aß plaque area in the cortex by 33% when compared to non-treatment controls. To further assess the therapeutic potential of both myeloablative and non-myeloablative bone marrow transplantation therapies, additional immunofluorescence, as well as immunohistochemistry, quantification of Aß plaque deposition will be performed. These preliminary results suggest non-myeloablative bone marrow transplantation is a potentially effective stem cell therapy in treating an Alzheimer's related pathology.

The Short-tailed Albatross (Phoebastria albatrus) is listed as endangered under the US Endangered Species Act (ESA) due to small population size, and limited breeding range. The Short-tailed Albatross (STAL) breeds on Torishima and Minami-kojima Islands off Japan and migrates to Alaskan waters during the summer. The NOAA Alaska Fisheries Science Center’s Observer Program, in collaboration with the USFWS, instructs observers to carry out seabird monitoring activities in addition to their recording of bycatch during fishing operations. Using Observer Program seabird sightings and vessel-bird interaction data from 1993-2009, we examined potential vessel interaction threats to the recovery of the population, as well as the frequency and geographic expansion of Short-tailed Albatross sightings. Our data indicate that Short-tailed Albatross sightings increased more than the Short-tailed Albatross population during this time period (6.5% population growth per year), with observer days remaining relatively stable. We also found that incidences of discard feeding and/or vessel following are not increasing disproportionately to population size as the population continues to grow, thus it is unlikely that vessel interactions threaten the STAL population recovery. Lastly, we found that the sightings of Short-tailed Albatross show an eastward expansion since 1993, thus suggesting an expansion of this species within their historic range.

My senior project explores the use of art to activate public spaces, specifically urban mixed-use alleys. It has two purposes. First, I want to determine whether an alley art walk event can enhance community wellness and revitalize alleys in the University District. And second, I want to explore how context shapes meaning by examining how the blunt contrast between fine art, typically reserved for an exclusive gallery setting, and a public alley, typically seen as a hub for crime and debauchery, can shape our perception of both art and alley. To achieve these goals, I have organized an event called Alley Art Walk that will be held in the University District in May, 2012 featuring UW student artwork and musicians. I have drawn on the advice of the non-profit The international Sustainability Institute to organize this event as well as my own research into street art events and alley activation methods. I will assess the project’s impact using interviews and observations of the event and its participants. The result of my work will be an established infrastructure for future Art Alley events, a greater sense of community and place in the University District, and a reconceptualization of alleys, art, and the relationship between the two.

Neurons contain two highly specialized compartments: the dendrite, which receives synaptic or sensory inputs, and the axon, which relays these signals to other cells. Different types of neurons often have unique, type-specific dendrite morphologies and proper dendrite patterning is important for normal neuronal function. Underscoring the importance of dendrite morphology to neuronal function, defects in dendrite patterning likely contribute to numerous neurological disease states and the cognitive decline that accompanies normal aging. However, the many genes that contribute to the complex dendrite patterns remain largely uncharacterized. To identify genes involved in this process, we conducted a genetic screen for mutants that alter the patterning of sensory neuron dendrites that innervate the body wall of fruit fly larvae. Briefly, we mutagenized fruit flies with EMS, a chemical mutagen, and screened for late-larval stage lethal mutations that perturb dendrite patterning using a fluorescent protein that allowed us to visualize a single functional class of sensory neurons in living larvae. Here, we report our analysis of a novel mutant, messi. Using live cell imaging and quantitative analysis, we found that messi leads to exuberant dendrite branching and intermingling of dendrites in sensory neurons. This latter defect is of particular interest since “self-avoidance” may represent a general mechanism for organizing sensory dendrites and little is known about the genetic basis for this phenomenon. Using time-lapse microscopy, we found that messi causes progressive dendrite defects: the dendrite patterning of messi mutants is indistinguishable from wild type early in development, but becomes abnormal later in development. Similarly, dendrite defects in many neurological disorders are progressive, therefore further analysis of messi may contribute to our understanding of how dendrite maintenance is deregulated in diseased states. Currently, we are working towards identifying the gene affected in messi mutants and determining whether messi affects dendrite patterning in other functional classes of sensory neurons.

While red blood cell transfusions require basic blood type matching (A+, B-, O+, etc...), effective platelet transfusions require complex histocompatibility matching, testing to make sure specific alleles of genes are the same between donor and recipient so as to prevent rejection; this is similar to the testing required for organ transplants. Currently, platelets are transfused from random donors until a patient shows signs of rejection, at which point a blood center must attempt to find a histocompatible donor out of its registry to donate on short notice. Using a canine model, the Slichter lab has created a treatment, through a combination of filtration leukoreduction to remove antigen presenting white cells (APCs) and irradiation to inactivate residual APCs, which may prevent transfused recipients from rejecting non-histocompatible donor platelets. In my research, I will focus on canine immune responses to platelet transfusions. The lab transfuses canines with mismatched, treated platelets and measures the recovery and survival of radiolabeled donor platelets to document rejection; antibody levels are also measured, to correlate decreased donor platelet recoveries and survivals as being immune mediated. I perform an Enzyme-Linked Immunoabsorbent spot (ELI-spot) assay to test the production of gamma interferon (IFN-g). IFN-g is produced primarily by activated T-h1 and CD8 lymphocytes as well as other cells such as macrophages and mast cells. As such, the ELI-spot serves as a direct indication of the very beginning of an immune response. My research aims to expand on the current antibody data and directly correlate the recipient’s response to transfused platelets with the results of the ELI-spot assay. This research allows a direct link between cell interactions and immune responses, which can then be compared to the donor’s platelet recovery and survival data to see if a correlation exists. This will allow us to better judge the effectiveness of various platelet treatments by identifying significant correlations between in vitro data and post-transfusion platelet responses. Not only can this lead to breakthroughs in platelet delivery, but the results may also be useful in detecting early organ transplant rejection.

The European Union committed to developing a Common European Asylum System by the year 2012. Having evolved from the desire to allocate responsibility among member states, the burden of asylum policy has now shifted away from focusing on national interests and into the realm of international standards of human rights. While this system is far from a successful example of harmonization at the community level, there has been progress nonetheless. Asylum seekers, those seeking refugee status in another country, are vulnerable to the inadequacies of the country that receives them, which is why efforts to harmonize are so significant. This evolution has been rooted in International law and the opinions of international institutions. European institutions, particularly the High Courts in Strasbourg and Luxembourg, have taken initiative to uphold the values of asylum protection under International law. This paper will explore how best practice policy prescriptions from the international level and European case law are working towards a Common European Asylum System that coincides with the minimum standards of international protection.

Mitochondrial dysfunction and oxidative stress have been proposed to contribute to organismal aging. In the nematode C. elegans, reduction of mitochondrial function through knockdown of genes encoding components of the electron transport chain (ETC) is sufficient to increase life span. The increased longevity is not solely the by-product of decreased oxidative damage generated by the ETC, but also involves induction of the mitochondrial unfolded protein response (UPR^mt), as evidenced by the observation that life span extension requires an intact UPR^mt. The cytoplasm, endoplasmic reticulum, and mitochondria have each evolved compartment-specific signal transduction pathways to alter nuclear gene expression in response to perturbations in protein homeostasis. However, little is known about the UPR^mt and the mechanism by which unfolded proteins are recognized in the mitochondria and signal changes in gene expression. Previous studies demonstrate that knockdown of ETC components and a subset of mitochondrial proteins induce the GFP reporters for mitochondrial chaperones hsp-6 and hsp-60. To identify novel genes involved in the UPR^mt, we are performing a forward genome-wide RNAi screen using the hsp-6::GFP reporter and measuring UPR^mt activity by fluorescent microscopy. Upon completion of the screen, we expect positive hits to include mitochondrial proteins, signaling molecules, and transcription factors that regulate the UPR^mt. Consistent with previous studies, gene knockdowns that have robustly induced the UPR^mt thus far in our screen are largely components of the ETC. In addition, the screen has yielded many novel hits including genes outside of the mitochondria and of unknown function. After the screen is complete, we will validate the RNAi clones that induce the UPR^mt and perform lifespan experiments to understand how the UPR^mt is involved in the aging process. Our screen will further understanding of how the mitochondria and nucleus communicate with one another in order to maintain mitochondrial proteostasis and illuminate how mitochondrial stress contributes to aging.

Singapore is renowned to be a multilingual and a multi-ethnic society where Chinese, Malay and Indian traditions coexist beneath the veneer of a western cosmopolitan metropolis. The result of this multiformity, however, shows a regressive trend of youths maintaining their Mother Tongue language. This research investigated 24 mature teenagers about their language attitudes towards their Mother Tongue as measured by the Language Attitude Questionnaire and interviews. Various results from other related published materials have also been used in the analysis. Ethnicity and education levels are the independent variables of this analysis. Statistical analysis report that the youth’s attitudes towards their Mother Tongue are off-putting and less esteemed than the English Language despite it being the language of their cultural identity. However, youths from the lower education level generally were found to have a more positive attitude towards their Mother Tongue compared to the youths from the medium and high level education. These findings confirm that the language attitude of the youth is remodeled by the rigidity of the education system and as well as social factors. Singapore’s insistence of the second language education could show signs of demise of language acquisition despite her ascertained objectives.

Glioblastoma Multiforme (GBM) is an aggressive type of primary brain tumor, which is treated by surgery followed by chemotherapy and radiation. A majority of cases prove to be highly resistant resulting in uniform fatality. At present, research has been moving towards developing a patient-centered model of treatment that is developed by finding the unique characteristics of a patient's tumor growth kinetics and response to therapy. GBM is a very heterogeneous disease despite having a generally poor prognosis. A promising method of investigating this heterogeneity has been through finding patterns in the molecular-genetic makeup of these tumors. Large-scale mathematical analysis on data from open-source repositories such as The Cancer Genome Atlas (TCGA) has already led to the discovery and validation of four GBM subclasses which point to characteristic areas of origination in the brain as well as differential growth behaviour. A limitation in this strictly data-oriented approach is the lack of meaningful clinical perspective applied which has resulted in the findings only being directed towards gauging patient survival. The focus of our research has been the discovery of information about individual characteristics of patients tumors that may have more clinical significance for each patient. Our hypothesis is that there is a correlation between the different biological subtypes classified by cluster analysis and the different kinetics of tumor growth measured by imaging. This work will be done by developing tools to investigate the genetic changes that may be driving different kinetics of disease progression (the proliferation and migration rates of the tumor cells) measured from actual patient imaging. This approach is guided by the belief that individual patient tumor biology can be used to inform the data analysis techniques and ultimately bring us closer to the goal of identifying the most discriminating treatment to effectively treat an individual's cancer.

Gliomas are invasive, fatal brain tumors that can be detected using magnetic resonance imaging (MRI). However, MRI does not reveal the entire size of tumor. By using a mathematical model developed by Kristin R. Swanson and colleagues, glioma growth can be quantified from the diffusion rate of the tumors cells, the net proliferation rate, and the carrying capacity of the tissue. These parameters are unique to each patient and can be determined by measuring the tumor volume from different MRI modalities as they change over time. Our lab collects data from patients consented to our study and records information about what treatments a given patient receives, since this can affect how the image appears. In my role as a member of the measurement team, I examine patient images to determine the extent of tumor burden on a given date. To obtain these measurements, I use Calcmri, a MATLAB program developed by our lab. Depending on the modality, enhancement on MRI slices can indicate tumor volume as well as other fluids. Calcmri can adjust the intensity threshold at which MRI enhancement will appear, which allows me to isolate the tumor and specify a region for the program to measure. I measure a series of two-dimensional cross section images in order to calculate a combined into 3-dimensional volume. These measurements are used to model the growth of the tumor, “in silico”. Our lab uses information from these models to discover clinical applications, such as to suggest more accurate treatment dosages and to predict life expectancy, which follows an overall goal to better capture the extent and invasion of tumor burden than what appears on MRI.

The geographic ranges of species are strongly influenced by climate. As temperatures increase, species are expected to shift poleward in latitude and upward in elevation, a prediction supported by observations of range shifts in recent decades. Species interactions also play a crucial role in setting geographic ranges of global biomes, and could be critical in determining the response of species to climate change. Due to limited data on interspecific competition in the boreal biome, Earth's largest land biome, it is largely unclear how climate change will affect the range limits of the individual tree species that occupy it. In recent decades, spruce trees (Picea engelmannii) have increased in abundance at high elevation locations formerly dominated by larch trees (Larix lyallii). This change is thought to result from improved climatic conditions for spruce establishment but has not been tested. I hypothesize that spruce have higher establishment rates than larch where the two co-occur when temperatures are high. To test this hypothesis, I will harvest 120 stems of each species at locations in the North Cascade Mountains in the summer of 2012. I will then count the number of annual growth rings for each sapling to determine establishment year. Next, I will model the relationship between establishment rates and climate in different decades of the last ~100 years for each species. Finally, I will compare the establishment-climate relationships of the two species to infer how the relative abundances of the species might shift with warming. These results have large-scale implications for changes we should expect to see in global biomes as warming continues. In particular, this hypothesis suggests that spruce will replace larch as climate change progresses.

The alginate polymer is a promising material emerging in the field of controlled release. Alginate is a naturally occurring anionic polysaccharide derived from the cell walls of green and brown algae. Alginate can be crossed-linked using divalent cations to create a hydrogel. Using a double emulsion process, the alginate can be formed into microparticles and loaded with a desired therapeutic such as protein, DNA, RNA, drugs, or other agents. However, under physiological conditions, ionically cross-linked alginate degrades rapidly, resulting in the burst release of the particle’s contents, leading to higher initial drug delivery and reduction in the effective lifetime of the delivery system. Previous research in the Bryers lab de3monstrated that the reaction of alginate with methacrylic anhydride results in a methacrylated alginate, which can then be covalently cross-linked via free radical polymerization to form a more stable alginate hydrogel. It has been suggested the methacrylated alginate polymers may degrade at a slow, consistent rate and are therefore hypothesized to allow for a prolonged, linear release of therapeutic agents. This project has tested this hypothesis by creating protein-loaded microparticles from methacrylated alginate as well as microparticles from ionically cross-linked alginate, which were subsequently coated with a methacrylated alginate shell. This investigation used bovine serum albumin (BSA) as a protein to model antibody delivery in vitro. The successfully release of BSA could lead to a novel vaccine delivery system. The implication of this research is broad, but may have the deepest impact in clinical studies, including less frequent administration of desired therapeutic leading to better patient compliance and increased convenience, reduced side effects due to the delivery of the effective concentration, less of therapeutic per patient and therefore lower cost per patient.

Our world is becoming increasingly integrated with motion sensor technology. However, the usefulness of motion sensor data is still vague and difficult to understand. Several applications using sensor infrastructure in the home, often referred to as smart homes, aim to support independence for older adults. The goal of this project is to try to understand smart homes for aging in place in general and complex motion sensor data within independent retirement communities. Our focus is in trying to understand how aggregated motion sensor data can be useful for clinicians, patients and family members, how to present aggregated motion sensor data, and how to proactively manage health to support aging in place. Our group is implementing ubiquitous motion sensors in independent retirement communities to assess mobility. Various parameters that influence mobility, including cognitive ability, psychosocial activity, and environmental characteristics, are noted and integrated into the data. The projects goal is to evaluate mobility in older adults and consider actions or treatments to prevent disease onset or discomfort. Preliminary findings from the ongoing longitudinal feasibility study provide strength to the argument that motion sensors may provide a supporting role for aging in place.

Engineered vehicles capable of matching the performance of natural systems in collision avoidance have not yet been developed. The purpose of our research is to translate the collision avoidance capability of schooling fish to an algorithm that could be applied to engineered vehicles. We want to determine if collision avoidance in schooling fish is related to an engineering method of collision avoidance termed collision cones. The collision cone is a set of velocities for one fish (or agent) that indicates it will collide with another fish (or agent). In order to avoid collision, the fish’s velocity vector must lie outside all collision cones. Constraints with this method are that it only works under certain conditions: each vehicle has constant velocities, uniform and full view sensing, noiseless measurements, and planar motion. This method already works well for engineered systems under these conditions. Our research is exploring how to alter the conditions to encompass the biological characteristics of the fish. As of now, the data that has been collected has revealed promising results. If further research reveals that collision cones do not match schooling fish’s collision avoidance capability, other algorithms will be explored. This research is significant in that it will impact the development of UAVs (Unmanned Aerial Vehicles) and other autonomous technology.

Variable stars are stars that fluctuate in brightness over time, usually with sinusoidal patterns. We can plot the brightness of variables over time to create light curves, which allow us to examine the periodicity of the stars. SX Phe variables are a specific type of star that have not been extensively studied and classified. We examined seven SX Phe candidates in order to more precisely determine their light curves. The periods of the candidates had been roughly estimated with data from the LINEAR survey. The goal of this project was to determine these periods more precisely and to image the stars in multiple filters, which will tell us more about their properties. At the University of Washington Manastash Ridge Observatory (MRO), these seven candidate SX Phe stars were observed in the Sloan g’ and r’ filters over at least 1.5 periods. Photometric images of the candidates were obtained from these observations, and light curves were produced. It was determined that the majority of candidates have periods of variability of about 1.35 hours, almost half as long as previously hypothesized. Further analysis of these more accurate light curves is needed to classify the candidates as SX Phe stars.

Within the previous year, over half of a million people died from malaria and ninety one percent of these deaths occurred in Africa. My research studies the living conditions of the Maasai tribe in correlation to the prevalence of malaria, intestinal parasites, and head fungus. During field research in Tanzania these were the three most widespread diseases among the three hundred patients treated. The life cycles and causes of each disease were studied individually to distinguish how specific environmental and household factors contributed to the transmission of the diseases. Relevant factors of the living conditions were identified. I hypothesized that the incidence of disease would be reflected in the prevalence of the elements relating to the transmission of disease. I collected data on the living conditions in Tanzania by visiting Maasai households and evaluating the following criteria: the presence of a fire inside the house, the presence of feces and/or garbage in the household, the number and size of the windows in each household, the number of people living there, the number of people who were sick living there, the presence of uncontained animals in the compound, the presence of mosquito nets, the type of material used to make the house, the presence of a toilet, and the presence of a cover on the toilet; if applicable. Analysis of the results suggests that for each disease, the relevant factors of living conditions matched expectations in all three diseases. These results suggest that by making certain improvements to the living conditions of the people in the Maasai village, it would be possible to reduce the prevalence of the tropical diseases of malaria, intestinal parasites, and head fungus.

In the last decade, Seattle, like many other cities across the world, has tried to encourage bicycling by developing new bicycle infrastructures, cultures, and policies. In many cities, these efforts often start nearly from ‘scratch’. However, in The Netherlands, bicycling has been an important part of the transportation network for more than 100 years, with comprehensive infrastructure in place from policies developed during the 1960’s and 70’s. Our team, composed of two members, spent several months in Groningen, The Netherlands, on an exchange where we collected data on the bicycle infrastructure success that this region of the world is renowned for. Working with the Multimodal Project Development team at Seattle Department of Transportation (SDOT), we brought the lessons-learned and design of the Netherlands to our home, Seattle. We have evaluated the design of four critical Seattle intersections: 43rd Ave NE and University Way, 7th Ave NE and NE 40th St., 25th Ave NE and the Burke Gilman Trail, and 34th Ave N and N Fremont Ave. and compared them to successful infrastructure in Groningen. Through background research, interviews, and observation, we have assessed the comfort, safety, and directness of these selected intersections using quantitative and qualitative measures. Based on this data, we have suggested two alternatives for each intersection: one based on Dutch design which is novel to Seattle and very ambitious, and one of which is more practical and less expensive. The possible results of this study are far-reaching and significant. Whether our designs are adopted in some form by SDOT or not, our final designs have influenced SDOT employees. We are taking a step towards making our community a safer, healthier, and more enjoyable place for all street users.

My research examines fairness and equity in the distribution of three wastewater treatment types across seven counties in the Puget Sound region. I begin my analysis with a thorough exploration into the concepts of fairness and equity, within the context of a variety of disciplines. Drawing on this analysis, I then look into the costs of these different systems, making sure to take into account all applicable considerations, including implementation, maintenance, and repair costs. Specifically, I investigate the costs of combined-sewer systems, separated sewer systems, and onsite septic systems at the household scale. Lastly, I use Geographical Information Systems and spatial analysis to compare the costs of these systems to their spatial distribution through the subject counties, and to the household median income within their respective census tracts. This methodology allows me to uncover any inequities in the way that the costs of these treatment types are distributed, and address a specific instance of fairness within urban planning that has yet to be investigated.

Cell migration and cell adhesion are crucial processes for embryonic development, homeostasis and cancer progression. Regulated changes in adhesion are coordinated with cytoskeletal change, which result in morphogenesis. Conversely, the loss of cell to cell adhesion can promote tumor cell metastasis and change in cell motility. Thus, examining the specific regulator of the adhesion and cytoskeleton is important in terms of furthering our understanding of the development and disease progression. We specifically study an important protein regulator called p120 catenin and its involvement in cell migration in the zebrafish embryo. An extensive literature implies that p120 catenin both positively and negatively regulates cell adhesiveness through phosphorylation. Cell cultures show that phosphorylation of serine residues strengthens the adhesion and that phosphorylation of tyrosine residues increases the cell mobility. After the morpholino knockdown of normal p120 catenin, I will co-inject the mutant Y228F p120 catenin. Then I will observe whether the mutant without the tryrosine phosphorylation rescued normal development. For this I will use in situ staining of the somites with myoD at the 3 to 15 somite stage. To observe migration and protein localization, we will use a confocal microscope with the embryos' cells labeled with cherry fluorescent p120 catenin, green fluorescent Rho GTPase, or a green fluorescent plasma membrane. If mutant p120 catenin, which cannot be phosphorylated, can rescue successfully, we conclude the phosphorylation site does not play an important role in cell-cell adhesion or cell migration. However, if it does not rescue the morpholino knockdown, tyrosine phosphorylation at the 228 site is important for p120 catenin’s modulation of cell–cell adhesion and cell migration.

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the United States and much of the world. NAFLD resembles alcohol-induced liver injury, but occurs in patients with little to no history of alcohol consumption. It is a fairly benign condition, but can progress to a more advanced disease known as nonalcoholic steatohepatitis (NASH); many factors have been implicated in the pathogenesis of this transition (ER stress, mitochondrial dysfunction, insulin resistance, oxidative damage), but the exact mechanism remains unclear. Iron, although essential to many cellular processes, leads to increased oxidative stress and may be significant to NASH development via dysregulation of microRNA expression. To test our hypothesis, we measured microRNAs known to regulate processes marking the transition of NAFLD to NASH, such as apoptosis, inflammation, and lipid metabolism with real-time reverse-transcription PCR in a NAFLD mouse model. By comparing microRNA levels from the liver tissue of iron-treated vs. non-iron-treated NAFLD mice, we can survey effect of iron in exacerbating NAFLD via differential microRNA expression. As a regulator of cellular gene expression by transcriptional inhibition of messenger RNA, microRNA have the capacity to predict cellular processes before physiological changes are seen in the affected tissue. Thus, our results can more specifically describe differentially regulated genes during NASH development in the context of iron. After profiling our treatment groups, we will use bioinformatics to identify gene targets of the significant microRNA and validate the relationship of microRNAs and target genes in vitro. We will also compare the microRNA expression profiles of liver tissue and serum to identify serum biomarkers of NASH. In addition to the mechanistic insights elucidating the pathogenesis of NASH, our findings may lead to alternative non-invasive methods for NASH diagnosis, as liver biopsy is currently the only method for diagnosing NASH.

Marine bacteria carry out nutrient transformations that maintain the chemistry of seawater. Most marine bacteria are uncultured and little is known about their specific roles in marine biogeochemical cycles. We identified several cultures from the beta-proteobacterial OM43 and gamma proteobacterial sulfur oxidizer (GSO) clades in a culturing experiment from the North Pacific. Members of the OM43 clade use single carbon compounds produced by phytoplankton, suggesting that they contribute to carbon cycling in surface waters. Members of the GSO clade use energy from sulfur oxidation to assimilate organic and inorganic carbon, suggesting that they contribute to carbon and sulfur cycling throughout the water column. We selected four OM43 and three GSO cultures to establish a culture collection. Several OM43 and GSO cultures were revived from freezer stocks and purified. Their identity was confirmed by 16S rRNA gene analyses and they were added to the UW marine bacterial culture collection. OM43 and GSO isolates obtained in this study will be used to further characterize the roles of these important groups of bacteria in marine carbon and sulfur cycles.

Mitochondria are organelles vital to all cells in the body, generating energy and regulating metabolism, calcium signaling and apoptosis. These diverse functions are made possible partly through constant remodeling of mitochondria via fission and fusion. Neurons are especially vulnerable to mitochondrial defects, and this is true for mutations arising in mitochondrial fusion/fission proteins. Mitofusins (Mfn) are key proteins for mitochondrial fusion. Presently, we do not have clinically useful drugs to modulate fission and fusion in order to prevent neuronal damage due to disease and injury. In order to characterize how mitochondrial phenotype affects the metabolic rate in mammalian cells and disease models, we genetically engineered a chemically inducible system that allowed us to manipulate the mitochondrial fusion machineries. Specifically, I helped produce a ligand-induced heterodimerization system to initiate assembly and activation of fusion protein complexes by a specific chemical cue or ligand. Rapamycin, an antibiotic, complexes with immunophilin FKBP-12 (FKB) and binds to the FKB-rapamycin-binding domain (FRB) of the serine/threonine protein kinase mTORC1. I assisted in genetically engineering FKB and FRB onto the functional ends of the Mfn proteins. These Mfn proteins were expressed in mutant cells lacking all Mfn proteins. Since they lack fusion proteins their mitochondria are highly fragmented and we hypothesized that they could be rescued by inducing fusion with this inducible system. When we express the modified Mfn proteins containing FKB and FRB in cells, they will only dimerize and express fusion activity in the presence of rapamycin, which acts as a chemical ligand uniting the two modified forms of Mfn. We used a Seahorse analyzer to measure the oxygen consumption rate of FRB/FKB Mfn cells exposed to rapamycin for different periods of time. This system will help to identify new drugs that regulate mitochondrial dynamics in disease and injury.

The present cross-cultural study was conducted among college students in the United States who were recruited through the social media website, Facebook, and directed to the online survey website, Survey Monkey. The purpose of the study was to examine the relationship between perfectionism and perceived external pressure for academic success among Korean international and European-descent American college students. Hypotheses were: 1) external pressure for academic success is positively correlated with perfectionism for both Korean international and Caucasian-American participants, 2) Korean students are more collectivistic than European-American students, 3) Korean students perceived a higher level of external pressure for academic success, especially from their parents, than European-American students and 4) Korean students’ level of perfectionism is higher than that of European-descent American college students. Forty-three students (20 European-American and 23 Korean students) responded to the survey. Although the study’s findings did not fully support all four hypotheses, there was a significant positive relationship between the level of perceived external pressure and the level of perfectionism among Korean international and European-descent American college students combined. The major implication of the results is that external pressure for academic success is an important aspect of the development of perfectionism regardless of culture. Future research with different cultures will be necessary to test the generality of the result.

Gastrulation is a crucial step in embryogenesis, creating differentiation between ectoderm, mesoderm, and endoderm, as well as forming necessary organs. Transmembrane and juxtamembrane proteins located at the adherens junction, such as cadherins and p120 catenin, work together to either promote cell motility or adhesion. Using Danio rerio embryos as a model organism, we hypothesized that when p120 catenin is at the plasma membrane it binds and stabilizes the cadherins, causing cell clustering and increased adhesion. When p120 catenin is in the cytoplasm it activates Rac1 and Cdc42 (two members of the Rho GTPase family), which causes cell motility. By using a “depletion-rescue” experimental approach, p120 catenin levels are depleted by injecting a splice-morpholino, then “rescued” by coinjecting wild-type Cdc42 or Rac1. This indicates that p120 catenin in healthy embryos works to activate Cdc42 and Rac1 during gastrulation, resulting in cellular motility. When dominant-negative and constitutively-active mutants of Cdc42 or Rac1 are injected in combination with morpholino, the embryos do not “rescue” well, if at all. We postulate that wild type GTPases “rescue” well because the can receive a signal and activate migration directionally while the constitutively-active GTPases activate migration in all directions. These studies on the regulation of cell motility can help to elucidate larger signaling pathways, leading to additional effects on cell survival, growth, and invasiveness, all of which may be caused by the upstream p120 catenin.

The development of satellite technology has enabled scientists to develop a greater understanding of the movement patterns of various animals. Specifically, the movement of polar bears in Greenland is of ecological interest due to sea ice loss in the Arctic. Researchers tag polar bears with satellite collars and collect various samples and measurements such as age, sex, body mass, and body condition. Bears are tracked using polar-orbiting satellites and the data are collected and transmitted by Advanced Research and Global Observation Satellite (ARGOS). The large volumes of data are reported in coded text files that are difficult to analyze and contain error. I developed a program to extract data from ARGOS written using the statistical programming language R. This program allows for covariates on individual bears to be merged with satellite location data. I created two error checked databases (filtered and unfiltered) on movement of polar bears in Greenland. This program will facilitate data analysis of the movement patterns of polar bears.

Wind is highly variable and unpredictable, unlike conventional generation resources such as coal. The U.S. grid system is ill-equipped to accommodate resources that are stochastic in nature. Policies exist at the federal, state, and local levels that attempt to subsidize the production cost of wind generation, but how will these incentives impact system operations? We explore how the power generation mixture will change due to policies that incentivize wind. Our approach involves an analysis of a case study of three different incentive schemes: a base case (un-incentivized), the federal production tax credit (PTC) for wind, and a feed-in tariff (FIT) system modeled on the FIT proposed in California. Computer simulations will be developed to qualitatively model how these policies impact system operations using the economic dispatch algorithm, which is used in practice to deploy generation resources to serve the load and meet all power system constraints at the lowest cost. Comparing these cases will show which of these incentives have an impact on the total energy cost over a given time frame, as well as give an idea about the resulting generation profile.

Gastrulation is the process during which cells migrate and tissue layers differentiate in early embryo development. This process requires a balance between cell-cell adhesion mediated by cadherin-catenin interactions and stimulation of cell migration. Our research focuses on p120 catenin (p120ctn) dependent cell migration during gastrulation in zebrafish. P120ctn stabilizes cadherins at the plasma membrane and interacts with Rac1 and Cdc42 GTPases to stimulate cell migration, and with RhoA GTPase to regulate cell-cell adhesion. P120 binds and translocates RhoA to the plasma membrane where a RhoA gunanine nucleotide exchange factor stimulates release of GDP and binding of GTP. GTP-RhoA activates RhoA kinase which activates myosin light chains, inducing cross links to stabilize actin filaments, thus increasing the strength of cell-cell adhesion. In this project we aim to address what the role of RhoA GTPase is in the p120ctn signaling pathway as well as how phosphorylation of p120ctn affects the RhoA-p120ctn binding interaction. By knocking down p120ctn and attempting to rescue developmental deficiencies, we can elucidate how p120ctn interacts with RhoA to regulate cell-cell adhesion. We hypothesize that injection of GDP-bound (DN) RhoA will rescue a splice-morpholino p120ctn knockdown allowing low concentrations of p120ctn to activate Rac1 and Cdc42 GTPases that promote cell migration. Our microinjections of DN-RhoA mRNA into one-cell zebrafish embryos have shown that DN-RhoA, and not WT-RhoA or CA-(GTP-bound) RhoA, is able to rescue p120ctn knockdown. Additionally, p120ctn is regulated by phosphorylation and we are currently interested in how tyrosine phosphorylation of p120ctn affects its ability to bind and regulate RhoA. We hypothesize that tyrosine phosphorylation site mutants will be unable to rescue splice-morpholino p120ctn knockdown, and therefore be essential regulation sites. Using confocal fluorescence microscopy and a binding assay to measure GTP-RhoA, we hope to elucidate whether these sites are directly involved in the p120ctn-RhoA binding interaction.

Drug resistant strains of Staphylococcus aureus are now possibly responsible for more deaths than any other infectious disease in the United States. Phosphosignaling enzymes are thought to constitute a major class of drug targets in humans, but their potential as drug targets in bacteria are yet to be known to their full extent. In this study, we sought to develop an assay to test activity of an S. aureus signaling molecule, the tyrosine kinase CapB, which controls capsule biosynthesis. By interfering with capsule biosynthesis, we hope to interfere with virulence of S. aureus, allowing better clearance of the infection by the immune system. To assay for kinase activity, we recombinantly expressed the known kinase substrate Cap5O. Cloning of the Cap5O insert into the pQE30 vector created an expression plasmid with a 6XHis-tag on the C-terminus of Cap5O. The plasmid was grown and harvested in Rosetta cells. Purification of the protein was carried out through Metal Affinity Chromatograpy to obtain pure protein for activity assays. The results of this study will provide the starting point for an assay to screen for compounds that interfere with capsule biosynthesis. To date, no screens for the bacterial tyrosine kinases have been developed.

The mitotic spindle orchestrates proper alignment of chromosomes during cell division. The spindle is composed of microtubules that attach to kinetochores, multi-protein complexes that assemble at the centromeres of chromosomes. Understanding kinetochore function is essential to understanding the process of cell division. Through mass spectrometry analysis, the Davis Lab has found an abundance of the urmylation component Uba4 at the kinetochore. The urmylation pathway is highly similar to ubiquitination, and involves conjugation of a ubiquitin related modifier (Urm1) to proteins and RNAs. The role of urmylation at the kinetochore is not known. We hypothesize that post-translational modification of kinetochore proteins through urmylation is a regulator of chromosome segregation. To examine the effects of urmylation on the kinetochore I will be using an Ncs2 mutant, a protein involved in the urmylation pathway, By fluorescently labeling the kinetochore protein Spc105 and spindle pole body protein Spc110, I am using fluorescence microscopy and computational analysis to look for abnormalities in spindle appearance. These results will help elucidate the role of the urmylation pathway in the regulation of cell division.

The spindle assembly checkpoint is important for detecting errors in spindle assembly during mitosis. When the checkpoint is activated, it arrests the cell cycle so that errors such as unattached kinetochores can be detected and corrected before progressing through the cell cycle. Problems with kinetochore attachment can be detrimental and lead to cells with an abnormal number of chromosomes which can then cause birth defects. Misregulation of the cell cycle can lead to abnormal cell division and cancer. Spindle pole bodies in yeast are functionally equivalent to human centrosomes, which organize microtubules in the cell cycle. Spindle pole bodies increase in size when the cell cycle is arrested at the checkpoint. Mad1 is an essential component of the checkpoint and interacts with the Nup60 protein in the nuclear pore complex, a channel through which information traffics between the nucleus and cytoplasm. The N-terminus of Mad1 protein is required to localize Mad1 to the nuclear pore complex, but is not required for the checkpoint arrest. We found previously that if Nup60 is deleted, the spindle pole bodies do not grow in cells arrested at the checkpoint. Mad1 mutants containing only the C-terminus of the protein will be constructed. I will test if the ability of Mad1 to bind to Nup60 is required for spindle pole body growth. Spindle pole body size will be measured by fluorescence microscopy after arresting the cells in metaphase. I hypothesize that although Mad1 interaction with Nup60 is not required for the cell cycle arrest, it is required to signal spindle pole body growth. If true, then deletion of the Nup60 binding domain of Mad1 should block spindle pole body growth. Discovering what interactions are vital in these cells will give us a deeper understanding of how regulation of the cell cycle is maintained.