Agressive cancers are resistant to apoptosis and stem-like cancer cells may be responsible for re-growth of cancerous tumors. This inspired this search for compounds that could aid in the destruction of cancer cells with stem-like properties. Drosophila germ-line stem cells under radiative or chemotoxic stress are protected by a molecular signal from apoptotic daughter cells via the TIE receptor. Thwarting this protective signal by the introduction of a small molecule may lead to the discovery of compounds that can be effective against stem-like cancer cells. The NCI Diversity Set of 1,596 small molecules was screened by undergraduate research students, in-vivo, to find compounds that can induce apoptosis in germ-line stem cells of Drosophila melanogaster. Four compounds have been found that induce apoptosis in both the male and female germ-line stem cells at a low 5 uM concentration. Future investigations will uncover the mechanism of action and efficacy against stem-like cancer cells.

Little is understood about how Supermassive black holes affect their host galaxies in terms of growth and shape. Using the Simulation Romulus25, we are able to study how galaxy properties correlate with black hole properties throughout time. The simulation is a cube with lengths of 25 Mpc on each side, which is about 75 million ly or 21000 Milky way galaxies. We look at how the properties of galaxies relate to the properties of their black holes. We present trends that distinguish star forming galaxies from quenched galaxies.

Retinitis Pigmentosa, a progressive neurodegenerative disease, is a significant contributor to loss of vision due to retinal degeneration. The retina is made up of light sensing cells called rods (for night vision) and cones (for day vision). In patients afflicted with this disease, there is a degeneration of rod photoreceptors over time, which leads to a decreased visual field and night blindness. At a certain point, the loss of rod cells leads to the breakdown and loss of cone cells, which are responsible for color vision. Mutations in the rod gene Rhodopsin have been linked to the development of this disease. By down regulating this defective gene, the degeneration of rods would likely be prevented. Subsequently, cone degeneration would also be prevented, limiting the loss of vision in afflicted individuals. The expression of Rhodopsin is controlled by a nuclear hormone-like receptor transcription factor called Nr2e3. In collaboration with another lab (Dr. Sheng Ding, UCSF), we have identified small drug-like molecules that can block Nr2e3, and we have called them CA88, CA95, and CA97. We predict these antagonists will lower the expression of rod genes. Wildtype mouse retinas were treated in culture with CA88, CA95, or CA97. The use of these small molecules resulted in the significant down regulation of a number of rod genes. These genes include Rhodopsin, NRL, NR2E3, and GNAT1.  Stained tissue sections further confirmed a decrease in Rhodopsin with treated retinas.  When retinal ex plants were done using mice with a P23H mutation in the Rhodopsin gene, treated retinas were found to have a significantly thicker photoreceptor layer than non-treated, indicating the ability for these compounds to prevent retinal degeneration. With a way to reliably down regulate problematic genes such as Rhodopsin, a potential avenue for treatment of humans affected by Retinitis Pigmentosa is opened.

Overnutrition and sleep loss are widespread problems in today’s society and major risk factors for metabolic diseases. As with overnutrition, sleep loss impairs glucose regulation, though the mechanisms underlying this effect are unclear. Hypothalamic neuroinflammation disrupts leptin and insulin functions, resulting in the promotion of obesity. Sleep loss also elicits neuroinflammation, though little research has focused on determining whether this occurs in brain regions that regulate glucose metabolism. To examine the role of neuroinflammation in insufficient sleep- and overnutrition-induced deficits in glucose regulation, adult C57BL/6J mice were subjected to one of four treatments: undisturbed sleep and standard chow (control); undisturbed sleep and high fat diet (HFD); 18 hours/day sleep fragmentation (SF) and standard chow; 18 h/d sleep fragmentation and high fat diet. After nine days of manipulation, a glucose tolerance test was conducted, and then brain tissues were obtained and processed for immunohistochemical analyses of microglial and astroglial activation in the hypothalamus and brainstem (n=6/group). Sleep fragmentation or high fat diet reduced glucose tolerance compared to the control, with the greatest deficits observed in mice subjected to both sleep fragmentation and high fat diet. Analyses of numbers of activated microglia and astrocytes will determine whether patterns of glial activation across treatments reflect changes in glucose tolerance. These findings will be important in determining the contributions of neuroinflammation to glucose tolerance within the context of chronic insufficient sleep and poor diet.

Most of the tissues in our body contain adult stem cells that in theory could combat many aging phenotypes observed in human. However, these stem cells do not regenerate the tissue during aging. To understand, and in the future govern adult stem cell regenerative capacity we need to study the regulators of human adult stem cells. DPSCs are adult mesenchymal stem cells with powerful regenerative capacity that can easily be isolated from waste product, extracted wisdom teeth. Due to low cost and easy accessibility, dental pulp is a more feasible source for mesenchymal stem cells than bone marrow. DPSCs are thought to have the ability to differentiate into multiple cell lineages, and thus hold great promises in tissue regeneration. However, little is known about the molecular markers, cellular regulators, and differentiation capacity of these cells. The goal of my research project is to generate a large diversity set of DPSC to carry on a careful analysis of true common markers and differentiation capacity of these cells. At the moment I have optimized the procedures and isolated DPSCs from over 50 patients in partnership with UW dental clinic. We have now identified the molecular markers of DPSCs, and evaluated their differentiability to better understand the key criteria in the self-renewal and differentiation capacity of these cells. Western blot and flow cytometry analysis shows that most of our DPSCs have a robust expression of CD29 and CD146, both molecular markers of mesenchymal stem cells, but displaying an unexpected diversity on the levels of these markers among individuals. In differentiation tests, we also observe diversity in cartilage and adipocyte differentiation efficiency. With this unprecedented diversity set of easily accessible adult stem cells we will now identify the key components and metabolites that enhance the stemness and regenerative capacity of these adult stem cells.

Ammonia-oxidizing archaea and bacteria (AOA, AOB) are important contributors to soil ecosystem function, as they convert nitrogen (N) as ammonium (NH4+) into nitrate (NO3-), a more readily available form for plant uptake. This study examines the abundance of AOA and AOB in forest soils of the Pacific Northwest that have experienced wildfire 31, 7, and 5 years previously. Charcoal, a common residue of wildfire, may play a significant role in stimulating nitrification in soils, possibly by adsorbing monoterpenes that may inhibit mono-oxegynase activity in nitrifying organisms. The goal of this study was twofold. We first hypothesized that charcoal would increase the quantity and quality of AOB and/or AOA in wildfire-affected soils. To test this hypothesis, we extracted and compared DNA between burned and unburned sites using real-time quantitative polymerase chain reaction (RT-qPCR). We expect to find a greater abundance of AOA and AOB nucleotides in the burned sites indicated by qPCR, and a larger array of species indicated by DGGE analysis. Secondly, we will introduce monoterpenes (α-pinene) into soils with charcoal present, and soils void of charcoal to assess the interaction between the terpenes and charcoal surfaces. We hypothesize that the addition of terpene will readily adsorb onto charcoal surfaces. Therefore, burned soils will show reduced nitrification inhibition compared to soils without charcoal present and result in higher nitrification rates. These data will be matched with an assessment of the AOA and AOB from the burned and unburned soils, with and without the addition of charcoal in order to reach a better understanding of wildfire effects on forest soils.

The University of Washington's Manastash Ridge Observatory is being upgraded with a telescope auto-guiding system and a replacement camera, funded by Student Technology Fund.  The new, in-house, upgrades call for a high-level software implementation from the ground up.  Utilizing the programming language Python, we build two graphic user interfaces (GUIs) for controlling the telescope and camera independently.  With a telescope control GUI, we supply the basic features to drive the telescope, while also ushering in the controls for the auto-guider, greatly enhancing the past capability.  Meanwhile, the camera GUI handles the different camera exposure settings, camera filters, and saving of images.  We construct the GUIs using the software package wxPython in conjunction with the package TwistedPython.  In tandem, these software comprise of the bulk underlining functionality; where we use the feature set of wxPython to receive top-level client input and then talk to our hardware systems with TwistedPython to convey the user's needs.  Ultimately, the move to completely new, high-level software allows us more control than proprietary solutions allowing us to implement an intuitive end-user experience that will run on any computer towards the future.

The Astronomy Undergraduate Engineering Group is building an attachment to improve the science capabilities of the Manastash Ridge Observatory 30 inch telescope. This attachment is an offset guider which will improve tracking capabilities allowing the telescope to stay within two arcseconds of a target star (seeing limit) for an extended period of time. The guider uses unused light from the main optical path that is reflected off with a pick-off mirror onto a detector. A rotating periscope design is used to take full advantage of all of the unused light by creating a simulated large field that the detector can use to increase the sampling area. The periscopes rotational position along this field will be driven by a high precision stepper motor for maximum control. Two linear actuators will als  o be used to check the primary focus of the telescope so that it may dynamically correct for any wandering of the focus.

The Astronomy Undergraduate Engineering Group's (AUEG) is designing and installing a new instrument multiplexer for the 0.76m telescope at the Manastash Ridge Observatory (MRO). The multiplexer includes mechanics for the focal reducing optics, guider, filter wheel, the Student Technology Fee (STF) funded high performance photometer, as well as the STF funded spectrograph. Most of the research effort is going into the quick-change, fiber fed spectrograph that will extend our capabilities into new areas of astronomical observations. This instrument will be capable of switching between imaging and spectroscopic observations within seconds, all while maintaining an on-sky lock on the target. It will also include several resolution modes allowing for a varied ability for the user to choose between high throughput and high resolution. Through the efforts of the AUEG and the funding by the STF and MRO will once again have a full suite of high performance instrumentation with the ability to take several minute exposures, both photometrically and spectroscopically. Expected final product completion date for the instrumentation upgrades is Fall 2016.

Arrhythmias kill 300,000 people annually and effective cardiac drugs are imperative in their management. However, heavy reliance on in vivo testing results in low throughput and ineffective preclinical prediction of human response. Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are a promising cell source for highly predictive, high-throughput in vitro testing. Unfortunately, culture conditions in current hPSC-CM assays leave hPSC-CM tissues immature, making them ineffective at modeling human myocardial drug responses. Tissue culture conditions that mimic the myocardial microenvironment promote the maturation of hPSC-CMs with higher efficiency than non-mimetic conditions. Taking advantage of this, our lab's NanoMEA system successfully melds biomimetically nanopatterned substrates with microelectrode arrays (MEAs) that perform high-throughput electrophysiological analyses of in vitro tissues. However, greater maturation efficiency is necessary to improve NanoMEA screening throughput. Electrically conductive environments promote hPSC-CM maturation, and numerous electrically conductive scaffolds exist. Yet, overlaying MEA electrodes with these substrates results in noisy signals that bar automatic processing. NanoMEA nanopatterns are made of Nafion, a nanoporous polymer that does not negatively impact the recordings from underlying MEAs. Since Nafion exhibits robust self-assembly with electrically conductive reduced Graphene-Oxide (rGO) molecules, we hypothesize that Nafion-reduced Graphene-Oxide (NrGO) nanopatterns will convey the benefits of conducting surfaces without impacting signal clarity. To investigate this, NrGO-nanopatterns are fabricated and characterized using Raman Spectroscopy, transmission electron microscopy, scanning electron microscopy, and conductive atomic force microscopy. Then, hPSC-CM monolayers are cultured on NrGO nanopatterns of varying rGO content and differences in morphological and transcriptional maturation markers are assessed. Promising NrGO nanopatterns are then integrated into a multiwell MEA platform to examine their effects on signal clarity and electrophysiological hPSC-CM maturation. If effective, we anticipate that this enhancement to the NanoMEA system will enable faster development of safer drugs, reducing animal model reliance, and improving the treatment of arrhythmias.

Ankle foot orthoses (AFOs) are commonly prescribed to improve gait in individuals with cerebral palsy to stabilize gait. AFOs have also shown additional benefits in reducing the metabolic cost of walking, preventing bone deformities, and providing support during gait. The advent of the affordable 3D-printer has provided a new tool in the manufacturing of AFOs which may be able to overcome many limitations of current production methods. The purpose of this study is to improve the manufacturability and functionality of AFOs by improving AFO design and manufacturing techniques. Validation testing through the use of material testing, and multiple subject gait experiments verified the study’s results. The subjects’ lower leg was scanned with a portable 3D scanner and using this scan the AFO was form fitted to the unique shape of the subject’s foot. Parametric and non-parametric computer aided design tools were used to design the AFOs. Using a fused deposition modeling 3D printer the AFOs were fabricated using polylactide (PLA) filament. In order to adjust the stiffness of the AFO, elastic polymer bands were fabricated with polyurethane. Since a single elastic polymer band only allows for one specific AFO stiffness, multiple of elastic polymer bands might be need to be used to control the wide range of AFO stiffness. To solve this issue, the AFO was designed to have a support structure that allows for the moment arm of the elastic polymer bands to be changed, thereby adjusting to a wide range of AFO stiffness with minimum number of elastic polymer bands. Designing an open-source, 3D-printed AFO that helps rehabilitate the user could allow for low-cost, easily accessible rehabilitation devices to be common place.

The study of neonatal neuroanatomy is a complex field because of the rapid changes occurring continuously. The physical development of tissues is critical to understanding the cognitive development of behavior and learning in the neonate. These structures can be visualized and analyzed with Magnetic Resonance Imaging (MRI). The hippocampal structure in particular is vital to memory consolidation and is therefore key to understanding how newborns build upon acquired knowledge and how this affects their behavior as they grow. This strucure has been studied at many different ages with parallel work analyzing how changes in anatomy result in observable cognitive differences and developments. This study in particular has a rare cohort of scans that were taken shortly after birth. Prematurity is an especially important factor to consider here as it affects physical and behavioral growth. Here we looked at 42 premature MRI subjects and used these to build a temporal model of brain development. Our primary aims of the study are to: (1) develop a protocol for labeling the hippocampus in premature neonate scans, (2) create a growth over time model of the structure in order to automatically segment a larger number of scans and (3) observe how volume varies with behavior as projected by Bayley's Scale of Infant and Toddler Development. So far aim 1 has been achieved and current work is increasing the previous atlas size of 32 scans to 42 in order to improve automatic segmentation. The overarching goal of premature neonatal MRI segmentation is to provide further data for early diagnosis of behavior abnormalities that could develop later in the subject. Results here could produce a meaningful indicator of cognitive development through MRI analysis as well as assist in improving the accuracy of MRI automatic segmentation algorithms. 

Airflow inside a telescope dome is crucial for the efficient collection of data. The purpose of this project is to analyze the airflow inside the dome of the 3.5 meter telescope at Apache Point Observatory. Air flow metrology was used to measure wind velocity at multiple points in the dome over several months. This data was reduced using numerical computation. With this data, analysis was performed for trends both computationally and using 3D visualization of vector flow patterns. This data will be used to improve the dome airflow by moving and replacing louvers throughout the dome. By doing so, the wind flow across the telescope light path will be optimized and the resolution of targets at this telescope will be improved.

College presents many challenges for students, and how students cope with these challenges can affect how well they fare academically and socially. First-generation college students (FGs: students whose parents do not have four-year degrees) face more social, academic, and financial challenges and have higher dropout rates than continuing-generation students (CGs: students with at least one parent with a four-year degree). Research has shown that when facing challenges in college, FGs are unlikely to seek university resources; however, it is not clear what FGs are doing in the face of challenge. This exploratory study uses a social and cultural-psychological lens to begin understanding how FGs respond to challenges in college. We presented 273 undergraduate students (70 FGs) with a series of vignettes describing academic, financial, and social challenges and asked students to predict how they would respond to each challenge. Initial analyses suggest that when faced with financial challenges, FGs were less likely than CGs to “seek resources they would need,” and when faced with academic and social challenges, FGs were more likely than CGs to seek social support, to distract themselves from thinking about the challenge, and to remove themselves from the situation. These findings suggest that FGs may struggle in particular when faced with financial challenges, as they do not seek the resources they need to overcome this type of challenge, perhaps because they do not have access to many financial resources. When facing academic or social challenges, rather than turning to the university, FGs may seek social support outside of the university or disengage from these situations altogether. Given that FGs tend to struggle more in college than CGs do, this research has implications for understanding how to help future FGs deal with challenges in the university.

Premature births, or births before 37 gestational weeks, are associated with structural and functional abnormalities in the brain. Magnetic Resonance Imaging (MRI) is used to examine brain injury in neonates. Previous work demonstrated correlations between neonatal cortical lobes volumes from MRI and scores on the Bayley Scales of Infant and Toddler Development-Third Edition (Bayley-III), which measures cognitive, motor, and language skills of infants. The occipital lobe is important to diagnosis of visual and neurodevelopmental delays. In this work, I examined the relationship between occipital lobe subdivision volumes and Bayley-III scores. In order to do this, I designed a parcellation or labeling protocol that divided the occipital lobe into two regions based on the calcarine sulcus, the cuneus region and the lingual region. I applied the protocol to the 32 MRI training dataset. Using this parcellation protocol, I created a spatio-temporal atlas of brain parcels, which is a time and space model of brain tissue and parcel probability estimates. This atlas was used to validate our protocol using a leave-one-out validation and to automatically parcellate the larger dataset using EM or Expectation-Maximization labeling. The dataset contained 270 T1-weighted MRI scans from premature neonates who took the Bayley-III at 18 months. Once the larger dataset was labeled, I used multi-variate linear regression, normalizing for head size, to examine the relationship between occipital lobe gray matter volumes and scores on the Bayley-III and analyzed the growth pattern of the regions of the occipital lobe. Both regions showed symmetric and exponential growth patterns. Statistically significant correlations between the lingual region of the occipital lobe and Bayley-III scores were found. This suggests that regional occipital lobe volumes are associated with developmental outcomes in premature neonates.

Since 1904, when the first voter-sponsored bill appeared on the ballot in Oregon, the frequency of initiatives and referenda has greatly increased, most especially over the last 40 years. While there were only 98 bills voted on nation-wide between 1960 and 1969, over 370 initiatives made it onto state ballots between 2000 and 2009. My research examines several underlying causes of this rising frequency in order to help understand trends in the increasing use of direct democracy. Previous work has focused on the increased participation by moneyed interest groups who use paid petitioners to circulate legislation; however, I am proposing a new, original theory which connects political alienation and dissatisfaction of representative democracy to increased participation in direct democracy. I have built an original dataset which will combine measures of polarization within government, public trust in Congress, and the number of initiatives and referenda throughout the multiple states in which they appear. With this dataset, I ran multivariate regressions to analyze statistical significance in the relationships between these variables. I expect to find that as political polarization in Congress increases, people will lose faith in traditional modes of representative democracy. I further hypothesize that as trust in government decreases, people are more likely to turn to modes of direct democracy to instill change in government, therefore increasing participation in the initiative and referendum process. If my hypothesis is correct, my research would serve as a tool for political scientists to use to predict the rise or fall in the political activity of voters, the implications of which could influence timing of legislation, outreach efforts, and a number of other participation-related issues.

This research project explores disenfranchisement in America. Today, citizens living in unincorporated US territories (Guam, Northern Marianas Islands, US Virgin Islands, Puerto Rico, and American Samoa) are considered “second-class Americans,” having all other fundamental rights as mainland Americans do except federal voting rights. To help understand this phenomenon, this project examines the circumstances under which the political elite had extended suffrage or had established additional protection for minority voters since the early 1900s. Since then, women, African-Americans, 18-year olds, and citizens living in US territories have used different movement techniques and strategies to achieve suffrage, such as establishing conventions, organizing violent and nonviolent protests, and committing to quid pro quo services like serving the country in times of war. This closes in on a theory where political will—defined as the mobilization of mass movements to gain the right to vote—helps explain why Congress votes to extend suffrage to previous disenfranchised groups. This variable is operationalized by counting the number of organized events and the number of people in the group lobbying for suffrage during the year prior to a congressional vote on the floor. I hypothesized that the greater amount of political will present in a year, the more bills will be introduced in Congress. The time frame of data used in this project is from 1910-2015. This presentation can serve as a guide to explain when suffrage extension happens, and what disenfranchised groups did to get what they wanted from big government.

Motor behavior is the result of neural programs emerging from the Primary Motor Cortex (PMC). To generate behavioral outputs the PMC integrates exogenous and endogenous sources of variance. Electrical activity from the PMC has been effectively used to operate minimally invasive brain-machine interfaces (BMIs) that can operate prosthetic limbs to achieve basic motor outcomes such as operating a joystick.  Further development of neuroprosthetic technology will rely on a deep understanding of sources of variance to the PMC and how the PMC compensates for this. The circadian system regulates physiology and behavior within the 24-hour time frame and it represents a predictable source of endogenous variance for the generation of motor behavior. The specific pathways by which the circadian clock(s) may modulate PMC motor programs is not understood, but preliminary results from our lab show that the circadian system modulates the PMC electrical activity associated with wheel running in mice. We implanted electrocorticographic (ECoG) electrodes onto the PMC of mice and recorded electrical activity while they ran on a wheel at different circadian times. This showed that the PMC electrical signals associated with wheel-running are modulated in a predictable manner by the circadian system. I propose to replicate these experiments in mice with a malfunctioning circadian clock. I hypothesize that the canonical molecular circadian clock is essential for this modulation. To test this hypothesis, I used ECoG electrodes to record PMC electrical activity of Bmal1^-/- mice, which have no copies of the clock gene BMAL1, and their wildtype (Bmal1^+/+) littermates. This determines whether the circadian modulation of the PMC depends on an intact molecular circadian clock. Understanding the regulatory effects of the circadian system on PMC brain wave activity is crucial for the design of BMIs and their effective operation throughout the 24-hour day.

Until today, the Coptic culture is seen and studied by most of its onlookers as a dead Egyptian culture of late antiquity, neglecting the fact that there are more than 20 million people who identify as Coptic and live across continents and cultures. Copts only lived in Egypt until about 60 years ago, and thus, the sudden incline in rates of migration to different countries raised concerns regarding the loss of their culture's identity(ies), and opened dialogues concerning cultural adaptation. In light of these concerns and dialogues, this study explores what it means to be Coptic in a diverse society such as the U.S. The Coptic culture is founded on Orthodox Christian beliefs that are embedded in the symbolic significance of the physical aspects of the culture (i.e music, art, etc). Dressing these religious values in the aspects of a culture is a concept in this research termed as the "immersive experience" and has also been thoroughly explored. The data needed for this study has been gathered through 35 interviews, four focus groups, full participant observation, and auto-ethnography in three specific Coptic communities: Copts in Washington DC, Seattle, and in Mallawi in Egypt. The findings of this study construct a framework of meanings that shapes how the Coptic faith is embodied in the Coptic culture and how different Copts who have settled here in the States negotiate their culturally-embodied faith with the cultures of their new homelands. The framework suggests a theoretical approach that can provide both a proper transition of faith to new homelands, and a successful way to maintain heritage. This work is not only helpful to Copts, but also to communities of similar religious structure, and communities who wish to remain unified but not uniformed with their peers across different spaces and cultures.

For the past twenty years, scientists have attempted to learn more about the effects of pollution on coral species. However, identifying coral species in today's scientific community is more of an art than a science. For the last five years, researchers have been attempting to address this problem by comparing the skeletal structures of different coral species. Coral calcification is distinctive because it involves the formation of rapid aragonite super saturation. Aragonite is a very unusual form of calcium carbonate. It is much less thermodynamically stable than the primary form of calcium carbonate--calcite. There are two lines of thought as to why aragonite is preferentially precipitated in coral skeletons. One, the proteins secreted by the polyps within the coral create microenvironments that promote aragonite precipitation. Two, the magnesium from the surrounding ocean water interacts with the proteins in such a way that aragonite becomes the more energetically favorable precipitate. Our research examined the proteins and water involved in these calcification sites and compared them among species of coral collected from the Mo’orea Islands using Thermo Gravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC), Energy Dispersive X-Ray Spectroscopy (EDS) and Fourier Transform Infrared Spectroscopy (FT-IR). In short, we wanted to compare the magnesium, water content, and protein content/functional groups between species in the hope of finding species or site-specific trends. Our results confirmed the correlation between magnesium and protein, and discovered that the way in which corals create their exoskeleton is highly evolutionarily conserved.

Due to the rise of pathogen genetic knowledge and implementation methods of diagnoses pathways for patients, an increase in access to speedy and efficacious therapies is needed. The development of inexpensive, high-performance point-of-care (POC) tests does not only improve healthcare in low resource settings, but also moves the diagnoses out of hospitals and into homes and primary care offices. Paper-based microfluidic devices help both identify and screen for pathogens by allowing for more rapid care and treatment. The multiplexed, autonomous, disposable nucleic acid amplification test devices fabricated in the Yager Laboratory performs sequential functions - sample preparation, nucleic acid amplification, and lateral flow detection – for target identification. My project aims to bridge the last two segments into a single unit by introducing a method of inhibitory competition that permits for measurable, fluorescent-based analysis of isothermal DNA amplification from dry reagents in porous media. To prove this concept, a simplified experimental model of a multi-region, paper-based nucleic acid amplification test was designed, and new interference amplification mixtures developed. The isothermal strand displacement amplification (iSDA) technique utilized in these devices incorporates a fluorescent hybridization probe that allows for the detection of the increase in amplicons using an optical detection method. By incorporating a dilution of comparable, secondary strand of DNA as an internal control, a competition for reagents is established which creates different chemical sensitivities in the amplification zones. As a result, target DNA from the pathogen is amplified against a competitive threshold in a range. In the long run, fluorescence imaging of all regions can yield a quantitative measure of the concentration of pathogens in a sample. Overall, this project tests the fundamental groundwork for a new family of optical-based, quantitative devices by testing the use of fluorescent detection for POC tests, and investigating the principle of inhibitory competition.

College retention in the United States has been a growing concern among minority populations for decades. However, the Asian American and Pacific Islander (AAPI) population is one of the most overlooked and understudied populations in higher education because of the stereotype that all AAPIs do well in academia. To better understand the various resources needed for AAPI subpopulations, data among this diverse population needs to be disaggregated. This also suggests how resources can be improved to help these specific groups in higher education institutions. Although there have been numerous studies on specific subgroups in the AAPI community, minimal research has included Hawai'i's population in higher education. Retention rates among students from Hawai'i remain invisible. Additionally, retention rates are unclear of why and how these rates occur among students from Hawai'i. This study explored the challenges of students from Hawai'i in a predominately-white institution in relation to retention rates. From semi-structured interviews, commonalities were found from analyzing student responses that attended a public, four-year, predominately-white institution in the Pacific Northwest. This study found that student retention factors affecting college adjustment is pertinent in higher education for student persistence.

The present study examines low-income Latina mothers' influence on their preschool aged children's self-regulation of caloric intake. There is limited research done on the minority population in regards to parenting styles associated with children's self-regulation of eating. The research conducted is part of a larger study and analyzes the children's self-regulation and parents pressuring their children to eat as contributors to childhood obesity in terms of several procedures. The total number of participants consisted of 187 low-income Head Start Latina mothers with the exception of 2 grandmothers and their preschool children. Mothers were recruited through Head Start, a federally funded preschool program for low-income families and their children. Four procedures are used in my study, which observe children in the eating in the absence of hunger task, caregiver reports of feeding practices, observed pressure to eat during meals, and anthropometrics. It is predicted that caregivers who pressure their children to eat at the first time point will have children who show low levels of self-regulation and higher BMI's 18 months later. These results will have implications for the development of programs to address childhood obesity.

Endophytes are symbionts that live in the intercellular spaces of host plants. They can be fungi, bacteria, actinomycetes and/or viruses. Initial investigations indicate that endophytes provide a number of benefits that promote plant growth including, but not limited to, dinitrogen fixation, plant hormone production, nutrient acquisition, stress tolerance and increased immunological response. In exchange, they receive domicile and photosynthates. Endophytic biological and ecological services hold great potential for bioengineering and evolutionary inquiries, particularly so for sustainable agriculture. Nitrogen has historically been the nutrient limiting factor in all crop production. Bioengineering endophytic biomes capable of alleviating input demands while ameliorating soils damaged from industrial agriculture stands to offer novel solutions. This two year student-independent research is evaluating the inoculation of three fruit species, Malus domestica, Prunus avium, and Fragaria × ananassa with an endophytic consortia isolated by the UW Doty Lab. Washington is a leading state in fruit crops with over a hundred thousand hectares dedicated to production. Sweet fruit crops require heavy nitrogen inputs to yield nutritionally and economically viable fruits. Our primary objective is to investigate the effect of inoculation on the aforementioned crop physiology and fruit production. We are examining these effects through ecophysiology metrics involving rates of photosynthesis, stomatal conductance, biomass accretion, chlorophyll content, fluorescence rate, drought response, fruit sucrose content and biostatistic analysis. We hypothesize that our inoculated fruit crops will out perform controls as indicated with greater total biomass, fruit production and quality. First season preliminary results point to greater fruit biomass with higher sucrose content in Malus domestica. With crops now well established after season one, we anticipate a continued trend of improved crop total yields, higher sucrose content and greater total biomass production in all three varieties.

In order to understand the paleoecology of extinct animals, it is useful to look at extant species for comparison. Due to the shared ancestry between the modern opossum, Didelphis virginiana, and the extinct marsupialiform, Didelphodon vorax, the opossum is often used as an analog for understanding the life history of D. vorax. Didelphodon vorax, which was the largest mammal from the latest Cretaceous of North America (~66 million years ago), is thought to have had an ovivorous (egg eating) or durophagous (hard-shelled eating) diet; however, little is known about its ontogenetic patterns and ecology. Therefore, we aim to construct an age series of D. vorax to gain insight into diet changes throughout its life. A mandibular bending strength analysis investigates the level of force the mandible is capable of withstanding during biting in both dorsoventral and labiolingual directions. Additionally, we can use it to determine variation in bending strength along the body of the jaw, which allows us to further explore feeding behavior. Here, we illuminate cranial ontogenetic patterns in D. vorax by examining different development stages to determine diet variation based on mandibular strength profiles. We analyzed mandibular cross-sectional properties and applied beam theory to 15 D. virginiana and seven D. vorax specimens. Each individual used in the study resulted with a relative force greater than one, which is indicative of an adaptation toward exerting forces directly on prey, whereas a ratio less than one would indicate an adaptation toward withstanding struggling motions or transverse stresses. Finally, we find similar patterns of ontogeny for both species at different tooth positions, which supports the notion that diet changes throughout ontogeny of these marsupials. Thus, comparison of mandibular bending strength between extinct and extant mammals has the ability to gain insight into their feeding behavior and morphological adaptations.

Mosquitoes, such as Aedes aegypti, mainly rely on olfaction to find a host to feed on. By exploring mosquitoes’ olfactory learning abilities, we can increase our knowledge of how they choose their hosts. Using an olfactometer, we have conducted behavioral experiments demonstrating mosquitoes can associate a single odorant, 1-octen-3-ol, with a punishment. To further these results, we tested if mosquitoes would use their experience to guide their host feeding preferences, even when confronted with strong appetitive stimuli such as heat and potential blood meal. We found mosquitoes are indeed capable of aversive conditioning in the context of feeding. In this present project, we investigate if mosquitoes can learn the association between more complex vertebrate body odor mixtures (e.g. rat, chicken, human) and a punishment. After sampling the body odors of various vertebrates, we will aversively train mosquitoes to these odor bouquets. Mosquitoes are trained by simultaneously pairing the delivery of the host odor with a negative stimulus (mechanical shock), mimicking host defensive behavior. Upon training the mosquitoes, we test them in an olfactometer giving them the choice between the aversively trained odor bouquet and the solvent used as a control. To examine whether learning affects mosquitoes’ preference between two individual hosts, we plan to use both olfactometer and blood feeding assays. Further analysis of chemical profiles of the vertebrates species using a gas-chromatograph coupled with a mass spectrometer (GC-MS) will provide insights on the interspecific variability that may be used by mosquitoes to discriminate between individual hosts. These results help to advance knowledge of the behavior and biology of disease transmitting mosquitoes and provide interesting cues to develop efficient tools (e.g. bait) to fight them.

Current drug delivery methods lack the ability to effectively deliver a drug to a targeted region and fail to escape from the endosome. The ability to gain greater control over a drug’s effective delivery would lead to an enhanced efficacy of existing drugs, decrease the amount administration sessions, and reduce the number of side effects. Nanotechnology is a means to address these issues as the unique quantum properties witnessed on this scale allow for enhanced targeting and greater control over the delivery of the targeted drug. However, biocompatibility and toxicity are concerns with many developments within nanotechnology. To address these concerns, we have designed a siRNA-aptamer chimera based on protein biosynthesized calcium phosphate (CaP) nanoparticles. This was done due to CaP’s well-known biocompatibility and biodegradability as the calcium phosphate dissolves within the endosome, therefore releasing the siRNA into the cytoplasm of the cell. Within this project, we have targeted cancer cells as a means to quantify the efficacy of our nanoparticles. Through engineering a dual-functional protein expressed in E.coli, we were capable of 1) biosynthesizing CaP nanoparticles utilizing the protein’s affinity to calcium phosphate, and 2) binding siRNA onto the designed protein for delivery, which is utilized to inhibit the translation of the targeted cancer cells. The biomineralized nanoparticles were characterized via DLS and TEM to reveal that we had synthesized uniform 100nm nanoparticles, a promising result which supports our goal of designing nanoparticles capable of establishing greater control over drug delivery. The completion of this project would entail the successful design of biocompatible nanoparticles that could be effectively used to silence cancer cells. As the protein’s affinity for a substrate can be manipulated, these siRNA-aptamer chimeras could see use with other drugs as well; effectively leading to a powerful and versatile drug delivery system.

Macrophages play a large part in the immune response to Mycobaterium tuberculosis (M.tb) infection, and its response to infection is modulated by pattern recognition receptors. CD43 is a receptor glycoprotein on the macrophagal surface that has been shown to be associated with differential response severity of TB. The mechanism behind CD43 involvement in the macrophage response to M.tb is still unknown. Our hypothesis is that CD43 controls M.tb growth in human macrophages by mediating pro-inflammatory modulators. We knocked out the CD43 gene in the monocytic cell line THP-1 using the gene editing system lentiviral CRISPR Cas9. Using this cell line, we investigated how the knocked-out cells were affected when infected with M.tb compared to wild-types. We did this by measuring replication of a luminescent M.tb strain. Additionally, since M.tb capsule protein CPN 60.2 is a known ligand of CD43, we used CPN 60.2 to stimulate a tumor necrosis factor (TNF) cytokine response in both wild-type and knocked-out cells. We evaluated the TNF response using an ELISA assay. We found a statistically significant higher rate of replication in the CD43 knocked-out cells compared to wild type cells, indicating that CD43 plays a significant role in the macrophage’s pathway of killing M.tb. We also found significantly lower TNF secretion in CD43 knocked-out cells when compared to wild type cells after stimulation with CPN 60.2, which shows that cytokine response to M.tb is likely modulated by CD43 as well. Taken together, these results show that CD43 is a novel receptor on the macrophage surface that modulates the innate immune response to M.tb by controlling growth and pro-inflammatory cytokines such as TNF. The next steps in this project are to explore the exact mechanisms, such as M.tb macrophagal uptake and phagosome formation, that CD43 targets to control M.tb growth to develop targeted therapies for better TB treatment.

Chronic epilepsy is attributed to dysfunctional ion channels, including hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels, which are regulated by a signal cascade mediated by p38 mitogen activated protein kinase (p38 MAPK). Previous researchers in the Poolos Lab manipulated this cascade and discovered an increase in activation of c-Jun N-terminal kinase (JNK), seen by increased phosphorylated JNK in animals experiencing seizures. This is a novel connection and my project explores the timeline of JNK activity during the development of epilepsy. I hypothesize that JNK activity precedes epilepsy onset and may be causal of chronic epilepsy. To study epilepsy, we administer research-bred rats a pilocarpine injection that induces status epilepticus (SE), a state of continuous seizures. After one hour, the rat receives a phenobarbital injection to halt SE. Seizures begin around one week post-SE and achieve steady-state frequency around six weeks. I analyze brain tissue taken after one hour, one day, and one week post-SE using Western blotting to observe JNK differences from pilocarpine-treated rats to control rats. There are three isoforms of JNK; JNK 1 and 3 run on a 46 kDa band and JNK 2 runs on a 54 kDa band. JNK 3 is thought to have most significance in modulating brain neuronal activity. I have discovered a significant increase of the 54 kDa band at one hour post-SE (130 ± 10%, p<0.05, n=8) and one day post-SE (129 ± 11%, p<0.05, n=11); however, the 46 kDa band was insignificantly changed at both one hour post-SE (104 ± 7%, p>0.5, n=9) and one day post-SE (120 ± 12%, p=0.11, n=11). Gathering data at one week post-SE will show us if JNK activation is potentially causative of epilepsy. By understanding JNK activation, we can explore ways to prevent epilepsy development or lessen its severity after brain injury, through antiepileptic drugs and other therapeutic options.

Since DNA replication and transcription are concurrent in most bacteria, collisions (or conflicts) occur between these two processes. Conflicts have deleterious effects on cells, including double strand breaks and mutagenesis, especially when a gene is transcribed head-on to replication. Because conflicts increase mutagenesis specifically in genes that are oriented head-on to replication, this process may be a conserved strategy for targeted evolution. Consistent with this, a bioinformatics analysis determined that many genes in the head-on orientation are involved in stress response. We previously showed in Bacillus subtilis that the error prone translesion synthesis (TLS) polymerase YqjH is required for the asymmetric mutagenesis of genes in the two orientations and that transcription-coupled nucleotide excision repair (TC-NER) is also involved in this repair pathway. Under DNA damaging conditions, however, a different TLS polymerase, YqjW appeared to be responsible for mutational asymmetry, though TC-NER appears to still be involved. To show this, I used RecA-GFP microscopy to measure rates of replisome stalling in Wildtype, YqjW deletion mutant, and YqjW/UvrA double-deletion mutant (WT, ΔyqjW, and ΔyqjW/ΔuvrA) in B. subtilis, along with measuring these same strains' survival rates in response to two types of DNA damage. The data I generated was supported by mutation rate data generated through reversion assays done by a technician in the lab, and these data led us to propose that during conflicts in the presence of DNA damage, YqjW outcompetes YqjH to fill in gaps in DNA during TCR.

Cholangiocarcinoma, better known as bile duct cancer, is a rare and aggressive form of cancer in the biliary system. Bile duct cancer has the third lowest 5-year survival rate among all forms of cancer in the US. Due to its location, access to the biliary system for detection or diagnosis is difficult without invasive methods. Early detection of bile duct cancer is crucial and could be achieved by using the multimodal scanning fiber endoscope (SFE) developed in our lab. The SFE is able to noninvasively enter the biliary tree through the digestive system and present realistic information about the potential malignancies or disease state. Typically, a phantom is used to mimic the in-vivo presentation of disease state in order to validate the use of a new medical device. To prepare the SFE for this kind of cancer detection, a bile duct phantom with three dimensional (3D) cell culture was developed to test the sensitivity and specificity of the real-time in-vivo imaging. A biocompatible and optically clear polydimethylsiloxane (PDMS) device was first made for the cast of the hydrogel phantom. The device was utilized for structural stability of the phantom like a cast. The phantom was constructed by folding a flat sheet of hydrogel into a cylindrical tube with a lumen that reflects the true diameter of bile duct. The cancer cells were suspended at specific locations in order for spatial validation of SFE. The end result was the development of a 3D cell culture phantom with fluorescent probes targeted to cancer biomarkers. The phantom was imaged with SFE to evaluate its ability to accurately locate malignancies, distinguishing cancer cells from normal cells. Future work will extend to validation of fluorescent probes and ultimately lead to development of a new cancer imaging method with SFE to reduce late diagnosis.

Melioidosis, a disease caused by Burkholderia pseudomallei, is the third most fatal infectious disease in Thailand and causes morbidity and mortality in many other Southeast Asian countries. Due to fears that this bacterium could be weaponized, the US government lists this bacterium as a tier 1 select agent. Current treatments involve weeks of IV-delivered antibiotics and months of pills to prevent reoccurrence of the infection. Despite the availability of these treatments mortality can be as high as 40% in some locations. This situation calls for a more effective means of treatment to reduce loss of life, treatment time, and cost involved in fighting melioidosis. In order to develop a more efficient treatment, I created a novel delivery system to deliver large doses of antibiotics and, potentially, prophylactically load cells with therapeutic to prevent infection. I formulated nanoparticles using reversible addition-fragmentation chain transfer (RAFT) polymerization and microemulsion. The particles were first formulated using an inert monomer to test uniformity of the constructs and optimize the microemulsion procedure. Once this procedure was optimized, I added a prodrug monomer containing ciprofloxacin to the construct and the new constructs were characterized for size, shape, and the kinetics of prodrug degradation to its active form. Cytotoxicity to mammalian cells was tested with MTS assays using RAW 264.7 cells. Planktonic assays were also performed to test the efficacy of this novel delivery system to combat Burkholderia as compared to free ciprofloxacin.

Hydrogen sulfide (H₂S) is an important signaling molecule in humans, however the mechanisms behind H₂S signaling and its toxicity, which is thought to be similar to hydrogen cyanide (HCN), are poorly understood. Caenorhabditis elegans (C. elegans) is a convenient model to study exposure to H₂S and HCN as the proteins that mediate the organismal responses are highly conserved. Our previous work has shown that low levels of H₂S can increase thermotolerance and lifespans in C. elegans, but at high levels H₂S has toxic effects. The disparate effects of signaling and toxicity of H₂S on C. elegans led us to ask how the response to HCN compares to that of H₂S. To investigate this, we exposed different C. elegans strains to gaseous H₂S and HCN in sealed chambers and scored the survival rates between the two gases. We see that while both H₂S and HCN are toxic to C. elegans, HCN leads to death at lower concentrations, suggesting different modes of toxicity. We confirmed that HIF-1, a key transcription factor in the response to both H₂S and HCN, is necessary for survival in both H₂S and HCN. To determine if there are mechanistic similarities between the responses to these gases we exposed mutants that suppress hif-1 lethality in H₂S to both H₂S and HCN, and found that mutants that increased survival in H₂S did not necessarily increase resistance to HCN. This allows us to identify proteins that play a role in the response to H₂S. Understanding the proteins which differentially mediate toxicity in H₂S versus HCN will help us better understand the signaling roles of H₂S.

Organic photovoltaics (OPV) have emerged as a focus in photovoltaic research due to low-cost, simple, and high-throughput manufacturing capabilities. Still high vacuum deposited metals such as silver (Ag) are required for the top electrode of the cell, limiting size due to the high cost of silver, and throughput. This will significantly limit the performance of OPVs as larger sizes are necessary for many practical applications. My research addresses these important engineering issues by developing an alternative deposition method with less expensive materials. Therefore I plan to replace vacuum deposited Ag with electroplated copper (Cu). Recently it has been shown that high vacuum deposition can be replaced with low-cost metallization techniques such as electroplating. Electroplating is a well-established industrial process that is relatively low-cost, and simple, making it a suitable choice for rapid processing. While electroplating technology has been adopted for silicon-based photovoltaics, its advantages and implications have yet to be explored in OPVs. Cu is a significantly lower-cost material when compared to Ag with comparable conductivity characteristics as to not harm OPV performance. My method of investigation involves testing OPV performance once they are fabricated, then electroplate a thick Cu electrode on top of the Ag electrode, followed by once again testing OPV performance. My plan is to then characterize the effects of the electroplated Cu on the power conversion efficiency (PCE) or the ability to convert the sun’s energy into electrical energy of the OPV. Successfully replacing a sophisticated manufacturing process with simple methods, and cheap materials such as electroplated Cu, would create opportunities for further technology to be developed for OPV.

The aim of this project has been the development of a Helium-I collisional-radiative model, so that the measured intensities of various helium spectral lines could be used to diagnose electron temperature and density in the HIT-SI3 device. The HIT-SI (Helicity Injected Torus - Steady Inductive) plasma research lab tests a novel confinement strategy in which the injection of current along helical magnetic fields forms a magnetic structure which confines the bulk plasma. Currently, the lab’s methods of measuring electron temperature (via Thompson scattering) and electron density (via a far-infra-red laser) are difficult, time consuming, and unreliable. Collisional-radiative modeling can fill both roles in a simple and inexpensive manner. In brief, it is an attempt to accurately model the expected emission profiles for various helium spectral lines of interest over a range of electron temperature and density values and then to extract those values which correspond to the lines’ measured intensities. Our model has been encoded following published methods, and takes into account electron impact excitation/de-excitation and ionization, radiative recombination, three body recombination, and spontaneous de-excitation. The first stage was the successful replication of both equilibrium and non-equilibrium published solutions. We extended these models to the HIT-SI3 operating regime by adding in ion recycling terms. The necessary optical systems for data collection were built, and then calibrated using a stabilized light source. Results so far show that equilibrium models should be sufficient, but have so far not produced useful results. However, when the density range is fixed to within known values, we find a temperature range of between 10-25 eV.

For my history thesis I am studying French intellectuals’ appropriation of World War II memory in debates over the Algerian war. My research involves close readings of the works of key French intellectuals, some of which were printed in major French periodicals like Le Monde, L’Express, and Les Temps modernes. I focus predominantly on the last Governor-General of Algeria Jacques Soustelle and philosopher Jean-Paul Sartre. In these intellectuals’ arguments, two opposing conceptions of national honor arise. Soustelle was a staunch supporter of French sovereignty in Algeria. He connected the war to France’s duty to combat totalitarian and tyrannical threats to democracy, embodied in his eyes in the FLN Algerian rebels. In contrast, Jean-Paul Sartre argued against the war and colonialism, disparaging France for resembling Germany during World War II and compromising its democratic values through the use of torture. Within the context of intellectual petitions and French military coup d’états, these opposing conceptions of honor polarized contemporary debates. These debates in turn contributed to an environment of political instability that brought about the fall of the Fourth French Republic in 1958 and pushed France to settle a cease-fire with the FLN in 1962. However, despite their differences, both Soustelle and Sartre’s conceptions of honor were rooted in the same democratic ideals of the French Resistance of World War II. My research thus also reveals the unique, powerful, yet also dangerous multiplicity of memory. Algerian war intellectual debates revealed that intellectuals could draw on the same collective memory of a previous conflict in order to support radically opposing contemporary arguments and agendas. This reminds us that contemporary conflicts and ensuing debates cannot be understood in a vacuum. Memory is a strong rhetorical tool, and in many ways must be considered central to political and historical scholarship.

A barrier to quality healthcare in low-resource, rural areas is the lack of surgical care, and current anesthetic delivery devices either are expensive or require resources such as electricity. The Bioengineers Without Borders have proposed a low-cost, point-of-care anesthetic vaporizer, and seek a tool to assist in designing the device. To this end, a finite element model was constructed to predict the performance of a device in different operating conditions. We have imported the prototype’s geometry into finite element multiphysics software and added a domain representing the liquid anesthetic. Conservation equations and boundary conditions for mass, momentum, and heat transfer were applied to the domains of the device and numerically solved over clinically relevant time periods. Physical properties of the liquid halothane, stainless steel, and air were approximated using literature values of similar compounds. The model is currently being validated by comparing the vaporizer’s benchtop measurements of concentration and temperature to the computational model’s prediction. Computational results indicate that a vaporizer with no external heat transfer will experience a significant temperature and concentration drop, which in turn lowers the amount of anesthetic vaporized. When validated, the model will prove useful to engineers as proposed modification may be tested computationally before production, allowing for design refinement and less chance of device failure.

Highly controllable adhesives refers to adhesives that can be activated to attach strongly when needed but deactivated for easy and non-damaging detachment. There currently is a need to develop highly controllable adhesives that work optimally in wet environments, like those found inside the human body. Single fimH proteins, found at the tip of E. coli type 1 fimbria, form bonds with mannose that can be activated to bind strongly when pulled at high speeds, but are not activated under low speeds and as a result bind weakly. We hypothesize that thin-films composed of E. coli type 1 fimbriae can act as a nanoscale locking seatbelt, where they lock in at high speeds but not at low speeds, and that we can use mechanical force to control the adhesive behavior. Using atomic force microscopy (AFM) we tested the adhesive behavior between fimbriae thin-films and mannose covered surfaces. We observed that the force required to break the surfaces apart, as well as the number of activated bonds formed, increased the faster the surfaces were pulled away from each other. Also, by using the AFM to preload the bonds with high force, we observed that we could increase the number of activated bonds by a near 4 fold, as opposed to pulls with no preload. Inactivation after preload was also observed by allowing enough time for bonds to inactivate under no force, which decreased the bonds activated to only a 2 fold increase. These results show that these adhesive thin-films are capable of acting like a nanoscale locking seatbelt and can be controlled through mechanical force. An adhesive that can display these properties can have the potential to be incorporated into devices like pill endoscopy, giving an increased ability of controlled precise movement in fields like medical micro-robotics.

Repeating earthquakes are a common feature of the seismicity of active volcanoes, defined as any number of earthquakes that share the same source and are detected based on the similarity of their waveforms. Often, the waveforms of these repeating earthquakes change subtly with time, indicative of changes in the volcanic system. We use the technique of coda-wave interferometry to determine if the source or medium (e.g., seismic velocity) is changing with time. It has been shown that seismic velocity changed significantly immediately prior to the 2004 eruption of Mount St. Helens, and that these changes correlated with changes in the amount of seismicity. We take a similar approach using a catalog of repeating earthquake swarms during the eruption of Redoubt Volcano in 2009, to determine if there is a similar correlation between velocity changes and seismicity changes prior to a different eruption. Initial results indicate that the velocity dropped prior to at least two explosions, coincident with an increase in seismicity. We attribute the change in velocity to an increase of pressure in the system, which props open cracks, causes local inflation, and reduces seismic velocity. Furthermore, the increased pressure would also drive an increase in seismicity. These techniques may prove useful as part of a monitoring system, providing we can demonstrate the phenomenon is unique to eruptions and ubiquitous among them.

Sediment cores were recovered from Limnaea Sø and Braya Sø, closed-basin lakes in Southwestern Greenland, to reconstruct temperatures during the Holocene epoch (past ~10,000 years). The closed-basin topography makes the lakes ideal for studying changes in evaporation and precipitation, and variations in past lake conditions are recorded by authigenic carbonates in the lake sediments. The sediment cores were analyzed by x-ray, magnetic susceptibility, and bulk density to allow stratigraphic correlation between cores and to determine changes in sedimentation rate and lithology. After sectioning, a series of samples taken 20 cm apart were sent for radiocarbon dating, which placed the samples between present day and 9.5 ka (Calendar age). Due to the deposition rate (~0.1 mm/yr), these sediments were sectioned at 0.5 to 1 cm intervals to achieve ~100 year resolution. A series of samples were analyzed for total organic carbon, which provided insight into the history of vegetative changes surrounding the lakes. Samples were then prepared for δ13C and δ18O isotopic analysis on the Kiel Carbonate system/isotope ratio mass spectrometer. The δ13C and δ18O data show periods of isotopic changes, indicating either a strong change in the hydrologic regime or changes in surface air temperatures. We are analyzing these abrupt periods using novel clumped-isotope paleothermometry to determine whether the isotopic variations are a response to lake temperature variations as previous alkenone analyses indicate, or shifts in precipitation/evaporation patterns. While work from ice cores show relatively stable temperatures during the Holocene epoch, recent lake sediment records have suggested that temperatures may have been more variable than thought. If our results show no significant temperature variations, it will confirm previous interpretations based on δ18O that large shifts in the hydrologic cycle occurred. The clumped isotope paleothermometry technique will be the first of its kind applied to Greenland lake sediments to produce a temperature reconstruction.

During the 1960s and 70s, jazz enters the curriculae of school music programs as a result of social protest in the wake of the Civil Rights and Black Power movements. In Seattle, this acceptance of jazz as an academic art form coincides with the downfall of its popularity in the once vibrant club scenes of Jackson Street and the Central District. While Seattle once boasted a jazz scene that nurtured the likes of Ray Charles, Quincy Jones, and Ernestine Anderson, by the 1960s, the tradition of jazz becomes confined within high school and college jazz ensembles. Thus, Seattle's jazz scene is distanced from its working class roots, and its accessibility limited to those students who could afford to study it. Yet, even within these programs, racial tensions persist, particularly in the development of the University of Washington jazz program within the School of Music. I will argue that the complicated racial politics and history of Seattle's high school and college level jazz programs through the 1960s, 70s, and 80s restricted the availability of formal jazz education in Seattle to the wealthy and privileged. While many students, educators, and musicians from this time period viewed jazz as free of racial tensions, citing integrated ensembles as evidence, this idealized perspective ignores the larger political and economic factors that have always affected equal access and opportunity to quality jazz education. I expect that if we examinine the complex history of jazz education in Seattle, we will gain a greater understanding of why we must strive to make music programs accessible for all students.

What Persian politicians dubbed as ‘the woman question’ in the early twentieth century towards the end of the Qajar Dynasty became, and still remains, a hotly debated topic in Iran that is undeniably intertwined with Iranian ideas of nationalism. The question asked what the new role of women should be in society and what should be done to accomplish it. My honors history thesis examines how both the Pahlavi monarchy (1925-1979) and the Islamic Republic of Iran (1979-present) used women to visualize the national state of wellbeing. This thesis is rooted in extensive research in primary sources conducted over five months; my main sources include oral interviews of local Iranian-Americans, Mohammad Reza Shah Pahlavi’s autobiography, Women and Her Rights in Islam by Ayatollah Motahari, Tehran’s most popular women’s magazine, Zan-e Ruz, private family photo collections, newspaper articles, and speeches by the main political figures of the time. I answer the questions: how did each of the respective governments use control of women’s clothing as a strategy to implement their contrasting nationalist ideologies, and what was their reasoning behind the specific compulsory dress codes? Through analysis of books and speeches by Mohammad Reza Shah and Ayatollahs Khomeini and Motahari [leading Shiite clerics of the creation of the Islamic Republic], I conclude that parallel to the cultural notion that women represent familial honor, both regimes viewed women as symbols of national honor, and thus sought to control their clothing and socialization. Through poetry, political cartoons, and advertisements found in Zan-e Ruz, I investigate the transitions between mandatory hijab to Western clothing in the 1930s and back to mandatory hijab after the Islamic Revolution in 1979. Using oral history methodology, I determine a paradox that shows that despite outward appearances, a new contrary culture developed in the private realm.

Regulation of metabolic pathways is often implicated in many normal as well as disease processes in organisms. Our previous work discovered changes in the metabolome associated with longevity in eleven different species of fruit flies. The metabolic pathways associated with longevity included gluconeogenesis, the Krebs Cycle, and amino acid degradation. However, it is still unknown how basic nutrient parameters influence metabolic pathways in flies. We used mass spectrometry coupled with liquid chromatography to quantify the small molecules present in whole fly tissue. After finding metabolites associated with age, we completed nutrition assays to determine if there were associations between nutrient parameters and metabolomic profiles. The measurement of basic nutrient parameters consisted of colorimetric assays for total glucose and protein levels. Data analysis revealed correlations between the levels of each nutrient found in whole fly tissue and corresponding metabolomic profiles. In our future work, we plan to manipulate metabolic pathways or nutrient parameters found to be significantly associated with age and observe whether there are changes in longevity.

In 2015, nearly 20% of China’s urban population were floating population who lived and worked in the cities (Ma, 2015). Substantial amount of them live in areas called “villages in the cities” (VICs). These are neighborhoods that are left underdeveloped from the government-led urbanization in the past three decades. Though VICs are often identified as “problematic areas” by government officials and surrounding urban residents, they are used as an important “landing place” for the migrants who cannot afford housings elsewhere. Because of that, VICs are also commonly known as “rural-urban fringe” amongst Chinese scholars and politicians. My research project examines the social relationship between migrants and indigenous in Cuiwei, a VIC located in a Pearl River Delta city called Zhuhai. By analyzing the descriptive records from tweenty migrants and indigenous villagers whom I have interviewed from Cuiwei village, I found that there is a lack of sense of community amongst not only the migrant, but also indigenous villagers in Cuiwei. On the one hand, my paper will suggest that this lack of sense of community is a part of the larger problems of Chinese urbanization and development. On the other hand, my paper will argue that this character is in part the cause of inadequacy in historic preservation, neighborhood security, and redevelopment bargaining in this VIC community.

Public restroom maintenance and management is expensive and varies throughout city establishments in terms of cleaning schedules, safety monitoring and funding sources. Neighborhood groups pursuing the installation of public restrooms often earn grant money from their city to install the restroom, but must develop their own localized funding and management plans for the daily upkeep of the facility, including contingency costs for restroom misuse and vandalism. This research proposed a community participation plan as a strategy for managing a public restroom. Neighborhood Watch, as well as ‘Adopt a Street’ programs that invite/implore community members to take ownership of their neighborhood’s safety and well-being through volunteer work inspired this plan. It was hypothesized that the adaptation of these neighborhood programs for a public restroom would aid in creating ownership and respect of the restroom and thus discourage inappropriate use, saving money in cleaning and repair fees. A literature review examined crime monitoring programs, building respect in public space, and the idea of self-surveillance as a basis for developing strategies to solicit community participation. An online survey aided in understanding public perceptions about safety, accessibility, and cleanliness of public restroom facilities and the public’s role as users in reporting problems and maintaining the proper function of the restroom. Initial survey results indicated that while people supported the idea of shared community responsibility in public restroom upkeep, management cannot solely depend on volunteer contributions, but could rather supplement the maintenance efforts of paid employees. Findings from this research were presented to the University District ULoo committee, a community group studying the feasibility of bringing a public restroom to the U District neighborhood.

The City of Seattle has entered a phase of development where economic growth is happening at unprecedented rates for many neighborhoods. As Seattle changes for years to come, that presents the opportunity for local communities to learn how they can grow and to have a say about how their neighborhood will transform in the future. Seattle expresses local public policy preferences through Neighborhood Plans, which urban planners use as a framework for directing economic development. A powerful tool of controlling economic change in Seattle is through regulatory zoning laws in our Neighborhood Plans. Often, the primary goal of using these economic zoning tools is to help create livable and equitable communities. This research project analyzed these plans and tools to create potential changes in local neighborhoods and asks: how does Seattle’s zoning for economic growth create changes in neighborhoods? I examined the neighborhood of Columbia City as a case study to represent the dynamic growth and possible tensions of a shifting economic system on a local scale. After establishing the baseline of the neighborhood and its economy, I evaluated Seattle’s implementation of zoning and measured the impact of those regulations. The economic metrics to determine policy results were: affordable housing, retail revenue, the composition of businesses present and business turnover, and if patterns for new development matched city expectations. These results were mapped using a Geographical Information System (GIS), which also modeled the economic findings in the area. With a baseline model of the area’s economy, I then compared past zoning to where growth has been concentrated to find the significance of correlations present. With correlations between zoning laws and economic effects, I predicted how current zoning laws and future growth will affect the development of Columbia City.

How has colonization affected Samoan culinary traditions, identity, and health? What is the process of reclaiming culture, health, and identity through food sovereignty for Samoan communities in the United States (King County)? For centuries, the effects of Western colonialism in the Pacific has left scars on both indigenous lands and the wellbeing of indigenous peoples. What once was a sustainable food system has transformed to a system reliant on commodified and imported foods. I argue that a shift in diet from a traditional to Western contribute to a high prevalence of obesity, type 2 diabetes, and other chronic illnesses among the Samoan population. This study critically examines Samoan food practices, colonial history in the South Pacific, and current health challenges for Samoan communities. Methods of research include oral and written interviews by Samoan students and community members, discourse analysis, and participant-observation. The aim of this project is to inform the general public of the importance of revitalizing and sustaining indigenous food traditions for the health and overall well-being of our indigenous communities.

In Filipino culture, family is arguably the most important and emphasized value. When Filipino parents or elders require care, it is customary in the Filipino culture to assume the role of a caretaker, often times until they pass. However, this traditional family structure and system of care can be compromised when practiced in the United States. Since 1990, the Philippines has been consistently among the top five countries of origin, accounting for 4.5% of the 41.3 million total immigrant population in the United States. As of the 2010 Census, Washington is home to the fifth largest Filipino American population of any single state in the nation, with an estimated 137,083 Filipinos in the region. Among this large Filipino immigrant and Filipino American population, a high proportion are nurses and health care workers. Despite the large population of immigrant Filipinos in the U.S., many elders experience isolation, acculturation stress and depression due to the cultural disconnection and shift of family structure. Considering the high volume of Filipino elders and health care workers, it is important to investigate the relationship between Filipino elders and health care workers. Cultural concordance plays a large role in developing trust and allowing for effective health treatment. Through the qualitative methods of interviews, participant observation and spatial analysis, I have explored the different elements of health and wellness that effect Filipino elders. I delved into the experiences of Filipino elders who are cared for by their families as well as those who receive end-of-life care. More generally, I aim to identify the key aspects of holistic health among elderly Filipinos through their communal involvement and wellbeing. Through this research, I aim to emphasize the importance of cultural relationality and concordance in health care and in the broader community for Filipino elders in Seattle.

How do current U.S. Government healthcare policies affect Micronesians? As legal "aliens," indicated in the Compact of Free Association (COFA), what challenges do Micronesians experience while navigating the healthcare system in Washington State? Our research demonstrates that for 30 years Micronesian families migrating to the U.S. in search of beneficial opportunities experience great amount of difficulty when accessing healthcare in Washington State. Current U.S. policies towards migrants from the Freely Associated States perpetuate Dr. Paul Farmer's theory of structural violence by failing to acknowledge the United States Government's role in the healthcare burdens residing in the bodies of COFA citizens, due to U.S. colonialism within the region. Preliminary results indicate that different subgroups have distinct experiences in comparison to others. Methods of research include interviews with Micronesian students and community members, specifically from March 1st, 2016, A Day of Remembrance --solidarity event with the Marshallese community at the Burke Museum on the anniversary of the largest nuclear weapon ever tested by the U.S. Government.

Epileptic encephalopathies (EE) are severe forms of childhood epilepsies. Recent studies have shown that some cases of pediatric EE are caused by copy number variants (CNV), which are chromosomal deletions, duplications, or insertions of DNA. CNVs may contain genes that are important for neural health, causing disease when there is a copy number change. I am investigating rare CNVs in EE patients where the genetic cause is not known. I will screen EE patients for CNVs using a technique called array comparative genomic hybridization (aCGH) to identify rare CNVs that may be disease-causing. If a CNV is found, I will conduct aCGH on parents to determine if the CNV is de novo (arising for the first time in that individual and not inherited from either parent). We also expect that in cases with multiple affected family members, patients may inherit rare mutations from an affected parent. Preliminary results show that out of 69 patients screened thus far, 15 rare CNVs that range in size and number of genes affected have been identified in 13 patients. Of these, 3 de novo CNVs were identified that include a single exon deletion of the gene SLC2A1, a partial deletion of the gene NRXN1, and a 2.4 mb deletion in chromosomal region 7q11.23, affecting 40 genes. In addition, 2 patients each have a 1.4-1.5 mb deletion encompassing the region 16p13.11, which has been reported to be associated with epilepsy and developmental delay. Parental and segregation testing is ongoing for many patients. Rare CNVs can highlight genes implicated for proper neural function and development. This will help advance our understanding of the pathology and genetic basis of epilepsy. Furthermore, identification of particular pathogenic genes will be useful in the clinical setting for genetic counseling of affected patients and families.

Cognitive impairment in the form of dementia is a hallmark of Alzheimer’s disease (AD), an aging-related neurodegenerative disorder that is characterized by increasing deficits in memory and cognition. To allow for targeted, early intervention, it is necessary to develop reliable prognostic tools that can identify individuals at risk of developing AD. Studies suggest that several neuroimaging markers may be predictive of cognitive decline; these include atrophy of medial temporal lobe structures, reduced cerebral blood flow to the hippocampus, reduced functional connectivity between memory-related structures, and lower density of cholinergic cells within the nucleus basalis. In this study, we modeled the relationship between episodic memory test scores from Wechsler’s Adult Intelligence Scale using both established and novel neuroimaging markers while controlling for age, sex and education. Standard neuropsychological battery test scores and structural, diffusion and resting-state functional MRI data were collected from 54 participants (n = 29 women) aged 65 and above (mean = 78.6 years) recruited from Group Health Research Institute’s Adult Changes in Thought study. We found left hippocampal and left entorhinal cortex (LEC) volumes to be significantly smaller in cognitively impaired subjects as compared to healthy controls (p <0.05), and episodic memory scores were most positively correlated with LEC volumes (r = 0.45, p < 0.05) as compared to other MRI measures. Stepwise regression analysis also showed that LEC volume explained a significant portion of variance in memory scores (R² = 0.31, F = 6.88, p <0.05). In comparison to structural MRI markers, functional connectivity measures did not add predictive value, suggesting that physiological measures play a more mediating role in the relationship between cortical structure and performance. Overall, volumetric MRI measures served as better predictors of cognitive performance than other examined MRI measures, and the inclusion of these measures in future AD risk assessments may help to predict cognitive decline with greater sensitivity.

From Caesar Augustus onward, various Roman emperors and their family members were officially declared to be gods.  The topic of this paper concerns the imperial deification process and the role subjectivity played in which emperors and imperial family members were accorded divine status.  Specifically, the personal and political considerations of the reigning emperor or senate that served as the basis as to why a certain individual obtained or was denied deification, and the evolution of the divinization process over time, are examined.  Conversely, an alternative act called damnatio memoriae, by which the memory of deposed emperors or other unwelcome persons was condemned to oblivion after their death by the state, is also compared.  The reactions (as preserved in the poetry and prose of ancient writers) of the Romans and imperial subjects to the imperial deification apparatus in general and the conferral of divinity upon specific persons are also noted.  The paper focuses in particular on the reign of Domitian, who upon his succession deified his brother and immediate predecessor Titus, and later his young son as well.  In contrast to past imperial customs of deifying emperors after their death, Domitian demanded to be hailed as a god during his own lifetime, and the paper investigates his justifications for this deviation from the precedent that only a deceased emperor or member of the imperial family could be granted apotheosis.  He suffered the condemnation of his memory after his assassination.  And while poets and writers bestowed voluminous adulations upon him in his lifetime and referred to him as a god, his reputation plummeted precipitously after his death.

Antibodies play a critical role in our health system, adding specificity to diagnostics and therapeutics with their strong binding capabilities. Unfortunately, the binding cannot be controlled over time, introducing contamination of the target and preventing further testing with the bound sample. We propose an alternative to antibodies: a switchable binding protein. This protein has affinity for its binding target which can be modulated by environmental change without directly altering the binding site, otherwise known as allosteric regulation. This presents the potential to later change the binding target to a medically relevant antigen. A binding protein FimH, found on the end of bacteria pili, was used as the scaffold for the design because its binding depends on a significant structural change. I predict that if this protein is locked in place with a cross-linker or covalent bond, which experiences a large structural change under a simple external stimulus, FimH binding could be precisely triggered. Inserting a disulfide bond or a photoswitchable linker are two methods I am investigating with their binding triggers being dithiothreitol (DTT) and ultra-violet (UV) light, respectively. The photoswitchable linker design is ideal because it would induce reversible binding, allowing for reuse of our protein. Using past structural knowledge, multiple mutation designs are being created and their binding tested under external stimulus. The design requires mutation placed far from the binding site in order to create this allosteric switch. Initial results indicate the design with a disulfide bond between residues 112 and 189 does switch binding affinity, triggered to unbind, when DTT is added. This research also has the potential to contribute a novel approach to regulating large proteins and add specificity in diagnostics by concentrating the target.

Bacterial endocarditis is an infection on the inner lining of the heart. When studying bacterial adhesion, researchers often ignore that blood is pumped through the heart in a pulsatile manner. Because of this, all studies have been done with constant flow. We hypothesize that pulsatile flow conditions play a critical role in this disease. We studied how Streptococcus gordonii, a strain of bacteria that is known to cause bacterial endocarditis, bound in constant and pulsatile flow. The rate of adhesion in both constant and pulsatile flow was measured at different shear stresses. When suspended in buffer, the bacteria bound at the same rate in both flow conditions. The overall trend showed the rate of bacterial adhesion was highest at 10 dyne/cm². At the shear stresses predicted to be present within the heart, 20 – 80 dyne/cm², only about 10% of bacteria bound as compared to the peak value. In a solution with 50% buffer and 50% red blood cells (RBCs), the percentage commonly found in the blood, there was a dramatic change in the trend of bacterial adhesion in constant flow. Instead of having a peak value, the rate of adhesion increased with the level of shear stress, allowing for a much higher rate of binding in the 20 – 80 dyne/cm² range. We were unable to repeat this experiment using pulsatile flow due to limitations in our flow device but this could mean a dramatic change in the trend observed in pulsatile flow as well. We have created a new device to further investigate our hypothesis and better simulate the conditions found in the heart.

Databases are growing too large for a single computer to handle; cloud-based platforms are capable of handling limitless amounts of information while big data is quickly becoming one of the most sought after fields for its many applications. My research focuses on adapting machine learning methods within the cloud-based computing platform: Microsoft Azure Machine Learning Studio (MAMLS), and comparing the results to the current state-of-the-art processes. Our goal is to create and automate a generalized flow that utilizes cloud-based resources for classification and regression tasks. In this work, classification tasks refer to data sets where each sample has a discrete label, i.e., class A, B, or C, while regression tasks refer to data sets where each sample has a continuous label, i.e., anywhere within the range from 1-10. In both cases, the goal is to correctly predict the label for each sample through the implementation of machine learning algorithms. The preliminary results imply that the MAMLS platform is a viable option for an automatic classification application because the overall process did not need to be tailored specifically for each data set. The automated decision-making process, including the choice of an optimal machine learning algorithm and parameter fine-tuning, has been realized through the inclusion of modules written in the ‘R’ programming language. My current work focus on an in-depth analysis of prior work regarding the data sets in study. Currently, the automated flow is capable of accepting a generalized input and synthesizing optimal, parameterized classification results with minimal manual supervision, this cloud-based flow can be applied to a wide range of vendor-based applications.

The purpose of this research is to design, build, and deploy an all-sky cloud monitor instrument for Apache Point Observatory. This camera will be used to monitor the sky surrounding the telescope and provide sight down to the horizon via visual and numerical feedback. This research will create automatic image analysis software that will calculate sky brightness and uniformity, both of which can be used to constrain the level of atmospheric blockage. The cloud camera system will also have weather metrology feedback which can alert observers using the telescopes to current hazardous weather conditions. As a self-contained unit, this camera, and associated sensors, will require no actions by on-site or remote observers to function. An instrument with this mode of operation will allow for safe remote observing with minimal (to zero) engineering support. The end users of this instrument will be astronomers using the telescopes remotely. This will allow remote users to see the current sky conditions, which can have a great effect on their data.

The models of the universe’s diffuse configuration of hydrogen and helium atoms, known as the Intergalactic Medium (IGM), have become increasingly accurate in predicting the mechanics of the universe. Simulations of the IGM can provide a foundation for cosmology to be built upon. The purpose of our research is to test the accuracy and precision of our latest model of the IGM. Using data from the Very Large Telescope (VLT) in Chile, we analyzed quasar spectra for absorption lines at the Lyman-Alpha wavelength, creating phenomena called the Lyman-Alpha forest. We then processed this data incorporating scripts written in the programming language, Python, in order to compare the probability distribution function of the Lyman-Alpha absorption of the observed quasar spectra to the simulated quasar spectra. Interpreting our data we found that our simulations fell within one standard deviation of the observed data. Further analysis of our data showed that the simulations were more accurate for quasars at a lower redshift - those which were moving away from us at a slower rate - than quasars at a higher redshift - those moving away from us most rapidly. The largest contributors to error stem from the effects of other material in the IGM causing metal lines, our methods of metal line removal, and the limits of the size and quality of our observational sample. Metal lines skew our understanding of the Lyman-Alpha forest and a larger sample would decrease the variance among the samples. We plan on continuing research and improving the techniques of comparing the observations to models. An increased understanding of an effective model of the IGM can be used as a cosmological map of time to predict the origins of the universe as well as its future.

The performance of polymer solar cells (PSC) have been a popular study in its applications and fabrication processes in the field of solar energy. Although the power conversion efficiency (PCE) for this type of organic solar cell increased to about 6%, there is a need for the improvement in its device architecture. Creating solar cells involve a strategic fabrication process that consists of several layers that must be built in sequence. Each layer serves a crucial role. The primary role in the performance of its PCE is in optimizing the parameter of transport layers that facilitate charge carriers from the active layer. Fabricating solar cells start with a premade indium-tin oxide (ITO) coated electrode glass slide, followed by ZnO, an electron transport layer (ETL) created with specific measurements. The active layer, P3HT:PCBM is then created with appropriate concentration levels. MoO₃, a hole transport layer (HTL), is deposited on top of the active layer, at a different thicknesses. Lastly, Ag is deposited to serve as our second electrode. Completing the solar cell with the second electrode completes the circuit. Electron charge carriers transport through ZnO to ITO, while the hole charge carriers transport through MoO₃ to Ag. My research, therefore, aims to address what is the optimized thickness of the hole transport layer (HTL), MoO₃, in order to further improve the PCE. In focusing on MoO₃, results determined that as the layer thickness of MoO₃ is reduced, the PCE increases. In opposition, as the layer thickness of MoO₃ increases, the PCE decreases. By controlling the thickness of the hole transport layer, this allowed me to find an optimized thickness to produce high PCEs. This research opens new possibilities and opportunities for future processes when optimizing a particular layer. 

The Joint United Nations Program on HIV/AIDS (UNAIDS) reported in 2014 that approximately 36.9 million people in the world are currently living with HIV/AIDS. Many of these individuals reside in low and middle income countries where access to STD prevention methods is limited and risk of infection is high. Electrospun nanofibers are a promising drug delivery platform in development, with the potential to provide either pericoital or sustained protection at an affordable cost. Here, we fabricate and characterize nanofibers composed of polyvinyl alcohol (PVA) and agarose (AGR), a naturally occurring polysaccharide that is both mechanically strong and biocompatible. Previous studies in our group have reported challenges in electrospinning polymer blends from AGR and PVA, likely due to the high gelling properties of agarose. Subsequently, a non-uniform distribution of fiber diameter resulted in variable mechanical properties with an undesirable burst release of hydrophilic small molecule drugs (tenofovir, TFV). In this study, the electrospinning process was improved to achieve higher AGR loading in the nanofibers. We used a melt-electrospinning technique where the polymer solution was heated at a constant temperature of approximately 60°C, which is below the glass transition temperature of PVA. Constant heating of the polymer solution reduced AGR gelation and improved fiber throughput. The melt-electrospinning process enabled fabrication of nanofibers with up to 30% AGR content. Mechanical testing on the nanofibers revealed that the Young’s Modulus was approximately 100 – 200 MPa. Drug release studies revealed that AGR loading in the nanofibers did not significantly affect the burst release of TFV from the fibers. Fiber properties indicate that the PVA-AGR system must be optimized to further validate experimental results. In general, the melt-electrospinning process was key to enable the fabrication of PVA-AGR nanofibers with increased AGR content, which allows for enhanced characterization of these fibers as an antiretroviral drug delivery platform.

Chronic inflammation in human immunodeficiency virus (HIV) infected individuals is associated with increased mortality, even in patients who are virally suppressed by antiretroviral therapy.The goal of this research is to understand how the gastrointestinal (GI) tract is damaged during early HIV/SIV infection. In many infections, neutrophils play an important part during early response to infection because of their microbial killing properties. The role of neutrophils in the establishment of HIV infection and subsequent chronic inflammation has not been examined. Our purpose was to study neutrophil supporting cytokines before and during acute simian immunodeficiency virus (SIV) infection and their potential role in the kinetics of the neutrophil response. We used SIV in the Rhesus macaque model instead of HIV so that we could obtain longitudinal samples very early after infection to observe the neutrophil kinetics. The neutrophil supporting cytokines we looked at were IL-8, IL-17, and G-CSF. We hypothesized neutrophils would decrease during acute SIV infection in peripheral blood in response to the decreasing neutrophil-supporting cytokines. We used Luminex to measure cytokine levels in the blood at each time point, and used Complete Blood Count to get blood neutrophil concentrations. After infection, neutrophils initially increased, but then 14 days post-infection there was a decrease in most of the animals. Prior to the post-infection decrease of neutrophils, we saw a decline of IL-8 levels, which may contribute to neutrophil decline. In contrast to other types of infection, we saw no increase in G-CSF or IL-17. However, we did observe increases in pro-inflammatory cytokines 14 days post-infection, and the pro-inflammatory cytokine IL-15 correlated with neutrophil decrease. These data suggest that reduced neutrophil supporting cytokines and increased pro-inflammatory cytokines may be contributing to the neutrophil decline observed in acute HIV and SIV infection.

Olfaction is an important method of communication for organisms such as mice. However, metabolism is significantly influenced by the integrity of sleep and the amount of dietary fat. Here I examined whether environmental factors such as sleep and diet could affect volatile profiles, because these may in turn affect the biological signals that are relayed between conspecifics. We hypothesized that the volatile profiles in mice would change following sleep disruption and/or increased fat levels intake. A group of one strain of mice was divided into two groups: one control group with undisturbed sleep and one experimental group that underwent sleep disturbance. Each group was divided again into two groups: one received regular chow diet and the other received high-fat diet. All mice were individually housed during the 4-week treatment period, and fecal samples were taken 2 weeks after cessation of sleep and diet manipulations through solid-phase microextraction (SPME). Following gas chromatography and mass spectroscopy (GC-MS) of these samples, I analyzed the data and found differences in abundance of volatile compounds among the experimental groups. Namely, production of pentanoic acid and benzaldehyde decreased considerably as a result of sleep disruption. Several other compounds were also found to undergo change in abundance as a result of fat level in diet or from a combination of both factors. My work in this project could potentially be a starting point in investigating the metabolic pathways associated with sleep disruption and diet that are linked to the above changes in volatile production.

Over the last 10 years, the number of undocumented immigrants in the United States has gradually begun to decline for the first time in decades. While previous research has looked at this change in the rate of undocumented immigrants across the country as a whole, there is very little information on how or why these trends have changed within and across states. Yet, some states are losing more undocumented immigrants than the nation as a whole, and some states still have a growing undocumented immigrant population. Why has the rate of undocumented immigration dropped so much more in particular states since the mid 2000s, when compared to the national rates since the same year? To answer this question, I employ statistical methods and examine the relationship between the number of undocumented immigrants within a state, as well as state immigration legislation. I expect that the number and severity of state laws regulating or deterring undocumented immigrants corresponds with a more significant drop in the number of undocumented immigrants.

Carnivorous plants inhabit low nitrogen soils and must consume insects for nutrition. They achieve this by using modified leaves, called traps, which can catch prey. Thus, the ability of carnivorous plants to attract prey is key for their survival. In this study, we tested the hypothesis that carnivorous plants use scents to lure insect prey. We considered two possible cases: 1) prey are lured by only trap scents, so they will only detect trap scents or 2) prey animals are lured by both trap and flower scents, so they will detect scents from both organs. We focused on Sarracenia pitcher plants, a genus that is indigenous to the southeastern United States, and their interactions with calliphorid flies (commonly known as blow flies), one of their major prey. We used electroanntenograms (EAGs) to determine whether flies were responding to specific smells. We did this by hooking up a whole fly prep to the EAG machine, pulsing specific scent compounds over the antennae, and recording the electrical responses produced by the fly. In our tests so far, we have found that flies respond most strongly to pulses of DMT, a compound which is found in the scents of traps that have captured prey. Flies also respond to beta-ionone, a compound that is found in pitcher plant flowers. Our preliminary results indicate that flies are able to detect both trap and flower scents, so this supports the hypothesis that pitcher plants use a combination of trap and flower scents to attract their prey. We plan on testing a wider range of trap and flower scents using both EAG pulses and gas chromatography - electroantennography (GC-EAG).

This project examines local government effort to combat persistent racial residential segregation. Although U.S. cities today are more diverse than ever, many continue to be characterized by black-white segregation. Because many local governments today do not implement a sufficient variety of policy solutions to address segregation, an important question arises: What might deter local government implementation of these policies? I hypothesize that fragmentation, a result of the fracturing of metropolitan statistical areas (MSA) into many smaller local governments, can explain this inaction. Because metropolitan areas vary regarding their level of fragmentation and therefore the political and economic competitiveness local governments face, local governments in more fragmented MSA’s will prioritize policy issues that will allow them to compete. In order to test my hypothesis, I use statistical methods to analyze local government effort to combat segregation for three U.S. cities, Baltimore, St. Louis, and Atlanta between 2011-2014. I draw on original research identifying key legislation and newspaper articles addressing residential segregation and examine the role of institutional fragmentation in each context, controlling for other factors. This project will offer a new understanding of local governments’ role in addressing a crucial aspect of racial inequality by revealing one reason many local governments do not treat racial residential segregation as an immediate issue to be addressed through public policy.

Francisella tularensis and Burkholderia pseudomallei, the agents of tularemia and melioidosis, respectively, have been identified by the Centers for Disease Control and Prevention (CDC) as bioterrorism agents that could lead to mass casualties and severe threat to public health. These pathogens are highly infectious and aerosolizable intracellular alveolar pathogens that can cause fatal respiratory tract infections. The intracellular compartmentalization of these pathogenic organisms within alveolar macrophages is a significant barrier to bacterial clearance and contributes to their associated morbidity and mortality. Currently, there is no effective treatment to eradicate melioidosis and tularemia other than prolonged antibiotic therapy and even with several months of intensive antibiotic treatment, complete clearance of these pathogens is not guaranteed. Therefore, there is an urgent clinical need to develop new therapeutic drug nanocarriers that can deliver antibiotics intracellularly to alveolar macrophages to increase treatment efficacy of tularemia and melioidosis. The goal of this project is to design biodegradable and nontoxic polymeric nanoparticles with various drug release rates and drug loading densities to overcome pathogens’ drug resistance mechanisms. The nanoparticle scaffolds will be synthesized using Polysorbate 80 via Thiol-ene and Thiol-Michael “click” reactions to maintain biocompatibility while incorporating functional groups that are amenable to chemical modification for enhanced drug conjugation. Once the nanoparticle scaffolds are characterized, they will be conjugated to antibiotics such as ciprofloxacin via hydrolytically degradable ester bonds. Drug release profiles will be characterized in serum containing media via reverse phase HPLC to evaluate their efficacies. Once ciprofloxacin is conjugated to the nanoparticle scaffolds, in vitro studies will be conducted to evaluate the polymeric nanoparticles’ therapeutic efficacy and toxicity in co-culture macrophage models of bacterial infection. Development of these polymeric nanoparticles will lead to rapid clearance of tularemia and melioidosis with shorter antibiotic administration while reducing the chances of relapse and antimicrobial resistance.

Blowflies are a major food source of pitcher plants. The main goal of this project is to observe if scents produced by the pitchers can attract blowflies. To test the hypothesis, experiments were conducted to determine the volatiles produced by pitcher plants and if flies have a preferred scent. We collected scents from pitcher traps through headspace sampling for a period of 24 hours (+/- 1hour), and ran them on a GCMS to identify the compounds. A Y-maze choice experiment was set up to determine if flies were attracted or repelled by any particular scent produced by pitcher plants. One arm in the Y-maze is set up as control, in which the scent emitted was purely mineral oil. While the other arm contained the scent that was being tested such as DMT or benzaldehyde. Each scent that was tested included 50 trials so that results due to random chance can be reduced. Initial experiments identified that traps produce a wide range of volatiles from sweet scents like ethyl tiglate to carrion-like scents such as DMT. On average, the flies went into the side arm with DMT scent diffused into it. The observed data can be explained by the possibility that flies have preference over the scent of DMT. I plan on testing additional scents produced by traps to determine if they are detectable and attractive to pitcher plant prey.

Point-of-care diagnostic tests allow clinicians or care providers to make rapid, informed treatment decisions in settings where patient follow-up is unlikely or not an option (i.e. rural regions in developing countries). The Anisotropic Ratchet Conveyors (ARC) platform developed in our laboratory can transport small, individual droplets with a passive surface pattern and orthogonal vibration. In this work, a novel ARC system is characterized for future use in automated point-of-care diagnostic devices. Effects of rung radius on droplet transport were characterized with respect to the acceleration amplitude of the vibration required to initiate transport. The acceleration amplitude was significantly lower on the 1000 µm radius and 1500 µm radius rungs compared to the 500 µm radius rungs and slightly lower on the 1000 µm radius rungs compared to the 1500 µm radius rungs. Interestingly, the radius of the rungs was also observed to influence the natural frequency of the transported droplets. The results of this work will be applied to optimize droplet transport across functionalized detection regions on chip. Thus, ongoing work aims to functionalize the silicon dioxide rungs for immunosensing. In order to demonstrate proof-of-concept immunosensing in droplets, antibodies (e.g. antibodies targeting human immunoglobulin gamma - anti-IgG) will be bound to the silicon dioxide rungs using a linking molecule (e.g. silane-PEG-NHS or APTES) via micro contact printing, a common technique used to transfer proteins to a surface with elastomeric stamps. This process will be optimized to control the density of bound antibodies. Fluorescent microscopy will be used to verify and characterize the capture of fluorescently tagged target molecules (e.g. FITC-IgG) suspended in droplets transported on ARC tracks. Experiments will also be performed to characterize how antibody capture affects the velocity droplets transported on rungs of each radius group. The ability to capture target molecules suspended in droplets will present the potential of using ARC devices as a platform for rapid, efficient healthcare diagnostics.

The model yeast, Saccharomyces cerevisiae, can evolve the ability to clump, a trait called flocculation that protects the yeast cells from stress factors including antimicrobial treatments. Understanding the genetics behind this trait could give us insight into treatment options for biofilm-related complications in hospitals as well as targets for microbe engineering in the case of industrial production. In this project, we are interested in identifying the mutations that occur when yeast evolve flocculation. We evolved S. cerevisiae from a non-flocculent ancestor strain for 300 generations in miniature chemostats, multiplexed culture devices that maintain a constant environment. Strains that flocculate have a selective advantage in these devices, and 35% of our final populations evolved this trait. In backcrossing these flocculent strains with their ancestor and dissecting the tetrads into four spores, 20 out of 22 strains segregated the flocculation trait with a 2:2 ratio, indicative of a mutation in a single gene causing the trait. We identified causal alleles using bulk segregant analysis, a pooling and sequencing approach, including a causal transposable element insertion in the promoter of FLO1, a gene known to control flocculation. We hypothesize that this mutation is responsible for changing how FLO1 is expressed and have now identified this mutation in 13 of the clones, some of which exhibit varying phenotypes. We believe that additional mutations may be responsible for this phenotypic variation and are using microscopy to target our sequencing for the gene(s) of interest. We also used these findings to engineer a new strain with FLO1 deleted, which we hypothesized would take longer to flocculate. We report the results of a new evolution experiment comparing flocculation time between the deletion strain and the wild-type strain and demonstrate that our engineering effectively decreases flocculation ability. This is a promising result for both medical and industrial applications.

Forests emit an array of reactive volatile organic compounds (VOCs), such as alpha-pinene (C₁₀H₁₆), to the atmosphere. Atmospheric oxidation can produce low volatility products, which contribute to the formation and growth of atmospheric particles, in turn modulating the amount of sunlight, or precipitation that reaches the surface. The chemistry behind this particle formation process is poorly understood. We present measurements and analysis of the gas- and particle-phase composition produced from alpha-pinene ozonolysis utilizing the University of Washington (UW) Chamber, a 0.7 m³ Teflon bag. The UW Chamber was operated in continuous flow mode, where ~70 ppb of alpha-pinene and excess ozone were constantly input and products constantly sampled with an Iodide adduct High Resolution – Time of Flight – Chemical Ionization Mass Spectrometer (HR-ToF-CIMS) coupled to the Filter Inlet for Gases and AEROsols (FIGAERO). This method provides elemental composition for each detected molecule, but does not provide structural information. To address this issue we employ a voltage scanning technique where we increase the electric field strength within the HR-ToF-CIMS to induce the declustering of reagent ion-molecule clusters. This technique causes a decrease in signal for most compounds, as the reagent-ion is no longer clustered to the molecule. It is hypothesized, that if the reagent-ion is clustered to a peroxy acid group, then enhanced declustering can promote reactive charge transfer reactions of the type I-(RC(O)OOH) -> HOI + RC(O)O -. We expect to observe decrease in signal from the parent I -(RC(O)OOH) adducts accompanied by a corresponding increase in carboxylate ion(RC(O)O-) signals. The mass spectrometer is able to resolve ions that do and do not contain an Iodide, and thus we can, for the first time, quantitatively determine online and in real time, how many peroxy acid products are present and their fractional contribution to the total of observed alpha-pinene oxidation products.

The security level of the interactions between human users and cyber systems is becoming more and more important in many areas. The traditional way of identifying a user is to utilize alphanumerical passwords, which are easy to realize but hard to memorize and vulnerable to various kinds of attack. To enhance security performance for user authentication, we take the advantage of the haptic interaction of new touchscreen devices that have recently been introduced. Previous studies show that how a person interacts with a haptic interface is unique and can be used for identification and authentication purposes. We applied this technique using the Microsoft Surface Pro 3, which has a pen, the N-trig digitizer. Having its API (ways for developers to talk to another site or services) made it easier to transfer data to the haptic password system. By developing an app on a writable windows tablet, we successfully captured ink data and pointer properties such as pressure, twist and orientation. We built a haptic password system and invited subjects to take specific tests. After data analysis, we found that this system is secure with good performance and forgery attack resistance. This system provides a complex but intuitive way of creating signature passwords. This haptic interaction technique can be applied to those pressure sensitive devices, such as tablets and signature touch screens. This could provide a much safer way of authorizing credit card transactions and lead to reduced transaction fraud.
 

Research has shown that online mindfulness training is an effective means to reduce stress and increase coping among university students. The beGreatful project builds on the findings of this research to create an online platform which students can use to participate in mindful practices. The platform operates around two key components. The first component is an online gratitude journal. This component is designed to encourage mindful thinking by guiding the user through the process of completing a journal entry. Our goal within this component is to help students build the habit of setting aside time to reflect upon their day. This helps foster the habit of positive thinking which can lead to increased resilience. The second component is an analytical feature designed to help users visualize patterns that occur in their journal entries so that they can become more aware of their thought patterns. This feature also reinforces the habit of writing in the journal daily by providing a snapshot of each day and showing the user’s improvement overtime. The online platform will serve as a low cost, accessible tool for college students to maintain a healthy mindset. We are currently in the design phase of the project. We have surveyed approximately 50 students at the University of Washington to gauge initial student interest in the project and have tested our first iteration of prototypes with 10 students. Based on these tests, we are working on our second iteration of prototypes which we will continue to test and improve. We will begin developing the platform next quarter and will have built the first live version of the beGreatful web application by the end of spring quarter.

Our Informatics capstone team of four is creating an Android application to help solve our research question: How do we create an efficient mobile platform that will display real-time airport conditions so that patrons of SeaTac International Airport can navigate through the airport in a more timely and hassle-free manner? We have conducted thorough user research in the form of an online survey and several interviews, aiming to understand the greatest frustrations users encounter while at the airport, and how features of our application could help solve these problems. We found that most people were frustrated by the TSA lines and not knowing how long they would have to wait in them. In the online survey, we collected around 150 responses. We used the survey results to help create interview questions, and then interviewed at least 2 people that fell under each persona category: Business Traveler, Recreational Traveler, International Traveler, and a Family Traveler. From this research we decided that our application would focus on three main features: predicting TSA wait times, predicting baggage check lines, and locating restaurants, shops, and amenities. We believe that our user research was very informative in helping us determine what features our application should support to most benefit users in navigating throughout the airport.  

Depression acts as one of the leading mental health diagnostics affecting college-aged students today. But with a societal stigma surrounding mental health and barriers to therapy, it is difficult for students to receive the support that they need to better manage their depressive state. Current literature delves into the causes of depression, and suggests that having a supportive social network is linked to lower levels of depression and anxiety. However, discussion of a highly accessible solution through technology was not found. Trellis is an exploratory project meant to discover whether a mobile application could be effectively used to support students through confronting the stigma of depression among college-aged students. To understand the needs of depressed college-aged students, an anonymous survey was posted on Facebook and Reddit, yielding 639 responses. The survey segmented participants into three groups related to depression and anxiety: those who were clinically diagnosed, those who felt they had symptoms but had not yet sought professional help, and those who are not personally struggling, but know of people who are. Participants were asked questions depending on the group they identified most with. Free response questions involved identifying coping strategies used and identifying what they wished they had to combat the symptoms. Likert scale questions were used to assess general attitudes towards why students hadn’t sought professional help, and the reasons as to why those that had friends exhibiting depressive symptoms did not yet broach the subject with them.

Using ATLAS.ti, a qualitative analysis was conducted to thoroughly vet the answers received. It was discovered that students with depression long for a caring, non-judgmental support group and better education about mental health, as the stigma makes is difficult to seek help.

Trellis is designed to connect those that want to get support, to those that want to give support.

According to the World Health Organization, more than 100 million people annually drop into poverty because of health care related costs. Point-of-care (POC) diagnostic testing works to alleviate this issue. Point-of-care diagnostics is testing that delivers cheap, accurate, and timely diagnosis in the hospital, the field, the office, or the home. In this way, POC testing can provide vital health information in a way that reduces the burden of health care globally. The lab of Dr. Paul Yager has developed a POC diagnostic device known as the multiplexed autonomous disposable nucleic acid amplification test, or MAD NAAT, which returns results in less than one hour. This device uses a two-dimensional paper network (2DPN) to automate the fluidic steps of a nucleic acid-based diagnostic assay, which detects the presence of one or more pathogens (e.g. MRSA, RSV) in a patient’s test sample. The downstream region of the 2DPN uses nitrocellulose strips to support a visual, colorimetric detection system. The detection system produces a series of visible red lines on the nitrocellulose strip that indicate the result of the test and associated controls. My research is focused on the optimization of the detection system, specifically: increasing the visible intensity of these red lines without increasing device cost. I have investigated the effects of varying the geometry of the 2DPN through the detection region. The goal of this research is to obtain the most intense test line signal with the least amount of expensive reagents, at the lowest possible pathogen count, in the least amount of time. I have also used MATLAB to implement patient sample analyzations for the MAD NAAT device. These efforts support further development of an affordable POC device, which will improve patient health outcomes in communities that lack proper healthcare.

Current tissue-engineered vascular grafts (TEVG) lack physiologically relevant internal structural organization which limits their mechanical properties and contractility. It has previously been shown that through the utilization of anisotropically nanopatterned scaffolds, vascular smooth muscle cells (vSMC) can be manipulated to express enhanced contractile phenotypes. We hypothesize that by using vSMCs cultured on nanopatterned surfaces we can create a TEVG, which exhibits native internal structure, that has increased mechanical properties and contains vSMCs with increased expression of contractile markers compared to a graft which lacks internal organization. In this study, we developed a flexible thermoresponsive nanofabricated substratum (fTNFS) which allows for the fabrication of multi-layered cell tubes with well defined internal structural configurations and diameters. Using the fTNFS, individual cell sheets can be stacked into a multi-layered tissue construct which can then be wrapped into a cylindrical shape. The cell tube structure can then be stabilized using a hydrogel. Here, we fabricated multi-layered vSMC tubes with structural characteristics similar to native blood vessels. The TEVGs were then immaged using immunofluorescence microscopy for expression of contractile proteins. The  vSMC tubes produced in this project maintauned internal structures analogous to native blood vessels and expressed contractile proteins.

Short-term inflammation processes are commonplace following traumatic brain injuries (TBI), as they are a normal defense mechanism the body elicits to heal itself. However, when prolonged or chronic, inflammation can become detrimental. One inflammatory cytokine, Interleukin-6, has been shown to be increased in cerebrospinal fluid and blood post-TBI. In other non-TBI related clinical studies, Interleukin-6 has been associated with pain, fatigue, sleep disturbance, and depression. In this study, we examined whether plasma levels of interleukin-6 were associated with a higher symptom levels of four symptoms (headache, fatigue, sleep disturbance and depression) in the post-acute phase in patients with mild TBIs. To answer this question, secondary data analysis from a study that is currently underway was used. In the parent study, interested participants were enrolled from the Harborview Medical Center ED if they were 21-54 years of age, had sustained a mild TBI within the last 24 hours, and met other inclusion/exclusion criteria which would have impacted the immune response. Endorsement of symptoms and total symptom burden at 3 and 6 months was measured using the Rivermead Post-Concussion Questionnaire. Interleukin-6 levels at 3 and 6 months post-injury were obtained from banked plasma samples using a multiplex assay (Millipore, Minneapolis, MN). The sample (N=84) had a mean age of 34.7 years (SD 9.4). At 3 months post-injury the percent of patients endorsing symptoms as a problem were, 35.9% for headaches, 44.9% for sleep disturbance, 50% for fatigue and 32% for feelings of depression. At 6 months, the percentage reporting the symptom was higher for headaches (38.2%). Data analysis is currently underway using chi-squared tests and regression analysis to assess for the association between Interleukin-6 levels. If such an association is shown, this understanding of disease progression in mild TBIs could bring new treatment modalities to the medical realm concerning chronic inflammation.

Mild traumatic brain injuries (MTBI) affect millions every year. Symptoms are typically transient in nature but recovery time can span weeks to months. The neurobehavioral disturbances resulting from MTBI are associated with lower functional outcomes. Research suggests that well-developed social support networks contributes to improved health outcomes. However, less is understood regarding the existence of a relationship between social support networks and MTBI outcomes specifically. The objective of this study is to establish whether or not there is a relationship between social support availability and perceived symptom burden after MTBI. This study is a secondary analysis of data captured by the AIm:TBI study, which tests whether poorer outcomes from TBI in older adult survivors are associated with an altered post-traumatic immune response. In the parent study, participants were enrolled from the ED if they were 21-54 years of age and had sustained a MTBI within the last 24 hours (N=78). Social support was measured by the MOS-Social Support Scale (range 19-95; higher scores mean more social support). Endorsement of symptoms and total symptom burden at 3 and 6 months was measured using the Rivermead Post-Concussion Questionnaire (range 0-64; higher scores mean more burden). At baseline, the average social support score was 79.7 (SD 14.9). At 3 and 6 months post-injury the mean total symptom burden was 16.2 (SD 14.4) and 15.5 (SD 15.0) respectively. Analysis of the relationship between the two includes the assessment of relative influence of the type of social support received on symptoms. If the results of this study suggest that there is an inverse relationship between the severity of an individual’s symptoms after MTBI and the quality of their social support network, it may justify the development of interventions to increase social support in specific areas in order to facilitate better outcomes for MTBI patients.

Duchenne muscular dystrophy (DMD) is an incurable disease affecting approximately 1 in every 3600 males in the United States that is caused by a genetic mutation leading to the loss of dystrophin expression in muscles. Dystrophin is a protein that links the cytoskeleton of muscle cells to the extracellular matrix (ECM), and a lack of dystrophin leads to extensive damage to muscle fibers and subsequent loss of muscle function. Proposed methods of treatment, such as direct stem cell injections, have not been effective due to poor cell viability and difficulties associated with the culture of muscle stem cells in vitro. However, the development of implantable, vascularized and functionally mature skeletal muscle tissue patches may be able to address some of these issues. These tissues are made by growing primary muscle cells on biodegradable nanopatterned scaffolds that have been functionalized with sphingosine 1-phosphate (S1P), a potent angiogenic and myogenic biomolecule. The nanopatterning of these scaffolds is designed to mimic the nanotopography of native muscle ECM such that the anisotropic alignment and maturation of cultured muscle cells is induced. With this combination of topographical and biochemical cues, there was an observed increase in the formation of mature, contracting myotubes and the presence of differentiated endothelial cells. Furthermore, increased expression of myogenic and angiogenic genetic markers were found in cells cultured on substrates functionalized with S1P. Current work is focused on the validation of these results with cells featuring a knockout of the S1P receptor 1 gene. Lack of this receptor should lead to S1P-functionalized substrates having little to no effect on cell differentiation and tissue maturation, thereby illustrating the importance of S1P on the observed results. With further research and development, these tissue constructs may be used in the future to treat chronic muscle diseases such as DMD.

Shear-enhanced adhesion is a mechanism in which binding is enhanced at high flow rates. Some species of bacteria within the genus Streptococcus demonstrate shear-enhanced adhesion under high flow conditions, which are present throughout the human body. The purpose of our research is to understand and compare the effect of constant and pulsatile flow in Streptococcus gordonii, a strain of bacteria that causes infections by binding to human platelets. Our research focuses primarily on cases of infective endocarditis, a life-threatening infection of heart valves caused by various strains of bacteria. Rates of incidence in a general population has been estimated between 2 and 6 cases per 100,000 person-years. In our model system, we utilized a flow chamber to mimic pulsatile flow conditions in heart valves, which oscillate between a low and high flow, with a maximum shear stress of 3 Pa. We took videos of S. gordonii, which uses a serine rich-repeat adhesin to bind to platelets, and determined the number of bacteria that bonded to the surface under constant low, peak, average, high, and pulsatile shear stresses. We analyzed the videos to determine the conditions that enhance adhesion and compared our results under pulsatile flow to constant flow for the same range of shear stresses. Our results indicated that pulsatile conditions promote low amounts of adhesion above 1-2 Pa, demonstrating that pulsatile flow does not explain how Streptococci bind to heart valves at 2-8 Pa. These results disproved our hypothesis that pulsatile flow enhances adhesion at 2-8 Pa. Further research may look to testing the mechanism behind which Streptococci bind to heart valves in bacterial lesions exposed up to 8 Pa in the circulatory system. By understanding the adhesive properties of S. gordonii, our research may contribute to the development of anti-adhesive therapies to treat bacterial endocarditis.

Circadian rhythms are vital to maintaining proper mental health. This project seeks to determine whether or not cyclic fear stimuli has the ability to override the natural entrainment of the circadian system to the light-dark (LD) cycle. This work is significant because there are few environmental stimuli that are capable of overriding entrainment of circadian rhythms by the LD cycle (e.g., temperature cycles, temporally restricted food access). Our laboratory has shown that nocturnal cyclic fear stimuli are sufficient to induce a shift in the natural nocturnal foraging and feeding activity to diurnal activity. This reflects the output of an endogenous circadian clock that is entrained to the fear stimuli because the timing of these behavioral rhythms is sustained under constant conditions. Our experimental design involves three stages. First, mice are entrained to a 12:12 light-dark cycle over a seven-day period. Then, mice are subjected to random nocturnal footshocks for fourteen days. Finally, mice are released into constant conditions to determine if diurnal behavior is sustained. Future experiments will examine the role of the amygdala and suprachiasmatic nucleus in generating the nocturnal-to-diurnal shift in behavior. Ultimately, if we know how and why fear changes circadian behavior, then we can potentially create new treatments for sleep disturbances associated with mental disorders that result from trauma, such as post-traumatic stress disorder.

Retinal degeneration is one of the leading causes for blindness in working-age people. It results from the loss of one or more of the seven different cell types in the retina which eventually disrupts the structure and signaling between the cells, ultimately leading to irreversible vision loss. Unfortunately, mammalian retinas cannot regenerate lost neurons, and current therapies only slow down disease progression. Alternatively, cell therapy using self-renewing, pluripotent embryonic stem cells (ESCs) could provide an unlimited source of replacement retinal cells. Many groups, including our own have developed protocols to derive retinal neurons from ESCs. While these can generate photoreceptors well, the generation of complete retinas from ESCs in a consistent and more efficient manner has remained elusive. Our research thus focused on optimizing the existing retinal differentiation protocols for mouse ESCs, with the goal of producing more laminated retinas consisting of all retinal cell types. In the current study, we used the three-dimensional method to produce embryoid bodies (EB) from our ESCs. We tested the effectiveness of Fetal Bovine Serum (FBS) and hyperoxia to enhance retinal differentiation by supplying them to our EBs. The samples were collected every week for five weeks and analyzed by immunohistochemistry. We found that both conditions increased production of inner retinal neurons such as ganglion cells and amacrine cells, and EBs grown under hyperoxia were healthier looking. We then compared the ESC-derived retinas to age-matured mouse retinas and found that both retinas were similar in structure with the different cell types organized in the correct arrangement. These results suggest that FBS and oxygen are additional factors that can be integrated into existing protocols to improve the differentiation of mouse and possibly also human ESCs into retinal neurons.

A Mycobacterium bovis-based Bacillus Calmette-Guerin (BCG) vaccine is protective against childhood TB meningitis but insufficient for controlling the disease. The development of efficacious vaccines requires mechanistic understanding of host immune response to MTb and the BCG vaccine. We have previously identified that single nucleotide polymorphisms in the gene HSP90B1 are associated with development of TB disease in South African children. HSP90B1 is a molecular chaperone for integrins and most Toll-like receptors (TLRs). TLRs recognize pathogen-associated molecular patterns (PAMPs), and are critical for the innate immune response to infection. In a mouse model, HSP90B1-deficient macrophages were unresponsive to ligands that target TLR2, 4, 5, 7, and 9. Our lab has generated an HSP90B1 gene knockout using CRISPR/Cas9 technology in a human monocyte cell line, and I have confirmed successful mutagenesis via a restriction fragment length polymorphism analysis. Our preliminary data indicates that exposure to TLR ligands PAM2, PAM3 and LPS, in addition to MTb whole cell lysate is correlated with a reduction in Tumor Necrosis Factor (TNF-α) secretion in the knockout cells compared to controls. We hypothesize that HSP90B1 is a critical modulator of the MTb-induced TLR signaling pathway, which drives the production of inflammatory cytokines and plays a key role in the immune response to MTb. My objective is to characterize the effects of HSP90B1 on the TLR signaling pathway by stimulating cells with TLR ligands such as flagellin for TLR5, imiquimod for TLR7, and performing cytokine quantification via enzyme-linked immunosorbent assays (ELISA). Moreover, I will conduct Griess assays to evaluate effects of HSP90B1 upon nitric oxide production, which is an important defense molecule in enhancing efferocytosis, the process of up taking apoptotic cells. These studies will improve our understanding of host immune responses to MTb and potentially lead to development of more efficacious TB vaccines.

Among middle school age youth, recent research estimates that approximately 1.3% of students identify as transgender (a gender identity that differs from the sex assigned at birth). Transgender youth are at considerable risk for depression, anxiety, and suicide associated with bullying at school or difficulties at home. School nurses are well positioned to identify these youth, intervene, and provide support. Public health study of cultural competence in caring for sexual minorities has begun to emerge, yet little of this research addresses the disparities of care experienced by transgender patients. Previous research has shown that school-based health professionals lack adequate skills and knowledge to care for transgender youth. This study focuses on the state of care within the school setting for transgender youth in Washington State. A survey of knowledge of transgender issues and experiences with transgender youth was conducted among Washington State school nurses serving youth grades 6-12. The UW Catalyst hosted questionnaire was distributed to members of the SNOW (School Nurses Organization of Washington) email list-serv. A snowball sampling approach enabled recipients to forward the survey link to additional respondents. Questions included demographic information (educational attainment, type of work settings, institution size, etc), confidence in ability to provide care to transgender youth, presence and enforcement of the school anti-bullying policy, willingness/interest in receiving additional education, knowledge of community resources, and awareness of/contact with transgender students in the school population. Data from this study provides a picture of the educational needs of Washington’s school nurses in order to care for this sensitive population successfully.

Recent incidents have shown a significant lack of compliance with traffic laws among cyclists. Previous research focusing on motor vehicle behavior in bicycle-related accidents is extensive, but there is limited research on cyclists’ behavior and compliance. In this study, observations of cyclist behavior and compliance at three major intersections in King County where bicycle-related accidents are most prevalent will be conducted. Also, motorists’ behavior will be observed at these intersections in order to fully understand the relationship and interaction between both modes of transportation. Additionally, a survey of 400 cyclists and motorists will assess their perception of bicycle safety. In addition, this study will evaluate the current infrastructure of the two modes of transportation, which is crucial for potentially establishing new policies and requirements. Observational data and survey analysis are currently in process. Based on trends of information gathered thus far, I anticipate an overall lack of knowledge and compliance of traffic laws from cyclists, and a desire for more bike lanes on roads from both cyclists and motorists. The expected outcome of this research study is to reduce bicycle-related accidents through the cooperation of cyclists and motorists, as well as collaborate with King County administration and law enforcement. The implications of improved infrastructure and policy for bicyclists and motorists include improvements for the environment, public health and better individual health outcomes.