Human stool sample collection is a non-invasive method of assessing the gut microbiome. Rapid changes in microbial composition upon defecation limit the use of fresh stool for microbial community analysis. This investigation tests the effects of stool sample storage and shipment conditions on bacterial DNA quality and microbial community structure to establish and validate a methodology for stool collection in human population-based studies. The goal is to establish a protocol that minimizes bias due to shipping conditions. Fresh stool samples were collected from three participants, homogenized, and aliquoted with or without a preservative (RNALater) within 48 hours of collection. To mimic sample transport conditions, we incubated samples from three individuals under the following conditions: -80°C without RNALater, 37°C, 22°C, 4°C, -80°C -5°C, or frozen samples packed in ice left at 22°C for 48 hours. Samples were then stored at -80°C for 48 hours after which fecal DNA was extracted. We used 16S rRNA gene sequencing of the V1-V3 region (Illumina Mi-seq) to measure the community composition. Multivariate analysis was used to test the effect of sample storage and shipping regime on the microbiome. On average, the phylum level distribution was 76% Firmicutes, 20% Bacteroidetes, 3% Actinobacteria, and <1% Lentisphaerae, Tenericutes, and Actinobacteria. A perMANOVA (F=2.25, p< 0.1) showed that there was no statistically significant difference in the phyla due to temperature and handling. Regardless of treatment, samples from each individual clustered together suggesting that between individual variation exceeds any differences due to shipping regimen. Our current protocol for stool collection and preservation shows no significant loss of bacterial DNA quality, nor does it significantly affect microbial community representation and is adequate for investigations on microbiome composition, structure and activity in human studies.

Enzymatic pathways comprising multi-step biochemical reactions in biological cells constitute a key part of life. Biomimetic reconstruction of these metabolic pathways holds tremendous promise for developing sustainably powered devices. In biological cells, enzymatic components are kept in strict compartments or in serial networks. To mimic this complex hierarchical assembly of enzymes found in nature, a common approach is immobilizing these enzymes on the surface of porous substrates i.e., anodic aluminum oxide (AAO) membrane. However, one common limitation has been immobilization of multiple enzymes with a single type surface chemistry. As a result, these approaches have failed to provide enough capability to control spatial localizations of enzymes on AAO surfaces. Solid-binding peptides (SBPs) offer a novel solution to circumvent these problems with their exquisite recognition and long range solid-coverage properties. The ease of genetic conjugation of these short peptides with large proteins makes them an ideal candidate in utilization as molecular linkers in designing new multi-enzymatic devices. In this study, the utilization of a gold binding peptide (AuBP) as a molecular linker in combination with histidine-tag to immobilize Lactate Dehydrogenase (LDH) and Formate Dehydrogenase (FDH) enzymes on AAO based flow bioreactor was demonstrated. The efficacy of the described approach was tested by monitoring the sequential lactate and formate break down by LDH and FDH enzymes spectrophotometrically. The overall sequential catalytic conversion with greater than 90% yield was observed. Furthermore, the surface selectivity of the SBP conjugated enzymes were tested by visualizing their localization on Ni-NTA patterned gold surface using fluorescence microscopy. Cumulatively, this study highlights the utility of solid binding peptides as a molecular linker for addressable immobilization of multiple enzymes in the AAO based devices.

The plant hormone auxin plays a role in nearly every aspect of plant growth and development. Auxin facilitates interactions between two protein families: the transcriptional repressor Aux/IAA family and the auxin receptor TIR1/AFB family. TIR1/AFB proteins act as the substrate recognition subunit of SCF ubiquitin ligase complexes. SCF^TIR1/AFB-auxin-Aux/IAA interactions lead to ubiquitination and degradation of Aux/IAA proteins, allowing transcription of auxin-responsive genes. Each of these protein families is comprised of many functionally distinct members, allowing auxin to drive numerous developmental responses in plants. This complex network can be decomposed and signaling dynamics of individual pairs of TIR1/AFB and fluorescently-labelled Aux/IAA proteins can be measured in a yeast synthetic system using time-lapse flow cytometry. This dynamic analysis can give insight into the behavior of developmental networks in planta. However, of the six TIR1/AFB genes in the model plant Arabidopsis thaliana, only TIR1 and AFB2 induce degradation of Aux/IAAs in yeast. We aim to engineer a variant of AFB5 that is functional in this synthetic system, as AFB5 is known to be the target of many agriculturally important herbicides, but little is known about its role in development. We hypothesize that AFB5 is non-functional in yeast because it cannot form an SCF complex with the native yeast proteins. This is potentially caused by the extended N-terminus of AFB5 or the sequence divergence within AFB5’s SCF binding domain. To test these hypotheses, several N-terminal truncations of AFB5 and chimeric AFB5 proteins with the SCF binding domain replaced by that of AFB2 or TIR1 will be individually tested for their ability to induce degradation of Aux/IAAs in yeast. Functional variants will allow identification of key AFB5-regulated Aux/IAAs and associated developmental networks. Additionally, this work will guide engineering and allow functional characterization of the remaining Arabidopsis AFB genes and AFB genes from other plant species.

Vascular injury causes platelets to form hemostatic plugs. Platelets are activated by high shear and collagen, and adhere and contract to protect a clot from mechanical forces. The role of collagen and the anticoagulants heparin and ASA (Acetylsalicylic Acid), which inhibit thrombin and TxA2 (Thromboxane A2) respectively, are not fully understood. Our lab has designed a microfluidic device to measure clot forces and area. Microfluidic channels with block-post sensors generate shear gradients that induce platelet adhesion. Clots grow towards the post and contract, pulling the post closer. Fluorescence microscopy allows post deflection to be analyzed with MATLAB code using Hooke's Law, and phase images monitor area. First, channels were coated with and without collagen. Then, channels were collagen-coated and blood inhibited with heparin or ASA. Blood was incubated with 15 USP (U.S. Pharmacopeia standard) heparin lithium in H2O or 0.3 mM ASA in DMSO for 20 min. Clots in uncoated channels had lower forces than in collagen-coated channels. Blood with ASA in DMSO had less platelet adhesion and contraction than in blood incubated with DMSO. Blood with heparin in H2O had lower force but higher clot area than without heparin. Reduced force of clots formed in uncoated channels relative to collagen-coated channels suggests that collagen is important in force. Inability of platelets to adhere or produce normal force with ASA indicates that TxA2 promotes platelet aggregation and force. Heparin reduced force but not platelet aggregation, thus thrombin is involved in force generation only. This clot-on-a-chip technology can shed light on the clotting process and diagnose patient clotting issues.

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 majority of the population living with HIV resides in African countries where the cost-effectiveness and ease of implementation of the technology is imperative. Our goal is to develop an assay that eliminates the need for expensive nucleic acid sequencing technology, to test and diagnose drug resistance by detecting variation in nucleic acid sequence of the virus. One of the missing pieces that will allow us to reach this overarching goal is to design a method for isolating the viral particles in a manner appropriate for point-of-care application. Our approach, which will contribute to the assay being developed at the same time, is to use protein G magnetic beads, which are affinity molecules, to isolate the HIV virus from plasma sample. The protein G on the magnetic beads interacts with the coat antibodies on the viral particles and facilitate their removal from plasma. We show that the protein G magnetic beads have comparable efficiency at isolating the viral particles compared to the gold standard, Qiagen extraction, without the use of strong chemical reagents and complicated instruments. Yet, further work is needed to demonstrate that the viral RNA can be extracted starting from clinical plasma specimens with a protocol applicable in point-of-care settings defined by limited use of complicated insturments and cost effectiveness of the solution. 

Eclipsing binaries are systems in which two stars orbit and pass in front of each other. They are important astrophysical tools we utilize to measure fundamental properties of stars, such as their masses, radii, and temperatures. Here, we analyzed photometric data acquired from the Kepler satellite in order to model the light as a function of time of specific eclipsing binary systems. We selected these targets from the Villanova Kepler Eclipsing Binary Catalog. For each system, we used a least-squares optimization method to determine the best fit solution between the model and the observed light curve. Our light curve model has a total of 13 parameters. They include stellar elements such as sum of radii and flux ratio, as well as orbital elements such as period and eccentricity. In addition to providing orbital solutions, our models can be used to search for the presence of additional bodies in the system, such as a third star or a circumbinary planet.

Trustworthiness is an invariant characteristic that is independent of changes in emotional expressions. However, the perception of trustworthiness is highly varied and is not often accurately portrayed. As an attempt to understand what causes variations in perceived facial trustworthiness, participants were asked to rate trustworthiness of facial expressions (sad, happy, neutral) presented individually and as a single unit. Results found participants viewed happy expressions as more trustworthy, but when presented with all emotional expressions, neutral expressions were more likely to be used as an indication of trustworthiness. Overall, this study suggests neutrality is a better indicator of personality traits.

Current synthesis for thermoresponsive magnetic nanoparticles such as iron oxide nanoparticles coated with poly(N-isopropylacrylamide), pNIPAm, usually requires extensive surface functionalization or high temperature procedure, and the yield is very limited. Here we present a simple and reproducible approach for the synthesis of thermosensitive iron oxide nanoparticles, via coprecipitation of Fe2+ and Fe3+ ions from basic aqueous solutions at room temperature in the presence of block copolymer, poly(N-isopropylacrylamide)-block-poly(acrylic acid) with a dodecyl tail following the acrylic acid block. The polymer facilitates iron oxide nanoparticle synthesis by forming micelles via hydrophobic dodecyl tail assembly and coordinating iron oxide formation via complexation with the poly(acrylic acid) segment. The block copolymers were synthesized through reversible addition-fragmentation chain transfer polymerization. Proton NMR characterization shows incorporation of 11 acrylic acid monomeric units to pNIPAm macro chain transfer reagent with 150 degree of polymerization. The new synthesis approach is rapid, taking one hour, and can be easily purified via size exclusion chromatography. The resulting magnetic nanoparticles’ surfaces display pNIPAm, which enables particle aggregation when the solution temperature is above 34°C. The particle aggregates exhibit high magnetophoretic mobility, which results in rapid and efficient magnetic separation, ≥95% in few minutes. The particle’s hydrodynamic diameter is ca. 30 nm, characterized using dynamic light scattering. This simple method overcomes the problem of using high temperatures while maintaining reproducibility, which could make it useful for larger scale synthesis.

Aging leads to the loss of physiological function such as cognition, mobility, and cardiovascular performance. One possibility for this loss is an age-dependent decrease in the generation of proteins necessary to support these functions at a youthful level. Many of these protein factors are secreted into the general circulation and can be detected in the serum of blood samples, this provides the opportunity to monitor their levels at various ages. The objective of this project was to determine if serum proteins could be identified that decreased with increasing age using mice as a preclinical model of aging. Mice with a mixed genetic background, designated as CB6F1, were used because they represent a heterogeneous gene pool and a co-morbid disease pattern similar to humans. Serum was collected from 8-month and 32-month old mice (comparable to 22 and 80 human years, respectively), and tested for 200 serum proteins using a slide capture array (RayBiotech). Levels for 23 proteins, involved in supporting blood vessels, the immune response, brain cells, skin, muscle and bones, were significantly decreased in old mice compared to young mice, correlating with an increase in frailty, fatigue, heart failure, and cognitive impairment. This preliminary data suggest specific serum proteins, alone or in combination, may be useful markers for aging. This provides the rationale to investigate the ability of anti-aging drugs to restore specific protein factors to their youthful levels and monitor for any delay or reversal of age-related functional decline.

Lung diseases, including chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis, are major health concerns in older people. There is currently a paucity of drugs available that are effective in treating these conditions.  A potential drug target in the lungs is a cell type known as fibroblasts. These cells are very abundant and are essential in providing support and structure for alveolar cells, which are responsible for the vital gaseous exchange of oxygen and carbon dioxide. A drug that has been shown to target fibroblasts in the skin, and currently used in skin creams, is a tripeptide designated as GHK. The objective of this project was to see if GHK could target lung fibroblasts collected from old mice by restoring functional capacity. Lung fibroblasts were grown in culture to a monolayer and a scratch wound assay was performed to measure the rate of closure. Immediately proceeding the scratch, cells were treated with different concentrations of GHK while one received a placebo treatment. The closure rate was then measured every 24 hours for a total of 72 hours. The highest concentration treatment of GHK had a significantly faster migration rate than that of the placebo treated monolayers, suggesting that GHK enhances fibroblast migration and restores functionality to more youthful levels. These results provide the rationale for preclinical studies in mice to help determine if GHK might be a potential drug to consider for treating chronic lung diseases in the elderly.     
 

With increasing age and as a result of mitochondrial-generated reactive oxygen species such as hydrogen peroxide, lung fibroblasts cells undergo DNA damage which is leading to a loss of function and premature ageing (senescence). The objective of this project was to assess whether the presence of the mitochondrial-specific antioxidant enzyme catalase (mCAT) could affect the levels of DNA damage and senescence in fibroblasts collected from the lungs of 24 month old mCAT mice versus control. Immunostaining of lung fibroblast cultures, using specific antibodies against markers of DNA damage/premature ageing showed, a significant decrease in DNA damage and a decrease in cell division in mCAT lung fibroblasts against control.
Aging is the most significant risk factor for developing cancer, and majority of malignant cancers that are treated in clinics, occur in older patients that are suffering from cellular senescence/aging and uncontrollable cell division, leading to cancer. Therefore, understanding the consequences of senescence may help with designing new strategies, such as anti-oxidant therapies that lead to prevention of DNA damage and age-related diseases, in the future.
 

Historically, only clinicians and researchers have been involved with decisions about what research topics to pursue, and patients have been left out of the process. This creates a gap between clinical application of research and patients’ experience. By expanding the scope of how researchers and clinicians obtain patient data to include research topic priorities, we explore how to incorporate patient perspectives better. Although there are many studies that aim to analyze patient registries, there are limited studies that attempt to elucidate the degree of the participants’ interest, or willingness to get involved in providing input on research activities. Through a study funded by the Patient-Centered Outcomes Research Institute (PCORI), we developed a two-phase approach to prioritize topics for low back pain research. In phase one, we invited participants from a patient registry of older adults with back pain , and in phase two, invited participants using Amazon Mechanical Turk (MTurk), an online crowd-sourcing platform. Participants completed an initial screening survey comprised of the Roland Morris Disability Questionnaire, a standard tool to identify individuals experiencing back pain. Those scoring 7 or higher on the RMDQ were sent a research topic prioritization survey. 1966 people completed the screening survey, and 480 qualified, of which 353 completed the prioritization survey (completion rate: 74%). Using both recruitment strategies, we had a high response rate, and participants are diverse in terms of pain, gender, and age. Responses show participants’ effort to fully answer the survey and voice their opinion, including providing additional topics that had not been identified previously.This work highlights that recruiting from a patient registry or using MTurk are both effective tools to obtain patient input, and increases the flow of information from the public/patient to the researcher, and inevitably the clinician; we expect incorporating these methods will increase patient voice in research.

After large loading events, such as earthquakes, buildings are inspected to determine the extent of damage done to the structural systems and whether it is still safe to use. These building inspections are completed mostly by observing visible damage and using engineering judgment to determine the residual strength of structural elements, or members. This approach is subjective, and accurate inspections demand a more robust approach. Non-destructive testing can be performed on structural steel that attempts to quantify a member’s strength, but these tests have marginal accuracy. Permanent instrumentation of a building can also provide data, but sensors must be powered and well maintained. An interdisciplinary team, led by Professors Dawn Lehman and Laura Lowes from the Department of Civil and Environmental Engineering and Professor AJ Boydston from the Department of Chemistry seeks to develop a polymer coating that can provide a better way to quantify strain in building members. The polymer is comprised of strain-sensitive units (mechanophores) that undergo molecular-level transformations as the polymer chains are extended. The chemical reactions provide visible outputs, such as intense changes in color and fluorescence properties. By changing the microstructure of the polymer and mechanophores, we will be able to control the threshold sensitivity and strain-dependent intensity of color changes. Once applied to a member, the polymer would effectively track the strain that the material undergoes through a change in color, which can be correlated to a residual strength. This color can be observed after earthquakes and other extreme events and allow inspectors to quickly and accurately determine structural health. Our research objectives include applying color-changing strain-responsive (mechanochromic) polymer coatings to building members and analyzing the response to applied strain. My contribution to the project is creating the metal samples and testing them after the polymer has been applied.

Childhood maltreatment is one of the most common adverse events in children and has been associated with a variety of negative effects on children’s social adjustment and mental well-being later in life. One explanation is that maltreated children may develop maladaptive emotion regulation skills, which mediate the pathway between maltreatment and psychopathology. Accumulating literature suggests that attachment security may be a protective factor against maladaptive emotion regulation skills in maltreated children. Prior research has investigated attachment as a mediator between childhood maltreatment and poor behavior outcomes. However, little research has examined attachment as a protective factor associated with better emotion regulation skills in maltreated children, which in turn results in better behavioral and emotional adjustment. The current study hypothesizes that, childhood maltreatment will have a less negative effect on children who are securely attached to one of their care givers, compare to those who have insecure attachment. In other words, secure attachment will serve as a protective factor for children exposed to adverse experiences, leading to better emotional and behavioral outcomes. Data from two separately collected samples of maltreated and control children (n= 221 and n= 124) are analyzed based on multiple linear regression models. We expect to find a significant difference between the effect of maltreatment on emotion regulation in high and low attachment individuals, such that children with more secure attachment are less affected by maltreatment. These findings would suggest that secure attachment may protect maltreated children from developing maladaptive emotion regulation skills which contribute to better general behavior outcomes in children.

We have obtained three epochs of observations of the nearby spiral galaxy, NGC 300, using the Chandra X-ray Observatory. Using this data, we searched for variability in the X-ray luminosity function (XLF) of NGC 300's X-ray point source population. When the entire X-ray source population was considered, the XLFs were best described by using a power law with a slope of ~0.6-0.7. However, the XLFs of intrinsically variable X-ray sources showed significant variability between observations, especially at low luminosities (< 10^37 erg/s). We created synthetic, variable X-ray sources to probe the characteristics of the X-ray point source population in NGC 300. In order to match the observations, our models required that the peak X-ray luminosity of variable sources are significantly lower than commonly assumed, which is characteristic of a mass transfer due to direct wind accretion at significantly sub-Eddington rates.

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.

In recent years there has been much speculation about how events that occur during childhood can have a lasting impact on a child’s development. There have been many studies that attempt to look at how the impact of child stress affects different parts of development: physical development, psychological development, and social-emotional development. The purpose of this research was to observe and learn how stress affects emotional and social development and consequently impacts the child's risk for mental health issues. Although stress is a multidimensional concept and can be measured by biological responses, the presence of challenging environmental factors, and self-reports, for the purpose of this research stress was defined as the presence of adverse environmental factors. For development, I specifically observed attachment and emotional regulation. My focus on mental health was internalizing psychopathology, especially anxiety and depression. To gain a better understanding of the emotional social development of a child suffering from toxic stress, I looked at multiple studies already done that observed the effects of stress on a child’s social-emotional development. I also used conclusions drawn from experience gained while working at the Stress and Development Lab directed by Dr. Katie McLaughlin. For this approach I reviewed papers that demonstrated a connection between stress and mental health, between stress and development, and between development and mental health. I also looked for and identified factors that showed evidence of mitigating the effects of stress on mental health and development. These factors are referred to as protective factors. Identifying the aspects of development influenced by toxic stress and the mitigating factors is crucial to creating and implementing intervention techniques to promote healthy development and to decreasing the risk of internalizing psychopathology.

The lateral habenula (LHb) in the brain is an important regulator of midbrain dopaminergic systems that are known to be involved in the reinforcing properties of cocaine. We have previously determined that activation of LHb neurons using Designer Receptors Exclusively Activated by Designer Drug (DREADD) technology decreased cocaine-induced locomotor activity and cocaine self-administration in rats. To determine if these effects were due to disruption in motor coordination, in this study, male Long-Evans rats underwent survival surgery and were injected with hM3Dq (2 microliters), which is an activating DREADD virus bilaterally into the LHb. They then went through a training period of 2 trials per day for 5 days to master the Rotarod, a test for motor co-ordination. The Rotarod test entails a rotating wheel in which rats must balance and walk, thus testing their coordination. The amount of time they remain on the wheel is recorded with the maximum time per trail being 120 seconds. After the training period is over they are subjected to testing days where the rats are then injected with 1 or 3 mg/kg i.p. clozapine-N-oxide, which is the inert ligand that activates DREADD receptors. Twenty minutes is elapsed before they are subjected to the test. The amount of time spent on the Rotarod is again collected. Interestingly, our results demonstrated that activating the LHb produced no change in the level of motor coordination. This is interesting because with our cocaine self-administration experiments, a decrease in lever pressing is observed. Our results tell us that inhibiting the LHb has no effect on coordination and thus the decreased lever pressing expressed in the cocaine self-administration rats is in fact not due to a decrease in coordination. These results helped us rule out a possibility as to why our self-administration rats decreased their lever pressing.

Unhealthy alcohol consumption can result in alcohol-related diseases such as hypertension, cancer and depression. One of the ways in which primary care settings have helped address unhealthy alcohol use has been through a method called screening and brief intervention (SBI). Latino immigrant day laborers are at a higher risk of unhealthy alcohol use; however, they are less likely to receive SBI due to barriers in accessing health care services. Vida PURA is a culturally adapted SBI designed to address such barriers by placing Spanish speaking promotores at a worker center. We evaluated the feasibility of providing brief interventions to Latino day laborers in a community setting. Interested men completed a screening survey and, if eligible, proceeded to take a baseline survey. Participants were then randomized to the culturally adapted BI or the control group and also completed a follow-up survey two weeks and eight weeks later. The recruitment, retention, and reach measures were recorded in logs and tracking forms kept by the promotores. I evaluated the feasibility of the intervention by analyzing these logs. After 28 weeks of data collection, 118 participants have been screened, of which, 67% were eligible for the study. Baseline surveys were completed by 78 participants, 51 were randomized, and 48 received the intervention. The participant retention rate was 91% for the two-week survey and 89% for the eight-week follow-up. Findings suggest the study is feasible in regards to recruitment, retention, and reach. This analysis highlights the importance of using promotores at a worker center to provide brief interventions to Latino immigrant day laborers, a population considered to be hard to reach. Future studies should consider the use of promotores to target other hard to reach and underserved populations to address unhealthy alcohol use.

Danon disease, a form of cardiomyopathy, results in deficient blood flow due to the weakening of heart muscles and can lead to a shortened lifespan. In collaboration with the Song lab at the University of Colorado, we aim to better understand the differences in contractile function between healthy cardiomyocytes and those from individuals with Danon disease. The Song lab obtained primary adult cells from two control groups—healthy individuals without cardiac problems—and three diseased groups—people suffering from Danon disease. The patient cells were used to generate induced pluripotent stem cells (iPSC), from which they derived cardiomyocytes that possess genetic information of the original donor. The Sniadecki lab has the technology to make micropost substrates from polydimethylsiloxane (PDMS), using a soft lithography process. The iPSC-cardiomyocytes were seeded onto the microposts. As the cardiomyocytes contract on the microposts, each post under the cell deflects. Videos were taken at the tips of the microposts underneath the beating cells, to record the post deflection over time. A still image was taken at the bottom of the microposts in order to determine the relative deflection of each post. From the deflection of the posts, we were able to measure contractile forces produced by the iPSC-cardiomyocytes using simple beam bending theory. For this experiment, we used microposts with following dimensions: height = 4.14 μm, diameter = 1.75 μm, and center-to-center spacing of 6 μm. These dimensions gave each post a stiffness = 56 nN/μm, which was used to calculate the force. We hypothesized that the diseased cells will produce lower contractile forces than the control cells. The results produced supported our hypothesis. We hope this study contributes to the effect of Danon disease on the contractile function of cardiomyocytes. Further, this work would exemplify a methodology to investigate cardiac disease modeling and treatments.

Glacial erratics are rocks that have been transported and deposited by glaciers. They are typically characterized by large size and a composition that differs from the surrounding geologic features, indicating a foreign source. Determining the source of these erratics provides evidence of ice flow direction, which helps to reconstruct glacial history of a region. Our project focuses on a glacial erratic located in West Seattle at the entrance to the South Seattle College campus. Our research has two main goals. Our first goal is to determine the composition of the glacial erratic through mineral property tests and optical analysis, and use this information to identify potential origins of the rock. Our second goal is to determine if the characteristics of the sediment underlying the erratic are consistent with recent glacial transport. Using sediment samples and existing borehole data, we have constructed subsurface cross-sections showing the stratigraphy of underlying deposits. Preliminary mineralogical and composition analyses indicate that this rock is not native to the Puget Sound basin, and may have been transported from as far away as the northern San Juan Islands or Canadian Cascades. Analysis of existing borehole data and sediment sampling indicate the underlying stratigraphy includes glacial till and outwash deposits consistent with our hypothesis that the erratic was deposited during one of the recent glacial pulses. Learning more about the glacial erratics in the Puget Sound area can help confirm the path and timeline of ice sheets that covered the area thousands of years ago.

Little is known about mammalian diversity in North America during the mid-Cretaceous (Albian-Cenomanian, 120-90 mya). This was an important interval in mammalian evolutionary history, during which metatherian (including marsupials) and eutherian (including placentals) mammals first appeared in North America and multituberculates (a now-extinct group of mammals) began to radiate. Unfortunately, our understanding of this period is poor because mid-Cretaceous mammal-bearing fossil localities are sparse in North America. Accordingly, each newly discovered specimen from this interval could provide important insights into therian and multituberculate diversity and their early stages of evolution. Recent paleontological fieldwork in the mid-Cretaceous (ca. 100 mya) Wayan Formation of eastern Idaho has led to the recovery of 30 mammalian specimens, including 15 metatherians and 13 multituberculates. These specimens, all isolated teeth, were discovered in situ and in the lab. Previous work by myself and other members of the Wilson Lab has focused on describing three metatherian species from this sample, as well as documenting a new occurrence of the genus Targheedelphys. Here, I focus on describing the multituberculates and analyzing their taxonomic diversity, as well as comparing them to those from a larger, contemporaneous sample from the Mussentuchit member of the Cedar Mountain formation of central Utah. Some of the Wayan specimens are attributed to new species and others are referred to previously known species. Current results indicate that multituberculate and metatherian diversity is approximately equal, with three species observed in each group, and each occupying close to fifty percent of the local fauna. The similarities and differences in taxonomic composition and diversity between these two localities will give us important insight about mid-Cretaceous mammalian evolution in North America. Additionally, this information fills a gap in the timeline of mammalian evolution that will further our understanding of mammal evolution through the K-Pg and onward into the Cenozoic.

With concern about climate change increasing, assessing how plant reproductive success is impacted by increases in temperature is crucial in order to fully understand how climate change influences ecosystem structure and dynamics. This study measures how population variation and the climate of different elevations affect the capsule size and seed mass of the high-elevation plant mountain monkeyflower, Mimulus tilingii, at Mt. Rainier National Park. If climate is the primary limiting factor determining the range of M. tilingii, plants within the species’ climate range will produce the most abundant capsules and seeds whereas plants grown outside the species’ distributional range will produce smaller amounts. Sample seedlings were planted at two elevation sites: 1)  M. tilingii’s range center and 2) below M. tilingii’s range to mimic the increase in temperature due to climate change. Populations were categorized as either within-population (for crosses within the same elevation site) or between-population (for crosses between the two elevation sites) with equal amounts at both sites. This study quantifies M. tilingii’s reproductive success both in the context of the site as well as the population type, allowing for comparisons on these two levels. Results show that parent plants from the lower site produced more flowers and grew faster, indicating that plants in the lower elevation site might be more successful. These unexpected results suggest that M. tilingii may be better adapted to a warmer environment and that climate change might even be beneficial for this reason. Determining the exact impact of temperature on reproductive success is crucial not only for measuring the species’ fitness but also for understanding how these new adaptations will play an even bigger role in competition for resources among different plant species and how those new interactions will alter the ecosystem as a whole as the climate warms.

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.

For a community suffering from collective trauma, unity is vital for building community resilience, which is the capacity to withstand, recover from, and respond positively to a collective crisis. Both the Native American Tulalip community and the predominantly White Marysville community were affected by an October 2014 school shooting in which five students (3 Native American; 2 European American) died. We sought to identify factors that contribute to community resilience. We surveyed 597 employees of the Marysville School District and assessed perceptions of unity prior to and after the shooting, as well as personal experiences following the shooting (i.e., negative and positive feelings). My project focuses on the relation between people’s individual experiences and their perceptions of community unity following the shooting. I conducted a series of regression analyses predicting unity from personal experiences and found that people who had more positive feelings following the shooting perceived the communities as more united, while people who had more negative feelings perceived the community as less united. Furthermore, these relationships were magnified among people who knew at least one victim of the shooting compared to those who did not know victims. These findings suggest that in cases of collective trauma, projections of negative feelings following the event have the potential to hinder efforts to rebuild the community, whereas positive feelings may serve to aid this effort, especially among people who are closely tied to the traumatic event. These results highlight the importance of understanding how to foster positive feelings in the promotion of post-trauma healing. Given the frequency of mass violence in contemporary society, it is increasingly important to examine not only preventative measures but also understand how to promote healing for those affected by these tragedies. This work seeks to begin answering this question.

We know that climate sensitivity can vary within species, but the factors that influence which climatic variables influence population dynamics remain unclear. In this study, I am assessing whether macroclimate influences the climate sensitivity of three prominent conifer species: Pacific silver fir (Abies amabilis), mountain hemlock (Tsuga mertensiana), and Alaska yellow cedar (Callitropsis nootkatensis) on Mt. Rainier. I am analyzing tree core data from three high elevation sites. Each site is located in a distinctly different climatic area on the mountain. I am comparing standardized tree growth to climate variables (mean growing-season temperature, total growing-season precipitation, snow duration, etc.) using linear mixed effect models. This will determine how influential climate variables differ by location and by species. Gaining more insight into which climate variables have the greatest influence on growth in different areas will allow us to better predict how specific plant populations will react to ongoing climate change. Moreover, studying tree communities at high elevations is particularly important, since behavior at treeline will determine whether a species’ range expands, contracts or shifts. Range expansion of one species could lead to the crowding or elimination of another. For example, conifer range expansion on Mt. Rainier could negatively affect the alpine wildflower meadows, a major attraction for tourists. Widespread range contractions could also decrease forest density and potentially reduce the ability of those forests to sequester carbon from the atmosphere. Thus, with better predictions of tree shifts, we can make more informed management decisions for ecotourism and conservation.

Sea ice plays a vital role in the Arctic ecosystem and is a good indicator of climate change, so it is important to understand the physical processes that control sea ice evolution in order to get a better sense of the detrimental effects of climate change on the environment. Thus, accurate measurements of the features of ice – such as ice concentration – are needed to provide a clearer picture of how and when the ice evolves. This project aims to document and quantify ice variability from airborne imagery during the summer melting season in the Beaufort Sea. Images were taken from US Coast Guard Arctic Domain Awareness (ADA) flights in June, July, August, and October of 2014, with data collection to be continued in coming summers, including this summer, the summer of 2015. Algorithms were developed to automate the identification and quantification of features of the sea ice and open water such as ice concentration, floe size, melt pond coverage, and melt pond size. This data will be charted over time and space (latitude) to identify and analyze patterns in the evolution of Arctic sea ice. Results from this study will be useful for verifying satellite data, evaluating models, and initializing predication schemes. This information will be helpful for quantifying and analyzing the effects of climate change on the Arctic ecosystem.

Masting refers to annually variable seed production; whereby plant species release large quantities of seeds one year, followed by one or more years of significantly lower seed production. Seed masting behavior is thought to be evolutionarily favorable, a technique for survival. Two main theories exist to explain mast seeding, predator satiation and increased pollination. The purpose of this research study was to determine A) if a group of six conifer species within Mt. Rainier National Park exhibit mast seeding behavior (i.e. synchronized seed production over large areas, annual variation in seed production exceeds annual climate variation); B) Whether seed viability is greater in 'boom' years than 'bust' years (which would support wind pollination efficiency as an evolutionary driver of masting); and C) whether these patterns vary by species and/or elevation. We examined six species of conifers: Abies amabilis, Callitropsis nootkatensis, pseudotsuga menziesii, Thuja plicata, Tsuga heterophylla, and Tsuga mertensiana. Data was collected from 108 seed traps located in 18 stands at multiple elevation ranges within Mt. Rainier National Park. Seeds were sorted based on tree species, and classified as filled (viable) vs. unfilled (not viable). We then calculated mean total seed production for each stand and used correlations to assess how correlated annual seed production is across 18 stands. Next, we compared annual variation in climate within each stand, to assess whether species showed higher variation in seed production in comparison to climatic variation. Finally, we compared results for our six focal species to assess species specific similarities and differences. Understanding the mechanisms behind masting is important, as masting can control tree population demography, and influences ecosystem dynamics. Moreover, our study may provide greater understanding of the implications of climate change on masting dynamics for forests at Mt. Rainier National Park.

Mature Red alder (Alnus rubra) forests are now found in large contiguous patches which stand as legacies of past intensive management (logging, conversion to agriculture, etc.) of previously conifer-dominated forests of the Puget lowlands. King County acknowledges that a disproportionate amount of land under their ownership is comprised of mature alder forests nearing the end of their lifespan. King County is concerned with these forests’ ability to meet certain ecological, social, and economic objectives, such as providing wildlife habitat, carbon sequestration, and riparian function. In this study, we analyzed the quantity, distribution, and current conditions of these forests across three watersheds in central King County to provide landscape context. We compare the effects of alternate management approaches of varying harvest intensities on carbon uptake, and examine the distribution of forest types in riparian areas. We predicted that greater intensities of hardwood harvesting with conifer replacement will result in the highest long-term carbon uptake, while improving riparian forest function. To test our hypothesis, we used a forest vegetation dataset that was compiled by Oregon State University’s Landscape Ecology, Modeling, Mapping & Analysis Group in 2014. We combined this data with visual surveys of representative forests on King County property to classify county land into narrow forest cover types, which we then used for further modeling. We used the US Forest Service Forest Vegetation Simulator (FVS) to model forest treatments and obtain carbon storage projections. We found that coniferous forests provide greater long-term carbon benefits than short-lived hardwood forests. We support increasing conifer presence in mature hardwood forests to increase function and longevity.

Tree lines play a vital role in plant community composition in montane ecosystems. Over the past several decades, increasing annual temperatures have led to shifts in tree lines in montane environments. However, little is known about how local topography may have an effect on tree line advance. My research incorporates historical and repeat, ground based and aerial photography to assess the change of alpine tree line in a range of topographical conditions in Mount Rainier National Park over the past century. My study quantifies changes in tree cover and tree-line elevation in ridge and cove environments of the park. To track treeline change, historical and recent photographs were aligned, and areas of the photograph were broken up into polygons based on their small-scale topography. Random points were overlaid in these polygons to assess the rate of change of tree line shift. By looking at the change in tree cover in each random point relative to the polygon type, we are able to determine the amount of tree thickening that has occurred. We predicted that tree lines on sun exposed ridges will shift more quickly than those in cove environments. Snow is prevalent for longer periods of time in concave valleys limiting the amount by which the trees can shift up. Our results thus far indicate that small-scale ridge regions have the highest rate of change for tree line shift followed by cove. Subalpine meadows often occur in cove topography. Tree thickening in these regions over time may impact the wildflower populations and decrease species richness in subalpine meadows. In all, our research adds to the growing body of evidence that tree lines are moving up in elevation as well as provides the National Park Service with information about tree line influences on the plant communities of the park.

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.

The McMurdo Dry Valleys in Antarctica is a cold desert with a frigid, hyperarid environment. Physical models predict that the sediments should have a net loss of water vapor, but in reality ice-cemented ground is pervasive within decimeters of the surface. Scarce, episodic snowfall is mostly lost to rapid sublimation; however, some water vapor may diffuse into the subsurface and possibly stabilize or form ground ice. This study investigates ice within a 30-m permafrost core that was collected from Beacon Valley in 2008 using a dry coring technique. The entire core is ice rich, ranging from 20-80% water content by weight and is largely composed of weathered sand with some fractured cobbles. The high ice content suggests that the ground surface inflated as the ice formed. Processes leading to the excess accumulation of ice are investigated using δ18O and δD. Potential sources of the ice include surface percolation, water vapor diffusion, and accumulation of snow into thermal contraction cracks. Subsamples of the ice-cemented core were cut from its interior, thawed, and the water was collected using a double-bottom centrifuge tube. Isotope analysis was also performed on water samples from hoarfrost collected from the abandoned core holes, snow, and glacier ice in Beacon Valley. The core’s isotope depth profiles will provide information on the origin of the ice and processes that modify it. This site serves as an analog for Mars, where excess ground ice has been confirmed at the Phoenix landing site, and will provide insight on ice accumulation there.

Oxygen transportation in red blood cells occurs via a protein called hemoglobin. When hemoglobin is either absent, flawed, or impaired, the transportation of oxygen is hindered and this is known as anemia. Due to the prevalence and dangers of anemia, our goal is to effectively measure the concentration of hemoglobin in small volumes of a patient’s blood in order to diagnose critical levels of anemia. In order to do this, we take advantage of Beer-Lambert’s Law – a physical law that states concentration scales linearly with absorbance (a measure of how much light a molecule can absorb at a given wavelength). With the use of a microfluidic device, whole blood flows through an 8 mm x 250 μm x 50 μm channel and is illuminated by a white LED. A portion of the light is then absorbed by hemoglobin and continues at a reduced intensity to a green filter to focus our measurements to the visible green spectra, because it is known that hemoglobin absorbs the most light at about 540 nm, which is in this region. We demonstrate that our devices can determine hemoglobin concentration effectively with less than 40 μL of blood and at a low cost. The immediate impact of hemoglobin measurements of small volumes is its use towards children. The long-term impact is a diagnostic point of care device to solve global needs.

Fear of predators may cause changes in prey species behavior with cascading impacts on the environment. When large herbivores such as deer are less sedentary, herbivory is dispersed and vegetation does not get browsed heavily in one area. As gray wolves (Canis lupus) naturally recolonize Washington state after a 70 year absence, deer behavior may shift in response to fear. Accordingly, under the hypothesis that greater movement may reduce encounters with wolves, we predicted that deer (Odocoileus spp.) would spend more time traveling in wolf-present areas compared with those from which wolves were absent. To test this prediction, we reviewed video clips recorded on deer-borne camera collars during the winters of 2013-2015 in the study areas and categorized the behavior of the deer. We compared the time deer spent traveling in wolf-present and wolf-absent areas. Our results will help us better understand the impacts of wolf recolonization on the ecosystem, including possible trophic cascades that may result from dispersed herbivory.

Research on Mexican-migrants in the United States usually focuses on the 1st and 2nd generations; 1st generation being the migrant who exits their home country, and the 2nd their children born in the Unites States. Often overlooked by the complexities of the two is the 1.5 generation; migrants who were brought to the United States as children and have been socialized here. This is relevant since the 1.5 generation has increasingly become an integral and significant force in the political agenda of Mexican-migrants in the United States. In spite of their contribution to the movement for comprehensive-immigration reform, and small successes such as the Dream Act and Deferred Action for Childhood Arrivals, there are many of the 1.5 generation that didn’t, and do not, benefit from these legislative efforts, and who have returned to their home country because of these and other circumstances.This proposed research project attempts to analyze how these individuals, specifically females of the 1.5 generation, lead their lives between and across borders by asking the following questions: 1) How do young transnational Mexican women form and reform identities when moving across borders? (2) How have they learned to navigate these transformations and adapt or readapt to U.S or Mexican society? and (3) What role has culture, tradition, community, machismo and the borderlands played in their process of self-identifying? Building on theories of transnationalism, identity and Chicana-feminism, this proposed research explores the themes of immigration, gender, globalization and community through the employment of qualitative methods including semi-structured interviews, participant observation and life histories, such as testimonios, with six women on both sides of the US-Mexico border. Although this is an exploratory study it will serve to better inform our perceptions of undocumented people in the United States who lead their lives across borders.

Women still represent a small percentage of the Oregon police force even 30 years after the first push for integration into the field. As increasing numbers of departments include more strategic efforts to be made to encourage women to pursue a career in the police force, it is important to recognize the difference in how male and female police officers react to crisis situations. Research has shown that policewomen are less physically aggressive which leads to fewer lethal police encounters. Building on prior research of policewomen, my results can add to the discussion to emphasize why women are less susceptible to reacting violently during crisis situations. Data will be gathered through the collection of systemic social observations and in-person interviews with policewomen. Through the lens of the hegemonic masculinity theory, the thematic results from the interviews can assess how the internalization of gender ideologies factors into the use of nonviolent tactics in the field. The goal of the proposed research is to examine these questions; (1) What is the experience of policewomen using nonviolent conflict resolution tactics in Hillsboro, Portland and Forest Grove, Oregon? (2) How do policewomen use de-escalation and nonviolent communication learned in their police training? (3) To what extent do policewomen feel the need to use their gun in a crisis situation? This research will more clearly demonstrate to police departments the increased need for the thorough training in verbal judo, de-escalation and other nonviolent communication skills in initial police training and ongoing training for male and female police officers.

Our research at the Applied Physics Laboratory of the University of Washington seeks to develop the controlled flux technique for measuring ocean turbulence for use from a ship in the presence of rainfall. This method has been shown to be effective at determining turbulence at the surface of the ocean under rain-free conditions. However, the application under development will use the technique in the field to measure oceanic turbulence due to various types of rainfall. My objective is to determine whether or not the technique and available equipment will work in the field. A 125 W CO₂ laser operating at a wavelength of 10.6 μm (i.e. in the infrared) was assembled, tested, and aligned so that the laser beam was directed at the surface of water in a small container. The laser was pulsed so that a small patch of water was heated. A fan provided varying amounts of turbulence and an infrared imager was positioned to take images of the heated patch of water. We expect to find that the temperature of the heated water will decay more quickly for greater amounts of wind, and surface turbulence. This is important because rain also generates turbulence at the ocean surface. It is thought that the difference in turbulence as a function of rain intensity will be enough to distinguish between different amounts of ocean rainfall. Using this method at sea will give oceanographers a greater level of insight into how rainfall affects oceanic turbulence. This information can be used to improve models of upper ocean dynamics that affects large-scale ocean circulation which in turn will improve performance of global climate models. This will help scientists better predict climate events and the associated weather patterns that affect the lives of billions of people.

Ecological imbalances have manifested as environmental, social, and political concerns worldwide. Simultaneously, technology, a continued rise in urban cities, innovation, and instant gratification place a disconnect between a majority of people and the workings of nature. Much research seeks to understand the demographic and internal factors, and implicit and explicit attitudes, that attribute to environmental knowledge, attitudes, and behaviors of everyday citizens in an effort to make leaps in sustainable development. Former and recent findings illustrate the reality that positive sentiments toward the environmental movement are common, yet behavior and activism is difficult to achieve. For this research project I explore environmental knowledge, attitudes, and everyday behaviors among first year and last year University of Washington students utilizing survey research and a focus group approach. More particularly, I explore the strength and power of normative influences that develops over this traditional four-year span. Seattle, a distinguished hub of sustainable values and actions, reflects environmentally-supportive intentions and behavior among its residents, with a novel capability to inspire visitors and newcomers with its visible and verbal support. These findings will contribute to the growing understanding of environmental awareness and activism, in addition to evaluating and mapping out the power of social influence within environmental contexts.

This abstract is no longer available. Please contact urp@uw.edu if you have any questions.

The Burmese political system has entered a period of gradual democratization since the rise of the pro-Western National League for Democracy (NLD) in 1988 against the longstanding military regime. Myanmar/Burma is progressing insofar as democratic ideals are theoretically implemented; however, these provisions realistically function primarily to position the state more favorably in the international arena. This project describes the evolution of foreign diplomacy and the relationship between economic liberalization and the most recent period of democratization. To approach this subject, I focus on the legacy of British colonialism as establishing weak public institutions that promoted political disorder and exacerbated domestic conflict with the politicization of race. I look into the shift of public discourse from this hopeful unification to a regime that adopted an instutional reinforcement of colonialist racial hierarchies through militarization. My research seeks to answer why Myanmar/Burma has oscillated between democracy and authoritarianism historically based on the effects of economic growth and the potential for economic crises related to the globally interconnected economy. I emphasize the contrasting ideas between foreign and domestic actors to explicitly contextualize the ways in which political order is developing with the emergence of democratic ideals. The focus is on building state capacity since independence by using the analytic tools of modern political economy as informed by the growing importance of foreign influence on the integration into a global economy. I use the internationalization of Burma's politics to analyze the impact of foreign political support on acting as a stabilizer of domestic conflict. I conclude that the implications of foreign values taking root in Myanmar/Burma undermine domestic growth by adopting the faulty assumption that democracy is both necessary and sufficient for producing positive social and economic policies.

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.

Hot flashes (HF) are acute vasomotor disturbances that cause facial flushing and sweating. They commonly occur in menopausal women as a result of a decreased production of estradiol from the aging ovary, which triggers an acute malfunction in the brain’s control of body temperature. However, the molecular and cellular mechanisms that generate HF are poorly understood. Recent studies suggest that super-activation of KNDy neurons in the hypothalamus, which occurs in response to either reduced levels of estradiol or artificial stimulation, can disrupt thermoregulatory centers in the brain. To test this, we are developing an optogenetic animal model for HF aimed at understanding their physiological origins and enabling preclinical testing of potential therapeutics. We have created a transgenic mouse that has a light-sensitive membrane channel (channelrhodopsin-2) inserted into KNDy neurons, which can be activated with a fiber optic probe inserted into the brain. Selective activation of KNDy neurons and the subsequent behavioral response of the animal along a thermal gradient allow us to explore the role of KNDy neurons in thermoregulation. We hypothesize that following activation of KNDy neurons, the thermoregulatory set-point for excess heat perception will be lowered, so the animal will move to a cooler place along the gradient. We have preliminary evidence to suggest that when activated with a different technology (Designer Receptor Exclusively Activated by Designer Drugs) animals do, in fact move to cooler temperatures. Testing this hypothesis is our primary objective. We believe development of an animal model for hot flashes will aid our understanding of their neurobiological basis and foster development of better and safer therapeutic options for treatment.
 

Universal health care has been a topic of controversy, largely due to the question of resource management. As part of an Exploration Seminar through the University of Washington, a team of students conducted interviews with health centers in Chile to investigate universal health care. Each team member was responsible for posing questions relevant to their area of study and reporting on the research after the program ended. The goal of the program was to assess health system disparities in Chile.This presentation focuses on the role of regional epidemiology, which studies the population in a local area and tailors the universal health care plan to that region. Open ended interviews with community health workers were conducted at twenty-two medical sites throughout Santiago and Southern Chile. The sites ranged from the private sector headquarters to rural outposts in the Southern Archipelago of Chiloé. Translations between English and Spanish were performed when necessary. The study found that Chile has an overburdened public health care system, particularly in specialty areas. Eighty percent of treatments are not as effective as standards per guidelines. Regional epidemiology decreases waste and increases productivity, especially in the areas of primary care and prevention. The strengthened primary care system reduces the burden of care on the tertiary health system. Regional epidemiology is currently expanding to cities outside of Castro and Chiloé Island. Regional epidemiology is an effective tool for improving the Chilean universal health care system. More research should be done to predict whether regional epidemiology will be effective in private health care and other universal health care systems.

Pain catastrophizing has been associated with increased pain experience and expression in children with chronic pain. Parental catastrophizing about child pain has been associated with increased parental distress and overprotection. This study sought to understand how catastrophizing might be reflected in pain-related parent-child communication. 70 children with chronic abdominal pain and their mothers participated. Mothers and children independently completed child- and parent-report versions of the Pain Catastrophizing Scale. Dyads then conversed for 10 minutes about the child’s pain. Conversations were audio-recorded, transcribed and reduced using a linguistic analysis program. Dependent variables were the percentage of negative affect words uttered, including anxiety, sad and angry words such as worried, grief and mad, respectively. Multilevel modeling was used to estimate an Actor-Partner Interdependence Model assessing the effects of role (mother versus child) and catastrophizing on the percentage of negative affect words uttered during the conversation. Main effects of role emerged for the higher level category of negative emotion words and the subcategory of sad words (p values < .001), such that mothers uttered more of these words than did children. A main effect of catastrophizing also emerged for negative emotion words, such that those higher in catastrophizing uttered more negative emotion words than did those lower in catastrophizing, regardless of role (p < .01). The analysis for anger words was more complex, yielding role x actor and role x partner interactions (p values < .05). In essence, maternal catastrophizing was positively associated with both maternal and child anger word usage, whereas child catastrophizing was inversely associated with maternal anger word usage. Findings extend the literature on behavioral and interpersonal correlates of catastrophizing. Future research is needed to fully elucidate parent-child interactional patterns in the context of chronic pain. Findings could inform the design of cognitive-behavioral interventions aimed at reducing symptoms and disability.

 In 1737, Gaspar Miguel de Berrio painted El Patrocinio de San José. Now housed in La Casa Nacional de Moneda de Bolivia, the canvas is one of reverent exuberance. In an aura of golden sand, Saint Joseph’s cloak gently shelters earthbound saints, separating them from the ethereal realm above. The holy figures appear attentive to Christ’s foster father, raptly gazing at the golden glinting figure. Like other Andean Baroque painters, de Berrio juxtaposed European and Pre-Columbian details, though his paintings in particular are exceptional in their subtle yet innovative reappropriations and combinations of motifs. In this presentation, I explore de Berrio’s choice to enclose the saints surrounding Joseph in relationship to Medieval images of the Virgin Mary. Though this connection has been marginally noted in the literature, a proper study of such a striking feature remains necessary to understand the adoption and modification of European iconography by Andean Baroque artists. Studying de Berrio’s oeuvre in relationship to European references, I argue that Gaspar Miguel de Berrio not only intentionally depicted Saint Joseph in a manner similar those medieval virgins in his El Patrocinio de San José , but that this artistic choice reveals the power of the Cult of Saint Joseph in the Viceroyalty of Peru.

The Odegaard Writing and Research Center (OWRC) is one of the most well-known and broadly focused writing support resources on the UW campus. Our staff of nearly 70 tutors offers about 500 bookable appointments each week; additionally, a consistent flow of unscheduled writers enter the center daily. To manage incoming traffic, two years ago, the OWRC instituted a concierge position with responsibilities that include answering general questions, assisting writers with booking appointments, notifying tutors of appointment arrivals, and conducting drop-in sessions. Still, traffic flow into the OWRC is occasionally overwhelming and concierge staff often mention the logistical challenges and frustrations inherent in the position. We decided to assess the concierge position from a design perspective, using focus groups, interviews, surveys and ethnographic observation. We wanted to know more about the nature of challenges faced by concierge staff and to identify measures that would improve our writers’ user experience. Preliminary results from this project point us to several recurring problems for which we plan to generate and test solutions iteratively. In addition to improving the experience our fellow Huskies have in the OWRC, our work may have implications for other institutions that experience high traffic flow and want to make their check-in experience more streamlined and welcoming.

Pursuing undergraduate education in developed countries has become a phenomenal trend in China over the past ten years. At the University of Washington (UW), among 7299 international students in 2014, 3845 are from China and over three-fourths of them are undergraduate students. Though Chinese students have been a significantly growing student body at UW, there has not been sufficient research to comprehensively understand them. My research is to create an ethnography of undergraduate Chinese international students at the University of Washington. The ethnography centers around the challenges they have faced at the crossroad of stepping into young adulthood and adjusting to American culture; and changes they have undergone in the U.S., including those of identities, beliefs, life styles, interests, and personalities. I aim to capture characteristics unique to this Chinese generation studying abroad who were born in 1990s under one-child policy, growing up in the era of economic reform in China and globalization; and to understand the sociopolitical, economic factors in China that made this studying abroad trend possible. The ethnography also focuses on students’ values and relationships with their families as singletons and how their transnational lives change the dynamics of their original families. I conducted in-depth interviews with ten junior and senior Chinese international students with various majors and backgrounds at UW. Reoccurring themes from fieldwork, which are being further investigated, include realization of being racial and ethnic minority in the U.S., challenges of assimilating into American society, social dynamics among Chinese and American peers, restrictions of working opportunities in the U.S., non-traditional definition on filial piety, etc. This ethnography intends to promote understanding of Chinese international students at UW and shed light on the only-child generation in China.
 

Fronts are dynamic regions in the ocean where contrasting water masses meet, characterized by rapid currents, sharp density gradients and high productivity. What drives the phytoplankton community structure in these regions is still not well understood, but it has been hypothesized that fronts could act as either a barrier or a blender. However, few observations exist to test this hypothesis. The Kuroshio Front off the coast of Japan, extending eastward into the North Pacific Ocean, is an important western boundary current front, known to be important for fisheries. During a cruise in October of 2009, fine-scale sampling was conducted, and diatom and dinoflagellate phytoplankton taxa were identified to the species level by microscopy. Concurrent measurements such as salinity, temperature and chlorophyll were also taken to relate the physical and biological characteristics of the sample region. My analysis has revealed that distinct water masses found in the frontal zone have significantly different phytoplankton diversity indices. Conversely, I found that the most frequently observed and most abundant species in these water masses were remarkably similar. Major differences between the water masses were driven by the diversity of rare species. I show the importance of rarity in driving diversity and highlight the disconnect between the physically distinct water masses observed and the structurally similar phytoplankton community. My results reflect the importance of lateral mixing, mingling species from distinct source regions along the front. Rare species most likely represent the least competitive constituents of those original source populations. This research suggests phytoplankton may mix into new water masses diferent than their initial environment even if the water masses themselves remain physically distinct.

Plastic pollution in the ocean is a global issue that continues to grow as manufacturing and consumption of plastic products increases. Both macro- and micro-plastics are often difficult to discern visually, the latter requiring a microscope, which makes scientific quantification and identification challenging. The full range of plastic’s impacts on/to the marine environment is not completely understood, particularly in New Zealand waters where there is a lack of research on the subject. During the six-week Sea Education Association S-256 research voyage around New Zealand’s North and South Islands, 44 surface water samples were taken to measure microplastic (0.02 – 0.33mm particles) concentrations and 34 neuston net tows were conducted to collect macroplastics (0.33 – 5mm particles). Overall, plastic concentrations in New Zealand waters varied in density and polymer type. However, when compared to major gyre systems such as the North Atlantic and North Pacific, macroplastic and microplastic concentrations in this region were considerably lower. Macroplastics were limited in quantity. 29 total were found along the cruise track, primarily polyethylene and polypropylene polymers; these plastic types come from single-use packaged goods and fishing gear. Microplastic densities were greatest in regions where strong currents converge, suggesting that surface ocean plastic particles are transported by circulation processes. 2,923 microplastic particles were observed, the majority of which were filaments likely indicative of fishing gear. This marine debris may be attributed to relatively high fishing efforts in portions of the New Zealand Exclusive Economic Zone.

Non-traditional isotopes have become increasingly important as tracers for geological and environmental processes on earth. Recently, renewed attention has been direct towards potassium (K) isotopes given the abundance of K in the earth and the potential for significant mass-dependent fractionation between ⁴¹K and ³⁹K. There is little existing research on K isotopes primarily due to analytical difficulties, however recent technological developments have made precise analysis possible. Seawater has the potential to be an excellent geostandard for K isotope geochemistry because of predicted ⁴¹K/³⁹K homogeneity through the water column, and its wide accessibility around the globe. A total of forty-seven, 30 mL samples were collected in July 2015 aboard the R/V Thomas G. Thompson on the VISIONS 2015 Expedition to Axial Seamount on the Juan de Fuca Ridge. Samples were collected from CTD (Conductivity Temperature Depth) casts as well as niskin bottles operated by the Remotely Operated Platform for Ocean Science (ROPOS). Seawater profile samples were taken at several locations from 7 m down to 2890 m. Evaluating the K isotopic composition at each depth and geographic location will determine if the K isotope composition of seawater is homogeneous and therefore if seawater may be useful as a future geostandard. If K behaves similarly to other non-traditional isotope systems, ³⁹K will preferentially be released into the hydrosphere during weathering, leaving the residual rock enriched in ⁴¹K. This behavior will be useful in constraining the process of granite weathering, and its effect on the K budget in the hydrosphere. In chemical oceanography, there is thought to be a missing sink for K, and it is theorized that clay formation, crustal fractures, or both may remove K from seawater. Determining the feasibility of seawater as a geostandard for K isotopes will further facilitate new research in these and other geochemical topics.

This project aims to develop a better model for testing gene therapy vectors in vitro. Gene therapy uses a modified virus to insert a functional copy of a gene into a patient’s cells, but testing new viral vectors on 2D cell culture does not accurately predict success in vivo. To address this need, I have designed a 3D-printed microfluidic device for optimized viral vector testing. Cells are cultured in 3D in one channel, while media and viral vector load can be easily adjusted in a connected channel through a gravity perfusion system. The device is currently undergoing tests for cell viability and demonstrating its utility for gene therapy applications. The primary advantage of this device is that cells cultured in 3D mature more similarly to true skeletal muscle and thus are better models for predicting the success of a viral vector in a patient. The small size and fine tune control over the cell’s environment also save time and money during testing, allowing the maximum number of options to be explored. A new, physiologically relevant model for testing viral vectors would expedite gene therapy research to help bring treatments faster to patients in need of gene replacement therapy.

The ideology of colorblindness is an issue prevalent in multiple areas of American society. The environment in which college students receive their education could affect whether or not they will develop racial awareness, particularly in terms of privilege. High school educators should have the opportunity to teach students about the topics of race and white privilege and how to recognize the myriad ways that race shapes individuals' lives as well as how they are still embedded in social institutions. Scholarship on this topic highlights how there are many factors that influence the ways in which privilege is (or is not) being taught to American students. White students who fail to realize the privileges that come with their race don't feel like they have social responsibility to others, specifically minorities. This study examines the freshmen college student's awareness of race and white privilege at a predominantly white university. Thus, for the purpose of this study, the colorblind ideology and symbolic interactionism theory of sociology are being used as the perspectives to analyze and interpret the data. The research uses a questionnaire containing many of Peggy McIntosh's questions on white privilege, to observe the racial awareness, particularly in terms of privilege, of the freshmen college students. The results will conclude whether there is a correlation between the student's racial awareness, particularly in terms of privilege and their educational context. Through this research, the discussion of mandating the implementation of a cultural studies course at a high school setting can potentially be opened for future scholars.

There are significant pregnancy health disparities experienced by American Indians in the Great Plains region that are not well understood. Community-based research projects (CBRPs) are one of the best ways to understand why these disparities exist and how we can reduce them. Conducting a CBRP requires building a trusting relationship with the American Indian community and the researchers. As well as having community members and researchers work together on the project will show that we value the community members and their input just as much as our own. It will also allow us to write the findings from a community perspective not just an outsider’s perspective. Our McNair research plan is to establish a trusting CBRP collaboration with the Turtle Mountain band of Chippewa Indians focusing on institutions that will help us conduct the Healthy American Indian Pregnancy Project that is under grant consideration.

I explore the role of Philosophy for Children (P4C) and critical pedagogy in middle-school education and argue that P4C is a crucial component of an emancipatory education. A critical P4C is necessary to provide students what education ought to provide, that is moral reasoning skills, tools for thinking, and ability to engage in discourse. Proponents often justify P4C claims that philosophy lessons in K-12 education by demonstrating the improvement of outcomes in other subjects and gains in cognitive skills. Instead, I argue for an intrinsic value to engaging in philosophy with children. Critical pedagogy, and the methods developed within its framework, are helpful here to examine the structure of educational practice and its role in dehumanization, which "is a distortion of the vocation of becoming more fully human"; critical pedagogy is intended to be a tool for both the oppressors and the oppressed to become aware of their dehumanization. First, I justify P4C by showing that precollege students can understand and engage in philosophical discussion using academic references and my own experience working with middle-school students at the Ivy School in Portland, Oregon. Next I examine the philosophical influences of P4C alongside critical pedagogy to show how they interact and compliment each other. Lastly, I envision pedagogical techniques for carrying out Critical P4C in the classroom. Implementing critical P4C has the capacity to create communities of inquiry around questions of agency and freedom that are central to critical pedagogy. Critical P4C offers strategies for engaging students in socio-political discussions and promises to break the boundaries between "school life" and the students' everyday life outside the classroom.

 Glioblastoma multiforme (GBM) is the most common and deadliest cancer of the central nervous system. The existence of stem-like cells within GBM tumors - Glioblastoma stem cells (GSCs) - may explain some of the malignant features of Glioblastoma multiforme (GBM) owing to their rapid self renewal and diffuse migratory behavior. Increasingly apparent is the role ion channels play in many cancer cell properties, including regulation of cell cycle progression and proliferation, tumor cell motility and invasion, and regulation of metabolic rate. We hypothesize that ion channel dysregulation contributes to GSC malignancy, including increased viability, proliferation, and migration. To test this, multiple GSC isolates derived from human GBM tumors were maintained in culture over many passages while retaining stem cell properties. RNA-seq expression profiles revealed ion channel families that were highly enriched in GSC samples. Real-time qPCR was next used to confirm increased expression of voltage gated calcium, sodium, and potassium channels, ionotropic glutamate channels and inwardly-rectifying potassium channels. Identifying ion channels uniquely enriched in GSCs led to functional analyses to determine how ion channel blockers affected their proliferative and migratory properties. We performed MTT cell viability assays to assess how ion channel blockers altered the viability of GSCs compared to a control neural stem cell line. We were able to show a significant decrease in cell viability across GSC lines compared to control at a variety of drug concentrations. Utilizing live-image cell tracking, we determined decreased migratory behavior and rates of these GSC lines with the same blockers. Finally, to elucidate the role of the extrinsic tumour microenvironment on the proliferation and migration of GSCs, unique coculture models involving GSCs cultured on mouse organotypic brain slices were utilized, and showed the affects of stimulating and inhibitory DREADD receptors to modulate local neuronal activity.

Cancers are fueled by mutations which impart new capabilities to incipient cancer cells. Spontaneous mutations are, however, more likely to be deleterious than beneficial based on random chance alone. Therefore, inducing more mutations in an heavily mutated population could lead to an “error catastrophe” once the mutation level rises past a certain threshold. Accumulating too many of these debilitating mutations consequently leads to a reduction in the overall population fitness. Our hypothesis is that mutagenic versions of nucleoside analogs (modified versions of the building blocks of DNA) can induce more mutations to reach this ‘error’ threshold and beyond, and that this can selectively kill cancer cells. To evaluate the effectiveness of this strategy, termed therapeutic mutagenesis, we conducted cell culture experiments on various human colon cancer cell lines: HCT116 (mismatch repair deficient colorectal cancer) cells, SWS620 (non-MMR-deficient colorectal cancer), and a control normal human fibroblast line. We screened a library of candidate nucleoside analogues (e.g. O4-Ethyl-Thymidine) for mutagenicity and viability at physiologically relevant concentrations. I then quantified the short-term viability of the treated cell lines with a clonogenic survival assay. I used the highly accurate Duplex genetic sequencing methodology to monitor the changes in a cell line’s overall mutation load after treatment. After validating the concept of therapeutic mutagenesis in cancer, our next steps will be to determine whether possible animal and clinical trials would be possible in the future. Our approach may open up new therapeutic possibilities for patients in the most advanced stages of cancer, especially in the context of complementing increasingly common immunotherapies.

Developmental phenotypic plasticity can be a vital means to buffer the sudden and persistent effects of anthropogenic climate change, through facilitation of species persistence and possible facilitation of species range shifts. Integrating our understanding of plastic physiological growth mechanisms with functional traits may prove useful for interpretation of the ecological impacts of climate change. We investigated the influence of water-stress and light limitation on leaf mass per area (LMA), leaf anatomy, and leaf gas exchange of juvenile Populus tremuloides trees. Leaves that developed while water-stressed had significantly elevated LMA, due to increased leaf density from significantly higher spongy mesophyll surface area per leaf area (A_smes/A) and reduced stomatal conductance (g_s) but only marginally reduced photosynthesis (Pmax). In shade, leaves had significantly reduced LMA, due to reduced thickness, density, and combined A_mes/A, but maintained the same A_smes/A, and reduced palisade mesophyll surface area per leaf area (A_pmes/A), which was coupled with a reduction of g_s and P_max. Furthermore, water-stressed leaves had elevated intrinsic water use efficiency (WUE_i: P_max/g_s) while the shaded leaves, despite reduced g_s, maintained similar WUE_i. Our results suggest that, under water-stress and full sunlight, greater A_smes/A conferred maintenance of photosynthetic rate possibly through reduction of mesophyll resistance (r_m), at the cost of reducing expansive leaf area (and increasing density) as leaves were more dense but were 20 % the area of control leaves. In shade, suppressing A_pmes/A while maintaining A_smes/A may be a plastic strategy to increase laminar light capture, as leaves had reduced density and thickness but were still 50 % the area of control leaves . Together, in P. tremuloides saplings, these stresses induced developmental plasticity in LMA with differing plastic underlying anatomy and function; we discuss future implications specifically in the context of developmental plasticity, growth trade-offs, and the ecological impacts of climate change.

Suction feeding is a valuable process to study since most aquatic vertebrates, which make up nearly half of all vertebrates, eat this way. Having a better understanding of this may give important insight into the evolution of vertebrates as a whole. During suction feeding the cranium elevates, causing bending in the vertebral column, resulting in a rotation of the cranium and body plane about an axis of rotation located on the vertebral column. We hypothesized that the vertebral column behaves like a flexible rod and accordingly asked if axial rotation is located more posteriorly with larger degrees of cranial elevation. Using video reconstruction of moving morphology and joint coordinate systems, which use coordinates to measure the 3D motions of bones in a anatomicaly meaningful coordinate space, we compared movement of the cranium in relation to the body in striped surfperch, largemouth bass, and Pacific staghorn sculpin. We found no significant correlation between degree of cranial elevation and location of axial rotation. However, the degree of cranial elevation and location of axial rotation varied among these species in a consistent way. These species’ unique ways of performing these movements could be related to their differences in morphologies.

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.

The Cretaceous-Paleogene (K-Pg) mass extinction and resulting biotic recovery mark a pivotal moment in mammal evolution. The recovery period, which spanned about 1 million years from the Puercan North American Land Mammal Age (NALMA) to the Torrejonian NALMA, represents a transition from species-poor “disaster” faunas directly following the extinction event to species-rich “recovery” faunas. Though previous research has broadly studied the faunal dynamics of the early Paleogene, the exact mode and tempo of the biotic recovery has not been well examined. To investigate the ecological trends of the “disaster” to “recovery” faunal transition, specifically changes in diet, we analyzed dental evolution within the periptychid and arctocyonid “archaic ungulate” lineages over a time period that spans from the Puercan NALMA to the Torrejonian NALMA. We measured relief index (RFI), a metric that determines the ratio between the 2D and 3D area of mammal teeth, on both the “archaic ungulates” and a set of ecologically diverse extant mammals to identify the dietary ecologies of the extinct mammals. Previous research has demonstrated a correlation between RFI and diet in extant mammals; high RFI values correspond to herbivory and insectivory, while low RFI values correspond to omnivory and frugivory. Our preliminary results suggest an increase in dietary diversity and an overall decrease in RFI during the biotic recovery. This reduction in RFI reflects a trend in “archaic ungulate” dietary preference from insectivory in the Puercan NALMA to omnivory and frugivory in the Torrejonian NALMA. The results of our study will help scientists understand how ecosystems recover from catastrophic events, such as mass extinctions, on large timescales.

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.

The microscopic cyanobacteria Prochlorococcus is the smallest and most abundant photosynthetic organism in the ocean, playing a large role in the global cycling of nutrients. Prochlorococcus form ecotypes, which are genetically variable lineages with differing physiological traits adapted to various environmental niches that enable them to be so widespread. They reside in oligotrophic (nutrient depleted) waters where certain required nutrients like phosphate can be scarce, and use a high affinity phosphate uptake pathway to take in phosphate. However, this pathway cannot completely differentiate a phosphate molecule from the physiochemically similar arsenate molecule, leading to the uptake of arsenic into cells, especially when the phosphate to arsenic ratio is low. Recent work performed by my mentors has studied the two pathways Prochlorococcus uses to detoxify arsenic, the efflux detoxification pathway, which was previously known, and the recently discovered putative methylation pathway, and they have found that strains of Prochlorococcus have different genomic capacities for arsenic detoxification. We are currently testing that genomic capacity for arsenic detoxification correlates to relative arsenic tolerance among lab strains of Prochlorococcus by batch culturing and comparing growth inhibition rates of four Prochlorococcus strains that differ in the pathway genes they contain, MED4, NATL2A, AS9601 and SS120. By inoculating the cultures in three different conditions with variable arsenate concentrations and calculating the inhibition rates, we will answer if Prochlorococcus genomic capacity correlates to relative arsenic tolerance. This would have impacts on how we look at the global circulation of arsenic because the two arsenic pathways have varying outputs that affect the circulation of arsenic and can influence the bioaccumulation of arsenic in upper trophic levels.

Glioblastoma multiforme (GBM) is the most common and highly malignant brain cancer diagnosed in adults. Due to its high invasiveness and difficulty of surgical removal, there is a need for novel therapeutics to treat this disease. Recent evidence suggests that cannabidiol (CBD), a non-psychoactive compound from the Cannabis plant, possesses antitumor properties in a number of cancers. However, the mechanism by which CBD acts to decrease tumor viability and proliferation is unclear. To better understand the antitumor properties of CBD, we tested this compound against standard of care chemotherapy drugs BCNU, Temozolomide, and Cisplatin in human GBM cell lines T98G, U87MG, and U251. Using the water soluble tetra-zolium salt (WST-1) reagent and bromodeoxyuridine (BrDU) assay in vitro, we assessed the dose response of CBD on GBM cell viability and proliferation, respectively. Using the same assays, we also investigated the effects of CBD in combination with standard of care chemotherapy. We found that CBD dose-dependently (IC50 = 3.1µM) suppressed viability and proliferation in all GBM cell lines tested, and that this response was more potent than standard of care chemotherapy. In addition, CBD exhibited additive effects when combined with standard of care chemotherapy in vitro. Implications for this research include development of novel cannabinoid-based cancer therapeutics.

When setting up interspecies crosses between female Caenorhabditis species 29 (C.sp.29) and male Caenorhabditis nouraguensis (C.n.), the resulting progeny are all dead. However, the reciprocal cross (mating male C.sp.29 with female C.n.) still results in mostly dead progeny, but there are rare progeny that survive. These rare, surviving progeny can either be sterile or fertile. My research focuses on studying what causes the sterility of the rare offspring genetically. Thus, I set up crosses between female C.n and male C.sp.29 and collect the resulting rare offspring to genotype them. Then I characterize these offspring based on their morphology and genetic differences such as homozygous or heterozygous type inheritance at each chromosome. The worm genome consists of six chromosomes and I am currently testing chromosome I and IV. So far, fertility is associated with only maternal inheritance at chromosome I, while sterility is associated with offspring being a hybrid (heterozygous) at chromosome I. The fertile progeny are able to survive possibly due to a process called gynogenesis. Gynogenesis is when the egg is activated by the sperm but sperm’s DNA is excluded in the offspring. Some offspring exhibit a homozygous genotype at one chromosome while a heterozygous genotype at another. Therefore, if a reoccurring pattern is observed where a sterile worm has a homozygous genotype at chromosome I and a heterozygote genotype at chromosome IV, then I could hypothesize that sterility of the offspring is due to this particular pattern of inheritance. This implies that there could be more than one combination of inheritance contributing to the degree of sterility of each offspring. The main goal of the project is to investigate the complexity and the genetic requirement for sterility that is caused as result of these crosses.

The Cretaceous-Paleogene (K-Pg) mass extinction event was a pivotal episode in the evolution of mammals. It is widely held that the extinction of non-avian dinosaurs allowed mammals to evolve rapidly into ecological niches previously occupied by dinosaurs. Studies of successive mammalian faunas from northeastern Montana have detailed this pattern, showing that (1) the earliest Paleogene (Puercan 1) ‘survival’ fauna from within 80,000 years of the K-Pg boundary was species poor and included many immigrant taxa and (2) full recovery and expansion of mammalian diversity only occurred 600 to 700 thousand years after the K-Pg event. To better resolve our view of the immediate aftermath following this mass extinction event, previous studies by myself and the Wilson Lab have analyzed a mammalian fossil assemblage from the Constenius locality (UWBM C1665), which documents a ‘survival’ fauna. The Constenius locality is bracketed to within 20,000 years after the K-Pg boundary, thus providing a time-constrained view into which mammals survived the mass extinction and how quickly immigrant taxa invaded this area. Here, I add to our understanding of this fossil assemblage by identifying and describing 23 newly recovered mammalian specimens from the Constenius locality. These specimens, which include isolated teeth and jaw fragments, were discovered in situ in the field and in the lab after screen washing more than 100 kg of bulk sediment. I compared the taxonomic composition and species richness of the Constenius mammalian assemblage to those from the Worm Coulee 1 locality (UWBM C1369), which is bracketed to within 80,000 years of the K/Pg boundary and likely represents a slightly younger assemblage. The results so far indicate that species richness and relative abundance is highest in archaic ungulates and lowest in multituberculates which is consistent and further strengthens previous research done at the Worm Coulee 1 locality within 80,000 years after the extinction event.

Protein homooligomers, multibodied assemblies built from identical polypeptide chains, comprise a large fraction of known cellular proteins. Homooligomers prove to be particularly amenable for many biological applications; they hold the potential as oligomerization domains, often have enzymatic functionality as a byproduct of their oligomeric configuration, and can serve as structural scaffolds for bionanomaterials. While there exists a multitude of protein homooligomers in the Protein Data Bank, the finite number of existing homooligomers limits the potential for custom applications. Our current work involves designing novel cyclic protein homooligomers from a set of de novo designed repeat proteins that share no sequence or structural homology to any known protein structures. We chose these proteins because of their modular properties, large variety of topologies, and unprecedented thermostability. Using the Rosetta software suite, we generated a set of de novo homooligomer models by designing the oligomeric interface to direct self-assembly into a target configuration with two to six identical chains. After a round of refinement, we will express the designs in Escherichia coli and purify them by immobilized metal affinity chromatography. Their oligomerization state will be validated by measuring the molecular weight in solution by size exclusion chromatography paired with multi-angled light scattering and comparing it to the predicted molecular weight of the design. Designs that exhibit the desired molecular weight will be submitted to collaborators for small angle X-ray scattering data and X-ray crystallography. The exclusive use of de novo proteins in homooligomer design grants a greater control over the shape and stability by nature of the repeats, thus making one successful interface design useful for a multitude of shapes and sizes. This variability opens up a wide scope of scaffolds for bionanomaterial engineering.  

Systemic immune activation (IA) is a proven key factor in human immunodeficiency virus type 1 (HIV) infection pathogenesis and progression to acquired immunodeficiency syndrome. The reproductive hormone progesterone plays a role in regulating the immune system, and most cells contain progesterone receptors. Previous studies have linked high-progestogen states in women, such as pregnancy and progestin-based contraception use, to increased infectivity in HIV-seropositive women and increased HIV acquisition in seronegative women. Progestin-based contraceptives such as depot-medroxyprogesterone acetate (DMPA) can create high plasma levels of progesterone analogs. Therefore, studying DMPA use by HIV-seropositive and seronegative women may clarify DMPA’s role in HIV-related IA and genital shedding, and immune changes related to HIV acquisition. We hypothesize that DMPA increases systemic IA. Increased IA could be clinically significant by contributing to increased HIV acquisition in high-risk HIV-seronegative women, and by increasing genital shedding and infectivity among HIV-seropositive women. To answer this question, peripheral blood mononuclear cells (PBMC) were collected at three postpartum time points over six months from 120 Kenyan women with both HIV-seropositive and seronegative status, including a sub-population in each category that elected to receive DMPA for contraception. Two immunophenotyping panels were developed to measure T-cell IA and cellular subsets of interest using flow cytometry (CD38, HLA-DR, Ki-67, Bcl-2 for T-cell activation; FOXP3, CD25, CD127 for regulatory T-cells; CCR7, CD45RA, CD27, CD28, CD57 for memory subsets; CCR5 for the HIV co-receptor). With preliminary analysis completed for most samples, specific antibody populations have been gated with FlowJo software. After completion, we will compare different population percentages in the four arms of the study, observing how these change with DMPA administration. These calculations will help elucidate expected differences in inflammatory and regulatory changes in both HIV-seropositive and seronegative women with respect to the relationships between DMPA, immune activation, and HIV susceptibility and infectivity.

A pressing issue for much of the world is finding energy resources alternative to fossil fuels. I conducted a literature review through databases such as JSTOR and ERIC that addresses fractal kinetics to describe the saccharification of lignocellulose. Lignocellulose is one of the most abundant biomass resources on earth found in plants and can be converted into a biofuel, ethanol. The process of converting lignocellulose to ethanol is similar to the process of converting starch, found in corn, into ethanol. In both processes the substrates go through saccharification, a procedure where they are broken down into glucose. The glucose is then fermented and is converted into ethanol chemicals. However, converting lignocellulose to ethanol has a very low conversion rate which inhibits the ability to use lignocellulose as a viable energy alternative. Primarily, the classical kinetics model is used to describe the saccharification of cellulose. Before the introduction of fractal geometry in the 1970s, the geometry of nature was considered too complex and irregular to describe analytically using Euclidean geometry. Since then, fractal geometry has been found to model natural phenomena. Fractal theory is important to helping scientists understand the saccharification of lignocellulose and develop models for efficient conversion in the future. With a consistent method to converting lignocellulose into a biofuel, society can move away from fossil fuels as our greatest energy source.

During pregnancy, women and the developing fetus face the risk of invasive bacterial infection, which can lead to adverse birth outcomes such as preterm birth or fetal death. Inflammatory cytokines play a key role during infection-related preterm birth. Previous studies have shown that lipopolysaccharide (LPS), a gram-negative cell wall component, causes increases in inflammatory cytokines and preterm birth in mice. However, limitations exist when comparing the pregnant mouse model to humans. Recently, we conducted a non-human primate (NHP) experiment to identify putative targets of inflammation caused by LPS. However, contrary to expectation, no signs of preterm labor were observed. To determine if the LPS batch used in the NHP model induced inflammation in immune cells, I used an in vitro human macrophage cell culture model.  A human immortalized monocyte cell line, THP-1 cells, was differentiated to macrophages using phorbol myristate acetate (PMA) and treated with a range of concentrations of LPS, similar to those used for the NHP experiment. Cytokines in the medium were quantified by the Enzyme-Linked Immunosorbent Assay (ELISA). LPS increased IL-1B in a dose-dependent manner. Additional inflammatory cytokines associated with preterm birth such as, IL-6, IL-8, and TNF-a, will also be measured. The results will be compared to the ELISA results of the same cytokines released in the NHP samples. This work will guide insight into addressing the inflammatory response associated with preterm birth.

This abstract is no longer available. Please contact urp@uw.edu if you have any questions.

Polio is on the cusp of worldwide eradication but remains endemic in Afghanistan and Pakistan. The Global Polio Eradication Initiative has implemented an environmental surveillance program to detect poliovirus (PV) in environmental samples such as sewage. Systematic environmental sampling provides supplemental data to disease-based clinical surveillance data. However, traditional PV detection methods from environmental samples, cell culture and quantitative reverse transcriptase polymerase chain reaction (RT-qPCR), are time-consuming and expensive. Development of a screening test has potential to streamline environmental surveillance of PV. Reverse transcriptase recombinase polymerase amplification (RT-RPA) is an isothermal molecular amplification technique with potential as a screening test. In this technique, virus particles are lysed to release RNA, which is converted to cDNA and amplified using enzymes. Amplified PV cDNA can then be detected through lateral flow detection. Collaborators at PATH have developed a RT-RPA protocol that has shown promise in rapid PV detection in stool samples. The aim of this research is to adapt PATH’s clinical PV RT-RPA protocol for use with environmental concentrates. Concentrates were obtained by filtering raw sewage from a Seattle wastewater treatment plant. Results of the RT-RPA test and subsequent visualization on lateral flow detection strip were compared to cell culture and RT-qPCR. We anticipate that RT-RPA will show similar PV recovery rates when compared to traditional methods and will be suitable as a rapid screening test for environmental concentrates. Future work will include designing primers to expand PV serotype detection and evaluating PV detection in environmental samples from existing sampling sites. Rapid PV detection with RT-RPA may streamline environmental surveillance methods, improve outbreak detection, and provide data for certification of polio-free status and global eradication.

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.

The central nervous system is protected by a specialized population of glial cells called microglia. In addition to other crucial functions, microglia function as resident macrophages of the brain and mount a coordinated response when activated by infection or injury. Although acute inflammation is a necessary component of repair after injury, chronic inflammation can have neurotoxic – rather than neuroprotective – effects. The dysregulation of microglia is associated with many neurodegenerative diseases and is an impetus for investigating the molecular mechanisms that regulate microglial changes in aging and their responses to neural disease and injury. The Garden Lab has previously identified a pathway by which reactive oxygen species or DNA damage modulate microglial anti-inflammatory functions through induction of the p53 transcription factor. Transcriptional activation by p53 leads to increased expression of microRNA’s that suppress the anti-inflammatory transcription factor, c-Maf. The goals for my project are to investigate how c-Maf influences microglial activation states and how changes in the environment influence the expression of c-Maf. In order to assess how c-Maf influences microglia activation, I quantified phagocytic activity in primary murine microglia by flow cytometry in conditions where c-Maf is overexpressed or knocked down. Overexpression or knock-down of c-Maf was accomplished by treatment with adeno-associated viruses (AAVs) containing CMV-promoter driven c-Maf or c-Maf-shRNA, respectively. I also evaluated microglia expression levels of pro-inflammatory and anti-inflammatory activation markers by qRT-PCR following modulation of c-Maf expression or treatment with cytokines. I observed that c-Maf overexpression resulted in increased expression of anti-inflammatory markers and decreased expression of pro-inflammatory markers, and vice versa for c-Maf knock-down. Through this project, we have a better understanding of the influence of c-Maf and inflammatory cytokines on the molecular regulation of microglial functions, and their roles in the pathogenesis of neurodegenerative disease.

Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of abnormal immature bone marrow progenitor cells (“blasts”). AML blasts reside in the bone marrow microenvironment via adhesion molecules such as CXCR-4 and VLA-4, which confer protection from chemotherapy in AML. L-selectin is a surface receptor utilized by leukocytes (white blood cells) for rolling on the endothelial lining of blood vessels and adhesion to sites of inflammation. CXCR-4 is a chemokine receptor for stromal derived factor (SDF-1, CXCL12) produced by bone marrow stromal cells. VLA4 is an α4β1 integrin that mediates adhesion to alternatively spliced fibronectin and cellular vascular cell adhesion molecule 1 (VCAM1). Previous studies in our laboratory and others suggested that expression of CXCR-4 and VLA-4 is associated with prognosis in AML, and L-selectin expression increases with older age in AML patients. The hypothesis of my project is that L-selectin expression level is associated with chemotherapy resistance in AML. We performed experiments on blasts with high vs. low L-selectin surface expression as measured by flow cytometry assessment of mean fluorescence intensity (MFI). We allowed the AML blasts to be attached to plates coated with PSGL-1, an L-selectin ligand, or bovine serum albumin (BSA), a control protein. Then blasts were treated with cytarabine (Ara-C), one of the most active chemotherapy drugs in AML, for 72 hours. Data were collected by manual counting of viable cells, Cell-Titer Glo luminescent viability assay, and flow cytometry for Annexin V, as a measure of apoptosis. Our data showed that PSGL-1 binding protected AML blasts from chemotherapy in 4/15 (27%) of the samples, which had higher L-selectin (p = 0.05), lower VLA-4 expression (p = 0.10) and higher CXCR-4 (p=0.11) surface expression. Therefore, these results suggest that differences in expression and function of L-selectin, CXCR-4 and VLA-4 are associated with chemotherapy sensitivity in AML blasts.

This project will inform a systems biology platform for identifying adverse responses to environmental compounds on testicular development in mice, a commonly used model system in the field of Toxicology. In order to validate the organotypic culture system, we have investigated the adverse effects of the known testicular toxicant, cadmium. To initiate the culture model, we isolate and plate testicular cells from immature mice on postnatal day (PND) 9 in order to capture a developmental window of susceptibility. Based on a literature search derived developmental timeline, we chose to treat the culture on days in vitro (DIV) 2, 5 and 15 with cadmium and quantify effects 24 hours later. We hypothesized that dosing with cadmium during these time points would correspond to impacts on steroid regulation, proliferation, and spermatogenesis processes. In order to evaluate a dose response relationship in our testicular culture, we treated the testis cells with 2.5, 5.0 and 10 uM concentrations of cadmium. To quantify the effects of cadmium in our cell culture model we evaluated; total protein, testosterone production, cell type specific proteins with western blots, LDH cytotoxicity, 3 color assay for live and dead cells and immunofluorescence to capture morphology for DIV 3,7 and 16, 24 hours post treatment for all three doses. Our initial studies have observed that cadmium treatment for all three doses impacted testosterone production, germ cell morphology and proliferation on DIV 7 and 16.  

The ability to recapitulate the dynamic presentation of signals in a stem cell’s microenvironment remains a major hurdle in tissue engineering. Controlling cell growth and differentiation in 4 dimensions (i.e., time and 3D space) would allow for heterogeneous synthetic tissues to be produced that match the complexity of their native counterparts. Combining strategies in both light-programmable hydrogels and recombinant protein engineering, we control the cellular microenvironment using proteins site-specifically modified with a bioorthogonal handle and able to covalently bind to a photocaged reactive group in the hydrogel. Previously we’ve demonstrated the ability to photopattern gels with fluorescent proteins that excite at different wavelengths, and have shown that multiple proteins can be patterned independently within the same material with 4D control. These techniques have many potential applications, including improving joint replacement. Current joint replacement therapies often involve use of metals, plastics, and ceramics, and commonly require future revision surgeries. We propose that through our techniques, we can generate a patterned bone/cartilage interface to improve joint replacement, creating a longer-term option for joint replacement. Towards this, we have generated two photopatternable recombinant growth factors, BMP-2 (bone morphogenic protein 2) and TGF-β (transforming growth factor β), known to direct human mesenchymal stem cell (hMSC) osteogenesis and chondrogenesis. I will encapsulate hMSCs in a hydrogel and direct cell differentiation and growth in 4D using a combination of photopatterned BMP-2 and TGF-β proteins. This research will have significant impact in tissue engineering, as it will enable recreation of complex physiological structures, grown outside the body with the patient’s own cells, that can be used for personalized medicine. Our approach is unique in that it allows for unprecedented control over microscale tissue structures, ultimately matching the complexity of native tissue.

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s Sarcoma (KS), a cancer of endothelial cell origin that commonly presents in immunocompromised individuals. While relatively rare in the United States, KS remains endemic to certain parts of Africa, where it is the most common cancer. Previous research has established that the number of peroxisomes is altered during latent KSHV infection. Peroxisomes are multifunctional cellular organelles involved in a variety of metabolic pathways important to KSHV pathogenesis. We propose to evaluate the cellular mechanism by which KSHV induces peroxisome biogenesis. I hypothesized that KSHV increases the transcription of specific regulatory genes responsible for the increase of peroxisome biogenesis. After mock and KSHV infecting cells, I evaluated gene expression of a known transcription factor, peroxisome proliferator-activated receptor alpha (PPARA), that has been shown to be responsible for peroxisome biogenesis. I used real time PCR to evaluate gene expression of the transcription factor PPARA. Our preliminary data shows that PPARA is increased, suggesting that PPARA regulates the expression of peroxisome associated genes and peroxisome biogenesis. Currently, I am evaluating if other peroxisome genes are increased, including those involved in peroxisome formation and enzyme activity. In addition, I am using small interfering RNA (siRNA) to transiently knock down PPARA. Silencing the expression of PPARA will determine its specific role in peroxisome biogenesis. I will mock and KSHV infect the cells in which PPARA is knocked down and use real time PCR to evaluate peroxisome biogenesis. In the absence of PPARA, I expect that PEX gene expression will be downregulated, which would suggest that PPARA regulates PEX genes at the gene transcription level. These results will help elucidate one of the key pathways involved in KSHV latency, and potentially contribute to the development of novel therapeutic avenues for KS treatment. 


Cancer cells can grow into life-threatening tumors and metastases partly because of their ability to evade the immune system. Immunotherapies combat cancer by boosting the natural immune response towards cancer cells. Immunotherapies are often more successful than standard treatments like chemotherapy because they are more targeted and have longer lasting effects with milder side-effects. A key component of immunotherapy is the identification of ligands that selectively target immune cells for drug delivery or immunomodulation. Peptide ligands are of special interest because they are inexpensive to synthesize and can be identified by a library screening technique called phage display. The purpose of this project is to identify peptide ligands to address two needs in cancer immunotherapy. The first need is to enable selective depletion of M2 tumor-associated macrophages, which promote tumor growth and suppress the adaptive immune response. We successfully identified 6 peptide ligands that preferentially bind murine M2 macrophages over M1 macrophages by using phage display and Illumina next-generation sequencing. The second need is to develop technologies for T-cell based immunotherapies. T-cells are an effective target for immunotherapies because they kill pathogens and regulate short-term and long-term immune responses. The identification of inexpensive peptide ligands to specific surface receptors on T-cells will be useful in increasing accessibility and efficacy of these treatments. We applied the successful next-generation sequencing methods from M2 macrophage ligand identification to target the CD28 and CD3e surface receptors on T-cells.

Locomotion is a ubiquitous human behavior. The analysis of locomotion patterns is critical for diagnosing and monitoring musculoskeletal disorders. However, current analysis methods are limited to gait laboratories equipped with accurate optical systems and force plates. To address this limitation, this work focuses on developing a process for manufacturing low-cost, individualized, flexible foot insoles equipped with force, acceleration, and gyroscopic sensors. The approach is a three stage three-dimensional (3-D) printing process: (1) 3-D print flexible base layer with electronic compartments; (2) install electronics; and (3) 3-D print flexible closing top layer. The design of the insole with respect to the sensor location is highly modifiable, resulting in subject specific sensor layouts. Moreover, any miniaturized sensor/transducer can be incorporated in the design. The resulting structure is a flexible instrumented insole worn in the user's shoe. Currently, the main application is for real-time sensing for use with a bionic ankle prosthesis. Future applications include real-time sports analysis, sweat sensing for analysis of body chemistry, and energy conversion using piezo electric transducers. Thus, the main contribution of this work is a manufacturing process for low-cost flexible 3-D printed insoles with embedded sensors.

The Cretaceous-Paleogene (K/Pg) mass extinction event (~66 million years ago) was a seminal episode in Earth's history. This event resulted in the extinction of up to 76% of all species and led to new evolutionary opportunities for the survivors (e.g., mammals). Accordingly, study of fossils spanning the K/Pg boundary is critical to understanding the dynamics of the extinction and resulting biotic recovery. However, K/Pg sections with vertebrate faunas are presently known only in North America. The Indian subcontinent was geographically isolated from approximately 88 MYA until 55-50 MYA, during which time massive volcanic eruptions (the Deccan Traps) occurred in western India during a four million year span across the K-Pg boundary. These eruptions and their effects have been implicated as causal mechanisms of the K-Pg mass extinction, but few studies have directly tested this hypothesis. Numerous vertebrate fossil localities have been found in India in the sedimentary rocks below (infratrappean) and between (intertrappean) the volcanic basalt flows. Historically, these fossil localities have been considered latest Cretaceous in age, but recent work has refined the stratigraphic and temporal relationships of the fossil localities. This allows us to track species diversity through time during the volcanic eruptions and leading up to and across the K-Pg boundary. In turn, these data can be compiled to determine the timing and magnitude of the extinctions within the context of Deccan volcanism and the mass extinction itself. We have compiled published records of over 1,653 fossil specimens from infra- and intertrappean localities throughout India. From the literature, we recorded demographic and locality information for our database. We will then use this database to characterize vertebrate faunal changes during the volcanic eruptions and across the K-Pg boundary in India, as well as compare the effects of the mass extinction in India with other parts of the world.

Dancers across all styles use their spine as a main form of design in their posture and movements. The shape of the lumbar spine of the lower back is of particular interest, because it defines the line of the body. We hypothesize, therefore, that dancers, who have danced for longer than ten years, are able to change the shape of their lower spine. Through this study we examine the variations in curvature of the lumbar spine between different dancers walking in multiple common dance forms. Nine females aged 18-30 years walked at a normal pace in four different forms: regular walking, toe-ball-heel and neutral pelvis, toe-ball-heel and posterior pelvic tilt, and posterior pelvic tilt with regular foot form. An 8-camera Qualisys system was used to measure 3D trajectories of markers placed on fixed anatomical landmarks. We determined the curvature of lumbar spine in the participants by fitting a circle through the position of the lumbar spine markers in each frame. We found that six of nine participants were able to change significantly the curvature of their spines (p < 0.05).

Using a similar study completed by José Franco Rodríguez in 2005, I have studied the districts in the City of Seattle to determine the ethnolinguistic vitality of the Spanish language in Seattle. In doing so, I searched through the busiest areas in two neighborhoods for each of the thirteen districts in Seattle to find where the presence of written Spanish was the most prominent. I hypothesized that the ethnolinguistic vitality of Spanish would be greatest in areas in which the population of Hispanic people was greatest, and used census data provided by the City of Seattle to determine the areas with the largest Hispanic population. In order to measure the ethnolinguistic vitality of the language in the city, I took pictures of Spanish signage throughout the city and codified the images based on where they were found, the actors responsible for their creation, the social realm in which the sign was found, and a variety of other factors. In conducting my research, I have also considered the existence of inequity between Spanish and English in the city of Seattle, and have found that signage presented by non-Hispanic entities are more likely to be discriminatory in nature and are more likely to contain grammatical and lexical errors. While I am still in the process of codifying the images, I am seeing a correlation between population of Hispanic people in a given area and presence of Spanish signage in that same area. At the Undergraduate Research Symposium, I will present my conclusions about the overall "health" of the Spanish language in Seattle and the various inequalities between Spanish and English that were encountered during data collection.

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.

All biological systems are dependent on properly folded protein molecules to function correctly. To enable major developments in biotechnology and medicine, an understanding of the protein folding process is needed. Advances in this field have been made, however most of the knowledge gained has been concentrated on structured beta-sheets and alpha-helices. Experimental studies of beta-strand association and the effects of conformational dynamics in unstructured loop regions remain scarce, in part because the timescales of the dynamics leave few spectroscopic methods available for measuring kinetics. Using a model system consisting of two beta-strands connected by a loop of variable length and composition, measurements of beta-strand association dynamics on microsecond to millisecond timescales have been made by employing Relaxation Dispersion Nuclear Magnetic Resonance (NMR) techniques. In addition, using multidimensional NMR and Circular Dichroism spectroscopy, sequence-specific thermodynamic effects in the folding of these peptides have been examined. Loop closure was originally thought to be so fast that it would be negligible in the protein folding process, however our measurements show that loop closure rates can vary significantly depending on size and composition. Peptides containing all-glycine loops of length 3 – 16 have been shown to have folding rate constants (1/kf) of 12.3 – 109 microseconds with unfolding rate constants (1/ku) of 636 – 191 microseconds at 300 Kelvin. Insertion of structured beta-turns into the loop region were shown to increase the rate of folding, from 231 microseconds for an all glycine 10-loop to 25.0 microseconds for a length-10 loop containing an organized turn. These measurements have shown that the interplay of conformational entropy and residual segmental motion are crucial to understanding the stability and dynamics of beta-sheets. Current and future work on this project seeks to understand how tuning the dynamics of beta-sheets will affect thermodynamics and kinetics of ligand binding in biologically relevant systems.

Using the UC Irvine Whole Air Sampler, I measured volatile organic compounds (VOCs) onboard the NASA DC-8 during the Student Airborne Research Program. High levels of the harmful chemical ozone were observed near the surface over the Sierra Nevada mountains, which led to the focus of my independent research project on the study of VOC data in order to investigate factors that contributed to ozone production. This was done by calculating the hydroxyl radical reactivity, which can, in proper conditions, be used to predict ozone formation potential. I divided the region into three boxes from east to west, based on wind direction, and the reactivity was analyzed over each region with respect to methane, non-methane alkanes, alkenes, aromatics, and biogenic compounds. In the westernmost box the reactivity was 1.7 ± 0.5 s-1 (1σ), in the middle section it was 1.4 ± 1 s-1, and in the easternmost region it was 0.8 ± 0.3 s-1. I compared the data in the Sierra Nevada region with a region known to be heavily polluted, the Los Angeles (LA) basin, and it was observed that the reactivity was 1.1 ± 0.6 s-1, lower than in two of the mountainous regions. In the Sierra Nevada mountains a major percentage of the hydroxyl radical reactivity was the result of biogenic influence, at 24% for the western box, 39% for the middle box, and 31% for the easternmost box, in contrast to only 2% biogenic contribution in LA. My work indicates that biogenic factors greatly contributed to overall ozone formation in the Sierra Nevada mountains. These mountains are strategically protected, and high pollution levels of ozone and other VOCs could lead to health impacts for visitors, vegetation, and wildlife.

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.

The marble plaque showing parturition scene, from 400BC-300CE Ostia, Italy, depicts three women attending to a mother in the midst of her labor. On the left, one of the assistants holds a newborn with cloth covered hands as she observes the midwife delivering the placenta. The final attendant rings out a cloth as she locks eyes with the mother. The marble’s poignant composition draws the viewer in with its forceful narrative of childbirth. Despite its uniqueness and significance, this artwork has been neglected in the scholarship. In order to supplement the resulting deficiency, in my presentation I explore the plaque in relationship to Roman midwifery practices through period visual and literary sources. Paying special attention to the medical writings of Soranus of Ephesus, my inquiry delves into the qualifications of Roman midwives, their training, social status, and prestige. The dynamic and naturalistic aspects of the piece articulates a careful attention to Roman obstetrical, medical knowledge. Moreover, the relief demonstrates the esteem midwives held in Roman society, which is especially relevant considering the funerary function of this relief. The status of midwives is in itself a debated topic in the scholarship due to a lack of documentation, and therefore a careful study of the plaque is vital to our understanding of midwifery and childbirth in antiquity as well as its depiction in art.

Myths of the quest for the Golden Fleece and Jason’s relationship with Medea have survived whole or in fragments for almost 3,000 years.  Our analysis of the many variants of the myth used a Google site we developed to facilitate collaboration.  We examined key literary works written over a span of roughly 1500 years, starting with Homer.  Our base text was a summary by “Apollodorus” (1st-2nd Century CE) supplemented by entire works such as Apollonius’ Argonautica, Pindar’s Pythian Ode 4, Euripides’ Medea and by many fragments from lost epics.  We identified many variations in the story as it developed over time observing major differences in the way key characters are depicted.  We also explored artistic representations of the myths that have survived, such as Greek vase paintings illustrating different interpretations of myth unknown in literature.  Our research found that early Greek colonization of territories bordering the Black Sea and later geopolitical factors affected the development of what once may have been a simple folktale.  We noted how authors (e.g. Ovid, Valerius Flaccus) manipulated the narrative to serve artistic and political purposes and hypothesized why.  We completed our survey with two cinematic adaptions of the myth (Jason and the Argonauts 1964, 2000) examining how modern conceptions of narrative have changed the stories.  Our project attempted to answer various questions.  Where did the myths originate?  Homer tells us that Jason’s expedition was well known at the time of his writing but does not mention Medea.  Why was Jason heroic to Homer, then clueless to Apollonius?  Why was Medea first a goddess, then heroine, witch, murderess, then filicide?   Why does Hercules haunt the myths?  How did Roman authors receive and develop the myths from their own cultural perspective? Through this project we observed first-hand how cultures collide but creatively coalesce.

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.

Immigrant agricultural workers experience a sense of cultural confusion, an interruption of their sense of identity, and a disconnection from their sense of Historical Self. I describe the Historical Self as a Self that is informed and complicated by history. Although many individuals survive in the dominant American culture, through assimilation or assimilation of their children, many still struggle with a sense of existential loss. In this paper, I use Henry Lefebvre’s concept of rhythmanalysis as a framework for analyzing space, time, and energy in the fandango, a practice of participatory community music. I argue that participatory, community experiences in traditional art and music provide one fulfillment of the demand for connections to culture, identity, and history.

Arctic areas such as coastal Alaska are experiencing some of the most severe effects of global climate change. These effects include melting of the permafrost, shorter winters and longer summers, more frequent and severe storms, and a drastic loss of shoreline. These factors have led to the endangering or destruction of many archaeological sites. Interdisciplinary scientists have worked together to form a model to help monitor the condition of coastal archaeological sites and the effect that the climate has upon them. However, in formulating this model they were unable to include the perspective of local indigenous groups and other local community members. The goal of this project is to add to the existing model a way of collecting and including the perspectives of the local communities and indigenous groups who often have better access to and knowledge of these sites than outside interests do. The fieldwork for this project takes place at an archaeological site near Barrow, Alaska which is currently eroding into the ocean due to shoreline loss. By utilizing the existing community ties that the archaeologists working at this site have cultivated I will show that through the involvement of all members of the local community the monitoring of local sites can be more comprehensive.

Nongovernmental organizations have become important actors and contributors to global governance as states have been superseded as the primary representatives of constituents since the neoliberal era. Many of the current studies on NGOs are moving beyond generalizations of NGO work that provide binary accounts of good and bad, successful and unsuccessful, taking an approach that studies the processes that occur in NGO work and highlighting issues of power. It is argued that NGOs, particularly those that work on issues of gender and women’s rights, are part of what Keck and Sikkink call “transnational advocacy networks” where a set of values and meaning are shared among various actors working on a particular issue at global, national, regional, and local levels. This study addresses the communication that occurs between the various, diverse actors of this transnational network and how those values and meaning are interpreted and shared at each level with a particular focus on NGOs as intermediaries. Organizations that work specifically on issues of women’s rights become new spaces for feminist activism and a renegotiation of prescribed identity. This study is a case study of a women’s organization, Réseau Siggil Jigeen, in Dakar, Senegal that relies on a series of qualitative interviews and a gender-based analysis of women in development to explore feminist struggles and transnationalism in Senegalese women’s organizations. The findings illustrate that actors within these networks hold power in various ways and that values are often negotiated or transformed throughout the network to fit the diverse contexts in which they function. This paper contributes to a broader understanding of transnationalism and transnational networks, where it is ideas that are shared across borders and how the re-negotiation of those ideas in different contexts can lead us to more inclusive discourses and research methods.

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiologic agent for Kaposi’s sarcoma (KS)—the most common malignancy of AIDS patients worldwide. Because KS is an endothelial cell based cancer, it relies on mechanisms unique to endothelial cells to proliferate. One such way is through expression of vascular endothelial growth factor receptors 1 and 3 (R1 and R3). The goal of my project is to determine the viral mechanisms by which KSHV upregulates these receptors. Because the majority of KSHV-infected cells are in latent phase, I hypothesized that latent genes are responsible for R1 and R3 upregulation. By infecting cells with an adenovirus modified to express only genes within KSHV latency-associated region (KLAR), I was able to confirm that KLAR genes are sufficient to upregulate R1, but not R3. To determine which KLAR genes are required for R1 upregulation, I created lentiviruses to express one viral gene at a time. By infecting cells with these lentiviruses and monitoring R1 mRNA transcript production by PCR, I was able to rule out three of the four genes in KLAR. Using a cell line modified to constituently express the remaining KLAR gene, latency-associated nuclear antigen (LANA), I found mRNA transcript levels for R1 were significantly higher in LANA-expressing cells than in control cells. This suggests LANA is responsible for R1 upregulation. I am currently conducting a luciferase assay to determine if LANA interacts with the R1 promoter to modify R1 expression. To narrow the search for genes involved in R3 upregulation, I will continue to make lentiviruses to test the involvement of viral genes not located in KLAR. I will present current work examining if conditioned media induces R3 to determine if virus induced secreted factors could be responsible for R3 upregulation. My research will contribute to the ongoing search for treatment strategies for KSHV and KS.

Kaposi’s sarcoma (KS) is the most common tumor found in sub-Saharan Africa and in AIDS patients worldwide. It is a highly angiogenic tumor caused by Kaposi’s sarcoma-associated herpesvirus (KSHV), which establishes a latent infection in endothelial cells. KSHV infected endothelial cells display many angiogenic phenotypes, including vascular tube formation and stabilization. Recent data shows a link between KSHV angiogenesis and the hypoxia inducible factors (HIF) pathway. HIFs are a family of heterodimeric transcription factors that respond to low levels of oxygen in the cell. The HIF pathway has been shown to activate pro-angiogenic genes, including vascular endothelial growth factor (VEGF). Our lab has previously shown that both HIF-1alpha and HIF-2alpha are upregulated during KSHV infection. Although HIF-1alpha is expressed ubiquitously, HIF-2alpha is specific to endothelial cells. I hypothesize that HIF-2alpha regulates angiogenesis during KSHV infection. To test this hypothesis, I knocked down HIF-2alpha expression in endothelial cells using an shRNA lentivirus, which successfully knocked down expression by 80%. I then conducted a capillary tube assay on mock and KSHV infected cells. This assay involves homogenous seeding of cells onto Matrigel, a basement membrane matrix for studying angiogenesis in vitro. The cells attach and migrate on the Matrigel to organize into capillary-like structures, which mimics the later stages of angiogenesis. Latent KSHV infection has been shown to form tubes at 6 hours post-plating in Matrigel and to stabilize tube formation at 24 hours, a time point when capillary-like formation normally regresses in uninfected cells. My preliminary data shows that when HIF-2alpha is knocked down, KSHV-induced tube formation is inhibited. Future work will explore the viral mechanism and the cellular significance of HIF-2alpha upregulation during latent KSHV infection. If HIF-2alpha is required for KSHV-induced angiogenesis, this transcription factor may be a promising therapeutic target for KS tumors.

The web has become a pervasive part of our lives, giving us previously unfathomable access to information and computation. The dynamic, interactive experience of the modern web is made possible only by the substantial engineering efforts put into making web browsers run correctly and with high efficiency. Towards this aim, software engineers have crafted complex, highly specialized algorithms and tuned their performance largely through informal and experimental techniques. Web browser layout engines are a case in point; Google has 10 full-time staff members specifically dedicated to this component of Google Chrome. In our research, we set out to develop a system to transform a high-level description of such computations on a restricted domain of tree-shaped data structures into an algorithm to perform the computations on any input from this domain with both efficiency and correctness. More generally, this kind of transformation, involving the automated construction of a program from a high-level, constrained description, is known as program synthesis, or optimal program synthesis when optimization is incorporated into the process. In our case, we optimize with respect to the time necessary to compute or update a prior result based on a change in input by exploiting parallel and incremental computation. Existing, domain-specific implementations already incorporate both concepts but often suboptimally and sometimes even incorrectly, as they are notoriously difficult to get right. In our approach, we employ an automated theorem prover to perform multiple compositional searches over the space of candidate algorithms and select the optimal candidate according to our efficiency approximation methods. In the process of accomplishing this, we have created a novel approach to decomposing complex, almost intractable problems in program synthesis. Currently, we are applying this work to synthesize a highly performant web layout engine with guaranteed layout correctness.

The compact core that remains after a star like our Sun dies is called a white dwarf. Some of these stars have close orbiting companion stars that they will accrete matter from constantly. This accretion eventually causes outburst events called dwarf novae. These binary star systems are known as cataclysmic variables. The six telescope observing targets for this project also undergo variable brightness pulsations due to temperature instabilities in the near pure hydrogen atmpspheres of these white dwarf stars.  These variable brightness pulsations make these stars ZZ Ceti pulsators in addition to being cataclysmic variables. We present time series photometry in the optical range from cataclysmic variable white dwarf ZZ Ceti pulsators as part of an ongoing long term investigation of accretion dynamics and white dwarf internal structure. These light curves are used in comparison with UV light curves gathered from the Hubble Space Telescope to probe the temperature and pulsation properties of these targets. Previous observations suggest a temperature instability strip that is broader than current models predict. This investigation will empirically measure the instability strip as our pulsator telescope targets cool and restart regular pulsations after dwarf nova outburst events that were observed near the start of this project. Measurements of the time it takes the pulsations to reappear allows for an estimation of accreted mass and heating that occurred during the dwarf nova outburst. These measurements have confirmed the target SDSS0755+14 as a ZZ Ceti pulsator in the target pool and allow for tighter constraints and refined models of binary and accretion interactions of white dwarf systems, especially Type Ia supernova progenitor models.

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.

Many biological, socioeconomic, and cultural factors increase women’s risk of acquiring HIV, especially in low-resource settings. Currently, there aren’t any options that allow women to discreetly protect themselves from HIV acquisition. To address this, we developed a topical nanofiber mesh to be inserted into the vagina to deliver antiretrovirals for HIV prevention. Benefits of this dosage form include high drug loading, tunable drug release, and imperceptibility to users while protecting them from HIV over the course of a week. We designed a “fiber-in-fiber” system: the “burst” release nanofiber delivers an initial bolus of drug, while the “sustained” release nanofiber (polyester) prolongs drug release over a week. Nanofibers are synthesized via electrospinning, which involves exposing a polymer and drug solution to an electric field to create a nanofiber mesh. After polyester fibers are electrospun, they are micronized using a food processor and electrospun directly into the burst release fibers. The final product is a burst release nanofiber mesh that contains small polyester fiber particles. Initially, the polyester fiber particle sizes were large and variable, ranging from 8 to 2000 micrometers. After optimizing the micronization process, the median particle size was reduced to 179 micrometers. We compared this to the median particle size of post-electrospinning, which was 26 micrometers. The data indicate that smaller nanofibers are more likely to be electrospun into the fiber-in-fiber mesh. Thus, minimizing particle size is essential to achieve the desired drug loading. Furthermore, loading the micronized fibers with a fluorescent dye revealed that they are evenly distributed throughout the burst release fiber mesh. Recent experiments assessed the drug release profiles of this fiber-in-fiber system, which showed that it is able to sustain drug release. Evaluating the drug release benefits of this fiber-in-fiber system will allow this system to be applied to other topic drug delivery systems.

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.

Though researchers have been studying marijuana for decades, little attention has been given to the role marijuana may play in an individual’s self-concept. Previous research has shown that drinking identity (the extent to which an individual views alcohol as part of his/her identity), as measured by the Alcohol Self-Concept Scale (ASCS), predicts alcohol consumption and alcohol-related problems. The current study sought to explore whether a similar pattern of results would be found for marijuana. Drawing from the ASCS, the newly developed Marijuana Self-Concept Scale (MSCS) seeks to evaluate how strongly individuals identify with marijuana. Stronger marijuana identity was predicted to be associated with more use and use-related problems. Men and non-college individuals were predicted to identify with marijuana more strongly than women and college students. Individuals of legal age (>21) were also hypothesized to be more likely to identify with marijuana. To test these hypotheses, participants (N=380, 54.8% female, ages 18-24) from the Seattle area completed a lab-based survey, which was a part of a larger study assessing the young adults’ developmental transitions and how those transitions relate to substance use. The MSCS and measures of marijuana use and problems were included in the survey. As expected, people who identified with marijuana tended to use more frequently and report more related problems. Men were more likely to identify with marijuana than women. However, we found no significant differences between non-college individuals and college students. In addition, being of legal age to use marijuana did not reveal a significance in identity. Findings suggest the MSCS may be a useful screening tool in future research and/or clinical application. By examining the relationship between marijuana identity and its subsequent use, we may also have the potential to develop more effective therapies and interventions for those who are at risk.

Marijuana is one of the most commonly used substances among young adults. Approximately 20% of college students at two major universities reported use in the past 30 days. Various methods of marijuana use are also becoming increasingly popular and may be perceived as less risky by young adults than smoking as a route of administration. Young adults are generally more aware of vaping (smoking vapor produced by an electronic device, e.g. vape pen or e-cig) than older individuals and the prevalence of vaping tobacco is highest among young adults. Dabbing (i.e., when an individual ingests heated butane hash oil) is another new method that young adults have reported using to consume marijuana. This research study investigated the behaviors and personal views of young adults (18-25 years old) regarding substance use and associated perceived health risks. Participants were recruited using online advertising and direct mailers within Washington State. Data was collected using an electronically delivered survey between April and August 2014 (n= 2,101) and June and November 2015 (n= 1,591). Results from the preliminary data on marijuana use suggest increased rates of new (vaping and dabbing; 5% in 2014, 10% in 2015) versus traditional (smoking and eating; 90% in 2014, 85% in 2015) methods (dabbing was added to the survey in 2015). The proposed research investigates whether there is a relationship between marijuana consumption methods and perceived physical, psychological, emotional, and cognitive risk. Considering the progression of relaxed policies on marijuana use and the lack of research on health risks associated with vaping and dabbing, significant results could influence and encourage further education of individuals, especially young adults, about the potential health risks of novel methods of marijuana use. 

Tooth discoloration is a common aesthetic concern for many individuals, and in response the dental profession and public expend considerable amounts of time and money to improve the appearance of stained teeth. Although many treatments are available to attempt whitening discolored teeth, these methods are typically expensive or cause more harm to the oral health of the individual due to the use of harsh chemicals, e.g. hydrogen peroxide, which often results in tooth hypersensitivity. The peptide-enabled aqueous whitening approach restores the color of teeth by forming a mineral layer on the tooth enamel and consequently masking the underlying discoloration, offering a suitable alternative to conventional bleaching methods. In this approach, peptides direct Ca²⁺ and PO₄^3- ions to form a new mineralized layer on the tooth surface. The aim of this study is to develop a suitable vehicle to deliver remineralization components to an oral environment, promoting enamel remineralization and built-in tooth whitening. With this aim, lozenges composed of varying concentrations of peptide, Ca2⁺, PO₄^3- and other inactive ingredients were manufactured using a hydraulic compression machine, and a suitable formulation was selected based on disintegration times optimized in artificial saliva. The whitening lozenge was then applied to human teeth samples under conditions mimicking the oral environment. Structural and optical properties of the resulting mineral layer were characterized using scanning electron microscopy and a chromameter, respectively. Our results demonstrate that surface discoloration has been successfully masked using whitening lozenges in vitro and, therefore, the color of the teeth was aesthetically improved. The technology developed in this study offers a simple oral hygiene product that acts biogenically in water and results in an additive treatment. The whitening lozenge is expected to considerably impact the dental and cosmetic industry as an over-the-counter product.

In the United States alone, over 3 million people have glaucoma, yet only half of those people have been diagnosed. Elevated intraocular pressure is the principal symptom checked to detect glaucoma. Current medical technology lacks the capability to capture the fluctuation of eye pressure during the day, essential for an accurate diagnosis and management of the disease. Implanted during cataract surgery, this intraocular pressure sensor increases monitoring capability, allowing early detection and diagnosis of glaucoma before irreversible nerve damage occurs. Our device is a passive capacitive sensor; no chip or battery is needed to detect the changing of pressure within the eye. The signal is sent and transmitted to an external readout via RF. The sensor is fabricated using microelectronic techniques and is made of biocompatible materials, such as polyimide and gold. Two parallel gold rings plus the empty cavity created between them form the capacitive sensor. The device itself is covered and packaged in polyimide. In relation to device fabrication, my research involved the optimization of various processes related with the production and testing of the intraocular pressure sensors. I performed the optimization of polyimide deposition parameters, as well as the timing and process flow of baking and curing steps. I also performed the testing of varying gold thicknesses, deposited via several different processes. Two layers of polyimide are bonded together using heat and pressure to form the cavity. The heat and pressure used to fuse the two polymer layers morphed the shape of the cavity, resulting in inconsistent signals given off by the antenna. We now seek to develop a process flow that does not necessitate the bonding of two separate layers to form a cavity.

The question of how to better represent harmonic and non-harmonic sounds with cochlear implants was addressed by reviewing journal articles on the subject and experimenting by simulation. By using electrodes to broadly stimulate the auditory nerves, cochlear implants can enable profoundly deaf individuals to understand a conversation in a quiet room. Because of this broad stimulation however, cochlear implant (CI) users have difficulty discerning pitch. The ability to discern pitch is not only nice for listening to music and necessary for understanding tonal languages like Chinese, but also has been shown to be important for aiding in the separation and understanding of speech in noisy environments. New processing strategies are being developed to represent pitch that rely on representing its fundamental frequency f_0 by amplitude modulating the carrier pulse trains sent to each electrode. This approach has improved users’ performance in timbre tests, melody recognition tests and Chinese tone recognition tasks but there is still much room for experiment and refinement. Since the harmonic components of pitched sound are evenly spaced in the frequency domain, two pitched sounds having fundamental frequencies related by a simple ratio will have overlapping harmonic components and be perceived as more consonant while notes with more complex relationships share fewer components and are perceived as more dissonant. Previous studies on normal hearing listeners as young as 9-months old have shown that it takes longer for subjects to notice and respond to a change in note sequences when the sequences switch from dissonant to consonant relationships than from consonant to dissonant ones. A better understanding of perceptual consonance and dissonance for CI users would aid in the development of better processing strategies and simulations. Experiments are proposed to investigate this perception by studying the reaction times of subjects to changes between electrode stimulation patterns.

A sizable obstacle to the success of wearable devices in supporting good health, independent living, and workplace safety is compliance: is the user wearing the device and wearing it as it was designed? According to the United States Department of Labor, thousands of people are blinded each year from work-related eye injuries; this costs the industry more than $300 million in lost production time, medical expenses, and worker compensation (“Safety and Health Topics | Eye and Face Protection,” n.d.). This loss easily could be prevented by the usage of protective eyewear; thus is it imperative to know whether workers are complying with safety standards. Occupational Safety and Health Administration (OSHA) requires that all protective equipment, including personal protective equipment for eyes, face, head and extremities be provided (“General requirements. - 1910.132,” n.d.). Therefore, any manual laborer worker is required comply with safety standards, including wearing protective eyewear. This research investigated inexpensive sensors to monitor compliance with regard to safety goggles and workplace safety. To ensure high fidelity and accurate data, it is paramount to understand user behavior in the wearing and use of these devices. Specifically, detailed knowledge regarding the subject’s usage of protective eyewear, including the orientation and location on the head directly to inform the quality of compliance to safety standards. However, the addition of compliance monitoring functionality is limited by size, power consumption, cost, and form factor constraints inherent to the wearable device of interest. These limitations restrict the types of sensors that can be used to achieve compliance monitoring. After literature review and feasibility study of compliance monitoring techniques and existing biomedical wearables, including assessing electrostatic field sensing, magnetic sensing, and various approaches to eye tracking, we have decided to pursue magnetic sensors as the most viable option for compliance sensing. We are optimistic that magnetic sensing may offer a low cost and low energy solution for the detection of direction and orientation of protective eyewear. Therefore, with magnetic sensing we will determine if the protective eyewear is being worn on the bridge of the nose, on top of the head, or completely off of the body to determine compliance with safety standards. A preliminary design has been modeled and simulated to be evaluated for feasibility.

In 2012, the World Health Organization (WHO) estimated that in low resource countries 4 in 10 deaths among children under the age of 15 were associated with infectious disease. Point-of-care diagnostic devices that can quickly and effectively identify the source of the infection will drastically improve patient treatment times increasing rates of survival. We therefore investigated whether traditional RNA handling techniques used in a laboratory setting are necessary for these point-of-care devices, by assessing the stability of RNA under various conditions. Using respiratory syncytial virus (RSV) as an example, we discovered that RSV can be thermally lysed without significantly degrading the integrity of the RNA. In addition, the use of RNase inhibitors or tRNA does not have a statistically significant effect on sample integrity. A comparison between RSV RNA derived directly from patient nasal swabs, with swabs containing purified RSV RNA, shows that RSV virions protect their RNA prior to lysis. Amplification by qRT-PCR, indicates that RSV RNA is directly amplifiable suggesting that RNases are inactivated at 95°C, and do not regain activity prior to amplification. Our data provides the necessary framework for performing point-of-care testing without the need for traditional RNA handling procedures. The results have important implications since we expect that the research concerning RNA handling and integrity will translate to other RNA based viruses which include Ebola haemorrhagic fever, influenza, hepatitis C, West Nile fever, polio, and measles. With recognition of these capabilities, we can implement minimal RNA sample processing into point-of-care devices.

Acute myeloid leukemia (AML) is a generally aggressive blood cancer with poor prognosis for which the fundamental treatment approach has not changed substantially. The need for new therapies is thus unquestioned. One therapy currently under phase I/II investigation at UW/SCCA for patients with newly diagnosed AML and those with relapsed or refractory disease, is G-CLAM (Granulocyte-colony stimulating factor, Cladribine, cytArabine, and Mitoxantrone). The phase I portion of the clinical trial involved evaluating the regimen for safety and escalating the dosage of mitoxantrone to determine the maximally tolerated dose. The main purpose of phase II, which is now ongoing, is to evaluate the effectiveness of the regimen, measured by the rates of complete remission and overall survival. Patients are accepted into the trial after having their medical history, laboratory, pathology and radiology results thoroughly reviewed to ensure all of the eligibility criteria have been met. As in all clinical trials the eligibility criteria are designed to help minimize risks to patients and homogenize the study population. However, the use of a set of criteria to define trial eligibility introduces a potential bias in the study and raises the question as to the degree to which findings can ultimately be extrapolated to the AML population at large. Studying the latter question is facilitated by the fact that a larger number of patients have received the same treatment off-protocol, e.g. because they were too sick to be eligible or did not have insurance coverage for study participation. We are collecting data on these off-study patients to compare their characteristics and treatment outcomes with those treated on-study. Findings are anticipated to answer whether the promising treatment results we have seen in the on-protocol patients carries over to those treated off-protocol as well and thus whether our results can be validly applied to the general AML population. 

The purpose of this survey was to evaluate the importance of international students’ organizations, in the wake of less funding and reduced support. The research on the imperativeness of international students' organizations is significant due to the notable increase in the number of international students in American institutions of higher learning. The gradual proliferation in the number of international students seeking tertiary education has resulted in the need to form friendly associations for students that play a pivotal role in aiding new students in the process of settling in and adjusting to the cultural shock that is experienced after relocating to a new social setting. The research therefore evaluates the practical need for supporting the students’ organizations as a means of ensuring safety and comfort for all the international students. The literature review supports the need for sustainable structures that support better cultural experience for international students. The research was conducted through qualitative methods with the adoption of an exploratory research design. The method included direct questionnaires to various students concerning the importance of supporting international students’ organizations. The results suggest that more students recognize and appreciate the role of student organizations and therefore support any actions meant to stabilize the various student organizations. This research therefore attempts to demystify the assumption that supporting international student organizations is a waste of time and funds.

Making the surrounding of a yellow target brighter will make the target appear darker and change its hue to brown. These changes are called darkness induction and brightness induction, respectively. Brown induction is interesting because the shift from yellow to a different dark hue, brown, is not found for the other basic colors—red, green, and blue. To assess whether the same neural and perceptual processes mediate brown and darkness induction, we explore the possible parallels with a checkerboard variation of White’s Illusion, which produces unexpected and theoretically controversial darkness induction effects. Surround stimuli consisted of a 20x10 black and white checkerboard grid. In a portion of the checkerboard grid, either the white or black squares were replaced by a 4x4 set of target squares, leaving the target squares surrounded by either only black or only white squares, respectively. For the darkness induction task, gray target squares were adjusted in luminance (physical light level) so that targets on white matched targets on black in perceived darkness. For the brown induction task, yellow/brown target squares were adjusted in luminance so that each target was right at the boundary between pure brown and yellowish brown, the “brown boundary.” The magnitude of the White’s Illusion effect was expressed as the difference in luminance between the two darkness-matched targets (darkness induction) or the two brown-adjusted targets (brown induction). Preliminary results show the White’s Illusion effect for brown induction to generally be in the same direction, but much weaker in magnitude, compared to darkness induction. This suggests that brown induction cannot simply be concluded as being darkness induction. These results help us to begin to understand the differences in the underlying perceptual and neural processes that mediate the two key properties of human vision, darkness induction and brown induction.

 Cyclic diadenosine monophosphate (c-di-AMP) is an essential nucleotide for bacterial virulence. C-di-AMP has been extensively studied in Listeria monocytogenes (Lm), but is also produced by other pathogens including E. coli, C. trachomatis, and M. tuberculosis. Although c-di-AMP is a signaling molecule in bacteria, host cells detect it as a pathogen-associated molecular pattern. During infection, the host receptor STING senses c-di-AMP and stimulates expression of interferon-beta, an anti-viral molecule. To date, STING is the only known sensor of c-di-AMP, and its promotion of an anti-viral versus anti-bacterial response has been somewhat perplexing. However, our lab has recently discovered another host c-di-AMP sensor, the murine aldo-keto reductase1C13 (AKR1C13) or “RECON”, that induces an alternative, anti-bacterial cellular response to infection. Based on the importance of bacterial clearance and the ubiquity of AKRs across species, we began to investigate whether other murine and human AKRs respond similarly to c-di-AMP. Sequence alignment of AKR genes and data on tissue-specific expression of these genes returned six candidates: the murine AKR1C12 as a potential paralogue, and human AKRs 1C1, 1C2, 1C3, and 1C4 as potential homologues. Cloning techniques allowed me to insert these genes into an E. coli expression vector that I used to purify recombinant protein via affinity chromatography. The binding affinity with c-di-AMP of each protein was tested with radio-ligand binding assays to determine dissociation constants (K_d) and we additionally used enzyme activity assays to quantify inhibition of protein activity. AKRs that bind c-di-AMP will be further characterized in vivo in mammalian cell lines in which expression has been knocked down via lentiviral transduction. Further work in cell lines may elucidate novel pathways that are activated downstream of c-di-AMP detection. Understanding the pathways that naturally clear infections is important to potential medical advances in bacterial infection management and prevention.

In mammals, fundamental differences evolved between the sex chromosomes of males (XY) and females (XX), resulting in specific regulatory mechanisms, which restore a balanced expression of X-linked genes between the sexes. To do this, one of the female’s X chromosomes is silenced (i.e. X inactivation). However, some genes escape this inactivation and remain bi-allelically expressed in females, resulting in higher expression levels potentially contributing to sex differences. The Car5b gene, which encodes a mitochondria carbonic anhydrase important for heart function, escapes X inactivation in both mouse and human. The CCCTC-binding factor (CTCF) often binds near the boundaries between escape and silenced genes. Car5b is inactivated in mouse brain, but it escapes silencing in embryonic kidney (Patski) cells derived from a F1 hybrid female mouse. Selective CTCF binding at a site near Car5b in Patski cells but not in brain suggests the possibility that a chromatin loop that includes the Car5b promoter may facilitate escape in the cell line. To test this looping escape model, we are deleting the CTCF binding site on the inactive X (BL6 allele) and will evaluate its effects on escape. To establish an allelic deletion at the Car5b locus, a CRISPR/cas9 approach (DNA modifier) is being used with two BL6-specific small guide RNAs spanning the CTCF binding site upstream of the Car5b promoter. We’ve completed single-cell cloning for Patski cells transfected with CRISPR constructs. These cell clones are currently being verified for correct deletion by PCR and Sanger sequencing. Results have shown a positive deletion in the cell cloning colony. Allelic expression of Car5b will then be examined in the clones to investigate whether deletion of the CTCF binding site affects its escape (chromatin architecture). If results are conclusive, such an approach will be utilized to examine other escape gene regions.

In collaboration with Booz Allen Hamilton, our E E 497/498 Entrepreneurial Design Capstone project addresses the challenge of taking precisely georeferenced photographs of the underwater domain. These photographs will be mapped onto existing bathymetric datasets (from sources like NASA and NOAA) to provide visual textures of static and dynamic underwater points of interest. Our team’s role is the design and implementation of the imaging system hardware, which will complement visualization software under development at Booz Allen Hamilton’s Seattle office. Our design extends the OpenROV 2.8 platform, a small open-source, tethered, remotely-operated vehicle (ROV), with emphasis on developing a successful prototype using commercial off-the-shelf (COTS) parts at minimal cost. In total, our team has implemented (1) the extension of OpenROV into an underwater imaging platform, carrying a payload enabling hemispherical imaging below the ROV; (2) the design of a tethered surface buoy system, with access to Differential GPS data to act as a reference for geolocating the ROV; (3) the design of an ROV-mounted acoustic transmitter and buoy-mounted acoustic receiver array to determine underwater distance between the ROV and each array element; (4) the design of an efficient trilateration algorithm using nonlinear and linear least-squares optimization to accurately position the ROV relative to the buoy based on (3). Our research has significant implications for improving access to the underwater domain, including low-cost maritime sensing and deployment applications and military training and simulation applications.

Seasonal influenza exhibits rapid evolutionary dynamics and successful prediction of its evolutionary future is extremely beneficial for public health. In this research we proposed a method that can infer the genotypes that are likely to dominate the influenza population from a sample of genome sequences. Our approach first requires to construct a time-scaled phylogenetic tree from the genome sample. By iterating over the subclades of the phylogenetic tree, we infer the effective population trajectory for each subclade using Bayesian Nonparmaetric Phylodynamic Reconstruction by Palacios JA et al. Finally, we estimate and rank each subclade’s population growth rate which enables us to identify the genotypes with the highest growth potential. We applied our method to seasonal influenza A/H3N2 sample data from 1995-2014, which predicted the progenitor lineage of the upcoming influenza season with near optimality in 5 out of 19 years and provide informative predictions in 14 out of 19 years. The results indicate that our method could help provide useful information for influenza vaccine selection process.

Multiple strains of rats and mice are used to evaluate differences in response after exposures to various toxicants at the molecular or cellular levels. However, neuronal toxicity in different strains of species has received much less attention. Therefore, the objective of our research was to compare and characterize fetal mouse micromass culture system using two different strains of mouse—C57BL/6 and A/J—which may be used to screen and prioritize variety of neurodevelopmental toxicants. Our mouse midbrain micromass culture system, a high-density in vitro cultures of primary midbrain cells, is an alternative method to in vivo neurodevelopmental testing because of the ability of cells within the cultures to differentiate in vitro without additional stimulants. Differentiation is purely driven by high cell density. For our 3D in vitro micromass culture system, we isolated the primary midbrain cells from fetus at gestational day 11 (for C57BL/6 mice) or 12 (for A/J mice). The embryos were surgically removed, and midbrain cells of fetal mice were digested into single neuronal cells. These primary in vitro neuronal cells were plated onto plates and cultured up to 22 days in vitro. When morphology was examined throughout 22 days in culture with a 400x phase microscope, cell proliferation, differentiation, and migration were observed for both strains of mice. Proliferation (PCNA, Nestin) and differentiation (B-tubulin, EN1, MAP-2) related protein expression levels were examined using western blot for both C57BL/6 and A/J mouse strains. Dynamics of protein expression levels in western blot indicated that proliferation may be at its highest point between DIV 4-6 while differentiation is between DIV 8-14. If midbrain cells from multiple mouse strains can be harvested at similar neurodevelopmental stages, differences in response due to genetic variability may be studied using our 3D fetal mouse micromass model.

 Protein aggregation is implicated in many human diseases. For example, Alzheimer’s disease is characterized by the misfolding of the amyloid beta (abeta) protein that disrupts cellular function by accumulating into fibrils with a characteristic cross-beta sheet structure. A wide variety of computational, sequence based tools are available to predict amyloidogenic “hot spots”; the regions in proteins that cause the formation of these toxic aggregates. Recently we have performed a comprehensive mutational analysis of abeta using a high throughput method termed Deep Mutational Scanning (DMS). Four hundred and fifty abeta variants were simultaneously assayed for solubility. An aggregation score that reflects the effect on the aggregation propensity of abeta was calculated for each variant. Using these data as a gold standard, we benchmarked aggregation prediction tools and assessed the ability of each algorithm to accurately predict aggregation. In particular, we were interested in identifying methodological weaknesses in these tools and then determining how to improve aggregation propensity prediction. I measured the correlation between several tools’ aggregation predictions for abeta single mutants with the measured aggregation scores. My initial analysis revealed that these tools are often insensitive and over-predict amyloidogenic regions, indicating an opportunity to improve these methods. Having comprehensively measured the relationship between abeta sequence and aggregation propensity, we are now in a position to assess and improve current aggregation prediction tools. Improving our ability to predict this critical process will enhance our understanding of diseases of protein aggregation.

The psychology literature delves into understanding the role of men's self perception of masculinity in help-seeking behavior as well as help-seeking behavior in men with cancer. Help-seeking behavior is behavior that explains the utilization of healthcare of a population or group. What is the role of self perceptions of masculinity in help-seeking behavior of men with prostate cancer? This literature review focuses on understanding this role in men specifically with prostate cancer. The resources used for the review are MedLine, PsycINFO, PsycArticles, PubMed, and references within articles. The majority of the literature used were qualitative studies due to the availability in the literature. The literature suggests that men believe that prostate cancer affects their masculinity in both physical and emotional ways such as their physical aspects like strength, ability to provide for and protect their families, reaction to physical pain through peer pressure and social norms, and being viewed as unmanly. There are men that efficiently seek help from healthcare professionals for this disease to preserve their masculinity. Men also inefficiently seek help due to the potential embarrassment of those qualities being diminished by the disease. The limitations to writing the review included small sample sizes, support group participants, and participants that were already diagnosed. The review is also limited because there was no research on men that focused on how masculinity may have contributed to their help-seeking in the initial stages. Healthcare services, such as interventions or programs, should focus on the following indicators when promoting help-seeking behavior to men with prostate cancer: stoicism, privacy, family providing and protection, and being viewed as unmanly due to the physical effects on a man's body. If the healthcare system can overcome these barriers, it will be able to reach men more efficiently and prevent further advancement of diseases like prostate cancer. 

Periodontitis is a serious infection that damages both soft (gingiva and periodontal ligaments-PDL) and hard tissues (dental cementum and alveolar bone) of the periodontium. Mineralization is an essential dynamic process for development and maintenance of the periodontium. The current study focuses on how mineralization of alveolar bone and the attachments of PDL are affected by experimental periodontitis in a pig model. Eight three-month-old pigs were periodically inoculated with 4 types of periodontal bacteria, along with a ligature around the last maxillary deciduous premolar for 8 weeks to induce periodontitis. Another group of 7 pigs without the ligatures and bacterial inoculations were taken as control. Bone labeling dyes, calcein and alizarin, were injected intraperitoneally 7 and 2 days respectively before euthanasia. The harvested upper molar blocks were embedded in micro-bed resin and successive sections were taken at 30μm thickness coronally. Three sections that contained the most intact mesial and distal roots of the target molar were selected and examined under epifluorescence. The interlabel distance between two vital markers at the surfaces of alveolar socket and trabeculae, cementum, and the attachment of PDL fiber bundles were measured, and the mineral apposition rates (MAR) were calculated. Preliminary results indicate that, as compared with control pigs, periodontitis pigs showed reduced MAR in the trabecular structures, more significantly in the regions underneath the molar furcation. The reduced MAR was also seen in the alveolar ridges in the periodontitis pigs but was not as significant as the region under the furcation. More data analysis is currently underway. These results suggest that experimental periodontitis may slow down periodontal mineralization in young growing pigs, in which alveolar bone underneath the root furcation and the cortical layer of the socket are mostly affected.

The study of crop foods, such as maize and corn, offer us important insights on how to create healthier and more abundant crop yields. The initiation and maintenance of callus tissue cultures is a process essential for researching transgenic plants and is constantly plagued by contamination. The media components can influence the formation of callus, shoot, or root tissue as well as culture longevity and general health. The goal of this project is to find an optimal medium for callus formation that contains anti-microbials in order to avoid contamination and promote callus, rather than shoot or root, production. The monocots used are rice and maize. The base medium used consists of Chu N6 Basal salts, 0.7% phytablend agar, and 3% various sugars. I grew tissues on the base media with varying amounts of hormones, additives, anti-microbials, and sugar blends and assessed callus, root, and shoot development as well as the presence or absence of tissue necrosis and microbial contamination. Various tissue cleaning procedures were also tested. I hypothesize that rinsing tissues in antibiotics before plating them would decrease initial contamination and that antibiotic plates could be used to eliminate contamination from already growing cultures. The presence of various hormones and chemicals, such as 2,4-D and silver nitrate, influenced tissue differentiation when applied at certain times. The use of anti-microbials in the washing process as well as in the initial cultures has eliminated most of the contamination issues. It appears that the use of an initial growth medium that promotes callus development and a long-term growth medium to keep cultures healthy will be the key to achieving long-lived callus cultures. The ability to create and maintain these cultures allows the study of transgenic plants and their DNA.

Nitrous oxide (N₂O) is a pharmacologically active gas used clinically in dentistry and medicine. It is also an abused inhalant. Our lab has an established rat model of N₂O-induced hypothermia that can assess changes in core temperature (Tc) as well as the determinants of Tc, i.e., heat production (HP) and heat loss (HL). Drug-induced hypothermia elicits hypothermia-opposing autonomic HP responses that account for individual differences in the degree of hypothermia observed during an initial N₂O administration. Furthermore, these individual differences in HP also predict the rate of tolerance development at the level of Tc, predict an individual’s subsequent self-administration of N₂O, and predict the degree of allostatic over-correction of Tc that develops over repeated N₂O administrations. This study was designed to determine whether a rat’s HP response to a non-drug, cold challenge is correlated to its HP response during an initial N₂O administration. Individual rats (N=20) were tested in two different sessions in counterbalanced order; one session involved a 60% N₂O challenge while the rat was at 22°C ambient temperature and the other session involved a cold (10°C) ambient temperature challenge while the rat was exposed to control air. The N2O challenge was achieved as a rapid exponential rise to a steady-state 60% concentration whereas the cold challenge was a ramp change starting from 22°C. The two challenges were given 7 days apart. During each 2-h challenge, 1200 HP measurements were collected using indirect calorimetry and median values were evaluated. Results found a correlation (r=0.57; p=0.009) between HP responses during a N₂O challenge and HP responses during a cold challenge. These findings have translational importance because they suggest that individual differences related to a young individual’s addictive vulnerability may be predicted using a non-drug challenge which facilitates human research pertinent to understanding the pathogenesis and treatment of drug addiction.

 Variations in sea ice extent have a large impact on the energy budget of the artic and, consequentially, temperature variations in the arctic region. It has been proposed that the recent arctic sea ice melt has influenced mid-latitude weather, yet others argue that arctic warming anomalies also respond to influences from other latitudes. The purpose of this project is to examine relationships between temperature fluctuations in the lower troposphere of the arctic and variations in weather at other latitudes. Using NOAA's 20th Century Reanalysis data, a recent analysis involving interpolation and assimilation of past weather observations, we identified global geopotential height trends during warm and cold years in the arctic region. Preliminary conclusions of these results suggest that warm temperatures over the arctic are associated with low 500mb geopotential heights over the northern Pacific Ocean during winter, spring and fall months as well as high 500mb geopotential heights over the southwestern Pacific Ocean in fall months when temperatures in the arctic are warmer than usual. Our next goal will be to compare the 500mb height maps created to El Nino temperature indices to assess the viability of a claim that arctic temperatures are correlated with El Nino events. As of now, the results indicate that a warm arctic temperatures can be associated with sea surface temperature variations. The conclusion that lower tropospheric arctic temperatures are correlated with El Nino events indicates that care must be taken in associating a warmed arctic with weather anomalies over the continental USA. We will attempt to distinguish the effects of historical El Nino variability from the effects of the recent human-induced arctic melting.

Peri-implantitis is an inflammation around dental implants due to bacterial infection that can ultimately damage both the soft and hard tissues of the jawbone. After recently discovering that Titanium (Ti) implants play a crucial role in the electrical conductivity of microbial community, we propose a twofold research approach to reduce Ti corrosion known to have detrimental effects to patients' oral health. Aim1 is to create a “stripe-spangled” implant design with a ceramic body coating that isolates the zones of Ti in order to eliminate the biofilm-generated electrical current. Independently, Aim2 uses an electrotherapeutic approach by providing an external power source to counteract the electrical current produced from oral microbiota. Therefore, this poster is primarily focusing on Aim2 to evaluate safety and efficacy of a new oral electrotherapy. We design an in-vitro experiment to simulate a patient's mouth and provide electrotherapy to examine the electrochemical behaviors generated by oral biofilm. Using actual oral microbiota from a volunteer, we found that providing a short-term electrical current affects the microbiota's electrochemical currents. To further our experiment, we will use dogs to test the efficacy of the electrotherapy in vivo. In a broader implication, this research will potentially alleviate medication and invasive surgery to combat peri-implantitis through electrotherapy.

Approximately one in four patients who receive dental implants experience peri-implantitis, an inflammation of soft tissue and bone around dental implants, within 11 years of implant placement. Peri-implantitis is one of the main causes for implant failure and with 500,000 implants being placed a year, it is critical to develop a product that increases the long-term success of implants. Prior research has shown that the electroconductive properties of titanium used in implants facilitate corrosion by oral bacteria, which in turn leads to an increased risk for peri-implantitis. The goal of this project is to create a composite implant of titanium and insulating ceramic that is biocompatible and capable of osseointegration, but not electroconductive. Our project uses solid ceramic implants that are coated with titanium using a vacuum evaporator. The titanium is deposited in isolated bands and chemically binds to the surface of the ceramic. These islands of titanium will provide a surface against which bone can grow, while the ceramic interrupts the flow of electrons. The implants are placed in a bone model in media mimicking the oral environment, and oral bacteria from a volunteer are injected. The media is then tested for titanium leaching. Going forward we will be testing the implants with osteoblasts in vitro to measure biocompatibility. The improvements to existing and widely used technology will serve to increase patient welfare tremendously. Once an implant fails and peri-implantitis sets in, no more implants can be placed in that area of the mouth. Extending the working lifespan of the implant will prevent a painful condition and the worsening of dental health. The product of this research will be a cost-effective and long-lasting implant that will be better able to withstand the oral environment.

The plasma protein von Willebrand Factor (VWF) is secreted by vascular endothelial cells. VWF’s primary function is to recruit platelets to the site of blood vessel injury. The interaction between VWF and platelets happens through binding between the VWF A1 domain and the platelet surface receptor, glycoprotein Ibα (GpIbα). VWF requires shear to be activated. Recently, it has been shown that oxidizing agents increase the platelet-binding activity of VWF, although the exact molecular mechanism is not understood. To explore whether neighboring domains of A1 play a role in the oxidant-induced activation of VWF, we used a flow chamber microscopy assay. Two experimental constructs of VWF, one containing the A1 domain and the neighboring A2 and A3 domains, the second containing A1 and the neighboring D`D3 domain were expressed and bound to separate plates. One control construct containing only the A1 domain was also expressed and bound to plates. Then GpIbα coated beads were washed at different shears over plates that had either been pre-oxidized or not. The movement of beads was recorded. Subsequently, rolling velocities and total number of beads were measured and analyzed using MATLAB. The results showed that, at high shear, both the A1A2A3 and the D`D3A1 constructs were more active in binding to beads when oxidized compared to the unoxidized controls. The control construct did not show a difference in binding to beads when oxidized compared to unoxidized controls. These findings suggest that the A2, A3 and D`D3 domains could have an inhibitory function on the A1 domain and that oxidation removes this inhibition resulting in an increased binding activity of VWF to platelets. Understanding how oxidation alters the function of VWF domains is necessary to explain the increased risk of thrombosis in patients suffering of chronic or acute inflammation.

Understanding composition of avifauna in different ecosystems has been the focus of a wide number of scientists in North America.  Knowledge of the structure of a bird community provides information about the species found in an area as well as their ecological roles. More importantly, a long-term monitoring of species composition in an ecosystem provides an important tool for assessing the status of their populations as well as responses to habitat changes.  University of Washington–Bothell campus North Creek wetlands present one of the most successful restoration efforts of the past 20 years. Faculty and students have been evaluating changes in vegetation composition, stream organisms, invertebrates and other ecological aspects associated with the establishment of the wetland. In the summer of 2015, an effort to establish a long-term monitoring of the bird community was started. We joined these efforts with the goal to determine the composition of the bird community in the winter and spring of 2016. In addition to the ecological research goals, we are also working on producing educational materials that help students and the general public become more familiar with the avifauna of the area. We are conducting auditory and visual point count and transect surveys to determine species composition. We are using distance methods to determine bird abundance along the different vegetation types found in the area. We are also collecting information on the natural history of the species, and documenting the observations with photographic materials that will be used in the elaboration of a photographic guide to birds of the UWB Wetlands. To date, we have registered a total of 51 species within 26 families that are distributed within 8 guilds (insectivores, filter-feeders, nectarivores, frugivores, and carnivores among others). We hope that our work provides important contributions to the long-term documentation of UWB bird communities.

Past studies in the Pollack Lab have discovered the existence of negatively charged solute-free "exclusion zones" adjacent to hydrophilic surfaces in aqueous solutions. One of these studies has shown that radiant energy expands exclusion zones adjacent to nonmetal surfaces based on wavelength. Another study indicated that these zones also exist adjacent to metal surfaces, but with positive charge. As a result, it is expected that radiant energy will have an opposite effect and decrease the size of the zone. My project explores the effects of radiant energy on these solute-free zones next to metals. To conduct these experiments, an aluminum sample is cleaned and placed into a customized chamber containing a diluted microsphere solution. The sample is left in the dark for 5 minutes to allow for formation of the zone. After the initial 5 minutes, the sample is subjected to the desired wavelength and intensity of light. Pictures are taken at 5 minute intervals to compare the size of the exclusion zones over 20 minutes. Initial results show that lower wavelengths have a larger effect on exclusion zones. However, varying intensities with the same wavelengths tend to produce unusual results where some intensities initially decrease the size of the zone then later causes an increase. More trials are necessary to validate these preliminary findings. Generally, the trends show that radiant energy tends to have a negative effect on these metal exclusion zones. These findings will give way for more research into areas such as electrochemical potential and energy harvesting as we discover the reasons for this behavior.

Water forms liquid crystal structures near hydrophilic (water-loving) surfaces such as human cells . Compounds are excluded from dissolution in the zone containing these structures, and thus this zone is known as the Exclusion Zone or EZ water. EZ is believed to contribute to cell properties and is thus important for healthy cellular function - therefore, it is essential to try and maximize EZ content as much as possible. We evaluated the EZ content of various purported therapeutic or crystallizing waters using the well-established technique of using a microscope to determine the width of the EZ around a piece of tubing. We concluded that different types of water have varying amounts of EZ, with the highest being those observed in KW and Crystal Energy Water. The effect of probiotics, helpful bacteria which reside in the intestine and have varied health benefits, was also investigated. The most clinically studied probiotic, Lactobacillus rhamnosus GG, is known to have positive effects on various body systems, including digestive and immune. This was theorized to be a result of their effects on the EZ content of body water. We investigated the effects of the probiotic by varying its concentration in DI water. It was found that EZ dramatically increased in the presence of probiotic, with a 50% increase over control observed for the recommended dose of probiotic. As a control, we conducted a heat-response study by heating a solution of the probiotic (1 mg/40 ml) to 90°C, at which temperature the bacteria would be killed. The EZ greatly declined, suggesting a large role for live probiotic in EZ formation and therefore health. This research has wide implications for health, suggesting that changing the type of water ingested and taking probiotics could greatly improve cell function and overall health.

There are many mutualistic interactions that occur naturally in the world. Some of these mutualistic relationships evolve to be obligate, where the presence of one species is dependent on the other for its survival. We study the evolution of an obligate relationship with two model organisms, a sulfate reducer, Desulfovibrio vulgaris, and a methanogen, Methanococcus maripaludis. 22 populations of these organisms have evolved in an environment that has forced their cooperation. When we sequenced these populations, we discovered that at least 13 of the 22 populations of D. vulgaris have lost the ability to reduce sulfate To confirm if these mutations are beneficial or not, we measured the fitness of mutants with knockouts in the sulfate-reducing gene pathway relative to the wild-type strain with either an ancestral or evolved M. maripaludis partner. The final population size of each D. vulgaris mutant will be measured using FREQ-Seq; a technique that quantifies frequencies of various mutations in an amplicon. In previous iterations of this experiment, results presented a discrepancy between replicates (I and II) due to a failed cell lysis technique. We found that only a small fraction of the cells were lysed. With a better cell lysis protocol, we expect to see an increase in D. vulgaris mutant frequencies when paired with either an ancestor or evolved M. maripaludis compared to the wild-type. The data collected from these experiments will help us have a better understanding whether losing the ability to reduce sulfate is a beneficial mutation for D. vulgaris or not.
 

Precedent Model Study (Fall 2015): the primary objective of the 2-week long project is to foster the ability to see and create architectural spaces that are sensitive to human needs and requirements in terms of materiality, scale, and use. Students work in teams to investigate a building, which is selected for its particular architectural language and relationship with its site. Students research, analyze and then create a 1/2" = 1'-0" section model of their building precedent. Then,they develop an evocative section perspective that communicates qualities of the building uncovered during their research, analysis, and model construction. Our group researched Glenn Murcutt's Marika-Alderton House, which was selected by our mentor for its particular architectural language and relationship with its site. Glenn Murcutt’s Marika-Alderton House stands as an attempt to apply modernism and bring about peace in the midst of the tense cultural and uniquely volatile natural landscape of far Northern Australia. His structure was created as a home for Aboriginal artist Banduk Marika and her family, drawing upon both the inspiration of the native people of Australia in their curved-bark long houses, and the inspiration of the European settlers, with their raised corrugated metal woolsheds. It is most essentially the interpretation of structure as elevated, shaded platform. The house “floats” on the air, raised on stilts with a permeable membrane of open windows, allowing the tropical winds to permeate the walls and floor and sweep upward through holes in the roof. The corrugated metal roof with deep eaves protects the house from the sun and heavy monsoon rains. It is intrinsically local, made of natural timber with a steel frame and built using unskilled labor. Glenn Murcutt’s Marika-Alderton House is an example of a structure dictated by the complex cultural and natural web into which it is placed.

Working in small groups, our studio collectively studied various residential projects, focusing on conceptual design, human scale, programmatic relationships, and the buildings' relationship to the site. Our group was assigned the Floodplain House designed by Paul Hirzel Architects. In order to gain a better understanding of the project, our group created 1/4" = 1' basswood section model. The Floodplain House was built to provide a live/work space for the client’s 70 acre winery. The live and work areas are housed in the main body, while a bedroom rests within a grove of cottonwood trees as its own private wing that flanks the main structure. The house sits on the edge of Potlach River to maximize the land for the vineyard, as well as provide an immersive experience for its owner and their guests. At 184 feet in length, a steel Howe truss rests on four thick concrete piers, allowing the house to cantilever above the river similar to a bridge. The structure is elevated at a height above the ‘500 year flood plane’ and to prevent rattlesnake infestations. Building on such a challenging site, the exoskeletal structure doubled as scaffolding during the construction to keep initial costs low. The external structural system allows the walls to be placed and angled freely in order to frame views and suggest movement. Paul Hirzel Architects' Floodplain House effectively incorporates the clients' needs and is responsive to the existing site conditions.

Depressive disorders are a significant public health concern, affecting 11.4% of youth, and are associated with a loss of interest in activities and anxiety, psychosocial problems such as academic difficulties, and psychosocial impairment in adulthood including increased risk for substance abuse and suicide. By providing adequate mental health treatment, adverse effects of depressive disorders in youth and adolescence may be mitigated. Although mental health services for youth are currently inaccessible for 70% of the youth population who would benefit from these services, healthcare is experiencing a trend towards increased access to mental health services both through the Affordable Care Act and the expansion of Medicaid. My study’s goal is to look at ways to provide these quality mental health services to youth. In order to provide quality health mental health care for youth with depressive disorder, a collaborative care model may be used. Collaborative care uses a multidisciplinary team of primary care providers, mental health specialists, and community support to deliver a multifaceted approach to patients with mental health issues through cognitive-behavioral therapy (CBT), pharmacotherapy, or both delivered by primary care providers in community health settings. To date, 3 RCTs have evaluated the effectiveness of collaborative care against usual care for youth depression. One mainstay treatment for youth depression has been CBT. While collaborative care is an emerging model of treatment for youth depression, it has not been compared to stand-alone CBT. In this investigation, benchmarking is used to find an applied effectiveness for both collaborative care and cognitive behavioral therapy. I searched through peer-reviewed journals using search engines such as Medline and PsychInfo to gather published studies. Using these results and data, I then used statistical analyses and benchmarking to compare the effectiveness of both CBT and collaborative care.

The inland waters of the Puget Sound, Washington, USA, and Georgia Basin, British Columba, Canada, is a complex system of high energy river inputs to lower energy large basins with direct connection to the open ocean through the Straits of Juan de Fuca. High energy systems acting as transport mechanisms for coarse sediment interact with low energy regions with transport deposition of finer sediments to create the vertical stratigraphy of the seafloor. In regions of high energy the seafloor expression is dominated by a rougher seafloor with more geomorphic features of coarser material, while low energy regions are expressed in a seafloor of uniform lamination. This research investigates the link between the surface expression of seafloor roughness and the underlying vertical structure of sediment deposition. Using a high resolution bathymetric surface derived from multibeam sonar synchronized with low frequency sub-bottom acoustic profiles, the depth of acoustic penetration is correlated with a focal calculation of seafloor roughness. Areas of lower acoustic impedance have a larger range in penetration, with lower ranges of penetration persisting in areas of high acoustic impedance. High acoustic impedance is indicative of harder sediments, such as sand, and low acoustic impedance indicates softer sediments, such as mud. The research is a comparative study between a high energy system adjacent to the mouth of the Elwha River and the low energy protected region of South Possession Sound. The research illustrates the strong link between seafloor geomorphology and the terrestrial sources of sediment input and mitigation of sediment transport energy.

When isolated subpopulations adapt to the particular features of the predators, prey, or cooperative partners that are specific to their local environment, populations may become specialized to their local partner and less able to interact with other populations. To what extent might this hypothesis explain the diversification of microbial species, which cooperate or compete with each other in complex communities? We tested whether specialization was a common outcome of evolution between the bacterium Desulfovibrio vulgaris and the archaeon Methanococcus maripaludis after they evolved together in a beneficial interaction for 1000 generations. To test if D. vulgaris populations tended to become specialized for the M. maripaludis populations they evolved with (and vice versa), we revived 6 independently-evolved communities, separating the D. vulgaris and M. maripaludis populations from one another, and then paired each population back up with its sympatric partner (evolved in the same community) or with 5 allopatrically-evolved partners (evolved in different communities). We used microscopy to quantify the density of D. vulgaris and M. maripaludis to test whether the absolute fitness of either species was higher in sympatric versus allopatric pairings. We also competed allopatrically-evolved and sympatrically-evolved D. vulgaris against one another. We conclude that variation across cocultures in population yield of D. vulgaris or M. maripaludis is not necessarily correlated with whether they evolved in sympatry or allopatry, suggesting that the first 1000 generations of adaptation to a new mutualism may not be characterized by specialization. Our results show that some sympatric pairings were more efficient than allopatric pairings;however no distinct trend was identified. Broader implications of our research include roles in  byproduct inhibition which is an important factor in global carbon cycling within diverse anaerobic environments, including bio-digestion for fuels, wastewater treatment, and experimental evolution. 

Do species evolve in diverse communities, similar to the simple community of our research? We are looking at the evolution that we've seen in a species of sulfate reducers found in our simple laboratory environment and comparing this evolution to that of a large, more complex anaerobic digester of the wastewater treatment plant. In our 'simple community', a methanogen, Methanoccocus maripaludis, and a sulfate reducer, Desulfovibrio vulgaris, were paired. When two species are forced to live together over time we expect to see evolution take place. It was found that after 1000 generations D. vulgaris loses its ability to reduce sulfate in this paired relationship. Using this laboratory pairing as a model, we have looked at the evolution of sulfate reducers in  these two different anaerobic digesters from the University of Washington and Brightwater Municipal Waste Water Treatment Center. Both digesters have similar conditions; they are both anaerobic with low levels of sulfate present. To test our hypothesis we have currently been extracting DNA from weekly samples of both digesters. The dsrAB gene is first amplified, as it is a conserved region throughout sulfate reducers and their relatives. We are now doing Illumina sequencing in order to better determine the diversity of sulfate reducers present. Using this information, we will be able to design primers for the sat apsA and apsB genes. This will show us if any mutations are present among the population of sulfate reducers in both digesters. This will be means for the comparison between real world and experimental conditions. Future work will look for mutations in the sat, apsA and apsB genes. By identifying these loss-of-function mutations in both the digesters, we will be able to see the impact of evolution on sulfate reducers in complex communities.

The model is a project from our architectural design studio. In this project, groups of students were assigned an existing building and tasked to build a scale model of it while making a section cut that helped give a better understanding of the building as a whole. Each was built primarily of basswood at 1/4" - 1' 0" scale. In doing so, we were able to compare and contrast the different forms and structures effectively. The building we had been assigned to was the Palmyra House in Maharashtra, India by Studio Mumbai, which was completed in 2007. Studying the house and its model gave us a better understanding of its relationship to its environment. Local craftsmen who had knowledge of traditional construction methods like interlocking joinery were employed for the House’s construction. Focusing on building by hand avoided the need for heavy machinery, which would have damaged part of the existing coconut plantation it is located in. The louvers help bring in air from the Arabian Sea or the plantation, cooling the interior spaces. They also prevent direct sunlight from reaching these rooms while still keeping them well lit with natural light. These characteristics let the Palmyra House naturally fit its site and also leave it undisturbed.

The cultivation of tomatoes is currently a 58 billion dollar industry worldwide. Over the past few years, tomato plants have been subjected to more severe and abrupt climatic fluctuations than ever before. In-depth understanding of the tomato leaf anatomy and physiology can have significant consequences in agriculture. Fluxes (fluid flow rate) in leaf water and sugar-conducting tissues, xylem and phloem, are challenging to visualize in real time. It is important to attempt this measurement using intact leaves as excision interrupts control of normal flow paths. The possibility that vein density and flux influence photosynthetic rate is being investigated here.  Optical Coherence Tomography (OCT) is a non-invasive imaging modality that performs high-resolution cross-sectional imaging, allowing to visualize the structure and motion in biological samples in 3D.  In this study, we have used a state-of-the-art OCT system with 7 μm resolution, operating at 1300 nm wavelength, to investigate leaf structure, venation and vein flow in live tomato leaves for the first time. The low intensity imaging beam (3 mW) is in the near IR spectral region and imaging is performed at high speed (4 ms/frame) hence, does not interfere with the leaf’s natural physiological processes. We have used Rutgers’ tomatoes for this study. To improve the image contrast in the leaf veins, we are investigating using dye and lipid particles to be taken up by the leaves

Women who experienced sexual assault are 2 - 3 times more likely to experience sexual revictimization (SR). Factors that predict risk of SR include emotion dysregulation, guilt, and lower heart rate reactivity when facing sexual threats. These factors overlap with tonic immobility (TI), which is characterized by victim's diminished or absent physical or vocal response during sexual assault ("freeze" response). Post-traumatic maladaptive cognitions also may increase risk for SR, either directly or through increasing risk of TI. Based on prior literature, my hypotheses are: 1. Higher TI will predict higher SV risk; 2. More severe maladaptive cognitions will predict higher SV risk; 3. TI will be predicted by maladaptive cognitions. Participants were female college students reporting prior child sexual abuse or adult sexual assault and high risk alcohol use (n=162) assessed at baseline and 1-month later. Relevant measures were Tonic Immobility Scale (TIS-A), Posttraumatic Cognitions Inventory, and Sexual Experiences Scale (SES). Thirty-seven women reported SR 1-month following the initial assessment (22.3%). In logistic regression analysis, after controlling for prior adult and child sexual victimization, SR was predicted by TI (p<0.05). Maladaptive cognitions and prior fear response during trauma, an aspect of TI, did not predict SR. Based on multiple regression analysis, TI was predicted by maladaptive cognitions about self but not by cognitions about the world or self-blame, after controlling for prior trauma history (p<0.01). Results suggest TI in women during prior trauma may increase risk of future SR. In addition, more negative beliefs about self, but not self-blame, predicts TI. Findings suggest that prevention efforts may want to target women who experienced prior TI as a means of preventing future revictimization. These prevention efforts may be more effective if they include cognitive interventions.

 Approximately 500,000 Americans undergo surgery for lower back problems each year. Despite dramatic improvements over the last decade in perioperative care, the outcome of spine surgery is associated with prolonged hospitalization and poor pain management. In April 2014, Harborview Medical Center introduced an enhanced recovery protocol, called the Perioperative Enhanced Recovery from Major Spine Surgery (PERMSS), which aims to reduce significant physiological stress and shorten hospitalization by implementing pre-operative nutrition supplement, standardized analgesic administration, and early mobilization. The purpose of this study is to investigate the efficacy of PERMSS on post-operative pain relief. This project takes a quantitative approach and follows the descriptive correlational design. From June 2015 to Feb 2016, fifty PERMSS and fifty non-PERMSS patients were recruited and interviewed in their hospital rooms on their first postoperative day. The validated International Pain Outcome survey was used to capture comprehensive data including patient demographics, comorbidity, surgical procedure, analgesic regimen, and patient-reported outcomes. In April 2016, data analysis will be conducted through Stata MP V13.1. to compare the difference between PERMSS and non-PERMSS patient outcomes. We expect a significant improvement in pain management, reflected by less time spent in severe pain, decreased interference in recovery activities, and improved patient satisfaction. The result of this study leads to two potential benefits: first, to introduce enhanced recovery protocol to other similar complex surgeries; and secondly, to reduce reliance on opioids especially in spinal patients who have a 15-30% likelihood to develop failed back surgery syndrome (FBSS) and become frequent victims of opioid use disorders. In contrast to traditional practice that relies heavily on opioids, PERMSS may help address this problem with its emphasis on multi-modal analgesic, which is a combination of opioid and non-opioid prescription.

This project intends to answer the following questions: (1) how knowledgeable are teens and young adults on how they can maintain confidentiality when seeking sensitive health care services while under their parent or guardian’s health insurance, and (2) what is the most effective tool to disseminate this kind of information? Although health care confidentiality is protected by law, there still remains the possibility that health information may be disclosed when documents such as the Explanation of Benefits (EOBs) and invoices are sent home. For adolescents and young adults insured under their parent or guardian’s health insurance plan, the potential breach of confidentiality may deter them from seeking appropriate health care. We hypothesize that teens and young adults have little knowledge about how to protect to their health care confidentiality and that a pamphlet is the most effective tool to educate them. To test this hypothesis, we created a pamphlet that provides options on how to maintain confidentiality when seeking sensitive services while on their parent or guardian’s health insurance. We will survey 20 adolescents, aged 13-25, on the pamphlet information, including the content and lay-out. Additionally, respondents are asked about other tools that would be effective in disseminating this information. Survey responses will be analyzed for themes. Thus far, we have interviewed 9 persons between ages 13 and 25. Each respondent stated that he/she was unaware of some information provided in the pamphlet. For example, one young adult stated, “I didn’t know that insurance or laboratory testing could accidentally make it easier for privacy to be lost in the billing process.” Respondents stated that tools such as a website or videos may be more effective to publicize this information. This project highlights the need to inform adolescents and young adults about their rights to maintain confidentiality when under their parents’ health insurance plans.

Besnoitia besnoiti is an emerging apicomplexan parasite that causes bovine besnoitiosis. Found originally in Africa, and now in many European countries. It causes, among many other things, decreased milk production, sterility in bulls, and an increased mortality rate, which all have severe economic affects. Currently, there is no cure, no publicly available genome sequence, and only a very unreliable vaccine. Our goal is to develop a new drug for the treatment of bovine besnoitiosis. To do this, we will find compounds that inhibit the enzymes that are crucial for the survival of B. besnoiti. Calcium dependant protein kinases (CDPKs) have shown to be promising targets in other closely related enzymes. They are essential for the survival of the parasite and can be targeted by bumped kinase inhibitors (BKIs) which bind to the ATP binding site of these enzymes. We have identified, cloned, expressed, and assayed recombinant BbCDPK1 for the inhibition of its enzyme activity with 63 BKI analogs using previously described luciferase assay. BbCDPK1 was inhibited by low concentrations of BKIs. Experiments so far have had around a 90% inhibition rate, and four compounds in particular have been very effective with only small amounts of compound. Further experiments are planned in vivo, as the BKIs have shown no toxicity in cattle. Our studies thus far indicate that this strategy could lead to non-toxic, selective CDPK1 inhibitors with good PK properties, and are thus excellent leads for further besnoitiosis drug development programs.

Good communication is crucial to a patient's healthcare experience and an integral part of a nurse's role in providing care. Patients with communication disorders are susceptible to poorer health outcomes and decreased satisfaction with services due to breakdowns in communication with nurses. Literature suggests that nurses should receive training on how to effectively communicate with these patients, but it is unclear whether this training is currently included in nursing school curriculum. What are nursing students at universities across Washington State being taught about how communication disorders impact medical interactions, or how to better communicate with patients who struggle? Are these students lacking the necessary education and training to provide quality care for patients with communication disorders? In an attempt to answer these questions, survey data will be collected from junior and senior nursing students at the University of Washington, as well as from faculty responsible for developing nursing student curriculum at UW and other in-state universities regarding the current communication skills curriculum being taught in this area. Based on preliminary findings we hypothesize that a gap exists in nursing student curriculum related to how to communicate effectively with this patient population, and that the survey data collected will show that nursing students in Washington State are not currently being taught about communicating with patients with communication disorders. The key implication of this study will either suggest a need for nursing school curriculum to implement communication skills training targeted toward patients with communication disorders or show that students are in fact receiving this training. The addition of education and training in this area can help nurses improve the quality of care for this patient population. 

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.

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.

People with leg amputations who use prosthetic feet during community ambulation encounter frequent environmental barriers. Uneven ground, such as grassy fields or sidewalks in disrepair, cause excessive forces at the interface between the artificial leg and the residual limb because of torques from the ground acting on the foot. These forces can cause pain, skin breakdown, and falls. Impulsive forces may be reduced by a prosthetic foot allowing medial-lateral rotation of the foot relative to the leg. This study compared the kinetic and kinematic outcomes of an investigational prosthetic (IP) foot to the participant’s usual prostheses. Eight study participants completed a single leg balance test and 5 walking conditions with their prescribed prosthetic (UF) and with the IP foot. The participants walked lengthwise along 10% and 15% side slopes and across domes (Botts’ dots) placed on flat ground. A 3-D motion capture system tracked 36 reflective dots which were placed on key landmarks so that joint angles and spatiotemporal metrics could be computed. One participant’s data was excluded from the ankle joint outcomes. Participants reported reduced forces at the residual limb-prosthesis interface. Preliminary results indicated that the UF and IP foot perform similarly in sagittal plane motion. The IP foot increased the ankle medial-lateral rotation for 5 out of 6 participants. Future research will include comparing a participant’s UF to the IP foot in community trials while collecting activity monitoring, GPS, and logbook data.

 The public consultation on “Equality between Women and Men in the EU," launched by the European Commission's Directorate-General for Justice and Consumers, received an astounding 4,896 contributions in 2015. In comparison, most public consultations garner less than 500 replies. Although each of the 28 European Union (EU) Member States contributed, 51.7% of the organizations were based in Germany, and 47.5% of contributing individuals lived in Germany. While this level of involvement merits attention by itself, a substantial group of individuals in Germany answered in an eerily similar negative manner to all questions of the consultation. Their responses were highly critical of gender equality policies and denounced action at an EU-level. Why did this group of individuals in Germany, in contrast to the other reponses of Germany organizations and individuals from other countries, react in this negative manner? Moreover, apparent from the patterned responses and almost-verbatim comments, how did this group with anti-feminist tendencies coordinate and mobilize? Our research examines this consultation on gender equality among several others addressing female genital mutiliation, paternity leave, and gender imbalance on corporate boards to analyze potential collaborative networks between European civil society. To organize our data, we code consultation responses into matrices, which allows us to view patterns that could indicate occuring collbaborations. From here, we attempt to unearth the motivations behind and intricancies of these mobilizing networks. Ultimately, our research seeks to explain this uniquely German anti-feminist phenomenon within the public consultation context. 

Proteins are naturally-occurring biopolymers that are useful in a wide range of therapeutic and imaging applications. Though natural proteins are comprised of just 20 monomeric amino acids, they can be post-translationally decorated to introduce expanded chemical functionality. Though several techniques have been developed, the majority do not provide site-specific modification nor stoichiometric conjugation necessary to preserve protein bioactivity. Additionally, proteins functionalized through these methods have proven difficult to purify after modification, thereby limiting potential clinical and industrial applications. Sortase-Tag Expressed Protein Ligation (STEPL) is a protein functionalization/purification method that solves many of these problems. This method allows functional probes to be site-specifically conjugated onto a protein, while simultaneously separating modified and unmodified proteins. Though this technique has been successfully demonstrated in the DeForest lab, a remaining challenge is to increase yield during protein expression. In our group, we exploit several microbiology techniques to optimize this process. Bacterial strain identity, growth conditions, reaction temperature, and protein solubility have all been shown to influence protein expression. Using Green Fluorescent Protein (GFP), we found that the STEPL yield increased when conducted for 4 hours at 37°C versus overnight at 18°C. This was determined through mass spectrometry, which showed hydrolyzed proteins after prolonged reaction. For some difficult to express proteins, including growth factors, the STEPL protocol resulted in a negligible protein yield. Through experimenting with a dialysis refolding protocol, functional growth factor Bone Morphogenic Protein-2 was produced at dramatically increased yields. Furthermore, experimenting with E. coli growth and STEPL reaction conditions has resulted in increased yield for many different functionalized proteins. Although progress has been made in producing functionalized protein with the STEPL method, yield remains below that obtained through other methods. Further experimentation to improve the robustness and yield of the STEPL protocol will increase the availability of functionalized proteins in biotherapeutics.

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.

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.

Studies have shown that Electrical Stimulation (ES), in the form of electric or electromagnetic field can enhance wound healing by promoting cellular proliferation and expression of growth factors. We hypothesized that ES mediated by negative electric charge is predominantly effective in inducing cellular rehydration of dehydrated mammalian cells, resulting in increased viability and survival. This was tested by analyzing the effects of ES induced in a cellular model through negative electric charge build-up in a parallel plate capacitor system. The system consisted of two identical gold-plated surfaces separated by two polytetrafluoroethylene pillars. Electric charge built up on the plate was manipulated by altering the voltage of the power supply connected in turn to the gold plated surface. Experiments were conducted on the commonly used standard cellular model of mouse embryonic fibroblast NIH/3T3 cells under sterile conditions to reduce extraneous variables. The strength of ES was predetermined through a quantitative and qualitative analysis of temperature, pH, and bubble formation in different standard solutions. Cells challenged by partial dehydration with an established range of sodium chloride concentrations will be subjected to the predetermined ES and transferred to different cell culture media- Phosphate Buffered Saline (PBS) or Dulbecco's Modified Eagle Medium (DMEM). Cellular viability will be analyzed by Trypan Blue dye-exclusion method. In this way, we will determine whether negative charge promotes viability.

In this experiment, the period of a complex pendulum was examined. The pendulum consisted of a long thin rod (physical pendulum) suspended from a pivot with a simple pendulum (a string of negligible mass holding a pendulum bob) suspended from the bottom of the physical pendulum. After release, the motion of the double pendulum is irregular and chaotic for a period of time until which the two pendula synchronize and behave as a single pendulum. It was hypothesized that the synchronization period of the complex pendulum would be longer than the natural period of the individual physical pendulum, due to the increased length. Initial findings indicate that when the length of the string of the simple pendulum and the angular displacement of the physical pendulum remain constant, the synchronization period of the system can be modeled as a simple pendulum and the synchronization time is constant. Further analysis of the complex pendulum will be conducted to examine how varying the simple pendulum length and the initial displacement impact the synchronization time and synchronization period to verify the synchronized simple pendulum model and further explore the complex nature of the system. Understanding the synchronization of chaotic systems can lead to the engineering of more complex systems.

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.

Marine ammonia-oxidizing archaea (AOA) are abundant marine microorganisms that compose their cell membranes with glycerol dialkyl glycerol tetraethers (GDGTs). These lipids are useful biomarkers for developing a record of sea surface temperature. Through the TEX86 temperature proxy, GDGTs have been able to provide insight into historic patterns of sea surface temperature through the relationship between annual average sea surface temperature and the composition of GDGTs. Existing data suggest that in addition to temperature, other environmental factors might influence TEX86. We postulate that varying light, salinity and peroxide concentrations would have an effect on the GDGT composition of AOA in culture. We conducted experiments with varying light, salinity and peroxide levels to test their effect on TEX86 on strains of AOA. We observed that light levels influenced the GDGT composition. The calculated TEX86 values were higher when the cells were exposed to light. Salinity concentrations above and below the optimal salinity of 25 resulted in lower calculated TEX86 (below 17°C). Peroxide levels did not affect calculated TEX86 temperatures, which suggest the presence of different adaptations that allow for archaea to acclimate to relatively extreme conditions. Our work demonstrates that different environmental stressors have an effect on lipid composition.

In 2015, the American Heart Association (AHA) stated that sudden cardiac arrest is still a primary cause of death in the United States. During cardiac arrest, lack of intervention to maintain the perfusion of tissues with oxygenated blood leads to irreparable damage to the brain and vital organs within minutes. In 2010, the A-B-C (airway, breathing, circulation) of CPR changed to C-A-B (circulation, airway, breathing) due to strong evidence that supports the idea that high-quality CPR chest compressions help sustain life until the underlying causes of cardiac arrest are addressed. The purpose of this study was to use technology to measure and review chest compression data collected during cardiac resuscitations, and evaluate specific compression parameters, in relation to AHA standards, for overall quality improvement. The CODE-STAT™ technology used in this study measured changes in thoracic pressure during a cardiac resuscitation, and then generated a report stating rate of chest compressions per minute, and total time spent on chest compressions. The data was then given to the hospital resuscitation teams so that they could visualize and discuss the quality of their performance in comparison to AHA and hospital standards. Thus far, results of the study have shown that in-hospital resuscitation teams have compression rates that are too fast and there are too many pauses, or times without chest compressions. A compression rate above 120 beats per minute can decrease sufficient blood return to the heart from the rest of the body, making subsequent compressions less effective at dispersing blood. Too many pauses in chest compressions can negatively impact the pressure gradients in the thoracic cavity that are required to maintain adequate cerebral and coronary blood flow. Hospitals must continue to implement technologies that measure CPR performance so that cardiac arrest patients receive the best possible outcomes for survival.

Chelating agents are widely used in plants and human industries to capture metal ions and control free metal ion concentrations. Constituent ions in soils (e.g. Ca²⁺, Mg²⁺) influence the exchange of a metal ion between two chelating agents. Predicting changes in reaction pathways and the magnitude of kinetic effects is fundamental to understanding dynamic metal speciation where strong chelating ligands control metal ion speciation. This research focuses on the influence of calcium ions on the exchange rate of Ni between nitrilotriacetic acid (NTA) and 1,2-cyclohexylenedinitrilotetraacetic acid (CDTA). Capillary electrophoresis was used to monitor the changes in free chelating agent and nickel-chelating agent complex concentration with time at different pHs and reactant concentrations. Reaction rates and order were compared to those in the absence of calcium ion. The presence of calcium ions reduces overall exchange rates and alters reaction order under the conditions studied. Kinetic modeling is used to support a proposed mechanism for the influence of calcium on this exchange reaction. Knowledge about dynamic metal speciation is fundamental to understanding the ideal soil compositions for plants’ uptake of essential metals and developing remediation methods for hazardous waste sites.

 The majority of Americans do not engage in regular physical activity. Fitness Zones, a program sponsored by The Trust for Public Land, aims to increase physical activity by providing free outdoor fitness equipment in public parks. This program has gained popularity across the United States; however, few evaluations exist on the effectiveness of the program. Additionally, the majority of previous Fitness Zones were installed in warm locations. The purpose of this study is to examine physical activity patterns of park users in two Seattle parks where Fitness Zones will be installed, as well as to evaluate the effect of weather on park attendance and Fitness Zone utilization in these participating parks. Data collection will be performed in two Seattle parks prior to installation of Fitness Zone equipment with follow up at one of the parks after installation using a combination of observation and survey/interviews of park users. Observations are performed using System of Observing Play and Recreation in Communities (SOPARC). Park attendance will be assessed using a Park User Log and weather condition data will be obtained through Underground Weather. Qualitative content analysis of park user responses and comparison of park user turnout during tolerable versus poor weather differentiated by temperature, wind speed, and precipitation will be used for analysis. In addition, we will use linear regressions to determine correlational strength between park user attendance and various weather conditions. The results will contribute to the understanding of park use, and how to improve physical activity levels of all people in Seattle parks. Results will also describe relationships between Seattle weather conditions, park user attendance, and Fitness Zone utilization. Ultimately, this study will add to the knowledge base about whether Fitness Zone installation in public parks is an effective method to increase physical activity in the Seattle area.

Arsenic is a toxic heavy metal to humans that can cause serious health damages. Exposure to arsenic can cause various health conditions such as skin damage, lung, bladder, kidney and liver cancer, as well as nerve and circulatory problems. Arsenic contamination in water and soil can be naturally sourced from local geology or human sourced from pesticide and preservative uses. Studies have shown that rice will uptake arsenic from water and soil. Rice is a very easily digestible grain which makes it very suitable source of nutrition for children, whom are more susceptible to toxins. Therefore, it is important to develop and continue the study of methods that can help to quantitatively detect arsenic in rice. For this experiment, the objective was to look at a previously published method used to detect arsenic and validate its effectiveness on five store-bought rice samples. The broader implication of this experiment is to validate a method and modify it to gain quantitative data in order to assess whether harmful levels can be detected and to determine background levels of arsenic in rice. Rice was powdered and 1.0 g of rice sample was digested in 10mL of 0.28M nitric acid for 90 minutes at 95°C. The samples were analyzed with ICP-MS to detect arsenic based on its mass. A calibration plot with a correlation coefficient of 0.96278 and a slope of 1856.48 was created. The calibration plot was made from concentration of 1ppb, 5 ppb, 10 ppb, and 50ppb in which all had intensities that were detectable. The detection value of the samples falls in between the calibration intensities. The data that is obtained suggests mean concentration of arsenic range from 1ppb to 30 ppb in 10mL solution of HNO3. This indicates that there is a range of 10 ppb to 300ppb per grams of rice. These data are corroborated by other studies analyzing levels of arsenic in rice.

Every year bee specialists report detection of larger numbers of bee colonies suffering from colony collapse disorder. One of the suggested causes of colony collapse disorder is the increasing use of neonicotinoid pesticides in farming agriculture. Neonicotinoids like clothianidin, thiacloprid and imidacloprid are effective insect neurotoxins created as a safer alternative to previous insecticides. Neonicotinoid pesticides have many distribution methods including dusting methods and application to soil and root systems; leading to their dispersion in a multitude of matrices. The quantity of these pesticides in water and soil samples needs to be measured to further asses the effect of these pesticides on bees and other species including fish and humans. However, differences in extraction methodology can lead to differences in analyte detection. Water and soil samples are complex matrices to be separated before being assessed through gas chromatography-mass spectrometry or liquid chromatography–mass spectrometry. Here I present my work in comparing methods for extracting imidacloprid, a specific pesticide in the neonicotinoid category. Results from determining a reliable and accurate method of imidacloprid will help to increase the ability for future research to be conducted on collected environmental samples.

Elevated levels of arsenic have been reported in surface waters of many urban lakes around the Puget Sound as a result of the widespread heavy metal contamination from the late ASARCO smelter in Ruston, Washington. Arsenic is a neurotoxin and carcinogen and a priority Superfund contaminant. However, the mobility and toxicity of arsenic is not fully understood. Physical and biogeochemical processes that lead to elevated arsenic concentrations in the water column and aquatic organisms have been studied well in thermally stratified lakes, but not in periodically mixed (polymictic) oxygenated lakes. This project examines the mobility, bioaccumulation and toxicity of arsenic in four urban lakes in south King County that range from seasonally stratified and oxygen depleted (anoxic) to polymictic and oxygenated (oxic). Specifically, we aim to discover why one of the lakes has elevated levels of arsenic (up to 40 ppb) in surface waters, yet regularly mixes and thus remains oxygenated. Typically, arsenic is only mobilized from sediments when a lake becomes anoxic during stratification. Monthly water quality parameters (temperature, pH, dissolved oxygen, and specific conductivity) were measured and water samples (alkalinity, chlorophyll, sulfide, iron, arsenic, and nutrients) were collected at multiple depths throughout the water column. Plankton samples were also collected using vertical net tows. Water and plankton samples were analyzed for dissolved and total arsenic (after digestion) by ICP-MS. Phytoplankton and zooplankton in polymictic oxic lakes accumulated more arsenic than plankton in thermally stratified lakes, even though aqueous arsenic concentrations were similar between the lakes. This data suggests that arsenic in polymictic urban lakes is not only bioavailable, but has the potential to travel up the food chain. This project aims to create a model for predicting arsenic bioavailability based on physical lake characteristics to better predict possible toxicity and, therefore, has important implications for lake management.

Blind programmers bring a unique perspective to the computer developer workplace, and make important contributions to the computer science field. However, blind programmers often cannot use computer development environments because they are inaccessible, and usage can be slow and tedious for blind developers who use screen readers. The goal of our research is to design and build plug-ins for various coding environments to make it easier for blind developers to code. In prior work, Ms. Baker made a plug-in called StructJumper for Eclipse, a Java Integrated Development Environment (IDE). The plug-in creates a navigable hieratical tree based on the nesting structure of a Java class, essentially creating an outline of key points (such as method headings and control flow statements) in the code structure. Blind programmers can switch between StructJumper’s TreeView and default Text Editor to navigate code with greater ease. The usability of StructJumper was tested by seven blind programmers, whose results showed a trend of completing tasks faster with the plug-in then without. This suggests that StructJumper is a viable plug-in to improve accessibility to blind developers. However Java is not the only major programming language developers’ use on a daily basis. Thus we are pursuing further research to extend StructJumper beyond Java and implement plug-ins/add-ons for other commonly used programming languages and development environments, such as for the programming language Python. My work is the start of coding StructJumper as a plug-in for Visual Studio (practically the only screen reader compatible Python IDE). This plug-in is written in Visual Studio using C#, .NET framework, and IronPython to parse Python files open in the IDE.

Sea otters (Enhydra lutris spp.) play a significant role as a keystone species in shaping nearshore marine ecosystems of the northern Pacific coast through their primary diet of bottom-dwelling invertebrates, like sea urchins. Northern sea otters (Enhydra lutris kenyoni) were hunted to extinction from Washington State in 1911 due the fur trade of the 18th and 19th centuries, and remained locally extinct until their reintroduction to Washington State from Alaska in 1969 and 1970. We studied the foraging ecology of this species since this reintroduction, specifically how the diversity of prey species consumed by sea otters has changed from the 1990s to the present day. The prey switching hypothesis suggests that predators preferentially consume the most abundant prey species, then as a given prey item becomes rare, the predator will add a prey item of the next highest rank to their diet, increasing their diet diversity. Based off of this hypothesis, we expected sea otters in the 1990s to consume a lower diversity of prey species compared to recent years. Using sea otter diet data we collected from 2014-2016 as well as data collected by the U.S. Geological Survey from 2010-2011, we compared prey species diversity from 1990s data to present day data with the Shannon-Wiener Diversity Index. Preliminary analyses suggest that sea otter diet in the 1990s consisted primarily of clams, while it consisted primarily of snails in the 2010s.

Dental hypersensitivity (DS) is one of the most common diseases in the United States, affecting the majority of the adult population. DS is commonly accompanied by gingival recession and occurs at the cervical third of the crown. DS is usually triggered externally, e.g. by cold, hot, acid, or basic conditions in the saliva, and produces a sharp pain at the root of the tooth. Our objective is to develop a biomimetic treatment protocol comprising a peptide gel formulation to treat DS. Current approaches include desensitizing nerve ends by blocking the axonic action via potassium salts, limiting the permeability of dentinal tubules using synthetic adhesive sealers, e.g. NaF, bioactive glasses, oxalic acid and glass ionomer cements, or forming coagulates inside the tubules using protein cross-linker agents. Although these agents may be effective, clinical validation is still lacking and their short durability against daily tooth brushing, various foods, or drinking of acidic beverages makes their occlusion effects incomplete. We propose to form a mechanically and thermally stable mineral layer and thereby occlude exposed dentinal tubules using a peptide-remineralization approach. Working closely with the Dental School, our approach involves exposing underlying dentin by removing cement tissue at the coronal root surface by scraping away dentin on extracted human tooth to mimic hypersensitivity conditions. The samples are next treated with peptide-enabled remineralization resulting in tens of micrometer-thick new layer over the damaged dentin. The stability of the newly formed layer is then mechanically and thermally evaluated using nanomechanical testing and thermal-cycling, respectively. Our results demonstrate that exposed dentinal tubules are successfully occluded by mechanically and thermally stable mineral layer. Through a molecular biomimetic approach, the method described herein offers a unique solution to dentinal hypersensitivity, which can be used as a platform technology to develop effective in-clinic and over-the-counter hypersensitivity treatments.

3D printing of materials has been expanding from a process used solely for manufacturing of parts and prototypes in industry to the medical fields during the last decades. The 3D printing process with hydrogels has been used for biomedical applications and the process is also gaining popularity in dental industry, though mainly for model and mold creation, although it has yet to be used for dental composites. The most common dental fillers are either metals, alloys, or resin-based composites. The traditional dental composites, such as ionomers and synthetic resins in addition to metal amalgam are non-adherent to tooth and have different thermal expansion coefficients, which can lead to cracking of the fillers and additional damage to patient’s tooth. Common fillers also have non-natural colors and can leach into the blood stream or oral cavity, causing allergic and harmful reactions. In this research, our aim is to develop a biogenic dental filler using micro-extrusion 3D printing process combined with biomineralizing hydrogel technology. For 3D printable tooth filler, alginate gel was used as the main molecular scaffold along with biomineralizing peptides. After optimizing the rheological characteristics of alginate gel by tuning its concentration, crosslinking properties as well as biomineralization, the efficacy has been characterized in vitro in the presence of Ca⁺² and PO₄^-3 precursor ions. Furthermore, nano- and microstructures of biomineralized dental filler have been tested using scanning electron microscopy and X-ray diffraction techniques. Our results so far indicate that 3D printable, biomineralizing tooth filler can successfully be developed and, when fully optimized, the technique will allow filler material to be custom-made for patient’s caries. In summary, while the novel tooth filler produces internal structures mimicking the natural tooth and well interfaced with the existing tissue, the filler material is also 3D easily fabricated for clinical implementations.

One of the leading causes of depression is stress, and yet not enough is known about the exact mechanism by which stress alters depression. Of the four opioid receptor systems (mu, delta, kappa, and opioid receptor like-1), the kappa opioid receptor (KOR) is what my research focuses on. KOR is activated by its endogenous ligand, dynorphin. This is responsible for promoting analgesia, and depression-like phenotypes such as swim-stress immobility. The mammalian target of rapamycin (mTOR) is a protein kinase involved in regulation of functions such as cell growth, and metabolism. When dysregulated, it may lead to obesity, depression or cancer. Both mTOR and KOR have been shown to independently regulate stress-induced depression. However, there are no studies which tie these two ideas together. One possible link could be the stimulation of p38 MAPK kinase. Stimulation of KOR causes G-protein coupled receptor kinase (GRK)-dependent activation of the p38. Additionally, it is known that p38 causes the inhibition of TSC2, promoting phosphorylation of mTOR. Based on our results, activation of KOR with U50,488 causes an increase in phosphorylation in mTOR in vitro. However, this is also present in negative control cells not expressing KOR, which could indicate that U50,488 also has an off-target effect on a non-KOR mediated pathway. A similar treatment on mice decreases phosphorylation of mTOR after 28 hours in the brain, indicating that after a stressful event, mTOR activation is transient and acute. Furthermore, decreased mTOR phosphorylation after 28 hours in the brain was found to be blocked in GRK3 knockout mice. This implies that decreased mTOR phosphorylation after 28 hours with U50,488, requires the GRK gene. Further experiments, including behavioral testing, will be needed to investigate a deeper relationship between KOR and mTOR. With further research, these studies may lead to developing novel anti-depressants, revolutionizing depression treatment.

Hydrogels have proven to be excellent 3D cell culture platforms, serving as frameworks for synthetic tissue substitutes. Though given the complexity of the native extracellular environment, control over mechanical and biochemical cues within hydrogels is important in mimicking the extracellular matrix (ECM), the dynamic framework about which cells function. We seek to provide spatiotemporal control over cell fate within hydrogels formed through photo-mediated oxime ligation, a novel approach to photopolymerization seldom interfering with biological species present in cell encapsulation. By conjugating a photo-cleavable ortho-nitro benzyl (NPPOC) functionality to an aminooxy group, this otherwise spontaneous reaction may be spatiotemporally regulated with UV light. Excitation of the aminooxy-NPPOC complex upon UV light exposure cleaves NPPOC, enabling aminooxy to undergo ligation with an aldehyde. We have demonstrated the successful synthesis of 4-arm poly(ethylene glycol) (PEG) molecules separately functionalized with benzaldehyde and aminooxy-NPPOC end-groups. We have additionally demonstrated hydrogel formation following UV light exposure to 4-arm PEG solutions of varying compositions, verifying photo-mediated oxime ligation’s viability as a photopolymerization strategy. Following gelation, photo-mediated oxime ligation may be extended towards the incorporation of biochemical ligands via 3-dimensionally patterning NPPOC-conjugated proteins. Combining control over hydrogel geometry and stiffness with protein patterning, this dynamic hydrogel platform will expectedly aid in better understanding cell behavior through emulating the ECM’s heterogeneity. Consequently, an improved understanding of cell-matrix interactions may aid in advancing synthetic tissue substitutes.

A neuropeptide called corticotropin-releasing factor (CRF) is shown to be necessary in fear behavior, but it is currently unknown whether upregulated CRF expression in the central amygdala is sufficient for enhancing fear behavior. An increase in CRF expression in a controlled manner will specifically test CRF's ability to enhance fear learning. To achieve this, a Cas9-CIBN complex will be directed towards CRF promoter by small-guiding RNAs where it will recruit the Cry-Vp64 complex. When these two complexes come together, they form a light-inducible transcriptional effector (LITE) that can recruit the transcriptional machinery to the CRF promoter and up-regulate CRF expression in the presence of light. LITE machinery will also provide a method of improved spatial and temporal control to the upregulation compared to currently used methods of upregulation. However, in order to accurately analyze this uniquely controlled method, certain comparable controls are required. This project will serve as the comparison to temporally controlled CRF expression by creating a constitutive CRF overexpression vector. This will upregulate CRF without temporal control and cannot be switched “off”. This continuous effect may elicit compensatory changes to the system over time and reveal important differences between constitutive and temporally controlled CRF expression. The three objectives of this project are to 1) clone the CRF gene into a DNA vector called adeno-associated virus vector (AAV vector), 2) package the AAV-CRF vector into virus, and 3) inject the packaged virus into central amygdala for behavioral analysis. The first objective has been achieved using a standard cloning protocol. The second and third objectives are still in the preliminary phase.