Research on the Zebra Finch song system represents a unique inter-disciplinary collaboration between physics and neurobiology to investigate trial-and-error learning. In trial-and-error, or reinforcement, learning, the “actor” explores random variations in motor outputs and is rewarded for those variations producing favorable outcomes. The potential components of a reinforcement learning scheme have been identified in the songbird system: songbirds learn their songs by trial and error, and the anatomy of this system has been well studied. The objective of this research project is to characterize the nature of the variability that remains in adult song, as this variability is presumably the basis for adult song maintenance, and the bird’s ongoing ability to learn song variations. We use the recorded vocalizations from four adult male zebra finches to analyze repetitive motifs in a song, in order to characterize song structure. By utilizing sound analysis, we aim to first identify the nature of the song syllables and then determine the variations in these syllables, particularly with respect to their pitch and timing. We will use this analysis to inform our models of the neurological activity driving such variation. The outcome sought from this research is to contribute to and constrain a mathematical model of injected variation that will allow us to predict the relationship between internal brain activity and the subsequent corresponding behaviors. By investigating such variables as timing and frequency across the songs of these four zebra finches, the identification of the degrees of freedom explored by neurally driven variation can inform our models of the manner in which trial-and-error through reinforcement learning occurs. This project demonstrates that the quantitative methods of physics can be applied within the context of neurobiology to analyze the underlying algorithms of neural computation.

In October 2015, a Yale administrator named Erika Christakis sent a school-wide email in defense of culturally appropriative Halloween outfits. This email broke the tension that had been accumulating around race issues at Yale, a historically all-white all-male institution, where the specter of racism still exists in instances of social and institutional discrimination. Meanwhile, at University of Missouri and across the country, student protesters received nation-wide media attention for demanding institutional support for students of color, and speaking out against race-related campus violence. My paper analyses media and popular reaction to these protests by examining articles, blog posts, and YouTube commentary that appeared in their wake. I show how criticisms of the protesters’ respectability are often couched in racist, sexist, and ageist rhetoric. Additionally, I add to Michelle Smith’s discourse on respectability politics by arguing that conservative media weaponizes the notion of “free speech” by propagating the false notion that freedom of speech shields an individual from criticism and personal consequences. I contend that the trend of dismissing safe spaces further marginalizes oppressed groups, as safe spaces often provide a forum for free speech that runs counter to popular opinion and, in particular, state rule. Ultimately, I conclude that there is no way to separate free speech from its uncivil form, as free speech is inherently subversive.

The fenestrations found on the vertical part of the maxillary bone of the order Lagomorpha are a defining trait of the order, and yet the function and evolutionary benefit is not well understood. The only study on the function of the fenestrations was by Moss and Feliciano, in 1977. They concluded that the "fenestrations are causally related to the normal lack of transmission of masticatory forces through the vertical plate." Here we argue that this conclusion is incomplete. Lack of masticatory forces in tooth bearing structures of many animals does not result in the pattern of fenestrations observed in lagomorphs. Even toothless mammals have intact maxillary bones. Using gross observational studies of skulls, imaging software, specimens treated with vascular fill agent, and histology, we suggest an additional function, specifically thermoregulation. The primary evidence is the proximity of the nasal cavity, which is exposed to ambient air, coupled with large blood vessels. Especially because rabbits are obligate nose breathers, these conditions suggest that this region of the skull serves to dissipate body heat to the environment. 

American consumers tend to prefer visually appealing fruits and vegetables, a fact that makes selling imperfect produce to food distributors difficult for producers. As a result, more than twenty percent of all produce grown for human consumption in the United States never enters the food supply chain due to minor superficial flaws, such as blemishes or deformities. Despite the significant impact of such consumer behavior, there has been little research into why consumers have an aversion to “ugly” produce, or how to go about changing their negative perceptions. To address these gaps and better understand consumer preferences for more attractive produce, this research investigates three areas. First, it provides a review of the literature on consumer decision-making, consumer perceptions of food, and food waste. Second, through interviews with local farmers, produce buyers, and produce sellers, it seeks to better understand the motivations for buying or wasting food along the food supply chain. Third, through extensive consumer surveys conducted at farmer’s markets and conventional grocery stores, it examines consumer-purchasing decisions and the misconceptions around imperfect produce. Drawing on the findings from this work, this study concludes with a series of recommendations for consumer-targeted programming and education that can help shift common negative perceptions of imperfect produce and reduce food waste throughout the food supply chain.

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

The Heesch number of a shape (or tile) is the maximum number of complete "layers" said shape can form around itself in a tiling. Regular hexagons can tile the two-dimensional plane in exactly one way, so tiling theorists impose "matching rules" on them to make things interesting. A matching rule on a regular hexagon dictates which of the six sides, when indexed, may touch which other sides and with what orientation. There are four possibilities: two sides cannot match, they can match with only the same orientation, they can match with only opposite orientations, or they can match in either manner. This yields approximately 4.4 trillion rule sets. The ultimate goal of this project is to use the computing cluster to find which of these rule sets give rise to finite Heesch numbers, but the existing code that exhaustively checks each rule set takes an exorbitant amount of time if the Heesch number is large or the rule set tiles the plane (has an infinite Heesch number). We are building filters that identify which rule sets tile the plane in a k-tile-transitive manner, currently as far as k=4. We hope that this will allow us to run the exhaustive Heesch number checking code on a much smaller data set, which would allow us to see results in a reasonable amount of time. 

Flavin containing monooxygenases (FMO) are a highly conserved and ancient protein family. They have been suggested to have evolved pre-Last Universal Common Ancestor (LUCA) and to be present in all kingdoms of life. FMOs are known as catalysts for detoxification of xenobiotic compounds, and their activity in the nematode Caenorhabditis elegans, animal model par excellence for aging research, has recently been found to modulate stress resistance and aging. However, the mechanisms by which FMOs affect these processes remain vastly undercharacterized. Our project seeks to define the subcellular localization and endogenous substrates of the C. elegans FMO, FMO-2, as well as investigate its role in redox balance and iron homeostasis. To compare fmo-2 knockout worms, FMO-2 overexpressor worms, and wild-type worms, we crossed the three strains into various established reporters, biochemically stained worms for changes in iron and fat, and performed stress epistasis experiments feeding them RNAi. We also assessed subcellular localization via several fluorescent translational fusion reporters including crossing them into organelle-marked worms. With FMOs’ newly uncovered role as longevity- and health-promoting enzymes, characterizing them more fully may lead in time to human therapies making use of these enzymes.

Coordination of the initiation of flowering with the optimum season is important for plants in both natural and agricultural systems. In the model plant, Arabidopsis thaliana, timing of flowering is strongly regulated by photoperiod. The main factors important for flowering are CONSTANS (CO) protein, which is an activator of flowering in response to photoperiod and FLOWERING LOCUS T (FT), the direct target of CO. FT protein is a mobile factor which can initiate flowering. Additionally there is a family of repressor transcription factors, the CYCLING DOF FACTOR (CDF) transcription factors that are able to limit the timing of both CO and FT expression so that flowering is repressed during short days. Functionally, CDF expression is controlled by the circadian clock so that their effect is constrained to the morning period of the day. In the afternoon of long days, CDF protein is degraded, enabling CO and FT to promote flowering. Recently, our laboratory has determined that CDFs may require a co-repressor protein, TOPLESS (TPL) to form a repressor complex to regulate flowering genes. To explore the importance of this repressor complex on flowering time, I observed how FT, CO, and other flowering genes expression levels change over the course of development in several genetic backgrounds. To remove TPL function where flowering time genes are expressed, we created a transgenic plant that expresses a dominant negative mutant of TPL in phloem companion cells. We hypothesized that this mutant would resemble a CDF loss of function, so I compared these lines and wild type plants over developmental time. Additionally, I am investigating the genetic interactions and epistasis of TPL with other flowering time pathway components by checking the flowering time and gene expression of transgenic plants which express mutated TPL and harbor mutations in other flowering time genes.

Our lab is using the nitrogen-vacancy (NV) center, which is a specific impurity in diamond, to measure magnetic fields on a microscopic scale. The ability to measure these fields unobtrusively and in real time will be a valuable tool for studying biological systems tagged with magnetic nanoparticles. The NV centers fluoresce when exposed to green light, but in the presence of a microwave field of a specific frequency this fluorescence decreases. The precise frequency at which this occurs is dependent on the local magnetic field strength and direction. Thus, by sweeping this microwave field over a range of frequencies, we can measure the magnetic field at the NV centers. Here we use computer software, HFSS, to design a resonator to produce the necessary microwave field. Critically, the resonator needs to produce a uniform microwave field over the imaging area on a diamond chip for a wide frequency bandwidth. It also needs to integrate with other aspects of the overall design; in particular it should be transparent at the center to allow us to image through it. Designs are fabricated at the University of Washington MakerSpace, and a comparison between the simulations and these fabricated devices will be presented.

Recent proposed guidelines for Alzheimer’s disease (AD) stress the importance of AD subtypes (DuBois et al., Lancet Neurology 2014). There are limited data available regarding incidence rates of AD- and non-AD dementia subtypes. Better understanding of these subtypes is an important objective for improving clinical diagnoses and planning future research targets. Using data from the Adult Changes in Thought (ACT) Study we identified groups of individuals with pronounced deficits in memory, executive functioning, language, visuospatial ability, and attention, defined as >1SD below their average score on the battery of cognitive tests administered at the dementia evaluation. We performed two sets of analyses on these groups. The first set of analyses was on the subset of the ACT cohort who died and came to autopsy (636 individuals). In this group, we analyzed Braak stage and CERAD level, which are measures of disease progression, using data from 274 cases and 344 controls, as well as the presence and location of microinfarcts, macroscopic infarcts, Lewy bodies, and amyloid angiopathy. The second set of analyses was on the entire ACT cohort regardless of autopsy status. In this group we analyzed dementia onset, years of education, self-reported race, and medical comorbidity as estimated from pharmacy data. We also analyzed APOE genotype in this group; one variant of this gene is a well-know risk factor for AD. In ACT, of 867 cases of dementia with probable or possible AD, 745 (86%) had complete data with non-missing scores for all cognitive domains. Of these, 517 (69%) had a typical cognitive profile while 228 (31%) had an atypical cognitive profile. We concluded that clinical AD with a typical pattern of cognitive deficits is the most common form of incident dementia in the community, and that clinical AD with an atypical pattern of cognitive deficits is more common than non-AD dementia. Further work may reveal associated risk factors for these groups.

A key goal of aging research is to identify cellular factors that slow aging in hopes of one day developing treatments to combat age related diseases. Caenorhabditis elegans is a roundworm that has been used extensively to study the biology of aging. Low oxygen (hypoxic) environments have been shown to increase the longevity of C. elegans significantly, but the specific mechanisms of hypoxia induced longevity are still not completely understood. Temperature is one of the key determinants of lifespan in cold-blooded (poikilothermic) animals and also greatly influences the physiological response to decreased oxygen. This study aims to identify the relationship between temperature, oxygen levels, and development in C. elegans. Using a temperature gradient within a sealed gas environment we analyzed C. elegans development, growth and reproduction over a wide range of temperatures and oxygen concentrations. Our results show that under normal atmospheric oxygen concentrations (21%) growth is fastest at 26.7C. Interestingly, at extremely low oxygen concentrations (0.1%), development was extremely slow and was fastest at 16C. We hypothesize that increased oxygen demand at normally optimal growth temperatures prevents growth in hypoxia leading to the observed decrease in maximum growth temperature. We are continuing our work with various mutant strains to identify the genetic factors controlling the responses to low oxygen across a range of temperatures. These findings will provide insight into the fundamentals mechanisms of development and aging, and may facilitate development of therapies to delay the progression of age related diseases in humans. 

Studies examining longitudinal change in white matter tracts are limited, especially those including modifiers of change.  We examined 4 year change in white matter tract diffusivity- (linked to degradation), over 3 occasions on participants of the Seattle Longitudinal Study.  Fractional anisotropy (FA), axial diffusivity (AD), and radial diffusivity (RD) were measured in 5 association tracts: superior longitudinal fasciculus (SLF), inferior longitudinal fasciculus (ILF), uncinate fasciculus (UNC), fornix (FNX), and cingulum (CING).  Multivariate multilevel models using a stepwise modeling procedure estimated longitudinal change. Participants were scanned on same 3T Philips Achieva MRI.  Data processed with FSL software (eddy correction, skull stripping, tensor computation).  Probtrackx was used for probabilistic fiber tracking.  A baseline model of change in the previously mentioned tracts was used to predict cross-sectional age differences (AGE) and individual differences in rate of change (TIME) in WM integrity.  This model was followed by the full model examining not only cross-sectional and longitudinal effects, but also moderator variables: APOE genotype and hypertension (HBP).  Cross-sectional AGE effects were found for all 5 tracts for FA and RD.  No AGE effect for AD was found for ILF or CING.  Longitudinal TIME effects were found for all tracts, but only AD and RD.  RD effects were found for all 5 tracts, supporting the importance of myelin-specific damage in association tract fibers.  Loss of white matter integrity was greater for older than middle age adults for ILF and SLF.  Almost no moderation of longitudinal change in tracts occured due to APOE or HBP, possibly due to the homogeneity of the participants.  Given the limited longitudinal research in old age on white matter integrity, the study findings are important in showing longitudinal change in a relatively brief period (six years), and suggesting the importance of AD and particularly RD for examination in future longitudinal studies.

The prefrontal cortex has the potential to play an important role in the development of future brain-computer interface technologies, which have the potential to greatly improve mobility and quality of life for people who suffer from central nervous system injuries or diseases . Most brain-computer interface systems collect neural signals from the motor cortex to control the effector; while this has long been the standard in the field, this approach is not viable if the motor cortex is damaged (e.g. by traumatic brain injury or stroke). The prefrontal cortex plays a role in executive function; it has signals that modulate with motor planning, is susceptible to operant conditioning, and its activity could possibly control brain-computer interfaces. This project aims to explore the efficacy of volitional control of local field potential signals in the prefrontal cortex for potential brain-computer interface applications. Two macaques were bilaterally implanted over the prefrontal, premotor, and motor cortices with dual surface-and-depth electrodes to collect differential local field potential signals. Through repeated training sessions with operant conditioning, the macaques learned to control the cursor on a computer screen, performing center-out tasks by modulating the frequency of local field potentials in the prefrontal cortex. These initial results show that volitional control of local field potentials in the prefrontal cortex is possible. My role in this project is to both collect and analyze data. Current and future work includes data collection from another macaque and examination of interactions between cortical sites during task performance.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder showing persistent deficits in social communication, social interaction across context and communication deficits (DSM-5, 2013). Research suggests that pre- and perinatal conditions such as low birth weight, small gestational age and intrapartum hypoxia (Briston et al., 1996) could be considered as potential risk factors for the development of ASD. Children with lower birth weight are significantly more likely to be diagnosed with autism (Lampi et al., 2012). The goal of this study is to extend the research on these risk factors by examining pre- and perinatal risk factors in a population of high functioning children, and between genders. Participants included children with ASD (n=20) and children with typical development (n=20) between the ages of 8 to 17 years. Parents of participants completed a medical history interview including information about pregnancy conditions and birth related problems. We compared birth weight, gestational age and other perinatal complications in children diagnosed with autism to our control group. We expect to find a lower average birth weight, an overall smaller gestational age, and a higher number of other related pregnancy complications in children diagnosed with ASD compared to our control group. We will then examine how pre- and perinatal conditions might differ for male and females who develop autism. Male children are nearly five times more likely than females to be diagnosed with ASD (CDC, 2014), and so this study, will also explore whether the rates of obstetric complications occur significantly higher in ASD males as well. The results of this study will add to our understanding of these potential risk factors, which may emphasize the importance of early screening and monitoring.

Corvids are fearless. This fearlessness coincides with their striking ability to problem solve and employ their advanced intellectual acuity. Mobbing is a widely utilized behavior reported in varying species of birds and across the mammalian spectrum. Why do these select organisms participate in this conspicuous behavior? I propose that this behavior is a crucial communication tool within a hover of Northwestern Crows (Corvus caurinus). By effectively communicating between individuals, crows can efficiently distract targeted predators and place increasing risk equally over participating members of the mob. I will analyze the audible and physical responses of crows to predatory stimuli in the field. I will also aim to test whether or not crows can adequately identify fake research decoys, as crows are notably intelligent and very effective communicators. I've done this by comparing the results of previous work on Northwestern Crows, which employed an obviously fake predator model, to my work with a more advanced predatory representative. The importance of this work stems on the crows responsiveness to my predatory stimuli. Understanding the way these birds communicate and recognize false predator decoys will only lead to more efficient work done with this species in the future.

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.

The Olympia oyster (Ostrea lurida) is a native oyster along the west coast of the U.S. that has been commercially extinct in Puget Sound since the 1940s. Recently they have been the subject of restoration efforts in Washington State. They are a beneficial part of the ecosystem by providing filtration and oyster beds that offer habitat, food, and increased speciation in estuaries. It has been documented that bivalves can travel vast distances of coastline as larvae in their planktonic life stage. This is a valuable stage in the O. luridia lifecycle as it is the only time that the oyster is mobile and can contribute to other populations. It is therefore important to track the oyster in its larval planktonic stage to help aid in restoration of the species. Plankton samples were collected from two bays in western Washington. Fidalgo Bay to the north, and Dyes Inlet in Central Puget Sound. Plankton samples were collected at the ebb tide and the flood tide from both locations, as well as from two different heights in the water column, 1m from the surface and 0.5 meter from the bottom of the bay. Samples were collected weekly for 5 weeks. The plankton samples were then hand counted visually using microscopy, and quantified with quantitative, real time PCR for comparison. The results will indicate what the larval oysters are doing at different tides. If higher densities of oysters are found in an ebb tide versus the flood tide, it is predicted that larval oysters are being exported. If the flood tide contains significantly higher densities then at ebb tide, then it is possible that larval oysters are being imported from other estuaries, or are being retained in their natal bay.

Cardiovascular disease is the leading cause of death worldwide due largely to the inability of the heart to respond effectively to injury through tissue regeneration. Coronary artery narrowing initiates cessation of arterial blood supply to the heart generating an ischemic injury, characterized by low oxygen and nutrient supply and the accumulation of metabolic waste. Currently, research approaches to study ischemia rely on high-cost and low-throughput in vivo models. As such, there is a need for an in vitro platform for mimicking ischemia/reperfusion injury in a three dimensional cellular environment. The research and design pursued here addresses this deficit in modeling capabilities by developing an in vitro ischemic injury and reperfusion model utilizing engineered cardiac micro tissues. Cardiomyocyte microtissue particles (MTPs) are formed through centrifugation of a single cell suspension of stem cell derived cardiomyocytes without scaffold materials into polydimethylsiloxane micro-wells. Ischemic injury is induced in MTPs by exposing tissue cultures to mineral oil layers on top of small volumes of spent culture media to restrict oxygen supply and metabolic waste exchange. This simulated injury results in an observable reduction in live cells as evidenced by a decreased live cell fluorescence signal associated with duration of injury from a calcein and EthD-1 live/dead stain. Optimization of this staining protocol for characterizing the extent of the induced injury in an adapted plate reader format is currently underway. Thus far, percent of live cells has been shown to positively correlate with normalized calcein fluorescence intensity and current efforts are directed towards increased efficacy of EthD-1 dead cell marking and sufficient tissue infiltration of the stain. Implementation of this protocol will create a baseline metric for monitoring the state of the engineered cardiac tissue during injury and reperfusion and provide a foundation for development of an accurate and cost effective cardiac ischemia injury model.

The fast evolution rate of influenza viruses allows it to avoid host immune systems. Vaccines must be updated yearly in an attempt to protect the population from reinfection. The surface protein haemagglutinin (HA) helps the virus infect the host cell and is the main target of host neutralizing antibodies. Mutations in epitope regions of the HA protein allow the virus to escape antibodies but also affect the protein’s stability. An unstable protein is prone to unfolding and decreased function so it’s hypothesized that stability is selected for during the evolution of HA. HA sequences from 1968-present were used to create a phylogenetic tree. From this tree, ancestral sequences were inferred so that a likely list of HA mutations was compiled. Using the computational program FoldX, changes in stability were estimated for all the mutations that occurred in HA during this time period. Mutations that occurred along the main trunk of the tree were on average more stabilizing than side branch and tip mutations. Epitope mutations that allow the virus to escape the immune system were found to be more destabilizing than mutations that did not occur in epitope regions. As influenza viruses evolve over time, viruses that survive longer generally have more stable haemagglutinin.

Previous studies have shown the importance of bitewing radiographs, xrays taken to detect caries (also known as cavities) in between teeth. Some dental schools have adopted individualized decision-making protocol in order to monitor the decay that lead to performing restorations. However, it is not clear if selective radiographic examinations based on caries risk have been applied routinely. The goals of this project are (1) to examine the frequency of dental radiographic examinations in both children and adult populations, and (2) to analyze the relationship between the frequency of dental examinations, bitewing radiograph prescriptions, and risk of dental caries. Factors that may influence how often radiographic examinations were prescribed, including patients’ age, gender, distance from clinics, and status of dental insurance, were investigated. Patients’ dental records and radiographic images at the University of Washington School of Dentistry from 2007 to 2015 were reviewed. Patients who have been examined for more than 3 visits over a span more than 2 years were selected. Data was collected from two clinics, the adult (n=109) and children's (n=172) clinics. Patients lacking posterior teeth, fewer than 3 exams, or no radiograph prescriptions were excluded from the study. The caries risk was calculated as the number of decay, missing, and filled teeth for the adult clinic and recorded as decay and filled teeth for the children's clinic. Missing teeth were not considered part of the caries risk due to the mixed dentition nature of most children. Our results showed no significant correlation between the clinical examination and radiograph prescription frequencies and the caries risk, age, gender, and distance from clinics. There are significant differences in both radiograph prescription frequencies between clinics and how soon patients return for their second visit among insurance statuses. Our data suggests that dental bitewing radiograph prescriptions were determined by clinic/providers, not caries risk factors.

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.

Copper metallization is an essential step to provide low electrical resistance and reduced electromigration for interconnecting electronic devices. Recently, 2.5D and 3D chip integration has emerged as a desirable packaging technology for advanced electronics. 2.5D uses dedicated silicon-based circuit boards with precise, thick conductor lines while 3D uses vertical connections call Through Silicon Vias (TSVs). Both rely on the process of advanced electroplating where copper is deposited onto the surface of a wafer to fill high aspect ratio structures (either trenches or TSVs). In order to have level plating on a wafer and minimize pinching off of the features, specific levels of organic additives are necessary in the solution. These additives include accelerator, suppressor and leveler, all of which contribute to a successful electroplating process. The analysis of the levels of the additives are discussed as well as their depletion over time due to evaporation or usage. Producing uniform electroplated Cu is dependent on specific concentrations of organic additives in the Cu electroplating bath, namely the accelerator, suppressor and leveler. In this work, we performed copper bath analysis to characterize the amount of the additives needed to achieve an optimal plating bath composition to yield pristine Cu thin films. During the electroplating process, we addressed key challenges by adjusting variables such as increasing current in small intervals to prevent contact failure and taking into account the high aspect ratio structures and plating times to completely fill the trenches/TSVs.

Previous research has established a link between social media and risky drinking behavior, indicating that social networking sites provide exposure to drinking norms that predict attitudes and willingness towards alcohol use. However, despite the growing usage of social media, there is little research on the effects of social networks (other than Facebook) on risky sexual behaviors. Risky sexual behaviors have been previously defined as behaviors that increase the risk of negative outcomes associated with sexual contact such as unwanted pregnancies or sexually transmitted infections. The purpose of the current study is to describe the relationship between having an account with various social networking platforms and risky sexual behavior among young adults. For the present study, risky sexual behavior was defined as having sex with casual partners, having multiple sexual partners, and the lack of condom usage. We hypothesize that being a member of currently popular social media platforms will be positively associated with the aforementioned risky behaviors, while this relationship will be mediated by positive attitudes held towards risky sex. To test our hypotheses, a national sample of 1002 young adults aged 18-20 (53.6% female) were asked to complete a one-time online survey on social media use, health behaviors and risk behaviors, including sexual behavior. Participants reported which social media platforms (Facebook, Twitter, Instagram, or Snapchat) they have accounts with and their attitudes regarding casual sexual behavior, multiple sexual partners, and condom use. Additionally, participants reported on their sexual behaviors within the past 3 months, including: number of casual sexual partners, number of total sexual partners, and the frequency of condom use during sexual encounters. Results of this study may provide a better understanding of the nature and dangers of social media usage, and can help shape protective actions or interventions for reducing sexual behavioral risk.

The nitrogen-vacancy (NV) center is a defect in diamond which shows promise as a solid-state qubit for scalable quantum computation. However, inhomogeneity and instability in the frequency of NV optical emission inhibits efficient quantum entanglement generation between NV centers, thus preventing the realization of quantum algorithms. This work implements two methods—one passive, one active—to mitigate these effects. First, high-temperature annealing improves the uniformity of the carbon lattice, which stabilizes the electro-magnetic environment of NV centers. Specifically, detrimental defects occupying nearby lattice-points diffuse out of the crystal. We build and test a system capable of non-destructively annealing diamond to 1200°C. Second, the application of strong local electric fields across NV centers enables active frequency control via the Stark Effect. To apply these fields, we fabricate gold electrodes directly on the surface of diamond containing near-surface NV centers. To determine the effectiveness of this method, we monitor the frequency of NV emission with photoluminescence excitation spectroscopy while fluctuating the applied electric field. Future work will involve the integration of these two systems with previously-demonstrated photonic circuits to realize efficient multi-qubit entanglement generation.

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.

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

The traumatic loss of one or both parents is difficult for children to manage, even under the best circumstances. For children in low- and middle-income countries, the effects of being orphaned can be devastating. In Kenya and Tanzania, it is hard to meet orphans’ basic needs, such as food and shelter, let alone their mental health needs. The present study is examining data from a large randomized controlled trial (RCT) of a mental health treatment for orphans in Kenya and Tanzania. In the intervention condition of the RCT, orphaned children in these countries who presented with posttraumatic stress or grief symptoms participated in a 12-week Trauma-Focused Cognitive Behavioral Therapy (TF-CBT) intervention, along with their guardians. TF-CBT was previously adapted to fit this cultural setting based on an earlier pilot study. This evidence-based treatment consisted of weekly group sessions led by trained local lay counselors following a predetermined schedule of TF-CBT components. We will be looking at data from 64 study participants’ qualitative interviews conducted 12 months post-treatment, in which children and their guardians reported their levels of satisfaction with the treatment they received. We are currently conducting content analysis on interview responses to identify common themes in the overall experiences, opinions, and life changes associated with participating in the TF-CBT intervention. Findings from this project have important implications for examining whether orphans and guardians in this setting found TF-CBT acceptable and worthwhile, helping inform future research and implementation efforts.

DNA replication is essential for cells to divide and is initiated at specific areas along chromosomes called origins. To better understand how perturbing the process of origin initiation affects cells, our lab created a mutant of the Pre Replication Complex in the model organism Saccharomyces cerevisiae. We observe interesting phenotypes in this mutant, including an altered replication pattern and a shortened Chr XII, due to a loss of ribosomal DNA repeats. The rDNA locus contains around 150 copies of a 9.1 kb repeated sequence which encodes the template needed for ribosome synthesis and also an origin of replication, called rARS. We find the activity of rARS is reduced in the mutant and believe the highly repetitive nature of this region and lack of origin initiation make this locus particularly sensitive to replication stress during S-phase. Interestingly, we have found in a different genetic background of yeast, cells harboring this same mutation in the Pre-RC can maintain a relatively large rDNA locus. My research specifically studies this phenomenon and attempts to explore the mechanisms by which this mutant can overcome replication stress in the rDNA region without reducing rDNA copy number. I am currently investigating several possibilities including using gene replacement to determine the role of a notable mutation in a DNA damage repair protein present in this background. This mutation could confer some stress relief to the cells, which would allow them to retain their large rDNA. I will use the genetic tools available in yeast to study this mutation and its effect on rDNA size variation by Pulsed Field Gel Electrophoresis. DNA replication is vital for cell growth and we hope these inquiries will better elucidate the mechanisms and factors involved in replication in order to better our overall understanding of cell biology.

Leigh Syndrome (LS), one of the most common childhood mitochondrial diseases, typically arises during the first year of life and results in a wide array of metabolic and motor deficiencies leading to death within a couple of years. LS is associated with mutations in any of several mitochondrially encoded genes, including NADH Dehydrogenase Subunit 2 (ND2). The ND2 gene codes for a subunit of complex I within the respiratory chain of the mitochondria. Among patients with the same ND2 mutation, the progression and pathology of LS varies widely. The variation might be due to the effects of variation at other genes that interact with ND2. To test this hypothesis, we have turned to a Drosophila model of LS, in which flies carry an ND2 loss-of-function mutation. Drosophila with the ND2 mutation experience LS-like symptoms, including decreased lifespan, metabolic dysfunction, and paralysis, when exposed to mechanical stress, termed ‘bang sensitivity’. To identify other genes that affect the ND2 mutation in Drosophila, we crossed female ND2 flies with males from the Drosophila Genetic Reference Panel (DGRP); a panel of 200 inbred, fully sequenced lines. The resulting offspring are aged 21 days and assayed for changes in bang sensitivity— the time it takes for individual flies to recover from paralysis. By comparing the effects of ND2 on the bang sensitivity phenotype in each DGRP background, we hope to identify specific genes that either worsen or ameliorate the phenotype. If successful, this study could help us identify genetic modifiers of this mitochondrial disease, and thus help us identify novel therapeutic targets.

In the Possession Sound area of the Whidbey Basin, Ocean Research College Academy (ORCA) students collected water samples to measure nitrate, ammonia, and nitrite levels to better understand seasonal nitrogen cycle changes in the Sound. ORCA is an early college program in cooperation with Everett Community College that allows students to pursue hands-on research in the Puget Sound region of the Salish Sea. We analyzed the archived data set from 2012-2015 with the hypothesis that nitrates would be highest in winter and spring, and lowest in summer and fall due to photosynthesis patterns. High ammonia counts follow high nitrate levels due to decomposition of organic matter, occurring in spring, summer, and fall, and be lowest in winter. Ammonia is fixed into nitrites by heterotrophic bacteria, leading to high nitrite levels in summer, fall, and winter, and low levels in spring. Data were gathered using a Niskin bottle to collect surface water samples, which were then analyzed for nutrient concentrations by the University of Washington Marine Chemistry Laboratory. The data partially supported the nitrate hypothesis, with high levels in the fall and winter, but spring and summer had seasonal variations ranging from 2.5 to 25 µM. The data did not support the ammonia hypothesis, with low spring levels of 1 µM and variation from 1-2.7 µM within summer, winter, and fall. Nitrites partially supported the hypothesis, with high winter and fall levels, but amounts varied within spring and summer, from below 0.05 to 0.1 µM. The patterns observed here lead to further questions regarding primary production by photosynthetic diatoms and their abundance patterns compared to nitrogenous nutrients and silicates used to form frustules. These results help to assess the overall health of the Possession Sound ecosystem by monitoring the abundance patterns that affect the entire food chain.
 

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

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. 

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.

Imidacloprid (IMI) is being sought as an alternative to the carbamate pesticide, carbaryl to control burrowing shrimp (ghost shrimp, Neotropea californiensis) in Willapa Bay and Grays Harbor. The shrimp destabilize sediments resulting in poor survival and low yields of the commercially harvested Pacific oyster. Previous laboratory tests indicate ghost shrimp are overtly affected (immobilized) when exposed to IMI at concentrations up to 1,500 ppb in artificial seawater (SW), but not killed and subsequently recover. Our objective was to determine the concentrations of IMI in SW that result in mortality of the shrimp and compare these levels to those known to affect other marine invertebrates, particularly Crustacea. Additionally, we quantified time to recovery in shrimp exposed to the concentrations tested. We exposed adult non-gravid females to 0, 10, 100, 1000, 10000, and 1000000 ppb (1,000 ppm) of the active ingredient (a.i.) (Nuprid® 2F) in SW for 48 h (24-h static renewal; 5 individual shrimp per concentration) and quantified overt behavior, survival and water quality. All shrimp at concentrations > 1 ppb were overtly affected, but none died. In the recovery test, 6-8 individual shrimp were exposed to 0, 10, 100, 1000, and 10000 ppb a.i. for 24 h (static) followed by 120 h in clean SW (static renewal). One shrimp exposed to 100 ppb died and time to recovery in survivors was concentration dependent. Results suggest ghost shrimp are very sensitive to IMI in terms of immobilization, but concentrations necessary to kill the shrimp exceed those for other marine invertebrates. The neurophysiology of Crustacea may not match the mode of action of IMI because most neural receptors in these species use glutamate as the neurotransmitter and not acetylcholine. Our results, coupled with the less than desired efficacy in the field, suggest IMI may not be an effective alternative to carbaryl.
 

Autism Spectrum Disorder (ASD) is a pervasive developmental disorder characterized by persistent difficulty responding appropriately to new environments with appropriate social behavior. Electroencephalography (EEG) is an electrophysiological test used to record brain activity. EEG is a noninvasive option for understanding abnormal neurological activity in ASD. Among the frequencies associated with observable cognitive processes is the mid-range alpha frequency (8-12Hz). The alpha band band reflects neural preparatory activity in resting, awake individuals, and plays a role in top-down processing in sensorimotor control, especially in limiting inappropriate responses. Studies using resting state EEG indicate a pattern of abnormality in alpha power in ASD, with decreased alpha power compared to individuals with typical development. However, more research is needed to elucidate consistent ASD patterns in larger sample sizes with clear diagnostic criteria, gender diversity, and a large number of electrodes. This study will compare EEG alpha power between larger groups of ASD and TD individuals and between male and female subgroups. Participants include children with typical development (n=30) or a diagnosis of ASD (n=30), between the ages of 8 and 18, with 15 boys and 15 girls in each group. High-density EEG data was collected while subjects viewed three sets of four 16-second videos, in which participants were reminded to keep still and limit blinking. We expect lower alpha band power in ASD individuals than in TD individuals. We will then compare alpha power between males and females in each group, in order to explore the possibility of gender differences in autism, with gender differences in TD as a comparison. This study will contribute to the body of research on biological, physical components of Autism Spectrum Disorder.

Formalin-fixed, paraffin-embedded (FFPE) tissue is the clinical standard for histopathological analysis. FFPE stores and protects for long-term clinical follow-up the tissues and biomarkers which may serve as detectors for cancers and other diseases. However, the traditional method of extracting RNA from FFPE tissue has been a challenge because formalin creates covalent bonds and often causes fragmentations during the extraction process. The goal of our project is to compare the traditional lysis buffer method alone and with the addition of the M220 focused-ultrasonicator. Measurable endpoints include four criteria: time, cost, quality and quantity of extracted RNA. I performed the RNA extraction processes for both protocols using 5 challenging FFPE samples (2 cell lines, 1 liver, 1 lung, and 1 kidney). To acquire the most accurate results, we used the Thermo Scientific UV-Vis micro volume spectrophotometer NanoDrop 1000, bioanalyzers, and a size ladder of polymerase chain reactions (PCR) to access the quality of the starting material. We measured and compared the concentration of RNA (ng/ml) and purity of RNA with the ratios 260/280 (the ratio of RNA over protein) and 260/230 (the ratio of RNA over contaminants) from two protocols. The results demonstrated that on average M220 (117.14 ng/ul) extracted less RNA than the traditional method (323.48 ng/ul). The 260/280 and 260/230 ratios of the RNA extract with M220 were lower than the traditional method. The traditional method kit (20 steps) costs $8.34 per sample, took 5 hours 30 minutes, while M220 (18 steps) costs $12 per sample, and took 4 hours 35 mins. In conclusion, in very preliminary studies M220 appears to decrease time process and complexity, but it doesn’t appear to improve extraction yield or quality of challenging specimens (over-fixed specimens, autopsy specimens).

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.

Antibiotic resistance in bacteria is rapidly rising and our garrison of effective drugs keeps dwindling. As the creation of new antibiotics is incredibly time-consuming and expensive, it’s crucial that we slow the rapid evolution of drug resistance to prolong the effectiveness of our current drugs. Recent studies suggest improving current drug cycling practices by exploiting a phenomenon known as collateral sensitivity, where resistance to one drug leaves bacteria more sensitive to a second. By selecting pairs of antibiotics that exhibit collateral sensitivity, this method causes one drug to become more effective at abolishing bacteria after resistance to another drug has occurred. However, it is not known if collateral sensitivity profiles are maintained after further evolution of the bacteria; information that is crucial if we want a long-term method of combating drug resistance. Through our experiments, we aim to test the null hypothesis that collateral sensitivity profiles do not change over evolutionary time. To do this, we first isolated an array of Gentamicin-resistant Escherichia coli that exhibit collateral sensitivity to Colistin. Then we evolved our resistant bacteria for ~200 generations and measured the minimum inhibitory concentration (MIC), the concentration of drug that inhibits bacterial growth, for both drugs. By comparing the MIC values before and after our evolution experiment, we can determine if collateral sensitivity changes. If collateral sensitivity increases after evolution, collaterally sensitive drug cycling treatments could prove to be more effective than we already assume. But if collateral sensitivity decreases, the efficacy of this style of treatment may be reduced, which is important to know when designing drug cycling treatments. Knowledge of collateral sensitivity patterns will influence the way we treat patients and combat future multidrug-resistant bacteria.

Possession Sound is located near the Port of Everett. Along with the freshwater input of the Snohomish River, the water chemistry of this area is influenced by runoff from nonpoint sources like agriculture and urban development. Our research group, part of the Ocean Research College Academy (ORCA), collected water column data by using a Niskin bottle. Nutrients were then analyzed by the University of Washington Marine Chemistry Laboratory. We hypothesized that the nutrient levels would be higher in areas closer to Everett. However, the data did not demonstrate a significant correlation between location and nutrient level. Average nitrate and nitrite levels were highest in the middle of Possession Sound, at 14.4 μmol and 1.7 μmol respectively. Ammonium levels were highest near the Snohomish River delta, at 1.6 μmol. This variance could in part be due to the transport of nonpoint sources of nitrite and ammonium from upriver, where ammonium is introduced from agricultural fertilizers and undergoes fixation through the nitrogen cycle into nitrite. If continued increases in nutrient levels from human activity is seen, an increase in harmful algal blooms could occur, leading to significant changes in water chemistry and phytoplankton biomass.

When two-dimensional materials, such as graphene, boron nitride, or transition metal dichalcogenides (TMDs) are stacked on one another, van der Waals forces bind the layers together to form vertical heterostructures. These have recently sparked interest in the device physics community. Heterostructures fabricated with two differing layers of transition metal dichalcogenides with type-II band alignment are of particular interest as they allow for the hole and electron to separate and be localized into the different monolayers of the heterostructure. Further, the separated charge carriers may bind together to form spatially indirect excitons at the interface. This species of exciton has been shown to exhibit a number of interesting properties including long-range drift-diffusion in the 2D plane, long-lived valley polarization, and an increase in the interlayer exciton lifetime by many orders of magnitude in WSe2–MoSe2heterostructures. A long exciton lifetime is particularly important for investigations of excitonic superfluidity and condensation, which are exciting phenomena in fundamental scientific research. Here, we use a hexagonal boron nitride (h-BN) monolayer to further separate the layers of the WSe2-MoSe2heterostructure and measure the change in the interlayer exciton lifetime. If the lifetime is long enough and exciton density high enough, these bound states can cool and condense into a degenerate Bose gas that exhibits superfluidity. We investigate the interlayer exciton lifetime in the MoSe2–h-BN–WSe2heterostructure by time-resolved photoluminescence. Further, the power dependence of the spatial distribution of the interlayer exciton photoluminescence will elucidate how these excitons migrate throughout the sample, which demonstrates the exciton superfluid phase transition. This research provokes further exploration into interlayer exciton condensation and other quantum-correlated effects in 2D heterostructures.

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

Olympia oysters (Ostrea lurida) were historically overharvested to near extinction. Populations have failed to recover naturally leading to a need for active restoration. O. lurida provide ecosystem services including filtering water, providing habitat, food, and increasing the overall diversity of the ecosystem. The intent of this research is to determine spatial patterns and connectivity of O. lurida planktonic larvae in Puget Sound, WA. We sampled larvae at two depths in the water column and at both ebb and flow tides. Larvae in the water can be sourced back to the natal populations using trace elemental fingerprinting. Trace metals embedded into shell during early life history is representative of the water body where the individual formed its shell. Analysis by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) will yield results that indicate trace elemental ratios with respect to calcium. This information will be used to analyze the distribution patterns of different source populations of O. lurida planktonic larvae in the bay. The big picture of this study is to provide useful information that will aid in restoration efforts.

Flowering time in plants is imperative to reproductive viability and is controlled by a variety of molecular regulatory systems drawing upon internal and external stimulus. We use Arabadopsis thaliana as a model to determine how plants incorporate photoperiodic sunlight cues in the production of flowers. Through the transcriptional regulation of certain molecular factors, plants are able to effectively control the temporal expression of the FT (FLOWERING LOCUS T) gene, FT protein is in leaves and then moves up the shoot apex to initiate flowering. Expression of the FT gene is initiated by a transcription factor called CO (CONSTANS) and suppressed by a protein called CDF1 (CYCLING DOF FACTOR 1) that are controlled by sunlight and the plant’s endogenous circadian clock. CDF1 inhibits CO transcription by binding to a series of four identical upstream DNA binding sites and is thought to do so in conjunction with a corepressor protein called TPL (TOPLESS). In this experiment we created a mutant background that was deficient in TPL activity in conjunction with a synthetic CO promoter fused to the bioluminescent enzyme firefly luciferase (LUC). We use this tool to assay if changes in binding site number and orientation in the presence or absence of TPL change the sensitivity of the promoter to photoperiodic sunlight inputs. We hypothesize that the removal of TPL will increase early-day CO expression regardless of daylength but CO expression will be unaffected by the amount of binding sites. We also expect that loss of TPL function attenuates CDF1 dependent repression of flowering, such that differences in CDF1 repression between different binding site architectures types will be unchanged in the absence of the corepressor. This would corroborate results from previous experiments. Should we obtain other results we might be made to reevaluate the role TPL plays in florigenesis in Arabidopsis.

Exposure to high levels of manganese (Mn) causes a form of Parkinsonism (PS) with clinical features similar to, but distinguishable from, Parkinson’s disease (PD). Though the clinical phenotype of Mn-induced PS is similar to PD, PD is characterized by neurodegeneration in the substantia nigra, whereas Mn-induced PS features striatal neurodegeneration. Mortalin, an important mitochondrial chaperone protein involved with the response to oxidative stress, has shown to be downregulated in PD. Moreover, in recent studies we found mortalin expression to be decreased in striatal astrocytes of Mn exposed miners and in astrocytes of the substania nigra of PD patients. Additionally, we found that in vitro, a reduction in mortalin expression impairs astrocytic protection of neurons. Importantly, Mn-induced astrocyte dysfunction is substantially reduced in cells lacking expression of α-Synuclein (α-Syn), suggesting that their interaction modulates astrocyte function, potentially affecting their neuro-protective role in PS. The interaction between α-Syn and mortalin was investigated in astrocytes isolated from brain regions associated with PD and of Mn-induced neurotoxicity. We employed an animal model of cultured astrocytes from the ventral mesencephalon, striatum, and cerebral cortex to examine this interaction. The cells were treated with 0, 10, or 100 μM Mn, then examined using western blotting and immunofluorescence microscopy. The relative levels of mortalin and α-Syn were then quantified and analyzed. We saw a decrease in the availability of functional astrocytic mortalin with increasing Mn in striatal cells compared to other regions and substantial aggregation of α-Syn, reflecting the astrocytic dysfunction. This study helps bring light to the potentially critical association between mortalin and α-Syn in motor-impaired neurodegenerative diseases and can have important implications for understanding the pathogenesis of α-Syn aggregation and ultimately, PS related neurodegeneration.
 

In developed regions, laboratory-based molecular assays are routinely performed to enable early diagnosis and improve patient outcomes. However, several key technology gaps prevent the widespread use of molecular assays in low-resource areas. For instance, the lack of trained laboratory personnel in resource-poor settings can limit their capacity to perform labor-intensive tests. Additionally, many commonly used enzymes (e.g. polymerase and ligase) require costly cold chain storage. To simplify molecular assays for use in sub-optimal laboratories, we are developing a dried reagent platform for drying, storing, and dispensing test reagents. Our current work is focused on optimizing the platform for PCR and ligation, which are key steps in the Oligonucleotide Ligation Assay (OLA)-based HIV drug-resistance test being developed by the Frenkel lab (Seattle Children’s Research Institute) and the Lai and Lutz labs (UW Bioengineering). Multiple formulas containing preservatives up to 10% w/v were evaluated based on their assay compatibility and enzyme-stabilizing effect during freeze-drying. We found that the presence of trehalose and poly(ethylene glycol) in the dried reagent mixtures best maintained assay performance for both PCR and ligation. Preliminary data also showed that ligation performance of the new formula with the dried reagent platform was comparable to the performance of freshly prepared mixtures and that the dried reagents remained stable after 28-days of ambient storage (<15% relative humidity, 20-25°C). Long-term storage studies with the preserved PCR mixture are still in progress but we have demonstrated that lyophilized mixtures stored overnight produce amplified products in the same range as those from freshly prepared PCR mix. Future work will aim to achieve dried reagent stability up to 3-months and incorporate the platform into the first prototype of our drug-resistance test. Ultimately, the platform will reduce user manipulation and assay preparation time for the OLA and could be expanded to simplify other complex molecular assays.

Students of the Ocean Research College Academy (ORCA), an early college Running Start program through Everett Community College, earn their associate's degree at the same time as their high school diploma. Students conduct boat-based research of multiple parameters in the local Snohomish River estuary system. Our study focused on using the historical data set to study the relationship between heavy metal concentrations and sediment size. Heavy metals can originate due to weathering and erosion from rainfall during storm events. Particles are deposited by size; finer sediments accumulate farther from shore while larger sediments remain closer to their point of origin. The hypothesis for our study was that the larger sediment sizes would retain more heavy metals, because of their larger surface area, which allowed for more absorption of the heavy metals. A Ponar grab was used for collection of benthic sediments and samples were sieved according to sediment size. Complimentary samples were analyzed for heavy metal abundance by the Everett Environmental Laboratory. These data collected from previous ORCA students were analyzed for spatial trends in mercury and lead abundance with sediment size at the three different locations from 2013 to 2015. Lead and mercury are neurotoxins that when found in high abundance can cause harmful effects to marine organisms.
 

The Ndufs4 gene knockout (Ndufs4-/-) mice show the phenotype of severe neurodegenerative mitochondrial disease analogous to human Leigh syndrome. Phosphoproteomics is a large-scale study of phosphorylated proteins, which are post-translational modifications that can turn on and off biological signaling pathways. Phosphoproteomics and proteomics experiments using mass spectrometry can allow us to quantify protein levels in mouse tissues. The broad goal of my project is to define the underlying mechanism of mitochondrial dysfunction using a phosphoproteomics approach in the Ndufs4-/- mouse model and translate the findings to improve the health of patients with severe mitochondrial disorders. Our lab previously showed that rapamycin, a drug that inhibits mTOR kinase, partially rescued the disease phenotype of Ndufs4-/- mice. However, the downstream biological pathways affected by rapamycin in this setting are not understood yet. Those may be discovered by analyzing differences in phosphorylated proteins among brain tissues of wildtype, Ndufs4-/-, and rapamycin treated Ndufs4-/- mice. For the initial analysis, protein data sets with quantitative measurements of more than 4,000 proteins were analyzed. Proteins that may be important and most affected by mitochondrial disease and rescued by rapamycin were pinpointed. After the analysis of the data was complete, the proteins that passed the filtering thresholds were quantified with Western blots, a biochemical technique to quantify protein level individually. We have already identified two signaling pathways from the phosphoproteomics and will test the effect of inhibitors of these pathways in the mice. It is our hope that a better mechanistic understanding of disease progression in this mitochondrial disease mouse model will yield new therapies to treat mitochondrial disease in patients for whom there is not currently any effective treatment.
 

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. 

This project aims to build a pulsed laser for lifetime measurements of nitrogen-vacancy (NV) centers in diamond. Such measurements are an important tool for characterizing the quantum information processing potential of NV-center-based photonic devices. Specifically, the radiative lifetime of an NV center is indicative of the proportion of photons being emitted at the useful zero phonon line (ZPL) wavelength. Optical emission at other wavelengths cannot be used for quantum information processing. As NV centers naturally emit only ~3% of photons at the ZPL wavelength, a major objective of our lab is to increase this quantity through photonic integration. Although lifetime measurements have been performed previously in our lab, the excitation source used had a pulse width of 4 ps, much shorter than needed and thus requiring a high optical intensity. This tended to damage the photonic devices under investigation. Therefore, a pulsed laser with a pulse width on the order of 10 ns is being constructed for future lifetime measurements. An important feature of this laser will be a pulse fall time significantly shorter than the NV center’s radiative lifetime. After the laser becomes operational, we will utilize it to implement lifetime measurements of NV centers coupled to photonic devices. This will lead to a better characterization of device performance, and ultimately to large scale NV-center-based quantum information processing.

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.

In the aging community, our ultimate goal is to lifespan and healthspan, the period of time that an individual lives healthily. Previous studies have found that aging results in decline of heart functions and increases prevalence of cardiovascular disease. Characteristics of cardiac aging include enlargement of the left ventricle, impaired diastolic functions, and reduced myocardial performance. Oxidative stress has been implicated as one of the mechanisms underlying cardiac aging. SS-31 peptide, a tetrapeptide that targets the inner membrane of the mitochondria, has been shown to interact with cardiolipin and enhance the electron carrying function of cytochrome c, an essential component of the electron transport chain. SS-31 peptide also limits oxidative damage to cardiolipin, a phospholipid that is almost exclusively located in the inner mitochondrial membrane, by reducing peroxidase activity of cytochrome C. SS-31 treatment has been shown to protect mitochondria in pressure-overload induced heart failure and oxidative injury in other tissues. In this study, we performed echocardiography and treadmill running and showed that 8 weeks of the SS-31 treatment improved diastolic function, myocardial performance, and enhanced exercise endurance in old mice. Using quantitative real-time PCR, I am assessing the gene expression changes regulated by the SS-31 treatment. Understanding the mechanism of how SS-31 improves cardiac aging will provide insight on potential therapies to improve cardiac health in the elderly populations.

An electron bound to a donor impurity in a semiconductor exhibits properties of a quantum system that could be used as a spin quantum bit (qubit) for quantum computing. For such a quantum system to be considered a candidate for a spin qubit there must be minimal interaction with its surrounding environment, maximizing the time the system can store quantum information. Longitudinal electron spin relaxation time (T1), the characteristic time for perturbed electron spins to return to thermal equilibrium, serves as a fundamental upper limit for quantum information storage time of an electron spin qubit. Theoretical calculations and previous electron spin resonance measurements of donor bound electrons in bulk ZnO provide promising predictions for long storage times of ZnO donor electrons. To date there has been no direct optical measurements of T1 for donor bound electrons in ZnO. Here I present the experimental method and results of measuring T1 for electrons bound to gallium and indium donor impurities in ZnO nanowires. A measurement of T1 on the order of milliseconds for donor bound electrons in ZnO would merit further research to determine if these donor electrons can be realized as qubits with good properties. The nanowire structure of our ZnO samples also has the potential to meet another requirement for the donor bound electrons to be considered candidates for spin qubits; they must have qubit-specific measurement capabilities. By isolating a single nanowire, with the right sample dopant concentrations, we would be able to spatially resolve a single qubit.

Cytomegalovirus (CMV) is a common herpes virus that causes severe illness in immunocompromised patients, such as transplant recipients. Due to scarcity of matching donors, it is sometimes necessary to give a patient who is CMV-negative hematopoietic stem cells from a donor who is positive, resulting in a 25% risk of infection. A study was performed 30 years ago to determine if giving patients immune globulin with high levels of CMV-specific antibodies (CMV-IVIG) could prevent infection. The hypothesis was that CMV-specific antibodies would bind to and neutralize the virus before it could establish infection in the patient. The results demonstrated decreased risk of infection among patients who received CMV-IVIG compared to those who did not (controls). However, because of the poor diagnostic and treatment options available for CMV at this time, there was no difference in the rate of illness or survival, so the strategy was abandoned. Using samples from this trial, we will measure the ability of antibodies to prevent CMV entry into epithelial cells utilizing a novel neutralizing-antibody (NAb) assay. A standard concentration of a green fluorescent protein (GFP) labeled, CMV strain is added to dilutions of patient sera. The virus and sera solutions are overlaid onto epithelial cells for one hour and then washed. The cells are incubated for one week and the intensity of GFP fluorescence is measured. We construct a standard curve and extrapolate the concentration of serum required to neutralize 50% of the virus (IC-50). We hypothesize that patients who received CMV-IVIG will have higher NAb activity than controls. We have completed testing of 17/63 patients. The mean log₂IC-50 of patients who received CMV-IVIG (n=8) was 6.25, compared to 5.33 in controls (n=9). Identification of a marker that predicts prevention of CMV infection would be important for CMV vaccine development.

Extracellular matrices are more than structural scaffolds used merely to provide mechanical support to cell and tissue organization—rather, they provide physical and biochemical signals to change the cell structure and function. Here, my project is to investigate on the diffusion properties of human kidney extracellular matrix (kECM) and their impact on proximal tubular epithelial cells (PTECs) in an engineered 3D physiological system. Outcomes of the project include: 1) diffusion coefficients of dextran of different sizes in the matrices made from pure type I collagen, pure kECM, and mixtures of type I collagen and kECM (3:1, 1:1, and 1:3). 2) A standard protocol and an assistive Matlab program for diffusion measurement and vessel perfusion experiments. 3) characterization of structure, morphology and transporters (Immunostaining) of proximal tubular epithelial cells inside the flow-derived microphysiological system. I expect the study to provide supportive understanding of cell-matrix interactions and facilitate the further development of the bioengineered human kidney microphysiological system to study kidney function and response to drugs and toxins.

Merkel cell carcinoma (MCC) is a rare, and often aggressive skin cancer with a disease-associated mortality of approximately 40%. About 1,500 cases of MCC are diagnosed annually, and the incidence is increasing. Following surgery, post-operative radiation therapy (PORT) is usually recommended to minimize local recurrences. However, it is unclear whether patients with low-risk Stage IA MCC arising on the limbs and trunk should also receive PORT. We retrospectively identified 80 low-risk patients from our database who met all of the following criteria: 1) primary tumor ≤2cm in diameter, 2) microscopically negative margins on surgical excision, 3) no microscopic evidence of nodal metastasis in the sentinel lymph node biopsy, and 4) absence of immunosuppression. Of these 80 patients, 20 patients were treated with surgery alone and 60 received surgery and PORT. There were no significant differences between the two groups in terms of demographics (age, sex, race), location of primary tumor, margin status, depth, or lympho-vascular spread. However, patients treated with PORT tended to have larger primary tumors (p=0.009). The median long-term follow up time was similar for both groups, and was > 4 years. We defined a local recurrence (LR) as a recurrence within 2 cm of the primary tumor operative bed, and Fisher’s exact (2 tailed) was used. There was no statistically significant difference in LR between patients treated with surgery alone versus surgery + PORT (p=0.25). One patient (5%), who had surgery alone, had a LR. There were no LRs among those who had PORT. There was also no statistical difference in regional nodal metastases (p=1), distant metastases (p=0.33), MCC specific survival (p=0.06), and overall survival (p=0.06) between the two groups of patients. In conclusion, PORT was not associated with a reduced risk of local recurrence in low-risk, Stage IA, MCC arising on the limbs and trunk.

3D integration of microelectronic structures are essential to addressing the demands of future high performance electronics. Current memory chips use wire bonding to connect memory cells but are reaching a limit due to assembly challenges. Through-silicon-vias (TSVs), which are vertical electrical connections through a silicon wafer, are a promising alternative to wire bonding and printed electrical interconnects. 3D integrated circuit architecture can be fabricated using TSVs to connect stacked memory cells to increase memory performance while reducing power consumption and chip area. The key to improved TSV technology relies on the conformity of the TaN diffusion barrier and dielectric layers (inside the TSV) prior to electroplating the Cu interconnects. In addition, longer and smaller TSVs form denser 3D microelectronic structures which could have major implications in maximizing data flow for memory cells. In this work, we focused primarily on fabricating ultra-high aspect ratio TSVs (20:1) through standard semiconductor fabrication techniques and used deep reactive-ion etching to create the TSVs. We addressed TSV fabrication process challenges, such as achieving conformal high aspect ratio metal interconnects, by utilizing a novel thin film deposition process called pulsed-CVD (chemical vapor deposition). Lastly, preliminary research on the annealing of the TaN barrier layer reveals a more uniform grain microstructure, which attributes to the TaN’s ability to resist ion diffusion.

Autism Spectrum Disorder (ASD) is characterized by deficits in social interactions, verbal and nonverbal communication, and restricted and repetitive patterns of behavior and interests. There is also variability in intellectual ability, such that about 46% of those individuals on the spectrum have average or above average intellectual abilities. Additionally, males are almost 5 times more likely to be diagnosed with ASD than females are: 1 in 42 males are identified as being on the spectrum compared to the 1 in 189 females. It is hypothesized that females with ASD may be under-diagnosed or be diagnosed at a later age due to their greater socio-communication ability and less repetitive behaviors compared to males. To test this, this study will investigate the possible relationship between autism severity and IQ, and then to further explore the role of gender within this correlation. The participants of this study were 20 males and 20 females ages 8 through 17 with a diagnosis of ASD. Autism severity was measured through clinician and child interaction using the Autistic Diagnostic Observation Schedule-2 (ADOS-2). Each participant’s verbal IQ was also identified through the Differential Abilities Scale 2 (DAS II). I predict that lower verbal IQ, for both sexes, will be associated with more severe autism behaviors. Second, females on average will have a higher mean verbal IQ in comparison to the males when matching on age and severity of ASD. This study identifies the complex and varying patterns of ASD by testing for relationships between severity of ASD, intellectual ability, and gender.

In this presentation, I wish to explore the question “what role has racism played in American Foreign Policy?” To answer this question, I look at the American colonization of the Philippines in 1898. Many scholars disagree and instead state American Foreign policy is strategically motivated in a mode that most efficiently eliminates foreign threats and secures American interests. I believe differently. Racism has historically played a role in American Foreign Policy, and continues to do so. Race and racism are social constructs, created and normalized by groups of people in response to how they feel about another group of people. One has a strong sense of identity with those who appear to be the same as them and will see them as sharing common interests. Conversely, if one is unable to associate with a group of people, they will perceive this group as some sort of threat, as they are unable to assimilate with these people. This threat perception influences decision-making. To support my argument, I will be looking at multiple theoretical approaches, included the role of cognitive and motivated biases in threat perception, race and racial identity, and how racist beliefs are formed. In order to answer this question, I looked at publications made by prominent Filipino and American leaders of the time Emilio Aguinaldo and Theodore Roosevelt, which helped me to determine the two parties’ attitudes towards one another. I also looked at historical data of the treatment of Filipinos under Spanish rule, and later as an American colony. I did a secondary review of the research, comparing and contrasting my findings with those of historians and political scientists, such as Zoltan Buzas. I believe that citizens have an obligation to be aware of the actions that reflect upon our nation as a whole. Though individuals most likely cannot change the actions of policymakers, we as a society, as a nation, can hold our elected officials accountable for their roles in American Foreign Policy, as it is a reflection of our values as a society.

Phenotypes of mutant alleles in a given environment can be used to determine which processes depend on the normal function of a gene. Although genes involved in specific biosynthesis pathways are well characterized in the model organism Saccharomyces cerevisiae, there are genes involved in these processes that still have uncharacterized function. The interaction between gene function and the environmental condition is complex, and requires a comparative approach across yeast species to identify the function of uncharacterized genes in a variety of conditions. We have used a Tn7 transposon insertion mutagenesis system in Saccharomyces uvarum to randomly mutate genes across the genome and pooled all resulting insertional mutants together. We used deep sequencing to identify the insertion sites, and previously predicted 809 genes to be essential for growth in standard laboratory conditions in S. uvarum. Using these same methods, we will apply different selective pressures to libraries of mutant yeast, and aim to understand which genes are critical for growth under specific conditions, such as glucose, phosphate, and sulfate limiting media. We expect that it will be more common to find genes that were non-essential in normal growth media to be essential in more limiting conditions, whereas most genes that were essential in normal growth media should also be essential in limiting conditions. Studying yeast in conditions where they are naturally found (such as grape-must) can provide insight into new, critical genes. This information can be used to make commercial processes such as fermentation more efficient by optimizing metabolic pathways. Additionally, this data can be used to improve gene annotations and increase our knowledge of the biochemical pathways that underlie these essential processes. Thus, acquiring phenotypic information of mutant genes across species and conditions can even help discover genes involved in previously well-studied pathways.

Point of care diagnostics devices are aimed at addressing health disparities in low resource settings. They must be cheap, easy to use and offer quick results. Nucleic acids (DNA, RNA) can be used to identify infectious pathogens, and employ molecular diagnostic tools such as PCR to do so. PCR is a process which utilizes DNA Denaturation, where the hydrogen bonds that form between DNA and complementary strands break under various temperatures, forming to single strands of DNA. The melt temperature, the point where half of a given solution is single stranded DNA, and half of the solution is double stranded DNA, can be calculated by using fundamental thermodynamic equations. Our goal is to create a lab teaching module in which students can perform experiments measuring the melt temperature of various pieces of DNA with its complementary strand. Learning Objectives were produced, and a lab was designed in order to fulfill each objective. The module consists of a prelab portion, in which students review the basic concepts behind thermodynamics, read and analyze scientific papers, and calculate melt temperatures (by using thermodynamic values as well as industry standard software). The actual lab portion consists of an experiment which tests the effect of DNA length on melt temperatures. Students will then interpret and analyze the melt curves generated in lab. Lastly, during the post lab portion students will brainstorm future experiments and solidify their understanding of how thermodynamic tools can be used to measure various nucleic acid processes, namely denaturation.

The drug rapamycin is a specific inhibitor of the mechanistic target of rapamycin (mTOR) and has been previously shown to increase lifespan in yeast, worms, flies, and mice. Rapamycin inhibits mTOR by binding the Fpr1 protein (FKBP12 in mammals); the rapamycin-Fpr1 complex then dissociates the mTOR complex I. In order to identify new, natural product inhibitors of mTOR that function similarly to rapamycin we have developed a high resolution assay for growth inhibition in yeast using a Bioscreen C MBR machine. We are currently testing twenty-two natural product compounds, and their mixes in this assay to determine if they inhibit the TOR pathway, change mitochondrial function, or have any effect on replicative lifespan in yeast. Each compound and mixture is being assessed for its ability to alter the growth kinetics of four yeast strains: wild-type, TOR1 deletion, FPR1 deletion, and SIT4 deletion. Tor1p is a kinase in the TOR complex, and deletion of TOR1 leads to rapamycin hypersensitivity. The fpr1Δ mutant is resistant to rapamycin. The sit4Δ deletion is sensitive to multiple drugs. Compounds were dissolved in the solvent DMSO, or in some cases other solvents, and diluted to 1 µg/ml, 10 µg/ml, and 100 µg/ml in culture medium. All tests were performed in yeast extract peptone dextrose (YEPD) solution. We used a Bioscreen C MBR analyzer to measure the optical density of growing yeast in the YEPD with the compounds. The bioscreen analyzer generates an optical density curve over time that can be further analyzed by using the web tool, Yeast Outgrowth Data Analyzer (YODA), to selectively examine and compute the doubling time of the cultured yeast cells. The doubling time data was used to evaluate the effect of supplements on growth rate compared to rapamycin, in order to identify compounds of interest for further study.

Storm events in Western Washington increase urban runoff which can transport sediments and deposit them in Puget Sound. These sediments can contain concentrations of different types of heavy metals. We hypothesized that when there was higher precipitation and river discharge, there would be a higher percentage heavy metals. The data that was being looked at was from 2012-2015 from three different stations near the Snohomish River estuary and the samples were collected by a Ponar grab. These sediment samples were later analyzed by the Everett Environmental Laboratory. The stations were labelled based on proximity to the mouth of the Snohomish River. Station 1 was closest, Station 2 was in between 1 and 3, and Station 3 was the farthest away from the Snohomish River. The river discharge at Station 1 had a median equal to 8,120 ft³/s with averages of heavy metal concentrations that were at 18.9 mg/kg of copper, 8.38 mg/kg of arsenic, 5.07 mg/kg of lead, and 48.06 mg/kg of zinc. The river discharge at Station 2 had a median of 10,000 ft³/s with averages of heavy metal concentrations that were 14.96 mg/kg of copper, 5.48 mg/kg of arsenic, 4.53 mg/kg of lead, and 35.22 mg/kg of zinc. The river discharge at Station 3 had a median equal to 10,550 ft³/s with averages of heavy metal concentrations at 4.94 mg/kg of copper, 2.59 mg/kg of arsenic, 3.14 mg/kg of lead, and 22.48 mg/kg of zinc. After looking at the data, we have concluded that there is no clear correlation between river discharge and heavy metal concentration. In the future, we would try to integrate a marine biology aspect into this project to see how the heavy metal concentrations affect the plankton near the stations.

There are many different Danio species that each have their own very unique pigment pattern. Even though each pattern is different, they are all made up of the same pigment cell types. Different interactions between black melanophores, yellow/orange xanthophores, and iridescent iridophores establish and maintain the Danio pigment patterns. Changes in these interactions allowed the species to diverge and created their own unique phenotype. Our project is focused on determining the differences that allow for the development of different pigment patterns within Danio species, such as Danio rerio, D. margaritatus, D. erythromicron, D. choprae, D. tinwini, D. alboliniatus, D. aesculapii, and D. nigrofasciatus. One of the more obvious differences in the development of these patterns is the order in which the adult pigment cells differentiate. In some species melanophores differentiate first, while in others xanthophores differentiate first, and in some species multiple pigment cell types differentiate at the same time. Previous studies have shown that xanthophores are very important in determining the final pigment pattern in D. rerio. In order to test what roles the xanthophores have in determining the final pattern for other species we generated colony stimulating factor 1 receptor (csf1r) mutants using CRISPR/cas9 mutagenesis. Without csf1r there cannot be any csf1 signaling, which is required for xanthophore development. By knocking out csf1r we can knock out xanthophores and the cell-to-cell signaling involving xanthophores that was necessary to form the normal pattern in Danios. So far we have created mutants for csf1r in D. rerio, D. alboliniatus, D. aesculapii, and D. choprae. We have also started to quantify the phenotypes for these mutants to determine the overall effect of knocking out xanthophores. Understanding the cellular mechanisms that allow for all the different patterns in Danios will help our understanding of the evolution of different Danio species.

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

The efficient production of cellular energy via the mitochondrial electron transport chain is necessary for the growth, health, and lifespan of all organisms. However, the genetic pathways that impact the regulation of energy production are still largely undefined. This is largely because the electron transport chain is so essential for life that genetic mutations which disrupt its functioning are lethal, preventing their study. The small roundworm Caenorhabditis elegans has been a useful model because its powerful genetics have allowed researchers to perform forward screens to identify mutations to electron transport chain proteins that can significantly reduce ATP production but are not severe enough to kill the animal. Preceding studies in my lab (Dr. Kaeberlein, Pathology) have identified how mutations that on the ISP-1 molecule itself can restore more normal functioning. My research focuses on identifying genes other than ISP-1 that can also functionally compensate for the reduction in ATP production efficiency. I am currently identifying the genetic loci of three mutations that suppress the loss of ATP production through single nucleotide polymorphism (SNP) gene mapping, and whole genome sequencing. These process require genetic crosses and high-throughput PCR and restriction digest protocol. Results from this experiment would give the first insights into the cellular pathways that can impact energy production.

Dopamine deficiency within the brain is a key characteristic observed in patients afflicted with Parkinson's disease. In the Darvas lab, we induce dopamine deficiency in mice by genetically targeting dopamine neurons to express the human diphtheria toxin (DT) receptor (DTR, Slc6a3^DTR mice), which allows us to selectively ablate targeted dopamine neurons in Slc6a3^DTR mice with intramuscular DT injections. After DT-mediated ablation of dopamine neurons in Slc6a3^DTR mice, we observe severe physiological changes including an inability to maintain motor balance on a rotating rod and, unfortunately, a precipitous drop in weight that results in mortality for a majority of mice. This loss of weight is attributed to a lack of appetite resulting from the dopamine depletion. In an attempt to increase the survival rate of dopamine-depleted adult Slc6a3^DTR mice, we have introduced a high-fat diet to both raise the body mass and stimulate the appetite of mice to prevent them from starving. Mice are weaned from their parents and put on the high-fat diet for 12 weeks after which they receive two DT injections, one 48 hours after the other. For 2 weeks post-injection mice are weighed daily and at 3 weeks are tested for motor balance to confirm successful dopamine depletion. There was no improvement in the survival rate of Slc6a3^DTR mice on the high-fat diet and severe dehydration was observed in a majority of Slc6a3^DTR mice past 10 days post-injection. Dopamine depletion in Slc6a3^DTR mice affects both appetite and thirst meaning the high-fat diet alone could not increase survival rate.

Students from the Ocean Research College Academy (ORCA), a program through Everett Community College for high school students that focuses on marine science research, have collected monthly water quality data from the Possession Sound (PS) over the past twelve years. This longitudinal data set is combined with collections of current water quality by this research group. Nutrients play an important role in the health of the PS ecosystem. We evaluated the variations in the levels of phosphates and nitrates in relation to season in the north Whidbey Basin of Puget Sound from 2012-2015. Data were collected monthly from four locations in PS and we averaged these values to analyze the resulting trends in nutrient amounts. Surface water temperature was used as a proxy for the seasonal changes in direct sunlight. Nutrients and sunlight are required by phytoplankton for photosynthesis, so as phytoplankton populations increase nutrients become less abundant as they are utilized. Nitrates and phosphates were hypothesized to decrease in spring months because there was more photosynthesis taking place during the spring with increased sunlight, while the nutrients would peak in the winter. The resulting trends supported this hypothesis with the highest average levels of nitrates in October, at 15.54 μmol, and phosphates peaking in February at 2.15 μmol. The lowest average nitrate and phosphate levels occurred in June, at 3.08 μmol and 0.43 μmol, respectively. Our study gives insight into the health of the PS ecosystem by analyzing nutrients that limit the primary production of phytoplankton. Future parameters to be studied in correlation with this research include silicate and chlorophyll levels.
 

In the context of the growing aging population and constantly improving medical advancement, studies aiming to delay or reverse age-related health issues and enhance longevity have become increasingly relevant, especially in pre-clinical trials with drug interventions. One pharmacological agent, rapamycin which inhibits mTOR (mechanistic target of rapamycin), has been shown to robustly promote longevity in multiple animal model systems. Previous studies in the Kaeberlein lab showed that transient rapamycin treatment in aged C57BL/6JNia mice dramatically extended life expectancy, improved measures of healthspan, and remodeled the gut microbiome. We were particularly interested in the last discovery—specifically whether the increased prevalence of segmented filamentous bacteria (SFB) or C. savagella, commensal microbes shown to modulate the gut immune response, plays a role in rapamycin’s robust effects on longevity and health. To test this hypothesis, we will transplant SFB into aged Balbc By mice, obtained from the National Institute of Aging (NIA), that do not harbor SFB in their gut. The effects of SFB inoculation, paired with transient rapamycin treatment in these mice, will be evaluated by measuring changes in their lifespan and healthspan. We will also assess the changes in their gut microbiome after rapamycin interventions. This set of experiments provides an avenue to evaluate two important aspects of rapamycin intervention. Firstly, since this drug has not been tested in Balbc By mice, we can assess the role of genetic background on rapamycin’s effect on longevity. Secondly, we can establish whether the remodeling of the gut microbiome is relevant to the drug’s role in longevity and health. Additionally, does SFB play a role in this process? Answers to these questions can have a significant impact on how we view the aging process and may help pave the way for possible clinical interventions that can attenuate the negative effects associated with human aging.

Autism spectrum disorder (ASD) is a complex developmental disorder that includes impairments in social interaction, communication skills and presence of repetitive behaviors. The CDC estimates that rates of autism are almost five times higher in boys than among girls. ASD children demonstrate less social involvement, such as fewer reciprocal relationships with friends, in comparison to typical children. This may be due to lower social communication skills in children with ASD. In a study of typically developing children, girls scored higher in non-verbal skills such as pretend play, compared to boys, suggesting that girls may be more likely to communicate socially than boys. This study will investigate if boys and girls with autism differ in their social communications abilities when matched for non- verbal intelligence. Forty children (20 girls and 20 boys) with ASD between the ages of 8 and 17 participated in this study. Social communication was measured using a child-clinical diagnostic interaction (Autism Diagnostic Observational Schedule) and non-social communication skills were measured using the Clinical Evaluation of Language Fundamentals (which measures verbal response to visual stimuli). Additionally, parents reported on their child’s social interactions using the Autism Diagnostic Interview. We hypothesized that ASD girls will have higher scores on both social and non-social forms of communication than ASD boys. To date, no study has included equivalent numbers of boys and girls in analyses. The results of this study will provide insight into gender differences in autism.

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.

The use of mobile applications for real-time self monitoring of patients’ conditions has been growing rapidly in medical research and healthcare fields.  I am working with a team to build a smart aging monitoring mobile app, which will be particularly prototyped among participants of Seattle Longitudinal Study (SLS). Many of them are subject to the risk of developing aging diseases such as the Alzheimer’s disease (AD). AD is a degenerative disorder that can destroy memory and other important mental functions.  Currently there have been 5.3 million Americans suffering from AD, and with the demographic shift towards an aging society, this number is expected to double in the next decade. We feel a strong calling to build senior people monitoring tools to help them stay away from such disorders, as well a tool that assists monitoring and early intervention among AD patients. Therefore, we started our research project, named as “CHI - Contemporaneous Health Index for Smart Monitoring of Aging. CHI comprises of a smart mobile application for aging condition monitoring, evaluation, and health promotion and a series of machine learning algorithms that support these functions. In order to build the app, I researched and read related papers and resources about hte AD and form the related tasks and games for the patients in the app. I also researched and talked with my mentor to determine the types of body condition data to collect. The app also provides user with easy access to record their body condition readings. Users can also get their task results and our feedback. I conducted the app tests and make several test users to test and improve the app. In the future we will conduct various user tasks specifically designed for Alzheimer’s patients and we will collect user results by working with SLS for further analysis. It is anticipated to be a powerful tool that mainly focuses on monitoring, evaluating, and intervening the aging process, to characterize the “aging trajectory” of individuals, to identify abnormal patterns, and to further provide personalized recommendation that help users stay healthier, active and happy lives.

Real-time quantification of chemical compounds in urban and non-urban environments has far-reaching prospective benefits for our society. Such a possibility could provide instantaneous detection of dangerous chemicals, identification of areas that require air quality restoration, estimation of agricultural effectivity, etc. However, currently, dynamic and efficient platforms to perform quantification do not exist and only a few static sensors are deployed in sparse locations, e.g., a typical city has only a handful of such sensors. While several mobile devices have been constructed, they are typically large, expensive and imprecise. These factors make them practically unrealizable for gathering environmental data in real-time from a wide variety of locations. In our project, we address this fascinating and challenging problem by building an inexpensive, mobile multi-sensor device, that communicates with a mobile phone. We designed the device to incorporate an array of inexpensive sensors, many of which have cross sensitivities to particles measured by other sensors. We had performed testing on a variety of sensors to identify most efficient and precise sensors. To improve performance of the device and obtain readings, we have implemented a neural network, based on olfactory system in moths. We have assembled a prototype of a multi-sensor device according to our design. Our preliminary results show that the network was capable of discriminating and tracking more precise values of contaminants, that could even include mixtures of compounds. We are currently working on implementing a server-side application that will integrate information from multiple devices and will produce a real-time “heat-map” of contaminants and pollution levels across a geographic area.

Exposure to manganese (Mn) causes a neurodegenerative syndrome with clinical manifestations of Parkinsonism (PS) similar to Parkinson’s disease (PD). Although both PD and Mn-induced PS feature movement dysfunction resulting from decreased striatal dopamine, pathologically, Mn-induced PS is thought to be related to striatal degeneration, while in PD, dopaminergic neuron bodies residing in the substantia nigra pars compacta are largely affected. Recent evidence has suggested that astrocytes, glial cells that play a vital role in maintaining homeostasis such as uptake and release of important molecules like precursors for neurotransmitters, may play a vital role in neuronal survival in PD and PS. In order to determine whether the regional differences in sensitivity to Mn are conferred by inherent differences in astrocytes from these brain regions I examined the role of such astrocytes in neuron survival. Contact co-cultures of two neuron-like immortalized cell lines, MES and SH-SY5Y cells, were made with astrocytes from the ventral mesencephalon (vm), striatum (str), and cortex (ctx). These were treated with 10μM and 100μM of Mn and stained for the markers MAP2, TH, and GFAP, imaged, and neurons were counted. Based on previous results, MES cells grown with str astrocytes are expected to have a lower survival rate when treated with Mn, versus those plated with vm and ctx astrocytes. If this trend is observed in the separate SH-SY5Y cell line, this would suggest other neuron-like cell lines and dopaminergic neurons respond similarly to Mn. By examining if Mn affects astrocytes, and in turn neuron survival, this could not only elucidate the pathogenesis of Mn-induced PS, but also elucidate the region specific astrocyte-neuron relationships in the brain.

Cellular growth and tissue elongation are critical features of development, but the mechanisms that regulate these processes remain poorly understood. Our lab, however, uses the fruit fly, Drosophila melanogaster, as a model organism to study these complex pathways and we recently discovered that a novel family of six growth factors may play a role in the development of the adult fly. IDGFs were first discovered by Dr. Peter Bryant in 1998 while attempting to culture individual cells taken from the wing imaginal disc. He found that the wing-disc cells secreted factors that would help cultured cells grow, but further experiments were not conducted to test their function in the wing disc. To begin to test whether these genes play a role in vivo, I am using in situ hybridization to localize the mRNA sequences. I found that IDGF 1, 2, 3, and 4 transcripts are present in the wing blade and hinge regions, and I am currently characterizing IDGF 5 and 6 expression. My long-term goal is to determine the function of the IDGFs; I will use a yeast transcription factor, Gal4, to drive expression of IDGFs from Upstream Activating Sequences (UAS) and examine whether over- or mis-expression alters the growth of the wing. I will also use Gal4/UAS to express RNA that interferes with RNAi in the same wing disc. Subsequently, I will measure potential abnormalities by examining outward defects and quantifying wing size relative to body size. These studies will contribute to our understanding of the mechanisms that regulate tissue growth during development. 

At the Snohomish River estuary, seafloor sediment composition correlates with river discharge. With an increase in river discharge mixing of sediments occurs and the heavy metal particles become suspended in the water column. With a decrease in river discharge sediment concentrations deposit on the sea floor. Ocean Research College Academy (ORCA) students, including ourselves, collected the data used in this investigation on monthly research cruises throughout 2015. We hypothesized that in 2015, higher levels of Snohomish River discharge would lead to lower concentrations of heavy metals in the sediment. River discharge data from the Snohomish River was collected three days prior to the date of sediment collection. Arsenic, copper, and lead concentrations were sampled from three sites in Possession Sound: Mount Baker Terminal (MBT), a buoy southwest of the jetty, and the delta. The results showed that heavy metal concentration decreased with increasing river discharge, with the exception of one site. At MBT, south of the Snohomish River, all of the heavy metal concentrations declined with the increase of river discharge. A rise in river discharge of 1,980 to 25,400ft^3/sec caused a decrease in arsenic from 4.84 to 2.49mg/kg, copper from 15.2 to 8.53, and lead from 7.17 to 2.81mg/kg. The site at the river delta followed the same trend, with a range in river discharge of 1,980 to 10,400ft^3/sec correlating with a decrease in arsenic from 9.34 to 6.06mg/kg, copper from 20.5 to 13.4mg/kg, and lead from 5.94 to 3.04mg/kg. The exception was Buoy, located to the southwest of the jetty. With an increase in river discharge from 3,910 to 29,300ft^3/sec, arsenic rose from 5.74 to 7.14mg/kg, copper from 15.4 to 21.5mg/kg, and lead from 4.31 to 5.78mg/kg. Heavy metal concentrations have been found to be harmful to marine organisms in high concentrations. Thus for further research we will be collecting data on heavy metal concentrations found in local plankton populations, in order to find a correlation between the two.

On a global scale, Australia attracts a minimal amount of asylum seekers but has adopted one of the strictest policies in dealing with these individuals. This paper will attempt to explain the two policies Australia has adopted for dealing with different asylum seekers based on arrival methods. It will draw upon historical and current asylum seeker policy documents and statistics published by the Australian government. It will also seek to analyze why Australia has adopted two separate policies for treating these two categories of asylum seekers. It will utilize scholarly articles and journals, as well as news articles to evaluate these two policies and why Australia has chosen to embrace this treatment.

Possession Sound, located in the northeast arm of the Whidbey Basin, is in close proximity to urbanized and industrialized areas where rainfall produces surface runoff throughout the year. Urban runoff carries a variety of pollutants and heavy metals into Possession Sound, increasing the levels in the aquatic environment. Students at the Ocean Research College Academy (ORCA) have been conducting research of biological, physical, and chemical parameters at five rotating sites since 2010, including collection of benthic sediments for heavy metal analysis. We compiled data records from this time period, as well as ongoing sampling, to observe trends between location and heavy metal concentration. The Everett Environmental Laboratory completes the analysis of six heavy metals; for this study, we selected lead (Pb), copper (Cu), and zinc (Zn) due to their potential to cause adverse effects in the marine environment. We hypothesized that sampling sites closer to shore would contain higher concentrations of Pb, Cu, and Zn compared to a sampling site farther away from cities and industrial areas. Using archived data from 2012-2015, and ongoing research in 2016, we compared three locations of varying distance from shore. The results showed higher levels of Pb near Mukilteo (closest to shore), with an average of 7.4 mg/kg. Contradicting the hypothesis, the location furthest from shore had the highest average values of Cu and Zn (6.7 mg/kg and 30.9 mg/kg, respectively). Considering these data, further monitoring of Possession Sound for anthropogenic influence will be conducted of sediment near storm drains adjacent to marine ecosystems in areas such as eelgrass beds, which act as a nursery for many invertebrate species in Possession Sound and have the ability to bioaccumulate heavy metals, removing them from the sediment.
 

Aging and severe mitochondrial disease are disparate, complex processes whose causes have yet to be fully understood. One protein involved in both is the mechanistic target of rapamycin (mTOR), which regulates cell growth and metabolism. mTOR protein is a component of two complexes, the mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2). Inhibiting mTORC1 with the drug rapamycin increases lifespan in model organisms and suppresses severe mitochondrial disease and shortened lifespan in the Ndufs4 knockout (KO) mouse model of Leigh Syndrome. In mouse models, KO of the S6K1 protein, a substrate of mTORC1, also increases lifespan. Therefore, we hypothesized that KO of S6K1 in the whole body and specific tissues (brain, liver, fat) would rescue the short lifespan of Ndufs4 KO mice. A breeding strategy utilizing Cre-recombinase mice, S6K1^Flox/Flox mice, and Ndufs4 +/- mice was employed to ultimately produce tissue-specific Cre +/- Ndufs4 -/- S6K1^Flox/Flox mice. PCR and Western blot analysis confirmed the whole body and tissue-specific deletion of S6K1 gene and depletion of the protein in each mouse. Our findings indicate that whole body and liver-specific S6K1 KO modestly increased lifespan and delayed the onset of neurological symptoms originating from the mitochondrial disease. However, S6K1 KO is still less effective in rescuing mitochondrial dysfunction than the optimal dose of rapamycin. We speculate that S6K1 partially contributes to the mitochondrial disease of Ndufs4 KO mice, and the liver may play an important role in regulating lifespan. In the long run, these findings may enable us to potentially produce drug treatments to extend the lifespan of healthy humans as well as Leigh Syndrome patients.

Propositions are cognitive structures centered on verbs of action or existences (e.g., Maria plays golf or Maria is a golfer). Implicit Association Tests (IATs) measure associations among concepts in the simpler form of categories that can often be represented by single words (e.g., nouns, adjectives, verbs). To test whether IATs can measure associations involving propositions, this research tested variations of an IAT measuring implicit-attitude associations of Democrat and Republican categories with valence. The first two variations replaced the two political party categories with concepts that could be exemplified by propositions (Democrat victory and Republican victory). A one-verb variation used exemplars in the form of recognizable names (e.g., Obama, Romney) followed by the verb “wins”. This worked successfully and was comparable in properties to the basic 2-category IAT. An opposed-verb variation used exemplars incorporating opposed verbs (e.g., Obama wins and Romney loses for the Democrat victory concept). This proved difficult for subjects, in addition to which the resulting IAT measure did not correlate as expected with self-reported political attitudes. A final phrase IAT variation returned to the two parties as concepts, but used exemplar stimuli in the form of short phrases (e.g., common core) extracted from full statements of Republican and Democrat policy positions (e.g., The U.S. government should specify basic requirements (‘common core’) for public education). Subjects received initial practice linking the short phrases to the full policy statements. The phrase IAT was easier for subjects than the opposed-verb IAT and correlated as expected with self-report measures, indicating its possibility of being used more generally to measure associations involving proposition-level concepts.

According to the most universally used scale for measuring psychological distress, the Holms and Rahe Readjustment Scale, becoming a widow holds top rank for the most taxing life-event. Unless specifically defined otherwise, it is generally understood that the term ‘widow’ refers to a heterosexual female. Consequently, few studies highlight the psychological distress of self-identified lesbian widows, with even fewer examining their resiliency. Resiliency is the capacity to recover from difficulties, where individuals use their personal skill sets to reengage themselves within their environment. To our knowledge, no current research directly compares features of both lesbian and heterosexual widow resiliency within the same qualitative analysis. We seek to understand key features and possible differences in resiliency between self-identified lesbian and self-identified heterosexual widows. Our intention is to learn what types of support best aid resiliency among widows, and whether these support systems are readily accessible to lesbian widows in mainstream heterosexist U.S. society. To measure resiliency, we are conducting voluntary, in-person, one-on-one tape-recorded interviews of 15 lesbian and 15 heterosexual widows. Inclusion criteria required participants be at least 45 years of age and widowed for a minimum of one year at the time of interview. We analyzed interview data through the constant comparative analysis method. We found differences between groups in a variety of themes related to resiliency (i.e., perception of available support systems, and effectiveness of those systems). Participants in the research will have given us an understanding of the underlying attitudes and social dynamics that influence resiliency in this context, helping us identify the conceptual framework needed to best improve resiliency among lesbian and heterosexual widowed populations.

Traumatic dental injury (TDI) is an important public health issue in the pediatric population. Patient demographics, hospital characteristics, and diagnoses present with TDI visits to emergency departments in the United States are poorly understood. The objective of this study was to provide nationally representative estimates of hospital-based emergency department (ED) visits for broken teeth and loss of teeth due to trauma in patients 21 years old and younger. Nationwide Emergency Department Sample (NEDS) for the year 2012 was used. All hospital-based ED visits occurring among 21-year-olds and younger with an International Classification of Diseases-Clinical Modifications, volume 9 code for broken or loss of teeth due to trauma were selected for analysis. Hospital and patient characteristics and external causes of injury were examined. In 2012, hospital-based ED visits with a dental injury diagnosis comprised an estimated total of 66,656 (0.18%) of all ED visits among 21-year-olds and younger in the United States. Of these, 64,732 (97%) had a diagnosis of broken teeth and 2,132 (3%) had loss of teeth due to trauma. Medicaid was the primary payer for 44% of dental injury ED visits. The majority (72%) of the total ED visits that had a diagnosis of dental injury were accompanied with other diagnoses. Of the dental injuries with at least one concurrent diagnoses, 42% were open wound to head or face, 10% were accompanied with facial fracture(s), and 4% had a concomitant diagnosis of concussion. Among specified causes of injury, "fall" and "struck by; against" were the most frequently reported causes of TDI (47% and 30%, respectively). The primary mechanism of injury in children 6 years of age and younger were falls as compared to middle and late adolescent age groups examined. Hospital-based ED visits that had a dental injury were rarely reported, and often accompanied with other diagnoses. 

 Neurodegeneration from proteostatic stress spreads from cell to cell. However, the cellular pathways that contribute to this spreading are poorly understood because there is no simple genetic model established to study this. We can use Caenorhabditis Elegans as the model system because the nematode secretes the ECVs outside into the extracellular environment. I have found that transgenic nematodes (Caenorhabditis elegans) that express human versions of the toxic proteins characteristic of Alzheimer's disease (Amyloid beta) are transported by extracellular vesicles (ECVs). Therefore, I am now developing this novel model system for studying extracellular vesicles signaling and its role in spreading age-related neurodegeneration. The powerful genetics of C. elegans will allow me to study the cellular pathways that contribute to that spreading of these toxic molecules. By harvesting the nematodes from growth plates and centrifuging the worm pellet in buffer, we are able to separate the worms from the raw wash, which contains the ECVs. The raw wash is then run through a size exclusion column to separate the ECVs, and the different size samples are either run through a BCA Protein Assay to determine amount of protein in each sample based on an absorbance reading, or run through an SDS-PAGE Protein Gel and treated with antibodies to isolate the aβ protein. My preliminary results show that the aβ protein is in fact located within a specific range of samples from the size exclusion column. The ability to isolate the extracellular vesicles and locate the source of aβ protein and its proliferation should have a significant impact on the future of Alzheimer’s therapy. If we know more about the exact location and behavior of the deleterious protein, we can apply the knowledge to studies on human cerebral spinal fluid and develop drugs that target this specific pathway in humans.

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

Chlamydia trachomatis is an obligate, intracellular, Gram-negative bacterium that infects approximately 106 million people annually, making it the most common cause of bacterial sexually transmitted infection worldwide. These staggering statistics reflect the substantial lack of scientific understanding regarding the pathogen’s developmental cycle, creating a huge obstacle for effective vaccine development. So far, it is known that after binding and host cell entry, Chlamydia replicates within a vacuole called an inclusion. Once replication is complete, exit occurs by two different pathways, one of which is the lysis pathway. This pathway specifically involves the release of free, infectious bacteria by inclusion and host cell rupture. Results from previous experiments strongly indicate that cysteine proteases serve a crucial role in inclusion membrane degradation central to the lysis pathway late in the developmental cycle (about 48 hours post-infection). My primary research goal is to apply a novel labeling approach called activity-based protein profiling (ABPP) to determine the identity of the specific chlamydial cysteine proteases involved as a critical first step towards determining the molecular mechanisms of the chlamydial lysis exit strategy. ABPP utilizes a specific probe consisting of a reactive group, which covalently binds to the active site of the protease, and a tag, which is usually a fluorophore or affinity label. After extensive optimization of probe concentrations, I exploited this beneficial specificity to isolate successfully labeled cysteine proteases from Chlamydia-infected cells and assess proper probe binding via SDS-PAGE gels. Following isolation and purification, samples will be sent to collaborator Dr. Aaron Wright at Pacific Northwest National Laboratory for mass spectrometry analysis. Successful identification of these proteases will confirm which specific proteases are essential to lysis, enhancing our understanding the Chlamydia lysis pathway and allowing for evaluation of future vaccine targets to reduce the global burden of Chlamydia transmission.
 

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

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

Aging is characterized by time-dependent deterioration of cellular and physiological functions. Due to the numerous challenges and limitations of studying aging in humans, model organisms are used to further extend our understanding of basic mechanisms of aging. The Kaeberlein laboratory uses the single celled budding yeast Saccharomyces cerevisiae as one such model. Advantages of this model organism include the ability to measure the lifespan of great numbers of organisms under various environmental conditions. One method of measuring a yeast cell’s longevity is by assaying its replicative lifespan (RLS). The RLS model refers to the number of daughter cells that can be produced by a mother cell before senescence. The number of budded daughters can be determined by micro-dissection with fiber optic needles from mother cells after each round of incubation. This process is repeated until mother cells no longer generate daughters. Approximately 600 mother cells are assessed weekly and incubation cycles last one month. Yeast lifespan can be manipulated through genetic changes, altering media content, addition of pharmacological agents, and change of temperature. Data collected is compared to control groups and to past and expected results. These results clarify how senescence is regulated. RLS is thought to be a better representation of senescence in mitotically active cells, like certain tissues in multicellular organisms. By analyzing thousands of cells, a variety of genes and environmental conditions that impact aging have been identified. These genes and interventions can be further studied and applied to other organisms. Studying budding yeast enhances our understanding of the molecular basis of aging.​

Since the beginning of the 21st century, as online access is increasingly available all over the world, we have seen the rise of social media platforms, where people can virtually interact and share information. Twitter is one popular outlet where users post short messages expressing their opinions and attitudes, share information, and respond to posted content. Recently, with the deaths of unarmed black men around the United States, Twitter and other social media have become places in which a racial discourse takes place. These discussions have been accompanied by the rise of two different ideologies: Black Lives Matter; and All Lives Matter. This research observes online communication surrounding three Twitter hashtags – #BlackLivesMatter, #AllLivesMatter, and #BlackHistoryMonth– in order to compare the similarities and differences within these groups when users talk about race in an online social setting. The data from this study is analyzed to examine both the demographics of participating Twitter users utilizing these hashtags as well as the discourse between these groups. Data was collected for the 72 hours period from February 24th – 26th, 2016. Although social media has received increased attention as a platform for racial discourse, little research has examined the social groups participating in these emerging conversations.

In the past few years waterborne pathogens have caused many outbreaks of disease after natural disasters. Water flux is influenced by climate change, so it will also have an effect on the epidemiology of these diseases. This means that diseases that are endemic in certain regions might migrate to other regions as the climate changes. This literature review focused on research pertinent to constructing a sanitation system that would, after a natural disaster, be feasibly built by the affected population. We explored existing sanitation system designs which can be easily built by the lay population in a limited time frame, without the need for outside help. Such a sanitation system would prevent waterborne diseases that are known to cause disease outbreaks, and be sturdy enough to withstand other catastrophes. We also presented other generalized models for sanitation systems which may be transposed in any other region with similar topography and climate. It was found that climate change will become increasingly devastating to populations around the world. Sanitation systems, while a better investment, would require more infrastructures which are not always possible in developing countries. It was determined that if an affected population is to avoid outbreaks, arborloos and urine diverting toilets were the simplest solutions, both economically and with regard to ease of construction, especially in developing countries. This literature review used several disciplinary lenses including economics, engineering, microbiology, health, geography, climate change, and finally the epidemiological lens. This project explored research in academic journals and other professional publications with keywords such as “sanitation system” and “waterborne infection.”

Zebrafish have recently emerged as a valuable model of human osteogenesis and bone remodeling pathways. However, the relationship between those pathways and energy metabolism has yet to be determined. In this experiment, energy metabolism was studied using three different compounds: botulinum toxin (botox), rhodamine 123, and cyclopamine. Botulinum toxin, a neurotoxin produced by the bacteria Clostridium botulinum, inhibits synaptic release of acetylcholine and is known to repress zebrafish fin regeneration and decrease bone mineralization levels. Rhodamine 123, a common chemical dye, serves as an indicator of mitochondrial activity. And cyclopamine, a steroidal alkaloid, inhibits the Sonic Hedgehog Pathway that is involved in proper development. After dosing zebrafish in these chemicals, NADH levels in the regenerating fin were quantified, serving as an indicator of energy metabolism specifically in the form of ATP. Comparing relative NADH levels across regeneration conditions allowed us to determine if each pathway that was inhibited had any direct effect on the production or use of energy as regeneration proceeded. In each experiment, fluorescent microscopy was used to quantify the level of NADH in the fin, measuring the auto-fluorescence of biological molecules (NADH) as they absorb and emit light at distinct wavelengths. Rhodamine 123 successfully allowed for the visualization of NADH under fluorescent microscopy, supporting its use as a marker of metabolism for future experiments. Cyclopamine did not cause any significant changes in NADH levels from the control, suggesting that the Sonic Hedgehog Pathway is not involved in metabolism in the regenerate. Finally, botox showed significantly higher levels of NADH in the first two days following injection, and higher levels in the first five days following amputation. These results suggest a relationship between metabolic levels and regeneration conditions specifically through Botulinum toxin, hinting at a possible relationship between the acetylcholine neurotransmitter system and proper energy metabolism.

Cone-beam computed tomography (CBCT) has been one of the newest innovative technologies introduced in the field of dentistry, and its role in diagnostic imaging has been greatly beneficial for patients in need of various treatment. The goal of this study is to utilize CBCT to investigate the effects of experimental periodontitis on molar roots and alveolar bone in a pig model by taking quantitative measurements from 3D models. Four normal pigs and eight with experimental periodontitis pigs were included in this study. Experimental periodontitis was induced by periodic inoculation with 4 types of periodontal bacteria, along with the suture ligature around the upper third deciduous molar for 8 weeks. Two sets of CBCT were taken for each experimental pig before and after the induction of periodontitis, but one set for control pigs. A custom-made seat was placed on the CBCT chair for CBCT scanning while the pig was intubated with 3% isoflurane. Obtained CBCT images were then used to create 3D models using the software ITK-Snap with the aid of Invivo5. Models were standardized by the region of interest selected for segmentation. Volumetric measurements were taken in the software. The volumes of molar roots and alveolar bone were then compared in the experimental and control pigs before and after the induction of periodontitis. The expected results should show significant volumetric reduction in the alveolar bone of the experimental pigs as compared with controls. Further in the project, the expected results should show that there is significant reduction in the volume of the roots as well. Understanding the use of CBCT and its role in 3D modeling and quantitative measurement will contribute cutting-edge treatment planning and diagnostic methodologies for all dental practitioners. 

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. 

 There have been major advancements in the use of Virtual Reality (VR) technologies in military, medical, and educational applications. However, it is not well understood how representations of spatial memory are encoded by the bi-modal, visual and audio sensory stimulation inherent to VR interactions. Previous studies have identified the hippocampus and entorhinal cortex as structures involved in the formation of spatial memory. Because Alzheimer’s pathology affects these medial temporal structures and is characterized by deficits in memory, spatiotemporal reasoning, and route finding, better understanding of spatial representations in medial temporal areas would help create VR with potentially therapeutic effects in patients with memory deficits. Using VR, non-human primates will utilize a joystick to move a first-person avatar and perform a foraging task wherein they must collect virtual objects to obtain food rewards. We hypothesize that monkeys will use a demonstrable strategy to optimize behavior in our VR task and propose experiments and computational methods to identify unique strategies wherein memory and route planning are being used. Preliminary results indicate that the three monkeys fully trained on this task utilize unique strategies to obtain food rewards. Furthermore, the evolution of individual strategies over the training period suggests that memory and other factors may play a role in route planning. Corresponding and ongoing research is aimed at identifying neural representations of complex spaces and encoded memory and planning elicited by our task.

Rapamycin, an FDA approved drug that inhibits the mTOR pathway, is known to prolong lifespan in yeast, invertebrates, and vertebrates. In aged mice, reports of lifespan extension had been demonstrated using continuous treatment. More recently, our lab showed that a shorter three-month transient treatment of rapamycin sufficiently extends lifespan. However, some questions remain. Is there an optimal rapamycin dosage and treatment length that results in a robust effect on healthspan and lifespan? We had noted a sex-specific increase in cancer incidence and no lifespan extension in females that received daily intraperitoneal (IP) injections of rapamycin, the same regimen that robustly extended lifespan in male mice. Currently, we are testing the effects of daily, once weekly, and twice weekly rapamycin injections in female mice. We have already uncovered an increased incidence of eye inflammation in the animals that received daily drug treatment compared to all the other cohorts. Interestingly, this increase in eye inflammation also occurred in mice that were fed high-dose rapamycin. These data suggest that high dosages present unwanted side effects in female mice and it is crucial to find an optimal treatment regimen to minimize the undesirable effects of rapamycin. Additional assays to measure physiological parameters such as body fat mass, body temperature, muscle function, cognitive function, and lifespan will be done in our study. We hope to reveal the proper drug dose and intervention frequency that provides the best outcome, enhancing longevity while minimizing or even abolishing the detrimental outcomes associated with rapamycin.

Nearly all psychiatry residents in the United States take the Psychiatry Resident-In-Training Examination (PRITE).  The PRITE is a 300-question examination administered annually to psychiatry residents that covers a variety of important topics related to general psychiatry training. After each test administration, residency programs receive a detailed computer analysis of the test performance of their residents. The computer-generated analysis provides details for comparing residents across different training programs with a similar level of training. In recent years, the University of Washington Psychiatry Residency Program has consistently ranked below the 50th percentile on the PRITE in the area of forensic psychiatry across all years of residency training. In this study, the authors reviewed PRITE questions over multiple years that were categorized as focusing on forensic psychiatry. Each question was then coded for a specific sub-topic within forensic psychiatry. This research reveals the sub-topics identified as important in the PRITE. The authors, using the data collected, also identify areas in need of further instruction or emphasis in the psychiatry residency didactic curriculum and provide recommendations for psychiatry training to cover the identified sub-topics. 

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

Hydrostatic pressure is important to many vascular processes, including endothelial activation (inflammation), vasodilation, vasoconstriction and angiogenesis (branching of new blood vessels from existing ones). The problem of pressure regulation in in vitro studies is usually solved by syringe pump based systems. Harvard Apparatus provides a catalogue of “Constant Pressure Syringe Pumps,” the cheapest of which costs $4500. This is prohibitively expensive for many applications. Thus, there is a need to create an affordable device that can reliably regulate hydrostatic pressure. I present a syringe pump based system that maintains liquid pressure within a flow chamber at a fraction of the cost of commercially available devices. My pump was designed from open-source and off the shelf components, including a pressure transducer and Arduino Microcontroller, at a total cost of ~$350. I have tested the pump’s ability to maintain constant liquid pressure across a high-impedance microfluidic system and have shown that it maintains pressure at a user-defined set point between 0 and 70 cmH2O of gauge pressure. This device illustrates the power of open-source software and hardware, 3D-printing and rapid prototyping to allow labs to design customized hardware to meet specific research needs at a reasonable price. Once completed, I will use it to study the pressure dependence of angiogenesis and vasculogenesis (formation of new blood vessels by endothelial cells embedded in interstitium). We will vary hydrostatic pressure to optimize and document blood vessel network formation. This is relevant to studying embryonic development and tumor vascularization and to engineering grafts to repair the damage from myocardial infarction (heart attack). Other possible applications include eliminating the confounding variable of pressure variation in Doppler echocardiography or in studies of endothelial cell response to variation in microvessel geometries.

Water chemistry and heavy metal data were collected from 2009 to summer 2015 by Ocean Research College Academy (ORCA) students and we continued sampling in Possession Sound in fall of 2015 to 2016. In June of 2015, the relocation of the Mukilteo Ferry Terminal began with the removal of the abandoned Tank Farm pier, at the Mukilteo location, eliminating creosote soaked pilings. It was hypothesized that the heavy metal concentrations in the sediments, as well as dissolved oxygen (DO) and pH levels, would differ both temporally, from before the removal of the pier in June of 2015 to January 2016, and spatially, between the Mukilteo site and Mount Baker Terminal (MBT) to the north. Benthic sediments were sampled offshore with a Ponar grab and analyzed by the Everett Environmental Laboratory for heavy metal concentration. DO and pH were sampled with a YSI-650. Copper, lead and zinc showed positive correlations, with an increase in the amount of heavy metals at Mukilteo from January 2009 to June 2015. Copper concentration increased by 503.31%, zinc concentration increased 573.33%, and lead concentration increased 437.20%. Additionally, amounts of heavy metals present in the sediment, regardless of temporal correlation, were consistently higher in samples from Mukilteo than samples from MBT, possibly due to proximity to the construction project. There was on average 154.27% more arsenic, 282.69% more mercury, 210.86% more cadmium, 157.95% more copper, 105.60% more lead, and 130.15% more zinc at Mukilteo. There appeared to be no changes to water chemistry in terms of DO and pH. Additionally, three other heavy metals, arsenic, mercury and cadmium, showed no temporal correlation. Further research on the bioaccumulation of heavy metals by marine organisms nearby would offer an intriguing look at the biological effects.
 

Phytoliths are microscopic silica bodies that are produced in the tissues of many vascular plants. Over the course of their lifetimes, certain plant cells become filled or encrusted with silica that the plants have absorbed from soil. Grasses produce a diverse range of phytolith shapes that distinguish them from phytoliths produced by other plants. We hypothesized that it would be possible to distinguish certain grass clades by the unique phytolith shapes they produce and the relative abundances of these shapes. We sampled a range of grass species across the grass-family phylogeny, including from grasses that diverged early on in the evolution of this clade. We isolated phytoliths from dried grass material and created permanent slides that were examined using a light microscope. For each grass species, we counted and categorized all phytolith shapes observed and calculated the relative abundance of each shape. These counts allowed us to identify grass clades based on the relative abundances of phytolith shapes they produced. Our results are a reference collection of phytoliths found in modern grasses that can be used as a key for identifying grasses in the fossil record. When applied to deep-time vegetation studies, this information can help identify grasses from ancient ecosystems. Because the spatial distribution of grass species vary depending on environmental factors such as temperature and humidity, our work can also help provide past climatic and environmental information. Studying grasses is important because they are an important part of Earth’s ecosystems and are a major food crop for humans.

The human Tumor Suppressing Subtransferable Candidate 1 (TSSC1) gene was first discovered in 1997 as a gene whose likely location was within a chromosomal region that suppressed tumor growth. A recent study reported that decreased TSSC1 gene expression results in increased metastasis of breast cancer cells to bone. However, the underlying mechanism by which the TSSC1 protein acts in cancer cells remains unknown. Interestingly, TSSC1 is a highly conserved protein among eukaryotes. We are using Drosophila melanogaster as a model organism to define the normal function of TSSC1. Previously, our lab showed that the Drosophila protein, dTSSC1, localizes near Trans-Golgi Network (TGN), the region of the Golgi that sorts and packages membrane and secreted proteins into vesicles for transport to post-Golgi destinations. We have also isolated two mutations in dTSSC1 and observed that they cause defective formation of the acrosome, a Golgi-derived organelle that is localized to the apical tip of mature sperm and is required for fertilization. Based on these observations, we propose that dTSSC1 acts in spermatids to regulate acrosomal protein and vesicular trafficking. We are expressing tagged membrane proteins to ask whether dTSSC1 is required specifically for trafficking of acrosomal proteins or if it has a more general impact on membrane protein trafficking. These studies use expression in the male germ line. Notably, dTSSC1 is expressed in many tissue types, similar to its counterpart in humans. Therefore, we are also investigating whether dTSSC1 mutations have effects on protein trafficking in somatic cells. Our results should define the normal cellular role of dTSSC1 in Drosophila and may also provide insight into the role of the human protein in normal and cancer cells.

The budding yeast, Saccharomyces cerevisiae, has been an invaluable model organism in the study of aging. Yeast cells divide asymmetrically. During division, the “mother” cell retains any accumulated cellular damage and produces a rejuvenated “daughter” cell. Thus, each yeast cell has a finite replicative lifespan defined by the number of daughter cells it produces before senescence. The historical belief in the field of aging has been that the asymmetrical inheritance of damage is absolute; until the last few divisions of a mother cell’s lifespan, daughters are born with a full lifespan potential, completely independent of the mother’s remaining lifespan. In this project we measure the replicative lifespans of daughter cells that budded off from mothers at different ages. We found a loss of daughter lifespan potential and an increase in mother-daughter remaining lifespan correlation in middle-aged mother cells. By tracking the granddaughter lifespans of aged mother cells, we find that this effect is compounded across generations. The implications of this research are to improve our understanding of yeast replication so as to better interpret the data gained from experiments that, as an example, use yeast aging as a model for human cell aging.

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.

During mammalian neural development, there are critical periods in which the brain is most plastic. These periods of plasticity are defined by the growth of neurons and formation of new synapses. Perineuronal nets (PNs) are specialized proteoglycan structures of the extracellular matrices that surround neurons in many parts of the brain. Their formation is thought to be triggered by appropriate sensory experience and to mark the end of plasticity by stabilizing the established synaptic connections. Density of PNs in mammalian brains varies across regions of the brain, and with age, but there have been few studies of the central auditory system. By studying the postnatal development of PNs in the central auditory system of the big brown bat, Eptesicus fuscus, a species in which the auditory pathways are exceptionally large and highly differentiated, we aim to increase our understanding of critical periods in the auditory centers of the brain. To visualize the distribution of PNs over the course of maturation, we used immunohistochemistry to label PNs and the associated cell bodies. More specifically, we used Wisteria floribunda lectin to label PNs, and parvalbumin, a calcium binding protein, to label neuron cell bodies. In counting parvalbumin-labeled cells and cells surrounded by PNs we hope to determine the patterns and trends of these critical periods. Our results suggest that there are distinct differences in the amount of area that PNs occupy and the number of cells which are netted across different ages. Each auditory nucleus has shown a unique pattern of development for PN staining. Our findings on the plasticity of the development of the auditory pathway may help further future studies of sensory systems.

Vessels of different organs have heterogeneous permeability to serve distinct physiological functions. Differences in basal vascular permeability may result from heterogeneity in the endothelial cells that line the vessel walls, which are influenced by many factors—including differences in the complexity of cell-cell junctions and the expression of various diaphragms that span the cell body. In addition, many diseased states are often associated with elevated levels of permeability, including viral hemorrhagic fever and tumor-induced angiogenesis. To understand such fundamental heterogeneity of the blood vessels and further investigate the change of vascular structure and function in disease scenarios, we characterized the permeability of endothelial cells harvested from different areas of the body. Human primary cells—including endothelial cells from various organs and epithelial cells from the proximal tubules of the kidney (PTECs)—were seeded on gelatin-coated transwells. We measured transendothelial electrical resistance (TEER) using a Millicell ERS Voltohmmeter, and determined solute permeability by tracking the perfusion of fluorescent dextran across the cell monolayer over time. Immunostaining was performed to observe monolayer formation, while transmission electron microscopy (TEM) was utilized to observe ultrastructure. Preliminary TEM images demonstrate distinct morphological differences between endothelial cell types, specifically in the complexity of cell-cell junctions. Investigations into the impact of these morphological differences on vascular permeability are ongoing, and a definitive conclusion will be made upon the study’s completion.

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.

There is no known therapy for the loss of cardiac function associated with aging. Aging has been long associated with oxidative damage from reactive oxygen species (ROS), which are mostly produced at the mitochondria. In mammalian cells, catalase is an enzyme located in peroxisomes that breaks down damaging hydrogen peroxide. Methods that target catalase to the mitochondria, where most of the oxidative damage occurs, have been shown to increase life span and attenuate age-related pathologies in mice. Adeno-associated virus (AAV) has been used for gene transfer in mice and humans for decades with no adverse effects. We are investigating if the presence of AAV-mCAT leads to an improvement in cardiac function, the percentage of cells in each tissue that are expressing AAV-mCAT at the time of improvement in function, and if mCAT is expressed in other tissues aside from the heart. My role in particular is to determine the expression levels of catalase in various tissues, which could affect cardiac function. We present evidence of improvement of diastolic function by longitudinal echocardiography, and expression of the mitochondrial-targeted catalase gene (MCAT) in various tissues, after injection of AAV expressing MCAT (AAV9-MCAT) into aged female mice. This pilot project shows that the AAV9-MCAT has the potential to be an eventual therapy for aging-related diastolic dysfunction, for which there is presently no effective therapy. Thus, AAV9-MCAT is a novel and promising method of reversing the effects of aging on cardiac health.

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

Sources of heavy metals in the Snohomish River estuary system are influenced by both point and nonpoint sources; therefore, areas near the Snohomish River estuary are expected to have higher concentrations of heavy metals in the sediment during periods of high river discharge. At the Ocean Research College Academy, students develop research based studies through hands-on data collection in Possession Sound (P.S.). Our study focused on the effects of non-point sources on heavy metal deposits in P.S., both spatially and temporally. In consideration of the recent removal of the oil dock at Mukilteo, we hypothesized that higher levels of mercury and copper would be present at Mount Baker Terminal (MBT). Collection of arsenic and copper data involved in our group’s research were taken by previous cohorts at three sites in P.S.: Buoy, located closest to the mouth of the Snohomish River; Dolphin 1 (DOL), farther from shore near Hat Island and MBT, adjacent to Mukilteo. A Ponar type sediment grab was used to retrieve sediment from the various locations to be analyzed for heavy metal concentration at the Everett Environmental Laboratory. From 2012-2015, Buoy had higher heavy metal content than the other two stations; an average of 5.5 mg/L arsenic and 15.5 mg/L copper. Furthermore, Buoy showed the strongest seasonal correlations in 2014; DOL and MBT did not. The highest concentrations of heavy metals occurred during winter; an average of 6.5 mg/L arsenic and 16.1 mg/L copper. Buoy is nearest to the mouth of the Snohomish River; therefore, it is possible that river runoff heavily influenced arsenic and copper deposits at this station. Increased levels of heavy metals can be toxic for marine life and humans, which poses health concerns in environments with high concentrations. For future studies, the effects of heavy metal contamination on marine plants will be investigated.
 

Global climate change causes weather patterns to be increasingly unpredictable, which has a major impact on plant productivity. Humans are dependent on the agricultural economy and loss of crop productivity would be devastating. Due to their sessile nature, plants are unable to escape environmental stresses and must be able to acclimate to rapidly changing conditions. Arabidopsis thaliana is an important plant model organism, which has around 30,000 genes (about as many as humans). Arabidopsis genes have been identified, but not fully characterized, which is why it is the optimal model organism to work with. There are also many genomic tools available in the reference organism Arabidopsis. One such tool is RNA interference. Using small RNAs, we knockdown an accumulation of gene products and screen to find which genes play important roles in that particular function – drought resistance, for example. In our Arabidopsis RNAi screen, we chose to use trans-acting small-interfering RNAs (tasiRNAs) for multiple reasons. TasiRNAs have a lower chance of off-target transcript silencing than other siRNAs. They are naturally occurring in plants and have a low chance of transgene silencing. Lastly, multiple tasiRNAs can be incorporated into the library at different positions at varying concentrations. Our RNAi screen includes tasiRNAs that target every gene in the Arabidopsis genome, which allows for easy identification of causative changes and the ability to screen for multiple phenotypes with one library. These screens allow us to identify essential genes and other complex interacting gene systems important to plants under various environmental stresses. In the future, this technology can be developed on a bigger scale with crops.

The purpose of this project was to record zooplankton abundance, distribution and diversity at two different study sites in the SJC (San Juan Channel) during the autumn of 2015, one with strong oceanic influence and one more estuarine, while continuing an annual, long-running dataset. Previous projects have focused on factors associated with distribution patterns, such as tides and tidal current speed. In this project, possible relationships between dissolved oxygen and the density of certain taxa were investigated using linear regression analysis both within the autumn 2015 dataset and over preceding years of data collection (2007-2015). Intra-seasonal temporal changes in abundance and distribution were observed during autumn 2015, some of which were consistent with that found during other years. While diversity was consistent across the years, the specific community assemblages found at the two sites varied. Dissolved oxygen was seen as a factor co-varying with abundance of certain taxa. If conditions are suboptimal for plankton survival (oxygen levels, nutrients, temperature) it may result in negative ecological consequences for animals farther up the food chain (Frederiksen, 2006). Information on plankton abundance as it relates to the changing oceans will be valuable in the years to come. In the SJC Caridean shrimp and gastropod larvae had positive relationships (p=0.008 and p=0.014) and polychaete trochophores had a negative relationship (p=0.018). However, these relationships did not all hold across the years. 

 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.

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.

Possession Sound is located within Puget Sound of western Washington. Students at the Ocean Research College Academy (ORCA), a dual enrollment program in conjunction with Everett Community College, have collected environmental data in Possession Sound such as pH, and dissolved oxygen (DO) concentrations since 2004. Our group participated in this academic year, 2015-2016. Based on seasonal trends, it was hypothesized that pH of Possession Sound would be higher during summer, due to usage of CO₂ for photosynthesis, and lower during winter due to lack of photosynthesis. ORCA students collected water chemistry data at the sample site, Mount Baker Terminal, using a YSI 650, and analyzed the monthly mean value from 2010-2015. These monthly mean values showed that pH levels were highest in late spring and early summer months. These data of summer seasons’ correlation to higher pH levels supports our conclusion that less direct sunlight in winter season is linked with a higher acidity and lower pH while more direct sunlight provided in summer season is linked with lower acidity and higher pH levels. The pH levels were lowest during winter, January and February, at a pH of 6.81. The average rose in the spring months of March, April, and May to 7.72 while the average pH peaked during the summer months of June, July, and August was at a high of 7.97. However, it was shown that late spring had consistently higher pH levels. DO levels followed similar trends when investigating those levels. The average DO levels during summer months was 11.4, while the lowest was Fall at 9.88 instead of in expected winter. Although further evidence is needed to connect the fluctuations in DO and chlorophyll via biological processes to these observations of pH. Once this investigation is done, there will be a better understanding of the pH parameters marine organisms can withstand in the Possesion Sound.

This research project focuses on the study of the mitochondrial Cytochrome -c-Oxidase 1 gene (MT-CO1) in salmon species of the Pacific Northwest. The MT-CO1 gene encodes for a protein located in most eukaryotic cells called Cytochrome-c-Oxidase 1. This protein is located in mitochondria and plays an extremely important role in cellular metabolism. The MT-CO1 gene has become one of the standard sequences for a technique called DNA Barcoding. The idea of this technique is to compile MT-CO1 gene sequences in a database that allows researchers to accurately identify species by using computer software, such as Mega Software. It also allows them to analyze the subtle differences between them from a small tissue sample available. Moreover, it helps taxonomists to accurately identify new species and track changes in a given population of organisms. In this project, we used the MT-CO1 Gene as a barcode to identify different samples of the Pacific Northwest salmon which were purchased from different local stores to find out whether they actually belong to Pacific Northwest salmon species. The laboratory techniques and methods used in this research project included polymerase chain reaction (PCR), gel electrophoresis, DNA imaging and gene sequencing. Our results indicated the expression of the identical MT-CO1 gene within the northwest salmon species. Gel electrophoresis confirms the successful replication of 660 base pair MT-CO1 gene. Further analysis of the sequences indicates that the tested salmon samples are of the species Oncorhynchus: nerka, tsawytscha, keta and kisutch. These species were confirmed by using alignment search tools, such as BLASTN and MEGA6. DNA barcoding can be used as a tool to track evolutionary changes, miss-labelled food products and identification of pathogen bacteria allowing to accurately identify and treat the diseases caused by these agents.

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.

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.

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.

At full capacity, the University of Washington-Seattle Campus plays host to nearly thirty thousand undergraduates and fourteen thousand graduate and professional students. UW-Seattle provides an enormous amount of information to help students navigate over one hundred and eighty majors and degree programs. Lack of standardization and the diaspora of information across many department websites, however, makes it very difficult for students to effectively discover and plan course work, especially over their entire undergraduate or graduate career at the university. The Coursector Project seeks to address this disparity between the amount of information available for students and unfortunately complex nature of its structure: much of the information about courses and offerings is simply in text, with no visual aids or recommendation engines for students. By building web-ready data visualizations about course prerequisite relationships, the project allows students to see links between courses, majors, and areas of their interest. These interactive visualizations are made up of data scraped from the UW course catalog. Beyond using it for practical course planning purposes, students can also simply mess with the visualizations for fun, discovering new classes and course pathways they had not previously thought of. Furthermore, because of the interwoven nature of many interdisciplinary offerings at the University of Washington, many departments rely on one another for prerequisite courses and instruction. The data analysis and visualizations performed by the Coursector Project will also allow school administrators to address so called choke point classes: those which unlock access to many upper level classes in any given department. The data is all there. The Coursector Project helps students and staff alike make sense of it.

M. tuberculosis (TB) infects one third of the global population and causes 1.5 million deaths annually. Most of the disease burden occurs in low-income countries. Although TB is curable, the lack of proper diagnostic tools in developing areas restricts treatment and propagates the spread of this highly contagious airborne disease. Currently, the gold standard for pulmonary TB detection is a sputum culture, which is not only time intensive, invasive, and requires a clinical setting with laboratory analysis, but also increases risk of transmission and is difficult to obtain. In collaboration with Dr. James Lai of UW Bioengineering and Dr. David Horne of UW Global Health, we are developing a noninvasive and highly sensitive TB test for point-of-care settings. We propose a sequence specific capture modality of TB transrenal DNA (trDNA) in easily collected urine samples. Recent literature has shown the ability to detect TB trDNA in patient urine samples, but the current methods target long trDNA fragments which are unlikely to pass through the renal system and lack both sensitivity and specificity. As a result from specific DNA capture and targeting short DNA fragments, the proposed protocol allows detection of TB trDNA fragments from urine at a thousand-fold lower concentration.

From blood vessels to the small intestine to the spinal cord, tubes are an essential part of nearly all living organisms. The study of the formation of biological tubes, called tubulogenesis, is therefore indispensible in the understanding of the developmental pathways that, when impaired, cause many of the birth defects that afflict infants today. Our lab uses the fruit fly Drosophila melanogaster as a model organism to study these complex pathways. Recently, we discovered that a family of genes known as Imaginal Disc Growth Factors (IDGFs) are linked to tubulogenesis in fruit flies. However, the mechanisms by which these genes act, and their involvement in the tubulogenesis pathway, remain unclear. My project investigates the function of a specific IDGF, the gene CG5210, using a powerful new method for deleting genes known as the CRISPR/Cas9 system. With this technique, I created flies lacking the CG5210 gene by first designing highly specific plasmid vectors, which encoded RNAs that bound to the target DNA. When injected into fly embryos, these RNAs directed the Cas9 protein to cleave the DNA on either side of CG5210. Cas9 then replaced the gene with DNA that encodes a red fluorescent protein expressed in the eyes of the fly. The fluorescent red eyes served as a marker for a successful deletion in my later experiments. If my initial hypothesis is correct, I expect to see unusual phenotypes in these mutant flies that correlate with tube formation or growth pathways. From there, the next phase of my research will include further exploration of this genetic pathway, including determining what other genes and pathways interact with CG5210 to cause similar mutant phenotypes. This information will be an important contribution to our understanding of tubulogenesis and provide new insight into disease pathways that cause defects such as spina bifida in newborns.

 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.

Cytomegalovirus (CMV) infection is a common chronic viral infection that can cause significant complications in bone marrow transplant (BMT) recipients and other immunocompromised people. Using stored serum from BMT patients who were CMV negative but had a CMV positive donor, we have identified a group of patients who appear to have had self-limited infection, where DNA from CMV was found in their serum then resolved without therapy. It is thought that donor-derived, entry specific neutralizing antibodies (NAbs) bind to the virus and prevent entry into cells and infection. In this study, we measured the CMV NAb activity in patients with self-limited infection and compared this to similar patients who developed chronic infection. Specifically, serially diluted patient sera was incubated with a standard quantity of CMV, and the relative decrease of cellular infection was assessed. Our CMV strain contains a green fluorescent protein (GFP) gene that is expressed by infected cells. The virus-serum mixture was incubated with human epithelial cells for one hour, and then washed away. On day 7, we measured the fluorescence emitted by infected cells and constructed a standard curve to compare the fluorescence of the cells with sera to those without virus and those without serum. We calculated the serum concentration required to neutralize 50% of the virus (IC-50). Because NAbs prevent CMV entry into cells, those with self-limited infection may have greater NAb activity (i.e. IC-50) than patients who develop infection. We have measured the IC-50 in serum from 7 healthy donors. These preliminary data indicated that people with high NAb activity have a log₂IC-50 of 9-11, where CMV negative people have a log₂IC-50 <3. We are now measuring the NAb activity of patient samples. If NAb activity is important for prevention of infection, this may aid development of CMV vaccines and therapeutics.

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.

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.

Only a small portion of the market sells printers that are compatible with Google cloud print. In the case where a customer purchases a printer that is not compatible with Google cloud print, the printer can only be used through a wireless, wired, or USB connection. With the aim of allowing users to print from anywhere and at anytime, our project intends to design a low-cost and user friendly device that is capable of converting a regular printer into a cloud printer. The project is being developed on a small portable Linux machine (raspberry pi) using a 16GB SD card and a small Wi-Fi adapter. The raspberry pi is initially configured as an access point, enabling the user to connect wirelessly to the device. Once connected, the user then navigates to a web page hosted on the device accessing a user friendly interface to set up the printer. After the initial setup has been completed, the raspberry pi will then turn into a Wi-Fi client which allows itself to receive instructions through the Internet. The device will then interface with the printer through a USB cable. The users then can log in to their Google cloud print account on any device from any place at any time to print on the registered printer. This device, once developed, would provide a low cost and user friendly alternative to the existing expensive cloud-ready printers and allow users to take advantage of Google cloud print.

In the United States, kidney cancer has consistently been in the top 10 most prevalent cancers with 62,700 new cases and 14,240 fatalities each year. Renal cell carcinoma (RCC) derives from the epithelium of the kidney’s proximal convoluted tubule, and comprises the overwhelming majority of all kidney cancers. A critical step in the formation and spread of all cancers, including RCC, is angiogenesis: the formation of new blood vessels. Cancerous cells secrete numerous signals to recruit endothelial cells to form new blood vessels; these vessels provide primary tumors with oxygen, nutrients, and a path to metastasize throughout the body. While cell and animal models have been utilized to study angiogenesis and test anti-angiogenesis drugs in RCC, successes fail to translate in clinical human studies. Because of the added complexity of the human body, a better model to represent human RCC is required to study angiogenesis in vitro. In order to address this need, we are developing a tissue engineered vascularized RCC microphysiological 3D system. Microfluidic devices will be utilized to recapitulate the angiogenic interaction between blood vessels and RCC cells. Sprouting from the endothelial-lined channel, simulating kidney microvasculature, toward collagen suspended RCC cells will be analyzed to determine the efficacy of our device. In addition, we have unprecedented access to normal and cancerous tissue sample pairs from the same kidney cancer patient at the UW Medical Center. Cultures from the tissue sample pairs will be utilized to validate the device and display differences in angiogenesis between RCC and normal kidney tissue. Tissue pairs were also utilized in qRT-PCR to determine up regulated pro-angiogenesis genes in RCC. Commercial drugs along with those currently in development or clinical trials will be administered to our device to determine their efficacy in preventing angiogenesis in RCC.

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

 Eukaryotic cells contain membrane-bound organelles that serve to compartmentalize certain cellular functions. Different organelles contain optimal pH levels necessary for the organelle function. The vacuolar ATPase (V-ATPase) is a highly evolutionarily conserved proton pump that is responsible for acidification of many organelles. This proton pump consists of various protein subunits and loss of any these subunits results in disruption of the entire protein complex, which in return is not compatible with life for most organisms. Within certain conditions, S.cerevisiae (yeast) is able to survive in the absence of a functional V-ATPase, which makes it an ideal model organism to study V-ATPase function. In yeast, the proteins that comprise the V-ATPase are encoded for by vacuolar membrane ATPase (VMA) genes. Loss of any individual VMA gene results in pleiotropic phenotypes including an inability to grow on nonfermentable carbon sources and shortened replicative lifespan. In order to understand more about how the V-ATPase functions, we have performed multiple screens to identify genes that when overexpressed or mutated can suppress the respiratory phenotype of VMA mutants. Our results implicate iron homeostasis as a process that is crucially disturbed when the V-ATPase is disrupted.

Long term evolutionary experiments involve continuous observation of populations of organisms in controlled environments. Continuous culture devices allow cultures to grow for extended over many generations. The Chemostat is a device that can maintain a desired growth rate and cell density by controlled delivery of nutrition for the cells. Another example is a Turbidostat, which can maintain desired cell density without affecting growth rates based on the optical measurements of population density. Such devices are usually expensive and unsatisfactory for traditional labs. The Klavins lab from the University of Washington developed low-cost, multiplexed Turbidostat using three-dimensionally printed components. We have made improvements for running the system as a Chemostat. Modifications included improved python based software, integration of new customized parts with commercial parts led to increase in reliability. These improvements led to consistent flow rates of nutrition within 10% variation. These modifications gave the original Turbidostat design adequate operations of a Chemostat for critical experiments, which allowed for more consistent growth rates. This type of system allows for versatility in observing growth of populations through a Turbidostat and a Chemostat while maintaining minimal cost.

Previous research has found that risky sexual behavior, including not using a condom, is associated with alcohol use prior to the sexual experience. However, little is known about whether these relations differ by prototype favorability (defined as the perceived favorability of the typical person who engages in a risk behavior) of individuals who do not use condoms. The present study investigated whether prototype favorability moderates the relationship between prior alcohol consumption and condom use during sex. We hypothesized that prior alcohol consumption is positively associated with not using a condom. Additionally, we hypothesized that this association is stronger for those who have higher prototype favorability for individuals who do not use condoms during sex. To test these hypotheses, the current study (n=1002) used data from a national sample of young adults, ages 18-20, who completed a one-time online survey about health and risk behaviors, including sexual behavior and alcohol use. Participants were asked to report the frequency that they engaged in any type of sex after or while drinking alcohol during the past 3 months and the number of times they used a condom when having sex after or while drinking. Participants were also asked to report on a scale from 1 (not at all) to 7 (extremely) how much the following words: "smart", "popular", "mature", "careless", "attractive", and "risky", describe their image of a typical male or female their age who has sex without a condom with a casual partner after having 4/5 or more drinks (prototype favorability). Regression analyses were conducted to determine the association between alcohol use and condom use, and if prototype favorability moderates the association. Results from this study will help interventions focus on specific beliefs, such as prototype favorabilty, and how they relate to alcohol-related risk behaviors.

Humans find it trivial to classify natural scenes, yet this same task is a significant challenge for artificial intelligence. Here we investigate which properties of natural scenes might allow computers to classify natural scenes more accurately. A set of 200 images of natural scenes (city, coast, country, forest, and mountain) were converted into gray scale. Each scene was then Fourier filtered to create a bank of images that each contained different spatial frequency and orientation information. Low-frequency information corresponds to large-scale modulations in luminance across the image (e.g., a coastline might be brighter in the upper half of the image and darker in the lower half of the image, which would be visible within the images created by filtering using a low-frequency grating in the horizontal direction). High-frequency gratings correspond to small-scale modulations in luminance (e.g., fine textures such as grass would be visible within images filtered using a high-frequency vertical filter). We then trained a computer algorithm to ‘guess’ which class (city, coast, country, forest or mountain) any given image belonged to, based on this filtered image bank, and used this training algorithm to determine which filtered images provided the most reliable information about which class the scene belonged to. Using novel images, this approach allows us to classify with greater than 75 percent accuracy. We are currently examining which filters are considered by the algorithm to be the most useful, with the eventual goal of examining if the information contained within these filters resembles that used by humans.

There are different types of programmed cell death: the well-understood apoptosis, and the inflammatory process of necroptosis. The enzyme Caspase-8 has been defined as a key initiator of apoptosis and inhibitor of necroptosis from studies using knockout mouse models. While Caspase-8 is found in both humans and rodents, a close homolog of the enzyme called Caspase-10, is not found in rodents. To add on, the role of Caspase-10 pertaining to the necroptosis pathway is still undefined. The goal of this project is to understand how Caspase-10 functions in human cells, and how the apoptotic and necroptotic roles of Caspase-8 described in rodents may be divided between Caspase-8 and Caspase-10 in humans. To investigate this idea, we silenced Caspase-8 and/or Caspase-10 expression in human cells, induced Necroptosis using chemical signals and inhibitory drugs, and investigated expression levels of proteins Caspase-10 may interact with. Our results will be critical in uncovering the role of Caspase-10 pertaining to necroptosis, as well as why Caspase-10 is present in humans but not mice.

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

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.

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

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

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

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.

Genetic robustness is the ability of an organism to gain mutations without changes to its fitness or functions. Evolutionary conditions that might select for genetic robustness are unclear, but some studies suggest that proteins that are more thermostable (able to fold properly at high temperatures) are also genetically robust to mutations. We are examining this relationship in phi-6, a virus that infects bacteria. We have evolved phi-6 for thermostability by subjecting it to high temperatures and then sequenced the viruses for mutations. We used homology-modeling programs to visualize the structures of mutated viral proteins and made predictions about the molecular basis of thermostability and genetic robustness. In order to evaluate whether the thermostable strains are genetically robust, we ran random mutagenesis on both thermostable mutants and the wild type virus. Our work shows that evolution for thermostability may be a viable mechanism to evolve genetic robustness.

While many community mental health agencies have shown increasing emphasis in the direction of evidence-based practices (EBP) for children’s mental health, most training efforts have not included consultation on intervention delivery following training. A rising body of evidence suggests that one-time training workshops do not provide enough support to sufficiently influence clinician adherence with respect to EBP delivery, and that ongoing expert consultation is vital for motivating providers towards satisfactory implementation. Though the literature outlines consultation broadly, the fundamental elements of consultation, to date, remain elusive, and further investigation into the underlying mechanisms of this critical training strategy is warranted. To investigate consultation, biweekly consultant-led call summary emails (N=73) generated by five Ph.D. level expert consultants following EBP trainings were examined via identification of thematic issues addressed among community therapists belonging to six-month-long training cohorts. To ensure inter-rater reliability—improving internal validity—three peer examiners were commissioned to offer concordant verification of identified themes in the coding process. Each coding team member independently reviewed summary transcriptions and developed a list of themes. These subcategory themes were evaluated, discussed, and consolidated by the coding team into a coding scheme for each subcategory. By the day of the symposium presentation, data analysis will reach completion and key findings will be reported. Prospective results may include emergent themes related to EBP delivery (i.e., frequently addressed clinical issues, therapeutic barriers to treatment, etc.) This study contributes to a larger effort of examining core consultation functions, which may have broad applicability in the assessment of the conceptual framework needed to best improve consultant-clinician training initiatives in community mental health.

 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 switch from vegetative to reproductive development in flowering plants is tightly regulated by a complex gene network, yet little is known about how this network evolved. The Arabidopsis thaliana flower meristem identity gene LEAFY (LFY) encodes a transcription factor that activates floral organ identity genes to initiate flower development; loss of function mutants develop leaf-like structures in place of floral organs. Genes homologous to LFY have been identified in representatives of more basal land plant lineages, including gymnosperms, ferns, and mosses. Moss LFY functions in early sporophyte development; knock-outs result in the zygote being arrested at the single-cell stage with no further development. To investigate the evolution of LFY, we have generated transgenic lines in the emerging model fern Ceratopteris richardii that use RNAi to silence CrLFY expression. We have validated lines with reduced LFY expression by RT-PCR showing a delay in sporophyte development and distinct leaf development. Our working hypothesis is that fern LFY may be crucial for early sporophyte development. To find evidence for this, we are currently analyzing gametophyte and early sporophyte development in detail using microscopy to determine the timing and location of the developmental defect (i.e. in gametangia, during fertilization, or in the early cell divisions of the zygote). Our research seeks to bridge the evolutionary gap between LFY function in moss and flowering plants by looking at its function in ferns (sister taxa to all seed plants) and to ultimately investigate how it became specified for flower development.

HIV remains a major global health problem due to high transmission levels and emergence of drug resistant strains. According to WHO, in 2014, sub-Saharan Africa had 25 million people living with HIV and 70% of new HIV infections globally. A high number of circulating drug resistant HIV remains undetected due to lack of affordable HIV genotyping methods. The lab based oligonucleotide ligation assay (OLA) is a highly sensitive method for detecting HIV drug resistance as an alternative to the expensive and complex complete-genome sequencing, but its reliance on moderately expensive lab equipment prevents its universal access.  Our lab, in collaboration with the Frenkel Lab (Seattle Children’s Research Institute) and the Lai Lab (UW BioE), focuses on developing a simplified OLA-based HIV drug resistance test. The ligation step of the OLA relies on the specificity of DNA ligase to target single nucleotide polymorphisms (SNP’s) that can confer HIV drug resistance. However, ligation currently requires a thermal cycler to cycle between 95 °C to de-hybridize target DNA and 37 °C for annealing of oligonucleotide probes to target DNA. Eliminating the temperature cycling component of ligation would be a key advantage because thermal cyclers are not widely available in low resource settings. We measured ligation at intervals from 25 °C to 70 °C and were able to pinpoint an optimal temperature range for isothermal ligation. We plan to further increase ligation yield, and therefore detection signal, by optimizing the concentrations of salts and cofactors, adjusting probe lengths, and modifying probe sequences.  With the development of isothermal ligation, the OLA will be further simplified for potential widespread use in low resource settings. This will allow HIV infected individuals to be accurately diagnosed and receive the proper line of HIV drugs, controlling transmission rates and reducing the evolution of drug resistant HIV within entire populations. 

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.

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

Students of Everett Community College’s Ocean College Research Academy (ORCA) analyzed pH trends in the Snohomish River estuary of Possession Sound using ten years of data. Influences on water chemistry include freshwater discharge from the Snohomish River and tidal currents in Possession Sound. In addition, high salinity, cold water from the Pacific Ocean may transport low pH water as a result of ocean acidification, when atmospheric carbon dioxide dissolves in seawater and decreases the pH. Students wanted to investigate whether average pH in Possession Sound had been decreasing over time. Data were analyzed during the winter months, November through March, from 2006 to 2016. We collected data from October 2015 through May 2016, with archived data collected by previous ORCA students. Water chemistry at three sample sites in the Possession Sound were compared. Recordings of pH from the surface to five meters were completed with a YSI 650 and averaged. The most significant decreases in pH occurred at locations in closer proximity to the shore, near south Whidbey Island and Mukilteo. Each had an overall decrease of 0.3, compared to only 0.1 in the middle of the sound near Hat Island. Decreased pH in an estuary system directly affects the development of many organisms, such as phytoplankton, which make up the primary levels of the trophic pyramid. Further investigation is ongoing about the effects of salinity and river discharge on these minimal decreases in pH, along with seasonal fluctuations in primary production by phytoplankton as well as the effects of decreased pH on phytoplankton.