Investigation of the phenotypic features of a putatively unaffected individual, in a family diagnosed with a multiple congenital contracture disorder called Distal Arthrogryposis Type 2B (DA2B), identified joint hypermobility, a phenotypic trait not commonly associated with DA2B. Review of the family history revealed joint hypermobility in multiple other family members extending back four generations. Analysis of exome data from the family, identified two candidate variants, one in exon 1 of the gene SRL and another in exon 8 of NPR3, which may explain the joint hypermobility observed in this family. Recently, we used Sanger sequencing to genotype five family members with hypermobility and four unaffected family members for the two candidate variants to see if either variant tracks with the hypermobility phenotype. Briefly, we amplified exons via polymerase chain reaction and verified product sizes using gel electrophoresis.  We then sequenced the amplicons using di-deoxy chain termination sequencing and generated electropherograms using an automated DNA sequencer. Using the computer program CodonCode, we aligned and examined the sequences. Analysis of the data is underway. Through pinpointing mutations that cause hypermobility, characterization of Distal Arthrogryposis syndromes will become more accurate which may lead to better patient outcomes for individuals with additional features like severe hypermobility.

Cell-to-cell interactions are necessary for proper cell function. In the peripheral nervous system, interactions between sensory neurons and the epidermis influence neuronal growth, survival and function. However, mediators of these neuron-epidermis interactions are largely unknown. Drosophila melanogaster provides a tractable genetic system to study these cell-cell interactions. In Drosophila, dendrites of larval sensory neurons are sandwiched between the epithelial cell and the extracellular matrix. Occasionally the epithelial cells form invaginations at the location of dendrites, and eventually the dendrites become embedded inside the epithelial cell. In a screen for markers that label plasma membrane-associated proteins that localize to sites of dendrite embedding, we identified components of gap junctions as candidate regulators of dendrite-epidermis interactions. Gap junctions connect two cells via their cytoplasms and allow signals to be passed from one cell to another. Innexins are a family of gap junction proteins in Drosophilia, one of which is encoded by the gene innexin3 (inx3). Our preliminary data showed that, when overexpressed, GFP-tagged Inx3 protein can localize to sites of epithelial dendrite ensheathment, thus we hypothesize that inx3 contributes to formation/stabilization of membrane invaginations that enclose dendrites. However, no tool exists to visualize endogenous Inx3 distribution, nor is there an Inx3 antibody for immunostaining. Using CRISPR/CAS9 genome editing we plan to generate a Drosophila line with endogenous Inx3 tagged with GFP (Inx3-GFP). Using this line, we will determine whether Inx3 indeed localizes to sites of epithelial dendrite ensheathment. If we observe Inx3 enrichment at sites of dendrite ensheathment, we will perform expansion microscopy, a technique that our lab has recently adapted for use in Drosophila, to determine whether Inx3 labels discrete domains in the epithelial membrane invaginations. Finally, using our inx3-GFP fly line, we will conduct genetic mosaic analysis to determine whether inx3 is necessary for epithelial enclosure of dendrites.

Due to their luminescent properties, semiconductor nanocrystals are promising tools for optical imaging of biological samples. This experiment explores how the surface chemistry of CdSe/CdS core-shell semiconductor nanocrystals impacts cell targeting and cytotoxicity. Growing a CdS shell on top of a CdSe core and then altering the surface chemistry allows functional control of how these nanocrystals interact with the surrounding environment. Cytotoxicity was analyzed as a function of surface chemistry, in order to identify biocompatible surface chemistries. Surface chemistries were also altered to allow targeting of different cell types. CdSe core nanocrystals were produced using a hot injection method, and UV-vis spectroscopy was used to relate peak absorbance wavelength to nanocrystal core size. To increase the quantum yield, a uniform CdS shell was grown using a slow-growth process with cadmium and sulfur precursors. A ligand exchange was performed to transfer the nanocrystals from an organic solvent to an aqueous solvent. A fluorimeter was used to determine the nanocrystal quantum yields after synthesis of cores, shell growth, and surface functionalization with transfer to aqueous solvent. Quantum yields increased after the shell growth, but decreased in general after surface functionalization and transfer to aqueous solvent. Decreased cytotoxicity was observed for surface chemistries with longer ligands, such as functionalized polyethylene glycol (PEG) chains. Further research will aim to tune the properties of CdSe/CdS core-shell nanocrystals and target a variety of cell types.

Researchers are working to determine in-depth information about the substructure of the proton. This includes the proton's fundamental charge and current distributions, described by functions called electric and magnetic form factors. These form factors have traditionally been determined by computing elastic electron-nucleon scattering cross sections, to first-order expansion in the electromagnetic fine structure constant, α_e—encompassing a process called one-photon exchange. Experimental discrepancies in the proton's electric-to-magnetic form factor ratio have prompted a need to compute cross sections to second order expansion in α_e, involving two-photon exchange (TPE) interactions. Two methods for calculating TPE cross section contributions exist: one based on hadronic degrees of freedom (suitable at low Q², where Q is the four-momentum transfer between the electron and nucleon) and the other on partonic (quark-level) degrees of freedom (applicable at high Q²). Both methods have been claimed to principally account for the form factor discrepancy. However, ambiguities exist in the separation of the parts of the cross sections independent of the underlying hadronic structure (“soft” parts) and the parts dependent on such structure (“hard” parts). We aim to resolve such ambiguities by first rederiving current quark-level calculations to better understand exactly how the hard and soft parts of the cross section are separated and the underlying physical motivations. Furthermore, we plan to compare these calculations to known behavior of the hard part of the cross section in the limit that the scattering angle goes to zero. Ultimately, our objective is to pave the way toward a unified description of TPE effects at all Q² values. Achieving this goal will further pin down the nature of the proton's interior, and the results in turn can be used to better understand the neutron and other hadrons.

Retinol Binding Protein (RBP) is a protein used by the body to transport Vitamin A and is often used to monitor short-term nutritional changes. Traditionally, RBP has been measured via a nephelometric immunoassay with a high sample requirement. In an attempt to reduce turnaround time and to reduce the volume of sample needed for testing, an in-house assay using liquid chromatography tandem-mass spectrometry (LC-MS/MS) technology is being developed.The method being developed is based on the Vitamin D Binding Protein assay which sets a precedent for LC-MS/MS methods targeted toward high-abundance globulins. This method consists of denaturation of RBP using heat and denaturation agents, then digested by trypsin into peptides which are detected by LC-MS/MS. Currently there are three peptides with multiple transitions being monitored for each (FSGTWYAMAK, YWGVASFLQK, and LIVHNGYC[+57]DGR).The assay is being developed and validated according to the document CLSI C-62A and the assay is currently in its pre-validation phase. Experiments done include standard curve verification and comparison to development data, simple repeatability 5x5, carryover and various troubleshooting experiments.Data analysis has exposed high control and internal standard variability in the assay which are being resolved, but progress looks promising.The RBP assay is still far from completion and further testing and troubleshooting needs to be done to reduce variability before it can enter the validation phase. Once optimized, the LC-MS/MS assay, while less automated than nephelometric platforms, should allow UW Medical Center to have better control over an in-house assay in terms of turnaround time, while also using much smaller volumes of sample. LC-MS/MS also has improved sensitivity when compared to the nephelometric assay. This increased performance may lead to assay utility with other conditions such as diabetes, liver disease and kidney disease.
 

The nitrogen-vacancy (NV) center is a defect in diamond formed by replacing two carbon atoms by a nitrogen atom and a vacant lattice site. The NV center is a promising qubit candidate for quantum information, and its sensitivity to magnetic fields allows it to measure these fields. Due to the lattice structure of diamond, the NV center can have one of four possible orientations. For quantum information and sensing applications, control over this orientation is desirable, and would enable the production of better quality devices. Ab initio models predict that the NV orientation can be controlled through annealing, however the model depends critically on the barrier heights for defect diffusion which are difficult to calculate quantitatively. Preliminary data from our group demonstrated that heating the diamond up to high temperatures (> 1000 C) can sometimes cause single NV centers to appear, disappear, or change orientations. However, information on the frequency at which these changes occur, and thus information on barriers for diffusion, were unknown. Here we conduct thousands of single defect studies to determine these relevant rates as a function of the annealing temperature and time. While NV centers fluoresce under green laser light, restricting the polarization of this light only allows NV centers in that direction to fluoresce. By taking multiple confocal images at several polarizations, two families of orientations can be distinguished. These images are taken before and after the annealing process and then are compared using customized computer software to gather statistical data on the dynamics of single NV centers.

Preliminary work has revealed genetic heterogeneity among Alzheimer’s disease (AD) subtypes defined by cognitive domain-specific impairments. There are currently no reports of risk factor associations for these AD subgroups. We used cognitive data from 825 Adult Changes in Thought (ACT) participants at the time they were identified with probable or possible AD to generate scores for memory, executive functioning/attention, language, and visuospatial ability. We determined individual mean scores across all domains, and identified specific impairments as >0.75 SD below each individual’s mean domain score. Depressive symptom severity was measured with the CES-D, and study staff collected self-reported data on traumatic brain injury (TBI) exposure. We used multinomial logistic regression with the “no prominent domain group” designated as the reference category. We determined risk ratios for depression and TBI for each subgroup vs. the no prominent domain subgroup, and tested significance of any heterogeneity with an omnibus test. We controlled for age, sex, APOE genotype, and years of education. Education's role as a risk factor varied across the five cognitively-defined AD subgroups (omnibus p=0.04). Education predicted development of memory prominent AD rather than AD with no prominent domain (risk ratio [RR] = 1.08 per year of education, 95% confidence interval (CI) 1.00, 1.16, p=0.05; omnibus p=0.04). Depression also varied across AD subgroups (omnibus p = 0.04). Higher CESD scores were associated with lower risk of developing memory prominent AD compared to no prominent domain AD (RR = 0.93 per point on the CESD, 95% CI 0.88, 0.98, p=0.01). We did not find differences in risk associated with TBI. Cognitively-defined AD subtypes show heterogeneity in their associations with depressive symptoms and education. It is possible that these risk factors are associated with biological differences across subgroups.

From intimate Baroque chamber halls to vast stadiums, architecture has long dictated music's performance and composition. The 20th century rise of acoustic science brought about a quantitative way of perceiving the interaction which was sometimes successful, and other times justified the creation of buildings like Leo Beranek’s Boston Philharmonic Hall, which failed to serve its experiential purpose. With this becoming the norm, it is increasingly important to analyze the way sounds construct spaces, rather than the reciprocal. Psychoacoustics, or the study of auditory perception, can be applied to create built environments which are sensitively and intimately related to the sounds performed or produced within. Raymond Murray Schafer and several other theorists proposed the idea of psychoacoustic ecology as a framework for viewing and shaping the large-scale urban environment. Acoustic ecology is the study of the relationship between humans and sounds in a given environment, and the larger societal systems framing the interaction. My research applies Schafer's lens to analyze the extent to which existing urban “sound spaces”, (or built environments as perceived by sound), underserve their occupants. Furthermore, Schafer’s perception of urban acoustic environments through the lens of music composition holds potential to inform new ways of structuring the built environment. My research critiques existing urban theories on silence through the writing and work of several prominent figures in the urban planning community. I analyze the repercussions of existing urban acoustic environments on the societies which occupy the spaces. Using in particular the theories of midcentury music composer John Cage, including his “emancipation of noise,” I propose an improved framework for viewing and creating urban acoustic ecologies to encourage more egalitarian, cooperative, and inclusive urban spaces.

The spike in commercialization of college sports programs raises the issues that student athletes’ are facing more difficulties to achieve academically. Collegiate athletes playing at the Division 1 level has shifted from mere competiton for students to a massive business enterprise that brings in millions amount of revenue to universities. The purpose of this study was to (1) determine the relationship between team subcultures, parental influence, coach/teammate influence, learning environment, training, financial aid, prior high school requirements of play and academic assistance influence academic achievement of Minority university athletes, (2) determine if differences exist between non-minority and minority student athletes’ within the same subculture of that team and (3) determine if there are differences between minority student athletes’ success in Division 1 men and Division 1 women, in regards to academic achievement within their respective teams subculture. Ultimately, were minority student athletes getting a chance to engage in the academics that are the school's trade-off for the profit it makes from students' athletic labor or does the team subculture emphasize the athletic aspect as opposed to academic achievement? Using convenience sampling, respondents were chosen from among the University of Washington football, basketball (men and women’s) and volleyball team. The sample consists of 50-student athletes from the University of Washington who are pursuing their studies while representing their university in one of the listed sports team. Respondents completed (a) an interview assessing the attitudes and behavior of their environment, by teammates and coaches, (b) an assessment scale of involvement with faculty pertaining to academics vs. athletics, (c) demographics Q&A which assess gender, race, athletic status, and prior high school academic achievement. Data were analyzed using descriptive statistics, descriptive analysis and logistic regression. This study concludes with a series of suggestions and recommendations on how to improve the academic achievement of the intercollegiate minority student athlete population.

The recent changes in our climate drive the need for a more comprehensive understanding of the workings of the environment so that we can more accurately simulate the changes taking place around the world. This project aims to do this by studying measurements of the optical depth of tropical clouds at different heights. The optical depth of a cloud is how opaque it is to visible radiation and determines how effective the cloud is at absorbing or scattering the solar radiation. By sifting through radar and lidar data collected by NASA’s CALIPSO and CloudSat satellites that orbit the earth simultaneously in a group called the A train, I am able to determine cloud optical depths as a function of altitude in different regions. I expect the optical depth of tropical clouds to decrease as their height increases due to the fact that lower, warmer clouds are able to hold more water and should therefore be thicker. My research adds additional information for climate models so that they may more accurately define the radiative budget.

Understanding how genes and regulatory networks evolve to promote innovation is a key question in evolution and development. Flowers represent a classic example of evolutionary innovation, one that propelled angiosperms into one of the most notable adaptive radiations. In angiosperms, the flower meristem identity gene LEAFY (LFY) is expressed after a shoot meristem is induced by long days, allowing flowers to develop. In the absence of LFY function, additional shoots with leaves develop instead of flowers. Surprisingly, knockouts of LFY homologs of moss, a representative of an early plant lineage, result in an arrested zygote that does not get passed the one-cell stage. Since ferns lie midway in the evolutionary tree between mosses and angiosperms, and are the sister group to seed plants, a functional study in the emerging model fern Ceratopteris richardii will provide much needed insight as to how this important gene evolved. We predict that in angiosperms LFY may have been recruited from a broader role as a meristem gene in the shoot apical meristem (SAM) and in indeterminate compound leaves, common in ferns. Expression data backs up this prediction, with CrLFY being found in the embryo SAM and later in the growing areas of compound leaves. We have taken a loss-of-function approach to elucidate the role of LFY homologs in ferns via RNA interference (RNAi). Currently, we are investigating the embryo within knock-down transgenic lines to determine whether it develops normally or if it arrests at any stage, and we are following its development into the compound leaf stage. By providing insight into the evolution of a master regulator of flowering, this projects has potential applications towards agriculture, where most of the crops for human consumption consist of grains or fruits that derive from flowers.

The Bengal Fan is the world’s largest active submarine fan, collecting sediment from the Himalaya in a fan-shaped depositional system. The fan has an active channel formed by turbidity currents. This active channel behaves much like a river system on land:it meanders, eroding and depositing material, building natural levees along its banks in the same way. In this research, we used samples collected next to the active channel by International Ocean Discovery Program (IODP) Expedition 354 to investigate the anisotropy of magnetic susceptibility in terms of the direction of turbidity currents during their deposition. The direction of the currents recorded in the sample gives us a map of where the channel is in relation to the time of deposition. Through successive sampling along the core we can see how the channel has migrated over time. This should tell us how long it takes an active channel to meander or migrate along the bottom of the ocean. Understanding how this fan system works is critical in understanding the changes on the ocean floor. Knowing the timeline for these changes has both economic and societal importance. It can tell us more about where to find economically important deposits of petroleum as the sediment structures that are made by turbidity currents in active channels are repositories for oil resources, and the sudden turbidity currents that run down active channels can cause damage to underwater structures like important seafloor cables.

The circumgalactic medium (CGM) is gas that is constantly being thrown out and being recycled back into galaxies. Learning more about the composition and location of this gas can give information about its origin and fate. However, this gas is exceedingly difficult to observe in emission, as it is very diffuse and ionized, and therefore must be observed in absorption at ultraviolet wavelengths. Fortunately, the Hubble Space Telescope (HST) Cosmic Origins Spectrograph (COS) installed in 2009 allows for very sensitive measurements of CGM UV absorption lines. As light from very bright quasi-stellar objects (QSOs) passes through the universe on its way to Earth, it encounters a galaxy’s gaseous CGM resulting in absorption lines from ionized gas in the QSO spectra. My research involves an analysis of many QSO spectra from HST/COS. I identify ionized elements seen in absorption at distinct redshifts along the QSO line of sight. The goal is to identify everything in the spectrum, and in doing so isolate the systems of gas that contain strong Lyman Series lines from Hydrogen and metals (elements heavier than hydrogen) with a corresponding redshift from the Milky Way. These redshifts can be used to reference various databases to actually look for the host galaxy halo at some projected distance from the QSO absorber system. With this information, the distance between the galaxy and the sightline of the QSO can be calculated giving a lower limit for the extent of its CGM. Additionally, the composition of the galaxy can be compared to that of the gas in its CGM. Ultimately, these data will further our understanding of the dynamic processes that drive galaxy formation.

Composite materials utilizing nanoparticles can exhibit improved properties and qualities. Silica (SiO₂) nanoparticles exhibit unique optical, electrical, and mechanical properties and are an ideal candidate for the dispersed phase in many applications, such as precursors for optical films with controlled optical properties and rheology. Atomic forces dominate when particles shrink to sizes below the visible wavelength spectrum, generating unique phenomena. One problematic phenomena, however, is the agglomeration of primary particles into a polydisperse collection of dimer, trimer, or larger secondary particles when calcined or mixed into the continuous phase of the composite. Monodisperse colloids and nanopowders are critical for consistent and optimized performance of composites and nano features. Silica particle synthesis has been well researched, but the practicality of producing pure, monodisperse, and non-agglomerated particles at scalable operations is still in question. This research investigates the factors leading to the agglomeration of spherical silica nanoparticles when synthesized with variations of the Stöber method, and evaluates changes in synthesis parameters that can reduce agglomeration in order to determine the most viable process for scalable production. Parameters that are manipulated include the ratio of ammonia catalyst with tetraethyl orthosilicate (TEOS) in ethanol or methanol solvents and the addition of anionic electrolytes. SEM imaging is then used to evaluate the distribution of the particles. Surface treatments for anti-agglomeration as incorporated into the synthesis process or as post processing are also evaluated, with minimal remnant impurities in the product as a priority. The end goal of this research is to successfully synthesize monodisperse sub-10 nanometer silica particles for pseudoplastic shear-thinning precursors used in fast throughput nanoimprinting of an antireflective layer for solar cells.

Necroptosis is a lytic and immunogenic form of programmed cell death (PCD), characterized by pro-inflammatory cytokine production and the release of intracellular molecules, including cell-associated antigens. In the context of tumor immunology, tumor cell death is a necessary step in causing the release of tumor antigens, allowing for antigen-specific tumor recognition by the immune system. However, how distinct forms of PCD within tumor cells could differentially instruct immune recognition of tumor-associated antigens remains poorly understood. Our research question addresses how the immune system responds to cancer cell death, and will help determine whether necroptosis can promote tumor immunity. We propose that induction of necroptosis within tumor cells could promote anti-tumor immune responses by releasing tumor antigens accompanied by pro-inflammatory signals, resulting in potent immune recognition of cancerous cells. To study the immune responses to cell death in tumors, we have modeled the effects of various cancer cell death programs using flank tumors implanted in B6/J mice. Using flank tumors engineered to express versions of various pro-death signaling proteins that can be activated, we show that induction of necroptosis within the tumor microenvironment leads to robust tumor control. Measuring serum cytokine levels, in addition to analyzing the identity and activation status of immune cells isolated from the tumor tissue following treatment, will yield critical insights towards the immune cell subsets and signaling axes responsible for the observed response to necroptosis. These experiments provide us with a comprehensive understanding of whether cell death in a solid tumor has a therapeutic benefit as well as the underlying mechanism of the immune response to dying cells within a solid tumor. Considering the pro-inflammatory nature of necroptosis, it represents a promising therapeutic target in the context of cancer immunology.

As the usage of electric vehicles (EV) expands around the world, there are numerous challenges to overcome. One of the biggest challenges encountered is the efficiency of EV charging systems. This research explores the trade-offs between maintaining availability of DC fast chargers and other variables including waiting times, station utilization, and cost per vehicle served. To determine the utilization rate of chargers, we created a queueing model by using characteristics of EV models and chargers such as charging rates, battery size, and range. A queueing system is a generic model that is comprised of three elements: a user source, a queue, and a user facility. For this research, the three elements of the queueing model are linked to a cost model to evaluate the attractiveness of private sector investments in charging infrastructure. Since there are many uncertainties and results are sensitive to assumptions, we developed an interactive R Shiny app that allows users to specify assumptions and visualize the relation between the number of vehicles served and key performance metrics. This visualization can help decision makers determine the optimal number of chargers required to balance the tradeoffs between availability of chargers and utilization rate in order to provide satisfying services for users and beneficial business for operators. Ultimately, our model shows that it is difficult to maintain high reliability of utilization and low cost per vehicle served, and that improving this trade-off demands significant growth in the total number of EVs on the road.

All physical systems are ultimately governed by the laws of quantum mechanics. Over the past decades, it has become clear that these laws enable new generations of quantum information technologies that can profoundly outperform their classical counterparts. However, this depends critically on (i) the ability to efficiently entangle quantum systems (qubits) at rates much faster than the rate of quantum decoherence and (ii) the ability to scale the system with reasonable cost per added qubit.
Color centers in diamond, such as the nitrogen-vacancy (NV) center, have emerged as a promising qubit candidate. Pairs of NV centers can be entangled via the interference and detection of emitted single photons. Entanglement generation with this method was previously demonstrated in a non-scalable manner; adding additional qubits would require the costly hand-assembly of macroscopic equipment. This project aims to develop integrated circuitry for quantum information, where each macroscopic device is shrunk to an equivalent piece of photonic circuit.
Such circuits are easy to devise, but are extremely difficult to realize in the non-ideal circumstances of reality. Two main effects contribute to this difficulty: (1) the optical properties of NV centers are damaged by local imperfections in the diamond environment and (2) comparatively low fabrication precision prevents ideal production of photonic circuitry. We are developing both (a) passive and (b) active methods to mitigate these errors. This includes (1a) high temperature annealing of our diamond to reduce local defect concentration, (1b) applying electric fields to dynamically stabilize the local electro-magnetic NV environment, (2a) improving etch quality by reducing sidewall roughness and slant, and (2b) developing a wet etch to deterministically correct circuit dimensions. Further progress depends on traversing large parameter spaces to determine the optimal settings for success. Thus, automated testing procedures are being developed to make this traversal possible.

Oxidative stress arises from an imbalance between reactive oxygen species and an organism’s ability to avoid or repair the damage caused by these reactive molecules. The fruit fly, Drosophila melanogaster, demonstrates varying degrees of resistance to oxidative stress. To understand the genetic basis of this variation, our lab analyzed a collection of inbred, fully sequenced Drosophila lines, the Drosophila Genetic Reference Panel (DGRP), and tested the associations between resistance and each of more than two million single-nucleotide polymorphism (SNP) markers throughout the genome. We found a particular SNP at the second chromosome located within the gene u-shaped (ush), had the strongest statistical relationship with oxidaive stress resistance. We then hypothesized that this gene contributes to the degree of resistance in the flies. For my research, I am evaluating this hypothesis by comparing the peroxide resistance of two sets of genotypes to confirm if the SNP at 2L:531863 bp contributes to the trait. For this comparison, I used two groups of lines, one with the ‘resistant’ and the other with the ‘sensitive’ version of the SNP, and distributed mated females from each line into vials with or without peroxide added into the food. I counted the number of dead flies at regular intervals and used these data to calculate the mean lifespan for each line, where lifespan is a measure of peroxide resistance. If both groups show similar lifespans, it suggests that this particular SNP does not affect peroxide resistance and I may test other SNPs at nearby loci with a similar procedure. However, if the two groups show significant differences in resistance, this result would support the connection between the SNP and peroxide resistance. I would then go on to manipulate the expression of ush using RNA interference to test whether changing mRNA levels impacts peroxide resistance.

Spinal cord injury (SCI) disrupts the communication between the body and the brain. As a result, people with SCI typically have significant sensorimotor deficits leading to a lower quality of life. Electrical epidural stimulation (EES)—that is, the stimulation of the spinal cord from the surface of the cord—has shown promise for enhancing recovery of the hindlimbs when applied to the thoracic spinal cord. The goal of this study is to determine whether this same therapy applied to the cervical spinal cord in rats with cervical injuries can improve forelimb function. Prior to injury, the rats perform multiple tasks: Irvine, Beatties and Bresnahan (IBB) task, Limb-use Asymmetry Test (LUAT), Automatic-pellet-reaching task, and a Lever task. Next, rats will receive a unilateral C4 hemicontusion and below the injury the rats will receive an epidural implant for stimulating the spinal cord. All of the rats will perform the former tasks—IBB and LUAT—once a week to track their recovery. Half of the rats will be stimulated via the epidural implant while performing the automatic-pellet-reaching task and Lever task in the hopes of inducing Hebbian plasticity to enhance functional recovery. We are currently testing different epidural implants to identify a method that provides robust, long-term EES. Post-injury performance will be compared to the rat’s pre-injury performance. Subsequently, the rats are perfused for tissue analysis. We are optimizing the tissue analysis protocols for identifying GAP-43 immunoreactivity to determine if there was an increase in plasticity and axonal growth. Cresyl violet and myelin staining will also be used to measure the magnitude of the injury by staining the spared neurons and myelin.

Single-junction solar cells that employ metal-halide perovskites have generated intense interest due to their rapid increase in demonstrated power conversion efficiency. In contrast with previously explored solar cell active materials, perovskites are solution-processable, tunable band-gap materials with small energetic losses. Because of this they are ideal candidates for use in tandem solar cells, which integrate a large-bandgap and a small-bandgap solar cell into one structure, significantly increasing maximum efficiency. Current tandem solar cells can have marked efficiency loss due to excess window layers and poor layer design leading to absorptive losses. Additionally, the comparatively poor understanding of perovskite processing methodology can result in suboptimal perovskite active layers. Our goal was to explore the feasibility of using a metal grid-type electrode collection layer in place of a standard transparent window layer, in order to minimize absorptive losses for successful integration into a tandem structure. Principally important to characterizing this structure was exploration of device fabrication and perovskite processing methods that resulted in effective carrier extraction. The mean diffusion length of charge carriers in a material is one of the primary factors that affect carrier extraction. Current literature gives a diffusion length ranging from 0.3 – 10 um for methylammonium lead iodide (MAPI) perovskite layers. We fabricated test cells with electrode grid pitches ranging from 0.4 – 10 um using photolithography techniques. We then explored the effect of variable deposition method, heat treatment and solution composition as well as observed layer morphology on diffusion length and charge extraction using photoluminescence spectroscopy.

Diamond magnetometry enables the measurement of small-scale magnetic fields using nitrogen vacancy (NV) defect centers in diamond. Nanoscale magnetic field detection has a range of applications in biology and chemistry, such as imaging of magnetically-tagged molecules for the study of biological processes. Diamond magnetometry uses optically detected magnetic resonance (ODMR), a technique which combines radio frequency (RF) magnetic fields with optical excitation to control the defect spin. To detect DC magnetic fields, typically continuous wave RF and optical fields are used. However it is well-understood that continuous optical excitation limits the sensitivity of the technique. This project demonstrates a pulsed ODMR system executed in LabVIEW, in which optical initialization and radio-frequency spin control are staggered in time and compares the performance against the continuous wave execution. This program will enable more sensitive measurements of biological systems where orientation matters.

The Amazon tidal river consists of the lowermost 800 km of the Amazon River that is affected by tides.  The effect of tides on surface suspended sediment concentration (SSC) in the Amazon has not yet been characterized, and may impact estimates of surface SSC as monitored through remote sensing.  To assess potential tidal influence on surface SSC, water samples were collected and filtered in field; published remote sensing maps were also collected and compared to field measurements.  Thus far, this project has identified discrepancies between in situ and remotely-sensed estimates of surface SSC, and constrained the influence of tides on the observed signals.  In situ surface SSCs more accurately matched with remote sensing maps on sites located directly in the Amazon mainstem, while tributaries showed exaggerated differences in surface SSC.  Field surface SSCs in the Amazon mainstem also did not vary significantly with tidal  seasons, suggesting that ocean tides play a smaller role in surface sediment transport than originally hypothesized.  Further conclusions will look into the roll that tides play on total bedload, especially at sites close to the river mouth where tidal influence is strongest.  Explanations for surface SSC discrepancies will also be included in the paper's conclusions; since many of the discrepancies occur in freshwater tribuataries, the seasonality of phytoplankton blooms will be cross-linked to satellite SSCs.  Finally, suggestions for future usage of remote sensing in strong tidal areas of the Amazon River will be given and the success rate/percentage of correlation of satellite surface SSC with field SSCs will be assessed.  With a better understanding of the effects of tides on surface SSC and how well remote sensing captures variability, we can better monitor sediment discharge into the tropical Atlantic Ocean as well as sediment delivery to the floodplain of the Amazon River during seasonal floods.

In this thesis I interrogate the “It Gets Better”(IGB) video project by Dan Savage, using an intersectional analysis to reveal the ways in which it reinforces politics of respectability, neoliberalism, and lacks an intersectional approach to the process of coming out across lines of gender identity, race/ethnicity, class, nationality, religion, and ability. To help frame the research of this paper, I will address the following questions: 1) who is the intended audience of “It Gets Better”? 2) How and in what ways do hierarchies get created within a single group, rather than between two groups? 3) What are the consequences of delivering a message that it will "get better"? 4) How does “It Gets Better” apply to individuals living with multiple, marginalized identities? 5) In what ways do racialized LGBTQ bodies feel torn between their racial/ethnic community and the LGBTQ community?  I chose to research this topic because as a genderqueer and queer person there have been instances that my life has not gotten better since coming out. By the same token, I have several friends who have had particularly difficult experiences because of coming out due to their race, ethnicity, socioeconomic status (SES), contending with gender dysphoria, nationality, religion, and inaccessibility to resources (e.g.- healthcare, education, housing) within the capitalist structures of the United States (U.S.). My goal in this thesis is to interrupt neoliberal notions of “getting better” and instead turn our attention to the structures in society that do not allow life to get better for all LGBTQ people after coming out.

In many parts of the world, the lack of fresh water is the single largest factor limiting sustainable development. Water scarcity contributes to poverty and poor public health outcomes, and it can exacerbate ethnic and international conflicts in arid regions. This study aims to determine whether forward osmosis (FO) is a viable method for desalination of seawater. FO is an emerging technology for desalination, in which osmotic pressure is used as a driving force for separation. By using a concentrated solution of high osmotic pressure, called the draw solution, water is induced to flow from saline water across the membrane, rejecting the salt. To obtain potable water, the diluted draw solution is recovered and then recycled. Two chemicals – ammonium bicarbonate (NH₄HCO₃) and magnesium chloride (MgCl₂) – were compared in order to determine which one results in a more effective FO process, in terms of flow and chemical composition of the produced water. The results showed that the FO process is viable in terms of water flow and salt rejection. The effectiveness of the FO process does not depend on the type of draw solution, but instead depends on concentration, volume ratio of feed and draw solutions, and type of mixing. More experiments are required in order to develop the optimal mathematical relationship between the concentration of draw solution, and volume ratio of feed solution to draw solution. Potable water that complies with EPA standards, was obtained only from recovery of MgCl₂ diluted draw solution. Methods of NH₄HCO₃ removal described in the FO scientific literature did not result in production of potable water. Further analysis is required to identify possible techniques for NH₄HCO₃ removal from draw solution.

Housing First, also referred to as harm reduction housing, entails the provision of immediate, permanent, low barrier, nonabstinence based housing to chronically homeless individuals. Beyond the provision of housing, supportive services are essential to the Housing First approach. This includes the provision of opportunities to engage in meaningful activities, such as artistic endeavors, outings, gardening, and talking circles. Participation in meaningful activity programming has been associated with positive outcomes, such as reductions in alcohol-related problems and overall alcohol use. However, no study to date has examined which characteristics are predictors of participation in meaningful activities. The objective of this study is to understand who is engaged by meaningful activities offered in a Housing First setting. To this end, we explored the association between participant characteristics (e.g., sociodemographic, substance use, community-orientation variables) and level of activity engagement. Participants (n = 66) in this secondary study were residents of a Housing First site. An enhanced intervention specialist worked with housing staff to track residents' involvement in programmed Life Enhancing Alcohol-management Program (LEAP) activities. Self-report data were collected to document participants’ baseline characteristics. Attendance sheets were used to track participation in meaningful activities. Bivariate correlations indicated that participation in meaningful activities was associated with female gender, greater community orientation, and unemployment. When these variables were tested in a multivariate model, only unemployment remained a statistically significant predictor of greater participation in meaningful activities. This study indicated that few sociodemographic, substance use and community orientation variables predicted differential participation in meaningful activities in a Housing First setting. Taking all potential factors into account, only one variable significantly predicted involvement—unemployment. In designing programming for Housing First, providers should take into account residents’ competing priorities (e.g., work) to give programming optimal reach.

Respiratory syncytial virus infection (RSV) is the most common cause of hospitalization in infants in the United States. It has now been increasingly recognized to cause disease in elderly adults and those with chronic lung disease. We aim to identify risk factors associated with hospitalization due to RSV, severity of infection, and the neutralizing antibody response to infection in adults acutely infected with RSV. Patients admitted to Harborview Medical Center (HMC) with RSV are enrolled and given a brief questionnaire about their family and home, health history, and their drug use. In addition, serum samples are collected and tested for neutralizing antibody response to RSV. Analyzing the titers from the neutralizing antibody test identifies patients with a higher antibody response to infection. This can lead to a better understanding of the characteristics associated with more virulent RSV symptoms. With these data we will be able to better understand the immune response to infection as well as other factors that may play a role in disease severity due to RSV.

This research explores what role the U.S. should adopt in the new nuclear era to ensure that the expansion of nuclear energy capabilities proceeds safely, securely, and without further proliferation of weapons. Does the U.S. need to expand its own reactor fleet, using advanced reactor technology, to maintain a position of influence? What policies and measures should it take, if any, with regard to Russia’s plan to become a nuclear superpower? Through a broad literature review and interviews with world-renowned experts, this research answers these questions, as well as provides key policy recommendations for the U.S. going forward. Ultimately, our findings make it clear that expanding nuclear energy is critical to meeting U.S. climate objectives, buffering national energy security, and becoming a leader in critical energy technology.

Recent research has been dedicated to investigating ways to promote angiogenesis using microphysiological systems that more accurately represent native organs. The Zheng lab has recently created a kidney microvascular model on a chip that utilizes primary isolated endothelial cells. However, this model requires the implementation of a biologically representative matrix and the incorporation of perivascular and parenchyma cells to better mimic the native microenvironment. We hypothesize that the incorporation of a biomimetic matrix will confer quiescence in the endothelium of the microvascular model and that the integration of perivascular cells within the matrix will promote improved vessel maturation and the establishment of a basal lamina. We have synthesized a biomimetic material from decellularized human kidney tissue that has a complex modulus of 930 Pa, making it stiff enough to use in semi-3D cell culture. Furthermore, use of this material has led to decreased endothelial migration and fewer alpha smooth muscle actin positive perivascular cells, indicating representative in vivo behavior of both cell types. In the microvascular model, we expect the integration of perivascular cells to the matrix will lead to increased endothelial quiescence. Results in collagen I matrices have shown irregular perivascular homing to and coverage of the endothelium, denoting increased but not complete vascular maturation. We expect the utilization of this technique in the biomimetic matrix to show increased perivascular coverage of the endothelium and the formation of a more complete basal lamina. If proven to be biologically accurate, implications of an in vitro kidney microphysiological model include use in therapeutic tissue regeneration studies as well as the ability to replace less accurate animal models during drug testing.

Organisms face a range of stressors over the course of their lifespans. As with most traits, we see significant variation in response to stress even between individuals within species. In our attempt to explain differences in stress responses between individuals, the Promislow lab studied the metabolome, the total profile of all small molecules in an organism, and found variation in stress response is correlated with variation in contents of the metabolome. Indeed, in a study of peroxide resistance in the fruit fly, Drosophila melanogaster, we found resistant flies tended to have increased galactose levels, compared to sensitive flies. This observation led to the novel hypothesis that flies fed supplemental galactose will have increased peroxide resistance compared to control flies. For this experiment, we chose flies among the most sensitive and resistant lines examined previously because the most sensitive flies, with low galactose levels, may show increased effects of supplemental galactose on lifespan. In this experiment, flies feed on food with varied galactose concentrations, including a negative control without galactose. We then place the flies into media with peroxide or water, the control. We record the number of flies that die in each condition multiple times a day, and the death rate provides a quantitative measure of peroxide resistance. By comparing the death rate of flies within a line kept in varying concentrations of galactose exposure, we can test the effect of galactose on resistance. If our hypothesis is correct, the flies receiving supplemental galactose should die at a slower rate than those without additional galactose. However, it is possible flies receiving supplemental galactose will die at faster rates, suggesting galactose makes flies more sensitive. Determining whether galactose makes flies more resistant or sensitive to peroxide may prove to be important in counteracting effects of oxidative stress in other organisms.

There is an urgent need to clarify the causes of Alzheimer’s Disease (AD) so targeted treatments can be developed. Mutations in Presenilin 2 (PSEN2) cause an inherited form of AD, but the mechanism for this relationship is not fully understood. PSEN2 protein (PS2) has been found to regulate pro-inflammatory microglial response and the expression of microRNA miR146, an innate immune regulator. These findings led us to pursue the effects of PSEN2 mutations on microglia function, peripheral immunity, and AD. Our aim is to study mechanisms of microglia-induced neuron injury in AD. We hypothesize that PS2 mutation-expressing microglia contribute to neuroinflammation in AD by cytotoxicity and synaptic pruning mechanisms. To study the impact of stimulated microglia on neurons, we employ co-cultures, where microglial (BV2) and neuronal (SY5Y) cell lines are cultured together. We used a lactose dehydrogenase (LDH) cytotoxicity assay to measure levels of microglia-induced neuronal death. After initial assay optimizations, we measured LDH of a BV2/SY5Y coculture to quantify baseline LDH and optimize the ratio of neuron to microglia plating. Fluorescent microscopy was used to observe microglia and neuron interactions morphologically and flow cytometry quantified the levels of neuron phagocytosis of microglia. Using these methods, we were able to demonstrate interactions between the cells and these same methods can be used to later study synaptic pruning. From here, we will determine whether there is a difference in synaptic pruning levels and cytotoxicity between microglia from a control mouse and a mouse expressing mutated PSEN2 transgene when co-cultured with neurons. If our hypothesis holds true, we expect to see increases in both cytotoxicity and synaptic pruning induced by mutated microglia. Determining and understanding PSEN2’s role in causing AD could lead to the development of targeted treatment for patients with these mutations.

In resource-limited settings, premature and small for gestational age (SGA) births are common and increase risk of infant mortality. During pregnancy, exposure to high pathogen levels and other health risks increases inflammation and may result in premature or SGA infants. Cytokines are small secreted proteins involved in the inflammatory immune response. This experiment examines variations in 25 cytokine levels in sera collected from pregnant women during the second trimester of gestation and again at the time of delivery. Samples selected from women who delivered full term SGA (n=50), preterm SGA (n=50), preterm appropriate for gestational age (AGA) (n=50), and full-term, AGA (n=50) infants were tested using a Luminex 25-Plex Magnetic Assay to compare cytokine level changes in these populations. I plan to conduct and analyze this assay which has not yet been completed, but preliminary data shows we should expect elevated levels of cytokines in those mothers with preterm and SGA infants. Overall this experiment provides a better understanding of cytokine profiles unique to preterm and SGA infants in resource poor conditions, and could provide novel therapeutic targets for the prevention of infant mortality associated with these conditions.

In online news, as in many forms of online and print media, the appearance of the content can influence the reader, perhaps even more than the content itself. Styling is chosen to make certain news sources look modern, traditional, or edgy, and these styling choices might affect readers’ judgments. At the same time, creating and hosting websites that anyone can access has never been easier than it is today, as seen in the explosion of fake news across social media outlets during the 2016 U.S. presidential election. On a daily basis, people shared misleading or false articles because those articles looked convincing and affirmed the biases of their readers. Certainly the content, timing, design, and layout of news articles might all contribute to their propagation across social media, but the relative import of each of these factors is still unknown. In this work, we are interested in how the appearance of news, independent of its content, influences consumers’ perceptions of an article’s veracity. Our research project examined how the presence of certain visual attributes (e.g., layout, links, fonts, and use and arrangement of photos and videos) in news articles affects people’s credibility judgments of unfamiliar news sources. We conducted an online experiment and semi-structured interviews to collect data from people currently attending universities. We showed them a series of content-neutral (i.e., “lorem ipsum”) news articles and asked them to rate the credibility of each one on a 1-7 Likert scale. We also provided opportunities for narrative responses for more in-depth opinions at the end of the study. Our results indicate that presentational aspects do indeed affect perceived veracity of online news sources. Designers can take these findings into account when seeking to communicate better with their users.

On June 16th, 2015 business mogul Donald J. Trump delivered a presidential announcement speech, announcing his candidacy for president of the United States, launching his ascension to the White House. Through a rhetorical analysis of Donald Trump’s Presidential Announcement Speech utilizing Kenneth Burke’s framework of dramatism, Trump’s speech is shown to mimic the effective rhetorical strategy of the United States Christian theological prosperity gospel movement. The speech establishes a negative status quo, provides testimony on a successful break from the status quo, and concludes with a plan for redemption, showing listeners how they, too, can break from the status quo utilizing an exemplary model. Trump serves as the exemplary model, claiming to know a path toward greatness, articulated with his campaign’s slogan, “Make America Great Again”. However, Trump’s imperfections, including his relationships with the elite and break from expected niceties in rhetoric, required mortification and scapegoating for justification to legitimately be seen as the exemplary model. The implications of Trump’s rhetorical strategy may inform future political candidates’ rhetoric and provide insight into President Trump’s framing of policy issues.

In 2013, buildings were single-handedly responsible for 44.6% of all CO₂ emissions generated in the United States. In order to confront the reality of climate change, the life-cycle assessment (LCA) approach has been developed as a way to quantify the carbon footprint of existing and projected structures from cradle to grave. Although the accuracy of LCA hinges on the ability to accurately predict the lifespan of a building, most conducted studies focusing on LCA are explicitly based on an arbitrary building lifetime ranging between 50 to 100 years. The goal of my research is to provide a probabilistic model of housing stock lifespan rooted in existing data as an alternative. The National Science Foundation has funded an interdisciplinary research project aimed at integrating sustainability and resilience into community decision making. The UW team is focusing on evaluating environmental and economic sustainability in residential construction using LCA. The models I developed of the expected lifetime of existing housing stock will increase the accuracy of that LCA through an application of building demolition over time derived from real-world trends of housing longevity. In order to estimate the longevity of housing stock, I compiled data from the American Housing Survey (AHS) and the New Residential Construction report. I split the existing housing stock into cohorts based on decade of construction to investigate a change in longevity over time. Building off of previous work done by Michael Gleeson over thirty years ago, I fit statistical curves to each data set and assessed them in order to enable probabilistic assessment of building lifespan.

Many cases of chronic kidney disease are caused by loss of podocytes, kidney cells that are part of the filtration barrier between the blood and urine, resulting in declining kidney function. Current therapies do not prevent podocyte loss and rely on systemic small-molecule drug delivery, which is less effective and can lead to significant complicating side effects. Therefore, targeted drug delivery to podocytes could more effectively protect against injury, prevent further loss, and halt disease progression to kidney failure. To effectively deliver drugs to these cells, ligands that bind with high affinity to proteins specific to podocytes must be developed. Aptamers, DNA- or RNA-based ligands, are advantageous because they can be generated using standard techniques and are easily reproduced. Here, systemic evolution of ligands by exponential enrichment (SELEX) was used to identify aptamers that bind to His-tagged nephrin and NEPH-1, two membrane proteins highly specific to podocytes. First, a large library (on the order of 6×1014 sequences) of randomized single-stranded DNA (ssDNA) was incubated with nephrin or NEPH-1, and protein-aptamer complexes were isolated using His-tag capture beads. Beads were washed to remove any unbound ssDNA, and bound ssDNA were then isolated. This pool will be narrowed further by applying additional selection stringencies over the course of several rounds, ultimately resulting in a small final pool of aptamers with high specificity and affinity to these desired targets. Libraries from selected rounds will be tested for binding to target proteins to monitor selection. Through SELEX, we anticipate finding a small pool of aptamers capable of binding to recombinant nephrin and NEPH-1, and will next validate individual aptamer sequences for their ability to bind to these proteins in vivo. These identified aptamers can be further used to develop a targeted drug delivery platform to podocytes.

PanOptes is a low-cost, wide-field robotic survey telescope that uses two DSLR camera bodies to take images. These camera bodies house CMOS chips, which are already used in astronomy today. The use of off-the-shelf hardware keeps the cost down while still taking valuable science data. The ultimate goal of the project is to ultimately track the brightness of stars in a field in order to find transiting exoplanets, and the current capacity of the project is responding to gamma ray bursts. A major part of this project will be constructing a data pipeline that is capable of reducing several gigabytes of data per night of data, and extracting brightness values for each stellar body in the image. From this, brightness values over time will be tracked, allowing for planet transits as well as variable objects to be monitored. This low budget, high value student driven instrument will be tied into a wider network of small robotic telescopes to further increase the scientific value of the project.

Aging is a phenomenon that brings about the onset of disease and eventually death. One of the hallmarks of aging is the decline in proteome maintenance that can lead to the accumulation of misfolded proteins. In extreme cases, protein misfolding can induce such devastating neurodegenerative diseases such as Huntington’s disease and Alzheimer’s for which very limited treatment is currently available. It has been observed previously that dietary restriction is a method that increases lifespan and delays the loss of function caused by age-associated pathologies. Specifically, complete food removal leads to robust increase in longevity in the roundworm Caenhorbabditis elegans, a popular model organism for aging research. Remarkably, when pre-reproductive adult worms are subjected to starvation, they enter a condition known as adult reproductive diapause (ARD). Upon reintroduction to food after prolonged starvation, ARD worms experience a pronounced morphological recovery and have normal lifespan. To understand how diapaused animals preserve this rejuvenation potential and normal lifespan we aim to analyze how proteome quality is maintained during the diapause. We hypothesize that proteome quality is either well maintained during the diapause or is restored back to youthful state upon exit from the diapause. To discriminate between these possibilities, we use C. elegans models of proteotoxicity wherein toxic protein species produced in muscle cells induce paralysis with age. By analyzing the accumulation of insoluble protein aggregates and motility during and after the diapause we will gain a better understanding of the physiological aspects of the ARD state. These insights will be useful in developing novel approaches to counter age-associated pathologies.

Direct verifications of the validity of Newton's equations for vacuum free-fall in introductory physics laboratories are notoriously difficult due to the presence of atmospheric interactions between falling objects and their environments. The theoretical result, for example, that the gravitational acceleration of an object is independent of its mass is rather easy for observant students to experimentally reject under normal laboratory conditions. What is not so easy is to experimentally verify the validity of mass-independence in-vacuo. This is hindered by inaccessibility to vacuum environments or access to one small enough to fit in a classroom; such access is limited to organizations like NASA. We present here the construction and testing of a portable 1.5m tall extruded-acrylic vacuum free-fall apparatus designed for repeated-measures experiments of time-of-fall with a 2.5g, 40mm diameter magnetic ball over atmospheric pressure ranges 10-4 Torr < p_chamber < 760 Torr. The apparatus includes 12V electromagnet catch and release system within its all-externally-housed actuating mechanisms, automatic digital data acquisition, and a planar optical laser detection system. By comparing time trials in atmosphere and in vacuum, the difference in free-fall times will be isolated and found to be due to air resistance which is not accounted for in the original Newtonian formula. Parameters for this apparatus can be modified to test other ideas for fluid dynamics, such as coefficients of drag and the effects of fluid density on objects as they move through a fluid while using the already present vacuum environment as a control.

 As the world looks for sources of clean energy, the recent advances in lead halide solar cells have shown great promise, increasing from 3% efficiency to 20% in the last few years. Many lead halide or perovskite devices provide the opportunity for low carbon solar cell manufacturing, yet they are still scaled to laboratory settings. By using additive solution based treatments, large-area high-efficiency solar films can be scalably processed through the rapid deposition of perovskite solvents onto roll to roll printers similar to the printing presses used in the newspaper industry. In order to allow for the scaling of the perovskite solar cells, areas of improvement are needed on the small scale with perovskite films on glass substrates, including the need for rapid thermal processing to reduce processing time from 30+ minutes to a matter of seconds. In our work, various methods of rapid thermal treatment on perovskite films were performed by using a xenon flash lamp under different experimental intensities and time series. The flash lamp uses high pulses of energy that interact with the film to rapidly heat it while avoiding degradation due to quick thermal dissipation. These samples will be characterized using X-ray Diffraction, UV-Vis Spectrometry, and Scanning Electron Microscope in order to examine the degradation and grain growth effects. Then, the results will be compared to samples thermally treated from 10 minutes to an hour. Future work of this heat treatment process will be used to optimize the rapid thermal processing needed to roll coat scalable perovskite solar cells films onto a flexible plastic substrate, polyethylene terephthalate (PET). The xenon flash lamp will be attached to the roll to roll printer which will print large area flexible perovskite solar cells to reduce wasted processing energy, and meet increasing energy production needs.

According to  research, polluted air causes the deaths of 5.5 million people every year, with inhalation of fine particles (PM2.5) being the leading cause. Some communities are privileged to have clean and healthy air. Others, especially those who are marginalized, are breathing in chemicals that are causing them to face serious health consequences. The Environmental Protection Agency, established the Clean Air Act in 1970 to set national standards for air pollutants that are harmful. In this research, I will focus on one of these pollutants, particulate matter (PM). PM2.5, are fine particles, 2.5 micrometers in diameter or less, and pose the most danger to the people’s health. They can get deep into your lungs and possibly your bloodstream and cause serious health problems in the future. The goal of this research is to understand if disadvantaged communities are exposed to higher levels of air pollution over time. I expect to see that counties with a low socioeconomic status (SES), and high concentrations of African Americans and Hispanics, will have the highest levels of air pollution. I used county level census data from 1980 and 2010, and looked at indicators including, education, income, and poverty levels as well as looking at differences across race/ethnic groups. Data on PM2.5 are measured based on EPA monitoring data which is then used to predict levels for each county in the US. I then mapped the air pollution levels in in a Geographic Information System known as ArcView, and looked at what communities are affected most, comparing higher SES counties to lower SES. Using my research, I hope to help influence policy decisions that will lead to healthier lives of marginalized communities.

Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a method of organism identification that is currently used widely in clinical microbiology. Compared to traditional biochemical testing, it offers a faster turnaround time and provides a more cost-efficient way to identify clinical isolates. Currently at the University of Washington clinical microbiology laboratory, if a yeast grows from any media other than inhibitory mold agar (IMA) media, it is subcultured onto IMA and incubated to test by MALDI-TOF the following day. This validation study will allow medical laboratory scientists (MLS) to bypass the subculturing step, which will decrease the turnaround time by approximately 24 hours. We evaluated five different media types and incubation conditions, with a sample size of 51 organisms. Through this validation study, it was concluded that the various media and incubation conditions had little to no effect on yeast identification by MALDI-TOF. Because the different conditions tested had no effect on the MALDI-TOF MS score values, this successful validation will allow for shorter turn-around time for yeast identification, which in turn will allow for faster and more accurate patient care.

The good news: According to a Governance & Accountability Institute report (2016), 81% of the U.S. S&P 500 companies have issued a sustainability report. These reports are free, widely available to download from corporate websites, and contain a wealth of longitudinal environmental and social responsibility data. The not so good news: These reports are extremely underutilized by society, due to real and perceived insufficient knowledge of and skills for assessing information and data in sustainability reports. It is important that all stakeholders, including university students, develop skills for using sustainability report information. Why? First, to acquire or deepen one’s understanding of the state of corporate environmental and social impacts, and, second, to make better informed decisions, as consumers, employees, and investors. The research goal was to create and deliver an educational tool for mentoring students in conducting corporate sustainability performance research using sustainability reports. More specifically, the SPA (Sustainability Performance Assessment) System was created by Paun (2016) as a teaching tool. The SPA System is based on the Global Reporting Initiative’s (2016) 91 indicators (i.e. environment, human rights, labor practices, product responsibility, and society). The guiding research hypothesis is that if students increase their sustainability knowledge, then there will be an increased motivation in their desire to work in the field of sustainability. A sample of 265 students in business sustainability courses completed an end-of-course questionnaire about the change in their sustainability knowledge and their motivation to find work related to sustainability. Excel was used to generate descriptive data and run T-test. Preliminary data analysis suggests a positive correlation between sustainability knowledge and the motivation to work in a sustainability capacity.

Previous research has recognized a link between drinking alcohol and later negative consequences such as physical, legal, academic, interpersonal, and sexual problems. Despite the well-known risks linked to heavy drinking, young adults continue to engage in risky drinking behavior especially when they have positive attitudes about heavy drinking. However, little is known about why the relationship between alcohol-related consequences and drinking exists. We propose that attitudes act as a mediator between consequences and drinking. We hypothesize that the more alcohol-related consequences a young adult has experienced, the more favorable their attitudes will be towards drinking, which will ultimately lead to more drinking. To test our hypothesis, a national sample of 1002 young adults aged 18-20 were asked to complete an online survey on young adult health, including drinking attitudes and alcohol consequences. Participants reported the number of drinks they consume on a typical week, the frequency of drinking they consider acceptable, and the number of drinks they consider acceptable to consume in one sitting. Additionally, participants reported whether or not they experienced any alcohol-related consequences in the past 3 months, including but not limited to: “blacking out”, vomiting, a hangover, or driving a car while drunk. In order to test mediation, bootstrap estimation multiple mediation analysis (SPSS Process macro) will be used. Results of this study will provide a better understanding about young adults’ cognitions regarding alcohol-related consequences and may help shape interventions by allowing individuals to draw from their past experiences to guide their future decision-making.

This study recorded the perspectives of people living as homeless and found some significant differences in environmental public health hazards and utilized communication methods between those living in city sanctioned encampments and non-sanctioned encampments. Seattle and King County, in Washington state, have had emergency levels of people living as -and becoming- homeless. In events such as extreme weather events, shelter food poisonings, changes in available resources, increased incidence of drug overdoses, or other emergent issues, public health departments will need tested communication infrastructure to distribute health related information to the homeless population. This study employed semi-structured interviews with question probes around environmental public health concerns and health communication methods in the local homeless population and amongst local agency leaders and health care practitioners. The study findings show that sanctioned encampments had better access to toilets, garbage disposal, and clean drinking water than non-sanctioned encampments. Additionally, the sanctioned encampments have security precautions and existing communication infrastructure such as camp meetings and camp phones that are not present in non-sanctioned encampments. Using the results of this study, there are some recommendations to improve communication between public health departments, homeless-focused organizations, and the homeless population.

Chlorophyll concentration is an indicator of plant health, but is challenging to quantify. As a result, normalized difference vegetation index (NDVI) imaging was developed to help solve this problem by making use of of chlorophyll’s varying reflectance of light waves. This is a proven and powerful tool for observing terrestrial vegetation, allowing for efficient monitoring of living plant populations worldwide. However, no research had been published regarding the use of NDVI for submerged aquatic vegetation, thus our team sought to apply the technique to an aquatic environment, specifically seagrass beds in Queensland, Australia. Seagrass provides both nutrition and habitat for marine life, as well as carbon dioxide storage. The ability to monitor seagrass ecosystems is essential to understand and, in turn, preserve them. We saw NDVI imaging as a potential improvement to current seagrass monitoring methods and conducted experiments to find what issues this technique has in the underwater environment. After testing many aspects of NDVI imaging on in-situ seagrass beds and other test environments, we ultimately found it was not a viable option. This is largely due to basic optical transmission characteristics of water.

An organism’s ability to sense, interpret, and respond to its environment is an essential requirement of life itself. At the cellular level, this process of connecting signals to behaviors is governed by a diverse set of mechanisms such as mitogen activated protein (MAP) kinase cascades, which are broadly conserved across animals, plants and fungi. Alterations to these connections that arise from evolution or disease can have significant phenotypic effects. MAP kinases transmit signals by colocalizing with a target protein and altering its structure through phosphorylation and thereby producing downstream behavioral changes in the cell. Engineering novel phosphorylation triggered interaction domains will allow MAP kinase signaling networks to be rewired to correct pathological dysfunction or to generate novel responses to environmental signals. We intend to use an engineered protein scaffold with a phosphorylatable motif and an occluded binding motif, which was designed by collaborators in the Baker lab, to create a phosphorylation triggered interaction motif in Saccharomyces cerevisiae. By rewiring the S. cerevisiae mating MAP kinase cascade to phosphorylate this scaffold and incorporating a yeast three hybrid output, we hope to demonstrate the function of this new class of interaction domains in vivo. We hypothesize that upon phosphorylation, the scaffold will undergo a conformational change revealing the previously occluded binding motif, allowing another protein to bind and produce downstream effects. Such novel interaction domains will serve as a “toolbox” to allow the rewiring of MAP kinase cascades in any context in which they naturally occur. This approach could be used to fix pathological miswiring of MAP kinase cascades that contribute to anomalies of development or diseases such as cancer. Additionally, the creation of new connections using these interaction domains could be utilized to engineer organisms or cells with useful functions such as plants with enhanced defensive traits or cancer targeting T-cells.

Emissions estimates from wildfires can be estimated from dynamic fuel loadings including litter, duff, and rotten wood. The accuracy and uncertainty in these estimates are generally not well understood which is the basis of our research. Initial wildfire emissions inventories were taken from the Environmental Protection Agency's 2011 National Emissions Inventory and builds on the Fuel Characteristic Classification System fuelbeds (FCCS). Analysis focused on using maximum likelihood to estimate empirical fuel loading distribution from a vegetation database compiled from multiple sources. We highlight the use of the marginal and joint distribution to determine the distribution fit of each fuel loading. After applying necessary data transformations, we then fit each fuel loading to the multivariate normal distributions. Using the multivariate fit, we can make draws from the data that quantifies the uncertainty in the emissions estimates. These results would create a more robust method of mapping fuel-loading distributions and would be used to create a geospatial mapping of fuel distributions.

Plasmids are small circular pieces of DNA that replicate separately from the chromosome. Plasmids often contain antibiotic resistance genes that allow their host bacteria to grow in environments containing that antibiotic. They can be transmitted both vertically during cell division, and horizontally via conjugation to new bacterial hosts, and thus spread antibiotic resistance through populations. Plasmids are often costly to their bacterial hosts when not in the presence of antibiotics, but the coevolution of a bacteria and plasmid can reduce these costs through compensatory mutations. Typically a reduction or an amelioration of plasmid cost is seen during plasmid/host coevolution, but not a fitness benefit. However, preliminary data has shown evidence of a fitness advantage to containing a plasmid for the bacterial host Pseudomonas sp. nov. H2 after it was evolved with the plasmid RP4. In this project, I determined whether the fitness benefit seen in the aforementioned plasmid/host pair also occurs in three other bacterial species with different plasmid types. For each of these pairs the plasmids initially conferred a cost to the host. We hypothesized that compensatory mutations (on either the host chromosome or the plasmid) would result in the reduction, amelioration or reversal of the initial high cost of maintaining a plasmid for all three pairs. To test this, we evolved three plasmid/host pairs in antibiotic-containing media for several hundred generations, selecting for antibiotic resistance genes on the plasmids. We ran competitions between an evolved host/evolved plasmid pair and an evolved host with the plasmid removed, to determine whether there remained a cost to containing a plasmid, or whether that cost has been reduced, ameliorated, or reversed. Our experiments will help explain why plasmid-conferred antibiotic resistance persists in bacterial populations.

Metatarsal stress fractures are among the most common injuries sustained in both recreational and competitive long-distance runners. However, current research lacks a proper understanding of how elevated plantar pressures may pose as a risk indication for stress fractures. Therefore we are proposing a research experiment investigating whether or not elevated plantar pressures exist in women with confirmed stress fractures. We hypothesize that elevated plantar pressures will retrospectively correlate to an increased likelihood of metatarsal stress fracture. In this study, each participant will have a personalized pressure mask of their feet designed that is specifically measured and scaled using their x-ray images. After the successful creation of the personalized mask, all data will be analyzed to investigate absolute, relative and cross-foot ratio comparison between the injured and non-injured contralateral foot. It is anticipated that patients with confirmed metatarsal stress fracture will have relatively larger plantar pressure under the respective fractumetatarsal. The information generated by this experiment may provide valuable insight into understanding metatarsal stress fracture pathogenesis. Further implications could even warrant a secondary study investigating the provision of personalized footwear that lower plantar pressures under the at-risk metatarsal.

Variation in gene expression can be used as a way to test for or track the progression of large scale diseases. Although existing methods to evaluate expression such as RNA sequencing or microarrays are widely used in medical research, clinical application is limited because of time and cost. By monitoring gene expression levels clinicians could perform earlier diagnosis, evaluate therapeutic efficacy and predict recurrence of disease. Gene profiling by a linear DNA-based molecular circuit to classify samples with varying gene expression patterns would provide a novel approach resulting in a rapid, cost-efficient and reliable alternative to existing gene expression diagnostics. Previous work done on the project shows that multi-stage strand displacement cascades can be engineered to perform catalytic signal amplification with high sensitivity, amplification and specificity. In the Seelig lab, already a linear DNA molecular classifier has been engineered to distinguish between bacterial and viral infections and could correctly label 94.0% and 80.5% samples respectively. Although the previous experimental data supports the mythology of the classifier, it is not an ideal representation of clinical use. For that reason, I am working to scale up the molecular circuit by using RNA derived directly from human cancer cell lines to see if the classifier can robustly identify the originating cell line. I will take amplified RNA from each cell and add it to the classifier. The accuracy of initial binding will be analyzed by a fluorescent readout measured across both channels, corresponding to successful strand displacement. Upon demonstration of rapid, cost-effective and accurate classification of human cancer cell lines I then hope to translate this research into classification of clinical samples with the goal to adapt the current methodology into a point of care diagnostics device.

With the rise of social media, politicians use these platforms as tools to reach out to the public, press, and their constituents. During the 2016 United States presidential election, social media platforms played a significant role in guiding political conversation, particularly with the press. Using Donald Trump’s tweets during the Access Hollywood tape scandal as a case study, my research focuses on how political Twitter accounts can impact press coverage. For my research, I analyzed newspaper articles during the first two weeks of the Access Hollywood tape scandal, tracking how the press reacted to Donald Trump’s tweets in their coverage. Through understanding Trump’s Twitter dynamics and how it influenced his media coverage during the presidential election, my project identified patterns in which the media reacts to Twitter and other political social media accounts. 

Inner ear hair cells are the sensory receptors in the auditory and vestibular system of vertebrates. Damage to these hair cells permanently decrease one’s hearing and balance due to inability to regenerate these cells. Transdifferentiation of inner ear support cells into hair cells is a potential method to regenerate hair cells. The Doublecortin(DCX) gene is exclusively expressed in support cells of the cristae in adult mice. We are interested in examining whether there is a correlation between DCX expression and the plasticity of inner ear progenitor. However, we must first examine the temporal and spatial expression of this gene. We hypothesized that DCX expression begins in all inner ear progenitor cells and later gets restricted to support cells. An alternative hypothesis is that only some of the progenitor cells express DCX and these go on to differentiate into support cells. To study this question, we obtained inner ear tissue from mice of varying embryonic and postnatal ages that are DCX-Cre ER heterozygous and Tdtomato homozygous positive. We fed pregnant female mice with tamoxifen one day prior to euthanization, which will activate the tomato reporter causing the DCX expressing cells to look red. We then used immunostaining to identify hair cells and support cells and look for double labeled cells. By better understanding DCX expression, we can develop a protocol using DCX to FACS (Fluorescence activated cell sorting) support cells and/or progenitor cells from the vestibular organs. In addition, we can continue our research to determine the importance of DCX in transdifferentiation of support cells.

Iron sufficiency is essential for optimal brain growth and development, particularly among preterm infants. Current guidelines for iron supplementation of these infants (2-4 mg/kg/day) may be inadequate to maintain iron sufficiency. Our objective was to evaluate zinc protoporphyrin-to-heme (ZnPP/H) ratio and ferritin as measures of iron status in neonates. Iron sufficiency over time was also assessed. All UWMC NICU inpatients who received paired ferritin and ZnPP/H measurements between October 2014 and May 2016 were evaluated retrospectively. Concordance of iron measures were evaluated, as were effects of sepsis, transfusion and iron supplementation over time. There were in total of 601 paired samples from 228 patients and the paired values were assessed during culture-positive sepsis, defined as positive blood culture within 2 days before or 1 day after ZnPP/H or ferritin measurement. Mean ZnPP/H in infants with and without sepsis were not significantly different whereas ferritin values were significantly higher during sepsis. Ferritin values were also more affected by red blood cell transfusion given within seven days prior to ferritin and ZnPP/H measurements. A trend toward worsened iron sufficiency in infants born to diabetic mothers was noted. Small for gestational age infants also showed a trend towards poorer iron status. The mean iron supplementation at 30, 60 and 90 days was 5.4 mg/kg/day, 6.9 mg/kg/day and 7.4 mg/kg/day. Despite this, ferritin values decreased with advancing postnatal age, with 66% of ferritin values <76 ng/dL. In conclusion, ferritin is more significantly affected by sepsis and transfusion, and therefore ZnPP/H may be a more reliable marker of iron status during proinflammatory states. Infants showed worsening iron sufficiency over time despite supplementation above AAP guidelines suggesting a potential need for more aggressive iron supplementation.

The purpose of this project is to develop an automotive “head unit” entertainment system which can be installed into existing vehicles. It employs several connectivity technologies such as bluetooth, Wi-Fi, cellular, USB, and radio. It is also integrated with the vehicle’s data bus for indoor temperature and fan speed control. It includes features for sending or receiving texts and calls from a bluetooth connected phone, playing music from multiple sources, Point of Interest search and navigation around local areas or to a specified location. In addition, it has over the air update and upgrade capabilities, allowing additional content to be added to the system after deployment. Users can interact with the system through both voice and touch inputs. This system is being built with a Dragonboard 410C at the heart, running a modified version of Android. Connected to this board will be a 7" touchscreen, a CAN bus controller, a software-defined radio, and a cell modem. Included inside the board is a bluetooth module, a WiFi module, and adequate internal storage. The voice recognition technology is supported by VoiceBox’s cloud platform - VIBE. This project was developed in collaboration with VoiceBox Technologies.

Crop production will have to double by 2050 to meet projected global food demands. Insect herbivory currently accounts for nearly 15% of global crop losses; thus, plants better able to repel insect attack should have a significant impact on food security. One successful strategy for engineering plants is the constitutive expression of insecticidal toxins such as Bacillus thuringiensis endotoxin (BT). However, the constant production of these toxins decreases crop yield and increases the development of BT-resistant pests. When plants are damaged by insects, they produce the phytohormone jasmonate. We propose a new plant engineering strategy that links the expression of BT to jasmonate signaling. To create this link we have built a synthetic transcription factor called a Jasmonate Degradable CRISPR Transcription Factor (JDCTF). This transcription factor is easily retargeted to any gene of interest by changing the dcas9-associated guide RNA. The JDCTF responds to jasmonate via a jasmonate sensitive degradation domain. Using the plant model Arabidopsis thaliana, we’ve generated transgenic plant lines expressing a JDCTF that targets a Venus-Luciferase reporter. We have shown the system works using a bioluminescence time course assay on seedlings treated with the jasmonate analog coronatine. After induction with coronatine, we observed an increase in bioluminescence in the treated seedlings and no increase in biolumescence for the control. Currently we are characterizing the dynamic response to both exogenous jasmonate, as well as simulated and real insect herbivory on mature leaves. Future work will focus on regulating BT expression with the JDCTF system. Our system has the potential to increase yields, increase consumer safety, and slow down the development of insecticide resistance in pests.

Ceftazidime as a cephalosporin antibiotic has become much less effective against Gram-negative bacterial infections because of the appearance of multi-drug resistant, β-lactamase-producing strains. One of the newly FDA-approved drug inhibitor combinations, ceftazidime-avibactam, is a promising solution to rapidly decreasing susceptibilities to ceftazidime-resistant bacteria. E-test is a well-known manual antimicrobial susceptibility testing method widely used in clinical laboratories as an alternative for the gold standard. This study aims to validate ceftazidime E-tests with a selected panel of non-fastidious Gram negatives consisting of Escherichia coli, Stenotrophomonas maltophilia , Acinetobacter baumannii calcoaceticus complex, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella typhi, Citrobacter spp., Enterobacter cloacae, Klebsiella oxytoca and Proteus mirabillis, against gold standards including TREK Sensitre® micro-broth dilution and agar dilution while performing ceftazidime-avibactam E-tests to generate more data for future investigations on the novel antibacterial drug and its resistance profiles at University of Washington Medical Center. Ceftazidime and ceftazidime-avibactam E-tests were done on all selected patient isolates, and agar dilution was performed only on Stenotrophomonas maltophilia as the reference method instead of TREK Sensitre®. Both the accuracy and precision study results support ceftazidime E-test as a valid susceptibility test, and ceftazidime-avibactam was found to restore sensitivity in most of the resistant strains that were tested. We conclude that ceftazidime E-test is verified and the comparison of ceftazidime and ceftazidime-avibactam yields consistent outcomes as previous research.

Fizikl is a company that uses UAVs to count inventory in warehouse. The goal of the company is to replace the manual inventory counting method that most of the companies uses. Our team worked on the barcode detection and scanning process, as well as the centering of the UAV. The first step to achieve autonomous warehouse is to pinpoint the UAV's waypoints and designate its flight plan. Then, the UAV will take pictures upon arrival at each destination point after centering itself according to the Aruco codes. The distance between the camera and the shelf is carefully set to a fixed value to capture all the items on the shelf. The pictures will then be sent to a ground station where barcode extraction and counting will happen. Th barcode scanner algorithm will also output the location on the pictures where it finds barcodes. We have optimized the barcode detection process by testing the barcode detection algorithm with different qualities of barcodes. We have experimentaly determined how many pictures the UAV should take at a certain destination. We have successfully built a inventory counting system to achieve autonomous warehouse.

Sudden unexpected death in epilepsy (SUDEP) is the most common type of death in people with intractable epilepsies, including Dravet syndrome (DS). DS is a treatment-resistant infantile-onset epilepsy syndrome with comorbidities of cognitive impairment and premature death. DS is caused by a heterozygous loss-of-function mutation in SCN1A, the gene encoding the α subunit of the type I voltage-gated sodium channel Na_v1.1. Cardiovascular dysfunctions have been identified as the main causes of SUDEP. Recent studies have indicated that changes in cardiorespiratory coupling can indicate signs of disease and predict disease susceptibility, such as schizophrenia. We used the established mouse model of DS, which carries a global knock out of Scn1a, and conducted an examination of cardiac and respiratory functions. We recorded video recordings, electroencephalogram (EEG), electrocardiogram (ECC), whole body plethysmography, and LabChart Software 8.0 (AD Instruments) in freely moving DS and wild type (WT) control mice. We then identified and characterized the defects in cardiorespiratory coupling strength associated with SUDEP risk in the DS mice. We hypothesize that cardiorespiratory coupling of DS mice, compared to the WT mice, is disturbed and results in increased complexity between the heart rate and respiration. Findings from these studies may indicate that cardiorespiratory coupling parameters can be used as biomarkers of susceptibility to sudden death in intractable epilepsies and in other severe neurological disorders.

NASA confronts a forward contamination problem with the launch of spacecraft and probes into extraterrestrial environments with potential for detection of life. Earth-origin microbes risk threatening planetary systems, compromising the data obtained, and require implementing microbial control for planetary protection from cross contamination. While generally effective, currently approved decontamination methods are costly, involve high heat and chemical treatments, and risk damaging thermally sensitive spacecraft materials and components. Alternative methods, including atmospheric pressure plasma jets (APPJs), show promise as effective technologies for microbial control. Researchers at Edmonds Community College partnered with Eagle Harbor Technologies (EHT) of Seattle, WA to test the capabilities of an APPJ developed by EHT, performing characterization of killing efficacy. Bacillus atrophaeus endospores were spread on tryptic soy agar plates to quantify killing efficacy of over 900 combinations of APPJ parameters including pulse width, frequency, voltage, distance, time, electrode placement, jet configuration, gas composition, and flow rate. Unprecedented independent control of APPJ pulse width, frequency, and voltage allowed researchers to identify combinations of these parameters resulting in greater than 4-log reduction of endospores. A decimal reduction time (D-value) was additionally determined at an average of 160 seconds on aluminum. High humidity and low concentrations of O₂ were identified as conditions that enhanced killing of endospores. Further characterization of higher voltage, frequency, and humidity, as well as variable pulse width and low O₂ should lead to improved APPJ killing efficacy with decreased exposure time and allow for development of an APPJ optimized for microbial reduction for large-area spacecraft.

Wound healing is a biological process that tissues use to repair themselves after damage. If wound healing is impaired, the tissue may scar or the wound may be fatal. Our lab uses the fruit fly Drosophila melanogaster as a model organism to study the cellular and molecular mechanisms involved in tissue growth, morphogenesis, and homeostasis. Recently while characterizing a novel family of growth factors, Imaginal Disc Growth Factors (IDGFs), our data suggested that one family member, IDGF3, may be upregulated following damage to imaginal discs, the future adult tissue. To explore the potential involvement of the IDGFs in wound healing, I have quantifed their expression by in situ hybridization and localized the mRNA sequences at wound sites in the Drosophila wing imaginal disc. Next, I plan to determine whether specific molecular pathways such as the canonical Wnt pathway or the beta-Akt pathway, which are known to play a role in innate immunity, interact with IDGFs during wound healing. Subsequently, I will use a yeast transcription factor, Gal4, to express RNAi that interferes with mRNA in the same wing disc to determine the relationship between the different pathways. These studies will contribute to our understanding of the mechanisms that regulate tissue healing during development.

Ichthyoplankton are a very important aspect of aquatic ecosystems. Larval fish populations can be a determining factor of the overall health of the ecosystem. Rockfish, for example, are known for their long lifespans and low survival rate past the larval stage. For this study, specific locations in Possession Sound were sampled for the presence of larval fish, with a specific interest in the potential presence of larval rockfish. Eelgrass beds are ideal spawning locations due to their sheltering and food source benefits. Therefore, a 500μm plankton net was horizontally towed over eelgrass beds located at southern Whidbey Island and the Mount Baker Terminal (MBT), as well as nearby offshore sites with a minimum depth of 20 meters. It was hypothesized that larval fish populations would be higher at the eelgrass bed sites compared to the offshore sites, due to eelgrass being a favorable habitat for the larval fish. Data collection occurred between the months of February 2017 and April 2017. Preliminary results support the hypothesis with a total of 24 individual larval fish being found in eelgrass beds, and only 12 being found in open water tows. The overarching goal of this study is to help determine whether or not the eelgrass beds in Possession Sound are current homes to larval rockfish. Due to their endangered status it is important to know where larval rockfish thrive in order to know how to protect them in the future.

The primary producers of the ocean are responsible for nearly 50% of the carbon fixation on Earth. Many eukaryotic primary producers such as globally important diatoms require Vitamin B₁₂, also known as cobalamin, as they lack the biosynthetic pathway for the metabolically expensive molecule. A symbiosis between eukaryotic autotrophs and some marine bacteria has been proposed as the source of cobalamin to these B₁₂-requiring phytoplankton, but the quantitative nature of this relationship is not fully understood. With advancements in analytical techniques in liquid chromatography-mass spectrometry, we can learn more about microbial symbiosis, including vitamin interchange in pelagic microbial communities. This research will investigate the null hypothesis that the mean production of cobalamin of two species of pelagic proteobacteria (Ruegeria pomeroyi DSS-3 and Sulfitobacter sp. SA11) is equal under three different treatments: growth in a limited-carbon environment, growth in an environment enriched with stress molecules from a well-studied model diatom (Thalassiosira pseudonana), and growth in media with stressed T. pseudonana filtrate added. The alternate hypotheses state that cobalamin output will be affected by these different treatments. Data resulting from the experiments will undergo one-way ANOVA tests to determine statistical differences between means. With a more complete understanding of how bacteria and eukaryotic autotrophs interact, the possibilities for this field are significantly expanded. Quantifying cobalamin production in marine bacteria on a per-cell basis under varying conditions is a possible benefit of this research, as well as understanding more about the level of control bacteria exert on their symbiosis with eukaryotic autotrophs.

Mutations are imbedded in every individual’s DNA. A key challenge in human genetics is to determine the functional phenotype of specific mutations. The goal of my research in the Monnat Lab is to develop an efficient, quantitative, cell-based assay to study the phenotype of mutations in a gene in parallel. Our target disease is Fanconi Anemia (FA), a recessive human genetic disease associated with cancer, bone marrow failure, and sensitivity to crosslinking agents such as mitomycin-C. Among of the 21 “FANC” genes that could result FA, we focused on FANCA gene as it is mutated in 2/3 of FA patients. A set of nearly 500 FANCA variants was then used to build a plasmid library encoding each protein variant. In order to achieve this, each variant, linked to a unique DNA molecular 'barcode', will be inserted at a unique chromosomal location in FANCA-mutant human cells in order to determine their cellular phenotype. We will assess cell survival as a function of mitomycin-C dose and the expressed transgene. Preliminary results have already been generated to confirm the feasibility of this approach. My effort thus far has been focused on generating a library of ~500 single nucleotide variants of FANCA. In addition to capturing each variant, I developed an optimized workflow to generate barcoded plasmids with only desired variant without additional mutations in the FANCA. In the coming quarter, I will work with other members to develop a corresponding cell library in which each of these FANCA variants is expressed in a common, FANCA-deficient background for functional phenotyping. Results of my research will help identify new and existing deleterious as well as innocuous FANCA variants, and thus will enable a more accurate molecular diagnosis of FA.

Previous research has emphasized that the basal forebrain partially controls high-order neural processes such as memory. For this reason, it has often been studied in the context of Alzheimer’s and Parkinson’s disease, which both correspond to impaired cognitive function. In spite of the importance of this research, however, there stands much to learn and even revise about our understanding of the neurons which populate the basal forebrain. Neurons expressing the gene T-Box Brain 1 (TBR1) found in the Horizontal Limb Diagonal Band (HDB) and the Substantia Innominata (SI)—both regions within the basal forebrain—have been identified in the past as cholinergic neurons, meaning that they employ acetylcholine as their neurotransmitter. However, immunohistochemical stains of mouse brain sections in the Hevner lab have revealed counterevidence to this claim. We have hypothesized instead that the neurons which populate the HDB and SI are actually glutamatergic neurons, not cholinergic. In order to test this claim, we harvested mouse brains from different ages, ranging from embryonic, postnatal, to adult mice. These brains were embedded in Optimal Cutting Temperature Compound then sectioned these into 12 μm thick slices. These slices were then mounted on slides and stained via immunohistochemical techniques or via endogenous expression. High-magnification images were then collected using AxioVision software to confirm morphology and colocalization of neurons. Employing the above techniques, we have concluded that Tbr1-expressing neurons in the HBD and SI are not cholingeric. Rather, they are glutamatergic neurons. This distinction will be important as research into Alzheimer’s and Parkinson’s diseases develop. An understanding of the precise physical bases for complex, intangible processes is the necessary prerequisite to developing effective therapies.

Ocean warming, due to climate change, is currently altering marine ecosystems. In the Salish Sea, temperature anomalies of up to 4°C per year have been reported. Sea urchins hold an important ecological role as community engineers with the ability to alter the ecosystem in which they are found. The green sea urchin (Strongylocentrotus droebachiensis) relies on phytoplankton as a food source for development in the field, but has been shown to consume kelp detritus in the laboratory. Studies have separately shown the effects of different diets and temperatures on larval growth but have not studied the stresses of increasing ocean temperature with changing food sources and abundance. Here we studied the combined effects of food concentration, food type, and temperature on sea urchin larval development. Contrary to prior studies, our results show that at warmer temperatures, larvae can develop under lower food concentrations, but in agreement with past studies we confirm that larvae develop best under a high concentration phytoplankton diet. Interestingly, we saw increased mortality for larvae grown under warm temperatures and fed a high concentration kelp detritus diet, potentially caused by the introduction of microbes that thrive at warmer temperatures. Warming ocean conditions, causing nutrient composition shifts, could be harmful for sea urchin larvae.

Esthesioneuroblastoma (ENB) is a rare neuroendocrine sinonasal malignancy that is derived from the olfactory epithelium. Optimal management is controversial across institutions despite improvements in treatment methods of this disease. A standard of care for the management of ENB has been hampered by the relatively low incidence, which ultimately prevents the creation of large clinical studies. Most patients undergo multimodality treatment with surgery and radiotherapy with or without chemotherapy. There have been substantial advances in surgery as well as radiotherapy (RT), which may offer improved cancer control and decreased toxicity. We reviewed the management approaches and long-term outcomes at our institution. Forty-two patients with ENB were treated at a single institution from 1986-2016, with pathology reviewed. Demographic, treatment, and clinical data were retrospectively collected from medical records. Patients underwent CT and/or MRI and were staged using the Kadish staging. Event outcomes were calculated from date of surgery to time of recurrence, death, or last follow-up. Survival statistics were calculated using the Kaplan-Meier (KM) method using SPSS Statistics 19. Despite a predominance of locally advanced disease at presentation, relatively favorable long term survival outcomes were achieved for ENB with surgery followed by postoperative RT. ENB has a long natural history with risk of both early and late locoregional and distant recurrences. Local recurrence remains a major problem despite aggressive local therapy. Treatment intensification should be explored in patients with Kadish C disease, including defining the role and optimal timing of systemic therapy.

Microglia are the resident immune cells of the central nervous system, and are responsible for acute inflammatory responses when injury or infection is detected. However, chronic neuroinflammation has been implicated as a key precursor to neurotoxicity, and thus microglia play crucial roles in neurodegenerative disorders. cMaf is an anti-inflammatory transcription factor that mediates neuroprotective functions of microglia such as tissue repair and phagocytosis of cell debris. In 2014, the Garden Lab published results detailing a hypothesized pathway in which cMaf is downregulated by the cell-cycle regulator p53. However, these results were observed in p53 knockout murine microglia that likely have developed compensatory molecular responses to the lack of this critical transcription factor. To determine if acute p53 deletion by Cre-recombinase in floxed-p53 murine microglia influences cMaf expression we utilized AAV-Cre to infect floxed-p53 microglia, which sheds new light upon the current hypothesis regarding the relationship between p53 and cMaf. In this project, we also explored the effect of overexpression of cMaf by infecting wild-type microglia with exogenous cMaf to overexpress cMaf and examine the resulting impact on microglial activation and phagocytosis of apoptotic bodies using flow cytometry. We use quantitative real-time PCR and Western Blot to analyze the immunological impacts of cMaf overexpression in microglia. The implications of this research extend to a wide range of neurodegenerative disorders, like ALS and Alzheimer’s disease, where dysfunctional inflammatory responses may contribute to disease pathology.

Discussing end-of-life care, especially for patients with serious illness, is an important way to ensure that clinicians understand their patients’ wishes and that patients therefore receive the types of care and treatments they want. Conversations about end-of-life care are often not a part of outpatient clinic visits even though the outpatient setting is the best place to have these conversations before a crisis occurs. In this randomized trial, we are investigating whether the use of a short feedback form, the “Jumpstart” form, can help facilitate improved communication about end-of-life care and treatment preferences. The “Jumpstart” form is based on survey questions that the patient completes at the time of enrollment into the study, and the form is shared with the patient, his/her family and clinician. The form provided to the clinician includes prompts to assist the clinician in discussing the patient’s end-of-life care and communication preferences. The effectiveness of this communication feedback intervention will be measured by comparing patients who received the “Jumpstart” form with patients who received usual care. If the “Jumpstart” intervention is effective, patients in the intervention group, as compared with those in the control group, should report improved frequency and quality of communication with their clinician and better agreement between the care they desire and the care they receive. These outcomes were measured by data in the electronic health record (EHR) and abstracted from clinic visit notes and from a series of surveys collected at three time points after the target visit, during which the intervention was implemented (2 weeks, 3 months and 6 months). If this intervention is successful, healthcare systems could implement the "Jumpstart" forms as a tool to improve patient care.

Quasi-stellar objects (also known as quasars/QSOs) are the most luminous type of all known astronomical objects and can be seen over vast cosmological distances (often parameterized in terms of the degree to which light is “redshifted” due to the expansion of the universe). Quasars are characterized by an intrinsic astronomical spectrum that features a very bright continuum, which makes them useful as standard “background sources” to assess foreground material, such as the circumgalactic and intergalactic media. These are the warm-hot gaseous regions of space between and surrounding galaxies that are not directly measurable or observable due to their incredibly diffuse nature. However, as the quasar photons interact with this gas, the intrinsic spectra of quasars is distorted as atomic elements (such as Hydrogen, Oxygen and Iron) absorb some of this light. In my work, I use a Python Graphical User Interface to display the entire processed spectral region of interest and manually scroll through redshifts to detect and identify possible absorption features. I identify hundreds of features as foreground gas at distinct redshifts and subsequently correlate it with the redshift distribution of galaxies nearby in projection along the line of sight for a quasar. I am focusing on QSO PG1407+265, a quasar with a high signal to noise spectrum from a Hubble survey taken with the Cosmic Origins Spectrograph (COS). From that spectrum I have produced absorption models that I am analyzing in conjunction with ground-based galaxy spectra in order to compare host galaxy and circumgalactic metallicities. This particular QSO has a galaxy and absorption system rich sightline that will ultimately serve as a powerful diagnostic of the cosmic baryon cycle, the fundamental driver for galaxy evolution.

What would it mean to be able to hear light? How could this new perspective on light illuminate the fundamental intricacies of light energy? In Gilbert Simondon's musings on individuation he argues that the individual is never given in advance but is constantly coming into being through a process of interacting with its milieu and realizing potentials out of huge pool of possibilities. This work uses Simondon's focus on individuation and life as a never ending process of development to understand how energy exists through a similar process of change and potentials. Utilizing solar panels hacked into speakers, this installation seeks to employ the construction of a new relationship to light as a methodology for thinking about how energy emerges. The solar panels in the installation transduce light energy into electrical energy which is then fed into speakers for the participants to hear. Energy is most essentially a process of change, disruption and movement. It demonstrates to us the myriad of potentials which lie within and between us and energy. Through the use of transduction of energies this installation allows us to peer into the minutiae of our relationship with energy and begin to conceive of how we absorb, alter, collaborate and connect with it on a daily basis.

The process of aging brings about susceptibility to disease and death, but its mechanisms are still poorly understood. Dietary restriction is a potent approach to slow down the aging process, which has shown efficacy in multiple species, including the roundworm, Caenorhabditis elegans, a popular model organism for aging studies. Specifically, pre-reproductive adult C. elegans subjected to starvation enter a state of adult reproductive diapause (ARD), which preserves their lifespan and reproductive potential. Intriguingly, diapaused animals show signs of age-related deterioration upon prolonged starvation, but exhibit dramatic morphological improvements and have normal lifespans following return to feeding. However, the mechanisms regulating this lifespan preservation and apparent rejuvenation are not known. In this project, we aim to identify the genes responsible for the recovery during diapause exit. For that purpose, we used an RNA interference (RNAi)-based screen to inactivate individual genes during exit from diapause and analyzed the resulting phenotypes. Our current results reveal many regulators of metabolism and cellular homeostasis as crucial mediators of post-diapause recovery. Further studies based on these findings will discover the critical steps required for post-diapause tissue rejuvenation and preservation of longevity.

The most common form of cancer treatment is the use of small-molecule chemotherapeutic agents. However, due to non-specific distribution and uptake, these drugs have a host of complications that limit their efficacy and usage. Polymer nanocarriers have been demonstrated to improve drug pharmacokinetics, enhancing therapeutic benefit of the drugs. The feasibility of cyclic micelle-like polymer nanoparticles for use as a delivery vehicle for doxorubicin (abbreviated as DOX), a potent chemotherapeutic drug, is discussed here. It is hypothesized that cyclic polymers will afford a more efficacious pharmacokinetic release profile than their linear counterparts. A linear polymer is functionalized with “click”able moieties at each end, which are then joined to create a single cyclized polymer. The polymer is decorated with poly(ethylene glycol) (PEG) chains to reduce immunogenicity, and carboxylic acid groups to electrostatically complex with the positively-charged DOX molecule. Upon addition of DOX, the polymer self-assembles into unimolecular micelle-like structures. When the construct accumulates in a tumor microenvironment due to the enhanced permeability and retention (EPR) effect, the low pH of the tumoral interstitium protonates the carboxylic acid groups, releasing DOX locally. Using a unimolecular micelle-like approach, less polymer can be used to deliver the same therapeutic payload, relative to other similar approaches that utilize pluralities of potentially toxic polymers to form micelle structures. The polymer’s average molecular weight is around 11530 Da and the polydispersity of the reaction is 1.067. Gel Permeation Chromatography, Nuclear Magnetic Resonance, Fourier-Transform Infrared Spectroscopy, Ultraviolet-Visible Spectroscopy and Dynamic Light Scattering are used to confirm chemical identity, drug loading efficiency, particle size, and polydispersity. Cytotoxicity studies conducted with MDA-MB-231 invasive ductal carcinoma cells in vitro demonstrate the feasibility of this construct.

The Bengal Fan represents much of the accumulation of sediment shed from the Himalaya throughout the course of their uplift. The rate of sediment accumulation places constraints on the amount of material eroded from Earth’s highest mountains. To determine the amount of material deposited on the Bengal Fan through time, we examine the record of Earth’s magnetic polarity captured by sediment cores taken from the Bengal Fan as part of International Ocean Discovery Program Expedition 354. Sediment containing magnetic minerals, such as magnetite, would have polarities that align with the direction of Earth’s magnetic field as the sediment settled into the fan. This makes Bengal Fan sediments an excellent resource for deciphering Earth’s paleomagnetic history. Our data supplement data collected on board ship during Expedition 354, and are being used to link magnetic polarities observed in the cores to a known reversal time scale.

Hemiparasitic plants have the ability to obtain water, nutrients, and secondary metabolites from nearby host plants, while also retaining the capacity to photosynthesize. Through haustorial connections that form on roots, they can have varying levels of influence on their host plants. Hemiparasites have been recognized as keystone species in some ecosystems, playing essential roles such as suppression of competitively dominant species and alteration of nutrient availability. Thus far, the impact of hemiparasites on grassland communities in the Northwest is largely unknown. In this greenhouse experiment, I am testing the effects of the following treatments: 1) hemiparasite identity (Castilleja levisecta versus C. hispida), 2) prevention of parasitism, and 3) drought, on the performance of one species of host plant, Achillea millefolium. I am measuring whether these treatments alter the size or photosynthetic rate of A. millefolium. I expect parasitism to have a substantial effect on the host plant, particularly under drought conditions, with hemiparasite identity being a less significant factor. Anticipated results will show the extent to which Castilleja reduces the host plant’s biomass and affects its CO2 assimilation rate. It would be interesting to expand this study by duplicating it in the field to gain a more comprehensive understanding of the broader ecological impacts of parasitism. These species-specific findings may also be translated to other plant groups and have significant implications for ecological restoration projects.

Autism spectrum disorder (ASD) is characterized by deficits in social communication, repetitive patterns of behavior, and sensory sensitivities. Notably, studies have found that greater ASD severity is associated with lower levels of anxiety and depression. This finding raises the question as to which of these defining ASD characteristics influences internalizing behaviors. We explored the influence of social communication and interaction (SCI) on internalizing behavior symptoms between children with ASD and two comparison groups: typically developing (TD) children and children with sensory processing challenges (SPC). It was hypothesized that children with ASD would show greater levels of internalizing behavior symptoms than both the TD and SPC groups, and that social dysfunction would have a greater influence on internalizing behavior in children with ASD than in our comparison groups. Analyses of variance (ANOVA) were conducted to test for group differences in the relationship between internalizing behavior scores and social subscales from the Vineland and Social Responsiveness Scale surveys. An overall group difference in internalizing behavior symptoms F(2, 42)=21.46, p < 0.001 was found. However, a follow-up t-test did not yield differences between symptoms in children with ASD and SPC t(25)=1.03, p=0.793. We then ran a multiple regression to test for group differences in the effect of SCI on internalizing behaviors. We found a significant group difference in the relationship between SCI on internalizing behaviors, significantly explained by the slope of the ASD group, R2 =.495, t(39)=2.988 p =.005. These results suggest that while children with ASD and SPC show similar rates of social deficits and internalizing behaviors, social dysfunction contributes to internalizing behaviors significantly more in children with ASD than children with SPC. This finding indicates that in children with ASD, social dysfunction may be a contributing factor to internalizing behaviors and consequently an important target for intervention.

The University of Washington’s Manastash Ridge Observatory, a facility utilized by undergraduates to train students in current observational astronomy methods, is being upgraded with a new spectrograph system. Our student-led upgrade is a redesign of all aspects of the existing spectrograph and calibration system. We have purchased a new camera and redesigned a pickoff system that will allow the telescope to switch between spectroscopy and direct imaging. The necessary focal reducing and transfer optics are simple, off-the-shelf items, while the pickoff mirror and slit viewer optics will be made by us. The new spectrograph will use fiber optic cables to take light from multiple locations in the image and extract several spectra simultaneously. This will allow for the spectra of the target, background sky, and a calibration source, which consists of mercury and neon lamps, to be directly compared. Our new method simplifies the process of data reduction and reduces any systematic errors that may occur from one exposure to the next. The light from the dedicated calibration fiber will provide a consistent reference with known emission lines from one exposure to the next, and provide the baseline needed to scale wavelength dispersion per pixel. Once completed, the spectrograph will allow University of Washington students to perform spectroscopy during observation, which is relevant to both undergraduate astronomy course work and modern astronomy research.

Mutations have a large range of effects on an organism’s observable characteristics, from neutral (no effect) to deleterious (lower an organism’s fitness) to beneficial (increase an organism’s fitness). I engineered three mutations into the virus phi-6 and evaluated their effects on viral thermotolerance and growth. Because these mutations were found in a population that had experienced high temperature heat shocks, I hypothesized that the mutant viruses would have a higher thermotolerance than the ancestral virus. To test the thermotolerance of these mutations, I heat shocked bacteria-free lysates of mutant virus and ancestral virus at various temperatures and then calculated the percent survival of the lysate at each temperature. The mutants were also evaluated for their fitness through growth competitions with a common competitor. I found that only one mutation conferred a higher thermotolerance than the ancestor. However, fitness competitions showed that all mutations and combinations of mutations did increase viral growth. This suggested that additional selective pressures may have been present in the evolution experiment. Specifically, the viruses had been grown at low temperatures between heat shocks, which may have resulted in the evolution of higher growth rates, even at the cost of thermotolerance. My research shows that all selective pressures must be taken into consideration when studying evolutionary trajectories. We cannot accurately predict how organisms will evolve in response to one selective pressure such as increased environmental heat without taking in to account the other selective pressures they experience.

What are the similarities and differences between mass political movements? In an important sense, all movements are unique. Yet movements as diverse as a series of protests that shut down one of the biggest cities in Bolivia over water utility privatization, an Arab ethnic-nationalist group in Sudan, and a peasant revolt against the Tsarist government in Georgia, also have important characteristics in common. This poster outlines the methods and process for identifying, understanding, and describing movements as part of the Mass Movements project. The Mass Movements project team is developing the first comprehensive, cross-national survey of the characteristics of mass movements with at least 1,000 participants from 1800 to 2012. Researchers have long studied questions about mass political movements by studying specific cases of mobilization; the data from the Mass Movements project will provide new analytical leverage for testing theories about where mass movements form, how they are organized, and their role in changing politics and policy. The project relies on extensive examination of secondary sources, and utilizes a consensus model for identifying movements and their characteristics requiring both in-depth independent fact-finding and close collaboration between researchers to determine how to describe movements. This method allows nuanced characterizations of and comparisons among diverse movements. The poster illustrates the process through the examples of the Cochabamba Water War in Bolivia, the Janjaweed militias in Sudan, and the Gurian peasant revolt in modern-day Georgia, three dramatically different movements that demonstrate the wide scope of the project and the ways in which researchers translate complex histories into reliable data.

In March of 2011 Dr. Bonita Brewer published a paper proposing a model to explain how a particular error in replication can lead to the amplification of chromosomal segments in an inverted orientation, such as those seen in classes of chromosomal rearrangements that arise in human developmental disorders and cancers. She hypothesized that when a replication fork encounters a short inverted repeat, the leading strands could erroneously become ligated to the lagging strand and produce an extrachromosomal palindromic DNA intermediate. Through my research I am investigating if this model can explain the amplification of the ADH4 locus in yeast, what features of the short inverted repeats lead to the inverted junctions, and what environmental or genetic factors influence this mode of gene amplification. Yeast cells that lack a functional copy of ADH1 (a gene that encodes the major form of alcohol dehydrogenase) become sensitive to the drug Antimycin-A. However, these cells can regain Antimycin-A resistance by amplification of ADH4 (a gene that encodes a minor form of alcohol dehydrogenase). Previously it has been found that the extra copies of ADH4 reside on an extrachromosomal palindromic DNA molecule. Through my research I aim to determine if the extrachromosomal amplification of ADH4 is occurring via this new model. To do so, I have created my own adh1∆:KanMX strain, confirmed that high copy number of ADH4 is sufficient to confer resistance to Antimycin-A, and will isolate the extrachromosomal fragment via pulse-field gel electrophoresis and characterize its structure in detail. In an extension of this work I will test whether genetic and environmental factors that stress the replication process influence the frequency of this form of gene amplification, possibly providing insights into amplification events that contribute to human developmental disorders and cancers.

 In today’s children, the increased use of electronic devices during early stages of development is providing more audio and visual stimulation than ever before. At the same time, attentional deficits later in life are becoming significantly more common. This has lead us to hypothesize that excessive sensory stimulation (ESS), from media sources like TV, Smartphones, video games, etc., during development increases the risk of neurological disorders, most notably attention deficit hyperactive disorder (ADHD). Previous studies in our lab have found that mice subjected to a model of excessive sensory stimulation have damaged cognitive abilities, are less risk-averse, and display hyperactive behavior compared to controls. Our current study aims to build on this data and investigate the impacts of ESS on attention and impulsivity by using the Five Choice Serial Reaction Time Task (5CSRTT), a behavioral test in which mice nose poke a temporarily illuminated target in order to receive a food reward. CD-1 mice were subjected to ESS in the form of flashing lights and sounds for six hours per day for a total of 42 days and subsequently trained and tested on the 5CSRTT. While there was no difference in accuracy between groups, ESS mice displayed significantly increased premature responses in comparison to the controls indicating higher levels of impulsive behavior. These findings suggest a causal link between excessive sensory stimulation and impulsivity, and further illustrate the possible ramifications of the increased use of technology during development.

Photovoltaic devices based on polycrystalline films of hybrid organic-inorganic lead perovskite semiconductors have demonstrated impressive power conversion efficiencies of over 22% while still retaining the advantage of low-cost solution processability. However, a fundamental understanding of many of the photophysical and charge transport properties of these materials must be further developed. In this project, we synthesize a series of n-type doped single crystals of organic-inorganic methylammonium lead bromide (CH₃NH₃Pb_1-xBi_xBr₃) and all-inorganic cesium lead bromide (CsPb_1-xBi_xBr₃) by varying the amounts of Bi3+ cation and use optical spectroscopy and x-ray diffraction to characterize their optical and structural properties. In collaboration with the Chu group in the UW Department of Physics, we use these crystals to compare the charge transport properties of organic-inorganic to all-inorganic perovskite as a function of temperature and doping concentration, in order to understand the mechanisms that determine the charge carrier mobility in these materials. Insight gained from studies on these crystals can be applied to improve device fabrication procedures, ultimately improving perovskite device performance and stability and thereby hastening the introduction of efficient perovskite-based materials into the emerging solar energy market.

Cancer survivors often experience memory and thinking problems after treatment. Cognitive rehabilitation has been shown to improve function in head injury patients. This study examined behavioral and neural responses to a group-based cognitive training intervention in cancer survivors with cognitive symptoms. Gynecologic cancer survivors (n=23) were randomized to treatment group (15) or attention control (8). A subset of participants were eligible for scanning from the treatment (6) and control (5) groups. Both groups attended a 7-session, weekly group-based workshop. The treatment group received education and practice in skills (e.g. method of loci), and the attention control group received only education on cognition and information processing. Prior to and following the 7-session group-based workshops, participants were evaluated with a comprehensive cognitive battery along with an in-scanner verbal memory task where they studied word-pairs (e.g. star–couch) for later recall. During the test phase of the word-pairs task, participants were shown original word-pairs, novel word-pairs, shuffled (old and new) word-pairs, or recombined (two old words not previously paired) word-pairs. Recall during the test phase was assessed at an item level, where responses were yes/no to the query “both old?” or at the relational level, where responses were yes/no to the query “together previously?” Participants in the treatment group showed significant improvement for in-scanner responses in accuracy in the Relational condition, p < .04. Image analysis of group comparison at second level revealed decreased activation in one region in anterior cingulate for the treatment group for item recall. Cognitive training in cancer survivors can improve both attention and verbal memory. Pre to post change in the anterior cingulate for the treatment group suggests additional attention recruitment, consistent with improvements in attention observed with out-of-scanner tasks (e.g. digit span). Overall, cognitive training may be a useful treatment for cancer patients suffering from cognitive symptoms.

Traditional gastrointestinal pathogen detection includes many bacterial, viral, and parasite tests that require clinicians to order many different tests that have various sensitivity and turn-around-time (TAT). As a result, pathogen detection can be delayed or missed, if the correct tests are not ordered. This ongoing study is evaluating the time-to-diagnosis of gastrointestinal infections using the FilmArray Gastrointestinal (GI) Panel test (BioFire Diagnostics, Salt Lake City, UT, USA) compared to conventional methods. The Filmarray GI test is a multiplex PCR test with targets for 22 gastrointestinal bacteria, viruses, and parasites. The study is also comparing the FilmArray GI test to conventional stool cultures, to evaluate the impact of the FilmArray GI test on clinical decision-making. In this interim analysis, the sample population was composed of 167 outpatient or recently admitted (<3 days) patients who had stool specimens submitted for the FilmArray GI test. The time from collection to result for the FilmArray GI test was compared to stool culture. Results from our interim analysis found that the mean time from collection to a FilmArray GI result was 9.8 hours, while the mean time from collection to first actionable stool culture result (if positive) was 62.9. The time from collection to final stool culture result was even longer (77.2 hours). We also found that the FilmArray GI test identified many more pathogens than stool culture: 38% of the samples were positive by FilmArray GI, while only 5% were positive by stool culture. Thus far, the FilmArray test has demonstrated more rapid results and higher sensitivity than stool culture. Ongoing work is evaluating the clinical impact of the FilmArray GI test, but this interim analysis shows that it is more rapid and sensitive than traditional stool culture. As such, it appears to be a promising test for promptly detecting gastrointestinal pathogens.

The ion exchanger monosodium titanate (MST) has been proposed to therapeutically deliver calcium ions in dental situations that require calcium. However, previous results suggest that MST limits cell growth in vitro by mechanisms that remain obscure. It is critical to understand these mechanisms for any successful therapeutic use of MST. The current study tested the hypothesis that MST limits cell growth in vitro by binding to culture polystyrene, reducing attachments sites available to cells, thereby limiting cell culture growth. MST was added to culture wells (8 concentrations between 0 and 200 mg/L) either 24 h after addition of L929 fibroblasts/OSC2 osteoblasts or prior to cell addition. Cell cultures (n = 8/condition) were left in contact with the MST for 72 h, after which cell growth was assessed using Cell TiterBlue®. Control groups received no MST; statistical differences were detected using ANOVA with Tukey post-hoc tests (α = 0.05). When MST was added after plating of the cells, cell growth was inhibited in a dose-dependent fashion to a maximum of 40% (p < 0.05 compared to no-MST controls). Yet when MST was added prior to the cells, the maximal inhibition of growth was 80% vs. controls. (p < 0.05). The addition of MST before cells significantly decreased growth in the cultures (relative to conditions where cells were established first). Microscopic inspection of the culture wells revealed more attachment of the MST to the culture polystyrene than when cells were added first. These results and observations are consistent with our hypothesis that the MST attaches the polystyrene and reduces the ability of cells to attach and proliferate. Further testing with other cell types and additional cell densities is in progress.

For efficient water management, quantifying the amount of water stored in mountains through accurate hydrologic modeling is critical. Snow is an essential aspect of water resources because it acts as a natural storage, and melted snow accounts for a large amount of our water supply. Snow forest interception is the process of trees blocking snow from reaching the ground. Forests cover almost 40% of snow covered regions, and trees can intercept up to 60% of the total annual snowfall. Thus, forest interception has a large influence over how much water is stored in surrounding watersheds. Current methods for modeling forest-snow interception are based on parameterizations from few observations in non diverse areas. Evaluation of such methods is necessary and improvements in modeling will lead to improved hydrologic forecasting and planning. To evaluate such forest-snow interception parameterizations, I used time-lapse photography and citizen science through a project called Snow Spotter. Snow Spotter is an online tool where users can answer questions about the presence of snow intercepted by trees, from time-lapse photography throughout the western United States. Based on the classifications of our users, I created a time series of data containing the interception patterns which I used to develop a temporal understanding of forest snow interception which I compared to modeled parameterizations. The differences outlined in my research allows the time-lapse photography to improve these parameterizations. Thus, it improves the modeling process and the quantification of water resources in general, enabling better water resource management in the future.

Human-associated bacteria are important for human health, but little is known about how these bacteria interact with each other. Bacteroides fragilis (B. fragilis) is a Gram-negative bacteria that is found in the human gut and assists in nutrition. B. fragilis genomes encode the type VI secretion system (T6SS), a needle-like structure that transports toxins into nearby competitor cells. T6SS is used to gain advantage over competitors, yet our lab has observed that B. fragilis strains in adults are four times more likely to lack T6SS than strains in infants, suggesting B. fragilis may lose this mechanism over time. Why would T6SS be lost if it is used to gain an advantage over competitors? I hypothesize that B. fragilis inactivates T6SS because it is no longer required. To test this, I passaged B. fragilis strains with T6SS under competition conditions in which the recipient is either susceptible or immune to the effects of T6SS-delivered toxins. I predicted that recipients with immunity will cause B. fragilis to inactivate its T6SS mechanism, while predicting recipients that are susceptible to be killed off by the toxins delivered via T6SS in B. fragilis. Competitions proceeded for 24 hours, followed with the selection of the donor strain by addition of antibiotics. After selection of donor strains, each were archived in glycerol for evolutionary documentation. Subsequent passages were commenced with newly selected donors. Every 5 generations, competitions proceeded to evaluate competitive fitness of T6SS; whether or not B. fragilis has inactivated its T6SS. Whole genome sequencing revealed the mechanism by which T6SS was inactivated at the level of DNA mutations. By using experimental evolution to study interbacterial interactions within the human gut, we will have a better understanding of the long-term dynamics of the human microbiome and its role in influencing human health.

Systemic Lupus Erythematosus (SLE) is one of the complicated chronic autoimmune diseases that can involve many different organs including liver, kidney and skin. There is evidence that proliferation and apoptosis (cell death) of autoreactive T lymphocytes are defective in SLE, sustaining the inflammatory response. One specific protein that may contribute to T cell dysregulation is CD30. The main goal of my project is to study the expression of CD30 on T cells from SLE patients, specifically Lupus Nephritis (LN) patients. CD30 is expressed on activated memory T cells and it regulates communication between T and B cells along with initiation of apoptosis. Previous studies suggest that there is elevated soluble CD30 in LN patients. There is an FDA approved drug that causes apoptosis by targeting CD30 expressing cells, which is used to treat lymphoma patients. The drug Brentuximab Vedotin could potentially replace chemotherapy for those who cannot tolerate its toxicity and used as a primary treatment. Results of this study provide principle data to support the approach of therapeutically targeting chronic T cell activation in SLE via CD30. I hypothesize that the LN patients with more severe disease will have higher numbers of CD30 expressing cells depending on their diagnosed classes. Patient samples are stained and evaluated by immunofluorescence. The expression of CD30 was correlated to disease status at the time biopsies or urine samples collection. We expect that the higher classes such as III and IV are more likely to have higher number of CD30 positive cells compared to classes I and II as well as non LN patients. Therefore, I compared the frequency of CD30 expressing cells in SLE patients to those without SLE and those with different classes of LN. This research has great implications for SLE patients and could replace previously expensive and highly toxic treatments.

Impacting approximately 400,000 people in the United States, multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system, and the leading cause of disability among young to middle aged people in the developed world. It causes demyelination of neural axons in brain tissue, with associated loss of central and peripheral function. The Mourad lab specializes in applications of focused ultrasound. We, among others, have shown that transcranial delivery of pulsed focused ultrasound (pFU) can non-destructively activate central neural circuits, while others have shown enhanced myelin remodeling of axons activated by laser light in an optogenetic mouse model. Here, we hypothesized that targeted, transcranial pFU activation of axons within MS lesions in a rodent model would decrease the animals’ de-myelination and increase their re-myelination. To this effect, we performed pilot studies. After a baseline MRI session, we simulated MS-like pathology by feeding the mice .2% Cuprizone chow over the course of 10 weeks. We subsequently used MRI imaging two weeks after the end of their Cuprizone course to document de-myelination. This was followed by five days of half-hour long therapeutic transcranial pFU sessions, with subdermal EEG monitoring on the first day to verify neural activation. After a final MRI session, we histologically analyzed the brains of the animals, comparing myelin-stained corpus callosum on the hemisphere of the brain to control tissue. Our pilot study suggests a statistically significant increase in re-myelination in a mouse-model of MS.

Quantum information research often require lasers to deliver energy to devices and to acquire data. The goal of this project is to create an inexpensive and easy-to-build tool to measure and control laser power to support our lab’s quantum information research. The tool interfaces with our lab’s existing data collection and analysis modules. A standalone module is also present for adoption outside of our lab. Some of the intended applications of this tool are the generation of saturation curves for quantum emitters, and performing photoluminescence excitation spectroscopy on samples, both of which require precise control of laser power. The system uses a National Instruments data acquisition device to record a voltage generated by a laser power sensor. The software module also interfaces with an Arduino microcontroller, which can be used to adjust the laser’s power. The software module allows the user to set, monitor in real-time, and record laser power from a graphical user interface. The data taken utilizing the developed power controller will advance the development of quantum computation hardware based on single photons and quantum spins. Quantum computers are theoretically predicted to solve certain classes of problems that are currently unsolvable on today's computers, including the factoring of large numbers which is at the heart of current secure communication protocols.

The obligate human pathogen, Mycobacterium tuberculosis (Mtb), is the primary causative agent of the infectious disease tuberculosis (TB) and ranks as one of the world’s deadliest pathogens; infecting about 1.5 billion people worldwide. Mtb evades the host immune response via intracellular persistence in alveolar macrophages, where it faces chemical stresses such as a drop in pH, various hydrolytic enzymes, increased toxic ion concentration, and highly reactive oxygen (ROI) and nitrogen intermediates (RNI). Modification of mycobacterial proteins by the prokaryotic ubiquitin-like protein (Pup) and their subsequent proteasomal degradation plays a critical role in Mtb survival in this harsh environment. Thus enzymes associated with protein pupylation may be valuable targets in anti-tubercular therapy. This knowledge is exploited in a rational approach to drug design wherein known structural information about the sole Pup ligase, PafA, is used to develop specifically targeted inhibitors. These inhibitors take the form of stabilized short α-helical peptides, which mimic the hydrophobic and electrostatic interactions in Pup essential for binding to PafA. Production of these compounds was achieved using both automated and manual solid-phase peptide synthesis, as well as 'Click' chemistry to modify cyclized variants. Quantitation of inhibitor performance was accomplished by densitometric analysis of SDS-PAGE results from in vitro pupylation assays with purified proteins. Here I report my work on the successful design, synthesis, and testing of helical peptides which display significant activity as PafA inhibitors.

Mycobacterium tuberculosis (M.tb) is the causative agent of tuberculosis, an infectious disease responsible for nearly two million deaths around the world every year. Mycobacteria express a number of cell wall lipids that activate our immune system. For example, T cells are activated by lipids when bound to highly conserved CD1 molecules on the surface of antigen-presenting cells. T cells express a unique T cell receptor (TCR) that is the result of genetic recombination and mutation. Thus, the DNA sequence of a TCR is specific for the antigen recognized by a T cell. Virulent M.tb strains contain sulfoglycolipids (SGLs), but the diversity of SGL-specific T cells has not been determined. This information could be helpful in distinguishing infection from exposure or vaccination. The objective of this work is to determine the diversity of TCRs expressed by SGL-specific T cells. We isolated mRNA from SGL-specific T-cells that were derived from a patient with a latent M.tb infection and used template-switched PCR to amplify the TCR sequences. We will present data summarizing the diversity and conservation of sequence motifs required for recognizing SGLs. The identification of conserved sequences could be utilized to develop novel TCR sequence based diagnostics for M.tb.

A tile is a closed shape and a tiling is a group of these tiles put together such that there are no gaps nor overlaps, much like the tile you would find on your bathroom floor. Our research question is an extension of a problem initially proposed by Ruby Chick and Dr. Casey Mann. In our project, we investigated how changing the edges of squares, rhombuses, pentagons, and hexagons affected the tilings that they admit. We altered the edges of these shapes to have different symmetries; the new shapes had rotational, reflectional, or asymmetric edges, or S-, C-, and J-curves on their edges. The end goal of this project was to find all equilateral, convex tiles that admit only edge-to-edge, edge-k-transitive tilings, where edge-k-transitive describes how the symmetries of the tiling can map one edge of the tiling to others. We restrict our research to only tilings of a single shape. Our hope with this research is to understand how the symmetry of the edges of a tile affect the tilings a tile would admit, which would give us a broader understanding of how tilings arise.

Stressed cells may be able to avoid elimination but continue to respond to compensatory growth signals and accumulate, resulting in tumor formation. This ability to avoid cell elimination processes, such as apoptosis, is one of the hallmarks of cancer. The Jun N-terminal Kinase (JNK) mediates cellular stress responses by inducing apoptosis of stressed cells and promoting compensatory cell proliferation. Using immunohistochemistry and the GAL4-UAS targeted gene expression system, we are able to distinguish intestinal stem cells (ISCs) from enteroblasts, enterocytes, and other intestinal cells through a confocal microscope. We found that activation of JNK in fruit fly intestinal stem cells (ISCs) induced temporary over-proliferation. On the other hand, persistent activation of JNK resulted in elimination of the ISCs. Strikingly, we discovered that ISCs with constitutive activation of JNK 'extrude' out from the epithelial layer of fly intestines. Our findings suggest that cell extrusion may be a mechanism for JNK-mediated tumor suppression, preventing the accumulation of cancerous cells. Alternatively, cell extrusion may be involved in metastasis, enabling cancerous cells to spread to other parts of the body. We aim to further investigate the molecular mechanisms and gene expression underlying cell extrusion in various genotypic backgrounds, which may be helpful to understand how cancerous cells evade cell elimination and undergo metastasis. 

Infantile Spasms (IS), classified as an epileptic encephalopathy (EE), is a severe epileptic syndrome that mostly occurs in newborn babies. Because these seizures are hard to treat, IS can lead to other forms of epilepsy and is often associated with intellectual disability. Many IS cases have an underlying genetic cause – specifically, mutations acquired during DNA replication that disrupt key genetic pathways of synaptic function and brain development. However, many IS cases remain without a genetic diagnoses due to the genetic heterogeneity of the disease. Because IS shares many phenotypic traits with other EEs, my research uses a candidate gene approach to identify genetic variants in the coding regions of 51 known EE genes in a cohort of 105 patients with IS of unknown cause. Sequencing these candidate genes from a population of patients with IS will determine if mutations in these EE genes cause IS. I used next-generation DNA sequencing to screen for variants in 51 known EE genes. I filtered the data to identify 1) variants that result in an alternative amino acid sequence, which may lead to the disrupted function of a protein, and 2) variants that are unreported in a healthy population – identifying 16 variants. IS is most commonly the result of de novo mutations, where the patient has a pathogenic genetic mutation that was not inherited from either healthy parent. I performed segregation testing to determine the inheritance of the 16 identified variants. Of the 105 patients with IS, I identified 4 de novo, pathogenic mutations in 3 genes and am currently waiting on parents to determine the mode of inheritance of 4 other variants. My lab has solved 10% of the IS cases in total. These new genetic discoveries will contribute to a better understanding of IS and lead to more accurate diagnoses.

Companies care of their image in the customers’ mind, then offer customer service to understand and take care of customers’ need. However, customer services seem to be overwhelmed, while they have to serve an increasing huge number of customers. Companies have to pay a lot of expenses for employing labor, while customers are not taken care of well enough. Customer Ticket Classification project offered by Tupl Inc. delivers an algorithm that takes in customer queries, then categorizes and generates responses to those queries. In detail, the algorithm classifies thousands of customers’ messages into different categories and automatically responds to these messages based on the detected categories by using data science and machine learning. In detail, the project employs new data science tools such as Spark and Zeppelin to improve effectiveness. Thus, this algorithm can help companies save man power or labor hours and expenses in operating customer services.

NASA confronts a forward contamination problem with the launch of spacecraft and probes into extraterrestrial environments with potential for detection of life. Microbial control is required in order to avoid cross contamination that would compromise data collected. Currently approved decontamination methods are costly and involve high heat and chemical treatments which risk damaging thermally sensitive spacecraft materials and components. Alternative methods, including atmospheric pressure plasma jets (APPJs), show promise as effective technologies for microbial control. Researchers at Edmonds Community College partnered with Eagle Harbor Technologies (EHT) of Seattle, WA to test the capabilities of an APPJ developed by EHT, performing characterization of killing efficacy and demonstrating proof of principle for large-area spacecraft sterilization. Research demonstrated killing capabilities of APPJ when applied to various conditions including different surface materials, meshes, tapered and elevated holes. The plume of the APPJ traveled through tapered and elevated holes yielding greater than 99% killing of endospores. Application of APPJ as a “brush” demonstrated greater than a 6 log reduction of endospores over 56.75 cm²/10 minute exposure. Findings suggest a brush composed of multiple jets could be effective for spacecraft sterilization over large surface areas of differing materials with capability to penetrate unusual shapes and surfaces. Anticipated improvements in killing efficacy resulting from better characterization of increased voltage, frequency, humidity, and the inclusion of low O₂ concentrations should lead to the development of an APPJ brush effective at spacecraft sterilization.

Development of antibody-based diagnostics, biomolecular sensors, and biomaterial with reactive surface requires the ability to control the adsorption of bioactive protein at a surface. All medical devices exposed in an in vivo biological environment are immediately coated with a layer of adsorbed protein that plays an important role in the body’s behaviors towards the devices and the effectiveness of the devices themselves. In this study, we use a multi-technique approach to characterize the effect of protein G B1 (6 kDa) orientation on multi-layer antibody binding. By conjugating a cysteine group at different positions along the protein’s surface, we can immobilize five variants of the protein (V21C, D35C, E42C, T11C, and WT) onto maleimide and bare gold surfaces. We have confirmed through X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry experiments that the proteins adsorb onto these surfaces. In addition, we introduced primary IgG and secondary F(ab’)2 antibodies to investigate if the protein’s orientation will affect the binding of the antibodies. The adsorbed mass are measured using quartz crystal microbalance with dissipation monitoring. We have demonstrated that the cysteine mutants orient better on maleimide surfaces and encourage more IgG binding. We will also study the effect of temperature on adsorption mass and extend the experiments to amine and carboxyl functionalized surfaces. Fully developed techniques to accurately characterize the orientation and quantify the amount of protein and secondary adsorption will significantly contribute to understanding the interactions of biomaterials with the biological environment.

  Protein homooligomers, multibodied assemblies built from identical polypeptide chains, comprise a large fraction of known cellular proteins. Homooligomers prove to be particularly amenable for many biological applications; they hold the potential as oligomerization domains, often have enzymatic functionality as a byproduct of their oligomeric configuration, and can serve as structural scaffolds for bionanomaterials. While there exists a multitude of protein homooligomers in the Protein Data Bank, the finite number of existing homooligomers limits the potential for custom applications. Our current work involves designing novel cyclic protein homooligomers from a set of de novo designed repeat proteins that bind the Fc region of antibodies. Using the Rosetta software suite, we generated a set of de novo homooligomer models by designing the oligomeric interface to direct self-assembly into a target configuration with three to six identical chains. After a round of refinement, we will express the designs in Escherichia coli and purify them by immobilized metal affinity chromatography. Their oligomerization state will be validated by measuring the molecular weight in solution by size exclusion chromatography paired with multi-angled light scattering and comparing it to the predicted molecular weight of the design. Designs that exhibit the desired molecular weight will be submitted to collaborators for small angle X-ray scattering data and X-ray crystallography. The exclusive use of de novo proteins in homooligomer design grants a greater control over the shape and stability by nature of the repeats, thus making one successful interface design useful for a multitude of shapes and sizes. This variability opens up a wide scope of scaffolds for using these homooligomers for near atomic scale structural characterization by cryo-EM.

The Possession Sound is formed where freshwater from the Snohomish River and the salt water from Puget Sound creates an estuarine habitat that supports biodiversity within this ecosystem. Decreases in pH make it difficult for calcifiers to produce their calcium-carbonate shells, thus decreasing their survival rate in a higher acidity environment. Ocean Research College Academy (ORCA) has been sampling water chemistry at multiple sites in Possession Sound for 11 years. This study utilized ORCA data to compare two sites, one near shore and a second in a deep, central location. The purpose of this investigation was to study the pH and salinity trends from 2008 to 2016, considering influence of surface runoff, temperature, river discharge, and climate variations. It was hypothesized that the pH would decrease, becoming more acidic over the eight year period, and the salinity would remain within normal limits. Salinity and pH data were collected in 1-meter increments using a YSI 650 instrument. Initial data demonstrates an inverse relationship between salinity and pH. In 2013, salinity ranged with depth from 22.2-29.5 ppt near shore and 19.2-30.2 ppt at the deep site, correlating with higher surface pH that decreased with depth of 6.8-7.3 near shore and 6.5-7.1 at the deep site. This relationship was consistently demonstrated over the eight-year period, with the exceptions of 2011 and 2015. Further investigations include exploring the impact of climate patterns on the Snohomish River discharge and its influence on pH and salinity trends, as well as looking for seasonal trends in primary productivity of phytoplankton and their impact on temporal and spatial trends.

Endothelial cells (ECs) are cells that line our blood vessel walls. They differ throughout the circulatory system. For example, high pressure arteries typically have tighter endothelial junctions/gaps than the leaky, low pressure veins. ECs are known to sense fluid shear stress and hydrostatic pressure. These cues play a large part in embryonic development of the vasculature and induce short term responses in adults, such as dilation and constriction of arterioles, but it is unknown if adult ECs adapt to them in the long term. This matters for many medical procedures, such as venous graft bypass surgery, where the saphenous vein is implanted to bypass a blocked artery. These grafts are often lifesaving successes, but they sometimes re-occlude. Venous and arterial endothelium are very distinct, and it is important to know if the venous ECs in the graft can adapt to their new arterial environment. If not, that could explain the pathological re-occlusion. Here, we measure adaptation by changes in gene expression from a venous to an arterial phenotype. We designed a novel in vitro pump system to expose a flow chamber with endothelial cells to controlled flow and pressure. HUVECs (human umbilical vein endothelial cells) were then cultured and seeded into the chamber. Finally, a quantitative real time polymerase chain reaction (qRT-PCR) will measure gene expression at various time points in the venous (20 cmH₂O, low flow) and arterial (60 cmH₂O, high flow) cases. We analyze the markers EphrinB4 (EphB4) (higher in veins), EphB2 (arteries), Cx40 (veins) and endomucin (arteries). We present preliminary gene expression data from the 24-hour time point. We hypothesized that HUVECs will respond to arterial conditions with increased arterial gene expression, while retaining their venous state in venous conditions. Supporting or falsifying this will illuminate endothelial cell response to changing conditions in the body.

Today’s teens are more affected by stress than any other age group. However, measuring stress in teens as it happens in the real world can be difficult. Pencil and paper surveys are burdensome and even computer and phone surveys can be tiresome. Ecological Momentary Assessment is a longitudinal approach to capturing events as they happen in real-time in the real world. Students and faculty in Human Centered Design and Engineering are developing a social robot to measure stress in teens in their real world - school. In order to be effective as a measurement tool, this robot needs to be likable and engaging to its teenage users. Faculty and students utilized a human-centered design approach to study teen-robot-interactions using a minimally functional robot. Observational and interview pilot data were gathered from a combination of peer user studies and EMAR interactions with Seattle area high school students, ages 14-18. Descriptive analysis of initial data provided three important findings. First, despite designing a genderless prototype, teenagers instinctively and unanimously assigned a male gender to EMAR. Second, even with a minimally functional design, teens were very engaged with EMAR, often repeating various interactions again and again. Third, even in a high-tech world, teens find EMAR’s boxy, low-tech prototype design appealing. Future research will involve further iteration of the EMAR prototype in order to better understand teen-robot interactions, focusing on engagement and likability. By capitalizing on these attributes, it is possible to design a robot that is truly engaging for teens, thereby able to capture teen stress and mood in the real world.

Inflammasomes are one of the key components of the innate immune system. They sense pathogen-associated molecular patterns (PAMPs) in the cytosol of the cell and are responsible for the activation of caspase-1 to induce processing of the inflammatory cytokine IL-1β and pyroptosis. Activation of caspase-1 cleaves pro-IL-1β to its active form, IL-1β. Pyroptosis is programmed and inflammatory cell death that occurs upon intracellular pathogen infection. Pyroptosis can be triggered by the cytosolic detection of lipopolysaccharides (LPS) and their main toxic component, lipid A, which are large molecules found on the outer membrane of gram negative bacteria. LPS and lipid A are also detected by Toll-like receptor 4 (TLR4) on the membranes of immune cells. To further characterize the function of inflammasomes, we transfected human monocytic THP-1 cells with LPS and lipid A to deliver these components to the cytosol. We then quantified the inflammatory response of the cells by quantifying IL-1β and pyroptosis. To quantify IL-1β, we performed ELISA in cell supernatants. To quantify pyroptosis, we measured release of lactate dehydrogenase (LDH), a cytosolic enzyme that is released upon cell lysis. We found that – in contrast to simple stimulation of the cell with LPS or lipid A – delivery of LPS and lipid A to the cell cytosol induced IL-1β release and pyroptosis, suggesting caspase-1-dependent inflammasome activation. In addition, we found that different transfection reagents were variably cytotoxic. Future experiments will investigate whether delivery of other bacterial PAMPs, such as flagellin or TLR2 agonists, to the cytosol activates a similar inflammasome response as LPS/lipid A. Our findings will have important implications in understanding the immune response to bacterial infections and could help to develop more effective treatments.

Analyzing complicated, extended source emissions in radio frequencies allows for going beyond typical point source models used for Epoch of Reionization analysis. Our research uses data from the Murchison Widefield Array, which is a radio telescope observing regions of the southern hemisphere to detect the faint signal from hydrogen during the formation of the first stars and galaxies. Extended source emissions can include celestial bodies ranging from active galactic nuclei emitting jets of synchrotron emission to the first galaxies that populated our universe. We anticipated the extended sources to show structural changes from day to day and in different frequencies, due to normalization errors, ionospheric disturbances, and physics of the frequency-dependent emission.We made histograms of the radio data of the extended source objects to create images in different frequencies and from different days to get a more accurate view of the extended sources. This process was also used to create difference images for direct comparison between frequencies and observations. These images can be incorporated into a formula that removes unwanted bright objects from our view of the Epoch of Reionization. We did, in fact, observe expected changes from day to day and in different frequencies, as well as observing changes that could be due to atmospheric disturbances or other potential sources of error. This has been taken into account along with the potential for improvements to normalization for the sake of comparison. The images created prove that we are statistically sampling at a higher resolution than expected due to the brightness of the extended source objects, which has important implications on our ability to work towards imaging and understanding the point just beyond the Epoch of Reionization, and from there, the early Universe.

Imidacloprid (IMI), a neonicotinoid, 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 million ppb in artificial seawater (SW), but not killed and subsequently recover. Our objective was to determine if emamectin benzoate (EB) is a better alternative to IMI. EB, the active ingredient (a.i.) in Slice(R), is currently registered for use in marine waters for the control of sea lice on farmed salmon. We simulated a 6-hour tidal exposure of adult non-gravid female ghost shrimp to concentrations of EB (as the insecticide Proclaim(R)) ranging from 0.01 to 100 ppb a.i. within artificial seawater alone or sediment + seawater. No treatment-related mortality was observed within the 96-hour test, but overt effects were observed, particularly at 100 ppb in both seawater (abnormal body position) and sediment (lethargy, inability to burrow). Results suggest that the 6-hour exposure was not sufficient to cause mortality. In a subsequent 96-hour test, we will expose the shrimp to EB mixed directly into the sediment simulated tidal cycle. As the shrimp re-establish their burrows, we anticipate increased exposure to the chemical and mortality. EB is more effective as a pesticide when ingested and, in comparison to IMI, targets the primary neurophysiology of crustaceans including sea lice and burrowing shrimp.

Mycobacterium tuberculosis complex (MTBC) infects one third of the global population, with 5-10% developing active tuberculosis. As a contemporary global health concern, highly effective tuberculosis detection methods are crucial for diagnosis and control. The gold standard approach involves hazardous, difficult collection of sputum samples, followed by pathogen detection either by molecular methods (PCR) or bacterial culture. Oral Swab Analysis (OSA) uniquely uses oral swabs to collect epithelial and bacterial cells from the interior of the mouth. The swabs are then analyzed using an in-house extraction and quantitative polymerase chain reaction (qPCR) protocol. In a previous study, OSA accurately detected MTBC in 90% of TB patients. OSA provides a non-invasive, simpler, and faster detection method for MTBC. The current project aimed to optimize the sample preparation and qPCR detection methodologies. Of particular interest is a modified DNA re-suspension step that originally took 60 minutes and was performed using 5ul of a storage buffer. We hypothesized that a reduction in incubation time in conjunction with increasing the re-suspension solution to 15ul would have a negligible effect on the final DNA yield. Using spiked samples at known dilutions, re-suspension incubations were tested at fifteen and sixty minutes. The modified protocol produced DNA yields that outperformed the original protocol. The average changes in qPCR signal strength for the three dilutions were by 3.9, 4.9 and 5.1 units. Based on this performance, the modified re-suspension has been adopted into the official protocol. The modified protocol conserves valuable lab time enabling continued expansion of OSA benefits. Generating a faster turnaround time is not only relevant for high priority samples of this project, but for future TB detection application on a global scale.

 Housing First, also referred to as harm-reduction housing, is one approach to addressing the unique needs of chronically homeless people who are often multiply affected by psychiatric, medical and substance use disorders. Housing First entails the provision of immediate, permanent, low-barrier, housing that does not require sobriety. Beyond the provision of housing, low-barrier, client-centered supportive services are essential to the Housing First approach. The Life Enhancing Alcohol-management Program (LEAP) was a three-phase community based participatory research project designed to facilitate the codevelopment and evaluation of client-driven harm-reduction programming for a Housing First setting. This study describes the content of and attendance at activities that were designed within the LEAP project. Participants (n = 66) were residents in a single-site Housing First program who had lived experience of chronic homelessness and alcohol use disorders. LEAP activities were developed by residents, researchers, and agency management and staff in community advisory board meetings. LEAP activities included a) administrative leadership (e.g., Welcoming Committee, LEAP Advisory Board), b) meaningful activities (e.g., gardening, art hours), and c) pathways to recovery (e.g., talking circles, one-on-one and group harm-reduction treatment). Sociodemographic information on participants was gathered in one-on-one interviews. Attendance records were used to assess participation in LEAP activities during the 6-month follow up. Of LEAP study participants in the Housing First project, 86% reported engaging in at least one activity. On average, residents participated in 16.76 activities (SD= 2.99). Of those who attended activities, 95% of participants attended more than once. Low-barrier activities reached a sizeable proportion of Housing First residents, and residents often remained committed to attending activities over the longer term. Findings may help housing providers design meaningful activity programming for Housing First settings.

Beavers create complex modifications to the physical and biological components of stream ecosystems through their creation of dams and wetland complexes. Beaver impoundments alter the movement of surface and subsurface waters through riparian systems, which substantially affects biotic and abiotic ecosystem processes that together make up habitats for different species. Although there is general agreement that beaver impoundments modify stream temperature, there has been very little focus on their effect at larger spatial scales. In prior research, traditional temperature assessment methods have failed to capture the full spatial breadth of riverine systems. The use of thermal infrared remote sensing (TIR) is an effective tool for measuring surface stream temperature variability at landscape scales. To better understand the role of beavers in the regulation of stream temperature, we evaluated TIR imagery collected within the Snoqualmie and Stillaguamish River basins in Washington State. Our objective was to identify whether TIR imagery could be used to identify areas where beaver dam complexes have measurable effects in decreasing downstream water temperature due to the upwelling of groundwater. We used an intrinsic potential beaver habitat model to identify areas within the TIR flight paths where beavers were likely present and surveyed these areas to confirm presence of beaver wetland complexes. We compared upstream and downstream surface temperature, thermal complexity, and heterogeneity within these areas using a suite of spatial statistics. Our results have the potential to demonstrate that the use of TIR is a novel approach for monitoring the effects of beaver on riparian systems. Its use provides for assessments at scales and breadth not previously possible using traditional approaches.

Mutations in the gene Presenilin 2 (PSEN2) cause familial Alzheimer’s disease (fAD). FAD shares clinical and pathological features of sporadic, late onset AD thus fAD cell models can be useful to study mechanisms relevant to all forms of AD which is critical to developing effective AD therapeutics. Presenilin 2 protein (PS2) forms the catalytic subunit of the γ-secretase complex, which cleaves amyloid precursor protein and releases Aβ1-42, considered a pathogenic contributor to Alzheimer’s disease (AD). Our laboratory is interested in a fAD associated PSEN2 mutation, a frameshift two base-pair deletion (PSEN2 K115Fx) . The PSEN2 K115Fx is predicted to either lead to a truncated protein suggesting that the mutation may create a shortened peptide that interferes with normal cellular function (dominant negative or toxic gain of function) or result in degradation of the RNA transcript and subsequent loss of normal amount of PS2 protein (loss of function). To better understand how PSEN2 mutations cause disease, we have two objectives. The first aim of this project is to determine if the PSEN2 K115Fx does indeed result in a truncated protein or influence levels of wildtype PS2. I will be collecting human cultured fibroblasts isolated from AD patients with the PSEN2 mutations or controls and prepare cell lysate for analysis by Western blot. My colleague will also be analyzing mRNA levels from those same samples to determine the stability of the PSEN2 mutant and wildtype transcripts in all cases. The second aim is to determine the impact of the mutation on PS2 enzymatic activity. I will culture the cells described above, then infect with a luciferase based enzyme reporter assay to compare the impact of PSEN2 mutations on γ-secretase mediated cleavage of APP. My work will help identify the candidate mechanisms by which the PSEN2 K115Fx mutation causes AD.

There are many age-related cardiac diseases that relate to impairment of muscle function, including heart failure and arrhythmia. Previous studies show that increased mitochondrial function results in the enhancement of cardiac and skeletal muscle function as mice age. In these studies, the SS-31 tetrapeptide was used, an agent that serves as an antioxidant by binding to cardiolipin in the inner mitochondrial membrane, enhancing electron transport and increasing ATP generation, and protecting against damage from Reactive Oxygen Species (ROS) by reducing their generation. However prior literature has suggested that ultrastructural morphology does not change in relation to age. The goal of this study is to quantitatively assess interfibrillar mitochondrial damage caused by these ROS', and to see if there is structural improvement after treatment with the SS-31 peptide. Eight 24 month-old mice were split into two treatment groups, four treated with SS-31 for 8 weeks and four untreated. Four 8 month-old untreated mice were used as controls for youthful, “ideal” mitochondrial structure. The mice were euthanized, and cardiac tissue was harvested, sectioned, and examined by transmission electron microscopy (TEM). Quantitative analysis using NIH ImageJ software allowed the comparison of the SS-31 treated and untreated old hearts to young hearts. This revealed stark differences when comparing the young and old ultrastructure. Untreated old mice exhibited higher amounts of vacuolation, greater lack of mitochondrial axial organization, and lower density of mitochondrial cristae than the younger untreated mice. Older mice treated with SS-31 appear to exhibit improvement in ultrastructural definition compared to untreated older mice, but additional quantitation is necessary to validate this observation. In further testing, we are examining the persistence of the SS-31 tetrapeptide's positive effects after its administration period ends, and how ultrastructure changes during this refractory period.

Alzheimer’s Disease (AD) is a debilitating neurodegenerative disease that currently affects over 5 million Americans. We have previously demonstrated genetic and neuropathology-based variation across cognitively-defined AD subgroups. Here we sought to determine whether patterns of vascular risk factors differed across cognitively defined subgroups. We used data from the Seattle-based Adult Changes in Thought (ACT) prospective cohort study of individuals age 65+ and dementia-free at enrollment. ACT follows people at 2-year intervals to identify incident dementia and AD. We used cognitive data at the time of AD diagnosis to determine scores for memory, visuospatial abilities, language, and executive functioning. We used these scores to determine each individual’s average cognition and then domain-specific deficits below that individual average. We used these data to define six groups: no prominent domain, memory-, visuospatial-, language-, or executive functioning-prominent. We evaluated risk factors for these six groups from self-reported medical conditions including diabetes, stroke, and hypertension, and diagnosed atrial fibrillation or coronary artery disease. We used multinomial logistic regression models with the no prominent domain group as the reference. To account for multiple comparisons, we present tests of the null that each risk factor is unrelated to each subgroup, and an omnibus test of the association between each risk factor and any subgroup. Of 825 cases, nearly half had no prominent domain, a few had multiple prominent domains, and a single domain was prominent for the remainder. Memory-prominent domain was more common in people with diabetes and executive functioning-prominent was less common, although the omnibus test did not reach statistical significance (p=0.08). Despite low statistical power due to small group sizes, our results suggest possible differences in risk associated with diabetes. Subsequent work will refine these investigations using medications and evaluating glucose levels over time. These results support additional efforts to further understand cognitively-defined AD subgroups

The plainfin midshipman fish, Porichthys notatus, is a species of teleost fish that produces social acoustic signals for intraspecific communication. One social signal used during reproduction is the male advertisement call or “hum”. The hum is essential for courtship and reproduction because females use it to localize males at night during the breeding season. The hum has been implicated in mate selection, because the nocturnal environment prevents visual assessment of males. Here, I aimed to test the hypothesis that the male hum is a condition-dependent or “honest” acoustic signal that provides information related to the quality of the sender. I plan to investigate whether the acoustic properties of the hum are related to size and/or other morphological characteristics of the type I male (i.e., the condition or quality of the sender). We characterized the sound pressure level (SPL) and first five harmonics (H1-H5) of each hum using an oscilloscope and Adobe Audition. Furthermore, we measured standard length (distance from the tip of the snout to the base of the caudal fin), total mass, gonad mass, swim bladder volume, and swim bladder mass to calculate condition factor (K, a measure of body volume that relates to animal condition), gonadosomatic index (GSI, a ratio of gonad mass to body mass), and swim bladder muscle index (SBMI, a ratio of swim bladder muscle mass to body mass). The hum’s harmonics and SPL were statistically analyzed for correlations with the morphometrics. Results indicate that the frequencies of the harmonics (H1-H5) were negatively correlated with male GSI, however our low sample size and statistical power lead us to conclude that further data collection will be needed. The results of this experiment will add key information related to the acoustic communication and behavior of the plainfin midshipman and will provide new directions to future behavioral experiments.
 

The need for energy efficient chemical reactions is growing in response to the world’s energy crisis. Reactions must not only be high yielding but also require low energy input. Many redox processes of interest involve the transfer of electrons from the surfaces of electrodes and need an electrical input as driving force. The ability to promote redox reactions photochemically would greatly reduce the energy input needed. As of yet, interfacing electrochemical reactions with colloidal photosensitizers in order to promote them photochemically has not been done. This project experiments with CdSe quantum dots as the colloidal photosensitizer by absorbing visible light from an LED light source and transferring an electron in order to reduce ferrocenium to ferrocene as a model reaction. The goal of this project is display the ability of CdSe in the productive electron transfer promoted by visible light to ferrocenium. Knowledge of this model system can be applied to more complex reactions in the future and the work done here will help understand how to drive industrial chemical reactions via sunlight. 

Research has shown that chronic inflammation can facilitate the progression of certain diseases, including cancer and diabetes. One way to prevent inflammatory-linked diseases is to reduce the occurrences of inflammation. Since much of society uses nature-derived approaches of healing and disease prevention, we focus on how natural products (i.e. compounds from nature) alter cellular inflammatory status. Fungi and fungal extracts provide a rich source of novel natural products. Fungi have been shown to have beneficial health properties, exemplified by the antibiotic penicillin, derived from the fungus Penicillium chrysogenum. By studying many different fungal extracts and chemically separated fractions of fungal extracts, we hope to find novel anti-inflammatory compounds. In this study, novel fungal extracts and fractions were tested for anti-inflammatory activity against the cellular transcription factor, nuclear factor kappa B (NF-kB), a major mediator of cellular inflammation. Prior single-dose screening resulted in extracts and fractions that were shown to inhibit NF-kB activity. From these, eight were tested in dose-response assays that measured NF-kB activity and cytotoxicity. Human hepatoma Huh7.5.1 cells were transfected with a luciferase reporter gene under control of the NF-kB promoter. Twenty-four hours later, transfected cells were incubated with either extracts or fractions for 30 minutes prior to activation of inflammation by tumor necrosis factor-alpha, (TNF-α). NF-kB activity and cellular ATP were measured by luminescence 3.5 hours later. The ultimate goal is to identify extracts, fractions, and pure compounds that inhibit NF-kB without causing cytotoxicity. Such compounds will be advanced for further study and possible application in chronic inflammatory disease states.

Arsenic, a known carcinogen, has been linked to numerous cancers, and its toxicity and persistence in the environment at low levels impact both human health and ecosystem integrity. Due to natural and anthropogenic factors, the concentration of arsenic has elevated in many areas. Phytoremediation is a cost-effective, eco-friendly technology that uses the natural ability of plants to remediate pollutants, such as arsenic, from contaminated soils. Endophytes, mutualistic microbes colonizing the internal tissues of plants, have been shown to increase host-plant tolerance to a wide range of environmental stressors, and we hypothesize that arsenic-tolerant endophytes may improve the tolerance of their host plants to arsenic. The arsenic-tolerant isolate PD12R, identified as Rahnella aquatilis, has been shown to grow at a higher concentration in the presence of arsenic, than it does without. We hypothesis that this unexpected result may have to do with its ability to form a protective biofilm. This biofilm is made up of a matrix of extracellular polymeric substances (EPS) which bacteria use as a protection against environmental stressors. EPS may be protecting PD12R from arsenic either by slowing diffusion to the cells, or by chemically chelating the arsenic in the EPS matrix. This has an important application in plants because it may indirectly help reduce free arsenic in planta by promoting plant tolerance, thereby enhancing the process of phytoremediation. We are currently testing PD12R, and two other isolates, to determine whether biofilm production is correlated with arsenic concentration in the media, and whether arsenic is bound by the EPS matrix by using a 96-well plate set up to test optical density and colony forming units. The results will then be compared to the EPS data which will be quantified using a crystal violet assay.

Previous research has shown that Implicit Association Test (IAT) scores on a suicide-relevant IAT significantly predict future suicidal behavior. Additionally, evidence suggests that social exclusion may be a significant risk factor for eventual suicide; however, given that previous studies have been mostly correlational in nature, inferences regarding the causal relationship between previously identified theorized risk factors and suicidal behavior remain elusive. This study sought to address this gap in literature by experimentally manipulating experiences of social exclusion and looking at its impact on both implicit and explicit measures of suicidality. Participants were 42 undergraduate students who were asked to play Cyberball, a virtual ball-throwing activity in which the participant was randomized either to be included or excluded by virtual players whom the participant believes to be real. Afterwards, participants filled out The Survival and Coping Beliefs Scale (SCBS), an explicit measure that has been shown to prospectively predict one’s future suicidal behavior, and they then performed a behavioral assessment of implicit suicide cognition using the death/suicide Implicit Association Test (d/s IAT). An independent sample's t-tests found no evidence for a statistically significant difference between experimental conditions in average SCBS scores regarding their self-reports of expectations for the future following the Cyberball task. However, participants in exclusion conditions scored significantly higher on d/s IAT compared to their counterparts, which suggests socially excluded groups identified more strongly to suicide than the inclusion conditions following the Cyberball task. This study provides proof-of-principle findings that this type of methodology may be able to be applied to other research questions investigating the link between established risk factors and suicide-related constructs. From these findings, we infer that there may be a causal impact of social exclusion on one’s relationship to suicide and death on implicit levels that may not correspond with explicit reports.

Small cell lung tumor (SCLC) is a type of lung tumor that accounts for 10-15% of new lung cancer cases. It is an aggressive cancer that is often not detected before metastasis occurs. Even with chemotherapy and radiotherapy, SCLC has a very high mortality rate and patients tend to develop chemoresistance quickly. Unlike other types of lung cancers, SCLC has no available gene-targeted therapies. This project examines the development of chemoresistance in SCLC genetic mouse models . This approach deletes tumor suppressor genes, such as Rb1 and Tp53, and/or activates oncogenes like lmyc, using a Cre-expressing virus in mouse lung tissue, which leads to the development of SCLC. My role included verifying tumor burden following magnetic resonance imaging (MRI) and quantification of tumor volume in the lungs using MRI data. Once MRI confirmed tumor burden, mice are treated with chemotherapy and tumor volume measured over three weeks of drug treatment. The tumor response to chemotherapy will be compared in different genetic mouse models. At the end of treatment, lung tumors are collected and I use immunohistochemistry to measure the response of the tumors collected from the genetic mouse models. I examine markers of cell proliferation and cell death to assess drug effectiveness. These results could be relevant clinically if certain genetic mutations are found to be associated with chemoresistance.

Bacteria are widely used in metabolic engineering because they can synthesize chemical products from cheap, renewable carbon sources. A major current problem, however, is that toxic intermediates can build up when bacteria express heterologous biosynthetic pathways. In principle, we can control metabolic gene expression levels so that downstream enzymes quickly consume toxic intermediates. To achieve this goal, we use a programmable gene regulatory tool called the CRISPR-Cas system. To optimize gene activation activity of CRISPR-Cas in bacteria, we sought to identify modular transcriptional activation domains that could be recruited to specific genes to activate transcription. This strategy has been previously used successfully in eukaryotic cells, but with only limited success in bacteria. We used CRISPR-Cas to recruit a number of potential synthetic transcriptional activators to specific loci in E. coli, and identified candidates that can activate a fluorescent reporter gene. We also used protein-engineering approaches to optimize the gene activation activity of our CRISPR-Cas system. The transcription factor screening and protein engineering we did gave an 80-100-fold increase in activation compared to basal transcription levels. To make this new tool useful for practical metabolic engineering, we plan to use this system to dynamically respond to metabolic stresses. This tool could potentially be used to optimize biosynthesis of useful polymer precursors such as lactate and p-aminostyrene. Production of these types of cheap, biosynthetic precursors will help us move towards a greener industrial future.

Cystic Fibrosis (CF) patients are highly susceptible to colonization and infection by Pseudomonas aeruginosa, a bacterium that is a major contributor to CF-associated morbidity and mortality. Inflammation is a key part of the immune response to bacterial infection. However, inflammation can damage the lung and in the case of cystic fibrosis, lead to permanent structural damage. Respiratory failure is the leading cause of death for CF patients. The inflammasome is a protein complex that, upon activation in macrophages, leads to release of signaling molecules, IL-1b, and pyroptotic cell death. P. aeruginosa interacts with the host cell to trigger a protein, NLRC4, that mediates inflammasome activation. We recently found that a common variant of the NLRC4 gene (rs212704) is associated with lower mRNA levels in monocytes and is a genetic marker of NLRC4 deficiency. The cellular and clinical consequences of human NLRC4 deficiency in response to bacterial pathogens are largely unknown. We hypothesize that NLRC4 deficiency regulates host macrophage responses to NLRC4 ligands and infection by Pseudomonas. To test this hypothesis, we stimulated macrophages with ligands known to induce NLRC4 mediated inflammasome activation as well as with P. aeruginosa. We established an optimal dose and exposure time to monitor IL-1b secretion and pyroptosis before applying this assay to monocytes collected from people with the rs212704 variant. We expect less IL-1b production and pyroptosis in macrophages with the variant compared to wild-type macrophages due to an altered inflammasome response in these cells. The common variant allows us to study the mechanisms by which inflammasome activation affects CF-like outcomes. Additionally, we aim to knockout the NLRC4 gene using CRISPR technology and study the impact that it will have on the inflammatory response. The results derived from the experiment will ultimately help in the identification of novel therapeutic targets for patients with cystic fibrosis.

Age related changes in brain composition contribute to cognitive and functional decline. It is established that there is a decrease in vascularity, neuron density and brain volume, but changes in the extracellular matrix (ECM) components that provide support to microvasculature and cellular networks are understudied. The brain ECM is comprised primarily of Hyaluronan (HA) and HA-associated ECM, such as chondroitin sulphate proteoglycans. HA is a non-sulfated glycosaminoglycan that is synthesized at high molecular weight, but readily degraded to low molecular weight HA that is neuroinflammatory and damaging to microvasculature. We have previously shown that brain microvascular density decreases with aging and that this decrease is associated with increased HA accumulation. We now examine regional localization of HA, HA-associated ECM and the brain microvasculature in aging. Young (4 months, n=15), Middle (14 months, n=5) and Aged (24-25 months, n=15) murine brains were examined. Mouse brain sections were labeled with biotinylated HA binding protein or an antibody against chrondroitin sulfate proteoglycans. Brain microvasculature was identified by labeling with solanum. The cerebral cortex, midbrain, forebrain, cerebellum, and striatum were imaged (a minimum of 3 sections per region) at 10x. The location, association with microvasculature, and intensity of staining were quantified by ImageJ. We find that with aging, there is an increase in HA throughout all regions of the brain that is most prominent in the cortex. In contrast, there were no significant differences in CSPG accumulation with aging in any of the regions examined. We propose that the increase in HA, without a concomitant increase in HA- associated ECM to provide stability, leads to greater amounts of neuroinflammatory low molecular weight HA in aged brains. We postulate these changes promote loss of microvascular density, which contributes to other deleterious changes in the brain with aging.

Open clusters are groups of gravitationally bound stars formed from the same molecular gas cloud. These clusters and their stellar metallicity enhance our knowledge of stellar evolution, stellar cluster characteristics, and the chemical evolution of the Milky Way (MW) Galactic disk. Stars that are actual members of the cluster must be identified within each cluster’s observed field of view. We present OCMAP, an Open-source Customizable Membership Analysis Program developed in python for use within the astronomy data science community. Cluster membership is determined using simulated star fields and stellar photometry magnitudes across multiple filters. OCMAP matches stars across images, plots color-magnitude diagrams (CMDs), standardizes stellar magnitudes, and calculates the local and field star density on a CMD for each prospective member in order to determine a probability of membership for each star. OCMAP was developed to ultimately determine the membership and metallicity of 42 open clusters observed with the Apache Point Observatory 3.5m telescope and Dominion Astrophysical Observatory 1.83m Plaskett telescope using Sloan and Strömgren filters, respectively. We tested OCMAP on 8 of the 42 open clusters we have observed, and now present the resulting members-only Sloan [u-g] vs. [g-r] and Strömgren [m1] vs. [b-y] metallicity plots, as well as Sloan [g] vs. [g-r] and Strömgren [y] vs. [b-y] color-magnitude diagrams for each open cluster.

We aim to find diversity in the HHV-6B genome via sequencing of the U90 gene. We have previously sequenced 120 whole genomes of HHV-6B from New York, Japan, and Fred Hutch chromosomally integrated (Ci-HHV6B) strains and found the U90 gene to encode the most diversity. Our hypothesis was that candidate U90 sequencing of clinical samples for which whole genome sequence could not be accomplished due to low viral concentrations would give the most amount of phylogenetic information of candidate loci available. Eleven excess serum samples from Seattle Cancer Care Alliance and Fred Hutch for which genome sequencing failed were amplified for the U90 locus using nested PCR, pooled, and Nextera/Illumina sequenced. Of those nine samples three had fewer than five changes across the 3kb locus, and one sample accounted for 95% of the diversity in the gene among these eleven samples. We found sequence clusters outside of sequences published to genbank, as well as clusters outside of the 120 whole genome sequences. Nine of the eleven samples clustered with the New York isolates. One shows significant genetic distance from the Japanese group, while another isolate shows similarity to the Z29 reference strain. This demonstrates an unexplored diversity in HHV6B genomes with much more diversity to be expected. Further U90 sequencing studies would expose more diversity in HHV-6B in a low cost, but effective, manner. 

Recent studies have shown that electrical stimulation of the spinal cord can manipulate spinal cord plasticity and may be effective in recovering motor function after spinal cord injury. The emerging field of optogenetics allows researchers to change a cell’s membrane potential using light. Cells are made to express light-dependent ion channels (channelrhodopsins) which cause a cell to depolarize or hyperpolarize after being triggered by specific light wavelengths. Our lab has shown that optogenetics can be used to elicit forelimb movements in rats by stimulating the cervical spinal cord. Long-term methods for providing light stimulation in vivo are needed to explore the treatment potential of optogenetics. Initial experiments by our group using a LED implant stimulator demonstrated that long-term optogenetic stimulation of the spinal cord results in increased GAP-43 staining. GAP-43 staining highlights areas of new neuronal growth, suggesting an increase in neuronal plasticity in optogenetically stimulated rats. Animals in this study, however, also exhibited unusual tissue morphology around the site of implant. Current research is working to understand the possible sources of this tissue disruption, including heat production from the LED and inflammation induced by LED stimulator implantation near a spinal cord injury. To investigate the possibility of heat production, I developed a new implant prototype that incorporates a thermistor to monitor temperature changes during long-term light stimulation. I tested this implant design in anesthetized and freely-moving rats to investigate how different light stimulation parameters affected implant temperature. I then performed histological tissue analysis at the site of the implants to assess the effects these temperature changes had on tissue condition. The results from this work will inform the next generation of light stimulation implants, and help to improve function following spinal cord injury via optogenetic activation of neural tissue.

This work develops a parallelized algorithm to compute the dynamic mode decomposition (DMD) on a graphics processing unit using the streaming method of snapshots singular value decomposition. This allows the algorithm to operate efficiently on streaming data by avoiding redundant inner-products as new data becomes available. In addition, it is possible to leverage the native compressed format of many data streams, such as HD video and computational physics codes that are represented sparsely in the Fourier domain, where a signal is analyzed in terms of sinusoidal frequencies rather than time. This massively reduces data transfer from central processing unit (CPU) to graphics processing unit (GPU) and enables sparse matrix multiplications. Taken together, these algorithms facilitate real-time streaming DMD on high-dimensional data streams. We demonstrate the proposed method on numerous high-dimensional data sets ranging from video background modeling to scientific computing applications, where DMD is becoming a mainstay algorithm. The computational framework is developed as an open-source library written in C++ with CUDA, and the algorithms may be generalized to include other DMD advances, such as compressed sensing DMD, multi resolution DMD, or DMD with control. Keywords: Singular value decomposition, dynamic mode decomposition, streaming computations, graphics processing unit, video background modeling, scientific computing.

Agricultural workers use pesticides to prevent insect damage to crops. There are state and federal regulations about how to handle pesticides safely. However, off-target drift is an undesirable consequence of pesticide application. The Washington State Department of Health tracks pesticide-related illnesses and found that orchard workers can experience pesticide drift exposure. The goal of this study was to use water sensitive paper (WSP) to measure pesticide drift downwind of an orchard where pesticides were being applied. First, we collected passive air samples by evenly distributing WSP at different downwind distances throughout the neighboring orchard in vertical and horizontal planes on two different days. On Day 1, we placed 15 horizontal samples 0.3 meters above the ground at distances 5, 26, and 52 meters downwind. One Day 2, we placed 4 vertical samples at 0, 2, 4, and 6 meters above the ground at the same 15 downwind locations (n=60). We then conducted an analysis to confirm the wind direction and speed. After drying, I analyzed the samples by taking pictures of the WSP and using photo-editing software to emphasize the contrast between the paper and droplet marks and correct perspective angles. I counted the droplets using bioimaging to measure the diameters of fine (106-235 um diameter), medium (236-340 um diameter), and coarse (341-403 um diameter) sized droplets. With this, I quantified the number and size of drift droplets on the WSP. We observed higher concentrations of droplets in the WSP closest to the sprayed orchard, yet all the WSP showed evidence of drift. The results of this study will help provide evidence of pesticide drift and of methods to estimate drift exposure. This is important because the observations provide motive to look into ways to keep orchard workers safe from pesticide exposure.

As part of an ongoing effort to maintain the current high standard of astronomical instrumentation at the Apache Point Observatory in New Mexico, the Astronomy Undergraduate Engineering Group is pursuing a series of instrument and facility upgrades. One such upgrade includes new optical slits for the Dual Instrument Spectrograph (DIS). This instrument is a “variable slit” aperture that has a series of fixed width slits that mount into a rotating wheel. With DIS, the user can rapidly switch the slits as needed for their observing program, which is a powerful feature of the spectrograph. DIS is used in long slit spectroscopy from observing the rotation curves of galaxies to the expansion of optically thin nebulae. The slits being replaced were machined from stainless steel, giving undesirable width and edge uniformity. To eliminate these issues, we have constructed the new series of DIS slits using microelectromechanical systems (MEMS) processing at the Washington Nanofabrication Facility in order to get slit widths with precision on a sub-micron scale and edge uniformity less than 1%. The MEMS processing involved laser lithography, wet etching silicon wafers with KOH, and thin film deposition of aluminum. Full characterization of the finished product was done with microscopy and Fraunhofer laser diffraction. This fabrication process will provide unprecedented spectroscopic accuracy, enabling astronomers from dozens of member institutions to gather data faster and more accurately than ever. The MEMS processing manufacturing technique also has the potential to be used at other sites as it allows a way to make a wide variety of slit configurations more efficiently and at a lower cost than ever before.

Previous research has found substance use disorders (SUDs) to be disproportionately high in HIV positive patients, with lesbian, gay, or bisexual (LGB) status adding another critical dimension of risk in HIV research, resulting in poor HIV-related health outcomes in these two populations.  Given these findings, the present study hypothesized that sexuality and substance use would interact to produce poorer quality of life (QOL) and greater cumulative viral burden in HIV positive persons.  The records of adult patients (n=1653) within three HIV care clinics were obtained from the Center for AIDS Research Network of Clinical Integrated Systems during the period 1/1/1995 to 12/29/2014.  Two parallel analyses of covariance were performed to analyze variations of both viral load and QOL between-groups using self-reported LGB status (absent, present) and SUD status (absent, present) as predictor variables, controlling for 5-year historical enrollment interval and for HIV care clinic.  Cumulative viral burden reflects the computational index of viral load over time, reported as viremia copy-years (VCY), whereas QOL was assessed using a validated self-report instrument (EuroQual).  These analyses indicated: 1) LGB and SUD status predicted differential VCY and QOL with LGB status predicting higher VCY and QOL and SUD presence predicting higher VCY and lower QOL.  2) LGB status and SUD presence interacted such that the poorest QOL was found among heterosexuals with SUD.  3) HIV care clinic and historical enrollment interval both accounted for significant variance in VCY, whereas only HIV care clinic accounted for significant variance in QOL.  These findings strengthen the claim that both constructs are reliable predictors of salient outcomes within HIV care.  Further studies that elucidate why viral load is higher in LGB and substance abusing populations may offer significant public health gains though lowered cumulative viral burden, and greatly improve the QOL of these populations.

My research addresses the deficit of diversity in race, gender, and culture in the urban planning profession. Diversity and equity are extremely important, studies have shown that diverse groups are known to be better problem solvers and help build stronger communities. Due to the ever-growing concern for safety and equity in cities and the lack of racial diversity in the urban planning profession, evaluating the undergraduate entrance into the urban planning field is imperative to see how issues of racial equity can be addressed. Therefore, this project evaluates outreach and admissions processes of the undergraduate urban planning program at the University of Washington - Community, Environment, and Planning (CEP). The project includes a literature review assessing definitions of diversity, equality, equity and outreach best practices; a qualitative survey addressing the thoughts of stakeholders; a demographic study comparing the racial percentages of students in the program to that of the Masters of Urban Planning Program and the University of Washington at large; and a formal outreach and diversity plan that will be used by CEP as a major-wide commitment to diversity and equity. This plan will help ensure that issues of racial equity are addressed by the future urban planners that graduate from University of Washington. Without diversity, equity, and inclusion in the CEP education process, the graduating planners would be unable to work in collaboration with citizens and address the needs of their communities. It is the responsibility of all planners of the future to take control of their education and learn about racial equity issues elucidated by this study to ensure that they are truly able to plan cities for everyone.

Studies have shown that alcohol consequences are associated with alcohol-related sexual consequences. Studies on young adults have found that alcohol use is linked to risky sexual behavior , and alcohol-related sexual consequences are common. Women absorb and metabolize alcohol differently than men, and literature has found gender differences in alcohol consequences. However, gender differences in alcohol-related sexual consequences and the association between alcohol consequences and alcohol-related sexual consequences have been understudied. The current study will examine (1) gender differences on subscales of alcohol consequences and alcohol-related sexual consequences and (2) associations among alcohol consequences and alcohol-related sexual consequences by gender. We hypothesize that women will exhibit higher scores than men on the subscales of academic/occupational consequences, blackout drinking, impaired control, risk behaviors, and self-care. Additionally, we hypothesize that women will exhibit higher scores than men on the subscales of disregard of personal boundaries, neglect to use birth control, and sex with someone they just met. The current study used baseline data from an intervention study focusing on drinking and sexual behavior among a national sample of young adults (N = 402), who completed an online survey. Participants reported if they experienced alcohol consequences (21 items), such as “While drinking, I have said or done embarrassing things.” Additionally, participants reported if they experienced alcohol-related sexual consequences (41 items), such as “I had digital sex I later regretted.” Regression analyses for count outcomes were conducted to test gender differences in alcohol consequences and alcohol-related sexual consequences, controlling for alcohol use and sexual behavior. Spearman correlations were also conducted. Results will provide a better understanding of the relation between alcohol and alcohol-related sexual consequences and help shape interventions for reducing behavioral risks.

Early childhood experiences determine future success in well-being, school, work, and in the community. Adversity creates an accumulated number of risks that are potentially damaging and could contribute to greater vulnerabilities for negative health and social outcomes, including the likelihood of entering the juvenile justice system. Recidivism of offending from the juvenile into the adult years is higher for people who start offending at an early age. My research project focused on examining the relationship between childhood adversity and early behavioral indicators of risks for entering the juvenile justice system and the role of cultural connection and social support as protective factors against the negative effects of adversity across different ethnic groups. Data was collected using baseline and Wave 9 data from the Fragile Families and Child Well-being Study (N=4,898). The measured variables were parental adversity, cultural connections, and social support to investigate the relationship between childhood adversity and externalizing behaviors. Findings provide evidence towards the potentially increased risk and vulnerabilities of children exposed to multiple adversities in childhood towards later involvement in the juvenile justice system. This study showed that there is a positive relationship between childhood adversity and externalizing behaviors, where greater adversity was significantly associated with worse externalizing behavior (p<.01). Social support was a significant protective factor for all ethnic groups. Additionally, results show that cultural connection and social support are promising resources that could mitigate adversity’s impact on behavioral risks and vulnerabilities of young children. Examining protective factors in the context of early exposure to adversity helps to identify potential targets for preventive interventions.

Most of the atomic matter in the universe lies in the diffuse ionized gas in the inter and circumgalactic medium, cycling in and out of galaxies over billions of years. Mapping this cosmic baryon cycle is the key to understanding galaxy properties and evolution. Because we cannot observe gas by its own emission, we use a technique called quasar absorption line spectroscopy to study the gas. Quasars serve as bright background sources, and as light passes through gas clouds and galaxy halos we can analyze absorption features in the spectra to determine elements that are present in the gas. These absorption features also give us information about the distance to each gaseous system. When an absorption system with a high density of elements is identified in proximity to a known galaxy, it is likely that the system is galactic halo gas that is cycling in and out of the galaxy. I present my analyses of three quasar spectra at redshifts z = 0.789, 0.88, and 0.99, with a list of identified gaseous systems that are potentially associated with known galaxies. The study of these systems will help us gain an understanding of how this cosmic baryon cycle has given rise to the visible structures in the universe

Entering the 2016 presidential election, Hillary Clinton stood poised to become the United States’ first woman president. An electoral win would have assigned Clinton status as a symbolic first, or a figure who comes to represent social change by becoming the first member of a social group to assume some position from which members of this group have been excluded. Drawn from previous literature on symbolic victories for social movements, our initial hypothesis predicted that a Clinton win would influence Americans to be less concerned with gender inequality and to think that future steps to promote equality were less important. Given Clinton’s defeat, however, we modified our hypothesis to be that gender inequality would become more salient and Americans would prioritize reducing this inequality more, compared to before the election. Within-subjects shifts in these attitudes were measured by administering self-report surveys before and after Election Day 2016. While participants’ perceptions of broad societal gender equality conditions did not change, participants’ support for specific policies aimed at remedying inequalities increased following Clinton’s defeat. We offer potential theoretical and contextual explanations for these findings. Additionally, we explore how individual differences contribute to these primary effects. Our findings suggest a window of opportunity to organize collective action around gender equality issues.

Merkel cell carcinoma (MCC) is an aggressive, neuroendocrine skin cancer and one-third of patients develop metastatic disease. Specific sites and timing of distant metastases are largely un-described and, if characterized, could inform staging and surveillance protocols as well as optimize clinical  management. A cohort of 292 patients with metastatic MCC were prospectively followed and then grouped by the site(s) and timing of their initial distant metastases. Initial distant metastases were defined as the first distant metastatic lesions detected clinically and/or radiologically. Presentation of multiple lesions in a single organ site only counted as one initial distant metastasis for that organ site. MCC-specific survival was analyzed using a competing-risks regression, where 200 patients died of MCC. 292 patients had 420 distant metastatic sites, most commonly non-regional lymph nodes (40% of 292 patients), skin / body wall (26%), liver (22%), bone (20%), lung (9%), pancreas (8%), and brain (4%). Patients with only liver lesions (HR 2.1; p=0.02) or patients with lesions in multiple sites (HR 2.7; p<0.01) were over twice as likely to die of MCC than patients with distant metastases limited to the skin / body wall. Additionally, patients whose first distant metastasis occurred >3 years after initial diagnosis were twice as likely to survive MCC than patients whose MCC metastasized within two years of diagnosis (HR 0.5; p=0.02). Site of primary MCC is associated with a distinct pattern of initial distant metastasis, which may help inform surveillance practices. Survival outcomes vary among patients with metastatic MCC and prognosis may be more accurately estimated with stratification by timing and site(s) of initial distant metastasis. Accounting for these patient characteristics will help inform surveillance imaging intervals and define sub-staging for patients diagnosed with metastatic MCC.

The incorporation of trivalent ytterbium ion (Yb³⁺) impurities, or dopants, into nanoscale materials is of significant interest due to the unique optical properties of the Yb³⁺ ion. The electron configuration of Yb³⁺, 4f¹³, is associated with just one f-f electronic transition (²F_5/2↔²F_7/2) that is narrow and lattice-independent with an energy of ~1.27 eV. This makes luminescent ytterbium doped colloidal semiconductor nanocrystals, which are solution processable, ideal for use in silicon-based solar energy applications like luminescent solar concentrators. Doping colloidal nanocrystals with ytterbium ions, however, is not necessarily sufficient for creating a material with luminescent ytterbium. It is necessary for ytterbium to be sensitized by energy transfer from a visible light absorber in order to be emissive. Previous synthetic work indicates that the most promising route for sensitizing ytterbium is the direct doping of ytterbium ions into visibly absorbing host nanocrystals such as chalcogenide semiconductors. Incorporating ytterbium ions into chalcogenide semiconductor hosts, however, poses a significant synthetic challenge. Additionally, it is essential to optimize synthetic reaction conditions such as growth temperature, growth time, coordinating solvent used, precursor concentration in coordinating solvent, and ytterbium dopant concentration in order to produce a material with luminescent ytterbium. These synthetic variations are informed by physical characterization of the morphology, absorbance, and photoluminescence of previously synthesized ytterbium doped colloidal nanocrystal samples by transmission electron microscopy, absorbance spectroscopy, and photoluminescence spectroscopy, respectively. It is expected that current efforts to optimize these synthetic parameters and interface ytterbium doped colloidal nanocrystals with compatible ionic materials in a process known as ‘shelling’ will allow the reproducible creation of a novel nanoscale material with bright ytterbium luminescence at room temperature. Upcoming fundamental studies of these ytterbium doped colloidal nanocrystals will probe the dynamics of energy transfer by time-resolved photoluminescence spectroscopy and provide insight into the kinetics of ytterbium sensitization.

Hair cells are mechanosensory receptors of the auditory and vestibular systems in vertebrates. Loss of hair cells or hair cell dysfunction, leads to defects in hearing and balance. There are several mitochondrial gene mutations that lead to hearing loss, however, whether these mutations affect hair cells directly remains unknown. Two mitochondrial proteins known to be involved in sensorineural hearing loss, CLPP protease, and Timm8a translocate, were chosen as the focus of this study. To investigate the role of these proteins in hair cell function and susceptibility, I used the zebrafish lateral line as a model. Lateral line hair cells are structurally and functionally similar to those in the mammalian inner ear, but instead detect changes in water flow. CRIPSPR/Cas9 was used to introduce dsDNA breaks in CLPP and Timm8a in zebrafish embryos. Non-homologous end repair following dsDNA breaks is error prone, and can introduce small insertions or deletions (indels) in the protein coding sequence which often leads to a loss of function in the protein. In order to quantify hair cell susceptibility, I treated embryos 5 days post-fertilization with varying concentrations of neomycin, a well characterized ototoxin, and counted the hair cells remaining after treatment. Future characterization of these mutants will involve examining mitochondrial activity and oxidation levels. These studies will provide insight into how mutations in CLPP and Timm8a affect hair cell function and susceptibility to damage. Additionally, they will more broadly inform our understanding of how changes in mitochondrial function can cause deafness.

Semiconductor materials are essential components for modern electronics, making them one of the most useful tools in the modern world. In recent years, scientists have discovered single layered, two-dimensional (2D) materials that exhibit semiconducting properties. These 2D semiconductors can be used to create light emitting diodes (LEDs), field-effect transistors (FETs) and are promising candidates for a new generation of high performance solar cells. The optical response of these 2D semiconductors are highly sensitive to the crystal purity; impurities within the crystal lattice can obscure their unique optical properties. Here, we use photoluminescence spectroscopy to characterize the optical properties of tungsten diselenide (WSe2) produced using a new high pressure growth technique at the National Institute for Materials Science and Engineering in Japan. We analyze the spectrum of emitted light to determine the crystal quality and compare the degree of circular polarization in the sample photoluminescence, a key indicator of crystal quality, with other samples found in the literature. We find the sample of WSe2 to be of good quality with few impurities, making this method a step forward in the production of high quality WSe2 crystals.

Tyrosine kinases are critical drug targets in oncology due to their role in tumorigenesis. Accordingly, the treatment of specific cancers has been revolutionized by the development of tyrosine kinase inhibitors (TKIs). However, the long-term effectiveness of TKIs is undermined by the emergence of drug resistance. This resistance is often caused by mutations that prevent drug binding. Understanding how a given mutation affects drug sensitivity can enable physicians to personalize their treatment based on a patient's specific tumor genotype. However, current methods to identify resistance mutations are laborious and can only isolate a small subset of possible mutations. Previously, our lab developed a technique to simultaneously measure the functional effect of all single mutations within a protein of interest. We leveraged this method in order to generate a novel system for the rapid and comprehensive characterization of resistance mutations in oncogenic tyrosine kinases, thus overcoming previous technical limitations. Key to this system was choosing a functional assay that could accurately discriminate between the mutations of interest (in our case, drug resistance mutations). Our functional assay was built around Ba/F3 cells; a mammalian cell line whose growth is uniquely dependent on oncogenic kinase signaling. The first step in this project was to validate this growth phenotype by using three clinically relevant oncogenes: FGFR2, ALK, and JAK2. To do this, I cloned each oncogene into a mammalian expression vector, transfected the cloned vectors into Ba/F3 cells, and measured the growth rates of each transfected cell line. As I anticipated, only cells harboring an oncogenic tyrosine kinase grew, thus validating the cell line for further development. These results represent the first step toward the generation of a system for widespread identification of drug resistance mutations in cancer relevant kinases.

A large body of research has examined the association between disadvantage and crime in neighborhoods, usually finding a strong positive association between neighborhood disadvantage and crime. Neighborhood disadvantage is associated to crime via a variety of pathways, including, but not limited to, reduced educational opportunities and reduced collective efficacy (i.e., the ability of residents to control or influence the behavior of other individuals and groups in the neighborhood). However, research that links neighborhood disadvantage to crime has not examined the effects of clustering, better understood as grouping, of neighborhoods on the relationship between neighborhood disadvantage and crime. In metropolitan areas, predominantly minority-occupied, disadvantaged neighborhoods are often grouped together into specific areas. In other words, poor neighborhoods are adjacent to other poor neighborhoods compounding the disadvantage that inhabitants of these neighborhoods face. This is important to understand because it means that segregation of neighborhoods may be helping to drive high crime rates within neighborhoods. I extend this body of research by considering the role of clustering in the relationship between neighborhood disadvantage and crime. I use data from the National Neighborhood Crime Study, which includes tract, city, and metropolitan level variables to analyze crime and spatial inequality. The poverty and spatial proximity data is provided by the Neighborhood Change Database, which includes tract level data for impoverished neighborhoods as well as longitude and latitude of said neighborhoods. I use these two data sets to analyze the effects of neighborhood clustering through various data analyses. Preliminary data analyses show a statistically positive relationship between spatial proximity and number of murders. From this, it is expected that spatial proximity will also have a statistically positive relationship with overall crime.

It is known that dietary restriction is a positive intervention in aging. Its efficiency was demonstrated in multiple species suggesting that dietary restriction acts through conserved mechanisms that are not well understood. Specifically, in Caenorhabditis elegans (C. elegans), dietary restriction can extend lifespan well beyond that of their fed counterparts. Remarkably, it has been found that upon starvation young adult C. elegans enter a state of adult reproductive diapause (ARD) that allows a full lifespan preservation. We aim to characterize the mechanism by which lifespan can be preserved and extended in the diapaused animals. To this end we will investigate whether ARD animals experience typical age-related changes during prolonged starvation and whether they are reset upon diapause exit. Through fluorescent microscopy, we intend to distinctively characterize phenotypic differences of the cytoskeleton and nuclear morphology between ARD individuals and their fed counterparts. We expect these age-related markers either remain intact throughout the diapause state, or repaired upon diapause exit. This will further allow a better understanding of aging as wells the mechanisms of lifespan and healthspan preservation.

Many mainstream video games involve difficult game levels and challenges such as boss-battles and puzzles, leading some gamers to become frustrated as they struggle to advance to the next game level. In some cases, this frustration may lead gamers to give up on playing the game entirely. Although walkthroughs for video games are available online to help gamers when they get stuck, the gamers need to manually locate where they are in the game to obtain appropriate hints. Not only can manually looking for hints be inconvenient and time consuming, but it can also expose gamers to spoilers. We hypothesize that we can improve the gaming experience by providing gamers with a system that can automatically determine their current location in a game and serve up a link to a walkthrough video that demonstrates how to proceed. The goal is to queue up a video from the spot where gamers are stuck without the gamer having to know the level, scene, and time in the walkthrough for the hint. Our proposal is to use Deep Neural Networks (DNN) to learn the association of location and appearance pattern in the game(s) in order to locate the current game level. We will use recorded game play to train a DNN classifier for the games INSIDE and Portal, and evaluate the performance of the classifiers with gamers. Our goal is to design a system for NVIDIA Shield™ that provides gamers with help when needed. We hope by providing gamers with such a system, we improve the overall gaming experience and fewer players will give up on a game.

Anodized aluminum oxide (AAO) with macroscopically-aligned, hexagonally-packed nanopores is an attractive substrate both for making nanomaterial templates and forming membranes. AAO has a tunable pore diameter, a well-defined pore structure, and is easily scalable. However, it is brittle which makes it difficult to work with and limits its applications. Here we present a method for synthesizing AAO nanoporous membranes that are flexible. We perform a two-step anodizing process using 99.999% pure aluminum foil in Oxalic acid. We make flexible AAO by patterning aluminum seams in a triangular grid to relieve stress. Additionally, fittings and a patterned gasket protect the aluminum strips from the anodizing solution. With flexible AAO, further research can be carried out on pharmaceutical separation applications and biochemical filtration. For this project I wrote up a protocol for my laboratory to make AAO on site for use in future research projects.

 Two in three American adults are considered overweight or obese and research done in the last decade has indicated possible treatment options through the introduction of probiotics to an individual's diet. While there is research indicating the efficacy of probiotic use in the management of obesity, there is little available regarding the specifics of how that process works. Previous studies have shown that Elongation Factor-Thermounstable (EF-Tu) mediates the binding of Lactobacillus to mucins and epithelial cells in the intestine, but not the stomach. Our goal was to evaluate if (and how) EF-Tu production would change as Lactobacillus moved from the low-pH environment in the stomach to the more neutral intestine. We hypothesized that the rate of external EF-Tu expression would increase at more neutral pHs to facilitate gut colonization. To quantify levels of EF-Tu in different parts of the cell, we measured bacterial growth and EF-Tu levels in cultures of pH 3, 6, and 7.4 representing the averages at each stage in the GI tract. This was done by culturing bacteria in an incubator at each pH for six hours and separating supernatant and cell fractions by centrifugation. Membrane and cytosol were separated using freeze-thaw lysis in liquid nitrogen. SDS-PAGE was then used to isolate EF-Tu, followed by in-gel tryptic digestion. LCMS (a method of molecule separation and identification) was used to detect and quantify EF-Tu from each fraction. Initial results from growth showed the highest turbidity (cloudiness) from the pH 3 culture. Turbidity began before inoculation, indicating turbidity at this pH is not a sufficient measure of cell growth. Understanding how Lactobacilli produce and deploy EF-Tu in different pH regimes may help to optimize the use of probiotics in controlling obesity and improving digestive health.

In the last 10 years, perovskite solar cell efficiencies have increased from four to over twenty percent. Perovskite materials possess great application in thin-film photovoltaics and roll to roll processing. Unlike in traditional silicon solar cells with layer thicknesses on the order of 100 microns, the perovskite layer in a thin-film photovoltaic can be fewer than 100 nanometers. This study looks at the suitability of zinc oxide nanoparticles for use as an electron transport layer in a lead halide perovskite thin-film. Of particular interest is the ability to adjoin the zinc oxide and perovskite layers without any degradation of the perovskite. The effects of solvents, additives (i.e. surfactants), and particle size are analyzed using a variety of methods such as x-ray diffraction, transmission electron microscopy, and photoluminescence spectroscopy to determine optimal interfacial properties and exciton separation in the electron transportation layer. The success of the ZnO layer is further analyzed by comparing the quantum efficiencies and current-voltage characteristic curves of the assembled solar device to an identical solar cell that uses PCBM as the electron transport layer. PCBM is one of the most effective electron transport layers, but due to high cost, the need for alternatives such as ZnO was made necessary. The overall goal of this project is to attain efficient solar cells, using cost-effective materials and processing methods. By doing so, it will open up the field of solar energy for a wider market and broader applications.

A turbidity current is a rapid, density-driven underwater current, laden with sediment, that moves down a slope. Like rivers, turbidity currents can erode or flow within channels, or they can spill over channel banks to form levees and inter-levee deposits. Although turbidity currents cannot be seen easily, some aspects are known: dense, coarse sediment accumulates first (at the base of a turbidite deposit), whereas finer sediment falls out of suspension later (toward the top of the deposit) as the current slows down. International Ocean Discovery Program Expedition 354 collected sediment cores containing turbidites from the Bengal Fan – the largest submarine fan on Earth – including one core from the active channel. Here we use magnetic anisotropy to examine differences in transport direction and processes between turbidite bases and tops across the submarine fan deposit. Magnetic anisotropy was measured with a Kappabridge susceptometer on cubes containing sediment from the cores. This will allow us to better understand the mechanics of turbidity currents and to add detail to models of turbidite sedimentation, a major mechanism by which both mineral material and carbon are transported from land to the oceans.

Neonicotinoid pesticides have been identified as a possible contributor to colony collapse disorder (CCD), decimating honeybee populations. Development of methods to extract neonicotinoids from environmental matrices are important in exploring the correlation between pesticide exposure and CCD. Imidacloprid was chosen as representative neonicotinoid given it is the most commonly used agricultural pesticide in its class. Two extraction methods, QuEChERS and SPE C18, were evaluated for their effectiveness in quantifying imidacloprid concentrations in honey and water. The effectiveness of each extraction method was evaluated using gas chromatography-mass spectrometry (GC-MS). QuEChERS kits use a buffered extraction technique to absorb excess water and stabilize the pH of the solution and cleanup with weak, anionic and cationic exchange resins to remove complex sugars/macro organic molecules. The SPE C18 extraction method used a non-polar solid phase to isolate Imidacloprid from other undesirable solutes in the solution. Preliminary experiments have indicated the SPE C18 extraction method appeared to have better performance with water based solutions. However, honey solutions were ineffective due to more organic interference. Additionally, QuEChERS extraction appears to be more efficient for isolating analyte, but did not concentrate as efficiently compared to SPE C18 extraction. We hypothesize that QuEChERS and SPE C18 extraction methods will be more effective in tandem, as QuEChERS will remove organic interference, while SPE C18 extraction will concentrate the samples. The impact of pH adjustment of samples on peak area and shape was also investigated in both polar and non-polar GC-MS columns. The results obtained will help identify best practices for extraction and detection of imidacloprid in honey samples.

Brassinosteroids and auxin are plant hormones that are crucial in plant growth development. Although it is known that brassinosteroids and auxin signaling interact, it is not known exactly how. We are focusing our attention on the question of how auxin and brassinosteroids interact during the formation of lateral roots. Lateral roots are roots that extend horizontally from the primary root and the developmental tradeoff between the primary and lateral root formation helps the plant optimize its water and nutrient uptake. Previous studies have demonstrated that auxin promotes specification of founder cells, the first step in making a new root. To test if brassinosteroids are also involved in this process, I am quantifying the density of founder cells in seedlings treated with brassinosteroids alone, auxin alone or both hormones together. In this study, I will be able to distinguish whether the hormones act additively or synergistically (a much greater effect than a simply addition of the effect of each hormone individually). Our study will deepen our understanding of root formation which will have agricultural significance as strong roots lead to effective nutrient and water intake and stability for the plant under varying weather conditions.

My research sought to study the effect of removing the egg jelly layer from the eggs of the sea urchin species Lytechinus pictus, on chemoattractant release. Sea urchins are broadcast spawners, meaning the males and females of the species release their sperm and eggs into the water to independently find each other and form zygotes. L. pictus eggs release a chemoattractant peptide called speract, which binds to receptors on sperm cells in order to guide their movements toward the eggs. Little is known about the mechanism of release or the site of production for these peptides. The purpose here was to further illuminate the egg jelly layer’s role in speract release. I removed the egg jelly layer in order to identify if the attractant is actively released from the egg, or simply stored in the egg jelly layer. To do this, I quantified the concentration of speract released from eggs that had their egg jelly removed and compared this to eggs with intact egg jelly as a control, both from the same female, over the course of half an hour. I used column chromatography to purify the peptides released from artificial sea water and high performance liquid chromatography (HPLC) to identify the specific peptides present. The results showed that lack of a jelly layer lowered the absolute concentration of speract but did not significantly change the rate of chemoattractant release. Understanding the workings of an important factor in fertility can give insight into urchin species’ reproduction, biodiversity and evolution.

A growing field of sociological research has provided evidence that Hispanic immigrants in the United States tend to have better health outcomes than their native-born counterparts. Despite the fact that Hispanic immigrants tend to be of a lower socioeconomic status and are less fluent in the English language compared to native-born Americans, immigrants show lower rates of both physical and mental health disorders. This phenomenon is commonly referred to as the “epidemiological paradox” or the “immigrant health paradox.” This study questions the nature of the epidemiological paradox as it applies to mental health disorders among Hispanic immigrants in Seattle. The primary aim of this research is to better understand why immigrants have low rates of mental disorders by examining factors such as perception of mental illness, interaction with and access to the American healthcare system, treatment of mental illness, social connectivity, and cultural determinants. I am conducting semi-structured interviews with first-generation immigrants attending the University of Washington (i.e. Hispanic immigrants born outside of the U.S who first moved to the country after age 16 and have resided in the country for less than 4 years). My sampling strategy involves contacting students through clubs on campus in addition to snowball sampling in order to generate a sufficient sample of 20 subjects for interview. Results from this research will contribute to an in-depth understanding of the nature and mechanisms behind the immigrant health paradox as it relates to rates of mental health disorders in the United States.

Our research involves microscopic deposits of silica within the leaves of grasses, called phytoliths. Grasses produce distinctive phytoliths which can be diagnostic at various taxonomic levels. Phytoliths are particularly important in paleobotanical work because they can help us reconstruct earth’s past vegetation and climate history. Currently, there is a severe lack of quantitative data on phytolith morphotypes and relative abundances within Poaceae, the grass family. We used confocal microscopy to create 3D images of phytoliths in the Bambusoideae, the Bamboo subfamily, and applied geometric morphometrics in order to quantify shape variation. The 3D objects will contribute to a family wide digital reference collection for use by paleobotanists and grass taxonomists worldwide.

Drug addiction is a serious public health problem in the United States that impacts our society on multiple levels. It is known that drug addiction has major effects on both cortex and striatum; however, the exact role of different corticostriatal pathways in drug addiction is not completely understood. Our recent projects aim to deconstruct these circuits by examining a major population of cortical neurons, PT-type neurons that project to the striatum and affect the rewarding properties of the drugs. For this current project, I selectively manipulated these PT neurons in rats by placing a designer receptor called a DREADD (Designer Receptor Exclusively Activated by Designer Drugs) and examining how it changes the behavioral expression of drug reward. Changes of the behavior to a drug’s rewarding properties are measured with a conditioning model called conditioned place preference (CPP). When rats are repeatedly given addictive drugs, such as cocaine, in a chamber with a specific environmental cue (walls with horizontal or vertical stripes), they learn to associate the cue with the rewarding properties of the drug. Rats will associate a specific chamber with either vertical or horizontal striped walls with the drug with or without PT-type neurons activation. Because of their projection patterns, I hypothesize that PT activation will decrease the rewarding effect of cocaine and thus the animals will spend less time in the chamber with PT neuron activation plus drug compared to the other chamber with the drug alone. This finding would be a major step towards disentangling the neural circuits underlying addiction, allowing development of new strategies for prevention and treatment.

Although questionnaires are helpful for identifying employee retention targets in research contexts, such surveys do not benefit employers in small, real-world organizations due to the inevitability of gathering biased data (e.g., due to social desirability or lack of anonymity). The purpose of the current study was to test a tool employers could use to more accurately identify turnover risk and targets for individualized retention strategies. This tool focuses on employee engagement, which research has shown to be related to employee turnover (i.e. high engagement is related to lower employee turnover intentions). This tool enabled us to determine employee level of engagement and predict employee group identification (i.e. long-term retention vs turnover). We hypothesized that higher levels of engagement will predict employee long-term group identity, whereas, low levels of engagement will predict turnover group identity. We conducted a qualitative study using a between-subjects design to compare semistructured phone interviews with 25 community mental health clinicians (13 long-term, 12 turnover), in which we asked clinicians what “ideal changes” they would like to implement in their agency. Using the Q12 Engagement Measurement Model, derived from Maslow’s Hierarchy of Needs, we determined clinician engagement levels, which we then used to predict their group identification. We predict our analyses will reveal that clinicians who suggest more personal-level changes are more likely to be in the turnover group, while clinicians who suggest more altruistic-level changes are more likely to be in the long-term retention group. The literature indicates that employees with higher engagement levels are less likely to turnover; therefore, if we achieve our predicted results, future implications of this study could be that employers could use this tool in their annual review process to more accurately assess employee turnover risk and improve employee retention strategies.

Climate change is threatening global food security. There is a pressing need for better crops that can prevent severe losses. We hope to apply our current understanding of plant developmental mechanisms that are involved in responses to harsh external stimuli to engineer more resistant crop varieties. The plant hormone auxin plays an important role in organogenesis, the process of new organ formation. Auxin controls organogenesis by accumulating in specific tissues at specific developmental times. These accumulations are due to the polar flow of auxin through the plant. These flows are in turn reinforced by auxin through a feedback mechanism called canalization. PIN1 is a an auxin efflux transporter that is required for polar auxin transport. Loss of PIN1 results in several developmental defects. These phenotypes and other analyses have led to mathematical models of organogenesis. We used these models to predict plant phenotype in response to increased canalization. We have engineered transgenic plants with a library of synthetic promoters with varying auxin sensitivity driving expression of PIN1. We are characterizing the shoot architectures of these plants, specifically the number of branches and the pattern of lateral organ initiation. We are also studying how the increased canalization affects the distribution of auxin in our plant lines using fluorescent reporters. We hope that our results will demonstrate how plant synthetic biology and predictive models can be used to rationally design plant developmental phenotypes.

Ocular dominance columns (ODCs) are neurons that are organized in V1 of the visual cortex to respond to input from either eye preferentially. ODCs create stripes on the surface of V1, which have been shown to be less pronounced when the animal loses visual input before the critical period of ODC formation. It was previously believed that these ODCs did not exist in rodents. ODCs correlate with connections from the corpus callosum, which can be seen as a patchy pattern of callosal connections. When rats were found to have similar patchy callosal connections, it was hypothesized that rats would have ODCs as well. As a result of this, our lab was able to find that Long Evans rats have segregated ocular dominance domains. In our current experiment, we looked at plasticity of ODC formation in rats who are either monocularly deprived or enucleated during the critical period of ODC formation. First, we performed either a monocular deprivation (by suturing the eyelid of the rat shut) or a monocular enucleation (by removing the eye) before the onset of the critical period. We performed anatomical analyses by injection of a label for callosal connections and ODCs in the cortex. V1 of the visual cortex was then removed and examined. Furthermore, we performed physiological tests using electrophysiology. In these experiments, we looked at visually evoked responses of both eyes from the monocularly deprived rats (after the suture was removed). The results of our experiments have shown that monocularly deprived and enucleated rats show less patchiness in ODCs contralateral to the closed/removed eye and less patchiness in callosal connections. Also, we found that there was greater ipsilateral response of the non-damaged eye to visual stimulation in rats. These results show that there is plasticity in rats deprived/enucleated before the critical period. 

Peer victimization is common throughout the adolescent years. Recent research has highlighted increases in psychopathology in adolescence accompanying greater exposure to peer victimization. Furthermore, rates of peer victimization of a relational nature are higher among female adolescents than among males. Research also suggests that females are more likely to be diagnosed with internalizing disorders than males. Given these disparities, it is important to identify the mechanisms behind how peer victimization may play a gender-specific role in the development of internalizing psychopathology. To do so, we examined the relationship between peer rejection and emotion regulation, and the extent to which this relationship is moderated by sex. We hypothesized that females would display worse emotion regulation after experiencing peer rejection than males. We also predicted that worse emotion regulation would be associated with greater internalizing symptoms. Adolescents (N = 287, ages 16 and 17) completed a computerized peer rejection task involving being rated by virtual “peers” as well as emotion regulation tasks measuring persistence on a difficult task (Paced Auditory Serial Addition Task) and automatic emotion regulation (Emotional Stroop Task). They also completed self-report questionnaires which assessed exposure to peer victimization (Peer Victimization Questionnaire) and internalizing psychopathology (Children’s Depression Inventory, Multidimensional Anxiety Scale for Children). A moderation analysis was used to characterize a relationship between peer rejection and emotion regulation based on sex, and a linear regression analysis to examine the association of emotion regulation with internalizing psychopathology. Better understanding the factors that increase risk for internalizing psychopathology among female adolescents could better inform interventions to identify and treat those at risk.

The majority of Latinos/Hispanics seek TV news for information and news that reflect their experiences and values. Univision is the largest Spanish television network, in which its audience heavily relies on it for political information that relates to their values. The aim of this study is to understand the relationship between what the Latino/Hispanic viewers said were important issues and the actual content of the media messages used in Noticiero Univision Seattle before the Election of 2016. A content analysis was conducted to discover how agenda-setting plays a role in Noticiero Univision news broadcast. Agenda-setting consists of the amount of attention that is given to an issue in the media, which affects the level of importance assigned to that issue by the public. Within the agenda-setting of Noticierio Univision Seattle, it provided little attention to political issues throughout its news segment, which leads to how it affects the level of importance over political issues of its Latino/Hispanic viewers. Furthermore, a focus group study, a diverse group of people assembled to participate in a guided discussion, was conducted with a survey to understand if Noticiero Univision Seattle is responsible for shaping conceptions of social reality (cultivation theory). I predict that the limited amount of political issues Noticiero Univision Seattle focused on during the Election 2016 does not reflect the important issues that the viewers (focus group) were impacted by. This study will help us explore the importance of providing effective news to viewers, especially during the election season.

The meeting of the fresh water from the Snohomish River and the salt water from Possession Sound creates a unique habitat that is important for many species that make up the biodiversity within this ecosystem. The purpose of this investigation was to observe seasonal variation trends from the pH, chlorophyll, dissolved oxygen (DO) and temperature data at the Deep site in the Possession Sound in Everett, Washington. The study was conducted using a Yellow Springs Instrument 85 and Exo Sonde to collect temperature, dissolved oxygen, pH, and chlorophyll data between 0-3 meters in comparison to 7-10 meters in the the water column. It was hypothesized that during the spring and summer months, there will be a higher chlorophyll concentration due to photosynthesis causing an increase in pH and DO throughout the water column. We also predicted during fall and winter months, there will be a decrease in photosynthesis causing a decrease in chlorophyll, pH, and DO. The hypothesis was not supported. There was an inverse relationship between temperature and dissolved oxygen; as temperature was increasing during the summer months, dissolved oxygen was decreasing. When the temperature was decreasing during the Fall and Winter months, there was a increase in dissolved oxygen.

European colonization has profound impacts on Native Americans; many of those impacts are nuanced and have become institutionalized within oppressive systems. European colonization introduced the notion of heteronormativity to native societies. Heteronormativity is inherently hegemonic and limits human ranges of identity and expression. When people experience this form of oppression, it is common for them to internalize the very notions that cause the most damage. They start to believe the erasure of their identity, and their culture is justified. Distancing themselves from their traditions and culture they seek safety in assimilation. In order to survive, native communities must break those cycles of hegemony that perpetuate their erasure. One instance in which that can be accomplished is through an analysis of the frameworks that native peoples currently operate within. From there insight can be gained with regards to the specific sites in which identity, or spirit, has become suppressed by colonialism. By partnering with the UW First Nations Club I will produce a report that may be used in future powwow planning efforts to explore and enact meaningful and decolonized methods of including two-spirit peoples. Similar to the term queer, two-spirit challenges western heteronormative standards of gender and sexuality. Powwows are unique cultural gathering spaces for indigenous peoples. Powwows are spaces in which culture is shared, passed on, and celebrated. In my report I identify the UW Spring Powwow as a space to work towards recognizing the need for healing in indigenous communities with specific regards to the inclusivity of two-spirit, gender variant, and queer individuals. In this powwow we can dance decolonized by transcending colonial identities. This represents an act of collective resistance; a move to protect sacred values. In this capacity indigenous people have unique positions to be leaders in a movement to create a transformative and empowering majority.

Vascular remodeling, the modification of preexisting vasculature, often occurs during events such as cardiovascular disease. Little is known about the perivascular factors controlling vascular remodeling. A small-diameter, single-channel arteriole model was developed to study vascular remodeling under various perivascular conditions, such as those of disease models or under the addition of drugs. The housing device consists of polydimethylsiloxane (PDMS), a non-toxic silicone-based polymer, held by a plexiglass casing. Type I collagen gel embedded with human coronary artery smooth muscle cells (HCASMCs) is cast within the housing, and the lumen is formed using a needle-based subtractive molding method with a 180um acupuncture needle. The original diameter of the lumen is retained while human umbilical vein endothelial cells (HUVECs) are seeded into the lumen by hand-perfusion. Migration and realignment of both the HCASMCs and the HUVECs is observed after applying physiological flow rates of growth media for 3 days in co-culture. Additionally, endothelial barrier function and smooth muscle contractile function are maintained. The functionality of the model is confirmed through observed calcium wave propagation and epinephrine treatments, where dilation of the arteriole occurs upon perfusion of the hormone. Current studies include observing the effects of combined pressure and flow on perivascular remodeling and function with a focus on modeling atherosclerosis and arterial thrombosis. This study will demonstrate the role of pressure in controlling the vascular remodeling process, specifically the migration and alignment of HCASMCs and HUVECs. It will also provide insight into vascular remodeling during coronary artery disease.

For our Jackson School of International Studies capstone class, Task Force, we created a strategic communications plan tied with a digital story to create a social media campaign. The goal of this campaign is to communicate Tribal Treaty Rights between tribal and non-tribal millennials in the Puget Sound area. The Treaty Rights target issues in the Puget Sound caused by climate change, including decreasing salmon populations and managing non-tribal fishing rights around the region. Most millennials are unaware of these rights, or these issues in general, despite living in the Puget Sound. Our research, primarily self-hosted surveys and focus groups, show a trend in millennials to be sensitive to cultural diversity and climate change acceptance, making them a prime demographic for a marketing campaign. After data collection, we created social media groups, including Facebook, Instagram, and a digital story for potential use in the Tulalip Tribes website. We worked closely with the Tulalip Tribes in Marysville, and visited their location, supervised by Tulalip Tribes' Public Affairs Coordinator Francesca Hillery. UW campus resources will be invaluable in our pursuits; we will contact the school newspaper "The Daily", as well as collaborate with various departments, such as the Intellectual House, to spread awareness and to set up relevant lectures. Millennials are apt to be interested in this topic, therefore, one of our main campaign goals is to create the knowledge in the first place. If successful, our social media campaign will grow towards increasing implementaion on campus and for the tribes themselves. Overall, this can lead to future, independent student involvement and efforts to make a change for themselves, for the tribes, and for all in the Salish Sea region. 

Food has long been recognized as the way that people assign identities to themselves and others. We interpret the type of food individuals consume as a factor that constructs their biological, sociological, and psychological images. As social media grows more pervasive, foodie culture and new methods of self-expression through food visuals have been introduced. For example, today there is a trend for social media users to share pictures of food and meals they consume online. The goal of this study is to examine behaviors, identities, and motivations of 18-30 years old foodies through the food visuals they choose to post on Instagram. The study aims to seek answers to the following questions: What motivates young foodies to post different kinds of food visuals; Is there a relationship between identities and food photos; and, Why food has become such a popular subject to share online? Multiple data collection methods, including surveys and direct observation, are used in this research. The study anticipates that young foodies use food visuals as a tool to create emotional connections in their own network and to put forward a visual version of their personalities and values. Food visuals can be many things: demonstrations of social status, reflections of self, replicate togetherness, and create community, to name just a few. The findings of this research are useful for understanding what motivates people to post food photos on social media, and what those photos represent about their sense of self, their values, and their sense of community. The findings can be a stepping stone for future research exploring the relationship between food, humans, and social media in a wider perspective.

Nickel sulfate hexahydrate (NiSO4.6H2O) is an important industrial compound most commonly used in the nickel-plating industry. Approximately 40,000 tons are produced and consumed each year by manufacturers requiring corrosion-resistant components ranging from consumer electronics to medical devices and aerospace engineering. Freitas et. al. found that zinc sulfate heptahydrate crystal growth increased by 38% under a magnetic field of 0.3-0.7T compared to crystallization under earth’s magnetic field alone, whereas Lundager et. al. have presented evidence that paramagnetic materials such as CuSO4.5H2O do not exhibit such magnetically-induced increases in crystal growth rate. We present here our progress on confirmatory experiments aimed at fitting Nyvlt theory of cumulative crystal weight fraction M(L) and average growth rate G in batch synthesis of diamagnetic ZnSO4.7H2O and paramagnetic NiSO4.6H2O under external, uniform, homogeneous magnetic fields 0.0T<B<1.0T. Our study will examine the differences in the growth rate of paramagnetic and diamagnetic sulfate crystals under the influence of a manipulated magnetic field. Recrystallization is a method of purification during the synthesis process of many compounds. If recrystallization can be improved to increase percent yield by influencing the magnetic field surrounding the compound, it may be a profitable method for drug manufacturers to consider.

Two basic goals for implementation science are to broaden the reach and promote sustainability of Evidence-based Practice (EBP) through effective and efficient dissemination and implementation methods. Research has consistently shown that clinicians need both training and expert consultation or EBP supervision to deliver EBPs. However, often there are only a limited number of EBP expert trainers available. In children’s mental health, a growing body of literature documents the science-to-practice divide, in which few of the many EBPs for children’s mental health are available in public mental health settings, where most children are served. The question guiding this study is whether the Train The Trainer (TTT) model of implementation that is currently being utilized for scale up of EBP is effective. The goal of this study was to analyze trainer candidate ratings under the TTT model and within the context of CBT+. Participants included expert trainers (N=5) as well as trainer candidates (N=7). Surveys were used to compare the performance and trainee perception of trainer candidates. To assess candidate trainer effectiveness, we examined clinicians’ self-report of knowledge gain/competency. Similarly, we assessed whether expert and peer ratings of candidates at the TTT training predicted clinicians’ ratings of the trainer candidates. The results from this study serve to inform further implementation research on how other initiatives can use TTT models to expand EBP reach. This study also provides empirical data that indicates problematic discrepancies between experts and candidate trainers in their CBT+ training.

Previous research has found that alcohol consumption among young adults is linked to an increased likelihood of engaging in risky sexual behaviors, including unprotected sex. When examining the likelihood of safe sex practices, additional research has found that having sex at a younger age (<14) is associated with a lower likelihood of using contraception. However, there is a gap in the literature around how number of sexual partners plays into this relationship. The current study aimed to investigate the association between age of first sex and number of lifetime sexual partners with condom use after alcohol consumption. We hypothesized age at first sexual experience would be positively correlated with condom use during penile-vaginal, anal, and oral sex while under the influence of alcohol in the past three months. Additionally, we hypothesized that the number of lifetime sexual partners would be negatively correlated with condom use in the past three months after alcohol consumption. To test these hypotheses, the present study (n = 1002) used data from a national sample of young adults, ages 18-20, who completed a one-time online survey. Participants were asked age at first penile-vaginal, anal, and oral sex as well as their number of lifetime sexual partners. Additionally, participants were asked number of times they had sex in the past three months after consuming alcohol and of those times, how often they used a condom. Regression analyses were conducted to determine the association between first age of sexual encounter and likelihood of using a condom, as well as number of lifetime partners and the likelihood of using a condom, both after consuming alcohol. Results from this study may help us understand how previous sexual experience is related to the likelihood of practicing safe sex after alcohol consumption.

There is a problem with teamwork nowadays because members are not in the same place at the same time. Communication media allows for teamwork to proceed regardless of where members are located. There are many types of media available including phone, email, and communication applications such as Skype, Messenger, WeChat and so on. However, the communication media itself is also an important factor influencing the effectiveness of teamwork. This research focuses on studying teamwork from the perspective of individual communication media preferences rather than just the objective productivity potential. I present my insights to date, drawn from a literature review about communication media and teamwork and lead to a theoretical framework about the way communication media preferences influence outcomes. The framework displays two approaches affecting outcomes: 1) the quantitative approach that affects the quantity of information being carried out during a given period, and 2) the qualitative approach of quality that impacts the precision, specificity and directness of information. Finally, my future research steps are presented including a survey for testing the theorized framework using students completing a team project, and potentially other workforce teams. The work will advance knowledge about effective teamwork that can help organizations be more productive.

Probiotics are living microorganisms that, when administered in adequate amounts, confer health benefits on the host. Many studies indicate that there are several ways in which probiotics, which include lactic acid bacteria (LAB), have health benefits. These bacteria survive in a wide range of temperatures and pHs, from storage to digestion. In this study, I investigated the effect of varying pH and temperature on LAB growth in a model stomach with MRS broth, one of the most common growth mediums used by microbiologists to grow LAB. I isolated LAB from Yogourmet® yogurt starter, which contains L. Bulgarius, S. Thermophilus, and L. Acidophilus, and grew the bacteria in MRS broth at temperatures of 4°C, 22°C, and 37°C to imitate conditions under which various probiotic products are stored. I also grew LAB at pHs of 2, 4, 6.2, and 8 to replicate variations of pH that come with digestion. I measured bacterial growth at optical density (OD) 600 after 24 hours for all trials. I found that optimal LAB growth at the standard pH of the MRS broth (6.2 ± 0.2) and at the standard temperature of the human stomach (37°C) was expected and confirmed through several trials. When conditions deviated from standard, there was always less LAB growth. I concluded that variations in pH and temperature from standard stomach conditions result in smaller amounts of probiotic growth. This finding is important because a smaller amount of bacterial growth in the stomach will result in reduced health benefits on the host.

Leigh syndrome (LS) is an infantile necrotizing brain disorder associated with progressive neurological deterioration of the central nervous system (CNS), and is caused by the loss of Ndufs4. The Ndufs4 gene codes for the iron-sulfur protein 4 subunit of Complex I (NADH dehydrogenase) in the electron transport chain. The absence of Ndufs4 causes deficiency in Complex I, which negatively impacts mitochondrial energy production and results in symptoms associated with LS. One of the symptoms LS patients experience is seizure activity. Seizures can be caused by inhibition of inhibitory neurons, resulting in hyperexcitibility of neurons. In this study, we sought to identify brain regions that are involved in the generation of seizure activity in a mouse model of LS using c-Fos immunocytochemistry. c-Fos proteins are activated by seizures, and therefore are treated as metabolic markers for tracking seizure pathways. The LS mouse model used is homozygous (Hmz) Ndufs-floxed crossed with Gad-Cre mice, which selectively removes the Ndufs4 gene in GABAergic inhibitory interneurons. We induce thermal seizures in LS mice using a heating lamp. Sham animals, of the same corresponding genotype, are processed in the same protocol but are not exposed to the heating lamp. The mice are perfused 90 minutes after the start of seizure activity, and the brain tissues are extracted and fixed with PFA. Fixed brains are sliced, and the slices are stained and imaged on a confocal microscope to map out sites of c-Fos immunoreactivity. We anticipate that our results will show that Hmz Ndufs/Gad-Cre(+) mice with thermal-induced seizures will express elevated levels of c-Fos in the hippocampus, thalamus, and cortex. The results will provide insights on potential treatment drugs targeted at these specific brain regions in LS patients. 

Childhood sexual abuse (CSA) in males is a significant public health concern in the United States.  Male survivors of CSA are less studied than female survivors, despite current literature suggesting that the CSA experience may differ by gender.  Multiple studies have found that CSA is associated with a range of negative long-term outcomes in both genders, including increased sexual risk taking in adulthood.  Sexual risk taking is typically defined as behaviors which increase the likelihood of contracting a sexually transmitted infection (STI) or experiencing an unplanned pregnancy, having multiple sexual partners, using alcohol or other substances before sexual activity, and forgoing condom use.  Past literature has highlighted several potential pathways from CSA to sexual risk behavior, including mental health, emotional regulation, and sexual motives.  These factors are negatively impacted by CSA, and may in turn increase the likelihood of sexual risk behavior.  The present study aims to evaluate (a) whether CSA and sexual risk taking are associated in a community sample of 321 adult males, and (b) whether the association between CSA and sexual risk taking is mediated by mental health, emotional regulation, and sex motives.  Data was taken from self-report questionnaires.  A T-test will determine whether CSA is associated with sexual risk taking in this sample. Mediation analyses will assess significant mediating factors linking CSA and sexual risk behavior.  It is expected that CSA and sexual risk taking will be significantly associated, with survivors of CSA reporting more sexual partners and more unplanned pregnancies.  Mental health, emotional regulation, and sex motives are expected to be significant mediators of the relationship between CSA and sexual risk taking.  The present study has implications for practice and future research by indicating potential intervention and research targets for male survivors of sexual abuse.

A dynamic membrane system with nanometer-thick electrodes is able to selectively bind genetically modified proteins with specific protein ligands and pump them across the membrane with sequential voltage pulses. The previous tests on this system show that after several separations of mixed proteins, the separation rate decreases due to biofouling; non-specific proteins lie on the surface of membrane and diminish the ligand’s affinity to target modified proteins. A colayer of non-fouling zwitterionic peptides and affinity ligands is functionalized to the membrane surface.We set up rubber chambers to mimic the working environment of the seperation system. Mixed protein separations are performed  in the chambers and permeates are quantified with UV-Vis spectroscopy. After introducing the zwitterionic non-fouling agent, the membrane maintains constant separation rates while retaining high binding capacity.

Pierre Robin Sequence (PRS) is a human congenital disorder manifesting as a combination of several orofacial anomalies that include a small lower jaw (micrognathia), posterior placement of the tongue (glossoptosis), and high incidence of cleft palate. The resulting airway obstruction in affected infants and young children can be life-threatening. While lower jaw growth is thought to permit tongue descent to allow palatal shelf elevation and fusion, it remains unclear how tongue malposition and cleft palate results from lower jaw malformation in PRS. The aim of this study is to analyze the physical interactions between the tongue and other orofacial structures, such as the palatal shelves and lower jaw, to determine if dysregulation of these interactions plays a role in the pathogenesis of PRS. We used a Wnt1-Cre driver, a method to specifically knockout genes in the craniofacial mesenchyme, to disrupt hyaluronic acid synthase 2 (Has2), an enzyme crucial to the extracellular matrix and overall craniofacial development. This allowed us to produce conditional knockout (CKO) mouse models that developed the entire spectrum of PRS phenotypes including micrognathia, cleft palate, and a high-arched tongue interfering with the nasopharynx. Combining histology with 3D imaging techniques, we analyzed morphological changes of the palatal shelves, tongue and lower jaw in Wnt1-Cre, Has2 CKO mice. Our results indicated that reduced lower jaw growth affects tongue growth and its interaction with the nasomaxillary complex, while reduced palatal shelf growth affects tongue shape changes. This suggests the abnormal shape and positioning of the tongue in PRS may result from abnormal orofacial tissue interactions due to defects in the lower jaw and palatal shelves. The implications of this research will allow us to better understand the regulatory mechanisms of orofacial development and the pathogenesis of PRS in humans, which is essential for diagnosis and treatment of this disorder.

High-powered electromagnets are used in many different fields of science such as quantum physics and synthesis chemistry. Some projects require a very strong magnetic field to work. This magnet will allow students the freedom to design complex projects that utilize a strong magnetic field However, they are generally quite expensive and only available for use at well-funded research facilities and universities. Thus, we present our research in the design and construction of a cost-effective electromagnet capable of producing a highly-uniform magnetic field that can be used to further undergraduate research at Edmonds Community College. Our principal focus is on the reduction of engineering, fabrication and maintenance costs through a novel radial-flow cooling system which can be easily 3D-printed using high-temperature plastics in conjunction with a solid Bitter-plate solenoid design, requiring far less intricate and less expensive machining processes than conventional staggered-channel Bitter-plate designs. In order to make meaningful comparisons of generated field and thermal profiles with other published designs, our design maintains general shape and structural congruence to a design by Sabulsky, et. al., yet differing significantly in the design of the cooling system.