Climate change has raised concern on the possibility of West Antarctic Ice Sheet collapsing in the future, in which the ice sheet thins substantially, resulting in a sea level rise. In assessing the possibility of future collapse, scientists are researching whether the West Antarctic Ice Sheet had collapsed during a warmer period in the past. Delta O-18 records from an ice core originating from Siple Dome, West Antarctica indicates that the deeper section of the Siple Dome ice sheet had originated from a much higher elevation area. This indication suggests that ice that was deposited in the high-elevation central West Antarctic could have flowed horizontally through a melting ice sheet to settle at the base of Siple Dome today. Here we modeled an age-depth relationship for an ice column at Siple Dome to test if it is possible to have a melting scenario here during the last interglacial period (about 110 000 years ago) based on this 1-D model. We traced the flow trajectory of the ice particles in the column back to the surface where it was first deposited as falling snow. We used a Dansgaard-Johnsen model with time-varying accumulation rate and ice sheet thickness, and included a melting variable for the interglacial scenario. Constraints on past thickness and accumulation rate and comparison of model result to available ice-core data allow us to determine whether this model may or may not describe the ice flow trajectories that make up the column of ice at Siple Dome today. If the result matches the ice core data, this implies that the model may be valid, and that some part of West Antarctica might have collapsed during that interglacial period.

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

Our research project was to design, construct, and launch a high powered rocket with the intention of pushing its velocity significantly past the speed of sound while simultaneously collecting data from which to interpret the max achieved acceleration, velocity, and altitude. The rocket's body has a three inch inner diameter made to fit the 3-inch motor casing without any extra room. This minimum diameter design reduced its weight so that less force was required to achieve higher acceleration, and it provided a smaller cross sectional area than a traditional rocket, thereby reducing the amount of drag force impeding its acceleration. Atypical of most high powered rocket designs, our rocket features a metal tipped nose cone to provide resistance to the heat caused by friction when breaking the sound barrier. At the speeds achieved, unmodified rocket fins will vibrate at extreme rates due to turbulent flow. In order to combat this destructive effect the fins were reinforced with carbon fiber to significantly stiffen them and reduce any resonant effects during flight. The payload consists of a StratoLogger SL100 Altimeter to keep track of the maximum altitude and velocities of our flights as well triggering two separate parachute deployments, achieving a safe landing while also minimizing drift time due to winds at altitude. It is our hope that our research rocket will push the boundaries of velocity and altitude achieved by a junior college rocket team as well as provide insight into ways to optimize our rocket designs to maximize future results.

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

Understanding the sources and salience of gender stereotypes in society is of huge interest to social scientists as well as the broader public.  Indeed, a large body of research has been devoted to examining gender stereotypes represented in different forms of media particularly digital and print media.  A burgeoning body of research has begun to examine gender stereotypes in video games.  There are 155 million Americans who play video games and four out of five U.S. households own a device used to play video games.  Therefore, gender stereotypes portrayed in video games may be an important way in which people understand gender.  In this research project, I examine trends of female gender stereotypes in both actions and appearances in top rated PC and console games from 1996 to 2015.  I use data from a video game review aggregation website to find the top ten rated games of each year and randomly select four from each year.  I code each game on the stereotypes shown through the actions and appearances of the female characters to determine the overall trends in gender portrayals throughout the years.  This study will help us to understand how women are represented in a wide-reaching media outlet and whether video game companies are displaying more, less, or the same amount of stereotypes in their games over the years.

Much of the topography of Eastern Washington was shaped by the recession of the Cordilleran Ice Sheet and by periodic flooding from Glacial Lake Missoula towards the end of the last ice age. The age of flooding is approximately known from Carbon-14 dates, but because the floods distributed granite boulders across much of Eastern Washington we can improve the chronology using exposure dating with cosmic-ray-produced nuclides. In this method, the build-up of Aluminum-26 and Beryllium-10, two isotopes produced in quartz by cosmic rays, indicates the length of time these boulders have been exposed. By applying this technique to selected deposits we can shed light on the age of the last floods, sources of floodwater, and how the extent of the Cordilleran Ice Sheet controlled the floodwater paths. Initial data show that the last floods through Grand Coulee occurred approximately 15,500 years ago, but younger floods passed down the Columbia Gorge until approximately 14,100 years ago. This final flood may represent breaching of the glacier-ice dam across the Columbia River, or a glacial outburst flood from a more distant source. We can distinguish these possibilities by dating glacial deposits on the Waterville Plateau and in the Okanogan Valley. One exposure age on a glacial erratic from north of the Columbia River near Brewster gives an age similar to the final flood, possibly suggesting that the flood resulted from breakup of the Columbia River ice dam. Chemical analysis and accelerator mass spectroscopy of additional samples will give us a more accurate picture of the chronology of the last of this catastrophic flooding.

During restoration of strip mines, a one meter soil cap is added to prevent metal contamination from buried coal spoil. Research has shown that recolonization by invasive grasses and soil compaction often prevents the return of native forests. To encourage recovery of forests on reclaimed mine sites, hybrids of American and Asian chestnut species (Castanea dentata × C. mollissima) are being used to accelerate succession on reclamation sites. In this study, we are testing whether soil treatments that remediate compaction and remove invasive grasses facilitate the movement of metals from buried spoil to the soil and/or tree foliage or flowers. Soil treatments included 1) plow disking, 2) deep soil ripping, 3) combination of plow disking plus deep-ripping, and 4) an undisturbed control. Metal concentrations were measured from soil, foliage, and flowers of chestnut trees by Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Our results indicate no significant differences in metal uptake in chestnut trees due to soil treatment after 8 growing seasons; however, the treatments that involved deep soil ripping resulted in a trend of elevated metal concentrations in foliar tissue for lead, copper, zinc, selenium and manganese. As these trees mature, these trends warrant further investigation with regard to the effect of deep soil ripping on metal uptake.

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

A myriad of health disparities exist among Somali refugee and immigrant children living in the United States. Child undernutrition is a prominent issue in the community that affects children at a critical point of development and can lead to negative health outcomes later in life. Recent data estimates that the percentage of underweight children in the United States is 0.5%, the rate of underweight children in Somalia is 23%, and the rate of underweight Somali refugee children living in America is as high as 22%. Field data for the Somali refugee and immigrant population was collected from October 2015 – February 2016 at the Refugee Women’s Alliance (ReWA) in South Seattle in a job readiness program. The data was used to assess possible barriers in accessing healthy food, as well as barriers in accessing services meant to combat nutritional disparities. Data was then juxtaposed with qualitative data and statistics on the social determinants of health, as well as the nutritional status and food insecurity levels, of Somali refugee and immigrant children living in Lewiston, Maine. The research shows that Somali refugee and immigrant children of King County are affected by the same social and structural barriers that led to the poor nutritional status of refugee children living in Lewiston, Maine. Furthermore, the purpose of this research is to find what factors contribute to the substandard nutritional status of Somali refugee and immigrant children in hopes to reduce the clear level of inequality present in King County.

Cysteine knot peptides (knottins) are small proteins found in a wide variety of organisms. Due to their durable cysteine knotted core and small size, knottins are a promising new drug scaffold. Optimized knottins (optides) bind with high specificity to certain cancer cell types indicating that optides have the potential to deliver drug payloads or be utilized as tumor imaging tools. In order to determine if optides are localizing to certain organs or tissues of interest they must be radiolabeled and injected in vivo. The goal of my project was to develop a method to recover radiolabeled optides from mouse plasma or tissue samples and confirm via liquid chromatography that the optides are intact and reaching their target. I developed a column chromatography extraction technique that filtered out plasma proteins in order to recover optides. Analysis of the optides using high performance liquid chromatography showed high recovery rates and preserved structural integrity. The second phase of the project was to do a plasma stability assay. I incubated samples in mouse plasma over a time course and used the extraction method to determine if samples were degraded by plasma proteases and found that there was no visible degradation after incubation. This project set the groundwork for a more detailed examination of optide modifications that could lead to longer optide half-life in plasma and greater drug delivery. This recovery technique is a critical tool for analyzing the pharmacokinetics and biodistribution of optide drug candidates. 

The Bengal Fan is a cone-shaped submarine deposit that contains the sedimentary record of the collision between India and southern Asia, the formation of the Himalayan mountain range, and the development of one of the largest deltas in the world. Erosion of different rock types as the Himalayan crustal blocks were uplifted has produced variations in sediment composition within the Bengal Fan. This study focuses on using frequency-dependent magnetic susceptibility combined with optical and electron microscopy to identify magnetic iron oxides and sulfides in core samples taken during International Ocean Discovery Project Expedition 354. I will identify differences in oxide and sulfide mineral assemblages through time and trace their provenance. This data can then be used to track sediment sources that contributed to the creation of the Bengal Fan and uplift processes that created the Himalayas.

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

Ultraviolet photodetectors have wide-ranging applications, including use for missile detection. Current devices employ indium tin oxide (ITO), making them rigid and fragile. Development of flexible organic devices is therefore desirable to make more adaptable photodetectors. This set of experiments focuses on optimization of the polymer active layer in flexible organic ultraviolet photodetectors. Controlling thickness and morphology of the active layer is key to improving device performance. The active layer consists of an electron donor, a polymer called F8T2, and an electron acceptor, PC71BM. Optimization in this set of experiments is achieved through variation of preparation conditions, most notably the solvent used in processing. Other parameters varied include molecular weight of polymer, and ratio of electron donor to acceptor. Analysis of resulting films is performed in several ways. UV/Vis-spectroscopy provides information about morphology, while atomic force microscopy (AFM) allows for surface imaging of films on the nanoscale. Profilometry provides measurements of thickness. These forms of analysis reveal which preparation conditions should be used for fabrication of devices. Initial profilometry data suggests that processing with a dichlorobenzene/chloroform mix as a solvent results in films with roughly twice the thickness of films processed using pure dichlorobenzene. Acquisition of more data will drive future experiments on preparation conditions, allowing for optimization of active film thickness/morphology, and thereby device performance. This will allow for production of a more flexible and reliable form of ultraviolet photodetector.

Humans have an intrinsically symbolic nature that leads individuals to seek a stronger connection to the physical world around them. At numerous archaeological sites all over the world, red ochre has been utilized as a decorative pigmentation with an evidently ritualistic and spritual purpose. For example, on the Kamchatka Peninsula in Russia, multiple Upper Paleolithic burial pits have been filled completely with red ochre, which covered the bones and related grave goods. Early hunter gatherers at the Tanginak Spring Site in Kodiak, Alaska coated their living surfaces with red ochre and archaeologists are divided about whether this paint is a byproduct of waterproofing tent seams or a purely ritual application of color to ritual spaces. In my research, I will attempt to test predictions regarding whether or not the the residents of this particular Ocean Bay 1 site were employing ochre for its abilities as a tent waterproofing agent or if its pigmentation served a purely spiritual purpose. Through experimental archaeology and an analysis of the ochre and ochre processing tools discovered at the Tanginak site, I will gather evidence to either support or disprove my hypothesis that ochre served both a practical and symbolic purpose. 

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

Plastic debris in the marine environment has been a growing concern due to its durability in the ocean environment and the potential to have a variety of impacts on marine organisms. Characterization of plastic debris is approached via size as macroplastics (> 5mm), microplastics (5-0.330mm), and nanoplastics (<0.330mm), all of which are located in surface waters, within the water column, on beaches and within seafloor sediments. This is a preliminary study on monitoring plastics debris in marine sediments in Puget Sound with the goal of establish a baseline to determine the concentrations of plastics in marine benthic communities and work to deepen our understanding of the impacts of plastic debris on marine ecosystems throughout the Pacific Northwest. In collaboration with the Washington State Department of Ecology’s, Marine Sediment Monitoring Team (MSMT) and the Puget Sound Ecosystem Monitoring Program (PSEMP), ten samples weighing 200 grams each were processed and analyzed from different stations around Puget Sound. Plastic fibers of various colors and sizes were found throughout the samples as well as white plastic shards; foam and film. After multiple density separations it was determined that Bellingham had the highest concentration of microplastics at 2.48E-03 milligram (mg) of microplastics per gram (g) of sediment. The lowest concentration was found at Sinclair Inlet with 4E-05 (mg/g) of microplastics. Further analysis was performed to determine whether there was a correlation between concentration of microplastics and particle size of sand, silt and clay at each of the ten stations sampled. When comparing percent of sand, silt and clay it was determined that there was no correlation with an R value of 0.04 for sand, 0.01 for silt and 0.1 for clay. Future studies include identifying each plastic fiber using infrared spectroscopy and processing/analyzing samples gathered from past years.

The brain's ability to learn and adapt in response to its environment lies in the plasticity of its synaptic connections. Studying these neuroadaptations is complicated by the tremendous heterogeneity of the brain. Simply isolating a portion of the brain and homogenizing it results in a preparation that includes irrelevant cell types like mitochondria and glia, as well as the specific synaptic targets under consideration. Thus, neurobiologists use synaptosome preparations, which are enriched for synaptic particles, to study synaptic proteins. These preparations are the foundation for the study of synaptic neurobiology. While these synaptosomes preps are of great use, they also have limitations in regards to specificity and purity, with non-synaptic neuronal contaminants occupying a large part of the preparation. Beyond the creation of “cleaner” preparations, it would also be desirable to isolate specific cell types or projections (eg. Thalamo-cortical vs. cortico-cortical synapses). To tackle this issue, we created the Fingr-Sare “TAG” construct, which will allow us to physically isolate synapses that express the construct with high specificity. The FINGR insert is a fibronectin intrabody that binds endogenous PSD-95 and localizes the construct to the synapse, while the “TAG” serves as a target for antibody-based magnetic sorting of glutamatergic synapses. Following transfection of neurons in culture, the construct shows correct dendritic spine localization, with the CD4 portion appearing extracellular of the synaptic membrane. We have been able to sort cells using the TAG construct, and future research will focus on isolating pure populations of “tagged” synaptosomes. Overall, the versatility of this construct could provide researchers with the opportunity to customize and pinpoint specific types synapses from the brain in the hopes of advancing future neurobiological research.
 

Xenobiotic biotransformation is a vital process in the body that detoxifies various drugs, dietary factors, and environmental toxicants. This process is mediated by various drug-metabolizing enzymes in Phase-I (oxidation, reduction, and hydrolysis) and Phase-II, as well as transporters. The hepatic nuclear factor 4alpha (HNF4α) is a master regulator that transcriptionally up-regulates a wide spectrum of drug-metabolizing enzymes and transporters in liver. HNF4α also plays an important role in liver development and nutrient homeostasis. Previously, it has been shown that HNF4α can trans-activate the constitutive androstane receptor (CAR), which is a major ligand-activated xenobiotic-sensing nuclear receptor. However, very little is known about the effect of CAR activation by xenobiotics on the regulation of HNF4α in liver. In the present study, male mice at either 5-day-old neonatal age or 60-day-old adult age in wild-type, CAR-null, or humanized CAR-transgenic (hCAR-TG) genotypes were treated with vehicle (corn oil, which served as the control), or a species-appropriate CAR ligand (TCPOBOP for mouse CAR and CITCO for hCAR), once daily for 4 days. A novel truncated coding exon 9 was observed for the HNF4α transcript variant in mouse liver (RNA-Seq). Isoform-specific RT-PCR and gel electrophoresis confirmed the presence of the novel HNF4α isoform. During development, both the known and the novel isoform had increased expression with age. The mouse CAR ligand, TCPOBOP, down-regulated HNF4α in a mouse CAR-dependent manner only at mice at age 60, whereas hCAR did not appear to regulate the expression of HNF4α at any ages. In conclusion, the present study has identified a novel HNF4α transcript variant in the mouse liver, and discovered that both the known and novel isoforms were regulated by CAR in a species and age-specific manner.

As environmental monitoring technology advances, people will increasingly have access to new data about their surrounding environmental quality. But, a challenging issue is the question of how can people best access the information? In this research project I focused on data collected from a new neighborhood air pollution monitoring study in Oakland, CA. Our research question is: How can we best express complex air pollution data so that it can be understood and acted upon by people with different educational backgrounds and community interests? I employed user experience research and design methods to answering this question by having the local community members at organizations like West Oakland Environmental Indicators Project, Communities for a Better Environment, La Clinica, and Bay Area Air Quality Management District respond to questionnaires and interviews related to their interest and concerns about air pollution. After gathering this information, I analyzed the air pollution data our research group and the government are currently collecting in the region. Later I used the sorted data to design personas and wireframes through Illustrator and prototyping tools for how the interface should look and have the community members test the prototypes by responding to surveys and interviews as to whether they can use the given data with ease. Lastly, I reported the results of our iterative interviews and questionnaires. I anticipate that the outcome of using user experience research and design methods will be an interface that is highly usable for the community partners in Oakland, CA. 

Drosophila suzukii are an invasive species of fly that can potentially have large negative impacts on berry agriculture in the United States. D. suzukii fill a unique niche relative to other members of its genus in that it lays eggs and develops in ripening fruit before it has fallen to the ground. Thus, in this species, the decision to pupate on or in their host fruit, or leave to settle in uncertain soil environments, may have larger fitness effects than is the case for other species of Drosophila. We expect that D. suzukii larvae will be particularly sensitive to environmental cues when deciding where to pupate. In this study, we manipulated the position of host fruits (suspended or on the ground) and presence of vibrational predator cues to determine whether these factors influence larval behavior. We have found effects of the position of fruit and the presence of vibrational cues associated with predation on larval behavior and pupation site selection. This research will offer insight into this invasive species behavior in the field, from which possible management practices can be derived.

This study investigates the effects of anthropogenic pollution and mitigation efforts in Elliot Bay, Puget Sound, by analyzing the relationships between pollutants and benthic foraminiferal assemblages from 1998, 2007 and 2013. Foraminifera are single-celled microorganisms, which are typically encased within secreted shells (tests) comprised of either calcium carbonate (calcareous) or cemented sediment grains (agglutinated). Foraminifera are commonly found in marine environments and are a valuable tool for monitoring environmental conditions of the past and present. Elliot Bay has an extensive history of pollution, beginning with the European settlers establishing lumber mills in the 1850’s, and continues to have many industrial and recreational sources of pollution today. For this study, a total of 45 samples collected by the Washington State Department of Ecology in 1998, 2007 and 2013 were analyzed to identify any changes or trends in foraminiferal assemblages. From these samples, 21 species were recovered and identified, most of which are stress-tolerant species found in estuaries around the world. Some species are more tolerant of pollution and stress, and so have been more informative of the environmental conditions in Elliott Bay. For example, the agglutinate species Eggerella advena, found abundantly in some 2013 samples, is an opportunistic colonizer of industrial and sewage outfalls. In addition, the calcareous species Buliminella elegantissima and Cribroelphidium excavatum, also widely present in the bay, are tolerant of low oxygen environments. Correlations of species density and diversity with heavy metals such as copper, zinc, lead, arsenic, cadmium, and mercury result in a better understanding of the impacts of pollution and mitigation in Elliott Bay.

In a country that provides free health care for patients living with HIV/AIDS, China has not recognized a growing health crisis: hepatitis C (HCV). In Yunnan Province alone, 77.7% of intravenous drug users (IDU) are co-infected with HIV and hepatitis C. While these patients can obtain free treatment for HIV, they cannot do so to treat their hepatitis C infection, a viral disease that leads to liver failure. Recent trends indicate that more co-infected patients are dying of HCV than HIV due to treatment inaccessibility. This study investigates the severity of HCV in China, the barriers to obtaining treatment, and what alternatives exist for patients infected by HCV. Over the course of one month, formal interviews were conducted with 18 intravenous drug users, two medical doctors, and one traditional Chinese medicine doctor. The answers were analyzed to compare the experience of patients to that of doctors and how this correlated with the shortfalls in HCV treatment accessibility. There are four findings which point to the underlying causes. First, there is a gap between what medical doctors assume to what patients experience. While doctors claimed that HCV treatment is highly successful, not a single IDU who was interviewed had successfully completed the regimen. Second, finances and social stigma serve as the largest barriers to obtaining treatment. Third, in order to cope with these barriers, patients find emotional reprieve in community support and alternative treatments. Fourth, the solution requires changes from both the Chinese health care system and foreign pharmaceutical companies. The goal of this research is to raise awareness about the gaps in knowledge and efforts surrounding hepatitis C in order to create a sense of urgency to fill them.

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

Associations between health outcomes and exposures are frequently tested in research because of the risk of adverse effects when exposed to toxic substances. There are also correlations that occur frequently between socioeconomic status (or other demographic features) and health outcomes. The purpose of this research is to develop an analysis tool application that will help to assess this association between potentially toxic exposures and health outcomes, while adjusting for confounding variables that are related to location; e.g. socioeconomic status, race/ethnicity and possibly other spatially-localized exposures. I have developed this analysis tool using the programming language R (an open-source standard for statistical computing and visualization). In this tool, I use partially linear additive models to adjust for location-based confounding, while testing for an association between exposure and health outcome. I use a model of the form: outcome = B0 + B1*exposure + f(latitude, longitude) + e. Here, B1 is the target of the inference, f is confounding based on location, and e is the random observation-specific error. I use Google Maps API data to aid in translating street addresses to latitude/longitude coordinates. I have also created visualizations as they are useful in developing a better understanding of these relationships. The ultimate goal of this research is to create a tool that will allow the assessment of associations with any exposure and outcome and have it as a web-based application to allow for greater use. For real data, I have applied the tool to re-analyse the air pollution data of Sheppard et al. (1999). This dataset contains air pollution measurements and non-elderly hospital admissions in Seattle over a 7-year period. In this dataset there is not spatial confounding, but instead potential temporal confounding –- I have extended the tool to evaluate associations in this scenario.

Consistently, young adults (ages 18-24), hereafter referred to as "youth" are slow to get involved in the governance process. Rates of engagement in the political and governance process are consistently lower among those with intersections of marginality (e.g. race, gender, level of education, etc.). Two components which impact a young person's activism and connection to civic and political engagement are political education and socialization. How a person is introduced to the political process and how their interactions with their community had helped to instill, or failed to instill, notions of democratic citizenry. The way a person is taught to engage with the political process has significant implications for an engaged citizenry, and there are educational and social systems which work to promote or discourage such democratic involvement, among marginalized groups. This research provides statistical comparisons which allow for quantitative analysis of participation rates among diverse youth, and addtionally provides a qualitative examination of constructions of citizenship, socialization and education, which might discourage participation in traditional democracy for youth and other marginalized groups. Variations in how educational institutions teach about youth political engagement impact how involved they become in their own governance. Pedagogy and constructions of citizenship play a major role in not only whether youth engage, but how they engage in the political process. While shifts in socialization may not be achievable through public policy solutions, implications of this research could offer alternatives and solutions to the problem of youth political participation, to both existing educational institutions and policymakers, when considering youth engagement in the governance process.

Methylomicrobium buryatense 5GB1c is a strain of methanotrophic bacteria that serves as an attractive model for production of valuable compounds from methane that can be used in industrial applications. Using this bacteria to transform cheap methane into a commercial commodity is not only a profitable venture, but an effective use of this potent greenhouse gas. This project attempted to genetically manipulate 5GB1 to increase its concentration of cellular lipids, which can be used as precursors to diesel, and introduce new metabolic pathways to produce three stereoisomers of 2,3-butanediol, a compound that can be used in the synthesis of materials such as rubber, plastics, and several others. 5GB1 has a complex membrane structure to support methane oxidation, from which the desired lipids can be utilized in fuel production. By overexpressing five genes previously determined to be involved in high-lipid generating conditions, we expected a greater yield of the product. To accomplish this, direct chromosomal insertion of a genetic construct with a highly active promoter increased transcription of the target genes. After this successful transformation of the cells through homologous recombination, sample cultures were analyzed to determine if the level of lipid production increased. A knockout of the cell-shape determining gene was also made in an attempt to increase lipid concentration; however it was lethal. For 2,3-butanediol biosynthesis, cells were transformed with plasmid constructs containing genes encoding enzymes that are downstream of existing pathways within 5GB1. Three different sets of plasmids were made for the three stereoisomers of the compound, resulting in the production of mostly pure diols. After transformation, 5GB1 was expected to be able to convert methane to the desired products. This process can be scaled up at the industrial level for manufacture and profit.

The miniaturization of electronic devices has driven modern advances in computing, consumer electronics and sensor technology. Digital integrated circuits and the transistor are the most widely produced microelectronics. The metal-oxide-semiconductor field effect transistor (MOSFET) is widely used in modern devices. The core of this device is the metal-oxide-semiconductor (MOS) capacitor. While the physics behind the use of MOS capacitors are well understood, real world fabrication provides unique challenges that require experimental work and process characterization to repeatedly produce viable devices. For this project, we fabricated microscale MOS capacitors on an n-type silicon substrate. The dimensions and properties of the dielectric material used in a MOS capacitor determines its electrical properties. We characterized the effects of variations in the processing method for the deposition of the silicon oxide layer.  We varied parameters such as deposition rate, chamber temperature and silicon oxide thin film thickness.  Current-voltage (I-V) characteristics and electronic properties such as capacitance and breakdown voltage were characterized with electrical probing. We hope to quantitatively evaluate relationships between processing method and the electrical performance of MOS capacitors fabricated using tools and materials available in the Washington Nanofabrication Facility (WNF). Characterization of these relationships assists users and researchers in their circuit design and choice of processing parameters.

Stille coupling, Suzuki coupling, and Kumada coupling are some of the most commonly used reactions in the synthesis of polymers for organic solar cells and organic electrical devices. They are highly effective in creating new carbon-carbon (C-C) bonds. However, when synthesizing a conjugated polymer for organic solar cell applications through these conventional reactions, the process can be challenging and lead to many synthetic steps. In addition, some of the materials used are expensive and extremely toxic to both human health and the environment. In this project, I work individually to synthesize a new benzobisoxazole-based compound which can potentially serves as the monomer for conjugated polymer of organic polymer. The goal of the project is to create a compound in which the inert carbon-hydrogen (C-H) bonds are strongly weakened and easily broken. Potentially, organic solar cells production via this new compound can be more efficient, and as a result, reduces the cost and makes it more environmentally friendly. Recently, the lab’s collaborators at Emory University synthesized a benzobisthiazole-based monomer with two solubilizing alkyl thiophene groups. However, the monomer has limited solubility in organic solvents as well as C-H activation ability. To improve the monomer, I attached a further 2-ethyl hexyl chain to the 2-position on each thiophene solubilizing group and also replaced thiazole with the more electron deficient oxazole unit. Right now, I have successfully synthesized the desired compound and been in the process of activating it using a Gold-based catalyst. If C-H activation is possible for this compound, oligomers of at least three monomers are expected to form.

Electric propulsion is an area of increasing research as it offers increased efficiency and versatility in operation. Electric propulsion systems ionize solid propellant and accelerate plasma out the back of spacecraft at high velocities using electric and magnetic fields to create thrust. Pulsed plasma thrusters (PPT) are an example of how electric propulsion offers a lightweight and cost-effective source of in-space propulsion for small spacecraft with space and power limitations. Traditional solid propellants like Teflon provide adequate fuel for PPTs but are limited by space and weight thresholds for small spacecraft. The Advanced Propulsion Lab (APL) at the University of Washington is interested in exploring the use of dust as a fuel source in PPTs. Dust would prolong the life and therefore research capabilities of such spacecraft due to its universal availability. In addition to using planetary/asteroid dust, we are interested in de-orbiting and using particle-sized pieces of retired space debris as a source for fuel. We hypothesize favorable thrust values for small spacecraft can be obtained by igniting dust in a PPT. The dust thruster is mounted inside a small vacuum and operates by using high frequency vibrations to agitate micrometer-sized particles into a plume of very fine dust that is sparked via firing a PPT. We are experimenting with Martian regolith simulant (a synthetic manufactured Mars dust), lunar regolith simulant (synthetic lunar dust), and aluminum powder, but the dust thruster can utilize virtually any dust sample. This experiment will serve as a proof of concept that dust particles can be used as a main fuel source for PPTs. The dust thruster is a sustainable system that will allow for longer missions and thus increase research capabilities, while proposing a sustainable solution to space debris traffic.

Gastrulation is a stage in embryogenesis in which most progenitor cells commit to a muscle or neural fate. However, a population of bipotential progentitor cels does not differentiate during gastrulation and allows the embryos to dynamically allocate neural and muscle tissue in the correct proportion as the body axis is formed. The regulation of this process is crucial for proper neuromuscular development. The maintenance of these bipotential progenitor cells requires the repression of tbx16, a transcription factor that progenitors express when they commit to a muscle fate. Here, we examine two genes of interest termed eve1 and vent, and investigate their roles in the regulation of tbx16. While previous studies relied on Morpholino anti-sense oloigonucleotides (MOs), the credibility of MOs has recently become seriously questioned because they can cause off-target effects, generating misleading effects that don't reflect genetic mutants. Revolutionary new gene-editing techonology known as CRISPR, is hailed as the new standard for gene analysis because it allows the production of true genetic mutants in specific genes. CRISPR accurately and efficiently creates small deletions in target genes, which can result in complete loss of function. Using the CRISPR method, we will generate F1 lines of zebrafish with eve1 and vent mutations. Through high-resolution melt anaylsis (HRM) and DNA sequencing, we have thus far identified two eve1 F0 founder fish. We will then test how the absence of eve1 and vent affects the expression of tbx16 during zebrafish embryogenesis using in-situ hybridizations. By analyzing how embryogenesis in normal zebrafish embryos differs from that of eve1 or vent mutant embryos, we can identify the role that these genes play during development. Ultimately, our goal is to gain a better understanding of how serious birth defects and genetic disorders arise from complications in development. 

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

Sec1/Munc18 related proteins (SM) are essential cofactors of SNARE–mediated membrane fusion. They function in conjunction with SNARE proteins, a family of zipper-like proteins that drive the two opposing membranes toward fusion, and other SNARE cofactors. Membrane fusion is one of the most fundamental cellular processes. However, universal mechanisms of SM function and regulation have been elusive to membrane biologists for a long time. Sly1 is an SM protein that functions at the Golgi. Here, we present genetic and biochemical results, which show how a SNARE–mediated tethering mechanism of Sly1 is regulated, and which suggest that key aspects of SM function are evolutionarily conserved across the SM family. Unlike other SMs, Sly1p contains a loop that covers a portion of domain 3a on the protein. Previous studies show that mutations at the tip of the loop can suppress requirements for the Rab GTPase Ypt1 and tethering protein Uso1. It was hypothesized that the loop serves an auto–inhibitory function. Moreover, the recent crystal structure of another SM, Vps33, shows that domain 3a serves as a binding site for the cognate R–SNARE. We performed a screen for Sly1 mutants that suppress the loss of the Golgi tether, Uso1. The new mutants, as well as limited proteolysis experiments, suggest that the entire loop swings away to reveal a SNARE binding site on domain 3a, thereby activating the tethering and SNARE assembly functions of Sly1. These experiments reveal new features of Sly1 regulation, and in addition to the results from Vps33, suggest a universal mechanism of SM–SNARE interaction during vesicle tethering.

Genetically modified T cells have the potential for a number of therapeutic uses in anti-cancer immunotherapy, but a current limitation is the low yield of modified cells. Methotrexate is an FDA-approved drug used to destroy rapidly dividing cells by blocking their metabolism of folic acid. With the addition of a construct containing a mutant DHFR (dihydrofolate reductase) for methotrexate resistance, modified cell populations can be selectively expanded. Our mutant DHFR gene, delivered by lentivirus, has a Tyr-22 mutation which confers methotrexate resistance by changing its binding site. The purpose of this study is to determine the optimal concentrations and timing for the addition of methotrexate for selection of our target cell population. First, we grew cultures of Jurkat cells, an immortal T cell line, to find their normal growth and viability curves. Next, we transduced the cells by the addition of lentivirus at 1 or 2 X 10^4 viruses per 10^6 cells. We measured gene expression of a green fluorescent protein reporter gene using flow cytometry, which showed the lower viral concentration produces a peak protein expression of 14% on day two. Finally, we used various concentrations of methotrexate and found the optimal dosage for chemoselection to be 50 nM, with around 90% of the population showing expression on day five. We demonstrate a six-fold increase in gene modified cells in the presence of methotrexate and that the growth rate of modified resistant cells is comparable to non-modified cells. Currently, we are testing this selection protocol in human CD4 T cells. Overall, this study has major implications for the use of gene therapy requiring T cell products in clinical trials.

For many French citizens, French is much more than just a language. French is the central criterion of Frenchness, the badge of French nationhood and patriotic honor. This ongoing project is designed to investigate preconceived notions associated with regional French-accented speakers in France by focusing particularly on the Parisian’s perception towards regional French-accented speakers and the negative connotation associated with regional accented speakers in France. These types of negative stereotypes create linguistic insecurities and have a psychological impact on French speakers from different rural regions. Sadly, some people have developed subjective attitudes towards their own accented language, deeming certain forms of speech as incorrect and unpleasant. Thus, I have recruited 10 French-native adults living in Seattle; 5 of them are Parisians and the other 5 are from other French regions. My primary objective is to interview the participants and explore their attitudes and perceptions about the creation of linguistic stereotypes and misjudgments against accented-speakers in France. I have predicted that these Parisians’ opinions will be quite different because living in Seattle and being surrounded by different accented people may have influenced their own perception about accented-speakers. Under these circumstances it is possible that minor differences in pronunciation may hold less social weight. These interviews may provide insights to altering the negative perceptions about accented French that divides Francophones in France and abroad. 

Treponema pallidum pertenue, an endemic treponemal disease, also known as yaws, is considered a neglected tropical disease by the World Health Organization (WHO). Approximately 65,000 new cases of yaws occur each year in thirteen endemic countries, with almost 85% of all infections occurring in Ghana, Papua New Guinea, and the Solomon Islands. The disease is predominantly seen in children, transmitted by direct contact with the skin. Wild nonhuman primates (NHP) in Africa have been shown to be infected with T. pallidum pertenue. These African NHP cases of infection add to the speculation that free-ranging NHP may serve as a mammalian reservoir of the pathogen. Interestingly, human and NHP cases of T. pallidum pertenue in Africa often occur in areas where the groups are sympatric. In Asia, the human-NHP interface is generally more widespread and diverse, characterized by pet primates, temple monkeys, and wild and urban primates. Yaws infections in humans continues to be pervasive in many of the areas where humans and NHP interact. The goal of our project’s screening efforts is to further characterize whether these Asian monkey populations are infected with T. pallidum pertenue. Using standard serological assays to detect treponemal antibodies, we have screened approximately 800 NHP serum samples from eight countries representing six contexts and ten species. Our preliminary results indicate that T. pallidum pertenue can be detected in discreet NHP populations particularly where there is enhanced interaction between the human and NHP populations, and the disease is still largely endemic in the human population. In order for a disease to become eradicable, it is imperative that there be no mammalian reservoir. As the WHO seeks to eradicate the disease via a second global campaign, this research will be able to tell us whether treponemal infections are present in NHP populations.

Matrix-Associated Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is a high-throughput instrument with the ability to provide rapid and accurate identification of organisms in the microbial clinical setting. This powerful instrument has greatly impacted patient care in the recent decade. It has provided physicians the identification of organisms within a shorter time frame enabling more appropriate antibiotic treatments. With a newly implemented MALDI-TOF MS system at Virginia Mason Medical Center, it was necessary to validate the claim from the Bruker MALDI Biotyper CA System® against FDA cleared library list of organisms was indeed accurate. Fifteen anaerobic and twenty-three yeast isolates were selected in order to validate the instrument’s ability to identify organisms in the claim. These organisms were plated on media best suited for their growth and were incubated at 24 hour, 48 hour, and 24-hour sub culture to validate colony age, viability, and reproducibility. The purpose of this study was to validate the performance of the Bruker MALDI Biotyper CA System® on previously sequenced strains of yeasts and anaerobes, and to reliably perform testing on these frequently isolated organisms. Of the 15 different anaerobic isolates, MALDI-TOF was able to yield an accuracy of 86.7% using direct transfer methods. On the other hand, of the 23 different yeast isolates, the instrument yielded an accuracy of 87.0% with the misidentification of only one yeast isolate, which was possibly due to the resemblance to its closely related family. The validation of yeasts and anaerobes was proven to provide accurate identification to the species level with a vast number of isolates. MALDI-TOF MS has now been proven as a powerful method to be utilized in the clinical setting in order to accurately identify pathogenic organisms from patient isolates with this high-throughput instrument.

Thioester hydrolysis plays important roles in many biological processes including the Krebs cycle and the biosynthesis of fatty acids. In addition many enzymes such as thioesterases, hydrolyze thioesters. Previous studies have investigated the hydrolysis mechanism of the thioester formylthiocholine (FTC) using kinetic isotope effects (KIEs) in enzyme-catalyzed and non-enzymatic conditions. The data suggested that both concerted and stepwise mechanisms are plausible. To further explore and understand the transition state structure for the hydrolysis of FTC, we are investigating the hydrolysis of the oxoester analog, formylcholine (FCh). The formyl-KIEs for the hydrolysis of FCh in acidic, neutral, and alkaline conditions have been determined by comparing rates of hydrolysis of the light and heavy derivatives of FCh, HFCh and DFCh, respectively. The rates of reaction are measured using nuclear magnetic resonance spectroscopy. In this poster, we report current progress and preliminary results on the formyl-H KIEs for the hydrolysis of FCh. This study will provide a comparison for the KIE data collected with FTC, and will aid in the future design of inhibitors for enzymes that utilize thioesters as substrates. 

Wildland firefighters are trained to combat forest fires by prescribed burning or wildfire suppression. Prescribed burning is a planned fire lit intentionally by firefighters to reduce fire hazard and to provide greater safety for firefighters and the public. Wildland firefighters often work on controlled burns using one of two work tasks: lighting, which consists of laying a strip of fire on the forest floor; and holding, keeping fire inside specified boundaries. It is the exposure inherent to these work tasks that our research is primarily concerned with. During these operations, firefighters are exposed to various combustion products, including fine particulate matter (PM2.5), carbon monoxide, and polycyclic aromatic hydrocarbons (PAHs). Many PAHs are carcinogens that undergo metabolism and are excreted in urine. In order to measure the PAH exposure severity, urine samples from wildland firefighters were collected before and after prescribed burn operations as well as on non-burn days. Urine samples were hydrolyzed by treatment with sulfatase and glucuronidase enzymes, and cleaned up with solid phase extraction. High performance liquid chromatography with fluorescence detection was used to analyze the samples for PAH metabolites. Our data analysis compares PAH exposure by work task, by season, and between burn and non-burn days. We anticipate that urinary concentrations of PAHs in firefighters will be higher after the prescribed fire operation compared to pre-burn levels. Findings of this research can be used to measure PAH exposure not only in wildland firefighters, but also in other occupational or residential settings where people are exposed to high concentrations of PAHs to reduce risk factors of developing cancer.

In the United States, kidney failure (end stage renal disease/ ESRD) affects more than 871,000 people and costs over 40 billion dollars for treatment. The majority of these ESRD patients can sustain their lives via dialysis, which requires blood access. Synthetic vascular grafts are one way of creating the access, but they oftentimes fail within the first two years, in part due to the lack of endothelial ingrowth into the vessel walls. Our lab is developing a synthetic vascular graft that rivals the performance of native blood vessels by promoting complete healing of native vessels (e.g. endothelial cells) into the graft. This pro-healing effect is made possible by a precision-engineered microporous structure. However, due to this device’s porous properties, a sealant is required to prevent bleeding (hemorrhage). In order to simultaneously prevent hemorrhages and promote endothelial in-growth during the healing process, I have engineered a series of cross-linked gelatin with tunable biodegradability, mechanical properties, and low toxicity. In particular, cross-linkers genipin and EDC/NHS were explored. The shear strength of the hydrogel was examined by coating the luminal surface of the graft with the gelatin, incorporating this model into a flow regime, and analyzing the resulting surface effects with Scanning Electron Microscopy (SEM). Toxicity was analyzed through mice fibroblast seeding on a cross-linked hydrogel, and biodegradability was estimated by soaking the gelatin in a polyphenylene sulfide (PPS) buffer solution (with a physiological pH of 7.4) and measuring the resulting Young’s modulus with a universal testing machine (UTM). While lower crosslinking densities have rendered a more rapid remodeling by the body, higher crosslinking densities tend to display more durable mechanical properties; the crosslinking density was optimized based on these trends, such that the gelatin can effectively prevent initial bleeding while maintaining the biodegradability to allow the native blood vessel to heal into.

There has been growing policy and research attention to undocumented populations in the United States. Recent statistics indicate that there are currently 42.5 million foreign-born persons living in the United States, of which 11.2 million are undocumented. Immigration enforcement plays a huge role in the lives of undocumented populations and their families. Enforcement may impact immigrants’ health and social well-being in important ways. Indeed, undocumented families experience “extrafamilial acculturative stress,” a term used to describe the fear of deportation which leads to stress and compromised well-being. Documented immigrants in places with high concentrations of undocumented immigrants may be exposed to stress by being connected to undocumented immigrants. They also may experience discrimination by being assumed as having undocumented status. These stressors may impede immigrant populations from accessing health care and obtaining education and employment. For this research project, I have examined some of the implications for immigrants who live in states with a high concentration of undocumented immigrants. More specifically, I examined the association between the concentration of an undocumented population in all 50 states and the well-being of immigrant populations including access to health care, graduation rates, and unemployment rates. I used data from the Pew Research Center to estimate the unauthorized immigrant population as well as the foreign-born population in 2012 and adjusted for the total population. I gathered state-level well-being measures of foreign-born populations from the Kids Count organization and the Henry J. Kaiser Family Foundation. I drew data from the University of Kentucky Center for Poverty Research to create control measures capturing economic conditions and other demographic characteristics of the state. My analysis used multiple linear regression models to analyze the relationship between the concentration of undocumented immigrants and documented immigrants’ well-being.
 

Once the most followed woman on Instagram with a net worth of over 85 million dollars, Kim Kardashian West has not only made herself a household name, but as well her whole family. Seen as one of the most recognizable families in the world, the Kardashians have developed a brand surrounding their bodies, style, and personalities. As their brand continues, so has their cooptation of blackness to maintain their image and status. As the course of their success continues so has the Kardashians’ use of black scripts and performance in order to maintain their successful brand. As we look at stereotyped black features within the Kardashians, Kim herself has been known for her curvy figure, youngest member Kylie has gained attention surrounding her lip injections, and Khloe Kardashian has generated controversy over her appropriated persona. My project asks, what aspects of black culture have the Kardashians used to propel and maintain their careers? What does their strong media following and general popularity say about society’s acceptance of black appropriation? While conducting my research, I found that through their performance of blackness the Kardashians are able to further remove themselves from their Armenian identity and thus become traditional “white” celebrities by mainstream media. This performance allows the family to succeed by using what’s “cool” while not having to deal with the real oppressions that come with being black. With this performance, they are able to elevate their status by benefiting from the coolness while reminding viewers that they are not black. As one of the most famous families in the United States—and famous for being themselves—it’s important to examine their performance because through this modern form of minstrelsy, it allows us to see how society interacts with blackness and what blackness means.

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

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

A method will be presented for dating the last time sub-glacial mountains in West Antarctica were fully exposed by measuring the cosmic-ray-produced isotope ⁴¹Ca. The use of ⁴¹Ca will add a new cosmogenic isotope to the existing toolbox to improve surficial dating. The advantage of ⁴¹Ca over other isotopes is its short half-life (99,000 years), which reduces the complication of prior exposure in natural samples. To accomplish this, calcium will be extracted from Antarctic bedrock samples, converted to oxalate, and then further treated by column ion exchange to produce pure calcium, free of problematic potassium contamination. The biggest challenge will be to produce calcium hydride for measurement by accelerator mass spectrometry (AMS) to determine the ⁴¹Ca/⁴⁰Ca ratio. Current AMS capabilities allow ratio measurements in the 10-10 or 10-11 range. Measurements of the hydride should allow us to extend this down to the 10-14 level necessary for geological applications. Successful measurements in this range will open up applications such as tests for whether sub-glacial bedrock in West Antarctica was exposed to cosmic rays during the last warm interglacial climate period, approximately 120,000 years ago. Perfecting this method and making it available to others in the field can open a door into the past to determine if current global warming trends are leading us down a path similar to the last deglaciation, which raised global sea level by several meters. Though we are working on a geological and glaciological issue, the ultimate product of this research touches areas of meteorology, biology, and sociology as the Earth adjusts to increases in global temperature.

A cell’s outer membrane displays a broad range of proteins and other biomolecules that play an essential role in mediating interactions between the cell and its environment. Some cell surface molecules, known as antigens, can be used by clinicians and researchers to identify specific cells for use in diagnostics and targeted therapies. Cell identification based on surface antigens is known as phenotyping, which is typically performed in the clinical laboratory using a flow cytometer. In flow cytometry, cells are labeled with fluorescently-labeled antibodies that bind to a specific antigen on the cell surface in order to identify the cell’s phenotype. Conventional platforms for flow cytometry are costly, and fluorescence-based phenotyping involves tedious labeling steps and advanced detection capabilities. For laboratory facilities without the resources or need for a flow cytometry platform, a method for simple, specific, and direct cell characterization is desirable. The Ratner Lab uses silicon photonic technology in biosensing applications to detect when mass binds to a sensing surface. In this project, the sensing region of the silicon photonic chip was coated with antibodies to target a specific antigen displayed by a cell. A silicon photonic sensor was functionalized to phenotype prostate carcinoma cell lines for prostate-specific membrane antigen (PSMA). The cells were fragmented to yield membrane microparticles that could be flowed across the antibody-coated photonic sensor in order to characterize the cells for the presence or absence of the cancer marker. This study employed model cell lines as a proof-of-concept for simple, label-free cell phenotyping, departing from traditional fluorescence-based methods for cellular analysis.

Our planetary next-door neighbor, Mars, is a top candidate for near-future human settlement. Resources such as water ice are known to exist inside Mars’ porous regolith, and the ability to find and utilize resources is an important step toward putting astronauts on Mars’ surface. Our project investigates the influence of ice on the thermal properties of planetary regolith. Models predict that a .01% increase in regolith ice increases thermal conductivity by a factor of 5. Because the stability of water ice has a strong dependency on its thermal environment on a planet with little atmosphere such as Mars, an understanding of how thermal properties of regolith are influenced by ice will provide great insight into where ice exists. However, this relationship is not yet well-supported with empirical evidence, so we are designing and testing an apparatus to measure thermal conductivity of regolith with varied amounts of ice content. The apparatus uses a thermoelectric cooler to cool the sample to -10° Celsius and create sinusoidal temperature waves that propagate through the sample. Temperature sensors at specific heights measure the wave properties to determine thermal conductivity. Currently we can take temperature and weight measurements from the apparatus, and our next steps are to control humidity in the experiment with nitrogen gas, and calibrate a fiber-optic spectroscopic measurement technique to determine regolith ice content to higher precision than allowed by weight measurements. Understanding how ice content affects regolith thermal conductivity will help us further understand the conditions under which regolith ice is stable, and allow us to predict the location of ice on a planet by analyzing thermal inertia data from remote-sensing satellites. This method of locating ice and similar resources will prove valuable in planning crewed missions and determining ideal locations for human colonization on Mars and elsewhere in the solar system.

Conjugated polymer semiconductors have received substantial attention for providing a path to low cost manufacturing of electronics such as organic field-effect transistors, light emitting diodes, and solar cells. This work explores the electronic and structural effects of doping colloidal poly(3-hexlythiophene) (P3HT) nanofibers in non-aqueous solution. Doping injects charge carriers into the organic semiconductor and allows for modulation of electrical and optical properties. In solution, increasing dopant concentration also typically leads to uncontrolled polymer aggregation. In this work, we will demonstrate that doping and colloidal stability can be obtained for self-assembled P3HT nanofibers. This work characterizes the conductivity, structure, and optical properties of P3HT nanofibers as a function of dopant concentration and dopant molecular structure. These findings contribute to improved development of transparent thin films for organic electronics by achieving both solution stability and increased conductivity.

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

Europa is one of Jupiter’s moons which is covered in ice. Further research on Europa is needed to determine if the moon can sustain life. One of the barriers that has affected our understanding of the moon is the large velocity requirements to land on Europa, which make a soft landing on the surface too costly. To overcome this problem, research has being performed on penetrator technology that can withstand a hypervelocity impact. The initial system involves the study of the performance of a two-stage penetrator. The first stage would break the ice, making way for the second stage. The second stage of the penetrator would encounter weaker ice and therefore have a higher probability of surviving the impact. The electronics would be located in the second stage. Projectiles have been tested on impact qualities and post-impact properties. Further experimentation has been performed with various designs and materials that have varying densities. Density is expected to play an important role in the depth of penetration and the resulting deceleration forces on the system. Penetrators made of Lexan have been used along with wood as impact material. Seven inches of penetration has been achieved when fired at speeds close to 1 km/s. Smaller scale testing, at lower speeds, has been performed on larger Lexan projectiles fired into ice resulted in approximately 1.5 in. of penetration. Projectiles made of aluminum have been tested and fired into a bucket of ice. The ice was kept at -20° C, which is still significantly warmer that the surface conditions of the moon. Once the penetrators are optimized for these temperature conditions, additional testing would involve liquid nitrogen to cool the ice to colder temperatures. The penetrator system could lead to the discovery of new life, future missions to Europa and possible habitation or resource extraction.

Systemic lupus erythematosus (SLE) is a life-threatening disease that affects over 500,000 individuals in the United States. One in five patients is diagnosed as a child and they are at higher risk for kidney disease, early mortality and infection due to current immunosuppressive medications that serve as the only treatments. The voltage-gated potassium channel Kv1.3 sustains intracellular calcium levels needed for the activation of effector memory T-lymphocytes (TEMs), a cell associated with serious complications of SLE including lupus nephritis (LN). Because Kv1.3 is highly expressed on TEMs, we hypothesize that it could serve as a viable drug target for SLE. Preliminary data suggests that Kv1.3 expression is high on peripheral blood CD4+ (helper) and CD8+ (cytotoxic) TEMs from SLE patients compared to controls, but the inflammatory cells of interest are found within the tissues. In order to test for the expression of Kv1.3 on immune cells active in LN, we are characterizing Kv1.3 expression on cells in urine from pediatric SLE LN patients. Urinary leukocytes were isolated from 16 patients and applied to slides for analysis via multicolor immunofluorescence for the co-expression of Kv1.3 and CD3 (as a marker for T lymphocytes). Kv1.3 expression was observed on CD4+ TEMs verified by flow cytometry analysis. Further evaluation of patient lymphocytes will be performed by immunofluorescence in conjunction with flow cytometry assays showing the dual expression of Kv1.3 and CD3 on TEMs, and other cell types with potential pathogenic roles in LN, including B lymphocytes (CD19), monocytes (CD14) and epithelial cells (cytokeratin). Positive results will indicate the viability of Kv1.3 as a drug target for SLE treatment. This research has great implications for patients with SLE and those with a wide range of autoimmune disorders including rheumatoid arthritis/juvenile idiopathic arthritis, uveitis, psoriasis, and multiple sclerosis.

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

Considering the current price and competitiveness of higher education, extra-institutional programs like Advanced Placement, International Baccalaureate, and Running Start are playing an increasingly critical role in public education. Unfortunately these programs, varying in curriculum, course structure, assessment, and aptitude, are not always consistent with the learning outcomes of universities. At University of Washington, Texts and Teachers, a part of the UW in the High School Program, attempts to bridge the gap between extra-institutional college curricula and university learning outcomes by creating collaborative course design, teaching common texts, using common culminating writing portfolios for assessment, and scheduling reciprocal faculty visits to high school classrooms and high school class visits to the linked UW classrooom. In order to assess the program’s success in meeting common learning outcomes, I have designed a research project guided by program instructor Professor Gary Handwerk which evaluates student portfolios for their demonstration of writing ability relative to the UW Expository Writing Program’s learning outcomes. Using a text-response oriented scoring pathway taken from Linda Flower’s 1990 text Reading to Write, I reviewed student portfolios from ENGL 111 and from T&T classes both on and off campus, assessing three primary trait categories: organizational strategies, concept development, and critical analysis. Once scored, I tested for statistically significant differences between class setting and course level and concluded that there was no significant difference between classes. In addition, this methodology distinguished average rates at which students improve their writing ability in each setting. This research provides evidence to support the compatibility of T&T and EWP writing instruction. It thus demonstrates the success of extra-institutional college curricula operating in a context specific to the learning outcomes of a particular university.

In order to protect wheat from the aggressive root fungal infection, Take-all, farmers have turned to biological methods. Bacteria that produce 2,4-diacetylphloroglucinol (DAPG) are one of the best methods of controlling it, but some strains work better. Psuedomonas fluorescens L5.1-96 is the most effective strain, so 1000 bp long genome segments, from a made genomic library, are being sequenced and analyzed. One segment, a heat shock protein, was found to be unique among strains studied for wheat root colonization. To find whether this protein is necessary for L5.1-96’s effectiveness, a proper assay needs to be created for the protein for future analysis. The gene had a 98% DNA match to Psuedomonas brassicacearum, so primers for PCR of the gene were created based on its DNA sequence. The amplified gene will be placed into a high efficiency plasmid for transforming competent E. coli cells, which will be analyzed for their protein composition, in order to create a Western Blot test for the protein. Once the test is created, the strain can be analyzed to find out whether this gene is important for root colonization.

Exposure to air pollution has been linked to increased risk of cardiovascular morbidity and mortality, with special concern about fine particulate matter and traffic-related air pollution such as diesel exhaust. One potential mechanism for this association is an impact on the smallest blood vessels, the microvasculature, which regulate blood pressure. The microvasculature can be directly visualized in the eye’s retinal vessels, and some studies have observed narrowing of retinal arterioles with exposure to pollutants. This project investigates changes in human retinal vessel diameter in response to diesel exhaust exposure. We hypothesize that retinal arterioles will contract in response to diesel exhaust exposure. For this study, we recruited healthy, young adults, who visited the lab on four study days—two with diesel exhaust inhalation and two with filtered air inhalation, in a double-blind controlled trial. We collected retinal photographs before and after exposure for 17 participants on study days. We use semi-automated grading of retinal vessel diameters from the photographs to determine the arteriolar diameters assessed as central retinal arteriolar equivalents (CRAE). We use paired t-tests to determine if diesel exhaust exposure is associated with temporary reduction in CRAE. We expect to see reductions in CRAE in response to diesel exhaust exposure and no change in CRAE in response to clean air exposure. These study results would support the idea that retinal arterioles contract with diesel exhaust exposure. Under the assumption that retinal arterioles model a change in the microvascular bed throughout the body in response to this traffic-related air pollutant mixture, the results would ultimately suggest that a microvascular effect is involved in the contribution of air pollutants to the burden of cardiovascular morbidity and mortality.

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

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

We validated the LIATEST® Antithrombin III (ATIII) antigen assay for use on the Stago® STA compact analyzer. The LIATEST® is an antibody agglutination assay that measures the amount of ATIII antigen in patients who are on cardiopulmonary support systems. The LIATEST® was chosen because is more stable than the STACHROM (chromogenic) gold standard.

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

More than 20 million Americans have some level of chronic kidney disease. With the constant deterioration of kidney function, treatments for this disease are in high demand. The only treatments available today include dialysis and kidney replacement. Unfortunately, these methods are not ideal due to a high dependency on the dialysis machine, long waiting lists, and possible rejection of the organ. Recently, protocols were developed that allow us to use pluripotent stem cells to generate kidney-like organoids. These organoids contain major structures of the nephron, the functional units of the kidney, which clean and filter the blood. For instance, podocytes, proximal tubules, distal tubules, and various cell types develop in these samples. This complexity that develops allows more accurate modeling of kidney disease than previous methods. A new protocol developed by our lab allows us to grow miniature organoids in microwells; this will allow us to perform large scale drug screens to search for treatments for various types of kidney disease. The miniature organoids were tested to see if they replicate the complexity seen in larger wells. Immunofluorescence was used to characterize the kidney organoids and the different cell types present within them. Additionally, proteins with the capability to perform biological functions, such as transporting glucose and other ions, are able to be studied as well. The results were compared to human fetal kidney tissue. The miniature organoids replicate all of the same structures found in the larger wells. Because of the strong similarities between miniature kidney organoids and the human kidney, they are optimal for drug testing. Impacts associated with new therapies will be easier to monitor through the miniature kidney models.

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

This project seeks to identify root colonization of ectomycorrhizal fungi (EMF) on Abies grandis (grand fir) seedlings that were planted at the former Lake Mills restoration site along the Elwha river. Ectomycorrhizal fungi are a root-dwelling fungus that form mutualistic symbioses with many tree species and fulfill an important role in nutrient cycling within forest ecosystems. EMF species from early successional river bed sites may contain more suitable types of EMF compared to EMF that inhabit late successional mature forest soil. We hypothesize that the two soil inoculant types will produce a difference in EMF root seedling colonization and potentially have an impact on the survival rate of conifer seedlings at the restoration site. In fall of 2014, A. grandis seedlings were planted using two treatments of soil inoculant. Mature forest soil (late successional), autoclaved forest soil (control), river bed soil (early successional), or autoclaved river bed soil (control) was mixed with the excavated soil and then used to replant each seedling at the field site. Laboratory extractions of 260 A. grandis root tip samples have been completed and we are currently focused on completing PCR and sequence analysis on the extracted root tips. My laboratory work includes DNA extraction, gel electrophoresis, PCR using ITS1F and ITS4 primers, and sequence analysis of fungal DNA using the Basic Local Alignment Search Tool (BLAST). The ectomycorrhizal taxa present will be identified using BLAST and then percent colonization and taxa diversity will be determined within each treatment. This genetic information will contribute to the greater body of knowledge on the diversity and range of ectomycorrhizal fungi in the Pacific Northwest and be potentially useful in restoration ecology work as we gain a better understanding of the role of ectomycorrhizal fungi on conifer seedling survival within the context of early successional conditions.

Alexandrium is a genus of dinoflagellate that produces saxitoxin, which is known to cause paralytic shellfish poisoning when shellfish contaminated with high concentrations of Alexandrium are consumed. Due to the possibility of toxicity and negative economic impacts, the presence of Alexandrium is regularly monitored throughout the Puget Sound. Alexandrium spends part of its life cycle as a cyst in the sediment before germinating to become a free-swimming dinoflagellate. Alexandrium cysts in surface sediments are used to determine the present spatial distribution of this organism. Cyst concentrations in sediment cores can be used to evaluate historical presence and temporal variability. A research project from 2005, funded by NOAA’s ECOHAB program, has shown that surface sediments in Quartermaster Harbor (QMH), a harbor with low flushing rates due to its geographical orientation, have the highest abundance of Alexandrium cysts in Puget Sound. In July 2010, sediment cores were collected from five locations in Puget Sound to determine the historical distribution of Alexandrium. The purpose of this study is to quantify Alexandrium cyst concentrations in a 202 cm Kasten core collected from the inner harbor of QMH. Sediments were prepared for by sieving material between 20 and 90 µm and staining with Primulin before being analyzed for Alexandrium presence under epifluorescence using an FITS filter on a compound microscope. Preliminary results show maximum cysts/mL sediment near the surface, regressing to 0 cysts/mL sediment below 30 cm. The core was characterized by analyzing the grain-size distribution and organic content of each sub-sample of the core in order to determine if there is a relationship between cyst abundance and these properties. 210Pb dating was completed in order to correlate cyst abundance and local changes to the harbor.

The Tritium Recoil-Ion Mass Spectrometer (TRIMS) experiment is designed to measure the branching ratio of molecular tritium to the helium-tritium molecular ion after beta decay. Tritium emits very low-energy beta particles and is difficult to detect. My research seeks to measure the background levels of tritium contamination on laboratory and apparatus surfaces by using a gas flow proportional counter. This type of counter consists of a gas filled metal tube with a high voltage wire in the center. Beta particles from tritium decay ionize the gas, and the high electric field causes avalanche multiplication, which is picked up as a signal on the wire. The size of the signal is proportional to the energy of the original particle. This apparatus allows for surveys for tritium contamination initially and throughout the lifetime of the TRIMS experiment, with real time indication.

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

Freshwater lakes are an important source of the greenhouse gas methane contributing around 6-16% of the total atmospheric methane budget. Methane oxidation in freshwater lakes is the result of different functional guilds of bacteria working together as opposed to just methanotrophs themselves. Microbial communities in methane-fed lake sediment microcosms have not only displayed a clear response to methane by methanotrophs, but also by non-methanotrophic methylotrophs. To obtain a better understanding of the interaction between methanotrophs and methylotrophs, we investigated the role of methanol as a key methane-derived carbon compound enabling stable co-culture formations between a non-methanotrophic methylotroph (Methylotenera mobilis JLW8) and a methanotroph (Methylobacter tundripaludum 31/32). Along with JLW8 wild type, we tested different mutants of Methylotenera with deletions in the methanol oxidation pathway; XoxF mutants 1170, 2048 and 48/70-9. By monitoring the populations of Methylobacter and Methylotenera in the co-cultures with the use of flow cytometry, we find evidence that methane-derived methanol is likely the growth substrate used by Methylotenera in the artificially created methane-fed microcosms. All co-cultures formed stable communities with the exception of the double mutant, which is unable to grow on methanol, indicating that methanol is the key methane-derived component in community establishment. The wild type and both single mutants established co-cultures in similar patterns resulting in somewhat equal distributions of Methylobacter and Methylotenera by the 4th week. Both single mutants, however, showed consistently higher abundances of Methylotenera in comparison to the wild type co-cultures. This data also suggests that both single mutants may be better at oxidizing methanol than the wild type although the mechanisms for this are still unclear. These results provide insight into the growing significance of methanol in facilitating the complex communities invovled in methane oxidation.

Sexual dimorphism in biacetabular breadth in modern humans is believed to have developed in response to selective pressures for both a short lever arm from the body center of gravity to the acetabulum and a relatively large birth canal. Biacetabular breadth is difficult to measure in living people without invasive imaging, which complicates understanding the effect of this "obstetrical dilemma". Proxy measurements, such as bitrochanteric or bicristale breadth, have been used, but how well either of these easily obtainable measurements predicts biacetabular breadth remains unknown. Consequently, we examine whether or not biacetabular breadth is predicted by bitrochanteric or bicristale breadth in males and females. Biacetabular breadth, bicristale breadth, bitrochanteric breadth, and left and right femoral head diameters were measured on 154 AP radiographs (from 61 females and 93 males; aged 18 to 65 years) collected from a radiograph database. Multiple linear regression was used to assess the ability of bitrochanteric or bicristale breadth to predict biacetabular breadth. We found that biacetabular breadth is predicted by bitrochanteric breadth in both males (r-squared=0.48) and females (r-squared=0.63). Bicristale breadth predicts less of the variation in biacetabular breadth in males (r-squared=0.13) than in females (r-squared=0.54). Including the effect of both bitrochanteric and bicristale breadth improved the predictive ability in females (r-squared=0.70) but not in males. (All p-values were <0.001). We conclude that bitrochanteric and bicristale breadth predict biacetabular breadth but that greater than 30% of the variability remains unexplained.

As social media platforms become more prominent in daily interpersonal interactions, there are also increasing developments of online communities associated with several mental health issues, some of which include mental health surrounding disordered eating patterns. Patterns of disordered eating include anorexia nervosa, bulimia nervosa, binge-eating disorder, orthorexia, and others. Prior research indicates that pro-eating disorder messages are increasingly prominent on social media sites including Facebook and Tumblr, and note the negative effects of this content in terms of self-image within those exposed to this content. However, little research has been conducted on the effects of online communities established with the purpose of providing support for internet users living with disordered eating patterns. This research surveys the opinions of Tumblr users who follow blogs providing support for those suffering with eating disorders, such as “Eating Disordered Confessions” (eatingdisorderconfession.tumblr.com). The survey used includes questions about participants’ opinions about available treatment options for disordered eating, whether they believe that they display some sort of disordered eating, if this has been influenced by the use of Tumblr, and several other questions that serve to indicate the extent of the disordered eating patterns of the participants. The responses to these questions are compared between groups separated by indicated amounts of time that the participants spend on Tumblr. Results from this research can help to inform the role of social media sites for helping or harming individuals suffering from stigmatized mental health disorders.

This research details the design, construction, modeling, launch and post-flight analysis of a high-powered rocket through the Earth and Space Sciences’ Rockets and Instrumentation course at the University of Washington. The primary goal was to build and test a multistage cluster rocket, scheduled to launch March 2016 in Black Rock, NV. To exploit the exponentially decreasing drag at high altitudes the rocket was initially designed as a two-stage, with eight external motors and two internal motors providing 43 kN-s of total thrust with a max velocity of 750 m/s. Risk assessment shows three-stage ignition as a safer option, providing a ground launch of 10 kN-s of thrust. Once the main engine burns for 2 seconds, the external cluster motors will ignite, providing 19 kN-s of impulse before separating from the main stage at around 20,000 feet. The sustainer motor then ignites at a final impulse of 14 kN-s and will reach an apogee of approximately 47,000 feet. The recovery package was designed with two separate systems of dual deployment for drogue and main parachutes, as well as a GPS and an altimeter, using two different flight computers, one in each stage. Previously untested commercial telemetry instrumentation was chosen and simulated with electromagnetic software before launching. If the rocket performs as designed, it will be the highest rocket built and flown by a University of Washington student group.

Due to society’s increasing energy demand and the push for technological innovation within key industries (e.g. consumer electronics and electric vehicles), major advancements in energy storage technology, specifically battery technology, are needed. While Li-ion batteries are currently regarded as one of the premier options for reusable energy storage, they are not as safe, environmentally-friendly, or cost-effective as currently researched alternatives. One promising alternative is the rechargeable Zn/MnO₂ battery which offers many benefits such as high energy density, low cost, and the ability to use non-corrosive electrolytes. In addition, the cathode material, MnO₂, can exist in a variety of crystal structures which will offer distinct pathways or mechanisms for Zn-ion transport. This project explores how the crystal structure of MnO₂ influences the electrochemical reaction mechanisms and subsequent performance of the Zn/MnO₂ battery. Three different phases of MnO₂ (α, β, and δ) were synthesized hydrothermally for use as cathode materials. Coin cells consisting of a Zn metal anode, MnO₂ cathode, and an aqueous ZnSO₄ electrolyte were then assembled and cycled to determine the charge/discharge behaviors of the batteries. Finally, the results of this project will help identify optimal cathode materials for improving the electrochemical performance of Zn/MnO₂ batteries. 

Molecular studies of plants’ photoperiodic flowering have helped improve crops in agriculture and horticulture by modulating growth patterns in plants. A photoperiod is a seasonal change in day length of daytime that is consistent from year to year. Plants maximize their reproductive success by adjusting their flowering time according to photoperiodic information. To better understand the effect of photoperiods in plants, we used Arabidopsis thaliana as a model organism. Scientists worldwide study A.thaliana due to its genomic simplicity, its fast growth and its efficient transformation by using Agrobacterium tumefaciens. In A. thaliana, the transcription of the CONSTANS (CO) gene is key for the regulation of seasonal flowering. Under long-day conditions, both transcriptional and post-transcriptional CO regulation maximize the CO protein accumulation towards the end of day, which induces the expression of FLOWERING LOCUS T (FT) gene, which encodes florigen and causes the plants to flower. TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL NUCLEAR ANTIGEN FACTOR (TCP) binding site is closely located to cis-elements of CO regulators, which indicates that they might interact in the same complex. To study the functional interaction between TCP and known CO regulators, including GIGANTEA (GI) and FLOWERING bHLH (FBH), we first studied the protein-protein interaction using yeast two hybrid analysis. The yeast two hybrid analysis confirmed protein-protein interaction between TCP4-GI, TCP4-FBH, and FBH-GI. Then, to validate the protein-protein interaction suggested by the yeast two hybrid analysis we performed flowering time measurement experiments on multiple combinations of these mutants, in order to investigate the genetic relation among CO regulators.

 

Proteins are the executors of life’s most essential processes, and the ability to express and purify proteins of interest is critical to studying their structure and function. Genetic fusions to small ubiquitin-like modifier (SUMO) tags generally increase the solubility and stability of target proteins during recombinant expression. Following purification, the fusion protein can be cleaved by the highly specific SUMO protease, leaving the target protein intact and unmodified. This specificity attests to the use of the SUMO protease as a powerful biotechnical tool. The current SUMO system relies on the Saccharomyces cerevisiae protease Ulp1. However, this protein has considerable limitations in that it is temperature sensitive and requires detergent to maintain stability, which can interfere with downstream applications. Furthermore, Ulp1 instability often leads to incomplete digestion of SUMOylated constructs and can nucleate aggregation of target proteins. We sought to improve the current system by two orthogonal approaches. First, we mined genomic information from thermophilic organisms for homologous proteins. We have identified and experimentally characterized a novel SUMO-protease system from, Chaetomium thermophilium, a eukaryote that can grow in compost up to 60°C. Second, we used computational protein design with Rosetta to reengineer S. cerevisiae Ulp1 to enhance the stability and solubility of this protein. Using a novel fluorescence resonance energy transfer (FRET) based reporter assay that we have developed to monitor protein cleavage, we can characterize the SUMO systems and evaluate their efficacy. This assay allows for assessment and optimization of protease digestion in varying temperature, pH, and salinity conditions. These SUMO protease systems that we have uncovered and redesigned allow for the ability to circumvent many of the issues associated with the current Ulp1 system by offering an alternative, enhanced tool for the purification and expression of recombinant protein in laboratory research settings.

Newborns and children are more vulnerable to xenobiotics (foreign chemical substances) partly because little is known regarding the developmental regulation of drug-processing genes (DPGs) by drugs and environmental chemicals. The xenobiotic-sensing nuclear receptors, namely the pregnane X receptor (PXR) and constitutive androstane receptor (CAR), are well-known to up-regulate many DPGs in liver. However, relatively less is known regarding the effect of developmental exposure to PXR- or CAR-activators on the expression of DPGs in intestine, where the biotransformation of orally-exposed xenobiotics takes place. Therefore, the goal of this study was to determine both the acute and the potential long-term effects of neonatal exposure to PXR- and CAR-activators on the regulation of DPGs in neonatal and adult intestine. Wild-type mice were pharmacologically administered the PXR-ligand PCN (the activator of PXR in mice), the CAR-ligand TCPOBOP (the activator of CAR in mice), or vehicle, at 3-day-old neonatal age. Intestines were collected 24h post-dose (whole intestine) or at 60-day-old adult age (duodenum, jejunum, ileum, and colon). Neonatal exposure to TCPOBOP and PCN up-regulated many DPGs 24h postdose. Interestingly, at 60-days adult age, neonatal exposure to TCPOBOP persistently up-regulated many DPGs especially in small intestine, but down-regulated particularly in colon (large intestine). Neonatal exposure to PCN persistently up-regulated 6 DPGs but down-regulated 11 DPGs in specific sections of intestine. In conclusion, this study has demonstrated that neonatal exposure to xenobiotics that activate PXR and CAR not only produce acute induction effect on the DPG expression in newborns, but also lead to persistent alterations on the expression of certain DPGs in adult intestine, and this may potentially alter the pharmacokinetics of orally-exposed chemicals in adults.

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

The Redbluff landslide, situated at Washington-Oregon state border, is part of the larger Bonneville landslide complex. In 1450 A.D., the Bonneville landslide dammed the Columbia River, but the river eventually breached it. In the present day, only one part of the landslide complex, namely the Redbluff landslide, is still slowly creeping into the Columbia River. It also poses a risk of damaging nearby public infrastructure. Interferometric synthetic aperture radar (InSAR) is a remote sensing technique used to measure millimeter-scale surface deformation. These satellite data are complemented by Light Detection Ranging (LiDAR), which is used to produce high-resolution topography images. Using these observations, I seek to understand how the movement of the Redbluff landslide relates to the surrounding geology and morphology. The downslope landslide movement is computed by back-projecting the line-of-sight InSAR observations onto a downslope vector, as done by previous InSAR glacier studies. ArcGIS software will be used to produce a higher-resolution model of the landslide movement. Furthermore, surface roughness will be computed as a geomorphic proxy of active movement on the slope. I expect that the InSAR surface displacement will show active movement in the regions with highest surface roughness. The InSAR and LiDAR data sets are highly complementary data sets and both help to better characterize landslide hazards along the Columbia River.

This project focused on redesigning the application and related sites for mPOWEr, a research project building a mobile post-operative wound evaluator to reduce surgical site infections. The redesign of the application’s overall aesthetic focused on improving usability and creating a more cohesive look. One of the major tasks in redesign was reimagining the patient-facing site. After brainstorming and interacting with the initial patient site, I realized the necessity of a distinct, categorized system for the website instead of a primarily single-document layout. I created basic wireframes, which turned into higher-fidelity prototypes, and eventually culminated in coding the live site. Through group critique, feedback, and continued iterations, the patient-site went through the steps of creative problem-solving to construct a cohesive identity for mPOWEr and provide compelling visuals that match the group’s purposes. After creating a new identity for the patient-facing site, similar design can be applied to the application itself, as well as other of marketing materials, to build cohesive aesthetic and distinctive design across all elements of the project.

Optical coherence tomography (OCT) is an non-invasive imaging technique that is able to produce micrometer resolution images of human tissue. Building upon this imaging technique, the Wang lab has developed novel OCT based techniques to image the microvasculature of the human eye. With these high resolution OCT images, it would be possible to provide quantitiatve measurements of ocular features that can assess eye diseases non-invasively. These measurements would include blood flow rate, vessel density, vessel tortuosity, fractal dimensions, etc. The goal in this research is to determine which of these physical parameters in the eye can provide objective measures that correlate well with the severity of diabetic retinopathy (DR), the leading cause of blindness worldwide. Specifically, this research focused on five quantifiable metrics - vessel diameter, vessel area density, vessel skeleton density, vessel perimeter index, and vessel complexity index - and their correlations with the progression of the disease. The main hypothesis was that at least one of these parameters would show significant correlation with DR progression.Each of these metrics were quantified from OCT images of patients with DR using semi-automated computer software. Then, statistical analysis was done to calculate the correlations of each metrics with disease progression. Finally, an evaluation was performed to see which of these objective parameters can serve as sensitive biomarkers, possessing the potential to be used in diagnosing or monitoring the therapeutic treatments of diabetic retinopathy. 

The conventional decaffeination processes consume a lot of energy and use many chemical solvents that can be harmful to both the environment and human health. Although there are four main methods of decaffeination, they all consume high amounts of energy and tend to degrade the taste of the decaffeinated coffee; some processes even use harmful chemicals such as methylene chloride. To address this problem, natural clay minerals are chosen as the adsorbents to extract caffeine from coffee beverages due to their unique micro and nano structures. Selective caffeine adsorption can be achieved by engineering the clay structures, including methods of interlayer spacing control, ion exchange, edge sites modification, secondary structure control, and structural polymerization. Three clay minerals have been tested, which are laponite, bentonite, and zeolite Y. For all three clay materials tested, they initially do not show any caffeine adsorption. However, with different engineering principles applied, different degrees of caffeine removal are achieved. The best result is 80% caffeine reduction after 2 minutes and 99.6% after 20 minutes in real coffee using 1 gram of clay per 100mL of coffee; this particular result was achieved through clay interlayer spacing control, secondary structure control, and structural polymerization of the bentonite clay. Moreover, with the HPLC analysis, the result showed that the material is fairly selective for the caffeine molecule, and during the decaffeinated coffee taste tests, most of the participants said that decaffeination with clay yield better taste coffee compared to conventional decaffeinated coffee. This new decaffeination process is much faster and versatile since it can reduce much of the caffeine in most of the beverages that contain caffeine in just a few minutes. Clay mineral structural engineering is a very promising technology for selectively removing caffeine molecules and has great potentials for the beverage industry.

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

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

Congenital heart disease is a problem with the structure of the heart that is present at birth. In the United States, about 40,000 babies are affected by this disease annually. In our lab, zebrafish are used to investigate the genetic causes of this disease. Previous research investigations from our lab have shown that two important genes that are responsible for the regulation of heart muscle are Pbx4 and Pbx2, which are homeodomain transcription factors. Pbx2 and Pbx4 are genes of interest because their roles in heart development are not completely understood. CRISPR/Cas9 method is a method that can be used to target specific DNA sequences and create modifications in the genome. We used this method to engineer different strains of zebrafish with a variety of Pbx gene alleles to determine the role of the Pbx factors in heart development. In order to figure out how the different alleles affect the Pbx genes, each of the strains were observed for phenotype. The null alleles of Pbx2 and Pbx4 were used to demonstrate that embryos lacking both of these factors have severe defects in heart muscle differentiation and outflow tract formation. Then, in-frame deletions were made in the Pbx4 gene demonstrating the importance of an alanine tract for critical functions in heart development. Next, a strain was engineered which contains a Pbx gene variant associated with congenital heart disease in humans. Crosses were set up between strains to compare the effect of each mutation. Thus, the use of genome engineering allowed us to conduct analyses of vital transcription factors involved in heart development.

Food security is the measure of an individual’s ability to access and utilize sufficient food to ensure a healthy and productive lifestyle. Previous research has highlighted this issue in various populations in the Seattle area. However, the effectiveness and coverage of the available nutritional programming has yet to be determined. The goals of this project were to 1) better understand which areas of Seattle are at the greatest risk of hunger and food insecurity as measured by income, and 2) to measure which areas are most underserved by nutrition programming. A visual representation of Seattle was created to identify specific census tracts with a population that is at-risk of food insecurity by incorporating economic, social, and demographic data from the 2013 American Community Survey [ACS] and the 2010 Decennial Census. From this map highlighting at-risk populations and data regarding numerous social programs run by nonprofits, governmental agencies, and businesses, a geographical analysis was performed to determine the coverage and the ability of these programs to fulfill the studied population’s nutritional needs. The results of this study will enable nutritional programs and future researchers to better serve at-risk populations by focusing their efforts on underserved areas and allow more efficient allocation of resources to ensure food equity in Seattle.

With 9.5 million new cases of active disease annually and 30% of the world latently infected, tuberculosis (TB) disease is a public health crisis on a massive scale. Despite decades of research, treatment options are still suboptimal, with standard drug regimens ranging from 6-12 months for drug-susceptible cases and up to 24 months in instances of drug resistance. Detection of drug resistance is essential to getting patients the appropriate treatment regimen, but the diagnosis of resistance can take 4-6 weeks using standard culturing approaches. Current TB research is often done with “batch culture” techniques, which are tests done on millions to billions of bacteria and the average response is used to make inferences about individual bacteria. While useful, batch culturing contributes to the lengthy diagnosis of drug resistance and is at odds with the clinical course of TB infections, where such numbers of bacteria are seen in only the most extreme cases of disease. To address this limitation we developed a platform to watch and track single cells responding to a variety of environments. Our platform features a semi-solid growth substrate, brightfield and fluorescent microscopy, and the ability to faithfully track  single cells for more than 5 days. Using our platform we tested TB susceptibility to isoniazid, a common first line TB drug. Benchmarking against batch culture, we found the killing dose of isoniazid to be comparable with our platform; however, unexpectedly, we found that sublethal doses of drug have the opposite effect: they increase bacterial growth rates. In addition to impacting knowledge about the basic biology of TB, our platform has the potential to evolve into a diagnostic test for drug resistance, with the ability to identify drug resistant strains of TB in <4 days.

In diagnostics, the ability to detect small quantities of molecules with high sensitivity and specificity is crucial for a quick and accurate diagnosis of the presence of target antigens. The ELISA assay, which uses fluorescence to detect the presence of target molecules, is a standard diagnostic and research method for antibody-antigen detection. However, current ELISA methods do not have fast binding kinetics at low target antigen concentrations, requiring several hours for complete results. Therefore, there is a significant need for development of a simple and inexpensive method to improve the molecular binding kinetics in ELISA assays. My hypothesis was that rotational stimulation during enzyme incubation would greatly increase the sensitivity of the assay in a much shorter amount of time. To test this hypothesis, I compared the measured fluorescence of two different types of incubations – the traditional static incubation and a rotational incubation method. I measured the fluorescence generated by each set of assays at varying enzyme concentrations to determine the limit of detection, the minimum concentration that can be detected in a sample, for each method. I also analyzed the binding kinetics of each method using time-based data of each method. It is expected that the rotational method increases the sensitivity of the assay using half the concentration of target molecules compared to that of the static method. It also significantly decreases the time required to reach a binding equilibrium state by several hours. Promising results would suggest that rotational stimulation could significantly improve the molecular binding kinetics in diagnostic assays and could be implemented in future protocols to produce a more efficient diagnostic assay procedure.

The striatum encodes voluntary movements and cue dependent behaviors, utilizing dopamine, GABA, and acetylcholine to modulate cortical input based on experience. Parkinson’s disease is characterized by a progressive loss of dopamine that reduces striatal function. This degeneration impacts the function of striatal tonically-active cholinergic interneurons (ChIs) that are the sole source of striatal acetylcholine. A main treatment for Parkinson’s disease is L-Dopa, which partially restores synaptic dopamine. Unfortunately, most Parkinson’s disease patients eventually develop L-Dopa-induced dyskinesias (LIDs). The cause of LIDs is unknown and there is no effective treatment.  Our lab and others have shown that ChIs fire in tonic, burst, and pause patterns. To determine how ChIs might respond to a progressive reduction in dopamine availability that emulates Parkinson’s disease, we generated mice that have a knock-in of the human diphtheria-toxin (DT) receptor (DTR) into the mouse Slc6a3 locus, which encodes the dopamine transporter (DAT). DT injection into DAT-DTR mice causes robust ablation of dopamine neurons, while leaving dopamine neurons in DT-treated wild-type (WT) mice [WT(DT)] intact. Preliminary electrophysiological experiments revealed that dopamine-depletion in these mice causes a reduction in firing that is generated by abnormal intrinsic hyperpolarization-activated cation (HCN) channels. We hypothesized the DA sensitive autonomous activity of the ChIs plays a critical role in the development of LIDs.  We generated and harvested the striata from diphtheria-treated DAT-DTR mice (n=10) and WT(DT) mice (n=10) 14 days following DT, when performance on the rotarod was reduced. Comparison with acute dopamine depletion was determined using reserpine (n=10) and saline-treated mice (n=10), sacrificed 13 hr after injection. Mice were crossed with RiboTag^+/+ x ChatCre^+/- mice which allowed collection of ribosomal-associated mRNA from ChIs following immunoprecipitation. Expression levels of choline-acetyltransferase and HCN 1-4 were determined using an optimized RT-qPCR reaction. Outcome will determine the mechanism underlying LIDs and lead to viral-mediated treatments.

Seattle’s young homeless population has long been underrepresented and misunderstood—their experiences are largely absent from public conscious. In the University District, young people often face discrimination, stereotypes, and violence rooted in negative perceptions from University of Washington students. These two groups share a history of mutual distrust and even fear. Exposure is creating a 3D interactive narrative to challenge stereotypes toward homeless youth and allow an audience of University of Washington students to step into the shoes of a young person experiencing homelessness as a way to confront misperceptions. We took a community-grounded approach to researching this marginalized group. Through volunteering with service organizations and meeting with community leaders, we have curated stories and experiences by which to design this dramatic narrative. We also draw upon existing literature on daily youth community practices as well as game design for addressing social issues. We have then developed requirements for key scenes and interactions for this narrative. For example, cell phones, which play a large role in managing young people's’ lives, will be represented in the narrative. The diversity of the community across race and gender identity will manifest as playable characters with narrative outcomes distinct to those identities. As of today, Exposure is completing a working prototype for this narrative which will then become a playable demo. Key elements of our narrative have been written and storyboarded. By exposing our audience to the youth community through this fictionalized interactive experience, we hope students will confront prevailing misperceptions of young people, develop empathy for this underrepresented community, and engage with movements addressing structural causes of homelessness. In the same way film and literature are used to communicate our lived experiences, we hope that the use of an interactive medium will be a novel and impactful approach to represent a community long neglected.

For this investigation, I developed a repeatable Geographic Information System (GIS) model using Esri's ArcMap software to test if and under what circumstances rivers preferentially erode along surface fault traces. The motivation for this study stemmed from the fact that geoscientists have long assumed that strain along faults weakens rock and leads to focused erosion. Such positive feedbacks between faulting and surface processes have yet to be investigated at the scale of major fault systems. River networks in New Zealand, an active obliquely convergent tectonic setting with hundreds of surface breaking faults, are examined. The goal is to identify river reaches that travel parallel and along the faults - a first step in estimating whether and under what circumstances preferential erosion exists. Two digital datasets were used: active fault data from GNS Science (New Zealand's geological survey) and river data from LINZ Data Service (New Zealand's national land mapping agency), both freely available. The GIS model uses the Model Builder feature in ArcMap to assign each fault a layer. The model then selects faults of a particular length and adds a buffer. The size of the buffer selects the rivers to be studied. The rivers selected are noted as either bisecting or traveling parallel to the fault. Rivers within the buffer and traveling parallel to fault strike are selected and can then be further analyzed to calculate metrics such as the percentage of the fault with river running along it, lengths of river segments that flow along faults, and other variables such as fault type, slip rate, and fault strike. This GIS model is meant to be transportable to other large fault systems such as the San Andreas Fault zone in California, with the ultimate goal of extracting tectonic information directly from earth's surface.

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

Disorders and diseases of chronic pain have placed a tremendous burden on modern society, imposing myriad consequences on many individuals and populations. Despite extensive investment to date, therapies to treat chronic and acute pain remain limited; the most-widely used, researched, and prescribed drugs often act generally upon the nervous system. This characteristic of most existing therapies carries with it many unintended consequences and unwanted effects for pain patients. The limitations of these therapies are often traceable to our limited understanding of the neuronal circuitry responsible for the sensation and transduction of noxious or other pain-inducing stimuli. We utilize zebrafish in our forward genetic screen to identify mutations that disrupt the ability to perceive pain. Behavioral tracking of larval zebrafish, specifically the progeny of mutated genetic lines, allows us to screen for a large number of potential phenotypic mutations. By identifying mutant lineages in this screen, we hope to further elucidate and characterize the neuron cell populations responsible for nociception. Our genetic screen has identified several lineage of fish that lacked the behavioral “escape” response typical of embryonic zebrafish when immersed in a noxious chemical environment, in this case, 10µM allyl isothiocyanate (AITC), the pungent compound in mustard oil. Subsequent complementation to known mutants suggested that one of these families carried a mutation in a previously identified nociceptive ion channel, TRPA1, which is specifically expressed in somatosensory neurons, and has been shown to be required for the pain response induced by noxious chemicals, including AITC. We have crossed mutants into well-characterized genetic backgrounds and used RNA-seq based mapping to narrow these lesions to a region of Linkage Group 9. Following fine-mapping, we will subsequently study the role these gene(s) play in the sensation of pain. Our findings suggest that our screening strategy is likely to be successful and is feasible for identifying genes involved in nociception.

Continued advances in energy technologies have allowed for the increased utilization of renewable energy sources. However, energy storage is needed to provide power during peak hours. Flow batteries offer a convenient solution to the problem of storing large amounts of energy while remaining relatively cost efficient. One of the most expensive parts of a flow battery is the proton conducting membrane that separates the two halves of the battery cell. The current state-of-the-art membrane is Nafion, which can be expensive to produce. The goal of this project is to create a membrane with characteristics that can rival those of Nafion but that can be produced using cheaper materials. Towards this end we are utilizing sodium silicate solutions to create flow battery membranes. Two main characteristics of these membranes were studied: 1) proton conductivity, which is essential to current flowing through the battery and 2) ion permeability, which dictates the rate at which the ions in the two halves of the battery cell mix and the battery quality deteriorates. Initial testing for proton conductivity revealed that the experimental membranes were performing within the same order of magnitude as Nafion. However, the experimental membranes showed high permeability relative to Nafion. Future work will focus on isolating variables that affect pore size and polydispersity in the synthesized membranes in order to size exclude redox ions from permeating the membrane while retaining effective proton conductivity.

Chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) is the gold standard for assaying the binding sites of chromatin-binding proteins and their modifications, such as histone tail modifications. One major limititation for this method is that it requires large amounts of starting material, therefore limiting applications in those cases where only a limited number of cells can be recovered, e.g. rare cell populations obtained directly from patients. In the last few years, great efforts have been made to develop new ChIP-seq protocols to overcome this limitation. In my lab, they have developed a method called carrier ChIP-seq (cChIP-seq). The method is based on the use of a DNA-free carrier to enhance recovery of DNA after IP. Using cChIP-seq they have been able to perform ChIP-seq on 10,000 cells for several histone tail modifications. I tested a series of modifications on the cChIP-seq protocol. The goal of my project was to develop a protocol that can be performed in one day. Currently the cChIP-seq protocol takes 3 days to be complete. This is mainly due to two overnight incubations. The first one is the immunoprecipitation, so I performed multiple trials to identity the minimum time sufficient for immunoprecitating the chromatin. The second overnight incubation is to reverse crosslink immuneprecipitated chromatin. I tested a version of the cChIP-seq protocol for native chromatin, meaning the DNA is not crosslinked. By optimizing and combining these two modifications I was able to shorten the cChIP-seq to a single day. Through my project I contributed to a larger project with the goal of scaling down the number of cells used for ChIP-seq.

Therapsids (mammal-like reptiles) document the transition to modern mammals and are an important study tool in examining how the past informs the present. Understanding diseases today requires understanding the deep evolutionary history in our fossil ancestors. We present an instance of dental pathology in a gorganopsid therapsid (~260 million years old). Using fossil histological techniques, we examine a gorganopsian canine and preliminary results reveal abnormal mixture of dental tissue next to the functional tooth. These individual ectopically expressed teeth have preserved tissue layers such as enamel, dentine and a pulp cavity. Based off of the histological characters of our specimen as compared to modern clinical studies we hypothesized two possible diagnoses: odontoma and enamel pearls. Enamel pearls show dento-enamel pearl nodules protruding from the enamel of a functional tooth. Odontoma presents as individual teeth with their own histological packaging (i.e. dentine and enamel). These results suggest that our specimen most likely had odontoma. In modern cases, this results in excess dentinal tissue growth and un-alignment of teeth. The cause of this odontoma in modern clinical practices is a result of either trauma or rapid tooth replacement. The canine tooth of this gorgonopsid was prone to trauma since it served to pierce prey and was subjected to intense forces. Alternatively, gorgonopsids replaced their teeth continuously. This continous replacement could have gone awry resulting in this disease. This study presents the oldest possible case of cancer in the fossil record and elucidates the evolution of such pathologies. This study has relevance in dental clinical studies because understanding how diseases operate in humans requires an understanding of how they evolved in our deep evolutionary history. 

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


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

Honeybees (Apis mellifera) use a caste system to organize individuals into different roles. The queen is the only bee in the hive to ingest royal jelly and the only fertile female. Many sterile workers perform different jobs in their short lives, moving from larvae-nurse to keeping the hive clean to foraging for food. At each stage the worker bees learn a new task. Such different phenotypes and behavior would indicate a difference in gene expression in the brain. In a population of organisms that are genetically similar, these changes in gene expression must be explained in chemical modifications of the genome, or the epigenome. Thus far, much attention has been given to DNA methylation as an epigenetic feature known to be associated with variation in gene expression. Royal jelly, however, contains butyrate, a histone deacetylase inhibitor, which suggests that histone tail modifications could be a major mechanism for regulating gene expression in queen bees. To further investigate the role of histone modification in determining honeybee caste division, we are performing chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-seq) to profile key chromatin modifications: H3K27ac, and H3K27me3. H3K27ac and H3K27me3 are histone modifications that have opposing effects; where H3K27ac marks active regions of the genome, and H3K27me3 is indicative of repressive chromatin. We anticipate when using ChIP-seq to map chromatin modification in the brains of queen and worker bees, we will observe key differences in genome regulation and be able to identify genes important to honeybee behavior. As an initial step toward achieving our goal, we describe the chromatin state of brains from forager honeybees.

Iohexol and Iothalamate are nonradioactive contrast reagents, and are used as a marker to determine glomerular filtration rate (GFR). GFR is commonly used to evaluate the overall function of the kidneys as it reflects the rate at which toxins are filtered. It is considered the best index of kidney function. In order to switch from iothalamate to iohexol, a method validation is required to switch protocols. The method being evaluated uses iohexol that is given by bolus IV (single injection), and quantitates the concentration by high performance liquid chromatography (HPLC). HPLC uses high pressure and the affinity of molecules to elute of a column at specific times, called retention times, allowing the the quantitation of iohexol in a sample. Iohexol methodology provides many advantages including using less invasive clinical techniques, needing fewer sampling, and being less expensive than most markers used to determine GFR. The methodology is validated on two Waters® HPLC setups with analysis using EZ Chrom® and EP Evaluator®. EZ Chrom® is the program that stores and analyzes the the information, such as retention times, in order to determine the amount of iohexol. EP Evaluator®, is a program which analyzes data by calculating statistics to determine the precision and accuracy of the results. Assays performed included, inter-assays, intra-assays, analytical sensitivities, linearity, carryover, interferences, analytical comparison and cost analysis. The data showed that within limits, iohexol testing is precise, accurate, and overall valid to implement at Seattle Children’s Hospital in order to determine GFR. This makes it possible for Seattle Children's Hospital to continue to improve patient care by providing a less invasive method to determine GFR.
 

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

Explosive boiling is characterized by an unstable, non-uniform liquid/vapor interface consisting of multiple gaseous lobes. Explosive boiling at microscales is a process of extreme interest in the studies of micromechanical systems and actuation due to the nearly instantaneous pace and large amounts of kinetic energy associated with the process. These characteristics that make the explosive boiling phenomenon highly attractive for certain microscale applications also hinders the study and understanding of the dynamics of the unstable liquid/vapor interface, and thus the prediction of the overall behavior of the process. The objective of my research is to overcome the challenges posed by the small temporal and spatial scales by designing and building an experimental apparatus to observe the explosive boiling phenomenon. This apparatus consists of a test chamber in which the explosive boiling of a droplet of test fluid will be controlled by the host fluid temperature gradient, and a high speed camera used to capture the process in a high level of detail. The experimental results will be compared with theoretical results acquired from direct numerical simulation to elucidate the dynamics of the liquid/vapor interface. The experimental apparatus design and preliminary imaging results are presented.

The mineral composition of marine sediments is an indicator of recent climate change. Long-term changes in global climate over the past 40 million years are likely both a cause and an effect of the rise and erosion of the Himalaya. The Ganges and Brahmaputra rivers have deposited most of the Himalayan sediment in the Bengal Fan. Sediment cores samples collected from the International Ocean Discovery Program Expedition 354 to the Bay of Bengal were analyzed using visible and UV diffuse reflectance spectroscopy to determine changes in mineralogy. A focused analysis of a set of ship-board data of the sedimentary record of the last glacial cycle (100,000 years),using non-negative matrix factorization, showed three endmembers corresponding to different mineral assemblages: one with a blue spectrum (peak wavelength of 400 nm), a second with reflectance in the 400-500 nm wavelength range, and the third with a red spectrum. The mineral content of these endmembers will be determined by comparing their reflectance to the NASA library of mineral spectra. Changes in composition through time will be compared to known climate proxy records over the same time period to determine new mineral climate proxies. These climate proxies can contribute to a better understanding of the relationships of Earth’s climate system to sediment sources and weathering.

Heart failure is one of the leading causes of morbidity and mortality worldwide. Heart failure (HF) is the inability of the heart to keep up with its workload, and at least half of HF patients suffer from decreased ventricular contractility or systolic dysfunction. Improving cardiomyocyte contraction is a potential therapy for diminished heart systolic function, but there is no current effective therapy that directly improves cardiomyocyte contraction. Previous studies from the Regnier Lab have shown that heart muscle exhibits a significant increase in contractility and force when naturally occurring 2-deoxyadenosine triphosphate (dATP) is used in place of adenosine triphosphate (ATP) as the substrate for contraction. Intracellular dATP levels can be elevated by the overexpression of the enzyme ribonucleotide reductase (RNR). In order to assess the efficacy of this alternative myosin binding substrate as a potential therapy, it is necessary to design a reliable and accurate method to quantify the dATP levels in cardiac tissue and/or cultured cells. The goal of this work was to design a protocol for tissue sample preparation to run using High Performance Liquid Chromatography-Tandem Mass Spectrometry (HPLC-MS/MS) for quantitative assessment of nucleotides. A standard curve was produced to allow for absolute quantification of the nucleotides. Finally, these methods were implemented to study the cardiac levels of nucleotides in a transgenic mouse that overexpressed the enzyme attributed for de novo dATP synthesis on dATP levels. Correlation of dATP levels and cardiac function can provide validation of the influence of elevated dATP to improve cardiac muscle contraction for use in studies of animal models of heart failure.

The CubeSat form-factor is an increasingly popular design of small satellites utilized by a range of research orginizations. Consisting of stacks of 10x10x10cm cubes, CubeSats offer a compact and inexpensive means to place equipment and instrumentation into low-earth orbit, but suffer from limited or non-existent maneuvering capabilities. Currently available propulsion options for CubeSats may offer limited abilities to modify the shape of an orbit near to Earth, but suffer constraints on propellant efficiency, thrust duration, and thrust force. A new design of compact pulsed plasma thruster from the University of Washington for use on small satellites offers improved abilities to maneuver in not just low-Earth orbit but also in lunar insertion, lunar orbit, Earth escape trajectory, and a variety of trajectories reaching beyond. The orbital mechanics team has been responsible for studying the motion of PPT powered satellites in space and for the plotting of trajectories to potential mission targets. As the PPT has significantly different levels of thrust and efficiency from conventional liquid-fueled rockets, unique solutions to conventional problems must be found.

While HIV-related immunosuppression is a well-studied risk factor of tuberculosis (TB) infection and reactivation, other forms of immune system modulation have yet to be explored in great depth. Mycobacterium tuberculosis complex (MTBC) infects one third of the global population, with 5-10% developing active TB. Understanding risk factors of a high burden infectious disease such as TB is critical to improving control and prevention in humans. This study uses a population of biomedical macaques to explore the relationship between pregnancy history and TB susceptibility. A correlation between the factors would flag pregnant women as a unique high-risk population. It is anticipated that the number of pregnancies will be predictive of increased TB susceptibility, with individuals who have had multiple pregnancies more likely to be infected with MTBC. Individuals without a history of pregnancy are expected to have similar rates of infection as males in our study. Nonhuman primate(s) (NHP) are used as models of human infectious diseases and are also susceptible to infection with MTBC. The Oral Swab PCR (OSP) uses a buccal swab to sample saliva and cells from the interior of a subject’s mouth. This protocol has been previously validated for the detection of MTBC in NHP and humans. We used an extensive archive of buccal swabs collected from biomedical macaques to screen for MTBC. Following OSP screening for MTBC, statistical tests were run to test for A) sex-specific differences in infection and B) the impact of number and frequency of pregnancies on infection within females. An association between pregnancy and TB supports existing research and furthers the question on how pregnancy relates to the reactivation of latent TB. Currently, mechanisms for reactivation of latent TB are poorly understood making it difficult to predict how, or why TB reactivation occurs. Further research is needed to examine immunosuppression and reactivation.

The Madjebebe archaeological site, located in the Arnhem Land region of the Northern Territory, Australia, contains evidence for first human occupation 50-60 thousand years ago (Roberts et al, 1990a). Because of the age of this site, Madjebebe has the potential to provide insight into the dispersal of modern homo sapiens out of Africa along the southern arc through Southeast Asia and into Australia. Clarkson et al. (2014) describe technological shifts that occur over the site’s history, particularly in the raw material used to fabricate lithic tools. They hypothesize that some of the technology changes may be explained by changes to the local environment due to climate change during the Holocene (Clarkson et al, 2014). However, their hypothesis has not yet been tested. Using bulk sediment samples collected at 5 centimeter intervals for the entire 4 meter depth of sediment preserved the site, we will examine the paleovegetation changes that have occurred during the site’s history. Because C₄ plants like grasses fixate CO₂ through a different pathway than C₃ plants such as shrubs and trees, C₄ plants are composed of a higher concentration of isotopically heavy ¹³C relative to C₃ plants (DeNiro, 1987). The presence of C₄ and C₃ type plants can be detected through the ¹²C/¹³C ratio that is left behind in the soil when the plants decay (Haslam et al, 2012). By analyzing the ¹²C/¹³C ratio of the sediment using a mass spectrometer, we hope to identify shifts in vegetation patterns that occurred at Madjebebe. Our findings could reveal a correlation with the patterns of human occupation and technology changes that occurred at Madjebebe during the site’s 50 thousand year history. Ultimately, we hope to better understand the conditions that lead to the late pleistocene migration of humans into Northern Australia.

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

People in agriculture commonly use pesticides to prevent insect damage on crops. One common pesticide is called acetamiprid (ACP). While this pesticide has low toxicity to mammals, there have been cases of acute toxicity from overexposure to this pesticide. In this study, we focused on pesticide handlers, people who apply pesticide to crops in the fields, from the Yakima valley and analyzed their urine samples to measure their exposure to the pesticide ACP. The primary goal of the study was to quantify urine biomarkers to ACP exposure, including the parent compound ACP, and two metabolites: acetamiprid-N-desmethyl (ACPDM) and 6-chloronicotinic acid (6-CNA). We collected urine samples from 10 pesticide handlers in the 24 hours after applying ACP in an orchard. Each person was given a liter sized sampling vial to collect each void. We collected 34 human samples in total. I identified and quantified the biomarkers in the human urine samples collected. I did this by processing the samples using Solid Phase Extraction (SPE) and then quantifying them by using high-performance liquid chromatography and tandem mass spectrometry (HPLC-MS/MS). We expected to see small amounts of each biomarker in each sample, but found relatively high concentrations of the metabolite ACPDM. The results of this study will help to improve our ability to measure urinary markers of exposure, better estimate exposure and risk to pesticide handlers, understand the kinetics of ACP in the human body, and think of means to minimize exposure to prevent acute toxicity.

Gene delivery has successfully been accomplished with the use of polycations, both in vivo and in vitro. However, a major problem in this category is the inherent cytotoxicity associated with a high density of positive charges. Polymers that can be degraded within the cells are typically better tolerated compared to their non-degradable counterparts. This research studies the use of disulfide bonds to reversibly connect cationic polymer moieties to a stable polymer backbone. Reducible and non-reducible, statistical co-polymers of 2-aminoethyl methacrylate (AEMA) and oligo(ethylene glycol) monomethyl ether methacrylate (OEGMA) were synthesized and evaluated for a comb-like, backbone chain. These monomers have been chosen due to their low cytotoxicity as well as their high degree of polymerization control in reversible addition-fragmentation chain transfer (RAFT) polymerization. Backbones containing 50 and 100 monomers per polymer have been successfully synthesized. The current phase of the project is to functionalize AEMA with a unique biomolecule called dibromomaelimide that contains two points for positively charged moieties. This final polymer will be used to transfect cells with genetic material to test its feasibility for gene delivery. Success of this project will create a well-defined polymer containing positively charged cations that are easily dispersed upon internalization by cells.

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

 1 in 600 people world-wide are diagnosed with polycystic kidney disease (PKD), which leads to reduced kidney function over time. A cure for PKD is not currently available, making it important that we find more effective therapies for this disorder. Our laboratory has successfully used pluripotent stem cells to generate kidney organoids that functionally model the physiology of the kidney. The goal of this study is to generate induced-pluripotent stem (iPS) cells, adult somatic cells which have been reprogrammed to an undifferentiated state, from individuals affected with PKD. The first step of the process is the isolation of the patient’s cells from hair and urine samples. We are then able to reprogram these disease-affected cells into iPS cells and later differentiate them into kidney cells to create a better model for the disorder and screen for novel drugs. The information we learn from this study will help us better understand how PKD progresses and improve its treatment. We also hope that one day we will be able to transplant healthy kidney cells back into their patients, eventually eradicating the need for kidney transplants.

Fed by a large upwelling of hot viscous rock originating deep in the Earth’s mantle, the Yellowstone hotspot has been carving its history into North America for over 50 million years. As the North American tectonic plate moves westward over the mantle plume, magma erupts through the crust creating a chain of large volcanic centers stretching from west to east, ending at the supervolcano under Yellowstone National Park. Despite its large size, tracing the history of the Yellowstone mantle plume is a difficult task. Geologic processes, including subsequent eruption of the subduction-related Cascade volcanoes, have altered the crust since its passage over the Yellowstone hotspot. In Washington and Oregon, young basalts (<5 million years old) erupted with unusual compositions similar to mantle-plume-related basalt such as found in Hawaii. However, these mantle-plume-like basalts erupted when the Yellowstone plume was far to the east, no longer located under Washington State. Our project uses isotope and trace element analyses to determine the origins of these unusual basalts in Oregon and Washington. We test the hypothesis that remnants of the Yellowstone plume continue to influence local volcanism. Rare-earth element abundances are typical of mantle-plume (e.g., Hawaiian) basalts. Our samples show high concentrations of the elements niobium and tantalum, indicating an origin outside of normal subduction processes. Most diagnostically, ²⁰⁶Pb/²⁰⁴Pb, ²⁰⁸Pb /²⁰⁴Pb, and ²⁰⁷Pb /²⁰⁴Pb isotopic ratios of our samples are similar to the Columbia River and Steens basalts in Eastern Washington and Oregon, two volcanic provinces formed by the Yellowstone Hotspot 16 million years ago. The results of our Pb and trace element analyses suggest the presence of a mantle plume component in recent volcanism west of the Cascadia volcanic arc. We hypothesize that this component reflects the melting of material incorporated from the Yellowstone plume head.

While there are currently drugs available to treat patients with human immunodeficiency virus (HIV), there is no known cure for this infection. As the HIV virus integrates into the host’s DNA, reservoirs of latent HIV are established. Because antiretroviral drugs only attack replicating HIV, the presence of these latent reservoirs prevents the eradication of the virus from the body. Once the use of anti-retroviral drugs is discontinued, the active virus reemerges in patients. The purpose of this project is to identify transcriptional and epigenetic pathways to reverse HIV latency, knowledge that could pave the way for new drug design to kill all existing virus in the body. To accomplish this goal, we are using a microplate-based matrix chromatin immunoprecipitation (ChIP) assay and quantitative polymerase chain reaction (qPCR) to measure more than one hundred different transcription and epigenetic events along the latent HIV genome upon its transcriptional activation. We applied cluster analysis to our data and have found that Protein Kinase A (PKA), a class of enzymes which phosphorylate proteins, and its target, the transcriptional factor CREB, are recruited to HIV genome. This finding, which has not previously been reported, suggests that PKA plays a role in HIV genome transcription, and if so, could be a possible path for developing pharmacological reversal of HIV latency.

Due to the complex nature of the steroidogenic pathway, which involves enzymes with multiple substrates as well as multiple enzymes acting upon the same substrates, rigorous methods for molecularly dissecting this pathway are required for understanding it’s role in AR signaling and prostate cancer. Over the course of current androgen deprivation treatments, many patients develop castration resistant prostate cancer (CRPC). When the disease reaches this stage it has been known that cancer utilizes multiple pathways, known as the backdoor or bypass pathways, in order to continue synthesizing the androgens which ultimately drive cancer progression. To learn more about these alternate pathways, isoform-specific CRISPR/Cas9-mediated knockouts of these highly similar genes can be used to determine the specific contributions of each of these factors to de novo androgen synthesis and androgen scavenging in prostate cancer tumors. These CRISPR constructs will be used to generate gene specific knockout prostate cancer cell lines. Validation of each line will be done using a T7 endonuclease assay followed by western blot to confirm knockout of the protein. Further analyses using these specific knockout cell lines will provide insight on which genes are involved in the new pathway when the classical pathway is shunted.

Speculation for the increasing trend in interdisciplinarity in the life sciences spans from financial incentives to social relevance with little focus on the possibility of economic instability as a key contributor. To understand how economic instability impacts interdisciplinarity in faculty positions in the life sciences, I extracted and analyzed data from job ads in the journal Science from 2002 and 2008 and compared the amount of interdisciplinary research and experience required by assistant professors before and during the recession. I concluded that more faculty members are required to have an interdisciplinary background across fields to satisfy the requirements of a single job postion in 2008 compared to 2002, and that interdisciplinary skills are especially relevant in times of economic down-turn. To fill the demand for interdisciplinary knowledge in life science faculty positions, I propose that the university incorporate interdisciplinary approaches in their graduate training programs to better equip doctoral students for future academic professorship positions.  

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

In order to successfully invade and survive within a host cell, pathogens such as the bacteria Shigella flexneri have to suppress the host cell’s immune response. To do this, Shigella flexneri inject bacterial effector proteins into the host cell that hamper the host cell’s ability to detect and respond to invasion. One such protein is IpaH4.5, a bacterial E3 ubiquitin ligase, which hijacks the host cell’s ubiquitylation machinery to transfer ubiquitin, a small signaling protein, to a substrate. Ubiquitin signaling impacts all aspects of eukaryotic cell biology. Often modification of a protein by ubiquitin serves to mark protein for destruction. IpaH4.5 targets proteins involved in the host cell’s immune response, dampening the host cell’s ability to respond to invasion by Shigella flexneri. I am investigating IpaH4.5 and its interactions with both host substrates and the host ubiquitin machinery. After sub cloning out the various domains of TbK1, a known substrate of IpaH4.5, I will perform ubiquitilation assays in order to determine which domain of TBK1 is polyubiquitilated, indicating that IpaH4.5 interacts with this domain. Then, this domain can be used for structural and mechanical analysis of IpaH4.5, such as determining how mutations in IpaH4.5 affect ubiquitilation through biochemical assays. Understanding how IpaH4.5 binds to and interacts with its substrates will increase our understanding of how Shigella flexneri dampens host immune response as well as help us better understand the mechanisms of bacterial E3 ubiquitin ligases. Since IpaH4.5 functions differently than eukaryotic E3 ubiquitin ligases, increasing our understanding of its mechanisms could allow us to use it as a target for future drug development. Finding new targets for drug development is becoming increasingly important with the spread of antibiotic resistant bacteria.

Studies suggest that Europa contains elements required to support life beneath its icy crust, but further data collection is required for verification. One of the largest issues in performing such a research expedition is the demanding cost of soft-landing an instrument on its surface to retrieve the data. To address this issue, research is currently being conducted for a new method involving a two-stage penetrator probe which would allow the hard-landing of the probe into the moon’s surface. The initial stage penetrator would weaken the ice and create a debris plume which would allow the second stage probe to decelerate and enter the surface intact. To optimize the system and further study its potential, the impact is being simulated in the ANSYS finite element analysis software. In working parallel with experimental data obtained from impact testing, the geometry and parameters within ANSYS were modeled to create a FEA explicit dynamics simulation of the impact. The analysis models the ice as concrete due to material properties of ice being difficult to obtain, and local mesh refinement methods were utilized to improve computational time. The focus of the simulation is to determine the optimal model in which the first stage penetrator has significant impact in the acceleration profile of the second stage probe. The impact pattern, the amount of material carved out, and the acceleration profile of the probe will be analyzed to relate the efficiency of various penetrator geometries at various speeds. Impacts involving the two stage system with various penetrator geometries show significant reductions in the acceleration profile of the probe. Future research will rely on refining the simulation parameters to derive a more accurate model of the impact.

Due to dwindling non-renewable energy sources, people have started to harvest clean and sustainable energy. Utilized to capture solar energy, organic photovoltaics (OPVs) are developed due to their ability to be printed on a flexible substrate, ease of production, and lightweight. Current researches are focused on improving the device efficiency and durability. Therefore, OPVs may compete with their inorganic counterparts, which are currently more popular although limited by the expensive material and manufacturing process. Phenyl-C61-butyric acid methyl ester (PC61BM) and poly(3-hexylthiophene-2,5-diyl) (P3HT) nanowires are widely-used acceptor and donor polymers, respectively, in an OPV’s active layer. A desirable morphology of the active layer is a bulk heterojunction structure. One of the factors that affect the morphology is the processing of these polymers. The purpose of this project is to investigate how the PC61BM addition affects the P3HT nanowire formation. The experiment involves nanowire development in three cases: (1) pure P3HT, (2) P3HT with PC61BM added after the formation, and (3) P3HT with PC61BM added before the formation. Samples from the three cases were characterized using UV-Visible spectroscopy and X-ray Diffractometer to determine the crystallinity and morphology of the polymer chains. The morphology of polymers is discussed as a function absorbance ratio, which indicates chain planarity, and crystallite size. The results were then compared with those from previously published papers. Due to considerable differences observed, the regioregularity of the P3HT precursor was tested using Nuclear Magnetic Resonance spectroscopy. The result was a lower regioregularity than that of P3HT which is typically used for photovoltaic applications. Therefore, a different batch of P3HT was used to investigate the morphological differences between the three cases. Assessment of the polymers’ morphology were correlated with OPV device performances in published literatures. A determination of the PC61BM-addition effect may assist future fabrication of OPV with superior performance.

Our project is to characterize the Caenorhabditis elegans (C. elegans) ortholog of PICK1 and we will henceforth refer to this C. elegans gene as pick-1. In other systems, PICK1 is involved with dense-core vesicle (DCV) biology and has been shown to affect the trafficking of AMPA glutamate receptors to the cell membrane, which are believed to be trafficked in a non-DCV process. DCVs are a specialized organelle in neuron and neuroendocrine cells that are loaded with, and release, several important neuromodulators. These DCV-release neuromodulators regulate a broad spectrum of biological processes such as blood glucose homeostasis, the plasticity of the nervous system, and even appetite. AMPA trafficking is crucial to signaling in the brain. Glutamate is the major transmitter of excitatory signals in the brain. Our project aims to figure out if, and how, pick-1 is affecting these processes in C. elegans. To investigate pick-1's involvement in DCV biology we tested its interaction with RIC-19 (ICA69 in mammalian systems), a protein that is known to interact with PICK1 systems. To test pick-1's interaction with AMPA receptors, we tested how PICK1 affects the localization of GLR-1 (an AMPA receptor). If PICK1 does not affect the localization of GLR-1, then we would expect to see GLR-1 not properly trafficked to the synapse. If PICK1 is involved in DCV biology, we would expect a deletion of pick-1 would create lower levels of RIC-19 in the worms. To this point, our raw data has suggested that PICK1 does not play a role in DCV biology or AMPA receptor trafficking in C. elegans.

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

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

Stroke accounts for more than half of all patients hospitalized for acute neurological disease in the United States, and is the second most common cause of death worldwide. Microglia, the brain’s specialized tissue macrophages, play a major role in the innate immune response to many neurological diseases including stroke. Ischemic preconditioning (IPC) is a brief period of cerebral ischemia that confers robust but transient tolerance to subsequent ischemic challenge. Elucidating the mechanisms of IPC is a critical challenge in stroke research. A major focus of investigation in the Weinstein lab is the cellular and molecular mechanisms of IPC with a particular emphasis on elucidating the role of microglia in this experimental phenomenon. The Weinstein laboratory has demonstrated using ex vivo flow cytometry that IPC induces a robust increase in the number of microglia that can be identified and sorted from the preconditioned (ipsilateral) cortex. Immunofluorescent microscopy and quantitative stereology on preconditioned mouse brain confirmed that IPC-induces a true in situ increase in the number of microglia. Recent efforts have sought to discriminate whether the origin of this in situ increase lies in cellular recruitment or cellular proliferation. My project has been to use immunofluorescent microscopy to evaluate the extent of double-staining present in preconditioned cortex when using antibodies targeted against cellular markers for microglia (Iba-1) and proliferating cells (Ki-67). Initial findings suggest that the increased counts observed in preconditioned cortex are the result of microglia cell proliferation. We have also begun to employ a protocol using Bromodeoxyuridine (BrdU), a stably incorporated cellular proliferation marker, followed by immunofluorescent microscopy/stereology to quantify the time course of microglial cell proliferation following IPC.

The federal government determines the poverty line in the United States by calculating untaxed income against the standardized cost of a calorically sufficient diet that is adjusted for inflation. The cost of living is much higher in cities; therefore, this methodology often fails to classify families living in urban areas as impoverished. The current methodology is unreasonable because it does not account for geographic variability in the cost of living for individual environments throughout the United States. There are other methods of measuring poverty, which attempt to acknowledge the shortcomings of an absolute poverty line, but these methods have shortcomings as well through the consistency of poverty measurement thresholds such as in the Supplemental Poverty Measurement. The European Union adopted a method of measuring poverty through a relational poverty line, which encourages the decrease of income inequality and also enables welfare policies to mark certain populations at risk for becoming impoverished. The goal of this project is to analyze and compare the use of the absolute and relative poverty measures in the United States to determine the differences in population size that would be eligible for government assistance. 

For over twenty years the Text Encoding Initiative (TEI) has managed and developed a set of encoding guidelines for the representation of humanities, social sciences, and linguistics -- to preserve and share -- texts in digital form. Using the Extensible Markup Language (XML) as its backbone, TEI is the generally accepted encoding model for the digital humanities. Due to XML’s extensible nature, it can often be difficult to share these files and even more problematic to make them interoperable. The goal of our project is to build a prototype Application Programming Interface (API) for TEI-XML documents that provides greater interoperability while at the same time being easy to use by an audience with backgrounds in the humanities, social sciences, and linguistics. Currently, we have produced a deliverable with two components. The first: an API that, once installed, can return multiple views of a TEI-XML file using a Uniform Resource Identifier (URI) as its query method. The second is a set of user-tested support documentation that is both easily discoverable and easliy usable by our target audience. In future iterations of our prototype we plan to include a more robust listing of return view types, the ability to support multiple TEI-XML files, and API key permissions support.

This thesis examines factors that contribute to the “leaky pipeline” between journalism programs and the newsroom. University journalism programs are predominately composed of women, yet sixty percent of journalists who work in newsrooms are men. Semi-structured interviews were conducted in person and over the phone with 20 women from the Seattle area – five journalism students, five recent graduates currently working in journalism, five experienced journalists, and five journalists who left the profession. Participants were located through snowball sampling and searches of newspaper bylines and social media sites, such as LinkedIn. Questions centered around the women’s career-path choices and the rationale for their career decisions; their motivations to remain in journalism or to leave the profession; and the challenges women face working in the newsroom. Many women stated that they went into journalism because of their passion for storytelling and writing. Some suggested that women still experience unintentional discrimination as journalists, while others believe that women are treated equally in the newsroom. Issues were raised surrounding the challenge of balancing family and a journalism career, the emotional toll of sexist comments from sources, and a lack of opportunities for women in some newsrooms. Gender inequality in the workplace is an issue at the forefront of contemporary American politics. It is an important topic for discussion, especially for female journalists trying to break into reporting.

Current chemotherapies exploit the larger pore size of tumor vasculature to reach cancer cells. However, this rudimentary form of targeting offers low selectivity and carries the risk of severe systemic toxicity. In addition, chemotherapy distribution to tumors is limited by the large distance between blood vessels in tumors, increased interstitial fluid pressure, and physiological resistance by the extracellular matrix (ECM). With the goal of addressing these limitations, researchers have developed drug-bearing polymers of various sizes and architectures that selectively target tumor cells. The Pun lab previously produced a novel drug delivery polymer, the sunflower polymer, that can be utilized for anticancer drug-delivery. The sunflower polymer is a macrocyclic brush polymer that can be functionalized with a folic acid targeting ligand and an anticancer drug, doxorubicin, that is released in the acidic tumor microenvironment. In order to maximize the potential of anti-cancer drug-delivery polymers such as this, the impact of polymer size and architecture on tumor penetration must be better understood. This is because the efficacy of any anticancer drug, regardless of its mechanism of action, is limited by its ability to navigate the tumor microenvironment and reach all viable cells in a tumor. This project seeks to discover how polymer size and architecture impacts tumor penetration by using a 3D in vitro perfusion chip model of the tumor microenvironment. The model consists of microfluidic channels seeded with KB carcinoma cells and ECM, and has been optimized using model polymers of polyethylene glycol (PEG) and dextran. Tumor penetration is studied by perfusing fluorescently labelled polymers of various morphologies through the seeded microfluidic channels. The information obtained from this project could potentially be used to optimize the size and architecture of drug-delivery polymers for tumor penetration. In turn, these optimizations could present a significant contribution to the development of anticancer drug-delivery polymers.

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

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

Current commercial Li-ion batteries use carbon-based anode materials, most commonly graphite. The low theoretical capacity (372 mAh/g) [1, 2] and slow Li-ion diffusion (10^-8cm²s^-1) [2] through graphite limits the batteries energy density and power capability. Molybdenum disulfide (MoS₂) is a promising graphite replacement. The layered structure of the 2H trigonal prismatic phase is very similar to graphite where van der Waals (vdW) interaction between layers of S-Mo-S slabs accommodates Li-ion intercalation [3, 1]. MoS₂ has high initial capacity (669 mAh/g), low discharge voltage (0.6V), and low diffusion barrier, but has poor cycling stability resulting in short cycle-life [2]. Herein it is proposed that the degradation in capacity over cycling could be mitigated by engineering a restacked MoS₂-polymer composite material using a one-pot wet chemical synthesis method. The MoS₂ slabs are first exfoliated and then restacked in the presence of a polymer, inserting organic layers in the vdW gap. This work probes the effectiveness of this synthesis technique by comparing materials prepared with PEO and PEDOT. Characterizations will be conducted with X-ray Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR), Thermogravimetric Analysis (TGA), and Differential Scanning Calorimetry (DSC) to confirm the synthesis of restacked MoS₂-polymer composites. XRD will be used to determine the d-spacing that correlates to an expansion in the c-direction, specifically looking for peak shifts of (002) or (004), and with no shifting of the (hk0) directions. FTIR will be used to verify the presence of PEO and PEDOT in the composite. TGA and DSC will be used to check the stoichiometry of the polymer in the prepared composites. Pristine MoS₂ and synthesized composite materials will be compared in Lithium half cells to determine effect of restacking on cycling stability. Restacked MoS₂ would be an ideal anode material for Li-ion batteries if it brings enhanced energy density and greater cycle-life.

Low wage (<$15 per hour) jobs are often structured in ways that expose workers to dangerous chemical and physical agents, as well as policies and practices (e.g., volatile work schedule, low job control, etc.) that may result in adverse stress-related health outcomes. These outcomes are compounded when social disparities such as race, immigration status, and gender are also present. This study will provide a comprehensive assessment of working conditions among low-wage workers and examine the relationship between work conditions, stress and health, and further, if this relationship is affected by union status. Two hundred and fifty low-wage workers from local community-based organizations and labor unions were recruited to participate. Each participant completed a survey describing his or her workplace exposures and health. A composite index of work-related psychosocial stressors was created by combining previously validated scales relating to job strain (control and demand), security, benefits, and overall satisfaction, and each worker was assigned individual scores of work-related psychosocial exposures. We described work-related stressors and health status by union status and other demographic variables. We then examined the association between stress and health, and between union status and health. We further assessed the interaction of belonging to a union and stress on health outcomes. We anticipate that these psychosocial exposures will be associated with stress-related health outcomes. Further, we anticipate that unionized low-wage workers will show less psychosocial exposures to workplace conditions and in turn, less stress-related health outcomes due to better job security, workplace empowerment, and less volatile work schedules. The study information collected from this population may also provide baseline data on which a future longitudinal study proposal can be developed to evaluate the effect of the increase in the minimum wage laws over the next few years.

 Diabetes affects about 10% of the US population and is the 7th leading cause of death. Diabetes results from either a lack of insulin production (Type 1) or resistance to it (Type 2). The active form of insulin is a 51 amino acid monomer which regulates homeostasis of blood-glucose levels. It is crucial for insulin to be structurally sound and not degraded, especially for people using insulin pumps. However, insulin has a shelf life of about 28 days unopened and only 14 days after opening the container. Efforts to improve the stability of insulin may facilitate the development of implantable pump technologies for insulin delivery and allow for longer storage of insulin. Based on a review of the literature, I hypothesize that solvation in an Ionic Liquid solution will decrease the degradation and increase the shelf-life of insulin. To better understand the stability of the insulin protein, I compared its activity at an air-water interface to an air-ionic liquid interface. The approach consists of modeling the structure of insulin using the simulation software GROMACS and PLUMED. 10 nanosecond trials in different air-liquid interfaces were then analyzed to optimize the best insulin backbone stability. The goal is to extrapolate an ammonium- or imidazolium-based ionic liquid solution that will decrease the aggregation of the insulin monomers. Compared to the bulk insulin form, we found that the ionic liquid-protein solution demonstrates a lower radius of gyration and a root-mean-square deviation value that levels out towards 1 Angstrom representing a stable protein. These results are also supported by a decreased hydrodynamic radius and an increased free energy of unfolding the insulin protein. These findings suggest that insulin in an ionic liquid solution will last longer in vitro than in a water-based solution.

Myocardial infarctions, ischemic strokes, and peripheral artery disease (PAD) are the most common causes of mortality and morbidity among citizens of the United States. p27^Kip1 (p27) is a cell cycle regulator that affects the human physiological response to acute arterial injury such as coronary angioplasty or arterial bypass vein grafts. Overexpression of the p27 gene inhibits angiogenesis in mice. Conversely mice knocked out for p27 have improved angiogenesis and arteriogenesis. Our preliminary data shows that p27^-/- (knockout) mice have increased vessel diameters after hind-limb ischemia, but the molecular pathways controlling this collateralization result are not well understood. Our lab is interested in conducting in-vitro assays upon p27^-/- and wild-type (WT) vascular smooth muscle cells (VSMCs) to study the role of the p27 gene in VSMCs under hypoxic conditions as opposed to normoxic conditions. We hypothesize that cell proliferation and migration of p27^-/-, p27^+/- (HET) and WT VSMCs under hypoxic conditions will better mimic the ischemic in-vivo model than VSMC under normoxic conditions, and provide better insight about the molecular basis of collateralization via genetic profiling. I am currently performing experiments to further develop a hypoxic experimental apparatus and conducting normoxic in-vitro cell proliferation and cell migration assays to compare with the hypoxic experimental model. Preliminary results reveal that p27^-/- VSMC proliferate and migrate more than WT VSMC in normoxia. We expect this difference to be magnified in hypoxia. The results of this project will enable us to establish the hypoxia in-vitro model in the laboratory, and better study gene expression changes in hypoxia between the two genotypes.

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

In recent years, heart rate variability biofeedback (HRVB) has been used to treat a variety of illnesses and disorders such as depression, hypertension, and asthma. HRVB method includes presenting to an individual his current heart rate (HR) on the screen and teaching him to increase/decrease his HR by breathing at frequency of 0.1Hz (6 breaths/min). Such breathing will elicits high-amplitude oscillations in HR and blood pressure (BP). Such oscillations arise since baroreflex, as a closed-loop system for BP control, has resonance property (i.e., produces high-amplitude oscillations in response to 0.1Hz stimulation). The benefits of HRVB are derived from these oscillations which train reflexes and improve cardiovascular regulation the same way physical exercises improve muscle condition and regulation. The purpose of this study was to evaluate the response of the baroreflex to paced 0.1Hz emotional stimulation and how alcohol affects this response. Seventy-two subjects were randomized into three beverage groups that received an active dose of alcohol, an inactive dose of alcohol (placebo), or no alcohol. Each performed eight 5-minute tasks: two baseline tasks (before and after beverage consumption), four emotional stimulation tasks (negative, positive, alcohol, and neutral picture cues paced at 0.1Hz), paced breathing task (using a moving bar), and paced breathing task (using alcohol images). ECG, beat-to-beat blood pressure, and respiration were collected. Alcohol reduced baroreflex activity across all tasks. There was a strong positive association between the amplitude of 0.1Hz HR oscillation with baroreflex gain (activity) in both alcohol and control groups. Paced 0.1Hz breathing significantly increased baroreflex gain in the control and placebo groups, but did not change it in the alcohol group. All emotional tasks decreased baroreflex gain. Paced breathing versus breathing plus emotional stimulation tended to increase baroreflex gain more. Results showed that the application of breathing in HRVB is more effective than emotional stimulation.

Many people say that voting is the duty of every American citizen. Despite this, voter turnout rates are endemically low; according to the US Census Bureau, turnout rates reached 60% in 2004, a time of peak political dissent and an unpopular war. Many political scientists and sociologists have sought to understand these falling turnout rates but have failed to incorporate intersectionality theory in their analyses. While racial background and socioeconomic standing are individually linked to a lack of political participation, a failure to examine how these demographic features affect one another results in a far less rich understanding of the non-voter. This study uses interview data to examine how people of various racial and class backgrounds make sense of their self-selection out of the political process. The results of this data will provide a more comprehensive understanding of the non-voting population and will offer guidance to organizations seeking to increase voter turnout rates.

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

 In order to accurately interpret paleoclimate data from ice-cores, scientists must know the delta age, or the age difference between the ice and bubbles of gas trapped within. In order to calculate delta age, a firn-densification model is used to find the depth and age of the firn when the bubbles become trapped. Firn densification rates are strongly influenced by temperature, and firn-densification models include heat diffusion to account for seasonal and long-term temperature changes. The rate of heat diffusion through firn is a function of the firn’s thermal conductivity. Numerous relationships have been proposed to describe the thermal conductivity as a function of the firn density. Here, we ran the transient Herron and Langway (1980) model forced with a seasonal temperature cycle and a temperature step change with each of the thermal conductivity parameterizations. We use the depth-integrated porosity and close-off depth and age as functions of time for each model run to investigate the sensitivity of the model to the thermal conductivity parameterization. We find significant disagreements among the model results, suggesting that density and temperature are imperfect proxies for more fundamental micro-structural properties that control conductivity.

Due to anthropogenic pollution, toxic heavy metals such as arsenic, silver, cadmium, copper, lead, zinc and selenium have been deposited into the environment along the west coast of North America. Fungi have been shown to uptake or accumulate heavy metals at concentrations that can exceed the environmental background levels. Foraging for wild edible mushrooms has been gaining popularity in recent years, but many edible mushrooms can take up toxic heavy metals, causing concern for public health. Previous work from our lab has shown that heavy metals uptake varies dramatically in our region, but we are now expanding the geographic range of the study. Samples of numerous species of edible fungi, as well as the surrounding soil and duff were collected along the west coast from California to northern Vancouver Island by researchers at Oregon State University. Metals analyses are currently in progress: samples are digested in Nitric acid, diluted and will be analyzed for heavy metal concentration using inductively coupled plasma - mass spectrometry. We predict that different fungal species will preferentially uptake different metals, and therefore some species of fungi will concentrate certain metals within their tissue at greater levels than others. The results of this study will be used to determine if certain fungal species that are now considered edible may be a health risk due to heavy metal concentrations that exceed the EPA recommended annual intake levels. Certain locations that have recieved excess pollution may also be pinpointed and the results of this study will be reported to mycological societies to educate the public about unsafe species and locations to pick mushrooms. Additionally, if any of these fungi can accumulate heavy metals at levels that greatly exceed levels present in soil or duff, we can assert that these species have potential for use in bioremediation of polluted lands. 

This research is being conducted in order to discover more about surface and subsurface ice on other planets—specifically Mars. Liquid water is considered one of the primary requirements of life, and we now know that Mars has a vast quantity of water, but nearly all of it in the form of ice in its large polar caps and shallow buried ground ice present at all latitudes above ~50 degrees. There is much geologic evidence that liquid water has flowed on Mars’ surface in the past, and possibly even the present day, but the properties and processes that control the stability and behavior of water on Mars are poorly known. Knowledge of the properties of ground ice would aid in understanding the polar ice caps, atmosphere, and climate of Mars; this is necessary in order to assess when and where life could have existed on the red planet. Our goal is to study this ice by building a vacuum chamber that will contain icy regolith, creating a temperature gradient in it, and taking in situ measurements of the results. These measurements will be conducted through fiber optics as well as by removing the samples and taking them to a cold room for analysis. Hopefully, these measurements will allow us to understand both the subsurface ice and the planet Mars itself.

Public service announcements have long been a marketing technique to educate the public on social issues. Recently, audiences have spotted PSAs during the broadcasts of a sport usually known for shilling commercial advertisements – professional football. But why the change from beer and truck commercials to PSAs? Most of the research examining advertising and the National Football League relates to consumer products and the impact of ads being viewed during games have on the consumption of that product. Relatively absent in current literature is the relationship between public service announcements and the NFL. This research aims to determine how successful public service announcements and campaigns like the “NO MORE Domestic Violence” campaign are in generating public awareness about a social issue. Additionally, this research investigates whether attitudes about domestic violence differ depending on who is delivering the PSA messaging. Because of the unique partnership the campaign has with the NFL and the league’s history with domestic violence, one element of this research will focus on changes within the league that have been made since the implementation of the partnership. Many believe that the partnership is simply one to save the reputation of the NFL due to their history of victim-shaming and light punitive action against players who have been accused. By examining responses after viewing celebrity and NFL ambassadors, this study will ascertain if there is a relationship between how the messages relating to domestic violence stigmas are received and who is associated with that message. Ultimately, this research may suggest that public service announcement-style campaigns can be an effective conduit for generating awareness about a social issue even in a social-media dominated landscape, where social movements are implemented as hashtags and national dialogues occur based on what’s trending online. This research will also unearth what societal notions exist surrounding domestic violence, and offer methods for rectifying stigmas.

Use of Computational Fluid Dynamics (CFD), as a design and investigation tool in fields of science and engineering, is rapidly increasing parallel to today’s rapid growth of economically affordable computational hardware and software resources. However, it is extremely important that methodological usages of CFD is established and taught to the current generation of engineers and scientists with an almost same pace compared to current evolution pace of CFD’s usage. Learning a goal-oriented and methodological approach to use CFD would guarantee a reliable, an efficient and economically feasible final engineering designs and products. The core idea of the current project (SFO Project) is to achieve this important task via developing and validating a family of CFD simulations for the most fundamental problems in field of Fluid Mechanics in three CFD packages. The steps of this development and validation process are documented in form of a goal-oriented and methodological approach and made publicly available for use and further development of young scientists and engineers on the web. As a cherry on top, the application of the developed CFD simulations to more complex and real-life problems will be addressed and investigated. The focus of the current presentation is on the CFD simulations development for the flow over a two-dimensional cylinder, as one of the most fundamental and applicable problem in field of Fluid Mechanics. The simulations were first developed for the laminar and steady flow over a cylinder (i.e. Reynolds < 200). The numerical results were compared and validated against previously published experimental and numerical results. These validated simulations are currently being used for simulation and investigation of unsteady laminar flow around a stationary and heated cylinder. In the end the potential application of these developed CFD simulations to the real life, scientific and engineering problems are addressed and investigated.

Pancreatic cancer is ranked fourth amongst the most lethal cancers in US and first in mortality due to its low five-year survival rate. Accurate, definitive diagnoses are determined by pathologists who visually inspect and evaluate tissue slices from patient-procured biopsies traditionally processed into 2D slides. 3D microscopy makes 3D pathology, consisting of the imaging, visualization, and evaluation of unsectioned tissue biopsies in 3D, become a reality. Similar to the advantages of CT over traditional X-ray, 3D pathology may enhance pancreatic cancer detection and further streamline the diagnostic process in pathology. However, similarities with traditional pathology in optical information needs to first be achieved in 3D pathology in order to pair with current skilled pathologists. Enough color contrast and resolution of intracellular and extracellular structures can provide desirable features of biopsies to pathologists. Hence 3D pathology project in Human Photonic Laboratory aims to accomplish this goal by performing staining, imaging, reconstruction, and 3D visualization for tissue biopsies. Preliminary result illustrates that the reconstruction algorithm with appropriate parameters based on frequency spectrum of data determines the resolution of reconstructed images. Specific 3D manipulation software Amira helps 3D visualization of reconstructed images and preserve color contrast using its colormapping feature. The investigation of proper colormapping protocol starts from colormapping in-silico image of processed 2D microscope slides. An imaging systems with designed image stitching program creates grayscale image of microscope slides. Spectrometer is used to take spectral reflectance measurement. A developing algorithm will take the data and calculate coordinate values of the specimen in color space of human vision. Those values will be used in Amira in colormapping for in-silico image of microscope slides to pair with full color image of slides. This colormapping technique has potentials to extend into unsectioned sample and hence combine with reconstruction algorithm to achieve colormapping for 3D visualization.

Staphylococcus aureus is a global human pathogen and a major cause of wound infections, food poisoning, and invasive disease. Its success as a pathogen requires virulence factors used to evade the human immune system and subvert host defenses. Protein A is a multifunctional immune evasion factor that inhibits bacterial uptake by immune cells, modulates inflammatory responses, and disrupts development of adaptive immunity. We found that protein A expression decreased when cultures of S. aureus were exposed to the antimicrobial molecule nitric oxide (NO). NO is a reactive radical produced at high levels by macrophages and other host cells during infection. Reverse transcriptase quantitative PCR (RT-qPCR) showed that transcription of the spa gene, encoding protein A, was significantly decreased in the presence of NO. Dose response curves were generated comparing the sensitivity of spa and other genes to NO as well as to hydrogen peroxide (H₂O₂), another host-produced antimicrobial compound. Western blots confirmed that NO inhibition of spa transcription resulted in reduced protein A levels. Through allelic exchange mutagenesis, we mutated multiple spa transcription factors of S. aureus and identified the regulator protein XdrA as a likely NO target. Given that NO modifies cysteine thiols of proteins, we hypothesized that XdrA is S-nitrosylated by NO, leading to inhibition of spa transcription and concurring decrease in protein A. Single cysteine mutants of XdrA (C54S, C73S) have shown partial resistance to NO inhibition. A double cysteine XdrA mutant will be tested to assess the cumulative effect that multiple NO modifications have on spa transcription. This will allow us to understand the molecular mechanism of NO dependent protein A inhibition. Additional experiments demonstrating that NO produced by macrophages inhibits production of an important S. aureus virulence factor would characterize one mechanism by which innate immunity controls bacterial infections.
 

Li-ion batteries (LIB), with flammable liquid organic electrolytes, show limited energy density, serious safety concerns, and high cost, which largely limit their mass-market applications in electric vehicles or for stationary energy storages. It seems that the major issues of conventional LIB can be well addressed by using a solid-state electrolyte in place of the traditional liquid one. All solid-state LIB constructed by using solid electrolytes such as LIPON, Li10GeP2S12 (LGPS), and Li7La3Zr2O12 (LLZTO), and a Li metal anode, can effectively eliminate the safety issues and largely improve the energy density. However, the use of solid electrolytes is non-trivial because Li-ion diffusion across solid-to-solid interfaces, such as electrolyte/cathode and electrolyte/Li interfaces, is much more difficult than conventional liquid to solid interface. This work is focused on establishing relationship between grain size of LLZTO and Li-ion conductivity at the solid-to-solid interfaces, and trying to improve the ionic conductivity by optimizing the interface density, interfacial polarization, and interfacial composition (surface coatings, etc.). LLZTO samples with various grain sizes were synthesized, processed, and tested in an effort to improve the interfacial behavior. Grain size was controlled by varying the ball milling time and confirmed by light-scattering particle size analyzer (PSA) and scanning electron microscopy (SEM). The highly dense (>95% theoretical density) pellets were sintered by a spark plasma sintering technique and the ionic conductivities were tested by an electrochemical impedance spectroscopy (EIS). With decreasing grain size, the ionic conductivity of LLZTO pellets changes significantly due to the varied interfacial resistance, and the interfacial behaviors of electrolyte/cathode and electrolyte/Li are also expected to be significantly altered. This fundamental understanding is necessary to reveal the solid-to-solid interfacial behaviors inside the all solid state LIB, and will shed some lights on improving their electrochemical performances.

 Our lab is investigating the process of horizontal transfer of mobile DNA molecules in microbes, focusing on plasmids of bacteria. A plasmid is a circular piece of DNA that replicates separately from the host chromosome and can be passed from one bacterial cell to another via conjugation, allowing advantageous traits to spread among diverse species. My work has focused on the pQil plasmid, which was originally found in pathogen Klebsiella pneumonia, but has been observed to transfer to other bacterial species in human hosts. The pQil plasmid encodes resistance to the carbapenem antibiotics, a class of antibiotics used to combat multi-drug resistant bacterial infections and important in the treatment of bacterial pneumonia. We are characterizing the mobility of the pQil plasmid to create a laboratory model of a multi-plasmid system. We paired pQil with the F plasmid in E. coli to measure the transfer of these plasmids in the laboratory. We mated a plasmid-free recipient with the E. coli donor strain containing pQil, F, or both. The recipient cells were then characterized for the presence of the plasmids. We determined that the frequency of transfer for pQil is increased in the presence of F’42 and that the transfer of F’42 is slightly inhibited by the presence of pQil. Continuing studies will analyze the mechanisms through which bacterial conjugation occurs. Ultimately our work will inform us on how complex microbial systems evolve in natural environments, such as humans infected with pathogenic bacteria. With this information we can begin to study ways to halt plasmid transfer to slow the global spread of antimicrobial resistance.

Epigenetic analysis is a rapidly growing field of interest within the research community, due to its potential to advance our knowledge of the origins of a variety of diseases. It involves analyzing modifications of DNA as well as modifications of proteins associated with DNA, which affect overall chromatin structure and lead to potentially detrimental effects on gene expression. Aberrant gene expression has been shown to be involved in the development of diseases such as cancer, diabetes, and kidney disease. The most commonly used method for epigenetic analysis is chromatin immunoprecipitation (ChIP). However, current ChIP assays involve time-consuming and labor-intensive pre-analytical sample preparation and have low throughput, resulting in concerns about accuracy and sample loss. Thus, the current assays are limited in their clinical utility. The purpose of this project is to design an optimized protocol for DNA-protein crosslinking and chromatin shearing using novel high-throughput ultrasound technology for increased efficiency and reduced sample loss in ChIP. Various conditions were tested with different stages of ChIP, including DNA-protein cross-linking, and chromatin shearing. Effects of these conditions on the ChIP assay were analyzed utilizing a microplate-based matrix ChIP assay and quantitative polymerase chain reaction (qPCR). Efficacy of chromatin shearing was analyzed using gel electrophoresis. My findings will contribute to the development of a fully automated platform for chromatin shearing and ChIP, and lead to advances in epigenetic biomarker research of diseases that burden our society. Its application to human tissues will allow for quick and accurate evaluation of chromatin alterations and gene-bound enzymes, factors, and receptors in a wide variety of human biospecimens. It will also allow for discovery of innovative diagnostic and therapeutic biomarkers based on epigenetic pathways, and determination of genomic pathways that are associated with drug resistance development.

As a response to the NASA Cubesat initiative, the UW ESS department started the effort to design and build a 3U Cubesat by the students from various technical backgrounds. 3U Cubesat is made of 3 units vertically stacked onto each other with each unit at 10x10x11.35cm. This team is assembled within the UW Cubesat project to work on the structure system of the Cubesat and is responsible for solving problems in structure system. Recent progress regarding the CAD modeling of the body, designing and manufacturing of the hinges, deployers, solar panel mounting and ideas about fixed solar array and launcher possibilities are discussed. Various models have been proposed and tested and the overall capability of the hinges is improved to better suit the mission. For getting the maximum exposure of sunlight and keeping the whole system optimal, different solar panel solutions were assessed. Deployer design to release the Cubesat from the launching system and to release the solar panels from the Cubesat body was studied. Before machining the deployer and hinge system at its actual size, multiple tests have been done on the enlarged 3D-printed versions of the deployer and hinge system to make sure the design works properly. Among our team members, the tasks to design and implement each section are collaborative and everybody made sizable contributions to the progress. The current results produced include a design of the full body CAD model for the 3U Cubesat and its major components, a preliminary design of the deployer and hinge system undergoing its initial testing stage, a decision to use existing design of PPOD launcher and a design of the location and dimensions of the solar panels. Multiple models and their respective numerical estimations have been used in multiple presentations and will be presented at the day of the Symposium.

Microparticles are 0.1-1.0 μm vesicles derived from cell membranes upon cell activation, injury, or apoptosis, and are believed to aid coagulation. Due to their clinical significance, a calibration method to quantify microparticles on an upgraded flow cytometer was developed in this study. Optimal settings were previously sest on the Apogee A40 flow cytometer. However, this flow cytometer has recently been internally upgraded to a newer model, Apogee A50, making re-calibration necessary for accurate microparticle measurements. The same beads used for calibration appeared to scatter even more light on the A50 using the same settings and no longer corresponded to the desired upper limit. As a result, steps were taken to re-calibrate the optimal settings for microparticle detection. These were achieved by using polystyrene and silica beads of known sizes, antibodies with fluorescent molecules attached, and normal patient platelet rich and platelet poor plasma. Instead of using the forward scatter curve as previously done on the A40, experiments on the A50 utilized the side scatter curve due to the histogram’s appearance. After adjusting the voltages and threshold, the 1 μm microparticle cutoff corresponded with 0.4 μm polystyrene and 0.7 μm silica beads. The compensation settings (subtraction values to correct for overlap of fluorescent light signals) also differed significantly on the A50 compared to the A40. Based on these results, the Apogee A50 needs to have these newly established settings applied in order to effectively quantitate and measure microparticles.

Recognizing partially occluded objects is a major challenge for even the most cutting edge computer vision systems even though humans recognize partially occluded objects effortlessly. To begin to understand the neural basis, past research studies have investigated the correlation between animal behavior and neural activity during recognition under occlusion. These studies have been done on stable occluded objects even though it is well known that stimulus motion can attract attention to objects and can facilitate segmentation of objects in clutter, for example, in breaking camouflage. We investigated whether motion of an occluded object facilitates its recognition. To address this question, we asked human subjects to report whether two stimuli were same or different by pressing keys, M or N, for match or non-match. We moved the second stimulus at different speeds behind a field of occluding dots and asked how the percent correct performance and reaction time were influenced by the speed of movement of the visual stimulus. We found that 4 of the 6 subjects we tested exhibited a decreased reaction time and increased percent correct performance with stimulus motion. To verify that this difference was not simply because motion revealed parts of objects that were previously occluded by dots, we designed a control where the occluded shape underwent random jumps as opposed to coherent motion. In this case we did not observe the benefit of motion on performance. Thus, our results support the hypothesis that motion of an occluded stimulus enhances its recognition and discriminability.