Through the Galaxy Zoo Project, a project that lets public volunteers classify galaxies taken by numerous telescopes, several spiral galaxies were found that appear to be red in color in the visible wavelengths. Typically, only elliptical galaxies are red, so finding spiral galaxies of this color is an oddity. Initial analysis and explanations of these objects claimed that this group of galaxies has no star formation. However, these galaxies seem to be emitting massive amounts of light in the ultraviolet (UV), which might indicate that star formation is actually occurring. For this project, we compared the radial fits of these objects in the optical and ultraviolet using data from GALEX (Galaxy Evolution Explorer) and the SDSS (Sloan Digital Sky Survey) to see if these objects are just regular high mass spirals or galaxies nearing the end of their star formation that have exhausted their gas supply. Preliminary results show that the galaxies are slightly brighter near their center in the optical compared to the UV, but in the disk of the galaxies, the UV images are brighter than the optical images. This could mean that these galaxies indeed have star formation occurring in them.

Conventional methods of biomolecular immobilization on metal surfaces entail surface functionalization by chemically prepared self-assembled monolayers (SAMs) conjugated with the desired biomolecules. Many such methods require multistep reactions under harsh environments, lack material selectivity, have low biomolecule coupling efficiencies, and often result in random-orientation during the adsorption of target biomolecules. Furthermore, the behavior and the stability of these synthetic molecules under physiologic conditions are still not well understood. During the last decade, bio-functionalization of surfaces using material binding peptides has been demonstrated to avoid such limitations. These peptide-based biomimetic approaches were demonstrated to functionalize surfaces on a variety of materials under aqueous environments. They offer a promising alternative to conventional chemical surface functionalization techniques, while providing the additional advantage of material specificity that chemical-based linkers lack. Further bioconjugation with functional biomolecules to the materials binding peptides provides the self-assembly of the conjugated product on the material surface in a single step. Here, we design a peptide exhibiting a strong binding affinity to gold substrates while immobilizing antibodies on the surfaces. Biocombinatorily selected gold-binding peptides (AuBPs) were conjugated to an antibody-binding domain (FcBP). The binding characteristics of the resulting constructs, i.e. AuBP-FcBPs, on gold substrates were evaluated using Surface Plasmon Resonance (SPR) spectroscopy. The coupling of different peptide functional domains into a single fused peptide has the risk of inducing structural changes in the resulting molecule due to intermolecular interactions. It is therefore critical to determine whether functionality of each region was maintained. The SPR experiments were carried out at different concentrations and resulted in Langmuir adsorption behavior, allowing the calculation of the binding constants. The resulting bi-functional bioprobe molecule can be employed in a wide range of diagnostic and therapeutic applications.

 This study attempts to help resolve our lack of knowledge concerning the effects of velocity and load-carrying on footprints and gait. Several archaeological sites worldwide have preserved footprints, and in the case of some sites, such as the Laetoli footprint trails in Kenya, proper analysis of the footprints could yield crucial information about hominids. We will examine how gait and footprints change, if at all, with changes in speed and carried weight. Twelve individuals, six male and six female undergraduate students, moved across 9.2 meters of tiled surface with and without an additional load on their back equal to 20% of their body weight, and at three different speeds – self-selected walking, jogging, and running velocities. As they walked this distance, they stepped across an RSscan mat that dynamically records pressure, generating a digital image of their footprint, while also being filmed in order to record gait. While foot, midfoot, and heel contact length and the contact width of the ball of the foot all varied without any clear pattern over the 216 tests, for almost all volunteers the width of midfoot contact increased significantly with speed. There was a significant increase in midfoot contact width from walking to a higher speed, and also overall from jogging to running. Carrying loads equal to or less than 20% of one’s bodymass has no significant affect upon midfooth width or other footprint dimensions. The average angle between the heel and trochanterion (the tip of the greater trochanter, a feature of the femur)  changed significantly with movement speed for most volunteers, but not in response to carried loads of equal to or less than 20% of one's bodymass. 

In adults, acute myeloid leukemia (AML) generally remains difficult-to-treat, and most patients are currently expected to die either of their disease or treatment-related toxicities. The need for novel therapies is thus unquestioned. With increasing availability of specific small molecule inhibitors, one line of research has focused on targeting signaling pathways that are pivotal for the in vivo growth, survival, and propagation of AML cells as a means to improve therapeutic outcomes in this disease. Emerging evidence suggests that the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathway, a key physiologic regulator of transcription, translation, cell cycle progression, differentiation, metabolism, and suppression of apoptosis, could provide a rational drug target in AML. Constitutive activation of AKT signaling is indeed observed in many patients with AML, and several groups have reported inferior relapse-free and overall survival in AML cases with AKT activation. Given these data, we recently conducted an early phase clinical trial testing MK-2206, a highly specific allosteric AKT inhibitor, in patients with relapsed AML. However, MK-2206 has insufficient anti-AML activity at tolerated doses. Therefore, the goal of my project in the preclinical studies that I am currently carrying out is to identify signaling pathways that are critically important for AML cell survival in the presence of MK-2206 with the goal of developing combination therapies that optimize chemosensitization that can be achieved with AKT inhibitors. This is being done by mixing the MK-2206 inhibitor with various conventional chemotherapic drugs and measuring their toxicity on different AML cell lines by use of flow cytometry.

Exposure to vocalizations from members of their own species can influence how infants learn to hear and communicate. Eptesicus fuscus is a social mammal that lives in large colonies and uses many types of vocalizations for both communication and echolocation. We hypothesize that due to the fact that they live in large, well organized social groups, big brown bats should be social learners. In order to test this, we presented altered calls that have been raised or lowered in frequency and bandwidth to bats as they developed from infancy to adulthood. In order to limit exposure to natural maternal vocalizations, pups were reversibly deafened with silicon earplugs whenever they were in the presence of other bats. Every other day, we isolated the pups, removed the earplugs, presented altered calls and recorded the pups’ response. At the end of the study, we tested changes in the organization of the auditory nuclei by measuring frequencies of neurons in several layers the inferior colliculus (IC), a central nucleus in the auditory system in response to auditory stimulation. We compared these results to each infant's twin, as Eptesicus fuscus is usually born in pairs. This gives us a genetically similar control raised in identical conditions. Our results suggest a divergence in call frequency beginning in week two, related to the exposure to lowered artificial stimuli. There is also a shift in the organization of the bands of the IC, with larger low frequency bands and smaller high frequency bands. This suggests that the pups not only altered their vocalizations in response to altered stimuli, but that the frequency organization in auditory structures of the brain remains plastic beyond birth. Humans, like bats, are social mammals, and research into mechanisms of IC plasticity may provide some insight into the development of human hearing.

Over the past year, I have conducted ethnographic and oral history research here in the Puget Sound-area to understand the role of urban parks and organic farming in the development of a bioregional concept of sustainability. Throughout the research process I have maintained a focus on the study of sense of place, as this is one important aspect of bioregional ethics and design principles. This study was completed using collaborative ethnographic methods including participant observation, talking circles, surveys, and interviews with forest stewards at Seattle’s Carkeek Park, and farmers at Viva Farms in Skagit Valley. Through this I discovered the role of autotopography, the expression of self through place shaping practices, a process that contributes to a developing sense of place and is often overlooked. Some members of the Carkeek Park forest stewards, or WEWO as they call themselves, and some of the farmers used the act of shaping landscapes to express themselves in ways unique to the individual, and my data supports that this act was, and is, important to their developing a sense of place.

This action-research project describes a particular student-lead model created to foster community and awareness of global health across campus. We, the student leaders, who form the Global Health Undergraduate Leadership Committee (GHULC), have shaped this model to best respond to an ongoing challenge of engaging all undergraduates in awareness and community building around global health issues. The model for this approach involves bimonthly meetings with the committee and two advisors in addition to attending events planned by the GHULC and the Department of Global Health. Methods we have taken to increase undergraduate involvement in the minor include regular information sessions about the minor, monthly student-planned Community Connections events on critical issues, a joint student- and faculty-run journal club, peer advising, walking tours of Global Health organizations in Seattle, and a GHULC blog. Preliminary quantitative data suggests that there has already been an increase in the number of students enrolled in the minor this year as well as an increase in the academic diversity of participating students. Our next step will be to develop a qualitative assessment of the GHULC’s impact by administering a feedback form to all Global Health minor students regarding their perception of and involvement in the minor. We intend to gather this information on a yearly basis in order to improve the minor as well as the GHULC’s role with the goal of continuing to increase diversity, engagement, and mentorship.

In the 20th century, mathematicians attempted to reduce mathematics to a set of axioms. One of the properties that David Hilbert, a famous mathematician, postulated was decidability. This refers to an algorithm that can determine whether or not another algorithm in the same system is actually computable. In his 1939 paper, Alan Turing proves decidability cannot occur in formal mathematical systems. Turing used an unconventional way to prove his argument—the Turing Machine. The machine is a theoretical computational device. This abstract device has revolutionized the way we think of computing and computers among other fields. It consists of four parts: a head that reads symbols, an infinite tape that stores inputs and outputs, a state register that holds the current state (or state of mind if you prefer), and a table that describes how the machine transitions from state to state. Turing machines can compute anything that is computable. Computability equates to being able to describe how to obtain the solution of some function with an algorithm. This abstract idea is interdisciplinary; which makes it a great educational tool. We have built a working Turing machine out of LEGOS. To both extend and improve functionality, we have added various components. These components cross over to other fields of study making the project great for students of various education paths to reproduce in a team setting. Our hope is that others can use our work and further devolop it. Besides providing a concrete example of an abstract idea,  building the Turing machine allows us to reaffirm findings.  It is in the spirit of scientific descovery to reproduce work. This research project allows us to follow in the foot steps of intellectual giants.

During the last glaciation (18,000–13,000 years ago) a lobe of the Cordilleran Ice Sheet advanced into the Puget Lowland, scouring and sculpting the previous landscape into the present-day topography. Prior to the Puget Lobe’s advance, Cascadian alpine glacial systems had reached their maximum extent and were depositing large volumes of sediment into the Puget Lowland basin. While the extensive glacio-fluvial deposits that are preserved in the Puget Lowland indicate a thick sequence of sediment had filled the basin prior to the Puget Lobe’s advance, there has been no previous research on the source (or provenance) of these sediments. Much of this outwash sediment is currently attributed to the Puget Lobe, although a significant volume was likely deposited by Cascadian glacier sources prior to the Puget Lobe’s advance. I have collected samples from glacio-fluvial sediment and Puget Lobe till at bluff exposures on Whidbey Island, as well as alluvium from present-day Cascadian river drainages (a proxy for paleo-Cascadian glacio-fluvial outwash) that can be used to obtain a modal analysis of the basin fill. I analyze these samples using a microprobe to evaluate the proportional occurrence of source-indicative minerals in order to determine the provenance of Puget Lowland sediments. My expected results are for minerals present in the Cascadian drainage sediments, e.g., garnets, to occur in larger proportions than in the Puget Lobe sediments due to source-bedrock composition. For example, the result of high garnet (or other indicator mineral) content in Lowland sediments would indicate that the sediment was deposited by Cascadian glacio-fluvial source rather than by the Puget Lobe, redefining which depositional units are attributed to each source. Knowing the relative volumes of sediment deposited by these two sources will allow me to calculate alpine versus continental glacier sedimentations rates in the region during the last glacial maximum.

Pre-erythrocytic malaria vaccines may need to target numerous sporozoite and/or liver-stage proteins to be effective. If the protective antigens could be identified, multi-component vaccines could be produced. Using a high-throughput T cell screening, our lab recently identified a CD8⁺ response against the Plasmodium yoelii L3 ribosomal protein in sporozoite-immunized BALB/c mice. Unlike the CD8⁺ T cell response against the circumsporozoite protein (CSP) that increases with each parasite exposure in our system, the L3-specific response is not boosted by repeated exposures to attenuated P. yoelii sporozoites. Our lab has also shown that L3-specific cells have no cell intrinsic defects that counteract their re-expansion or function but rather that broad antisporozoite immune responses in secondary or later exposures eliminate expression of L3, thereby preventing any opportunity for activation of memory L3-specific CD8⁺ T cells. This T cell outcome following immunization may be emblematic of other T cells with liver-stage targets as well. In my project, we are studying the L3-specific T cell response in other murine parasite species (P. berghei) and other mouse strains (C57BL/6) by immunizing BALB/c and C57BL/6 mice with both species of Plasmodium and monitoring L3-specific CD8⁺ T cell responses via IFNγ ELISPOT to determine if this phenomenon is conserved in related models. Further, we are testing whether or not heterologous immunization of BALB/c mice with radio-attenuated P. berghei and P. yoelii followed by genetically-attenuated P. yoelii sporozoites bypasses the anti-CSP response and allows for boosting of late liver-stage antigens. If this occurs, such approaches could potentially yield more protective outcomes in human challenge studies and lead to more effective malaria vaccines in the future.

Fertility rates amongst women in Romania have been declining since the collapse of Communism in 1989. Data provided by the World Health Organization has shown the rapid growth of impairing diseases that have rendered some women infertile. With only 4% of Romania’s GDP allocated to the public health system, Romanian healthcare has struggled in providing women with quality treatment. The current study performed in Romania, investigates the effects of Romania’s Communist past on the ideologies of Romanian women. It considers how social networks, entrenched by these ideologies, have come to affect how women view the healthcare system and seek treatment. Using qualitative methods such as participant observation, in-depth interviews, and discourse analysis, this research will explore how Communist and post-Communist health policies have influenced attitudes towards fecundity and reproductive health for women and medical practitioners. By considering the ways in which ideologies construct the reproductive health network of Romanian women, this research shows that residual expectations of State responsibility in its role as a healthcare provider have prompted women to discuss and construct public healthcare as an illegitimate and inadequate government institution. Ultimately,  the emergence of this type of discourse in the female sphere is beginning to influence cultural notions of reproductive care and treatment. 

The unique geography and ice dynamics of the West Antarctic Ice Sheet (WAIS) are believed to make it susceptible to instability and rapid collapse. Predictions of WAIS stability in a warming world rely heavily on ice sheet model simulations; one drawback is that ground truth for these models comes from the last ice age, when the climate was colder. Geologic evidence of ice sheet behavior during warm interglacial periods is currently hidden beneath the Antarctic and Greenland ice sheets. We expect WAIS to have been thinner and less extensive under warmer conditions, and we ultimately plan to determine its past extent with cosmic ray exposure dating of subglacial bedrock. As a prelude to subglacial sampling, during January-February 2013 we collected samples from elevation transects of exposed granitic bedrock at three WAIS nunatak sites: the Pirrit Hills, Nash Hills, and Whitmore Mountains. We also conducted radar reconnaissance surveys to evaluate potential sites for future subglacial rock sampling, which will extend the transects beneath the ice sheet. We have separated out the quartz and potassium feldspar content of our samples for measurement of cosmogenic beryllium-10/aluminum-26, and chlorine-36 respectively. We are using the results of these analyses to determine the history of exposure and ice cover in the past 1-2 million years at each sampled elevation. Based on field observations, we expect our samples to show evidence of prolonged exposure, suggesting that presently subglacial surfaces were also exposed in the past. Ultimately our work will determine whether rock surfaces beneath the WAIS have ever been exposed to cosmic rays, providing clear evidence for or against a thinner ice sheet in the past. Such data will be useful in tuning ice sheet model conditions and establishing WAIS vulnerability to collapse, which is crucial to forecasting future sea level change.

Glioblastoma Multiforme, the most prevalent form of primary brain tumors, is characterized by its aggressive, invasive nature and short patient lifespan post-diagnosis - approximately 12 months. Through gene analysis of RNA sequencing data, we have found two miRNAs, miR-149 and miR-181, that target gene products whose increased expression has been shown to promote invasion and migration of U-87 human glioblastoma cells. miRNAs are short, non-coding RNAs that bind to messenger RNAs (mRNAs) - the body’s method of transferring genetic information, and target them to be degraded or prevent them from being translated into protein. As the miRNAs and the genes are inversely related, treatment of U-87 cells with the miRNAs would cause a decrease in migration, and blocking the miRNAs would cause an increase in migration. To quantify migration, we have employed a scratch test or wound healing assay, in which glioblastoma cells are grown on a dish and the middle of the plate is scratched, leaving space for the cells to migrate. The cells are treated with the miRNAs, and the percent of the gap filled after 24 hours is measured. We expect changes in miRNAs to affect the amount of migration in the gap compared to control - providing evidence that these miRNAs inhibit migration. miRNAs have been investigated as markers for disease, and the presence or absence of this miRNA in a patient’s glioblastoma may have implications as to the severity of their case. Additionally, characterizing these miRNAs adds to the database of knowledge concerning glioblastoma. The more that is known about this disease, the closer scientists are to finding a practical treatment.

Despite recent sweeping advances in DNA sequencing technology, whole genome sequencing remains impractical as a routine medical service. Nevertheless, recent work suggests that rare genetic mutations may play large roles in modulating disease progression. More affordable targeted DNA sequencing is currently necessary to study variants of low frequency in the human population and attain sufficient statistical power to link these variants with specific disease phenotypes. Previous studies have demonstrated the effectiveness of a capture by circularization approach using molecular inversion probes (MIPs) whereby thousands of individual sites in the genome can be captured simultaneously for DNA sequencing. Yet, non-uniformity across large numbers of targeted sites persists as a major barrier to more widespread adoption. In this work, we show that statistical analysis of past MIP sequencing runs readily informs modifications to the process of probe design and selection. Additionally, logistic regression on carefully selected MIP features enhances in silico identification of ineffective probes that leave gaps in sequence coverage. Richer data sets from MIP sequencing runs representing a broader range of MIP characteristics and interactions may offer further guidance in perfecting the design of MIPs, achieving greater uniformity across targeted sites and ultimately lowering the cost of sequencing.

Many individuals with severe depression experience chronic symptoms despite the aid of pharmacological interventions. This population may benefit from further interventions such as deep brain stimulation (DBS). Indeed, promising studies have illustrated the antidepressant effects of DBS on brain reward centers in patients with severe depression. However, these studies are limited by a lack of regulation of DBS delivery. We proposed that stimulation may be more effective if it is not delivered continuously, but only when needed. For example, DBS could be given when some physiological measure of depression increases. Therefore, we sought to provide proof-of-concept that an animal could learn to volitionally modulate a specific neural signal in order to receive DBS. To accomplish this goal, we used an operant conditioning paradigm wherein a rat gradually learns to volitionally modulate brain activity recorded from the surface of the cerebral cortex. The reinforcement consists of electrical stimulation in an area of the brain known as the medial forebrain bundle (MFB). When activated by electrical stimulation, neurons coursing through the MFB release dopamine, creating a strong reward sensation. We associated activity-dependent stimulation with a green light which served as an external cue to the rat. DBS was delivered only during times in which this light was on. Initially, results revealed that the production of the intended behavior was not correlated with the external cue. Over the course of repeated experimental sessions however, the desired neural activity became dramatically elevated during periods of activity-dependent stimulation. This finding suggests that through repetitive conditioning, the animal did in fact learn to volitionally control the neural signal to receive MFB stimulation. Despite these encouraging early findings, future work to determine the long term effects of DBS, as well as the optimal stimulation parameters, will be critical to the ultimate clinical implementation of this technology.

Alcohol is the only abusive substance from which withdrawal symptoms can be fatal. As such, the recovery processes from alcohol abuse are mentally, physically, and spiritually challenging. When alcoholics begin to move through the recovery process, they initiate a critical transition phase that shapes their identity as an alcoholic and as a human being within society. This study seeks to better understand how the recovery process transforms the identities of alcoholics. Furthermore, this research investigates how recovery alters the relationships between alcoholics and their communities. Through participant observation and interviews, this study examines the narratives of healthcare professionals, treatment facility employees, community members, family members, and alcoholics. Data from these groups were collected from individuals, treatment facilities, and Alcoholics Anonymous (AA) and affiliated meetings in order to provide a holistic perspective on how alcoholics move through the recovery process. This research expands our understanding of the effects of alcoholism as a social phenomenon by incorporating the perspectives of recovering alcoholics into the discourse while preserving individual anonymity. By providing a comprehensive conceptualization of alcoholism, this work has the potential to provide a framework for new modes of treatment that not only give alcoholics the agency to make a positive recovery, but also change the way society perceives the family disease of alcoholism.

 In Perlmutter lab’s ongoing study, a combination of activity-based motor training and EMG-triggered electrical spinal stimulation is used as therapeutic intervention for rats with spinal cord injuries (SCI). In addition to the reach training being a form of physical therapy, electromyogram (EMG) electrodes are implemented into rat’s impaired arm and on the spinal cord area that receives related motor commands from the brain. By detecting electrical potentials produced by the skeletal muscle, the electrodes then carry out electrical stimulation on the spinal cord. In response to repetitive and consistent transmission from a presynaptic neuron to a postsynaptic neuron, the connection between two neurons is reinforced as a result of Hebbian “plasticity” or the ability to strengthen or create new synaptic connections with the associated neurons. Although preliminary data suggested greater functional recovery in this novel intervention, many rats did not recover fully. This may be due to discrepancies in the timing between the EMG and the descending command arrival in the spinal cord, preventing optimal timing of the electrical spinal stimulation. In my proposed experiment, I hypothesize that triggering the electrical stimulation from the source of the descending motor commands, the brain, rather than from residual muscle activity will enable better synchronization of the stimulation, hence optimizing the intervention. Instead of EMG electrodes, electrocorticographic (ECoG) electrodes that are designed to detect brain electrical activity will be implanted on the surface of the brain. During the 12-week intervention along with the reaching exercise, a device called the Neurochip will record and trigger the stimulation of spinal cord. The ECoG technique may provide a less noisy signal by recording directly from the brain and enable a better estimate of the occurrence of spinal stimulation, thus maximizing the therapeutic potential of the intervention.

Individual bees often show flower constancy, specializing on a floral resource while avoiding switches to newly available resources. The familiar plant species benefits by receiving high rates of visitation even when competing floral resources become available. However, the phenology of some plants is shifting more rapidly than others in response to climate change, resulting in a changed sequence of floral resources bees encounter. To determine whether this affects plant fitness, we asked how pollinator visitation to competing plant species depends on the order in which those species bloom. We used two plant species with overlapping phenology and a common pollinator, Hypochaeris radicata and Campanula rotundifolia. We allowed Bombus impatiens to forage in floral arrays representing three phenological progressions: (1) CR Early, with C. rotundifolia decreasing from 100% to 0% while H. radicata gradually increased from 0% to 100%; (2) HR Early, with H. radicata decreasing from 100% to 0% while C. rotundifolia gradually increased from 0% to 100%; and (3) a Control with both species at 50% throughout. We quantified visitation rate to both species, and seed production by H. radicata. Overall, the number of bee visits received by both species was significantly higher when that species was introduced first than when it was introduced after its competitor. In treatments where the proportion of the early species decreased over time, the visitation rate per flower to that species increased, for both species and across all stages of experimental treatments. Seed set for H. radicata showed a similar pattern to visitation. Our results corroborate other work suggesting that individual bees learn and become specialized on a single floral resource and are slow to switch to a newly emerging resource. As a result, the flower species that blooms first can benefit from higher bee visitation and thus, potentially higher reproductive success.

Cellular noise is the variability in a biological quantity due to randomness. It is mathematically defined as the quotient of the quantity’s standard deviation and mean. Systems of genotypically identical cells may exhibit noisy gene expression—there are often differences between cells in terms of protein abundance. We are interested in developing a model to better understand this noise. Many factors contribute to gene expression noise, one of which is alternative splicing. RNA splicing is when sequences of RNA are “cut out”, leaving only the regions that will be translated into protein. Alternative splicing is when pre-mRNA transcripts are spliced differently, resulting in similar yet different specialized proteins. This is common in eukaryotes and increases protein diversity, allowing cells to take on particular functions and thereby playing a role in cellular decision making. To model the noise, we began by cloning different plasmids, each of which had two fluorescent reporter genes, citrine and mCherry. To better understand the alternative splicing mechanism, one of our plasmids contained an extra sequence of bases, an intron, in citrine. We used our two reporters to produce fluorescence readouts of correct versus incorrect splicing. We measured the fluorescence with a flow cytometer and the noise could be quantified by determining the spread and mean of the data. We hypothesize that as mRNA concentration increases, noise in expression will decrease, since variation decreases with increasing sample size. We also hypothesize that the plasmid with the intron will be noisier than that without since the alternative splicing mechanism will have a greater length sequence to splice. Alternative splicing will sometimes produce abnormal transcripts that are found to be in high concentration in cancerous cells. So in modeling the noise and gaining a better understanding of this mechanism, we may improve understanding of how cancer develops.

Pancreatic cancer is the fourth most common cause of cancer-related deaths in the United States. The overall survival rate is low because current therapies are ineffective. However there is growing research that High-Intensity Focused Ultrasound (HIFU) can be used to significantly improve current therapies for treating pancreatic cancer. HIFU works by accumulating ultrasound waves (i.e. energy), which generates heat causing tissue damage (i.e. hyperthermia). The thermal damage caused is measured by using thermal dose. Thermal dose describes the temperature the tissue is treated at and how long that treatment occurs. The theory of thermal dose has been tied to hyperthermia of cancer cells since at least the 1980s and there is a lot of strong mathematical background behind the time-temperature relationship. However with the rapid development of clinical hyperthermia for cancer therapy there is a need for accuracy when it comes to predicting thermal dose. My research focuses on whether or not equivalent thermal doses actually mean equivalent cell death (with cell types Panc-1 and MIA PaCa) and if this can be translated into a clinical setting where higher acoustic power can be used (i.e. using higher energy with HIFU to get lower time of treatment). I simulate HIFU by treating pancreatic cancer cells in water baths at equivalent thermal doses and measure cell survival with spectroscopy. My initial results suggest that the thermal dose relationship is accurate in relating amounts of cell death. An early conclusion from this is that thermal dose can be used to provide better calculations in a clinical setting and help evaluate data. Patients may even be able to experience shorter treatment times through using higher acoustic power with HIFU resulting in a more comfortable experience.

A Hamiltonian cycle is a path that goes through all vertices exactly one and comes back at the starting vertex. Finding Hamiltonian cycles is a well-known problem in graph theory. While necessary and sufficient conditions for Hamiltonian cycles remain unknown, we have developed an algorithm for finding Hamiltonian cycles in polynomial time in certain types of graphs presented in the paper. The algorithm involves finding k cyclic subgraphs within the original graph by deleting edges and then reconstructing some specific edges to create one single Hamiltonian cycle. Along with several algorithms developed earlier, this can contribute to a more general solution, or solutions of the classic Travelling Salesman Problem. 

We assessed the impacts of the Carpenter Creek Estuary Restoration Project, headed by Stillwaters Environmental Center of Kingston, WA, in regard to the goals of habitat restoration and preservation. Due to diversions and development, the altered hydrology and sedimentation regime of the stream and intertidal estuarine habitats led to unfavorable conditions for local wildlife, in particular, native salmonids such as Cutthroat trout (Oncorhynchus clarkii), Coho (kisutch), Chum (keta), and endangered Chinook salmon (tshawytscha). With the completion of the first phase of the restoration in 2011, the replacement of a ten foot culvert under S. Kingston Road with a ninety foot bridge, we began gauging the efficacy of the restoration by analyzing water quality, sediment samples, rates of sedimentation, and the extent and composition of intertidal vegetation islands in relation to the presence and abundance of salmonids using diachronous data from pre- and post-bridge construction. We collected and analyzed sediment samples taken in 2011 and 2012 from thirty three transects/quadrats along the estuary banks using Wentworth’s Classification of Coarser Sediments Based on Size of Particles and a gravelometer. These data reveal a decrease in total fine sediment volumes and an increase in larger grain sized pebbles and sand more conducive to salmonid spawning. We evaluated shifts in sedimentation rates and the size and species composition of vegetation islands in the estuary using vegetation surveys and geographic information systems (GIS). We gauged fish presence and abundance utilizing on-site observation, the online Habitat Work Schedule, and reports by local individuals and organizations, with indications of increased habitat health and availability based on geospatial analyses and fish presence. The results of this study are not yet conclusive, but implicate significant progress in the creation of habitat more suitable for returning salmonids, warranting additional research and funding for the completion of the restoration project.

Egalitarianism is a central value in the United States, with the strive for equal treatment for all individuals evident in law, policy, and education. In contrast, for East Asian cultures, which are deeply rooted in Confucianism, the existence of social hierarchy is seen as natural and justified, and more value is placed on harmoniously maintaining it than it is for achieving social equality. As biculturals, immigrants from East Asian cultures are socialized into both sets of norms, values, and behaviors, and can identify with both cultures. Given such incompatible values surrounding equality, how might experiencing discrimination affect feelings of conflict in an Asian immigrant's bicultural identity? In Study 1, first-generation Asian females completed scales of perceived sexism in the United States as well as the Bicultural Identity Integration Scale, a measure assessing the degree of compatibility a bicultural finds between their two identities. Results showed that the more participants perceived personally being a victim of sexism in the United States, the more conflict they felt between their two identities, even after controlling for perceptions of immigrant-related discrimination. In Study 2, female Asian immigrants were exposed to a scenario in which they anticipated receiving a grade that did or did not stem from sexism. Consistent with hypotheses, participants who considered experiencing sexism reported more cultural conflict between their Asian and American identities compared to participants who did not consider sexism. Together, these studies raise the possibility that differing cultural values placed on egalitarianism can create feelings of identity conflict for immigrants when they face discrimination.

My research focuses on Hanford, the former Cold War plutonium processing facility, located in southeastern Washington. Hanford produced plutonium for the nuclear bomb detonated over Nagasaki, Japan. Today, Hanford is a clean up site dealing with radiological and toxic waste challenges, and is considered the most contaminated site in the northern hemisphere. My independent research from 2012 focused on the dissemination of information on Hanford. I found that a majority of the people were unaware of the history of Hanford. This year, the focus of my research is the experiences of whistleblowers from Hanford, people who risked their jobs to make sure the public understood the real dangers that exist at Hanford. For the first part of the research I will conduct an interview with a whistleblower from Hanford and work on transcribing it for a book to be published on Hanford. When I  searched for sources I could use to find information on Hanford whistleblowers, I was surprised to find that what I was looking for did not exist yet. This vital information is often missing from the public discourse, and perhaps was the reason why many people were unaware of the issue. For the second part of the research, I chose to use the historical background, experiences, and the lessons we learned from the whistleblowers interviews and utilize them to address the current cleanup process and the potential nuclear accidents we could be prepared to avoid what Fukushima, Japan had to witness might potentially be the future of Hanford. I will investigate the issues at Fukushima and how it parallels the situation at Hanford. The health and safety violations that occurred at Fukushima continue to occur at Hanford and therefore need immediate attention. With Hanford located a mere three hours away from where we live, it is a shock that majority of people was not aware of this place. It is an issue that affects our health, the environment we live in, and moreover, our future generations.

Does climate change affect food security and health in Indonesia? In this project I studied the history of food security and health in Indonesia and analyzed how climate change phenomena, such as floods, droughts, increase in temperature, and rising sea levels, affect food security and health in Indonesia. Furthermore, I applied theories of structural inequality, risk society, and globalization to analyzing the impact of climate change on food security and health in Indonesia. I investigated the hypothesis that climate change phenomena drastically reduce the Indonesian food production, ultimately having a negative effect on the Indonesian economy and the health of the Indonesian people. My method was to look at current research of climate change phenomena in Indonesia and speak with Indonesian institutions, such as the secretary of health and environment, to learn the situation of food security and health in Indonesia and the various impacts of climate change. The research that I have done so far on this project suggests that climate change is having a negative effect on availability of food, cost of food, and access to adequate nutrition.

Possession Sound is an estuary system on the North East arm of Puget Sound, where the delta of the Snohomish River is located. Along the shoreline lies a highly industrial and populated area where there are large amounts of CO2 being put into the atmosphere. Because the ocean is a carbon sink, most of the CO2 that is put into the atmosphere dissolves in the water, and as a result of the excess H+ ions the pH lowers, acidifying the water. With the lowered pH, carbonate becomes less available and it could become increasingly difficult for planktonic organisms with calcium carbonate shells to survive, possibly decreasing their abundance at the halocline (depth of rapid increase or decrease in salinity), while the planktonic organisms with silica shells could possibly thrive in this environment because of decreased predation and competition. To study this, pH data was collected using a multiparameter probe, and plankton samples, using a 20µm net and cod end, were collected at the halocline for three consecutive years in the fall (using only November data), to see if a change in pH was followed by a change in the planktonic organisms present. Quantified species include Chaetoceros, Odontella, Psuedonitscha, Barnacle nauplius, Crab Zoea, Amphipod. The pH ranged from 5.89-7.9. In the data collected, there were more planktonic organisms with silica shells when there were lower pH levels, although more data is needed to rule out other contributing factors. The working hypothesis is, as the pH levels decrease, the planktonic organisms with calcium carbonate shells will decrease.

Our research study investigates if covert visual attention (knowing something visual will appear in your periphery) affects sensitivity to binaural cues (sound localization with both ears). The peripheral visual system has an area called the fovea that is used when sharp attention to detail is required, and this study hopes to see if there is a similar “fovea” in the auditory system. While a subject’s eyes are tracked, they are asked to fixate on a dot displayed on a screen. Once they are fixated, a sound occurs that appears to move a small distance either from right to left or from left to right. In half of the trials, a diamond also appears on the screen and it is informative of where the sound will occur. The subject is then asked to identify which way the sound moved. I ran the subjects, did statistical analysis on the data, and will be compiling that data into a meaningful result. In a previous study, an overt informative visual primer significantly increased binaural sensitivity, and we believe that a covert visual primer will help similarly. This suggests that the two modalities work together to contribute to a unified map of our environment. The short term goal of this research is to understand how the gaze control system modulates auditory attention. The twenty-year goal of the lab is to help create hearing aids and cochlear implants that can imitate a functioning hearing system’s ability to follow an auditory signal, eliminating a difficulty that pervades hearing devices today called the “cocktail party problem” which arises when attempting to understand speech in a noisy environment. Whether covert visual attention has a significant effect on hearing is as yet unknown, but it may have a valuable long-term impact on the lives of those living with hearing loss.

The Learn and Serve Environmental Anthropology Field (LEAF) School at Edmonds Community College has partnered with Nikkei Manor and the Wing Luke Museum to develop the Nikkei Concerns Oral History Project. Through this project, students have the opportunity to serve as both mentors and mentees. Eight students have undergone training, interviewed and recorded the experiences of Japanese Americans who were interned during World War II. From these survivors we are learning more than the easy to record factual history, we are learning about experience, about the diversity of coping strategies, adaptive solutions, and emotional struggles these Americans lived. We found unexpected stories relating to aspects of control and freedom within the camps, as well as humor, acceptance, bitterness and forgiveness. The hope in a project such as this is to develop a greater understanding of the experience of these people, to record their stories and create awareness of what they faced. This is a unique opportunity for students to hear firsthand accounts from internment survivors and participating students will continue to learn about the internment era while transcribing the stories shared by Nikkei residents, and mentoring their classmates in the transcription process. While there has been much research elsewhere, the story of internment in the Northwest has received less attention. This project has allowed for student engagement and development as well meeting the needs of the Nikkei residents who wished to share their stories. Recordings will be kept both by the Wing Luke museum and Edmonds community college.

The project explores the effects of social media on investing activities. The social media tool explored was Twitter, and the analysis was done on the amount and content of 'tweets.' Research was done to see if there was any correlation between the amount of tweets about a certain stock (Apple was used as the company for the study) and how the stock price fluctuated. Research was found to be inconclusive, but did find that tweets are being used to talk about stock (investment) sentiment. Whether or not individuals would make investments based on what they heard through tweets is something to study more as Twitter becomes more popular, socially and primarily the financial industry.  

Autism Spectrum Disorder (ASD) is defined as impairment in three areas of development: social skills, communication, and repetitive behavior. In typically developing children, there is a significant relationship between the development of communication and the use of joint attention (JA). Impairments in JA could also be related to some of the core features of ASD. This thesis will use data collected at the University of Washington as part of the larger, multisite Infant Brain Imaging Study (IBIS) Autism Center of Excellence (HD055741). The IBIS investigates brain and behavioral development in infants with older siblings with ASD, who are at high risk for ASD and related disabilities. This thesis project investigates the relationship between JA and early communication in high-risk infants. Our hypothesis is that high-risk infants with deficits in JA will also demonstrate more delayed language development than infants without these deficits. We have studied approximately 55 12-month-old high-risk infants and approximately 35 low-risk infants with a typically developing sibling. Language ability was assessed with the MacArthur Communicative Development Inventories (CDI) and joint attention was assessed with the Communication and Symbolic Behavior Scales (CSBS). Correlations between scores from 12-month-old high-risk and low-risk infants on the CDI and CSBS were then reported. This research will have implications on our understanding of the relationship between joint attention and language development as it applies to social interaction and learning in children with ASD. This thesis will expand on earlier research that has shown that joint attention plays a pivotal role in social interaction and language learning.

My research focuses on the ethnobotanical uses of plants by the Monte Salvado native community of the Las Piedras River in the Amazon Rainforest of Peru. One-fourth of all Western pharmaceuticals, including very common drugs such as aspirin, have their origin in rainforests. Much of the knowledge surrounding the use of these plants comes from indigenous communities living in the Amazon. Many of these communities, such as the Monte Salvado, use plants as both medicine for anything from stomach aches to snack bites, as well as a spiritual agent.  My research centers on the medicinal and spiritual purposes of plants such as Curare, Suma, and Clavillia. My research questions include, “What are the main purposes of and beliefs about plants in this community? How are these plants used and what are their effects? How do women use plants to aid in maternal and menstrual health? The prepatory work leading up to my community immersion this summer is creating a research proposal, as well as learning and practicing Anthropological research methods. 

My research uses ethnographic methods to examine personal histories and subsistence strategies of health workers in Sierra Leone. The project is designed to ‘study up’ (Nadar 1969), that is, to use ethnography as a tool to understand the macro- political, social, and economic context of people’s day-to-day experiences. I look to understand the impacts of Sierra Leone’s post-conflict economic restructurings on the quality of life, employment distribution, and clinical practices of healthcare providers. My project includes a preparatory stage at the University of Washington and, subsequently, six weeks field research in Sierra Leone. My work particularly considers Sierra Leone’s debt-relationship to International Financial Institutions (IFIs), such as the International Monetary Foundation (IMF) and World Bank. Loans issued by IFIs stipulate shifts in governmental spending and regulation that, in terms of healthcare services, translate to reduced funding for governmental healthcare services, the development of a private healthcare sector, and use of NGOs to funnel aid money into the nation. These shifts, inspired by neoliberal market fundamentalism, result in fewer jobs and lower wages for health workers, as well as a discordant healthcare system fractured between NGO, private, and government services. Globally, anthropologists have worked to document the collateral damage to health from neoliberal economics. However, there is a dearth of ethnographic work explicitly considering economic restructuring’s effects on health in Sierra Leone. Health workers are integral to health services and their stories incisively reflect the toll of neoliberal economic agendas on health. My research adds to the anthropological evidence that these agendas are systematically denying people health services and undermining health in developing countries.

The field of synthetic biology aims to modularize gene-networks within microorganisms for the purpose of using them as well characterized parts in building novel, useful biological systems. Realizing this goal is vital because biology’s inherent practicality holds the key to needed energy efficient technologies. As the human population increases, energy efficient technologies will become more and more a necessity. The first step in realizing this vision of adapting biology into an engineering discipline is through properly characterizing gene expression and enzyme function within engineered and natural biological systems. To do this, I have developed a turbidostat with mixture control and fluorescence sensing capabilities. A turbidostat is a continuous culture bioreactor that maintains constant culture volume and microbe density through a feedback loop between turbidity measurements and dilution with fresh media. The constant culture environment and microbe density allows the cultured microbes to reach a “steady state” where growth and all environmental conditions are kept constant. By maintaining microbes at steady state, variables that effect microbial processes are minimized, which facilitates accurate examining of gene-network dynamics. The mixture control ability of the turbidostat allows for the concentration of a given molecule within the culture environment to be modulated through time without altering any other environment variables. Through mixture control, a molecule that acts as an input to a gene-network (i.e. an inducer molecule that initializes a gene-network) can be varied in concentration through time within the culture environment. Since most gene-networks utilize fluorescent protein production as their output, the turbidostat’s fluorometer (a fluorescence detector) can monitor the output of a gene-network while the input to the network is modulated. We believe that the ability of this turbidostat to look at the input-output dynamics of gene-networks under defined environmental conditions will yield enhanced behavioral understandings, aiding to the modularity of these systems.

Evaluative priming (EP) is an unobtrusive measure of attitude.  Participants' responses to a target stimulus (a face) are either facilitated or slowed by immediate prior exposure to a prime (pleasant or unpleasant word). If pleasant primes ellicit speedy responses to faces of one social category more so than faces of another, this is interpreted as preference for the first category. Unfortunately, EP has been plagued by low internal consistency, reliability and convergent validity with other measures. The present project proposes a modification to EP procedure, known as homogeneous blocks priming (HBP). In HBP, prime-target pairs consistent with prevailing attitudes (such as pleasant+young and unpleasant+old) are presented in one block, while prime-target pairs that are inconsistent with prevailing attitudes (pleasant+old and unpleasant+young) are presented in a different block. Previous research has hinted that HBP will outperform traditional EP procedures, but they have never been compared within the same experiment. The present experiment tests age attitudes using a traditional EP measure, the new HBP measure, and an Implicit Association Test (IAT), a much more widely used implicit measure of attitude. HBP and traditional EP will be compared on the basis of internal consistency, reliability, and correlation with the IAT. The study is ongoing now, but pilot data reveal that the HBP task correlates more strongly with the IAT than EP does, and the HBP effect size is especially strong for participants who respond very rapidly.

Pulsed plasma thrusters are a modular electric propulsion technology with extensive flight heritage. Flight-ready PPTs are tailored to a specific mission based on the power and mass budget of a mission. The lower bound for both parameters is far less than competing electric propulsion (EP) technologies, such as Arcjets and Hall Thrusters, which makes them desirable as spacecraft size decreases. The variable components of PPTs are typically electrode geometry, capacitor size, spark plug geometry, and fuel feeding system, but rarely if ever does a space mission select an unusual fuel. Teflon is used almost exclusively, and PPT fuel research is effectively stagnant. This investigation has concluded that alternative fuels are indeed significant. The sulfur PPT (SPPT) is inspired by natural sulfur plasmas in the Jovian magnetosphere. Thrust stand tests over the course of six months have demonstrated clearly that the specific thrust (thrust per unit power) is three times higher than in a corresponding test using a Teflon PPT of the same electrode geometry. Both pure sulfur and a sulfur-epoxy binder have been considered, and show the same specific thrust within error of the experiment. Pure sulfur will outgas in space, and may not be suitable for long missions, but the sulfur-epoxy fuel could potentially solve this problem. Additionally, an insulated semi-conductive bismuth sulfide compound shows similar thrust characteristics to the Teflon fuel, albeit at a lower exhaust velocity. This investigation is ongoing, with a parallel application project performing the SPPT experiment on a high-altitude balloon airship. This mission will demonstrate systems control, test the SPPT in a non-laboratory environment, build flight heritage, and represent and important advancement in PPT applications.

Vasodilator-stimulated phosphoprotein (VASP) is a focal adhesion protein that regulates actin filament polymerization, a process necessary for cell motility. Through cell locomotion, endothelial cells migrate to designated locations to form new capillaries (angiogenesis). Previous studies have shown that VASP regulates endothelial cell migration in human umbilical veins and during human placental development. Given VASP's role in endothelial cell movement, we hypothesized that VASP is required for angiogenesis. We are investigating VASP’s role in angiogenesis through both in vitro and in vivo assays in VASP null and wildtype mice. In addition, we measured blood flow recovery in VASP null and wildtype mice after hindlimb ischemia by laser Doppler perfusion imaging. The in vitro assays compare microvessel outgrowth from either tibialis anterior muscle or descending thoracic aorta in response to the vascular endothelial growth factor (VEGF). The in vivo assays compare capillary ingrowth into matrigel plugs containing (VEGF) and capillary angiogenesis stimulated by hindlimb ischemia generated by unilateral femoral artery ligation. Capillaries are identified through immunohistochemistry. Significant difference for the hindlimb ischemia blood flow recovery rate and capillary counts was evaluated through the T-test and the Analysis of Variance test, respectively. So far, we have identified no significant difference between VASP null and wildtype mice in blood flow recovery by laser Doppler perfusion imaging; however, this process is more dependent on arteriogenesis than capillary angiogenesis. Identification of potential regulators of angiogenesis would further our understanding of processes such as wound healing, growth and development, and recovery from ischemia, where capillary formation plays a key role.

Dysregulation of the Epidermal Growth Factor Receptor (EGFR) pathway has been implicated in 50-60% of glioblastoma multiforme (GBM) tumors. The EGFR signaling network regulates cell proliferation, differentiation, growth, and apoptosis. The binding of an extracellular ligand activates the EGFR molecule, initiating a cascade in which proteins are serially activated and deactivated through phosphorylation and dephosphorylation. This process is time-sensitive: proper function depends upon each protein remaining active for the proper interval. Wild-type astrocyte proteins respond to phosphorylation by tyrosine kinase, dephosphorylating within five to ten minutes. A dysfunction of EGFR resulting in sustained low-intensity activity or over-activity of the EGFR pathway causes distal abnormalities, including the aplastic over-proliferation and aggressive invasion of astrocytes endemic to GBM. A detailed temporal map of signal transduction through various components of EGFR pathway is needed to find the proteins contributing to the deviant cell behavior. To that end, we will create a 7-time point model of the EGFR pathway in GBM. The GBM cell line will be exposed to EGF for various lengths of time starting from 5 minutes through 24 hours. At each time point the phosphorylation status of pathway proteins will be profiled and quantified.  This assay is anticipated to yield approximately 500 phosphorylated proteins. We will use high throughput phosphoproteomics strategy, in which quantitative mass spectrometry will be utilized to measure phosphorylation levels of each component of the pathway. Information generated through phosphoproteomics will be overlaid on the computational EGFR network for each time point resulting in seven different EGFR pathway models. We will compare the network at each time point with the other to track the signal transduction through different proteins in the pathway. At the end of this project, we will have seven detailed EGFR networks, which can elucidate the dynamics of signal transduction from ligand exposure to the cell’s response through gene activation.

Within the last 20 years, global climate change has become well accepted. Research on plant dynamics has documented species shifting their ranges to higher elevations in order to remain within physiologically optimal conditions. This general observation has motivated my investigation of elevation as a driver of life history traits within alpine and subalpine plants. Specifically I’m interested in sex-ratios among the subalpine flower Erythronium montanum. This species of flower has been shown to exhibit a unique trait known as androdioecy, wherein some individuals produce male-only flowers instead of hermaphroditic flowers. In other species this trait has been attributed to sexual dimorphism, the variability between the sexes in terms of morphology and/or phenology. The discovery of this trait in E. montanum has inspired my research project with two distinct goals: To determine whether 1) abiotic factors such as elevation, soil moisture and time of flowering and 2) biotic factors such as canopy cover, and flowering density, influence sex-ratios within E. montanum. Surveys done at Mt. Rainier in 2011 and 2012 by the Hille Ris Lambers lab provide data on multiple factors which should allow me to test a number of possible hypotheses. Preliminary data analysis spanning both elevation and flowering time, show biased sex-ratios where the number of males to hermaphrodites decreases at higher elevations, late in the season. A future look at the extent of sexual dimorphism within the population can help to shed light on the mechanism behind sex-ratio bias and increase our understanding of plant reproductive-ecology over an altitudinal gradient. As many species begin a slow but steady march up the mountain, it’s paramount that we have a better understanding of how and why life-history traits fundamental to reproduction (e.g. sexual dimorphism) vary with elevation. Ultimately, future generations and plant communities rely on what is happening today.

Research has made tremendous gains in therapy efficacy for children and adolescents, yet the therapies have not effectively been implemented into usual care settings. The mental health field has recently initiated a huge drive to disseminate Evidence Supported Therapies, or ESTs, in order to better serve our children. Do clinicians trained in ESTs deliver the clinically relevant components to their clients and utilize important structural elements of EST such as agenda setting, assigning/reviewing homework? If clinicians are not utilizing the components and structure supported for the specific clinical target, then children may not be receiving efficacious therapy. Clinicians across Washington State were invited to participate in the Washington State Initiative and receive components based Cognitive Behavioral Therapy, or CBT Plus. The training included components for Anxiety, Depression, Behavioral Problems and PTSD. Each clinician involved in the study entered assessment data on his/her cases as well as what components and structural elements were delivered. Research has shown that clinicians are reluctant to deliver exposure.  For instance, if a child has PTSD and has a panic attack each time he hears an ambulance, exposure to ambulances reduces the related anxiety.  It is predicted that clinicians delivering CBT Plus with a clinical target of anxiety or PTSD will be less likely to deliver the adequate components due to this exposure reluctance. The preliminary data shows that many clinicians did not consistently provide the necessary components and structure for their clients’ clinical presentations. If clinicians delivering EST are not utilizing the relevant components, then the children are not receiving the best care possible and the ESTs are not being effectively disseminated. Training for ESTs would thus need to focus more strongly on combating clinicians’ negative perceptions of exposure. This may be achieved through more thorough psychoeducation and theory explanation during EST training.

Heart disease is often responsible for morbidity and mortality in the United States. Current treatments aim to slow the progression of the disease by modifying calcium handling in the heart, but do not restore function to healthy levels. Endogenous troponin C (TnC) is the calcium binding subunit of troponin, a complex that regulates contraction in muscle. The amino acid substitution of leucine for glutamine at position 48, L48Q, in cTnC has been shown to increase calcium binding affinity of the troponin complex. We hypothesize that the expression of engineered protein L48Q-cTnC will increase calcium sensitivity of a failing heart and restore function without disrupting calcium handling. The aim of this study is to determine the expression pattern of this engineered protein in vivo in healthy rat hearts after various dosages of adeno-associated viral vectors of serotype 6 (AAV6) containing L48Q-cTnC. In addition, we aim to determine the correlation between vector dosage and changes heart function. We will achieve these goals by administering our AAV6 virus to healthy rats and monitoring whole heart function over the next four weeks. Heart function will be assessed in vivo with non-invasive echocardiography ex vivo on a Neely whole heart apparatus four weeks post-injection. The Neely apparatus allows us to control the environment of the heart while measuring function, which is not possible in vivo. The expression of L48Q-cTnC will be determined by immunohistochemistry and Western blotting. From this data, we will be able to calculate the dosage necessary to achieve maximum expression and increased heart function in our healthy heart model. This initial study it vital to characterizing the expression and efficacy of a potential heart failure therapeutic and will directly impact the design of future studies in disease models.

My research focuses on mTOR (mammalian target of Rapamycin)-dependent signaling and its involvement in neurodegeneration and neurofibrillary degeneration. A lot of studies have shown that Rapamycin, which is an mTOR inhibitor, is able to provide protection in models of neurodegenerative diseases especially Alzheimer's and Parkinson's disease. Rapamycin is involved in a lot of cellular processes including cell growth, proliferation, and it accelerates clearance of these toxins. My project focuses on important neuronal proteins levels such as alpha synuclein, DJ1, Beta Amyloid, tau, and phosphorylated tau in Rapamycin treated control, old, and young cortex and cerebellum samples using the Luminex machine. Altered levels of the mentioned proteins have been associated with Alzheimer's and Parkinson’s disease. In the Luminex Instrument, cell lysates are combined with a biotinylated double stranded consensus binding sequence for the transcription factor family of interest. Fluorescently labeled magnetic beads, which have been conjugated to antibodies that target the individual transcription factor family members, are used to capture the transcription factor-bound DNA. At the end, a dye called Streptavidin-phycoerythrin is used to bind the biotinylated oligo and determine the magnitude of the signal. We hope to see a significant difference in the levels of the mentioned proteins in Rapamycin treated mice vs. the control group especially in the cerebrum group.

The late Oligocene-early Miocene fossil record (30-18.8 million years ago) of North America includes an abundant fauna of entoptychine gophers (Rodentia: Geomyidae: Entoptychinae). These burrowers make up as much as 20% of the mammalian individuals of the faunas they are part of, and can be involved in habitat partitioning or competition with other burrowing herbivores. The wide geographic range of these animals and their use in constraining the age of the fossil assemblages of the Cabbage Patch beds (western Montana) and John Day Formation (eastern Oregon) makes them critical to understanding the biogeographic relationships among these fossil faunas. To understand these spatiotemporal patterns, I am evaluating the taxonomic richness of entoptychine gophers. Previous studies have discriminated among these gopher species by using morphological features of skulls and dentaries. However, anatomical elements are rarely preserved in fossil assemblages, and isolated teeth are commonly the only material available for identification. Since the occlusal surfaces of the cheek teeth are usually worn down as a consequence of feeding, they lack discrete features for species identification. Instead, some researchers have hypothesized that the more continuous variation in the enamel outline of select cheek teeth could be used for discrimination. Here, I use semi landmark-based geometric morphometrics (an arithmetical comparison of geometric coordinates) on the upper last premolar and molar. Applying this method to 98 modern geomyine gopher specimens (Geomyidae: Geomyinae), representing 10 taxa, helps quantify intra- and interspecific tooth shape variation and offers guidelines for recognizing fossil gopher species. Preliminary analyses indicate that tooth shape is species-specific in modern gophers, supporting the use of this method to differentiate fossil gopher taxa. Applied to 96 specimens of fossil gophers, I found a strong overlap of fossil taxa in the morphospace, suggesting that previous researchers may have overestimated the species diversity of some fossil gophers.

The objective of this research is to produce bio-oils from biomass at high temperature in water or ethanol at different pressures. The high pressures and temperatures takes the solvents near or into supercritical conditions where small changes in pressure have great effects on the solvents' physiochemical properties. Conditions are tailored to increase the yield of bio-oil that can be hydrogenated and then refined in existing petroleum refineries to produce high-quality level jet fuel. Char, coke, and tar - unwanted byproducts - must be decreased to a minimum as they deactivate catalysts and clog reactors. These unwanted byproducts are a ubiquitous problem in biomass themro-chemical conversion; removing them would help the industry develop. It is possible to get no char, coke and tar produced, as I have been able to attain, though a better understanding of how to reproduce it consistently and at larger scales is necessary. Temperature are adjusted within the sand-bath - apparatus for heat transfer- and to increase pressure more reactants are placed into the chamber to which the pressure can be calculated.  

Influenza has long plagued the human population, and continues to cause sickness throughout the world. As an enveloped virus that utilizes the process of endocytosis to enter and infect cells, it must fuse its membrane with the host’s endosomal membrane in order to deliver its genetic material to the cell. This specific process is mediated by the viral glycoprotein hemagglutinin. Through my research, I hope to determine the underlying mechanisms of the HA-mediated fusion process. One aspect of the membrane fusion process that remains poorly understood involves the association between HA and the internal structural protein M1 or matrix protein. It has been hypothesized that these work together to keep the virus intact while the host membrane is remodeled. The M1 protein is located between the viral envelope and ribonuclear core, and is believed to be a bridge between these two layers. We hypothesize that the interactions between the cytoplasmic tail of HA and the M1 protein layer in the virus interior are disrupted in a low pH environment. To test this hypothesis, I have isolated and purifyed the influenza matrix protein from whole virus particles. Having obtained a pure matrix protein, I can further study the oligomerization process and start to determine the behavior of the M1 protein in solution. I hope to be able to use dynamic light scattering and gel filtration chromatography to observe the M1-M1 complexes. I will also examine how M1 interacts with membranes of different compositions using lipid flotation gradients and electron microscopy. By understanding the dynamics of M1 secondary structure and HA membrane fusion, my research could help to generate information for rational drug and vaccine targets against the influenza virus.

It is important that animals be able to modulate the rate at which they learn. Without such a capacity animals might form habits based on single events, or fail to respond to changing circumstances. Previous work suggests that two populations of inhibitory striatal neurons may play antagonistic roles in modulating learning rates. Inactivation of D1 receptor expressing striatonigral neurons slows that rate at which animals learn operant tasks, while inactivation of D2 receptor expressing striatopallidal neurons speeds the rate at which animals learn. This suggests that the normal activity of striatonigral neurons supports learning while the normal activity of striatopallidal neurons suppresses learning. We assessed a maze-based operant learning task that may be useful for examining the roles of these neuronal populations in modulating learning rate. In this task, animals are repeatedly faced with the choice of a right or left turn. One of these turns consistently results in the animal receiving a large reward, while the other results in a small reward. The animal performs twenty trials per day. If after the first ten trials in a day the animal selects the large reward for at least nine trials, saline vehicle or a D1 or D2 receptor specific antagonist is infused into the nucleus accumbens of the animal and the rewarded turn is switched. This allows the assessment of learning rates under conditions of D1 and D2 receptor antagonism within individual animals. Preliminary results are not yet sufficiently extreme to establish a difference between D1 antagonism, D2 antagonism, and vehicle administration. This may result from insufficiently distinct reward magnitudes, an insufficient number of subjects, or from an insufficiently difficult task. Alternatively, it may be that while D1 and D2 receptor expressing neurons contribute antagonistically to learning rate, the activity of D1 and D2 receptors on these neurons does not.

Ischemic Preconditioning (IPC) is a neuroprotective phenomenon in which a brief ischemic exposure increases resistance to serious injury from subsequent ischemia. Understanding the basic mechanisms of IPC and taking advantage of this knowledge may provide better treatment options for those at high risk for stroke. We hypothesize that ischemia induces brain tissue release of endogenous Toll-like receptor (TLRs) agonists (sometimes referred to as damage association molecular patterns (DAMPS)) that stimulate microglia Toll-like receptors, thus releasing interferon (IFN) α/β to trigger the transcription of neuroprotective interferon stimulated genes (ISG). Our objective was to culture mouse microglial cells and stimulate the various microglia TLR receptors with their respective agonists to identify the receptors that mediate ISG release. We also wanted to demonstrate TLR-agonist induced release of IFN α/β, especially because IFNs are already effective FDA-approved treatments for Multiple Sclerosis and could serve to increase ischemic tolerance for patients at high risk for strokes. Due to results from previous experimental paradigms strongly suggesting that IPC-mediated neuroprotection is TLR4-dependent, we proposed that stimulation of TLR4 generates release of IFNs that in turn induce transcription of ISGs. Our preliminary results revealed that activation of multiple TLRs (TLR 3, 4, and 9) could mediate the release of ISG chemokines, with notable ISG release following TLR3 and TLR4 activation. IFN release was not detected through TLR4 but instead TLR3. We are currently exploring the possibility of a synergistic relationship between TLR3 and TLR4 in regulating IPC-mediated neuroprotection.

 Among individuals diagnosed with autism spectrum disorder (ASD), a delay or diminishment of the development of language and communication is found to be a core feature of the disorder. Children with ASD are also found to have more difficulty with verbal working memory tasks when compared to typically developing individuals, although findings have been mixed. In other clinical populations in which communication is impaired, one aspect of language that has been found to be related to verbal working memory is narrative ability, though this has not been thoroughly tested among children with ASD. Previous work has shown that verbal working memory relates to communication skills in children with ASD, albeit this study did not investigate narrative ability specifically. The current study had the goal of investigating the relation between verbal working memory and narrative ability in children with ASD. Data was collected from 21 participants. Participants were children from 6 to 11 years of age with autism spectrum disorder and average or above average IQ. Working memory was measured with the Children’s Memory Scale Numbers subtest, and narrative ability was coded from a speech sample obtained during the Autism Diagnostic Observation Schedule. The planned analysis was a partial correlation between verbal working memory and narrative ability controlling for IQ. Our prediction was that better verbal working memory would be a predictor for stronger narrative ability above and beyond IQ.

One of the functions of the vestibular system is to engage neural reflexes, which ensures the stabilization of a visual image during head movements. This is accomplished through the stimulation of vestibular hair cells, which respond to accelerations, and then produce compensatory eye movements opposing head motion. This called the vestibulo-ocular reflex (VOR). Hair cell loss results in vestibular deficits, and for these individuals, this loss of function is debilitating and results in vertigo and decreased visual acuity. To address these deficits, the Phillips lab has developed a vestibular prosthesis, which aims to use electrical stimulation to restore function by artificially activating individual branches of the vestibular nerve. However, it is not known precisely how the system changes after hair cell loss; this may have implications for the effectiveness of the prosthesis in treating vestibular loss. To explore this, we examined the interaction between the electrical activity and residual vestibular activity after vestibular loss. We first introduced a vestibular deficit in a rhesus macaque through successive gentamicin injections into the middle ear to destroy vestibular hair cells, and measured VOR responses to verify the progressive vestibular loss. Next, we recorded eye velocities in response to electrical stimulation to characterize changes in the efficacy of stimulation, thus providing insight into the prosthetic mechanism. Finally, modulated electrical stimulation was provided during rotation of the rhesus macaque to test the efficacy of the prosthesis in restoring VOR in conjunction with residual vestibular activity. Characterizing prosthetic function during increasing vestibular deficit is important in determining the mechanism of stimulation, the physiological responses succeeding hair cell loss, and ultimately a model for the prosthetic efficacy for human patients.

Motivated by current interest in one-dimensional materials for their ideality and potential in the next generation of electronics, a device consisting of a microscopic four-point probe was developed with electron beam lithography (EBL) to investigate the conductance and resistivity of manganese-doped copper oxide (Mn:CuO) nanowires. Mn:CuO nanowires were chosen because they are known to be ferromagnetic and conductive below a critical temperature of 80K, while maintaining semiconductor properties and low resistance at room temperature. Nanowire samples were obtained from the Yang Group in Nanjing, China, and were deposited with ethanol onto silicon dioxide wafers to obtain a rough monolayer for easy isolation of individual nanowires. A pattern consisting of four contact lines was created with DesignCAD and conditions were optimized to obtain an adequate dose (charge/unit area). A subsequent process of precise alignment was performed to ensure complete overlap between the nanowire and pattern on a nanometer scale. With accurate alignment, the pattern was then etched onto a single nanowire, developed, and coated in a 50 nm thin film of gold to enable conduction between the nanowire and the four-point pattern. From this point, the current and voltage can be measured through the nanowire macroscopically. Consequently, the anisotropic resistivity of the material as well as gate voltage effects can be studied to verify the material’s applicability to future spintronics devices such as field-effect transistors.

Diatoms are major players in Earth’s biogeochemical cycling, accounting for approximately 20% of global primary production. Their dominance in several aquatic ecosystems is a testament to adaptations that provide an advantage in nutrient acquisition and growth. Ocean fertilization experiments have demonstrated that iron is the primary limiting nutrient in many open ocean ecosystems. This metal is critical to the functioning of numerous important proteins, particularly in photoautotrophs such as diatoms. An excess of intracellular iron, however, can cause oxidative damage to the cell. This project investigates genes related to iron metabolism in the recently sequenced transcriptomes of 21 diatoms and select outgroup species. Of particular interest are genes coding for ferritin subunits. Ferritin is a multimeric protein that serves as an iron storage unit, safely sequestering iron atoms in an oxidized state and releasing them back into the cytoplasm when iron supply is low. Ferritin in diatoms was previously thought to exist only in pennate diatoms. Here we show that ferritin-coding genes are expressed in members of every major diatom group. 13 out of 21 diatom transcriptomes contain full-length sequences, forming a clear monophyletic clade most closely related to cyanobacterial ferritins. Additionally, 7 of the 21 transcriptomes surveyed reveal two distinct ferritin genes, possibly due to an ancient duplication event. The presence of ferritin helps to explain the success of some diatom species in iron-poor waters, and our expanded understanding of which diatoms possess ferritin genes will help to predict the responses of this important group to a dynamic ocean environment.

The Kiss1 gene encodes a neurotransmitter whose expression in the brain is essential for reproduction. Previous studies with in situ hybridization and immunocytochemistry have identified Kiss1 expression in several hypothalamic nuclei, including the arcuate. To determine whether Kiss1 expression is limited to the hypothalamus, we developed a transgenic mouse that expresses a marker gene (tdTomato) if and only if Kiss1 expression is turned on. tdTomato encodes a red marker protein that is constitutively expressed, labeling the cell forever as having once expressed Kiss1. We looked for tdTomato labeling in brain sections to identify areas that reveal expression of Kiss1 at some time during development. Surprisingly, we found tdTomato labeling outside of the hypothalamus. Possible causes include Kiss1 expression early in development or low-level Kiss1 expression in adulthood. Distinguishing between these possibilities has important implications for developing tools to genetically manipulate Kiss1 neurons in adult animals. We will test the hypothesis that Kiss1 is widely expressed at low levels in the adult brain. Kiss1 transcription will be mapped in two ways. First, brain sections will be examined for the presence of green fluorescent protein (GFP). GFP is expressed under the Kiss1 promoter, but it may not mark low levels of Kiss1 transcription. Therefore, Kiss1 expression in adulthood will also be tested by in situ hybridization. In situ hybridization radioactively marks Kiss1 mRNA, illuminating even low levels of transcription. Comparing in situ hybridization between wild-type and Kiss1 knockout mice may reveal low levels of Kiss1 mRNA outside the adult hypothalamus— and open new possibilities for a physiological role of Kiss1 signaling that extends beyond reproduction.

This project’s goal is producing microporous scaffold for tissue growth. These scaffolds are made out of crosslinked 2-hydroxyethyl methacrylate (HEMA), a hydrogel. They are formed by polymerizing the HEMA around polymethyl methacrylate (PMMA) beads that are of a constrained and predetermined size. The PMMA is washed away and we’re left with a porous scaffold of precise pore size. These scaffolds are used to encourage tissue growth and reduce inflammation and the foreign body reaction. The purpose of my research is to investigate blood vessel penetration into scaffolds by producing the largest sized scaffolds I can using novel techniques. We are currently limited to tissue scaffolds of a maximum thickness of 1 mm using our current techniques. With a larger thickness, our scaffolds could be used for many more applications that are presently unavailable with a thin scaffold. Our methods are varied and include creating multiple mold designs, polymerizing techniques, and chemical washing techniques. Once I can create these larger scaffolds we will test them in vivo to evaluate the foreign body reaction as well as angiogenesis in the region. There is a large range of possible future applications for these scaffolds. They could be tuned to encourage many different types of tissue growth.

Proton radiation therapy is an emerging modality for the treatment of cancer. Clinical use of protons is growing around the world because of their favorable energy deposition patterns in tissues, but many unknowns remain in terms of the radiobiology of proton radiotherapy. Therefore, more preclinical research is needed. To this end the UWMC is developing a first-of-its kind experimental proton beam specifically designed for preclinical laboratory studies. The goal of this experiment is to compare biological endpoints of DNA damage and repair to radiation dose deposition patterns of the proton beam. As the proton beam passes through tissues it loses energy exponentially. At the end of its track it reaches very high levels of linear energy transfer, LET, i.e. – the energy deposited per unit length. We hypothesize that cells within high-LET regions of the beam are subject to more DNA damage. A549 lung cancer cells were grown to confluence in chamber slides, irradiated with protons or ¹³⁷Cs gamma rays (control), and fixed in methanol at 0, 15, 30, 60, 120, and 1440 minutes post-irradiation. DNA double-strand breaks were indirectly measured by immunohistochemical staining for γH2AX, a histone protein modified at sites of double strand breaks. The resulting biodosimetric assay will provide valuable information concerning DNA damage as a function of varying LET. Future work will extend the results to an in vivo model of mouse brain tissue with the goal of analyzing normal tissue toxicity in high-LET regions of the proton beam. This research has implications for current cancer treatment planning by, for example, avoiding proton beams directed at an organ at risk, or correcting normal tissue toxicity tolerances currently accepted by the academic community.

The distribution of temperature and precipitation on our planet (i.e. our climate), affects plant growth, animal habitats, and the livability of Earth's varied regions. In order to predict future climate we need to know about our past climate. This is important to better understand how temperature and weather conditions change when the radiative forcing (e.g. CO2 greenhouse effect) on our atmosphere increases. The best way to predict these changes is researching past radiative forcing increases and how these events impacted Earth’s climate. Some details of our past climate are discovered by analyzing polar ice and the gas bubbles trapped within. Firn is fallen snow that compacts and eventually turns into glacial ice. During this process gas can move relatively freely throughout the firn. When the firn densifies enough to block the air passageways, young gases are trapped in significantly older ice. This work is building a web-based community firn densification model that allows the user to accurately determine the difference between the age of a gas sample and the age of the ice surrounding it. Our transient model determines this delta age more accurately than current steady-state models by accounting for changing conditions as the firn turns into ice, instead of assuming conditions remain static throughout the firn evolution. This model is open-source, and written using the Python programming language, along with the NumPy library, allowing the model to be free and usable by anyone. Because the model is modular, users can easily change it to fit specific conditions or to incorporate different physical processes. Our goal is to provide a model that is simple to use, freely available, and helpful for developing a more accurate understanding of our past climate.

Nitrogen is a commonly limiting nutrient for Douglas-fir growth in commercial stands throughout the Pacific Northwest. Fertilizer nitrogen is applied to mitigate these deficiencies though some studies estimate that only about 30% of the nitrogen is actually taken up by the trees. Knowing where the rest of the nitrogen goes will help determine the best way to fertilize trees and reduce excess use of nitrogen fertilizers. This is beneficial both to stand managers looking to reduce costs associated with fertilization and to the environment as excessive fertilization can lead to increased nitrates in water. For this study, fertilizers labeled with 15N were used to track to the movement of nitrogen within a commercial Douglas-fir ecosystem. Nitrogen-15 is a stable isotope of nitrogen and is often used to trace nitrogen compounds in the environment. Three enhanced fertilizers designed to increase fertilizer N uptake by reducing volatile loss of N and one industry standard fertilizer were used on ten different commercial Douglas–fir stands throughout the Pacific Northwest. The fertilizers were applied at same rate over a period of one year. For the purpose of this study we will be looking specifically at two of the stands. Mineral soil (up to 60cm depth) and foliage samples were collected prior to fertilization to determine the background abundance levels of 15N. Following fertilization, mineral soil and foliage samples were collected at regular intervals to quantify the amount of N15 recovered over time and final sampling was conducted one year after fertilization. Mineral soil and foliage samples were prepared and analyzed for N15. To quantify the amount of N15 taken up by each component, background abundance of N15 was subtracted from the amount of N15 recovered in both the mineral soil fractions and the foliage. We anticipate that the enhanced fertilizers will increase N uptake.

Breast cancer continues to be a major threat to women’s health. For survivors, breast cancer often recurs 2 to 15 years after the initial treatment, either locally in the same or contralateral breast or at a distant recurrent site (metastasis). Currently, the performance of traditional methods, such as mammography and genetic markers, for screening breast cancer recurrence is limited, and alternative methods is strongly desired. Because of their sensitivity to biological status, metabolite markers may provide better diagnostic accuracy and earlier detection. Therefore, metabolomics, which focuses on the parallel measurement of hundreds of small molecule metabolites, has emerged as a powerful methodology for understanding biochemical systems and metabolic changes due to cancer. The Raftery group identified 11 metabolites (lactate, glutamic acid, etc.) that are useful for breast cancer recurrence detection. This model provides an earlier and more accurate approach to detect recurrence compared to the current standard, cancer antigen 27.29 (a FDA-approved blood immunoassay for breast cancer treatment monitoring). Recently, they have developed a targeted liquid chromatography mass spectrometry method (LC-MS), which enables us to simultaneously monitor changes of more than 150 metabolites in 25 different metabolic pathways (such as Glycolysis and the TCA cycle) that are of potential significance to breast cancer. In our present work we are validating their previous results and expanding this research to investigate a more comprehensive metabolic profile. Our specific task in this project is to prepare the samples and analyze them using the LC-MS platform. Using commercial serum samples from recurrent and non-recurrent breast cancer patients, we anticipate additional metabolite biomarkers that will be very valuable for developing a better diagnostic test for detecting breast cancer recurrence. In the long run, these markers should be useful for improving survival rates of breast cancer patients and thus for reducing social and financial burden. 

Lily blooming has recently been suggested to result from differential growth of the petals. The tissue expands along the edges, making them longer than the midrib. To accommodate for this excess length, the petal reverses its curvature, causing the bud to open. This is the growth driven mechanism for lily blooming. We inquired into the shape of the ripples resulting from edge growth and if we could observe direct evidence of the growth. We first investigated rippling, another consequence of edge growth. When the growth rate is high enough, lily petals ripple and their edges adopt their characteristic wavy shape. Using time-lapse imaging, we observed lily petals' edges rippling. We monitored the formation of several generations of ripples, with a fractal-like pattern of smaller waves superimposed onto larger ones. We also measured the temporal evolution of the ripples' wavelength, amplitude and arc length. We found that these quantities could be related using a geometric argument. Agreement between our prediction and observations is excellent. This indicates that in addition to biology, physics plays a significant role in determining the shape of lily petals. Second, we sought to quantify edge growth. We took quantitative measurements of the different growth rates, by tracking the positions of marks along the edge and along the midrib. We found that the growth rate is 35% larger along the edge than along the midrib, supporting the edge growth driven blooming model. We now want to measure the growth rates of different lily species, and investigate whether smaller growth rates can correlate to the absence of ripples. The purpose was to understand the 3D shape resulting from growth in a 2D sheet to supply knowledge leading to understanding plant development. It will also lead to applications in the packaging industry where flat shapes are made into 3D objects.

Barrett’s Esophagus (BE) is an inflammation of the lower esophagus. This inflammation can progress to cancer through a stage called High Grade Dysplasia (HGD). One approach to early detection of HGD is the use of light emitting “beacons “consisting of fluorescently labeled peptides targeted to HGD tissue biomarkers. Our laser based Scanning Fiber Endoscope (SFE) possesses the ability to capture live images of the esophagus during examinations and also excite and locate fluorescently tagged targets. Refining SFE fluorescence imaging for clinical use requires mathematical algorithms such as image stitching and distance compensation. Image stitching combines a series of partial views of a 3-D surface into a composite view of the entire surface. Distance compensation addresses the issue of fluorescence signal reduction as the distance between the light emitting beacon and endoscope increases. Phantoms are synthetic mimics of disease conditions used to refine and calibrate new medical devices. This research was directed toward the development of a low-cost, flexible, and durable esophagus phantom with color matching to provide a realistic model of BE. The color of inflamed BE tissue and healthy tissue were matched using quantitative combinations of commercial acrylic paints to create recipes for both tissue types. The resulting paint mixtures were applied to the interior of a latex cast cylinder mimicking the dimensions of an adult esophagus. The painted latex models were shown to a panel of gastroenterologists for approval. The end result was the development of a color realistic phantom onto which fluorescent targets could be affixed. The phantom was imaged using the SFE and demonstrates 2D stitching with distance compensation. (C. Yang, V. Hou, L. Nelson, E. Seibel. J. Biomed. Optics, Feb 2013) Future work extends similar techniques to develop brain tissue phantoms for the calibration of the SFE after integration onto the RAVEN surgical robot.

Porous membrane-based lateral flow assays have become extremely popular for their inexpensive and user-friendly diagnosis of many conditions. However, commercial lateral flow assays typically only run single-step processes that may lead to inaccurate results for low concentration analytes. Our goal is to create more sophisticated assays that can perform automated multi-step processes to achieve higher sensitivity detection. In order to achieve this goal, porous fluidic valves for the precise regulation of fluid flow in these devices are needed. We have developed a simple shut-off valve that passes a well-defined volume of fluid before permanent shut-off. These dissolvable bridges offer a way to automate the metering of reagent volumes that would otherwise require the user to pipet exact volumes into the device. We have characterized the operation of the valves and demonstrated their tunability using parameters such as geometry and composition of the dissolvable bridge. In addition, we have demonstrated the utility of dissolvable bridges in the important context of automated delivery of multiple volumes from a common source to different locations in an assay for simple device loading and activation. Dissolvable bridges have the potential to help bring advanced testing using porous membrane networks to limited-resource settings.

Heart disease and stroke are the first and third leading causes of death for men and women in the U.S. and together account for more than a third of all U.S. deaths. It has been shown there is a correlation between decreased intercellular forces in the endothelial cells in the artery and higher permeability of the arterial lining. This can lead to atherosclerosis, a disease defined by hardening of the arteries, a major underlying cause of heart attacks and strokes. The focus of this research was to determine how different blood flow rates affect the intercellular forces of the endothelial cells that line the arterial wall. The first step was to fabricate microposts. Negative molds of the posts were cast off of a master array of microposts for which the spacing, height and diameter of the microposts were known. A positive mold was then cast off of the negative mold to produce a substrate on which the cells could be cultured. Next a flow chamber was designed for these experiments. Human Pulmonary Artery Endothelial Cells (HPAECs) were then cultured and transferred onto the microposts which were stamped with fibronectin, a protein that would help the cells bind to the tips of the microposts. The stamping portion of the experiment required much trouble shooting and ultimately the experiments were halted here. If the research had continued the experiments would have run for 14 hours, after which the cells would be fixed in place, stained with a fluorescent dye and imaged using microscopy. These images would then be transferred to a custom written Matlab code that would calculate the deflection of the microposts and the forces induced by cells. This data could then be used to determine the effect of varying blood flow rates on the permeability of the arterial wall.

Recent techniques now allow us to study the developing fetal brain anatomy in 3D from the reconstruction of motion corrected sets of multiple 2D images. The use of iterative, as opposed to interpolation based, reconstruction to form a 3D image from the slice data can provide improved anatomical detail. However, the lack of strategy on deciding the regularization parameter has prevented us from getting the optimal result. Here we implemented the L-curve method, which took into account of the trade-off between the fit and the data error, on choosing the optimal regularization parameter. We reviewed the 3D reconstruction quality from clinically acquired data through the examination of tissue contrast and spatial resolution and compared the results against interpolation methods. In this study, we analyzed a series of T2-weighted MRI scans from the developing fetuses and focused on the main fetal brain sectors –cortical plate (CP), deep gray nuclei (DG), germinal matrix (GMAT), subplate and intermediate zone (SP+IZ), and ventricles (VENT). Through these evaluations, we were able to obtain the optimal iterative reconstructed images that work best with different numbers of image stacks, image resolution, image signal strength as well as presenting clear anatomical details within critical brain regions.

The mountain pine beetle (MPB) infestation in British Columbia (BC) forests ranks among the largest scale ecological disturbances recorded to date and thus presents a unique testbed for understanding forest dynamics and associated climatic feedbacks. Previous work has shown that BC MPB infestation affects the local surface energy balance, decreasing evapotranspiration and increasing surface temperature. Based on this study and related physics, we hypothesized that there may be greater cloud cover over affected areas of BC post-disturbance relative to pre-disturbance. To explore this hypothesis, we used forest inventory data together with data from the Geostationary Operational Environmental Satellite (GOES) imager to quantify the impact of the devastation on summertime cloud development. Using published calibrations, we transformed raw counts at visible and infrared wavelengths to reflectance and temperature, respectively. We then made cloud maps by applying threshold criteria to the derived reflectance and temperature. Visual inspection of the cloud maps compared to the forest mortality map suggests no obvious difference between the pre- and post-disturbance cloud scenes. Ongoing work is attempting to verify and quantify this qualitative result. Because cloud development processes can have an important influence on the local climate, our research will show whether climatic effects of this ecological disturbance could raise additional concerns about the MPB issue in BC.

The fact that hydrogen isotope deuterium/protium (D/H) ratios in algal lipids co-vary with their surrounding water D/H ratios is well established. Paleoclimatologists have taken advantage of this relationship in their compound-specific D/H analyses, but little is known about the individual environmental parameters, such as temperature, salinity, light levels, and nutrient concentrations that influence D/H fractionation, or the state of unequal isotope composition. Laboratory experiments conducted with batch cultured green algae, Eudorina unicocca and Volvox aureus, grown at temperatures of 15°C and 25°C suggest that there is increased fractionation with increased temperature. The work presented here aims to elucidate the magnitude of D/H fractionation in a natural population of algae where temperature is the primary environmental variable. To test this relationship, surface water was sampled from Lake Washington once a month for one year, with a surface temperature range from ~8°C in February to ~24°C in August. Phytoplankton were filtered from the water and lipids are extracted and analyzed by gas-chromatography isotope ratio mass spectrometry (GC-IRMS) to determine the extent of D/H fractionation. We found that there was a positive correlation between temperature and D/H fractionation, in which fractionation increased with increasing temperature. The results from this research, as well as the results of similar experiments with other environmental parameters, will give paleoclimatologists accurate modern-day calibrations to apply to the analysis of lipids extracted from sediment cores in order to reveal climatic variations for the past.

While corporations provide essential goods and services, they also create externalities with negative, sometimes lasting (e.g. climate change), impacts on stakeholders. Freeman (1984) defines a “stakeholder” as anyone who affects or is affected by a business. Since its inception, stakeholder theory has broadened to include as stakeholders other biotic entities such as ecosystems and the entire living system of earth, i.e. Gaia. Neither government regulation nor consumer purchasing selectivity can eliminate all negative externalities on the planet and society, so market-based and financial incentives are key to encouraging quicker, broader corporate actions for the greater good. This research investigates potential correlations among social responsibility performance (SP), environmental performance (EP), and financial performance (FP). The hypotheses, based on Freeman’s stakeholder theory, are: H1: Higher social responsibility performance will lead to higher financial performance. H2: Higher environmental performance will lead to higher financial performance. The sample includes publically traded corporations from around the world in multiple industries. Measures of SP and EP are derived using Global Reporting Initiative (GRI) indicators while FP is based on Generally Accepted Accounting Principles (GAAP). Data is extracted from annual financial and sustainability reports and analyzed using a variety of statistical tests. This research may contribute to the academic literature and managerial practices through revealing which environmental and social responsibility practices are most correlated with higher profitability.

Using the lens of contemporary Egyptian archaeology, this research examines how the roles of Egyptian archaeology and archaeologists have changed since George Reisner first excavated the Menkaure Valley Temple over a hundred years ago in 1910. By examining the changes in archaeological practices, and the profession of archaeology in Egypt, this study seeks to explore a new perspective on how the application of archaeology has changed within the last century. There are many different ways of excavation, and methodologies have advanced dramatically over the past century. By comparing and contrasting old archaeological practices used by George Reisner in 1910 while excavating the Menkarure Valley Temple, Ancient Egypt Research Associates (AERA) is re-excavating the same structure and using Reisner’s old work combined with new archaeological practices to develop a new understanding of the temple and its many modifications, and changes of use throughout the history of Ancient Egypt. By using myself as an archaeologist and Reisner’s work along with the research conducted by the AERA team members as the investigative perspective, I will present a story that is relatively unknown, as well as introduce a new perspective on how the methods and practice of archaeology in Egypt have evolved. The project has the following steps:1. Compare Reisner’s methods of excavation strategy, artifact analysis, dating (etc.—focus on methods) to 21st century AERA methods. 2. Discuss how contemporary archaeologists in AERA use old data collected by Reisner—problems, challenges, and solutions 3. How does all of this change the way we interpret the Menkarure Valley Temple?

Possession Sound, an estuary system located at the mouth of the Snohomish River in Everett, Washington, is home to a large group of industrial sites which greatly influence the types of runoff affecting the ecosystem. Industrial sites often output heavy metals, which can be dangerous at certain levels, as determined by the Environmental Protection Agency (EPA). Possession Sound is home to three primary industries with historical evidence of leaching copper, lead, and arsenic into the ecosystem: the Everett Naval base, the Kimberly-Clark paper mill, and American Smelting and Refining Company (ASARCO), respectively. We hypothesize that higher levels of these heavy metals will be found in areas close in proximity to the aforementioned industrial sites and combined sewer outfalls. To show these correlations we utilized Washington Department of Ecology 2009 data in conjunction with independent heavy metal sampling at two additional locations: one location offshore, near the historically influential sites and another two nautical miles westward, away from the shore. After collecting samples with a Ponar grab, they were analyzed for heavy metal concentrations through the Everett Environmental Lab per EPA approved methods. Results have shown high concentrations of heavy metals terrestrially, which has caused mandated cleanups of the area. Marine sampling demonstrates a seasonal trend. The concentrations of heavy metals are higher in the spring, correlating with a higher river discharge. Other variables that contribute to these trends include dredging of the river. Should concentrations of heavy metals in the sediments in Possession Sound reach levels deemed unsafe by the EPA, the health of the local aquatic ecosystems may be put at risk through bioaccumulation, particularly near industrial sites.

One of the current challenges in developing an effective microbicide is the ability to provide both short-term and long-lasting protection against HIV with a single application. In this project we seek to develop a nanofiber material that will be used to deliver HIV neutralizing antibodies from poly(vinyl) alcohol (PVA) nanofibers of different degree of hydrolysis to be used as a female controlled vaginal microbicide, using bovine serum albumin (BSA) as a model release protein. We hypothesize that the differences in the degree of hydrolysis of PVA will allow for controllable release of the BSA protein, because a higher degree of hydrolysis allows for a more crystalline structure, which may slow release. PVA was chosen for the nanofibers because of its quick-dissolving abilities and biocompatibility. We are using two compositions of PVA, 87-88% and 99+% degree of hydrolysis. We optimized electrospinning parameters to create PVA nanofibers with high mass yield and consistent fiber diameters that will be used to deliver the antibodies. The time to dissolution was measured by visually determining when no distinguishable fiber pieces were present when added to water at 37C. We found the time to dissolution of 87-88% degree of hydrolysis nanofibers to be approximately 15 minutes compared to greater than 3 days for the 99+% degree of hydrolysis. We incorporated 1% and 2% w/v BSA as a model protein in the PVA nanofibers. Using enzyme-linked immunosorbent assay (ELISA) we characterized the protein release of the fibers and compared the relationship between degree of hydrolysis and release patterns of the proteins. We expect that this project will provide a proof of concept for antibody encapsulating nanofibers for vaginal drug delivery.

Osteoarthritis (OA) is a degenerative joint disease present in most older individuals. The macaque, a New World monkey (genus Macaca), is an excellent proxy of the human condition in the study of the progression of osteoarthritis in humans, as the disease exhibits similar development in both. The key covariates of OA are age and body mass, but a longitudinal study of the development and severity of osteoarthritis in diet-restricted (n=259) and control monkeys (n=310) is ongoing (total data n=569) to establish whether or not diet plays a role in OA. The average development and severity of osteophytes (OST) and the level of disc space narrowing (DSN) from the thoracic and lumbar vertebrae were scored using previously-established methods. Based on averages of OST and DSN, it appears that diet-restricted monkeys do not show significantly different levels of severity from controls. Age and mass combine to explain 31% of the variation in spinal osteoarthritis (R2=.3091, p<0.001 and p<0.001, respectively for OST). Age, mass, and species explain 32% of variation in DSN (R2=.32, p<0.001, p=.001, p<0.001, respectively). Diet does not have a significant role in the development of osteophytes (p=0.16).

In 2005, Hurricane Katrina devastated the Lower Ninth Ward community of New Orleans, Louisiana. Eight years later, New Orleans has yet to fully recover from the destruction of Katrina. However, in 2012, New York advertising agency, GLU, partnered with New Orleans native Lil' Wayne and Mountain Dew to construct a community skatepark, branded the "DEWeezy Skatepark." The park is meant to act as a central hub for community members, promoting community cohesion, encouraging futher development, and providing a unique environment for youth to build character through the medium of sports. The purpose of this proposal will be to evaluate whether or not corporate and celebrity partners were successful in their efforts to bring "rebirth" to this devastated community. Both positivist logical and participatory frameworks will be considered as methods for evaluation. If research supports the DEWeezy skatepark as a success, the model could be replicated in other devastated communities as a method for development. 

Cigarette smoking is the leading cause of preventable death in the United States. The adverse health effects from tobacco use account for about one of every five deaths each year in the United States. Moreover, smokers with depressive symptoms have lower cessation rates and more difficulties while quitting than the general population of smokers. Treating smokers with depressive symptoms effectively is challenging and new smoking cessation interventions are always needed. In order to determine how recent smoking cessation treatments are benefiting smokers with depressive symptoms, the present study examines an existing web-based treatment using the innovative Acceptance and Commitment Therapy (ACT). ACT provides mindfulness-based techniques that help smokers dealing with the urges, thoughts and negative feelings associated with smoking while quitting. The study aimed to determine the users: (1) willingness to experience smoking cues, and (2) 3-months post randomization smoking status. Adult participants were recruited nationally into the double-blind randomized controlled pilot trial which compared web-based ACT for smoking cessation (webquit.org) with smokefree.gov—the national standard for web-based smoking cessation interventions. The present study will report the outcomes for smokers with depressive symptoms. Data analysis is ongoing. Based on previous research, we expect the web-based ACT intervention to be more effective than the standard treatment (smokefree.gov). This trial will provide insights for ongoing research in smoking cessation interventions to help smokers with depressive symptoms to quit smoking.

Drug resistance is a growing problem in the fights against cancer, malaria, and various bacterial and viral pathogens. Recently, strands of Mycobacterium tuberculosis in India, Iran, and Italy have been found to be resistant to nearly all effective drugs, highlighting the need for drug resistance research. The anti-malarial drug artemisinin and its derivatives have been shown to exhibit cytotoxicity and high selectivity in targeting various types of cancer. We selected a strain of MOLT-4 leukemia cells for resistance to the artemisinin derivative dihydroartemisinin (DHA). The project goals were to characterize these cells by analyzing specifics such as growth rate, genetic expression, DNA repair ability, and cell viability across various conditions. Cancer stem cells are known to be involved in drug resistance, thus we hypothesized that the resistant population would contain a higher percentage of stem cells. Techniques employed include the single cell gel electrophoresis assay (Comet Assay), suspension cell culture, and immunoglobulin assays. When applicable, cell samples were counted using a hemocytometer, and statistical tests were conducted using GraphPad Prizm software. We have currently found the resistant cells to exhibit a five times greater LD50 to DHA than the control MOLT-4 cells, a slower growth rate, and the ability to grow in media containing 12.4 μM DHA – an otherwise cytotoxic concentration. Results suggest the mechanisms of resistance include a thicker cellular membrane and improved DNA repair ability, but we have yet to determine whether cytoplasmic iron requital and DHA effusion play a part as well. We expect to find elevated levels of aldehyde dehydrogenase in resistant cells, strongly indicating the presence of stem cells. The information found will be useful for cancer and malaria drug therapy design, and will further the connection between cancer stem cells and drug resistance.

According to the American Cancer Society, pancreatic cancer has a five-year survival rate of less than 15 percent and is the fourth leading cause of death from cancer in the United States. Present-day chemotherapy treatments attempt to lengthen the lives of patients but are often unsuccessful due to the nature of the disease. Doxorubicin and Gemcitabine are already commonly prescribed as pancreatic cancer treatments while Thermodox®, a lysolipid thermally-sensitive liposome (LTSL) technology, is still undergoing clinical trials. LTSLs encapsulate Doxorubicin releasing the drug when the agent is exposed to temperatures greater than 40 degrees C. The goal of this study is to compare the in vitro cytotoxicity of four chemotherapeutic conditions: unheated Thermodox®, heated Thermodox®, Doxorubicin, and Gemcitabine. Varying concentrations of each drug condition are applied to LMP, PANC-1, and Mia-PaCa cell lines, which originate from mouse and human pancreas carcinoma. The remaining post-treatment viable cells and relevent controls are then stained with a fluorescent dye (Hoechst 33342) and analyzed by a fluorescent plate reader, from which cell death can be determined. Preliminary results show that that unheated Thermodox is not toxic to cells, and heated Thermodox®, Doxorubicin, and Gemcitabine is toxic to cells. The results of this experiment can lead to greater knowledge of the cytotoxicity of current chemotherapy agents as well as new technologies in cancer treatment.

UVC is ultraviolet light in the wavelengths 280 – 100nm. UVC’s germicidal ability has been employed to prevent forward contamination, or the contamination of a pure planetary body with terrestrial organisms. Scientists have used UVC to sterilize equipment on land and water, but the effective dose of UV needed to prevent contamination when probing a pure ice environment is still unknown. In order to safely explore pure icy environments, data of bacterial response to UVC in ice are needed. To create these data, we first irradiated Escherichia coli in water as there is a known decimation curve for this experiment, which serves to standardize our irradiation set up and techniques. After matching the decimation curve of Escherichia coli of previous UV sterilization experiments, we will then proceed to irradiate bacteria in ice. In addition to irradiating commonly tested bacteria such as Escherichia coli and Bacillus subtilus, we will also irradiate samples of glacial isolates that would be more likely contaminants in an icy environment. Each sample of bacteria will be assessed before and after radiation using the Most Probable Number technique, or MPN. The MPN method uses serial dilutions of a sample bacterial culture until no colony forming bacteria are present to determine the concentration of bacteria present in the original sample. From our irradiations, we will create curves of UV dose versus survival of bacteria that will allow future equipment used in the exploration of pure icy environments to employ the correct dosage of UVC light to minimize forward contamination.

AL 288-1, better known as Lucy, is a 3.2 million-year-old Australopithecus afarensis partial skeleton. KSD-VP-1/1 is a recently described 3.6 million-year-old hominin partial skeleton that has been assigned to A. afarensis. Recent analysis, however, indicates that the estimated lower limb length (eLLL) for KSD-VP-1/1 (0.763 – 0.791m) is substantially longer than that of AL-288-1 (0.525m). The ratio of shorter to longer eLLL for these specimens ranges from 1.44 to 1.51, which raises the question of whether or not these two are likely to belong to the same paleospecies (Australopithecus afarensis). In order to determine the probability of randomly selecting two members of the same group with an eLLL ratio ≥ 1.44, 66 primate groups were examined: 19 non-human primates, 46 modern human populations, and a combined sample that represents species-level human variation. Virtual populations of 10,000 individuals were created using the descriptive statistics of the groups because only 11 out of the 66 groups included two individuals who could generate a ratio ≥ 1.44. The virtual populations allowed for the existence of individuals that can produce the sought ratio for all groups. 1,000 sets of two individuals were drawn from each virtual population. The probability of two randomly selected individuals generating an eLLL ratio ≥ 1.44 ranges from 0 (Hylobates, Presbytis, Trachypithecus, Andaman Islanders) to 0.0076 (Macaca mulatta). If the distribution and variability of early hominin lower limb lengths is adequately represented by extant primates, these results indicate that it is unlikely that two individuals as different in their eLLL’s as KSD-VP-1/1 and AL-288-1 could have come from the same paleospecies. More work is needed, however, to understand the morphological variability of paleospecies, particularly that introduced by time.

Deficiencies of monoamine neurotransmitters including serotonin, norepinephrine, and/or dopamine have been associated with many CNS diseases including depression, schizophrenia, ADHD, autism, Parkinson’s disease, and Tourette syndrome. The intensity and duration of monoamine signaling is mainly determined by the clearance of the released transmitters through uptake1 and uptake2 transporters. The recently discovered uptake2 transporters including the plasma membrane monoamine transporter (PMAT) and organic cation tansporter3 (OCT3) have been less studied partly due to the lack of specific inhibitors. Recently, inhibition of PMAT and/or OCT3 has been proposed as a strategy for the development of antidepressant drugs with improved efficacy and faster onset of actions. The goal of this project is to characterize specific chemical inhibitors for PMAT and OCT3. Previously, 10-40 small molecule inhibitors for PMAT and OCT3 were identified from high throughput screening. We will choose two to three inhibitors for PMAT and OCT3 obtained from the initial screen and further analyze their potency, specificity and mechanism of inhibition towards PMAT and OCT3. We first will determine their inhibition potencies (IC50) towards PMAT and OCT3 using radiotracer uptake assays in cell lines stably expressing these transporters. Preliminary data showed that two compounds inhibited OCT3 with IC50 values of 1.97 ± 0.766 and 2.86 ± 0.532 µM. One compound inhibited PMAT with an IC50 value of 2.15 ± 0.537 µM. Further studies will be performed to determine the specificity and mechanism of inhibition for these inhibitors. The proposed studies may lead to novel, highly specific and potent PMAT and OCT3 inhibitors that could be further evaluated and developed in preclinical models for the treatment of depression and other monoamine-related diseases.

Different groups of smokers are commonly discussed in the research literature on tobacco use and nicotine dependence. Examples include heavy smokers, light smokers, intermittent smokers or social smokers. While forming such groupings may be scientifically useful, there are not standardized definitions for group membership, leading to a lack of clarity and comparability across studies. In tobacco research, groups are commonly formed via cutoff scores. That is, if one is below a certain score, one is in group A, otherwise one is in group B. However the lack of clear group definitions has lead to different researchers using different cutoff scores. For example, one researcher may use smoking five or fewer cigarettes a day as a cutoff to define the “light smoker” group, where another researcher may use smoking ten or fewer cigarettes a day to define the same group. A further potential weakness of the use of cutoff scores is that they enforce absolute distinctions and thereby ignore within group variability as well as measurement error. Rather than using cutoff scores to define groups, we can use statistical models, such as latent class analysis (LCA), to empirically group observations. LCA is a multivariate statistical model often used for exploratory analysis, It identifies homogeneous subgroups (or classes) in a population on the basis of item associations. The purpose of this study is to compare group differences between groups formed via cutoff scores with groups from LCA. The question of interest is if results in these analyses differ or parallel each other. Specifically, we examined the differences in the associations between group membership and relevant demographic covariates as well as measures of nicotine dependence.

The frequency of premature birth has risen to almost one in every eight births. Although most preterm infants survive, there is growing evidence of adverse neurodevelopmental outcomes due to alterations in brain structure and function. However, the relationship between morphometric changes and final neurological outcome is unknown. This project aims to locate specific structural bio-markers of delayed or decreased brain folding that correlate with decreased neurocognitive abilities, by implementing different quantifications of gyrification. Gyrification, or curvature of the brain, has been identified as a promising structural marker for neurodevelopment. Curvature measurements are heavily dependent on size of the surface which drastically increases during this brief developmental time period; therefore our framework includes normalization and ratio based measures for improved consistency. Our image analysis framework proposes a novel atlas-based automatic tissue segmentation which utilizes age-specific tissue probability maps to serve as a source of spatial priors. We propose to adapt an atlas-based segmentation technique from fetal to preterm analysis with the addition of lobe segmentations that increase the precision of segmentation and registration. This will allow for brain surface extraction by tessellation of tissue maps to reconstruct topology correct representations of the inner and outer cortical surfaces, in which our unique vertex-wise gyrification analysis will be mapped onto a population-average surface by volumetric unbiased template-free groupwise registration. Statistical modeling will be performed for each vertex to detect local and regional patterns of folding and asymmetry. This project has the opportunity to directly relate these measures of early brain folding against later measures of developmental outcomes derived from the Bayley's Scale of Infant Development (BSID) with the goal of predicting neurocognitive outcomes. Achieving this goal will allow for the possibility of earlier clinical diagnostics permitting timely neurodevelopmental interventions.

On Mars, the properties of CO₂ radiation frost formed in a CO₂ atmosphere are basically unknown, but are important to understanding the polar caps, atmosphere, and climate of Mars. The broad-band solar albedo and infrared emissivity of Martian seasonal frost deposits dominate the annual polar heat balance, which controls a significant amount of seasonal variation in atmospheric mass as well as the potential for atmospheric collapse at the extremes of Mars epochal obliquity variations. Our goal is to perform realistic laboratory simulations of the thermal and radiative environment on the surface of Mars and produce the first-ever samples of carbon dioxide frost formed the same way it does on Mars, by radiative cooling in a nearly-pure CO₂ atmosphere. To create and analyze simulated Mars CO₂ frost, we have been constructing a Radiation Frost Chamber (RFC). The outer shell of the chamber has already been constructed so my specific role in the research and development process is to help acquire, design, build, and test components to be used for measurements and experiments in the RFC; specifically, a fiberscope, a calibration cup, quartz beads, and other Martian soil analog materials. The fiberscope will be used to view and record the physical morphology and texture of the CO₂ frost. Also, its output light will help measure the broadband and spectral albedo of the frost. The quartz beads are being used for testing a theoretical model for thermal conductivity of planetary soils and the calibration cup is going to be used for testing techniques to measure ice content of soil. The base will contain the Mars analog soil at about 600 Pa of pressure of CO₂ in order to simulate the Martian environment. Once the RFC has been built it is our goal to finally simulate the Martian environment in a lab setting accurately.

The immune system has evolved to achieve a fine balance between recognizing and attacking foreign pathogens and preserving unresponsiveness to self-antigens. T cells that are unresponsive to self-antigens are called self-tolerant T cells and a hallmark of such tolerant T cells is their inability to attack cells expressing self-antigens in order to prevent autoimmunity. However, tolerance to these proteins impedes anti-tumor T cell immune responses because many cancer antigens that are targeted in immunotherapy are in fact self-antigens. Thus, a critical challenge in tumor immunology is to develop strategies that break T cell tolerance to tumor antigens without causing unacceptable autoimmune injury. It has been shown that tolerant T cells lack important proteins normally required for T cell effector functions, including two master transcription factors, Tbet and Eomes, which have been found to be critical for T cell function by repressing the expression of inhibitory molecules and mediating the expression of effector molecules. Therefore, the decreased expression of Tbet and Eomes in tolerant T cells might cause their functional unresponsiveness. Using a transgenic tumor mouse model, my research project investigates if enforced over-expression of Tbet and/or Eomes in tolerant tumor-specific T cells can re-program such tolerant T cells and restore effector functions, allowing re-programmed T cells to recognize and attack cancer cells. Tolerant T cells will be isolated from spleens of transgenic mice, retrovirally transduced in vitro to over-express Tbet and Eomes, and subsequently transferred into tumor-bearing mice. The main focus of my research will then be to analyze Tbet-, Eomes-, and/or control-transduced donor T cells for anti-tumor effector function in vivo to understand if and by what mechanism(s) T cells can be re-programmed via the over-expression of the master transcription factors and whether such re-programming could possibly become an effective strategy for the treatment of cancers in humans.

Do you worry more about getting cancer or having heat stroke? If you chose cancer, you are among the majority because cancer has a relatively higher risk perception. Risk perception describes how people emotionally and psychologically perceive hazards. It is different from risk assessment, which often analyzes risks quantitatively. Therefore, some risks may have minimal hazards but elevated risk perceptions, and vice versa. Understanding how businesses perceive climate risks is crucial to effectively approach climate change. My research aimed to determine whether businesses perceive climate change as a substantial risk to alter business behaviors. As such, I first interned at the U.S. Environmental Protection Agency to evaluate the risk perception associated with polychlorinated biphenyls (PCBs) and whether higher risk perception encourages action. I discovered that PCB contaminations in NY schools were associated with a high risk perception, which consequently pressured authorities to take proactive and remediation measures. Alongside my internship, I conducted a literature reveiw and verified that higher risk perception triggers higher chances of action. However, there are limited evidences that willingness to act may plunge when people find benefits associated with risks, entrust others to manage risks, or lack resources. In applying these findings, I conducted additional literature review to evaluate the willingness to invest by businesses for climate change, through looking at their risk perceptions. My results indicate that businesses have moderate risk perception of climate change, but low willingness to act. Most managers believe that regulators will tell them what to do, implying that they entrust the government to manage climate change. I conclude that businesses will not pay to prepare for climate change at this point in time. This implies that government must mandate businesses to change. Future studies must assess willingness of businesses to take actions as climate risks become greater.

Aging in the budding yeast Saccharomyces cerevisiae can be measured by its replicative life span, which is defined by the finite number of mitotic divisions of mother cells. The Kaeberlein lab measures the replicative life span of S. cerevisiae through the microdissection of dividing mother cells. This laborious process separates daughter cells from their mothers, which quantifies the replicative life span. We are assessing how various environmental factors affect the replicative life span of the cells. Our research project involves paraquat, a commonly used pesticide that produces reactive oxygen species within cells. This substance is normally considered to be toxic, and as expected, we have observed that the replicative lifespan of yeast is decreased in the presence of high concentrations of paraquat. However, we have also found that low concentrations of paraquat increased the replicative life span of the yeast. This observation is an example of hormesis- a phenomenon where beneficial effects are obtained at low doses of an agent that is otherwise toxic when given at higher doses. These findings are significant because a similar effect has been published with the nematode worm, Caenorhabditis elegans. C. elegans and S. cerevisiae are evolutionarily separated by approximately one billion years, suggesting that there is a conserved mechanism of life span extension influenced by paraquat. We are currently characterizing the effect of paraquat and other environmental conditions that will help us to find conserved pathways that modulate longevity.

There are currently an estimated 350 million people worldwide chronically infected with the Hepatitis B virus (HBV). These individuals, over the course of their life, are at an increased risk of developing liver cancer. While antiviral drugs can suppress HBV replication, latent HBV viruses, lying dormant but still potent in the hosts’ cells, so far have proven difficult to eradicate. Homing endonucleases (HE), enzymes that recognize long DNA sequences and induce DNA double strand breaks, could be a means to target and inactivate latent HBV. In particular, we aim to modify the recognition site of the WT I-GzeII homing endonuclease specific to the HBV genome and introduce DNA double-strand breaks. By exploiting the error prone nature of non-homologous end joining, the cellular process to repair double-strand breaks, these modified HEs will have a mutagenic effect on target sequences. Repeated HE activity will eventually cripple the replicative ability of latent viruses. To selectively modify the structure of homing endonucleases, a variant library of the I-GzeII gene is generated with randomized bases corresponding to the amino acid residues that interact with the DNA substrate. Variants that encoded for active HEs with the appropriate recognition site are selected for by In Vitro Compartmentalization (IVC). The selected variants will then be run through bacterial selection and in vitro cleavage assays to further select for structurally stable variants that function in vitro. The final step is to test the HE product on an in vitro HBV cell line. Through our research, we hope to prove that the target of I-GzeII recognition sites can be effectively altered and that latent viruses can be targeted and inactivated through mutagenesis by homing endonucleases. Hopefully, our research will be the first step to a more permanent cure for HBV infections and help to reduce incidences of liver cancer.

Stress can have a major impact on the cognitive functions of the brain in both humans and animals. One of the possible areas affected is the hippocampus, a structure known to be important in consolidation of short and long-term declarative memory and spatial memory. Previous studies have shown that stress can reduce long-term potentiation, impair spatial memory, and affect the firing rate of location-specific place cells in rats. This study aims to investigate the effects of temporary hippocampus impairment during stress on risky foraging behaviors in rats using APV, an NMDA receptor antagonist that inhibits the synaptic plasticity of local neurons at the site of injection. Rats were trained to retrieve food pellets from a simulated foraging environment and return to a safe nest, and APV infusions were then made via implanted cannulas into the rats’ hippocampus 30 min prior to stress. Foraging behavior in the presence of a robot predator was assessed in comparison to control rats infused with artificial cerebrospinal fluid. Hippocampal dysfunction is hypothesized to contribute to faulty contextual fear conditioning and memory formation, thus rats with an impaired hippocampus may exhibit excessive, contextually-inappropriate fear behavior in the presence of an artificial predator. The results of this study may help us understand the affects of stress and its role in the behaviors of individuals with post-traumatic stress disorder.

Over the past decade, measurements of hydrogen isotopes of lipid biomarkers, in particular leaf waxes, have been used to reconstruct past climate change. This method is appealing because lipids are well preserved in sediment and their hydrogen isotope ratio is primarily controlled by the hydrogen isotope ratio of their source water, which itself is controlled by factors such as precipitation amount and temperature. However, it has been shown that the isotopic difference between source water and lipids is distinctive among different plant species. In particular, it has been shown that salinity strongly affects the hydrogen isotope ratio of lipids produced by mangroves, but the mechanism that controls this relationship is unknown. Plants, including mangroves, take in water mainly from surrounding source water, but the deuterium to hydrogen ratio within the plant may be impacted by differences in transpiration rate, photosynthetic rate and respiratory water production. The photosynthetic rate (mol CO2 m-2s-1), internal carbon, (μmol CO2/ mol air) and conductance (mol H2O m-2s-1) of three species of mangrove, Rhizophora apiculata, Avicennia germinans, and Xylocarpus granatum, were measured at six different salinities from 5 to 30 ppt. The date, time, and leaf number were also recorded as additional measurements. Determining whether salinity, time of day and/or differences among species affects photosynthetic rate, internal carbon, and conductance is important in comparing the biosynthetic pathways of the three species of mangroves. It will allow us to investigate the cause of increased deuterium discrimination in mangroves at high salinity.

Paternal effect mutations provide experimental tools to identify the unique contributions that fathers provide to their offspring. We are studying the ddbt (deadbeat) gene of Drosophila melanogaster, which encodes a chromosomal protein that is incorporated into spermatid nuclei during spermatogenesis and is required for normal embryogenesis. Embryos fathered by ddbt mutant males have extensive chromosome damage and embryogenesis terminates prematurely. This study asks whether ddbt-induced damage is a consequence of improper mitotic chromosome segregation in the embryo, or if the damage is independent of chromosome segregation. To address these alternatives, ddbt males will be mated to females carrying the giant nuclei (gnu) mutation. This maternal effect mutation permits repeated rounds of DNA replication but prevents chromosome segregation in the embryo. If DNA replicates to the same extent in embryos produced by gnu mothers and ddbt fathers compared to those of control fathers, this would suggest that ddbt-induced breaks occur during chromosome segregation. The alternative is that the chromosomes of ddbt fathers have preexisting damage, in which case replication would arrest due to preexisting DNA breaks. We are examining nuclear size and morphology in experimental and control embryos using confocal microscopy and assay for chromosome damage using techniques that detect breaks in DNA. Investigation of ddbt promises to improve our understanding of the paternal contributions to embryonic development.

Ischemic preconditioning (IPC) is a neuroprotective phenomenon in which a short ischemic episode confers resistance to prolonged subsequent ischemic attacks, and is dependent upon functional Toll-Like Receptor 4 (TLR4) and possibly downstream interferon (IFN)-related signaling. Understanding this mechanism and being able to mimic it pharmaceutically may lead to better stroke therapy and treatment. In our current study, we use the optic nerve—a pure axonal tract—as our model in determining the effects of stroke in white matter. Roughly half the human brain is composed of white matter—the myelinated axons and supporting cellular milieu that connect neurons into networks. In our experimental paradigm, we induce IPC in vivo by performing common carotid artery occlusion (CCAO) and then expose ipsilateral (IPC-induced) and contralateral (control) optic nerves to ex vivo oxygen-glucose deprivation (OGD) (in order to model ischemic or “stroke” related injury). We then characterize electrophysiological properties and axonal integrity of the isolated optic nerves. In addition, we characterize glutamate receptor isoform expression and interferon stimulated gene induction. IPC-exposed optic nerves showed improved compound action potential (CAP) recovery following OGD in wild-type versus TLR4-/- mice. Using immunohistochemical techniques we show that oligodendrocytes are protected from OGD-induced death. Likewise, axonal integrity is maintained better in IPC-treated optic nerves as shown by immunohistochemistry of phosphorylated neurofilaments. Glutamate receptor (GluR) isoform variants flip and flop can exhibit different channel opening kinetics by affecting rates of receptor desensitization—possibly influencing how CAPs respond following IPC. However, our data indicated little regulation of GluR mRNA transcript isoforms. We did however observe upregulation of several interferon-stimulated genes (ISGs) following IPC in optic nerve, which may contribute to the mechanism by which IPC can mitigate the injurious effects of stroke. Studying IPC and stroke pathophysiology in the optic nerve may lead to potential therapeutics specific to white matter.

Our 800,000-year climate record is dependent primarily on data obtained from ice cores. Analyzing and dating the ice, gas, and sediment in these cores allows us to construct a remarkably accurate historical record of Earth's climate and atmosphere. However, the dating and chronology of the ice record is not as exact as we would like it to be, especially deeper in the ice. Our ability to date ice cores with accuracy depends on our understanding the evolution of glacial firn, fallen snow that gradually compacts into ice. Researchers have developed many different models of firn evolution. The aim of this project is to run these models against each other under the same boundary conditions, so that we may compare their responses and determine the strengths of each model. Participants have submitted their model output and our results have been returned to them. A second inter-comparison will be organized to address issues brought up by our initial results. These comparisons will improve future efforts in firn-modeling, ultimately leading to a better understanding of our climate record.

During the last ice age the Missoula Floods – huge cataclysmic floods caused by failure of the glacier dam that impounded Lake Missoula, a massive ephemeral meltwater lake – spilled across eastern Washington in periods of a few days. Repeated floods transformed the Eastern Washington landscape, eroding coulees and re-working the resulting sediment into extensive sand, gravel, and boulder deposits. Although widely studied, debate persists over the number and timing of the floods. Flooding is known to have spanned a period of several thousand years; this is constrained by several areas of research including radiocarbon dates, dated volcanic ashes, and examination of the interbedding of Missoula Flood deposits with those of the 18,000 yr BP Bonneville Flood on the Snake River. To further constrain the chronology of flooding, we plan to measure the cosmic ray produced isotope Beryllium-10 in granitic quartz from boulder deposits near Ephrata, and at Priest Rapids on the Columbia River. Concentrations of Be-10, accumulated since the boulders were deposited, will allow us to determine their exposure ages. So far, we have collected several samples from the Ephrata boulder fan and from the Priest Rapids deposit. We have sampled high-standing, water-polished boulders to avoid the effects of past sediment cover and post-depositional erosion, both of which can lead to erroneous age estimates. We have crushed the samples and separated quartz in preparation for Be-10 analysis. After further purification, the quartz will be dissolved for extraction and isotopic analysis of Beryllium. We expect results of this work to better constrain the relative timing of the deposits at Ephrata and Priest Rapids, and the age of the floods that produced them, the last to pass through the Grand Coulee and Sentinel Gap, respectively.  

Auxin is one of the most important plant hormones that regulates almost every developmental process during plant life cycle. Auxin response factors (ARFs), are DNA-binding transcription factors that regulate auxin-mediated transcription by activation or repression. In Arabidopsis, ARFs are encoded by a family of 28 genes, and each member is thought to play a central role in various auxin-mediated developmental processes. ARF2 has shown to be a transcriptional repressor. Nemhauser lab uses Arabidopsis seedling hypocotyl, the embryonic stem, as a model to study growth. Loss of ARF2 alters hypocotyl growth in Arabidopsis seedlings. arf2-9 is a single point mutation in DNA-binding domain that results in loss of ARF2 function. I have analyzed the hypocotyl growth in arf2-9 mutant in presence and absence of exogenously applied auxin. The results indicate that arf2-9 exhibits longer hypocotyl in comparison with wild type seedlings not only in control untreated condition but also in response to auxin application. This data suggests that ARF2 is a negative regulator of hypocotyl elongation. To investigate the mechanisms how ARF2 regulates hypocotyl growth and elongation, I have crossed arf2-9 mutant with a reporter line P_PKS4::GUS that marks actively growing hypocotyl region. I have used dCAP genotyping method for arf2-9 single point mutation and Basta resistance selection for P_PKS4::GUS transgene to isolate double homozygous arf2-9 X P_PKS4::GUS plants. My hypothesis is that long hypocotyl in arf2-9 is a consequence of indeterminate growth. Given that, my prediction is that GUS staining pattern of P_PKS4::GUS will be different in arf2-9 genetic background compared to the original line. This includes possibility of having GUS staining in different regions of hypocotyl or extended staining pattern over the time when in wild type background P_PKS4::GUS marker is no longer active. Those differences will help us understand the function of ARF2 better.

Current computers' knowledge in our 3D world is mainly based on "depth data" collected form reflection of radiations (like infared or laser). Such data give the measurement the distance between points in space and can be used to reconstruct the original environment in 3D, hence enable computers to get an idea of what our world "looks" like. The unsatisfying points would be it takes time and considerate amount of memory to get such depth data and computers don't "learn" during such process. I've been looking into an alternative way to teach computers to view our world in 3D, that is through 2D images. This is inspired by the fact that human can understand 3D world through 2D information collected by our eyes. In my research, I first train a computer to pull out geometric information in 2D images, then relate such 2D geometry to a 3D geometry data base to get 3D geometric structure. The decision making through the process is controlled by supervised learning. The goal of this reasearch is to let computers see our 3D world through normal cameras without the necessary help from extra visual aids and train them to become an intelligent helper intead of just a mere measuring tool.

Diffusion tensor imaging (DTI) has been successfully used to map 3D brain structure due to its ability to characterize water diffusion rate, anisotropy, and direction. However, DTI-based 3D fiber tracking has not yet been done in human breast. The objective of this study is to develop an approach for 3D fiber tracking of the breast ductal network. In the study, an optimized DTI pulse sequence has been determined by testing on different parameter combinations. Intra-subject reproducibility has also been characterized to assess the reliability of the DTI data and post-processing methods. Lastly, 3D fiber tracking of the breast ductal network is under development using DTI measures obtained from scanning the breast of healthy volunteers. The resulting information on 3D trajectory of breast ducts can benefit the study of the anatomy and development of the breast. It may also help detect early malignancy within the ducts because of the disruption of the ductal system.

Understanding the complex signaling pathways that lead to tumor formation is essential for developing methods the diagnosis, prognosis and treatment of cancer. As the proteins implicated in these pathways are often overexpressed or constitutively activated, the technology for detecting these proteins is necessary for this area of research. Recently, studies have suggested the importance of subcellular localization of these proteins in diagnosing cancer subtype and survival rate. However, the current analytical methods for detecting specific proteins do not provide enough spatial or quantitative information for single-molecule resolution. Quantum dots are nano-sized fluorescent crystals that can label single molecules and be more accurately quantified than fluorescent dye, which is currently used. Quantum dot labeling technology offers the high spatial and temporal resolution that is needed to study the localization of cancer-relevant proteins. We studied the correlation of the protein Akt, which has previously been suggested to preferentially localize in the nucleus or cytoplasm depending on the breast cancer subtype. We used a combination of quantum dot labeling and cellular compartment staining on a breast cancer cell line, and stimulated with insulin to activate Akt for varying amounts of time. Cells were imaged via fluorescent microscopy and the localization of proteins was conducted through MATLAB. Our results showed increased activation of Akt in the stimulated cells over non-stimulated cells, as measured with our quantum dot probe. We also showed an insulin stimulation-dependent localization of Akt. This project suggests that quantum dots can effectively label Akt in breast cancer cell lines at a high spatial and temporal resolution and offer a new platform for studying the mechanisms of cancer signaling proteins.

Because of its unique immune characteristics, the vaginal tract is highly susceptible to attacks from sexually transmitted infections (STIs) and other pathogens. Therefore, there is a need for vaccines that can be delivered directly to the vaginal mucosa and locally protect against STIs. Due to the high vascularization of the vaginal tract, free drug may traffic to other parts of the body before it has the ability to noticeably impact the mucosal immune environment. To address these challenges, we propose utilizing a vaccine encapsulating, lipid nanoparticle that is capable of storing drug, that can be retained in the vaginal tract until it directly interacts with local immune cells capable of mounting a strong local immune response. The Woodrow Lab (at the University of Washington Department of Bioengineering) has been working on developing a protocol to synthesize a stable, biocompatible lipid nanoparticle that can encapsulate a multi-component vaccine. The particles are synthesized by cross-linking together concentric polar-lipid bilayers to form stable nanoparticles. The multi-bilayer cross-linked nature of these nanoparticles increases stability and allows them to be retained within the tissue longer than simple single-bilayer particle systems. Here we show that our particles exhibit better material efficiency and have the potential to encapsulate greater levels of drug than similar lipid particle platforms. Through electron microscopy we have demonstrated that our protocol successfully produces particles with the characteristic uniform multi-bilayer morphology that we expected. We are currently working on optimizing our production process for scale-up production of the particles for larger trials. In future experiments we plan to encapsulate vaccine in the particles and use in vivo mouse models to demonstrate that our particle-vaccine system creates a more potent and longer lasting immune response than free vaccine alone. This method of vaccine delivery may prove effective at preventing several STIs including herpes and HIV.

Seabird distribution and abundance can be used as indicators of the health of the coastal ecosystem. In the Gulf of Alaska over the last four decades there has been growing evidence of climate change and ocean acidification. The largest oil spill in the United States, the Exxon Valdez, occurred here. We used data from the Coastal Observation and Seabird Survey Team (COASST), a citizen science, beached bird survey program with 14 years of surveys from beaches in the Pacific Northwest, and eight years of data from Alaska. We seek to compare U.S. Fish and Wildlife Service (USFWS) data from historical surveys in the Gulf of Alaska (1970-1989), to the current beached bird data collected through the COASST program (2005-present). Historic data include monthly surveys of sites from the Kenai Peninsula to Yakutat Bay, and one offshore island, Middleton (n>250 surveys). Current COASST data cover this same range, include additional surveys from Kodiak Island, but exclude Middleton (n>1200 surveys). These data will be analyzed to examine the differences in monthly encounter rate (carcasses/km) averaged over this region, cumulative species diversity, and oiling rate (percent of recorded carcasses that are oiled). This comparison will provide insight into possible changes in the encounter rate index in the Gulf of Alaska over the past 40 years.

Single-molecule force spectroscopy is a powerful tool for studying mechanical forces on proteins and other biological molecules. Magnetic tweezers (MT), optical tweezers, and atomic force microscopy (AFM) are specific examples of high-resolution tools that allow users to investigate how changes in the biomechanical function of a single protein, for example, can lead to larger effects in the complete organism. We have chosen to develop and implement an MT apparatus due to its unique potential to expand our current capabilities by allowing many single-molecule measurements in parallel. In this system, molecules are tethered to a glass surface and to magnetic beads, and a magnetic field is applied to pull on the beads and thus the molecules. We then used a bead-tracking algorithm to derive quantitative force measurements. We hope that multiplexing will allow for a more efficient study of how mechanical forces regulate molecular structure and function. Ultimately, this knowledge can be applied to both engineering innovative materials and designing therapeutic interventions. For example, we are using our MT to investigate how mutations in a blood clotting protein called von Willebrand factor (VWF) can lead to bleeding disorders. We intend to accomplish this by measuring how VWF’s sensitivity to forces comparable to those in the blood affect its roles in platelet binding. VWF also plays a major role in stroke and myocardial infarction, which we hope to study and quantify using our MT system.

Dopamine (DA) modulation is important in treating neurological disorders such as Parkinson's disease. Available methods fail to deliver DA into the brain due to its inability to cross the blood brain barrier (BBB). Attempts have been made to overcome this limitation, such as the development of L-DOPA. Despite its ability to cross the BBB, the pro-drug still causes many unwanted side effects. The demand for new DA delivery led to the development of my DA nanoprobe. This newly designed nanoprobe is modified to cross the BBB and can be safely uptake into the brain. The addition of a fluorophore allows for in vitro detection while the iron oxide core allows for in vivo real-time magnetic resonance (MR) imaging. The ability for the DA nanoprobe to cross the BBB and to be detected through optical/MR imaging provides new applications to many diagnostics and therapeutics of central nervous system disorder.

Asymmetric cell division creates diverse cell-types that are critical for stem-cell maintenance and tissue patterning in multicellular organisms, including ourselves. Therefore, understanding the mechanism of asymmetric divisions can have a huge impact on regenerative medicine. In plants, asymmetric divisions are important for producing proper patterns of stomata, which are microscopic valves that regulate proper exchange of carbon dioxide and oxygen while simultaneously minimizing water loss. A precursor of stomata, called a meristemoid, divides asymmetrically and renews itself, while its daughter cell, called a stomatal-lineage ground cell (SLGC), shows rapid polar expansion and loses stomatal precursor fate. How can a meristemoid create two daughter cells with contrasting characters? Lines of evidence suggests that rapid expansion of SLGC associated with polar localization of novel proteins is essential for cell fate determination. In this study, I will test this hypothesis within Arabidopsis thaliana by expressing a known regulator of cell polarity, Rho-GTPase2 (ROP2), in stomatal cell lineages. I have generated transgenic plants expressing green fluorescent protein (GFP) tagged Rho-GTPases (ROPs) driven by the stomatal-lineage specific POLAR promoter, which is short for POLAR LOCALIZATION DURING ASYMMETRIC DIVISION AND REDISTRIBUTION (POLAR) in order to view potential ROP localizations using confocal microscopy within stomatal cells. I expressed three forms of ROP2: a wild type form, a constitutively active form (CA ROP2) that always binds GTP and causes isotropic cell expansion, and a dominant negative form (DN ROP2) which always binds GDP and in inhibits cell expansion. Visualization of these ROPs may provide evidence indicating their presence is a requirement for meristemoid differentiation. Because ROPs are present in both plants and animals, this study is an important player in understanding stem cell differentiations, which may resolve the modern challenges we face with respect to regenerative medicine, world hunger, and biomechanical operations.

Defects in joint cartilage are a common pathology found in the knee. Operative management aims at alleviating symptoms and decreasing the potential of progressing to osteoarthritis. One method of repair involves the insertion of a plug of analogous cartilage tissue taken from a cadaver, called an osteochondral allograft, providing function restoration of the affected joint surface. Traditionally "fresh" grafts were used within 24-48 hours and resulted in good clinical outcomes. Currently concerns with possible disease transmission have resulted in longer delays from graft harvest until surgical implementation. Prolonged graft storage however leads to death of chondrocytes, the cells that are responsible for producing cartilage. Trehalose is a linked form of two glucoses, and is present in bacteria, plants, and invertebrate animals. These organisms drastically increase cellular concentrations of trehalose during times of cellular stress such as severe dehydration, heating, exposure to cold, or oxidative stress. Following these observations, studies were conducted that have shown trehalose to be a useful cyroprotectant in the cold storage of cells and various tissues. The purpose of this study was to determine if supplementing standard storage medium with trehalose would preserve chondrocyte cell viability after prolonged graft storage. Osteochonral plugs were taken from rabbit joints and stored in two types of medium, one supplemented with trehalose and one without. At various time points after storage (0, 14, and 24 days) plugs were taken and analyzed for markings of apoptosis (self programmed cell death) and articular cartilage integrity. Trehalose medium preserved osteochondral grafts better then the control group after prolonged cell storage. Additional research is needed to determine success of trehalose stored grafts in the clinical setting, and in trehalose's role in the storage of other tissues.

 Double electron electron resonance (DEER) and electron nuclear double resonance (ENDOR) are two variants of electron paramagnetic resonance (EPR) spectroscopy that are useful in investigating the structures of chemical species with unpaired electrons. DEER is used to measure the distances between unpaired electrons, and ENDOR is used to measure the effect that nearby nuclear spins have on unpaired electrons. EPR experiments are conducted using microwave frequencies, with the X band (~10 GHz) and Q band (~34 GHz) being commonly used. Pulsed variants of DEER require the use of a resonator with a wide resonant bandwidth in order to accomodate two microwave pulses of different frequencies and to minimize measurement deadtime, while ENDOR requires the device to accomodate a wire coil through which radio frequency signals are sent to induce nuclear transitions, posing a technical challenge. Based on previous computational work, an tunable cylindrical resonator with a resonant frequency of ~34 GHz, has been built. The goal of this work is to evaluate the efficacy of this resonator design in pulsed EPR experiments. In addition, a radio frequency coil for use with ENDOR will be computationally designed and optimized using CST Microwave Studio, an electromagnetics modeling software package. 

Past research has shown that figures of authority, media representation, emotionality, and perceived outcome of an event can all play a role in confounding eyewitness recall. The current research tested the effects of post event information and encouraging/leading statements on eyewitness event recall. Participants watched a short video clip, after which they filled out a questionnaire to assess their recall of the event. Results confirmed that leading questions and post event information confound eyewitness recall. These results have implications for both the ethical use of eyewitness questioning methods and the validity of using eyewitness testimony in the courtroom.

Possession Sound is a complex estuary system branching off of NE Puget Sound. It is home to an abundance of organisms, primarily birds and mammals, and a multitude of environmental factors which influence them constantly, including the Snohomish River, tides, and anthropogenic factors. Buoy, the station we studied, is one of four stations in Possession Sound used by Ocean Research College Academy (ORCA) students to collect data on the state of Possession Sound. Its position in the Sound, at the mouth of the Snohomish River, allowed us to analyze data that is more diversified than the information from other stations. We compared dissolved oxygen (DO) and temperature trends from past years at the Buoy station. We found that in the winter of 2012, in comparison to 2010 winter data, the range was less extreme, with DO ranging from 7.58 mg/L at 8 meters and 11.02 mg/L at sea level, while winter data from 2012 showed DO being 11.47 mg/L at 0 meters and 6.91 at 7 meters. Based on our findings at Buoy we can infer that there has been a change in the seasonal conditions affecting DO and temperature between 2010 and 2012, resulting in increasingly extreme ranges of data in the water column. This suggests that DO and temperature trends could develop wider ranges of data in the future if the factors contributing to the increase in variability of the ranges of these two parameters remain prevalent.

It is well documented that low levels of antibiotics are present in both surface water sources and in soil near industrial, large-scale farms. However, very little work has been done exploring the selective pressure for the evolution of resistance at these sub-inhibitory antibiotic concentrations. It is our concern that mutations acquired in a low antibiotic environment may be “potentiating:” that is, the presence of these first mutations opens more mutational paths after a shift to a high antibiotic environment. The converse may also be true in terms of “dooming” mutations that close off evolutionary paths in the new environment. Here we aim to investigate the prevalence of potentiating and dooming mutations and to understand their role in adaptive evolution. We study these phenomena by performing evolution experiments with Escherichia coli grown in a permissive environment (low drug concentration) followed later by a sudden shift to a new environment that imposes a strong selective pressure (high drug concentration). Here the permissive environment serves to generate mutational diversity and the harsh selective environment serves to assess the evolutionary potential of mutant isolates relative to their wild type ancestor. This will increase our knowledge of the evolution of antibiotic resistance and as well as the unintended but potentially dangerous effects of long term selection in the presence of low levels of antibiotics.

Climate change is likely to affect the altitudinal range limits of conifers in the Pacific Northwest as population performance declines at lower elevations and populations expand into upper elevations. However, it is possible that populations are locally adapted, thus influencing range shift dynamics. To assess the potential for local adaptation for three conifer species, Abies amabilis, Tsuga heterophylla, and Tsuga mertensiana, we monitored bud set and bud dormancy in seedlings collected from two to three different source elevations at Mt. Rainier National Park. Phenotypic differences in bud set and bud dormancy influence the length of the growing season, and thus, have impacts on fitness. However, source elevations from which we collected seeds differ strongly in climate, meaning that the optimal climatic triggers for bud set and dormancy are likely to differ. Observations on apical (terminal) bud formation were taken for one year in a common garden at the UW Greenhouse, to correct for environmental differences. Our study thus provides a glimpse at whether or not populations of one species in different locations on Mount Rainier are producing seeds with similar or different phenological traits when observed in the same climate. If seeds of the same species from different locations have inherent differences in the timing of key ecological events, a species may experience difficulty shifting its range when between-population interactions from different elevations become necessary because of climate. Dormancy and bud set differences at the seedling level could influence how conifer population dynamics on Mount Rainier and in other places around the Pacific Northwest will change. In preliminary analyses, we found that seedlings differ in budset and dormancy by species, and there is a trend for differences by elevation within species.

The Vera Member of the Sarmiento Formation in Southern Argentina contains the only continuous fossil record across the Eocene-Oligocene Transition (EOT) in the Southern Hemisphere. Marine records indicate that the EOT was a time of dramatic climate change; plant fossils also suggest cooler environments with a transition from subtropical to temperate forests at middle latitudes during this interval. Phytoliths from the Vera Member, however, indicate a wetter climate and relatively stable plant communities, and oxygen isotope data from tooth enamel also suggests minimal climate change across the EOT. The goal of this research project is to use clay mineralogy to examine the environment and local climate conditions in which the Vera Member was deposited, giving a context for plant and animal evolution. Common clay minerals such as montmorillonite, illite, chlorite, kaolinite, as well as cristobalite and tridymite were found to at least partially explain the x-ray diffraction (XRD) patterns produced from the Vera Member <2µm fraction. Kaolinite in particular is often formed within a much more humid environment than what conditions are currently present in Southern Argentina. If present, kaolinite would indicate that the climate may have been more humid during the EOT. Although the various clay mineral XRD data were a good match, it is difficult to ascertain exact mineral matches with the patterns that were produced. The results of this research project are inconclusive about the various climate proxies, but suggest that more detailed clay work could lead to a clearer understanding of the Vera Member and its unique geological timeline.

In the auditory system the first site of neuronal auditory processing occurs in the cochlear nucleus (CN). All vertebrates studied to date depend on afferent sensory input during a critical period of young life for the normal development of the CN. We are investigating the intercellular and intracellular signaling pathways that lead to neuronal cell death (or survival) following the elimination of sensory input to the mammalian CN using a unique mouse model for deafness. The mouse variant (DTR) has a gene that codes for diphtheria toxin (DTx) sensitivity inserted behind the promoter that controls sensory hair cells. Wildtype mice will have no response to DTx but the DTR mice will have their sensory hair cells destroyed after an injection of DTx. The mice are injected with DTx at 5 days and 30 days of age. At 2 days post injection the majority of the sensory hair cells in the cochlea are destroyed. At the appropriate survival times, 6 and 10 days, the mice will be anesthetized and perfused with paraformaldehyde. Brain tissue will be collected and stained and we will be employing several visualization techniques to quantify and characterize different cell populations in the tissue. We predict that the DTR mice receiving DTx injections will show significantly more neuronal death in the CN as compared to any of the control groups. The amount of cellular death shown will depend on the age at which the mouse received the DTx injection, with younger mice showing increased cell death and the mice of 14 days and older showing less cell death with the neuronal survival rates being dependent on the age at which they received the DTx injection. And thus we will be able to specify more exactly the critical period regarding neuronal survival in the CN of this mouse variant.

Being the main entertainment of our everyday lives, athletes are constantly judged for their performance and behaviors during the games. One key criterion of athletic performance focuses on the shift from collective to individualistic gameplay by athletes. The main drive behind this shift hasn’t been discussed due to the overall change in the society, and the adaptation of people into this new manner. One of the fields where this shift is present and more visible is sports such as basketball, which is a collective game but the players and fans aim is seem to be more individualistic. To come closer to the main stimulant of this change, I have done research in the girls and boys basketball game in the U.S. and Europe. My research was based on interviews (email, and in person), participant observation in basketball games, photo voice, and analysis of media; of basketball players, fans, and children. By comparing two different cultures, that of Kosovo in southeastern Europe and Seattle in Washington, I found some of the main factors that are driving this shift. Those factors are: racial segregation, gender, country conflicts, and globalization. I related my research to Claudia L.Kernan and Patricia M. Greenfield, who did a research in the issue of individualism and collectivism in a girl’s high school basketball game. The researcher is focused on children, and how the culture and racial segregation plays a role in their world view. Likewise, my research shows that the shift to individualism is an effect of the above mentioned factors, while the cause of these factors differs in the culture of Kosovo and Seattle.

Possession Sound is a smaller estuary within the northeast arm of Puget Sound, with influence from the Snohomish River. As a result of the watershed runoff into the Snohomish River, fecal coliform and other bacteria are present in the Possession Sound water column. We hypothesized that the most fecal coliform and other bacteria would be found at the surface and halocline (the zone of rapid increase in salinity) of the water column. The density difference would therefore trap the bacteria in or above the halocline. Low salinity surface water from the Snohomish River is the vector of fecal coliform due to warm-blooded animals. To determine the distribution of fecal coliform and other bacteria we referenced historical data from past State of Possession Sound (SOPS) cruises collected by Ocean Research College Academy (ORCA) students at the research station Buoy. The location Buoy is near the Snohomish River and therefore has a strong influence from the river discharge. We tested for fecal coliform at North Jetty (NJ) another location near the river. Using a sediment grab we collected samples of sediment and tested them for fecal as well. River discharge and watershed runoff change seasonally, affecting the depth and strength of the halocline so we categorized the data by season in order to find any correlation. The data shows during times of strong stratification, only a single fecal coliform at the surface, whereas an average of twenty other bacteria colonies were found at the surface. At the halocline there were no fecal coliform, but on average four other bacteria. In the deep layer there were no fecal coliform and on average two other bacteria found. The seasonal analysis of the same data demonstrates that fall months had the highest concentration of other bacteria and winter contained the most fecal.

Autism is a neurodevelopmental disorder, with symptoms related to social communication and repetitive behavior. In addition to these symptoms, a significant number of children with autism exhibit anxiety. One way to understand the biological underpinnings of anxiety is to measure responses of the automonic nervous system. Children with autism spectrum disorders (ASD) have shown hyper sympathetic responses to some tasks, while showing hypo sympathetic responses to others. In this study we examine two questions. The first objective of our study is to compare the behavior and skin conductance of typically developing children and children with ASD during a working memory task. Our second objective is to test whether individual differences in skin conductance within the group with ASD correlate to internalizing behaviors. Twenty-one 6 and 7 year old children with idiopathic ASD and 21 typically developing children participated. There were no group differences in age, IQ, or sex ratio. Continuous recordings of the skin conductance response (SCR) signals were collected during the digit span task for both groups of children. Internalizing behaviors were assessed via the Behavior Assessment System for Children, second edition. We expect to find higher level of SCR for the group of children with ASD, given previous reports of increased SCR among children with ASD in tasks that were cognitively or socially demanding. For the second part of the study we predict that there will be a positive correlation between the level of SCR and internalizing behaviors. Our results may illuminate what biological features correlate with these challenging internalizing behaviors. This could identify a subgroup of children with higher levels of anxiety and increase our understanding and treatment of anxiety in individuals with autism spectrum disorders.

This study used the Hamilton Search and Set Breaking tasks to assess working memory, cognitive flexibility and inhibition control of a variety of domestic dog breeds. This memory task has been tested on pigtail macaque monkeys, as well as, other species. The Hamilton Search task consisted of 4 containers which the dog was allowed to search to find a randomly placed food reward. The latency and search patterns were recorded to determine performance of the task. After 5 sessions of Hamilton Search testing, the dogs moved on to the Set Breaking protocol. Set Breaking consisted of placing the reward in the same container every trial until the dog reached criterion by searching the correct location first 5 times consecutively. The container that the food reward was placed in was determined by calculating the container which was visited the least often during the pervious Hamilton Search trials. The results from this study will be compared across species and within the species of domestic dogs. Enough dogs of very diverse breeds were tested to allow us to analyze for similarities and differences between breeds. The results showed that dogs approached this task much differently than the pigtailed macaque monkeys. Current data suggests that the dogs, not dependent on breed, are approaching this task in a very systematic manner starting a search pattern at one end and working towards the other end. With this approach, rechecking a container is very rare, demonstrating perfect memory, but in fact the dogs are using a systematic approach that is less flexible, but efficient alternative to the use of memory. Results of this study can be applied to help refine training techniques and to establish the validity of these tasks for studying canine spatial learning and memory.

Ischemic preconditioning (IPC) refers to the neuroprotective phenomenon in which a brief ischemic exposure in the brain increases resistance to injurious effects of subsequent prolonged ischemia. Ischemia is the restriction of blood to tissues. Interferons (IFNs) are cytokines released during ischemic exposure to activate the Interferon alpha receptor (IFNAR)  complex and trigger the transcription of interferon stimulated genes (ISG). ISG gene products may contribute to IPC-mediated neuroprotection. However, IFN receptors are expressed on myeloid cells as well as neural cells; the cell type-specific contribution of IFN signaling in IPC is not established. Microglia are the resident immune cells in the brain and are central in the inflammatory responses to stroke. Data from our lab strongly suggest that microglia exposed to ischemia both in vitro or in vivo demonstrate a robust expression of ISGs. We hypothesize that expression of IFNAR1 and intact IFN signaling on microglia is required for IPC mediated neuroprotection. Thus, the administration of IFNβ prior to stroke will mimic IPC in the wild type (WT) but not in myeloid cell targeted IFNAR1 (Cre/loxP) knockdown mice. We obtained IFNAR1fl/fl strains through collaboration and purchased LysM-Cre. We then used selective breeding and PCR genomic strategies to generate mice that are combined for homozygous IFNAR1fl/fl and heterozygous for LysM-Cre and wild type (WT) genes. We are also currently optimizing our method to administer IFN β using a stereotactic injection system through the lateral ventricle of the brain. We have recently confirmed the appropriate positioning of the intracerebroventicular (ICV) injection and plan to carry out ICV injection of IFN β on the WT and IFNAR1fl/fl /LysM-Cre strains. After inducing stroke, we will quantify and compare the infarct volume and neurobehavioral outcomes. This study will demonstrate the cell-type specific contribution of microglia in IFN-mediated neuroprotection. If successful, our findings can be used to develop pharmaceutical therapies for stroke and gene therapy remedies.

Planarians are one of the earliest organisms to have a primitive bilateral nervous system enabling them to sense and avoid certain light wavelengths through their photoreceptors. Additionally, planarians have the ability to regenerate completely due to stem cells that are activated after the planarian has been severed. In connection to photoreceptors, decapitation of the planarian prohibits planarians from sensing light until processes from the photoreceptors properly connect to the cephalic ganglion. This study asks if light stimulus is necessary to establish correct photoreceptor connections to the brain during regeneration, something that is seen in mammals during development. All planarians were placed in two groups: 12 hr day-12 hr night (Light/dark) cycle, 24 hr night (dark) cycle. We measured the percentage of time planarian spent in the darkest quadrant (Q4) of a shadow box (6.5cm X 3cm X 1.8cm) separated into four quadrants with the lightest being quadrant 1 (Q1) nearest the light source. Data was gathered on days 3-7 after decapitations illustrating no delay in regeneration between the two photoperiod cycles as both reached pre-cut levels on day 5 of regeneration. This suggests that light stimulus is not necessary to establish the proper connections from the photoreceptors to the cephalic ganglion and regain their functionality. The surprising un-reliance on activity-dependent regeneration may be one reason why planarians are such master regenerators.

In order to elicit an effective immunological response against diseases such as HIV, tuberculosis, and malaria, vaccines aimed at combating these diseases need to induce a potent CD8+ cytotoxic T cell response (CTL). CTL activation typically requires antigen delivery to the cytoplasm of antigen presenting cells. Current vaccine delivery vehicles generally lack the ability to elicit such responses, as they cannot efficiently mediate the delivery of antigenic payloads into the cytosol. To address this shortcoming, the Stayton lab has developed a novel micellar, pH-responsive protein-polymer carrier capable of endosomal escape that enables protein delivery to the cytosol. When the carrier is in the low pH environment of the endosomal compartments, the polymer is able to undergo a conformational change that disrupts the endosomal membrane and allows the protein to escape into the cytosol. In order to confirm endosomal escape and cytosolic delivery, this project aims to establish methods to study the intracellular trafficking of the protein-polymer conjugate in a murine dendritic cell line. The project employs two approaches: i) the conjugate’s location in either cytosolic or vesicular compartments is identified via subcellular and differential fractionation, and ii) the conjugate’s location is identified based on compartmental pH by fluorescently labeling the conjugate with pH sensitive and pH in-sensitive dyes, and imaging via live cell fluorescent microscopy. Finally, the project uses the developed methods to characterize the intracellular trafficking of a non-pH responsive and a glycosylated micellar carrier. Results from these intracellular trafficking studies will help identify potential areas for future improvements and optimization of the delivery vehicle.

Commercial fish stock populations can be linked to the health of forage fish populations. The Pacific sand lance, Ammodytes hexapterus, is an essential link between zooplankton and higher trophic levels such as birds, marine mammals, and fishes. Understanding the behavior and habitat of Pacific sand lance is key to ensuring the long-term sustainability of sand lance populations. Sand lance spend most of their time either schooling in the water column or buried beneath the substrate. We performed paired preference trials during daylight hours to compare burrowing tendencies between sediment sizes. Sediments were collected on San Juan Island and sorted using a RoTap sediment analyzer. The grain sizes chosen for the trial were medium sand (0.25 – 0.5 mm), coarse sand (0.5 – 1.0 mm), very coarse sand (1.0 – 2.0 mm), and very fine gravel (2.0 – 4.0 mm). The study was conducted on sub adults (8.5-11.5cm total length) to account for any ontogenetic variability in burrowing behavior. We found that sand lance could burrow into all of the provided substrates, but they prefer coarse sand. Observations have shown that Pacific sand lance spend the majority of the night buried under the sediment. We also conducted nocturnal preference experiments during night time hours (2300 – 0300). At night, A. hexapterus displayed no preference between coarse sand and very coarse sand, but did prefer coarse sand over medium sand. At night, when visual clues are eliminated, the preference for substrate type is relaxed. However, preference is also being evaluated by other sensory systems as there is still a notable distinction in the proportion of buried sand lance between substrates.

Standard orthopedic surgical procedures fail for reasons that are currently not understood. Joint replacements become unexpectedly stiff, well-fixed implants become loose and fusions fail to heal. These failures are costly to the patient and the healthcare system, especially if they result in substantial number of these ‘aseptic’ failures may be due to pernicious infection with relatively low virulence organisms, such as Propionibacteria, that do not stimulate the body’s usual immune response or usual clinical evidence of infection. P. acnes is aerotolerant anaerobic, slow-growing, and found in the skin’s sebaceous gland as commensal microbial flora. The Bumgarner group has sequenced a large number of P. acnes isolated from prosthetic implants. There is a strong interest in understanding the genes responsible for variation in biofilm forming capacity. My project within the Bumgarner group involves measuring biofilm production capacity across several strains of P. acnes and a related species, P. humerusii. The goal is to catalog and associate the phenotypes with the genotypes associated with pathogenic strains. This will contribute to the understanding of surgical pathology, and lead to improved aseptic practice in future operations.

GCS1 is a protein that plays a crucial role in angiosperm plant fertilization. Surprisingly, comparative studies show that GCS1-like proteins exist within a wide variety of eukaryotic species. In Drosophila, the protein Pskl is predicted to have a GCS1-like domain that affects male gametes, but its exact role in sperm formation and sperm function is not well characterized. Studying Pskl is imperative towards broadening our understanding of sexual reproduction in eukaryotes. Comparisons of Pskl to its homologs in angiosperms, algae, and protists may provide insight into mechanisms of fertilization that are evolutionarily conserved across diverse species. Furthermore, defining how the protein works could contribute to the development of reproductive therapeutics or drugs that inhibit the procreation of illness-causing organisms. The goal of this research is to understand how Pskl regulates fertility by defining its functional domains. Through gene deletions generated by imprecise excisions of a transposable element called MiMIC, analysis of both the molecular and phenotypic consequences can improve our understanding of sequences necessary for normal pskl expression. If male flies with the chromosomal derivative are sterile or have reduced fertility, then removed sequences flanking the MiMIC insertion site are likely crucial for successful fertilization. Alternatively, generated deletions may extend in either or both direction of the insertion site and impact viability, shedding light on whether pskl or its adjacent genes are essential for development. In this report, we describe the nature and consequences of the transposon excisions in pskl, both molecularly and phenotypically.

Thirty-four million people worldwide currently live with HIV-1. Despite the availability of highly-active antiretroviral therapy (HAART) which may prolong the lifespan of HIV patients, HAART does not target the latent viral reservoir in infected cells, enabling viral rebound in the absence of treatment. Introducing genetically-engineered DNA cutting enzymes (endonucleases) into HIV-infected cells may disrupt the integrated provirus. The site-specific DNA cutting activity of these endonucleases operating in conjunction with cellular error-prone DNA repair mechanisms may result in sustained damage to the integrated viral genome and prevent the virus from replicating. We are investigating 3 classes of engineered endonucleases: homing endonucleases (HEs), zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENS). While the large DNA-binding domains of these endonucleases allow for customization to a desired target sequence, delivering these enzymes to a cell (vectorization) poses a challenge. TALENS in particular require a DNA coding sequence beyond the capacity of many viral vectors. As such, a method of co-transduction must be pursued, whereby two halves of the endonuclease coding sequence are delivered by separate viral vectors and coordinately expressed in the HIV-infected cell. My project aims to determine the optimal multiplicity of infection (MOI) for co-transducing HIV-infected cells using adeno-associated virus (AAV) vectors. I have determined AAV-1 to be the optimal serotype of AAV for infecting SupT1 cells, a cell line used as a model for HIV-infected T-cells. I have constructed two sets of AAV-1 viral vectors to express either Green Fluorescent Protein (GFP) or a red fluorescent protein (mCherry) as surrogates for endonuclease genes and infected SupT1 cells with both sets of vectors at variable MOIs, using flow cytometry to determine the rate of co-transduction. Through this method, I have successfully co-transduced cells with two AAV-1 viral vectors. These results may have applications in future HIV research and clinical therapy.

Observations suggest that the intracluster medium in galaxy clusters is strongly influenced by supermassive black holes residing in cluster centers. We investigate the consequences a black hole can have on the thermodynamics of the gas in galaxy clusters by comparing the properties of a simulated galaxy cluster without black holes to X-ray observations of real clusters, which have black holes. For our data we used Python to manipulate a cosmological simulation made with ChaNGa, a code capable of simulating gravity, thermodynamics, and other things. Our cluster simulation includes gravity, hydrodynamics, gas cooling, star formation, and stellar feedback in a fully cosmological setting. However, this simulation lacks black hole formation, growth, and feedback, allowing us to pinpoint the effects of these processes on the cluster by comparing to observations. In our investigation, we found only minor differences in the density, temperature, and pressures of the gas between the observed and simulated galaxy clusters in the cluster outskirts. However, we found significant deviations between the simulation and observations near the cluster centers, where a large spike in star formation is present in the simulated cluster, not seen in the observations. Our results suggest that black hole formation and feedback in galaxy clusters most strongly affect the cluster in the central regions, where it can significantly decrease star formation by heating the gas.

The application of Magnetic Resonance Imaging (MRI) in medicine and research has seen a stable growth in magnetic field strength. It is therefore essential to determine if motion correction algorithms developed for low field MRI show comparable results for higher field MRI, by observing quantifiable parameters like signal and contrast to noise ratios (SNR and CNR). The goal of this research study is to study the variations in signal-to-noise ratio (SNR) in 3 Tesla and 1.5 Tesla fetal brain Magnetic Resonance Images for slice-intersection based motion-correction (SIMC) algorithms. The SIMC approach aligns the individual MRI slices by considering slice-to-slice matching directly and improves the final image alignment accuracy, thereby reducing motion related image artifacts. In order to perform suitable analysis, SNR is first measured in raw MRI data by evaluating the signal levels in transient tissue regions of the brain against background noise and then compared with the SNR for motion-corrected data in 3T and 1.5T fetal brains. Grey and white matter regions from adult brains are used as a reference to determine the transient tissue regions of interest. Since a higher SNR is produced for 3T in comparison to 1.5T fetal brain MRI for raw data, we expect significant increase in the SNR values for motion-corrected 3T data as well. We also expect that the SIMC method significantly improves motion-related image artifacts, while preserving the image quality for high-field data. The results from this study can help establish 3T field strength as one suitable for imaging fetal brains, due to higher signal and higher image contrast. Moreover, it can help ascertain the efficacy of the SIMC method for a range of MRI field strengths.

Mogadishu, the capital of Somalia, is overcoming over twenty years of violence, political chaos, and lack of economic growth. Now, for the first time in twenty years, with a recognized government and renewed international investment, Mogadishu has a chance to escape the cyclical patterns of poverty and hunger. However, this cannot be simply done through a top to bottom format of political changes; the political inequalities ingrained in the population need to be alleviated. The people who are most vulnerable, women, particularly young women, and minorities have to be given economic opportunities. I went to Mogadishu to find out more about the economic situation of the city, particularly, the economic situation of young women in Mogadishu through observation and conversations with this population. I visited busy market places and very small kiosks. I spoke with women who graduated from Universities and women who were illiterate about their situation and perspective of Mogadishu's economy. I found out that the Mogadishu economy is alive, changing rapidly, and there are many people who are living decent lives. However, there are many more women who are poor, illiterate or with little education, and/or come from tribes that are politically marginalized. If these women, and others in similar economic situation, are not systematically given beneficial economic opportunities, the cycle of poverty, violence, and disease will continue.

Stuttering is a high-prevalence speech disorder that often develops into a chronic, life-long problem with severe social implications. The ultimate causes are unknown, but recent studies have revealed structural and functional neural deficits that impact sensorimotor functioning, the interaction between motor control and sensory feedback. Our laboratory has shown that stuttering adults differ from nonstuttering adults in their ability to adapt to conditions with novel sensorimotor mappings. We suggest that individuals who stutter may have difficulties with the learning of stored neural representations of the mapping between motor commands and sensory consequences. We investigate whether stuttering individuals' difficulties in sensorimotor adaptation tasks are associated with (a) increased interference by competing sensorimotor mappings and/or (b) an impaired ability to generalize learned sensorimotor mappings to unpracticed movements. We used a design that allows an examination of anterograde interference (learning task B interferes with the subsequent learning of task C), retrograde interference (learning task C interferes when re-tested on task B), and generalization (adaptation transfers to an unpracticed task). In this design, groups of stuttering adults and nonstuttering adults produced monosyllabic words in different conditions of formant-shifted auditory feedback and a non-shifted control condition. Additionally, in each condition, all subjects produced 4 different words without altered auditory feedback but in the presence of masking noise. All productions were recorded for off-line acoustic analyses. We will present descriptive and inferential statistical data comparing stuttering and nonstuttering subjects with regard to retrograde interference, anterograde interference, and generalization in this speech sensorimotor adaptation task. We will present these findings in light of previous suggestions that individuals who stutter may have difficulty with the learning, updating, or activation of internal models used in the planning and execution of speech movements. The results will motivate improvements and adjustments in our current model of the sensorimotor mechanisms underlying stuttering.

Skeletal muscle myosin can use a variety of nucleotides to varying effectiveness as substrates for contraction. We previously demonstrated that complete replacement of ATP with 2 deoxy-ATP (dATP) in activation solutions increases contraction of demembranated rabbit skeletal muscle and that enhanced performance results from increased myosin binding and cycling kinetics, especially during sub-maximal calcium activation. Here we report on a transgenic mouse (Tg-RR) that overexpresses the enzyme, ribonucleotide reductase, which converts ADP to dADP, which is rapidly phosphorylated to dATP. This results in a 10-fold increase in dATP content of skeletal muscle, which still constitutes less than 2% of the adenosine triphosphate nucleotide pool. We are examining the contractile and metabolic properties of skeletal muscle in this transgenic model. Preliminary data indicates the phosphocreatine to ATP (PCr:ATP) ratio of Tg-RR mice is significantly elevated relative to wild type mice, suggesting the Tg-RR mice may have an energetic advantage due to increased high energy phosphate reserves. Furthermore, the Tg-RR mice ran for a longer period of time at increased speed and for longer distances in a graded exercise test. Direct in situ stimulation of the gastrocnemius muscle indicates improved resistance to fatigue, consistent with both the exercise and the metabolic (PCr:ATP) findings. Interestingly, our preliminary experiments suggest the Tg-RR mice produce significantly less peak force and show signs of atrophy. Ongoing experiments are examining changes in mitochondrial content and function as well as contractile properties of isolated muscles to determine the mechanisms underlying the increased fatigue resistance of the Tg-RR mice. These results suggest a new direction for developing interventions to improve exercise tolerance in human patients.

Chitin is the second most abundant polysaccharide extracted from the cuticles of insects and crustaceans. Chitin is known for its biocompatibility and superior mechanical strength. Silk fibroin is produced by the Bombyx mori silkworm and is known for its biocompatibility and superior toughness. Composites of chitin and silk fibroin would possess each biomaterial's unmatched mechanical strength and toughness, making them ideal candidates for biomedical applications requiring such mechanical properties. Here, squid pen β-chitin and Bombyx mori silkworm cocoon silk were blended in Hexafluoroisopropanol (HFIP) solution in specified ratios to synthesize the nanocomposites. As a result, chitin/silk hybrid nanocomposite thin films were produced to test the mechanical properties. Studies of both X-Ray Diffraction (XRD) and Fourier Transform-Infrared (FTIR) Spectroscopy revealed a successful effective interaction between the chitin nanofibers and the silk proteins matrix, which was most likely caused by hydrogen bonding. Results of the self-assembled chitin nanofibers embedded in the silk matrix showed a noticeable enhancement in mechanical properties. The tensile strength, flexibility, and toughness of the biomaterial nanocomposites were enhanced compared to just pure chitin or pure silk fibroin. Due to the improvement in mechanical properties, these chitin/silk engineered nanocomposites can be utilized in biomedical applications such as hybrid scaffolds for bone tissue engineering or microneedles to serve as a new methodology for drug delivery systems.

Waves carry a significant amount of energy, but this energy has not been thoroughly explored for human use. There are a myriad of different ways to harness this energy. One very promising method is through the vertical oscillation of a buoy as waves pass beneath it. The Applied Physics Lab (APL) has teamed up with Oscilla Power to test an APL buoy design paired with an Oscilla power generator. This pairing has been tested over a matter of months on Lake Washington, just off of Sand Point. The buoy itself is anchored to the bottom of the lake by three anchors, and a weight consisting of two railroad wheels hangs in the water column beneath the buoy. The Oscilla Power energy-generating device attaches mid-line above the hanging weight. There are a number of data acquisition devices onboard measuring the motion of the buoy via accelerometers, the loading on the tether, and electrical output of the Oscilla Power device. The results of this test show a relation between wave height and power output via tether loading, verifying the buoy design. Optimal power output coincides with optimal wave heights and frequencies, and the results of this test and subsequent data analysis reveal these values. This information is crucial to the design of future moorings for wave energy conversion devices. This work may be scaled up to provide power to open ocean research buoys, extending the battery life of these devices. If these tests are promising, additional uses for this energy on a larger scale could be explored.

Manganism, a movement disorder characterized by neuronal death in the basal ganglia and symptomatology similar to Parkinson’s disease, has been shown to involve manganese-mediated increase of toxic reactive oxygen species (ROS) production in mitochondria. The protein alpha-synuclein, a product of the SNCA gene, has been implicated in glial and neuronal degeneration in Parkinson’s disease, and preliminary data from our laboratory suggests that removal of alpha-synuclein from astrocytes confers some protection against ROS toxicity. Astrocytic hydrogen peroxide metabolism has been shown to produce ROS capable of damaging a variety of cellular macromolecules. The present study seeks to compare the effectiveness of toxicant attenuation in SNCA knock-out and wild type astrocytes in response to hydrogen peroxide after gradated 24-hour manganese pre-treatments. Calcium imaging with fluo-4 dye will be performed to measure astrocytic calcium by quantifying the amplitudes and durations of induced calcium waves, known to form an important mechanism of astrocytic communication, after addition of hydrogen peroxide. Based on previous studies, we predict that increased manganese dosages will correlate with elevated calcium wave amplitudes in both SNCA knock-out and control cultures. We further predict significantly lower calcium wave amplitudes in wild type cultures after each manganese treatment.

Previous research on infant auditory development has shown that infants are poor in discriminating between vowels in a background of fluctuating noise. In those studies, however, the voice speaking the vowel has always been a male voice. The question is whether infants would perform better if the voice were female. Female vowels (/i/ or /a/) are presented in a 4-Hz amplitude modulated noise. The vowel is played at 75 dB SPL and the noise is played at 60 dB SPL to the right ear. The observer-based approach is used to study 7- to -9-month-old infants’ ability to tell that a repeated vowel changed from /a/ to /i/ or from /i/ to /a/. Preliminary results indicated that compared to previous studies conducted using male vowels, infants did not show a difference in vowel discrimination based on gender. Similar performance was obtained regardless of whether male or female vowels were used. One explanation for these results is the infants are inefficient in segregating auditory streams to focus on target acoustic information. This may suggest that infants have immature listening strategies as opposed auditory processing immaturity. Future directions of the studies need to focus on auditory stream segregation and its developmental trajectory using natural, complex sounds.

Juvenile Idiopathic Arthritis (JIA) is an autoimmune disease with an unknown cause. Children experience joint inflammation, pain, fatigue and sleep disturbances. Sleep disturbances such as sleep disordered breathing and insufficient amounts of sleep may contribute to lower quality of life and poor health outcomes in JIA. In a recent study from our laboratory 40% of a sample of children with JIA showed signs of sleep disordered breathing. The aim of this study is to describe and compare sleep disturbances in JIA and age, sex matched control children, and its relation to quality of life (QoL). Forty-six children (6-to-11 years) participated in the study. Of the 46 children, 23 were diagnosed with JIA and 23 were age-matched typically developing children. Parents completed the Children’s Sleep Habits Questionnaires (CSHQ), a 45-item measure of their child’s sleep habits and quality over the previous week. Children underwent 1 night of polysomnography in the UW School of Nursing sleep laboratory, and completed the Pediatric Quality of Life (PedsQL) questionnaire, a 23-item report that assesses health-related QoL (day-to-day activities) and disease specific symptoms. The specific domains include physical, emotional, social, and school function during the month prior to completion of the questionnaire. The PedsQL 4.0 yields a total score for overall health-related QoL, physical and psychosocial function and 4 subscales: physical, emotional, social, and school function. Data will be analyzed using SPSS for Windows version 18.0 (SPSS Inc, Chicago, Ill). Data analyses will be blocked into conceptual categories and then analyzed for group differences. Findings from this study may provide new knowledge about sleep disturbances and QoL in JIA children. Missed days from school and lower QoL in JIA often are attributed to pain and fatigue, but untreated sleep disturbances and sleep disorders may be an important etiology that is unrecognized by both clinicians and parents.

Possession Sound is an estuarine system in Puget Sound’s northeast arm that is influenced by freshwater input from the Snohomish River. The Snohomish River carries sediments from upriver and deposits them in Possession Sound. Over the past three years, Ocean Research College Academy (ORCA) students have collected sediment samples at specific locations within Possession Sound that are analyzed by Everett Environmental Laboratory for concentrations of various heavy metals: mercury, zinc, copper, cadmium, lead, and arsenic. This area’s history of industrial development, including the Asarco Smelter in Everett 1900s, focused our attention on the lead and arsenic concentrations in Possession Sound. The purpose of this research is to discern any changes in concentrations of lead and arsenic observed at three stations within Possession Sound in the last three years. It was hypothesized that the station Buoy would experience greater fluctuations than the other two stations due to its proximity to the Snohomish River. The heavy metal concentrations are expected to be greater in the spring than during the other seasons because of increased river discharge from melting ice in the mountains, which results in increased stirring of benthic sediments. Dolphin 1 is a shallower location near Hat Island that is expected to have similar fluctuations that correlate with ice melt in the spring. Mukilteo is located farther south in Possession Sound, which would lead to a subtler influence from the Snohomish River, if any at all. Other factors that may impact the concentrations of lead and arsenic at Mukilteo include its proximity to the Mukilteo Ferry, a potential source of runoff containing toxins from human sources.

In natural environments, animals seeking resources face potential perils associated with foraging behavior, namely predation. Thus, animals must balance their needs with risks by utilizing adaptive behavioral strategies. One such strategy is hypothesized to be provided by the fear system through adapting foraging behavior in the presence of environmental threats. The advent of new molecular biological techniques such as Designer Receptors Exclusively Activated by Designer Drugs (DREADD) and optogenetics has provided novel approaches to investigating the amygdala’s modulating role in fear behavior. DREADDs are based on the G-protein coupled receptor pathways in which the receptors are activated by systemic injections of clozapine-N-oxide to stimulate or inhibit neurons initially and affect a host of downstream cellular signaling pathways that results in changes to cell function. Optogenetics uses receptors that immediately open in response to certain wavelengths of light to allow the passage of relevant ions in order to activate or inhibit the cells. The current project utilizes these targeted approaches to remotely activate or inhibit the basolateral amygdala and the central amygdala. The animal's ability of fear learning will be assessed using the Pavlovian fear conditioning paradigm. The effect of activating or inhibiting the amygdala in a semi-naturalistic setting will be evaluated using the Robogator paradigm. After habituation and training, rats will be placed in the chamber in which a predatory presence, known as a Robogator, will surge and snap when the animals attempt to grab a food pellet. The analyzed behavioral results in control animals and experimental DREADD and optogenetic animals can be compared to affirm the use of DREADD and optogenetic in behavioral research while providing new information as to how different groups of neurons and their connectivity in the amygdala affect fear behavior.

Does a genetic predisposition towards excessive alcohol consumption influence the acquisition of habits? The study of alcohol dependency and its effects on learning and behavior continues to be a subject of growing importance. With an animal model of alcoholism, we sought to uncover some of these potential behavioral consequences. We focused on the development of both flexible and habitual spatial behaviors in rats selectively bred for High Alcohol Drinking (HAD) and Low Alcohol Drinking (LAD). Using a standard plus-maze task, rats were trained to run to an unchanging reward arm. We hypothesized that HAD rats would rely more on response learning strategies than spatial strategies, and would develop a habit more quickly than LAD rats. Initially, visual cues were placed around the room, and two probes were conducted to assess the progress of habitual behaviors in each animal. Later, cues were removed and one last probe was conducted. Preliminary data analysis revealed some unexpected findings, the most striking of which was seen in the LAD rats’ behavior. We expected both groups of animals to form a habitual response by the end of testing, however the percentage of LAD rats using spatial strategies increased with each successive probe. HAD rats, on the other hand, did appear to increasingly rely on response strategies over time, suggesting that they may be more prone towards developing a habitual behavior under these conditions. Additionally, a large number of HAD rats consistently omitted trials and demonstrated increased latencies when compared to LAD rats, possibly indicating that receiving a reward was not enough of an incentive to run the task. These preliminary findings may suggest that genetic preferences for alcohol consumption could influence the learning strategies employed in solving simple behavioral tasks.

Knowing the sources of archaeological materials is helpful in understanding how they were acquired, that is, by trade or travel, and how these methods change over time. We analyzed magnetic susceptibility and elemental concentrations in ochre samples from four South African Middle Stone Age sites spanning 60-20 ky BP. We measured elemental concentrations on 13 geological ochre samples and 60 archaeological ochre samples using portable x-ray fluorescence spectroscopy (pXRF). Magnetic susceptibility, a sample’s ability to be magnetized, was also measured on these samples using the the Bartington MS2. These analyses will help distinguish between each sample and identify different types of ochre. Analysis of these data will determine provenance of the archaeological samples of ochre, an important step towards understanding the process by which they were procured. We show how procurement strategies varied between the four sites and over time.

Each summer, millions of Pacific salmon (Oncorhynchus spp.) leave the ocean to return to the streams and lakes where they were born several years earlier. These fish provide a rich resource of nutrients (e.g. eggs, carcasses) to a wide variety of consumers in their spawning watersheds; from insects to fishes, birds and apex consumers like the coastal brown bear (Ursus arctos). While most fish are consumed by bears in the spawning areas of streams, some proportion of the total population of fish is moved into adjacent riparian zones by the bears for later consumption. Although the importance of this subsidy is well documented, few studies have attempted to measure the population level impact of bear consumption on spawning salmon. We quantified the extent and geographic range of bear consumption and carcass movement in a small stream in Bristol Bay, Alaska by conducting daily surveys on the riparian trails used by bears and counting carcasses found there. Our surveys built upon nearly 50 years of in-stream salmon counts where the daily number of dead and alive fish, as well as the degree of consumption of each fish has been measured. We found that 31% of the total fish population was moved into riparian zones during the 2012 season. The mean distance moved was 3.68 meters and the maximum distance recorded was 30 meters. We found no significant differences in the distance moved between sexes of salmon, or in carcass consumption as a function of distance moved. The large quantity of salmon removed from the stream by bears indicates that salmon abundance estimates obtained through manual stream surveys in 2012 significantly undercounted the returning population of salmon. We suggest that riparian carcass removal be factored into future stream surveys for salmon abundance estimation, and present potential methods for further quantifying this effect.

In the spring of 2012, I traveled to Tahiti to examine the health and health seeking behaviors of the inhabitants of French Polynesia. I looked at the current healthcare system, which is modeled after the socialist French system, as well as traditional Tahitian Ra’au. I was able to compare and contrast the two different health systems by conducting interviews of both a French physician and a traditional Tahitian healer. I was also interested in learning how local Tahitians themselves view their health and their healthcare system. I especially wanted to focus on the cultural relationship between the local Tahitian patients and the foreign French physicians, and whether this relationship enriches or impoverishes the quality of health care that is delivered to Tahitians. The methodology I used for this portion of my research was participant observation and interviewing. I interviewed several Tahitians to get insight on their views of health and the healthcare system in Tahiti. My preliminary findings indicate that there is some cultural tension between doctors and patients and between traditional medicine and western medicine. However, many feel that overcoming differences is possible if a relationship is forged between the two opposing groups. This cultural difference can be problematic if healthcare providers do not respect the views of their patients because it can negatively impact the care that they provide. This research topic may also connect to healthcare in the United States, where some underrepresented minority groups in medicine may feel there is a cultural barrier between doctors and patients. I hope to use the information I have gained on cultural competency to better understand my future role in the healthcare field and to improve the care I will one day bring to patients.

Multi-Legged terrestrial biological systems demonstrate complex forms of locomotion by utilizing different gait patterns and leg motions for different environmental conditions. Typically, the footpath of biological systems consists of a smooth flat region when the foot is in contact with the ground where the forward motion of the body occurs. The following research focuses on designing a mechanical linkage-based leg mechanism to effectively mimic the step of a biological system. A simulation of the linkage was performed using MATLAB in order to analyze the dynamics of the foot path and duration of stepping phase that the foot was in contact with the ground. After analyzing the foot motion, the linkage-based leg designs were then constructed using the LEGO Mindstorms NXT robotics kit and tested with various walking patterns. Further analysis of the linkage-based leg motion was done by comparing the resulting motion to biological leg motion; successful linkage-based leg designs should display similar stepping characteristics to the biological motion.

The ZaP Flow Z-Pinch Project researches the stabilizing effects of sheared axial flow on Z-pinch plasmas. Stable plasmas are necessary to harness nuclear fusion. Nuclear fusion is an essentially limitless source of power, but the difficulty of creating long-lived plasma stability has hindered the development of controlled nuclear fusion. The ZaP experiment forms a Z-pinch plasma by ionizing hydrogen gas into plasma and dynamically forming a 100 cm long column approximately 1 cm in radius. Z-pinches are extremely susceptible to instabilities, which tend to disrupt the plasma on the order of 10-8 s. With a sheared flow, the ZaP experiment has observed a Z-pinch plasma lifetime of 10-5 s. These successful research results have led to a new experiment, ZaP-HD, the goal of which is to produce and observe high energy-density plasma pinches. This new experiment will be modeled with MACH2, a two-dimensional magnetohydrodynamic equation-based simulation code. The design that is modeled will use a similar design to the current ZaP Flow Z-Pinch experiment, however it will have significant modifications to its geometry and operating conditions. These will be reflected in the simulation by changes to the code’s input file, which consists of a matrix of points to form the geometry and parameters that determine the running conditions. Two major design changes include the addition of a third electrode and a second power supply. These modifications allow for independent control of the motion of the plasma through the two phases of the experiment. The simulation data collected will provide the team with a complex and detailed view of how this new experiment, ZaP-HD, will operate as well as any changes that need to be made to the planned design.

Sulawesi, in northern Indonesia, is strategically positioned to test competing models of modern human expansion, and trajectories of cultural change and interaction. Recent excavations in South Sulawesi have revealed a long and continuous archaeological sequence spanning most of the Holocene. We used sedimentological methods to investigate site formation and the environment of deposition at Gua Mo'o hono. These methods include the analyses of chemical and physical attributres of sediments, and particle size analysis. For determining the basic chemical  properties of the Sulewesi sediment samples, we used measurements of pH, electrical conductivity, organic carbon proportion by mass, and carbonate proportion by mass. For determining the basic physical properties of the sediment samples, we determined the color using the Munsell color chart by analyzing hue, value, chroma, viewing conditions, sample freshness, and the moisture content, as well as by measuring the magnetic susceptibility of the samples. Lastly, for dertermining particle size distribution of sediment samples, we use the pipette method and camsizer method of sediment granulometry. Our results present the environmental context to human occupation at the site. We discuss the relationship between the environmental and major cultural changes such as the introduction of ceramics at this site. The expected results are an improved understanding of the environment of site formation and the climatic conditions for humans that occupied the site.

Algae play an important role in the food chain of marine ecosystems; however environmental conditions can negatively alter their balance. A harmful algal bloom (HAB) occurs when certain types of algae grow quickly in water, often in response to changes in land use patterns which disrupt nutrient conditions. These HABs impact other organisms via introduction of natural toxins into the food chain, and are the cause of shellfish poisonings. This study focuses on mapping historical conditions of HABs, with the purpose of discovering the ecological conditions driving the current phenomenon. A protocol for diatom isolation was established for ongoing processing of core samples. One hundred diatoms per surface sampling location were identified to the species level. The main taxa present in all locations were Paralia sulcata and Thalassiosira eccentric. Purified frustules were quantified and found to have and average Shannon entropy value of 2.49. The entropy value is within the normal range, but is lower than comparable studies of Puget Sound. Quantification and identification data was assessed to determine environmental conditions at the time of deposition. Based on the ecological niches of diatoms identified the temperature range in Sequim Bay was between 10.5° and 16°C. Additional habitat conditions were determined to be: a salinity range of 31.9-34.6 PPS; a nitrate range of 1.9-2.1 µmol/L; an oxygen range of 0.57-.059 ‰; a phosphate range of 0.19-0.27 µmol/L; and a silicate bioavailability between 2.4 and 7.9 µmol/L. Further processing of core samples will allow for historical trends to be correlated to land-use patterns surround Sequim Bay.

Learning to effectively cope with stress is an important protective factor against the development of psychopathology. Developmental factors, such as the parenting environment, and immediate factors, such as self-regulation resources, have been suggested to influence individuals’ use of specific coping strategies in the face of stress. The goal of these linked studies was to understand what factors influence how people respond to stress, and particularly what factors predict using maladaptive coping strategies, such as drug and alcohol use. The first study tested how self-regulation depletion affected coping in an experimental paradigm, while the second study used an online survey to explore the links between parenting styles and coping styles. For study one, 80 college students were recruited from the Online Psychology Subject Pool (OSPP) at the University of Washington, and randomly assigned to a self-regulation depletion group or a control group. Self-regulation is a personality trait that controls decision-making, and it can be exhausted, resulting in unhealthy decisions. After the depletion task, participants completed the Trier Social Stress Test, where they were given a speech in front of confederate judges and provided with negative feedback. Following the stress task, coping was coded using behavioral observations. We hypothesized that individuals in the depletion condition will be more likely to utilize avoidant coping than those in the control condition. In study two, 400 participants from the OSPP completed an online survey on the environment of their family of origin and their coping styles. We expected that individuals from high conflict and chaotic households tend to report greater use of maladaptive coping strategies. Results of the study will attempt to provide further evidence that family factors can predict preferred coping styles. Overall, these studies will help us to better understand the risk pathways associated with psychopathology.

Tissue engineered skin is a candidate for skin therapies since detrimental wounds require replacement of both the epidermal and dermal layers. For successful replacements, it is important to mimic the skin structure consisting of two layers: a top epidermis layer with a dermis layer beneath, which is made up of keratinocytes and fibroblasts respectively. In the present study, we developed the skin graft by seeding the two types of skin cells, keratinocytes (HeCat) and fibroblasts (hFF), on opposite sides of a porous, biodegradable, and biocompatible 3D natural polymer-based scaffold. The skin graft was investigated by using Alamar Blue Assay, Histology, and SEM. The results showed that (1) the HeCat and hFF proliferated better in co-culture on the scaffold, (2) HeCat forms differentiate into 5 layers, compared with control. This infers that the 3D structure of the scaffold not only acts as a mechanically sufficient substrate for cells to grow and receive nutrients, but also creates a good environment for signaling between the two types of skin cells. These findings indicate that the integration of a natural polymer-based scaffold with co-cultured HeCat and hFF in vitro can be used for a living skin graft in vivo.

Multiculturalism has been a progressively addressed topic in psychology. While there has been a collection of empirical literatures on bicultural conflict relying on explicit measures, not much has been done to explore the topic of bicultural conflict with implicit measures. Although self-report measures, such as Bicultural Identity Integration Scale-2, are effective in measuring bicultural conflict, there are always limitations when subjects fail to report accurately. This research answers 1) whether it is possible to measure bicultural conflict implicitly, and if so, then 2) how explicit and implicit measures of bicultural conflict correlate. We took advantage of the large size of Chinese American and Chinese international student body at the University of Washington to test our theories. This research uses a balanced identity design that includes three Implicit Association Tests (IATs). The three pairs of concepts in our balanced identity design are “self” and “other,” “China” and “U.S.,” and “family” and “college life.” Our hypothesis was that a more unbalanced identity is associated with a higher level of bicultural conflict. The balanced-ness of an identity is calculated with mathematical algorithms from the three IAT scores. The level of bicultural conflict was scored based on several explicit measures—Bicultural Identity Integration Scale-2, Vancouver Index Acculturation, Multi-Item Identification, and a cultural value ranking survey. This research tests a new method to implicitly measure people’s bicultural conflict by correlating the balanced-ness of one’s identity and the level of one’s bicultural conflict. This research calls for future studies to examine the effect(s) of bicultural conflict by making correlations between people’s implicit bicultural conflict and other aspects of their lives. Since implicit measures are powerful in detecting things people are not aware about themselves, these studies are helpful in developing coping mechanisms to help foreigners and immigrants.

In the United States prostate cancer (PCa) is one of the most commonly diagnosed cancers and estimated to affect 239,000 men in 2013. Although few prognostic biomarkers are currently used in the clinical setting, biomarkers that predict the risk of disease aggressiveness leading to prostate specific antigen (PSA) failure after prostatectomy may assist clinicians in selecting adjuvant therapies following prostatectomy. In studies utilizing co-registered pre-operative imaging data with post-operative pathology data, validated prognostic biomarkers may also be highly useful as “gold standards” against which to train imaging methods to assess disease aggressiveness pre-operatively. We previously identified 33 potentially prognostic biomarkers from the analysis of multiple gene expression datasets and current literature. Using tissue microarrays containing PCa tissue from 170 prostatectomy specimens from men with detailed PSA and follow up data, we quantified immunohistochemical (IHC) staining for these markers within selective tissue sub-regions (malignant epithelium) and identified 16 of the 33 biomarkers which were associated with shorter time to PSA failure. While our aim is to use validated biomarkers to pre-operatively train in vivo imaging methods, current imaging capabilities have lower resolution than digital histology and it is unclear whether biomarker expression in total tumor areas (encompassing malignant epithelium, benign epithelium, stroma, and other tissue structures) which are resolvable by imaging methods will also be prognostic. In this study, we have re-evaluated our list of 16 strong candidate biomarkers to determine if IHC expression within total tumor areas are associated with PCa aggressiveness (PSA failure following prostatectomy) using our TMA cohort.

The San Juan Archipelago is a unique cluster of islands supporting many marine mammals including the harbor porpoise (Phocoena phocoena) and harbor seal (Phoca vitulina). Use of the San Juan Archipelago by these two species is poorly understood, hindering effective management decisions. Accordingly, I use data from transect surveys to examine the effects of bathymetry over a flooding tide on harbor porpoise and harbor seal abundance. During the fall transition of 2012 my research group and I conducted 57 strip transects, 48 of which were usable, from the south end of Griffin bay (48 ̊ 28,256’N, 122 ̊ 57,517’W) to the north end (48 ̊ 30,250’N, 122 ̊ 57,837’W). The total length of the transect was 4km and the search area was 1.6 km². Bathymetry in the area studied contains a distinct feature where the depth changes from deep (~ 165 m) to shallow (~ 70 m). This report will examines densities along transects, assigning tidal states based on the tidal curve. Plankton and salinity/temperature data were collected at the start of each transect. Marine mammal point count data were also taken on one day close to the south end of the transect. On that day, numbers of harbor porpoises and harbor seals were recorded, along with temperature and plankton data, through the flooding tide. The results of this study can be used to reduce anthropogenic effects on marine mammals by enhancing our understanding of their space through behavior and distribution. This study also will underscore the value of small temporal scale studies for examining patterns of marine mammal habitat use.

Induced Pluripotent Stem cells (iPSCs) have the capability to differentiate into beating cardiomyocytes, therefore have the potential to regenerate injured heart. Structural and metabolic maturation is important to support the increase in energetic demand during the differentiation process. These metabolic and energetic requirements of iPSCs during their differentiation into iPSCs-derived cardiomyocytes (iPSC-CM) are largely unexplored. The aim of this project is to study the changes in metabolic pathways in iPSCs during differentiation processes, using state-of-the-art, extracellular flux (XF) analyzer manufactured by Seahorse Bioscience (Massachusetts, USA). IPSCs were differentiated into cardiomyocytes in 96-well plates using directed differentiation protocol. Oxidative phosphorylation and glycolysis rates were measured in plate using XF machines on different time points of differentiation. The XF machine monitors the changes in energy producing pathways by measuring the amount of oxygen consumption and the acidification rate. Our findings showed significant difference in the energetic requirements of undifferentiated and differentiated stem cells. We found that undifferentiated iPSCs have active mitochondrial metabolism reflected by high respiratory rate. During differentiation of iPSCs, their metabolism shifts to a more glycolytic pathway. Fully matured cardiomyocytes demonstrate greater metabolic flexibility characterized by quick shift of energy production from oxidative phosphorylation to glycolysis in conditions where mitochondrial respiration is impaired. To our knowledge, this is the first study to measure the changes in energy metabolism in iPSCs during differentiation into cardiomyocytes by XF analyzer. The protocol developed in this study will provide novel platform for analyzing the energetics of other cells types during differentiation processes. The results of the study will provide an insight into metabolic processes underlying cardiomyocyte differentiation of iPSCs and might be useful for establishing metabolic targets to regulate cardiogenesis and cell maturation.

The wintering migration of marine birds in Possession Sound due to tidal influence is a complex and challenging study. Possession Sound provides habitat for the Pacific Flyway migration of marine birds, and the dynamic estuarine environment influences distribution of these birds due to tidal variation. The working hypothesis of this study was that birds were more active feeding during high tides in the morning hours. The data collected for this study was done by land surveys and small vessel trips along transects on North Jetty Island near the Port of Everett. The species of interest included Bald Eagles, Buffleheads, Common Loons, Double Crested Cormorants, Northern Pintails, and Pigeon Guillemots. The status of recovery from the Washington Department of Fish and Wildlife was compared to data collected. Preliminary data suggests that high tides influence the sandy substrate in Possession Sound, which provides optimum feeding grounds for Buffleheads, Northern Pintails, and Pigeon Guillemots as they have been observed more frequently.

Heart disease has been the leading cause of death in the United States for nearly 100 years. The term heart disease covers a wide variety of cardiovascular complications but myocardial infarctions (MI) occur most frequently with nearly 1 million Americans projected to have a heart attack every year. The heart undergoes MI when the myocardial cells are starved of oxygen and permanently die. The process results in scarred tissue, which may induce arrhythmias and heart failure. Currently, there is no available therapy to restore the scarred tissue function. Vascularized heart tissue has the potential to replace the infarcted region to help restore normal heart function. There is a need for vasculature that can withstand physiological conditions with a perfusion system. Here, I will generate a collagen-based microvessel network by using sodium alginate as a sacrificial template. Sodium alginate is a hydrogel synthesized from alginic acid (C₆H₈O₆) and calcium chloride (CaCl₂). This gel is unique in the fact that it can be reversibly cross-linked or dissolved by ionic solutions. This property of alginate has proved useful to generate 3D features in collagen-like hydrogels. Sodium alginate constructs of varying sizes of microvasculature will be created from existing molds. These constructs will then be placed in collagen and dissolved by EDTA to generate cylindrical networks. The morphology and long-term stability of the microvessel will be characterized. Afterward, endothelial cells will be seeded into the network to form a 3D microvessel system. In addition to these microvessel systems, a macroscopic vessel will be created with sodium alginate and collagen to serve as the surgical junction tube between this system and in vivo vasculature. The goal of this research is to produce viable 3D microvessel systems in a collagen matrix as infrastructures for building implantable thick cardiac tissues.

Pareiasaurs were a group of herbivorous reptiles that lived during the Middle to Late Permian (~265–252 mya) in what is modern day Europe, Asia, and Africa. Fieldwork in the Moradi Formation of Niger has produced three scapulocoracoids of the pareiasaur Bunostegos akokanensis, two of which were identified to taxon by associated skull material, with the third not found in association with a skull. The considerable size disparity and slight morphological variation among the scapulocoracoids suggest that they are from different ontogenetic stages ranging from juvenile to adult. This variation permits the first description of ontogenetic change in the scapulocoracoid in pareiasaurs. An increase in overall size is associated with morphological change in each region of the scapulocoracoid, including the expansion of the anterior coracoid, the reduction of the posterior coracoid, increased robustness of the scapula, increased depth of the glenoid fossa, and a higher angle of the acromion process. To analyze these trends, precise measurements were taken from important physical landmarks in order to quantify ontogenetic shape change. Following a description of the morphology and ontogeny, an analysis of phylogenetic relationships will be conducted based on morphological characters, comparing Bunostegos to other pareiasaurs and their closest relatives. This research will further understanding of ontogenetic change in pareiasaurs, but more importantly, it will form the basis for further hypotheses regarding function, locomotion, and ecology in this important group of Permian reptiles.

In the Puget Sound marine ecosystem, a large estuary complex located in the Pacific Northwest, plankton species are impacted by both seasonal variations and water chemistry. Salinity and pH data are collected monthly by Ocean Research College Academy (ORCA) students during State of Possession Sound (SOPS) trips, near the urban center of Everett and the Snohomish River delta. We studied salinity and pH data in parallel to plankton samples collected in a vertical tow by a 20µ plankton net. By collecting these data at different stations within the Possession Sound subsystem, we are able to compare varied salinity and pH data to account for spatial differences, in tangent with the collected plankton samples. We focused on Coscinodiscus spp.,  Pseudo-nitzschia spp.,  and adult Copepoda spp., for our plankton species, as they were typically the largest populations in every cruise. The data we collected showed that plankton were most numerous within water of a pH between 6.3-6.7 and a salinity of 28ppt-31ppt. Samples collected that strayed from the 6.3-6.7 pH range or went above or below 26-31ppt had either no, or significantly fewer amounts of plankton.

Nearly half of the US population is living with a chronic disease. A chronic disease is a prolonged illness that cannot be spontaneously resolved and can rarely be cured completely. Chronically ill patients feel more resentful, isolated, and prone to depression, stress, and anxiety; known factors which diminish a patient’s health. Studies indicate that support groups help patients to alleviate stress, depression, and cope with their illnesses. Currently there are many online support groups that help connect fellow patients of a chronic disease with each other while medical tools like WebMD help connect patients to an expert (not necessarily the patient’s own doctor). Triage is a system we are designing to bring together these connection mediums and provide chronic disease patients with a communication hub where they can connect with fellow patients, their own doctors, and researchers. Patients can share with fellow patients their personal journeys through the chronic disease, become friends with them, form groups, and view top posts from other patients. Patient to doctor communication will entail quick questions to the patient’s doctor, and short messages to the doctor that could easily answered without an appointment. Patients can also interact with researchers of their particular chronic disease who are looking for participants for their studies, can participate in studies, and get updates about new research in the field. Multiple usability tests will be conducted involving doctors, patients and researchers to evaluate and improve the overall design of the Triage project.

Aging is a process characterized by the degeneration of bodily components and functions. Scientists are limited in their ability to study this process in humans, in part because a human lifespan is too long to conveniently study. Instead, model organisms are studied extensively in the hope that discoveries made will be applicable to another organism of interest. Model organisms are usually short-lived, easy to manipulate, and easy to handle. One of the best examples of a model organism is the budding yeast Saccharomyces cerevisiae. S. cerevisiae lifespans are easy to measure and reproduce, and since they have a short lifespan we can study a large amount at one time. Aging in Saccharomyces can be measured in two different ways. A yeast cell can be kept in a non-dividing, nutrient limited environment and tested to see if it can successfully re-enter the cell cycle, when it cannot, its lifespan has ended. This method is used to measure the chronological lifespan, and the model can be applied to human cells that are no longer replicating (post-mitotic cells). There is another model we can use to understand a different aging process, called the replicative lifespan. The replicative lifespan refers to the number of times a mother cell can divide to produce daughter cells, and is a much better representation of cells that are still dividing (mitotically active cells) in other organisms. As undergraduates, we help study this process by physcially separating daughter cells from the mothers using fiberoptic needles (dissecting) and counting them at regular intervals. When the mother cell no longer produces daughter cells, the replicative lifespan has ended. The data collected can be compared to past and expected results in order to help us gauge how well the cells are dividing. By manipulating the environment that each cell line is grown in, we can gain insight towards specific drugs and conditions that mother cells divide best in, and apply this to other mitotically active cells in other organisms. Both measurements of lifespan can be manipulated in similar ways, and many labs have started to establish a bank of genes and environmental factors that can be manipulated in order to change the outcomes.

The discovery of 2003 VB12, or “Sedna”, far beyond Pluto has suggested a new class of Solar System objects. These objects are not members of the Kuiper belt, a large disk of icy objects spanning roughly 30 AU to 50 AU from the sun; nor do they reach far enough to be considered members of the Classical Oort Cloud, which is comprised of Long Period Comets (LPCs) and distant objects that may take millions of years to orbit the sun. Both of these groups and this new class of objects are likely debris from the planets’ formation, making them surviving “fossils” from the Solar System’s early history that can be directly examined. Despite the great numbers of this population, however, the vast majority is undetectably dim, a problem that observers hope to address by peering deeper than ever with the upcoming Large Synoptic Survey Telescope (LSST). Sedna-class objects may be unique in that they provide clues about the Solar System’s interaction with the Galaxy over its history. Because they orbit beyond the boundaries of planetary perturbations, they could have resulted from the sun’s migration close to the galactic center. I, along with Alexia Lewis, ran simulations of the Solar System’s formation with this migration model. I then analyzed them alongside “static” model simulations, which could be compared to past survey data and be used to predict the numbers of comets and Sedna-like objects that will be seen by the LSST. Later verification by the LSST will constrain models of the inner Oort cloud (where LPCs are expected to be abundant) and the region of Sedna-like objects, provide exciting new clues toward our models of how the Solar System was formed, and whether it has migrated from the center of the Galaxy over its history.

What are the barriers to fitness for Marshallese women living in the U.S.? Marshallese populations suffer from especially high rates of cancer and Type 2 Diabetes. It is common knowledge that exercise and overall fitness contributes to better health. I have explored the barriers through various research methods, including: Participant-observation, focus groups and field notes. This work is important for the long-term health of the community. Through research into discovering the barriers to fitness for Marshallese women I am helping the community to work towards breaking down some of those barriers and empowering  these women to take control of their fitness and their overall health. It is my intent to have a positive ongoing impact on the Marshallese women’s fitness level not just for current members of the community but also for future generations. Women that learn fitness skills now will be able to pass on those skills to the next generation of women.

Borderline personality disorder (BPD) and alcohol use disorders (AUDs) frequently co-occur and are each associated with an increased risk of suicide. However, little research has been conducted comparing individuals with comorbid BPD and AUDs to individuals with BPD only. The present study sought to determine whether individuals with comorbid BPD and AUDs exhibit more non-suicidal self-injury (NSSI), suicidal behaviors, and emotion dysregulation than individuals with BPD and no history of AUDs. Data from previously conducted research studies were analyzed via multivariate analysis of variance (MANOVA). It was expected that the group with comorbid BPD and AUDs would more frequently engage in NSSI and suicidal behaviors, and would have more emotion dysregulation, on average, than the group with BPD and no AUDs. The results of this study have implications for the treatment of individuals with comorbid BPD and AUDs. In addition, results may provide evidence for increasing AUD prevention efforts among those with BPD in order to improve the likelihood of positive future outcomes for these individuals.

Even though many women engage in subsistence activities that require movement in varied terrains, little is known about the effects of burden and gradient on the energy expenditure of women. Additionally, it remains unclear which anthropometric characteristics predict variability among women in these situations. To begin to understand this better, 10 women walked on a treadmill for 14 randomized trials, divided into 2 or 3 testing sessions. Each trial consisted of different combinations of three variables. The women walked at self-selected slow, medium, and fast velocities; at gradients of 0, 5%, and 10%; and with and without a 10 kg burden carried in a backpack. Walking trials lasted 5 minutes, with 4 minutes of resting between each trial. VO₂ and VCO₂ were accessed (using a Sensormedics Vmax 29c metabolic cart) and cadence was determined during each trial. Standard anthropometrics (such as body mass, stature, limb segment lengths) were measured. Cost of transport (CoT) was calculated as the average VO₂ of the last 2 minutes of the 5-minute trial divided by velocity. Gradient (p<0.001), burden (p=0.004), mass (p<0.001), and burden/mass (0.019) were positively correlated with CoT (r²=0.71), while cadence (p<0.001) was negatively correlated. Our analysis shows that these variables predict variability within individuals (r²=0.72) better than among individuals (r²=0.64). Stature (p=0.52) and lower limb length (p=0.28) were not predictive. Future work should investigate how additional anthropometric measurements (such as crural index) interact with gait and terrain characteristics (burden, gradient, etc).

 The Washington State TF-CBT and CBT+ Initiative offers training in Cognitive Behavioral Therapy (CBT) for clinicians working in public mental health across Washington State. While CBT has been shown in previous studies to be an effective therapy for anxiety, depression, behavior problems, and Post-Traumatic Stress Disorder, its use is limited in public mental health because of the lack of available training. The purpose of the study is to examine whether clinician orientation affects clinician learning of CBT for anxiety, depression, behavior problems, and PTSD. Our first hypothesis is that clinicians with a cognitive behavioral orientation will have a higher skill level before training in comparison to clinician of other orientations. The second hypothesis is that clinicians of other orientations will have a higher skill level after the training than those clinicians with a cognitive behavioral orientation due to a higher rate of improvement. Clinician self-reported efficacy in elements of CBT for anxiety, depression, behavior problems, and PTSD, was assessed before the three-day training, after training, and after 6 months of bi-weekly phone consultations with a CBT expert, and will be compared for each theoretical orientation. The participating clinicians in this study vary in theoretical orientation, including integrative/eclectic, biological, interpersonal, cognitive behavioral, psychodynamic/analytic, systems, humanistic/existential and others. We plan to integrate the results of the study implications for future clinician training of CBT. If our hypotheses are supported, it will suggest that clinicians with a cognitive behavioral orientation may need specialized training in CBT that takes into account their previous knowledge and offers more advanced training options for those with past experience in CBT.

Approximately 30% of patients who receive standard therapy for Acute Myeloid Leukemia survive the treatment, but do not enter complete remission. These patients are classified as resistant to the first course, and it must be decided if they should receive a second course of standard therapy or switch to a new therapy in a clinical trial. The complete remission rate produced by a clinical trial is by definition unknown, so the probability of a patient achieving a complete remission with a second course of standard therapy must be used. In this study, we aim to determine which factors can be used by physicians to predict if a patient will enter complete remission with a second course of standard therapy. Medical records from three separate clinical trials conducted by the Southwest Oncology Group were analyzed to find patients who received two courses of standard therapy. Specific information such as blast percentage and marrow cellularity before and after treatment was then recorded. A multivariate analysis of this data will be performed to determine which factors can predict response to the second course of standard therapy. This information has the potential to be used in making the decision to treat patients with a second course of standard therapy or to switch to a new therapy in a clinical trial.

Essentially all growth and developmental processes in plants require action of the hormone auxin. Auxin regulates gene expression by mediating the degradation of repressor proteins called IAAs. A subset of IAA proteins are involved in the initiation of new lateral roots, which are important for overall root architecture and function. Members of the Nemhauser lab have shown that proteins within this subset from Arabidopsis thaliana have varying auxin-induced degradation rates, using degradation assays in a heterologous yeast system. I hypothesize that differences observed between the degradation rates of the IAAs contribute to the specificity and diversity of auxin responses. When one of these lateral-root expressed IAA genes, IAA28, is mutated so that it is completely unable to be degraded, the plant does not form lateral roots. I predict that small changes to the degradation rate of IAA28 will lead to differences in plant phenotype, specifically the developmental stages and numbers of lateral roots that develop, as is suggested by preliminary data from work with IAA14. Currently, I am engineering and testing modified versions of IAA28 with the goal of obtaining a range of degradation rates. It is difficult using plant-based system to measure the degradation rates of modified IAA28 proteins due to feedback and the inability to control auxin. To test the degradation rates of modified versions of IAA28, I am expressing them in the yeast, Saccharomyces cerevisiae. Once I have obtained a cohort of modified IAA28 proteins that display a range of degradation rates, I will transform these proteins into plants. I predict that my observations of plant phenotypes will allow me to determine whether the precision of IAA28 degradation rates matters. The results of my research may partially explain the importance of the differences between IAA degradation rates in determining specificity of auxin response phenotypes in the plant.

During the postembryonic transformation from larva to adult, zebrafish undergo a dramatic metamorphosis in pigment pattern. New pigment cells differentiate, interact, and migrate to form stripes of black cells (melanophores) and the interstripe regions of yellow cells (xanthophores); this pigment pattern characterizes adult zebrafish. My project investigates the roles of thyroid hormone (TH) in this dramatic transformation. We have produced a stable transgenic line expressing a transgene for nitroreductase exclusively in the thyroid gland. When I expose these transgenic fish to the drug metronidazole, toxic byproducts are produced in the thyroid gland, causing cell death and ablating the gland and preventing the fish from producing any TH. Using these thyroid ablated fish, I have characterized pigment cell differentiation and pattern formation in the absence of TH. I find that these thyroid ablated individuals do not develop xanthophores and show resulting disruptions in stripe boundary formation. Our lab has also found a zebrafish pigment mutant (opallus), which produces an excess of xanthophores. Mapping data from this mutant leads us to hypothesize that the phenotype is caused by a gain-of-function mutation in the receptor that stimulates TH production in the thyroid gland. I test the prediction that the excess xanthophore phenotype is caused by overproduction of TH by blocking TH synthesis using the drug methimazole, and show that these treatments rescue the opallus pigment phenotype, returning them to a wild-type pigment pattern. Moreover, I test the prediction that exposing wild-type zebrafish to exogenous TH produces an opallus-like pigment pattern. Thus, by quantifying the number of melanophores and xanthophores and their distribution across the flank in these hypothyroid and hyperthyroid backgrounds, I show that TH is both necessary and sufficient for xanthophore differentiation, and that both too much and too little thyroid hormone during the adult transformation grossly disrupts the formation of adult stripes.

Energy-harvesting electrochromic windows are windows that combine electrochromic windows, which change color when a voltage is applied, with dye-sensitized solar cells to harvest solar energy. These can be placed in buildings and used to reduce the amount of air-condition costs by blocking sunlight in the dark state and providing a self-sufficient renewable energy source. Dye-sensitized solar cells with dyes that may be used for color-switching applications are being tested and compared to other types of dye. The solar cells must have a high efficiency in order to be practical for energy-harvesting applications and work with an electrolyte that can be used for electro-chromic applications. Different methods of fabrication and different dyes and electrolytes were tested. The goal is to compare different types of dyes with different combinations of electrolytes to optimize the properties and performance. Solar cells were fabricated using a platinum counter electrode, varying working electrodes and different electrolytes. Working electrodes were fabricated by screen printing titanium dioxide. These were soaked in different types of dye. The cells with these different combinations were measured for efficiency. One type of dye that has some electro-chromic properties yielded fairly high conversion efficiencies with a relevant electrolyte. Different combinations are being tested in order to find one with ideal electrochromic properties that yields high efficiencies.

Pollination syndromes refer to suites of floral traits that influence biotic or abiotic vectors transporting pollen from one flower to another. These traits include flower color, position, shape, size, scent and reward. Scent is a major component of pollination, as the volatile organic compounds (VOCs) that compose “scent” often attract pollinators or deter predators. The genus Thalictrum in the Ranunculaceae (buttercup family) possesses both insect- and wind-pollinated species, enabling comparisons of the role of scent in floral diversification among recently diverged taxa with distinct pollination syndromes. To characterize floral scent, we identified and compared the bouquet of VOCs emitted by insect- and wind-pollination species, as well as by floral vs. vegetative tissue. Focusing on twelve species representative of the two pollination syndromes and spanning the Thalictrum phylogeny, we identified 8 primary compounds of interest. These compounds are known to be chemical communicators for various insects, including bees and syrphid flies, reported to visit Thalictrum. The overall purpose of this project is to determine the differences in scent emissions between species in an evolutionary context, and identify the key volatiles involved in pollination syndrome variation. This will further illuminate our understanding of the biochemical and, ultimately, the genetic basis of these starkly different pollination syndromes. In addition, the variation in distribution of VOCs across species will also be used to test implications of patterns of compound development and reuse during evolution.

As Seattle's light rail system expands, one branch is being designed to cross the I-90 floating bridge in order to connect downtown to Redmond. The challenges associated with designing a rail system over a floating bridge are significant. Traditional train rail systems are not built to accommodate the wide range of movements undergone by a floating bridge but Parsons Brinckerhoff have designed a new kind of rail called CESURA that will allow this new branch of Link light rail to exist. I have been helping to construct and test a full-scale replica of part of the CESURA system and my personal research has focused on the specific stiffnesses of the rubber fasteners which hold the rails to the rest of the system. These stiffnesses are very difficult to determine without a specialized test to isolate their properties. A hydraulic actuator was used to provide loads that would either rotate or linearly translate a rail that was secured by a single fastener. Various instruments were calibrated and placed throughout the system in order to monitor the fastener's behavior in response to different loadings. The newly discovered fastener properties will improve computer models of CESURA and allow Parsons Brinckerhoff to more accurately understand how the entire system behaves. Armed with this new knowledge Parsons Brinckerhoff will be better prepared for their next test in Pueblo, CO with an actual Link light rail train running over the full CESURA system.

Estrogen has been shown to directly influence auditory function, with high levels of estrogen receptor expression in the central auditory system of mice correlated with elevated high-frequency auditory thresholds. These findings and others raise the possibility that hormonal modulation might be used to treat some hearing deficiencies. The big brown bat, Eptesicus fuscus, provides a unique opportunity to study an easily accessible, complex auditory pathway in a highly social mammalian species. Bats experience large seasonal differences in both estrogen levels and behavior. During fall mating season, males produce “song” calls to attract females. During winter torpor, a state of decreased physiological activity, the need for hearing is greatly reduced. During spring gestation, estrogen levels are high to support a healthy pregnancy and, after giving birth, females are sensitive to the call frequency of their pups. We hypothesized that seasonally fluctuating estrogen levels in the bat brain have a direct effect on auditory processing which varies throughout the year. We measured blood estrogen levels of male and female bats over the course of the year, and recorded sound-evoked responses of single neurons in the central nucleus of the inferior colliculus (IC), the midbrain auditory center. We specifically measured changes in basic response properties such as call selectivity, frequency tuning, and threshold changes. Afterwards, we perfused the bat, sliced the brain into 40µ sections, and stained for estrogen receptors. These measurements enabled us to correlate blood estrogen levels with both estrogen receptor expression throughout the central auditory system of the brain and functional measurements of neural sensitivity and selectivity across the audible frequency range.

Trichloroethylene (TCE) is a widely found pollutant that is carcinogenic and hazardous to humans. Phytoremediation, which uses plants to degrade toxins, offers a more economical solution to removing toxic wastes from the environment. The Doty lab has isolated an endophyte (microbes living inside plants) from hybrid poplar that can degrade TCE, an enterobacter sp. strain PDN3. In this study, we are determining its potential to colonize the plants, protect against TCE toxicity and its ability to help plants degrade TCE. Colonization was studied using fluorescent microscopy, using plant tissues of S365 (Salix discolor) inoculated with fluorescent PDN3 through either foliar spray or root inoculation. The presence of the inoculated endophyte in roots of root-inoculated plants suggests that PDN3’s can colonize roots. We also tagged PD1(a phenanthrene degrader) with a red fluorescent marker to study co-colonization by both PD1 and PDN3 in S365 so that we can understand their preferred methods of colonization and their potential use in remediating sites contaminated with multiple pollutants. Because PDN3 is known to degrade TCE, we want to see whether it enhances the plants’ capacity to degrade TCE. In the next study we inoculated S365 with PDN3 and exposed them to TCE in hydroponics solution to monitor TCE removal and chloride release (metabolite of TCE). In a previous study, clone SX64 (Salix miyabeana) showed decreased biomass when exposed to TCE. So we want to examine if adding PDN3 would help the plants against the toxic effects of TCE. We are also screening other willows and poplar clones for phytotoxicity to TCE and the data generated in these studies will help us in developing a cost effective clean up technology.

Over the past few decades various electrical propulsion systems have been developed to facilitate space exploration. Plasma propulsion is a form of electrical propulsion of particular interest, in that it is especially efficient for the purposes of long-duration interplanetary space travel. Specifically, the high power helicon (HPH) thruster is a plasma propulsion system that utilizes a helicon antenna to ionize a neutral gas and create high energy plasma. This project has focused on the production of a B-dot probe to measure magnetic field perturbations in the plume of the HPH double-gun configuration. The configuration will have two HPH thrusters mounted next to each other and fired simultaneously. It is known by Faraday’s law of induction that time-varying magnetic flux through a closed circuit induces an electromotive force in the circuit. At the end of the B-dot probe are three coils of wire, whose circular loops are arranged into a sphere. Using the B-dot probe, the time derivative of the magnetic field component normal to each loop can be found, for each of the three vector components. The time derivative of the magnetic field can then be integrated over time to find the changes in the magnetic field. These changes in the magnetic field will be compared to those that result when only a single HPH thruster is fired. It is expected that the double-gun configuration will produce stronger magnetic field perturbations downstream than will a single HPH thruster. Measuring changes in the magnetic field with the use of a B-dot probe will provide a better understanding of the performance of the double-gun configuration and how it can be improved.

Research has demonstrated that early intervention for young children with autism has a significant positive impact on child progress. However, little is known about the effectiveness of early autism intervention and language acquisition for children with different levels of sociodemographic risk factors (SDR). We examined the effect of these risk factors on the efficacy of the Early Start Denver Model (ESDM) intervention. We aimed to develop a scale of SDR factors and examine the relationship of this scale to child and family factors in order to investigate the validity of this measure. We hypothesized that families with a greater number of risk factors will have children with significantly lower communication abilities. We created the SDR scale from existing variables in a multisite,randomized,controlled trial of early intervention using the ESDM. These data are from a subset of 74 families, when the child with autism was 12-24 months old. Items are from the Life Experiences Survey, CHARGE family characteristics questionnaire, and enrollment interviews. For each factor endorsed by the parent, a point was given, for a possible score of 16 points. Item-level analysis of SDR revealed the following: child not living with both parents 10.8%, mother with high school degree or less 16.2%, father with high school degree or less 10.8%, unemployed father 6.8%, family income below $50,000, 23%, one/both parents born outside the US 21.6% resided in US for < 10 years, 17.6%, parents with primary language other than English, 25.7%, sibling with a disability, 29.7% (mean = 2.47, SD = 1.753, median = 2, mode = 2). The results suggest that the SDR scale may be a useful tool to investigate variability in response to intervention and parent learning. These family risk factors may have implications for individualization of intervention.

The nematode Caenorhabditis elegans is a powerful model for the analysis of the conserved mechanisms that modulate healthy aging, from organismal to molecular levels. As animals age, tissues deteriorate at different rates. It has been shown previously in the Kaeberlein lab that deletion of the hypoxia-inducible factor, HIF-1, extended lifespan of worms at high temperature (25°C), but did not do so at low temperature (15°C). Accordingly, it was speculated that at low temperature, worms were not as healthy. At low temperature, we noticed an abnormal vulva phenotype and called it age-related vulva integrity defect (Avid). As worms age, their vulvae protrude and rupture, causing internal organs such as the intestine to erupt out of their bodies. Through investigation, we realized that animals lacking oocytes tend to show more Avid phenotype, compared with the animals that produce enough oocyte. It has been shown before that at 15°C worms produce around 300 fertilized and unfertilized oocytes, while at 25°C this number increases to 400. My preliminary results suggest that germline is involved in the progress of Avid. I studied animals with germline defects and observed 100% Avid phenotype in germless mutants. Avid is a sign of healthspan as animals age, and decline in germline fecundity due to aging can induce Avid. Healthspan is defined as the period of life spent in relatively good health, and maintenance of healthspan is an important component of aging. Our data indicate that Avid can be used as a measurement tool of the age-related healthspan of worms.

Huntington’s disease (HD) is a devastating hereditary neurodegenerative disease characterized by motor and cognitive dysfunction. One of the earliest molecular events in HD pathogenesis is the down-regulation of the cannabinoid 1 receptor (CB₁) in medium spiny neurons (MSNs), cells that play a key role in movement and degenerate in HD patients. Our goal is to rescue the specific loss of CB₁ in striatal MSNs to understand the role of this event in HD pathology. To do this, we inserted flox-stop CB₁ (fsCB₁) into striatal MSNs of R6/2 mice, the best characterized HD mouse model, and confirmed its localization. To validate the functionality of the knock-in fsCB₁ protein, we crossed fsCB₁ mice into a CB₁-/- background, so that the resulting mice lacked endogenous CB₁ receptors, and crossed them with globally-expressed Cre, so that fsCB₁ receptors became globally-expressed. We then demonstrated that replacing endogenous CB₁ with fsCB₁ did not alter responses in four classic cannabinoid behaviors (analgesia, hypolocomotion, catalepsy, and hypothermia) by injecting these mice with cannabinoid agonists. Once the knocked-in mice were validated, we measured changes in motor phenotype and synaptic integrity between R6/2 and fsCB₁-R6/2 mice. Motor phenotype was measured using rotarod, open field, clasping behavior, and Catwalk assay biweekly from 4 to 12 weeks of age. Synaptic loss was measured in the striatum, globus pallidus and substantia nigra reticulata by costaining with synaptophysin and either PSD95 or neuroligin 2 to resolve excitatory and inhibitory synapses, respectively. Preliminary results indicate that CB₁ rescue did not improve motor phenotype, but did reverse loss of excitatory synapses in the dorsal-medial striatum. Our future goals are to identify the specific subset of excitatory synapses being lost. By understanding which synapses are lost and how CB₁ rescue improves this loss, we hope to obtain greater insight into the pathophysiology of HD.