In the nervous system proper signal conduction velocity through myelinated axons is maintained by an optimal physiological ratio between axon size and myelin length and thickness. Demyelination after spinal cord injury blocks signal conduction and can lead to axonal death, inhibiting functional recovery. Remyelination can spare a denuded axon, but it occurs inefficiently and leads to formation of myelin segments that are shorter and thinner than normal, slowing conduction through spared axons. The enhancement of remyelination is therefore an important clinical target for demyelinating injuries or diseases. Neuregulin-1 (NRG1) proteins are the only growth factors shown to regulate timing and thickness of myelination during development. We previously observed that treating with NRG1 after spinal cord injury can influence myelin thickness during remyelination and found indirect evidence that it also altered internode length. To examine this phenomenon directly, we asked whether NRG1 can change myelin length in an in vitro model of myelination, the developing cerebellar slice. We applied soluble and virally delivered NRG1 to P10 rat cerebellar slice preparations for two weeks and measured internode lengths on Purkinje axons. We found that soluble NRG1 increased or decreased internode length, depending upon the isoform of NRG1 applied. This is the first work to show that modulating levels of NRG1 within the developing and injured central nervous system alters the length of myelin internodes and has implications for therapeutic interventions in spinal cord injury and other demyelinating conditions.

Imagine a country/society without rules or a Constitution.  Dar-fur is an example where the national government has failed to protect human rights and promote social or political rights. Whether the government continues to control people without their will, the people of Dar-fur know that their rights have been violated, because Dar-fur does not have a Constitution and the national government has been failing to protect their human rights. In order to improve the access to law and rights, Dar-fur will need an enforceable Constitution that will be binding in Dar-fur region. While the need for a Constitution is clear, a crucial question remains—what is an effective constitution? In 2010, I began researching this question by looking at work by political scientists and legal scholars that have theorized about the conditions that have led to the creation of effective constitutions. Dar-fur needs to regulate and enforce laws that pertain to its unique environment.  However, there may be lessons from other cases that can be useful to create an effective Constitutional. For this presentation, I will utilize qualitative analysis methods drawing on theories developed by scholars of constitutional and comparative law. First, I discuss with Political and Constitution Law professors to examine the critical components of a Constitution. Second, I analyze and compare Comparative Law literatures such as Referendums around the World and Comparative Constitutions Project to explore methods of drafting a Constitution for Dar-fur. Third, I research different countries’ government structure to find the greatest separation of power structure and oversight strategies that will work in Dar-fur. Thus, this Constitution will be accessible to anyone in Dar-fur. The result of this research will reveal the critical components that an effective Constitution must have in order to protect human rights and promote stability in Dar-fur.

Crush-injured soldiers suffer from a hypobaric hypoxia when transported by air for medical treatment from the battle field. We know that if crush injury syndrome remains untreated it can lead to acute renal failure. Crush injury leads to inflammatory responses which can result in acute renal failure due to disturbance in cell integrity and leakage of cellular content. Since oxygen is an essential component of wound healing, acute hypobaric hypoxia can exacerbate combat injuries and prolong recovery. One way to potentially reverse the effects of hypobaric hypoxia is through treatment with estrogen. In this study we will focus on the current evidence of how estrogen may counteract hypobaric hypoxia and limit an exacerbation of crush muscle injury. To collect evidence, we researched research articles and reviews on PubMed using key words such as crush muscle injury, hypoxia, muscle, skeletal muscle, and estrogen. Studies have shown that hormones such as estrogen and testosterone have emerged as important modifiers of acute inflammatory responses to injury by reducing leukocyte movement. Furthermore, estrogen promotes water retention in the human body, which may help prevent acute renal failure in muscle crush injury. Future studies are needed to understand the protective effects of estrogen more in-depth. Animal models are underway to understand if single doses of estrogen will decrease the inflammation and injury time so the muscle crush injury can be effectively treated without the risk of developing renal failure due to hypoxia.

Previous studies have shown several molecular mechanisms of physiological aging. Among these are 1) oxidative damage to proteins, lipids, and nucleic acids which over time induce cell death, 2) accumulation of DNA damage, and 3) proteins adopting faulty conformations which cause a cascade of events leading to cell death. A common feature of many long-lived mutants is resistance to different types of stress, which may reflect an enhanced ability to withstand age-related damage. Here we report studies in the budding yeast, Saccharomyces cerevisiae, to determine how long-lived mutants respond to different stresses. Several chemicals known to cause damage were used. Yeast were subjected to oxidative damage with paraquat, DNA damage with MMS, protein misfolding with heat shock, and protein accumulation in the endoplasmic reticulum with tunicamysin. Growth rate curves obtained from bioscreens and viability tests of yeast in the different drug conditions revealed that many long-lived mutants including translation mutants are resistant to paraquat, MMS, tunicamysin, and heat shock; however, many other mutants were not. These findings suggest that longevity may not result solely from enhanced resistance to damage and may explain why there are multiple pathways that can extend lifespan.

Ctenophores are basal metazoans with potential to contribute to regenerative medicine. Rapid regeneration has been documented in multiple species of ctenophore, across multiple orders. Many of the studies were conducted in the early or late 1900s, some featuring small data sets. The ctenophore species Bolinopsis infundibulum and Pleurobrachia bachei were collected from the dock at Friday Harbor Laboratories, Friday Harbor, WA and kept at local sea water temperature in sea table aquaria. Aboral regions (including polar fields, statocyst and ciliated furrows) from both species were excised and the progress of regeneration was documented at regular intervals. In B. infundibulum statocysts appeared on average 3.9 days after dissection (n=8). Statocysts were fully formed an average of 5.9 days after dissection (n=8) and regeneration of the polar fields continued through the end of the experiment (15 days). P. bachei healed the site of injury but did not regenerate aboral organ structures (n = 8). B. infundibulum may be a useful model organism for studying regeneration in basal groups.

The Himalayas are among the highest and most rapidly eroding active mountain ranges in the world. The Tsangpo-Brahmaputra River cuts a deep gorge through the Eastern Himalayas and is thought to contain the fastest and most focused river erosion rates. However, how focused and for what duration of time has this erosion persisted are the unanswered questions. This study examines the provenance and sediment mixing of modern fluvial sands in the drainage basins of the Brahmaputra River in India to investigate the pattern of erosion around the gorge. Using the dense mineral components of modern fluvial sands, this study classifies their provenance by determining the degree of metamorphism they experienced. Mixing models determine the contribution from each source of sediment, and allow us to determine relative erosion rates in different tributary catchments along the river. The study area contains Lesser Himalayan and High Himalayan lithotectonic units, which vary significantly in metamorphic grade and are distinguishable by their unique fine sand fraction (63-250 micron) components. We used a standard mineral separation technique to isolate the dense (~2.77g/mL) sand fraction of the samples. With the use of an Electron Microprobe, we calculated modal abundances of key igneous and metamorphic index minerals from backscattered images. By using a mixing model to estimate the relative amount of sediment from specific sources, we approximate more accurate provenance locations. Refining provenance locations will benefit erosion and sediment studies of the Eastern Himalayan region for further research. Using this study of modern sediments as a guide, future studies will constrain ancient focused erosion patterns using ancient river sediments stored in the drainage basins and alluvial fans. With the help of dating techniques, we can then determine when the fast and focused erosion started that we observe today in the Tsangpo Gorge.

HIV related fatigue (HRF) is the most common complaint of HIV patients; which impacts patients’ physical and mental health significantly. Mitochondrial dysfunction is one potential cause for the profound fatigue. We analyzed the plasma of fatigued HIV patients versus healthy controls using proteomics to get mitochondrial protein profiles for each group. We hypothesize that there are distinctly different mitochondrial proteins in fatigued (>7 on a 0-10 Piper Fatigue scale) HIV patients compared to healthy controls. We used a depletion column to remove the seven most abundant proteins. The remaining proteins underwent trypsinization into peptides to be identified using shotgun mass spectrometry. The peptide sequences are representative of different proteins. We used Protein databases such as Proxeon Protein Center for protein identification. Thus far we have identified 15 unique mitochondrial proteins in fatigued HIV patients, 20 unique mitochondrial proteins in the healthy controls, and 20 mitochondrial proteins common between both groups. The mitochondrial proteins we found are associated with a number of pathways, including fatty acid metabolism, respiration, and membrane transport. Two of the proteins found only in the healthy controls are particularly of interest: 3-oxoacyl-CoA thiolase, which catalyzes the last step of fatty acid beta oxidation; and creatine kinase, which catalyzes a reaction that rapidly regenerates ATP. The importance of these proteins in energy production leads us to inquire why they were not as abundant in the fatigued HIV patients as they were in the healthy controls. Future research is needed to confirm the differential expression of these two proteins and future studies need to determine their relationship to mitochondrial dysfunction and HRF. We are also conducting a follow-up study in which we have added more groups with varying levels of fatigue in order to find any correlation between proteins and HRF.

 Glioblastoma multiforme (GBM) is a diffuse primary brain tumor that is universally fatal, with an estimated prognosis of a year or less. A subset of these lesions develop fluid filled cysts. A recent study on 22 patients suggests that cysts in GBMs incur a significant survival advantage for these patients (Maldaun, J Neurosurg 2004). We hypothesize that these two types of tumors must have different growth dynamics leading to different prognoses for the same disease. Modern science has combined the fields of math and biology to produce many mathematical models of cancer growth, with some simulating glioma growth. Our patient-specific math model extracts net proliferation rate (ρ), net diffusion rate (D), and velocity of radial tumor growth from pre-treatment MRIs. The model-predicted survival time to reach a fatal tumor burden (FTB) of 30 mm tumor radius on T1Gd MRI is estimated through model simulations, as this is approximately the average tumor burden at time of patient death. We propose that a different method of parameter extraction for cystic gliomas is necessary to differentiate the growth, and consequently predict survival advantage of cystic glioma patients. Rather than including the cyst volume as part of the bulk tumour mass, it will be excluded. Cyst fluid is not composed of proliferating tumor cells and should not be treated as such. Instead the cyst volume will be included in our T2 MRI measurement, and the combination of these two measurements will be used to calculate a rate of cellular diffusion. The survival predictions from the two methods are compared to actual patient survival to evaluate quality of the method. This modified method provides a more biologically realistic simulation of growth, characterizing the differences between cystic and non cystic gliomas, allowing more accurate predictions of patient prognosis to be made.

Due to the National Environmental Policy Act (NEPA), projects undertaken by agencies in the U.S. that affect the environment must involve the creation of Environmental Impact Statements (EIS’s). These are detailed statements describing the impact that their proposed projects will have on the environment. While the government adheres to this act and creates these documents, recent research at the College of Forest Resources into the readability of EIS’s finds them to be difficult to understand and navigate by interested parties, which include court juries and local residents. This research identifies multi-author collaboration and final compilation difficulties as some of the problems leading to these deficiencies. After a draft is created, these documents go through a Request for Comments (RFC) period where there are limited opportunities to comment on a draft, but commenting requires physical attendance at local meetings. NEPA documents are then used in court when the project laid out in the EIS document conflicts with the affected populace’s expectations. Using this research, we have developed “Impresario”, a web application that facilitates the creation of quality NEPA documents. Impresario guides the authors to write at an appropriate reading level to improve understanding and automatically generates tables of contents to facilitate navigating through complex documents. Impresario allows multiple editors to collaborate in a structured manner, thereby removing formatting errors identified with the creation of poor EIS documents. Additionally, Impresario allows for public comments to be posted about a document, to increase participation in the RFC phases. The US Forest Service currently has plans to evaluate Impresario in order to improve EIS creation in their own organization.

The advanced plasma propulsion lab is focusing on the High Power Helicon as a plasma source to determine its feasibility as a deep space propulsion engine. As a plasma source, the helicon antenna ionizes and accelerates the plasma through multiple electromagnetic nozzles that confine the beam. The plasma created by the helical antenna contains an electromagnetic wave propagating in the plasma as well as other magnetic fields created by driving the plasma through the electromagnetic nozzles. I am designing and constructing a large magnetic flux probe that will move perpendicular to the plasma beam to measure the magnetic fields farther away from the center of the beam and near the edge of the chamber. This data provides a better picture of magnetic field created by the plasma. The primary goals of these experiments are to understand more about the helicon plasma source, as well as to improve our current setup maximizing plasma density and acceleration larger distances from the source.

Penn Cove is a marine bay in the Whidbey Basin of Puget Sound that experiences low dissolved oxygen (DO). We are examining the structure and function of pelagic bacterial and archeal communities in relation to nutrient loads, phytoplankton, and physical conditions across different seasons. These can be affected by several external influences including natural and anthropogenic. The nearby Skagit River may exert a strong influence on pelagic microbial communities by transporting freshwater, sediments, and nutrients into the bay. Anthropogenic impacts, such as sewage treatment plant outfalls and terrestrial runoff, are additional modifying factors. Total heterotrophic production was positively correlated with the abundance of high nucleic acid bacteria/archea and negatively correlated with water depth in the summer (r2 ≥ 0.6). However, in the winter, total production was uniformly low regardless of depth, nutrient level, or dissolved oxygen. The photosynthetic bacterium, Synechococcus, was detected primarily in winter, and abundance in winter was negatively correlated with water temperature and positively correlated with dissolved oxygen (r2 ≥ 0.7). Although the abundances of large and small phytoplankton were strongly positively correlated with dissolved oxygen in both summer and winter (r2 ≥ 0.7), the corresponding abundances of total bacteria/archea were more weakly correlated (r2 ≈ 0.35). While nitrate concentrations were higher at all sites in winter, abundances of plankton, Synechococcus, and bacteria/archea were negatively correlated with nitrate levels in both summer and winter. Surprisingly, abundances of these three groups of microbes tended to be negatively correlated with dissolved nutrient concentrations. Additional analyses of genetic diversity and particle association are underway as well as analysis into microbial particle affinity using DAPI staining microscopy. This study should provide insights into the relationship of pelagic microbial communities to physical conditions in Penn Cove.

Age is the most significant risk factor in a variety of diseases, including heart disease, cancer, and stroke, the three leading causes of death in the United States. Determining which genes influence aging, and the molecular mechanisms behind that influence, will help us develop treatments to slow the aging process and fight these diseases. In this project, we are studying 25 genes for which reduced expression has been shown to increase longevity in both the budding yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. These model organisms are separated by ~1.5 billion years of evolution. While neither system is mammalian, identifying aging genes and pathways that play a conserved role in both organisms will likely be applicable to humans, which are separated from nematodes by only ~1 billion years of evolution. Our primary goal is to place the 25 genes into, or out of, known aging pathways using yeast. We are examining the interaction between each of the 25 conserved aging genes and a set of genes that play a role in known conserved aging pathways using genetic epistasis analysis as applied to replicative lifespan in yeast. Any interactions will be verified with biochemical analysis specific to the given known aging pathway. The screen has already produced several key findings. First, ADH1 and PMR1 gene deletions do not extend lifespan after all. Original reports were tested in a background with the incorrect genotype. Second, we have found that under dietary restriction, which normally extends replicative lifespan, pmr1Δ strains are very short lived. PMR1 encodes a Ca2+/Mn2+ transporter in the golgi, suggesting a necessity for cation homeostasis for a normal response to bacterial deprivation. Finally, no long lived gene deletions that we have tested extend lifespan in a sir2Δ background, contrary to what we had expected.

With a growing number of children coping with the after effects of surviving pediatric cancer, increased attention has been given to the quality of their survivorship. Current research suggests not all survivors experience adjustment problems, but there is a subset of children who have significant difficulties post-treatment, including higher levels of depression, anxiety, post-traumatic stress symptoms, lower self-esteem and quality of life. Understanding the underlying mechanisms associated with this disparity in adjustment problems is important for the development of treatment interventions for children who are at risk for poor adjustment. The current study will test the hypothesis that the quality of parent-child interactions will act as a moderator between a cancer diagnosis and poor adjustment post-treatment. Participants for this study included 26 mothers and their children who were survivors of pediatric cancer, as well as 25 age, gender and ethnically matched healthy controls and their mothers. Participants filled out questionnaires about quality of life and symptoms of depression, anxiety and post-traumatic stress. The quality of the parent-child interaction was investigated through a 10 minute videotaped discussion between mother and child. If a moderating effect is found it will suggest that the quality of the parent child interactions is important to ensuring positive outcomes for all survivors of pediatric cancer, and future research should consider possible treatment interventions to help build positive interactions.

The King County Community Corrections Division (CCD) was established within the Department of Adult and Juvenile Detention (DAJD) in 2002. Currently, a day reporting program was added to the existing work release and electronic home monitoring programs. However, data for defendants in the various community corrections alternatives were not integrated into a unified system thus hindering the ability of the CCD to evaluate who has been assigned to which community corrections alternatives and who is successful in each of the alternatives. King County Community Corrections has asked the University of Washington Sociology Department to begin developing a research plan to address these questions. As these alternative programs are used to different degrees across the country for pre-trial and sentenced offenders, it is important to have a better understanding of which types of offenders are better served by each of the various types of programs. Our role in this partnership with King County is to evaluate the effectiveness of these alternatives to incarceration focusing on pre-trial defendants. We designed and carried out a research project that will provide Community Corrections staff with empirical information about 1) who is in the various alternatives to incarceration, 2) the extent of whether these alternatives are effective, and 3) for which the defendants are successful, where they show up for trial with no new violations. After analyzing previous literature, we established and developed background information on previous work that has been cited in regards to the effectiveness of these alternatives. We contacted judges from the courts in Downtown Seattle and Kent to seek their participation. We conducted interviews to understand their decision making process when issuing defendants into the certain programs. Finally, our team developed interview protocol questions for conducting our interviews with staff members from the specific alternative programs.

Over the past several years, it has emerged that electronics-compatible silicon-on-insulator wafers can be used to build a variety of photonic devices. While silicon is not a traditional material for optics, working in this material is highly advantageous because of the large investments made by the electronics industry in CMOS processing technology. By leveraging this existing infrastructure, it is possible to quickly and efficiently manufacture integrated electronic-photonic systems in silicon involving both optical devices and transistor-based control electronics. This technology has been highlighted for its potential to transform computing, telecommunications, and, recently, biochemical detection. We are able to utilize silicon photonic devices to build revolutionary biosensors by integrating the entire sensor system onto a single chip, including the relevant control electronics. Such systems have the potential to make a significant impact in healthcare, biomedical research, pharmaceuticals, and environmental monitoring, since they may dramatically reduce the cost of diagnostics. In this work, we use silicon microring resonators, which serve as a platform for label-free detection of chemical and biological analytes. By functionalizing the surface of these rings with appropriate selective capture agents, the concentration of target molecules in solution can be measured. Since the devices are roughly 30 microns in diameter, thousands of individual sensors can be incorporated onto a single chip. Our long-term goal is to develop these sensors into portable, inexpensive, high throughput devices capable of quantitatively measuring a large panel of disease specific biomarkers in solution. The purpose of our current work is to optimize the fundamental sensitivity of the individual microring sensors and to develop fluidics integration necessary for consistent and controlled sensing. By taking advantage of electron-beam based rapid prototyping, we can explore new device architectures in days, instead of the months required for commercial manufacturing.

Syphilis is a significant problem for global health and one of the most common sexually transmitted infections worldwide. The estimated yearly incidence of syphilis is 12 million cases worldwide. It is caused by Treponema pallidum subspecies pallidum (T.pallidum), a highly virulent, invasive and genetically intractable spirochete. The failure of existing public health efforts to control syphilis worldwide emphasizes the need for more effective methods of syphilis prevention such as a vaccine. This requires a better understanding, at the molecular level, of the immunogens that elicit sterilizing immunity in human populations. Outer membrane proteins are molecules pathogens use to evade the host immune response and are frequently targeted as vaccine candidates. Compared to other organisms, T. pallidum has very few outer membrane proteins exposed on the surface of the organism. Structural predictions show that Tp0126 is an OmpW homolog in Escherichia coli; OmpW is involved in the transport of small hydrophobic molecules from the extracellular milieu into the periplasmic space. In the promoter region of tp0126, we identified a poly-guanidine (G) tract with varying numbers of Gs between typical sigma70 signatures. Such homopolymeric repeats of different lengths are involved in phase variation mechanisms in other bacteria. Recombinant Tp0126 was expressed in E. coli with a N-terminal His tag and purified by nickel chromatography. To summarize, recombinant Tp0126 is available now for testing its immunogenic properties in immunization experiments and during active syphilitic infection. Tp0126 is likely to undergo phase variation and, consequently, to contribute to the immune evasiveness of T.pallidum.

There has been a growing interest in the large scale patterning of nanometer-sized features in order to promote the proliferation of nanostructure based electronic devices. A promising approach is to take existing fabrication methods and perform them in a parallel fashion on a larger scale. Recently, our group has demonstrated the use of an atomic force microscope (AFM) (an instrument that uses an atomically sharp tip to "feel" the surface of a sample) to write single lines of germanium and silicon. A bias is applied to an AFM tip immersed in diphenylgermane or diphenylsilane precursors to create a highly localized electric field. Within the field, the liquid precursors undergo a chemical reaction that results in the deposition of pure germanium and silicon onto the surface below. Here, we introduce the patterning of germanium and silicon in parallel fashion using a gold-coated polydimethylsiloxane soft stamp. Our new method differs in that the AFM tip is replaced with a soft stamp. This allows for much faster pattern construction while keeping nanometer precision of deposition placement.  This novel method of fabricating nanostructures made from semiconducting materials is a step toward next generation electronics fabrication techniques.

 It has been known for several years that planetary nebulae (PNe) follow a different relationship from other objects which have sulfur and oxygen emission lines in their spectra, e.g., H II regions (star forming regions), and Blue Compact Galaxies (BCGs) when log(S/H) is plotted versus log(O/H). Log in this case means logarithm. The HII regions and BCGs show a rather tight linear relationship between log(S/H) and log(O/H) over several orders of magnitude in these abundances. However, PNe concentrate towards higher values of both log(S/H) and log(O/H) (except for a few halo PNe which have lower values) and generally don't follow the relationship defined by the HII regions and BCGs. We are investigating the cause of this apparent “sulfur anomaly” by using a sample of about 160 PNe which have abundances determined in a uniform fashion. We consider the derived abundances in combination with other nebular and stellar properties to investigate various possibilities that have been proposed (ionization correction factors don't account correctly for sulfur emission lines in IR/UV, sulfur not observed due to presence in grains/molecules, PNe oxygen abundances more enhanced than previously predicted).

Recent studies at the University of Washington have shown that Ovarian Cancer usually begins in the fallopian tubes and is later detected in the ovaries and the uterus. This conclusion is forcing a shift from biopsies and hysteroscopic images taken of the uterus to monitoring the fallopian tubes for cancer using laser-based biomarker detection and direct visual inspection using thin, flexible endoscopes. However, the fallopian tubes are soft and flaccid and have a proximal sphincter with an average diameter of 1 mm as well as an intricate series of folds, which can hide cancerous tumors. These problems make imaging the fallopian tubes incredibly difficult. To prove that endoscopes can be used to monitor the fallopian tubes for cancer, I prepared synthetic models of the fallopian tubes using silicone to simulate the same limp nature of real fallopian tubes. This process included hand-carving wax structures to simulate the folds of the fimbriae in the fallopian tubes and then applying a release agent to the wax before applying several thin coats of silicone. Special care was taken to make sure that the folds in the fimbriae could be opened up after the silicone was removed from the wax structure. After the fallopian tubes were created they were attached to a synthetic uterus to serve as a training model for the doctor who will be performing fallopian tube inspection in the future. I also performed fallopian tube inspection on the fallopian tube model in order to write up a testing procedure, which would increase efficiency and decrease any discomfort for the patient. These contributions will greatly increase the likelihood of success during the in-vivo testing. Hopefully, the future in-vivo testing will prove that the SFE effectively be used to visually inspect the fallopian tubes, safely and with minimal invasiveness.

Many important results in continuous mathematics revolve around computing volumes and integrals. In order for our computational algorithms for these problems to be useful in practical applications, it is crucial to know that they are both accurate and efficient. Theoretical computer science not only gives us a mathematical framework for analyzing the efficiency of known algorithms, but also gives us tools for demonstrating the inherent intractability of some of these problems. In particular, we can show that relatively simple problem of exactly integrating a polynomial function over a simplex in arbitrarily many dimensions is NP-hard, hence conjectured to be intractable. Since one often uses polynomials and simplices to approximate general functions and regions, the ramification is that it is computationally difficult to tackle the general integration problem using these approximations. This basic problem of integrating a polynomial over a simplex is the core motivation for our research, and we are presently working on various extensions of the above result. Our primary goal is to develop a hardness of approximation result for the integration problem. That is, we suspect that it is also NP-hard to approximate the value of such an integral to within an appropriate constant multiple. In this presentation, we survey prior hardness of approximation results for related continuous problems, such as volume and centroid computation. Furthermore, we discuss how we can apply their proof techniques to the particular problem at hand, and describe the progress we have made toward a consequential hardness of approximation result. We hope that by studying this problem, we can develop techniques that are more generally applicable at the interface between complexity theory and continuous mathematics.

University Health Education Leadership Program (UHELP) is a Peer Health Education group on the University of Washington campus in conjunction with being a part of the BACCHUS Network a nationwide peer health organization, provides a variety of services. One of them being dynamic health presentations, UHELP facilitates to over 70 Freshman Interest Groups (FIGs) consisting of 22-25 students under the First Year Program. This project provides cost effective evaluation methods assessing the impact of peer presentations, in particular the “Condom Olympics” which provides vital information on sexual health resources, different contraception available and sexually transmitted infections. This longitudinal study collected data from the freshman in the FIGs over the 2010 Autumn Quarter. Catalyst and paper based pre, post, and follow up questionnaires examined the willingness to get tested for STIs, knowledge of contraceptives, and awareness of sexual health resources on and off campus. The distribution of each questionnaire was done at different times, the pre-test link was sent via-email one week prior to presentation, the post-test was paper based handed out after the presentation, and the follow up was sent via-email 3-4 weeks later. The data analysis of the 220 pre-test, 270 post-test, and 41 follow up responses is still underway. The project thus far offers some limitations for instance keeping track of an individual’s responses as it was an anonymous survey, participants did not consistently answer the ID questions and providing a strong incentive for retention was challenging as the follow up survey only captured about 15% of initial participants. However areas to highlight are: the use of catalyst provided easy accessibility for participants to use and researcher to observe data. This evaluation project can serve as a model for other Peer Health groups as it is able to record participants’ responses of peer intervention.

There are six extant species that comprise the nautiloid cephalopods, commonly referred to as chambered nautiluses, which differ from their modern coleoid cephalopod counterparts by possessing an external spiraled aragonitic shell. The common name “chambered nautilus” refers to internal compartments of its shell separated by partitions called septa which are continuously formed throughout development and discontinue once the animal has reached maturity; however, not much is known about the mechanism in which septa are formed. Apatitic concrements found in the renal appendages of Nautilus pompilius were discovered in 1865 and have been hypothesized to be mineral storage structures, but there have been no studies that have made a conclusive link between these deposits and septa formation. In this study, we used x-ray analysis to view concrements in the renal appendages of juvenile Nautilus pompilius and observed that these concrements are present and absent in what appears to be weekly cycles whereas it was observed in previous x-ray analyses of adult specimens that no concrements were present. Once concrements were confirmed to be absent, we measured the septa directly from the radiographs. We propose a mechanism of septa formation in which the apatitic concrements in the renal appendages form the septa and that this process continues throughout development until maturity is reached.

Historically, rhododendrons and other plants were classified using traits such as flower and leaf morphology or geographical location to posit relationships. This practice is limited by the number of phenotypic traits detectible between species. Phylogenetic analysis based on DNA sequence reveals numerous new traits consisting of Single Nucleotide Polymorphisms (SNPs) and other mutations among and between species and has made it possible to directly infer lineages. My research is focused on Rhododendron subsection Fortunea, comprising some 45 species. The goal is to gather DNA sequence information from many parts of the genome and to use it in establishing a phylogenetic tree for Fortunea. This requires finding insertion or deletion (indel) markers throughout the genome that are specific to some species, but not others. Previous research in the lab has produced a phylogeny of Fortunea; however, the data used to construct the tree was from three specific genes, cataloguing every SNP and mutation for each species in those genes. My research is aimed at unveiling large indels within many disparate regions of the genome: I theorize that combining the intergenomic data I am collecting with the data from specific genes will generate a more highly resolved phylogeny of subsection Fortunea than presently exists. To collect this data, I use PCR primers to amplify sections of the genome (specifically introns and intergenic regions) in six diverse species and compare the Fortunea sequence to the known sequence of a related subsection. I then design specific Fortunea primers to amplify regions spanning any indels that I find, using these to genotype all of the species in the subsection. So far, I have isolated six promising mutations for which I have genotyped most of the species in the subsection, revealing a foundation that I will elaborate on as I find more mutations.

The ability to manipulate gene expression in a directed fashion has provided invaluable insight into gene function. In the fruit fly Drosophila melanogaster, the yeast-derived GAL4/UAS binary expression system has been extensively used to drive gene expression in a precise spatiotemporal pattern. The LexA::VP16-LexAop binary expression system has recently been developed for use in Drosophila, independently or in combination with other genetic tools (such as the GAL4/UAS system), allowing for an additional level of control and versatility for labeling distinct tissue and cell types. To complement the GAL4 system, we report the application of the LexA-LexAop binary system. We have generated a collection of LexA::VP16 (a bacterial-viral fusion protein) enhancer traps by P-element mediated insertion into the Drosophila genome. In this way, expression of LexA::VP16 is placed under control of the animal’s own endogenous genomic enhancers. To determine which of these putative enhancer traps drives expression of LexA::VP16, and to document the pattern of LexA expression, we have systematically crossed these enhancer trap lines to fly stocks bearing a LexA-responsive green fluorescent protein (GFP) transgene; in the presence of this transgene, cells expressing LexA will be labeled with GFP. Using confocal microscopy, we have documented larval expression patterns for ~200 enhancer traps, many of which drive expression of GFP by the LexA reporter in specific subsets of cells. In combination with the GAL4/UAS system, the LexA-LexAop system will allow for simultaneous and unique labeling (and manipulation) of two distinct cell types. In this way, one could dissect neural circuits by performing multiple tasks at identical times and in distinct locales, all within the same animal.

Routine screening of high-risk individuals by medical doctors through cystoscopy is standard clinical practice for the treatment and detection of bladder cancer. Regrettably, the current methodology for these procedures is inefficient and expensive, making bladder cancer the most expensive cancer to treat in the United States. New technology needs to be developed to improve the quality of bladder cancer screening with reduced cost per procedure. An automated bladder cancer screening system is being developed in the Human Photonics Laboratory at the University of Washington combining an automated cystoscopy tool, an endoscopic imaging device, and 3D mosaicing software. Automation of the bladder scanning process allows the procedure to be performed by any medical staff capable of inserting a urinary catheter and the mosaicing software provides verification of a complete scan with diagnostic images available to clinicians after the procedure. These cystoscopy screening advancements would improve accuracy and precision of bladder cancer surveillance, while eliminating the need for a medical doctor to perform the procedure, significantly reducing procedural costs. Initial designs of potential cystoscopy tools that have potential for automation and provide a track-able scan pattern in the bladder have been developed. Two tool designs were developed, one using a pre-curved cannula extended from a rigid sheath and the second, a urinary catheter combined with a flexible scope that has pull-wire steering. These tools were tested in vitro using an excised pig bladder to develop an optimized tool, which was then tested in vivo during a live pig experiment .  Results from these experiments indicated that initial designs using the pre-curved cannula could not achieve a small enough bend radius to image the entire bladder. Successful mosacing of the bladder was achieved in vitro with the catheter and steerable scope, and further experiments are being conducted to evaluate this device.

Thin, flexible, solid polymer electrolytes (SPE) show great technological potential towards electrochemical devices with ion conductivities that have shown to gradually reach the ion conductivity of traditional liquid electrolyte lithium batteries (≈ 10mS/cm). Advantages of polymer electrolytes are their flexibility in geometry design, light weight, durability, and potentially low manufacturing cost. Different methods are utilized to enhance the ion conductivity of SPE that often involve the creation of interfaces within the membranes in form of, for instance, composites or liquid swollen or filled solid polymer matrices and microporous systems. Atomic force microscopy and scanning electron microscopy technology are utilized to analyze the surface characteristics.Our group is investigating a microporous polymer electrolyte (MPE) membrane, P(VdF-HFP)-PEO, introduced by Deka et al. (2009) that is prepared by simple phase inversion technique. Phase inversion is a technique where you cast a polymer solution and evaporate the solvent and non-solvent. The non-solvent leaving then forms pores. We will report our findings on pore size control as a function of the preparation conditions and interfacial constraints in thin films.

Basic algal physiology is important for large-scale algal growth facilities since they need to know optimal growth conditions for algal to produce the most desirable products. Algae produce lipids that are used for biofuel and other products such as proteins used for animal feeding or dietary supplements. Fatty acids from algae can be substituted for omega 3 fatty acids from fish. In this project, we wanted to know how changing light intensity and temperature from minimal levels for curations of cultures to standard growth conditions would affect algae growth. Our standard conditions were 20 °C, 100 uEm^-2 sec^-1 illumination with or without 60 revolutions per minute agitation and grown in seawater or freshwater media depending on the species. Microalgal growth could be hard to monitor by machines such as a Beckman Coulter Counter because of small size and colony formation, so I used a hemocytometer. Hemocytometer was a special type of microscope slide designed to facilitate accurate counting of cell concentration and used with an epifluorescent microscope to count the number of cells from inoculation through stationary phase growth. Then, I collected samples for lipid analysis to determine the types of fatty acids present in each species. These results were used to identify algal strains for a larger scale growth experiment by choosing the strains which produced abundant lipid in a short period of time.

Renal interstitial fibrosis is a final common pathway of all chronic kidney diseases (CKD). Capillary loss has been observed in human CKD and is correlated with disease severity. Studies in animal models of CKD have shown that the renal microcirculation undergoes major structural and functional changes including increased vascular permeability in addition to capillary loss. These changes are thought to depend on a variety of growth factors, possibly including Placental Growth Factor (PlGF). PlGF is a known pro-angiogenic growth factor, which may stimulate capillary proliferation in the event of fibrosis. However, PlGF is also known to activate macrophages, which induce inflammation. We are using the mouse unilateral ureteral obstruction (UUO) model of renal fibrosis to investigate the role of PlGF in CKD. Using PlGF-/- (knockout) and PlGF+/+ (wild-type) mice, we performed UUO or Sham surgery and harvest the kidneys 7, 14, and 21 days afterwards. To assess the extent of fibrotic damage, we measured total collagen content using the hydroxyproline assay. We have observed a negligible difference in total collagen between PlGF-/- and PlGF+/+ mice. This suggests that PlGF is not likely involved in fibrosis. Currently, we are investigating the effect of PlGF on vascular remodeling. Using Platelet Endothelial Cell Adhesion Molecule-1 (PECAM-1) as a marker for endothelial cells, I will be performing immunohistochemistry to quantify changes in capillary density. If there is a difference between PlGF-/- and PlGF+/+ mice, I will investigate other possible effects of PlGF, including changes in vascular permeability, that may play a role in CKD.

As scientists look into the future of computing devices, the building of quantum computers had become a popular field of research due their potential high speed and problem solving capabilities. This presentation reports the experimental results of an ultrahigh vacuum (UHV) system that can be used to implement scalable trapped-ion quantum computers. Such devices would use micro-fabricated ion traps as fundamental building blocks. Current challenges for setting up the ion trap are the routing of large number of chip pins and the difficulty to filter out noise during operation. The novelty of this system resides in our design, material selection, mechanical liability, low complexity of assembly, and reduced signal interference between DC and RF electrodes. Our system utilizes RF isolation and onsite-filtering topologies to attenuate AC signals generated from the resonator. We use a UHV compatible printed circuit board (PCB) material to perform DC signal routing, while the RF high and RF ground received separated routing via wire-bonding. The standard PCB fabrication process enabled us to implement ceramic-based filter components adjacent to the chip trap. The DC electrodes are connected to air-side electrical feed through using four 25D adaptors made with polyether ether ketone (PEEK). The assembly process of this system is straight forward and in-chamber structure is self-supporting. We report on initial testing of this concept with a linear chip trap fabricated by the Sandia National Labs. In the future, the quantum computing devices implemented in this experiment may prove to have valuable military applications.

In recent years, there has been growing interest in brain-computer interfaces (BCIs) for controlling robotic devices and prosthetics directly using brain signals. Non-invasive BCIs, such as those based on electroencephalographic (EEG) signals, suffer from low signal-to-noise ratio, limiting the bandwidth of control. Invasive BCIs, on the other hand, allow fine-grained control but can leave users exhausted over long periods of time because of the amount of attention required for control on a moment-by-moment basis. We address these problems using a new adaptive and hierarchical approach to brain-computer interfacing. The approach allows a user to teach the BCI system new skills on-the-fly; these learned skills are later invoked directly as high-level commands, relieving the user of tedious lower-level control. We demonstrate the approach using a hierarchical EEG-based BCI for controlling a humanoid robot. In a study involving four human subjects controlling the robot in a simulated home environment, each subject successfully used the BCI to teach the robot a new navigational task. They later were able to execute the same task by selecting the newly learned command from the BCI's adaptive menu, avoiding the need for low-level control. A comparison of the performance of the system under low-level and hierarchical control revealed that hierarchical control is both faster and more accurate. Our results suggest that hierarchical BCIs can provide a flexible and robust way of controlling complex robotic devices, satisfying the dual goals of decreasing the cognitive load on the user while maintaining the ability to adapt to the user's needs.

Ninety percent of patients that die of prostate cancer (PCa) have bone metastasis. Growth of PCa cells in the bone can lead to bone marrow replacement, spinal cord compression, severe bone pain, cachexia and death. Characteristically, PCa bone metastases exhibit a bone-forming (osteoblastic) response. We have set out to identify the tumor-derived secreted factor(s) responsible for osteoblastic bone growth in PCa bone metastasis. LuCaP 23.1 is a PCa xenograft that causes an osteoblastic response in bone. To determine whether a secreted factor is responsible for the osteoblastic bone response, conditioned media (CM) isolated from LuCaP 23.1 xenografts were added to MC3T3-E1 (mouse osteoblasts) cells. Deposition of calcium phosphate (mineralization) was assessed by the presence of alizarin red dye. Additionally, mass spectrometry in combination with gene expression arrays was used to identify potential osteoblastic factor(s) secreted by the LuCaP 23.1 xenograft. To identify molecular pathways altered in osteoblasts in response to the secreted osteoblastic factor(s), we compared gene expression in LuCaP 23.1 CM-treated vs control human osteoblasts using gene expression arrays. These results were validated by real-time PCR. Our results showed that LuCaP 23.1 CM promoted mineralization of MC3T3-E1 cells and upregulated mineralization-associated genes in human osteoblasts. Additionally, phosphoglycerate kinase 1 (PGK1), a factor shown to promote bone formation, was identified as a potential secreted osteoblastic factor in the osteoblastic LuCaP 23.1 xenograft. Further research will be conducted to verify whether PGK1 is responsible for the osteoblastic response in PCa in the bone. Identifying and targeting the osteoblastic factor(s) could alleviate the pain and suffering associated with osteoblastic bone formation in PCa bone metastasis.

Nearly every organism needs iron to survive. Pathogenic bacteria must acquire iron from their hosts and have evolved multiple mechanisms to capture iron or iron-containing heme in the bloodstream or tissues. In response, mammals have developed several defense mechanisms to keep iron away from invading bacteria. For example, the liver secretes hepcidin in response to infection, causing the degradation of the iron exporter ferroportin and in turn decreasing gastrointestinal iron absorption. Much of the body’s iron store does not exist as free iron but is instead complexed with heme. The Feline leukemia virus, subgroup C (FeLV-C), receptor, FLVCR, is a heme export protein. It is unknown whether FLVCR plays a role in regulating heme-iron after infection, however, given that heme regulatory proteins such as heme oxygenase-1 are up-regulated in macrophages in response to bacterial infection, we hypothesize that macrophages dynamically regulate FLVCR. To test this hypothesis, we will use lipopolysaccharide (LPS), a membrane component of gram-negative bacteria, to activate macrophages and measure the response of heme regulatory genes. We will derive macrophages from wild-type mice, stimulate them with LPS, and measure macrophage FLVCR and heme oxygenase-1 mRNA expression using quantitative real-time PCR. If we find that macrophages up-regulate FLVCR, we could determine whether FLVCR knockout macrophages are defective in controlling the growth of intracellular bacteria. On the other hand, if macrophages down-regulate FLVCR, this would suggest that they are acting to keep heme-iron away from extracellular bacteria. Through these studies, we aim to understand the role of FLVCR and heme export in the macrophage response to bacterial infection.

Severe Myoclonic Epilepsy in Infancy (SMEI), or Dravet’s syndrome, is a childhood epilepsy syndrome that is non-responsive to current treatment plans. At 6-9 months of age, SMEI patients begin to suffer from spontaneous and febrile seizures, which are followed by decline in their motor and cognitive abilities. SMEI is associated with loss of-function mutation in the Nav1.1, a brain-specific sodium channel that is crucial for neuronal excitability. By introducing the same mutation in mice, the Catterall Lab has developed a mouse model of SMEI, which experiences the similar seizures as the SMEI patients. In addition, the mutation reduced the sodium current in GABAergic inhibitory interneurons, causing weakened inhibition against neuronal excitation in the brain. It is likely that this causes the seizures and comorbidities. The lab hypothesized that drugs that strengthen GABAergic inhibitory signals will be most effective in preventing seizures. We are seeking treatment plans that will maximize the protective effects of antiepileptic drugs while minimizing the side effects for optimal therapy. To accomplish this goal, we chose Tiagabine and Clonazepam, which are drugs that increase GABA transmission. We observed their effectiveness in protecting against seizures when administered separately and compared the results to when they were used in combination. The results indicated that the two drugs may exhibit some synergy. When administered together, they yielded an effect that significantly exceeded the level of protection offered when they were used separately. At the same time, the side effects associated with the drugs at high doses were abolished. Once we complete these short-term treatment studies, we will move onto designing long-term therapy plans. My work will result in a better understanding of the molecular mechanisms of SMEI and contribute to better treatment strategies.

Global climate change is a widely discussed topic in the United States. Yet the task of reducing greenhouse gas (GHG) emissions is not entirely a technological one but one of economics and policy. Wastewater Treatment Facilities (WWTFs) provide a great opportunity to employ combined heat and power (CHP) and reduce greenhouse gas emissions. There are over 16,000 WWTFs in the United States and of those, 3,500 employ anaerobic digesters, which create biogas. Biogas is a fuel that can be used for CHP. Evaluating Washington State’s policy for renewable energy revealed gaps between the current available best practices and the State’s policies. A 2005 prefeasibility study performed by the United States Environmental Protection Agency Combined Heat and Power Partnership for the Brightwater Wastewater Treatment Facility in King County provided the background information to execute this case study. Using the same assessment tool from the 2005 study, I examined the impact of each of the four scenarios: no incentives with current energy prices, 5 megawatt net metering, a cogeneration credit, and a change in the market price of electricity (e.g., as the result of a carbon tax). After dissecting the proposed policy solutions and determining the impact on prices and incentive payments, the data was then inserted into the tool, where upon economic feasibility was determined. For the scenarios with a positive annual savings an annuity formula was used to calculate the payback period for the combined heat and power system. Findings for each scenario conclude with whether a CHP system should be installed based on annual energy savings over a 20-year payback period with no change in energy prices. As a result, I was able to make recommendations based on which of the policy options were the most effective at improving the economic feasibility of combined heat and power.

Findings from early studies in children with Autism Spectrum Disorders (ASD) have suggested ear abnormalities to be a discriminating factor between ASD and normal controls. Previous investigations have also suggested that low-set ears may be associated with chronic and problematic otitis media in children with ASD. In this project frequency of tympanostomy procedures used to treat chronic otitis media (OM) are examined in relation to ear position in children with ASD to identify the possible relationships between external and internal ear abnormalities. Ear measurements are analyzed using 2D facial software and compared with a control group of siblings unaffected by ASD. The examination of procedures for the treatment for chronic and severe OM in children with ASD could provide further information into the nature of chronic OM in ASD populations. Furthermore, examining ear placement in children with ASD may be utilized to serve as a clinical marker for ASD symptomology and aid in identifying specific subgroups within the disorder.  

Paraoxonase-1 (PON1) protects the body by hydrolyzing the toxic metabolites of organophosphate compounds (OPs), like the insecticides widely used in agriculture. PON1 status, comprised of plasma PON1 activity levels and the PON1Q192R polymorphism, is predictive of sensitivity to specific OPs as shown by previous studies in adult mice. To characterize human PON1 status as a biomarker for OP sensitivity after gestational exposure, we used four lines of mice: PON1-wild-type (WT), PON1-knockouts (KO), and tgHuPON1_R192 and tgHuPON1_Q192 (PON1 knockouts expressing the human PON1 transgenes). Based on previous studies we expect tgPON1_R192 to be more protective like WT, while tgPON1_Q192 is expected to be more sensitive, like KO mice. The first step was finding the optimal dose of CPO (chlorpyrifos-oxon, the metabolite of the insecticide Dursban) where toxic effects like tremors and lacrimation are not apparent in the dam, but fetal OP-sensitive enzymes are inhibited. For this experiment, WT and KO mice were chosen because they show the extremes of sensitivity to toxicity. Three doses of CPO were administered dermally to pregnant females during gestational days 6-17. Enzyme assays were run on fetal and maternal tissues to measure inhibition of the OP target enzymes cholinesterase (ChE) and carboxylesterase (CES). Both genotypes of females showed no visible signs of toxicity at the highest dose (0.75mg/kg/day). ChE and CES in maternal tissues and fetal blood plasma were inhibited, but not in fetal brain, even KOs. We hypothesized this was due to rapid re-synthesis of these enzymes during development. Based on these dose-finding data, we will extend our studies to all genotypes and examine several endpoints, including behavior and brain gene expression. These experiments will provide insight into the effects of maternal and fetal PON1 status on sensitivity to OP exposure, which can then be applied to the public health field.

Stream hydrographs are a helpful way to visualize discharge patterns in a watershed. Discharge patterns are the result of the physical and biological characteristics of the watershed, including anthropogenic effects such as land use changes and urbanization. Using these stream hydrographs and other metrics, including the fraction of the year annual mean discharge is exceeded (TQmean), several small, undeveloped watersheds are analyzed to examine these patterns. The La Cangreja National Park watershed in Costa Rica exhibits the unusual pattern of very “flashy” discharge, which is usually associated with more urban and developed watersheds. This is primarily due to the shallow soils and to high rain intensities. This study statistically compares the runoff patterns of several different watersheds in a variety of biomes, including urbanized watersheds in the Puget Sound (which are expected to have flashier discharge patterns), undeveloped watersheds on the east coast of the United States (as designated by USGS), and the tropical, undeveloped La Cangreja watershed in Costa Rica. A broader understanding of runoff patterns is essential to management planning. Flashy runoff can have significant impacts on erosion, sedimentation, and flooding, which can in turn effect urban populations as well as local wildlife.

The subjects and focus of this research were members of the Biker culture, and how American Bikers define their community, their identity, and their place within American society. This research was based within a theoretical framework that investigated the sociological claim that there are more differences within a culture, than between cultures. I traveled thousands of miles with fellow Bikers in the summer of 2010, some as the driver of my own motorcycle, and some on the back of a motorcycle as a passenger. These road trips brought me to many locations where I conducted participant observation and other forms of research. Additionally, a quantitative electronic survey was administered investigating many concepts including gender roles, trust of law enforcement, and chosen family versus biological family. Demographic information was collected in order to run statistical analysis in comparison with data collected by government sources from the American public in general. As a result of this research, I have had the opportunity to share with the academic community some of the process in which members of the Biker culture have developed legislation in order to ensure fair and equal treatment under the law, the Motorcycle Profiling Bill. By providing accurate, valid, and reliable information inside and outside of the American Biker culture, I offer this research in the hopes of facilitating a greater understanding of who American Bikers are individually and as a cultural group. I further hope that this research will help to debunk destructive stereotypes and shed some light on cultural truths, not only for outsiders to the Biker culture, but for Bikers and Motorcycle Enthusiasts as well.

In 2008 University of Washington students discovered labor rights violations in Nike apparel factories in Honduras that supplied the University of Washington with collegiate apparel. This issue was brought to the attention of ACTL (Advisory Committee on Trademarks and Licensing) who then recommended that the UW put Nike on formal notice that their business relationship was in jeopardy if these labor rights violations went un-remedied. After claiming no legal obligation to enforce the actions of Honduran sub-contractors, Nike finally announced a $2 million settlement in July 2010. What motivates apparel manufacturers to act in a socially responsible manner? We use a close examination of the Nike case to investigate why Nike and similar corporations chose to uphold their social responsibility and compensate transgressed workers. We rely on ongoing interviews with key stakeholders to draw out themes relating to student activist groups, third party auditors, university committees, material interests and legal responsibility. We will identify the most important factors in compelling multi-national corporations to uphold responsibility throughout the supply chain. Preliminary results indicate that the combination of strong student groups and leadership may have played an important role in Nike's decision. This research is fundamental in understanding the consumer power of universities in their interactions with multi-national corporations. 

Over the past nine years we have established a Chemical Garden that supplies our research and teaching labs with a sustainable source of plant materials suited for laboratory science and chemical analysis. This garden is located at the Organic Farm, which is part of The Evergreen State College campus. Our interest has been with plants that produce volatile oils as these plants lend themselves well to extraction by steam or ethereal solvents. The extracted constituents are readily analyzed via Gas Chromatography-Mass Spectrometry (GC/MS), our primary analytical tool. The plants we have focused on are garlic, St John’s Wort, hops and mints. This poster reports on our progress toward characterizing the essential oils extracted from the flowering tops of different strains of lavender as a function of drying time. The lavender samples were distilled fresh and after set drying times. This process was repeated continuously throughout the year. All isolated essential oil samples were analyzed using GC/MS. These results showed only slight changes in the major constituents as a function of drying time. We then looked at how the aging of an essential oil sample or exposure to sunlight and molecular oxygen changed the oils. We next examined commercial lavender essential oils purchased locally. This research wil provide information on the differences between organically grown lavender oils and commercially produced oils, as well as providing knowledge of the rate of degradation of essential oils.

Puget Sound lowland prairies are the most endangered ecosystem in Washington State. Restoration ecologists are actively restoring these sensitive areas by controlling exotic species and seeding native species. The effectiveness of seeding depends on seed germination and viability, which can vary among species. Furthermore, germination and viability can also vary within species among populations collected from different geographic areas or in different years. I am examining this variation for 4 species: Lomatium utriculatum, Camassia quamash, Aquilegia formosa and Microseris laciniata. This work is within the scope of a larger project of determining the germination and viability of 143 different collections of 42 different native species, the dates of collection range from 1994-2010. Four hundred seeds of each collection are placed in growth chambers set to mimic spring/fall (8-16°C and 12 hours of light), summer (14-23°C and 14 hours of light) or winter (5°C and 10 hours of light) conditions. Seeds are checked periodically and those which have germinated are counted and removed; these seedlings are grown out for use in restoration projects. Seeds that do not germinate are subject to a tetrazolium test to determine if they are viable. Tetrazolium reacts with enzymes within live tissues in seeds and stains them pink; dead seeds remain un-stained. The proportion of all tested seeds that germinate or are viable is the percent live seed in the collected population. Knowledge about variation in germination and viability among species will help restoration ecologists improve their seeding efforts. Variation among collections from different locations and years will give insight into how variable populations within a species are, and into how long seeds can be stored before outplanting.

Development pressure from human population expansion results in extensive land use modifications that can have a negative impact on stream and river health. This study assessed the correlations between various land uses and stream ecosystem integrity. As a part of the Snohomish County Critical Areas Monitoring and Adaptive Management Program, benthic macroinvertebrate samples were collected from 22 headwater stream basins in Snohomish County, Washington during the summer of 2009. These samples were scored using the multimetric Benthic Index of Biotic Integrity for the Puget Sound Lowlands (B-IBI), an indicator of stream ecological health, and then compared to land cover composition at four different spatial scales. Within each headwater basin, the scales included a 50-foot buffer surrounding all streams, a 100-foot buffer, a 150-foot buffer, and the entire basin. Land cover compositions were calculated from a model that combined color infrared satellite imagery, a LiDAR-based flow accumulation model, and ancillary geographic datasets to compile 2007 and 2009 land cover maps that included six cover classifications (wetlands, grass, scrub/shrub, forest, impervious surface, and bare earth). The correlation between land cover and B-IBI score was significant and negative for a combination of bare earth and impervious surface at all spatial scales, implying that these land use modifications, which often indicate development, negatively affect stream ecosystems. These results are consistent with previous research and provide valuable information that can influence land-use management strategies.

Low clouds are a negative forcing on the climate system, acting to radiatively cool the earth. The feedbacks associated with these clouds are the greatest source of uncertainty in estimates of climate sensitivity, primarily due to a lack of understanding of the processes that influence their behavior. Previous studies have investigated marine stratocumulus clouds and found strong correlations between the boundary layer inversion and cloud fraction. In this study, a subtropical inversion model, which considers a boundary layer in radiative equilibrium with radiatively-driven subsidence, is applied to the subtropical Pacific and Southern Hemisphere midlatitude marine boundary layers using observational and reanalysis data. Comparison with the estimated inversion strength demonstrates that the subtropical model is unable to reproduce the magnitude of the inversion in the midlatitudes. Other processes that are hypothesized to be important in the energy budget of the boundary layer are studied to attempt to resolve this discrepancy. Additionally, the seasonal cycle and variability of marine stratocumulus are briefly characterized and contrasted between the two regions.

Although mixed 'race' populations in the United States are growing, the spaces for dialogue in academic settings are still too few, and the lack of multi-racial/multi-ethnic perspectives within academic classes and texts is not often acknowledged. In response to this lack of representation and space for critical mixed race discourse on campus we designed a project intending to create a space for mixed experiences be heard and recognized as providing important contributions to the body of academic research and scholarship. We were interested in what conversations about “mixedness” could look like when the experiences and lives of people in the room were centered, and the students themselves were considered to be the most knowledgeable on the subject being studied. Based on this question, we designed a year-long project that involves collecting sources from the existing body of research and scholarship on mixed race experiences, designing a ten-week curriculum incorporating themes and perspectives we considered to be most relevant and pressing, and then facilitating the course as a way to both provide space for dialogue about ‘mixedness’ and to contribute to the knowledge base of critical mixed race studies.

Previous studies have indicated that electrical activity from the brain changes during the perception of pain. Electroencephalography (EEG) is often used to measure the size and frequency this activity. Beta waves are a category of small, rapid electrical waves that have been associated with attention, vigilance and active thought. Additionally, beta waves have been associated with the perception of pain, especially in the sensory integration areas found in the brain’s temporal lobes. The purpose of our research is to explore the relationship between perceived, self-reported pain ratings in spinal cord injury (SCI) participants with chronic pain, and the density of their beta waves, as measured by (EEG). SCI Participants with chronic pain were asked to rate their pain before, during and after each EEG session. Preliminary results may reveal a relationship between the frequency of beta wave activity and self-reported pain, in SCI participants with chronic pain. Understanding the relationship between SCI patients’ self-reported pain and their frequency of beta waves, may assist researchers in evaluating the efficacy of pain treatments for people with chronic pain.

The high level of organization achieved in an adult organism has its origins in a very early developmental process called gastrulation. During gastrulation, a young embryo arranges its cells into three layers—the endoderm, mesoderm, and ectoderm—which will later give rise to specific tissues and organs in the adult. As can be imagined, the profound embryonic shift from a nearly amorphous mass of cells to a highly organized system of layers requires an incredible level of coordination. Any single cell is not only required to move, but also to coordinate this movement in a highly dynamic environment populated by countless other cells which are also en route to their final location and orientation. This movement, or cellular migration, is regulated by a large number of proteins and their interactions with each other. One such protein is p120 catenin, which works as a kind of binary switch, cycling cells between their motile and immotile states. We are interested in how p120 catenin regulates the motile state by interacting with a class of proteins called GTPases, which rearrange the internal architecture of a cell, and thereby propel it into motion.We hypothesize that one such GTPase, CDC42, is regulated by p120 catenin in a manner that is critical to proper cell migration during gastrulation. To explore this, we employed a “depletion-rescue” experimental approach, utilizing zebrafish as our model organism. First, p120 catenin levels are depleted by injecting a morpholino into young embryos. Normally, this results in defective gastrulation, and a variety of morphological abnormalities. However, by coinjecting CDC42, we are able to “rescue” these embryos—that is, restore normal development. This indicates that p120 catenin in healthy embryos works to activate CDC42 during gastrulation, resulting in cellular motility.

Does similarity in political regime and culture affect what countries the United States cooperates bilaterally with? I hypothesize that the U.S. will experience more instances of bilateral cooperation with countries with which it shares a similar political system and/or culture because shared political and cultural norms fosters growth of collective identities and interest formation. This hypothesis emerges from theories of democratic peace and constructivism, but diverges from the realist perspective that material interests, not shared culture, are the driving forces behind international cooperation. Existing scholarship on the relationship of political regime type, culture and international cooperation has produced robust findings that democracies virtually never fight wars as enemies, are prone to enter alliances, and cultural similarity between countries can predict alliance behavior. However, empirical scholarship has left unexplored the relationship of political regime, culture and non-alliance bilateral cooperation between the U.S. and other countries. The author uses a dataset containing all the international agreements between the United States and other countries for the year 2000. Each country is given a code for political regime and cultural similarity to the United States. After controlling for each country’s population and GDP, I expect to find that there are more instances of bilateral cooperation between the United States and countries predominantly Christian and/or are functioning democracies.

Few incidences of congenital abnormalities in pinnipeds have been published. This paper documents eight cases of congenital defects found in 176 (4.6%) harbor seal (Phoca vitulina) pups that were collected dead and examined on or near harbor seal haul out sites in southern Puget Sound Washington between 2004 and 2010. Our role in this research included: specimen collection, conducting necropsies, and compiling relevant data from participating stranding network agencies, for descriptive analysis. The anomalies include four pups with varying severities of orofacial anomalies (cleft palate and lip), three pups presenting a condition similar to chondrodysplasia or dwarfism and one case of a hydronephrosis, a kidney disorder, found during gross necropsy. While the causes of these malformations are not yet known, these genetic defects may reflect the overall health of the southern Puget Sound harbor seal population.

Most of the current literature on sexual motivation focuses on the effects of sexual motivations on risky sexual behaviors. Sexual motivations or reasons why individuals report having sex, are often categorized by assessing two different dimensions: the type of reinforcement (positive or negative) and sociality of the behavior (social and self) (Cooper et al. 1998). The current study will focus specifically on partner and peer-related motives. Individuals who report this motive may use sex as a way of gaining peer/partner approval. One way of examining the impact of sexual motivations is to determine how they predict actual sexual behavior. Research by Cooper et al. (1998) indicated that different sexual motivations predict different pattern of sexual risk taking. However, there has not been much research examining the effects of sexual motivations on drinking behavior. Based on research that has shown anxiety is associated with partner and peer sexual motivations (Walker-Bauer, 2006), it is possible that individuals with partner and pee-related sexual motivations use alcohol to deal with their sexual-motivation-induced anxiety. Based on previous literature, it is hypothesized that individuals with partner and peer-related sexual motivations are more likely to drink prior or in conjunction with sexual behavior. The present study utilized measures from a larger study on risky sexual behavior in college. The 1,055 students (ages 18-30) that completed the study were paid 20 dollars for their time. Specific measures for the present analyses include: the Sexual and Alcohol-Related Sexual Behaviors Scale (Cooper et al. 1998 & Lewis, et al. 2006) and the Sex Motives Scale (Cooper et al, 1998). The findings from this study will broaden the understanding of the associations between partner and peer related sexual motivations and sex related drinking.

Individuals with autism spectrum disorders (ASD) can show impairments in social cognition at a young age. Previous electrophysiological studies show that, in healthy individuals, the processing of faces evokes an early negative event-related brain potential (ERP) component at 170ms (N170) after the stimulus. One way of measuring this is taking an electroencephalogram (EEG) recording at the surface of the scalp. Young children with autism have an N170 that is larger in amplitude and faster for objects than faces; typically developing children show the opposite pattern (Webb et al., 2006). Little is known about the development of the face and object-specific N170 in children with ASD. The goal of this study is to compare how the relationship of the face and object N170 develops between children who show more social improvement versus children who do not. Participants included 31 children with ASD and 23 children with typical development. Children with ASD were diagnosed using gold standard research and clinical assessment tools. In the ERP experiment, participants watched images of repeating faces and objects while high-density electrophysiology was recorded. The pictures of faces were of the child’s caregiver (familiar) and a picture of an unfamiliar face. The objects shown were pictures of the child’s favorite toy and a picture of an unfamiliar toy. To provide a measure of social development, each child’s primary caregiver completed the Vineland Adaptive Behavior Scales at age 6 and 9-years. Two groups of ASD children were separated in terms of amount of social improvement over the 3 year period. We predict that as an individual with ASD socially improves, we will see a decrease in latency, and greater amplitude for the face-specific N170 relative to the object-specific. Results may have implications for theories of the relation between social behavior and face processing impairments in autism.

This project is the product of continued conversations with homeless and street-involved informants as well as analysis of interviews, articles, and books from popular media and academic circulations. Research took place between September 2009 and December 2010. Initial interests were how people without homes use urban space and how in turn the physical geography of the U-District affects the habits and lifestyles of the homeless. Though these aims were kept in mind throughout the project, the ways that people without homes interact with their physical environment proved to be diverse and particular to the circumstances that had led them into homelessness. Understanding these interactions became a task of beginning to understand issues such as late-stage alcoholism and addiction, inefficiencies in the welfare and foster care systems, unhealthy family dynamics, and mental illness. In taking the stance that homelessness is a shared symptom of diverse social processes this project challenged several common assumptions about homelessness: It is possible or even plausible to discern who is homeless, those who are homeless share a common culture, and the “solution” to homelessness is to provide services or new information that creates an outlet to this culture. As a learning tool, this project provided lessons in applied research methods, ethics in anthropology, and interpretation of collected data in terms of social theory.  

Paralytic shellfish poisoning (PSP) has become a significant problem in Puget Sound, causing repeated closures of shellfish beds which affect both commercial and recreational harvests. In addition, the increased frequency of such events has both ecological and human health implications. Alexandrium sp. is one of the primary dinoflagellate algae responsible for producing toxins that cause PSP in this region. When environmental conditions become favorable, resting cysts of Alexandrium sp. bloom releasing toxins into the water which spread through the marine environment (Cox et al, 2008). These cysts have been found in the sediments of various regions in Puget Sound and have been previously identified as the species Alexandrium catenella. There has, however, been very little definitive confirmation of their identity through molecular techniques. This study uses the polymerase chain reaction (PCR) on individual cysts to identify them positively as toxin producing algae. The PCR results show the cysts present in Puget Sound are from the toxic species Alexandrium tamarense. DNA sequencing will further resolve the taxonomic uncertainty, making it possible to accurately map the spatial distribution of the cysts in sediments. Further research on individual algae cysts will help develop a better understanding of the timing and mode of Alexandrium sp. introduction to the Puget Sound Basin. This will contribute to preventing toxic algal blooms in the future and may help reduce the risk from PSP in Puget Sound.

Trade studies are needed to evaluate different designs and manufacturing processes for a large-scale production system, such as building airplanes. Decision factors in manufacturing processes can include flow time, work load balance, cost, etc. In this paper, we provide a decision analysis matrix by considering various numeric and subjective decision factors. In particular, we propose some statistical analysis and simulation methods to study uncertainty of the decision factors. The confidence intervals of the total weighted decision analysis scores are provided for the trade scenarios. The proposed decision matrix analysis is illustrated by a case study where four different manufacturing process alternatives in an aerospace manufacturing envirnoment are studied.

Anecdotal evidence suggests that adults who suffer from one chronic illness such as heart disease or hypertension often suffer from several others. Discovering why these individuals are more prone to disease has important implications for determining the best treatment for them, both before and after they have begun to fall ill. It was thought that there may be some genetic reason for this tendency towards illness, but the difficulty of collecting enough data to do a feasible study was prohibitive. Recently, however, a large database of sequenced exomes, the expressed part of the genome, became available to facilitate studies of this sort. We hypothesize that adults who are more prone to chronic conditions may carry mutations in important genes that have widespread effects. To assess importance, we have isolated portions of the DNA sequence that code for proteins, called exons, that have fewer mutations within the database’s population than would be expected based on the average mutation rate; these exons are referred to as highly conserved. This lowered mutation rate indicates that highly deleterious mutations in those genes strongly reduce reproductive fitness, meaning the products of these genes must be especially important. We have chosen to compare a group of people who have slightly deleterious mutations at these sites to a control group in order to see if people with mutations in these important genes have chronic health conditions in common. I wrote computer programs that isolated highly conserved sites as well as a control group. To continue the project I will be isolating data from the exome and medical history database that corresponds to these sites and performing a statistical analysis to see if mutations in important genes correlates with a higher rate of complex disease.

Recent research has indicated that genetic variations of DNA repair genes not only play a causal role in cancer occurrence in humans, but also affect the therapeutic efficacy of many anti-cancer regimens using chemo- and radio-therapeutics. The human MutS homolog 5 (hMSH5) is a member of the MutS family of proteins that are involved in DNA mismatch repair, meiotic and mitotic recombination, and DNA damage response. However the functional impact of hMSH5 polymorphic variants on these two critical cellular processes is largely unknown. To this end, we have begun a series of functional analyses for six out of the seven common hMSH5 polymorphic variants, including L85F, Y202C, V206F, R351G, L377F, and P786F. Specifically, expression constructs harboring these polymorphic variants have been generated and used to create a series of 293TLα and 293T cell lines stably expressing the variant proteins. Immunoblotting experiments with individual clones indicated that, in comparison to the widetype, none of the polymorphic variants significantly affected the level of protein expression. Clonogenic survival and cell cycle analyses—experiments designed to decipher the potential functional effects on DNA repair and cellular damage response—are presently ongoing in the laboratory. A detailed understanding of the potential functional deviation of hMSH5 polymorphic variants in DNA repair and damage response will be a critical foundation for the development of effective individualized anti-cancer strategies.

Currently governments around the world are pouring money into research pertaining to advancing and increasing the efficiency and reliability of our current power grid. These systems promise to prevent blackouts by evenly distributing power throughout the day and reduce costs associated with the maintenance and operations. Though their goals may seem straight forward our research primarily focuses on some of the current and potential security lapses. We are as a whole seeking to find the weak spots in what has been billed as a fool proof system. Our initial approach focused on discovering the guidelines set forth by federal agencies. This included talking to local officials at Seattle City Light and conversing with university affiliated personal. The end objective was to find out what could be made better with the current and future systems around the country. Our research yielded many points of concern for the nation’s smart grid. We found out that by adding in digital controls third parties such as terrorists or thieves now have the possibility of causing a remote catastrophic failure or a systematic disarmament of a victim within our power grid. Through research conducted by students like ourselves we hope to prevent problems before they arise on our path to a nationwide smart grid.

Temperature determines whether incoming precipitation will fall as rain or snow, as well as how fast snow melts. Significant spatial variability of temperature within a basin may be very important to hydrological forecasting efforts. As a member of the Mountain Hydrology Research Group, led by Professor Jessica Lundquist, I am analyzing air temperature variations in the complex terrain of the American River basin near Sacramento, California. The project is based largely on the analysis of a network of surface sensors deployed in the basin as part of the National Oceanic and Atmospheric Administration’s (NOAA) Hydrometeorology Testbed. To measure the presence of snow in the basin, ground temperature data series are examined to find periods when the sensor recorded untypically constant temperatures below 3.5°C for extended periods of time indicating that the sensor was covered (and insulated) by snow. In addition to snow presence, I am also investigating lapse rate variability resulting from local temperature patterns influenced by atmospheric conditions and topography. The lapse rate of an air parcel is characterized as the rate at which temperature decreases with elevation (usually measured in °C/km). A typical lapse rate that is used in many west coast hydrological models is -6.5°C /km. My initial findings indicate that a standard lapse rate of -6.5°C /km may not be applicable to mountainous terrain in the Northern Sierra due to complex, local variations in temperature. Additionally, I am investigating the accuracy of the predicted 0 °C elevation (point at which snow turns into rain) by comparing our calculated lapse rates with those used in current practices. As current modeling of snow pack accumulation and precipitation patterns in mountain basins improves, damages caused by flooding events may be reduced while improving current water availability forecasting methods.

.The debate over the purpose and usefulness of nuclear weapons shifted significantly in the wake of the collapse of the Soviet Union and after the events of September 11, 2001. For many experts—particularly nuclear terrorism experts—fears about proliferation to rogue states and transnational actors began to supersede traditional considerations like Soviet ICBM limits or the efficacy of mutually assured destruction, and new and restructured organizations sprang up to meet these new challenges . The 2007 Wall Street Journal article by Henry Kissinger, George Shultz, William Perry, and Sam Nunn, advocating for the abolition of nuclear weapons in light of a changing world full of new threats, is perhaps the most widely recognized evidence of this shift, but the change in interest group activity long predated this article. Is it possible to systematically document this shift by examining nuclear weapons policymaking in Congress over time? Previous research has shown that an increase in interest group activity surrounding a particular issue initiates a shift in the way Congress address that issue. In order to determine whether the increase in interest group activity following these two events caused Congress to change the way it addresses nuclear weapons policy, I look at Congressional hearings on nuclear weapons-related topics over the past 40 years. To measure change, I code hearing content based on five categories of nuclear weapons subtopics, and use indicators such as hearing length and committee referrals in order to detect subtle shifts in the politics surrounding this issue. I expect to find that the politics of nuclear weapons policy changed after both 1991 and 2001, but I predict that the effect will be weaker after 9/11 than it was after the fall of the Soviet Union, as the later represented a more fundamental shift in the nuclear weapons international environment.

When studying Congressional actions in shaping a given law, researchers and observers often focus on its development only up to its receipt of signature by the President. In reality, these laws continue to be shaped by amendments made long after their original passage; their provisions may be expanded, weakened, or repealed altogether. There is reason to believe that certain aspects of both the original legislation and the environment in which it was created may have a significant effect on post-passage action. Previous research in this area has focused on explaining how these factors affect the speed with which the law is amended, but this tells us little about how the amendment effects the original law; this project seeks to explore how the aforementioned factors effect whether a law is strengthened or weakened by its later amendment. I expect to find that when, at the time of passage, government is divided, the legislation is carried by a slim margin, or the public disapproves of government action, a given law is at increased risk of later unraveling by amendment; alternatively, when the law creates new rights for the general public, it stands a greater chance of later being expanded upon. These independent variables, operationalized by using Congressional voting records, were developed by Forrest Maltzman and Charles Shipan, whose work I build upon. I develop my own dependent variable (expansion/contraction) by examining explanatory language used by articles referring to selected laws in Congressional Quarterly. By better understanding the interaction of these variables, researchers may better predict the longevity and developmental path of a program or law, and legislators may better strategize to maximize the likelihood that their legislation evolves in a favorable manner.

Good communication between healthcare providers and patients is essential to a successful medical encounter. However, achieving effective patient-provider communication (PPC) can be difficult when the patient has a speech, language or cognitive-communication disability. Quality of care can be compromised when patients are unable to understand what a physician is saying or to verbalize their questions and concerns. Similarly, if a physician is unable to understand a patient he or she can find it more difficult to get a case history, accurately diagnose the problem, and form a relationship with that patient, which can increase the risk of medical errors and patient dissatisfaction. While studies have shown that effective PPC is a critical part of a good medical encounter, healthcare providers receive little instruction on how to achieve this effective communication, especially with patients who have special communication needs. This research project seeks to evaluate the effectiveness of a training program for fourth-year medical students to impart specific strategies for effective interactions with communicatively impaired patients. Information is provided through lecture, video demonstrations and demonstrations with simulated patients to increase awareness about communication strategies to use with patients with communication disorders. Student progress is tracked by analyzing pre- and post-training self-assessment surveys. While this research is ongoing, preliminary results have shown statistically significant positive improvement in student knowledge, attitudes and confidence regarding communicating with patients with communication disorders upon completion of this training seminar.

There is a misunderstanding with the word patriotism which Howard Zinn explained during an interview when he said: “Dissent is the highest form of patriotism.” Despite numerous revolts in our history as mentioned and explained by Howard Zinn in A People History of the United States, dissent is a very long process that often results in a two steps forward one step back doctrine. I will explore through recent news articles and magazines such as Time and Newsweek, as well as scholarly journals and Chomsky and Zinn’s works, the factors which prevent the American people who take action, by dissenting, to make much change in the status quo. I am going to focus on the controversy of the Tea Party as the example of an attempt to analyze the role of the American citizen in the political arena.

The phenomenon of lying is central to the human condition, relevant to almost all human affairs. Studies have shown that lie/truth detection capabilities average at less than 55% accuracy rates – especially when individuals judge the veracity of strangers, in real-time, with no special aids. This phenomenon is especially present in situations where the “truthful character” of the person making the statement is called into question (e.g., during police interrogations). Thus, it appears deception judgment is related more to the context and perceived credibility of the person making statements than any other individual difference – i.e. people are more likely to perceive someone as lying if they are looking for a lie, even if the speaker is being truthful. This is the specific phenomenon investigated in the current study. We hypothesized that participants would not perform better than chance at distinguishing between truthful and false statements. Moreover, we predicted that when primed to look for deception, participants would be more likely to perceive truthful statements as lies compared to unprimed participants. To test our hypothesis, we used biased written and verbal instructions to prime participants to detect deception, truthfulness, or neither (neutral control). Participants were then shown a pre-recorded video of individuals telling both truthful and false statements and asked to judge the veracity of those statements. Quantitative analyses were conducted by running descriptive and inferential statistics to examine correlations and outcomes. Analyses showed that our hypothesis was not supported and that the type of priming used had no impact on deception judgment. However, an unexpected discovery was that participants were either more or less likely to judge a statement as dishonest depending on whether it was negative or affirmative. These findings suggest that even the basic linguistic composition of a statement has a significant impact on its believability.

Contamination of the world’s waterways with plastics has been a cause of concern for many years (Barnes et al. 2009). Microplastics, or those ranging from 0.1 to 5.0 mm in size, have been a far less noticeable component of the total plastic load of aquatic environments. These microplastics are of particular concern due to their ease of ingestion and capacity to accumulate persistent organic pollutants (Mato et al. 2001). The objective of this study is to create a library of AFM images to assist with the identification of these microplastics and to better understand the process of mechanical weathering they experience. To accomplish this, various virgin plastics were examined using AFM and compared to weathered samples collected from urban run-off in Seattle. This collection of images will help future researchers identify microplastics collected from a variety of sources and enable them to observe how exposure to physical abrasion and UV radiation affects their structure

It has been observed that water at hydrophilic surfaces exists in an ordered, liquid crystalline state. This crystalline region has been termed the exclusion zone, because like other crystals, it excludes many solutes. The exclusion zone is amplified by incident radiant energy. The focus of this experiment was to observe exclusion-zone behavior during the application of another kind of energy - ultrasonic acoustic energy. Using a 7.5MHz ultrasound immersion transducer, various ultrasound amplitudes and durations were applied to the exclusion zone next to submerged Nafion tubing. Poly-carboxylate microspheres were used to define the extent of the exclusion zone. Observations showed that the exclusion zone was compressed during the application of high amplitude ultrasound. Upon turnoff, the exclusion zone built well beyond its control size for several minutes, eventually dropping off and returning to its control size. While the mechanism for this behavior is not yet clear, it is well known that ultrasound can create cavitation bubbles in water. This might be mechanistically relevant. Thus, after cavitation, the sequential migration of micro-bubbles towards the exclusion zone and accumulation next to that zone could be the major contributing factor to its expanded character. Apart from its intrinsic scientific interest, near-surface water behavior in the presence of ultrasound has major implications for sonochemistry and for applications to the biomedical fields of tissue-imaging and ultrasound therapies.

A significant limitation of current lithium ion batteries is their cycle life. Most consumer-grade batteries lose half of their design capacity within 300 to 1000 charge and discharge cycles. This translates into an approximate lifetime of one to three years before the batteries are rendered effectively useless, and must be replaced. The cause of this limited lifetime is two-fold. First, the ceramic cathodes react irreversibly with lithium ions, forming a new phase that no longer contributes to the battery’s charge capacity. The second challenge is that the movement of lithium ions into and out of the cathode physically strains the ceramic lattice, and damages or even fractures it. In order to combat this second effect, this project is explores microstructural design concepts to make the cathode more strain tolerant. One of the attractive approaches is to make the cathodes with aligned pore channels. Results are presented from the freeze casting apparatus used to make ceramics with aligned pores and microstructures.

Part of The Baryon Oscillation Sky Survey (BOSS) is a spectrograph which allows observation of one thousand different specta in a single exposure because each object can be observed with its own individual optical fiber. BOSS contains millions of spectra (including galaxies, quasars, and many other celestial objects) in its database. This allows both for inadvertently found spectra of low mass stars as well as 4000 specifically selected low mass star targets. Using the 'Hammer' (a spectral typing software) we have determined the spectral types for this sample of approximately 8000 low mass stars. We will discuss our spectral classification program and compare the characteristics of our sample of low mass stars with previous large spectral databases.

The corpus callosum facilitates communication between the two cerebral hemispheres via contralaterally projecting cortico-cortical and corticostriatal connections. Understanding the rules that govern this striatal circuitry can lead to an understanding of motor learning, motor function, and neurodevelopmental disorders originating in the cortico-basal ganglia system. However, an unexplored issue remains. Although selection of appropriate cortical inputs to the striatum appeared to be a major function of dopamine, the only inputs that have been characterized were those that projected to the ipsilateral striatum. However, roughly half of the corticostriatal inputs originate from the contralateral cortex. In order to explore the function of cross cortical connections, a unique two cut approach was developed to sever the corpus callosum. After surgeries, the callosotomy was verified by observing brain slices. This technique contains advantages. It avoids the hippocampus and yields minimal ventricle damage. Another advantage was that a partial callosotomy, limited to the posterior and anterior parts of the corpus callosum, can be performed. This may yield different results compared to mice with complete agenesis of the corpus callosum. These callosotomy mice were then used in a variety of behaviorial tasks in order to determine any behavioral abnormalities. First, they were observed performing a tail flick test to determine basic neurological reflexes. These callosotomy mice then were evaluated using a rotor rod task to determine motor coordination, followed by a tail suspension task to assess motivation. Finally, learning and memory were tested using a Morris Water Maze task. All data was compared to controls of the same age, in this case six weeks, that underwent a sham surgery. This data, along with converging electrophysiology data, optical FM-143 imaging, and genetic knockout mice, can be used to further understand the function of the corpus callosum. This could allow a more complete understanding of corticostriatal connections originating from the contralateral cortex.

Recent studies on human aggression have found that females are not less aggressive than males. Rather, they are more likely than males to exhibit relational aggression, particularly during adolescence. This indirect aggressive behavior coincides with the onset of puberty, suggesting the phenomenon could be explained by evolutionary factors. Some aggression and risk-taking behavior among males is seen as an adaptive mating strategy shaped by intrasexual selection. My project explores the idea that relational aggression may also be a form of intrasexual mate competition in adolescent females. To explore the association between sexual maturity and aggression, I recruited 70 girls between the ages 11 and 13 through the Seattle Youth Soccer Association (SYSA). Each girl completed a five-page questionnaire that included questions on: (a) her involvement with the three most common forms of relational aggression: gossiping, rumor spreading, and exclusion from groups; (b) a self-assessment of her own sexual maturity using Tanner stage drawings; and, (c) her opposite-sex relationship history. These data were analyzed to assess their conformity to predictions derived from evolutionary theory: that the patterns observed would make sense as an adaptation shaped by intrasexual selection. The girls were dichotomized as either premature or mature to evaluate the role of sexual maturity on aggressor-target relationships. Contrary to previous suggestions that later-maturing girls will target earlier-maturing girls (earlier-maturing girls have longer reproductive life-spans, and therefore “first-pick” of valuable mates if left unabated), I found that girls tend to target others of the same maturity level. In addition, boyfriends were more commonly reported among those with higher levels of aggression. I argue that this pattern of aggressive behavior is consistent with an adaptive mating strategy whereby girls target direct competitors as opposed to those who pose little threat, or against whom one is unlikely to out compete.

Mountain beavers (Aplodontia rufa) are a common, yet understudied, species in the Pacific Northwest. These burrowing animals favor areas previously disturbed by human activities such as logging, and they are conspicuous members of the communities of large Seattle urban parks. Their tunneling behaviors aerate the soil and promote drainage, and may bring nutrients deep below the topsoil, as do pocket gophers, their subterranean counterpart. Studies on the impacts of other burrowing animals, such as pocket gophers, have shown that the frequent disturbance they provide serves to increase plant species diversity locally and to provide transient patchy habitat for early successional species. The hypothesis being tested is that while the activities of Aplodontia rufa may negatively affect areas of human habitation, the soil cycling and eating activities promotes species rotation and increases plant biodiversity in these locations. Specifically, plant richness and abundance within mountain beaver territories will be compared to control locations in the same parks, where the animals are absent. Observing the impact of mountain beavers on rates of soil turnover, plant biodiversity, and canopy cover could help Seattle parks personnel create a wildlife management plan for these animals. Unlike the pocket gopher, whose effects on plant diversity and succession have been reported in other papers, the mountain beaver's effect on natural habitat remains largely unknown. We predict that the activities of A. rufa increase local plant diversity and produce habitat for early successional plant species within a community dominated by late successional species. 

Embedded in every leaf are stomata; special cellular valves on the epidermis of plants. These stomata act as gatekeepers in transpiration, an essential gas exchange with the atmosphere performed by plants. Stomatal patterning describes the density and spacing of stomata in the epidermis of the Arabidopsis plant; a flowering annual closely related to mustard. The density of stomata can affect the plant's capability to thrive in arid environments, which makes stomatal development research of particular interest to biologists. It has recently been established that small, non-protein-coding fragments of RNA participate in a system called RNA silencing. RNA silencing allows plant cells to repress harmful gene expression, as well as regulate normal gene expression. In this process, small interfering RNA (siRNA) binds with a corresponding sequence of messenger RNA before translation and uses RNA-induced silencing complex, a nuclease complex known as RISC, to cleave and degrade the targeted sequence. By imaging the epidermis of Arabidopsis with genotypes defective in small RNA pathways, I am attempting to discover a role of small RNA silencing in stomatal patterning by phenotypic analysis. Through light microscopy, the relative densities of various cell types as well as the physical appearance of the cells can be compared to the genetically normal wild type. Cell counting is used to determine differences in the raw number of each cell type compared to the control, and the cell densities are extrapolated from this data. In addition, I am also looking for anomalies in cell structure or patterning that would not be interpreted by quantitative data. This research may reveal subtle changes in Arabidopsis epidermal phenotypes that result from a defect in particular RNA silencing pathways. These small, previously overlooked abnormalities may help clarify the function of small RNA silencing in the differentiation of cells in Arabidopsis.

HIV has infected over 30 million people worldwide and has resulted in the loss of millions in healthcare costs. HIV vaccines have the potential to prevent infection and drastically reduce infection rates. A potential strategy for vaccine development is to elicit a mucosal immune response, since sexual transmission of the virus is the leading cause of new infections. A successful functioning vaccine could deliver a HIV antigen, such as the highly conserved HIV membrane surface peptides gp41 and gp120, and an adjuvant, such as the synthetic organic molecule R848 or the CpG oligonucleotide, through mucosal and cellular barriers. Here, we develop a delivery vehicle for a complex HIV vaccine by using a nanoprecipitation method to formulate a polymeric nanoparticle consisting of a biodegradable polymer core surrounded by a lipid layer. Previous work involving nanoparticles with lipid layers has shown controlled surface chemistry and greater particle stability, since the lipid layer prevents rapid degradation of the polymer core. However, nanoprecipitation traditionally results in low polymer yield and drug encapsulation efficiency, two factors important in designing a reproducible vaccine system, since nanoprecipitation involves poor mixing of the polymer and adjuvant in the lipid solution. We propose a fluidic system that automates the nanoprecipitation to generate particles with controlled uniform particle size profiles and low polydispersity. The adjuvant encapsulation was integrated into the fluidic system to allow partitioning of the adjuvants within the hydrophobic polymer core or to be associated with the lipid shell. The encapsulation efficiency was measured via liquid chromatography (HPLC), while in vitro assays, such as ELISA and cell culture studies, were used to test for the controlled release and immunogenicity of the immunogens. These results demonstrate a more controlled design for creating nanoparticle vaccine delivery vehicles that may elicit a more comprehensive immune response against HIV.

The goal of this project is to explore the concepts of Living Buildings and Living Cities as proposed by the International Living Building Institute and to apply the framework to a redevelopment project located in the Roosevelt neighborhood, envisioning it as a Living City in 2035.  Using a literature review focused on the latest theory and technology, we explain the concept of a living building, highlight existing examples, discuss the the expansion of the concept from a single building to the neighborhood or city scale, and explore current applications of the Living Buildings concept.  We use site analysis to identify the strengths and weaknesses of the Roosevelt site, including renovation and re-use opportunities for existing buildings, potential opportunities to use natural systems processes such as solar or water circulation patterns, and connections to the surrounding community.  We identify a few of the components critical to the establishment of a Living City: technology that can provide a decentralized and sophisticated power grid, eco-districts that will create economies of scale, and systems for the on-site treatement and recycling of waste.  We then visually apply these concepts to the Roosevelt site in order to envision it as a thriving Living City, providing a clear representation of what is possible for the future of the area within this framework.

Obesity is currently the leading preventable cause of death worldwide. It is a foundation for chronic diseases, such as cardiovascular disease, hypertension, stroke, cancer, musculoskeletal disorders, and type 2 diabetes. Alcohol use may pose a risk for becoming overweight or obese. However, evidence suggests moderate consumption of alcohol may protect against weight-related disease, namely type 2 diabetes and cardiovascular disease. Preference for specific alcoholic beverages may interact with lifestyle choices such as diet and physical activity in determining overall risk for disease. Researchers have largely explored the relationship between red wine consumption and coronary heart disease, but few have investigated preference for specific alcoholic beverages in relation to other behaviors. The current study explores relationships between preference for specific alcoholic beverages (i.e., red wine, white or rosé wine, beer, liquor, and mixed drinks), dietary habits, physical activity, and socio-demographic information via cross-sectional survey. Specifically, better adherence to recommended USDA dietary guidelines is associated with a preference for wine compared with other alcoholic beverages. Socio-demographic characteristics are explored as potential moderators of this relationship, and associations between socio-demographic characteristics and the tendency to exhibit beverage preference are examined. These findings add to the growing body of literature examining the complex links between alcohol, diet, exercise, and other personal characteristics, which have direct implications for prevention of chronic disease.

News media frames content much like a picture frame does: the organization of the frame, the perspective it enforces, the establishment of foreground, background, angle and positioning all operate to activate particular frames of seeing (and not seeing). In parsing Western media’s portrayal of the Egyptian Revolution predominantly as a “Facebook Revolution,” we are exploring what the media’s taking-up of one narrative (that Facebook is a liberator’s tool and a liberating media) indicates about the technology and its service of imperial subject formation. We deploy Lisa Lowe’s theoretical development of notions of assimilation, nation formation and citizenship to assist us in historically situating our argument. Facebook in the dominant media’s account is figured as an actor, its presence determining the outcome of the ‘revolution’ and predetermining the technologized user-consumers produced. The “Facebook Revolution” organizes and supports a narrative of the nation as one of democratic inclusion and propagation rather than as an engine of war, re-constituted and sustained through imperial campaigns in the Middle East. Our research reveals how Western media uses Facebook as an organizing narrative tool to overdetermine the Internet’s uses and weave it within a uniform and predictable trajectory of globalization and modernization. We demonstrate how these various media accounts when taken together articulate and valorize Western/U.S. national and global aspirations, and that these frames elide the violence of ongoing imperial interventions. Our research opens up a space for the creative interpretation and co-option of Internet technologies that, when informed, can disrupt unidirectional movement and unilateral effect from the Western center to its local peripheries. This intervention is important if we are to question these technoscientific narratives and their ideological underpinnings; the awareness of these frames can enable a more empowering albeit problematic navigation of the Internet and its dominant publics, and their place within globalizing processes.

Systemic Lupus Erythematosus (SLE) is an immune complex (IC) mediated disease. Previously, the Elkon Lab has shown that C1q blocks interferon alpha (IFNα) and other inflammatory cytokines after peripheral blood mononuclear cell (PBMC) stimulation with immune complexes (ICs). Given that osteopontin (OPN) is associated with inflammation, we hypothesized that OPN would also be downregulated however, microarray studies revealed that OPN was upregulated. The goal of my project is to understand how C1q regulates OPN. OPN is a highly phosphorylated glycoprotein that is overexpressed in tumor cells and individuals with autoimmune disease, such as Systemic Lupus Erythematosus (SLE). There are two forms of OPN - secreted OPN (sOPN) and intracellular osteopontin (iOPN). While OPN is expressed by many cell types, the primary isoform produced varies with cell type and cell activation. The current understanding of OPN expression is derived from studies using murine models. My first goal was to explore whether or not our in vitro mRNA expression studies of OPN were similar at the protein level and to the results of published murine studies. The concentration of OPN was measured by a homemade ELISA in the cell culture supernatant and cell lysate of human monocyte-derived macrophages after stimulation with IFNα. Detection of OPN in the supernatant of macrophages stimulated with IFNα suggests that the upregulation of sOPN is not IFNα dose-dependent. Futher experiments need to be completed before conclusions can be made with regard to the effect of IFNα on iOPN. Additionally, experiments studying the affect that C1q has on OPN protein expression in PBMCs and monocyte-derived dendritic cells after exposure to ICs are underway. Taken together, these studies will help elucidate the role of OPN and C1q in modulating SLE disease activity in humans.

The mammalian inner ear contains mechanosensory hair cells that act as receptors and transducers of environmental stimuli. These hair cells are susceptible to ototoxicity, and specifically sensitive to aminoglycoside antibiotics such as neomycin. Damage to the inner ear causes deafness and affects balance, and mammalian hair cells cannot regenerate once they are damaged. The non-mammalian vertebrates, zebrafish, also possess mechanosensory hair cells. However, zebrafish are able to regenerate their damaged hair cells. Zebrafish also have an additional mechanosensory organ called the lateral line, with neuromasts or groups of hair cells that can detect water flow. We use the lateral line to study hair cell regeneration in zebrafish, and in particular I am identifying genes that regulate how hair cells regenerate after damage. Those who sustain damage to their inner ear hair cells suffer from hearing loss and possible deafness. By understanding the genetics about how zebrafish regenerate their hair cells, we may be able to apply this knowledge to fix an otherwise permanent deaf condition. To identify genes that regulate hair cell regeneration we performed a mutagenesis screen. Eight families were identified with mutations that cause abnormal hair cell regeneration and I am mapping the Moby mutation. Moby is a homozygous lethal, recessive mutation that has been stably transmitted over several generation. Moby mutants display ~50% hair cell regeneration as compared to wild-type siblings and fail to completely regenerate even after 7 days of recovery. I am currently using linkage analysis to map the mutated gene by comparing polymorphisms from DNA extracted from mutants to that of DNA extracted from wild-type siblings. Mapping is ongoing however, Preliminary mapping results suggest that the mutation is likely on Linkage Group 10 or 5.

The objective of this research is to explore the use of silver nanoprisms in sensing applications. Silver nanoprisms exhibit a unique resonance involving the delocalized conduction electrons called surface plasmon resonance. This resonance responds to light, and as a consequence the nanoprisms strongly absorb, scatter, and concentrate specific wavelengths of optical energy. The position of the resonance is highly sensitive to the size of the prism and the characteristics of the prism’s surroundings. This quality allows prisms to offer information about binding of analytes to the prism surface. In this research, we synthesized silver nanoprisms of varying sizes and different plasmon resonances. Silver nanoprisms are unstable in a variety of solvents and are oxidized easily, and we coated them in a protective layer of silica. We found the silica coating decreased the reactivity of the silver while preserving the optical properties of the plasmon resonance. We are currently studying functionalization of the silica-encapsulated nanoprisms with DNA and the use of these DNA-covered, silica-coated silver particles in biosensing applications. The prisms will ideally eventually signify a change in the state of the DNA through a shift in the absorption spectrum, and so could indicate the presence of specific DNA sequences or proteins.

The budding yeast Saccharomyces cerevisiae is commonly used in aging research. The ease with which this organism can be altered genetically or its environment changed makes Saccharomyces cerevisiae an ideal organism to study factors which influence aging. However, few age-related phenotypes can be easily measured in yeast; therefore aging-related studies have primarily examined life span. Currently two different methods are used to measure life span in Saccharomyces cerevisiae. Chronological Life Span (CLS) is defined as the length of time a culture of yeast cells can survive in stationary phase (a non-dividing state in which the cells have exhausted the nutrients available) and is thought to model aging in somatic cells. In contrast, Replicative Life Span (RLS) is defined as the total number of daughter cells produced by a single mother cell and is thought to model aging in actively dividing cells. To further investigate the relationship between the two models of yeast life span we measured the RLS of cells taken from various time points within a CLS experiment. Mother cells subjected to chronological aging generated fewer daughter cells with increased time spent in stationary phase. Interestingly, this reduction in RLS could be delayed by interventions which have been previously demonstrated to extend chronological life span, such as reduced glucose levels (dietary restriction) and use of glycerol as the primary carbon source. These results suggest that certain aspects of aging are shared between dividing and non-dividing cells and that some life span extending interventions, such as dietary restriction, act on both types of cell populations.

Autism Spectrum Disorder (ASD) is a pervasive developmental disorder affecting approximately 1 out of 88 males. Theoretical conceptions of ASD and human neuroimaging studies suggest abnormalities in connections among distributed neural systems in ASD. To investigate possible differences in neural function and connectivity in adults with ASD, we evaluated narrow band dense array electroencephalogram (EEG) responses from 18 males with ASD and 18 age & IQ matched control males. All participants were tested under four conditions: eyes closed resting, eyes closed counting, eyes open resting, eyes open counting. Preliminary analysis of spontaneous brain activity confirms previous reports of decreased lower alpha range (8-10 Hz) power in the ASD group during rest conditions. Coherence, a measure of functional brain connectivity, was also reduced in the ASD group and group power differences are predominant across frontal regions. Similarly, functional connectivity estimates reflect reduced lower alpha coherence both within frontal regions and between frontal and all other scalp regions. These data support hypothesized atypical connectivity across neuronal populations in individuals with ASD, compared to individuals with typical development.

Traditionally there has been a clear distinction between infotainment and news broadcasting. In the past decade this distinction has been blurred by new shows, such as, The Daily Show with Jon Stewart which combines advertiser’s preferences for comedy with viewer’s preferences for news content. Scholars of infotainment claim that through entertainment based programing viewers glean political information as a by-product of watching the said program. Others argue, in the recent literature focused on The Daily Show with Jon Stewart, viewers must be politically aware in order to understand the entertainment presented in the show. I posit it is these politically inclined viewers is the explanation behind White House Press Secretary Robert Gibbs citing The Daily Show with Jon Stewart, as instrumental to the changed outcome of the 9/11 Health Care Bill (H.R. 847) in 2010. I consider the political implications of this new media by investigating the political characteristics of its viewers in conjunction with the bill passage of H.R.847. I use a telephone survey conducted by Pew Research Center to determine if there is a unique political characteristic within viewers who watch The Daily Show with John Stewart, and shows like his, which link advertisers and viewers preferences. I will link this politically inclined demographic to theories of congressional responsiveness to further explain Mr. Gibb’s claim regarding H.R. 874.

All animals need oxygen to survive. When cells do not have enough oxygen to function, there can be damaging physiological effects. As some proteins tend to aggregate under stressful conditions, quantification of protein aggregation can be used to study this delicate homeostasis. I am using the small nematode C. elegans with an aggregation-prone and fluorescent-tagged transgene (Q35-YFP), to investigate different concentrations of oxygen in these live animals. In this model, I count the number of aggregates per nematode at multiple time points to quantify aggregation in hypoxia as compared to room air (about 200,000 ppm oxygen). By this assay, I have demonstrated that protein homeostasis is lost upon exposure to hypoxic concentration of oxygen. My results show that protein aggregation occurs in 1000 ppm oxygen. However, in <10 ppm oxygen, aggregation occurs during only after return to room air. Furthermore, I have shown that the loss of protein homeostasis is more strongly correlated with the time and concentration of oxygen exposure than with the reperfusion event. I have shown that mutations in aak-2 (lacking a subunit of a kinase related to cellular energetics) or hif-1 (lacking a protein vital to the cell’s response to stress) effect protein homeostasis. My goal with this project is to find molecular components that maintain the cell’s ability to function even when exposed to aggregation-inducing conditions. Understanding the responses to hypoxia and reperfusion in C. elegans may reveal new strategies for the treatment of human conditions that result from insufficient oxygen supply, such as stroke, myocardial infarct and cardiovascular disease.

Americans use hundreds of millions of gallons of oil per day. Fossil fuels are not renewable and their consumption is a major source of air pollution and greenhouse gasses. Using microalgae for biofuel production has strong potential as an alternative fuel source; the oil yield per area is high, it can be grown on non-agricultural land and it requires little fresh water or pesticides. Much research has been done studying the green microalga, Botryococcus braunii, which stores hydrocarbon oil outside of its primary cell wall and has shown great promise as a microalgal fuel source under controlled lab conditions on a small scale. However, little research has been done to explore the capability of this alga to be cultivated in a larger-scale system. Growth in a photobioreactor offers protection and good control of variables. This study applies physical and chemical stress to B. braunii grown in a 13 L vertical, tubular photobioreactor to maximize lipid production. Careful analysis of the lipid composition and yield under these varying conditions provides a model system for large-scale production of biofuel from this alga. Further research into B. braunii and other microalgae for oil may provide a good source of renewable oil for the ever-increasing demand of Americans.

The goal of this project is to better understand new data returned from NASA’s Phoenix Lander spacecraft, which landed on Mars in 2008. Specifically, we are analyzing data gathered from an experiment called the Wet Chemistry Lab (WCL) where Martian soil was mixed with water and ions released from soluble salts were measured. The WCL collected voltage data from 15 ion-specific electrodes (ISEs), which can be used to determine the composition of the soil. However, the ISE data obtained is noisy and must be filtered. The algorithm being used is a Kalman smoother, which filters and smoothes the results using a predictor-corrector method. From the filtered results, we can calculate the concentration of different ions and their statistical uncertainties as well as work backwards to determine what salts and other compounds were present before and after dissolution. We are also interested in examining rates of dissolution in order to calculate limits on crystal size related to the kinetics of solubility. With this information we will be able to compare the soil of Mars to places with similar properties on the Earth and gain more insight into the surface conditions and habitability of Mars.

Women’s underrepresentation in computer science may be fueled by societal norms that deter women from expressing and pursuing an interest in this field. Compared to men, women may show less interest in computer science because computer science is perceived as masculine and women may face backlash from their peers for expressing an interest in masculine domains. Two experiments tested the hypothesis that social pressure might cause women to express less interest in computer science. Experiment 1 indicates that women, compared to men, imagine they would feel less comfortable joining a computer-programming club. However, both women and men felt that joining a computer-programming club would fit equally well with their identity. This suggests that women believe an interest in computer science could be compatible with their interests, but it is not approved of socially. In Experiment 2, women and men stated their interest in computer science either out loud to an experimenter (publically) or on an anonymous questionnaire (privately). Preliminary data suggest that women express less interest in computer science publically than privately, supporting our hypothesis that social pressure plays a role in shaping women’s interest in computer science. Together, our data indicate that social pressure may be one of the many factors influencing women’s underrepresentation in computer science. Understanding this social pressure and finding ways to reduce its impact are necessary in order to encourage more women to participate in the field of computer science.

The purpose of this investigation is to learn about and characterize behaviors involved in human haptic exploration. Specifically, participants are asked to explore a two-dimensional surface in search of particular features using their hands with only their sense of touch. There will be various paths that act as cues to provided information about the location of the feature. The use of the provided cues, path, strategy and other remarkable behavioral patterns executed by participants will be observed and quantitatively analyzed. It is anticipated that varying path features, such as amplitude or frequency, will result in different behaviors and that certain path features will be more useful in helping people build mental models of the surface. The collection of behaviors will be studied and findings will be extrapolated to encompass more general shapes and features to create a prediction method. The method will attempt to predict the behaviors or path of travel to be executed. A successful prediction method will aid in developing a computational model of human exploration behaviors and towards better robotic or prosthetic hand control.

Interfacial interactions carry tremendous importance in many areas of science and thus attract great interest in how they impact technology and industrial manufacturing. Adsorption energetics influence the size and sinter resistance of supported metal catalysts. Larger adsorption energy results in adsorbed metal atoms that grow in smaller clusters which are ideal for maintaining a large surface-to-bulk ratio for the catalytically active metal. However, too strong of an adsorption energy will decrease catalytic activity by reducing the adsorbates’ ability to bind molecules. Adsorption energies can therefore be used to tune the catalytic activity of a system. Unfortunately, these values are simply not known for many systems. In the Campbell group, we use a unique microcalorimetric approach to measure heats of adsorption of atoms and molecules onto single crystalline substrates. We have recently constructed a new ultrahigh vacuum adsorption microcalorimeter that employs an electron beam evaporator to produce temporally and spatially well-defined gaseous metal atom pulses that are deposited onto thin metal oxide surfaces. The evaporator metal flux is stabilized using a quartz crystal microbalance, the signal acting as a feedback loop to control the e-beam emission current. Adsorption of the metal atoms causes a transient temperature rise which is measured as a change in voltage across a pyroelectric ribbon that is in gentle contact with the back of the sample. The response is compared to a laser pulse of known energy to calculate the adsorption energy. Directly measuring these thermodynamically important values will allow for intelligent design of industrial catalytic processes and will also produce important benchmarks for improving theoretical methods.

Digital receipt systems have been implemented in an attempt to reduce the 228.7 million pounds of paper that is used to print receipts annually, but have not come into widespread use. We believe this is because these systems have overlooked the importance of involving target users in the design process. We conducted an online survey comprised of 129 respondents and gathered feedback from a 10 person focus group and discovered that privacy, ease of making returns, maintaining a history of purchases, and retaining proof of purchase are the fundamental user values that consumers would like to have in a digital receipt system. Using an iterative design process we designed a digital receipt system, entitled Freeceipt, which incorporates the fundamental user values we discovered. Freeceipt allows users to manage their receipts through an online web application as well as make returns and provide proof of purchases via an accompanying smart phone application, all just by providing an email address. We evaluated Freeceipt with several iterations of user testing and followup surveys and found that it fulfills the fundamental user needs of a digital receipt system while remaining simple and easy to use.

Many generations of students have left school with the common feeling of remembering only bits and pieces of information taught in class, never fully grasping a complete understanding of classroom material. Current teaching methods such as lectures and demonstrations often fail to adequately impart knowledge due to a lack of interaction between students and teachers. Also, these traditional methods often fail to visualize information. To address these issues, we present an adaptation of multi-touch technology for use in education settings to increase learning through visualizing of information and engaging interactions. We constructed a multi-touch table with an interactive 24” by 18” acrylic surface and used Community Core Vision (CCV) open-source software with a modified Windows 7 driver. To test our table, we created a flash card application to practice elementary arithmetic. We tested our prototype with 13 elementary and middle school students at the King County Library System’s K-12 after school tutoring program. Students were asked to use the elementary arithmetic flash card application on the prototype table. We received feedback through a 3-question paper survey and interviews. Our survey found that 13/13 students liked using the table. When asked if they would like to use study tools like ours to study other subjects, students gave an average rating of 4.53 (SD = 0.66) on a 1 (unlikely) to 5 (likely) scale. In terms of ease of use, students gave an average rating of 3.85 (SD = 0.80). Students enjoyed using our table to study elementary arithmetic. These findings suggest that students may enjoy using visual and interactive mediums such as a multi-touch table to study other subjects.

Plankton is crucial to the biogeochemical cycle of the planet to recycle and reuse carbon in the atmosphere. Recent research focused on environmental factors such as global warming and industrialization in Puget Sound and their effects on plankton abundance. Our research was designed to test the vertical distribution of plankton with regards to salinity. To better understand plankton abundance in Possession Sound we looked at data collected by students of the Ocean Research College Academy (ORCA). Monthly research cruises since September of 2003 at five different locations collected basic water quality data. Plankton sampling was completed using both a 253 and 20 micrometer net for horizontal and vertical tows at each station. The data collected shows the predicted abundance in plankton at and around the halocline, as opposed to the reduced amount of plankton found within other areas in the water column. With the data previously acquired and the methods we have used, we will to continue our research throughout the course of the year to rule out variables such as the seasonal effects on plankton abundance and halocline depth.

The movement and melting of glaciers causes seismic events known as icequakes. These are like earthquakes, but they propagate through the ice and are caused by elastic deformation of the ice as well as water flow in subglacial channels. Our goal was to locate icequakes from summer 2007 in one section of western Greenland and determine whether they involved bulk sliding or formation of crevasses, based on the motion of the ice during the passage of the wave. Seismograms from sensors in the North Lake and South Lake region were obtained, and the cleanest wave signals were picked. The segments of each waveform, including the primary, shear, and coda waves, were identified with a MATLAB program, and several MATLAB scripts were written that model ice particle motion during these different wave segments. The models were then run using real data, giving us visual and graphical information that allowed us to both estimate the direction of the incoming waves and describe the events. From seismogram analysis, we saw a shift from bulk motion events to cracking events over the course of the summer. This was accompanied by a shift in the location of the quakes, which came from the west, or down the ice, in early and middle summer and from the east, or up the ice, in late summer. We concluded that this was linked to changes in hydrology during the summer melt season, possibly related to drainage of glacial lakes. We now have more information about the nature of icequakes in western Greenland, and our particle motion program can be used to understand future seismic activity and how they might bring about long-term changes in the ice sheet, especially in the face of climate change.

Aging is a degenerative process characterized by a progressive deterioration of cellular components and organelles resulting in mortality. The budding yeast Saccharomyces cerevisiae has been used extensively to study the biology of aging, and several determinants of yeast longevity have been shown to be conserved in multicellular eukaryotes, including worms, flies, and mice. Due to the lack of easily quantified age-associated phenotypes, aging in yeast has been assayed almost exclusively by measuring the life span of cells in different contexts, with two different life span paradigms in common usage. Chronological life span refers to the length of time that a mother cell can survive in a non-dividing, quiescence-like state, and is proposed to serve as a model for aging of post-mitotic cells in multicellular eukaryotes. Replicative life span, in contrast, refers the number of daughter cells produced by a mother cell prior to senescence, and is thought to provide a model of aging in mitotically active cells. In the Kaeberlein lab, we are quantifying replicative life span for each of more than 4500 single gene deletion strains contained in the yeast ORF deletion collection. This represents the first quantitative genomic analysis of longevity in any species. A team of more than 15 undergraduates, graduate students, and research scientists work together to measure life span for approximately 1200 mother cells each week. This project has already uncovered several dozen novel longevity factors, many of which play a similar role in the aging of multicellular eukaryotes.

Current approaches in in vitro toxicology, drug screening, and cellular biology focus on the analysis of single cell behavior and functional changes under different environments. Among many techniques, impedance sensors have been used to monitor these functional changes (i.e. cell attachment, spreading, morphology, and cell-induced chemical changes to the environment around the sensor). However, it is rather challenging to analyze cells that are randomly moving and oriented with respect to their differences in shapes, morphologies, growth and different stages of vitality. The immobilization of single cells on sensor probes may alleviate many of these problems. Current immobilization methods include surface functionalizations using mostly synthetic molecules such as thiols. This type of immobilization approach, however, is nonspecific and requires many lengthy steps and the use of toxic chemicals. To overcome these shortcomings, we biocombinatorially selected inorganic-binding peptides (GEPI) that bind to inorganic surfaces with high material selectivity and affinity. These peptides can then be optimized to perform a multitude of tasks, making them a novel and powerful tool for assembly, coupling and synthesis of materials. Our project focuses on the use of gold binding (AuBP)–RGD bi-functional peptide constructs to specifically direct the assembly of single cells onto gold surface, and PEG-peptide conjugates to create non-fouling surfaces that prevent cell adhesion. The binding affinity of peptide based molecular contructs was quantified using Surface Plasmon Resonance. The effectiveness of surface functionalization on cell adhesion was tested in conjunction with various peptide deposition techniques, and visualized using fluorescence microscopy. Peptide based approaches for surface functionalization offer the advantages of green processing through integration of biological routes to material science and engineering, and providing a solid substrate specificity, controlled orientation of biological molecules, and biocompatibility.

 There is a large amount of research currently devoted to developing quantum computers.  In order to realize this goal, advances are needed to move away from the traditional bit to a qubit, or quantum bit, which would allow for complex information to be stored per unit of computation in a computer.  In order to understand systems that could act as a qubit, research is being performed on dilute magnetic semiconductors (DMS).  These materials, when quantum confined, create an environment where there is a great deal of control over the electronic structure of the material as well as a large number of ways to easily probe the current state of electrons through spectroscopy. Exploring how the electronic structure changes when additional electrons are introduced into the conduction band of the semiconductor is desirable for developing a better understanding of these materials. This research studies how surface ligands on the nanocrystal change the behavior of electrons excited into the conduction band.  Experiments are also dedicated to understanding how size and the introduction of impurities into the crystal affects the energies at which electronic transitions occur within these DMS’s.  Observations were made via UV/ViS absorption/luminescence as well as supported with time dependent density functional theory calculations. Results support that small changes to the crystal can influence the electronic structure greatly and in predictable ways which will help allow for a greater understanding of making materials that will make quantum computing a possibility.

The Short-tailed Albatross (Phoebastria albatrus) and Red-legged Kittiwake (Rissa brevirostris) are U.S. Fish and Wildlife Service (USFWS) species of interest due to limited breeding and foraging ranges. The Short-tailed Albatross, a USFWS Endangered Species Act (ESA) listed species, migrates from Japan to Alaskan waters to feed during the summer, whereas the Red-legged Kittiwake, a USFWS non-ESA “species of concern,” is an Alaskan resident, primarily restricted to the North Pacific. USFWS, in collaboration with National Ocean and Atmospheric Administration’s North Pacific Groundfish Observer Program (NPGOP) seabird observers, monitor the status of these species. Using NPGOP seabird sightings and vessel-bird interaction data, we compared the change in fishing effort, measured as boat days (i.e., sum of the number of boats fishing in a given year times the number of days each boat fished), with the number of Short-tailed Albatross sightings from 1993-2005. Our data indicate that Short-tailed Albatross sightings increased more than the population during this time period (6.5% per year) with only a slight increase in fishing effort. Also, these sightings have expanded eastward. We then evaluated the incidence of active feeding by both species as a function of boat days to understand potential negative vessel-bird interactions (e.g., bird mortality caused by entanglement in vessel gear). Active discard feeding by Short-tailed Albatross does occur, and they target (i.e., follow) vessels to feed on discard more often than Red-legged Kittiwakes where the two species overlap along the western Bering Sea shelf.

Cell transplantation has been shown to improve cardiac function following myocardial infarction (MI). Previous studies in our lab found that neonatal rat cardiomyocyte (NRC) grafts increased Ca²⁺ sensitivity of force in surviving host myocardium, which likely accounted for the graft-associated 10% increase in in vivo fractional shortening. The mechanisms behind improved function are not entirely clear, but correlated with changes in myofilament protein phosphorylation, which likely affect Ca²⁺ and length-dependent (preload) changes in force. This project was designed to test the hypotheses that 1) responsiveness to ventricular filling (Frank-Starling relationship) will decrease following MI, and 2) NRC transplantation after infarction will ameliorate this loss of function. One week after induction of MI (permanent ligation of the left anterior descending coronary artery), fluorescently labeled NRCs were injected into the area of infarction of some of the animals. Sham-operated rats (pneumothorax only) served as control. After 4-6 weeks, cardiac performance for all groups was preliminarily assessed using echocardiography. Then, whole working heart preparations were used to collect systolic and diastolic pressures and coronary and aortic output under controlled preload, afterload, and heart rate, testing the heart’s ability to follow the Frank-Starling relationship. NRC-injected hearts exhibited higher average power and response to ventricular filling than sham (media-only) injected hearts, indicating that NRC-engraftment significantly ameliorates MI-induced decreases in preload responsiveness. Force and Ca²⁺ sensitivity (pCa50) were then assessed using demembranated myocardial strips from these hearts. Myocardial strips from NRC-injected hearts had a length associated change in pCa50 that was similar to uninfarcted hearts (0.07 ± .02 vs. 0.1 ± .03, respectively), which was significantly improved as compared to untreated, infarcted animals (0.0 ± .03). These results indicate that loss of preload dependence following MI is, at least in part, due to altered myofilament function that is reversed following NRC engraftment.

Previous studies have found that certain lipids in mangrove leaves can be useful indicators for the presence and abundance of mangroves in the geologic past. The triterpenoid taraxerol is among the most relatively abundant lipid in the species Rhizophora stylosa and Rhizophora mangle. Due to its high abundance in the genus Rhizophora taraxerol has the potential to be an excellent biomarker (i.e. molecular fossil) for paleoclimate reconstructions, and its hydrogen isotope ratio may be a powerful tool for reconstructing past rainfall in globally extensive mangrove swamps where Rhizophora is present. In this study we are determining whether all four species of Rhizophora on the island of Kosrae in the Federated States of Micronesia (FSM) have similarly large abundances of taraxerol. We are also investigating if each species produces taraxerol with the same hydrogen isotope ratio relative to the water in which it is growing, and whether the salinity of that water affects the hydrogen isotopes of taraxerol. To achieve these goals, leaves from each of the four species of the Rhizophora in Kosrae (Rhizophora apiculata, Rhizophora mucronata, Rhizophora stylosa, Rhizophora lamarckii) were collected along the Nefalil estuary across a wide range of salinities, along with samples of the adjacent water and surface sediment. Lipids from the leaves were extracted and identified by gas chromatography-mass spectrometry, and the compounds were quantified via a gas chromatograph-flame ionization detector. A gas chromatograph-isotope ratio mass spectrometer was utilized to then measure the hydrogen isotope ratios of purified taraxerol from the leaves. Our initial results indicate that all four species of Rhizophora on Kosrae produce high amounts of taraxerol. The effect of species and salinity on the hydrogen isotope ratio of taraxerol must be assessed before using it as a tool for reconstructing past rainfall changes in Kosrae, Micronesia.

    In this paper I seek to answer the question: How does the homogeneity of racial-minority populations in a U.S. Congressional district affect the responsiveness of the representative to issues pertinent to racial minorities? The issue of representative responsiveness is important because it has implications for redistricting after decennial censuses. I expect to find that as the racial-minority population within a district grows, representatives will be more sensitive to racial-minority issues. However, I also expect that districts with more homogeneous racial-minority populations will elect representatives more sensitive to racial-minority issues than districts with more heterogeneous racial-minority populations. Furthermore, majority-minority districts should produce representatives that are more sensitive to racial-minority issues than white-majority districts, regardless of racial-minority population homogeneity. I anticipate a difference of racial-minority issue sensitivity between districts of varying levels of homogeneity to be a product of agenda diversity, where districts with high levels of heterogeneity will have a highly diverse set of agendas which will result in less attention to minority-constituent issues. Instead, representatives will appeal to more encompassing issues that run less risk of upsetting any one particular subset of their constituency. If representatives are found to be less responsive to districts with highly heterogeneous minority populations, it may suggest the need for re-evaluation of procedures for determining district boundaries. This study will focus on U.S. Congressional districts during the 110th Congress, based on population statistics from the 2000 Census. In this study I measure racial-minority population homogeneity using the Herfindahl (or Simpson) index which ranges between 0 for high heterogeneity, and 1 for high homogeneity. Representative responsiveness to racial-minority issues is measured by a variety of voting-record indexes (Leadership Conference on Civil Rights, Americans for Democratic Action, and the AFL-CIO) that score representative responsiveness to minority issues based on whether their votes in Congress matched the position of the respective institution, and sponsorship/co-sponsorship of racial-minority issue legislation in the House of Representatives.

Sentiment-override is a cognitive process in which individuals in intimate relationships perceive their partners’ behaviors either more positively or more negatively than the behaviors appear to others. Most studies, however, have evaluated sentiment-override within middle- and upper-income couples. There appears to be no previous work that has evaluated how sentiment-override manifests itself in low-income populations. The current study aimed to fill this gap by evaluating sentiment-override in sample of low-income couples (N=36) who were receiving public assistance. We examined whether sentiment-override in low-income couples was related to couples’ observed interaction patterns. Interaction patterns were measured using the Specific Affect Coding System (SPAFF), which captures positive and negative affective interaction patterns (e.g., defensiveness, validation), while couples engaged in a conflict discussion. Sentiment-override was captured by comparing outside-observers’ ratings of couple behavior during the interaction to ratings given by each partner of the spouses behavior during the interaction. Scores for positive and negative sentiment-override were created by comparing the ratings of each partner’s behavior provided by the outsider-observer and the spouse. Bivariate correlations showed that male negative sentiment-override was positively related to male tension and male physical affection and negatively related to male neutral behavior. Male positive sentiment-override was positively related to female validation. Female negative sentiment-override was positively related to male domineering and female validation. Female positive sentiment-override was positively related to male humor and female affection. Male negative-sentiment override was related solely to male behaviors whereas female negative sentiment-override was related to both female and male behaviors. Positive sentiment-override was related to the other partner’s behaviors for both genders. Although past research within other income levels has found relationships between spousal behavior and negative sentiment-override, the link between behavior and positive sentiment-override in low-income couples appears to be stronger than in other income levels.

The transition from vegetative growth to flower production occurs when a plant is stimulated by its optimal photoperiod (=duration of light within a day). In the model plant Arabidopsis thaliana, flowering is promoted by long day conditions. A long day photoperiod induces the flowering response through a signaling cascade featuring CONSTANS (CO), a transcriptional regulator that induces the expression of the mobile floral-induction signal, FLOWERING LOCUS T (FT) protein. Transcriptional regulation of CO expression is a crucial component of day-length dependent flowering mechanism. However, the mechanism that regulates CO transcription has still been largely unknown. We identified that a basic-helix-loop-helix (bHLH) protein binds to the CO promoter in yeast.We hypothesized that if the bHLH protein is involved in the regulation of CO in vivo, overexpression of the bHLH may cause changes in the expression of CO, and subsequently would change timing of flowering. When the bHLH gene was overexpressed in the transgenic plants, they demonstrated an early flowering phenotype. This result indicated that the bHLH may increase CO expression, and in turn elevated CO expression may induce early flowering. We found that the CO expression level was elevated in the transgenic lines. Based on sequence homology, three additional bHLHs were discovered as close homologs. Individual overexpression lines for these bHLH genes also demonstrated a similar early flowering phenotype. We are currently analyzing whether these bHLH proteins also regulate CO transcription. Through our research, we will obtain insight into CO transcriptional regulation, which is the core of the day-length sensing mechanism.

Rehospitalization in inpatient psychiatric facilities is stressful for patients and families, is costly, and generally indicates that the patient is experiencing serious distress. Several studies have found that forty to fifty percent of psychiatric inpatients are rehospitalized within a year. Some degree of psychiatric readmission may be unavoidable and even beneficial to those seeking care, however it is generally felt that seeking readmission within a short period of time, usually during a period of six months or less, is unnecessary and potentially preventable given appropriately targeted interventions. It is especially remarkable that numerous patients are discharged and readmitted within the same month, a phenomenon that pointedly calls attention to potentially preventable readmissions. Given the emotional and financial costs of requiring such a high level of care within a short period of time, it is valuable to gain a greater understanding of risk factors for rehospitalization in an attempt to better target services to assist this population. To learn more about this phenomenon, a retrospective chart review was completed, aimed at exploring a variety of individual characteristics for the purpose of examining which factors correlate most strongly with inpatient readmission within 30 days. The study focused on patients ages 18 and older who were voluntarily admitted at their most recent admission. Patients admitted for detoxification only are not included. Understanding factors influencing readmission within 30 days may help facilitate creation of more targeted interventions to help stabilize and support individuals in their transition out of the hospital. Results should inform discharge planning and add to the existing body of research on inpatient psychiatric readmission.

Despite major advancements in our understanding of the neural systems involved in persistent developmental stuttering (PDS), the causal mechanisms underlying acquired neurogenic stuttering (ANS) remain poorly understood. ANS typically occurs after stroke, and its primary symptoms resemble those of PDS (i.e., within-word dysfluencies). However, individuals with ANS often show no adaptation effect and no fluency-enhancement with altered auditory feedback. To date, little is known about differences and similarities between ANS and PDS in terms of loci of stuttering--that is, the locations of stuttering moments within spoken utterances. Brown's research on PDS has shown that stuttering is more likely to occur on (1) longer words, (2) words that occur early in the sentence, (3) content words, and (4) words that start with a consonant. In this study, we therefore compared ANS and PDS with regard to the distribution of stuttering moments as quantified by Brown's word weights (for each stuttered or fluent word, 0-4 points are assigned based on the aforementioned four factors). As expected, adults with PDS showed greater word weights for stuttered versus fluent words. Individuals with ANS showed a highly similar pattern with greater word weights for stuttered versus fluent words. Calculating word weights for each factor separately (word length, sentence position, grammatical class, initial consonant) revealed that the ANS group also did not differ from the PDS group in the relative influence of each individual factor. Thus, although there are several known differences between acquired neurogenic and developmental stuttering, the loci of stuttering appear to be influenced by similar factors in both disorders. Of those factors, word length and grammatical class had the strongest influence on the occurrence of dysfluencies in both groups. These findings can be used to generate new hypotheses regarding the neural basis of fluent and dysfluent speech production.

Though we have observed the Galilean satellites (Jupiter’s moons Io, Europa, Ganymede, and Callisto) since they were discovered by their namesake in 1610, there are some phenomena that remain unexplained. Without an understanding of why and how certain landforms and characteristics develop in different locations, it is difficult to determine how these moons fit into the larger solar system. Specifically, in this project we will explore 1) the evolution of knobs, or remnants of crater rims, on Callisto and 2) the presence of frost deposits at specific points on the three icy satellites (Europa, Ganymede, and Callisto), both of which are featured prominently in Galileo images. The first to attempt systematic quantitative modeling of landscape evolution for these satellites, we will develop a 3D model which simulates sublimation and re-condensation of volatiles, solar and radiative heating and cooling, and thermal diffusion at the surface and subsurface levels. These models will allow us to essentially reverse engineer the past and to understand what present appearances imply about the initial shape and composition of these surfaces, as well as subsequent geomorphological processes.

 Heart attack is one of the leading causes of death. In the United States alone, 1 heart attack occurs every 34 seconds (Reference AHA). Heart attack, also known as Myocardial Infarction (MI) occurs when blood flow to the heart is obstructed, resulting in an inadequate amount of oxygen supply for the cardiomyocytes (CMs) to survive, which results in CM cell death and ultimately scar formation. Since the heart is unable to regenerate on its own, interventional therapies are necessary to promote myocardial repair following heart attack. One of the major limitations of many current cell- and tissue- based therapies is lack of survivability following implantation. Heme oxygenase-1 (HO-1) is an enzymatic membrane protein that is endogenously up-regulated in response to oxidative stress. HO-1 breaks down heme molecules, resulting in by-products that have cytoprotective effects; therefore, HO-1 is currently being investigated as a therapeutic tool to promote the survival of cell and tissue implantations following heart failure. It is yet unknown, however, whether there are any functional effects of modulating HO-1 in vitro and in vivo. In the HAMM lab, we are currently seeking to understand whether altering HO-1 activity affects the contractile or calcium handling properties of intact adult rat cardiomyocytes (ARCs). My role is to efficiently quantify the amount of HO-1 expression in the cell samples. Western blots prove to be an excellent technique for protein profiling, because we can specifically identify both the protein in question as well as the amount of the protein in question. We can then compare the cell samples’ function with the amount of HO-1 in the sample, thus adding to our understanding of the HO-1 pathway.

Large plastic debris in marine environments has received considerable attention from scientists, policy makers and the media. Only recently, however, has much consideration been given to the unique problems presented by microplastics (5.0mm - 0.33mm) in aquatic habitats. The small size of these plastic particulates makes them difficult to study and potentially more hazardous to marine and freshwater environments. While initial efforts to quantify microplastics have concentrated in marine environments, this study investigates microplastics load in freshwater runoff by sampling Lake Washington and the surrounding watershed. Water samples were obtained with flow meter-equipped plankton nets modified for accurate surface collection, and then processed using an oxidation reaction and visual inspection method developed by UW Tacoma. Results suggest significant freshwater origins for microplastics found in the Puget Sound Basin, underscoring the contribution of nonpoint sources to marine microplastic pollution.

MobileASL, a software program enabling sign-language video on mobile devices over conventional U.S. cellular networks, was evaluated in a preliminary three-week field study during the summer of 2010. Through a series of interviews, questionnaires, and a focus group, we asked participants about their behavior with and perceptions of MobileASL. In addition, we used on-device experience sampling and usage logging to observe how MobileASL was used. Initial results indicate that although participants felt that MobileASL’s short battery life limited its use, participants took advantage of the mobility of the technology and used it for in-the-moment information gathering in places like buses and restaurants or while travelling. In preparation for our main field study this summer, we will port MobileASL to Android. To do this, we plan to add the MobileASL video encoder, field study data collection tools, and power-saving algorithms to an existing open-source video chat application called IMSdroid. The port to Android will also allow MobileASL to be used on newer and faster smartphones that have front facing cameras. In the future, we will also conduct studies to compare MobileASL’s battery use and video quality to that of commercial software, such as Fring and Apple’s FaceTime. MobileASL will continue to be a competitive program with its unique high quality, low bit rate video encoder.

Systemic lupus erythematosus (SLE) is an autoimmune disease that chronically affects multiple organ systems. It is a difficult disease to accurately and efficiently diagnose in a clinical setting, as the signs of lupus resemble severe infection or malignancy. Programmed death-ligand 1 (PD-L1) is a regulatory protein that controls peripheral T cell tolerance that may be abnormal in SLE. It has been shown previously that patients with infections express high levels of PD-L1 whereas patients with active SLE fail to express PD-L1 on antigen-presenting cells such as monocytes and myeloid dendritic cells. Thus, PD-L1 may be a marker to diagnose and monitor patients with SLE. Rather than relying on the intensive practice of measuring PD-L1 protein levels in a laboratory setting, this study investigates the clinical implication PD-L1 messenger ribonucleic acid (mRNA) may have as a potential biomarker for SLE disease activity. Patients were classified by SLE Disease Activity Index (SLEDAI), where active disease was defined by SLEDAI>4. Peripheral venous blood samples were collected using PAXgene tubes. Total RNA was extracted from whole blood. PD-L1 mRNA expression was determined by reverse transcription real-time quantitative polymerase chain reaction and normalized to glyceraldehyde-3-phosphate dehydrogenase expression. Mann-Whitney rank-sum was used to test for a difference in PD-L1 mRNA expression between SLE patients and age-matched healthy controls. We found decreased PD-L1 mRNA expression in 2 patients with active disease. In contrast, control subjects and patients with disease remission showed similar level of mRNA expression. The preliminary data justifies further analysis of PD-L1 mRNA expression as a potential biomarker to predict SLE disease activity. PD-L1 gene expression in whole blood could serve as a clinical application to distinguish patients with SLE from those with other forms of autoimmunity, infection or malignancy.

The most debilitating type of chronic pain is peripheral neuropathic pain, which is intense, unremitting and often resistant to all available therapies. Several animal models were developed to better understand chronic pain development that clinically leads to allodynia and hyperalgesia. A new model of neuropathic pain was developed recently: partial infra-orbital trigeminal nerve ligation (pIONL) (Xu, Aita et al. 2008). The frequent lack of effect of morphine to treat neuropathic pain led to the development of other therapies. The actual study aims at evaluating the impact of pregabalin treatment to decrease neuropathic pain in animals that were exposed to pIONL. Three groups of animals were evaluated: group 1 (G1 = the placebo group) received preoperative saline, pIONL on D0 and postoperative saline for 21 days (D21). G2 (= curative group), received preoperative saline, pIONL, and postoperative pregabalin (30mg/kg) on D7 until D21. G3 (= preventative strategy), received preoperative pregabalin, pIONL D0, and postoperative pregabalin D1 until D21. Pregabalin or saline treatment (30mg/kg) was given to mice intra-peritoneal twice a day for a duration reported above. Nociceptive threshold was evaluated with von Frey filaments. When administered before the surgery, intra-peritoneal pregabalin given twice daily to rats was able to decrease postoperative hyperalgesia and rats’ nociceptive threshold were able to return to normal in few days (G3) as opposed to rats treated with saline (G1 and G2) that developed neuropathic pain and sustainable hyperalgesia for several days. The preventive pregabalin strategy was able to oppose early on the development of postoperative facial neuropathic pain. This is a new model of surgery-induced neuropathy, which is clinically relevant to all the patients undergoing invasive facial surgery for cancer. This would lead to propose a preventive strategy with pregabalin before patients are scheduled for traumatic surgery with high likelihood of developing chronic neuropathic pain.

The addition of transgenes to crop plants can introduce valuable agronomic traits such as pesticide resistance and increased yields. When performing transformations with plant DNA, transgenes have typically been introduced into the nuclear genome. An alternative is to introduce transgenes into the plastid (chloroplast) genome. This alternative provides a natural biological containment against dispersal by pollen to non-target plants due to the maternal inheritance of plastids. There is also a potential for higher expression of the transgene in the plastid. With current methods the efficiency of plastid transformation has been low, approximately 5 transformants per particle bombardment with tobacco plants. Our goal is to improve the efficiency using tobacco leaves. Two possible ways of increasing plastid transformation efficiency are to modify the form (or structure) of the plasmid DNA used to introduce the transgene as well as to vary the age of leaf tissue. For the former, linearized plasmids may increase efficiency compared to the standard circular form of the plasmid. For the latter, transformation may improve with younger tissue, where plastid DNA (ptDNA) replication is highest. We have used particle bombardment to deliver either circular or linearized plasmid DNA to plastids in tobacco leaves. In addition, the plastid transformation process was performed on young and old tobacco leaves. Our initial experiments do, in fact, show improved results using the linear form of the plasmid. Current and future experiments include more testing using different bombardment parameters and growth media to find the optimal conditions for increased transformation efficiency. To verify insertion of the transgene, we isolate total DNA from positive (callused) tobacco leaves and use PCR to amplify the wild type or transgenic DNA. We will then apply any insights for increasing transformation efficiency that we gain to other crop plants including maize.

Past research on midlife has indicated that it is a period of relative stability for many lifestyle domains, including personality and cognition. These studies looked at group averages across time, but when individual change trajectories are identified, it seems that while most do indeed remain stable, a subset of the population declines in episodic memory during midlife, while another subset experiences memory gain during this period. My project aims to identify some of the lifestyle differences between these two subsets. This will hopefully elucidate some of the patterns that in the future may lead to a discovery of the mechanisms behind cognitive changes in aging. My project uses data from the Seattle Longitudinal Study, a longitudinal study of cognitive aging that samples from the Group Health Cooperative. Subjects were identified as gainers or decliners in episodic memory if after a 14 year period (two 7-year intervals) they differed by at least one Standard Error of Measurement from their baseline scores. I compared gainers and decliners on lifestyle variables in the domains that are common predictors of cognitive change in old age to see if they predict similar change in a midlife population. These domains include demographic and personality variables, environment (family, social, and cognitive), daily activities (physical, social, and cognitive), health, and occupation factors. I found that several variables within these domains predict cognitive status in the hypothesized direction, especially in the areas of daily social and cognitive activities. Future research should attempt to uncover more of these patterns within the midlife population in other areas of cognition.

Previous research has suggested a strong link between maternal depression and potential adverse impacts on children’s mental health. Children whose mothers suffer from moderate to severe depressive symptoms seem to be at risk for developing psychopathology (Gotlib & Goodman, 1999; Kouros & Garber, 2010). Maternal depression has been implicated in negatively impacting mothers’ parenting behaviors, which may subsequently contribute to the development of children’s depression, anxiety or abnormal functioning (Letourneau, Salmani, & Duffett-Leger, 2010). Additionally, low household income has been correlated with higher levels of depression in mothers (Rafferty, Griffin, & Robokos, 2010). In this study, the relationship between mothers’ self-reported depressive symptoms and their reports on their children’s depressive and anxiety symptoms were examined, along with the role of income in relation to maternal depression. Subjects were mothers and their pre-school aged children (N=299) who were recruited as part of a larger longitudinal study called Project 1,2,3, Go! at the University of Washington. Preliminary data analyses suggested that mothers who scored higher on depression using the CES-D also scored their children higher on symptoms of anxiety and depression on the CBCL (r = 0.19, p = .001; r = 0.30, p < .001 respectively). Additionally, results suggested a significant negative correlation between maternal depression and family income (r = -0.33, p < .001). Final analyses will examine the relation of these variables over multiple time points. Our research can raise further awareness of the importance of early detection and treatment of maternal depression so as to minimize the risk of adverse effects on children’s overall mental health and behavioral problems.

Cancer remains a leading cause of death worldwide. Surgery, chemotherapy and radiation have been the standard treatment for solid cancers but these regimens do not always result in a cure. Recently there has been increasing evidence suggesting that our immune system (T and B cells) can be manipulated to recognize and attack tumors. Naïve T-cells (T_N), mature T-cells yet to encounter antigen, have been used for anti-cancer T-cell therapy in both mice and humans, but their therapeutic success has been limited in part due to their inability to persist in tumor-bearing hosts. Unlike T_N, memory T-cells (T_M) have previously encountered antigen. T_M have been studied in infection models but little is known about their potential anti-cancer functions. In infectious models it was demonstrated that T_M persist in hosts and upon re-encountering the pathogen they proliferate and mount a vigorous immune response. Since proliferative and survival potentials of transferred tumor-reactive T-cells are major determinants of anti-cancer efficacy. The question arises whether T_M have an increased therapeutic efficacy for treating cancers. In order to develop effective anti-cancer T-cell therapies for humans, there is a need for accurate pre-clinical mouse tumor models which reflect tumor genesis in humans. Since most pre-clinical cancer studies are performed with transplantation tumors in mice, which does not reflect the clinical situation, translation into the clinic is difficult and only of limited success. A mouse liver cancer model was developed, which precisely mirrors the formation of liver tumors in humans, using transgenic mice containing the oncogene SV40 as a transgene in liver cells. These mice spontaneously develop SV40-expressing liver tumors. Furthermore, we have generated SV40-specific T_M to target SV40-expressing liver tumors in adoptive T cell therapy studies. Our model represents a unique physiological pre-clinical system which allows elucidating the requirements for effective T cell-based anti-cancer therapies.

Diatoms are important photosynthetic eukaryotes found in the lighted portion of the oceans and lakes of the world. They fix carbon into organic matter, producing oxygen in the process, and become food for other organisms. One hypothesis of why diatoms are so successful is that they have great physiological and genetic diversity even among closely related strains. As the first diatom to have its whole genome sequenced, Thalassiosira pseudonana (Strain 1335) is a well-studied diatom. T. pseudonana has been isolated from different ocean basins around the world and characterized. The new strain I am working with is from the saline lake, Copper Basin, in CA, U.S.A, making it the first non-marine strain to be studied. Our new strain is believed to belong to the T. pseudonana species based on light microscope identification, but since it is from a non-marine origin I expect it to be very different genetically and physiologically from the other strains. To compare this new strain to the known strains of T. pseudonana, I cultured, isolated single colonies, and made them axenic. I will investigate the genetic variation and phylogenetic relationship of this new strain to the other cultured strains using 18S ribosomal DNA. To compare the physiology of this new strain to previously characterized strains, I will determine its growth rate under different light levels. Interestingly, the growth rates of axenic isolated cultures have appeared to be lower than the original cultures with bacteria. This could indicate that this new strain has a mutualistic relationship with the natural bacteria, but more work is needed to find what benefits the new strain is getting from the bacteria. By finding the similarities and differences between the new strain and the known strains, we can better understand how diversity helps diatoms be so successful.

Arabidopsis receptor-like kinase (ERECTA) signaling pathway has in previous studies shown to be a key player in stomatal development and organ morphogenesis. It has been proposed that during development ERECTA receives signals encoded by a family of small secretory peptides, Epidermal Patterning Factor (EPF) and EPFL-LIKE ligands. Previous research has shown EPF1 and EPF2 ligands play an important role in the ERECTA mediated process of stomatal development. Our project is based on the hypothesis that EPFLs are ligands for ERECTA-family RKs not just for stomatal patterning and differentiation (mediated by EPF1 and EPF2), but also for diverse growth regulations that include shoot meristem maintenance, aerial organ growth, inflorescence architecture, and vascular tissue differentiation. By taking a genetic approach we have been able to obtain and confirm T-DNA insertion lines of null alleles of EPFL. Through genotyping using polymerase chain reaction (PCR) we have been able to observe variations in the phenotype of plants with a variety of potential knocked out EPFL ligands. We are currently testing our hypothesis through detailed morphometric analysis of these mutant plants in order to compare their developmental patterns and morphology with known erecta mutants. The link between EPFL and ERECTA should be further studied in order to elucidate the mechanism by which a single receptor can participate in multiple pathways but still retain specificity for both the input ant output signals.

Extensive cognitive development research has shown that humans orient their visual attention in response to social cues such as the direction of someone else's gaze. The ability to use eye-gaze plays a crucial role in the understanding of another individual's state of mind such as focus of attention and desire. Individuals with neurodevelopment disorders such as Autism Spectrum Disorder (ASD) and Fragile X Syndrome (FXS) show developmental deficits especially within the context of socio-communicative interactions.The present study investigates if individuals with FXS and ASD show similar patterns of using social (eye gaze, hands) and nonsocial cues (arrows) to direct their attention. Participants aged 13- 40 years old with ASD, FXS, or neurotypical (NT) development were administered a social and non-social cueing task. Participants observed three conditions. In the baseline condition, a central cue stimulus did not provide any information as to the target location (face remained still and neutral, the signs did not change, and the hands pointed forward). In the cuing condition, the central stimulus cued the participant’s attention to the left or right (eyes on a face shifted left or right, hands pointed left or right, or arrows pointed left or right). The target appeared on the same side (congruent trial) or opposite side (incongruent trial). Participants were to then respond by pressing a button with their right or left hand that matched the side that the target appeared. Preliminary results suggest that the FXS group is slower to react to a target regardless of whether it is congruent or incongruent with the cue. However, the ASD and NT groups’ reaction times were facilitated by congruent cues, both social and non-social. We expect to see faster overall facilitated reaction time in typical developing individuals and in social versus non-social cues for both ASD and typical groups.

A significant health risk for astronauts assigned to long-duration spaceflight is the loss of bone mineral density (BMD) as well as decrements in muscle and bone strength. It is believed that maintenance of bone health is dependent on mechanical loading. This project utilizes two wireless tri-axial accelerometer/gyroscope sensors to detect load-bearing activities associated with maintenance of bone health in space. The enhanced Zero-Gravity Locomotion Simulator (eZLS) and Combined Countermeasure Device (CCD) are being used as space mission analog devices for data collection. Subjects are asked to perform sets of resistance and cycling exercise that are typical of crewmembers during spaceflight. A decision-tree initialized artificial neural network has been developed to autonomously recognize user activity based on the signals from the sensors. The magnitude and frequency of loading from each individual activity is then weighted through a function called the Enhanced Daily Load Stimulus (EDLS) to quantify osteogenic stimulation from mechanical loading. Real-time monitoring of osteogenic stimulus can then be recorded as a percentage of the daily amount required to maintain bone health. Although this project is primarily oriented primarily towards application in space, the development of a functional Bone Health Monitor (BHM) has significant Earth-based application as well. Such a device could be invaluable in efficiently and non-invasively recording activity and loading histories to help estimate the benefit of load bearing activity on BMD in patients at risk for osteoporosis. This project is funded by the National Space and Biomedical Research Institute.

According to the American College Health Association (2008), sexually active students reported using condoms during vaginal intercourse only 53.5% of the time. Surveying attitudes about condoms may be insufficient in determining if an individual will engage in safer sex; researchers have proposed alternative methods of measuring condom use. Condom self-efficacy focuses on actual condom use behaviors by measuring one’s confidence in condom use across a variety of situations. Using principles of Bandura’s social cognitive theory, O’Leary and colleagues (2008) proposed that those with higher condom self-efficacy would be more likely to discuss condom use with a partner, exert more effort in using condoms, and exhibit more consistent condom use. Another way to examine condom use behavior is through sexual motives: individual motivations for engaging in sexual intercourse. Previous studies have found that having sex to please one’s partner is negatively related to condom use, suggesting that other-directed sexual motives may be associated with condom use (Cooper et al., 1998). The current study will further examine the relationship between sexual motives and condom use and determine whether condom self-efficacy mediates this relationship. It is hypothesized that individuals high in peer and partner sex motives (other-directed) may be less confident in their abilities to communicate about safer sex practices to their partners (exhibiting low condom self-efficacy), leading to a lower likelihood of condom use. A random sample of 1,055 undergraduate students ages 18-30 completed an online survey examining risky sexual behavior. It included measures of sexual motives, condom self-efficacy, and condom use. Results from this study will assist in further development of risky sexual behavior interventions by taking into account the influence of sex motivation, as mediated by condom self-efficacy, on condom use.

Prior to the 1997 Asian Financial Crisis, Thailand was known as one of the countries undergoing rapid economic growth as a result of its growth in trade. Despite its growth and its strong recovery after the crisis, Thailand recently has been experiencing unceasing civil unrest, which has raised many heated discussions regarding the root causes of the discontent. Income and social inequality are among ones of the most discussed factors. While many studies have indicated a conclusive relationship between trade liberalization, economic growth and absolute poverty reduction, previous studies by Edwards and Dollar and Kraay have not shown conclusive empirical evidences on the relationship between trade liberalization and income inequality. Hence, in this paper, I will examine the possible correlation between trade openness and income inequality in Thailand with the attempt to address the issue of sustained income inequality in Thailand. I will be using ordinary least square (OLS) regression with variables such as the GINI Index and other trade openness representative, before and after 1992 when the ASEAN Free Trade Agreement was established, with a data set going back to 1975 through 2008.

Prenatal cocaine exposure (PCE) is a significant health problem that can cause abnormal cognitive and behavioral development, as well as movement disorders. Preliminary data from our laboratory shows that cocaine exposure in utero produces over-inhibition in the striatum. The striatum is the primary brain nucleus for cortical information entering the basal ganglia and it regulates motor control, cognition, and habit learning. Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter that modulates striatal signals by binding to trans-membrane GABA_A receptors (R) and GABA_BRs that are fundamental in organizing and controlling striatal output. Thus, examining their expression could provide insight into how cocaine alters striatal activity. We hypothesized that excessive GABAergic inhibition following PCE is produced by overly-functioning GABA interneurons, with secondary effects on GABAR expression and sensitivity. Immunoblotting assays determined if there were alterations in the expression of GABA_AR and GABA_BR subunits. Mice exposed to cocaine, saline, or saline pair-fed (SPF) controls in utero were sacrificed at 60 days of life and striatal tissue was removed and processed for immunoblot analysis. Immunoblot intensities to GABA_Aα1, GABA_B1, and GABA_B2 primary antibodies were quantified and their intensities were compared for each treatment group. Preliminary findings show alterations in GABA_Aα1 receptor expression for the cocaine group and data collection is ongoing. This study will be used to determine the mechanisms whereby congenital cocaine exposure might produce the behavioral phenotype and might further establish clinical treatments for drug-exposed children.

The expressive arts are part of a growing field of research on the humanities in health care; these arts continue to gain respect as auxiliary treatment modalities. We are doing a meta-summary of the literature on  the use of one expressive art form, the fiber arts (for example, quilting or knitting) in health care. In the review of approximately 60 articles, we analyze which fiber art has been used most widely, what populations have utilized or benefited from them, in which health care contexts they have been used, and how their use has changed over the past 40 years. The articles were found by searching CINAHL, Pubmed, and Complete Academic using 20 search terms pertaining to fiber arts including knit* and quilt*, and in association with therapy. Preliminary findings show that fiber arts have been used therapeutically to deal with grieving and addiction, within hospital and nursing home settings as well as inthe community, and often involve collaboration between groups of patients or patients and caregivers. This meta-summary is significant because it wil explicate the status of fiber arts in health care. We hope to use this meta-summary to determine suggestions for future studies that are empirically based.

Malaria is a globally prevalent infectious disease with 247 million annual cases leading to 1-2 million deaths.  An array of anti-malarial treatments exist today, however, drug resistance has rendered many of the commonly used drugs ineffective, such as chloroquine and pyrimethamine-sulfadoxine.  Continual exposure of malarial parasite populations to different drugs may have selected not only for resistance to individual drugs, but also for genetic traits that favor initiation of resistance to novel, unrelated anti-malarials.  Parasites that acquire resistance at significantly higher frequencies than other strains are labeled with the Accelerated Resistance to Multiple Drugs (ARMD) phenotype.  Previous studies in the Rathod laboratory indicate that ARMD parasites employ hypermutagenesis and genomic rearrangements to escape selective pressures.  We use chemical tools to explore the breadth of resistance mechanisms utilized by ARMD parasites.  In the current study we are using selective, triazolopyrimidine-based inhibitors that target malarial dihydroorotate dehydrogenase (DHODH), an essential enzyme of pyrimidine biosynthesis.  My project is focused on quantifying the capacity of ARMD parasites to acquire resistance by conducting a series of selection experiments using potent DHODH inhibitors.  PCR, quantitative PCR, and comparative genomic hybridization were done to evaluate the presence of Plasmodium falciparum DHODH (Pf DHODH) mutations and gene amplifications.  The goal of these studies is to shed additional light on the genetic strategies initiated by ARMD parasites under stress that allow them to rapidly and successfully evolve.

Prostate cancer is one of the most common forms of cancer and is highly associated with advanced age. It is classified as epithelial in origin and recent research has shown that changes to the epithelial extracellular matrix, such as those associated with aging, can alter the behavior of prostatic cells in a manner that promotes tumorigenesis. We used a benign prostatic hyperplasia (BPH-1) epithelial cell line and aged 3D collagen to simulate the aged extracellular matrix. BPH-1 cells placed in young collagen served as a control. We tested the hypothesis that aged collagen stimulates more aggressive growth. The outcome of placing BPH-1 cells in aged collagen was analyzed in terms of phenotype, proliferation, migration, gene expression, chemokine secretion, and the novel gene GOLM1. In terms of phenotype, BPH-1 cells did not exhibit epithelial to mesenchymal transition when placed in aged collagen relative to young collagen. However, there was less evidence of epithelial cytokeratin expression when BPH-1 cells were placed in aged collagen. BPH-1 cells displayed increased proliferation and migration when placed in aged collagen relative to young collagen. The expression of pro-growth cytokines, such as CCL2, was increased in BPH-1 cells when placed in aged collagen. Expression of GOLM1 did not change when the BPH-1 cells were placed in aged collagen. We propose that aged 3D collagen promotes features associated with tumorigenesis in BPH-1 cells. These include decreased cytokeratin expression, increased proliferation and migration, and the expression of pro-growth chemokines.

L. plena and L. scutulata are sympatric in most of their geographical range. These species represent potential model systems sympatric speciation. Our team investigated the Littorina species compositions of these two species at various sites in the San Juan Islands, WA. Species composition is defined as the percent of a species present in a location. Our aim was to find any pattern in the species distribution and species characteristics of these snails. Such species distributional data could lend support toward our two major hypotheses on how these two Littorina species diverged. Our results suggest that allopatry is unlikely, but do not lend full support for the sympatry hypothesis. Allopatric speciation is a divergence that occur due to selective pressure from different geographic locations. Sympatric speciation is when the divergence event is caused by difference in selective pressure within the same geographic location. On the other hand our data suggests various external traits, shell size and egg capsule sizes for example, can be used to look at these organisms. In the end, our data are not conclusive and should be viewed with certain parameters in mind. Measurements of various traits of the samples suggested that follow up research to be done as prescribed in the paper.

The evolution of the web and the independent development of web browsers have led to poor web design practices and inconsistencies in rendering by browsers. This led to the development of web standards, supported by organizations like the World Wide Web Consortium (W3C) and the Web Standards Project (WaSP). Work on the HTML5 standard commenced in 2004, the standard entered the Working Draft stage in 2011, and is expected to reach Candidate Recommendation in 2012. These standards stress accessibility of information by the separation of content, presentation, and behavior. Content is held by HTML, presentation is in stylesheets, and behavior is dictated by scripts. Our project goal was to redesign the Space Grant website so that it met the web standards laid out by the W3C and WaSP. Because the majority of the site design took place during the summer of 2010, many decisions had to be made about which standards to follow, and which ones were too costly to consider. The final implementation of web standards for the site included the design of a new layout and an intuitive navigation system. The website was made accessible across various devices such as mobile phones, screen readers, low resolution monitors, and with stylesheets or Javascript turned off. We used free open source tools for the development to keep costs low and increase future maintainability. Loading times and overall usability were also taken into consideration. Ultimately, the website will be accessible to a wider group of people and be easier to use, increasing traffic to the website. The site content will also be editable even by those unfamiliar with web development, and maintenance to conform to future standards will be a more trivial task.

The purpose of our research is to develop pressure and temperature sensitive (PTS) beads that will allow scientists to generate highly accurate models for turbulent flows. Traditionally, scientists have measured surface pressure and temperature distributions using extensive embedded arrays of pressure taps and temperature sensors. This allows engineers to pinpoint high-pressure areas on wings. A less intrusive method for creating pressure and temperature distribution models involves the use of pressure sensitive (PS) and temperature sensitive (TS) dyes that luminesce as functions of pressure or temperature. PS dyes that luminesce at different wavelengths than TS dyes allow scientists to simultaneously generate pressure and temperature curves. Unlike PS and TS dyes, microbeads can be used to model temperature and pressure distributions in turbulent flows. We are testing to find the combination of a reference dye, a PS dye, and a TS dye that will form a PTS bead that emits light at different wavelengths at the highest intensities and with the fastest reaction times. Stern-Volmer pressure sensitivity plots and temperature coefficient plots, which are generated using a specially-constructed apparatus, will allow us to find an optimal composition for a PTS bead. PTS beads will allow scientists to generate high-resolution models of turbulent flows and three-dimensional particle velocimetry. Thus far in our research, we have discovered that the reaction times of different dyes change when they are converted into bead form. In testing PtOEP Max, a PS dye with a fast reaction time in its dye form, it was found that the PS beads created using PtOEP Max had a much slower reaction time than PtOEP Max in its dye form. Further testing will be needed to determine the optimal combination of PS dye, TS dye, and reference dye to form a PTS bead with the shortest reaction time.

Practicing speech language pathologists drastically underuse the only test specifically created to diagnose specific language impairment (SLI), the Test of Early Grammatical Impairment (TEGI).  Children with SLI show receptive and expressive language deficits, but no cognitive or hearing impairment.  Given that approximately 7.4% of five-year-old children have SLI, speech language pathologists must be equipped with the proper tools for diagnosis, which can then lead to successful intervention.  One of the most diagnostically accurate tools for SLI is childrens' percentage correct use of tense and agreement marking, also referred to as finiteness. The current study investigates three different measures of finiteness marking: spontaneous language samples, the Structured Photographic Expressive Language Test (SPELT), and the TEGI.  Language samples are the most naturalistic way to assess use of finiteness, but also the most time consuming.  The SPELT was created to detect expressive language impairment, but not SLI specifically, and only 30% of the items address finiteness.  The TEGI was designed as a diagnostic tool for SLI and 100% of the items target finiteness. These three measures will be administered to two participant groups, children with language impairment and typically developing children.  The main questions of interest are:  1. Does a child’s accuracy in producing finiteness marking differ based on the test administration method and 2. Do the differences in method have a similar impact on typically developing children and children with SLI.  If test administration methods differ, the next question will be which of the methods is the most accurate.  Data will be statistically analyzed using an ANOVA in order to compare how much the three methods of test administration differ in terms of percentage correct use of finiteness marking. Results will determine the most accurate and efficient way for speech language pathologists to diagnose SLI.

Cryptobiotic crusts commonly cover the surface of soils in arctic, alpine, desert, and grassland ecosystems. These crusts are composed of varying proportions and species of lichens, mosses, fungi, bacteria, and cyanobacteria. The ecological roles of such crusts have been investigated in a variety of desert and arctic ecosystems, but relatively little is known about their roles in alpine ecosystems. Recent studies in the Olympic and Cascade Mountains indicated that crusts play an important role in altering near-surface soil temperatures. Such alterations could have important implications for seed germination and seedling success of plants, but this has not been studied in alpine ecosystems. To examine this we investigated the influence of eight different crust surfaces that occur in the northern Cascades on the germination of seven alpine plant species under controlled laboratory conditions.  We found that crusts generally do not inhibit germination compared to bare soil surfaces and in many cases actually promote higher rates of germination, though this varied with crust type and plant species. Crusts dominated by moss strongly enhanced germination of both dicot and monocot species. In contrast, a crustose lichen surface had germination rates similar to those of bare soil. The six different fruticose lichen surfaces varied in their effects on germination. Similar to the dark-colored moss crusts, the dark-colored Cetraria islandica crust strongly promoted germination. The lighter-colored fruticose lichens with loose structures tended to promote germination weakly while those with dense structure more often had germination rates similar to bare soil. These general patterns of germination effects held for most, but not all alpine plant species, with some crusts promoting germination of monocots while others promoting more germination of dicots. Understanding crust influences on surface temperatures and alpine plant germination will be important for long term management under conditions of climate warming and advancing treelines.

Because of very high temperatures and densities, plasma analysis must be done using indirect methods, often with lasers or visual analysis of the plasma. The ZaP Flow Z-Pinch Experiment (ZaP) lab studies the stabilizing characteristics of sheared plasma flow in a Z-pinch configuration using a variety of these indirect methods. My work has been designing a housing to convert an ultrahigh-speed, film-based IMACON 790 camera that photographs the plasma into a digital format. Currently, the IMACON 790 uses Polaroid film packs that have a failure rate of about 30%, resulting in lost time, money, and data. Using a Charge-Coupled Device (CCD) sensor, images could be digitally recorded, stored, and reviewed in the existing ZaP database. The CCD, in the form of a digital camera, will mount in place of the film. The image is focused onto the sensor and software then stores this photo, with additional information, in a database. This conversion will provide us with regular visual records of the experiment, instant analysis of the plasma, and a digitized database of images. This will add greater flexibility to the IMACON, including adding filters for specific experiments, and more opportunities and methods to better analyze the plasma’s behavior.

With peak fossil fuel production upon us, we must look to alternative sources of energy. Algal-based biofuels represent an attractive alternative given that some algae produce as much as 40% of their dry mass as fat that can be processed to fuel. The goal of this project is to identify media conditions that support the increased production of these fats. The parameter that will be assessed is the effect of a lipid precursor when added to culture medium. Algal cultures are assayed every third, sixth, and ninth day for cell growth and for lipid analysis. In order to assess the quantity of fatty acids that are present per cell, the lipids must be converted into a form better suited for separation, known as fatty acid methyl esters. To chemically transform the raw oil, it is heated for one hour with boron trifluoride and methanol producing the methyl esters as the desired products. A subsequent sub-microscale liquid-liquid extraction is performed to separate the esters followed by quantitation using GC/MS with grading against an internal standard. Prior experiments show that an increase in concentration of sodium acetate in the media positively influences the amount (thirty percent over the control) of fatty acid per cell in a small golden-brown algal that serves as our model organism. Should these results be confirmed, productivity of fatty acid synthesis can be increased at minimal cost using a nontoxic media additive.

American crows, Corvus brachyrhynchos, have shown a suite of abilities to help with predator recognition and avoidance. In particular, crows have shown the ability to recognize dangerous humans based off facial features. However, their ability to recognize human gaze and modify behavior accordingly is largely unknown. With expanding urban sprawl displacing many native species and habitats, this ability may play a key role in crows’ success in an urban environment. We observed crows in several parks and neighborhoods in Seattle metropolitan and rural areas. We approached crows providing direct eye contact or no contact and recorded the crow’s resulting flight initiation distance. We found that there is a positive trend between human gaze and flight initiation distance; crows tended to fly sooner when eye contact was made upon approach. The crows also showed behavior implying a greater level of fleeing urgency when eye contact was made. Our results suggested that crows may be able to respond to human intentions by distinguishing when humans are paying attention to them. These results indicated the importance of gaze recognition in urban adaptability. It will allow for better analysis and conservation of species that are poorly adapted to urban areas or better management of species with booming populations taking advantage of the urban environemnt.

Previous studies have shown that neurologically healthy subjects learn to generate adaptive motor commands when either sensory feedback (e.g., visual or auditory information) or the movements themselves (e.g., arm movements for reaching or jaw movements for speech) are experimentally perturbed—a phenomenon known as sensorimotor adaptation. In parallel, a different line of research has shown that for both nonspeech and speech movements the central nervous system (CNS) differentiates between self-generated and externally-caused sensory input by comparing actual and predicted inputs—a detected mismatch causes the input to be attributed to external sources. Here, we investigate these two phenomena in combination by means of a paradigm examining whether sensorimotor adaptation in speech production is diminished, or even completely abolished, when formant-shifted auditory feedback is played back with a delay rather than in real-time. We hypothesize that increasingly longer delays in the feedback signal will cause the CNS to increasingly interpret the perceived error as an external manipulation rather than a production error that requires adaptive corrections in future trials. Acoustic analyses are used to determine adjustments in subjects’ produced formant frequencies from a baseline phase (unaltered feedback) to the perturbation phase (formant-shifted feedback) across conditions with either real-time feedback or delayed feedback.

After the Supreme Court laid down the Chevron Doctrine in Chevron U.S.A., Inc. v. Natural Resources Defense Council, Inc., it was expected that the court’s widely criticized ability to shape policy through judicial review would be eliminated. However, although Chevron called for judicial deference to any reasonable interpretation of the law by agencies, these expectations have not been realized. Under what conditions do courts defer to or reject an agency’s interpretation of the law? This question, the focus of my research, considers the appropriate role of courts in a democratic society. Recent scholarship suggests that the judiciary, despite its insulation from the American people, has strong incentives to be concerned about its public standing and will adapt its behavior in response to congressional signals. I add to this literature by expanding my investigation beyond the Supreme Court to include lower courts and use a unique and subtler variable for observing court behavior. With an original dataset on court cases that invoked the Chevron Doctrine, I observe when judges defer interpretation of the law to agencies. I also utilize an existing dataset on legislation that strips court jurisdiction to measure congressional signals of waning support. Assuming that a court which invalidates agency decisions and slows down policy implementation will displease Congress and the public, I hypothesize that courts are more likely to defer to agency interpretation of the law when the percentage of “jurisdiction stripping” laws passed by Congress increases. This is because justices have strong incentives to be concerned about their waning public standing and institutional legitimacy.

Cervial spinal cord injury (SCI) causes severe damage to many of the descending pathways in the nervous system, one of which is the human rubrospinal tract. This tract plays a major role in voluntary movement of the extremities, and damage to the area can cause serious impairments in movement. Currently there is no cure for chronic SCI, and there are only minimal palliative therapies, thus it is imperative to explore treatment methods. In this study we are exploring a treatment that involves transplanting stem cells into rat’s injured spinal cords in hopes of improving upper extremity function. Specifically, we modify a fibroblast into a pluripotent state (iPS cell), then differentiate the cell to a precursor of an oligodendrocyte, a type of neural cell that helps the movement and speed of electrical impulses along an axon by increasing insulation. With SCI many of the remaining axons just need myelin to regain their function, thus if you can populate a site that has damaged or missing oligodendrocytes with new healthy cells or their precursors, then in theory the function in the damaged area can be improved. The rats are trained to perform two behavioral tests that involve volitional movement of their upper extremities. They then receive a contusion injury on their spinal cord at the level of the C4 vertebra resulting in unilateral forelimb deficits on their previously determined dominant side. One month post-surgery the injury site is injected with the iPS cells. We continue the behavioral assessment throughout and determine if their injury can improve as a result of the treatment. The purpose of the project is to test the efficacy of this procedure, and the data I will be helping to collect is required before it can be tried on humans.

Most angiosperms have conical cells on the adaxial epidermis of petals to attract insect pollinators. In the apetalous genus Thalictrum, the MYB transcription factor TMYBML2, an ortholog of the Antirrhinum Mixta-like 2, is responsible for making conical cells and giving petaloid appearance to sepals or stamens. Virus-induced gene silencing, the plant version of RNAi, was performed on the two closely related species T. clavatum and T. thalictroides, which have conical cells primarily in the stamens and sepals respectively. Treated flowers were validated molecularly by quantitative PCR for downregulation of the target gene. The absence of conical epidermal cells was observed by scanning electron microscopy in sepals of T. thalictroides, stamens of T. clavatum, and stigmatic papillae of both species. This study demonstrates at the molecular level that our target gene can confer ectopic petaloid characteristics to sepals and stamens. Additionally, a new role for this gene has been discovered in stigmatic papillae.

The United States is a primary actor in most international human rights organizations and is a permanent member of the United Nations Security Council. As such, it is important that U.S. international human rights policy serves as an appropriate model for other countries to adopt and follow. To the contrary, studies have indicated that U.S. human rights policy may be motivated by factors other than the alleged drive to enforce international human rights standards. I answer the question: Why is United States international human rights policy more lenient toward some countries than others? Specifically, I address whether or not U.S. human rights policy is more lenient towards countries that are (1) rich in natural resources and (2) strategically valuable to the U.S. In an increasingly unstable world with dwindling natural resources, I predict that U.S. human rights policy will be more lenient toward countries rich in natural resources and high in strategic value because economic and security concerns prevail over the responsibility to protect human rights. I employ data from international governmental organizations (World Bank, the United Nations, and the International Monetary Fund) and data from U.S. agencies (USAID, the United States International Trade Commission, and the Department of Defense). I capture the ‘leniency of U.S. human rights policy’ by including a measure of total net U.S. bilateral assistance to a recipient country. I use a regression model to empirically test the validity of my hypotheses. My findings have implications for the debate in Congress and the American public over how to reconcile the professed U.S. obligation to uphold international human rights with economic and security demands.

Pulsed, low intensity ultrasound (PLIUS) has long been researched as a possible method to accelerate cell growth. More recently, PLIUS has been used to boost the growth rates of several species of bacteria. Boosting bacterial growth rates could have a significant impact on increasing the rates of vaccine and pharmaceutical production. In order to study the effects of PLIUS on bacteria growth more completely, we have proposed the design of an ultrasonic bath that can fit into a standard bacteria incubator. The bath is powered by a 9 volt battery, and creates pulses of ultrasound at a 1/2 duty cycle. Users can vary the pulse frequency and intensity of the ultrasound supplied. The primary goal of this project is to enable further research of PLIUS, using a low-cost, low-power device that does not require specialized bacteria culture techniques. We hope to use this bath to confirm that PLIUS can increase the growth rate of E. coli. Then, we hope to determine which implementable parameters (application time, pulse frequency, intensity etc.) will optimize E. coli growth.

Recently the theory of aneuploidy causing cancer has gained much credit. Aneuploidy is the unequal segregation of chromosomes in cell division and can lead to the formation of tumors and development of cancer if not fixed. My project is about discovering which protein binds to and activates the Cse4 degrading enzyme Psh1, using yeast two hybrid screening, which is a research technique designed to discover protein to protein interactions. This is important because if Cse4 finds its way onto a sister chromatid, an extra kinetochore will form there. This is unacceptable because later, when the cell is dividing, extra microtubules, from the opposite pole can attach onto the extra kinetochore(s) and cause breakage during cell division. When this breakage occurs more genetic information will be pulled into one cell resulting in aneuploidy. I didn't figure out which protein binds to and activates Psh1, but when this is figured out, pharmaceutical companies will be able to use this basic research to create better cancer fighting drugs.

Kuali Student is a multi-university, next generation academic software suite. The objective of Kuali Student is to provide an open source solution for managing academic information, such as course offerings, at institutions of higher education. As part of the part of the planning process for implementing Kuali Student at the University of Washington, our client, the Student Information Systems Program from UW Information Technology, expressed a need for an evaluation of the requirements and challenges of moving data from the current legacy systems to the Kuali Student environment. To evaluate the challenges of moving data into Kuali Student, we created a data migration tool that reads the UW’s course data from the current legacy system, transforms the data to fit the Kuali Student environment, and inserts it into our own custom UW instance of Kuali Student. Additionally, we customized the Kuali Student interface, branding it as a University of Washington application. We extensively documented our work to provide a lasting account of our processes and struggles to aid future UW implementations of Kuali Student. By successfully migrating 98% of 15,622 courses into our custom instance of Kuali Student, we met the goals set by our client, and satisfied the need for a proof of concept for a UW implementation of Kuali Student. We submitted our data migration tool, documentation, and an instance of Kuali Student populated with UW course data to UW Information Technology, who plans on using our proof of concept to aid their future full-scale implementation of Kuali Student at the University of Washington.

Epiphytes (plants that grow on trees) play important roles in forest communities, providing many ecosystem services and representing a large portion of the world’s biodiversity.  A better understanding of environmental factors important for epiphyte communities is needed to improve management of biodiversity and ecosystem health.  This study aimed to identify epiphytic species and determine the influence of aspect, height in tree, and incline of the growing surface on the abundance and distribution of epiphytes in big leaf maples (Acer macrophyllum).  A study of bryophytes, macrolichens and vascular plants growing on the trunk of A. macrophyllum was performed in the Queets River temperate rainforest of the Olympic National Park.  Data was collected on the lower two-thirds of the tree using arborist tree-climbing techniques.  Rectangular quadrats spaced vertically every 30 cm on the N, S, E and W sides of the trunk (10 cm x 20 cm wide) were used to quantify relative species cover.  Aspect, vertical angle of the growing surface and height in the tree were measured at each quadrat and analyzed for correlations with epiphyte abundance, diversity and distribution.  The abundance and domination of mosses observed throughout measured portions of the tree will be presented.  This research has implications for conservation efforts, improving our understanding of epiphytic communities and encouraging management practices that maintain epiphyte abundance and minimize biodiversity losses.

Over the course of the past few decades, a dramatic increase in the prevalence of obesity has been seen in the United States. The CDC revealed that over thirty percent of the adult population was considered obese in 2008, with the number expected to rise in the coming years. Alongside this trend, many have worked to counteract this national problem on an individual level through the utilization of diet, exercise and surgical options available to undergo the massive weight loss necessary to get back in shape after obesity. At the same time a changing trend in care of surgical patients in the United States has prompted the use of accredited outpatient facilities for many surgical procedures. Traditionally massive weight loss body contouring was done in an inpatient fashion however with these changing trends more is being done on an outpatient basis. In order to establish the efficacy and safety of this changing trend we conducted a 6-year retrospective review of 260 consecutive patients who underwent 544 procedures. These were all done in an accredited outpatient facility with presence of board certified anesthesiologist, and were all discharged to home or a hotel with appropriate and detailed postoperative care instructions. The review included 241 women and 19 men with an average age of 42. 89.2% had bariatric surgery and 10.8% were involved with self-directed weight loss. The average weight loss in this group of patients was 130 lbs. The average operating time was 330 min. The average recovery time was 186 min prior to discharge. Patients followed up 8 times on the average. The complication rate was acceptable with minor wound separations being most common (15.4%). There were no deaths and no inpatient readmissions. The re-operative rate was 4.23%. With appropriate patient selection and detailed and comprehensive attention to post operative follow up, massive weight loss body contouring cases can be done safely and effectively in an outpatient setting.

Off the coast of Washington, Oregon, and northern California, the oceanic Juan de Fuca plate is being forced under the continental North American plate, a subduction zone. The presence of the subduction zone results in a risk of three types of earthquakes: earthquakes associated with internal deformation of the subduction slab (intraplate earthquakes), earthquakes on the interface between the subducting plate and the overriding plate (interface earthquakes), and earthquakes in the crust of the overriding plate (crustal earthquakes). Washington has many more small Cascadia intraplate and interface subduction zone earthquakes than Oregon which indicates a difference in the conditions of the subduction zone. One plausible explanation for the difference in background seismicity is a difference in heat flow beneath Washington and Oregon. The PNSN, Pacific Northwest Seismic Network, catalog of earthquakes in Washington and Oregon since 1990 will be used to search for interface and intraplate earthquakes in Oregon. Using the location, depth, and focal mechanics of an earthquake, it can be determined whether or not the earthquake was an intraplate or interface earthquake. A better catalog of interface and intraplate earthquakes beneath Oregon will help to understand what causes the difference in seismicity between Washington and Oregon.

Quantitative Microbial Risk Assessment (QMRA) is the assessment of exposures to microbiological agents and the resulting likelihood of infection. Dose response models attempt to determine the probability of infection as a function of microbial dose. To represent the probability of infection we use a cumulative distribution function (CDF). A CDF is a monotonically increasing function that ranges from zero to one. The objective to determine the best fit parameters for each potential CDF is achieved by using the Maximum Likelihood Estimation method. The goal of this study is to determine the best fit parameters and assess uncertainty for the exponential and Beta Poisson CDFs fit to several dose response data sets. To accomplish this, a bootstrap method is used to calculate the confidence intervals of our best fit estimations. In addition, we have migrated from a Microsoft Excel-based Solver solution to R. Excel is a closed source application with no way to verify the integrity of its results. In contrast, R is a free software environment for statistical computing specifically designed to perform statistical modeling. To make the use of R convenient as well as powerful, we developed a Java-based graphical user interface to R optimized for a dose response modeling workflow.

Over the last decade there has been a push from NGOs to reach a larger number of people and to reach them in more isolated and impoverished regions. However, the success rates of these projects, particularly drinking-water projects, is quite low and in some cases can leave the people they were designed to help in worse conditions than before the addition of the project. In the 2007-2008 academic year and again in the summer of 2010, I conducted an independent research project in the mountains of southwest China to gain insight into why these success rates are so low. My research was located in two Nuosu villages called Yangjuan and Pianshui which had received 5 water projects from various NGO groups. I analyzed these projects to see how they affected the villagers and whether or not they still were functioning to their original design intentions and if not, why. I used this data as a foundation for my own critique of the development process by placing it in the theoretical discussion of past and current scholars. I begin my thesis conducting an overview of the theoretical progression of development in both the western world and in China. Next, I move to current critiques. Finally I use the water projects to create my own critique. With the water projects in Yangjuan we have an opportunity to use these projects as a case study to critique the methods and means used by development agencies to try and determine what worked well and what did not. This type of knowledge, while grounded in development theory of Escobar, Rist, Bebbington, and Scott to name a few, can add significant insight into the work of development firms. Preliminary findings suggest some of the project failures were due to NGOs focusing too much on the technology behind the project and not enough on the social constructs of the communities they were placed in.

Neutrinos and antineutrinos are elementary particles with no electric charge and a very small mass. While difficult to detect, they are abundant on Earth, as they originate from the sun, nuclear power plants, and the Earth itself. In particular, electron antineutrinos are produced by the Earth’s interior from the radioactive decay of uranium, thorium, and potassium. By measuring these antineutrinos, we could estimate with improved accuracy the amount of radioactive uranium, thorium, and potassium contained in the Earth, and in turn the radiogenic heat produced by the Earth. This research investigates the merit of a hypothetical neutrino detector that would make such measurements. The detector would consist of an array of acrylic tubes filled with liquid scintillator, with photomultiplier tubes at each end. This design minimizes costs so that detectors could be placed at numerous locations in order to obtain accurate measurements. My involvement has consisted of developing and modifying code to simulate the detection of particles in this device. Specifically, I have used ROOT to generate functions that reconstruct the position and energy of a detected particle. Once we create realistic simulations, we will be in a position to decide whether or not this detector design is adequate, and thus whether or not it should be built.

Dendrite arborization patterns are an important determinant of neuronal function, yet the mechanisms underlying dendrite maintenance are not well understood. Using the Drosophila peripheral nervous system (PNS) as a model system, we are performing a forward genetic screen to identify mutations in genes are required for dendrite maintenance. By inducing lethal mutations that permit the organism to survive through late-larval stages, I can readily track the mutation via confocal microscopy and monitor defects in dendrite maintenance in homozygous mutants at the relevant stages of development. To date, we have screened over 900 different mutations and found several mutations that affect dendrite development. I will use time-lapse imaging to determine which (if any) of these mutants specifically affects dendrite maintenance, and meiotic recombination to determine the gene affected by the most interesting mutants. Successful characterization of substrate-derived signaling pathways that specifically function to regulate maintenance of dendrite arborization patterns will be an important step for deeper understanding of neuronal pathologies including schizophrenia, Alzheimer’s disease, and Parkinson’s disease.

Molecular assays of tumors are becoming increasingly important for the management of patients with cancer. To perform these molecular assays requires quality RNA. Where tissue quality or RNA quality is poor, the outcome will result in false negatives, or decreased signal thereby negating the effectiveness of the assay. Some of the issues associated with the isolation of RNA from tissue include time to tissue acquisition, duration of warm ischemia (restriction in blood supply), temperature (over time), location of the organ within the body, and therapy. For autopsies, time interval since death is another factor that might promote RNA degradation. To determine the changes in gene expression that occur in patient tissues, we assessed the quality of preservation of RNA in human tissues isolated at surgery and autopsy. For RNAlater (an RNA stabilization solution) preserved samples acquired at surgery, we measured the tissue processing time and the RIN (RNA integrity number) in forty patients. For flash RNAlater preserved samples acquired at autopsy, we measured the time since death, tissue processing time, and the RIN in twenty patients. For samples acquired at surgery, we have determined that short tissue processing times yield samples with a high RIN suggesting high quality RNA. For samples acquired at rapid autopsy, surprisingly, time to death does not impact RIN and the quality of the RNA. Instead, we have observed patient to patient and tissue site to tissue site variability in sample quality. These experiments will give us greater insight into effectiveness of the methods currently used to isolate RNA and the value of tissue isolated for molecular analysis from patients at time of surgery and autopsy. This knowledge can be directly translated into the development of molecular tools and techniques that will aid in the diagnosis of and molecular profiling of cancer.

Methylobacterium extorquens (AM1) is a methylotroph that metabolizes reduced C₁ compounds such as methanol (MeOH). A detailed understanding of methylotrophic metabolic processes is crucial for engineering strains for bioremediation purposes and redirecting the industry towards more renewable, non-polluting bioprocesses. The oxidation of MeOH by M. extorquens requires two cofactors: tetrahydromethanopterin (H₄MPT) and tetrahydrofolate (H₄F). MeOH is first oxidized to formaldehyde, a highly toxic compound. MtdB is involved in the oxidation of formaldehyde to formate using H₄MPT as a cofactor and both NAD+ and NADP+ as co-substrates. Formate is the branching point for either further oxidation to CO₂ or assimilation. MtdA is an H₄F-specific enzyme that uses NADP+ to generate methylen-H₄F, the intermediate that enters the serine cycle, and resumes in assimilation. Previous studies have shown that in vitro, MtdA is capable of using H₄MPT and H₄F as cofactors and interestingly is more efficient using H₄MPT. This suggests that it may have a role in both the oxidation and assimilation step of MeOH. However, in vivo, MtdA is unable to fully substitute MtdB as an mtdB mutant does not grow on MeOH. However, when MtdA was over-expressed the same mutant was no longer formaldehyde sensitive. This observation poses two questions: 1) What is the role of MtdA in the H₄MPT pathway? and 2) Why MtdA is unable to allow growth in MeOH when MtdB is not present? We proposed that if MtdA has a double role in assimilation and oxidation, MtdA is the key regulator to balance both processes. In order to answer these questions, constructs expressing different ratios of MtdA and MtdB have been used for phenotypic studies along with other constructs that releases metabolic and reducing power limitations.

Game play and altruistic behavior appear fundamental to human development and well-being. This research explores their intersection in the context of the digital age where gaming has been virtualized, making games easy to obtain and more accessible. The online gaming industry has increased game adoption and profits by fine-tuning the technical and psychological mechanisms by which games attract and engage players, including the easy socialization of casual games through social networking, increased micro-feedback, and the wide adoption of micro-transactions. Similar trends can be found in philanthropy, where many non-profit organizations funded through donations have moved towards smaller donations through easier transfer mediums (e.g. cell phones, the internet, etc). Our research investigates how non-profits can employ the core mechanisms that have fueled the gaming industry’s success to expand their user base, increase donations, and encourage donor activity. Specifically, we conducted research on “gamifying philanthropy” with Jolkona, an online non-profit that provides an easy and cost-effective way for other organizations to provide visual and textual feedback for micro-donations. Research methods included conceptual analysis of stakeholders (e.g. players, donors, beneficiaries, etc) as well as interviews and online surveys with gamers and donors to understand how their values might affect potential game design models for the non-profit. Analyses are underway. Preliminary findings suggest there are distinct value tensions among privacy, transparency, and anonymity when investigating ways to socialize feedback from beneficiaries of donations to the players and their social networks. Ethical and moral dilemmas are expected to emerge when rewards, loss aversion, and achievement mechanisms are used to promote the act of giving. Furthermore, maintaining the user experience of existing donors can be a unique challenge. Discussion addresses design features to support philanthropic gaming, obstacles for design, and value tensions among stakeholders.

As a public space, the Internet provides affordances for communities of users to interact at times anonymously and at other times to represent their true identities online. This duality – of anonymity and of identity – often presents a challenging value tension when it occurs within the same community. Should design features privilege anonymity over identity? How can technology be leveraged to strike a balance between the two conflicting representations? To help address these design challenges, the goal of our research was two-fold: (1) to formulate a conceptual framework for the values of anonymity and identity, their tensions, and their implications in online interactions; and (2) to apply the findings from our conceptual analysis to the context of dating websites in order to derive design specifications for a proposed relationship-building site. In Phase One of our research, we analyzed six websites (three dedicated to anonymous casual online interactions [Omegle.com, Craigslist.com, Mixi.com] and three that used identity to support authority [Yelp.com, Amazon.com, Quora.com]) in order to identify common site practices. Two key findings emerged: the use of anonymity to ease user-to-user communication, and the reliance on identity to encourage user-to-user trust. In Phase Two (in progress), we use our conceptual framework and findings from the website analysis to address anonymity and identity in the context of online dating. Specifically, we will explore further the construct of anonymity to ease social interactions, but adjust our focus of identity to study it as an indicator of personal commitment. Drawing on Value Sensitive Design, we will engage stakeholder values by employing the value dams and flows method to generate design specifications for a proposed relationship-building website. More generally, we seek to develop design guidelines for online spaces that encourage the formation of honest, meaningful relationships while still allowing a level of ease through anonymous interactions.

Obtaining drinking water from seawater still serves to be a major problem because of the high energy requiring mechanisms, limiting practicality. Prior research has indicated that particles and solutes exclude from the vicinity of hydrophilic surfaces under incident light, leaving large microsphere-free regions known as exclusion zones (EZs). EZs have been shown to extend for distances of up to several hundred micrometers from the nucleating surface. These observations were made on large, extended surfaces, leaving open the question whether EZ size might depend on the characteristic dimension of the excluding surface. We placed an ion-exchange resin bead with diameters varied from 15 um to 300 um into cuvettes. The beads were suffused with aqueous microsphere suspensions for observing the surfaces’ exclusionary behavior. Results showed a direct relation between bead size and exclusion-zone size over the full range of bead diameter, implying a similar relation for smaller particles, perhaps extending beyond the resolution of the light microscope. Based on these results, we are currently quantifying the direction and flow of these particles in solution around resin beads under both infrared and ultraviolet light and measuring the resulting EZs. These experiments will contribute to our understanding of the behavior of colloidal particles in our attempt to scale up this process to collect particle-free water in an economically-feasible way, reducing the risk of waterborne diseases.

Research has shown that risky sexual behaviors (defined as condom non-use, having multiple partners, and greater frequency of sexual intercourse) are frequent in college populations (Desiderato & Crawford, 1995). These risky behaviors can result in serious consequences such as sexually transmitted diseases and unwanted pregnancies (American College Health Association, 2008). Undergraduates typically overestimate the number of sexual partners and frequency of sex amongst their peers, while underestimating the rate of condom use amongst the student population (Scholly et al., 2005). Research (Lewis et al., 2007) has shown that undergraduate student’s perceived descriptive norms about their peers’ sexual behavior is positively associated with their own behavior; the more risky sex one has, (i.e. having a lot of sexual partners) the more they perceive their peers to have. However, less research has examined if this norm-behavior relationship holds for other measures of risky sexual behavior such as condom use and frequency of sex. The current study will explore the association between personal risky sexual behavior and perceived descriptive norms for several risky sexual behaviors. This cross-sectional study involves 1,055 undergraduate students, ages 18-30, who were paid $20 for their involvement. Measures of perceptions of sex-related risk, perceived sexual and alcohol-related sexual behaviors, and actual sexual and alcohol-related sexual behaviors will be included in all analyses. It is hypothesized that there will be 1) a negative association between personal condom use and perceptions of student’s condom use; 2) a positive association between one’s total number of partners and the number of partners they perceive other students as having; 3) a positive association between one’s frequency of sexual intercourse and the perceived frequency among other students. The information derived from this study could aid in a better understanding of risky sexual practices and inform education outreach programs in college populations.

The transplantation of human embryonic stem cell-derived cardiomyocytes (hESC-CMs) is being explored as a novel therapy to replace lost muscle due to myocardial infarction. For eventual safe clinical use, the preparations of hESC-CMs must be sufficiently pure, so we explored two complementary approaches to obtain enriched populations of cardiomyocytes: improved methods of guided differentiation (specifically, elimination of insulin signaling) and genetic selection (using a novel muscle-specific promoter). We previously reported a cardiac induction protocol capable of generating large quantities of hESC-CMs of 30-80% cardiac purity. Others have reported that activation of insulin signaling has a detrimental effect on the purity of hESC-CMs generated using an alternative induction protocol. *To test the hypothesis that the elimination of insulin signaling would improve cardiogenesis in our own system, we used flow cytometry with an anti-cardiac troponin T antibody to compare the percentage of cardiomyocytes in preparations differentiated in insulin-containing and insulin–free media. In preliminary studies, we found that the omission of insulin increases the purity of cardiomyocytes by nearly 3-fold. In ongoing studies, we have also tested whether the cardiac purity of hESC-CMs can be further enriched by genetic selection with a muscle-specific promoter. For this, hESCs were transduced with a lentiviral vector in which a regulatory element from the muscle creatine kinase (CK7) gene drives expression of the fluorescent protein, mCherry, and puromycin resistance. Our preliminary results suggest that the omission of insulin during the cardiac induction of hESCs increases the purity of the resultant cardiomyocytes. Work is in progress to see if such hESC-CMs can be further purified by genetic selection with a novel CK7-based transgene.

The Thomson scattering diagnostic measures the local electron temperature and density of plasmas. The ZaP Flow Z-Pinch Experiment (herein referred to as ZaP) uses this diagnostic to characterize its plasmas. This characterization is necessary for ZaP’s study of sheared-flow stabilization, which has applications in fusion, space propulsion, and astrophysics. The ZaP Thomson scattering system is comprised primarily of a ruby laser, an imaging spectrometer, and photomultiplier tubes (PMTs). The effects of attenuation, PMT response, dispersion, spectral filtering, spectral blurring, and wavelength binning must all be properly accounted for in order to make reliable measurements. A preliminary calibration of the system was completed by measuring the response to a white light input. This allowed initial electron temperature measurements to be made. A more refined calibration using white light, bandpass filtering, and more elaborate analysis techniques is presented here. The refined calibration will provide more accurate measurements of temperature and, eventually, density.

Computers, mobile devices, and search engines have made our lives easier by eliminating the need for tasks such as mentally calculating change or recalling phone numbers, dates, and directions. Our goal, as part of the Interfaces that Make Us Think Research Group (IMUT), is to research how computing interfaces can make us think more rather than less and to design interfaces and methods that achieve better retention of information and overall brain health. We are interested in determining opportune times to make tasks cognitively challenging, what methods are acceptable to make users think more without being frustrated or annoyed, and how mentally stimulating tasks can be seamlessly integrated into everyday habits. Based on our literature review and focusing on user-centered design principles, we brainstormed almost 100 concepts that would stimulate cognitive processes. These were narrowed down to five designs to storyboard, prototype, and test. We created a user survey to determine when, where, and for how long individuals are willing to perform such tasks, which cognitive tasks would be most compatible when incorporated into one’s daily schedule, and which of the prototypes were most appealing and useful. We also investigated technologies that would effectively deliver these types of activities to users, such as augmented reality games, social media, and household devices. The findings of this research will allow us to refine our prototypes into functional interfaces and devices. The products we produce will be tested for usability and whether cognitive processes are improved after using these interfaces and participating in the methods we design.

Heart disease often results from damage to cardiomyocytes, which have limited regenerative potential. Recent reports have demonstrated that fibroblasts can be reprogrammed directly into functioning induced cardiomyocytes (iCMs) using retroviral delivery of the three cardiac transcription factors, Gata4, Mef2c, and Tbx5 (collectively referred to as GMT), and have suggested that this technique may be useful in regenerating damaged heart muscle. Viral delivery, however, often results in insertional mutagenesis, which is a consequence of integrating the viral DNA into the host cell's genome, and may be detrimental to iCMs. To avoid this potential complication, we are using recombinant GMT proteins in place of retroviruses to achieve reprogramming. We cloned the GMT transcription factor genes into a bacterial protein expression vector to express large amounts of our proteins. Each protein contains a polyhistidine tag, which will allow purification through column chromatography, and a cellular permeability peptide, which will allow isolated GMT proteins to pass through the cellular membrane. We will introduce purified GMT proteins to embryonic fibroblasts in culture media and also test the effects of CHF1 on differentiation efficiency of these iCMs. CHF1 is our lab's molecule of interest, and is a cardiac transcription factor that has been shown to play critical roles during ventricular development. Due to its important role in cardiac maturation, we are optimistic that CHF1 will be a good target molecule to improve the efficiency of iCM production. We will test this hypothesis by using embryonic fibroblasts isolated from CHF1 wild type, null, and transgenic mice.

One in eight new mothers experiences a postpartum mood disorder (PPMD), most commonly postpartum depression. Maternal depression has been associated with higher rates of suicide, decreased duration of breastfeeding, developmental delays in infants of depressed mothers, and lower rates of vaccination and basic home safety interventions. It is common practice for mothers to be screened for depression during an outpatient visit at six weeks postpartum, though there is evidence that women suffering from depression are less likely to attend such visits. Screening women for mood disorders during their postpartum hospital stay would capture more of the risk population. As a result, women might receive earlier and more intensive follow-up for PPMD, reducing associated maternal and infant morbidities. The objectives of this project were to examine current practices for mood disorder screening in the inpatient maternity setting, and to determine best practices for timing of mood disorder screening. Ten hospitals in the greater Seattle metropolitan area were contacted by telephone and asked a series of questions regarding their practices for screening inpatient postpartum mothers for mood disorders. A literature review was conducted to determine the best evidence for timing of mood disorder screening. Of the hospitals surveyed, none had a policy, procedure or practice for routinely screening inpatient postpartum mothers for mood disorders. The literature review found that the first three days postpartum was an accessible and valid time to screen for depression.

Human hematopoietic stem cells (HSC) are multipotent stem cells that have the ability to self-regenerate and give rise to all types of blood cell. Understanding of developmental pathway of the blood formation in human body by hematopoietic stem cells may benefit human in numerous ways, including HSC transplantation. Therefore, by studying the molecular mechanism in hematopoietic stem cells, we wish to uncover the key fate determinants that are involved in replenishing all types of blood cell in our daily life. Our lab has constructed a short hairpin RNA (shRNA) library, which contains ten thousands shRNAs targeting known transcription factors, kinases, and oncogenes. Genome-wide shRNA screening was first performed in human granulocyte-colony stimulating factor (G-CSF) mobilized common myeloid progenitor cells (CMP) to identify critical components necessary for self-renewal and differentiation. Three days post treatment, cells were sorted into three populations (CMP, MEP, GMP) and shRNA level is then examined in each population. To validate involvement of any specific gene, RNA interference will be utilized to knockdown the target gene expression for observation of corresponding phenotype. Ultimately, finding of these novel biological interactions will provide a deeper insight to developmental biology.

Chloropyrifos (CP), a widely used organophosphate (OP) pesticide, has been reported to be associated with childrens' altered neurodevelopment. In this study, we established a human neural progenitor cells (hNPCs) model to examine the adverse effects of CP during proliferation and differentiation. hNPCs cells were expanded in serum free proliferation expansion medium (MEM) and differentiated in HyClone neural differentiation medium (HDM). Cells were incubated for 72 hours in either MEM or HDM with CP (0-20 μg/mL). Using this in vitro model, we examined morphology, cell viability, and neuronal protein markers for proliferation (PCNA), differentiation (MAP-2, b-tubulin III), and induction of apoptosis (cleaved caspase-3) after treatment. Dose-dependent decreases of cell viability were observed in both cells cultured in proliferation MEM and differentiation HDM medium, with significantly greater effects of CP on cells in HDM than in the MEM at concentrations of CP 20 μg/mL. We observed no changes in PCNA, but significant dose-dependent decreases were shown in MAP-2 in both proliferating and differentiating cells. Dose-dependent decreases in b-tubulin III were detected during differentiation with less change during proliferation. Cleaved caspase-3 shows a dose-dependent increase in proliferating cells, but a dose-dependent decrease in differentiating cells. Our results demonstrated a differential effect of CP on the neuronal cells during proliferation and differentiation. Differential alterations of neuronal protein markers during proliferation and differentiation by CP treatment may provide cell stage specific molecular and cellular mechanistic clues for the neurodevelopment.

According to the 2006- 2008 census, 8.6 % of the United States population spoke a primary language other than English and reported that their English speaking was less than "very good." Traditionally the roles of addressing English teaching and pronunciation skills have fallen under the realm of English as a Second Language (ESL) teachers. More recently the fields of Speech-Language Pathology and ESL have been collaborating with regard to the pronunciation skills of non-native speakers of English. This pilot study, conducted from the view point of the Speech-Language Pathologist, examines the speech samples from four male speakers of Spanish. Each speaker was recorded as he read aloud six sentences that varied in length from five to twenty syllables. Each speaker's sentence productions were phonetically transcribed and analyzed for speech sound accuracy using Percent Consonant Correct (PCC) and Percent Vowel Correct (PVC). Observed speech sound patterns were also analyzed. The findings are disscussed with respect to appropriate training targets for pronunciation instruction in Spanish speakers of English.

Alexandrium catenella is a dinoflagellate that increases levels of saxitoxin in bivalve mollusks, through bioaccumulation. Human exposure to saxitoxin by consumption of bivalves can be toxic and even deadly. Harmful algal blooms of A. catenella have a significant impact on Pacific Northwest commerce via shellfish bed closures. Previous hypotheses implied that increased Sea Surface Temperatures (SST) and severity of storm events during strong El Niño years increased total hectares and time of closures by favoring propagation of A. catenella. Recent studies suggest bloom increases are more closely tied to changes to the Pacific Decadal Oscillation (PDO) and show no statistical significance in the increase of shellfish bed closures due to El Niño events. This study examines the changes in seasonal weather and water properties due to the onset of the 2008-2009 El Niño (ENSO), including the subsequent 2009-2010 La Niña event, and their relation to the A.catenella populations in Quartermaster Harbor (QMH). Monthly samples were taken from QMH of water properties and plankton ecology, along with hourly meteorological data from the UW Tacoma Weather Station and graphed using Grapher software. Results continue to suggest no statistical significance in shellfish bed closures due to El Niño/La Niña events.

World War I’s dramatic violence not only produced widespread casualties, destruction, and cultural shell-shock, but also reverberated throughout 1910s artistic culture. WWI-era art and literature illuminates the dramatic effect of war’s never-ending violence on artists and authors alike. Just as shell shock disconnected soldiers from the realities of their surroundings, modernism jarred its viewers and readers by challenging the norms of artistic production. Aldous Huxley’s novel Crome Yellow (1921) captures the alarming qualities of modern form in the novel, whereas Mark Gertler’s painting, Merry Go Round (1916) rejects linear formalist structure and narrative. Both works feature endless cycles; the meaningless narrative structure represents Huxley and Gertler’s reaction to WWI. Both men defy their pacifist lifestyles; through their laborious production of art, they eschew literal blood and violence but ultimately leave their viewers with distress analogous to that displayed on the battlefield. In Crome Yellow, Huxley rejects plot, character development, and climax and leaves the reader to analyze the characters without guidance. Notably, the novel ends where it begins. Gertler’s Merry Go Round similarly rejects formalist artistic styles of the early twentieth century; he portrays soldiers rotating endlessly and pointlessly around the Merry-Go-Round, where the beginning is the end. The lack of purpose for the characters in Crome Yellow as well as the bereft individuality in the riders of the Merry-Go-Round mimic the mass of unidentified soldiers endlessly fighting in battle. Both Huxley and Gertler decry a war that united the masses against each other, evoked death and bloodshed, and most of all, expunged individuality for an entire generation of men and women. Ultimately, this essay argues that Huxley and Gertler’s works indicate not only their mutual distaste for the war, but also their own vexed relationship to pacifism, engaged in art and intellectualism while their countrymen died in battle.

Deuterostome adult body plans greatly differ between echinoderms, chordates and hemichordates. In order to understand the evolution of deuterostomes and the relationships between species, we may eventually have complete genomic sequences available for comparison, but we do not yet have the genome for Ptychodera flava. This information, along with gene expression data, gives insight to the similarities in developmental patterns between phyla as well as insight to their evolution. In this project, we are sequencing the genomic organization of the Hox genes in P. flava, an indirect developer of the hemichordates, which has larvae that are morphologically similar to echinoderms. Our purpose is to complete the genomic organization P. flava Hox genes in order to learn more about deuterostome evolution. We have analyzed a set of clones with Hox sequences inserted into bacterial artificial chromosomes (BACs). These BACs have been sequenced with primers made to individual Hox genes. We are mapping the exons of the genes in the Hox gene complex and the position of the BACs relative to the P. flava chromosome. Then, by sequencing the BACs we can piece together overlapping portions of the Hox genes. The overlapping sequences will reveal the order of the P. flava Hox genes on the chromosome. We are specifically interested in whether the Hox complex is rearranged, as in echinoderms, or co-linear, as in chordates.

Avian song learning is an important animal model for human speech development. The songbird brain has two circuits dedicated to song function, the song production pathway, and the anterior forebrain pathway (AFP). The two pathways are connected, with the AFP influencing the song production pathway. The song production pathway is a motor pathway that controls respiration and the syrinx, the vocal organ. The AFP is a specialized songbird circuit necessary for vocal learning, comprised of a basal ganglia - thalamo - cortical circuit. The AFP is believed in be involved in auditory feedback and correcting the song production pathway. Short latency information flow through this pathway is hypothesized to be crucial for fine motor control of song production or other aspects of learning. One synaptic connection in this pathway is the inhibitory projection of basal ganglia nucleus Area X onto the medial portion of the dorsolateral nucleus of the thalamus (DLM). Latency through this synapse is very short, and recent studies suggest that short response times are driven by a rebounding mechanism whereby inhibitory input results in cellular excitation. In other cells such rebound mechanisms have much longer latencies. To investigate this question, we developed a model in the NEURON software environment. Starting with a model of a mammalian thalamic cell, we asked what specializations of cellular currents were necessary to explain a shorter response latency. We have adjusted model parameters to match properties recorded in DLM cells. This model will help focus experimental measurements of the biophysical properties of the song learning circuit, and offer support to rebound based mechanisms of DLM firing latency.

The human body has been the subject of paintings, sculptures, music, dance, and film, inspiring masters across cultures and disciplines. However, in literary contexts, the human body frequently appears only through metaphors or veiled references. Authors are disinclined to deal with the corporeal, except in unavoidable situations such as trauma, illness, or death. Many writers have also noted an undeniable dearth of language accurately describing trauma and physicality. This shortcoming contributes to misunderstandings and ambiguity in textual analysis, which impedes consideration of the body as a substantial literary element. Rebecca West in The Return of the Soldier (1918), and Dorothy L. Sayers in Whose Body? (1923) experiment with the human body, portraying it as an aesthetic object. To this end, they apply modernist conventions such as minimalism, depersonalizing language, and photographic realism. Superimposing poetic stylistic conventions onto realism articulates intense and complex experiences that are hampered by inadequacies in the language of concrete prose. By eliminating abstractions from their descriptions of the human form, these writers explicitly engage with the body as an object and an image. Both Sayers and West effectively employ poetic imagery to overcome shortcomings in traditional narrative language, and reveal the aesthetic capacity of human bodies. This project discusses how, by objectifying the body and stripping away abstract human characteristics and emotions, these compositions transcend raw physicality and place the body in the context of literary art.

Sleep is an important component in children’s physical and intellectual growth and development. Yet, 25% of the children in the US have some type of sleep disturbance. Sleep disturbances are associated with particular sleep disorders (e.g. sleep disordered breathing), are often co-morbid with acute and chronic illness (e.g. arthritis, asthma), or manifest during developmental transitions (e.g. childhood, adolescence). Untreated disrupted sleep in typically developing children pose significant daytime consequences, and place children at considerable risk for adverse health outcomes including decrements in neurobehavioral performance (attention, memory) and poorer health-related quality of life. Children with chronic illnesses, such as asthma are likely to be particularly vulnerable to adverse health outcomes from unrecognized and untreated sleep disturbances. Asthma is the most common pediatric chronic condition. Sleep disturbances can disrupt nighttime sleep as well as exacerbate disease-related symptoms and thus interrupts daily routines. The purpose of this study was to gain a better understanding about the nature of sleep disturbances as measured by polysomnography (PSG) in school-age children with and without asthma. Similar research studies documented in this field will be compared to our information to assess similarities and differences. Several statistical tests such as T-test for equality of means, Chi- square tests, Levene’s test were used to determine the independent and dependent variables correlation between the effects of sleep in children with or without asthma. Such examinations are needed in determining if any relationships exist between variables, specifically age, height, weight, tested for in our group statistics recorded in a sleep lab with our selected 9-11 year old children.

The field of quantum computing is rapidly progressing in hopes to become a promising and efficient means of computation in the future. In mathematical abstraction, the field is rich and promising with elegant algorithms based on high dimensional linear algebra and statistics. My research explores numerical simulations of elegant representations of a particularly symmetric but rich subset of quantum mechanical states using weighted finite state automata. Finite state automata are the most basic models of computation and hence are a popular topic in introductory computing theory courses. Finite state automata represent computation on a string of N characters in a particular alphabet as a diagram of state nodes and state transitions. In terms of arbitrary N element 0-1 binary strings, a particular finite state automaton may be used to represent some subset of the total possible strings in a manageable form. By representing automata using matrices, we can add numerical weights to the transitions to better capture quantum states and operators; in particular, a nice (but still rich) subset of quantum states and operators that can be represented as weighted, non-deterministic sets of “strings”, we can describe them using a state machine with a multidimensional output. For particular N-bit quantum mechanical systems representable in this form, such as electron spin chains, we can compute by using arrays of tensors (multidimensional arrays) various quantities of interest of the system, such as the magnetization and average energy. We plan to run test simulations of the transverse Ising model, a well known model which has an explicit solution and an understood phase transition, to compute the minimum energy and “frustration” (a quantity based on the uncertainty principle) of the system. With a working computation infrastructure we can then explore more complicated but less understood systems important to Quantum Computing.

Electrochemists have hypothesized that the electron transfer pathway through heme-containing proteins is a function of protein orientation. In this study, we tested this hypothesis by inducing horse heart cytochrome c (12 kDa) into two orientations and measuring the electrode resistivity. To achieve these orientations, cytochrome c was adsorbed, via electrostatic interactions, onto self-assembled monolayers (SAMs) of 11-amino-1-undecane and 11-mercapto undecanoic acid thiols. The cytochrome c surface concentration was calculated from X-ray photoelectron spectroscopy (XPS) nitrogen signals, showing normalized coverage of 5.78 ± 0.80 and 8.72 ± 0.83 on amine and carboxylic surfaces respectively. An isotherm plot was constructed from the normalized XPS nitrogen signal and showed that monolayer coverage is achieved when adsorption is carried out at solution concentrations above 50 uM cytochrome c. Asymmetrically-distributed amino acids were identified via time-of-flight secondary ion mass spectroscopy (ToF-SIMS) and characterized as ‘electrode view’ (Glutamine, Threonine, Phenylalanine, Proline) and ‘solution view’ (Arginine, Asparagine, Aspartic acid, Glutamic Acid, Histidine, Tyrosine) based on a hypothesized orientation on the carboxylic substrate. Ratio plots of solution view versus electrode view were constructed from fragment peaks of the asymmetrically located amino acids. A ratio of 3.6 ± 0.09 was observed on amine-terminated SAMs while a value of 4.2 ± 0.18 was calculated for carboxylic-terminated SAMs. These large differences in values indicate that the protein was induced into two orientations. Cyclic voltammetry experiments (PBS, pH 7.0, 540 mM KCl) of the protein adsorbed onto an amine-terminated surface presented 167 kilo-ohms of resistance; conversely on carboxylic-terminated SAMs, 200 kilo-ohms of resistance was observed. This difference suggests greater electron conduction through cytochrome c on amine-terminated SAMs. These results illustrate a potential for heme containing proteins, like cytochrome c, to be arranged into different conductive pathways.

Near Smalley, in the UK East Midlands, outcrops of Pennsylvanian age coal are being mined in an open pit mine. The mine provides an unusual opportunity to examine coal-bearing rocks and to determine the ancient environments in which they formed. Coal is typically concentrated as individual layers, or coal seams, interbedded with other sedimentary rocks; it forms in wetland environments where low oxygen prevents or slows the breakdown of plant and organic material. At the Smalley mine, intervals between coal seams have been identified that are approximately 10-12 meters thick. Rock samples were collected at 20 cm spacing from one of these intervals. Most samples appear to consist of mudrock and siltstones. Mudrock and siltstones tend to be deposited in calm water, low energy environments, such as lakes. Field observations have indicated that the depositional environment for the mudrock and siltstone interval between the coals is a delta system that infilled a shallow lake. I am analyzing the collected samples for their TOC (total organic content) and grain size distribution. TOC analysis reveals trends in carbon content, which can reflect the amount of oxygen in the original depositional environment. The grain-size analyses will help determine the energy of the depositional environment as well as determine the rock type. Both data sets will be synthesized with the field data to further characterize depositional environments and compare previous research on coal formation.

A significant amount of money is spent annually converting software to run on new environments. However, there is no quantitative way to evaluate the portability of software running on multiple devices. The state-of-the-art technique involves running unit tests on multiple devices and then fixing any portability problems that arise. As unit tests usually only cover a small subset of the software’s functionality, these may only provide weak assurances of software portability. This work constructs a set of quantitative measures for software portability that work both in the lab and on practically deployed systems. A programmer builds a formal model of the software, similar to a simulation, in the same language as the original program. This model can be used to iteratively explore the program’s state space on testing machines, providing a quantitative assessment of the portability on these machines. This model may also be deployed on production systems to do run-time portability verification of system behavior where a conformance failure results in the creation of a test case that demonstrates the failure. We will be deploying this technique on two widely used portable APIs, Java and POSIX. We have also used this technique on our own Seattle API, which is a testbed deployed across many diverse systems. Our use of formal modeling has provided a simple and robust mechanism for testing and validating portability across thousands of systems.

The elegant ABC model of flower development emerged from the study of homeotic mutants in Arabidopsis and Antirrhinum, two core Eudicots. The ABC model summarizes how the presence or absence of different transcription factors affects the development of various floral organs. A long-standing question in developmental evolutionary biology is whether this model, which provides a mechanistic basis for floral patterning, applies throughout the angiosperm phylogeny and how it can be used to explain their diversification. My study system is the basal eudicot species Thalictrum thalictroides (“Rue Anemone”), chosen due to its impressive floral diversity, its pivotal phylogenetic position, and its retention of ancestral floral features. My goals are: 1- Test the hypothesis that unisexual flowers in this genus likely evolved by homeosis through loss of B function; 2- determine the degree of conservation of B class gene function within this lineage. To that end, I am using the RNAi-based knockdown method of Virus-Induced Gene Silencing (VIGS) to silence the Thalictrum copy of the B class gene PISTILLATA (TtPI), which controls stamen and petal identity. Silenced floral phenotypes consist of homeotic conversions of stamens into carpels; resulting in female flowers derived from a hermaphroditic flower. The conversion of organs within floral whorls is comparable to that observed for Arabidopsis and rice pi mutants, supporting conservation of B class gene function across angiosperms. These results also provide a potential one-step genetic mechanism for breeding system transitions during the evolution of this diverse genus.

The number one killer of Americans today is heart disease and one of the most damaging effects of heart disease is heart attack. Every year approximately 1,255,000 Americans have a heart attack. A heart attack occurs when a blood clot blocks an artery carrying oxygenated blood to the heart, and lack of oxygen kills heart tissue. Our goal was to image and quantify oxygen deprivation throughout cardiac arteries after heart attack by phosphorescence quenching analysis. Phosphorescence quenching analyses is a new technique to 3-dimensionally image and quantify oxygen concentrations in deoxygenated tissues such as those found post heart attack. Our specific aim was to perfuse rat hearts with polystyrene microspheres containing luminescent porphyrin dyes, whose phosphorescence is quenched by triplet oxygen. After microsphere perfusion, an artificial heart attack was surgically induced and the heart flash-frozen, thus preserving the metabolic state of the tissue. To collect data, the microsphere filled heart is serially sectioned and photographed using an Imaging CryomicrotomeTM (ICM). The series of images are compiled into a 3D volume. This 3D image will provide the exact location of every microsphere within the heart, and each microsphere provides one measurement of oxygen concentration. Deoxygenated heart tissue is characterized by microspheres with brighter phosphorescence. A single rat heart will contain 5,000 – 10,000 microspheres providing a sufficient number of measurements thus allowing good statistical analysis showing the distribution of oxygen concentration within the heart. We hope to expand the current understanding of the damage caused by heart attacks by 3-dimensionally mapping the distribution of oxygen in heart tissue after a heart attack. With a better picture of the mechanism of ischemia, the treatment of heart attacks can be made more effective.

The military as an institution stands to impact society on a large scale. According to the Department of Defense (DoD) Base Structure Report for 2010 there were 1,628,188 authorized Active Duty Personnel for the 4,249 bases located within the United States as well as 769,415 authorized civilians. A majority of these civilians are employed by the DoD or their respective installation. This research employs two competing hypotheses 1) Crime Rates will increase with military presence due to inherent qualities of military life. (i.e. young male population, high mobility) hypothesis 2) Crime rates will maintain or decrease because of economic impact that comes with many military installations. Much of the literature exploring interactions between the military and society have largely examined the psychological effects of service on service members and the effects of veteran status on life outcomes. This research investigates the larger effect of the military institution on society. Using data from the Federal Bureau of Investigation Uniform Crime Reports and DoD Base Structure Reports this research questions the existence of a relationship between Military Presence in an Area and Crime Rates in that area for the states; Arizona, California, Hawaii, Idaho, Nevada, Oregon, Utah and Washington .

The motor cortex in primates controls hand movement with direct connections of neurons to muscles in the arm. The question to consider is how flexible is a neuron’s control of its target muscle(s)? After implanting micro-wires to record neuron activity, I locate a neuron whose activity directly correlates with the activation or depression of two muscles with similar actions in the arm (muscle ‘A’ and muscle ‘B’). I then devise a task in which the monkey must disassociate the two target muscles from each other. This is done by having the monkey move the cursor into one of four different activation boxes: muscle ‘A’ activation, muscle ‘B’ activation, neither activated and co-activated. This task is repeated during which the activity of the neuron as well as the muscle activity of the two target muscles are recorded. The two things to look for when analyzing these data are whether the monkey was able to successfully control each muscle independently and the neuron’s activity throughout the task. The fact that the monkey could disassociate the muscles supports the hypothesis that this system has great plasticity. However, the neuron’s activity for each of the four types of activation varies greatly and is therefore not conclusive. Thus, many successful experiments with different combinations of muscles are required for further analysis and to observe any pattern that might emerge in these types of experiments. These results are important in understanding how the nervous system adapts to new environments and situations. These data could be used to develop and perfect a brain-computer interface. Such a device could serve as a fix for a broken link between the brain and specific muscles in a paralyzed victim, for instance. It is essential to understand how to rewire the nervous system to accomplish such a task.

Emergence of the deciduous teeth, or baby teeth, has been argued to be unaffected by moderate environmental risk factors such as malnutrition and disease.  Consequently, because of this argument, deciduous tooth emergence has been used to assess growth and age estimation in children without consideration of environmental factors.  In this paper we will examine the way nutrition and other covariates affected the timing of deciduous tooth emergence in a Bangladeshi sample.  We used data from a three year longitudinal study that prospectively followed 397 Bangladeshi children from the time of 1974 famine to 1977.   We used a parametric survival analysis to quantify the effects of nutritional status on the timing of tooth emergence in order to test the hypothesis that poor nutritional status does not delay the emergence of deciduous dentition.

Following the financial crisis of 2008, the ability of financial institutions to accurately quantify their risk and maintain suitable capital reverses has become a focal point of the financial industry. However, risk managers face some significant challenges when attempting to quantify their risk using the value-at-risk measure, which has recently become the de-facto industry standard. The value-at-risk measure, or VaR as it is most commonly known, is a measure of risk that attempts to answer a very important question—what is the most I can lose on this investment? VaR does this by measuring the potential loss of an asset or portfolio, with a given confidence interval over a set period of time, usually one day. For instance, a VaR measure of $10,000 over one day with a 95% confidence interval, would tell the investor that there is a 5% chance that their investment could lose $10,000 or more over that day. Although the concept of the VaR measure is well defined, there are many different ways to calculated it, many of which can lead to very different results. In order to assess these varying results, a historical simulation methodology will be used to observe the performance of the different VaR’s over the last five years using historical price data. In order to provide better insight into their performance characteristics, the VaR measures will be tested on commodities and currencies in addition to equities. The analysis of these observations, which include the financial crisis, should provide some additional insight into the robustness of different VaR measures during times of increased uncertainty.  These insights could be used by risk managers to more accurately quantify their risk and to establish more precise capital requirements, which would contribute to more stability in the financial industry.

Proper placement of stomata, valves on the plant surface essential for photosynthesis and transpiration, is necessary to allow gas exchange and minimize water loss. Cell-to-cell communication is required during stomatal development and is thought to use a complex ligand-receptor signaling pathway to ensure correct density and spacing of stomata on the epidermis. Small peptides Epidermal Patterning Factor 1 (EPF1) and EPF2 are expressed by cells at different stages of stomatal development and act to negatively regulate stomatal formation. To determine the distance over which these ligands affect stomatal patterning, the Cre-lox recombination system was used to create mosaic epidermal tissues that marked sectors overexpressing EPF1 or EPF2. By examining the number of stomata developing in the wild-type cells adjacent to the recombined sectors, the distance the ligands can act on stomatal precursor cells to coordinate stomatal patterning can be determined. The system will also be used to study the putative ligand EPFL9, which promotes stomatal formation and is expressed in the mesophyll, suggesting that it moves between cell layers to communicate with cells in the epidermis. This could lead to novel insight into the molecular communication regulating stomatal patterning.

Nematodes (soil worms) deprived of food (bacteria) have extended lifespans and exhibit substantially reduced translational activity (i.e., protein synthesis). In a previous study in this lab, translation in worms starved for 3 hours was significantly decreased but partially restored by 27 hours. Furthermore, mutations that decrease translation have been shown to extend lifespan in many model organisms including yeast, worms, and flies. Moreover, calorie restriction (CR) by growth in 0.05% glucose extends lifespan in yeast. As translation of some mRNAs is required for cell survival, we have analyzed translational activity in yeast in response to total sugar deprivation to identify key time points for changes in general translational efficiency via polysome profile analysis. Cells grown in rich medium were shifted to the same medium lacking glucose and samples for analysis were taken at the following timepoints: 10 min prior to the medium shift (MS), 10 min after MS, 1 hr after MS, and either 2 hrs or 4 hrs after MS. Directly after the MS, translation drastically drops off. At 1 hr after the MS, cells show a partial recovery in translational activity with a gradual decline thereafter. We then analyzed several mRNAs suspected to be affected by CR for transcriptional and/or translational changes, including mRNAs for heat shock proteins, pentose phosphate pathway, mitochondrial and cytoplasmic rRNA, and RNA polymerase (RNAP). Of the mRNAs analyzed in the RNA polymerase group, subunits of RNAP(II) (which transcribes mRNA) had elevated transcript levels at all time points relative to 10 min prior to MS. Analysis of polysome fractions by qPCR for RNAP(II) showed a similar trend in translation efficiency, indicating an increase in RNAP(II) protein synthesis. Despite the overall low levels of translation during CR, elevated levels of RNAP(II) suggest the production of new mRNAs needed for a conditional response to CR.

Maternal microchimerism is the trafficking of cells from the mother to the fetus during pregnancy. Surprisingly, maternal cells may remain in the fetus for years after birth, and recent research has linked the persistence of these maternal cells to some autoimmune diseases. Pediatric Lupus Erythematosus (PLE) is one such disease that may be influenced by a loss of T lymphocyte tolerance to chimeric maternal antigens. Our research aims to determine the role of microchimerism in T cell activation, along with determining the affects of premature birth on the prevalence of PLE. To determine the relationship between T cell activation and maternal microchimerism, peripheral blood mononuclear cells (PBMCs) were obtained from 26 PLE patients and age-matched controls. An immune response was elicited from the patients’ PBMCs by presenting them with self, maternal, or an unrelated donor PBMCs for 5 days. The level of immune response was determined by assaying cytokine expression and proliferation by flow cytometry. To determine levels of maternal microchimerism in PLE patients, non-inherited maternal antigens (NIMAs) were amplified using Real-Time PCR. Associations between premature birth and PLE were determined using premature delivery data from parental reports. Our results show that PLE patients have an increased prevalence of premature birth, which may allow for more maternal-fetal cell trafficking. This cell trafficking could then influence future immune responses to maternal antigens. The T lymphocyte response to maternal PBMCs in PLE patients was higher than in control groups, indicating that persistent activation of the T lymphocytes due to maternal antigens may be contributing to the inflammation in PLE. Maternal microchimerism levels in PLE patients were lower than in controls, indicating possible elimination of microchimeric cells by the activated T lymphocytes. Thus, further research on birth weight, microchimerism, and T lymphocyte activation may lead to a clearer picture of PLE, as well as targeted therapeutic approaches.

Operations research models can significantly improve decision making processes by optimizing certain objectives valued by the end user. Many real-world systems have more than one objective that can conflict with one another, and multi-objective optimization is a tool used to help a decision maker find a preferred balance between them. These models have been crucial to breakthroughs in areas such as scheduling and logistics. Though using these analytical techniques to solve practical business problems can yield impactful results, designing them is still challenging. For example, representing expert knowledge with mathematical expressions has conventionally been required to optimize systems with operations research algorithms. Furthermore, the inflexible nature of most mathematical expressions prevents models from accurately representing a constantly changing, real-world system. The language disparity between mathematics and the decision maker’s objectives also presents a challenge. Huseyin Onur Mete’s dissertation on Multi-Objective Optimization of Complex Systems Defined by Rules discusses how a multi-objective, rule based algorithm can address these limitations and can be used to optimize a hypothetical hospital evacuation strategy. The first steps of this research involved deciphering and learning to execute this particular algorithm in C++. We have also verified the algorithm’s performance with a mathematical example, by comparing graphs of the algorithm’s generated solutions with the true mathematical solutions. By conducting a literature review we were also able to better understand multi-objective optimization with rules and its applications to healthcare systems. We are now extending Mete’s results to demonstrate the algorithm’s potential for interactive use in a more complex evacuation situation by modifying the algorithm’s parameters and variables. A numerical demonstration of the methodology will be presented.

Acoustic levitation has been used in various capacities to study the effects of bubble oscillations in applications ranging from sonochemical studies, surfactant related studies, destruction of bacteria and malignant cells, intracellular drug delivery, noncontact materials manipulations, and various studies of cloud physics, among many others. With many applications and sensitive processes benefiting from acoustic levitation, all under ultrasonic frequencies, it is fundamental to understand the key behaviors that the most basic form of oscillation encompasses. One theory asserts there are upper and lower equilibrium positions within close proximity of the pressure nodes that allow for the support of droplets or any other particle for indefinite time periods. A different theory asserts the presence of a Bjerknes force that contributes to the stability of oscillating bubbles near pressure antinodes of the acoustic levitating field when an air bubble is smaller than resonance size. In this study, a water droplet is placed in an acoustic levitating field to determine the forces, equilibrium positions, and minimum energy density required for stable acoustic levitation under room temperature conditions. The water droplet is suspended against gravity by counterbalancing forces due to acoustic pressure and is located between equilibrium points. A curved reflector surface made of metal serves as pressure boundary to help create a standing wave for droplet stability. It is hypothesized that equilibrium is achieved in areas of least pressure variation within the acoustic field and that the minimum energy density required is proportional to the speed of the sound wave through the medium.

In 2008, the World Health Organization estimated that 33.4 million people globally were infected with human immunodeficiency virus (HIV), and that 2.7 million people became newly infected that year alone. Heterosexual transmission of HIV accounts for the majority of new HIV infections, with women being affected disproportionately. Microbicides, which are agents that can be applied topically to the vaginal or rectal mucosa to prevent HIV transmission, have tremendous potential for curbing this pandemic through offering a low cost and female initiated means of protection. A recent clinical study has demonstrated the protective efficacy of an antiretroviral (ARV) based vaginal gel. However, many potent ARVs, such as protease inhibitors, have characteristics causing poor topical mucosal penetration or are difficult to deliver in combination. Here we show the ability to create and control characteristics of micro- and nano-scale poly(lactic-co-glycolic acid) (PLGA) particles for ARV encapsulation and characterize their transport in the vaginal niche. We can formulate particles of variable size (~100 nm to ~500 nm) and surface chemistry through nanoprecipitation and emulsion formulation techniques. Cervical vaginal mucus (CVM) mimics were created to exhibit realistic log-linear shear-thinning of viscosity. Subsequent particle tracking studies in the CVM mimic were completed to show how size and surface chemistry affect particle diffusion through this barrier. CVM mimic diffusion studies reveal the validity of the mimic for transport studies and reflect the extent that particle diffusion is affected by the rheological properties of CVM. Results demonstrate we can alter characteristics of nanoparticles and evaluate its effects on particle transport. These studies are important for improving biomaterial properties to enhance nanoparticle based microbicide delivery. Optimization of drug delivery will allow drugs to penetrate the tissue and CVM layers more effectively, increasing the bioavailability of drugs at the site of HIV transfer.

Many of the glomerulonephritis present recurrent acute inflammation episodes. With time these conditions often lead to progressive fibrosis and chronic renal failure. Interleukin-6 (IL-6) is considered one of the most proinflammatory cytokines; herein we will study the role of IL-6 using the nephrotoxic serum nephritis mouse model. The ubiquitous expression of IL-6 makes it a challenge to study this interleukin. Therefore we hvae initiated our first studies with genetically engineered mice with ablated IL-6. Subsequently we will deplete the IL-6 in the F4/80+ macrophages and the Ytgax (CD11c+) dendritic cells. We have genetically engineered miec that express the Cre enzyme under the F4/80+ or Ytgax promoters, then we will breed either of these mice with IL-6 or IL6Ralpha-floxed mice, to ablate IL-6 expression only in those F4/80+ or Ytgax+ cells. IL-6 +/+ (IL6WT) and -/- mice (IL6KO) were injected with Nephrotoxic serum (NTS) in the tail vein. Mice were placed in metabolic cages for seven days to collect urine at 0,  3 and 7 days to measure renal failure and progression of the disease. Mice were sacrificed at 7 days after the injection and both kidneys harvested and sectioned. Sections were saved for RNA, protein, frozen section and paraffin embedded histopathology analysis. Extraction, quantification and quaility analysis (RNA integrity number) from the IL6WT and IL6KO frozen kidney samples were conducted and later synthesis of cDNA was made. Quanitative PCR (qPCR) reaction will be carried out to analyze gene expression of IL-6 family genes. Protein analysis of these genes will be carried out using western blot analysis and quantification of those no- and phosphorylated proteins will be determined. Measurements of creatinine and albumin by HPLC analysis will be carried out and used as indicators of renal function. Pathological anlaysis on frozen or paraffin embedded tissue will be done to assess glomerular and interstitial damage. 

Concentrated solar power is an attractive energy generation approach with zero greenhouse emissions. However, the existing systems and approaches have a very high capital cost and/or have been developed for utility-scale power generation. We are working on a stand-alone solar power system which is configured to 1) use recent developments in solar absorber and turbine technologies and 2) leverage high volume/ low cost components from existing industries. With this strategy, we will design an economical small-scale generator capable of producing enough electricity for the basic electricity needs of a single household (a minimum of 2kWh per day). We will also build and test a smaller scale prototype. The system consists of a volumetric solar absorber used as a heat collector to transfer the energy to a fluid. The heated fluid is used to generate pressurized steam for the powering the turbine and alternator assembly. Preliminary results demonstrate a functional low cost turbine in combination with a coated heat collector capable of transferring energy at slightly higher rates than ordinarily. With further refining of project efficiency can be optimized.

Vascular calcification is one of the complications that often occurs in Type II diabetic (T2D) patients. There is a growing consideration for the notion that smooth muscle cells (SMC) found in T2D blood vessels can express bone-regulatory proteins due to abnormal stimuli in their environment. These phenotype-changed SMCs behave more like osetochondogenic cells capable of contributing to the rise of vascular calcification. Studies have shown that osetochondogenic cells can differentiate into chondrocytes, which terminally differentiate into mature hypertrophic chondrocytes and are able to synthesize a cartilage matrix including Collagen Type X and alkaline phosphatase. Cartilage matrix can eventually calcify and be replaced by bone. One abnormal stimulus experienced by the SMCs in T2D condition is hyperglycemia. This high blood glucose level in diseased blood vessels can lead to a non-enzymatic glycosylation of various proteins, forming what are termed Advanced Glycated End-products (AGEs). High accumulation of these AGEs in the blood is hypothesized to serve as a signal or stimulus giving rise to many complications among which can be vascular calcification. In this study, I will perform immunohistochemical staining for Collagen Type X and it will be carried out on vessels collected form T2D animal models to check for the presence of mature hypertrophic chondrocytes. Calcifying Vessels are expected to have a positive Collagen Type X staining observed in the extracellular space. Ion-exchange column chromatography and spectrophotometry will be used on blood samples to determine the level of one type of AGE called glycohemoglobin. It is expected that the blood sample from T2D animal models will have higher glycohemoglobin level than the control group which will be revealed by the spectrophotometry optical density readings. The quantitative measurement of AGE concentrations will be correlated with the extent of Collagen Type X staining and the observed vascular calcification.

Botulinum toxin (Botox®) has been used for cosmetic and therapeutic purposes to induce paralysis in chewing muscles (innervated by the trigeminal nerve). The masseter muscle is a frequent target of such injections. Although paralysis induced by a single Botox® injection is traditionally believed to last 3-4 months, recent studies have shown that the muscles take longer to recover from atrophy. One possibility for this extended recovery time is that Botox® induces death of neurons in the trigeminal nucleus, specifically the trigeminal motor neurons. To investigate these effects, we injected one masseter of rabbits (left or right) with either Botox or an equivalent volume of saline. The brains were then removed, and the pons (which houses the trigeminal nucleus) was removed and sectioned. Alternate pons sections were stained with cresyl violet to count total trigeminal neurons. If Botox® leads to motor neuron death, the injected side of the brain in these animals should have lower counts than the uninjected side, whereas in saline-treated animals the sides should not differ. This has implications on dosage levels during treatments and raises concerns over the long-term health of patients undergoing procedures utilizing Botox®, since the trigeminal neurons control chewing muscles. Of the brains processed, neither the Botox® nor the saline group showed differences between sides (paired t-tests, p=0.35, n=4 and 0.59, n=3 respectively). The average counts on the injected side were actually slightly higher than those of the uninjected side in both groups, although not significantly (936 vs 909 for Botox®, 1120 vs 1078 for saline). The overall difference between groups was also not significant (p=0.61). These results suggest that the prolonged atrophy of jaw muscles after Botox® injection is not due to a loss of trigeminal motor neurons in rabbits. It remains possible that repeated Botox® injections could have such an effect, however.

As many seasonally breeding species do, the white-crowned sparrow (WCS) responds to seasonal changes in day length (or photoperiod) with alterations in physiology. These alterations include changes in the reproductive system and alterations in morphology (e.g. size and shape) of regions in the brain responsible for song production, courtship and territory maintenance. As photoperiod increases in early spring, males of the subspecies of WCS I study, Zonotrichia leucophrus gambelli, exhibit an increase in gonads size, which increases bloodstream concentrations of testosterone. Greater circulation of testosterone promotes a dramatic growth in HVC, a brain region necessary for producing song, via an incorporation of new neurons and growth of existing neurons. As photoperiod shortens at the end of the breeding season, the sparrows’ gonads regress, circulating testosterone levels drop, and HVC regresses through apoptosis-mediated neuronal death. This seasonal birth and death of new neurons in adult WCSs is the crux of my study: I am quantifying the rates of neuronal recruitment and death in HVC during the transition from breeding to non-breeding conditions. Using BrdU, a thymadine analog that incorporates into newly divided cells, I labeled adult born neurons in HVC while WCSs are in breeding condition (i.e. long photoperiods and high testosterone levels). I then permitted regression of HVC by transferring WCSs to non-breeding conditions (i.e. short photoperiods and low testosterone levels). Using immunohistochemistry, I am quantifying the recently incorporated neurons and apoptotic neurons in HVC at various time points after transition to non-breeding conditions. My project will provide insight into fundamental processes of neural plasticity in the avian brain. This resulting knowledge can be applied towards further understanding the neural basis of plasticity in regards to learning and memory in mammals, and thus ultimately understanding the etiology of many neural pathologies.

Post-translational modification of eukaryotic proteins by the small protein ubiquitin (Ub) is a signal for their proteasomal degradation. In some prokaryotes, such as Mycobacterium tuberculosis (Mtb), the 64 amino acid prokaryotic ubiquitin-like protein (Pup) is attached to target proteins prior to their degradation by the bacterial 20S proteasome. The proteasome accessory factor A (PafA) protein is the sole enzyme responsible for conjugating the C-terminal glutamic acid of Pup to lysine side-chain amines of its protein substrates. The two-step process of Pupylation (modification by Pup) involves transfer of the terminal phosphate of ATP to Pup in order to generate a phosphorylated Pup intermediate, which undergoes subsequent nucleophilic attack by lysine side-chains in substrate proteins. In order to further probe the mechanism of protein Pupylation, we have synthesized a novel fluorescent substrate of PafA and demonstrated its utility in measuring PafA activity in vitro and in cell lysates. Based on the proposed pathway of Pup activation, we have also synthesized a bi-substate analog that mimics the transition state of phosphate transfer, and have demonstrated its ability to inhibit the essential enzyme PafA in vitro. This holds promise for the future design of antitubercular agents targeting this key pathway in Mycobacterium tuberculosis.

In 2009, over 17% of all international adoptions to the United States were from Ethiopia.  This accounts for over an 800% increase in the past five years.  Ethiopian adoptees have also shown to have better health outcomes than adoptees from other regions of the world.  Despite this increasingly prevalent phenomenon, virtually no research has been done on the complex processes of trans-racial family building and identity formation experienced specifically by Ethiopian adoptees and their families.  While adoptees are integrated into new social and cultural settings, adoptive parents are forced to navigate their family through a new social and cultural space within a heavily racialized society, and facilitate identity formation for their children and themselves.  This project aims to investigate and analyze the lived experience of Ethiopian adoption by Euro-American parents in order to better understand these complex and poorly understood processes, and identify any strategies and resources they have used or created to facilitate these transitions.  Through semi-structured interviews, this research will generate case studies of the adoption process from the perspective of couples that have added to their family through Ethiopian adoption.  The sample population will consist of six Euro-American adoptive couples living in the Seattle area that have adopted at least one child from Ethiopia, found through convenience and snowball sampling.  Data will be qualitative and the analysis interpretive with a goal of understanding these complex and difficult processes of identity making/re-making, cultural reconciliation, trans-racial family building, and other complicated transitions.  As current adoption literature is in many ways inapplicable to the general experience of adoption from Ethiopia, this research will provide a basis from which those involved in this process can begin to seek relevant information for their individual experiences in order to facilitate the navigation of these complex processes of transition.

Development of new methods for detection and diagnosis of breast cancer is always in an urgent need for the medical community. Research has shown that the human immune system responds to tumor-specific antigens and produces specific antibodies even in the pre-malignant stage of breast cancer. We propose that these tumor-specific serum antibodies could be detected and used as biomarkers for detection of breast cancer. We use the neu transgenic mice developing estrogen receptor (ER) negative, HER-2/neu (HER2) positive breast cancers, which recapitulates human pre-menopausal ER-negative, HER2-positive malignant breast cancers. We have previously identified a few tumor antigens in the late stage of the neu-induced breast cancer. The mouse tumors have similar immunogenicity as their human counterparts due to the fact that some of these antigens are also immunogenic in human. Indeed, we have found that one mouse antigen called SRPK1, shares 91% homology with its human counterpart. We then performed an ELISA analysis on SRPK1 to test whether it qualifies to be a diagnostic biomarker. We found that SRPK1 alone detects 59% of HER2 breast cancer cases from the serum samples of 57 cancer patients (10 ovarian and 47 HER2-positive breast cancer samples) and 45 normal donors. Combination of SRPK1 and p53 markers detects more than 80% of cases in the same population. Furthermore, combination of SRPK1, p53, and HER2 markers increases the assay sensitivity to 82% of cases. In summary, we conclude that identification of SRPK1 in the neu transgenic animal model and assessing its human serum antibody responses is useful for the discovery of serum antibody biomarkers for detection and diagnosis of human breast cancer.

In nanoscale bioimaging and diagnostics, engineering bio-material interface has been one of the major challenges. Hybrid gold nanoparticles are long sought after as promising targeting contrast candidates for bioimaging and diagnostic applications due to their unique optical properties, strong light absorption and scattering, as well as high electron density. Conventionally, hybrid gold nanostructures have been produced by complex, multi-step synthetic and chemical cross-linking bioconjugation procedures which usually involve nonbiological stringent conditions, e.g. high temperatures, organic solvents and harsh reducing agents. To overcome difficulties related to complex conventional chemical synthesis and cross-linking methods, we adapted combinatorial peptide selection protocols, namely cell surface display (CSD), to select peptides that can interact with numerous solids with high affinity and material specificities. Specifically in this work we fused combinatorially selected gold-binding peptides (AuBP) conjugated with cell-targeting motifs (integrin binding, i.e. RGD- and glioma-binding) producing novel heterofuctional chimeric peptides. Here the gold-binding peptides (AuBPs) provide biological functionalization of gold nanoparticles resulting in hetero-functional nanoprobes that are biocompatible and capable of targeted cell bioimaging. The nanoprobes functionalized with designed chimeric peptides retained exceptional stability in high salt content buffer solutions in different stability assays, dynamic light scattering, and agarose gel electrophoresis. Furthermore, the resulting peptide-functionalized nanoprobes were successfully demonstrated to specifically target various cell receptors using fluorescence microscopy bioimaging experiments. The produced biocompatible, self-assembled gold nanoprobes have a great potential for development of clinically feasible nanoprobe tools for cell-targeted diagnostics and therapeutics applications.

Congenital heart defects are the most common form of birth defect, affecting about one out of every 100 newborns in the US. Ten percent of these afflicted newborns will face a narrowing of their aorta, formally called coarctation of the aorta. When a baby has this defect, his or her aorta begins to narrow, which can result in extreme hypoxia in tissues that do not receive sufficient blood supply, and eventual congestive heart failure. Surgical repair is required for the infant to regain normal circulation. Coarctation has been linked in many cases to migration of cells from the ductus arteriosus into the aorta. The ductus arteriosus is a fetal vessel that must close at birth, and does so by constriction of its smooth muscle cells until its lumen is occluded. If these contractile cells migrate into the aorta, they can cause constriction, and thus narrowing of the aortic lumen. Preliminary data from experiments on the region where the ductus inserts into the aorta show a differential expression of chemorepulsive signaling proteins from the Slit-Robo family in ductal versus aortic tissue, suggesting that a distinct tissue boundary forms in this region. In order to elucidate the role that Slit-Robo proteins play in determining the ductus-aorta boundary, I use reverse transcription PCR and microarray analysis to examine the expression of Slit-Robo ligand and receptor proteins in perinatal ductal and aortic tissue. By comparing expression in normal samples with samples from patients with coarctation, more insight into the influence of Slit-Robo chemorepulsive signaling on boundary formation will be gained. Characterization of the ductus-aorta boundary by identification of differential ligand-receptor expression is critical to understanding the role that abnormal boundary formation plays in coarctation of the aorta.

Quantum systems can store a fundamentally different type of information than what we are accustomed to. This quantum information enables us to perform computations that were previously infeasible. However, quantum information is also fragile to the slightest disturbances from thermodynamic noise. To circumvent this fragility, error-correcting codes have been developed to prevent and correct these errors. Though not yet physically implemented, these codes are mathematical techniques that process and arrange information in ways that theoretically works to preserve the stored data. This is akin to the way that CDs encode data to be recoverable even after losing some information to scratches. However, many of the interesting codes developed so far are not spacially local in our three-dimensional space: they require interactions between pairs of particles that are far away and that cannot be brought closer together without causing some other interacting pair to become separated. This is a major obstacle to practical implementation. We develop a mathematical method that converts a major subset of these codes--called "stabilizer codes"--to a spacially local form at the expense of requiring more information storage to encode the same data. This method brings together the two fields of error-correcting codes and measurement-based quantum computing. The application of this method to some known codes yields some previously unattained milestones in the effectiveness of spacially local codes.

Dietary restriction (DR), the limitation of calorie intake while maintaining proper nutrition, has been found to extend life span and delay the onset of age-associated disease in a wide range of species including yeast, flies, worms, mice, and primates. Previous studies have suggested that DR can reduce the lethality of environmental toxins. To further examine the role of DR in toxin response, we measured life spans of the nematode Cenorhabditis elegans treated with the mutagenic polyaromatic hydrocarbon, fluoranthene (FA). Treatment with 5μg/ml FA shortened the life spans of ad libitum fed nematodes compared with untreated controls. Animals subjected to DR showed increased sensitivity to FA compared to ad libitum fed counterparts. To determine the role of detoxifying enzymes in the toxicity of FA, we tested nematodes with mutations in Mediator (MDT-15), a transcription factor that regulates genes involved in fatty acid metabolism and detoxification. Mutation of MDT-15 increased the life span of FA treated animals compared to wild-type animals with no difference observed between DR and ad libitum fed MDT-15 animals. We also examined mutants with altered signaling in the Insulin-IFG1 (IIS) pathway, which regulates life span and stress resistance in C. elegans independently of DR. Constitutive activation of the IIS pathway through mutation of daf-2 or inactivation of the pathway through mutation of daf-16 did not alter the animals susceptibility to FA compared to wild type. Taken together, our results suggest that certain compounds increased in toxicity when combined with a DR regimen through increased metabolic activation. This work has important implications for the use of DR in the general population for the purpose of increasing general health. Our findings suggest environmental pollutants will play an important role in the efficacy of aging-related interventions .

A number of extensions to the Standard Model, the central paradigm of particle physics, have suggested the possibility of long-lived neutral particles inhabiting Hidden Sectors that are extremely difficult to detect. One such candidate event is the Higgs particle decay to Hidden Sector neutral pions that subsequently decay to a pair of bottom quarks, which create jets. Jets are conglomerations of particles and energy expelled in a cone shaped region. The UW Physics Department is engaged in the development of advanced analysis techniques, software algorithms that require large simulated data samples in order to identify patterns and to utilize correlations between several different important event quantities, for the identification and study of these particles. Because these processes are so infrequent, it is important to be able to separate the signal events from background. By examining the differences between signal and simulated background data, I developed selection criteria that could be applied to data to improve the signal-to-background ratio. A significant background process that I studied is the formation of Quantum Chromodynamic (QCD) di-jets that have a signature similar to signal events. These background QCD events were simulated by pseudodata called Monte Carlo. The signal events are comprised of 40 inverse picobarns of proton-proton interaction data recorded in 2010 at 7 TeV center of mass energies by the ATLAS detector on the Large Hadron Collider (LHC) ring in CERN, Geneva. I conducted my analysis with the aid of software developed at CERN such as the ROOT Data Analysis Framework that generates plots and distributions of data. The long term implication of my results is to aid in the discovery of new particles that will lead to a paradigm shift in Standard Model physics.

Time and causation are relatively well understood for the physics of general relativity, but not for generalized Newtonian conceptions of the universe. I examine the causal structure of Newtonian gravitation theory and compare it with the causal structure of general relativity. I reformulate the causality conditions of general relativity as Newtonian analogs. Many of these analogous conditions were subsequently found to be violated by all Newtonian spacetimes, meaning they are not useful as causal properties to understand Newtonian gravitation theory. By investigating how causal properties differ between these two theories of spacetime we can determine which are then most likely to apply to newly developing theories, such as quantum gravity. I also discuss the impact of these failures on future research regarding the fundamental properties of space and time.

It has long been difficult for researchers to collect data from planets and moons other than our own, so probes and satellites have been sent to the outer planets in hopes of learning more about them. The goal of this project is to analyze infrared spectral images taken by the Cassini orbiter in 2006 to create a model for the texture of the water ice on Enceladus, one of Saturn’s moons. This is done by comparing the modeled bidirectional reflectance (BDR) of the ice to the data. Ice scatters and absorbs light according to different sizes of ice crystals that make it up. Currently the models we have made use of only one grain size in a single ‘infinite’ optical depth layer. We know that there are layers of ice on top which has smaller grain size ice because Enceladus sweeps through the thickest part of the E-ring, a ring of small grain ice ejected by geysers on Enceladus, making it a prime target for investigation. This layer explains the errors between the BDR models and the actual data. By using layering techniques that incorporate more than one grain size, we hope to create a model that better fits the data.

InGen is a hand-held device capable of generating haptic feedback without the need for a battery. The InGen project focuses on two aspects of embedded devices; power harvesting and haptic feedback. Power harvesting is the ability to gather the power from the environment. The more power drawn from the environment, the less a computing system must rely on internal power storage (such as a battery). Haptic feedback is a useful means of conveying information to a user without requiring audible or visual cues. Many mobile phones use haptics to assist with virtual keyboards use by giving a quick vibration when an on-screen button is pressed. The vibration is minimally distracting to others, yet lets the user know the status of their action. InGen uses a modified servomotor to perform two functions: 1. Generate power for wireless communications and embedded electronics and 2. Provide haptic feedback. As InGen’s knob is turned, the servomotor generates power for an internal microprocessor, which relays information about movement to a near-by computer through wireless link. The computer can send information back to InGen to present haptic feedback to the user by increasing the amount of rotation resistance they experience. This resistance increase can be short or long-lasting. In the case of a short pulse the user will feel a bump, where-as the long-lasting response will make it difficult to turn the knob in one or both directions. Using InGen to scroll through a list of images on a computer screen, the ‘bumps’ can be used to let the user know when they scroll past an image that may interest them based on previous images viewed, while the longer resistance increase can signal to the user that they have reached one of the ends of the list.

M dwarfs are the most numerous stars in our galaxy. The optical spectra of these low mass stars are known for their distinguishing molecular absorption bands. We use the Sloan Digital Sky Survey (SDSS) DR7 spectroscopic catalog of 70,000 low mass stars to investigate the changes in atomic and molecular features that occur with differing mass, temperature, metallicity, and level of magnetic activity. In particular, we have found that stars with high activity levels show a lower amount of TiO2 absorption for a given amount of TiO4 in their photosphere. With time, we hope to define a relationship between the strength of either the TiO2 absorption band or other absorption bands and the amount of activity so that these molecular features can be used as activity flags.

Antiretroviral therapy (ART) has been shown to significantly increase life expectancy in HIV patients. The nucleoside reverse transcriptase inhibitor azidothymidine (AZT) is a backbone of ART, but its usefulness is limited because of its toxic effects on mitochondrial production of adenosine-triphosphate (ATP) for energy, resulting in reduced muscle function. Previously, up-regulation in gene expression of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) in AZT treatment was observed. The purpose of this investigation was to evaluate the literature for evidence of the role of PGC-1α in skeletal muscle function and to illustrate a model for its regulatory pathway. Databases used in this research included PubMed and OMIM, using the keywords “PGC-1 and skeletal muscle,” “PGC-1 and regulation,” etc. PGC-1α has been extensively described as a key regulator of mitochondrial biogenesis and coactivator of transcription factors that impact whole-body energy output. Early studies demonstrated that high amounts of PGC-1α lead to increased energy expenditure by coordinately increasing mitochondrial biogenesis, cellular respiration, and oxidative metabolism for energy production. To do so, PGC-1α directly activates a plethora of transcription coactivators, suggesting that many signaling cascades important in muscle physiology depend directly on PGC-1α activity. Several studies also explored the role of PGC-1s in skeletal muscle diseases such as Duchenne muscular dystrophy and various myopathies, demonstrating the critical role of PGC-1α in maintaining muscle fiber integrity. These results have furthered our understanding of the role of PGC-1α in mitochondrial function and muscle responses to pathological conditions such as HIV. However, subsequent research must investigate which pathways induce PGC-1α during external cues like exercise and disease as well as how PGC-1s protect against muscular atrophy and dystrophy. Future studies will focus on the role of PGC-1α in AZT-induced mitochondrial dysfunction by examining genes regulated by PGC-1α and theorize how and why this coactivator is induced.

Mechanical forces play a critical role in biology from cellular differentiation to the formation of blood clots. However, there are currently limited quantitative methods of measuring these intrinsic molecular forces. The development of fluorogen-activating proteins (FAPs) that are capable of allowing normally dark fluorogen dye molecules to fluoresce offers a unique possibility for the design of a novel force sensor with piconewton sensitivity. These proteins consist of two single-chain antibodies that must dimerize in order to bind and activate a fluorogen dye molecule for excitation. The force sensor itself consists of a single FAP with a flexible linker connecting the two chains such that they are held in close proximity to each other. In the presence of tensile mechanical force applied across the complex, the two antibody chains will be pulled away from each other, disrupting the binding of the fluorogen dye and subsequently decreasing the fluorescence intensity. The purpose of this project is to develop an in vitro testing system to demonstrate that the protein is responsive to applied forces. In order to apply tensile forces in a controllable manner, two high-affinity attachment tags (biotin and SNAP-tag) were added on the N and C termini of the complex. These ligands will be utilized to attach the force sensor to paramagnetic beads and a streptavidin-coated surface. Introducing a magnetic field will result in force simultaneously being applied across a large number of proteins and a detectable decrease in fluorescence intensity as the fluorogen dyes unbind. Positive confirmation of the relationship between fluorescence and force will validate the protein as a force sensor and allow for future development in implementing the probe in a cellular system.

The purpose of this study was to describe and compare sleep patterns as measured by actigraphy in children with active and inactive Juvenile Idiopathic Arthritis (JIA). JIA is one of the most chronic rheumatologic conditions in childhood. Children with JIA experience joint pain, inflammation, fatigue, and limited mobility. Children also experience sleep disturbances, including difficulty falling asleep and fragmented sleep. Sixty-nine children 6-to-11 years of age (mean 8.5 ± 1.96SD) with JIA (58 girls) participated in the study. Of the 69 children, 46.4% (n=32) were diagnosed with inactive disease and 53.6% (n=37) had active disease. Each child wore an actigraph and completed a sleep diary for 7 consecutive days. Our result shows average total sleep time was 496.6 ± 42.4 minutes for the entire sample. Diary bedtimes and rise times did not differ in children with active and inactive JIA. No group differences were found for total sleep time, wake after sleep onset, and sleep efficiency. These findings suggest that sleep patterns as measured by actigraphy did not differ in children with active and inactive JIA. The majority of children with JIA had low disease activity which may contribute to our findings. Further studies are warranted on sleep patterns in JIA children with more severe disease. 

Diabetes is a growing epidemic associated with many serious health complications. The Center for Disease Control estimates that about 25.8 million Americans are afflicted with diabetes resulting in total costs of $174 billion dollars annually. Today, no treatment options have been proven effective in curing Type II Diabetes Mellitus (T2DM). Recent research has shown that patients undergoing Roux-en-Y Gastric Bypass (RYGB) surgery show a near immediate remission of T2DM. The molecular mechanisms mediating the weight loss-independent anti-diabetes impact of the surgery are unknown. We hypothesize that RYGB surgery has a direct impact on the expression profile of gut peptides, resulting in an improved glucose homeostasis and insulin expression of the pancreas. To tests this hypothesis, 44 Ossabaw pigs are fed a standardized high fat diet for 180 days prior to surgery resulting in the development of obesity and T2DM. The pigs are randomized into five study groups receiving either Roux-en Y Gastric Bypass (n=10), Roux-en y Gastric Bypass with Vagotomy (n=10), Gastrojejunostomy (n=10), Gastrojejunostomy with a duodenal exclusion (n=10) or a sham (n=4) operation. Animals undergo an intravenous glucose tolerance test (IVGTT) and meal tolerance test (MTT) at the time points: 7 days pre-operative and again 14 and 60 days post-surgery. Gastrointestinal tissue and pancreatic samples are collected during surgery and at necropsy (day 60) at the following sites: proximal and distal duodenum, proximal and distal jejunum, and proximal and distal ileum. IVGTT and MTT samples will analyze the response on systemic glucose, insulin, glucagon-like peptide-1 (GLP-1), peptide YY (PYY), glucose-dependent insulinotropic polypeptide (GIP), and ghrelin levels. Histological and mRNA analysis of the gastrointestinal and pancreatic tissues will provide insight on changes in the expression patterns of these hormones at the different sampling sites. The findings of this study will provide greater clarity in our understanding of the T2DM remission.

Fear conditioning is a form of aversion-induced learning where a neutral conditioned stimulus (CS) is paired with an aversive unconditioned stimulus (US). After multiple CS (usually a tone)-US (usually a footshock) pairings, CS alone will result in conditioned fear responses. The amygdala has long been considered the center in the brain where fear-based US-CS plasticity primarily occurs. However, it has not been well studied how the US directs CS-US association in the amygdala. In this study, we addressed this issue by investigating whether the electrical stimulation of the amygdala or periaqueductal gray (PAG) could serve as a US in the fear conditioning. Male Sprague-Dawley rats were implanted with stimulating electrodes in their amygdala or dorsal PAG (dPAG) bilaterally. For training, a tone (2.9 kHz, 85 dB, 20 sec) was used as a CS and electrical stimulation (0.1-ms width, 100 Hz, 2 sec) of the amygdala or dPAG as a US, which co-terminated with the CS. Next day, 8-min tone was presented continuously as a tone testing, and the following day, 8-min exposure to the training chamber was given to the rats as a context testing. Freezing was measured as a dependent variable throughout the sessions. During the training, both amygdala and dPAG stimulation groups showed freezing (unconditioned response) to the electrical stimulation. However, during the testing, only dPAG stimulation group showed conditioned freezing to the tone, indicating fear conditioning occurred in this group. This result suggests that electrical stimulation of dPAG, not amygdala, can serve as a US in tone fear conditioning, and that dPAG might be a key structure in relaying US information to the amygdala during fear conditioning.

Despite recent advances, some strains of influenza virus pose significant obstacles to vaccine development. This challenge, coupled with the rapid emergence of drug-resistance, highlights the need for new, broadly acting antivirals against influenza. In previous work, a library of six- or eight-residue cyclic D,L-alpha-peptides was screened for activity against influenza virus in a cell culture-based assay. For our current mechanistic studies, a small subset of the most potent compounds was re-synthesized. We found that the re-synthesized peptides were less potent (>five-fold) than those identified in the initial screen using the same cell culture assay. In addition, all of the peptides were non-cytotoxic in an Alamar Blue assay for metabolic activity. Using two peptides that retained antiviral activity against influenza at non-cytotoxic concentrations, we have selected for influenza viruses that are resistant to peptide-mediated inhibition to gain insight into the molecular basis for their activity. The resistant viruses are selected for by passaging the virus in the presence of a high concentration of inhibitory peptide, which prevents the non-resistant virus from propagating while allowing the resistant viruses to replicate. The previously described inhibitor, tert-butylhydroquinone (TBHQ), has been included in our studies as a positive control to optimize our selection protocol. Over multiple rounds of selection, we have not observed resistance in either the TBHQ-treated controls or the peptide-selected samples. Based on these results, we are modifying our selection strategy and isolating individual plaque-purified clones for continued study.

Many plants sense changes in day length (photoperiod) to coordinate the timing of important developmental transition, such as flowering. The regulation of CONSTANS (CO) gene expression and FLOWERING LOCUS T (FT) gene expression is an important aspect of photoperiodic flowering mechanism in Arabidopsis. We have previously shown that FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) protein-mediated mechanism regulates CO transcription. Recently, the computational analysis indicated that FKF1 may also directly regulate FT transcription. CYCLING DOF FACTOR 1 (CDF1) is a repressor of CO transcription. To regulate CO transcription, FKF1 controls the degradation of CDF1 protein. We hypothesized that the same FKF1 dependent mechanism is involved in the regulation of FT transcription. If our hypothesis is correct, CDF1 not only binds to the promoter of CO, but CDF1 also would directly bind to the promoter of FT. We examined this possibility and found the evidence that CDF1 may bind to the FT promoter directly. We also demonstrated that CDF1 suppressed FT expression. Our results indicate that CDF1 is a link for the FKF1-mediated mechanism to regulate both CO and FT transcription.

Chronic mild traumatic brain injury (mTBI) is a persistent post-concussive syndrome with lingering symptoms of the initial injury. The most common symptom is fatigue that interferes with daily activities. Single photon emission computerized tomography (SPECT) imaging revealed that chronic mTBI patients exhibit increased dorsolateral prefrontal and insular cortex activation and a decrease in cerebellar activation compared to healthy controls during a working memory task (Hattori et al., 2009). This raises questions about the integrity of frontocerebellar connections in chronic mTBI patients. Are these connections interrupted in chronic mTBI patients and could this account for the nagging fatigue these patients experience? To explore these questions, chronic mTBI patients and matched controls will perform an n-back task in the fMRI scanner to engage working memory. We hope to replicate the findings found in the SPECT research as well as to examine changes in the strength of frontocerebellar connnections, differences in white matter tract integrity, and changes in resting state networks. We will also look for a correlation between neural activation and subjective measures of fatigue and perceived effort to examine the neural basis of fatigue. We hope the results from this study can offer insight into chronic mTBI—a difficult condition lacking any objective measures to confirm its diagnosis. Furthermore, if changes in neural networks are detected, specifically in the frontocerebellar connections, this could help us better understand the role of frontocerebellar connections in working memory and fatigue. All of our analyses will help us identify possible targets for more detailed and extensive future studies.

The Scribbler robot can sketch lines using programmed instructions and is linked to the computer with a wireless bluetooth dongle. Scribbler can also use its visible camera to discriminate between different visible patterns using image analysis. The goal of this project is to use Python to control the robot and have it locate Pepsi and Coke cans in a room and determine can type (Pepsi or Coke) for each can and to count the number of cans of each type. To accomplish the above goal, the robot will move towards the individual cans, using the IR sensors and stall sensors to avoid obstacles. Various obstacles and can configurations will be used to test the robots ability.

Autism is a neural development disorder characterized by impaired social function, communication, and rigid and repetitive behaviors. In studying Autism Spectrum Disorders (ASD), the capacities of the phonological loop, responsible for memory related to auditory information, are of particular interest. Individuals with ASD have been found to have shorter phonological loops, meaning they can recall less auditory information from memory. Research on autism genetics has established genetic heritability, however the exact mechanism remains unclear as autism has yet to be traced to a single-gene mutation or chromosome abnormality. There is a complex combination of factors involving interaction between multiple genes, environment, and factors which don't change DNA but can be inherited and interfere with gene expression (epigenetic factors). In looking for genetic connections with the causation of ASDs, it follows that families with children with the disorder may too exhibit evidence of shorter phonological loops. This can be tested using non-word repetition tests. The measure is evaluated for its scoring reliability in person as the test is administered. Scoring in person limits the administrator to hearing each said word once in real time. In contrast, scoring done after administration through taped recordings allows one to investigate the specific nature of the phonetic errors. The three groups in the study are neurologically typical participants with no history of autism within their families, simplex families with one child with ASD, and multiplex families with two or more children with ASD. If performance is heritable, then we predict that more first degree relatives in the multiplex group will show impairments on this measure and will show a greater number of phonemes missed.

Mineral growth is regulated by several critical factors such as phosphate (Pi), calcium, pyrophosphate (PPi) and a regulatory enzyme, tissue nonspecific alkaline phosphatase (TNAP). TNAP activity produces Pi from hydrolysis of PPi and functions as a regulator of skeletal mineralization by removing a mineralization inhibitor, PPi, and increasing Pi. Previous reports both in humans and mice have shown that TNAP is an essential factor in the formation of acellular cementum, with limited effects on dentin formation. Studies here aimed to further define the role of TNAP in root dentin development by analyzing tooth root development from TNAP homozygous gene knock-out mice (Akp2-/- mice) and wild type (WT). Tissues were analyzed using histology, histomorphometry and immunohistochemistry (IHC) at 33 and 39 days post coital (dpc). Histological analysis of Akp2-/- mice revealed defective dentin mineralization along the root of first molars and incisors. Interestingly, the extent of the defect varied within the same tooth, i.e. lingual dentin often revealed more severe effects with disordered odontoblasts and absence of mineralized dentin than buccal dentin. Histomorphometry was employed to detect changes in dimensions of dentin and determine if surrounding tissues were altered. Measurements of dentin in Akp2-/- mice showed the lingual side exhibited decreased width of mineralized dentin and increased width of predentin and the buccal side exhibited similar values as WT. IHC revealed differences in distribution of selected proteins, Bsp, Opn and Dmp1, in the dentin from the Akp2 KO mice vs. WT mice, suggesting that expression of these factors is vital for dentinogenesis. These results suggest that TNAP is crucial for both cementogenesis and dentinogenesis in mice, with a need to confirm these findings in humans with mutations in Akp2.

Efficient thermoelectric materials will possess low thermal conductivities, high electrical conductivities, and high Seebeck coefficients. The Seebeck coefficient is defined as the magnitude of the electric potential established when a sample is presented with a temperature gradient. We hope to enhance the efficiency of certain thermoelectric materials, such as Sodium Cobalt Oxide (NaCo2O4), by reducing the grain size of these materials. More specifically, a smaller grain size will produce more grain boundaries, which will lower the thermal conductivity and increase the Seebeck coefficient, without decreasing the electrical conductivity. The grain size will be reduced by implementing the electrospinning method, which utilizes a high-density electric field to pull a droplet into a fiber only a few hundred nanometers thick. The final grain size of samples can be determined using Scanning Electron Microscopy (SEM), and the thermal conductivity can be determined through a Laser Flash Thermal Diffusivity test. We established our own experimental measurement system to determine the Seebeck Coefficient and electrical conductivity of our bulk samples at temperatures up to 1100 degrees Celsius. Our measurement system utilizes two thermocouple probes that measure the voltage and temperature at two points along the length of the sample when subjected to a temperature gradient by a localized heating element. Moreover, since thermoelectric materials are mostly employed in high temperature conditions, the measurement system can also be inserted into a high temperature tube furnace in order to understand how grain structure would actually impact thermoelectric efficiency in real world applications. Currently, Sodium Cobalt exhibits a thermal conductivity of about 4 (W/m-K), with a Seebeck Coefficient of around 100 (µV/K). We expect the improved nanofiber grain structure to decrease the thermal conductivity to approximately 1 (W/m-K), while maintaining or possibly increasing the Seebeck coefficient, which would increase the efficiency of thermoelectric devices by at least 400%.

Activation of cardiac contraction is initiated by binding of Ca²⁺ to troponin C (cTnC) and regulated by cooperative strong cross-bridge binding. We have previously shown that passive exchange with L48Q cTnC increased Ca²⁺ sensitivity of force development and eliminated sarcomere length (SL) dependence of Ca²⁺ sensitivity of force in rat cardiac trabeculae. This was shown to be due to decreased reliance on strong cross-bridge binding for full thin-filament activation. Here we test the hypothesis that incorporation of a cTnC variant with decreased Ca²⁺ binding affinity, L57Q cTnC, will result in increased reliance on cross-bridge binding for full activation. As expected, results indicate rat cardiac muscle passively exchanged with L57Q cTnC display decreased Ca²⁺ sensitivity compared to WT cTnC at a given [Ca²⁺]. Interestingly, L57Q cTnC-cTn also mildly increased the SL-dependence of Ca²⁺ sensitivity of force and also significantly decreased maximal force. These findings suggest that reducing cTnC Ca²⁺ affinity per se can reduce Ca²⁺ sensitivity of contractile activation to the point of limited overall force production, which may enhance cross-bridge dependence of cooperative thin filament activation. Additional experiments have shown that stabilizing cross-bridges with either 2’-deoxy-ATP or rigor conditions increases force with L57Q cTnC to near WT cTnC levels. These results suggest that a ‘weakened’ Ca²⁺ activation pathway does not necessarily prevent maximal activation. Instead, reduced Ca²⁺ activation merely impairs the ability of cross-bridges to fully activate the system. NIH-HL65497(MR), AHA-2310117(FSK).

Because of its involvement in sensing painful stimuli, TRPV1 is a prime target in developing more effective pain medications. Encoded by the TRPV1 gene in mammals, it is an ion channel activated by capsaicin, the active component in chili peppers. Though it is often difficult to harvest large quantities of membrane proteins, much success has been found by expressing and purifying TRPV1 from yeast. I compare TRPV1 expression in two different strains of Saccharomyces cerevisiae, BJ4549 and FGY217. FGY217 was used for original expression, but this strain has multiple proteases which degrade the TRPV1 membrane protein. Using an efficient, multistep protocol consisting transforming TRPV1 DNA into the yeast, inducing the yeast to express the channel, and purifying the channel using affinity to a Nickel column, TRPV1 membrane protein will be screened and purified. I will use analytical chromatography and gel electrophoresis to determine which expression mode gives the greatest and most pure protein yield. After successfully purifying larger amounts of TRPV1, functional assessment will be possible by reconstitution into synthetic lipid membranes known as giant unilamellar vesicles (GUVS). Optimizing TRPV1 expression will facilitate our lab’s efforts to determine its precise role in human pain sensation.

Research has suggested two different approaches to behavior initiation; reasoned and reactive behavior. For example, substance use can occur as a result of a plan to use or as an unplanned, reactive event. At the same time, individuals differ in their tendencies to engage in planned or reactive behavior. This has been previously called a lack of premeditation, or forethought, and poor premeditation itself has been linked to alcohol use. The current study examined how individual differences in premeditation may alter how reasoned and reactive behavior pathways may be related to recent alcohol use. We tested how reasons for drinking (i.e. alcohol-related attitudes and subjective norms) and individuals’ prototypes about drinkers were related to expectations to drink and use alcohol in the past month, using ordinary least squares regression, and tested whether premeditation moderated either pathway. Data were collected through an anonymous web-based survey on impulsivity, substance use, and substance use cognitions. The collected sample (n=304) was of college students, with 65.7% female, 51.3% Caucasian, 42.1% Asian American, and a median age of 19. Results indicated that premeditation moderated the effects of subjective norms on both recent alcohol use and expectations to drink in the future, such that individuals who were low on premeditation were more influenced by subjective norms than those high on premeditation. These findings may imply that different sets of cognitions are accessed for both hot and cold emotional states when making decisions about substance use. This has ramifications for prevention programs aimed at reducing drinking through subjective norm beliefs, as our results indicate that the influence of these beliefs differ depending on personality characteristics.

One of the puzzling features of wild populations is that despite the abundance of genetic variation, organisms tend to have stable physical traits. To explain this phenomenon researchers postulated that molecular buffers must exist, which keep phenotypes stable in the presence of genetic and environmental perturbations. One such buffer that has been well characterized is the highly conserved, molecular chaperone protein HSP90. Reducing HSP90 function in plants, fish, and flies leads to a dramatic increase in phenotypic variation. In the plant, Arabidopsis thaliana, the embryonic stem length in wild-type populations has a narrow normal distribution about a mean. However, when HSP90 function is inhibited, the resulting distribution of the stem length has significantly increased variance. That is, inhibiting HSP90 increases stem length variance and decreased stability of the trait.The goal of this project was to identify and characterize the gene that contained the variation, which contributed to the changes in stability due to interactions (either directly or indirectly) with HSP90. Previous work in the lab narrowed down the list candidate genes to five genes in Chromosome 2 of A. Thaliana. We then tested the response to HSP90 inhibition in knockout lines of these 5 genes. Only the PFK5 knockout line showed no response to HSP90 inhibition, which made it the most likely candidate to contain the causal variation.

Presented here is a low-cost microfluidic origami device for point-of-care extraction of bacterial DNA from raw viscous samples -- a challenge for conventional microfluidic systems. The core idea is a novel method for sequencing arbitrarily complex chemical and physical processing steps through sequential folding of 2D surfaces. This folding creates temporary paper fluidic circuits substituting capillary flow for pumps, and folding and unfolding for valves. Demonstrated here is room temperature cell lysis and DNA extraction from E. coli spiked pig mucin (simulating sputum) without the use of external power. Device fabrication takes less than 30 min, and can be adapted for mass production in the developing world.

While construction projects mainly focus on the quality of the end product, it is equally important to monitor construction workers’ wellbeing. The construction industry has already identified best practices for safe weight handling. These bending and lifting techniques have already been designed to limit exposure to wrong postures and movements that could result in musculoskeletal disorders. Nevertheless, musculoskeletal disorders are still a major concern within the construction industry mainly due to unsafe bending practices. However, construction companies have not developed efficient methods for monitoring unsafe bending behaviors. How can construction companies assess if their workers are following material handling safe procedures? The purpose of our research is to determine if we can use physiological status monitors (PSMs) to collect posture data from human subjects as they conduct construction-simulated activities to answer this question. Taking an experimental approach to our research, we will design multiple construction task scenarios for subjects to complete while wearing PSM devices. Posture data will be collected and video cameras will record the experiment to provide an actual visual comparison. Analyzing PSM posture data, we will estimate how many times a subject follows safe material handling procedures. Our prediction will be compared against the ground truth as determined by the video analysis. If posture data can accurately predict worker behavior, we would be able to measure how often construction workers follow safety procedures. Moving forward, these results would suggest to construction companies new ways for improving the safety and long-term occupational health of construction workers.

Being able to adequately categorize your subjects in a research study is pivotal in obtaining consistent data. Drug sensitization studies rely heavily upon the classifications of subjects, whether human or other animals. Current ethanol sensitization studies performed on rats used several methods of classifying animal subjects, including High Responder/Low Responder (HR/LR) and High Rearing Activity/Low Rearing Activity (HRA/LRA) models. Although a small body of research has recently shown a sensitization effect for ethanol in rats, no studies to date have explored the sensitization effects which occur when using a sweetened gelatin vehicle. Increased exploratory behavior in a novel environment has been hypothesized to predict increased self-administration of drugs in rodents. Twenty female Long Evans rats were exposed to an open field for five minutes, during which distance travelled, rearing activity, and immobility, among other behaviors, were recorded and measured. Fourteen rats were provided ethanol (in a 10% concentration) in a sweetened gelatin for seven days followed by a three-week delay before a single challenge dose was given. Our study aims to determine the most effective way of categorizing rats into high novelty seeking and low novelty seeking groups as a predictor of self-administration of ethanol. We expect to see a significant difference between the two methods of subject classification.

Electric DC motors that convert electric current to torque are the most common type of actuators used in haptic interfaces. However, high currents necessary to deliver large haptic forces can generate heat in the electromagnetic coils, and in the extreme can cause malfunctions due to overheating. It is therefore necessary to add thermal protection mechanisms to limit the output current. While this is a common feature of haptic devices it is not clear what makes a superior current limiting method or what effect such limits have on haptic psychophysical thresholds, task performance using haptics, or the subjective experience of haptic realism. The current work evaluates three methods for current limiting: limit output to zero, limit output to a safe steady-state current, limit output current in linear proportion to temperature. Using both quantitative and qualitative metrics, these are compared to a control case with no current limit. Human subjects use one finger of a multi-finger haptic device to perform a psychophysical thresholding experiment designed to measure human perception of small haptic effects, while forcing the device to heat up. All methods are shown to effectively regulate temperature and show no statistically significant difference in psychophysical threshold value. Users show a slight preference for the linear method, while the zero output method requires less time spent interacting with current limited conditions.

Douglas-fir is the major species used in timber production in the Pacific Northwest. It grows across the Pacific Northwest in various climates, soil parent materials, and topographic features. Though it is taken up from the atmosphere and not from soil, carbon is a key nutrient in plant productivity and gaining a better understanding of how they are allocated within Douglas-fir trees and elsewhere within forest ecosystems would be beneficial for forest research and timber production. In this study I look at carbon allocation in 21 different sites around the Pacific Northwest to see where they are concentrated between foliage, forest floor litter, and soil in relation to climate data to understand how climate affects them. In addition to climate, carbon data will also be examined with respect to geographic location. These sites are part of a paired-tree fertilization study through the Washington Stand Management Co-operative in which each site has a nitrogen fertilized stand and a control stand. The climate data used here is the average of total rainfall from each site during the growing season of 2008-2010 along with average of the minimum and maximum temperatures during this season from each site. Understanding how climate and geographic location affect carbon allocation within stands could improve future forest management practices. 

Seagliders are autonomous underwater vehicles used by oceanographers to observe climate change and gather ocean data such as temperature, salinity, and dissolved oxygen. The purpose of this research is to determine more accurate methods of locating a seaglider using long-baseline (LBL) ranging. This method requires sound velocity information in order to position the glider because the calculation for position is based on how long sound takes to travel from a transponder to the seaglider. Sound velocity in seawater varies with depth, temperature, and salinity. These variables are expected to impact the determination of the sea glider position. Measurements for depth, temperature, and salinity were used in the Mackenzie equation for sound velocity in seawater to determine how sound velocity varies with depth at Port Susan. A sound velocity profile (SVP) was created from this equation and tested to determine its significance against a calculation using average sound velocity in seawater across all depths. This study shows that using the SVP does not provide significant amounts of accuracy to range estimates in Port Susan, and using an average velocity is a more simple approach that can be employed without loss of accuracy.

Retrotransposons exist as genetic elements within chromosomal DNA that can replicate themselves and move to new locations within a genome, using a process involving an RNA intermediate. Retrotransposons are the most widespread class of transposable elements, being abundant in the genomes of humans, insects, yeast and plants, where they comprise as much as 70% of the genome. The two most common retrotransposon families, Ty1-copia and Ty3-gypsy, occur across eukaryotic phyla and have a similar genetic organization. In their chromosomal form, they are flanked by direct repeats of a regulatory sequence called the long terminal repeat (LTR). The region between the two LTR’s contains sequences that encode a core RNA binding protein (GAG) and a polyprotein made up of protease, integrase, reverse transcriptase and RNAase H domains: all of them enzymes required for Ty element replication. This project has involved a search of genomic sequences from Rhododendron williamsianum for Ty1-copia elements, using their LTR and protein-coding regions as queries. We obtained sequences of several intact and many incomplete Ty1-copia retrotransposons from R. williamsianum. Most of the copies encountered are nonfunctional ones, either because of deletions of essential sequences or the occurrence of other types of mutations, for example nonsense or frameshift changes. Given that some of the individual Ty-1 insertions have been present at the same site through long periods of Rhododendron species divergence, the nonfunctional mutant Ty-1 copies are considered to be ancient. We estimated that there are about 200 active Ty1s in the genome. The location of a specific Ty1-copia LTR sequence in the genome was used as a phylogenetic marker to compare R. williamsianum with other species of Rhododendron. We also used the sequences to study the evolutionary history of the Ty1-copias within the genome as a whole.

The plainfin midshipman fish (Porichthys notatus) is a seasonal breeding teleost fish that uses acoustic signals for communication during social and reproductive behaviors. There are three adult morphs that include females and two types of males: type I or “singing” males build nests, produce seasonal advertisement calls or “hums” to attract mates and provide parental care for young, whereas type II or “sneaker” males do not build nests nor “sing” but instead practice cuckoldry or sneak spawn to steal fertilizations from type I males. During the summer reproductive season, type I males generate hums by rapidly contracting their sonic muscles that are attached to their swim bladder and can sustain these high contraction rates (approx 100 Hz) for long durations (on the order of mins to hrs). We hypothesize the production and maintenance of the sonic muscle and the seasonal developed testes would be metabolically costly. Thus, we predict that basal metabolic rate (BMR) should be higher in reproductive (summer) type I males than in non-reproductive (winter) type I males. Here, we examine the BMR of non-reproductive and reproductive type I males using a respirometer (YSI Model 52 Dissolved Oxygen Meter) to measure rate of O2 consumption. Standard length, body mass, sonic muscle mass, and GSI were measured for a wide range in size of type I males and compared the BMR of these fish across the reproductive and non-reproductive seasons. Preliminary results suggest that reproductive males have a higher metabolic cost than non-reproductive males. Current work includes measuring the metabolic costs of advertisement call production. The ultimate goal of this study is to determine if the cost of signal production and sustained calling is correlated with reproductive fitness and whether the acoustic signal can be used by females as a condition-dependent indicator of mate quality.

Traveling internationally lets people relax, explore new cultures, and just have fun. To gain an understanding of users’ motivations, we surveyed 53 UW college students and asked for their opinions regarding traveling internationally. Our user research showed that 87% of participants said trying new food motivates them to travel. Similarly, 68% travel to explore a culture and gain a new perspective. Issues such as not knowing what to eat and being unfamiliar with the culture and language make the experience cumbersome. Travel Bite is an Android application that eases these problems when finding food in international travel. Using Travel Bite, users can explore cultural dishes, history, customs and learn how to order food in the foreign location. Travel Bite also supports offline capabilities, which allows users to find food without the need of an internet connection. We refined our design through three iterations of user testing. Each iteration involved users walking through our PDF prototype displayed on an Android phone. Afterward, users were asked follow-up questions regarding their experience. In the first two iterations we asked primarily qualitative questions to learn why users liked or dislike certain features. This was followed by rigorous qualitative data analysis. The final iteration focused on asking quantitative questions evaluating our design. We aimed to answer one question: does our application help users find food and gain cultural insight? Results show that four out of five users would personally use Travel Bite. Three out of five users learned something new about the location in our test scenario. Overall, Travel Bite was highly successful in providing a solution to finding food internationally and moderately successful in providing cultural insight.

Chronic kidney disease (CKD) afflicts 1 out of 8 people in the United States. Every case of CKD undergoes the process of interstitial fibrosis regardless of its origins, yet it is unclear how fibrogenesis occurs. CKD mouse model studies suggest that the microvasculature of kidneys play an important role in the initiation of fibrosis. The same studies point to vascular endothelial cadherin (VE-cadherin), an adhesion molecule between endothelial cells, as the initiator in interstitial renal fibrosis. It is observed that VE-cadherin heterozygote (VE +/-) mice have greater amounts of interstitial myofibroblasts and activation of collagen genes compared to wild type mice (WT). There is also a lower amount of pericytes in VE +/- compared to WT. Pericytes are undifferentiated vessel support cells that have been observed to detach from endothelial cells and subsequently transform into fibroblasts and secrete collagen in the interstitium. The adhesion molecule neural cadherin (N-cadherin) mediates interaction between endothelial cells and pericytes. We hypothesize that changes in VE-cadherin expression alter the interaction between endothelial cells and pericytes. My work aims to elucidate the relationship between VE-cadherin and N-cadherin through in vitro studies. In order to determine the effect of VE-cadherin on N-cadherin expression, knockdown of VE-cadherin in endothelial cells is achieved via siRNA transfection. Preliminary results suggest that knockdown of VE-cadherin expression reduces N-cadherin expression. To understand the effect, expression levels of intracellular signaling molecules, alpha-catenin, beta-catenin, and p120 catenin, are investigated since they regulate VE-cadherin and N-cadherin. Unraveling the relationship between VE-cadherin and N-cadherin will help us understand the mechanisms of renal fibrosis and provide greater knowledge for a potential therapy in patients.

Heme is essential for all mammalian cells; however, free heme through oxidative stress causes cell damage or death. The Abkowitz lab showed that FLVCR, a heme export protein, is required for red blood cell differentiation (Science 319:825-8, 2008). Subsequent work demonstrated that loss of FLVCR blocked thymic T cell development at the CD4CD8 doublepositive (DP) stage. We hypothesize that FLVCR loss increases intracellular free heme (IFH) and thus blocks T cell development. IFH is difficult to measure, therefore the first goal of my project was to determine whether mRNA levels of genes regulated by heme (Alas1, encoding the first enzyme in the heme synthesis pathway, and Hmox1, encoding a heme-degrading enzyme) could be used as an indirect measure of IFH. I validated a multiplex quantitative RT-PCR assay to measure Alas1, Hmox1, and Flvcr mRNA levels and used this method to measure gene expression in developing thymocytes isolated from mice. Heme pathway genes are expressed at high levels during early thymic development in normal mice and subsequently down-regulated. I found that Hmox1 expression was higher in FLVCR-null DP, CD4, and CD8 thymocytes compared to controls, suggesting that the loss of FLVCR leads to increased IFH. This observation of HMOX1 overexpression in FLVCR KO thymocytes suggests that HMOX1 compensates for FLVCR loss and excess heme. This leads to the hypothesis that forced overexpression of HMOX1 could rescue FLVCR KO T cell development. To test this hypothesis, I will retrovirally infect FLVCR KO bone marrow cells with a Hmox1 construct, transplant the Hmox1-transduced bone marrow cells into Rag1KO mice, and observe whether HMOX1 overexpression can rescue the KO T cell development. If HMOX1 overexpression rescues FLVCR KO T cell development, this would imply that the block in FLVCR KO T cell development is caused by excess heme.

Interactions between proteins and DNA are critical for life. Despite this, exactly how these interactions occur in three dimensions is unknown for many of them. Although three dimensional structures of these interactions can be determined via physical methods such as x-ray crystallography, such methods are often costly and time-consuming, rendering them inefficient for determining the structures of large numbers of interactions. However, databases of three dimensional structural information for some interactions between proteins and DNA already exist. This data enables the computational prediction and modeling of many more interactions. This project deals with an important part of the computational interaction problem, creating three-dimensional predictions of protein and DNA interactions. It takes known three-dimensional structures of protein and DNA interactions, and uses them as templates for construction of models of the target interaction. Similarity between the template sequences and the target sequences results in increased likelihood of the resultant model being accurate. By selecting templates which have sequences most similar to the target sequences, predictions which are more likely accurate are generated. We expect this method to be of use as a tool to predict and infer information about interactions between proteins and DNA, with many possible applications in the field.