We present reform, a system that envisions roles for both programmers and end users in enhancing existing websites to support new goals. First, programmers author a traditional mashup or browser extension -- such as an alternate visualization or an extra set of tools for a website. However, where previous approaches would have necessitated the development of a web scraper (a program to extract data from the web page), reform uses a scraping-by-example interface that allows users to develop (or "train") a scraper interactively. Reform makes enhancements easier to program while also carrying the benefit that end users can apply the enhancements to any number of new websites. My work on reform involved developing a software interface to one of our components, so that it could be integrated with the whole -- making reform easier to install. We present reform's architecture, user interface, and interactive by-example extraction algorithm for novices. This is a step toward write-once, apply-anywhere user interface enhancements.

Environmental education varies dramatically from nation to nation due to a variety of factors. This talk will present the findings of a comparative evaluation of the environmental education systems in three case study locations: Stockholm, Sweden; Brussels, Belgium; and Seattle, Washington. While all age groups were considered, this research focuses on students 8-12 years old as this is an age where advanced reading and comprehension skills are commonly emphasized in school programs. The methodology featured a visit to each study location during the summer months of 2009 and in-depth interviews with the community leaders in charge of the sustainable education curriculum of each city. Both formal, in-class and informal, out-of-class instruction was considered. In addition, curricula pertaining to environmental issues were examined, as were reports about the efficacy of governmental education in each locale. My results explain how each level of government, independent organizations and green spaces influence the way environmental issues are taught in school. Additionally, the amount and types of literature on environmental topic made available to young students is discussed in depth. The research is informing my efforts to write a young adult fiction novel that contains themes related to environmental education and climate change.

For the male golden and white collared manikins, a species of tropical bird in Central America, the primary means of attracting females is by performing a "dance" over an arena which they have built on the rainforest floor. There is evidence that the arena helps to highlight a male's plumage as he performs his dance. Thus it is likely there is strong environmental and sexual selection to optimize arena structure to benefit the displaying male. Given that the golden and white collared manakins have different plumage colors, we hypothesized that arena structure would differ between these two species and that manakins living in a hybrid zone would build hybridized arena’s. In the first component of our research, we observed that the arena areas of the two species are different. We measured the overall area of the arenas and found that golden collared manakin arenas were smaller than white collared manakin arenas. Selection hypotheses presume that arena-building is a genetically determined behavior rather than learned. We continued our research and tested this by looking at arenas across a large geographic range in either species, and across a hybrid zone between the two species. If arena building is genetically determined we hypothesized that there would be high stereotypy in arena structure across the hybrid zone and that the arenas built by hybrids would be an intermediate between the white collared and golden collared manakin. Conversely, cultural hypotheses predict that there should be little stereotypy, and a high degree of local variation in arena structure across each species, therefore hybrids should copy the behavior of one species or the other. We found that arena structure varies little across geographic distance within parental species, and that hybrids occasionally produce arenas intermediate in structure. These results suggest that arena building is in fact genetically controlled.

Phosphorus is often regarded as the main culprit in cases of eutrophication in lakes subjected to point source pollution from sewage. The phosphorus species in water after applying alum are still under research. The Spokane City/County Municipal Wastewater Treatment Plant (WWTP) will be treating its effluent to remove nutrients (specifically phosphorus) to extremely low levels using an alum flocculation process. Preliminary data indicate this effluent has extremely low total phosphorus (TP) and accounts for a small amount of bio-available phosphorus. However, it has a high proportion of "non-reactive phosphorus" (NRP), which is not bio-available and can’t be used for algae growth. It’s quite likely that this NRP is aluminum bound phosphorus, i.e. AlPO4. Previous research on phosphorus speciation in sediment after alum treatment has been done using sequential extraction schemes to selectively remove phosphorus from different compounds in the sediment. The objective of this project will be to develop a standard method for quantifying aluminum bound phosphorus by applying the sequential extraction method to WWTP effluent samples collected from the Spokane Facility to prove the assumption that the NRP is mainly aluminum bound phosphorus. This project also aims to understand more about the phosphorus speciation in wastewater for the sake of further study in this area. Preliminary results of those analyses will also be presented.

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 and of the correct cardiac subtype (i.e. ventricular cardiomyocytes), to minimize the risk of teratomas and arrhythmias. In this study, we are exploring two complementary approaches to obtain such pure populations: improved methods of guided differentiation (specifically, elimination of insulin signaling) and genetic selection (using a novel muscle-specific promoter). Colleagues at the University of Washington have 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 puromcyin 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.

Kaposi’ Sarcoma (KS) was the first AIDS defining illness and is the most common tumor among AIDS patients world-wide. Currently, KS, is the most common tumor in parts of Africa. KS is a highly vascularized tumor and the main cell type found within the tumor is the spindle cell, a cell of endothelial cell origin. The etiologic agent of KS is Kaposi's sarcoma-associated herpesvirus (KSHV), a gamma-herpesvirus. KSHV is present in all spindle cells of KS tumor. My research focuses on how KSHV causes KS. An important aspect of KSHV pathogenesis is the ability of the virus to drive the differentiation of blood endothelial cells to lymphatic endothelial cells. My goal is to discover which KSHV genes are sufficient to cause this transformation from one cell type to another. Each KSHV gene was isolated, cloned into expression plasmids in bacteria, amplified, and will be transfected individually into human blood vessel cells. The infected cells will then be screened by changes in their surface receptors for indications of differentiation into lymphatic cells. This research marks the first steps in the understanding of how KSHV causes the further differentiation of endothelial cells and may shed light on how this virus can cause cancer.

It has been demonstrated that silicon nanophotonic waveguides can be used to construct all of the components of a photonic data transmission system on a single chip. Complex electro-photonic integrated circuits can be constructed from the integration of nanophotonic waveguides and CMOS electronics. It has also been shown that the high field confinement of silicon nanoscale guides enables a variety of new applications, including chip-scale nonlinear optics, as well as biosensors and light-force activated devices. Currently, the majority of experiments with silicon waveguides have been at wavelengths in the near-infrared, between 1.1-2 µm. Our research demonstrates that by using a material system which lacks a high index substrate, single-mode silicon nano-waveguides can be used at mid-infrared wavelengths, in particular at 4.5 µm, or 2222.2 cm^-1. This idea has appeared in theoretical literature, but experimental realization has been elusive. This result represents the first practical integrated waveguide system for the mid-infrared in silicon, and enables a range of new applications.

In adults, the classical electroencephalogram (EEG) alpha rhythm is a distinct 8-12 Hz frequency band that predominates over occipital scalp during eyes-closed relaxation. Although its precise developmental trajectory is not well understood, the EEG alpha rhythm undergoes significant temporal and spatial development during early childhood. Infancy marks a particularly critical period for aberrant brain maturation in children with autism, a developmental disorder associated with rapid brain overgrowth that begins between 6-12 months of age. To simulate eyes-closed relaxation in adults, room lights were turned on and off at one minute intervals while EEG was recorded from infants at 6 and at 12 months of age. We characterize the spatial and temporal development of the infant EEG alpha rhythm and contrast it with that of infants at risk for autism. Because it has been established that autism reflects dysfunctional global brain activity, we hypothesize that an abnormal trajectory of brain development (as indexed by alpha band activity) will be visible in infants who go on to develop autism.

 In the Pacific Northwest, over the next several decades, scientists have projected that both the average temperature and the frequency of extreme precipitation will continue to increase. These trends may lead to shifts in species' distributions and impose adverse impacts on species vulnerable to environmental change. Although resource managers and conservation specialists have developed tools to mitigate climate change, it is still important to assess the potential vulnerability of species to climate change and to identify the species that are most sensitive. Such an evaluation helps managers to set conservation priorities for different species and to make efficient conservation-investment decisions with limited resources. At this stage of the ongoing sensitivity assessment project, we are aiming to assess the sensitivity to climate change of species in Washington, Oregon and Idaho. We classify species into 14 categories: fungi, non-tree plants, tree plants, clitellata, gastropoda, malacostraca, bivalves, insects, lamprey, fish, amphibians, reptiles, birds and mammals. In the assessment of species sensitivity, we adopt two independent methodologies: synthesis from literature review and direct contact with species experts. For each species, we base our estimation of sensitivity on factors including dispersal ability, dependence on disturbance regimes (e.g. fire, flood), dependence on other species, physiological sensitivity to physical conditions (e.g. temperature, salinity, precipitation), reproductive strategy and susceptibility of the habitat to climate change. We are working with species experts both individually and in workshops to help them enter their rankings of sensitivity of species into the online database. For the final product, we will produce a database of species sensitivity to climate change, which will assist conservation planners and resource managers in setting conservation priorities and maximizing return on conservation investment.

Cyclic aminoalcohols are a class of small molecules with diverse therapeutical activities as antibiotics, antivirals and drugs against HIV, cancer, and neurodegeneration. Our project aims to contribute to the development of fast and economical syntheses of these important precursors. Many existing synthetic pathways depend on palladium-catalyzed chemistry, but metals are expensive and potentially toxic. Our current work with metal-free oxidative cyclization of aminoalkenes has shown that various acids mediate this reaction under mild conditions. Previous data from the Michael lab has shown that racemic BINOL phosphoric acid, a mild Bronsted acid, is effective in this reaction. When racemic acid is used, the resulting cyclic aminoalcohol derivative is also racemic, meaning that it is a 50:50 mixture of its two enantiomers (or non-identical mirror images of each other, just like left and right hands.) Enantiomers are hard to separate, however, and many drugs are effective only in one of their enantiomeric forms; they may even have adverse effects in their other form. Thus, we seek to control the enantioselectivity of this reaction using enantiopure (R)- or (S)-BINOL phosphoric acid. In a plausible reaction mechanism, BINOL phosphoric acid would linger as a counterion, creating a chiral environment and directing the enantioselective closing of the ring. To optimize this reaction, we are synthesizing a variety of substituted BINOL phosphoric acids with various steric and electronic properties.

Heart disease, the leading cause of death in the U.S. and other developing countries, is characterized by a decrease in cardiac output. Conventional methods for treating heart failure have adverse side effects, including arrhythmia due to alterations in the intracellular calcium transients. Our group has taken a novel approach to repair cardiac output by altering the Ca2+ binding efficiency of cardiac troponin C (cTnC), the calcium sensing protein complex found in the contractile myofilaments. This was accomplished with a single amino acid substitution (L48Q) that has been shown to increase the rate and extent of contraction in healthy rat cardiomyocytes without altering relaxation (diastolic function). The purpose of this study is to investigate the effectiveness of L48Q in restoring post-infarction rat cardiomyocyte contractility over a range of stimulation frequencies. We hypothesized that under L48Q treatment, the rate and extent of contraction in cardiomyocytes from infarcted hearts increases to approach the contractile properties of healthy cardiomyocytes, while relaxation and Ca2+ transients would remain unaltered. Ventricles from infarcted and normal rat hearts were first harvested and digested to isolate intact cardiomyocytes and these cells were then transduced with adenoviral or lentiviral vectors carrying the cDNA L48Q insert. After 48 hours, changes in cell length, sarcomere length, and Ca2+ transients were monitored with video microscopy (IonOptix) at 0.5, 1, and 2 Hz stimulation frequencies. Preliminary evidence suggests cells from infracted hearts cannot follow higher pacing frequencies. Further results of these studies will be presented in my poster. Future studies will determine the effect of these treatments in animal models of heart disease. Optimization of these myofilament targeted gene therapy approaches may lead to the development of an effective means to increase or restore cardiac output in humans, with minimal side effects.

 Cardiovascular disease is a chief concern for medical research as it remains the leading cause of morbidity and mortality in the United States. The cardiac cycle of contraction and relaxation is regulated by the binding of calcium ions (Ca2+) to the regulatory protein troponin C (cTnC). Heart failure can be caused by reduced sensitivity to Ca2+ or a decreased number of active cells, which manifests as decreased contractility. Our laboratory has engineered cTnC with a single amino acid substitution, L48Q, which shows promise as an effective treatment for calcium insensitivity due to enhanced Ca2+ binding. While the ultimate goal of the research is to utilize gene therapy strategies to deliver L48Q cTnC, we currently study this protein by exchanging native troponin complex (cTn) with cTn containing L48Q within specific rat heart muscles (trabeculae). Although changes in calcium sensitivity between native and L48Q cTnC-Tn exchanged trabeculae have previously been reported, the amount of L48Q cTnC-Tn that has been incorporated within the trabeculae during our exchanges must be quantified because gene therapy will likely not replace all of the native cTnC. The main goal of my current work is to determine the fraction of native cTn left after exchange by utilizing the fact that exchanged proteins are produced by E.coli and not phosphorylated. The amount of successfully exchanged cTn is determined by western blot analysis using antibodies that specifically bind to cTnI which has been phosphorylated at serine positions 23 and 24. This quantity will be correlated to the shift seen in the Ca2+ sensitivity of force measured in the same preparations. Preliminary results indicate that this method provides the necessary sensitivity to detect a variable amount of non-exchanged cTn and that our established protocol results in approximately 90-95% exchange. This project will provide valuable data for a number of other projects within the laboratory.

Male western song sparrows usually share at least part of their song repertoires with song sparrows in neighboring territories (usually 2-4 songs out of 8 songs in their repertoire). Therefore, most birds have the ability to use their shared songs in their interactions with their neighbors. In particular, when a challenger (usually a neighbor) sings a song that is shared with the opponent, the latter can reply with the same song type, which is called song-type matching. Song-type matching in song sparrow territorial interactions has long been considered a signal of aggressive intentions; however, previous studies have not conclusively shown that type matching necessarily predicts aggression. Recent studies have revealed that there are individual differences in aggression which are consistent over time (i.e. some birds are more aggressive than others). In extension of this, we asked whether type matching is a characteristic of individual birds, i.e. whether some birds will consistently type match and some will consistently not. To answer these questions, we challenged male song sparrows repeatedly by playing songs from their own repertoires from within their respective territories, allowing them to potentially type match the playback. We recorded the songs with which they replied as well as their behavior to get a measure of aggressive response. If type matching predicts aggression, type-matching males are expected to respond more aggressively than non-type-matching males. Furthermore, males that are more consistently more aggressive are expected to have a higher probability of type matching than males that are not aggressive.

Marine debris is a continuing threat to coastal wildlife, including marine birds, marine mammals, and sea turtles. Every year, 1000s of these charismatic marine vertebrates die from ingestion or entanglement of/in debris commonly found along Pacific Northwest beaches. This study aims to quantify the taxon-specific threats posed by marine debris commonly found along Pacific Northwest beaches. To assess threat level, we conducted a review of 141 peer-reviewed scientific articles, government reports and outreach materials, and categorized all mentioned debris as likely to produce death, injury, or distress to all referenced species. Where possible, we combined species into larger taxonomic groups (e.g., gulls). Plastics, either whole or fragmented, posed the greatest ingestion risk across all species. Entanglement in recreational and commercial fishing gear and other synthetic material was also a persistent source of mortality. We also conducted field surveys at four sties on the Washington coast and combined these data with historical surveys. Our surveys showed that plastic bags, and plastic and Styrofoam fragments were among the most common items. Fishing gear was found less frequently. We conclude that the most persistent types of litter found on Pacific Northwest beaches are also amongst the most common marine debris found on beaches worldwide, and may be particularly harmful to marine mammals, seabirds, and sea turtles. The final product of our research will be a threat-based guide to marine debris to help prioritize beach clean-up efforts by identifying which debris types are most threatening to local coastal wildlife, and – more broadly – to raise public awareness about coastal pollution sources and solutions.

Many animal species use signals to mediate conflict over breeding resources, and as a way of preventing violent physical encounters. Most birds use songs as their signal. Male Manakins (Manacus) have very simple, but highly variable calls which they use in male-male conflict. We hypothesize that this variation is correlated with the degree of aggressive intent. We measured frequency and time characteristics of multiple calls from multiple individuals engaged in an experiment that simulated a high aggression condition and a low aggression condition. So far we have not found any characteristics that correlate with aggression level, but analyses are ongoing. This is one of the first studies to look for a complex signaling system in the Sub-Oscine group, a group of birds known for relatively simple, genetically inherited calls.

At petroleum refineries, much precaution is taken to prevent equipment from over-pressuring, which can result in safety, health, and environmental hazards. When equipment does begin to over-pressure, vents and valves are opened to relieve the waste streams that build up. Valves may be opened to the refinery’s flare system, where waste gas streams are combusted. Environmental regulations require refinery operators to report flaring events when emissions exceed certain reportable quantities stipulated in environmental regulations and permits. In these events, the agencies must be notified within a short period of time. Flaring events, however, are undesirable; they contribute harmful pollution to the surrounding environment, leading to potential health risks for both humans and ecosystems. Through field experience at a Washington refinery and through a survey of the existing literature, I researched the environmental impacts of flares and opportunities for emissions reductions. I found that refineries should explore ways in which flaring can be reduced, through technology such as flare gas recovery systems, mobile variable flare tips, and swirl flow, and through changes in operational practices such as Advanced Process Control (APC). Cost is the largest barrier to implementation of flare gas recovery systems, although facilities that have constructed these units have recouped the capital costs within several years, due to the reduced usage of fuel gas and steam. On the other hand, mobile variable flare tips, swirl flow, and APC are new technologies that have so far been limited to pilot projects. As fuel costs climb and the results of these pilot projects are shared amongst industry professionals, these technologies are likely to become more widely implemented.

The Republic of the Marshall Islands (RMI), a group of 29 atolls and low-lying islands in the central Pacific Ocean, has a population of more than 60,000. The RMI has a mean height of only 2 meters above sea level. The Intergovernmental Panel on Climate Change (IPCC) projects that global average sea level will rise 0.4 to 1.4 meters by the end of this century. However, IPCC estimates of sea level rise are based only on thermal expansion. When complete glacial retreat and small ice cap loss is considered, an additional 0.2 to 0.7 meter global average sea level rise is expected. Consequently, the people of the RMI will be among the first to feel the effects of climate change in the 21st century. This qualitative study was conducted in order to understand the barriers to climate change adaptation and to explore available strategies for overcoming such barriers. The data collected included peer-reviewed journals, government documents and 23 interviews with government officials, educators and local scientists. Meetings with participants ranged from impromptu to formal, semi-structured interviews with open-ended questions. Currently, the major barriers preventing the RMI from planning for climate change adaptation include constrained financial resources, lack of professional and technical staff, and concerns of more immediate social and public health issues. These results lend to certain policy recommendations aimed at facilitating climate change assessments and implementation of adaptation plans in the RMI. The policy recommendations include technical and financial assistance, as well as professional development and educational exchange programs.

The final result of my capstone research is a documentary film, Yurtprints. This documentary asks viewers to examine their carbon footprint in respects to their home. It focuses on alternative housing in general, and yurts in particular, as a way to lower one's carbon footprint. Featuring interviews with yurt dwellers, green housing authorities, and other experts and scholars, the film compares the environmental impacts of conventional housing, "green" housing, and yurts (as both primary dwellings and vacation properties). Although yurts serve a very small niche in the housing market, that niche is growing and the utility of yurts is being recognized by a wider segment of the population. My talk to the Undergraduate Research Symposium will briefly describe my research on the environmental impacts of housing and present a few short clips from the documentary.

Viruses are the most abundant biological entities in the ocean. Though minute in size, they are thought to be responsible for controlling large-scale processes such as bloom and bust oscillations of algal blooms, lateral gene transfer, and global carbon and nutrient cycles. Viruses are both abundant and diverse, for they infect every life form on the planet and exhibit host selectivity at the species or strain level. Isolating and characterizing marine viruses is an integral step in understanding how viruses mediate communities in the sea. Pseudo-nitzschia is a cosmopolitan diatom genus that is particularly common in the Pacific Northwest. These phytoplankton are of particular importance because some species are capable of producing domoic acid, a neurotoxin. During blooms this compound bioaccumulates and can be deadly to humans, marine birds and mammals. Although it has been hypothesized that viruses play an integral role in phytoplankton ecology, only six diatom viruses have been characterized, none of which infect Pseudo-nitzschia. Water samples were taken during three Pseudo-nitzschia blooms in the Pacific Northwest in the summer of 2009. Single cells or chains of Pseudo-nitzschia were isolated, propagated in culture, and then identified at the species level. Molecular techniques were used for identification because Pseudo-nitzschia are indistinguishable by light microscopy alone. DNA extractions and polymerase chain reactions (PCR) were used to amplify a region of the genome called the intergenic transcribed spacer (ITS) for each isolate. This region has a high degree of variability across a genus and can thus be used to differentiate between species. A database of known Pseudo-nitzschia ITS sequences was then used for identification. These identified isolates will ultimately be used as hosts during virus isolation experiments. Because of viral host specificity, knowing the species of Pseudo-nitzschia lab cultures is essential for future experimentation.

The increasing occurrence of cardiac damaging events in the United States has led to a dire need for new methods to regenerate wounded heart tissue. The surgical implantation of engineered tissue grown on cell delivery devices is one proposed method for cardiac repair. A promising example of one such device is the novel microporous and microchanneled fibrin scaffold being developed by the Heart and Muscle Mechanics Lab at the University of Washington. This scaffold has been shown to direct proper cardiomyocyte alignment and promote cell adhesion to the scaffold material. It is my goal to optimize the passive mechanical properties of these fibrin scaffolds for tissue engineering applications by investigating parameters such as scaffold stiffness and rate of degradation. Because fibrin is a tunable polymer, slight variations in the way the scaffolds are constructed can affect their material properties. In order to determine which method of construction provides the most viable tissue engineering scaffolds, a selection of fibrin scaffolds are being made by varying parameters in the fibrin polymerization and scaffold preparation processes. The mechanical properties of these scaffolds are then assessed using stress-strain analysis. Of the parameters being varied, the concentration of fibrinogen (fibrin monomer), the extent of fibrin cross-linking, and the length of acetone exposure are expected to have the greatest influence on the mechanical properties of the scaffolds. Both scaffold stiffness and degradation time are expected to increase with increases in these factors. Duration of alcohol exposure was found to have no significant impact on scaffold stiffness, indicating alcohol as a potentially viable storage solution. Optimizing the passive mechanical properties of these fibrin scaffolds will further the development of a novel scaffold for cardiac tissue engineering and help prepare them for use in future in vitro studies.