The heritability of Autism Spectrum Disorders (ASD) has been documented by previous studies looking at the diagnostic concordance for autism in dizygotic (DZ) and monozygotic (MZ) twins. However, literature examining the genetic etiology of specific characteristics within the three symptom domains of ASD is scarce. Pragmatic (social) language ability, a kind of communication that relies on verbal (e.g., intent and appropriateness of utterances) and nonverbal (e.g., gaze maintenance, facial expressions) skills is a core deficit in the language and communication domain. This study will look at the heritability of pragmatic language in verbally fluent individuals with ASD. MZ and DZ twin pairs both concordant and disconcordrant for ASD will participate in the study. The Pragmatic Rating Scale-Modified will be used to rate pragmatic language ability based on an interview with participants. This study has two aims: First, an analysis will be conducted to confirm that there is a significant difference in pragmatic language ability between individuals with ASD and individuals with typical development. Second, analyses will be carried out to determine if the pattern of heritability for pragmatic language is the same for twins with ASD versus typically developing twins. This will be the first study to quantify the concordance of pragmatic language.

More than 50 percent of stars are found in binary systems. A cataclysmic variable star is a binary system consisting of a white dwarf and a larger, cooler star in an orbit with a period of only a few hours. These stars are so close that the white dwarf distorts the gravitational field of the other star and mass is transferred from the cool star to the white dwarf via an accretion disk. The defining characteristic of the type of cataclysmic variable called dwarf novae is that they irregularly increase and decrease in brightness. The increases (called outbursts) are caused by an instability in the accretion disk that causes an increase in accretion. After an outburst, these stars steadily decline in brightness until they return to their original state. However, the subgroup of dwarf novae called Z Cam systems sometimes become stuck in a state called a standstill, where they stay at a brightness near outburst level, and then decline to their original level. Using data taken at Kitt Peak National Observatory and Apache Point observatory over a series of five months, we were able to analyze spectra of two unusual objects as they go through their outbursts. We can find out what state they are in by comparing their spectra to light curves from the American Association of Variable Star Observers. What is unusual about these objects is that rather than fade to their original state after standstills, they go up to another outburst. Using these spectra, we hope to find the accretion rates of the stars at standstill, and then compare to other stars of the same type to better understand why they have this peculiar behavior.

Cyclotrons are devices used to accelerate charged particles to high kinetic energies.  Their applications range from experimental studies in fundamental high-energy particle physics to serving as proton sources for medical use in the treatment of cancerous tumors.  We present here an overview of the design and engineering of a 2-MeV cyclotron currently under construction at EdCC by the Undergraduate Research Students Association (URSA), including detailed work being pursued by each of the seven student teams working on the project: HEP Theory Team, Ion-Injection Team, Vacuum Team, Materials Engineering Team, Magnetics Team, Sensors and Acquisition Team, and the Computational Modeling Team. The long-term goal of the URSA Cyclotron Project is to provide future EdCC students with a starting platform for continued multidisciplinary research in high-energy physics, mechanical and electrical engineering, and computer science. The first near-term project goal is to create and measure the electron-positron pair production process $\gamma \rightarrow \e^+ - \e^-$ by scattering of ~2.2 MeV protons from tungsten target nuclei and looking for $\e^+ - e^- \rightarrow 2\gamma$ annihilation signatures with an event-coincidence detector comprised of bismuth germanium oxide scintillators. At 2MeV, this accelerator will not likely make significant direct contributions to the extant pool of PDG data; but it may make significant indirect contributions by introducing and engaging future practitioners in the field earlier in their educations.

Drug resistant strains of Staphylococcus aureus are now possibly responsible for more deaths than any other infectious disease in the United States. Phosphosignaling enzymes are thought to constitute a major class of drug targets in humans, but their potential as drug targets in bacteria are yet to be known to their full extent. In this study, we sought to develop an assay to test activity of an S. aureus signaling molecule, the tyrosine kinase CapB, which controls capsule biosynthesis. By interfering with capsule biosynthesis, we hope to interfere with virulence of S. aureus, allowing better clearance of the infection by the immune system. To assay for kinase activity, we recombinantly expressed the known kinase substrate Cap5O. Cloning of the Cap5O insert into the pQE30 vector created an expression plasmid with a 6XHis-tag on the C-terminus of Cap5O. The plasmid was grown and harvested in Rosetta cells. Purification of the protein was carried out through Metal Affinity Chromatograpy to obtain pure protein for activity assays. The results of this study will provide the starting point for an assay to screen for compounds that interfere with capsule biosynthesis. To date, no screens for the bacterial tyrosine kinases have been developed.

Cell labeling and tracking hold enormous potential to illuminate cellular pathway mechanisms. Because current labeling methods are either unsafe or unavailable for humans, a need exists for a safe and effective cell labeling technique suitable to track cells administered for cell therapy. The stable carbon isotope, C13, is safe for human use, incorporates into cellular DNA when taken up as C13 glucose in culture medium, and can be detected by GC mass spectrometry. We proposed to evaluate the use of C13 to label and track exogenous bone marrow derived macrophages (BMMCs) administered after myocardial infarct (MI). To confirm exogenous BMMCs can be detected in the heart, we injected green fluorescent protein (GFP) labeled BMMCs into the tail vein of mice three days following MI. Some heart sections were assessed for GFP positive cells by immunohistochemistry. Other hearts underwent dispersion and isolation of macrophages. Quantitation revealed the percentage of exogenously delivered C13 labeled GFP BMMCs in the cardiac macrophage population was 10 percent. Preliminary cell proliferation assay results suggest no considerable difference between the growth of BMMCs with or without C13 glucose. Finally, we cultured GFP BMMCs for ten days in 100% C13 glucose media for tail vein injections to mice following MI. Three days later, we excised the hearts to isolate cardiac macrophages. Cultured heart cells and macrophages were analyzed via GC mass spectrometer to quantify labeled DNA. Although we could detect C13 in in vitro labeled macrophages, increased C13 cellular label could not be detected in isolated macrophages. Unlabeled macrophages appropriately had no increase in label. Ultimately, while this study was unsuccessful in detecting a C13 cellular label in vivo with a GC mass spectrometer, in vitro successes suggest technique refinement could lead to a powerful and safe therapeutic stem cell label.

In developing countries nearly 80% of all diseases are linked to water and sanitation issues; globally, over two million people die annually from water-born diarrheal disease. It has long been known that some metals can exhibit powerful anti-bacterial properties. Copper has been used for hundreds of years as a means to purify drinking water but only recently have scientists begun to elucidate the mode of action for copper induced microbial death. In 2008 the U.S. Environmental Protection Agency officially registered copper alloys as biocidal agents. Now these alloys need to be studied to determine efficacy at different concentrations and with a variety of disease-causing microbes. This study investigates the powerful bactericidal effects of copper as a low cost accessible method to purify drinking water of pathogenic waterborne microorganisms. More specifically, E. coli was used as a model organism to test the efficacy of solid copper at killing microorganisms in drinking water over variable amounts of time. Efficacy of cell death was assessed with viable plate counts. Results show that ≥48cm2 of solid copper in 100 mL of water can kill E. coli (at an average concentration of 3.1x105 CFU/mL) within 24 hours. Further research is needed to determine the optimal copper to water volume ratio as well as the precise timing of cell death. It is also essential that the copper ion concentrations remain below EPA limits of 1.3 mg/L; preliminary findings produced inconsistent values. The results of this research could be beneficial to those living in locations where safe potable water is not readily available, or for those travelling to remote or foreign locations as well as hikers and campers.

The mitotic spindle orchestrates proper alignment of chromosomes during cell division. The spindle is composed of microtubules that attach to kinetochores, multi-protein complexes that assemble at the centromeres of chromosomes. Understanding kinetochore function is essential to understanding the process of cell division. Through mass spectrometry analysis, the Davis Lab has found an abundance of the urmylation component Uba4 at the kinetochore. The urmylation pathway is highly similar to ubiquitination, and involves conjugation of a ubiquitin related modifier (Urm1) to proteins and RNAs. The role of urmylation at the kinetochore is not known. We hypothesize that post-translational modification of kinetochore proteins through urmylation is a regulator of chromosome segregation. To examine the effects of urmylation on the kinetochore I will be using an Ncs2 mutant, a protein involved in the urmylation pathway, By fluorescently labeling the kinetochore protein Spc105 and spindle pole body protein Spc110, I am using fluorescence microscopy and computational analysis to look for abnormalities in spindle appearance. These results will help elucidate the role of the urmylation pathway in the regulation of cell division.

 The deep-divide between urban residents and rural migrants living in Shanghai has grown increasingly apparent over the last two decades. This so called "dual society" in which rural migrants do not have the same privileges as locals in Chinese cities, is a result of  the social disadvantages of the rural people in comparison to urban residents, government policies surrounding migration, and of a broader discourse of modernity in Chinese society that encourages discrimination against the rural population.  This study seeks to understand how migrants with different backgrounds and varying experiences have developed strategies for upward mobility (social mobility strategies). The term "social mobility strategies" refers to the various ways that rural migrants attempt to elevate their social status through employment and skill training. This study will examine how these strategies have been shaped by the educational and financial disadvantages, administrative and social barriers and difficult living and working situations that migrants face. My research was conducted over a period of fifteen months in Shanghai, China. During this time, I conducted extended semi-structured and structured interviews with ten migrant workers.This study will describe in detail the migration narratives of four migrants and will analyze their social mobility strategies in the context of their migration process. It will explore each individual's personal background and experiences in relation to their mobility strategies. I also conducted  participant observation in rural Anhui province to understand the rural background of migrants. In Shanghai,  I attended a hair-styling academy and spent time in a hair salon, to examine how migrants acquire and utilize technical skills. While each story of migration and mobility strategies have common themes with one another, this study shows the personal specificities of each individual's narrative. It then relates these stories to broader issues surrounding migration in China.  

It is a common dilemma for undergraduate students to feel like their class material is inapplicable to the real world. This project aims to enhance traditional homework assignments with problems based on current scientific literature. The current class of interest is Physical Chemistry for Biochemists I at the University of Washington, taught by Dr. Munira Khalil. I developed homework questions using journal articles that focused on concepts of thermodynamics important in biochemistry. The questions test the students’ comprehension of the article and their ability to solve quantitative problems based on research presented in the article. These questions were integrated with traditional assignments already given in this course. Dr. Khalil’s class in Fall 2011 served as a test run for the literature focused homework assignments. At the end of this course, students evaluate the homework through an online survey. These evaluations were used to adjust the homework assignments for the same course in Winter 2012. Information from both quarters of surveys gave insight into how learning about research influenced a student’s interest and performance in the class.

Large waves of synchronized, spontaneous electrical activity (SSA) play an important role in many aspects of mammalian central nervous system development, such as regulating changes in neurons' ion channel properties and strengthening synapses through coincidence detection mechanisms. Questions still remain about the mechanisms of wave generation and propagation, and it is unclear what factors limit SSA to only a short critical period in development. Around the time of birth, much of the SSA is generated by neurons that release the neurotransmitter GABA. Our aim in this project is to clarify the roles of two ionotropic GABA receptor subtypes, GABAa and GABAa-rho, which respond differently to GABA stimulation and may have different distributions within the cell membrane. We selectively block either the GABAa or GABAa-rho receptor subtype in cultured slices of neonatal mouse brain and use calcium imaging to observe changes in the spatial and temporal properties of SSA. Current data suggest that activation of GABAa receptors is the dominant factor in SSA generation, but GABAa-rho receptors (or receptors with a mixed subunit composition) are also necessary for normal wave frequency.

This paper explores why state governments choose to expand Medicaid family planning provisions. It will compare the demographics, rates of family planning consequences, and state budget of the 28 states expanding Medicaid against the 22 states who are not. Family planning Medicaid has documented savings, and for nearly every $1 invested, there is a savings of approximately $4.02. It has also been shown to improve women’s life chances, provide access to healthcare for the poor, and to prevent unintended pregnancies. Yet, only 28 states have chosen to expand Family planning Medicaid at this point in time. What differentiates the states that invest in Medicaid from those who do not? By using data from the Guttmacher Institute along with data from the Census, I will conduct a macro-level analysis of these states. Moral beliefs, religiosity, and level of education are likely to influence this decision more than the cost savings provided by Medicaid. By better understanding the logic behind Medicaid investment in state government, the decision making process to provide this essential service to the poor can be demystified. This analysis will cast light on the reasons states choose not to invest in Medicaid, as the cost savings and health benefits of the program can be great assets to any state.

Since political violence first broke out in 1999, Côte d’Ivoire has experienced a drastic loss of medical equipment, drugs, and skilled health personnel. Two civil wars in the past decade have posed significant challenges to outside intervention from international NGOs, and the weakening economy has provided little support for a state-funded health system. Currently, Côte d’Ivoire suffers from some of the highest maternal and neonatal mortality rates in the world, resulting from problems ranging from infection and hemorrhages to the compound effects of malaria, malnutrition, and HIV/AIDS. My research responds to these challenges by exploring what would be needed in a grant proposal to The Global Fund, a global funding agency that supports the fight against HIV/AIDS, malaria, and tuberculosis in developing countries. Of the thirteen Global Fund grants approved for Côte d’Ivoire in the past, none specifically address the problems of maternal and neonatal mortality. This project aims to understand why this gap in maternal and neonatal care persists and how it can be diminished in the context of political instability. To assess the efficacy of attempts to address health care gaps in Côte d’Ivoire, I analyzed the interventions currently in place to see if they were meeting their established goals and if not, why. Building upon this data and development theory, I created a proposal for improving maternal and neonatal mortality through a self-sufficient system that can remain in place should political violence persist. Preliminary research suggests that weak medical assistance is a leading cause of birth complications. Increased health monitoring during and immediately following pregnancy, as well as greater education for mothers on the crucial steps during this time period are vital to reducing mortality. Establishing self-sustaining health systems that are resilient in the face of violence and political uncertainty is invaluable across the developing world.

The spindle assembly checkpoint is important for detecting errors in spindle assembly during mitosis. When the checkpoint is activated, it arrests the cell cycle so that errors such as unattached kinetochores can be detected and corrected before progressing through the cell cycle. Problems with kinetochore attachment can be detrimental and lead to cells with an abnormal number of chromosomes which can then cause birth defects. Misregulation of the cell cycle can lead to abnormal cell division and cancer. Spindle pole bodies in yeast are functionally equivalent to human centrosomes, which organize microtubules in the cell cycle. Spindle pole bodies increase in size when the cell cycle is arrested at the checkpoint. Mad1 is an essential component of the checkpoint and interacts with the Nup60 protein in the nuclear pore complex, a channel through which information traffics between the nucleus and cytoplasm. The N-terminus of Mad1 protein is required to localize Mad1 to the nuclear pore complex, but is not required for the checkpoint arrest. We found previously that if Nup60 is deleted, the spindle pole bodies do not grow in cells arrested at the checkpoint. Mad1 mutants containing only the C-terminus of the protein will be constructed. I will test if the ability of Mad1 to bind to Nup60 is required for spindle pole body growth. Spindle pole body size will be measured by fluorescence microscopy after arresting the cells in metaphase. I hypothesize that although Mad1 interaction with Nup60 is not required for the cell cycle arrest, it is required to signal spindle pole body growth. If true, then deletion of the Nup60 binding domain of Mad1 should block spindle pole body growth. Discovering what interactions are vital in these cells will give us a deeper understanding of how regulation of the cell cycle is maintained.

The Dunham group studies the costs and benefits of changes in gene and chromosome copy number (aneuploidy) in S. cerevisiae. Gene copy number change is a common evolutionary mechanism, and is often seen in cancers. Previously, the lab carried out a series of experiments to determine the consequences of changing the copy number of every gene in the yeast genome. 4383 yeast strains, each carrying a plasmid containing a yeast gene and a unique barcode sequence, were competed in nutrient-limited continuous-culture environments. The relative success of each strain was found by performing high-throughput sequencing on the barcodes. Our project explored three assumptions of this experiment, using direct chemostat competition assays. First, we confirmed that fitness effects observed in the pooled experiment could be repeated in individual experiments. We performed competition experiments using 22 genes from the experiment that were found to either be beneficial in certain environments or potentially harmful when duplicated. We also found that the plasmid alone had a fitness effect, by competing a strain containing a plasmid without a gene insert against a wild-type strain. Finally we tested the fitness effects of Autonomously Replicating Sequences (ARSs), which are origins of DNA replication found in many of the loci we are investigating. In a competition between a strain transformed with a plasmid with two ARSs and a strain with a plasmid containing a single ARS, a fitness benefit was observed for the presence of an extra ARS on the plasmid. These data are important controls for the pooled experiments previously performed in the Dunham lab and will help to identify the precise molecular causes of fitness changes associated with aneuploidy, and, perhaps in the future, provide some new insights into cancer biology.

Domoic acid (DA) is a toxin that accumulates in edible shellfish through filter feeding and is the causing agent of a serious neurological condition known as amnesic shellfish poisoning. The increasing intensity and frequency of DA-producing algal blooms has drawn more attention to develop fast and effective ways to detect and quantify DA. At Yu Lab, we developed an effective method for the fast detection and quantification of DA using a surface plasmon resonance coupler and disperser (SPRCD) sensor. The SPRCD sensor is an optical instrument based on the coupling of light to electronic oscillations at the interface between a gold surface and a dielectric material. The sensor measures changes in the optical properties of the interface caused by the binding of a specific molecule to the gold surface. By modifying the gold surface such that only the molecule of interest adsorbs, we are able to detect and quantify low concentrations of the toxin in a sample. Using our method, we can detect concentrations of DA as low as 0.1ng/ml and quantify DA in concentrations ranging from 5ng/ml to 10ug/ml.

When proteins are built, the gene is first transcribed into messenger RNA (mRNA) as an intermediate product which is later translated into a protein. Thus, by disrupting the structure of the mRNA we are able to inhibit the expression of its corresponding protein. In our lab, we work on engineering RNA enzymes (ribozymes) that can target and cleave any mRNA of known sequence expressed in vivo. To achieve this, we take advantage of the natural properties of a bacterial E. coli RNA enzyme, called RNase P, to cleave precursor transfer RNA (ptRNA) molecules. The natural RNase P holoenzyme has two subunits: a catalytic RNA subunit (M1 RNA) which cleaves an RNA helix that resembles the acceptor stem and T-stem structure of its natural tRNA substrate and a protein subunit (C5 protein) that facilitates this process. It is possible to convert the M1 catalytic RNA subunit into a sequence specific endonuclease (M1GS ribozyme) by covalently linking it to an antisense, 12 to 18 nucleotides long, guide sequence (GS) complementary to a target mRNA. We have now designed and manufactured our first M1GS ribozymes with guiding sequences complementary to different sites of the mRNA of GFP (green fluorescent protein). The next step would be to test our M1GS constructs on fluorescent cells expressing the target gene GFP. If our ribozymes are effective we would expect a significant decrease in the fluorescence due to the silencing of the GFP expression. Preliminary data is promising and the next step would be to start testing our constructs on targeting other genes. We hope to be able to design an efficient M1GS ribozyme that could target any gene of interest for applications in both basic research and clinical therapy.

Individuals with significant barriers to achievement in our society, such as homelessness, unemployment, mental distress, and chemical dependency, often commit low-level, non-violent crimes and continually cycle through the criminal justice system. To reduce recidivism, Community Court programs have been established to reduce crime through a problem-solving and community-focused approach. Community Court was introduced in Seattle in 2005 to specifically target these chronic offenders. My research focuses on Seattle Community Court defendants who have been charged with committing a misdemeanor theft offense. Using completed assessment forms made available through Probation Services in the Municipal Court of Seattle; I will examine the defendants’ current situational context (specifically homelessness and chemical dependency), along with other variables like age, race, gender, literacy, and mental health, to gain a better understanding as to why defendants commit a non-violent misdemeanor theft offense. Furthermore, by using Seattle police reports I will examine the type and monetary value of item stolen; this analysis will lead me towards more conclusive determinants which may explain the defendants' misdemeanor theft charge and/or disparities amongst those examined. I hypothesize that defendants who are homeless will steal an item with higher monetary value including clothing and/or appliances. Additionally, I expect that defendants who are chemically dependant are likely to steal an item with less monetary value like: food, beverage, and/or alcoholic related. If my hypotheses are in fact incorrect, I will have learned that the chronic offenders entering Seattle Community Court are multifaceted and the above characteristics do not necessarily account for why these offenders have committed a non-violent theft.

The spinal cord represents a key site of convergence for sensory feedback and cortical commands, but determining how each contributes to movement has not been uncovered.  Understanding how spinal circuits are structured and utilized to generate complex movements will be necessary to understand how the nervous system processes multiple inputs.  One approach to understanding motor circuits is to know how the output effects of neurons change between tasks.  Here we investigate the state of the spinal cord by stimulating at specific sites in the cord and recording electromyographic activity (EMG) in the forelimb muscles of a non-human primate.  By comparing the output effects of stimulation between two behaviors, a flexion/extension wrist task and a reaching task, we hope to understand the effects of cortical and sensory interactions in shaping motor output.  In addition, by creating a spinal map of stimulus triggered EMG activity, we hope to reveal the functional organization of spinal outputs during the behaviors.  In this experiment, we compare the effects of stimulus triggered averages of EMG between these two tasks at various sties in the cord.  Our results show a change in the effects on EMG activity dependent on the behavior performed in roughly 2/3 of sites.  Indicating that the configuration of the circuit that our electrode stimulates is dependent on the task performed.  When the non-human primate performs a wrist task, cortical input and sensory feedback recruit specific spinal pathways to activity certain muscles in order to perform the task.  When the task is altered, different cortical inputs and sensory feedback may inhibit or further excite that circuit, changing EMG activity.  Understanding the circuits responsible for the control of arm movements and how these circuits change with varying tasks, may allow us to utilize and exploit these spinal circuits to treat patients with spinal cord injury.

In order to understand the development of typhoons in the Indian Ocean, our team will deploy three subsurface moorings for up to one year. Attached to these underwater buoys are instruments that measure water conductivity, temperature, pressure, and velocity. Given that these moorings lie at such depths that GPS instrumentation cannot function, our goal is to create a program using Python that will triangulate their positions using acoustic signals so these expensive instruments can be retrieved. A command from the ship is transmitted to an acoustic release device on the mooring which gives the range between the two and the device is located anywhere in a circle surrounding the ship with that given range as the radius. Once this process is repeated two or more times from different locations, these circles converge at the mooring’s location. The program receives latitude, longitude, and distance input from the user, suggests locations for triangulation, and gives the mooring’s final location. Also included in the program is a graphical mapping component, allowing the user to visualize the circles to ensure they converge. Given the relative proximity of the triangulation points to the mooring’s location, we expect the calculations to be accurate within a hundred meters. Upon the program’s successful completion, the team plans to use it for mooring cruises in other parts of the world, minimizing the time required to do guesswork or triangulation calculations by hand.

Telemetry is concerned with the problem of making automatic, real-time measurements of remote data which are transmitted to base stations for further analysis. We present here an overview of our work in rocket telemetry for a Stage II Rocket which focuses on problems related to real-time telemetric data acquisition from high-speed, high-altitude projectiles, with detailed overviews of contributions from the six student teams, including: Airframe Team, Propulsion Team, Software, Sensors and Acquisition Team, Computational Physics Team, Launch and Recovery Team and the Computer Modeling Team. The Airframe Team designs the mounting apparatuses for the interior of the rocket. Our Propulsion Team synthesized and thrust tested the fuel we will use for rocket propellant, which is comprised of (Ammonium Nitrate-Oxidizer), C12H22O11 (Sucrose[Sugar]-Fuel) and HTPB(Hydroxyl-Terminated Polybutadiene- Fuel and Binder). The Software, Sensors and Acquisition Team is responsible for designing and programming the scientific equipment that will be onboard the rocket (Steering fins, an Arduino Microcontroller and a Two-Axis Accelerometer to maintain a linear flight path). Our data will be video, 3 axis acceleration, tilt, and altitude. The Computational Physics Team derived models to predict the rockets performance and they worked with the Computer Modeling Team to make CAD sketches. The Launch and Recovery Team make sure we follow safety precautions in launch and will use GPS tracking to retrieve the rocket when landed. The broader goal of this project is to recruit and invigorate future scientists at community colleges specializing in aerospace studies by providing a basic starting point from which they can learn and on which they can improve. We expect that by sharing our initial discoveries and experiences this multi-disciplinary research project, we will help to encourage other students at community colleges to actively participate in realistic team aerospace projects at an earlier stage in their educations.

Type 1 Diabetes Mellitus (T1D) is caused by a permanent destruction of insulin-producing β-cells of the pancreas by autoreactive T cells. Despite advances in insulin therapy, patients often face serious cardiovascular and neurological complications. Since most patients are children and young adults it is imperative to identify therapeutic targets to prevent the disease without causing generalized immunosuppression. Using autoimmune prone non-obese diabetic (NOD) mice (the widely used model of T1D) with spontaneous gene mutations in either Fas (lpr) or FasL (gld), we hypothesize the involvement of a specific population of B cells in the disease process. These B cells express Fas ligand (FasL), which is part of the pathway involved with T cell homeostasis. FasL expressed in these cells break immune tolerance in autoimmune prone NOD mice. Using flow cytometry B cell populations were characterized in spleen, pancreatic and inguinal lymph nodes, and in peritoneal cavity of NOD mice as well as in C57BL/6 and Balb/c mice. We detected FasL expressing B cells in spleen of all three mouse strains tested (NOD, C57BL/6, and Balb/c), but higher levels were detected in NOD mice. In addition, gld/gld mice B cells did not up-regulate FasL, CD23, or CD86 like the NOD wild-type mice which was illustrated by activation with LPS and anti-IgM. We looked for apoptosis among FasL+ B cells in the spleen of NOD, B6 and Balb/c and found higher annexin V levels in B6 and Balb/c than NOD, supporting the hypothesis that B cells in NOD mice, are pathogenic.

The field of gene therapy relies on vehicles that can introduce exogenous genetic material into target cells in order to affect the production of a desired therapeutic protein. Viruses have long been used as delivery vehicles, but concerns over immunogenicity have fueled efforts to develop alternative nonviral delivery vehicles. Current polycationic polymers used in gene delivery methods generally exhibit poor transfection efficiencies and also dose-dependent cell toxicity. This project seeks to address these parameters through the synthesis of a novel copolymer of 2-hydroxypropyl methacrylate (HPMA) and a methacryated oligoarginine peptide (MaAhxR10). In phase one, the HPMA-oligoarginine copolymer was synthesized and tested for basic functionality. Transfections of HeLa cell populations demonstrated that the transfection capabilities of this polymer were comparable to those of the oligolysine standard, but the toxicity was significantly enhanced. Phase two consisted of modifying the peptide with neutral amino acid residues (such as glycine) to reduce the charge density of the polycationic peptides. Further, a more efficient approach to preparing arginine peptides was developed by chemically guanidinylating lysine residues. This approach was used to generate a lysine and a homoarginine version of each polymer. The resulting copolymers were tested for transfection efficiency and cell toxicity in cultured mammalian cells. Copolymers made from the resulting ‘spaced’ peptides (MaAhx(GK)5 and MaAhx(GhR)5) demonstrated reduced cytotoxicity compared the MaAhxR10 and PEI standards, but were still comparable in transfection efficiency to the oligolysine standard. While the delivery vehicle has not performed as expected, the project may have revealed a relationship between charge density (and therefore accessibility of charge) and cytotoxicity. The next step will be to generate another panel of polymers, this time with even more spacing between positive charge residues. This will allow for the identification of a correlation between charge density and cytotoxicity.

Although previous research has looked at the popularity of drinking games (DG) among college students and the positive correlation between alcohol use and related problems, there is a dearth of research focusing on the demographic correlates of participation in DG and associations of DG with alcohol-related protective behavioral strategies (PBS). The aims of this study were to a) detect demographic groups of college students who are more likely to engage in DG participation and b) determine whether frequency of DG participation was correlated with alcohol use, alcohol-related problems, and the use of PBS (e.g., limiting drinking, changing the manner in which one drinks, avoiding serious alcohol-related harm). Participants (N= 1096) were college students who completed an online self-report survey on drinking and related health behaviors. Findings showed that participants who belonged to a Greek organization, lived in a sorority/fraternity house and were White/European-American reported higher levels of DG participation than students who did not belong to a Greek organization, lived in other types of housing, and were not White/European-American, respectively. Furthermore, frequent participation in DG during the previous month was correlated with heavier and more frequent drinking, increased level of alcohol-related problems and decreased use of PBS. Current findings corresponded to those in the literature, which have shown that participation in DG puts college students at higher risk for alcohol-related problems. This study expanded upon the literature by more comprehensively evaluating demographic characteristics that put students at higher risk and by testing the correlation between DG participation and the use of safer drinking strategies. Future studies may investigate whether interventions encouraging the use of PBS can reduce alcohol use and related problems among college students who engage in DG.

Rare earth element (REE) concentrations in Mount St. Helens (MSH) volcanic units remain constant (or slightly decrease) with increasing silica (from andesites to dacites). Owing to the commonly held view that REE are incompatible with typical mineral assemblages in mafic to intermediate magmas, crystal fractionation was not considered to be a viable mechanism for generating dacitic melts. Instead, partial melting of a low REE crustal source was considered more likely. REE are, however, highly compatible in apatite and there is evidence of its early crystallization in mafic to intermediate magmas. Hence, we have reevaluated models for crystal fractionation in order to determine a possible mineral assemblage (including apatite) required to reproduce REE trends. Using published partition coefficients, reasonable modal amounts of the major minerals (amphibole, clinopyroxene, Fe-oxides, and plagioclase) and 1-2% apatite, it appears possible to closely mimic the REE patterns in dacites, particularly if considering some assimilation of depleted lithologies in the deep crust.

The treatment of a disease is often based on that disease's progression. In cancer, such information is derived from indicators such as the location and extent of tumor within tissue. In addition to determining the presence of a disease, biopsies are often taken with the goal of finding these indicators. Unlike cell biopsy, samples from tissue biopsy preserve biological architecture, allowing these indicators to be more easily determined. For this project, Thin Needle Core Biopsy (TNCB) is used to obtain small cylindrical tissue samples 250µm in diameter and up to 2cm in length. Tissue samples are imaged with Optical Projection Tomography Microscopy (OPTM), which is currently used to generate high-resolution three-dimensional (3D) images of individual cells. Imaging through the tissue is facilitated by axial scanning through the optically cleared tissue; however, the microscope has limited lateral field of view and the TNCB specimen must be imaged in a series of 3D images. This project has three focuses. First, stitch a series of OPTM images using morphological operations, histogram manipulation, and phase correlation. Second, perform image reconstruction to create a single continuous 3D image of all cells within the biopsy. Third, present the 3D images to pathologists in a user-friendly interface. In addition to displaying the 3D image, the computer interface allows clinicians to view cross-sections of the 3D image in the x-, y- , and z-planes to simulate pathological tissue slices. The results allow pathologists to analyze the entire tissue sample, not just samples of cells, and have potential to reduce sources of error in making diagnoses.

Gene therapy is the treatment of disease by inserting genes or altering them in a subject’s cells and tissues. The Pun lab develops cationic polymer-based delivery vehicles. Our agenda was to determine the intracellular fate of drug delivery vehicles carrying the therapeutic genes in order to better understand cellular barriers that limit efficient delivery. For this project, we applied two methods to study the intracellular trafficking of polyplexes (polymer-DNA complexes). The first approach is a quantitative method using subcellular fractionation to separate organelles and determine the distribution of polyplexes in various cellular compartments after internalization. We hypothesized that by using methods of centrifugation, organelle-specific enzyme assays, and radiolabeling, polyplex distribution could be quantitatively analyzed. We demonstrated successful separation and quantification of organelles using a combination of differential and density-gradient centrifugation. The polyplex distribution in each fraction was determined through radiolabeling. In this way, a quantitative “snapshot” was taken of the distribution of polyplexes inside the cell, and yielded information for the identification of potential bottlenecks in trafficking to the nucleus. Our second approach is to study the intracellular trafficking of drug delivery vehicles by time-lapse fluorescence imaging combined with single-particle tracking. This complementary approach reveals both the time-course and behavior of particles as they are trafficked within the cell. By fluorescently -labeling the polymer and applying the polyplexes to cells, we successfully observed their motion within a single cell. We further optimized the quantity of polyplexes delivered and the image capture techniques to robustly track polyplexes within a single cell. Our work therefore provides improved methods for determining the mechanism and efficacy of gene delivery systems and potentially any particle-based drug delivery system. For future work, we plan to investigate the process of unpackaging of the polyplexes inside cells.

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the United States and much of the world. NAFLD resembles alcohol-induced liver injury, but occurs in patients with little to no history of alcohol consumption. It is a fairly benign condition, but can progress to a more advanced disease known as nonalcoholic steatohepatitis (NASH); many factors have been implicated in the pathogenesis of this transition (ER stress, mitochondrial dysfunction, insulin resistance, oxidative damage), but the exact mechanism remains unclear. Iron, although essential to many cellular processes, leads to increased oxidative stress and may be significant to NASH development via dysregulation of microRNA expression. To test our hypothesis, we measured microRNAs known to regulate processes marking the transition of NAFLD to NASH, such as apoptosis, inflammation, and lipid metabolism with real-time reverse-transcription PCR in a NAFLD mouse model. By comparing microRNA levels from the liver tissue of iron-treated vs. non-iron-treated NAFLD mice, we can survey effect of iron in exacerbating NAFLD via differential microRNA expression. As a regulator of cellular gene expression by transcriptional inhibition of messenger RNA, microRNA have the capacity to predict cellular processes before physiological changes are seen in the affected tissue. Thus, our results can more specifically describe differentially regulated genes during NASH development in the context of iron. After profiling our treatment groups, we will use bioinformatics to identify gene targets of the significant microRNA and validate the relationship of microRNAs and target genes in vitro. We will also compare the microRNA expression profiles of liver tissue and serum to identify serum biomarkers of NASH. In addition to the mechanistic insights elucidating the pathogenesis of NASH, our findings may lead to alternative non-invasive methods for NASH diagnosis, as liver biopsy is currently the only method for diagnosing NASH.

HIV-2 is endemic in West Africa, but has a much more limited spread worldwide than HIV-1. Compared to HIV-1 infection, HIV-2 is characterized by a much longer asymptomatic stage, lower plasma viral loads, slower decrease in CD4 cell count, decreased AIDS associated mortality rate, and lower rates of genital tract shedding, mother to child transmission, and sexual transmission. Nonetheless, a signficant proportion of HIV-2 infected individuals will eventually progress to AIDS, and many of these individuals will benefit from antiretroviral therapy (ART). However HIV-2 is intrinsically resistant to nonnucleoside reverse-transcriptase inhibitors (NNRTI's) and the fusion inhibitor T-20, and reports suggest HIV-2 may be partially resistant to protease inhibitors. However the mutations in HIV-2 that confer resistance are not well characterized. Improving treatment of infected individuals requires a thorough understanding of the mutations that occur in the HIV-2 strains of ART treated patients and the effect of these mutations on the efficacy of ART. Plasma samples used in this study were obtained from ARV-treated HIV-2 infected individuals participating in the Senegalese Initiative for Access to Antiretrovirals (ISAARV) program. A phylogenetic analysis approach was used to identify common mutations occuring in the HIV-2 strains of individuals receiving protease inhibitor (PI) based therapy. Gaining an understanding of the mutations that occur in the HIV-2 strains of indiviuals receiving PI-based ART and their effect on ART efficacy is a first step in improving treatment of HIV-2 infected individuals to prevent progression to AIDS.

The hippocampus is well known for its role in spatial memory. A better understanding of how the hippocampus functions will provide us with insight into how memories are made and stored. This knowledge may ultimately lead to improved preventative and treatment strategies under conditions in which the hippocampus is altered, such as after traumatic brain injury or in cases of age-related memory impairment. Within the hippocampus there are cells commonly known as “place cells”. These cells are most likely to fire when a navigating organism is in a certain space in an environment, known as that cell’s “place field”. The activity of place cells may be modulated by dopamine input, which can be released tonically or phasically. For example, when overall dopamine input from the ventral tegmental area is disrupted, the place fields of cells within the CA1 subregion of the hippocampus are disrupted and spatial memory deficits occur. To test the idea that phasic dopamine, in particular, is necessary for normal place cell activity and spatial memory performance, we tested spatial working memory while recording electrophysiological activity of neurons in the hippocampus in normal mice and genetically engineered ‘knockout’ mice whose phasic dopamine signaling was selectively disrupted. Preliminary electrophysiological results show differences between the groups, including a nearly significant increase in the spatial selectivity that corresponds to a significant decrease in the size of place fields from the knockout mice when compared to controls. Behaviorally, knockout mice adapt more quickly than control mice following a change in the location of a reward, indicating that phasic dopamine input is not required to perform this task. Rather, removal of the phasic firing pattern may have unmasked a potential facilitating role of tonic dopamine release in flexible goal directed behaviors.

Inhibitor of differentiation (Id) is a transcription factor that negatively regulates basic helix-loop-helix (bHLH) transcription factors. Of four Ids identified (Id1-4), Id1 and Id3 have been shown to regulate glial development in the central nervous system. In the retina, there is a special type of glia called the Müller glia. Currently, it is not known whether the Ids are important for Müller glial development. Knockout studies in mice demonstrated that Id1/Id3 double knockout (KO) are embryonic lethal, while either Id1 or Id3 KO mice develop grossly normal. We investigated if Id1/Id3 are necessary for Müller glial development by performing Id1 shRNA knockdown (KD) in Id3 KO retinas. Five Id1 shRNAs were tested for their efficiency in NIH 3T3 cells (mouse fibroblast cell line), and the Western blot results showed over 90% decrease in Id1 expression using three shRNAs. We will electroporate Id3 KO retinal explants with these Id1 shRNAs and determine the effects of Id1/Id3 loss on Muller glial development. We expect to see a reduction in the number of Müller glia if Id1/Id3 play a role in their development.

Research studies suggest that up to 40% of hepatocellular carcinomas may be caused by liver stem cell carcinogenesis, in which stem cells, due to their high proliferative abilities, become neoplastic and maintain cancer growth and metastasis. MicroRNA are post-transcriptional gene regulators that have been found to be involved in many cellular processes such as differentiation of stem cells. This project focused on the role microRNA play specifically in liver stem cell differentiation. Finding which microRNA are important in liver cell differentiation could provide new methods for diagnosis and treatment of liver cancer originating from stem cells. I used a stem-cell-like liver progenitor cell line capable of differentiating into mature liver tissue from a proliferative state, providing an ideal in vitro model for liver stem cell differentiation. Relative quantification of microRNA by real-time PCR and microarray was performed on samples taken from various time points during differentiation leading to the characterization of two microRNAs strongly upregulated in differentiation. In order to validate the importance of these microRNAs, I will use a viral vector to induce their overexpression and monitor any subsequent changes in the differentiation process. In the end, this project may provide additional insights into neoplastic liver stem cells.

Over the past ten years we have analyzed a variety of plants that produce volatile oils grown in our Chemical Garden on The Evergreen State College campus. These plants lend themselves well to extraction by steam or ethereal solvents and are easily analyzed through Gas-Chromatography Mass Spectrometry (GC/MS). The plants we have focused on are garlic, St. John's Wort, hops, mints, and lavender. This poster reports on our progress towards isolating and identifying individual constituents of Devil's Club (Oplopanax horridus), a local plant with a long history of use as a medicine. We have been curious as to the best time of year to harvest the plant, as there is some debate in the herbalism community on this point. The Devil's Club was distilled at different times of the year and analyzed using GC/MS. The non volatile constituents were extracted using a number of different solvents and analyzed using Thin Layer Chromatography (TLC). This research will provide information on the effects of harvest time on constituent levels, as well as providing knowledge of the chemical make up of this plant.

In 1986, the United States’ Centers for Disease Control and Prevention (CDC) established the Gonococcal Isolate Surveillance Project (GISP) to monitor the trends of increasing antimicrobial resistance of urethral Neisseria gonorrhoeae isolates from men who have sex with men (MSM). Since then, such strains of N. gonorrhoeae, the bacterium that causes gonorrhea, have been observed to repeatedly develop resistance to antimicrobials including sulfonamides, penicillin, tetracyclines, and most recently, fluoroquinolones. The effectiveness of the cephalosporins, the last remaining option for empirical first-line treatment of gonorrhea, is threatened by declining gonococcal susceptibility to cephalosporins in the US and worldwide. In correlation with the University of Washington Neisseria Reference Laboratory, N. gonorrhoeae isolates recovered from non-urethral sites were screened for antimicrobial resistance, in an attempt to identify these previously unmonitored trends. Prior to this, there was no data concerning antimicrobial resistance trends of extra-genital N. gonorrhoeae isolates. The experimental approach employed was disk diffusion of cefpodoxime (cephalosporin) and azithromycin (macrolide). Diameters of zones of inhibited growth, which can be seen directly on agar plates, were measured. Analysis of results was visual, and it was often clear whether or not an isolate was resistant to an antimicrobial agent. By observing non-urethral isolates, information is gained regarding the management and treatment of gonorrhea based on other anatomical sites. Experimental analysis spanning two years of isolates (2008-2009) suggests similar susceptibility trends when compared to prior GISP data. While more exact trends will be determined based on a longer span of time, totaling ten years, completion of this work will inform treatment guidelines that consider a larger variety of N. gonorrhoeae isolates.

Wind tunnels are devices used to simulate real-world aerodynamic conditions and characteristics using small-scale models that will be experienced by larger-scale engineering structures such as aircraft, buildings, bridges, windmills, and even cities. They are useful for studying and addressing problems of the stability, efficiency, and feasibility of engineering designs on a small-scale before scaling-up to larger and more-expensive engineering projects. We present here an overview of the design, construction, and testing of the EdCC Undergraduate Research Students Association (URSA) research-grade wind tunnel which was conceived to support further student studies in aerodynamics across the Physics, Engineering, and Materials Sciences departments at EdCC, including detailed contributions from the four student teams involved with the project: Aerodynamic Theory Team, Engineering and Construction Team, Software, Sensors and Acquisition Team, and the Computational Physics Team.

Iodinated trihalomethanes (I-THMs) can be found as disinfection byproducts (DBPs) in treated drinking waters where chloramines are used as a secondary disinfectant and iodide is present in the source water. Chlorinated and brominated THMs are regulated DBPs by the US EPA at parts per billion (ppb) levels and are known human carcinogens. I-THMs are not EPA regulated, but can occur at sub ppb levels and studies have shown these compounds to be much more cytotoxic. This greater toxicity underlines the need to study the occurrence of I-DBPs and to determine the likelihood of human exposure. To measure I-DBP formation during a treatment plant process, we collected and analyzed samples of raw water, plant effluent, and distribution system water, from five different drinking water treatment plants. We applied headspace solid-phase micro-extraction (HS-SPME) as a method to extract compounds from samples and gas chromatography with electron capture detection (GC/ECD) as the analytical method for measuring I-THMs. Compared to the standard methods of liquid-liquid extraction to isolate THMs, the SPME method has a greater analyte concentration factor and consumes less solvent, which minimizes solvent exposure to the lab technician. This research project will provide occurrence data for future exposure assessments. When combined with toxicological assessments of I-DBPs, our findings could support future risk analysis of human exposure to drinking water DBPs.

Childbirth is considered one of the most painful events a woman may experience. Labor analgesia with an epidural or intrathecal opioids is an option that most women opt to receive nowadays. It has been hypothesized that genetic variability explains, at least in part, the large inter-individual variability in the observed response to neuraxial opioids. Pain perception and the analgesic response to opioids are most likely polygenic (affected by multiple single nucleotide polymorphisms across different candidate genes). The Landau Lab is investigating the association between the analgesic effect (potency) and duration of action of intrathecal fentanyl (ITF) in parturients and common polymorphisms of µ-opioid receptor gene (OPRM1) and catechol-O-methyltransferase (COMT) gene. We hypothesized that duration of ITF will be longer in A118 homozygotes of OPRM1 and Met158 of COMT (A/A-Met/Met) compared to women carrying a different allelic combination. We performed a secondary analysis on data from a study on 184 parturients receiving a combined-spinal epidural for labor analgesia. The primary outcome was duration of analgesia from ITF dose (25mcg) to request for additional analgesia (via epidural). There was no significant difference between genotypic groups (p=0.358) although there was a trend for longer duration of ITF in A/A-Met/Met women [n=38; 81min (CI 95% 70, 92)] compared to Met/Met not A/A women [n=11; 63min (CI 95% 46, 80]. These findings suggest that genetic variants of OPRM1 and COMT genes may affect the response to intrathecal fentanyl for labor analgesia and warrant further investigation as this may have relevant clinical implications.

Syphilis is a disease that is increasing in the United States. It is estimated that, every year, twelve million new syphilis infections occur globally. The development of a vaccine is therefore a high priority. Proteins in the outer membrane of the bacterium that causes syphilis, Treponema pallidum subsp.pallidum (T. pallidum) and surface-exposed epitopes that are recognized by the immune system must be identified to be used as targets for vaccines and new serological tests. One promising target for vaccine development is TprC, a predicted outer membrane protein with surface-exposed loops. This project will determine whether these predicted surface loops on the TprC protein are recognized by antibodies. TprC also varies among syphilis strains in discrete regions of the protein. The protein TprC was synthesized as small peptide fragments consisting of 20 amino acids, with 10 amino acids of overlap between each peptide. All of the peptides fragments including peptides of variable regions will be tested using anti serum from each strain. These peptides are exposed to antibodies from infected rabbit sera and visualized by a labeled secondary antibody. Those peptides visualized by the secondary antibody are regions of TprC recognized by the immune system. These ongoing experiments will determine whether the surface-exposed regions of Tpr C are the major targets of the antibody response and whether antibodies induced by infection of one strain will be effective against another strain; both crucial in vaccine design.

Duchenne Muscular Dystrophy (DMD) patients have mutated dystrophin genes and suffer from muscular degeneration, which leads to cardiac, respiratory and general skeletal muscle disabilities. Potential treatment of DMD patients could involve gene therapy in which Adeno-Associated Viruses (AAV) deliver functional dystrophin cDNA ligated to muscle specific regulatory cassettes that express dystrophin exclusively in striated muscle tissues. The Hauschka lab has been designing regulatory cassettes (e.g. MHCK7) that contain control regions from genes that are highly active in skeletal muscles such as the muscle Creatine Kinase (MCK) and α-Myosin Heavy Chain (α-MHC) genes. Due to the limited size of DNA that can fit into AAV capsids, the cassettes need to be as compact as possible. My goal is to test whether adding a small intronic enhancer (SIE) from the MCK gene, that is known to have high activity in skeletal muscle in vitro, will improve transcriptional activity in cardiac and skeletal muscle cultures compared to MHCK7. The SIE was isolated and cloned immediately 5’ of MHCK7. After sequencing to confirm the SIE orientation, we carried out a pilot study in which 5’-SIE-MHCK7 was transiently transfected into skeletal muscle cultures. 5’-SIE-MHCK7 activity, as measured by the reporter gene firefly luciferase, was several fold higher than MHCK7. This suggests that the addition of the SIE to two known muscle specific enhancers increases transcriptional activity in skeletal muscle cells. Future studies will focus on confirming this result, and comparing 5’-SIE-MHCK7 activity to aMHCK7-SIE cassette in which the SIE is located 3’ of the luciferase reporter, so as to mimic its normal location in the MCK gene. The 5’-SIE-MHCK7 cassette will also be tested in cardiomyocyte cultures, and smaller cassette versions will be designed that eliminates additional non-conserved DNA sequences from the SIE and MHCK7 components.

New information is emerging on the current status of the harbor porpoise (Phocoena phocoena) population in Washington’s southern Puget Sound region. In the 1940s harbor porpoise were considered one of the most abundant cetaceans in the waters south of the Tacoma Narrows Bridge (47 26N, 122 57W). By the 1970s they had almost completely disappeared and remained absent until about 2007. In 2007, sightings of adult animals as well as calves and juveniles were documented and appeared to increase over the next few years. Available sighting and stranding records were reviewed and plotted for spatial analysis; however at this point biases in effort prohibit the determination of seasonal and annual trends. Several potential factors have been speculated for the initial decline, including fishery interactions, contaminant burdens, and reduction in prey availability, but the cause for their disappearance is unclear. The underlying reasons for their comeback are not clear although it may be related to the increases in the population in the Strait of Juan de Fuca/San Juan Island area over the past 20 years, problems in other parts of their range in Washington and Oregon where there was an Unusual Mortality Event just prior to their return to Puget Sound, and possibly improvements in prey availability in Puget Sound. The reoccurrence of the harbor porpoise to southern Puget Sound also suggests anthropogenic impacts have lessened in this area allowing the return of this top predator. Understanding of the past and present abundance of harbor porpoise and the factors that may affect their presence is crucial to effectively manage of this sentinel species.

Vashon-Maury Island has always had a fascinating history, involving both its people and the land. As Vashon-Maury Island became more populated around the 1880s, citizens began to recognize the true benefits that the island was able to offer. Industries began to bloom, creating an inordinate economic growth for the community which led to a greater recognition of the island. One of the consequences of the economic boom was that industries were situated throughout the island, especially around Quartermaster Harbor. Research various documents and data have been compiled to understand the relationship between the population impacts on the environment especially around the island. Studies that were being conducted for this experiment included examining literature reviews from previous researchers, and compilation reviews from environmental journals. The conclusion from researchers state that the pollution of bacteria from the waters was not only accumulating directly from industries but also the homes and recreational activities. In order to understand the holistic impact of changes in relation to water pollution scientists took samples of soil and other marine organisms at Quartermaster Harbor and it has been revealed that the water has been significantly polluted over the past 100 years. Bacteria such as Escherichia coli have been recorded as having an immense population growth due to decades of activities. Remarkably, it appears that outdoor activities ranging from boating, picnicking, swimming and other recreational events have led to massive inputs of pollution. By understanding these conditions, future and present researchers are able to educate and inform the public on ways they can prevent future contamination to the harbor. With the right education and deliverance of information the community has the potential to increase the health of the environment on land and water.

The development of satellite technology has enabled scientists to develop a greater understanding of the movement patterns of various animals. Specifically, the movement of polar bears in Greenland is of ecological interest due to sea ice loss in the Arctic. Researchers tag polar bears with satellite collars and collect various samples and measurements such as age, sex, body mass, and body condition. Bears are tracked using polar-orbiting satellites and the data are collected and transmitted by Advanced Research and Global Observation Satellite (ARGOS). The large volumes of data are reported in coded text files that are difficult to analyze and contain error. I developed a program to extract data from ARGOS written using the statistical programming language R. This program allows for covariates on individual bears to be merged with satellite location data. I created two error checked databases (filtered and unfiltered) on movement of polar bears in Greenland. This program will facilitate data analysis of the movement patterns of polar bears.

Understanding the genetic and molecular mechanisms behind development is necessary for identifying and treating genetic disorders. A key developmental process is tube formation (tubulogenesis), which produces structures such as the vascular system, bronchi, and the embryonic neural tube. Our lab uses the model organism Drosophila melanogaster, a fruit fly, to study the formation of a tubular organ called the dorsal appendage (DA). Two DA tubes form during oogenesis, creating extensions of the eggshell used for gas exchange once the egg is laid. DA formation resembles neural tube formation in vertebrates. To understand the molecular mechanisms that underlie DA formation, we disrupt specific genes and proteins and then analyze how their loss affects DA formation. This project focuses on tiggrin, a gene that encodes an extra-cellular matrix protein that interacts with cell surface receptors to shape tissues. A previous genetic screen identified tiggrin as a potential regulator of DA formation. To understand tiggrin’s role, we have made 24 potential deletions of the tiggrin gene by excising a P-element transposon just upstream of tiggrin. We are using the polymerase chain reaction (PCR) to determine if we have produced any actual deletions of or within tiggrin. Once we determine which lines contain deletions, we will analyze their effect on DA formation. We are breeding lines with potential tiggrin deletions to determine if they are homozygous viable or fertile. We are crossing any lines that do not result in adult tig/tig individuals to a previously established line with a large deletion that removes tiggrin (and neighboring genes) to see if the resulting flies are viable and fertile. Also, we will determine the spatial and temporal expression of tiggrin protein during oogenesis using immunostaining. Adding tiggrin to our study of DA formation will broaden our holistic understanding of the molecular mechanisms of tubulogenesis.

The neuromodulator dopamine is important for motivated behavior. Past research provides evidence that dopamine neurons encode the expected value of reward-predicting stimuli in situations with a single option. The current project investigated dopamine transmission when multiple options are present, as previous studies have arrived at conflicting conclusions. One study found that dopamine neurons encode the value of the subsequently chosen option, regardless of the expected value of the option foregone; whereas the other concluded that dopamine neurons encode the value of the greater available reward, regardless of which option was actually chosen. To address this discrepancy, we recorded changes in nucleus accumbens dopamine concentration using fast-scan cyclic voltammetry in rats performing a decision-making task in operant chambers. Sessions included single-option trials intermixed with choices between two options that differed in reward size (number of food pellets) and effort requirement (number of lever presses). When rats were presented with a low-reward/low-effort option (1 pellet for 4 presses) and a high-reward/intermediate-effort option (4 pellets for 8 presses), they preferred the high-reward/intermediate-effort option. In separate sessions, when presented with the low-reward/low-effort and a high-reward/high-effort (4 pellets for 32 presses) options, the rats preferred the low-reward/low-effort option. Preliminary voltammetry results from single option trials suggested that dopamine release was greater following the presentation of the high-reward/intermediate-effort option compared to the presentation of the low-reward/low-effort option. In the other session type, however, dopamine concentration did not differ between the high-reward/high-effort option and the low-reward/low-effort option. In two-option choice trials, dopamine release associated with each reward/effort combination was similar to that in the corresponding single-option trials. Thus far, these results are more consistent with the claim that dopamine encodes for the option subsequently chosen, but the interaction between behavioral preference and encoding of expected reward value requires further investigation.

E. coli are a species of bacteria that naturally inhabit the mammalian intestinal tract. They can thrive in environments with high fluid shear like the colon or the urinary tract due to their sticky hair-like projections called fimbriae which allow them to grip epithelial lining. These fimbriae are primarily composed of a coiled chain of a repeating protein unit called FimA. This helical coil unwinds in a gradual fashion when pulled and our goal is to see how mutating certain amino acids (all proteins are made of sequences of amino acids) inside FimA can affect the energy required to uncoil the helix. A microscopic cantilever is applied to different mutants for E. coli fimbria and an atomic force microscope records how much force the fimbria exerts back during a pull, indicating the helix uncoiling and how much force it requires. We hope to find mutants that uncoil more easily or not at all which would illuminate which amino acids in FimA are active in maintaining the helix and its uncoiling flexibility. The findings would have many applications practically and for expanding research. Rigid helices are a valuable test group for examining fimbria behavior independent of the effects uncoiling while the amino acids isolated as important can help design target drugs against E. coli infections in urinary tracts by weakening their binding. The protein structure knowledge earned is also of biomedical value as it can help design novel adhesives using bacterial fimbrial protein.

The harvest of oil from large-scale algal cultivation has become an attractive source of alternative and sustainable biofuel to replace traditional fossil fuels. Understanding how algae store and breakdown their synthesized oils sequestered within specialized organelles known as lipid bodies is key to improving algae oil production. My study is to: a) propose a model alga, b) cytologically probe lipid body architecture, c) and document lipase activity gaining access to oils within lipid bodies. To select a model alga for my studies, I conducted a survey of my laboratory’s algae culture collection looking at organisms across a variety of taxa, lipid body morphology, spatial arrangement, and total number of lipid bodies. BODIPY 505/515, a lipophilic dye, was used to integrate the lipid bodies of these organisms. Chrysochromulina sp. was identified as the best model organism for its simple compliment of two large lipid bodies. Counterstained lipid bodies indicate a strong co-localization of an endoplasmic reticulum membrane with lipid bodies. Fluorescein diacetate was used as a fluorescent indicator for lipase activity. Over a 24-hr time course study, flow cytometric data showed fluorescein diacetate fluorescence increasing as BODIPY 505/515 fluorescence decreased. Cytological studies also show fluorescein diacetate localizing to lipid bodies during its peak fluorescence. These results indicate an endoplasmic reticulum membrane surrounds Chrysochromulina sp.’s lipid bodies and lipases are involved in gaining access to fatty acids through the endoplasmic reticulum membrane. In determining effective algal lipid harvesting protocols it is paramount to first understand cellular lipid usage. Developing the most efficient methods of converting algal lipid bodies to biofuels will accelerate the viability of the global transition to alternative fuel sources.

The mu rhythm is a continuous electroencephalogram (EEG) component that is typically suppressed when executing actions and observing the actions of others. Individuals with autism spectrum disorder (ASD), an impairment in social understanding and ability, show EEG mu suppression to self-movement but not when observing the movement of others. Inability to perceive and understand the actions of others may lead to disruptions in social development and is hypothesized as one of the core disruptions in individuals with ASD. The purpose of this study is to examine the relation between EEG mu rhythm and the degree of social impairment in individuals with ASD. Participants in the study will include children and adolescents with ASD and typical development. Degree of social impairment for the subjects with autism was assessed using the Social Responsiveness Scale (SRS), a 65-item parent report questionnaire. To record mu rhythm, EEG was recorded while the participant was at-rest and during the observation of biological and non-biological motion. We hypothesize that greater social impairment, indicated by higher scores on the SRS, will be associated with decreased mu suppression during observation of biological motion; social impairment will not be related to mu suppression during observation of non-biological motion. Results from this study may help in understanding the relation between mu rhythm, biological motion, and social understanding.

A strong understanding of the intricacies of blood coagulation is essential for proper treatment of coagulopathies such as hemophilia, hemorrhage, Von Willebrand’s disease, and numerous thrombosis related conditions. The coagulation behavior of blood is directly related to the structure of the supporting protein networks. Fibrinogen is a protein found in human blood that, upon polymerization into cross-linked fibers, forms the scaffold-like support structure of a blood clot. Based on the observation that emergency room patients with traumatic injuries experience a greater extent of hemorrhage and abnormal hemostasis, our group has investigated the effect of acidic oxidation on the structure and mechanical properties of fibrin gels. Purified fibrinogen was oxidized using hypochlorous acid to simulate the acidification of blood during trauma and shock. Rheological, x-ray scattering, and turbidity studies were performed to characterize the structural and mechanical differences between oxidized and normal fibrin gels. Preliminary results from these studies indicate the oxidation causes a delay in fibrin gelation as well as a decrease in the elastic modulus of the fiber network. Additionally, evidence from turbidity studies suggests that oxidation prevents lateral aggregation between protofibrils leading to an overall reduction in fiber diameter.

Vesicular Glutamate Transporters (VGLUTs) are proteins that package glutamate into vesicles prior to synaptic transmission. Three VGLUT proteins have been identified (VGLUT1-3) in mammals, with VGLUT1 and VGLUT2 showing complementary patterns of expression, and VGLUT3 co-localizing with both VGLUT1 and VGLUT2. In mammals, VGLUT1 is mainly found in the cortex, hippocampus, and cerebellum, and VGLUT2 is present in the thalamus, hypothalamus and brainstem. Intriguingly, birds appear to have no VGLUT1 homologue, though common ancestors of mammals and birds have homologues of both VGLUT1 and VGLUT2. This is an interesting development in the long disputed question of the evolutionary relationship between the pallium of the avian brain and the mammalian cortex. Because birds lack VGLUT1 and have VGLUT2 expression similar to the combined pattern of both VGLUT1 and VGLUT2 in mammals, the pattern of VGLUT2 activity in the bird brain could be important in understanding the different evolutionary paths of these two structures. In addition, knockout mice for the VGLUT1 gene die shortly after weaning, indicating a crucial role for VGLUT1 in development in mammals. However, birds function without VGLUT1, suggesting an increased functional role of VGLUT2 in the avian brain. To explore the distribution and role of VGLUT2 in the brain of the zebra finch, we used anterograde tracing and immunostaining for VGLUT2 to test whether synaptic terminals that originate in the pallium contain the VGLUT2 protein. Electron microscopy was then used to analyze VLGUT2-positive terminals in four different song nuclei (nucleus HVC, Area X, robust nucleus of the arcopallium, and medial portion of the dorsolateral thalamic nucleus) for size, number of synapses, and identity of postsynaptic elements. Overall, we find that VGLUT2 is expressed where VGLUT1 is found in mammals. These observations also help us characterize the glutamatergic terminals in these song nuclei of the zebra finch.

Vashon-Murray Island boarders a bay called Quartermaster Harbor which has many pollution problems including periodic algal blooms and chronic hypoxia events. It also has notably high nitrate levels. King County reports one creek that feeds Quartermaster Harbor, Mileta Creek, also has high nitrate levels: between one to two orders of magnitude higher concentrations than what would be typical for such as stream. These levels tend to peak during the late fall and early winter and drop off during the rest of the year. To better understand when and what is happening, we took nitrate samples more frequently and in at more sites than previously tested. This data was collected using a Satlantic SUNA ultraviolet absorbance nitrate sensor from samples taken along Melita Creek at eight sites between November 6th, 2011 and January 8th, 2012. Because we used the SUNA device, we were able to see results instantly and pinpoint these high nitrate levels while still on-site. The results showed elevated nitrate levels as high as 16.25 mg/l. The source is still unknown. We would like to continue our research to gather more data over a longer period of time at the same site to pinpoint when these levels reach their peak.

Information from rods and cones influences color vision because all signals travel on the same neural pathways. We are studying the rod effects on hue for small foveal stimuli compared with those of large peripheral stimuli in order to understand the neural mechanisms of rod influence on small foveal stimuli. Using a CRT display, we measured the rod hue biases that shift the balance point of the four unique hues (red, green, blue, yellow) at low light levels for foveal stimuli of varying sizes: 0.5°, 1°, and 2° diameters, and compared them to results for large peripheral stimuli. We are assessing the reliability of rod hue biases across subjects. So far, we have data on three observers, and more in progress. The hypothesis that direct stimulation of adjacent rods and cones is needed to produce rod hue biases predicts that we would not find foveal effects because there are few rods in the fovea. Results so far vary among observers, both in the specific unique hues that show rod effects, and in the dependence of these effects on stimulus size. For one observer, all rod hue biases disappear for stimuli smaller than 2° diameter. For two other observers, some specific rod hue biases persist for the smaller sizes. In addition, the pattern of rod effects for specific unique hues does not match for foveal and peripheral stimuli. These results suggest that, at least for some observers, foveal rod hue biases are mediated by neural interactions acting laterally across the retina. Further testing will address alternative explanations based on differential eye movements and attempt to understand the basis for foveal-peripheral differences. These results will allow for greater understanding of the rod influences on the fovea and of neural mechanisms of color vision.

The Sarmiento formation in the Gran Barranca region of Argentina is comprised of eolian, fluvial and volcanic sediment formed between twenty and forty million years ago. Climate change, sea level variation and tectonics driving subsidence were all important factors in the deposition of the Sarmiento Formation and research on the paleoenvironments of the region includes study of eolian and fluvial processes, paleoclimate and the evolution of grasslands. The sediment of the 33.581 million year old Vera section of the Sarmiento Formation is the focus of this study. To better understand the environments of deposition of this section, grain size and magnetic susceptibility were analyzed for over fifty sediment samples. A particle size analyzer was used to provide grain size distributions for each sample, which were then used to look for loess signatures in the sediment. Loess (wind blown sediment) is predominantly composed of fine sand and silt sized particles, and its detection can be evidence of arid, windy climates. Ongoing sedimentary analysis has revealed a predominance of silt sized particles, indicating a loess signature. Magnetic susceptibility analysis is a process that identifies iron-bearing minerals in sediment. The amount of iron present in the Vera sediment can be an indication of chemical weathering in Gran Barranca during the Eocene. Extent of weathering can also indicate past climate conditions. The results of the grain size and magnetic susceptibility analysis for each individual sample will be related to stratigraphic height and age so that a history of climate and environmental change for the Sarmiento Formation can be created.

The secretion of signals or toxins is a vital aspect of bacterial communication with its environment. We recently found that type VI secretion systems (T6SSs) in Gram-negative bacteria mediate interbacterial interactions by translocating protein effectors into neighboring bacterial cells, providing a large fitness advantage. One protein exported by the T6SS is a type VI-exported (Tse) cell wall amidase that degrades peptidoglycan, and secretion of this effector, Tse1, results in target cell lysis. Bacteria can also self-intoxicate by T6S, potentially posing a problem for the survival of a given species. However, bacteria encode cognate immunity (Tsi) proteins that bind and inactivate their Tse partners. As we identify more T6 effectors, it is becoming clear that Tse–Tsi pairs are part of a widespread protein–protein recognition network underlying bacterial diversity and community structure. This study sheds light on how this network influences interbacterial interactions by uncovering the mechanism of Tsi1-dependent inhibition of Tse1 and defining the molecular determinants of this recognition. I have reconstituted the complex in vitro by using recombinant proteins to probe for direct interaction. Then, by mapping conserved residues onto the recently solved structure of Tse1, I have identified and mutationally analyzed candidate surface residues that may be involved in Tsi1 recognition. Further understanding the determinants of this interaction may allow us to predict which bacterial species are vulnerable to Tse1 or provide a template for the design of novel effector-immunity complexes that escape recognition in naturally occurring bacteria as an antibacterial strategy.

Ubiquitin is a protein modifier that is essential for many eukaryotic cellular processes. Attachment of ubiquitin to substrate proteins (ubiquitination) occurs in a three-step cascade that involves a ubiquitin activase, ubiquitin conjugase, and ubiquitin ligase; it is the ligase that targets substrate proteins. One challenge for the ubiquitin field is identification of substrate cohorts for ubiquitin ligases. Although ubiquitination only occurs naturally in eukaryotic organisms, we have previously reconstituted the ubiqutination cascade in E. coli. Isolation of the ubiquitin pathway within a prokaryotic cell, such as E. coli, allows for the investigation and modification of individual components of the pathway and the measurement of immediate effects of these changes upon the overall process of ubiquitination. This project, which consists of the construction of a split protein assay, aims to address the abovementioned challenge by building on our previous work reconstituting ubiquitination in E. coli. The assay uses two fragments of the protein dihydrofolate reductase (DHFR) to detect the ubiquitination of proteins in E. coli, outside of the natural eukaryotic environment of ubiquitin. All of the essential components of the ubiquitination pathway, including individual fragments of DHFR fused to ubiquitin and a substrate protein of interest, are transformed into the bacterial cell. The assay tests for the covalent attachment of ubiquitin to the substrate protein through growth on selective medium, which is possible only through the combination of the separated fragments of DHFR. This reporter system allows for experimentation regarding the interaction and selectivity of the ubiquitin ligase with the substrate protein of interest. Thus, a functional reporter system will allow for the streamlined analysis and determination of the substrate cohort for a given ubiquitin ligase. Changes to the components of the system may include using different ubiquitin ligases and substrate proteins.

Pedaliaceae (Sesame Family) are a small family of plants, about 14 genera with approximately 70 species that occur mainly in arid regions and deserts of the Old World, with their center of distribution in Southern Africa. Contained in Pedaliaceae are two widely known species: Sesamum indicum, which is cultivated and provides sesame seed and Harpagophytum procumbens, Devils Claw, an endangered species which is harvested wild and used for medicinal purposes. Evolutionary relationships (phylogeny) within the family are currently not very well understood. Previous classification systems have included the Martyniaceae, a small New World family, which occurs in similar environments and exhibits similar fruit morphology, with the Pedaliaceae but this inclusion of has since been questioned. In order to infer a phylogeny for the Pedaliaceae I am using the chloroplast loci ndhF and tnrL-tnrF which generally provide good resolution to determine the relationships between families and major lineages within a family of plants. Preliminary analyses based on these two loci indicate that the genus Sesamum is not monophyletic. To achieve resolution of the relationships of the species within Sesamum, I am sequencing two commonly used nuclear loci: ETS and ITS, the external and internal transcribed spacers of the nuclear ribosomal repeat, and one of the many loci in the pentatricopeptide repeat (PPR) which have only recently been developed for phylogenetic study in the Olmstead Lab. The goal of this project is to infer a phylogenetic tree of the Pedaliaceae on the species level, resolve their relationship to Martyniaceae and the genus Trapella, as well as the placement of these groups within the larger tree of the Lamiales.

Many important enzymatic reactions require the transport of electrons to function properly. This transport is commonly achieved by passing an electron to several different residues on the peptide chain which composes the enzyme. Tryptophan, a common amino acid, participates in this electron transfer by way of an oxidized radical tryptophan intermediate. We hypothesize that hydrogen bonding characteristics have significant influence on the electron transfer behavior of tryptophan. Understanding the effects and implications of hydrogen bonding would greatly affect how we engineer enzyme structure for reactions involving this type of mechanism. Using EPR (electron paramagnetic resonance) spectroscopy, we recently discovered that the strength and position of the hydrogen bond correlates directly to shifts in the g-tensor, a proportionality constant used to describe the resonance condition of the radical electron. Using computational chemistry software, we are gathering data to better understand how g-tensors change as the geometry of the hydrogen bond is altered. Our main goal is to determine trends which describe how changing specific structural features alters the corresponding g-tensor values of the radical tryptophan. We hope these trends will allow us to understand if and how hydrogen bonding is occurring at a radical tryptophan.

This study investigates the impact of success or failure of a university’s marquee sports programs on student academic success. I analyzed data from schools in four National Collegiate Athletics Association (NCAA) Division I athletic conferences each having both of the money-generating sports programs, football and men's basketball. I am interested in determining whether the success or failure of a school’s teams affects student performance, both among student athletes and among the general student body. Anecdotal evidence and some prior studies indicate that student performance can suffer when a school team does well, but this effect is short-term. This study looks at short-term as well as more long-term measures of academic success as measured by overall graduation rates for undergraduates and graduation measures used by the NCAA and the US federal government, to track student athlete academic success. I also consider associations with other covariates such as school size (number of enrolled undergraduate students), school location, public vs. private institutions, racial make-up of the school and regional location, on the afore mentioned relationships. I expect these relationships to be different for small schools than for large schools. My hypothesis is that student-athletes as a group have higher graduation rates than the general student population and in larger schools student-athletes are less affected by athletic results than the general student body.

Mitochondria are organelles vital to all cells in the body, generating energy and regulating metabolism, calcium signaling and apoptosis. These diverse functions are made possible partly through constant remodeling of mitochondria via fission and fusion. Neurons are especially vulnerable to mitochondrial defects, and this is true for mutations arising in mitochondrial fusion/fission proteins. Mitofusins (Mfn) are key proteins for mitochondrial fusion. Presently, we do not have clinically useful drugs to modulate fission and fusion in order to prevent neuronal damage due to disease and injury. In order to characterize how mitochondrial phenotype affects the metabolic rate in mammalian cells and disease models, we genetically engineered a chemically inducible system that allowed us to manipulate the mitochondrial fusion machineries. Specifically, I helped produce a ligand-induced heterodimerization system to initiate assembly and activation of fusion protein complexes by a specific chemical cue or ligand. Rapamycin, an antibiotic, complexes with immunophilin FKBP-12 (FKB) and binds to the FKB-rapamycin-binding domain (FRB) of the serine/threonine protein kinase mTORC1. I assisted in genetically engineering FKB and FRB onto the functional ends of the Mfn proteins. These Mfn proteins were expressed in mutant cells lacking all Mfn proteins. Since they lack fusion proteins their mitochondria are highly fragmented and we hypothesized that they could be rescued by inducing fusion with this inducible system. When we express the modified Mfn proteins containing FKB and FRB in cells, they will only dimerize and express fusion activity in the presence of rapamycin, which acts as a chemical ligand uniting the two modified forms of Mfn. We used a Seahorse analyzer to measure the oxygen consumption rate of FRB/FKB Mfn cells exposed to rapamycin for different periods of time. This system will help to identify new drugs that regulate mitochondrial dynamics in disease and injury.

In recent years, nanoscience has become a major focus: from technologies in solar cell coatings, to developments in biomolecular detection methods. Utilization of unique optical absorption properties of noble metals, such as gold or silver, opens the door for harnessing photons in new and innovative ways. For these reasons, great emphasis has been placed on the synthesis and characterization of nanostructures. The Pozzo Group has recently shown that structured gold clusters can be formed in solution by exploiting the hydrophobic and steric interactions in self-assembling nanoparticles. Hydrophilic polyethylene-glycol (PEG) chains control long-range steric interactions, while hydrophobic alkane-thiol chains induce clustering through short-range attraction. This simple method has the potential to be a cheap and viable option for nanoscale fabrication; starting from the molecular level and building up. This method of nanoclustering yields multi-particle aggregates in solution. Clusters of different geometries and sizes are formed based on the number of consistuent gold particles in each aggregate. It has been shown that the total amount of PEG adhered to the surface of the gold particle impacts the extent of clustering. At lower PEG concentrations, more diverse populations of nanoclusters are observed. In this project, size-exclusion chromatography (SEC) is being utilized for separating cluster populations. A cluster dispersion is pumped through a column that is packed with a porous stationary phase. By size-exclusion, the largest clusters exit the bottom of the column first, while the smaller clusters have a higher retention time as they navigate the pores of the matrix. The viability of SEC for controlled separation of cluster populations is being investigated on different systems, with the goal of isolating populations of similar aggregation types. Population analysis with SEC is simple and can be used to identify the fundamental parameters that lead to polydispersity in cluster size and shape.

Evolutionary biology studies how populations change over time. For evolution to occur, there must be genetic variation, ultimately from mutation. Any mutation in a given environment may have a positive, negative, or neutral effect on fitness. Evolving populations tend to increase in fitness. A metaphoric “fitness landscape” is useful for visualizing this, with genotypes linked by mutations and elevation being their fitness. Fitness “peaks” denote genotypes from which all mutations are deleterious (downhill). If the landscape is smooth (possessing only one peak) then populations will always converge there by natural selection. However, if the landscape is rugged (multi-peaked), populations might get stuck on a low-fitness peak. This population must cross the “valley” between peaks to reach the higher peak. We are studying how migration patterns between subpopulations of Escherichia coli influence adaptation. Structured populations only allowed migration between nearby subpopulations of bacteria, while unstructured migrations occurred between any of the 95 other subpopulations of bacteria. We found that structured populations reached a higher fitness than unstructured ones. My project is investigating the genetic mechanisms behind these results. Using Illumina technology, I have completed whole genome sequencing and targeted sequencing on these populations. I am using these results to determine the type and frequency of mutations acquired in structured vs. unstructured populations. We have two hypotheses explaining structure’s effect on adaptation: the Mutational Distance Hypothesis and the Diversity Hypothesis. The Mutational Distance Hypothesis predicts that there will be more mutations accumulated in the structured populations than the unstructured, whereas the Diversity Hypothesis predicts that structured populations will have greater genetic diversity than unstructured populations. This work will lead to a greater understanding of adaptation and may have medical implications concerning the understanding bacterial evolution.

Fatty acids are vital for proper cell function, serving as a source of energy, a structural component of the plasma membrane, and a signaling molecule. Imbalance of these fatty acids can change the homeostasis of the cell and can lead to major consequences, including cancer. We propose that lipid levels could be analyzed and serve as a diagnostic and preventative measure for human hepatocellular carcinoma (HCC). In our study, we use a hepatic-specific PTEN knockout mouse which recapitulates the progression of HCC. Phosphatase-and-tensin homologue (PTEN) is a tumor suppressor gene involved in cell cycle regulation and mutations have been observed in many types of cancers, including HCC. We collected plasma and liver tissue from 12 month old PTEN KO mice and proper controls to undergo quantitative lipid analysis. Human serum samples from cirrhotic patients with and without HCC underwent similar lipid analysis. This analysis was done for 4 lipid fractions (FFA (free fatty acids), PL (Phospholipids), TG (Triglycerides) and CE (Cholesterol esters) and determined the relative abundance of nearly 30 lipids. In addition, we quantified the abundance of several genes important in lipid metabolism using q-RT PCR. We found several lipids that showed strong correlation to tumor development. Further, the abundance of the genes involved in metabolism of these specific lipids was altered in the PTEN KO mice and showed significant correlation to both lipid levels and tumor development. Similar results were found through analysis of human samples of HCC compared to the cirrhotic controls. This infers that analyzing lipid levels and related gene expression may serve as a potential method for diagnosis and, eventually, prevention of human HCC.

Autism Spectrum Disorders (ASD) are characterized by atypical social development, decreased verbal and non-verbal communication, and repetitive behaviors. Infants with siblings who have been diagnosed with ASD are considered at high-risk for also developing ASD. Previous findings suggest that high-risk infants show deficits in attention regulation, which may indicate future social and communication impairments. To evaluate visual attention performance in this population, we studied high-risk infants at 6 and 12 month time points. Participants were administered the “gap overlap” task, in which they were seated in front of a screen and introduced to three conditions, each of which showed a central visual stimulus (sun) and a peripheral visual target (balloon): 1) baseline, in which the stimulus disappeared as the target appeared, 2) gap, in which the stimulus disappeared before the target appeared, 3) overlap, during where the stimulus remained on the screen when the target appeared. We measured the latency for the infant to disengage from the stimulus and saccade toward the target. By studying participants at two time points, we were able to measure changes in visual attention performance over time. Data analysis is ongoing. Based on previous findings, we expect those at high-risk for ASD to exhibit a significant difference in latency between the overlap and baseline conditions, thus exhibiting a reduced efficiency in disengagement. We also expect to see increased variation in overlap and baseline latency at 12 months compared to data collected at 6 months. The results of this study could aid in early identification of ASD, which could lead to early diagnosis and intervention.

Lithium batteries have been used in electronics and increasingly in hybrid and all electrical vehicles due to their lightweight and improved electrochemical performance. However, there are still several limitations with these batteries including slow charging rate, incomplete discharge and cyclic degradation in performance. Most of these problems have been related to the performance of the cathode. This project is focused on optimizing the microstructure of the porous cathode. We are investigating LiMnPO₄, which has a high theoretical capacity (171 mAh g-1) and better electrochemical stability compared to other lithium-based metal oxide cathode materials. Unfortunately LiMnPO₄ has a low electrical conductivity, which is improved by mixing it with carbon.  LiMnPO₄ powder is synthesized using the polyol process. This produces extremely fine high surface area particles. By using directional freeze casting with different weight percentages of solids and freezing rates, it is possible to create aligned pores throughout the structure, which have the potential to increase the energy density and reduce the transport distances. We are making cathodes with a broad range of microstructures and investigating their electrochemical performance.  Another process to enhance the performance is through partial sintering to make cathodes with uniform porous microstructures. By controlling the sintering temperature between 500 º-700º C, cathodes with a range of uniform isotropic porosity are being made. Structural and physical characterization will be conducted for both types of cathodes to evaluate the microstructure. The electrochemical performance of the two types of cathodes at different densities will be compared in order to optimize the microstructure.

Highly soluble perchlorate and nitrate salts have been found to accumulate on Mars, which is a cold planet with no liquid water cycling at the surface. On Earth, the only places where nitrate and perchlorate salts are known to accumulate are the Atacama and Mojave deserts, two of the driest places on Earth. By characterizing the mobility of these salts in Earth's soil, we can better understand what the vertical distribution of these salts can tell us about past rainfall patterns on Earth and, by extension, past aqueous processes that may have affected Mars. We created and calibrated Ion-Selective Electrodes (ISEs) to measure concentrations of salts in the soil. ISE and Ion Chromatography measurements will be compared to determine the reliability of the ISEs. We are running controlled laboratory experiments where we simulate rainfall and track the real time moisture content of soils. Our results so far suggest a higher abundance of these salts in drier areas, and varying levels of these salts at different depths, which are assumed due to varying amounts of precipitation. In the future, we hope to simulate diurnal cycles in temperature and relative humidity under terrestrial and Mars-like conditions.

Effective social communication requires the ability to interpret social cues, communicate internal thoughts, and is necessary for participation in appropriate social exchanges and emotional interactions (Constantino, 2003). Individuals with Autism Spectrum Disorder (ASD) are often impaired in this domain. The Social Responsiveness Scale (SRS) is one measure that can be used to examine social communication skills (Constantino, 2003). This questionnaire allows parent or teacher to report about the child. This is ideal because researchers can acquire perspectives about the child’s social communication in different contexts. However, research has yielded conflicting data regarding parent/teacher agreement in reporting communication abilities. Some research suggests there is a disparity in parent/teacher reporting, especially when the child suffers from a developmental disorder like ASD (Tassé and Lecavalier, 2000; Murray, Ruble, Willis, and Molloy, 2009). The Pragmatic Rating Scale - Modified (PRS-M) (Russer et al., 2007) circumvents the issue of reporting bias, as it provides an experimental measure of an individual’s pragmatic (social) language skills. Participants are rated by unbiased coders on a number of pragmatic language skills including eye contact, emotional language usage, and ability to stay on topic. In this study individuals with and without ASD between the ages of 7 and 18 completed a short interview which was coded using the PRS-M. We will compare scores on PRS-M with parent and teacher reports of social communication on the SRS. We expect the teacher report SRS will more closely predict performance on the PRS-M than parent report due to parental bias. Identifying differences in reporting can inform researchers about the accuracy of questionnaire data being collected about social communication.

Organic photovoltaics (OPVs) are a promising low-cost option in developing renewable energies. OPVs are solar cells made from organic semiconductors instead of the more traditionally used inorganic semiconductors such as silicon. OPVs have several advantages including: low cost, ease of processing, physical flexibility, and highly tunable properties. Therefore, if the efficiency of OPVs can be increased, they could become a major, inexpensive renewable energy source. Electron-accepting materials used in OPVs have traditionally been fullerene-based due to their high electron mobility. However, fullerenes contribute little to light harvesting in an OPV as they have negligible absorption in the solar spectrum. Thus, our goal was to develop new electron-accepting materials for OPVs that absorb significantly in the solar spectrum as a means to increase light harvesting and therefore OPV efficiency. A series of novel oligomers with an oligothiophene-naphthalene diimide (NDI) structure was synthesized. All oligomers exhibited absorption in the visible region with band gaps ranging from 1.39 eV to 2.06 eV, and could therefore contribute to light harvesting in an OPV. Solution-processed solar cells using the new oligomers as the electron-acceptors showed power conversion efficiencies up to 1.5%. Overall, these new materials exhibited that non-fullerenes can function as the electron-accepting material in OPVs while contributing to light harvesting. This approach therefore shows promise for increasing OPV efficiency to make OPVs a viable, cost-effective renewable energy source.

Sediment was deposited in the Gran Barranca region of Argentina from 55.8-33.9 millions of years ago (middle Eocene to the lower Miocene). A group of researchers from UW is studying this sediment and the fossils it contains to better understand the paleoclimate and paleocology of the area at this time. Our contribution to this research focuses on the origin of sediments from the Gran Barrancan Member Sarmiento Formation, in particular if they were wind transported and deposited (eolian). Windblown sediments are known as loess. Loess sediment has variable amounts of clay, silt and sand particles, but contains more than 50 percent silt. The collected sedimentary samples were analyzed for grain size using a Particle Size Analyzer (PSA) and for magnetic susceptibility using a magnetic susceptometer. The majority of the samples had greater than 50 percent silt, which is characteristic of loess sediment. Testing a sample’s magnetic susceptibility is important in determining the amount of iron bearing particles. Loess sediment is mostly silt and consists of mainly quartz and clay minerals so the amount of iron bearing particles in a sample should be miniscule. When comparing percent silt to magnetic susceptibility for each member, there is a small but noticeable pattern; the younger the member the more iron bearing particles. We suggest that the sediment records changes in climate and humidity. The increase in humidity would contribute to the dissociation of the iron particles in the sediment, which as a result, lowers susceptibility. The high percent silt coupled with the low magnetic susceptibility suggests the samples are windblown loess sediment. Loess sediment indicates dry and windy climate conditions during time of deposition.

Model membranes are important tools for investigating physical properties of lipid bilayers. Unfortunately, current techniques for producing giant unilamellar vesicles (GUVs) with biologically and physically relevant properties (namely: inclusion of charged lipids, encapsulation of high salt buffer, and compositional asymmetry between the inner and outer leaflets) are difficult, unreliable, and/or low throughput. We examine a method called cDICE, developed by Abkarian et al., that has the potential to address all of these issues. Our results here for charged lipids in high salt buffers are promising, whereas asymmetry has proven difficult to measure.

 The ability to resist nonspecific protein adsorption, low fouling, is an essential surface property necessary for medical implants and biosensors. Mixed-charge surfaces with net neutral uniformly distributed charged amino acid residues have been shown experimentally to highly resistant to nonspecific protein adsorption, and thus have become a new field for biomaterial design. These mixed-charge surfaces have analogues in nature: The interior surfaces, or cavities, of molecular chaperone protein complexes. In addition to assisting hundreds of proteins folding through nonspecific interaction, the cavities usually show transition between a more charged residues state when assisting protein folding and a less charged residues state when actively unfolding proteins. Thus if these interior cavities are well studied, they can be mimicked to create new surface designs. In this study, GroEL-GroES, one of the most well characterized chaperon complexes, is used along with 528 substrate proteins found in Escherichia coli (E.coli). We hypothesized that the interior surface of GroEL-GroES will interact nonspecifically and assist the substrate proteins in folding by lowering their folding free energy. In order to quantitatively calculate these values, we have extended entropic models by introducing a new enthalpy term derived from the knowledge of the residues on the cavity surface. The model not only includes entropic confinement effects but also accounts for energetic interactions between residues found on GroEL-GroES and the substrate protein. Applied to the substrate proteins, our model presents results that match the experimentally observed changes in folding free energies. Furthermore, the optimization of the surface residues distribution of the cavity suggested by this model shows which residues contribute most to stabilized folding. This study provides a better understanding of GroEL-GroES’s ability to nonspecifically assist protein folding. Finally, it also gives insight into the mixed-charge surface design projects where low fouling materials are used as medical devices or sensors.

Chemostats are a continuous culture system in which cells are grown in a tightly controlled, chemically constant environment where culture density is constrained by limiting specific nutrients. Unlike batch cultures, the selective pressure imposed in a chemostat is constant. This has made them a desirable tool for evolution and competition experiments. Traditionally chemostat experiments with S. cerevisiae have been constrained due to the limited number of cultures that can be run at once. In order to solve this problem our team is working with a new culturing system that allows 64 chemostats to be run simultaneously. In our experiment we evolved 32 biological replicates of haploid MATa yeast cells under constant sulfur-limitation for 250 generations. We are now using a variety of techniques including whole genome sequencing of evolved populations to characterize mutations that have been selected for during the course of these evolutions. Changes in the genome can be correlated to changes in relative fitness, which we assayed through competition with a GFP (a green fluorescent protein that exhibits bright green fluorescence when exposed to ultraviolet blue light) expressing ancestral strain every 50 generations. Ultimately it is our hope that higher replicate number will better reveal the spectrum of genes important for adaptive growth in a sulfur-limited environment. Furthermore we would like to use these methods to understand what genes are important in a wide variety of nutrient limited environments.

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

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. Certain lipids found in mangroves have the potential to be excellent biomarkers (i.e. molecular fossils) for paleoclimate reconstructions. These reconstructions based on sediment cores are important in determining past sea level changes and local climactic conditions. Although certain sterols and triterpenols can be good biomarkers of mangroves, it is often unclear what function they serve. In this study, I investigated how salinity of surrounding water influences lipid distributions in different species of mangroves. To achieve these goals, I created an artificial tidal cycle in four tubs of differing salinities. Within each tub I cultivated four species of mangrove propagules (Rhizophora apiculata, Rhizophora mangle, Laguncularia racemosa, and Avicennia germinans). The mangroves were grown to a harvest size of ten leaves and then processed to analyze lipid distributions within leaves and stems of each plant via gas chromatography techniques. These mangroves cope with living in saline conditions with different mechanisms (i.e. secreting, excluding). By comparing the differences of lipid distributions of mangroves with different salt management strategies, I will determine if there is a correlation between these two factors.

Embryonic diapause or delayed implantation is an occurrence that effectively lengthens the gestation period of the embryo and allows offspring to be born into optimal conditions. In response to adverse environmental conditions, the mouse blastocyst enters a reversible state of cell quiescence, or extremely slowed development, resulting in delayed implantation. Our aim is to uncover the mechanisms that occur in diapause that allow stem cells to endure stressful environments. Theoretically we could generate “super” stem cells that retain pluripotency for longer periods and withstand harsh in vitro treatments. Gene expression profiling of the stem cell compartment of diapause embryos showed that the transcription factor Runx1 is upregulated and might be required to initiate diapause. Runx1 thus far has shown to induce a state of cell quiescence in haematopoietic stem cells (HSCs) and is responsible for haematopoiesis, the formation of blood cellular components, in early development1. Runx1 is also known as acute myeloid leukemia 1 protein (AML1) because mutations in it are the most common aberrations found in acute leukemia2. Additionally, we observed up-regulation of RUNX1 protein expression level in the primitive endoderm (PE) layer of the diapause embryos. We hypothesize that the increased expression of RUNX1 is required to maintain pluripotency of the stem cell compartments in the embryos. In vivo mouse models of Runx1 wild-type (+/+), heterozygous (+/-), and deficient (-/-) diapause embryos will be examined using confocal microscopy with antibodies against RUNX1, pluripotency marker (OCT4), and PE marker (GATA4), and the resulting morphologies of the Runx1 embryos will also be characterized.

Disparities between males and females is problematic in India and this is apparent in the countries’ gender composition. India’s population has increased exponentially over the past century, but during that time India’s sex ratio (defined as the number of females divided by the number of males) has been abnormally low. The natural sex ratio at birth is approximately .95, but during the last century India’s sex ratio has dropped from .96 to .91. Scholars suggest that the abnormal sex ratios are due to social and cultural factors. My research utilizes data from 2001 and 2011 Indian Censuses to examine the relationship between the sex ratios of young children (ages 0 – 6) in the 35 states of India and social/cultural factors in those states, such as female literacy rates, female labor force participation and religious practices that preference males. My data runs statistical analyses and I hope to show a positive relationship between the sex ratios and the social factors. My study shows the extent to which cultural and social conditions that lead to male preference in India may have produced the low sex ratios observed during the past century. This disparity is important to understand because it is a human rights issue and I hope my research can help us better understand the cultural and social aspects in order to obtain gender equality in India.

Intramuscular injection of Botulinum toxin(BTX) is a common approach to reduce muscular mass for cosmetic effect and to relieve symptoms of muscle spasm and pain through the mechanism of paralysing nerve-muscle junctions of the target muscle. However, the consequences of this neuromuscular blockage in masticatory muscles have not been evaluated. The goal of my research is to investigate the short- and long-term effect of the use of BTX on masseter muscles by evaluating evoked electromyography (EMG) in a rabbit model. Of 22 rabbits, 10 were injected once with 10 units of BTX in one masseter and examined 4 and 12 weeks after the injection (5 each); 7 were injected 3 times at 0, 12 and 24 weeks and examined 36 weeks after the first injection; and 5 were intact animals. My work is to assess masseter EMG signals evoked by electric stimulations of ipsilateral masseteric nerve, and to evaluate the regional effects of neuromuscular blockage based on a wire-electrode array placed on the masseter across various time points with single or multiple BTX injections. I use both time- and frequency-domain methods to analyze these signals and to compare their amplitude, timing, and frequency between injected and non-injected sides, single and multiple injections, and injected and intact animals. The study design also allows me to elucidate the recovery effects over time. The preliminary results indicate that a single BTX application significantly affected the responses of injected muscles to nerve stimulations, presented as an ~80% reduction in EMG amplitude at 4 weeks, and ~65% reduction at 12 weeks. At 36 weeks, the sides differed little if at all, suggesting partial recovery had occurred even though multiple injections were applied. My work is continuing to find out whether the masseter’s neural transduction (timing) and firing (frequency) are affected by BTX application.

Complexity of today’s financial markets and its services demand high degree of financial knowledge than ever before from individuals in order to make prudent financial decision. Early studies have shown that financial illiteracy is widespread and that those who are financially illiterate display both poor borrowing and saving behavior. Using household data from HRS (Health and Retirement Study), I test the hypothesis that financial literacy is a strong determinant of accumulation of wealth. That is, those who possess greater financial knowledge accumulate more wealth than those who have low or no financial knowledge. Moreover, I extend the analysis in an attempt to answer what drives individuals to acquire financial knowledge. My first hypothesis is that poor living circumstances at young age make individuals become more aware of the importance of finance: hence, it is a driver of financial knowledge. My second hypothesis is that past experiences (loss of portfolio value from recession and poor health) play a role. Data on several components of wealth, financial literacy, and past information were compiled and will be used to run regression to answer underlying questions. Finally, I explain what it means to be financially literate. The purpose of this analysis is to stress the importance of being financially literate and that finance class should be part of school’s core curriculum. This will better prepare our descendents for far more complex financial markets that lie ahead.

Acute Myeloid Leukemia (AML) is a malignancy of blood cells due to the proliferation of undifferentiated cells leading to hematopoietic insufficiency. It is known that genetic changes are causally associated with AML. FLT3 gene (Fms-Like Tyrosine kinase 3) is essential in regulating normal hematopoiesis, and mutations in these genes have been shown to be common in AML and lead to autonomous cell growth. In addition to mutations, our lab has identified novel transcript variants in FLT3 gene that may have biologic and clinical significance. These novel variants are a result of alternative splicing of exons, a regulatory developmental process that can result in production of different proteins from the same gene. My project is to study these novel FLT3 variants via molecular techniques and to determine the prevalence of these transcript variants from a cohort of patients with AML. I tested for the presence of FLT3 transcript variants in AML patient specimens relative to normal bone marrow. I analyzed my amplified products with a software called Gene Mapper, which identifies variations in size and expression rate of gene transcripts. In the normal bone marrow control, only one (wild type) product was identified. However, in the leukemic specimens, 4 different transcript variants were identified at different frequencies. The most intriguing transcript was missing exons 19 and 20. This would cause the tyrosine kinase receptor to have a truncation of the functional, kinase domain of the receptor. This variant would lead to the translation of a protein product that is devoid of kinase activity. I plan to correlate our data with clinical outcome to determine the clinical significance of these transcript variants. If associated with poor outcome, patients can get placed into a higher risk category, where they can be treated with more intensive chemotherapy followed by bone marrow transplantation.

Stroke is one of the top causes of death in the United States; however, due to the apoptotic death of neuronal cells from lack of oxygenated blood, prognosis and recovery is not always favorable even if the event is survived. Our lab focuses on finding agents that are already clinically relevant in other areas, but might also show neuroprotective qualities in cerebral ischemic events. The compounds we have focused on in this study are progesterone and its metabolite allopregnanolone. Previous studies have shown that both compounds have neuroprotective qualities in vitro and that progesterone administration in vivo suppresses inflammatory response and subsequent edema. Our hypothesis is that both progesterone and allopregnanolone would show neuroprotective, as well as neurogenic, qualities in vivo. This is tested through a mouse stroke model using progesterone receptor knockout mice and wild type mice, both being subjected to a middle cerebral artery occlusion. Different groups are treated with different compounds or control. The brains are then perfused, fixed, and sliced to be put through immunohistochemistry, where cells are identified by certain neurogenic markers (bromodeoxyuridine incorporation and doublecortin labeling). Slides are finally analyzed through confocal microscopy to look for these markers in certain areas such as the hippocampus, striatum, and lateral cortex. Finally, positive cells are counted in both the ipsilateral (stroked) and contralateral hemispheres. We anticipate an increase in the number of bromodeoxyuridine and doublecortin labeled cells in mice subjected to progesterone and allopregnanolone, and we also expect this to be more dramatic in the ipsilateral side due to new cell migration to the injury site. Hopefully, these results will allow for a greater push in implementing progesterone and allopregnanolone in clinical use for the recovery of ischemic stroke.

Sepsis is a complex, incompletely understood and often fatal disorder that is one of the most common causes of death in children worldwide. The overlapping pro- and anti-inflammatory responses, and resulting complications contribute to the complexity of sepsis and have made it difficult to find biomarkers and therapeutics targets for this disorder. Mast cells and basophils are well-known for being key players in allergic responses. However, it is less known whether these cells can influence the outcome of bacterial infections. We hypothesize that mast cells and/or basophils can limit the severity of the inflammatory response against bacterial infections to preven sepsis. We found that mast cell and basophil deficient mice (Cpa3-Cre; Mcl-1^flox/flox mice) exhibit signs of morbidity (reduced body temperature), kidney dysfunction (high blood urea nitrogen levels), and are unable to govern the inflammatory response induced by cecal ligation and puncture (CLP), a well-established model of sepsis. The inability to regulate the inflammatory response induced by CLP is shown by the increased number of neutrophils in the peritoneal cavity of the mast cell and basophil deficient mice. Our initial results indicate that Cpa3-Cre; Mcl-1^flox/flox mice that have been previously engrafted with mast cells show similar signs of morbidity, kidney dysfunction, and neutrophil numbers in the peritoneal cavity than non-engrafted mice. These results could indicate that basophils are more responsible than mast cells for the down-regulation of inflammation and reduced morbidity after CLP. Considering these new results, the next step will be to obtain basophil deficient mice to see the response after CLP and what effect basophils might have on the anti-inflammatory response during sepsis. 

Despite the numerous studies of the bacteria E. Coli, the basic motion of macromolecules confined to the cellular cytoplasm, such as mRNA, remains uncharacterized. I employ a technique called fluorescent correlation microscopy, which consists of binding synthesized mRNA with fluorescent proteins, imaging the cell throughout its lifetime, and analyzing the images using statistical autocorrelation. This technique allows me to determine the diffusion constant (D) as a function of cellular location while bypassing the error caused by higher order analysis. We predict that D is primarily dependent on the molecular crowding at its position, and there exists a tendency for mRNA to gather in the less crowded spaces in the cell, e.g. at the poles.

Weather prediction has become an integral tool in our society, giving us the ability to prepare for storms and route aircraft and ships around dangerous weather. Achieving a better understanding of lightning, its causes, and the patterns involved in it will allow further improvement of weather modeling as well as better interpretation of existing data. We aim to better understand the electrical evolution of these storms and the local control of stroke power by using the World Wide Lightning Location Network (WWLLN) to track oceanic thunderstorms in a variety of environments while examining the radiated power of the lightning. The analysis of WWLLN data using MATLAB will allow us to evaluate trends as well as the factors affecting those trends, and the development of MATLAB tools and techniques will allow said evaluation to proceed quickly and smoothly. The goal of this project was to develop the tools required in order to lay the groundwork for future study into the way oceanic thunderstorms change and evolve.

Gastrulation is a crucial step in embryogenesis, creating differentiation between ectoderm, mesoderm, and endoderm, as well as forming necessary organs. Transmembrane and juxtamembrane proteins located at the adherens junction, such as cadherins and p120 catenin, work together to either promote cell motility or adhesion. Using Danio rerio embryos as a model organism, we hypothesized that when p120 catenin is at the plasma membrane it binds and stabilizes the cadherins, causing cell clustering and increased adhesion. When p120 catenin is in the cytoplasm it activates Rac1 and Cdc42 (two members of the Rho GTPase family), which causes cell motility. By using a “depletion-rescue” experimental approach, p120 catenin levels are depleted by injecting a splice-morpholino, then “rescued” by coinjecting wild-type Cdc42 or Rac1. This indicates that p120 catenin in healthy embryos works to activate Cdc42 and Rac1 during gastrulation, resulting in cellular motility. When dominant-negative and constitutively-active mutants of Cdc42 or Rac1 are injected in combination with morpholino, the embryos do not “rescue” well, if at all. We postulate that wild type GTPases “rescue” well because the can receive a signal and activate migration directionally while the constitutively-active GTPases activate migration in all directions. These studies on the regulation of cell motility can help to elucidate larger signaling pathways, leading to additional effects on cell survival, growth, and invasiveness, all of which may be caused by the upstream p120 catenin.

According to the 2011 Urban Mobility Report, roadway congestion cost a total of $101 billion dollars and a total delay of 4.8 billion hours in the US in 2010, with approximately 60% of the congestion occurring on freeways. Given the severity and economic costs of freeway congestion, strategies to mitigate congestion based on real-time data and cutting edge technologies have obtained broad attention. Integrated Corridor Management (ICM) is an emerging management strategy in this category. ICM aims to understand how non-recurrent congestion causes, such as incidents, affect both freeway and nearby arterial corridors, and how network-wide congestion could be mitigated by diverting traffic to nearby arterials with extra capacity. This study investigates the effectiveness of the ICM technology and possible impacts on local streets for the Seattle Department of Transportation. A microscopic simulation model was built in VISSIM (a software often utilized to model the study area and traffic behavior) to conduct what-if analyses under the ICM strategy. The model studies the SODO area network, which includes northbound I-5 and the nearby major parallel arterials. To simulate practical and reliable results, the model first needs to be calibrated to ensure the model output can replicate observed field data. The sensitivity analysis between different driving behavior parameters in VISSIM, such as headway time, standstill distance, and maximum deceleration for lane changing, and the modeled vehicle throughput was performed during the calibration process. Results of this research can be useful by providing logical rationale for how driving behavior parameters can be adjusted to achieve desired volume results. This specific calibrated model serves as the stepping-stone for future research in the ICM project, where dynamic routing is implemented to investigate how traffic is diverged during accidents within the study network.

Children with Autistic Spectrum Disorders (ASD) frequently suffer from severe sleep difficulties of unknown origins. Sleep irregularities have been noticed as early as infancy and may serve as an early indication of increased risk for autism. Additional studies indicate that sleep difficulties in children with an intellectual disability can be a source of stress for families, particularly those with a child with ASD. Infant sleep problems can have an effect on parental mental health and consequently have strong correlations to postnatal depression. The infant sleep and maternal depression duality is important, not only because of its high prevalence, but also because of the potential to lead to further psychological distress for the primary care provider. This study investigates the relationship between infant sleep patterns and parental postnatal depression at 6 and 12 months. Participants were primary caregivers of infants at low and high risk (infants with siblings diagnosed with ASD) for autism. At both time points, primary caregivers reported their infant’s sleep patterns using the Sleep and Settle Questionnaire, and their own psychological symptoms on the Brief Symptom Inventory (BSI), which assesses depression and psychological distress. Based on previous findings, we hypothesize that infants at high risk for autism compared to those at low risk would have more sleep disruption, and would be related to a higher prevalence of self-assessed depression in their primary care givers/ parents (Quine, 1991). We also hypothesize that sleep disruptions and parental depression will increase with infant age. If these correlations are found, this information could expand understanding of how infant sleep and parental depression relate to early markers for autism, as well as inform resources to alleviate parent stress due to irregularities in infant sleep habits.

The mechanism to direct auditory attention consciously is not well understood. For hearing impaired people, it is very hard to direct attention efficiently between conversations with background noise. My project investigated the differences between maintaining and switching attention prompted by visual cues. In the behavioral task, two streams were presented simultaneously, one with high pitch and the other, low. Each stream consisted two triplets of spoken letters and the two triplets were separated by a silent gap that varied in duration. In the beginning of each trial, subjects were prompted by two spoken letters which stream (high or low) to pay attention to initially. Simultaneously, a visual cue directed subjects to either stay or switch between two streams during the silent gap period. Subjects were asked to respond when they heard the second ‘E’ from one of two streams that they attended to as quickly and accurately as possible. Preliminary results suggest that subjects needed more time to respond when they had to switch between streams. As expected, there were no differences between subjects attending to the high or low pitch stream. We also hypothesized that the shorter the gap period, the longer the response time will be—I hope to test this hypothesis through more in-depth data analysis. The result from this project will be analyzed together with neural data obtained using magnetoencephalography where subjects will be performing a similar task. The findings of this project will provide insight into the underlying mechanism of switching of auditory attention—a task that hearing impaired people find difficult to perform in a noisy environment, even with the help of hearing aids or other augmentative devices.

In this study, chitosan, a biocompatible, biodegradable, and nontoxic polymer obtained from crab shells, was used to produce 3D scaffolds which closely resemble the mechanical and physical properties of human bone tissue. One of the critical stages in tissue engineering for successful regeneration is to design a scaffold that mimics the architecture of actual human tissue. While chitosan has been acknowledged for its potential to be used in human tissue engineering, its weak mechanical strength restrained chitosan usage in bone tissue engineering. In order to cope with the drawbacks, mechanical properties of 3D chitosan scaffolds were examined in relation to different chitosan concentration (4, 6, 8, 12 wt%). Compression test and tensile test were done on each scaffold to measure the mechanical properties and study the relationship between increasing chitosan concentration and mechanical strengths. Then, MG-63 osteoblasts were seeded on each scaffold to examine attachment and proliferation of the cells. Immunoblotting will be performed to detect the levels of osteocalcin expression on walls of the scaffolds, and Scanning Electron Microscope imaging will be used to assess the proliferation pattern of MG-63. Upon completion of the study, we predict to observe direct relations between the concentration of chitosan and mechanical properties of the scaffolds.

The present cross-cultural study was conducted among college students in the United States who were recruited through the social media website, Facebook, and directed to the online survey website, Survey Monkey. The purpose of the study was to examine the relationship between perfectionism and perceived external pressure for academic success among Korean international and European-descent American college students. Hypotheses were: 1) external pressure for academic success is positively correlated with perfectionism for both Korean international and Caucasian-American participants, 2) Korean students are more collectivistic than European-American students, 3) Korean students perceived a higher level of external pressure for academic success, especially from their parents, than European-American students and 4) Korean students’ level of perfectionism is higher than that of European-descent American college students. Forty-three students (20 European-American and 23 Korean students) responded to the survey. Although the study’s findings did not fully support all four hypotheses, there was a significant positive relationship between the level of perceived external pressure and the level of perfectionism among Korean international and European-descent American college students combined. The major implication of the results is that external pressure for academic success is an important aspect of the development of perfectionism regardless of culture. Future research with different cultures will be necessary to test the generality of the result.

Polymer-derived SiC and Si₃N₄ ceramics exhibit excellent high temperature properties and thermal shock resistance. Using polymeric precursors is attractive from a processing point of view since a wide variety of components can be produced. Finally, this approach allows the composition to be tailored at the molecular level. In this poster, we present our results on the use of this approach to make ceramics for two specific applications. Volumetric thermal absorbers are an integral component of the emerging field solar thermal energy conversion. The goal of the research is to work on developing the most efficient material for use as a volumetric thermal absorber. The most efficient absorbers typically have high permeability, high cell density, high porosity, good radial heat transport, and high absorption. Materials typically used are advanced fiber mesh cellular ceramics, SiC catalysts, and SiC foams. We are exploring the use of Si-based polymers (e.g. siloxanes) to make SiOC foams and investigating their thermal and optical properties for this application. The second project is on the processing and properties of Si₃N₄ – SiC composites for high temperature applications. In our project we are starting with polycarbosilane (SMP-10) which is a precursor for SiC. By heat treating it in ammonia, we are able to molecularly incorporate nitrogen. By controlling the heat treatment temperature and atmosphere we are able to produce a precursor that can make a wide spectrum of composites in the Si₃N₄ – SiC systems. Results on the effect of heat treatment temperature and atmosphere on the composition of the resultant composites will be presented.

Marine bacteria carry out nutrient transformations that maintain the chemistry of seawater. Most marine bacteria are uncultured and little is known about their specific roles in marine biogeochemical cycles. We identified several cultures from the beta-proteobacterial OM43 and gamma proteobacterial sulfur oxidizer (GSO) clades in a culturing experiment from the North Pacific. Members of the OM43 clade use single carbon compounds produced by phytoplankton, suggesting that they contribute to carbon cycling in surface waters. Members of the GSO clade use energy from sulfur oxidation to assimilate organic and inorganic carbon, suggesting that they contribute to carbon and sulfur cycling throughout the water column. We selected four OM43 and three GSO cultures to establish a culture collection. Several OM43 and GSO cultures were revived from freezer stocks and purified. Their identity was confirmed by 16S rRNA gene analyses and they were added to the UW marine bacterial culture collection. OM43 and GSO isolates obtained in this study will be used to further characterize the roles of these important groups of bacteria in marine carbon and sulfur cycles.

Stellar flares are the explosive release of energy caused by the reconnection of magnetic fields on stars. Flares release large amounts of UV and X-ray radiation, and may affect the possibility of life on exoplanets, planets orbiting stars other than our own Sun. A star's mass and age greatly affect the frequency, duration, and energy of flares. Therefore, it is important to understand these aspects for a variety of masses and ages. The age of a star is related to the rate of its rotation as well as the rate at which it flares; older stars spin much more slowly and also flare less frequently than younger stars. M dwarfs, stars less than half the mass of the Sun, are commonly used in stellar flare research because they make up the majority of stars in the Milky Way galaxy. To conduct our research, we used two months of data from the NASA Kepler spacecraft to study the light curves of one young and three old M dwarfs. We were able to identify flares in these light curves and measured their durations and energies. We found that the vast majority of flares on all four stars have a short rise time and a long decay time. We also found that flares with long durations have larger total energies, and that older stars have fewer large energy flares compared to younger stars. Through using the light curves, larger, more prominent flares were easily detectable in comparison to smaller flares. Further research would concentrate on more accurate ways toward detecting such small flares.

The structure and assembly of a protein determines its function and role in a biological system.  By attaching a pair of spin labels to a protein, it is possible to measure the distance between the two spin labels using double electron-electron resonance spectroscopy (DEER).  A spin label is an organic molecule with an unpaired electron.  The spin label concentration is measured using an electron paramagnetic resonance (EPR) spectrometer.  There is a positive linear relationship between the amplitude of a spectra and the concentration of spin labels.  The goal of this experiment is to develop a protocol that will accurately and reproducibly measure spin label concentration in a sample.  This is achieved by obtaining spectra for 10, 20, 50, 100, and 200 uM of TEMPO spin labels so we can determine a standard calibration curve.  By obtaining more spectra, we will be able to minimize the discrepancies of the amplitude based on the calibration curve for a given concentration.  Using the calibration curve, the number of pairs of spin labels that are attached to a protein in a given protein sample can be determined using DEER.  Establishing this protocol is important because it will allow us to monitor the labeling efficiency which is crucial for the distance measurements.

The ability of the semiconductor FeS₂, or iron pyrite, to absorb sunlight makes it a cheap and abundant potential material for use in solar cells. Current photovoltaic studies using nanocrystalline pyrite rely on the synthesis of small, uniform crystals. However, pyrite naturally takes different crystal shapes depending on the conditions of its formation. Even the same shapes can have different surface chemistry, which directly impacts crystal growth direction. The mechanisms behind pyrite synthesis are not fully understood and are difficult to discern out of the complexity of real reaction mixtures. Density functional theory (DFT), a method for simplifying and calculating the quantum mechanics behind a physical system, allows for the numerical approximation of pyrite’s material properties. Our group performed DFT calculations of two common pyrite surfaces using the supercell approach. Slabs of pyrite separated by artificial vacuums were allowed to come to energy minimums. We hypothesized that the energetic and electronic properties of real pyrite surfaces would match those of the DFT-optimized supercells. Preliminary results agreed with published experimental data. After ensuring that our computations could reproduce physical properties, we put small molecules that could be found in reaction mixtures into contact with the lowest-energy pyrite surface and optimized using the same methods. The most-favorable interaction sites between pyrite and the reactants needed to make it are key components to the mechanisms of pyrite growth. Once these mechanisms are known, synthesis conditions can be controlled to produce only crystals fit for use in photovoltaic cells.

MRI is by far the most sensitive technique for screening high-risk women and assessing the extent of breast cancer. However, dynamic contrast-enhanced imaging (DCE-MRI), the standard breast MRI method, produces many false positives. As the American Cancer Society now recommends annual MRI screening for high-risk woman, estimated to affect up to 1.8 million women in the US, there is a quickly growing need to reduce the false-positive rate of breast MRI in order to reduce the number of unnecessary biopsies that could result. Our research explores the diagnostic potential of diffusion-weighted imaging (DWI), a MRI technique that depicts the diffusivity of water molecules in the tissue as a way to characterize the cellularity of breast lesions. Research has shown that DWI has the potential to increase the diagnostic accuracy of breast cancer, serving as a promising adjunct tool to DCE-MRI for reducing false positives. Our goal is to evaluate the ability of DWI for non-invasively discriminating benign and malignant breast lesions that were identified as suspicious on conventional breast MRI. Specifically, we will investigate image registration to improve alignment of DWI images, the effects of the contrast agent used in DCE-MRI on DWI measures, and the optimal diffusion sensitization of DWI in discriminating benign and malignant breast lesions. These characterizations of DWI can potentially help to optimize the acquisition and processing of DWI scans for future clinical implementation and help guide the appropriate use of DWI as an adjunct tool in radiological diagnosis of breast cancer.

Electron paramagnetic resonance (EPR) spectroscopy is a technique for analyzing chemical species with unpaired electrons (spin centers). An EPR spectrum provides information on the structure of the spin center as well as the total number of spin centers in a sample. The ability to use EPR to quantitatively determine the spin concentration of a sample is contingent on accurate comparison to a known concentration standard. For biological systems, a commonly used standard is a complex of copper(II) and EDTA (ethylenediaminetetraacetic acid); however, the presence of multiple species of copper-ligand complexes results in an EPR spectrum with overlapping signals that are not easily quantifiable. In an effort to develop a more accurate single-species standard, the coordination of EDTA to copper(II) as a function of acidity and its effect on the EPR spectrum is explored. Analysis of these spectra shows a single species of a copper(II) EDTA complex at pH three, with potential for use as a spin concentration standard.

Manipulation of inflation reports is a rarely known tool that policymakers use to generate temporary growth and more revenue than they would with an explicit monetary expansion. The Argentine government has intervened in its Statistic Department since early 2007. Several private estimates and scholarly studies have shown that the real inflation rate is in fact between two or three times the officially reported inflation rate. However, the current studies have only produced price indexes from December 2007 to present, which does not include the crucial period when the manipulation in inflation reports was first implemented. In this project, I will create an alternative price index from January 2006 to January 2009, which will bridge the gap from when the Argentine Statistic Department was still respectable to when its was widely known of misreporting inflation rate. I will assess the validity of my index by comparison with the published studies for 2008, the year that already has an alternative price index. From my index, I will be able to determine an accurate date when the misreporting inflation date started, and by also having the data for that crucial period, I will contribute to the study on the cost of misreporting inflation. I will be using the monthly average prices of 60 representative goods to construct an alternative price index comparable to the officially reported one. This valuable dataset includes the publications of the Consumer Action League and receipt records in a supermarket’s archives. Both database are rare to find because the Argentine government started to censor and punish domestic independent studies on inflation with heavy fines beginning on 2011. The preliminary results show that the manipulation of reported inflation started in February 2007.

Alzheimer’s Disease (AD) is a costly, debilitating, and irreversible neurodegenerative disease that affects at least 15 million people worldwide. There is no accurate early diagnosis for AD. When symptoms are noticeable, it is often at the end stage when treatment is of little use. Current treatment of AD cannot cure the disease, and is only able to slow its progression. Thus, an early diagnosis may prevent people from experiencing late-stage AD because people can begin treatments early and could slow disease progression significantly. The goal of this project is to explore the feasibility of such a diagnostic approach through Optical Coherence Tomography (OCT) imaging of ex vivo human lens. Specifically, I am writing MATLAB code that can screen OCT images for supranuclear cataracts. Goldstein et al. have described unique supranuclear cataracts in the lens of post-mortem AD patients. I will also correlate OCT findings to histology of the lens and current known AD biomarkers for a more definitive confirmation of AD. If supranuclear cataracts are indeed unique to AD and OCT is able to detect supranuclear cataracts, a diagnosis for AD through in vivo OCT imaging of the lens is promising.

Volatile organic compounds (VOCs) in indoor household air are carcinogens that many people are exposed to everyday. Examples of VOCs in the home are benzene, chloroform, and trichloroethylene. Genetically transformed plants are capable of degrading these VOCs by oxidizing them into less harmful compounds. The Strand lab has previously shown that poplar trees and tobacco, genetically transformed with cytochrome P450 2E1 (a rabbit gene expressed in the liver), successfully phytoremediated VOCs (phytoremediation is the use of plants in environmental treatment). My project at the Strand lab is to transform a houseplant with the same 2E1 gene, so people may raise this plant in their home to degrade indoor VOCs. Epipremnum aureum, a house ivy under the common name of pothos, was chosen for this project because the project follows the protocol for pothos transformation published by Kotsuka and Tada. Additionally, pothos does not flower, so the spread of the 2E1 gene can be kept in check. The project was executed in three steps: transformation, regeneration, and confirmation. The first part was to transform explants (pieces of pothos) by way of Agrobacterium infection, in which the bacteria insert the 2E1 gene into the pothos genome. The second step was to induce growth of calli in the explants, from which a new, genetically identical plant could be regenerated. The last step is to confirm that the new pothos was actually transformed and capable of degrading VOCs. This will be done through such tests as PCR, rtPCR, Western blot, and activity assays. I expect the pothos to be able to degrade VOCs as did the transgenic poplar and tobacco. These VOCs include trichloroethylene, vinyl chloride, chloroform, carbon tetrachloride, and benzene. If this result is not achieved, then future work may be devoted to find why the 2E1 gene is not compatible with pothos.

Every year, 700,000 people in the US alone suffer a stroke. Out of this, 87% of these incidences comprise of ischemic strokes. Ischemic strokes occur when normal blood flow to the brain is inhibited by some sort of blockage, thus starving the brain of oxygen and glucose. This results in neural tissue damage. HDACs (Histone Deacetylases) seem to play a major role in promoting neural tissue damage, thus using an HDAC inhibitor should protect already existing neurons from insult resulting from ischemia or any other traumatic brain injury. We believe that the recently developed HDAC inhibitor, MI-192, has the potential to show strong affinity towards a key HDAC involved in disease pathogenesis and thus confer neuroprotective effects. We have analyzed drug affinity for HDAC 3 and the effects of MI-192 on neuronal damage and on infarct size using western blotting and a variety of histological methods, respectively. MI-192 may have the potential to make it to clinical trials.

The Rock Detective Program is a non-profit organization that creates geo-science teaching kits for K-12 teaching professionals.  Students and teachers are able to explore geoscience using a hands-on approach to learning with real geological samples that are fun and educational.  As an intern with the Rock Detective Program, I am creating two geo-mysteries based on Fossil Turtles, specifically Emydid turtles.  Each mystery focuses on a specific age group - primary school and middle school aged children. Mysteries are then used as teaching tools to facilitate teachers and engage children in learning fundamental skills about geo-science not normally learned in a classroom.  Visual analyses, figuring out the approximate age of the specimens, and a final identification and confirmation from experts in the fields of vertebrate paleontology helped to give the mysteries a foundation.  To develop the geomysteries, I researched library and online literature and spoke further with experts.  The resultant mysteries will include information about the physical attributes of the fossil turtle as well as how turtles can provide information about past environment and climate.  I plan to test the mysteries at a local school and use my experience to fine tune the mysteries.  The final versions of the geomysteries will permanently be added to the Rock Detective Program's library.

Bacterial conjugation is the process of transferring genetic material from one cell to another. In the case of F-plasmid of Escherichia coli, the conjugation system is composed of inter-membrane proteins as well as hairlike appendages called pili encoded by the plasmid. Current interest in the characterization of F-plasmid lies with its ability to not only transfer itself to other cells but also its potential to mobilize auxiliary genes, such as antibiotic resistance, that yield some selective advantage. However, many basic details about the F-plasmid system, such as how donor cells recognize recipients and the function of the protruding pili, remain unknown. Through the use of an optical tweezer setup, I am able to isolate individual, fluorescently labeled E. coli cells in close proximity to each other. Once in close proximity, I will monitor the forces applied by donor cells on recipient cells and compare those forces to the forces potentially applied by donor cells on other donor cells. In addition, by utilizing the same optical tweezer setup, I will explore the statistical behavior of F-plasmid transfer as a function of cell-to-cell separation to investigate the potential function of the pili as transfer conduits.

This project will investigate the hypothesis that in utero exposure to clinically relevant doses of diagnostic ultrasound increases the risk for the manifestation of symptoms of autism. It is hypothesized that autism is caused by a triple hit of risk factors: a genetic susceptibility, a developmental time window of vulnerability, and an environmental factor. Diagnostic ultrasound is a candidate environmental factor within this “Triple Hit Hypothesis” for autism. To take the first steps toward testing our hypothesis, we propose to assay for ultrasound-associated changes in behavior and neuroanatomy of three mouse strains that have been well characterized in terms of social behavior. One strain is known for normal social behavior and the other two are known to exhibit autistic-like behaviors. Specifically, standard diagnostic ultrasound will be applied to mice at a key developmental time point during pregnancy to half of a group of mothers, and the other half will undergo the same procedure, but the ultrasound will not be turned on (sham application). At three weeks of age, the social, repetitive, and other relevant behaviors of the pups will be assayed using a battery of tests that includes a social approach test, a juvenile play test, open field observation, and several other methods. We will then analyze the data for significant differences in magnitude or occurrence of these behaviors within the three strains of mice based on their ultrasound exposure group. If the magnitude and/or occurrence of these behaviors are greater in the ultrasound-exposed group compared to the sham group in at least one of these strains, then our hypothesis will be supported and further experiments will be critical.

The purpose of the study is to contribute to the development of HIV prevention efforts by determining primary sources of reproductive health information for Luo youth of Western Kenya. In 2006, there were an estimated 55,000 new HIV infections in Kenya; the majority affected youth aged 15-24. HIV prevalence is highest, 20.2%, among the Luo ethnic group. The high infection rate among youth generally, and among the Luo in particular, stresses the need for HIV prevention tailored for Luo youth, which can be informed by existing survey data. The Asembo Baseline Cross Sectional Survey (Asembo BCS) was conducted by the Kenya Medical Research Institute & Centers for Disease Control and Prevention’s HIV Research Branch in 2003-2004 in the rural, predominately Luo community of Asembo. Interviewers collected data on health information-seeking behaviors, sexuality, gender norms, and HIV prevalence and risk factors from 1822 randomly selected Asembo residents. We conducted a secondary analysis using the Asembo BCS database, focusing on Luo youth respondents ages 13-24 (n=1,283). Factors examined included identification of the most important and preferred source of sexual health information, types of sexual health issues typically discussed with parents and friends, comfort level speaking with parents about sexuality, sources of HIV/AIDS information, and whether the youth had recently received HIV/AIDS information. Using descriptive statistics we characterized the distribution, dispersion, and central tendency of these factors. Preliminary results suggest that important and preferred sources of reproductive health information include schools, media and friends. Additional analyses are being conducted to describe parent-youth communication and recent exposure to HIV/AIDS information. Findings regarding where and from whom Luo youth receive information about sexual and reproductive health will be used to inform the design of targeted HIV prevention for Luo youth.

Hepatocellular Carcinoma (HCC) and Cholangiocarcinoma (CC) are the two prominent forms of liver cancer in humans. Current treatments show limited success. To further study the molecular mechanism of these diseases, I have made use of a genetically modified mouse model in which two tumor suppressor genes, Tsc1 and Pten, have been knocked out in the liver. I treated these mice with rapamycin, an inhibitor of mammalian target of rapamycin complex 1 (mTORC1) to determine its contribution in tumor development. mTOR is an important pathway involved in the regulation of cell growth, cell proliferation, and protein synthesis, and is implicated in tumor development. The livers of these mice phenotypically display an early onset of HCC and CC by twelve weeks of age. I hypothesized that treatment of these mice with rapamycin would result in decreased mTORC1 activity, which would negatively impact the growth of one or both types of tumors. Additionally, I predicted that mTORC1 activity would have an impact on hepatic steatosis (fatty liver disease). Following a two week treatment with rapamycin, liver tissue was harvested and analyzed for protein expression and activity using western blotting techniques and immunohistochemistry staining. Preliminary results suggest that rapamycin was effective in downregulating mTORC1 activity and in reducing cell and tumor size. Additionally, I witnessed a greater reduction in HCC lesions compared to CC in the treated livers, as well as an increase in steatosis. If future studies confirm these observations, the results suggest that 1) mTORC1 plays a functional role in the development of primary liver tumors, 2) HCC and CC respond to mTORC1 inhibition separately, and 3) rapamycin promotes steatosis. These findings may have implications in the treatment of liver cancers.

Diluted magnetic semiconductor (DMS) technology combines the properties of a semiconductor with ferromagnetism. Nanoparticles doped with magnetic elements such as Manganese offer a prime example of this type of material. Our specific task was to analyze the effects of p-type doping with nitrogen in ZnO quantum dots (QD) of 2.4 nm in diameter. p-type doping in this material involves the replacement of an O^2- ion with an N^2- ion, which has one less electron resulting in a hole due to an empty N^2- p-orbital. We hypothesize that when p-type doping is combined with paramagnetic Mn²⁺ doping, the unpaired 3d electrons of two Mn²⁺ ions separated by an N^2- ion will adopt a ferromagnetic orientation as opposed to their traditional antiferromagnetic state. Testing for this experiment was done with the development version of Gaussian. Energy calculations within this program and further data analysis reveal information such as the total energy of each state of the system, molecular orbital data, and energy diagrams concerning the semiconductor properties of these materials. Results show that the lowest energy state occurs when the Mn²⁺ ions adopt a ferromagnetic arrangement with the N^2- hole sharing this alignment. The potential for this QD and others with similar properties is extreme as many semiconductor applications could be revolutionized by DMS's. New applications such as solar cells made of DMS's are also under consideration.

Interspecific hybridization is common in flowering plants.  Hybrids tend to exhibit characteristics intermediate between both parents, and to grow more vigorously.  A novel specimen of the genus Heuchera (alumroot) found in a garden setting in Seattle is thought to be a hybrid between the commonly cultivated Heuchera sanguinea and the PNW native H. cylindrica.  In nature, H. cylindrica and H. sanguinea have non-overlapping geographic distributions.  Heuchera cylindrica is native to the western United States and Canada, whereas H. sanguinea is native to New Mexico and Arizona and it is not known if interbreeding between the two species is possible.  The unknown specimen in question shows intermediate characteristics of both species, which include flower color, inflorescence architecture and more vigorous growth.  To determine the relationship of the putative hybrid specimen with the two suspected parents, fixed differences in the Internal Transcribed Spacer (ITS) regions of nuclear ribosomal DNA of H. cylindrica and H. sanguinea were compared .  ITS regions were amplified using PCR and were then sequenced.  The results were edited, assembled and aligned to look for differences in the parents' ITS regions.  The differences in the parents' ITS regions are present in combination in the unknown specimen's DNA and shows that it is the hybrid of H. cylindrica and H. sanguinea.  A further test, using the maternally inherited chloroplast genome (cpDNA), was conducted in a similar fashion, with the expectation that the putative hybrid should contain the cpDNA of the species that is the maternal parent.

Ultrasonic neuromodulation is the process of stimulating different neural pathways in the brain through the use of transcranially delivered ultrasound in order to induce clinically relevant emotional, cognitive, physical or behavioral reactions. My research goal is to find out if it is possible to add anatomical specificity to neuromodulation through the use of modulated focused ultrasound (mFU), where 'modulated' refers to adding complex temporal structure to the waveform to optimize neuromodulation. Since mFU has a small focus relative to the brain, the acoustic power from the ultrasound can be moved within the brain; previous experiments have used unfocused ultrasound which sends ultrasound through the entire brain. We hypothesize that we can map varying physical reactions through stimulation of different parts of the brain, with our initial emphasis on the motor cortex because stimulation there produces readily observable results. With lightly anesthetized mice as our subjects, and always delivering ultrasound through the skin and skull, we began neuromodulation with unfocused transducers to transmit our ultrasound. This critical step was done to determine the optimal intensity, waveform shape and carrier frequency of ultrasound that created a robust observable effect. Next we translated these ultrasound parameters to our mFU transducer. The current stage of the process includes moving through different parts of each hemisphere and recording the associated motor response such as leg movements and tail flicks. We have already seen a change in activity between activating the quadrant of the brain containing motor cortex relative to the opposite quadrant. Going forward, we intend to see if we could produce varied motor movements as we change the point of stimulation within the brain hemisphere containing the motor cortex, along with changes in applied intensity, and duration of stimulation. Clinical implications for neuromodulation research include retraining brain function after injury.

DEER (double electron electron resonance) is a pulsed EPR (electron paramagnetic resonance) spectroscopy technique that is used to measure distances between unpaired electrons. DEER can be applied in structural biology to accurately characterize the structure of spin-labeled proteins, at the scale of several nanometers. EPR is commonly conducted using microwave frequencies at around 10 GHz (X-band), but spectral resolution and sensitivity can be improved by increasing the microwave frequencies to around 35 GHz (Q-band). Microwaves are concentrated on the sample of interest through the use of a resonator. Resonators developed for use with traditional continuous wave (CW) EPR experiments are designed with a high quality factor (i.e. most efficient storage of microwave energy) at a single resonance frequency. However, DEER requires a wide resonance bandwidth, which means that the quality factor of the resonator must be lowered, often at the expense of sensitivity. The goal of this project is to develop a Q-band resonant cavity for use with DEER that combines a bandwidth of 60-70 MHz with high accuracy and sensitivity. The resonator is designed using CST Microwave Studio, an electromagnetics modeling software package, to maximize its bandwidth and power conversion efficiency. A cylindrical cavity geometry is chosen due its ease of construction and simple tuning procedure. We anticipate that, after further development and testing, this initial design will serve as a platform that can be easily modified to accomodate other advanced EPR techniques.

Self-assembling silver nanoparticles have been of great interest to the scientific community due to their unique optical properties and potential use in areas such as cancer therapy and semiconductors. This research explores using a simple one-pot technique to produce self-assembling silver nanoparticles with controllable geometries based on steric interactions. The core advantage of this method is that it employs a bottom-up approach using commonly available and relatively inexpensive materials. Successive doping of long hydrophilic polyethylene glycol (PEG) chains followed by a short hydrophobic alkane-thiol renders the nanoparticles amphiphilic. Clusters of different sizes self-assemble depending on the concentration of PEG added to the silver dispersion. As PEG concentration increases, the extent of clustering decreases as the long chained PEG molecules create a corona around the silver particles and inhibit functionalization with alkane-thiol. This synthesis method is analyzed with Dynamic Light Scattering (DLS), Small Angle X-ray Scattering (SAXS), and Transmission Electron Microscopy (TEM). While the samples follow the expected clustering size trends, data indicates that monodisperse silver is critical to the reproducibility of the technique.

All solid materials have a stress limit beyond which cracks and ultimately fractures will develop; we are analyzing the possibility of uneven solar heating as a process that causes cracking. Research at the Universities of New Mexico and North Carolina drew attention to patterns of near vertical cracks in desert rocks, which known weathering processes cannot sufficiently explain. To investigate, temperature and strain data as well as cracking events were recorded using an instrumented boulder. We created a 3D-Finite-Element-simulation of the boulder incorporating thermal radiation, heat conduction, and thermo-mechanical stress analysis. Simulation provides the link between insolation and stresses, allowing us to assess size and shape effects on tensile stresses. We are validating our model by comparing measured and simulated temperature and strain data. As an example, we are calculating the maximum and minimum strain for each surface collection point and validating them against provided data. We expect to find that uneven heating from the diurnal cycle of the sun creates tensile stresses sufficient to cause cracking in these rocks. Future research will include a comprehensive data analysis concerning stress distribution and orientation within spherical boulders of various sizes, and an assessment of potential crack growth rates and crack orientation.

Gliomas are a uniformly fatal type of primary brain cancer characterized by their diffuse and invasive nature. Dr. Kristin Swanson and her team have developed a mathematical model of glioma growth that uses an individual’s unique tumor characteristics to derive metrics that enable the prediction of patient specific growth patterns and survival times. To date, relatively few studies have looked at predicting clinical progression of disease, which may be a function of disease localization. Clinical progression of disease incorporates variables such as mental cognition and impairment and is typically quantified using the widely used Karnofsky Performance Score (KPS). KPS is an accepted prognostic marker of a patient’s likelihood of tolerating chemotherapy and radiotherapy. In one study accessing functional status after gross total resection (GTR) of a patient’s enhancing tumor region, only 28% of patients had higher KPS post-operatively. 49% had stable scores, while 23% had declines in KPS of 10 to 30 points (Barker 1998). The variability in post GTR KPS scores suggests that there are patient-specific drivers of KPS. We will do a multivariate analysis to investigate which functional brain regions influence the mental and physical impairments that determine KPS scoring. We will identify brain regions, “functional drivers of KPS”, where tumor presence, as calculated by Dr. Swanson’s mathematical model, is well associated with a particular range of KPS scores. For each functional driver, we will use the region’s tumor cell concentration at time of tumor diagnosis, to quantify the future KPS. We will compare the predicted KPS to the actual KPS. If the initial and next time points are located pre and post- radiotherapy, chemotherapy, or resection, this will allow us another way of assessing the efficacy of therapies in palliating symptoms.

When we decide to go somewhere, we must also decide how we will get there. Any choice, whether it be by car or bike, will have a unique route associated with it. This route can play a role in the decision making process. With this in mind, it is important to understand differences in the routes taken by both bikers and motorists. This study uses Google Maps as a tool used to do just that. 32 Routes were created randomly, and ran for both cars and bikes. The outputs were then compared with regards to length, duration, and complexity. Overall length of the two routes showed little variance, while the duration for automobiles was predictably much shorter. Less predictable was the increased complexity for bike routes, which were calculated to be over 250% more complex than car routes. This increased complexity may have an effect on whether people chose to ride their bike or drive their car. Furthermore, it highlights another challenge that cyclist must face. In the future, communities should plan and invest in the type of infrastructure that fosters transportation equality

Insect-eating animals like birds are considered to be beneficial to farmers, since they help control insect pests. However, it has often been difficult to determine the extent to which agricultural pests make up the diets of predators like birds, since it can be difficult to actually observe them feeding on harmful insects. However, if we collect samples of feces from birds captured in farms, we can use molecular methods to look for the DNA of insect pests in these samples, a method that has been successfully used to study the diets of bats in agricultural areas. We extracted DNA from approximately 200 samples of bird feces and bird stomach contents form birds captured in coffee plantations in 2000 and 2001 as part of a study on the diversity of birds in coffee plantations. However, it has proven difficult to recover amplifiable insect DNA from these samples, possibly due to their age (the DNA is probably degraded). Of the over 200 samples, fewer than 20 have yielded insect DNA. Of these, none have tested positive for DNA from any of the insects that are the worst pests of coffee in our study area. This is in contrast to bats from the same study area; over 10% of fecal samples have DNA from one of these three coffee pests. There are a number of reasons why this might be. First of all, the bird samples were all collected in the dry season (our winter) when there are fewer insect pests. Also, the bird samples were collected in a different year, so there might not have been many pests at that time. Finally, the migratory songbirds might not be the birds that most feed on insect pests.

Oil operations that took place in the Northeast Ecuadorian Amazon between 1964 and 1992 have altered the ecological functions of thousands of acres of land by dumping crude in open pits, burying oil extraction byproducts, and burning unwanted oil without proper treatment. Many people in the area experience a number of health issues including flu, respiratory problems, skin issues, stomach aches, and headaches possibly associated with air and water contamination. My research focuses on the analysis and mapping of water quality, specifically of 5 parameters: temperature, dissolved oxygen, turbidity, conductivity, and pH. My colleagues and I collected 55 geo-referenced water samples within the Pacayacu and Sacha River watersheds, where oil operations have taken place. Preliminary data shows extremely acidic drinking water (pH<5.0) along with decreased oxygen levels means of 1.9 mg/L. My hypothesis is that sample sites such as wells and streams that are closer to oil production features such as residual pools, pumps, and oil refineries have inferior water quality to those located further away. I used geographic information systems to map and operationalize spatial variables such as path distance from the sites to oil operation features among other topographic factors. I will test the hypothesis using ordinary least square regression analysis. The results of this study will inform local organizations about the direct impacts on water quality and public health of oil operations in the area. We hope this study will help direct conservation and restoration efforts towards reversing anthropogenic environmental degradation in the area.

Diabetes is a serious and prevalent disease affecting the lives of many people. Studies have shown that cardiovascular calcification, or calcium-phosphate mineral deposition in blood vessels, cardiac valves, and myocardium, is prominent in patients with Type II diabetes (T2D), accounting for the heightened cardiovascular morbidity and mortality in this population. Using a T2D mouse model, our laboratory has shown a positive correlation of hyperglycemia with cardiovascular calcification. A multi-ligand receptor, namely the receptor for advanced glycation-end products (RAGE), was high in cartilaginous and calcific areas of blood vessels and aortic valves and translocated to the cell membrane of the cells with osteochodrogenic (bone and cartilage precursor) and chondrocytic (cartilage) properties. To study whether RAGE is involved in the early signaling of osteochodrogenic differentiation and calcification of cardiac valves, we cultured bovine valve interstitial cells (BVICs) in procalcific medium containing normal and high glucose in a range of hyperglycemia. We found that high glucose increased calcification of BVICs by up to 3 folds. Expression levels of RAGE and its ligands are determined by reverse-transcription PCR and Western blot analysis. The biological activity of RAGE are blocked by a commercially available neutralizing antibody to see whether RAGE is required for the high glucose-associated BVIC calcification. Our results show a decrease in BVIC calcification when RAGE activity is blocked by a neutralizing antibody. For future studies, we will create a cell line with lower expression levels of RAGE via small RNA interference.

Cancer vaccines offer a promising method of manipulating the immune system to seek and destroy malignant cells. However, there have been many limitations on their ability to enhance stimulation and persistence of CD4+ Type 1 helper (Th1) and CD8+ cytotoxic T lymphocytes (CTL) necessary to promote adequate tumor regression. The long-term goal of this research is to use polymeric carriers to deliver antigens and immunomodulatory siRNA to antigen presenting cells (APCs), in order to promote anti-tumor cellular immunity. We have designed pH-responsive, endosomolytic, “smart” polymers that are capable of being conjugated to antigens and complexed to siRNA. Also, we have demonstrated the ability of these polymers to enhance class I antigen presentation by APCs. In addition, we have shown that polymeric delivery of siRNA promotes knock down of a model gene, glyceraldehyde 3-phosphate dehydrogenase, in dendritic cells. We plan to demonstrate similar results with other immune cells, both immortalized and primary, and genes of interest, as well as extend this technology to relevant tumor-associated antigens. These data point to the modular nature of our polymeric delivery systems, as they provide a promising way of approaching challenges in cancer immunotherapy through multiple delivery modalities.

Food desert research is filling journals across academic disciplines. Food deserts refer to urban and rural areas, which lack easy and affordable access to healthy, nutritious foods. These studies emphasize the influence of inequality in relation to poor access to healthy food as well as the political and social processes that limit the diet of low-income areas. Food desert research has not explored the importance of age on food choice or how and if college campuses can and should be defined as food deserts. Poor diet habits cemented in the emerging adult phase, age 18-25, are indicative of future adult decisions. The habits of this age group should therefore be identified in order to understand and create programs that insure healthy habits among this age group. This approach will reduce unhealthy lifelong habits that contribute to rising obesity rates and chronic disease. My research examines available food choices on college campuses. My research reveals that food choices are severely limited, and the students are vulnerable to forging non-nutritious diet patterns. Students responding to a survey administered in a sample of the University of Washington's cafés, dining halls, and markets provide the basis for my findings.

The Banda Islands in Indonesia have been important cultural and trade centers for centuries. With their unique native nutmeg production, they have attracted merchants from around the world including Islamic spice traders and Dutch and British merchant companies. The site of BN1 located on Banda Neira Island may contain an important archaeological record of early contact with Islam. Following the thinking that behavioral and dietary changes soon follow religious conversions, this study looks to the presence and use of pigs as a proxy for Islamic versus Animistic religious orientation. I examine the density of pig skeletal remains through time by using tradeware ceramics as chronological markers. Additionally, I investigate the site formation processes with geochemical methods and search for chemical evidence of pig presence in the form of fecal lipid biomarkers. Gas Chromatography-Mass Spectrometry of total lipid extracts from the BN1 archaeological sediments can determine with greater resolution and accuracy the presence or absence of pigs at the site based on known sterol lipid ratios derived from decomposed feces. This suite of archaeological and geochemical data will provide an insightful picture of local-level impacts of Islam in the Banda Islands.

Digital microfluidics is an advantageous lab-on-a-chip platform that prevents cross contamination between samples and avoids dilution by diffusion. The majority of digital microfluidic technologies transport drops by establishing thermodynamic gradients. An emerging alternative to gradient transport is ratcheting. Ratchets utilize a predetermined asymmetry (either in input actuation or fabrication) to rectify an energy input into controlled microfluidic droplet transport. To realize a ratchet on a flat surface, we introduce chemically patterned hydrophilic regions on a hydrophobic background. The flat surface ratchet utilizes a semi-circular periodic chemically heterogeneous pattern to induce asymmetric contact angle hysteresis. Chemical ratchets reduce the actuation amplitudes of previously reported texture ratchets by over 3x for a 10 µl droplet. They are optically flat making it possible for fully transparent devices. The microscopically flat device has a simple fabrication (that could be achieved in a number of ways), is easily cleaned, integrated with electrodes and sensors and is compatible for down-scaling to nanoscale features for improved performance. We report two surface modification techniques using both oxide and gold adhering self-assembled monolayers (SAMs) to pattern the wettability of a surface (trimethylsilanol-dodecanethiol), as well as a trimethylsilanol-perfluorooctyltrichlorosilane pattern. In this report, we investigate the role of rung curvatures in establishing asymmetry and improving performance in flat surface ratchets. We compare the minimum energy input required to achieve droplet transport across a variety of ratchet designs, and identify design characteristics which result in the most efficient operation. Future applications of this improved technology include enhancements to lab-on-a-chip diagnostic devices for disease detection, and surface coatings on components such as windshields or condensers to enhance water removal capabilities.

The flux of oxygen between the ocean and atmosphere is a measure of net biological oxygen and carbon production in the euphotic zone of the ocean, which are key fluxes in the global carbon cycle. Seasonal measurements of O2 in the surface ocean are necessary to determine the flux. To date these measurements have been made in only a few time-series sites in the world’s oceans, but it may soon be possible to determine the global flux by deploying oxygen sensors on the world-wide Argo profiling float program. Before this can be achieved the accuracy of oxygen sensors deployed on these floats must be improved. My project will evaluate a series of calibration methods for increasing oxygen sensor accuracy to better than ±0.5% and establish a standard calibration protocol. Ten Aanderaa oxygen sensors will be submerged in a constant-temperature water bath under different oxygen concentrations. The sensor response will be determined along with the oxygen concentration measured by Winkler titration at each temperature and pOOxy value. The sensors will then be cycled in a separate housing between water and air at 100% humidity, constant temperature, and known atmospheric pressure to determine the oxygen sensor response in air. Laboratory-calibrated oxygen sensors will be deployed on the University of Washington vessel, R. V. Thompson in Northwest Pacific Kuroshio current in winter of 2012/13 to demonstrate increased accuracy and test in-situ calibration capabilities. The establishment of a standard calibration protocol will expand the spatial and temporal scale of dissolved oxygen oceanographic research.

I am doing research on the history of the Nisqually Wildlife Refuge and the role of Ducks Unlimited in the restoration of habitat in the Refuge from 2000-2010. Studies have shown that if habitat restoration is conducted, many species benefit from this restoration. These benefits are often wide-ranging past the scope of the original project, which was to restore endangered Chinook salmon habitat. These benefits include increased habitat for over 200 species of birds, waterfowl, and raptors as well as numerous species of trees, native plants, and flowers. Ducks Unlimited motivation has been questioned in the past as to only include the habitat restoration for migratory waterfowl as a hunting resource. Research shows that Ducks Unlimited’s role in this restoration by acquiring land and using their engineering and technical expertise, has improved the overall health and habitat of the whole ecosystem, not just for waterfowl. The research will show the role DU has had in the habitat restoration at Nisqually NWR and put to rest some of these criticisms that Ducks Unlimited has faced in the public eye by showing the incredible success that has been achieved. Information will be given on the partnerships between DU, various government agencies, and native tribes. Extensive database research and various articles will show the positive impact these partnerships have had on the overall health of the refuge. These articles will come from Ducks Unlimited articles, U. S. Fish and Wildlife reports as well as other federal and state agencies and an in person tour of the Refuge itself. This project is significant in that it shows the incredible importance and wide ranging impact of habitat and ecological restoration and the invaluable partnerships that can be formed between government and private entities as well as the public’s role in discussion on the project.

Glioblastoma multiforms (GBMs) are malignant brain tumors and are among the most lethal cancers in the United States. Current clinical treatments involve surgical resection followed by chemo radiation therapy. Temozolomide (TMZ) is a DNA methylating agent that has shown promise in post-operative chemo radiation therapy, yet its effects are mediated greatly by the DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT). The addition of DNA repair inhibitor O6-benzylguanine (BG) as part of a concurrent treatment with TMZ has shown promise, but suffers from unacceptable toxicity due to BGs poor pharmacokinetics. Here we report the development of nanoparticles (NPs) loaded with a BG payload that can efficiently cross the blood brain barrier (BBB) and with the addition of targeting agents may be a more effective method for drug delivery by reducing toxicity in healthy tissue. These NPs are composed of a magnetic core and biocompatible polymer surface coating. The NPs are then conjugated with BG (NP-BG) by attachment to the polymer surface. NP-BG is further modified with chlorotoxin (NP-BG-CTX), a tumor targeting peptide, through a polyethylene glycol linker. NP-BG-CTX had a mean hydrodynamic size of 75nm with a surface charge of about +4mV and have demonstrated specific targeting in vitro of GBM cell line SF767. Finally, we have shown that NP-BG substantially reduces MGMT activity in SF767 cells in vitro. These results suggest that NP-BG-CTX have a higher specificity to tumor cells than normal healthy cells in cancer patients. This would decrease drug toxicity in patients and reduce tumor resistance to TMZ, potentially providing a more effective treatment and improve clinical outcome.

 The research conducted by the Kaeberlein Lab is focused on identifying conserved longevity genes in evolutionarily divergent model organisms. The research methods discussed here concentrate particularly on the mechanism of aging in budding yeast. Aging in the budding yeast Saccharomyces cerevisiae was described more than fifty years ago with the observation that mother cells produce a finite number of daughter cells and then cease replication. Our poster describes the method utilized in our lab for quantifying replicative lifespan. In short, individual yeast cells are grown on solid media and monitored from their initial undivided state until they undergo senescence. Mother cells that produce more daughter cells are defined as having a longer replicative lifespan. Over the past several years, we have measured replicative lifespan on several hundred thousand mother cells, resulting in the identification of dozens of genes that modulate aging in yeast.  By identifying these genes and determining their mechanism of action it may be possible to one day develop therapies that delay the onset of aging and age-related disorders in people. 

Many plastics such as water bottles and poly vinyl chloride (PVC) pipes have phthalates added as plasticizers. Phthalates are a class of compounds that have the potential to leach out into groundwater and soil from plastics and storm water runoff. This is the cause for many health concerns since phthalates are hormone disruptors and neurotoxins. First Creek in Tacoma, Washington, was once a salmon-bearing stream, now used as a storm drain that feeds into the Puyallup River, and the Puget Sound. Parts of this watershed have also been used as a dumpsite by locals. I measured concentrations of bis-2-ethylhexyl phthalate (C₂₄H₃₈O₄), dimethyl phthalate (C₁₀H₁₀O₄), diethyl phthalate (C₁₂H₁₄O₄), dibutyl phthalate (C₁₆H₂₂O₄), butylbenzyl phthalate (C₁₉H₂₀O₄), and di-n-octyl phthalate (C₂₄H₃₈O₄) in creek sediment. I extracted the phthalates from the sediment using accelerated solvent extraction, and analyzed via Gas chromatography-Mass spectrometry (GC-MS). Only bis-2-ethylhexyl phthalate and dimethyl phthalate was detected in higher concentrations than the blank samples. The concentrations measured will be compared to those in other studies to determine relative contamination of First Creek. Determining phthalate concentrations is the first step in defining the health of the creek and restoring it to its former state.

In Acute Myeloid Leukemia (AML) the adhesion interaction between the AML blast cells and the bone marrow microenvironment confers resistance of the leukemia cells to the chemotherapy drugs. One possible receptor that might facilitate this adhesion is the VLA-6 integrin. Our laboratory has been found it to be highly expressed in the AML stem cells, the cells that are believed to give rise to leukemic relapse. To investigate the role of the VLA-6 receptor, I performed assays to observe the effects of blocking this receptor on cell adhesion as well as the chemotherapy resistance. The adhesion assay consists of measuring AML patient cell binding to laminin-coated wells, as laminin is the ligand for the VLA-6 adhesion receptor. Adhesion mediated by VLA-6 is assessed by measuring binding in the presence or absence of the anti-VLA-6 antibody. The chemotherapy resistance assay involved the same conditions as the adhesion assay. We expected that blocking the VLA- 6 receptor would prevent the cells from adhering to the laminin and that this would also lead to lessened drug resistance. However, for the cells from one patient studied so far, there has not been a significant difference between the amount of adhered cells in these conditions. Additional experiments are in progress with more patient samples to elucidate the significance of the VLA-6 receptor in AML physiology and survival.

Income inequality in the United States is at its highest level in at least the last half century, and official measures of poverty have remained relatively stable prior to the 2008 financial crisis. Since that time, the percent of the population considered poor has steadily increased. Previous research has shown that both income inequality and poverty, individually, are related to incarceration rates. This paper presents results of an analysis of the relative effects of income inequality and poverty on incarceration rates. Using state-level data for the United States, I use multiple regression analysis to determine the degree to which each can account for states’ incarceration rates.

Stroke is the leading cause of adult disability in the United States. Motor impairments often remain even after extensive physical therapy. To improve rehabilitation outcomes in severely affected individuals, we hypothesize that electrical stimulation could rewire the brain such that non-lesioned brain areas take over the function of lesioned areas. Mechanisms that modify connections in the brain rely on temporal associations on the order of tens of milliseconds. For targeted rewiring, we propose stimulation of the non-lesioned areas be triggered from activation of muscles weakened by stroke. This will provide a tight temporal association between muscle activity and brain activation and should boost the neural drive to the affected muscles. As an initial test of the proposed stimulation therapy, we trained neurologically-intact pigtailed macaques to make bimanual hand movements in response to visual cues. The macaques were implanted with electrodes at the surface of the brain that stimulated and recorded neural activity. Electrodes were located over left and right motor areas and over areas with less direct involvement in hand movements. Experimental sessions began with baseline neural activity recordings while the animal performed bimanual hand movements in the absence of stimulation. Next, movement-triggered stimulation was applied for 2-6 hours. Across sessions, a number of parameters were explored in this phase including the stimulus timing relative to movement, the stimulus intensity, and whether a motor or non-motor electrode was being stimulated. Each session ended with another recording in the absence of stimulation. The stimulation effect was quantified by changes in neural activity and behavior (i.e. reaction time between visual cue and movement onset) between pre-stimulus and post-stimulus recordings in each session. Significant stimulus-induced changes in reaction time were found to be a function of both stimulus timing and stimulus location. The results indicate that movement-triggered stimulation can powerfully modulate motor output.

Heart disease is the leading cause of death in the US. Current therapies are limited, and most slow progression of the disease but do not address restoring function. Dr. Regnier’s laboratory is pursuing a novel heart disease treatment. The lab discovered that a nucleotide analog of ATP, 2-deoxy-ATP (dATP), which is produced in heart cells (cardiomyocytes), greatly improves cardiac performance by increasing myofilament contraction. We have established a transgenic mouse line that overexpresses ribonucleotide reductase (RR), the enzyme that converts ATP to dATP. In addition, we have developed viral vectors to overexpress RR specifically in the heart. Both methods of RR overexpression elevate intracellular dATP, improving contractile strength of cardiomyocytes and cardiac function. An added benefit is increased rate of relaxation by dATP, as is the decay of the calcium transient. The calcium transient behavior is primarily governed by proteins of the sarcoplasmic reticulum (SR), which is the storage site for intracellular calcium. I am studying what causes the improved rate of calcium decay. I measure calcium handling protein expression and activity modification via western blots, and measure contraction and relaxation of isolated cardiomyocytes. I am comparing healthy and infarcted hearts from transgenic and viral RR overexpression mice. Mechanical measurements demonstrate the frequency dependence of the amplitude and kinetics of contraction, relaxation, and the calcium transient. Western blots reveal if faster calcium transient decay is due to SR changes in relation to RR overexpression. The infarct hearts have loss of function due to the death of muscle tissue, but we predict that RR overexpression and subsequent increased concentration of dATP will increase myofilament calcium sensitivity, thus rescuing cardiac function and restoring damaged cells to regular contractile strength. RR gene therapy may be a breakthrough treatment of heart trauma if damaged cells are rescued and normal contraction is achieved.

There are numerous applications of porous ceramics, including electrodes for solid oxide fuel cell, membranes and filters, and thermal insulation.  Most of these applications utilize uniform isotropic porous ceramics. Directional freeze-casting offers a novel way to make porous ceramics with tailored microstructures. Using this process, followed by partial sintering, we are able to fabricate ceramics with directionally aligned and hierarchical porosity. Freeze-casting involves directional freezing of a liquid suspension and then sublimation of the solvent by freeze drying in order to achieve uni-directional pores. Overall porosity and pore size and alignment can be controlled by several variables including: solvent to powder ratio, freezing rate, and sintering temperature. Our research focuses on two different applications of anisotropic porous zirconia ceramics. One project focuses on creating filters for catalytic hydrogen peroxide decomposition. Hydrogen peroxide (H₂O₂) is an undesirable byproduct and hindrance of a new process to produce chlorine using solar radiation. Porous ceramics provide the means of developing a filter with sufficient surface area and structure for photochemical reactor solutions to be continuously scrubbed of H₂O₂; thereby enabling unhindered chlorine production by this photochemical process at levels sufficient for water purification. The other project focuses on developing a glass-infiltrated reusable ablative ceramic surface for high temperature aeronautical applications. Porous yttrium stabilized zirconia is used as a substrate through which glass can be both initially infiltrated and subsequently drawn to a high temperature surface through capillary action for ablative purposes. At high use temperatures, the glass rises in the capillaries reaching the hot surface where it is ablated. The heating required for ablation reduces the surface temperature of the system.

Over the past fifteen years Washington State Juvenile Justice department has been developing an evidence-based rehabilitative system to reduce crime among adolescents cost effectively. One way legislators are encouraging this is through state funding grants. Up until 2010 funding from the state was distributed in the form of a categorical grant, which allocate funds to the 33 juvenile justice courts of Washington based on county level variables. In conjunction with the move towards research oriented methods for applying justice, the Department of Social and Human Services (DSHS) formed the Models for Change initiative to find ways to ensure minority youth received the same treatment and benefits from the rehabilitative programs as whites. Although these two developments are intended to provide equality to all, their implementation is so new that DSHS has yet to fully develop quality assurance tests to assess whether the grants are working as intended. My research examines how state funding affects the sentencing dispositions of minorities and whites across counties. Sixty-eight percent of the categorical grant funding is based on the youth population, so counties in more rural regions typically receive less money from the grant. Using data from the Juvenile Rehabilitation Administration (JRA) and the Census of Juveniles in Residential Placement data book, I measure the extent to which variation between rural and urban county funding affects the proportion of minorities and whites assigned to confinement. Keeping in mind the goals of the Models for Change initiative, I examine the ways in which urban and rural counties differ in their assignments of rehabilitation, with the hope of gaining further insight into how legislators deal with discrimination in contemporary legal processes.

Phytoremediation is the use of specific plants to remove pollutants and toxins from soil and water.  Phytoremediating plants can have problems surviving in highly polluted industrial environments, known as Super Fund sites. The Doty Lab has isolated an endophyte bacteria designated "PD.1" that has shown the ability to give plants the strength to become estabilished and productive in these highly toxic environments.  The term endophyte refers to a class of mutually beneficial, symbiotic microbes, which live in the intracellular spaces between cells of inoculated plants, and have been shown to release growth hormones, provide tolerance to drought, flood and high salt environments and can give plants the ability to break down large human-made chemicals into smaller molecules which the plant and microbes can use as a nutrient source . This presentation will show the results of several experiments conducted in hydroponic solutions, and in soil dosed with the Polycyclic Aromatic Hydrocarbon, phenantherene. Several different species of Salix and Populous trees were dosed with high levels of phenantherene after being inoculated with an endophyte bacteria isolated from a Populous deltoids. Growth, plant mortality rates and plant uptake of the pollutant phenantherene were recorded.  In several of these studies there was a dramatic decline in mortality of inoculated plants in highly polluted environments and also signifigant increases in shoot growth of inoculated plants. This research adds to the growing body of work that is demonstrating that the use of plants, inoculated with a corresponding symbiotic, endophytic bacteria can be a viable tool in pollution remediation of soil and water.

This project is an interpretation of high-resolution bathymetric data from the Norwegian Mapping Authority (Statens Kartverk), acquired between 2004 and 2008 at Engelskbukta, a bay located in West Spitsbergen in the Norwegian high arctic archipelago of Svalbard. Engelskbukta is bordered on the southeast by Comfortlessbreen, a large, surge-type tidewater glacier, and on the northeast by Uversøyra, a delta formed by the melting and outwash of the land-anchored Uversbreen glacier. The dataset was imported using CARIS processing software and was analyzed with ESRI ArcGIS. Initial interpretations of the seafloor morphology indicate a retreat moraine series, representative of long-term warming and recession of the glacier terminus, and larger thrust moraines indicative of active surging phases. Fluvial features, such as glacier-proximal grounding line fans and channels, indicate zones of past and present subglacial sediment flux from Comfortlessbreen and deltaic flux from the Uversøyra delta. These features can offer significant negative feedbacks against terminus melting by marine heat flux. Satellite and aerial imagery, descriptive models of surge-type glacier processes, and in-situ sediment dating from the adjacent Kongsfjorden offer further opportunities to constrain both retreat rate and surge frequency and predict future glaciodynamic responses to climate forcing.

The Earth’s magnetic field deflects most of the energetic particles contained in solar wind, but some are captured and trapped in regions called radiation belts. Sometimes, high-energy particles migrate from the radiation belts into Earth’s upper atmosphere, where they interact with matter to produce X-rays. Our project focuses on attempting to understand radiation belt loss processes by analyzing the X-ray data. Professor Michael McCarthy and I modeled an existing X-ray detector on the computer and simulated electron populations (having various energy distributions) as they move through the upper atmosphere. We recorded the energy distribution of X-rays captured in the detector. We then compared this distribution with the actual X-ray energy distribution recorded by real experiments. This method of working backwards limits what the energy distribution of the original charged particles may have been. This is significant, because knowing the energy distribution of charged particles in radiation belts and understanding how they move into the upper atmosphere will allow engineers to design spacecraft and satellites that are more resistant to damage from high-energy particles and X-rays. It is also an interesting research question that will teach us about the radiation belts of other planets in the universe that have magnetic fields. Our project will be applied to more experiments; in December 2012, the research team will return to Antarctica to release more balloons equipped with X-ray detectors into the upper atmosphere. Another extension of this work is to model the effects of high-energy protons from solar wind on Earth’s upper atmosphere.

Ocean Research College Academy (ORCA) students partake in monthly State of Possession Sound (SOPS) cruises to collect data from various sites in the Snohomish River estuary near Everett. The focus of this SOPS research is on dissolved oxygen fluctuations in Possession Sound and the Snohomish River. Large fresh water inputs into Possession Sound bring sediment, organic matter, nutrients, and pollutants from both natural and human influences, which may impact the dissolved oxygen (DO) levels of the water. In addition, the tides affect the amount of DO in the Snohomish River during flood tide and ebb tide. The hypothesis formulated for this research was that less populated areas upriver would have a higher DO content rather than more populated areas downriver. Measurements were taken at four different locations along the Snohomish River and at the delta during ebb tide to negate the tidal effects. The parameters collected with a YSI 85 were DO, temperature, and salinity in order to find the influences that determine levels of DO in the areas of interest. Future temporal studies based off of this research could directly link anthropogenic and seasonal influences on specific respiring marine organisms in the ecosystems of Possession Sound.

Electric vehicle infrastructure is the support network that allows electric vehicles (EVs) to travel farther than battery capabilities currently make possible. The infrastructure includes privately and publicly owned charging stations, upgraded electrical utilities capable of handling the output demanded by charging stations, and the internet technologies that give drivers the latest information on charging station locations and availability. This research investigated and developed a process to install a charging station on a roadway project in order to encourage expansion of electric vehicle infrastructure. This process could be recognized as a potential sustainable activity in the Greenroads Rating System. The rating system assigns points for completion of a number of sustainable activities on a roadway project that contribute to creating a "greener" road. Laying out such a process is especially challenging because it must remain applicable to many types of roadways in diverse environments, even with future advancements in electric vehicles, charging stations, and battery technologies. Two types of roadway projects were studied as cases: projects that have already installed charging stations and others that were considering installing charging stations. Through communication with professional design engineers on these projects and exploring numerous government EV infrastructure documents, preliminary findings determined that location characteristics, local markets for EVs, and local rules and regulations were the three key components to establishing EV infrastructure. Using these components, a short rubric was created, that allows project engineers to evaluate the feasibility of installing a charging station on a road project.

Photoactivation of compounds such as chlorophyll derivatives results in the excitation of oxygen into a highly reactive singlet state which causes cellular damage and death. This property is used as a cancer therapy, specifically in photodynamic therapy (PDT.) Although PDT has been proven to be effective at eradicating cancer, it has not been widely adopted due to poor penetration of light into body tissues. To avoid this limitation, photosensitizing molecules that absorb light at longer wavelengths are being synthesized to allow deeper tissue penetration. It is possible that the modification of a chlorophyll derivative called chlorin e6 (Ce6) via cycloaddition reactions, such as the Diels-Alder reaction, will lead to a molecule with a wavelength absorption long enough (750-800 nm) to obtain good tissue penetration. Such a molecule will eventually be attached to a cancer-targeting antibody to increase its tumor concentration, which will boost treatment effectiveness and minimize healthy tissue damage. Among the methods employed in the organic syntheses being studied are high-performance liquid chromatography (HPLC), ultraviolet-visible spectroscopy (UV/Vis), nuclear magnetic resonance (NMR), and mass spectroscopy (MS.) The cycloaddition reactions of a Ce6 derivative with a synthesized molecule are currently under investigation. If successful, PDT with this compound can be applied to treat a wider variety of cancers in a targeted and systematic way, while avoiding the nasty side effects of chemotherapy.

Gastrulation is the process during which cells migrate and tissue layers differentiate in early embryo development. This process requires a balance between cell-cell adhesion mediated by cadherin-catenin interactions and stimulation of cell migration. Our research focuses on p120 catenin (p120ctn) dependent cell migration during gastrulation in zebrafish. P120ctn stabilizes cadherins at the plasma membrane and interacts with Rac1 and Cdc42 GTPases to stimulate cell migration, and with RhoA GTPase to regulate cell-cell adhesion. P120 binds and translocates RhoA to the plasma membrane where a RhoA gunanine nucleotide exchange factor stimulates release of GDP and binding of GTP. GTP-RhoA activates RhoA kinase which activates myosin light chains, inducing cross links to stabilize actin filaments, thus increasing the strength of cell-cell adhesion. In this project we aim to address what the role of RhoA GTPase is in the p120ctn signaling pathway as well as how phosphorylation of p120ctn affects the RhoA-p120ctn binding interaction. By knocking down p120ctn and attempting to rescue developmental deficiencies, we can elucidate how p120ctn interacts with RhoA to regulate cell-cell adhesion. We hypothesize that injection of GDP-bound (DN) RhoA will rescue a splice-morpholino p120ctn knockdown allowing low concentrations of p120ctn to activate Rac1 and Cdc42 GTPases that promote cell migration. Our microinjections of DN-RhoA mRNA into one-cell zebrafish embryos have shown that DN-RhoA, and not WT-RhoA or CA-(GTP-bound) RhoA, is able to rescue p120ctn knockdown. Additionally, p120ctn is regulated by phosphorylation and we are currently interested in how tyrosine phosphorylation of p120ctn affects its ability to bind and regulate RhoA. We hypothesize that tyrosine phosphorylation site mutants will be unable to rescue splice-morpholino p120ctn knockdown, and therefore be essential regulation sites. Using confocal fluorescence microscopy and a binding assay to measure GTP-RhoA, we hope to elucidate whether these sites are directly involved in the p120ctn-RhoA binding interaction.

Malaria is a complex disease that poses an immense global public health burden with an annual death rate estimated between 1.5 and 2.5 million. An inclusive understanding of transmission dynamics is essential for the continuing development, improvement, and implementation of vector control strategies. Success will depend on extensive taxonomic research and advanced knowledge of malaria vectors, malaria parasites, and their developing resistance to insecticides and drugs. Examinations into host-parasite relationships among nonhuman primate malarias are needed to identify other likely species of Plasmodium malaria parasites capable of causing zoonoses. The vectors of malaria belong to the mosquito genus Anopheles and there are more than a dozen species of Anopheles malaria vectors affecting Indonesia. In July, I will travel to Tinjil Island, located off the coast of West Java. There is no current record of mosquito fauna for Tinjil and consequently no data regarding which malaria parasites affect it. My investigations into these matters will be essential to the operation of local fisherman camps and the natural habitat breeding colony of Macaca fascicularis, the long-tailed macaque. I will collect samples of larvae, pupae and adult forms of mosquitoes on mainland Java for confirmation of the Anopheles genus before heading to Tinjil. On Tinjil I will collect samples of larvae, pupae and adult forms for genus and species identification by utilizing an onsite stereomicroscope. I expect to follow up this initial entomological survey with molecular detection methods to identify possible members of a species complex, morphologically indistinguishable Anopheles taxa, which may display differing abilities to transmit malaria. By identifying these species of mosquito, the implementation of integrated vector management policies needed to improve the current vector control strategies for West Java and surrounding areas will be possible.

Measurements of the rotation of galaxies indicate that visible matter cannot account for all of a galaxy's mass. The prevailing theory is that each galaxy is surrounded by a halo of dark matter. Dark matter halo mass can be determined by measuring the velocities of dwarf satellite galaxies orbiting a central galaxy. We used data from the Sloan Digital Sky Survey (SDSS) DR8 and HyperLeda databases to identify massive, isolated galaxies including M94, M101, and NGC 2841 and prioritize their satellites for observation. Next we will make spectrographic observations to determine satellite velocities and use these results to infer the mass of the central galaxy. By comparing this value to the amount of visible mass in the galaxy, we will determine the mass of the dark matter halo.

Ultracold molecules are a new frontier in atomic physics that have many possible applications which include tests of fundamental physical theories and the development of quantum information science. One method of creating such molecules is through the process of photo-association (PA), where two ultracold atoms are optically excited into a bound molecular state. We will present the design and construction of an extended cavity laser diode system that will be used for PA of ultracold Lithium (Li) and Ytterbium (Yb) atoms. The exact energies for molecule formation are not known a-priori, so the laser has to be tunable over a wide range of frequencies near the wavelength of 556nm. To maximize the “mode hope free” (MHF) range where the laser frequency varies smoothly, we will simultaneously vary the current powering the diode and the length of the laser cavity. Once the MHF range has been maximized, the laser will be used in PA spectroscopy in order to form Li-Yb molecules and characterize their energy structure.

Routine ingestion of, and contact with, myriad chemical compounds in our environment impacts all aspects of human health, from psychiatric to oncological to acute and chronic toxicities. However, health outcomes resulting from exposure events are strongly influenced by genetic variability present in genes underlying pertinent metabolic pathways. There are four genes that have been identified in the literature as playing crucial roles in multiple and interrelated biochemical pathways, and which may have broad implications for human health. These genes include DRD4, which codes for the dopamine D4 receptor and has been linked to numerous neurological conditions including addictions, schizophrenia, bipolar disorder, and Parkinson’s disease; 5-HTTLPR, the serotonin-transporter-linked region that codes for the serotonin receptor and may be involved in a host of behaviors including affective disorders and addictions; CYP2E1, a member of the cytochrome P450 family involved with the metabolism of many endogenous and exogenous chemicals including ethanol; and GSTT1, which is involved with the metabolism of toxic compounds including many carcinogens. In order to offer an accessible advanced preventative health screening tool to patients addressing numerous potential conditions, we attempted to implement a multiplexed polymerase chain reaction that would allow us to simultaneously assay these four genetic variants. We were able to combine the GSTT1 and CYP2E1 assays into a single reaction, however we were unable to find compatible reaction conditions for 5-HTTLPR and DRD4 either together or with GSTT1 and CYP2E1.

Connections based on composition, location, and origination will improve our ability to assess the future impacts of microplastics in the oceans. Microplastics are synthetic polymers classified by their size, must be ≤5mm, and vary in composition. This study will categorize each microplastic particle by shape, size, as well as composition through Fourier-transform infrared spectroscopy (FTIR). The FTIR creates a molecular fingerprint by transmitting infrared radiation at the microplastic particle, producing an output infrared spectrum. These spectrums can be cross-referenced to other known plastics’ fingerprints for identification. An entire sample may then be analyzed using this method to compare proportions of different types of plastic found at each sample site. Of the 218 samples analyzed 64% were polyethylene, 15% polypropylene, 10% polyvinyl chloride, 3% mixed polyvinyl chloride and polyethylene, 2% high-density polyethylene, and 6% unknown polymers. Additionally the particles scanned have been found to contain an unidentified chemical signature attached to its fingerprint. This FTIR research has yielded important and promising data, for future risk assessment, by allowing analysis of microplastics at spectroscopic level.

Droughts and floods are pervasive natural hazards. Accurate precipitation estimates are essential for model predictions. However, it is challenging to generate accurate precipitation estimates only using gage observation data, especially over data sparse regions. Satellite sensors, used in combination, have the potential to improve the accuracy, coverage, and resolution of precipitation estimates. We evaluate the Tropical Rainfall Measuring Mission (TRMM) Multi satellite Precipitation Analysis (TMPA) 0.25 degree real-time product in comparison with the TMPA gauge-adjusted research product for the period from January 2003 to June 2011 over Africa. We calculate the maximum dry period lengths for each water year based on both daily and monthly TMPA data. We also calculate several performance indicators including frequency bias index, probability of detection, false alarm ration and equitable threat score. From the results, we evaluate the spatial and temporal patterns of errors of the real-time product compared to the gauge-adjusted product. Specifically, we show spatial variability in monthly and annual precipitation bias in the real-time product and the performance indicators for select location distributed across the continent. We also demonstrate the effect that changes in the TMPA real-time algorithms have had on these performance metrics. This poster describes the TMPA algorithms, our evaluation methods, and our results, with particular attention to the error analysis over the central region of the African continent using daily TMPA data.

Genus Rhododendron consists of over 1000 species of woody plants.  While the overall phylogeny of the genus is known, the relationships between species are not.  My research focuses on a small and unusual retrotransposon, Cassandra, and its possible use for evolutionary studies.  Retrotransposons are sequences that are able to move to new DNA chromosomal locations via mechanisms simlar to retroviral DNA replication.  Transposition involves transcription of an integrated DNA copy through an RNA product that acts as a template for reverse transcription, and finally integration of the resulting DNA at new sites in the plant genome.  Like other retrotransposons, Cassandra has no mechanism for complete excision from a site it has occupied.  Thus, once the element is inserted into a genomic site, all or part of it is retained at this position as a stable marker.  Consequently, a Cassandra insertion at a given site is a shared derived trait, suitable for evolutionary tree-building.  Ultimately, knowing these sequences of transposition may shed light on the pattern of evolutionary divergence of Rhododendron and Ericaceae plants.  Based on one insertion site, my data suggests that thus far, only a solo LTR version of the Cassandra element is found in most species of the subgenus Hymenanthes (primarily in East Asia), with an empty site found in the subsection Pontica (more geographically diverse).  Interestingly, for a few species within Hymenanthes that lack the element, another conserved insertion (approx. 450 bp) is found in the DNA instead.  Moving forward, I will look at additional insertion sites, to gain further information on Rhododendron phylogeny.

Previous studies have found deficits in visual attention and socio-communicative behavior to be characteristics of Autism Spectrum Disorder (ASD) (van der Geest, Kemner, Camfferman, Verbaten, & Van Engeland, 2001). Recently, researchers have investigated these deficits in young infants with the likelihood of a later autism diagnosis. One study indicates that infants at high risk for ASD will exhibit an atypical profile for visual disengagement (Elsabbagh et al., 2009). Our research aims to replicate these results by administering the ‘gap-overlap’ task to participants 12 months of age, separated into two categories: ‘high risk’, or those that have an older sibling with an ASD diagnosis, or ‘low risk,’ indicating no familial risk of ASD. The ‘gap-overlap’ task, a 5-10 minute measure consisting of 36 total trials, assesses infant ability to transfer visual attention from a central stimulus to a peripheral target. The infant views a random sequence of three trial types: 1) baseline, in which a central stimulus is immediately replaced by a peripheral target; 2) overlap, where the target appears peripherally while the stimulus remains in the center; and 3) gap, in which the central stimulus’ disappearance and the peripheral target’s appearance are separated by an interval of time. We measured the latency period, or the amount of time between the appearance of the peripheral stimulus and the infant’s saccade toward the target. Based on previous studies’ results, we hypothesize that the high-risk infants will exhibit longer latency periods in the gap and overlap trial types (Elsabbagh et al., 2009). This reduced ability to transfer visual attention may be a predictor for a later autism diagnosis. It is hoped that by identifying these early markers, new opportunities will be created for effective treatment and intervention.

Angiogenesis is the development of new blood vessels from pre-existing vasculature and is a hallmark of Kaposi’s sarcoma (KS), a highly vascularized neoplasm prevalent among immunosuppressed individuals. The etiological agent of KS, Kaposi’s sarcoma herpesvirus (KSHV), induces angiogenic phenotypes in endothelial cells during latent infection. Interestingly, KSHV infection leads to down-regulation of transforming growth factor-beta 2 (TGF-beta2), an anti-angiogenic cytokine. In addition to six viral genes, KSHV also encodes 17 recently discovered microRNAs (miRNAs) during latent infection that appear to directly contribute to pathogenesis and angiogenesis by targeting host gene expression.  These endogenously encoded RNAs of 19-23 nucleotides post-transcriptionally regulate gene expression through basepairing interactions with the 3’ untranslated region (UTR) of target messenger RNAs (mRNAs) and either mark them for degradation or prevent ribosomal binding. We have screened the miRNAs of KSHV to determine if any are involved in the downregulation of TGF-beta2 by KSHV. We found that two KSHV miRNAs, miK-K3 and miR-K8, are sufficient to downregulate TGF-beta2. To determine if these miRNAs act directly on the mRNA of TGF-beta2 as opposed to altering genes that affect its expression, I proposed two aims: (1) use quantitative RT-PCR to determine the levels of TGF-beta2 expression during KSHV infection when miR-K3 and miR-K8 are inhibited by antagomirs, small antisense inhibitors of miRNAs, and (2) determine if miK-K3 and miR-K8 directly bind to the 3ʼ UTR of TGF-beta2 mRNA using luciferase reporter constructs. By identifying specific targets of KSHVʼs miRNAs such as TGF-beta2, we can improve our understanding of how KSHV is able to maintain latent infection and disrupt the normal regulation of cell proliferation. These studies are the first steps to better understanding KSHV pathogenesis and to developing targets that disrupt KSHV replication.

In eukaryotic organisms, ubiquitin is a small protein modifier that is attached to proteins and targets them for proteasomal degradation. In an analogous fashion, in Mycobacterium tuberculosis (Mtb), the prokaryotic ubiquitin-like protein (Pup) is conjugated to lysine side-chains of substrate proteins and targets them for degradation by the Mtb 20S proteasome. This pathway has been shown to be essential for Mtb infection in mice, and is a potential target for theraputic reseach. The enzyme PafA is responsible for attaching Pup to its substrates and has previously been shown to be essential for lethal infections by Mtb in mice. We have developed a fluorescent activity-based probe to monitor PafA activity in vitro by conjugating Fluorescein isothiocyanate (FITC) to free lysine, a known substrate of PafA. FITC-Lys demonstrates a high degree of specificity for PafA, even in the presence of cell lysates. This probe was employed to visualize PafA activity by in-gel fluorescence. It has allowed us to identify a minimal sequence of Pup, the C-terminal 26 amino acids, that is recognized by PafA. Alanine mutants of the 25th and 26th C-terminal residues demonstrate that leucines at these positions are critical for PafA interaction.

No commercial mining has been attempted in the glacier basin area surrounding the ghost town of Monte Cristo, Washington since 1920. My research investigates the ecological history of mining in the Monte Cristo area and the impacts which are still evident today. Mining in Monte Cristo has/had three direct impacts on the ecology of its surroundings; runoff, tailings at each mining site, and the discarded “waste” from the mineral concentrator. The ore concentrator is long gone and had not been in operation for nearly a century. However the tailings at the mines remain and water continues to run from the scars ripped into the hillside, infiltrating the flow with pollutants. I did an in-depth historical analysis of newspaper articles along with interpretation of historical photographs to create a clear image of the indirect impacts mining had to the glacier basin area. The ancillary impacts included logging, grading and tunnel building from the railroad construction and building of a complete township. My analysis of historical photographic evidence and the contrasting photos from my recent visit to the area show that the wilderness has regained a foothold by the regrown thick forest and destruction of most of the man-made structures in what was once a booming mining town. Ongoing research shows that the ecological recovery of the Monte Cristo mines is a tenacious battle. Much physical evidence remains yet the environmental disturbances of the Monte Cristo mineral mines are being alleviated by nature.

Multi-Legged terrestrial biological systems demonstrate complex forms of locomotion by utilizing different gait patterns. These complex forms of locomotion provide a path for promising advancements in the development of biomimetic systems. In previous research, we analyzed various multi-legged terrestrial systems and several variables that effect the selection of the gait pattern became apparent. It was found that the number of legs, stability of the system, and velocity of the system all had a significant effect on the gait patterns selected and the gait patterns that are available for use in the system. This research focuses on constructing biomimetic walking systems, using LEGO Mindstorms NXT robotic kit, which implement the carious characteristics of animal locomotion to determine the effect of these variables on the gait patterns. The current systems under analysis consist of six legs controlled by interactive servo motors and an NXT micro-computer which allow the system to move with several distinct gait patterns. From the biomimetic system, it is shown that some gait patterns are inefficient under certain conditions and this may lead to determination of when a gait pattern change is necessary in both the biological and biomimetic systems. Application of this research include pattern selection in mechanical systems and design influence on biomimetic systmes.

Blindness is a condition that impacts people across the globe. Some of these people are born blind due to a genetic defect while others become blind through an accident or as the result of disease. Thus, dissecting the underlying molecular causes of blindness is a critical component in improving the lives of many people. To study causes of blindness, we are analyzing disease causing mutations in the model organism Danio Rerio, or zebrafish. The recessive ZVM10 mutation causes early degeneration of the retinal photoreceptors, causing complete blindness. To study this mutation we are determining the identity of the mutated gene. The first step is to determine the position of the mutation within the zebrafish genome (i.e. map the mutation). This is done by mating the ZVM10 AB fish with a polymorphic fish strain. The crossovers between the different DNAs are traced, and used to identify the area homozygous for the AB allele. By continually reducing this region we specify a small group of genes that potentially have mutated. Using this method, I have established a general region on chromosome 20 between Z markers G40149 and G47173 containing the ZVM10 mutation. Identification and study of this mutation will enable scientists to better understand the role of this gene in vision. It will also permit the identification of people who are blind due to this genetic mutation, through genetic screening of the patient. Finally, if this gene is also involved in human blindness, it will become a candidate for rescuing blindness through gene therapy.

All-atom molecular dynamics (MD) simulations are increasingly being used to predict protein motion and to represent the range of dynamic structures populated. MD simulations are now commonly done on nanosecond to microsecond timescales for improved sampling of biologically relevant processes. With the increasing size of simulation data, data visualization has become a challenge. In this research project, we address this problem by building an interactive 2D/3D rendering software based on Windows Forms and Windows Presentation Forms (WPF) within Microsoft’s .NET 4.0 Framework. The Protein Dashboard (PD) exists as several plugins for the in-house software program called DIVE (Data Intensive Visualization Engine). The Protein Dashboard offers 2D plots for rendering protein properties as well as 3D rendering for protein structures. Datapoints in both 2D and 3D plots are fully interactive. As plugins of DIVE, PD offers microscripting for both novice and advanced users. With microscripting, users can manipulate both 2D and 3D plots to examine data in various ways. All DIVE plugins have the capability of receiving and outputting data to one another. Thus, users can examine their data in different depth by connecting two different 2D plots and have the latter display the subset. The flexibility and interactivity of PD will allow researchers to explore MD simulation data much more efficiently and ultimately speed up scientific discovery.

The Dickinson lab studies the neurobiology of fruit flies. Particularly, we tested the effects of the neurotransmitter octopamine on a fly's ability to respond to visual stimuli while flying and walking. Evidence shows that a set of visually sensitive cells that are thought to be involved in stabilizing reflexes during flight have different responsive properties with and without octopamine. To further investigate the role of octopamine in this system, we looked for optomotor response deficits in flies that do not produce octopamine. We used mutant Drosophila melanogaster flies that no longer have the gene for enzyme tyramine-beta-hydroxylase, which converts tyramine to octopamine. As a result, these flies build up an excess of tyramine and are unable to produce octopamine. We tethered a fly to a metal pin, and placed it an LED light arena, where we presented it with different moving stripe patterns. We placed an infrared light above the fly, and an infrared sensor below it. Infrared light was used because it is outside the visual range of the fly and would not interfere with our intended visual stimuli. The fly cast a shadow on the sensor, from which we computed the wingbeat frequency and amplitude. We used the left and right wingbeat amplitudes to determine the fly's torque, which indicates its turning response. We analyzed this turning response to measure the fly's ability to respond to the visual stimuli. Lastly, we compared the octopamine-null fly's response to wild type flies. These experiments will further our understanding of the role of octopamine in the optomotor response system of fruit flies.

T lymphocytes protect against the universe of pathogens by generating a diverse repertoire of antigen receptors called T cell receptors (TCRs). Each individual T cell expresses TCRs with a single antigen specificity. The induction of self-tolerance is crucial to the health of the individual because it culls the T cell population of those cells that bear self-antigen reactive receptors. Such autoreactive T cells are the driving force behind autoimmune diseases. One mechanism for inducing self-tolerance is TCR revision, by which peripheral T cells replace self-reactive TCRs with newly generated, non-autoreactive TCRs. This replacement results in cell rescue and involves cleaving DNA, which requires implementation of many controls to protect genome stability. Cells undergoing TCR revision appear to be localized in the spleen and lymph nodes inside a confined microenvironment known as the germinal center (GC), and this constrainment may provide a means for controlling this process. Given the rarity of revising T cells, my project focused on potential means for increasing the frequency of cells undergoing TCR revision using as a model system TCR transgenic mice, in which the majority of T cells express TCRs of the same antigen specificity. We hypothesized that expanding the GC T cell compartment would increase the frequency of cells undergoing TCR revision. I carried out injections of lipopolysaccharide, sheep red blood cells, and anti-CD40 antibody into TCR transgenic mice in an effort to induce GC formation. I then analyzed the accumulation of post-revision and revising T cell populations by flow cytometry. Use of any of these agents to increase TCR revision would facilitate the isolation of post-revision and revising T cells and allow further investigation into the mechanistic details of this tolerance process. Our goal is to understand how the challenging balance between having a diverse T cell repertoire and avoiding autoimmunity is maintained.

Wind is highly variable and unpredictable, unlike conventional generation resources such as coal. The U.S. grid system is ill-equipped to accommodate resources that are stochastic in nature. Policies exist at the federal, state, and local levels that attempt to subsidize the production cost of wind generation, but how will these incentives impact system operations? We explore how the power generation mixture will change due to policies that incentivize wind. Our approach involves an analysis of a case study of three different incentive schemes: a base case (un-incentivized), the federal production tax credit (PTC) for wind, and a feed-in tariff (FIT) system modeled on the FIT proposed in California. Computer simulations will be developed to qualitatively model how these policies impact system operations using the economic dispatch algorithm, which is used in practice to deploy generation resources to serve the load and meet all power system constraints at the lowest cost. Comparing these cases will show which of these incentives have an impact on the total energy cost over a given time frame, as well as give an idea about the resulting generation profile.

Nitrous oxide (N₂O, dinitrogen monoxide, commonly called laughing gas) is an important greenhouse gas with a global warming potential, over a 100 year time scale, about 298 times higher than that of CO₂. N₂O is also the major source of NO in the atmosphere, which is a natural agent of stratospheric ozone destruction. The ocean is an important natural source of N₂O providing up to 25% of emissions to the atmosphere. However, although it is known the ocean is a net source for atmospheric N₂O, our understanding of the distribution and magnitude of the oceanic source is limited. Eastern-boundary upwelling zones which contain large oxygen-depleted intermediate waters, like the Eastern tropical North Pacific (ETNP), act as large sources of N₂O to the atmosphere but have not been adequately studied. I investigated the concentration of N₂O in the ETNP aboard the R/V Thompson between March 16th and 27th 2012. Water samples were collected at 6 locations between 20°N and 32.5°N along the west coast of Mexico on board the R/V Thompson and N2O concentrations measured on board the ship using gas chromatography. Using these results I plotted depth profiles of N₂O and O₂ from each station in order to characterize the vertical distribution of N₂O and compare the stations to see how N₂O concentration varies on a North-South axis. I consistently found a large peak in N₂O concentrations at around 200 m depth at the oxic-suboxic boundary. I used surface N₂O concentrations and known atmospheric N₂O concentrations to calculate the flux of N₂O across the air-sea boundary to determine the magnitude of the source of atmospheric N₂O in the ETNP and to explore the spatial and temporal variability of N₂O production in the region.

The Atacama Desert is currently named the "driest place on earth", specifically Yungay in the Atacama's center. These records are based on experiments done by using rain gauges to measure approximate rainfall but there are said to be nearby areas much drier. In regions where hardly any rain falls, it is nearly impossible to measure rainfall by means of rain gauges. The goal of this project is to find a way to measure rainfall in an area with low amounts of rainfall. To do this, we are investigating the correlation between amount of rainfall and the salt distribution in a given region. Generally in non-arid regions, soluble salts such as nitrates and perchlorates wash away into groundwater and the ocean. However, in deserts where salts are allowed to accumulate, the occasional rain dissolves these salts and moves them vertically through the soil column. If we can determine how much rain it takes to dissolve and move salts to certain depths, then we will be able to use a vertical soil profile as a means to determine how much rain has fallen in an area in a given period of time. The method will involve performing desert soil extractions, for which salt concentrations can be measured using ion-chromatography techniques. Ion specific electrodes will be designed and used to run experiments in which known concentrations of salts are added to desert soils and subjected to simulated rainfall rates which will allow us to determine the maximum rainfall that correlates with various distributions of salts. Thus far, tests on samples from “km 40,” a region of the Atacama Desert have shown its salt distribution to be very similar to those of perchlorates found on Mars. We hope the results will indicate that “km 40” is even drier than Yungay, the current “driest place on earth.”

Populus trichocarpa, or Black Cottonwood, form a mutualistic relationship with diazotrophic bacteria, in which nitrogen is provided to the host plant in exchange for protection and energy. Understanding this form of symbiosis is essential in determining how biologically available nitrogen is cycled throughout our planet’s biomes. A well-known diazotrophic mutualism is found between leguminous species and Rhizobia or Frankia bacteria, where colonies are established inside root nodules of the host plant. Black Cottonwoods differ from legumes in that they form an endosymbiosis with nitrogen-fixing bacteria recruited from the environment, where the bacteria form colonies throughout the plant tissue. To determine the endophyte source, bacterial samples were obtained from sand, river water, and seed collected at the Three Forks Park in Washington to determine where in the environment Black Cottonwoods are coming into contact with these endophytes, and which species are found at each source. Nitrogen-fixing species were selected for by culturing bacteria using nitrogen free media, and were then subjected to PCR for amplification of the nitrogenase gene for confirmation. Species identification was performed by amplifying the 16sRNA, followed by sequencing and local alignment matching. Of the 29 samples collected from the Three Forks site, 27 were found to carry the nitrogenase gene, and species identification underway. Black Cottonwoods, in addition to other poplar species, have been found to be very useful industrially as biofuels and in the bioremediation of environmental pollutants. Nitrogen-fixation provides a major benefit for using poplars, where the use of fertilizers is reduced. It is thought that there is a common evolutionary link between more plant species and diazotrophic bacteria than is currently known, and understanding which species exist outside of the plant hosts may lead to the reduction of nitrogen-based fertilizer in other industrially useful plants.

Graphene is a novel two-dimensional carbon material whose recent discovery has been awarded the 2010 Nobel Prize in Physics. The extraordinary electronic and mechanical properties of graphene such as its extremely high electron mobility and record breaking thermal conductivity have made it a promising candidate for countless applications, including integrated circuits, solar cells, and ultracapacitors. Graphene has also demonstrated usefulness in biological applications, and it was recently shown that mesenchymal stem cells cultured on the surface of graphene experience accelerated differentiation into bone cells. This has motivated research into the interaction of graphene with other types of cells, and we investigate the effects of culturing cardiomyocytes (heart muscle cells) on the surface of graphene. With cardiovascular disease being the leading cause of death globally there is currently a large effort to develop treatments based on engineered heart tissue, but no tissue engineering methods have thus far been able to produce cells that are sufficiently mature to provide the force generation necessary in a beating heart. Two methods currently showing promise for the maturation of cardiomyocytes are designed to mimic the environment of native heart tissue using electrical stimulation, and culturing on micropatterned substrates.  By culturing cardiomyocytes on the surface of micropatterned graphene that is electrically contacted through gold electrodes, we explore graphene’s potential to act as a versatile platform that could combine both methods.

The Institute of Medicine‘s (IOM) report on health disparities, “Unequal Treatment”, identified the medical system’s inability to distinguish minority groups with meaningful specificity as a primary barrier to recognizing critical disparities in health care and outcomes. A recent follow-up report on “Race, Ethnicity, and Language Data” called for more detailed demographic data collection. This study evaluated the validity of self-reported primary language to detect disparities in diabetes care across language groups of first generation, mostly non-English speaking outpatients at an international clinic. The REALL (Race, Ethnicity and Language proficiency Level) study is a cross-sectional pilot study, surveying a convenience sample of immigrant and refugee patients receiving primary care at an urban, county hospital. Participants were eligible for this study if they had diabetes based on medical record data and completed the REALL survey question about how many and what languages they speak, their reading ability in those languages, and the culture they most identify with. Survey data were linked with medical record data that included hemoglobin A1C (HA1C), low density lipoprotein (LDL) and systolic blood pressure (SBP). Diabetes control was evaluated across the 6 largest language groups. 250 patients were eligible for the study. The survey data were 90.84% concordant with registration data for primary language. Mean HA1Cs were lowest among Vietnamese patients, significantly lower than Somali patients and Cambodian patients. While 52% of Vietnamese patients had HA1C<7, only 26% of Somali patients had HA1C<7. There were no statistically significant differences across language groups in mean LDL level or SBP. Results suggest that there is variability in diabetic outcomes across language groups in first generation immigrant communities. Recent refugee communities are potentially more stressed due to lack of acculturation and community establishment. Further inquiry into their duration in the US, the clinical care system, and their dietary practices are advised.

Vietnam, which is experiencing a heath transition from communicable to non-communicable diseases, has an increased burden of stroke. Understanding its risk factors, including stress, are needed. The goal of this study was to evaluate the relationship of chronic stress and stroke symptoms (which are indicative of a potential stroke) as well as hypertension and diabetes in participants ages 35 and older in Da Nang, Viet Nam. We randomly identified adults, age 35 and older using voter registration lists for inclusion in this study. Interviews and health procedures were conducted either at the local health clinic or participants’ homes depending on preference. Stress was measured using the chronic stress burden scale assessing problems occurring in five domains: problems with one’s own health, with another’s health, job difficulties, financial strain, and relationship problems. Hypertensions was defined as self-reported or measured systolic blood pressure of 140 mm Hg or diastolic of 90 mm Hg and higher. Stroke was ascertained as a self-report of symptoms related to stroke or transient ischemic attack collected by the Questionnaire to Verify Stroke-Free Status (QVSFS). Multiple logistic regressions assessed the odds of increased risk of stroke related to level of stress categorized as no stress, 1 or 2 symptoms, and 3 to 5 symptoms in unadjusted and adjusted models. After adjustment for demographic, health characteristics, as well as diabetes and hypertension, individuals experiencing stress at the highest level (3-5 domains) were more than eight times as likely to report stroke symptoms as those with no stress (OR: 8.13, 4.43-14.91). Lower levels of stress (1-2 domains) also increased significantly the risk of stroke symptoms (OR: 3.27, 95% CI: 2.01-5.34). After adjusting for diabetes and hypertension, along with other potential confounding factors, we found stress to be independently associated with risk of stroke as measured by stroke symptoms.

 Harbor seals (Phoca vitulina concolor) are widely distributed across the North Atlantic and the North Pacific oceans.   Foraging opportunistically on seasonally abundant species, much of what is known about pinniped diet has been determined from analyzing stomach and intestinal contents. The use of fish otoliths recovered from pinniped fecal material (scat) has proven an effective tool to understand foraging habits Because fish otoliths (fish ear bones) are species-distinct and do not completely erode in the digestive tract, frequency of particular prey species can be identified through scat collection and subsequent identification of recovered otoliths. Within Great Bay, New Jersey a population of habor seals has been steadily increasing since observations began in 1994. In the winter of 2011 58 scat samples were obtained and 270 otoliths were recovered, photographed, identified, and measured. Fishes from the order Clupeiformes (herring) dominated recovered otoliths (32%), followed by Gadiformes (cod) (21%) and Pleuronectiformes (flat fish) (12%). Dominant species included Brevortia tyrannus (bunker), Clupea harengus (american herring), Urophycis sp. (red and spotted hake), and Ammodytes americanus (sandlance). Foraging preference varied monthly as indicated by temporal shifts in determined fish orders. This monthly variation in foraging preferences is consistent with annual fish migrations and food availability. Based on back-calculated prey lengths, these harbor seals likely feed both inside and outside the estuary. By understanding the foraging patterns and preferences of harbor seals within a dynamic ecosystem can assist in understanding their ecological significance. These frequencies can be compared between geographic locations, and across years and seasons.

In the 1960 United States Census, the federal government first gave official recognition to the Pacific Islander community by adding "Hawaiian or Part Hawaiian" to the options available under the category of "American Indian."  Between 1970 and 1990, however, the Census Bureau grouped Pacific Islanders in the category "Asian Americans," and statistically analyzed only this aggregate category.  In the 2000 census the Census Bureau constructed the category "Native Hawaiian and Other Pacific Islander," thereby recognizing the possible separate status of non-Hawaiian Pacific Islanders.  Official definitions of racial and ethnic groups are important because the federal government uses them to allocate resources to various state and local governmental units.  For example, schools in the United States categorize and analyze the academic performance and needs of students by using the racial categories as defined by the U.S. Census.  Many Washington state school districts, however, still group Asian American students and Pacific Islander students into an aggregate category when assessing academic performance and identifying students who perform below expectations and are in need of academic assistance.  Using data from the Washington Office of Superintendent of Public Instruction, I examine the graduation rates and standardized test scores of Asian American students and Pacific Islander students in the 17 school districts in the Seattle and Tacoma metropolis that contain the largest number of Pacific Islander students in the state. My objective is to gain a better understanding of the social-structural factors that produce variation in outcomes among the officially defined subgroups of students.

This project is aimed to examine the ways gender stereotypes are reinforced in sports. Particularly I wanted to investigate the impact this has on transgendered, intersex or otherwise gender nonconforming student athletes. This connects to current research published in the National Transgender Discrimination Study, examples of homophobia in women’s college basketball, the impact of genetic testing on athletes competing in the Olympic Games, the publication of the NCAA Inclusion of Transgender Student-Athletes, and the recent critical analysis of transgender legislation politics by Spade. For this I implemented the following methods: Literature review, focused analysis of data collected by Grant et al., social media analysis of internet blogs and websites, photo voice, critical discourse analysis and review of documentary films. These different approaches were intended to help me in the investigation of my research question by approaching the subject from multiple angles. With my research I hope to constructively contribute to the ongoing dispute of lingering discrimination based upon sexual orientation, gender politics and human rights in the United States and around the globe. Furthermore I aim to show how the struggle for acceptance of gender nonconforming students is still complicated by barriers raised on the grounds of biases and unfounded stereotypes. This project therefore shows how, despite the claims of policies aimed to end discrimination on the basis of race, creed, ethnicity, nationality, gender, sexual orientation or ability, not all students are treated equally. Finally it also connects to my undergraduate honors research project where I examine the transgender experience and quality of life in connection to gender reassignment surgery in the United States and Germany.

This project explores the innate immunity of the earthworm species Eisenia fetida during development in context of its symbiotic relationship with Verminephrobacter eiseniae, a known bacterial symbiont. Innate immunity, unlike adaptive, has largely unspecific properties against foreign particles yet many organisms that possess only innate immunity manage to allow select beneficial symbionts to thrive within their body while at the same time defending against pathogenic infection. In this study I begin to explore involvement of innate immunity in the relationship between E. fetida and its symbiont V. eiseniae. This project examines expression of a common innate response, oxidative stress, in early stages of V. eiseniae colonization of its host E. fetida. We hypothesize that innate immunity activity is spatially separated from colonization of bacterial symbionts. To test this hypothesis, I will stain for nitric oxide synthase (NOS), an enzyme commonly involved in oxidative stress, during the development of E. fetida in the presence of V. eiseniae. I will then proceed to compare the location of NOS to the location of V. eiseniae. If the hypothesis is correct, then oxidative stress response in the worm eliminates foreign organisms everywhere except where the symbionts reside. On the other hand, if oxidative stress is at the same location as the known symbionts at the same time during development, then the oxidative stress may eliminate other foreign organisms except the symbionts, which have developed a mechanism for overcoming the stress. The results of this research can reveal how innate immunity overcomes the dilemma of accommodating symbionts. In addition, if E. fetida is particularly easy to work with for this type of experimentation, then E. fetida could prove to be an ideal model organism for studying innate immunity. Furthermore, insights into innate immunity may hold the key to new innovative ways of combating disease.

Nearly half the world’s population lives in a coastal watershed where all anthropogenic input to the hydrologic network are transported downstream and onto the continental shelf. This connectivity then extends to the movement of terrestrial matter by submarine canyon channels. The morphology and evolution of these two essential coastal transport systems have been shown by previous literature to be strongly linked. I investigate the changes in channel morphology across a coastal zone on the Baja peninsula, and quantifying the link between river and submarine channel complexity through measurements of channel sinuosity, network slope gradient, and order length. Quantifying the changes in channel complexity across the coastal zone provides the means to monitor anthropogenic impacts upon terrestrial riverine system on submarine canyons.

During early development, spontaneous waves of electrical activity propagate across many different structures in the central nervous system. These waves are a critical feature of neuronal development, regulating neuronal migration, physiological maturation, and synaptic connectivity. In slices of mouse cerebral cortex taken at early stages (embryonic day 18 – postnatal day 1), we observed circular clusters of cells (domains) that were synchronously active during times when the slice was not generating spontaneous waves of activity. The domains consisted of approximately 10 to 50 cells and activity appeared to initiate from a center cell before the synchronous activation of the surrounding cluster of cells. We hypothesize that domains may form the functional basis of activity that propagates across the entire cortex. We have applied a range of drugs to elucidate the mechanism that triggers these small coactive domains. The domains do not appear to be dependent on electrical activity, they are not mediated by the neurotransmitters gamma-aminobutyric acid (GABA) or glutamate, and they are not dependent on calcium channels or the release of internal stores of calcium. Application of the gap junction blocker octanol inhibited the appearance of domains, but questions remain as to the specificity of octanol. Future work will identify the type of cell that triggers the domain and further study the relationship between the presence of domains and development of the neocortex.

Through much of the 20th century, the ASARCO copper smelter in Tacoma released heavy metal-rich ash, contaminating local soils and sediments. However, the smelter plant is not the only source of contamination: arsenate pesticides and other heavy metal sources contributed to soil contamination. Understanding the source of contamination can lead to remediation or replacement of contaminated soil. Here we use soil magnetic properties to identify minerals associated with smelter contamination. Specifically, iron bearing minerals can uniquely identify emissions generated from the smelting process. We use magnetic susceptibility (both high and low field), coercivity and magnetic remanence to produce a “magnetic fingerprint” of minerals from smelter dust. These properties are affected by grain size and mineralogy of magnetic particles. Remanance (Mr/Ms) and susceptibility/coercivity (LF/Hc) ratios are similar in all soils regardless of degree of contamination. However, high field susceptibility does appear to be related to arsenic concentrations of smelter contamination (R2= 0.4656). Further sampling and testing are being conducted to extend that relationship to other sites. Our results suggest that magnetic properties and testing can be used to efficiently and cheaply assess smelter contamination throughout the South Puget Sound region.

Cues from predation can have strong effects on prey behavior and development, but antipredator responses can reduce fitness in other ways. Costly responses to predators should be, and often are, proportional to the level of risk (i.e., threat-sensitive); however, the mechanisms by which prey assess risk are not fully understood. In mesocosm experiments, red-eyed treefrogs (Agalychnis callidryas) show threat-sensitive growth reduction in response to predation cues from giant water bugs (Belostoma) and dragonfly naiads (Anax). We reared A. callidryas tadpoles from hatching in individual 400 ml microcosms in an open-air laboratory in Panama to assess their growth responses to variation in water-borne chemical cues from predation on conspecifics. In an experiment manipulating cue concentration, cues from predation by both Anax and Belostoma elicited a similar, dose-dependent reduction in growth. We then investigated effects of the frequency of chemical cueing by holding the total cue amount constant across treatments, but delivering it in fewer larger doses or more frequent smaller doses. We found a strong negative correlation between tadpole growth and the frequency of cue events. These results suggest that the frequency of predation cue events is more important than the biomass of prey consumed, or amount of cue delivered per event, for assessment of predation risk. This is consistent with results from mesocosm experiments wherein tadpoles responded more strongly to predation on small tadpoles, via multiple predation events, than they did to predation of an equivalent biomass of larger tadpoles.

Cell migration and cell adhesion are crucial processes for embryonic development, homeostasis and cancer progression. Regulated changes in adhesion are coordinated with cytoskeletal change, which result in morphogenesis. Conversely, the loss of cell to cell adhesion can promote tumor cell metastasis and change in cell motility. Thus, examining the specific regulator of the adhesion and cytoskeleton is important in terms of furthering our understanding of the development and disease progression. We specifically study an important protein regulator called p120 catenin and its involvement in cell migration in the zebrafish embryo. An extensive literature implies that p120 catenin both positively and negatively regulates cell adhesiveness through phosphorylation. Cell cultures show that phosphorylation of serine residues strengthens the adhesion and that phosphorylation of tyrosine residues increases the cell mobility. After the morpholino knockdown of normal p120 catenin, I will co-inject the mutant Y228F p120 catenin. Then I will observe whether the mutant without the tryrosine phosphorylation rescued normal development. For this I will use in situ staining of the somites with myoD at the 3 to 15 somite stage. To observe migration and protein localization, we will use a confocal microscope with the embryos' cells labeled with cherry fluorescent p120 catenin, green fluorescent Rho GTPase, or a green fluorescent plasma membrane. If mutant p120 catenin, which cannot be phosphorylated, can rescue successfully, we conclude the phosphorylation site does not play an important role in cell-cell adhesion or cell migration. However, if it does not rescue the morpholino knockdown, tyrosine phosphorylation at the 228 site is important for p120 catenin’s modulation of cell–cell adhesion and cell migration.

The nature of Systemic Lupus Erythematosus (SLE) involves a complex network of uncontrolled activations of signals, which leads to a vast range of symptoms. SLE is an autoimmune disease that manifests itself when the immune system attacks the body’s cells and tissues, resulting in inflammations in joints, organs, and skin. The course of the disease is unpredictable and much more is to be understood about the mechanisms of the illness and the background of the patients who are prone to the disease. This study explores both the mechanistic and clinical aspect of SLE in an attempt to gain a broader view of the disease. Using 3 interferon stimulated genes, MX1, PKR, and CXCL10, we evaluated interferon scores of 66 patients. We then utilized cluster analysis to divide patients into two main groups based on interferon scores: Group 1 consisted of controls and SLE patients with low interferon scores (0.4), Group 2 consisted of SLE patients with high interferon scores (10.4). These groups were compared with interferon stimulated genes, RNase1 and Toll-Like Receptors 7 (TLR7), which positively correlated with interferon scores. A system called Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) is often utilized to quantitatively assess patients’ disease activity. The criteria in the evaluation of patients included symptoms often associated with SLE. The score in SLEDAI reflected the disease activity of the patient. In this study, we investigated the relationship between SLEDAI and interferon score, in which we found no correlation. However, when we examined Group 2, there was a trend towards better correlation with SLEDAI. In the clinical aspect, we examined age, race, and gender of SLE patients. In addition, we collected information on autoantibody titers such as double stranded DNA (dsDNA), antiphospholipid antibodies, and antinuclear antibodies (ANA), all of which may be important indicators of disease activity.

Many soldiers acquire traumatic brain injuries (TBI), such as edema, hemorrhage, and traumatic axonal injury, from improvised explosive devices. Currently there are no adequate brain-imaging devices for use near the battle field. Patients with TBI may require a complete hemicraniectomy to examine the extent and location of the injury. This presents a great need for field-deployable imaging devices optimized for brain imaging with the spatial resolution of CT scans. Previous work has shown that intraoperative ultrasound, ultrasound used during surgery, can create images of brain-based tissue stiffness. For this project, rats have been given TBI using controlled cortical impact methods and their brains have been imaged using shear wave imaging to quantify the stiffness of brain tissue. The ultrasound images have shown patterns of brain stiffness that exhibit the extent and location of TBI. After the brain tissue stiffness for TBI was quantified using shear wave ultrasound, the data was used to optimize ultrasound machines for imaging moderate TBI. The Verasonics ultrasound device in the lab was optimized to image brain tissue by tracking the shear wave, generated by the transducer, as it propagates through brain tissue and correlating propagation speed with stiffness values. The images obtained from the ultrasound device were compared against histology. The success of this project would ultimately lead to increased quality of care for soldiers with TBI near the battlefield.

Stroke is the degeneration of brain tissue caused by blockage of blood flow to the brain. It is one of the leading causes of adult disability and death worldwide. We used ultrasound elastography, a technique that measures local tissue deformation from ultrasound-induced shear wave propagation, to measure shear modulus, the ratio of shear stress to the shear strain, of brain tissue after ischemic infarction, loss of brain function due to low brain blood supply, to determine changes in individual hemisphere due to that injury. We imaged live mice that were 3 hours (hyperacute), 24 hours (acute) and 72 hours (subacute) after surgical occlusion of the middle cerebral artery, and measured the shear modulus of ipsilateral and contralateral brain hemispheres compared to corresponding values of control mice. The mice with hyperacute stroke showed statistically significant increase in shear modulus in both hemispheres compared with control animals. The mice with acute stroke showed a significantly decreased shear modulus in ipsilateral hemisphere and a significantly increased shear modulus in contralateral hemispheres compared to control mice. The mice with subacute stroke showed no significant difference in shear modulus compared to control mice. Significant differences were shown between ipsilateral and contralateral shear modulus values measured 24 hours and 72 hours after infarction. We hypothesize that the shear modulus differences among hyperacute, acute, and subacute stroke mice reflect the initial development of edema and reduction of cerebral blood flow in the ipsilateral hemisphere, and the initial reduction of blood flow then later development of edema in the contralateral hemisphere. Thus, ultrasound elastography may be a sensitive method to detect subtle changes in brain elasticity post stroke. Future work will include an attempt to remove the imaging artifact through the design of a new elastic imaging machine. This research will be a key step toward exploring the ultrasound parameters for imaging stroke, which will ultimately contribute to the development of a better imaging tool for potential stroke patients.

The aim of our research was to collect and synthesize best business practices and lessons learned about the ecotourism industry from a) the primary literature and b) interviews with a selection of ecotourism brokers from private, government, and civil society sectors. We then presented this information to the S. Korean Government in order to aid in the sustainable development of ecotourism on the Korean coastlines. We first examined the primary literature and created inventories of journal articles and books that outline contemporary paradigms of ecotourism. From these resources we established our own working definition of ecotourism as a baseline, represented through each section of the study: 1) Broker Types, 2) Ecotourism Production Process: Broker Perspective, 3) Triple Bottom Line Sustainability, and 4) Interview Framework. We then developed an interview protocol, and selected a series of case studies in which we interviewed a series of broker from different countries representing ecotourism industries and geographies similar to that of the Korean coastline. The framework of these interviews was based on a Triple Bottom Line Sustainability business model, which creates a balance between brokers, locals and the tourists. Results suggest that Triple Bottom Line Sustainability is appropriate for the development of ecotourism in S. Korea.

Huntington’s disease is a hereditary neurodegenerative disease that is characterized by motor and cognitive dysfunction and currently has no known cure. One of the earliest molecular events in Huntington’s disease pathogenesis is the down-regulation of the cannabinoid 1 receptor (CB₁), occurring prior to symptom onset and loss of any other receptor. Though the exact mechanism is unclear, it has been shown that CB₁ loss occurs almost exclusively in medium spiny neurons (MSNs), cells that play a key role in movement and degenerate later in disease progression. CB₁ knockouts in mouse models also exhibit exacerbated disease phenotype. Previous studies have attempted to rescue CB₁ function in mouse models by administering chronic cannabinoid agonists, but have produced inconclusive results. Our study investigates the effects of CB₁ receptor rescue from a genetic approach, by inserting flox-stop CB₁ (fsCB₁) specifically activated in striatal MSNs of R6/2 mice, the best characterized Huntington’s disease mouse model. We first confirmed the localization and functionality of the knocked-in fsCB₁ in R6/2 and CB₁ null mice (control), and then measured motor phenotype and synaptic integrity over time. Performance of R6/2 mice with and without fsCB₁ rescue was measured using rotarod, open field, novel object recognition, and clasping behavior tests biweekly from weeks 4 to 12 of age. MSN axon integrity was measured by IHC staining for caspase-6 and NPY-Y1R, markers for Wallerian-type degeneration. By observing behavior and axon integrity from pre- through late-symptomatic stages, we hope to establish a relationship between early MSN axonal loss and impaired motor phenotype in R6/2 mice, as well as link CB₁ function to axonal integrity through R6/2 and fsCB₁-R6/2 comparisons. This research will increase the present understanding of molecular mechanisms behind Huntington’s disease and provide insight into CB₁ as a therapeutic target.