The vertebrate body forms through a process called embryogenesis. In my research, I focused on the establishment of body length during embryogenesis of the model organism zebrafish (Danio rerio). Under normal conditions, the cells of the developing body intercalate towards the back, or dorsal side, of the embryo, and extend longitudinally to grow the body axis. One observed defect in this process blocks cell intercalation, thus leading to underdeveloped bodies, which is known as a convergent extension phenotype. In my research, I studied the role of Microtubule-Associated Serine/Threonine kinase-Like (MASTL) RNA in body axis formation. Because of a known role for MASTL in regulating chromosome segregation, I hypothesized that overexpression of MASTL would interfere with normal cell function and lead to a convergent extension phenotype with a shortened body axis in the developing zebrafish embryo. To test this hypothesis, I injected embryos with different concentrations of RNA and allowed them to develop. Overexpression of MASTL shortened body lengths at all but the lowest concentration of RNA. I then chose a low but effective concentration of MASTL RNA, injected embryos and quantified embryo length. Finally, I performed RNA in situ hybridizations, a process by which labeled probes are used to localize specific RNA transcripts in embryos. Using a variety of labeled probes, I found in addition to shortened body length, the distribution of the prospective spinal cord cells and muscle cells were abnormal in MASTL-injected embryos. The results of these experiments clearly show that overexpression of MASTL leads to a convergent extension phenotype. To continue this research, I will look at whether or not MASTL affects body length formation through Protein Phosphatase 2a, a known target of MASTL. The results of my research will lead to a better understanding of the role MASTL in cell intercalation and vertebrate body elongation.

It is known that exercise improves cancer survival, however, there is an unknown molecular link between physical activity and cancer occurrence. The purpose of this study was to determine the feasibility of studying biologic mechanisms related to exercise and cancer survival in the LIVESTRONG YMCA program. Eligible subjects were males and females who were diagnosed with prostate or breast cancer in the last three years, between 35-80 years of age, willing to provide urine samples at four time points, and enrollment in the 12-week LIVESTRONG YMCA program. Through a partnership with the University of Washington (UW) Mass Spectrometry Center and the UW Office of Nursing Research, two specific biomarkers were analyzed from the urine specimens. One of these markers is Estrogen DNA Adduct (EDA), an estrogen metabolite that binds to DNA and creates an increased potential of DNA mutation and cancer development. The other is 8-OH-dG, a biomarker related to oxidation. To determine the feasibility, we administered questionnaires to better determine patient satisfaction and calculate the percentage of participation and retention. One questionnaire surveyed the acceptability of our biospecimen collection procedures to participants, anticipated acceptability of additional biospecimen collection (blood and tissue samples) for future projects, and willingness to have a DEXA scan (for compensation). In order to determine the feasibility of conducting the study on a larger scale, we evaluated the percentage of participants enrolled out of those recruited, percentage of participants who provided urine samples out of those enrolled, and the percentage of participants who completed the program. Continuing to invest in our therapeutic, diagnostic and genetic understanding of cancer means that in the future, patients will have options based on scientific evidence.

HIV remains a serious health challenge particularly in developing countries. This can be attributed in part to the fact that many common diagnostic procedures in high-income countries are too expensive and technically complex to be practical in low-income countries. While there are several strategies for diagnosing HIV, one promising method is using the detection of the p24 antigen. The p24 antigen is a viral protein that can be detected within two weeks after HIV infection. This is useful because it allows for the detection of HIV infection sooner than the commonly used HIV antibody detection tests and rivals the more technologically complex nucleic acid detection methods. Our goal is to develop this test using a paper-based lateral flow membrane and a technique called immune complex dissociation (ICD) to reduce cost and increase sensitivity. The laboratory p24 antigen test was adapted into a paper format using the same reagents as the laboratory test. By comparing the results of the respective methods, we found that the paper test performed well compared to the laboratory test. This performance indicates that there is value in using the paper format and in exploring methods to increase the sensitivity of the assay. Test sensitivity can be compromised by the presence of antibodies that form complexes with the p24 antigen. These complexes reduce the amount of antigen that is free for detection. ICD restores this sensitivity by dissociating the antigen from these complexes. We tested the ICD process, to show that it is compatible with the paper format and improves sensitivity, by running parallel tests with and without ICD to demonstrate the efficacy of that procedure. The completion of this project will bring the paper-based assay one step closer to making a previously expensive, technology intensive, and operationally complicated test, accessible to those in low-resource settings.

A major focus of breast cancer research has involved the catechol estrogen pathway. Estrogen DNA Adduct (EDA) is a novel biomarker that is hypothesized to play a role in initiating breast cancer. Pilot studies have shown elevated levels of EDA in women at high risk for breast cancer and with breast cancer. The overall purpose of this project was to determine whether the EDA biomarker has potential for clinical use for breast cancer prevention. The first step toward this goal was to examine the extent to which the biomarker varies over time in the same individual. The specific aim was to determine whether the variation between urine samples taken at two points in time is significantly different from samples taken at a single point in time. We utilized a convenience sample from the DEEM (Diet, Exercise and Estrogen Metabolites) study of 6 urine samples from 3 women at 2 separate clinic visits, conducted 3 months apart. Triple quadrupole mass spectrometry was used to process 37 estrogen metabolites in the urine samples. The fragmentation pattern of each metabolite was analyzed and compared to a panel of known estrogen metabolites in which the elution times were known. The correlation coefficient between the 2 clinical visits was 0.49. The results from this analysis indicate moderate correlation between 2 time points. We will await the results from the larger study to decide whether a one point in time urine collection is adequate for the overall project. The implications of the overall project are important because determining breast cancer risk from urine samples would be a sensitive and non-invasive method that could allow healthcare providers to better target the women that should receive careful monitoring, testing, and interventions.

Cochlear implants (CI) are neural prostheses that provide individuals with profound hearing loss the ability to hear through artificial electrical stimulation to the inner ear. Despite the relative success of cochlear implants in providing speech in quiet settings, listening to complex signals such as music or speech in background noise is still difficult. Spectral resolution, the ability to extract frequency information from a signal, is important for interpreting complex signals, and this ability is impaired in CI users. In this study we compared two measures of spectral resolution: a pitch discrimination task and vowel identification. An individual’s ability to identify vowels depends on how well they can distinguish characteristic concentrations of energy at specific frequencies. Pitch discrimination is the ability to perceive small directional changes of sound frequencies between two pitches, and like vowel identification, relies heavily on one’s ability to discern frequency information. In this study we tested the pitch discrimination ability of CI users through the Clinical Assessment of Music Perception (CAMP) test (Kang et al., 2009), where participants were presented two tones 1-12 semitones apart and asked to identify the higher of the two. We then compared performance on the pitch perception test to the CI users’ scores on a vowel identification test, which included a closed set of ten vowel stimuli presented by a male or female speaker. Since spectral resolution is integral to both tasks, we expect to find that CI users with low scores on vowel identification also perform poorly on the pitch discrimination task. By understanding pitch and vowel perception we might inform the development of new signal processing that can optimize the transmission of music to cochlear implant listeners.

Endocrine disrupting compounds (EDCs) present in wastewater treatment plant (WWTP) effluents are a significant water quality issue. EDCs have been demonstrated to have adverse effects on aquatic life at extremely low concentrations. The synthetic estrogen, 17α-ethinylestradiol (EE2), is a particularly potent EDC of concern in WWTP effluents. Biological degradation is a critical mechanism for EDC removal in WWTPs. The goal of this research was to isolate and identify bacteria capable of degrading EE2 with an eventual goal of using the bacteria to improve WWTPs’ removal efficiencies. The experiments started with enrichments established in pH-buffered mineral salts media containing 1000 µg/L EE2 as the only added carbon and energy source, which were originally inoculated with activated sludge obtained from a local WWTP. Vitamin solutions were added to overcome loss of EE2 degradation abilities that were seen in earlier isolation attempts, and the new enrichments were monitored weekly for EE2 concentration using High-Performance Liquid Chromatograph with UV detection (HPLC-UV). Of the eight enrichments, three were found to degrade EE2 to below 200 µg/L within 54 days, as opposed to 120 days in the other enrichments. These were transferred to fresh media to reduce inactive bacteria concentrations through dilution and were monitored for degradation. Two of the three were transferred again after 78 days to fresh media and monitored for continued degradation. Transfer of the liquid cultures to solid media is currently underway to allow selection to single colony isolated cultures that can be assessed for their EE2 degradation abilities. This work is a promising advancement in the isolation of an EE2 degrader that will have a positive impact in bioaugmentation for the removal of EDCs from WWTP effluents.

Youth in the U.S. juvenile justice system are faced with various physical and mental health disparities, such as sexually transmitted diseases, and mental illness. Youth are at elevated levels of risk of contracting chlamydia and gonorrhea. People under 25 years old make up 15% to 30% of HIV cases (Morris, et al., 2006). It has also been found that many externalizing disorders such as attention-deficit/hyper-activity disorder, conduct disorder, and oppositional defiant disorder are also associated with delinquency (Wareham & Boots, 2012). Given these health disparities, it is essential that consistent health care be readily available and accessible to this high-risk population. However, many communities do not have efficient resources to identify possible factors that hinder the consistency of health and mental health care for adjudicated youth. The current research project focuses on risk factors preventing continuity of health care (both physical and mental) among youth in the King County Juvenile Justice system. Through analyzing and coding over twenty qualitative interviews, risk factors preventing youth’s access to care are identified. The study explores how factors such as lack of knowledge on how to navigate the medical system and youth’s rights to independently access care, create unique barriers for youth seeking and receiving care. As a result of these obstacles, many high-risk youth receive much of their primary care while in detention facilities. Based on analyzing the interviews and a literature review on programs fostering access to health care among adults, I will propose a model to promote continuity of care among this high-risk youth population.

Transforming growth factor-beta (TGF-β) signaling in smooth muscle cells (SMC) contributes to normal vascular development but may also play a significant role in the progression of aortic disease. Accordingly, TGF-β signaling is emerging as a therapeutic target, with strategies to block TGF-β signaling proposed as a means of preventing human aortic disease, including aortic aneurysms and dissections. However, because TGF-β signaling contributes to normal vascular development, blockade of TGF-β signaling could be harmful. We hypothesized that elimination of TGF-β signaling in aortic SMC of adult mice would cause aortic disease. We used inducible Cre-lox recombination technology to knock out Tgfbr2 in adult murine SMC. Tgfbr2 encodes TGF-β receptor II, believed to be essential for all TGF-β signaling. Mice were euthanized 4-14 weeks after SMC Tgfbr2 knockout, and effects of Tgfbr2 knockout (compared to control mice) were assessed by gross observation of aortas as well as sectioning and staining of aortic tissue. We found intramural hematomas, penetrating aortic ulcers, aortic dissection, and aortic dilation as well as significant thickening of the medial wall and adventitia in the knockout mice. Our data strongly suggest that loss of TGF-β signaling in SMC has a negative effect on aortic health and support a cautious approach in pursuing blockade of TGF-β signaling as a therapeutic strategy.

Protection of old buildings is one of the tools for reinforcing well-being of our communities and ensuring their sustainable development. Today, older built stock is challenged by demands for rapid urban growth and modernization, and so are challenged cultural identities of our neighborhoods. Preservation of historic urban fabric is necessary as transformations and growth occur. The question this project seeks to answer is how can we secure balance between protecting authentic character and ensuring economic vitality in historic urban cores? The primary methods are assessment of historic properties in the Old Town Neighborhood of Redmond and research of effective placemaking solutions among downtown revitalization case studies. The final report features a set of design suggestions regarding the public realm within Old Town's Historic Core and is meant to help preserve, promote, and celebrate the neighborhood. This project is a part of a planning process intended to develop architectural design standards for Redmond’s Historic Core.

 Breast cancer is the most common type of cancer in women, and 40,996 women died of cancer in 2010. I am working with Dr. Keryn Reding from the School of Nursing on examining estrogen DNA adducts (EDA) for their clinical utility as a biomarker for breast cancer. EDA is formed when estrone or estrodial are oxidized to form quinones. These compounds then attach to DNA, causing mutations that lead to cancerous cell growth. The EDA are then excised and released into the blood stream and excreted through urine. I will analyze urine samples in a triple quadrupole mass spectrometer in order to see if the ratio of EDA to parent estrogens is higher in women with breast cancer than women who did not develop breast cancer. My analysis will investigate the inter-variability of EDA in premenopausal and postmenopausal women to see if this biomarker can be accurate and reliable for women of all ages. We expect results to show that premenopausal women will have less EDA due to their younger age and lower risk of developing breast cancer. By May when I present at the URP, I will have results from the mass spectrometer and I will use the McNemar's test for statistical significance. We are investigating a hypothesis that a high EDA ratio will be associated with breast cancer risk, and thus the EDA ratio may have clinical applications for breast cancer prevention and screening. Because it is a non-invasive method of measuring the risk of developing breast cancer, it could be an ideal complement to current screening approaches, such as mammograms or biopsies.

The plant genus Thalictrum (meadow-rues) contains numerous shifts in ploidy number, ranging from diploid (2x) in the earliest diverging species to 24x in recently derived species. Polyploidy can result from a whole genome duplication event within an individual (autopolyploidy) or following a hybridization event (allopolyploidy). The rates and evolutionary consequences of these two mechanisms of polyploidy are currently under debate, and I am therefore attempting to estimate their relative roles within this genus using a phylogenetic approach. The current Thalictrum phylogeny relies on chloroplast DNA and nuclear ribosomal regions, which tend to underestimate the role of hybridization due to maternal inheritance and concerted evolution patterns, respectively. I am using single-copy nuclear genes to uncover potential hybridization signals in Thalictrum’s evolutionary history. This information will be used to compare the relative numbers of autopolyploids and allopolyploids in the genus. I hypothesize that allopolyploidy played a larger role in shaping the diversity of this genus, due to its potential for differential survival and reproduction as a consequence of immediate, novel gene expression in hybrid progeny. Furthermore, this analysis will estimate the hybrid origins of particular alleles within a species. In the future, this information will be applied to questions on the evolution of genes involved in flower development after whole genome duplications.

Pollination syndrome refers to suites of floral traits that influence biotic or abiotic vectors transporting pollen from one flower to another. These traits typically include flower color, position, shape, size, scent and reward. Scent is a major component of pollination syndrome, as the volatile organic compounds (VOCs) that compose “scent” often attract pollinators or deter predators. The genus Thalictrum in the Ranunculaceae (buttercup family) includes both insect- and wind-pollinated species, enabling comparisons of the role of scent in floral diversification among recently diverged taxa with distinct pollination syndromes. To characterize floral scent, we identified and compared the bouquet of VOCs emitted by insect- and wind-pollination species, as well as by floral vs. vegetative tissue. Scent was collected from tissue samples by traps in a filtered air system, then eluted and analyzed with gas chromatography mass spectrometry. Quantitation and emission rate were calculated to generate floral bouquets. Electroantennograms were performed on selected compounds to examine pollinator response. Focusing on eleven species representative of the two pollination syndromes and spanning the Thalictrum phylogeny, we identified ten key compounds of which five are deterrents against herbivory, two are pollinator attractants, and three have unknown functions. Given that these scent profiles consist primarily of defensive rather than attractive compounds, we hypothesize that repeated transitions from insect- to wind-pollination in Thalictrum may be due to the breakdown of an ancestrally weak insect pollination syndrome. Moreover, scent bouquets appear to follow phylogenetic patterns more so than pollination mode. The variation in distribution of VOCs across species in a phylogenetic framework allows us to test evolutionary patterns of compound co-option during evolution.

In the model organism Arabidopsis thaliana, the B-class genes of flower development are responsible for proper formation of petals and stamens in a flower. Studies in Thalictrum thalictroides, a representative of the sister lineage to all other eudicots provides insight into the ancestral function of the B-class genes. Unlike Arabidopsis, the flowers of T. thalictroides lack petals, and yet the sepals are large and colored similar to petals. Here, we investigate the function of B-class proteins in T. thalictroides through the study of the horticultural mutant known as ‘Betty Blake.’ The ‘Betty Blake’ mutant phenotype consists of many non-petaloid (green) sepals and carpels but no stamens. We have previously shown reduced expression of most B class genes in ‘Betty Blake’, yet we were not able to find any meaningful mutations in these loci. Therefore, we hypothesize that an upstream regulator of the B-class genes may be mutated in ‘Betty Blake’. UNUSUAL FLORAL ORGAN (UFO) is a known upstream regulator of the B-class genes and is therefore a logical candidate. We hypothesize that the UFO mutation is the cause of the B class phenotype in ‘Betty Blake.’ The investigation of B-class function in this non-core eudicot has provided us with insight into the evolution of gene regulatory networks affecting ectopic petaloidy and stamen identity that we will continue to pursue in future experiments.

 The first floral mutations ever documented, double flowers have been prized for centuries for their beauty. The double mutant variants ‘Shoaf’s Double’ and ‘Cameo’ are found in Thalictrum thalictroides, a member of the buttercup family. The purpose of this research is to determine the genetic mutation underlying this desirable phenotype. We predicted that a mutation in a C-class floral organ identity gene would cause the homeotic transformation (conversion of one organ type to another) of stamens and carpels to petalloid sepals in this species. C-class genes are also involved in floral determinacy, the termination of floral organ growth, which is why double flowers appear to have a second flower nested inside the first. As expected, the expression of the C-class gene ThtAG1 was greatly reduced in our mutants. Finding no changes in the coding region from wild type, we further investigated the entire genomic locus, where we found evidence of the action of a transposable element in both mutants. In ‘Shoaf’s Double’ a Mutator Like Element (MuLE) has inserted itself into a regulatory intron of TthAG1, disrupting its function. In ‘Cameo’ a ‘footprint’ at the exact same place in the sequence indicates that the same element may have jumped out, deleting a section of the intron. We hypothesize that the double phenotype in ‘Cameo’ is likely due to the accumulation of mutations before the MuLE jumped out. Since the MuLE’s transposase is expressed in ‘Shoaf’s Double’ (but not in wildtype), these results illustrate the rare case of an autonomous transposable element underlying a regulatory mutation that results in a visible phenotype. We hope that our work will provide insight into the genetic basis for the double phenotype of popular commercial flowers such as roses, camellias and carnations.

Since 2009, students in First Creek Middle School's Environmental Science Club have been collecting water samples from a local creek running behind their campus as a part of an ongoing service learning partnership with the University of Washington Tacoma. These monthly samples, along with samples taken at two other locations along the stream, have been analyzed for several potential contaminants: select metals, nutrients, and emerging environmental contaminants known as perfluorinated organic acids. Analysis was conducted using various laboratory-grade analytical techniques and equipment including Graphite Furnace Atomic Absorption Spectroscopy (GF-AAS), SmartChem Discrete Nutrient Analyzer, and Liquid Chromatography-Tandem Mass Spectrometry (LCMS). The results were compared with data spanning back to the beginning of the service learning project and correlated with rain events in order to track contaminant levels over time and identify the effects of stormwater on pollutant levels. These results are also being used to help Science Club students better understand environmental processes and challenges associated with ecological restoration, while encouraging advanced learning through classroom based analyses which they have conducted themselves. Through improved understanding of pollutant transport and stormwater contamination, results may also be useful in identifying and quantifying the need for further community-based stewardship programs designed to help improve Tacoma’s green spaces.

 North American river otter (Lontra canadensis) populations are difficult to assess by means such as live-capture; however, non-invasive fecal sampling has become a viable way to assess many aspects of river otter ecology including diet and genetics. L. canadensis uses specific locations called latrines to regularly defecate and scent mark. Fecal samples collected from latrine sites can be used for DNA analysis to distinguish unique individuals and evaluate genetic diversity in a population. Within Possession Sound, minimal research on the abundance and diversity of L. canadensis has been conducted. In fall of 2012, students at the Ocean Research College Academy (ORCA) became the first to study the species in this area. As of fall 2013, two latrine sites of L. canadensis in Possession Sound have been monitored using motion-sensing camera traps. Weekly checks for fresh scat and anal jellies are performed, with 153 samples collected so far. Diet is assessed by identifying prey remains present in feces. Currently, 27 scat samples have gone through DNA extraction, and Polymerase Chain Reaction (PCR) will be performed in the near future using the primers RIO-05, RIO-10, LUT-701, and LUT-801. DNA analysis results will provide information about population size, which is difficult to estimate using camera footage. It is expected that DNA analysis will identify a relatively small number of individuals, as the maximum number of otters simultaneously captured on camera footage is seven. With a small population size, we also expect some amount of genetic interrelatedness in the individuals identified through DNA analysis.

Lontra canadensis, more commonly known as the North American river otter, is a resident in many riparian and coastal ecosystems across the continent. The behaviors of mainland populations – the inhabitants of freshwater lakes and rivers – have been well documented and studied over the years. The impact of tides on coastal and estuarine populations, however, is still largely unknown. Therefore in 2012, members of the Ocean Research College Academy, a dual enrollment program run through Everett Community College, began studying otters in Possession Sound. Preliminary diet analysis of scats retrieved from local latrine sites revealed target prey consisting of mostly saltwater species. Due to the high metabolic rate of otters necessitating large daily food intake and prey availability in estuaries being driven by tidal cycles, it was then hypothesized a correlation existed between tides and the presence of otters in the sound. Specifically, it was predicted otters would be present at high salinity tides when the water chemistry could sustain their prey species. To test this, game cameras were installed at latrine sites on Jetty Island and the Hat Island ferry dock in Everett, Washington. Visits by otters were documented and time stamped, with corresponding tide stages and heights recorded. The majority of visitations occurred at tide heights above 4 feet (81% of visits) with considerably fewer camera captures during low salinity tides. Further research is currently being done into the possible impacts of other local factors on river otter behavior, including spring-neap tidal cycles and river discharge.

Possession Sound as a part of the larger Puget Sound is located between the Whidbey and Snohomish county shoreline. This location has significant influence from both freshwater and nutrient inflow from the Snohomish River as well as saline water resulting from tidal exchange. Students at the Ocean Research College Academy (ORCA), an early college program at Everett Community College, have been conducting baseline estuarine monitoring since 2007. The Washington State Department of Ecology has been aerially monitoring phytoplankton blooms and maintains a long-term collection of nutrient data throughout Puget Sound. According to this data set there has been a nutrient shift that is hypothesized to impact diatom abundance. This project combines the ORCA data set of plankton levels and nutrient concentrations to see if a similar shift is occurring in Possession Sound. Additionally, temperature variation is analyzed. Two hypotheses combine to identify special and temporal distribution of nutrients and plankton abundance. First, when silicate levels decline, diatomaceous phytoplankton are limited by this reduction. Second, the deep water location further from the river will have less variation in temperature, less nutrient availability and subsequently less phytoplankton abundance and diversity. The location nearest to the mouth of the Snohomish Riveris predicted to experience dramatic temperature variation and higher seasonal nutrient levels. The conclusions from this work will influence future plankton enumeration protocols at ORCA.

The source and fate of hazardous material released into rivers and estuaries is critically important to protecting environmental health, especially in highly industrialized areas such as the Puget Sound. This study focuses on determining the legacy of heavy metal distribution (Pb-Cu-Zn-As) from a demolished ASARCO smelter site in north Everett, WA near the mouth of the Snohomish River. The Snohomish is a complex riverine system with many potential point and non-point sources of contaminants. This site is the target of remedial actions under the Model Toxics Control Act cleanup regulation developed by the Washington Department of Ecology due to widespread As and Pb contamination in the early 1900’s. Previous studies showed a correlation between heavy metal concentrations in benthic sediment of Possession Sound and proximity to industrial sites near the mouth of the Snohomish River. If the source is the ASARCO smelter, we should be able to trace Pb contamination downstream from the site. No data are available from within the river to constrain the specific sources of anthropogenic metals. In our study, we use Pb isotope variability between natural and anthropogenic Pb to establish the extent of dispersion of contaminants derived from ASARCO. The sample suite we collected consists of: three one-meter-long river-bottom sediment cores collected 1) near the mouth of the Snohomish River, 2) near the ASARCO site, and 3) up river to compare natural baseline values with near site and downriver sites; and 4) slag samples to serve as reference isotopic signature of ASARCO Pb. Purification of Pb from the samples is complete, and the isotopic analyses of the Pb are in progress utilizing an inductively coupled plasma mass spectrometer under the advisory of Dr. Bruce Nelson at the University of Washington. This research will identify spatial and temporal relationships among fluvial processes and Pb deposition.

The location of anthropogenic plastics in the marine environment is influenced by current speeds generated by wind and estuarine influences. Local, estuary-based studies by undergraduates at the Ocean Research College Academy (ORCA), an early college program through Everett Community College, conducted surface sampling of the Possession Sound water column for microplastics in the spring and fall of 2013 and winter of 2014. These investigations examine the influence of current speed on the distribution of microplastics in Possession Sound. Two public access docks on opposite sides of Possession Sound (Everett, WA and Langley, WA) were compared to examine spatial trends in current speed as well as proximity to potential land-based sources of pollutants. Samples were collected using a 20 μm plankton and current speed was recorded by flow meter. Water samples were analyzed for plastics using a Wet Peroxide Oxidation to remove organic compounds. It is hypothesized that higher plastic levels will correlate with lower current speeds and increased proximity to urban sources near Everett.

When considering fluctuations in temperature, salinity and dissolved oxygen, tides and currents are two influential factors that affect an estuary system. Monthly research cruises since the fall of 2007 to the Snohomish River delta with the Ocean Research College Academy (ORCA), an early college program through Everett Community College located at the Everett waterfront, monitor the local marine system and provide a historical data set for use in analysis. Changes in the cline were first analyzed by isolating tidal and river flow variables as well as seasonal changes. The changes between different cycles of spring and neap tides as well as variations in river outflow are points of interest due to the hypothesized signature these events exhibit on the cline. The research sites of Mukilteo, Buoy, and the Snohomish River were used to analyze the impact of distance from the river, tides and currents, and river flow on salinity, temperature, and dissolved oxygen. In addition to these sites, current flow data was primarily taken along with water column measurements along the mouth of the Snohomish River and to the north east of Jetty Island. Surface current measurements were take by GPS enabled drogue. It was initially hypothesized that spatial differences and river flow would have a greater impact than tides on the pycnocline depth. However, after initial data collection the reverse appeared to be accurate, with changes in the current speed and water column being more closely tied to tidal patterns rather than river influence.

The Possession Sound, located within the Puget Sound, is a diverse estuarine environment where freshwater from the Snohomish River mixes with the ocean water from the Strait of Juan de Fuca. A key variable that influences fluctuations in an estuary system is tidal stage changes that result in mixing and stratification that influence water chemistry. The working hypothesis is that increased high salinity, cold water during high tide will result in decreased pH and increased dissolved oxygen (D.O.) Data from 2010 to 2013 were collected monthly at the Mukilteo and Mount Baker Terminal stations. YSI 85 and 650 data for salinity, temperature, pH, and D.O. were organized based on tidal stages. The data did not support our hypothesis; trend lines indicate that as tidal stages increase pH increases from 7.5 to 7.6. On average, D.O. decreased as tidal stages increased, from 9.1mg/L to 8.4 mg/L. Chemical levels in the water column are also influenced by phytoplankton through photosynthesis and respiration. Future research will be conducted to determine the correlation between the amount of plankton in the water and the levels of pH and D.O. in the water column.

The genomic RNA packing enhancer (GRPE) is an RNA element found in the HIV-1 genome that is implicated in the packing of HIV-1 genomic RNA (gRNA). This 140 base-pair sequence is found within the p1-p6 region of gag and is believed to fold into a structure that interacts with viral components to enhance packing, most likely by recruiting the nucleocapsid protein. Understanding this RNA structure would provide molecular understanding of the GRPE’s function in gRNA packing, which would in turn shed light on how HIV-1 assembles. Ultimately, it could also facilitate the design of new anti-HIV therapeutics. The goal of this study is to determine the structure of GRPE using nuclear magnetic resonance (NMR) spectroscopy. Using previously published chemical mapping data, I designed an optimal sequence to study and cloned the resulting 140 base-pair DNA sequence corresponding to the GRPE RNA into a high copy number plasmid for the purpose of generating sufficient amounts of DNA template for transcription. The transcription of GRPE was optimized, and I am in the process of synthesizing and purifying sufficient amounts of GRPE to conduct NMR spectroscopy studies using large scale gel electrophoresis and flash chromatography. Once this is done, I will use NMR spectroscopy to elucidate the GRPE structure.

Possession Sound is located in the northeast arm of Whidbey Basin of Puget Sound. Students at the Ocean Research College Academy, a Running Start program at Everett Community College, conduct monthly research cruises to collect oceanographic metrics in Possession Sound. Initial questions about seasonal changes, demonstrated by water temperature, influencing photosynthesis led to questions about correlations with dissolved oxygen, chlorophyll and silicate levels. We hypothesize that dissolved oxygen (D.O.) and chlorophyll concentrations will increase during the spring and summer due to increased photosynthesis with rising temperatures as a result of increased direct sunlight. Additionally, diatomaceous phytoplankton make silica shells out of the silicate nutrients absorbed from the water. Therefore, the silicate levels will decrease during the spring and summer because of an increase in the abundance of diatoms. Water chemistry data were compared seasonally at Mukilteo (MUK) during 2012-2014. The YSI 650 was deployed in meter increments, from the surface to a maximum of 20 meters, to collect temperature, D.O., and chlorophyll data. The Niskin was deployed at the surface and cline, and was used to collect silicate nutrient concentration trends with depth. For quantitative analysis of nutrient data - done by the University of Washington Marine Chemistry Laboratory - the silicate levels correspond to the depth the halocline, which varied for each deployment. Our data show that dissolved oxygen (D.O.) and chlorophyll both increased during the spring and summer, which supports our original hypothesis. Phytoplankton data samples were collected at the halocline with a 20 µm net for a three minute horizontal tow. Further studies on identifying diatom bloom events through plankton species abundance will further support seasonal trends and identify other factors that affect primary production in the local estuary system.

At the Ocean Research College Academy (ORCA), data is collected monthly at five locations in Possession Sound and is used to create a bigger picture of the health of the sound. Previous studies demonstrate that heavy metal concentrations in the sediment of Possession Sound and the Snohomish River vary with location. Upriver and point source anthropogenic influences contribute heavy metals, including zinc, lead and arsenic, to seafloor sediment and adversely affect the quality of the sediment. This study focused on bottom sediment at three different locations in Possession Sound and in the Snohomish River to investigate spatial patterns in heavy metal concentrations due to river influence. The sites, with increasing distance from the river, are three upriver samples, and three sites in Possession Sound. The river site sediment was potentially affected by the legacy of the ASARCO smelter in North Everett. Sites 1 and 2 are located near the mouth of the Snohomish River. Site 3 includes Mukilteo and Mount Baker Terminal data, both near busy ports and recreational areas. At these three sites, sediment samples were collected by utilizing a ponar grab. These samples were analyzed in the lab, and showed the heavy metal levels for each site. United States Geological Survey river flow data was also accessed to tie the high heavy metal patterns due to high river flow and greater discharge of sediments. Further research could be conducted to measure the biological impact that these metals have through bioaccumulation, based on our findings of heavy metal hot spots.

 The Ocean Research College Academy (ORCA) is a Running Start program through Everett Community College. Monthly State of Possession Sound (SOPS) cruises are conducted that analyze the overall health of the Possession Sound ecosystem. By monitoring physical, chemical, biological, and geological parameters through these cruises, conclusions can be drawn from the data collected. Sediment samples were gathered from different locations throughout Possession Sound--a smaller portion of the Puget Sound located between Whidbey Island and Snohomish County in Washington where the Snohomish River converges with Puget Sound . These samples were analyzed for the relative concentrations of arsenic, copper, and lead by the Everett Environmental Laboratory and distribution and relative concentrations at each site were further examined. The effects of human interaction on the environment--farming, industry, transportation, and recreation--as well as natural fluctuations in tides, currents, and precipitation influence heavy metal deposition in certain locations. The impact of heavy metals spreads to the overall marine health, affecting the food chain through bioaccumulation of these metals in plankton at the basis of the food chain and concentrating further through consumption by other marine life and animals that eat marine life. From the heavy metal information produced by our study, we plan to continue mirroring similar bay studies conducted by the Department of Ecology (DOE), where we can compare heavy metal data collected from this study with water chemistry data and the overall marine health of the Possession Sound ecosystem.

During the 2012-2013 school year, foundational research on the diet of the Possession Sound river otter (Lontra canadensis) population was performed by students of the Ocean Research College Academy (ORCA), a dual enrollment program at Everett Community College. This study included diet analysis of scat samples, visual surveys using motion-sensing game cameras, and tests for protozoa presence. The diet analysis showed the otter population to have a primarily marine crustacean diet. Further research during the 2013-2014 school year focused on gathering information about river otter abundance though camera traps and diet analysis of scat samples from communal “latrine sites.” This research aims to compare results from two latrine sites regularly studied in the Everett Marina to a new site established three miles up the Snohomish River, at Langus Riverfront Park. The highest number of river otters observed on camera simultaneously has been seven. It is hypothesized that these otters form one group which transit up and down river with the tidal cycle, resulting in the same groups of otters frequenting all the camera locations. It is assumed that otters will frequent upriver sites at high tide, following the marine species from Possession Sound with the more saline water. This will result in the upriver site having increased visitation at high tide noted in the camera trap data and no significant variation in prey types compared to the marina.

Possession Sound is located between the coastline of Snohomish county and Southeast of the Whidbey Island Basin within the Puget Sound. The freshwater Snohomish River is the second greatest input to the Puget Sound and greatly affects the overall health of Possession Sound. Monthly since 2009, the Ocean Research College Academy (ORCA) students collect samples in the Possession Sound with a Niskin bottle, to send to the University of Washington Marine Chemistry Lab which provides nutrient concentrations which can fluctuate with season, weather, river discharge, marine organisms, and anthropogenic influences, specifically waste water outfall. Focal analysis of a site close to the Snohomish River were compared to other locations up river. Discharge data corresponds with fluctuating levels of nitrates, nitrites (NOx) and ammonia throughout the year. NOx data corresponds with river discharge with an exception to spring where there is a general decrease. In April of 2013, for example, the discharge is at a high 18,300 ft³/second, but the NOx concentrations are at lows, at 3.04 μm/L. The subtle changes in ammonia concentrations seem to correlate with the extremes in river discharge. For example, between May and June of 2010, the river discharge data increases from 12,550 ft³/second to 15,090 ft³/second. Ammonia concentration follows, in May the concentration is 36.8 μm/L, which increases in June to 49.8 μm/L. The hypothesis was partially supported. Ammonia data correlated with river discharge, raising as river discharge flow increases. Comparatively, the NOx data varied independently of river discharge. Further research into ammonia concentrations and waste water outfall in addition to utilization of NOx by plankton species such as Thalassiosira spp. and Copepod spp. populations is yet to be conducted.

Puget Sound consists of many smaller bodies of water including Possession Sound, located between the cities of Everett and Mukilteo, Washington. The Asarco Smelter, located in North Everett was active around 100 years ago, resulting in heavy pollutants such as lead into the Snohomish River leading to Possession Sound. The Ocean Research College Academy (ORCA) students sample Possession Sound for sediments monthly. It can be hypothesized that the lead concentration will be higher at the location Buoy, because it is closer to the fresh water outputs such as the Snohomish River. Consequently, the location Mukilteo/Mount Baker Terminal (MUK/MBT), that is further south in Possession Sound, will have a lower lead concentration since it is further away from the Snohomish River in comparison to Buoy. According to the data collected, from 2009 to 2013, Buoy had a higher amount of lead concentration in comparison to MBT/MUK. However, factors to be considered are other anthropogenic influences, river discharge, tidal stages, time such as time of day, what season and the time of year the data was collected, as well as water currents that could impact the lead concentration in Possession Sound. Future studies will consist of scrutinizing organic matter in sediments in correlation with lead concentration to analyze if biological organisms are impacted by the amount of lead present in sediment.

The brain is the most powerful computer in existence, possessing roughly 100 billion neurons with one-quadrillion synapse connections between them. Mimicking the synapse of a neuron could lead to increasing processing power, a better understanding of brain functions, or enhanced biomedical device integration. We have previously demonstrated proton-conducting devices with synaptic behaviors utilizing protons as charge carriers in a palladium source-drain system. Altering the design of these devices to become more useful to the biomedical field would be highly advantageous. Due to nature’s naturally curved geometry, we aim to develop flexible devices capable of matching these parameters for biomedical integrations. Flexible devices allow a much broader scope of applications, including health sensors on the human body that might require soft or curved morphologies. The mechanical engineering and processing conditions to create flexible devices is currently being investigated. I propose starting device fabrication with a pre-strained substrate. When palladium is deposited on this substrate, it will compress and exhibit wave-like patterning upon the release of the substrate’s strain. This is critical to the device flexibility, as previous palladium tension tests showed a high fracture rate. With a pre-induced compression in the palladium, tension would result in a more relaxed state and limit fracture in the devices to allow flexibility. Future works involve determining buckling strains for various palladium thicknesses to obtain wave-like patterns of compression, determining a suitable substrate material, and comparison of electrical properties to our current palladium devices.

Adolescent obesity is a growing epidemic and has tripled in the past 20 years in the United States. This is a major public health concern as we are now observing numerous health conditions commonly associated with adult obesity in the adolescent population. The goal of our study is to determine how total sleep time (TST) affects body composition, activity level, and nutrition in adolescents. Our study population consists of 100 healthy 13-17 year old adolescents. We are currently collecting and will analyze data from sleep/hunger/satiety diaries and questionnaires, a watch that records daytime/nighttime activity, 24-hour diet recalls, serum metabolic markers, appetite regulating hormones, salivary cortisol, an air displacement device, and questionnaires that assess lifestyle factors. We anticipate our results will demonstrate differences between sleep-deprived adolescents with age, BMI, sex matched control adolescents in diet, food cravings, physical/sedentary activity, and appetite regulation. Further, we anticipate our results will demonstrate an inverse correlation between TST and body composition. The intent of this study is to provide preliminary information to suggest a need for further research in this area. We hope to apply this scientific understanding to the development and testing of innovative interventions to improve sleep and decrease adolescent obesity and metabolic risk.

Transcranial ultrasound can alter brain function transiently and nondestructively, offering a new tool to study brain function and inform future therapies. Previous research on neuromodulation implemented pulsed low frequency (250–700 kHz) ultrasound with spatial peak temporal average intensities (ISPTA) of 0.1–10 W/cm2. That work used transducers that either insonified relatively large volumes of mouse brain (several mL) with relatively low frequency ultrasound and produced bilateral motor responses, or relatively small volumes of brain (on the order of 0.06 mL) with relatively high frequency ultrasound that produced unilateral motor responses. Our work seeks to increase anatomical specificity to neuromodulation with modulated focused ultrasound (mFU). Here, ‘modulated’ means modifying a focused 2-MHz carrier signal dynamically with a 500-kHz signal as in vibro-acoustography, thereby creating a low frequency, but small volume (approximately 0.015 mL) source of neuromodulation. Application of transcranial mFU to lightly anesthetized mice produced various motor movements with high spatial selectivity (on the order of 1 mm) that scaled with the temporal average ultrasound intensity. Alone, mFU and focused ultrasound (FUS) each induced motor activity, including unilateral motions, though anatomical location and type of motion varied. Of interest is the exploration of potential research and clinical applications for targeted, transcranial neuromodulation created by modulated focused ultrasound, especially mFU’s ability to produce compact sources of ultrasound at the very low frequencies (10–100s of Hertz) that are commensurate with the natural frequencies of the brain. Currently, I am working to incorporate mFU with electroencephalography (EEG) to aid researchers and clinicians in localizing neural activity. Theoretically, the vibro-acoustography paradigm allows a small volume of neural tissue to be tagged with a specific difference frequency; EEG will determine the origin of this signal.

Biological systems coordinate themselves through cues such as ion currents and membrane electric potentials. This communication utilizing membrane proteins such as membrane receptors, channels, and pumps allows biological systems to form hierarchies of control over their systems that have yet to be achieved in conventional electronic systems. Integrating such biological components with nanoelectronics could allow exciting new developments in the field of biomimetic energy conversion. However, this approach requires the seamless incorporation of biological structures into electronics. In order to use membrane proteins, they must be integrated with a lipid bilayer which is essential to create a cell membrane mimicking environment. Lipid bilayers have previously been integrated on solid substrates for electrophysiological measurements and the construction of organic-inorganic hybrid devices, but have yet to be formed on PdH_x. In this work, we build the foundation towards harnessing this biology-based method of control by forming a lipid bilayer composed of DPhPC/DPhPE/PI/Cholesterol on PdH_x contacts. The formation and deposition of electrochemically robust liposomes on a PdH_x surface was confirmed using dynamic light scattering (DLS) measurements, atomic force microscopy (AFM), and resistance measurements with a PdH_x proton field effect transistor (H⁺-FET). Vesicle formation was proven through DLS by determining size of the lipid structures in aqueous solutions. These vesicles were then deposited onto a PdH_x contact and formed solid-supported bilayers on PdH_x surfaces by the process of spontaneous vesicle adsorption and rupture as confirmed by AFM. Finally, the electrical stability of the bi-lipid membrane was characterized through electrical measurements with an H⁺-FET, confirming minimal H⁺ leakage across the bilayer. Future work includes embedding an ion pumping membrane protein, bacteriorhodopsin, into the bi-lipid membrane to enable electrochemical gating of the PdH_x H⁺-FET through optical or other environmental cues for biomimetic energy conversion.

Parent engagement has been found to have direct implications in the academic success of students. Knowing the ways that parents are or are not engaged is vital to developing ways to improve parent engagement. Additionally, it is important to reveal the ways in which parent engagement is defined in current school settings. Increasingly, school, and community based organizations are in need of understanding how well they are doing in engaging parents. To help us understand ways to assess parent engagement, this study examines parent engagement measures found in literature from 1993 to the present with a focus on its representation in urban communities. Specifically, we examine how equitable and traditional forms of parent engagement are or are not represented in the constructs used to measure parent engagement in urban settings. We synthesized literature into Excel templates and then coded using MAXQDA software. This allows us to analyze the data and more easily view patterns, differences, and commonalities among the literature. Using our coding database, we found preliminary results that indicate that parent engagement studies of urban school settings were more frequent in comparison to suburban, rural, or mixed school settings. We found that within the urban setting, when studying parent-engagement behaviors, over fifty percent of the time the behaviors studied were home-based. These findings suggest that the quantitative measures and studies of parent involvement over the last twenty years largely reflect the traditional approaches that qualitative studies have found to be inhibiting, particularly for the participation of non-dominant parents such as minorities or parents from low-income background in school-based or community-based parent engagement. These findings suggest the need to examine beyond the scope of traditional measures in order to begin to understand the potential of equitable parent, school, and community collaboration for improving student learning and success.

As scientific studies have been focusing on generating alternative renewable energy sources, attention has been drawn to the need to store energy from the sun. One strategy is to develop catalysts capable of producing the energy-dense molecule hydrogen from the reduction of water. This kind of solar fuels system would allow for on-demand release of the energy that is stored in the chemical bonds of hydrogen through environmentally benign, carbon-free combustion. We are interested in the potential of catalyzing proton reduction with cobalt in a diimine-dioximato ligand framework. Previous studies on cobalt diglyoxime complexes have demonstrated the viability of such catalysts for proton reduction. Our research is focused on synthesizing bimetallic complexes using the same framework and studying the effect of another metal center on catalytic activity. Our entry into this chemistry relies on the initial synthesis of a doubly-deprotonated diimine dioximate complex of cobalt as a starting material, which can be considered as a “metalloligand”. The physical and electronic properties of this cobalt metalloligand and its multimetallic derivatives are studied by X-ray crystallography, 1H- and 13C-NMR, UV-visible spectroscopy, and cyclic voltammetry.

The Snohomish River flows through an area where anthropogenic factors may affect the water chemistry due to industry and agriculture. The lower reaches of the Snohomish River are near industrial sources. At the Ocean Research College Academy (ORCA) in Everett, Washington, students are encouraged to derive and conduct independent research studies in the Snohomish River estuary system on monthly State of Possession Sound (SOPS) research cruises. It is expected that data will change in relation to distance from anthropogenic influences and the mouth of the Snohomish River. The pH up river is expected to be, overall, lower than that of the salt water, and even lower with the influence of farm waste and factory runoff. The waste from these sources releases CO2 into the river causing the pH to decrease. Sampling sites for the data collection of this study were selected with consideration to farms and factories along the river. The data collected includes dissolved oxygen (D.O.), salinity, temperature, and pH. A handheld YSI 650 and YSI 85 were used. Nutrient samples were collected at approximately half a meter below the surface. From the data it can be determined how farms and other anthropogenic factors affect pH. Further research on how these factors affect the marine life in the Snohomish River estuary system and Possession Sound are planned for future studies to determine how changes in water chemistry may have a negative impact on estuarine ecosystems.
 

Chronic Obstructive Pulmonary Disease (COPD) is the third leading cause of death in the United States. About 50% of people who suffer from COPD die from cardiovascular diseases (CVD). The Metabolic Syndrome (MS), a group of risk factors associated with CVD, is increasingly recognized in COPD. In the general population, fatty liver disease (FL) is a risk factor for MS. The goal of this project was to assess the association between FL and MS in smokers at risk for and with COPD. We also sought to determine the relationship between FL and inflammation biomarkers. We measured the liver and spleen attenuations on CT scans from two large epidemiological studies in smokers. Study A enrolled smokers 45-80 years old in 21 centers across the US. Study B enrolled smokers 45-85 years old in the US and European countries. The liver to spleen attenuation (LSR) was calculated by dividing liver attenuation by spleen attenuation. FL is defined as a LSR ≤1.10 (approx≥30% infiltration of fat). In Study B we used the Spearman Correlation Coefficients to assess the correlation between LSR and inflammatory biomarkers in order to understand a potential mechanism linking FL and MS. In Study A, 18% had FL. FL was significantly associated with diabetes (odds ratio [OR] 2.49 [95% confidence interval [CI] 1.59-3.89]), hypertension (OR 1.52 [1.06-2.17]), and overweight/obesity (OR 2.24 [1.49-3.39]) in adjusted models. Female subjects in Study B, LSR was significantly associated with highly sensitive C-reactive protein (r, -0.41; P<0.021) and fibrinogen (R, -0.40; P<0.020). No such associations were observed in males. In smokers with and without COPD, FL increases the risk for MS. In females, inflammation may be involved in the association between FL and MS.

Malaria, due to parasitic infection by Plasmodium protozoa, is a severe global disease with 300 million annual cases leading to 1-2 million deaths. While a few anti-malarial treatments continue to work, the continual emergence of new drug resistant parasites is an urgent public health concern. Previous studies in the Rathod laboratory suggest that chemical tools can be used to distinguish variations in evolutionary capabilities of different malaria parasite strains. Some strains such as Dd2 display the Accelerated Resistance to Multiple Drugs (ARMD) phenotype, whereas the HB3 strain displays the non-ARMD phenotype. In previous studies, Dd2 strain acquires resistance to several antimalarials at a significantly higher frequency than the HB3 strain. In this experiment, a cyclopropyl carboxamide (GSK2645947), a novel class of antimalarial agent, was used to select for resistant parasites from Dd2 and HB3 with the aim of comparing their relative frequencies of resistance to GSK2645947. A series of selection experiments were carried out utilizing different concentrations of GSK2645947 and different numbers of starting parasites. The parasites acquired resistance to GSK2645947 at similar frequencies in Dd2 and HB3 cells. The extent of resistance to GSK2645947, measured using EC50 assays, was similar in Dd2 and HB3 resistant clones; resistant parasites from neither lines showed cross-resistance to other antimalarial drugs. The present results point to a novel mechanism for rapidly acquiring resistance to GSK2645947, a mechanism that is equally prevalent in Dd2 and HB3 strains of P. falciparum parasites.

High school students doing college-level coursework by participating in specialized programs, such as Running Start, can be put under large amounts of stress. It was hypothesized that as stress increases, health will, in turn, decrease and that there is a significant correlation between perceived stress levels and health. Surveys were designed for voluntary participants to report stress, health, and overall well-being through a series of questions where the participants ranked their levels on a Likert scale. The surveys were implemented 6 times throughout the quarter to help identify trends in perceptions of stress as the quarter progresses with correlations to changes in lifestyle, sense of self, and overall health. However, this data set is limited. Because of the relatively small population size studied within a limited period of time, one restriction was identifying specific stress factors for each individual. Whether or not this kind of stress is harmful to teenagers undergoing rigorous course loads is not yet clear.

The discipline of Pathology has an enormous scope and students are constantly challenged to determine which topics are essential for clinical patient care and for the National Medical Board exams. There is a significant gap between the material presented in pathology textbooks and the material outlined in medical board review books. In addition, much of the practical knowledge that is most useful for medical students and physicians falls in between this gap. To address this need, we created PocketPath, a web-based modular teaching system, to help students and physicians consume Pathology material more efficiently. PocketPath is designed in an easy to read format that delivers an optimal amount of high yield pathology content, which includes USMLE Step 1 Board Review-style questions and important research papers. Using student surveys, interviews and web usage data, we determined how students consumed PocketPath’s content and improved their pathology test scores. Initial data suggests that PocketPath may replace lecture time, promote active learning, and potentially change the way students prepare for Board exams.

Traumatic Brain Injury (TBI) is a leading cause of mortality and permanent neurological disability. Microglial activation and inflammation contribute to the onset and progression of TBI-induced pathology. In this study we aimed to identify the factors that activate brain inflammatory pathways in the early responses to TBI, and the mechanisms by which inflammation is sustained during the late stages of pathology. We have previously demonstrated that the microglial expressed receptor, CX3CR1, regulates microglia activity. We have also shown that lack of CX3CR1 leads to deficits in cognitive function and synaptic plasticity. Here we hypothesized that the loss of the CX3CR1 receptor - and consequently, the loss of normal microglia function - would increase pathologic conditions in the brain after TBI and cause measurable defects in behavioral and cognitive abilities. To this end, three month old male CX3CR1 wild type and CX3CR1 knockout mice were subjected to a mild TBI (0.5mm depth) using a controlled cortical impact (CCI) animal model. Control mice (sham operations) received the same anesthesia and craniotomy, but were not subjected to CCI. All animals were humanely euthanized and transcardially perfused at fifteen and thirty days following TBI. I specifically participated in assisting TBI surgeries, behavioral testing, transcardial perfusions, brain sectioning, and immunohistochemistry. Our results indicate that lack of CX3CR1 at early time points protects neuromotor function, reduces cell death, and is associated with expression of microglia that have an anti-inflammatory phenotype. However, the long term effect of CX3CR1 receptor loss following TBI induces neuronal cell death, as well as neurobehavioral and cognitive deficits, which are associated with an increase in expression of microglia that have a proinflammatory phenotype. These results point to the presence of CX3CR1 in the early stages following a TBI as essential in slowing the progression of the neuropathology. In conclusion, CX3CR1, the fractalkine signaling receptor, plays a central role in regulating neuroinflammation after a TBI.

Autism Spectrum Disorder (ASD), including previously diagnosed Autistic Disorder, Asperger’s Syndrome, and Pervasive Developmental Disorder-Not Otherwise Specified, are all biologically based neurodevelopmental disorders that are characterized by an increased lack of social communication, social interaction skills, and restricted, repetitive behaviors or interests. College students who are either diagnosed with ASD or have similar behavioral traits might have a tougher time coping with the demands of a college lifestyle. In the past, little empirical data have shown if there is a link between Autistic traits found in the general population of college students and academic factors. For my project, I will briefly survey approximately 200 college students using similar questions taken from the Autism Quotient and Social Responsiveness Scale to test and see if the presence of Autistic traits affects college students academic performance and adjustment to college life. Additionally, I will interview students who are registered with Center for Disability Services with an ASD diagnosis at Everett Community College to better understand their challenges. Because of the difficulties Autistic students have to face in a college campus, such as social communication, navigating the campus, and a change in their once regular routines, it is hypothesized students who display Autistic like characteristics will decline in their academic performance compared to those who show an absence of Autistic traits. Suggestions for transitioning and coping to college life are discussed

Immunohistochemistry (IHC) is a valuable technique used to validate biomarkers, not only because it provides direct visualization of biomarker expression in histologically relevant regions of examined tissues, but also because validated IHC assays may be implemented readily into clinical practice. IHC assays have traditionally been semi-quantified by pathologists, but this method is significantly costly, inherently subjective, and produces ordinal rather than continuous variable data. Computer-aided analysis of digitized whole slide images may address these serious limitations. Using tissue microarrays (TMAs) representing 578 prostate cancer (PCa) specimens stained for estrogen receptor β2, I evaluated the degree to which data obtained using computer-aided methods correlated with data obtained by pathologist visual scoring. Digital images were obtained using a whole slide scanner. Under pathologist supervision I annotated TMA spots using annotation software. Images were preprocessed using the Genie Histology Pattern Recognition software suite to segment tissues into three user-defined Image Classes (tumor, stroma, glass). Malignant epithelial DAB staining was separately quantified within cytoplasmic and nuclear regions using the Cytoplasmic algorithm using a continuous variable metric that incorporates both the staining strength and the percentage of positive pixels in cytoplasmic/nuclear malignant epithelial areas. I compared the IHC intensity data derived from the Cytoplasmic algorithm with pathologist visual scores and identified high Spearman correlations. This study demonstrated that computer-aided methods to quantify IHC staining within carcinomatous areas of PCa tissue specimens can produce highly similar data to visual evaluation by a pathologist. This will allow further research studies to be performed using less time consuming and more technician based image anaylsis methods instead of costly pathologist consultations.

 Little is known about the conditions that permitted photosynthetic life to survive the global glaciation events known as Snowball Earth events. During this time, sea glaciers covered the Earth’s oceans, prohibiting the transmission of light. Without liquid water and sunlight, where did photosynthetic life survive? Research has shown that under certain climatic conditions, areas of sufficiently thin ice known as refugia could have existed at the landward ends of narrow channels where sea glaciers would be unable to penetrate. The idealized channels used in sea-glacier flow models allow for refugia under a restrictive range of climate conditions. However, experiments varying the channel entrance width have shown that a less restrictive range of climate conditions are needed for these refugia than has been previously thought. I hypothesize that moderate variations in channel entrance and sidewall geometries could both 1) expand the range of climate conditions that allow for a refugium at the landward end of the sea glacier and 2) generate thin ice zones in additional locations within the channel, likely near the entrance and on leeward sides of promontories. Utilizing finite element modeling techniques to simulate rectangular, trapezoidal, and round-sided channel entrances and promontories,  I will determine the locations of regions of zero or near-zero ice thickness in idealized channels. Combined with reconstructions of real-world Neoproterozoic geomorphology, these results could help us understand the conditions under which photosynthetic life survived Snowball Earth and even help to locate evidence of Snowball Earth-era photosynthetic life on the modern Earth.

 In eukaryotic organisms, regulation of gene transcription depends on the presence or absence of transcription factors, which are proteins that bind to promoter sequences on DNA. One common promoter element is the TATA box, and transcription is initiated when a protein complex called TFIID (which stands for transcription factor for RNA Polymerase II, D subunit) binds to it. TFIID is a multi-subunit machine, made of a TATA-binding protein (TBP) and TBP-associated factors (TAFs). Our lab has previously shown that an interaction between TAF1 and TAF7 inhibits TFIID's ability to initiate transcription of select genes. If TFIID cannot function properly, TATA-box controlled genes will be transcribed when they should be repressed. Some of these genes are cyclins, which are important for regulating the cell cycle. If they are misexpressed, a cell could proliferate with damaged DNA. This type of uncontrollable proliferation is a key component of cancers. Therefore, I am studying the interaction between TAF1 and TAF7 to determine the nature of TFIID inhibition. TAF7 is the proposed inhibitor in this model. I have cloned wild-type and mutant TAF7 genes, expressed and purified protein, and plan to use co-immunoprecipitation to determine if TAF1 and TAF7 associate. If the wild-type and mutant molecules have different affinities for TAF1, then I can conclude that the residue I've mutated is essential for TAF1 association. Later, I would like to study the difference in TAF1 activity in the presence of wild-type or mutant TAF7. This research asserts its relevance through the ubiquity of TFIID-mediated transcription regulation in every one of our cells, as well as the implication that TAF7 misexpression could lead to aberrant cell growth and possibly cancer.