Triclosan is a type of antibacterial agent found in consumer products such as lotions, tooth paste, soaps, shaving gel, and acne wash treatments. Presence of Triclosan in various products contributes to substantial exposure, which people across all spectrums may experience. Continuity in Triclosan exposure has several side effects including skin irritation, endocrine disruption, bacterial and antibiotic resistance, thyroid hormone imbalances, and infertility. The purpose of this research is to detect and compare Triclosan levels in medicated versus non medicated consumer products. High Performance Liquid Chromatography UV (HPLC-UV) will be used to analyze several name brand gels, washes and lotions. The concentration of Triclosan found in each of the consumer samples will be reported.

The purpose of this experiment was to determine how concentrations of tocopheryl acetate are affected in Vitamin E skin moisturizing oils by exposure to air and light. This commonly known synthetic form of Vitamin E is used in skincare products that claim to enhance protection against ultraviolet rays, promote skin healing, and make skin firmer and stronger. Vitamin E degrades by photo-oxidation, and is highly susceptible to this degradation immediately upon exposure to air and light. After exposure, the Vitamin E concentration in skin care products; therefore, every time a bottle of oil containing Vitamin E is opened or put into a clear container, it immediately starts to lose the amount of the potentially beneficial antioxidant within it. Reverse-Phase High-Pressure Liquid Chromatography (HPLC) was used to evaluate polar solutes, and Vitamin E in standard solutions, to validate our testing method upon completion of a calibration curve. Comparative skin care samples with Vitamin E (one exposed to only air, one exposed to only light, one exposed to both air and light, and one remaining inside the bottle) were then tested using Reverse Phase HPLC, and the results indicated that the original hypothesis was valid.

Research suggests that weathering by early cryptogams provided an overall negative feedback on atmospheric CO2 and an overall positive feedback on biologically available inorganic nutrients during the Ordovician. This process is considered to have contributed to global cooling and to the formation of Earth’s first soils. Although there is no known analogue to Earth’s first land plants, mosses possess the most shared spore and sporophyte features with the early cryptophyte fossil, Partitatheca, when compared to other bryophytes. They therefore present a plausible model organism for examining how the first land plants irreversibly altered Earth's geochemistry. However, before Earth's first land plants, lichens are known to have been colonizing the Earth’s surface since the Devonian. The role of lichens in this early Earth process is even more uncertain and in situ studies of lichen weathering have yet to be attempted. Here, I propose to extend the scope of a previous microcosm study of biologically induced weathering to investigate an additional lithic moss species and a lichen species, and to determine if an interaction exists between the groups. This study will enhance our understanding of the rate at which lichens and different lithic moss species weather bare rock and will provide insights into how mutualistic relationships could affect weathering in areas of primary succession.

Located in the Whidbey Basin, Possession Sound is a body of water within the Puget Sound that is directly influenced by the Snohomish River. Water runoff from rain events takes phosphorus from the soil and eroded rocks, and introduces it into the Snohomish River, which eventually travels into Possession Sound. Additionally, irrigation, agriculture, construction and other human influences on the environment affect the chemistry of the water. Students of the Ocean Research College Academy (ORCA), a Running Start program through Everett Community College, have been collecting water chemistry and nutrient data in Possession Sound for the past ten years. Our research group compiled data from previous years to study the relationship between phosphorus concentration and salinity. Salinity levels were determined by EXO Sonde or YSI 650 and water samples were captured with a Niskin bottle, which were sent to the University of Washington Marine Chemistry Laboratory for nutrient analysis. The data were collected at three different research stations. Two sites are located near the mouth of the Snohomish River and the Port of Everett, while the third is further south and not as directly impacted by the freshwater from the Snohomish River, however there is some freshwater impact due to storm drains near the data collection site. It was hypothesized that, higher phosphate levels would be found in lower salinity water nearest the Snohomish River. Over several years, we expected to see different patterns in phosphorus levels based on Snohomish River discharge. Data and findings from this research project will aid in our understanding on our Spring Quarter research project, which will focus on plankton concentrations in the Possession Sound.

Traditional antibiotics are known to wipe out many species of bacteria, but often leave several resistant microbes to dominate. These resistant bacteria are a huge concern for human health. Medical researchers are on the hunt for new approaches to combat bacterial infections on a large scale. It has recently been discovered that bacteria communicate through Quorum Sensing (QS), which if inhibited, presents a promising strategy to control these pathogenic bacteria. Instead of eliminating the weakest strain of bacteria resulting in a proliferation of antibiotic resistance, inhibition of quorum sensing silences gene expression, virulence and pathogenicity. A variety of marine organisms have demonstrated quorum sensing inhibition (QSI) potential, however there are many marine organisms that have yet to be screened for QSI compounds. In this study, three species of marine algae native to the Pacific Northwest were investigated for quorum sensing inhibition (QSI) capabilities. Ulva Lactuca, Chondracanthus exasperatus, and Iridaea Cordata were subjected to QSI capability testing that involved use of the indicator strain Chromobacterium violaceum Bergonzini (ATC 12472). The indicator bacterium uses the QS signal N-acyl-homoserine lactone (AHL) to produce a purple pigment. Each species of algae was overlaid with agar inoculated with Chromobacterium violaceum and incubated overnight. Absence of pigment in the indicator strain suggested the presence of a QSI compound. Preliminary evidence indicated that two of the three species of algae tested demonstrated QSI activity. The next step of this research involves identification of the specific compounds involved in QSI, thereby contributing to the expanding catalogue of known QSI molecules from marine environments. Ultimately this work aims to make a contribution to the fight against antibiotic resistant pathogens.

Genetic variation plays an important role in an individual’s susceptibility to Mycobacterium tuberculosis. Common variation in the rs5743854 polymorphism was found to regulate Toll Interacting Protein (TOLLIP) mRNA levels in the TLR signal pathway in macrophages. Decreased TOLLIP mRNA was associated with an increase in inflammatory cytokines and decrease in disease-specific TCM cells, leading to increased tuberculosis susceptibility in adults. We are investigating the role of a long non-coding RNA, TOLLIP Antisense 1 (TOLLIP-AS1), which houses rs5743854 and is located immediately upstream of TOLLIP. We hypothesize that TOLLIP-AS1 regulates TOLLIP mRNA expression and therefore plays an important role in regulating immune responses during tuberculosis. We performed RT-PCR experiments using primary monocytes from multiple ethnic cohorts and plotted mRNA expression levels of TOLLIP against TOLLIP-AS1. We also generated overexpression and knockdown TOLLIP-AS1 cell and measured any subsequent effects on TOLLIP expression. The long non-coding RNA TOLLIP-AS1 may prove to be critical intermediate in regulating gene expression and provide new targets for TB host-directed therapeutics and vaccine adjuvants.

The appearance of plastic in the world’s oceans has increased since the early 1970s. As these plastics get older, they begin to break down and erode, which causes microscopic fibers of these plastics to end up in the ecosystem. These microplastics end up in the world’s oceans through runoff and other freshwater inputs. The main issue with these plastics is that they can be toxic to marine organisms. This study can bring awareness to this problem that the world is facing. A localized study in Possession Sound to monitor these microplastics incorporates two components: visual surveys from plankton tows and a targeted sieving of seawater. I hypothesize that there will be higher concentrations of microplastics in areas that are closer to the Snohomish River. The data that is being looked at is from 2013 plankton counts to present day, as well as data that I have collected by pumping surface seawater through three different sieves (with mesh sizes of 60 microns, 150 microns, and 250 microns) for three minutes. With the data collected by plankton counts, the most microplastics were found at a station called Buoy (an area just outside of the Snohomish River) with 42 counted, and the least plastics that were found was at North Jetty (an area that is adjacent to the mouth of the Snohomish River) with one plastic fiber counted. My hypothesis was not supported because there was only one fiber that was found at the mouth of the river, while 42 fibers were counted were counted further away from the river.

This research project focuses on the study of the mitochondrial Cytochrome -c-Oxidase 1 gene (MT-CO1), in salmon species of the Pacific Northwest. The MT-CO1 gene encodes for a protein located in most eukaryotic cells called Cytochrome-c-Oxidase 1. This protein is located in mitochondria and plays an extremely important role in cellular metabolism. The MT-CO1 gene has become one of the standard sequences for a technique called DNA Barcoding. The idea of this technique is to compile MT-CO1 gene sequences in a database in which researchers can use computer software, such as Mega Software, to accurately identify species and analyze the subtle differences between them from a small tissue sample available. This allows taxonomists to accurately identify new species and track changes in a given population of organisms. In this project, we used the MT-CO1 Gene as a barcode to identify different samples of the salmon which were purchased from different local stores to find out whether they belong to the Pacific Northwest Salmon species. The laboratory techniques used in this research project included DNA extraction, polymerase chain reaction (PCR), gel electrophoresis, DNA imaging, gene sequencing and analysis. Our results indicated the expression of the identical MT-CO1 gene within the Northwest salmon species. Gel electrophoresis confirms the successful replication of 660 base pair MT-CO1 gene. Further analysis of the sequences indicates these salmon samples are of the species Oncorhynchus: nerka, tsawytscha, keta, and kisutch. This was confirmed using alignment search tools, such as blastn and MEGA6. The implication of this study is that DNA Barcoding using the MT-CO1 gene or other specific gene sequences can be used as a supplementary identification tool to track evolutionary changes, mis-labeled food products and identification of pathogen bacteria allowing the medical practitioners to accurately identify and treat the diseases caused by these agents.

The Ocean Research College Academy (ORCA), a running start program in partnership with Everett Community College has been conducting research in the Possession Sound since 2004. Those carrying out this investigation added to ORCA’s longitudinal data set in 2016 and 2017. Possession Sound is part of the north Whidbey Basin of the Puget Sound and is bordered by Snohomish County to the east and Whidbey Island to the west. Dissolved oxygen (DO) is an important factor in the survival of many aquatic species, and the loss of these species due to a lack of dissolved oxygen can disrupt the lives of other predatory animals and negatively affect marine industries. As DO levels fall below 4 mg/L, waters become hypoxic which can be fatal to marine life. This study investigates the effect of temperature on DO levels in the Possession Sound from a single site location (referred to as Deep) during 2015 and 2016. Water samples were collected from a depth of about 20 meters by deploying a Niskin sampling bottle. Then DO and temperature were measured with a YSI-85 handheld instrument. Results show that DO levels are lower in waters with warmer temperature. For instance, a DO level of 7.7 mg/L was observed at 11oC, while a DO level of 4.78 mg/L was surveyed at 12.16oC. These results are attributed to water molecules being less dense in colder water, allowing for more volume to be occupied by dissolved oxygen. This suggests that warmer temperatures in Possession Sound may not be suitable for sustaining diverse and healthy marine life. Since this research only investigated dissolved oxygen at 20 meters deep, it would be of interest to investigate DO levels of surface waters in order to probe the effect of photosynthesis on DO in the future.

Increasing atmospheric CO2 has lead to increased uptake of CO2 by oceans causing ocean acidification. Ocean acidification is the long-term reduction of pH that can have negative effects on marine organisms, especially young calcifying organisms. In Puget Sound, ocean acidification has already caused large-scale oyster larval mortality, negatively affecting a significant contributor to the Pacific Northwest economy. The native eelgrass in Puget Sound, Zostera marina, may be a local mitigation strategy for ocean acidification. Marine plants take up CO2 through photosynthesis to create biomass increasing the pH of the water. In this study, water samples were collected from several depths within the water column above eelgrass beds and surrounding mudflats in Padilla Bay. Water samples were analyzed for pH, total alkalinity, dissolved oxygen, dissolved inorganic carbon, and chlorophyll A. Eelgrass shoots and density were measured for leaf area index and the Padilla Bay National Estuary Research Reserve weather stations were used to calculate solar irradiance to estimate the photosynthetic activity of the eelgrass beds. Results suggest that eelgrass beds, in addition to providing critical habitat, may also help locally mitigate ocean acidification beyond the area of the eelgrass beds. Future research analyzing the input and output of carbon in eelgrass beds will be critical to developing large-scale carbon and pH models in marine environments.

 We will use the roundworm Caenorhabditis elegans to study the process of meiosis, which is involved in the formation of gametes (sperm and eggs). Its small size, rapid life cycle, transparency and well-annotated genome allows researchers to track the effects of mutations that disrupt gametogenesis. Our preliminary data demonstrated that a genetic screen for mutations that increase the viability of embryos produced by worms lacking SPO-11, a critical factor regulating meiotic chromosomal inheritance, can identify genes required for the accurate transmission of the genome from one generation to the next. To further test this hypothesis, we will continue this screen to identify additional regulators of meiosis. Our results will be relevant to human genetics, since key regulators of gametogenesis are highly conserved in both worms and vertebrates. Thus, we can learn about the causes of human birth defects by examining worm development. Consequently, these mechanisms will be relevant to understanding gametogenesis in humans and may aide in preventing genetic instability.

Meiosis produces four daughter cells that are genetically distinct. A crucial step of production is the pairing of homologous chromosomes; however, how these chromosomes align by homologous pairing remains a mystery. One contributing factor to alignment is tension within kinetochores. Experimentation with budding yeast reveals that a lack of tension will influence the spindle checkpoint until all sister chromatids are attached to the fiber. In the same manner, we will use budding yeast to investigate homologous interaction as the yeast provides us with an ideal model of recombination rates and life cycles similar to higher eukaryotes. The question of homologous behavior is also presented in DNA double-strand breaks. During prophase, these breaks (DSBs) create interactions between homologs along with inducing repair of homologous recombination. The strand is able to be repaired by the sister chromatids; however, the DSBs prefer interactions with homologous chromatid. How are the homologous chromatids found and used to repair the strand? These types of questions will be better understood with our research focused on how homologous chromosomes align initially during meiosis.

Plasmids are small circular pieces of DNA that replicate separately from the chromosome. Plasmids often contain antibiotic resistance genes that allow their host bacteria to grow in environments containing that antibiotic. They can be transmitted both vertically during cell division, and horizontally via conjugation to new bacterial hosts, and thus spread antibiotic resistance through populations. Plasmids are often costly to their bacterial hosts when not in the presence of antibiotics, but the coevolution of a bacteria and plasmid can reduce these costs through compensatory mutations. Typically a reduction or an amelioration of plasmid cost is seen during plasmid/host coevolution, but not a fitness benefit. However, preliminary data has shown evidence of a fitness advantage to containing a plasmid for the bacterial host Pseudomonas sp. nov. H2 after it was evolved with the plasmid RP4. In this project, I determined whether the fitness benefit seen in the aforementioned plasmid/host pair also occurs in three other bacterial species with different plasmid types. For each of these pairs the plasmids initially conferred a cost to the host. We hypothesized that compensatory mutations (on either the host chromosome or the plasmid) would result in the reduction, amelioration or reversal of the initial high cost of maintaining a plasmid for all three pairs. To test this, we evolved three plasmid/host pairs in antibiotic-containing media for several hundred generations, selecting for antibiotic resistance genes on the plasmids. We ran competitions between an evolved host/evolved plasmid pair and an evolved host with the plasmid removed, to determine whether there remained a cost to containing a plasmid, or whether that cost has been reduced, ameliorated, or reversed. Our experiments will help explain why plasmid-conferred antibiotic resistance persists in bacterial populations.

The process of aging brings about susceptibility to disease and death, but its mechanisms are still poorly understood. Dietary restriction is a potent approach to slow down the aging process, which has shown efficacy in multiple species, including the roundworm, Caenorhabditis elegans, a popular model organism for aging studies. Specifically, pre-reproductive adult C. elegans subjected to starvation enter a state of adult reproductive diapause (ARD), which preserves their lifespan and reproductive potential. Intriguingly, diapaused animals show signs of age-related deterioration upon prolonged starvation, but exhibit dramatic morphological improvements and have normal lifespans following return to feeding. However, the mechanisms regulating this lifespan preservation and apparent rejuvenation are not known. In this project, we aim to identify the genes responsible for the recovery during diapause exit. For that purpose, we used an RNA interference (RNAi)-based screen to inactivate individual genes during exit from diapause and analyzed the resulting phenotypes. Our current results reveal many regulators of metabolism and cellular homeostasis as crucial mediators of post-diapause recovery. Further studies based on these findings will discover the critical steps required for post-diapause tissue rejuvenation and preservation of longevity.

Nickel sulfate hexahydrate (NiSO4.6H2O) is an important industrial compound most commonly used in the nickel-plating industry. Approximately 40,000 tons are produced and consumed each year by manufacturers requiring corrosion-resistant components ranging from consumer electronics to medical devices and aerospace engineering. Freitas et. al. found that zinc sulfate heptahydrate crystal growth increased by 38% under a magnetic field of 0.3-0.7T compared to crystallization under earth’s magnetic field alone, whereas Lundager et. al. have presented evidence that paramagnetic materials such as CuSO4.5H2O do not exhibit such magnetically-induced increases in crystal growth rate. We present here our progress on confirmatory experiments aimed at fitting Nyvlt theory of cumulative crystal weight fraction M(L) and average growth rate G in batch synthesis of diamagnetic ZnSO4.7H2O and paramagnetic NiSO4.6H2O under external, uniform, homogeneous magnetic fields 0.0T<B<1.0T. Our study will examine the differences in the growth rate of paramagnetic and diamagnetic sulfate crystals under the influence of a manipulated magnetic field. Recrystallization is a method of purification during the synthesis process of many compounds. If recrystallization can be improved to increase percent yield by influencing the magnetic field surrounding the compound, it may be a profitable method for drug manufacturers to consider.

The Possession Sound is formed where freshwater from the Snohomish River and the salt water from Puget Sound creates an estuarine habitat that supports biodiversity within this ecosystem. Decreases in pH make it difficult for calcifiers to produce their calcium-carbonate shells, thus decreasing their survival rate in a higher acidity environment. Ocean Research College Academy (ORCA) has been sampling water chemistry at multiple sites in Possession Sound for 11 years. This study utilized ORCA data to compare two sites, one near shore and a second in a deep, central location. The purpose of this investigation was to study the pH and salinity trends from 2008 to 2016, considering influence of surface runoff, temperature, river discharge, and climate variations. It was hypothesized that the pH would decrease, becoming more acidic over the eight year period, and the salinity would remain within normal limits. Salinity and pH data were collected in 1-meter increments using a YSI 650 instrument. Initial data demonstrates an inverse relationship between salinity and pH. In 2013, salinity ranged with depth from 22.2-29.5 ppt near shore and 19.2-30.2 ppt at the deep site, correlating with higher surface pH that decreased with depth of 6.8-7.3 near shore and 6.5-7.1 at the deep site. This relationship was consistently demonstrated over the eight-year period, with the exceptions of 2011 and 2015. Further investigations include exploring the impact of climate patterns on the Snohomish River discharge and its influence on pH and salinity trends, as well as looking for seasonal trends in primary productivity of phytoplankton and their impact on temporal and spatial trends.

Despite their inability to express proteins, long intervening noncoding RNAs (lincRNAs) have demonstrated significant biological function; they regulate both cancer and physiological epidermal development and target chromatin-remodeling genes. Their repertoire of activity is constantly growing with the discovery of each new lincRNA. The lincRNA OIP5-AS1 (Cyrano) is a 4.5kb transcript required for proper embryogenesis in zebrafish, and unlike most lincRNAs, possesses multiple stretches of conservation found in at least 52 vertebrates. While the mechanism for how Cyrano regulates embryogenesis is unknown, it is believed that Cyrano functions primarily through a 26-nucleotide region that is perfectly conserved in every tetrapod; perturbation of this region resulted in a lack of proper development of zebrafish embryos. The secondary structure of the 26-nucleotide conserved region was revealed to contain an RNA binding domain, 5’–CCAU-3’, for RBMX, an RNA binding protein that is highly conserved in mammalian species. I hypothesize that Cyrano interacts with RBMX to aid in the process of embryogenesis, not only in zebrafish, but in other species as well. By using in vitro gel shift assays and in cellulo pull-down experiments, I aim to determine if the lincRNA Cyrano binds to the RBMX protein. Understanding this protein-lincRNA interaction will give more insight to the process of embryogenesis, and how lincRNAs function overall.

MicroRNAs (miRNA) are non-coding RNA (ncRNA) which post-transcriptionally regulate gene expression. In cancer, many miRNAs are overexpressed leading to the down-regulation of tumor suppressing genes. While the general processing steps of miRNA are known, the specific reason certain miRNAs are overexpressed in cancer remains unclear. Our particular miRNA of interest is miR-21, which inhibits genes encoding tumor suppressing proteins, and upregulation is associated with cancer. Specifically, we are interested in understanding how the pre-miRNA-21 processing step is regulated to generate functionally mature miRNA, and what proteins are involved in this process. Many RNA binding proteins are involved in miRNA biogenesis and influence transcription levels. This project explores the possible role of the RNA binding protein NOVA. NOVA is a neuron-specific RNA-binding protein exclusively expressed in the brain and neuronal tissues except for patients with Paraneoplastic opsoclonus-myoclonus ataxia, where it is found site of malignancy. NOVA is composed of 3 K-homology RNA binding domains selective for the sequence 5’ -YCAY-3’ (Y = pyrimidine). This KH domain recognition sequence is present in the hairpin loop in pre-miR-21. Additionally, in-vitro DICER processing of pre-miR21 is very slow relative to other miRNAs, however, if NOVA interacts with the pre-miR-21, this could stimulate its processing. We are trying to determine a possible mechanism of NOVA stimulated miR-21 expression through binding a conserved YCAY sequence. MiR-21 and NOVA have been isolated and purified, and their binding affinities are being evaluated using electro mobility shift assays. If binding is indicated, gene knockdowns will be preformed in cells to assess how NOVA affects miR-21 levels. It is difficult to design microRNA specific inhibitors, however, finding inhibitors for proteins is possible. If NOVA is found to lead to miR-21 up-regulation, a possible cancer treatment could be designed by targeting NOVA to lower levels of miR-21. 

Identifying the bacteria that inhabit a stream is important to determine the overall health of the stream and its inhabitants. Previous studies have stated Proteobacteria, Bacteriodetes and Firmicutes to be the dominant phyla found in water microbiomes, while Flavobacterium, a microbe responsible for many salmon diseases, is the dominant genus. For this project, we performed a microbial analysis of Alder and Fry Creek through biochemical assays. 8 water samples, each from different sites, were plated onto Mannitol and MacConkey plates to determine the relative proportions of fecal coliforms within the aerobic bacterial population. Additionally, the Alder Creek samples were characterized through 16S sequencing. Our findings are in agreement with previous studies, with the exception of two sites, which were located at the intersection of residential areas and natural habitat. These sites were consistent with the major phyla expectation, except their major genus were Arcobacter and Crenothrix. Arcobacter species are typically found in sewage and some are human pathogens. Infections from some Arcobacter species are similar to a Campylobacter jejuni infection. The Crenothrix genus contains iron precipitating species that have been known to form deposits that clog or stain pipes and make water look unappealing. These findings contribute to our understanding of the health of the water, specifically related to fish bearing streams running through residential and industrial regions. This project will continue as a three-year study to monitor changes in the microbiome during the course of stream restoration.