CYCLOIDEA (CYC) is a member of the TCP family of transcription factors, whose name stands for TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS.  The members of this transcription factor family are involved in regulating plant growth and cell proliferation by binding to DNA. Previous studies show that CYC has duplicated at least twice in the core eudicot angiosperms and that the CYC2 paralog is involved in controlling flower symmetry. The goal of our research was to characterize duplications of CYC in Rhododendron, with the long-term goal of seeing how these duplications affect flower symmetry. To accomplish this task, we used the R. williamsianum genome sequence to design primers specific to each paralog in order to PCR-amplify the CYC genes from four Rhododendron species, representing two subgenera (Hymenanthes, Rhododendron). Amplified products were cloned and sequenced to recover all alleles. We used our Rhododendron sequences and sequences from the conserved TCP and R domains of other species as out-groups in a Bayesian analysis to reconstruct the gene tree. From this tree, we have identified 2 main duplications in Rhododendron CYC genes as seen in other core eudicots. We also found that the CYC2 paralog has undergone at least 2 gene duplications and that the CYC1 paralog underwent one. Future research will focus on finding when CYC2 duplications occurred in rhododendrons and determining if, where, and when these CYC2 duplicates are expressed in Rhododendron flowers.

Organic acids are crucial factors in creating the aromas and flavors in wine, each adding their own qualities and characteristics. Winemakers regularly use various forms of technology to quantitatively determine the contents of wine. Analytical tools such as enzymatic spectrophotometry, paper chromatography, and high-performance liquid chromatography offer methods to quantify chemical components including acetic, malic, lactic, tartaric, and citric acids, as well as sulfates and sulfites. Although ion chromatography (IC) has not been a widely studied method to analyze organic acid content in wine, it offers the potential to simultaneously analyze multiple ions with greater specificity and sensitivity than other approaches. This project examines the various ways that IC can be used to analyze the components of wine, allowing for further application within the wine industry. The malolactic fermentation process was tracked to measure the changes of malic and lactic acids within the wine. Sulfites and sulfates were measured as the wine was exposed to oxygen during the aeration process. The results show that IC provides greater accuracy than paper chromatography and enzymatic spectrophotometry, the most commonly used methods in wineries. This increased accuracy provides additional knowledge that allows winemakers to further understand and evaluate the chemical components in the wines that they create. This is a useful step towards making the characterization and marketing of the wines less subjective.

Antibiotics are present in nearly every facet of our lives including personal hygiene, medicine, food processing, and the treatment of infectious diseases. Because of this widespread exposure, antibiotic resistance occurs in dangerous pathogens around the world. Novel antibiotics are needed to combat these resistant organisms and reduce both the loss of lives and treatment costs. Most antibiotics originated in microorganisms cultured from soil, but very few novel compounds have been discovered in this environment over the last several decades. It is imperative that other environments are screened for antibiotic producing microbes. We sampled the Puget Sound, isolating and culturing bacteria from the surface. Isolated cultures were tested against reference strains of common pathogens for antibiotic potential by measuring the zones of inhibition they produced via agar diffusion. Phylogenetic analysis with 16s ribosomal RNA was used for identification of cultures with inhibitory activity. This type of analysis, especially if scaled-up, has potential to identify novel therapeutic compounds that may elude common resistance mechanisms.

Improving the efficiency of photosynthesis has the potential to help attain a net reduction of atmospheric carbon dioxide (CO₂). Cyanobacteria are an enticing target phylum as they contribute an estimated twenty five percent of global photosynthesis. Under ideal conditions, cyanobacteria grow and reproduce rapidly yielding numerous generations over a relatively short time span. Most research on cyanobacteria carbon fixation has been conducted under increased concentrations of CO₂. In contrast, this research investigated: 1) whether cyanobacteria subjected to CO₂-limited conditions will produce successive populations that have improved carbon fixation efficiency, 2) the viability of those adapted populations in present day atmospheric conditions, and 3) whether the survivors fix carbon at an increased rate compared to control cyanobacteria. To answer these questions, control cyanobacteria were maintained in ambient air conditions while an experimental population of cyanobacteria was developed under a range of CO₂-limited conditions. Half of the adapted populations were then returned to ambient air conditions. The rate of carbon fixation under both CO₂-limited and ambient air conditions was approximated by measuring biomass. This research could provide a laboratory-scale proof of concept for net reduction of atmospheric CO₂ by low energy biological means. This method could also eliminate the need for direct gene manipulation by capitalizing on an evolutionary process. Future experiments could replicate this study with different species of cyanobacteria to develop regionally compatible cyanobacteria with more efficient carbon fixation resulting in a net reduction of atmospheric CO₂ in an environmentally sustainable manner.

I examine the aesthetic representation of autism in two contemporary Spanish graphic novels that successfully counteract the typical medical presentation of disability: María y Yo (2007) and María Cumple 20 Años (2015), both written and drawn by Miguel Gallardo with his daughter Maria. Each text incorporates purposeful visual techniques in order to present the peculiar characteristics of Maria’s autism as well as her father’s preoccupations with her future. I share how their presentation facilitates educational discourse, empowers the disabled and their families, and reflects the capability of the graphic novel to give authority to groups who are often overlooked.

Kaposi’s sarcoma (KS) is the most common tumor found in sub-Saharan Africa and in AIDS patients worldwide. It is a highly angiogenic tumor caused by Kaposi’s sarcoma-associated herpesvirus (KSHV), which establishes a latent infection in endothelial cells. KSHV infected endothelial cells display many angiogenic phenotypes, including vascular tube formation and stabilization. Recent data shows a link between KSHV angiogenesis and the hypoxia inducible factors (HIF) pathway. HIFs are a family of heterodimeric transcription factors that respond to low levels of oxygen in the cell. The HIF pathway has been shown to activate pro-angiogenic genes, including vascular endothelial growth factor (VEGF). Our lab has previously shown that both HIF-1alpha and HIF-2alpha are upregulated during KSHV infection. Although HIF-1alpha is expressed ubiquitously, HIF-2alpha is specific to endothelial cells. I hypothesize that HIF-2alpha regulates angiogenesis during KSHV infection. To test this hypothesis, I knocked down HIF-2alpha expression in endothelial cells using an shRNA lentivirus, which successfully knocked down expression by 80%. I then conducted a capillary tube assay on mock and KSHV infected cells. This assay involves homogenous seeding of cells onto Matrigel, a basement membrane matrix for studying angiogenesis in vitro. The cells attach and migrate on the Matrigel to organize into capillary-like structures, which mimics the later stages of angiogenesis. Latent KSHV infection has been shown to form tubes at 6 hours post-plating in Matrigel and to stabilize tube formation at 24 hours, a time point when capillary-like formation normally regresses in uninfected cells. My preliminary data shows that when HIF-2alpha is knocked down, KSHV-induced tube formation is inhibited. Future work will explore the viral mechanism and the cellular significance of HIF-2alpha upregulation during latent KSHV infection. If HIF-2alpha is required for KSHV-induced angiogenesis, this transcription factor may be a promising therapeutic target for KS tumors.

The purpose of this project was to record zooplankton abundance, distribution and diversity at two different study sites in the SJC (San Juan Channel) during the autumn of 2015, one with strong oceanic influence and one more estuarine, while continuing an annual, long-running dataset. Previous projects have focused on factors associated with distribution patterns, such as tides and tidal current speed. In this project, possible relationships between dissolved oxygen and the density of certain taxa were investigated using linear regression analysis both within the autumn 2015 dataset and over preceding years of data collection (2007-2015). Intra-seasonal temporal changes in abundance and distribution were observed during autumn 2015, some of which were consistent with that found during other years. While diversity was consistent across the years, the specific community assemblages found at the two sites varied. Dissolved oxygen was seen as a factor co-varying with abundance of certain taxa. If conditions are suboptimal for plankton survival (oxygen levels, nutrients, temperature) it may result in negative ecological consequences for animals farther up the food chain (Frederiksen, 2006). Information on plankton abundance as it relates to the changing oceans will be valuable in the years to come. In the SJC Caridean shrimp and gastropod larvae had positive relationships (p=0.008 and p=0.014) and polychaete trochophores had a negative relationship (p=0.018). However, these relationships did not all hold across the years. 

Students of Everett Community College’s Ocean College Research Academy (ORCA) analyzed pH trends in the Snohomish River estuary of Possession Sound using ten years of data. Influences on water chemistry include freshwater discharge from the Snohomish River and tidal currents in Possession Sound. In addition, high salinity, cold water from the Pacific Ocean may transport low pH water as a result of ocean acidification, when atmospheric carbon dioxide dissolves in seawater and decreases the pH. Students wanted to investigate whether average pH in Possession Sound had been decreasing over time. Data were analyzed during the winter months, November through March, from 2006 to 2016. We collected data from October 2015 through May 2016, with archived data collected by previous ORCA students. Water chemistry at three sample sites in the Possession Sound were compared. Recordings of pH from the surface to five meters were completed with a YSI 650 and averaged. The most significant decreases in pH occurred at locations in closer proximity to the shore, near south Whidbey Island and Mukilteo. Each had an overall decrease of 0.3, compared to only 0.1 in the middle of the sound near Hat Island. Decreased pH in an estuary system directly affects the development of many organisms, such as phytoplankton, which make up the primary levels of the trophic pyramid. Further investigation is ongoing about the effects of salinity and river discharge on these minimal decreases in pH, along with seasonal fluctuations in primary production by phytoplankton as well as the effects of decreased pH on phytoplankton.

The cultivation of tomatoes is currently a 58 billion dollar industry worldwide. Over the past few years, tomato plants have been subjected to more severe and abrupt climatic fluctuations than ever before. In-depth understanding of the tomato leaf anatomy and physiology can have significant consequences in agriculture. Fluxes (fluid flow rate) in leaf water and sugar-conducting tissues, xylem and phloem, are challenging to visualize in real time. It is important to attempt this measurement using intact leaves as excision interrupts control of normal flow paths. The possibility that vein density and flux influence photosynthetic rate is being investigated here.  Optical Coherence Tomography (OCT) is a non-invasive imaging modality that performs high-resolution cross-sectional imaging, allowing to visualize the structure and motion in biological samples in 3D.  In this study, we have used a state-of-the-art OCT system with 7 μm resolution, operating at 1300 nm wavelength, to investigate leaf structure, venation and vein flow in live tomato leaves for the first time. The low intensity imaging beam (3 mW) is in the near IR spectral region and imaging is performed at high speed (4 ms/frame) hence, does not interfere with the leaf’s natural physiological processes. We have used Rutgers’ tomatoes for this study. To improve the image contrast in the leaf veins, we are investigating using dye and lipid particles to be taken up by the leaves