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«Strengthening the Nation through Diversity, Innovation & Leadership in STEM San Antonio,Texas · October 3-6, 2013 Get Connected! Connect with the ...»

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Folagbayi Arowolo1, Dhanansayan Shanmuganayagam2, Jess Reed2, Chris Krueger2.

University of Pittsburgh, Pittsburgh, PA, 2University of Wisconsin, Madison, WI.

1 Food spoilage accounts for billions of dollars in lost revenue for the food industry. Fruit rot alone accounts for approximately 10% of food spoilage. Additionally, economies that depend on soft-fruit exports suffer in agricultural returns from fruit rot. The most common agent of fruit rot is Colletotrichum acutatum, a fungal pathogen that infects soft fruits through bruised regions on the skin. We have developed a biopolymer composed of tannins and chitosan, derived from specific plant sources and shrimp shells, respectively. Our preliminary studies indicate that tanninchitosan biopolymers inhibit the growth of C. acutatum. However, tannins are complex polyphenolic compounds with large structural heterogeneity that confers a large diversity in biological properties. We will examine how specific structural features of tannins affect the antifungal properties of tannin-chitosan biopolymers. The study focuses on three distinct features: A-type linkages, from cranberry; B-type linkages, from grape seed; and hydrolysable tannins, from pomegranate. Tannins will be extracted from the sources and characterized by MALDI TOF mass spectrometry.

Three tannin-chitosan biopolymers will be synthesized from the three tannin sources, and their ability to inhibit the

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Linda Onyirimba1, Emily Yau1, Lisa Morano1, Kenneth Johnson1, Jay Neal2, Aaron Corsi2.

University of Houston-Downtown, Houston, TX, 2University of Houston, Houston, TX.

1 Terrior is the set of characteristics such as geography, geology, and climate, of a certain place and how those characteristics impact crops growing there. Terrior has been hypothesized to impact wine quality. This study focuses on the analysis of soil texture characteristics to investigate the connection between soil texture and viticulture parameters such as stem weight. We will analyze soil texture from 24 individual vine locations: 4 replicate Syrah vines from 6 different vineyards in the Texas Hill Country. We obtained soil samples at two different depths (30 cm and 50 cm), and analyzed the soil textures of the samples to determine the concentration of sand, silt, and clay. Preliminary data collected last year suggest that a higher percent composition of clay in the soil correlates with heavier stem weights of the grapevine. We will make wines from each of the vines in this year’s study. We will describe wine quality by analyzing characteristics such as aroma, pH, level of anthocyanins, Brix (concentration of sugar), phenols, and tannins. These characteristics will not only help define our wine quality, but also assist us in determining the interaction between wine quality and soil texture. Our goal is to determine if soil texture indirectly affects wine quality and flavor by impacting the vigor of our vines.



SLICES Irene Yim1, Wen-Xian Du2, Roberto Avena-Bustillos2, Tara McHugh2.

Skyline College, San Bruno, CA, 2Western Regional Research Center, United States Department of Agriculture, 1 Albany, CA.

Activation of phenylalanine ammonia-lyase and chalcone synthase through abiotic stress caused by UV-B treatment provides the basis for a novel value-added processing method that can enhance the nutrient content of specialty crops. This process increases the synthesis of secondary metabolites including terpenes, polyphenolic compounds, and nitrogen-containing compounds. We will evaluate the application of wounding followed by mild UV-B exposure to enhance the nutrient content of sliced carrots by stimulating the synthesis of secondary metabolites before cold storage. Recently harvested commercial, orange carrots will be sliced at 3 mm thickness. Both top and bottom sliced surfaces will be exposed to three different total energy doses and a bimodal peak UV-B irradiance of 20 mW/cm2. The slices will then be incubated at 15 °C for 3 days to allow for a biological response to the stresses followed by storage at 2 °C for 15 days. The change in total soluble phenolic contents (TSP) in response to the treatment conditions will be assessed using the Folin–Ciocalteu assay, and the resulting antioxidant capacity (AC) will be assessed by the 1,1-diphenyl-2-picrylhydrazyl radical method. Wounding stress from slicing and UV-B exposure at 60, 90, and 120 mJ/cm2 are expected to increase the TSP and AC of carrot slices at least 2-fold after 15 days of storage at 2 °C, compared to whole carrot controls under similar storage conditions. Our results may suggest that UV-B light exposure could be used as an additional industrial processing step on fresh-cut carrot slices to enhance their nutritional value.

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Mario Farias1, Ernesto Alvarado2.

Heritage University, Toppenish, WA, 2School of Envrionmental and Forest Sciences, University of Washington, 1 Seattle, WA.

The Tapash Sustainable Forest Collaborative is a project to restore ecosystem health in eastern Washington. The collaborative involves the US Forest Service, Washington State DNR and FWS, the Yakama Indian Nation, TNC, and private owners. This project analyzes the changes from 1992 through 2009 in forest species composition, cover, structure, and correlated management along the riparian areas of sampled watersheds. The initial change analysis was performed from 1949 through 1994 using historical, aerial photography and GIS. The objective of this project is to analyze the vegetation changes from 1994 through 2009 by using recent aerial photography available from the USDA NAIP. The vegetation found in these transitional areas between aquatic and terrestrial environments serves to reduce soil and nutrient loss due to stream runoff, serves as a form of flood control, and furthermore, dictates forest fire severity. ArcGIS will then be used to create vegetation layers to quantify the types of vegetation surrounding riparian areas in the Tapash area and to calculate vegetation coverage. Information found through this study will be used to determine fire prevention strategies and help define future reference conditions for landscape restoration among these fire-prone ecosystems.



Ruben Zamora, David Wood, Brice McPherson.

University of California, Berkeley, Berkeley, CA.

Phytophthora ramorum, an oomycete plant pathogen, was introduced to California approximately 2 decades ago.

P. ramorum causes sudden oak death throughout coastal forests of central and northern California. Coast live oak (Quercus agrifolia), a native California species, is highly susceptible to P. ramorum, and infections have led to high mortality rates. The goal of this study is to determine the severity and location of Sudden Oak Death in coast live oak populations throughout Tilden Park. To estimate the proportion of trees infected by the pathogen, both the point centered quarter (PCQ) population density estimation method and complete inventory plots were used. Sampling nodes were established across transects at 40 meter intervals, and one coast live oak was selected for analysis in each cardinal direction (N, S, E, and W). Because the disease follows a reproducible sequence of symptom expression, we can rate the severity of the disease on each sample tree from 1 to 5 where 1 is asymptomatic and 5 is dead with symptoms of the disease. Data collected will be used in the development of models to monitor the disease through time by updating data collected on the infection and mortality in 2009. Models are intended to predict the advancement of the disease in the East Bay Park District and will be used to better understand the long-term effects of this epidemic on California’s coastal forests. Although very little is known about the ecology of this pathogen, its long-term negative effects are likely to be highly significant.

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Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV; OMIM#265380) is a lethal genetic disease that affects the lungs during development. Diagnosis is done mostly by post-mortem autopsy, but some biopsies have also been done. The key characteristics are immature lungs, misalignment of pulmonary veins, and drastic lack of normally positioned alveolar capillaries which lead to hypertension and respiratory failure. A very high percentage (85%) of patients with ACD/MPV also present with anomalies of the gastrointestinal, cardiovascular, and genitourinary systems. Mutations in the FOXF1 gene cause ACD/MPV. While most of the cases are sporadic, some (~10%) of the samples in our cohort of over 100 patients have been identified as familial. We hypothesized that the DNA binding domain of FOXF1 is important for its function as a transcription factor. To investigate the mutations, DNA from patients and immediate family members were isolated to carry out polymerase chain reaction (PCR).

Amplification of the coding sequence of FOXF1 was done using specific primers. The amplicons were visualized on agarose gel by electrophoresis and were purified using sephadex columns. The wild type DNA and the mutant DNA were sequenced using an Applied Biosystems ABI3130XL genetic analyzer. The mutations identified were located on the DNA binding domain of the protein (FOXF1), thereby supporting our hypothesis. We will use this data to further investigate the role of the specific amino acids in the DNA binding domain of FOXF1 in accomplishing its function as a transcription factor.



Shawntel Okonkwo, Daniel Hart.

University of California, San Francisco, San Francisco, CA.

Though heritability for red blood cell traits is high, their genetic determinants remain largely unknown. Several single nucleotide polymorphisms (SNPs) are associated with high mean corpuscular hemoglobin concentration (MCHC), an RBC trait indicating abnormal erythropoiesis where RBCs become spherocytes instead of normal bi-concave disks.

A recent genome-wide association study (GWAS) showed that an intronic SNP of TATA-binding protein associated factor 3 (TAF3) has a particularly strong statistical correlation to the SNPs associated with high MCHC. It has also been shown that TAF3 is specifically required for proper erythropoiesis in zebrafish and mice, although the same requirement in human erythropoiesis has not been demonstrated. Our goal was to determine if there is a similar relationship between TAF3 and high MCHC, as suggested by the GWAS data. We hypothesized that TAF3 is a key transcriptional regulator of the genes encoding major proteins of the erythrocyte cytoskeleton (namely Ankyrin and α-Spectrin) thereby causing elevation in MCHC. We performed chromatin immunoprecipitation to determine occupancy of TAF3 in the gene promoters and found recruitment relatively high. We knocked down TAF3 in K562 cells (pro-erythrocytes) using shRNAs, and quantified gene expression of Ankyrin and α-Spectrin using QRT-PCR.

Our results conclusively indicated TAF3 knockdown downregulates α-Spectrin but not Ankyrin. In future studies, we aim to elucidate the mechanisms underlying this phenomenon by investigating epigenetic mechanisms such as histone modifications and chromatin crosstalk. This potentially novel role of TAF3 in human erythropoiesis may aid our understanding of the genetic determinants underlying RBC traits indicative of RBC membrane diseases.



Jasmine Johnson, Sue McClatchy, Gary Churchill.

Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME.

In recent decades, sleep deprivation has been linked to physical and behavioral diseases, particularly obesity.

Studies have identified a relationship between sleep deprivation and obesity, but the intricacies of this relationship remain unknown. We have set out to identify individual genes that regulate sleep traits and relate these genes to


metabolic disorder and obesity in order to further our understanding of the mechanisms underlying sleep and its effect on our bodies. We conducted quantitative trait locus (QTL) analysis on data from sleep-deprived mice with 28,054 gene expression traits from the hypothalamus, thalamus, and anterior cortex as well as various sleep-wake traits. We narrowed down a gene list from 28,054 to 7 candidate gene regulators of sleep. We identified Sncb, Ssr1, Psmg4, Adarb2, Spock1, Elmo1, and Txndc5 as genes related to sleep in addition to having relationships with body homeostasis, various neurodegenerative diseases, metabolism, and body weight. These candidate gene regulators have the potential for use in knockout models for elucidating the function of sleep and its relation to disease.



Ashley DeAguero, Melanie Adams, Richard Cripps.

University of New Mexico, Albuquerque, NM.

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