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Biomedical Sciences Seminar Series

Winter 2011 Poster Presentation
January 28, 2011 at 1 pm
Physical Sciences Lobby

Poster #1- Brenda Andrade

Quinoxaline-Spanned Heterocapsule for Improved Molecular
Guest Trapping Design Evolution

The previously reported Triquinoxaline heterocapsule by Tunstad et al. showed no significant guest binding.1, 2 The second generation of these heterocapsules with a more rigidified cavity afforded by benzal bridging of resorcinarene hydroxyls has been prepared and their binding studies are pending.2, 3 The newest generation of heterocapsules will incorporate quinoxaline, methylene, and phosphonate bridges that may allow the capsule to open and close and provide a more rigid scaffold for our capsules. The new design features a diquinoxaline monomethylene or monophosphonate bridged base that will create a cleft for guest binding, while the other capsule will have interdigitated quinoxaline moieties for a fully enclosed cavity. Synthesis of capsule precursors will be prepared using literature methods by condensation of resorcinol with hexanal. The resulting resorcin[4]arene will be incorporated with four quinoxaline moieties that will be selectively excised to provide Triquinoxaline diol and distal Diquinoxaline tetrol cavitands. The exposed hydroxyls of the quinoxaline-incorporated homologs will be bridged with methylenes or phosphonates to provide initial conformation studies.4, 5,6 Conformation studies via variable temperature, acid/base titration, and variable solvent 1HMR of our proposed capsule’s precursor cavitands, Diquinoxaline dimethylene cavitand and Triquinoxaline monomethylene, should provide insight to the opening, closing and binding abilities of the ultimate capsules


Poster #2- Diane Rico

Genetic Tests of Biophysical Models for the Caribbean

Understanding genetic connectivity among marine populations is essential for conserva-tion efforts such as establishing marine protected areas, managing fisheries, and assessing environmental impacts. Since benthic invertebrates do not have extensive swimming ca-pabilities, movement between populations must occur during a free-swimming larval stage that differs in duration between species. Different developmental strategies deter-mine three general PLD ranges. Species with long-lived planktonic larvae have a PLD of many weeks to months. Species with short-lived larvae persist in the plankton for hours to days, whereas species with intracapsular metamorphosis have no PLD. Planktonic larval duration is expected to proportionally correspond to dispersal between populations. A recent biophysical model for the Caribbean that incorporates currents, general larval swimming behavior, PLD, and spawning strategies predicts four distinct regions, each containing four to six subregions, between which larval dispersal is un-likely. A geophysical barrier was predicted to separate the Eastern and Western Carib-bean along the Mona Passage. However, studies on sea slugs from the genus Elysia re-vealed genetic discontinuities, or breaks in gene flow that counter the predictions. My project will evaluate genetic markers from four additional sea slug species ranging in PLDs to compare model predictions with actual gene flow and to determine whether or not there are congruent breaks across species. My results will determine whether dispersal patterns of marine invertebrates can be accu-rately predicted using a general ocean circulation model and larval PLD. If genetic data confirm that PLD is not correlated with dispersal, other factors must influence larval mi-gration. Integrating species-specific larval swimming behavior might then be necessary to improve the accuracy of models used in marine conservation.


Poster #3- Jose Cisneros

Virtual Yang-Baxter cocycle invariants

We extended the Yang-Baxter 2-cocycle invariants of knots and links, enhancements of the biquandle counting invariant, to include an operation at virtual crossings. These invariants coincide with the classical Yang-Baxter cocycle invariants for classical knots but provide extra information about virtual knots and links. In particular, they provide a method for detecting non-classicality of virtual knots and links.


Poster #4- Michelle Roa

Optimization of Analytical Techniques for the Detection of Oxygenated Polycyclic Aromatic Hydrocarbons on Environmental Surfaces

Polycyclic aromatic hydrocarbons (PAH) are formed in incomplete combustion processes including the burning of fossil fuels, and tobacco. Heavy PAH (those that contain 4 or more fused benzene rings) tend to reside on environmental surfaces such as particulate matter, soils and sediments. Photodegradation of PAHs may induce carcinogenic activity by forming oxygenated PAH with ketone, hydroxyl, or epoxide functional groups. Benzo[a]pyrene (BaP) is a PAH that has been studied extensively due to its carcinogenic potential. In the presence of sunlight and oxygen, oxygenated BaP derivatives, including isomeric benzo[a]oyrene-diones, are formed. Consequently, it is imperative to develop sensitive and selective analytical techniques to identify and quantify oxy-PAH on environmental surfaces. This paper will discuss preliminary results designed to optimize the extraction an oxy-PAH (BaP-dione) from silica gels that serve as surrogates for environmental dust, soil and sediment. The silica will be spiked with a known concentration of BaP-dione and dried. To extract the BaP-dione from the silica gel, a range of methanol : methylene chloride solutions will be used to reconstitute the BaP-dione in an ultrasonic bath. An Accela high performance-liquid chromatograph (HPLC) equipped with a photodiode array (PDA) detector will be used to measure the concentrations of BaP-dione in solution after extraction. The results of these experiments will be used to determine the optimal ratio of methanol to methylene chloride for the extraction of oxy-PAH from environmental surfaces. The results of this study will further help to understand the risk of oxy-PAH present in actual environmental samples.

Poster #5- Natalie Martinez

Applying Combinatorial Methods to Find Graph Eigenvalues

Finding eigenvalues for a specific graph can be very time-consuming yet provides considerable information about a graph. The number of closed walks of length k in the graph equals the sum of the kth powers of the eigenvalues of the graph. One can use combinatorial techniques to calculate the number of closed walks of a given length, thereby providing information about the eigenvalues. We illustrate this technique with small two-vertex multigraphs. Thank you, Natalie C Martinez


Poster #6- Richard Albay

The Effects of Lifetime Exercise and Environmental Enrichment on Brain Function, Innate Immunity and Lifespan.

The study is designed to test the hypothesis that engaging in voluntary wheel-running exercise, ingestion of a natural whole-food diet, ingestion of an nervous system-supporting herb, and living in an enriched living environment (EE model) throughout the lifetime of a rodent will each enhance mental functioning, measures of innate immunity and lifespan. There is emerging clinical evidence that physical activity and other important lifestyle interventions (such as diet and environmental enrichment) can improve lifespan, mental functioning and resistance to disease. The study of lifelong behaviors, dietary patterns and environmental conditions in laboratory animals is relatively new, and provides the opportunity to systematically measure important outcomes of interest to human clinical medicine.

Poster #7- Tanisha Williams

M.S. Environmental Science, Option in Environmental Biology

Identification of California Populus species and hybrids through single nucleotide polymorphism genotyping and morphological analyses Populus is a model tree with qualities that make it suitable for such research areas as forest restoration and biotechnology. Hybridization of Populus species has been researched for many years to provide insights into species interactions and the broader consequences of hybridization on native ecological systems. Thirty years ago, a morphological analysis was performed to describe hybrid zones between two native species (Populus fremontii and P. trichocarpa) and one European exotic (P. nigra) throughout California. These hybrid zones will be revisited (n = 480 samples) and all individuals sampled will be genotyped using a 42 single nucleotide polymorphism (SNP) assay (14 SNPs that diagnose each species). The genotypic data will be used to assess the frequency of hybrid events at each sampling site, the patterns of gene flow between pure species and hybrid individuals, and the presence of advance generation hybrids. In addition, leaf samples will be taken for further morphological analyses off site. The off site analyses will consist of a series of eight measurements of each leaf sample and these data will then be analyzed statistically to predict the species membership of each sample based on the eight measurements. The identities of samples based on molecular and morphological data will also be compared to assess the diagnostic utility of previously used morphological characters in identifying pure species and their hybrids. Leaf morphology will also be compared to genotypic data to determine whether the morphological characteristics expressed by hybrids are intermediate between the pure parental species, and if advanced generation hybrids occur, whether the resulting leaf morphologies are intermediate between the two parental species or if there is a trend towards a dominant pure parental species. The results of this study will increase our knowledge of population genomics and the consequences of gene flow in California Populus, and can help focus conservation efforts to maximize biodiversity.


Poster #8- Tram Duong

The Role of MyoD in activating transcription of Id2 gene

Id2 (inhibitor of differentiation 2) is a helix-loop-helix (HLH) protein known to inhibit the function of MyoD, a muscle-specific transcription factor. MyoD promotes skeletal muscle differentiation by binding and transactivating the expression of muscle-specific genes. Recent genome-wide analysis of MyoD binding suggests that MyoD may be regulating the expression of genes that are not muscle-specific as evidenced by the binding of MyoD at the Id2 promoter in undifferentiated myoblasts. We hypothesized that MyoD is activating transcription of the Id2 gene. To test this hypothesis, we will determine if there is a higher accumulation of Id2 mRNA in non-muscle cell lines expressing MyoD from a transgene in comparison to non-muscle cell lines lacking MyoD. RNA will be collected from the various cell lines and qRT-PCR will be used to assay for the difference in Id2 mRNA accumulation. From our results, we expect to see a higher accumulation of Id2 mRNA in non-muscle cell lines expressing MyoD from a transgene than non-muscle cell lines lacking MyoD. If our hypothesis is correct, then MyoD may have activating and repressive functions, which regulate the progression of muscle differentiation. Our results will provide further understanding of MyoD and Id2 contribution in normal muscle development.


Poster #9- Carlos Anguiano

Romanticism as a Function of Age, Sex, and Ethnicity

By adulthood, most people have developed a vast array of (sometimes inaccurate) beliefs about the nature of love and the features of romantic relationships. These idealized romantic beliefs, called romanticism, are associated with two demographic factors – age and sex. The association between romanticism and ethnicity is unknown. The goal of this study was to extend previous research by examining whether romanticism would differ as a function of age, sex, and ethnicity. A multi-ethnic community sample of 436 adults (average age = 27.2) completed Sprecher and Metts’ (1989) Romantic Beliefs Scale. Results revealed that: (1) Age was negatively correlated with average romanticism score (r = -.11, p


Poster #10- Angela Guerrero

Photooxidation of the Antioxidant Trans-Resveratrol

Resveratrol has received much attention as a polyphenolic antioxidant. However, its reactivity with other reactive oxygen species such as singlet dioxygen, has been unexplored. We present an investigation of the chemistry of trans-resveratrol, with singlet oxygen, an electrophilic reactive oxygen species. We found two reactivity channels, namely [2+2] addition followed by cleavage of the resveratrol trans double bond leading to the corresponding aldehydes, and [4+2] addition leading to endoperoxide formation. Trans-resveratrol removes singlet oxygen efficiently with a rate constant of 1.4 x 106 M-1sec -1. The fraction of the total singlet oxygen removal rate that leads to products was determined by determined competition experiments with known singlet oxygen traps. The implications of this kinetic data will be discussed.


Poster #11- Tiifanny Kilbas

Predicting Trends in Cysteine Oxidation: A Look at Sulfinic Acid

Cysteine oxidation is essential to protein regulation and function. Some forms of cysteine oxidation are reversible which means this oxidation can switch on or off a protein. However, cysteine sulfinic acid generally serves as an intermediate to further oxidation which leads to permanent protein damage and therefore halts normal protein function. However, studies indicate that oxidation of the active site cysteine of some peroxiredoxins to cysteine sulfinic acid is reversible. Because cysteine oxidationhas such critical roles in protein function it is important to know which proteins contain cysteines that are susceptible to oxidation to sulfinic acid. Trends in previously sequenced and crystallized proteins that are known to contain cysteine sulfinic acid can be observed and analyzed in order to design algorithms which predict which cysteines are susceptible to oxidation. In order to show that these trends are specific to cysteines that are susceptible to oxidation they must be compared to cysteines that are known not to be susceptible to oxidation this would be the control. To begin discovering these trends the sequences of the proteins were analyzed by entering data into a weblogo generator which provides a figure showing a rough estimation for which amino acid is expected to be most common at a given position ranging from -10 to +10. A graph was then designed which indicates the percent amino acid which exhibits certain chemical properties at a given position. The amino acids are divided into three groups, where group I corresponds to non-polar amino acids, group II to polar amino acids and group IIIA/IIIB to acidic/basic amino acids (charged) . Secondary structures were then analyzed by determining percent secondary structure at a given amino acid position, where the secondary structures include: isolated beta-bridge, hydrogen bonded turn, extended strand (participates in beta ladder), bend, no secondary structure assigned, 3-helix(3/10 helix), alpha helix and no data available. The secondary structures of cysteines known to become sulfinic acid and those amino acids in the relative -10 to +10 positions were also analyzed to ensure that protein structure was conserved upon oxidation. The future goals are to look at crystal structures of proteins and analyze trends of atoms at different spherical layers surrounding the oxidation susceptible thiol sulfur.


Poster #12- Arriana Valdez

Search for Homology of DNA and Clock DNA Among Acetabularia
and Other Organisms

Circadian rhythms are biochemical, physiological, and behavioral processes in living organisms that follow a roughly 24-hour cycle. The mechanism for the generation of circadian rhythmicity in most circadian systems is modeled by a transcription/translation feedback oscillation in which clock proteins feedback (negatively) on their own nuclear transcription to produce rhythmic levels of protein and mRNAs. Yet, enucleated Acetabularia is able to maintain rhythmicity for up to seven weeks, and the inhibition of nuclear RNA synthesis does not eliminate rhythmicity in this organism. This demonstrates that rhythmic transcription of any nuclear gene is not required to maintain a circadian rhythm in Acetabularia. Since organelle-DNA is present in enucleated Acetabularia, the presence of clock genes in the cytoplasm should be tested. General primers corresponding to circadian genes in other organisms are being tested on the Acetabularia chloroplast DNA using the polymerase chain reaction.  


Poster #13- Alberto Villegas

Circadian rhythms are biochemical, physiological, and behavioral processes in living organisms that follow a roughly 24-hour cycle. The mechanism for the generation of circadian rhythmicity in most circadian systems is modeled by a transcription/translation feedback oscillation in which clock proteins feedback (negatively) on their own nuclear transcription to produce rhythmic levels of protein and mRNAs. Yet, enucleated Acetabularia is able to maintain rhythmicity for up to seven weeks, and the inhibition of nuclear RNA synthesis does not eliminate rhythmicity in this organism. This demonstrates that rhythmic transcription of any nuclear gene is not required to maintain a circadian rhythm in Acetabularia. Since organelle-DNA is present in enucleated Acetabularia, the presence of clock genes in the cytoplasm should be tested. General primers corresponding to circadian genes in other organisms are being tested on the Acetabularia chloroplast DNA using the polymerase chain reaction.


Poster #14- Jhanisus Melendez

The Importance of Lysine 918 to the Catalytic Function of
Phosphoenolpyruvate Carboxylase

Phosphoenolpyruvate carboxylase (PEPc) is an essential photosynthetic enzyme for C4 plants. In monocotyledonous C4 plants such as maize (but not in dicotyledonous C4 plants) PEPc is allosterically activated by the amino acid glycine. The aim of this research is to test the role of the lysine residue at position 918 in glycine activation. Results obtained by multiple sequence alignment using the program ClustalW have shown this lysine residue is strongly conserved in sequences of PEPc from monocots, whereas in dicots there is a conserved histidine in this position. Using site-directed mutagenesis we replaced lysine 918 in the enzyme from maize (a monocot) with histidine. This mutation was confirmed by sequencing and the K918H mutant was expressed in E.coli. The recombinant enzyme was purified by Ni ion chromatography but, surprisingly, was found to be catalytically inactive. Since lysine 918 is quite distant from the catalytic site, this unexpected loss of catalytic function in K918H may stem from folding problems in vivo or from structural instability of the mutant protein during purification.


Poster #15- Na'il Mitchell

The Role of Magnetite in Amyloid Beta Fibril Formation

Magnetite has gathered considerable attention in an array of different research fields due to its low toxic effects, paramagnetic properties, and controllable size distribution; and may play a role in the formation of amyloid beta fibrils, the central landmark of Alzheimer’s diesease . Magnetite has been found to be present in the plaques of people with Alzhemier’s disease [1, 2], leading some to believe it is aiding in the formation of amyloid beta fibrils. Research has been done to see if it aids in the formation of the fibrils [3, 4]; none of the results indicating that it catalyzes the formation of amyloid fibrils. The research however involved surfactant based magnetite, which would not be present in-vivo and involved amyloid systems that were not amyloid beta. It is because of this that we wish to study uncoated magnetite and coated magnetite’s effect, if any, on the formation of amyloid beta fibrils.

Poster #16- Michael Mendoza

Protein Purification of Wild Type p53 DNA Binding Domain

The ability of a cell to appropriately respond to stresses and maintain its redox potential is essential for life. Stressors that can alter the redox potential in the cell include UV light, reactive oxygen intermediates (ROI), heat shock, ionizing radiation, and DNA damage. Adverse changes in redox potential can alter the tertiary structure of proteins and affect their ability to perform their functions. It has been shown that the tumor suppressor protein p53 is subjected to a reversible form of modification called S-glutathionylation. (Velu et al. 2007) p53 is tetramer protein, containing two identical dimer subunits that together form a fully functional protein which can bind to DNA. Human p53 contains six solvent exposed cysteine residues: Cys 124, Cys 176, Cys 182, Cys 229, Cys 242, and Cys 277 within the DNA binding domain. Maintaining the reduced states of these cysteine residues is vital for p53 to remain functional.

Poster #17- Evelyn Barrios
Combinatorial Game Theory
A look at Greedy Nim In a combinatorial game two players take turns moving alternately until no legal moves are available. Greedy Nim is a variation on nim where the players are restricted to choosing stones from only the largest pile(s).and the last player able to make a move wins
Poster #18- Marcela Leyva

Understanding the Mechanism of Decrease Production of F1-R Sendai Virus.

Sendai virus is a negative sense RNA virus which causes a respiratory infection in mice similar to the infection in humans caused by the Human Parainfluenza virus. A variant of Sendai virus call F1-R causes a systemic infection which makes it more virulent than wild type (Wt) virus. To identify which mutations are responsible for the F1-R systemic phenotype, reverse genetics was use to create variants of Sendai virus with various combinations of the F1-R gene mutations. One such variant, RGV0, has all the same mutations as F1-R except for mutations in the P and L gene. Animal studies showed that RGV0 causes a systemic infection in mice, but it appeared to be more virulent than either wt or F1-R. Tissue culture studies showed that RGV0 is replicates more like wt, consistently producing at least 10-fold more viruses then F1-R. This lead us to suggest that RGV0 is more virulent than wt because it causes a systemic infection, and that it is more virulent than F1-R because produces more viruses than F1-R . Given that the only difference between F1-R and RGV0 is that RGV0 lacks the P and L gene mutations it is believed that the mutations in the P and/ or L gene are responsible for the decrease production of F1-R. To gain a better understanding of the mechanism of decreased virus production in F1-R infections and determine if the decrease is due to an overall decrease in viruses being produced or a decrease in the production of infectious versus non-infectious virus, we have assayed the viruses via hemagglutinin, egg infectious dose assays, tissue culture infectious does assays, plaque assays and multiple round of replication assays. The results thus far may indicate that the decrease is in infectious virus production. We are currently developing both one-step and two step QRT-PCR protocols that can be used to accurately quantify the number of overall viruses and the ratio of infectious to non-infectious viruses produced during infections of the different variants of Sendai virus. An internal RNA control that utilizes the same primers and generates a product of the same size, but with a different internal sequence, has been made and it will be spiked into each experimental sample to correct for variations in amplification efficiency and for the presence of inhibitory substances. The two products will be distinguished based on the use of differentially labeled fluorescent probes. The results of the QRT-PCR assays will be compared to the results of a plaque assays, an egg infectious dose assays, a HA assay as well as a two step RT-PCR to determine if the difference in virulence is due to the amount of infectious virus being produced.

Poster #19- Anthony Obesisan


Caridad Wilson
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