Summer 2008 REU Program Projects 1. Prediction and validation of HCV virus-derived miRNAs and their targets: The objectives of the research were to validate computationally-predicted virus-derived miRNAs (vmiRNAs) in HCV (Heptatitis C virus) -infected human hepatocyte cells (HHC) and to determine putative target genes of validated vmiRNAs. Several predicted vmiRNAs were found present in experimental HCV HHC. 2. Observation of motifs that participate in alternative splicing: This project was investigating segments of the primary mRNA that take part in the regulation of alternative splicing. They were believed to function in pairs. By using combinatorial and statistical methods, the occurrences of such pairs in different mRNA sequences were analyzed, in order to make biological conclusions as to how they function in the process of alternative splicing. 3. Using nanosphere lithography to fabricate hexagonally arranged gold nanoparticles: Nanosphere lithography was thought to be a simple and cost-effective technique for the creation of gold nanoparticles. Glass substrates were coated with polystyrene latex nanospheres to become monolayer arrays. Gold was then deposited on top of these arrays and the spheres were removed. 4. Chromatin structure and epigenetics on repetitive elements: a genomic study: The repetitive DNA sequences in their bendability to wrap around the histone complex to form a nucleosome were studied. Then profiles were set up for the histones by mapping them onto the repetitive elements. 5. Multi-locus sequence typing for Necator americanus: The project was looking into the possibility of creating a more species-specific hookworm vaccine, while trying to eliminate the current assumption in research that most hookworms in all locations are genetically identical. 6. Vesicle phase dynamics and the effect of nanoparticle characteristics on vesicle internalization: This project provides insight into the interactions that occur between gold nanoparticles and lipid bilayer vesicles which serve as models for biological cells. This is accomplished using a dynamic light scattering (DLS) system. 7. Positive feedback induction of amylin aggregation by externalized phosphatidylserine in the development of Type II diabetes mellitus The interaction of human islet amyloid polypeptide (hIAPP) aggregates, labeled by IAPP aggregate-specific thioflavin-T fluorescent dye, with synthetic lipids in vitro by spectrophotometric analysis was studied. 8. Identifying genes in the drosophila genome: Is CG12207 the red malpighian tubules gene in Drosophila melanogaster? PCR and cloning techniques were used and constructs were made containing the transcript A cDNA of CG12207. Those constructs would be used to make transgenic flies to test whether a normal copy of CG12207 can cause flies that are homozygous for the red gene to have the normal wildtype eye color. 9. Locating the Cardinal (cd) eye color gene Cardinal gene causes the distinctive orange eye color in Drosophila melanogaster. The CG6969 transcript in larvae, pupae, and adult flies were amplified. The highest level of expression was expressed in pupae, the stage of life when eye color pigment is deposited. Hence, CG6969 is the cardinal gene. 10. Degradation of oxidized proteins in glyoxysomes Isocitrate lyase (ICL) is a unique enzyme of the glyoxylate cycle in glyoxysomes. The extent of ICL oxidation by hydrogen peroxide was studied to determine how the activity of proteins is affected by oxidation. 11. Systematics of species in the catch-all genus Knodus Morphological, histological and molecular characters were analyzed between the undescribed collections, which are tentatively classified in the genus Knodus, and Knodus meridae. The morphological and histological characters are sufficiently different between them and indicates a more distant relationship. 12. The role of 185/333 proteins in the immune system of the purple sea urchin, Strongylocentrotus purpuratus The immune response system in purple sea urchin was studied and it was found that the 185/333 family proteins would bind to a variety of bacteria, which suggests a high level of diversity within invertebrate immune response. 13. Group facilitation of Acharia stimulea The Acharia stimulea caterpillars group feeding behavior was studied. It was found that group feeding may protect well-defended caterpillars from predators because of their negative experience in capturing caterpillars. Group feeding may also facilitate growth by altering host plant quality. 14. Role of catecholamines in heart tube formation in developing chicken embryos The project was looking at the possible roles of norepinehprine (NE) and epinephrine (E), two catecholamines that can be synthesized from dopamine, in chicken heart development. It was found that sodium diethydithiocarbamate (DDC) and LY-134046 (LY) would partially block the closure of the anterior intestinal portal and produced embryos with short and/or split hearts, while other organ systems were not affected. 15. Tricyclics and their effects on lipid vesicles The project was looking into tricyclic drugs, which can act against the multi-drug resistance in cancerous cells. The focus was on clozapine, a tricyclic drug, on the phase dynamics of lipid membranes.
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