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
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
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,
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