Student Projects, Archives - ISR

Past student ISR projects have included:

The source of HIV and its relationship to multiple types of SIV

by Abbey Sellers '12
Currently the process of aligning approximately 150 strands of DNA (from the gag to the pol region) using Meta X software. The 150 strands consist of a combination of HIV I, HIV II, and multiple different types of SIV. These sequences must be correctly aligned from the gag to pol gene in order to compare and contrast the different strands and to correctly identify which strand evolved from the other otherwise known as the order of evolution of the virus. In the end, the goal is to create a “family tree” of HIV/SIV showing which strands are most closely related and how they are related. As of right now, the process of aligning the DNA sequences is still underway.
Woodward Mentor: Mr. David Alvord
Project Advisor: Shozo Yokoyama, Ph.D.

Fragile X-associated Tremor/Ataxia Syndrome in Drosophila melanogaster

by John Yamin '11
Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is the result of 60-200 CGG trinucleotide repeats located upstream from the FMR1 gene in the X chromosome. Individuals with FXTAS undergo normal brain development; however, at around 50 years of age, they start to show neurodegeneration, tremors, and dementia. The genetics behind FXTAS can be studied using a Drosophila melanogaster (fruit fly) model system. By taking CGG repeats from humans, cloning and injecting it into flies, transgenic flies are made that carry FXTAS. By comparing other genotypes of flies, such as wild type flies, to the CGG FXTAS flies with the use of spectrophotometry and DNA microarrays, the mechanisms behind FXTAS can be further studied.
Woodward Mentor: Ms. Jessica Echols (past faculty)
Project Advisors: Peng Jin, Ph.D. and Abrar Qurashi, Ph.D., Emory University, Department of Human Genetics

Effects of the D192G mutation of Apn1 on the DNA repair capacity of Saccharomyces cerevisae

by Ben Coleman '10
DNA is subject to many types of damage. Certain types of DNA damage can be very deleterious to cells, and can induce apoptosis (cell suicide) or mutations. When mutations accumulate, they can lead to diseases such as cancer. To maintain genetic fidelity, cells have evolves many DNA damage repair and tolerance pathways. In the model system Saccharomyces cerevisae (baker’s yeast), one protein that governs the base excision repair (BER) pathway is Apn1. The D192G mutation of Apn1 occurs on the active site of the protein that governs DNA repair. It is possible that the mutant form of Apn1 has the same effect on the ability of the cell top repair DNA as a knockout of that same protein. An alternative is that the D192G mutation could be dominant negative, meaning that the DNA repair capacity of the mutant would be more compromised compared to the knockout. In order to determine the effect of the mutant and knockout proteins on DNA repair, the mutation rates of different yeast strains were determined with an assay designed to observe spontaneous mutation. In order to determine the true effect of the D192G mutation, several genes that code for other DNA repair proteins had to be knocked out, which eliminated the presence of the coded proteins.
Woodward Mentor: Ms. Kristin Namenye (past faculty)
Project Advisors: Paul Doetsch, Ph.D., and Lydia Morris

Imaging of Joint Attention in Aspergers

by Elizabeth DuPre '10
Joint attention is a social cognitive process wherein one individual alerts another to a salient stimulus in a nonverbal manner, such as pointing or gazing. It is a skill acquired in social cognitively normal individuals around one year of age, and is highly important in later development of theory of the mind abilities. However, children suffering from Autism Spectrum Disorders (ASD)—a range of disorders that includes autism, Aspergers, and pervasive developmental disorders, not otherwise specified (PDD-NOS)—display impaired ability in joint attention processes. By using functional magnetic resonance imaging (fMRI), we hope to identify the specific brain areas that function differently during this process in Aspergers patients. This will be done with the intention of enhancing scientific understanding of the developmental process for individuals with ASD and eventually developing methods to combat the innate neural differences between ASD and neurologically normal individuals.
Woodward Mentor: Mrs. Paula Nettles
Project Advisors: Amy Anderson and Dr. Clint Kilts at Emory University

The Use of Microbial Mats in Wastewater Treatment

by McKenzie Hudgins '10
Microbial mats are complacent cyanobacteria that can clean just about anything from wastewater to acid mine drainage. They are not true algae or plant but a blue-green “algae” that’s not actually a living organism. The microbial mat has an aerobic zone and an anaerobic zone which is only mm to cm in height but can stretch expansive distances in width. In these zones the microbial mat effectively removes or degrades organic, metallic, and other inorganic compounds from the water. Thus functioning like a filtering system. This is an effective way of cleaning wastewater and leachate because a microbial mat is a naturally occurring, fast-growing photoautotroph, can survive harsh environmental condition, and has harvestable biomass that can be processed for bioenergy.
Woodward Mentor: Mr. Ethan Greenberg
Project Advisor: Dr. Valentine Nzengung at The University of Georgia

Construction of a Bioengineered Human Artery

Due to the relative scarcity of ex vivo arteries available for study, it has become necessary to engineer arteries representative of that of a human artery. These arteries are grown in vitro under conditions controlled by the experimenter and can be influenced to acquire specific diseases for study and experimentation. The ultimate goal is to engineer such arteries to have them available for organ repair in patients with vascular disease and to utilize these arteries as a substitute to induce and to treat vasculitis in vitro. To accomplish this goal, lipopolysaccharide (LPS), a component of bacteria cell membranes, was used to mature dendritic cells (DCs), highly activated macrophages, which were used as antigen-presenting cells (APCs) to cause infiltration by specific T cell subsets. In order to confirm DC adherence and T cell infiltration and to type the infiltrating T cells, immunofluorescence staining, and real time PCR have been used. Data suggests that infiltrating T cells are primarily T helper memory cells.
Woodward Mentor: Ms. Chery Gibson (past faculty)
Project Advisor: Dr. Cornelia Weyand, director of Kathleen B. and Mason I. Lowance Center for Human Immunology, Emory University

Copper-plating Nitex Nylon Meshes

Copper has a very high thermal and electrical conductivity, which allows it to withstand higher temperatures. Determining the surface are of a nylon mesh and then determining the surface area of the nylon mesh after copper-plating can help determine the thickness of the copper around the nylon fibers. After burning out the nylon mesh, the copper plating remains to create a copper tubing. This copper tubing is perfect for catalysis, and because of its high thermal conductivity it can withstand the temperature of the chemical reaction going on around the tubing. This experiment can determine how thick the copper plating on the fibers has to be to create successful tubing for catalysis.
Woodward mentor: Dr. Kevin Hurysz
Project Advisor: Dr. Jason Nadler, Georgia Tech Research Institute

Investigations of Pancreatitis Caused by Nucleoside Reverse Transcriptase Inhibitors (NRTIs)

by Josh Cohen '08
Nucleoside reverse transcriptase inhibitors (NRTIs) are molecular analogs used in the treatment of the human immunodeficiency virus (HIV).  Because of their similarity in structure to biological nucleosides, NRTIs are capable of inhibiting HIV viral replication.  However, NRTIs can be toxic if they are incorporated into cellular DNA, leading to various side effects such as pancreatitis.  NRTI induced mitochondrial DNA toxicity is a common hypothesis for explaining the pancreatitis side effect.  Using the human pancreatic carcinoma cell line (PANC-1), mitochondrial DNA toxicity was quantified using real-time PCR.  Results indicated depletion in levels of mitochondrial DNA when cells were treated with NRTIs known to cause pancreatitis.  As a result, this same occurrence may be leading to NRTI induced pancreatitis in clinical trial patients.
Woodward Mentor: Ms. Chery Gibson (past faculty)
Project Advisor: Leda Bassit, Ph.D. and Raymond F. Schinazi, Ph.D., D.Sc. (Hon.), Emory University, Laboratory of Biomedical Pharmacology

Laccase-Based Biological Direct Methanol Fuel Cells

by Jason Dunn '09
Energy generation is one of the most significant global problems for the foreseeable future. Fossil fuels are polluting and their reserves are rapidly diminishing, and alternative fuel sources are either scarce or not cost efficient. For nearly a decade now, fuel cells have been touted as the most affordable and viable alternative to current energy generation methods. Fuel cells rely on oxidation and reduction half cell reactions to convert chemical energy into electrical energy. However, there are some problems with state-of-the-art fuel cells such as the expensive catalysts that are used and their poor efficiency. Platinum, as a result of poor kinetics, does not allow a fuel cell to reach even 2/3 of its theoretical potential, and it is affected by methanol that passes through the membrane that separates the anode and cathode. Laccase, from Tramales Versicolor, is an enzyme that may be a promising substitute for the platinum cathode.
Woodward Mentor: Mrs. Paula Nettles
Project Advisor: Dr. Paul Kohl, a Regents’ Professor and Institute Fellow at The Georgia Institute of Technology; Ford Environmental Sciences and Technologies Building

Ephrin B Expression during Adult Neurogenesis in Panulirus Argus

by Omar Haque '09
Adult neurogenesis takes place in the lateral flagellum (LF) of the Panulirus argus (spiny lobster). However, the mechanisms regulating this process, along with the role molt stage plays in neurogenesis are currently unknown. Ephrin B, a ligand for Eph receptors, is a gene that is hypothesized to play role (such as an up regulator for the production of new neurons) in adult neurogenesis. Preliminary work shows that an ephrin homologue was cloned from the LF of the spiny lobster. Ten clones were created containing the ephrin domain. Thus, ephrin B is present in the LF but the location of the cells that express it is unknown. Through the use of in situ hybridization (ISH) with NBT/BCIP detection, ephrin B will be localized, specifically in the proliferation zone (PZ) where new neurons are being born and the mature zone (MZ) of premolt and intermolt lobsters. From these results, it will be determined whether ephrin B is associated with adult neurogenesis. Knowledge of different genes and mechanisms regulating adult neurogenesis will enable a better understanding of this phenomenon.
Woodward Mentor: Ms. Zasha Mickey (past faculty)
Project Advisors: Tizeta Tadesse and Dr. Charles Derby at Georgia State University

Flow Visualization in a Mechanical Heart Valve

by Vishnu Koganti '09
Mitral regurgitation and mitral valve failure are leading concerns in the cardiology field.  Mechanical heart valves are one of the leading solutions to mitral valve regurgitation and failure.  Although these mechanical heart valves provide a solution, there are many problems with side effects and efficiency of the valves such as blood damage.  Increasing the effectiveness of mechanical heart valves would prove to be a major improvement in the biomedical engineering field.  One technique used to determine the efficiency of the valves is flow visualization.  Flow visualization lets a person view the flow and see how it is acting as it passes through the valve by using a type of particle.  These experiments use the technique of flow visualization to try and improve the flow through the valve and make it more efficient.
Woodward Mentor: Mr. David Alvord
Project Advisors: Dr. Ajit Yoganathan, David Murphy, and Prasad L. Dasi at The Wallace H. Coulter Department of Biomedical Engineering

The Effect of Estrogen on the Immune Response to the Tuberculosis Vaccine

by Ravi Patel '08
He is studying the effects of Estrogen on the Tuberculosis Vaccine.  Vaccines are currently tested primarily on young women with high levels of estrogen but are administered to the elderly and the young, who have very low levels of estrogen.  Also Estrogen has been shown to modulate the immune response, so its absence could have a significant effect on the effectiveness of vaccines in the elderly and young.
Woodward Mentor: Ms. Kristin Namenye (past faculty)
Project Advisors: Dr. Roberta Attanasio at Georgia State University

Pancreatitis Caused by Nucleoside Reverse Transcriptase Inhibitors (NRTI)

by Emily Lee '07
Nucleoside Reverse Transcriptase Inhibitors (NRTI) are drugs commonly used for the treatment of HIV. In clinical trials, NRTI have been known to cause pancreatitis in patients. Pancreatitis is the digestion of the pancreas with its own enzymes chymotrypsin and trypsin, and it is marked by elevated lipase and amylase enzyme levels. A common hypothesis for explaining NRTI side effects such as pancreatitis is mitochondrial toxicity; the malfunctioning of mitochondria due to mitochondrial toxicity influences enzyme secretion. The AR42J cell line, rat pancreatic acinar cells, were used to show an increase in lactic acid in the supernatant for cells growing in the presence of NRTI, an indication of mitochondrial toxicity. Amylase, lipase, and general toxicity assays done with the AR42J cells did not reflect what was seen in the clinical trials. Because rat cells will behave differently than human cells, Panc-1 and Hs 766T, both human pancreatic ductal cell lines, will be used to show mitochondrial toxicity and pancreatitis using the same assays done with the AR42J.
Woodward Mentor: Mr. David Alvord
Project Advisor: Matthew Bennett and Dr. Raymond Schinazi, Emory University School of Medicine, Pediatrics Department

The Effect of the Endocrine Disruptor Fenitrothion on the Male Rotifer

by Andrew Mauro '07
Endocrine disrupters are currently a concern of many environmentalists because of their ability to cause unwanted changes in the bodies of many organisms. Fenitrothion, an andromimetic substance, has been shown in the past to affect rotifer reproduction, affecting the males specifically. Further investigation is needed to identify how Fenitrothion affects the male rotifers. Fenitrothion may affect the sperm of the rotifers, making them misshaped or decreased in number; it may change the morphology of the males; or it may disrupt the behavior of the rotifers themselves, causing the rotifers to lose the ability to recognize the female, to acknowledge the female for the needed amount of time, or to physically fertilize the female. Therefore, this project’s goal is to investigate those different possible effects of Fenitrothion.
Woodward Mentor: Ms. Anne Dervan (past faculty)
Project Advisor: Dr. Terry Snell, Georgia Institute of Technology, School of Biology

Mutagenesis of the TCR Zeta Chain at the 3’ Untranslated Region

by Ishita Patel '07
The T Cell Receptor (TCR) plays an important role in the intracellular portion of the signaling in the immune system. The ζ chain portion is an integral part of this signaling. In the disease systemic lupus erythematosus (SLE), T cells display reduced expression and activity of the TCR ζ protein. In T cells from SLE patients, the TCR ζ protein is derived from an alternatively spliced (AS) form that undergoes splice deletion of 562 nucleotides within the 3’ untranslated region (3’ UTR) of TCR ζ mRNA. This mutated region may lead to faulty signaling in SLE T Cells. The research aim was to focus on this sequence and promote mutagenesis through RT-PCR. Starting with previously isolated samples of TCR ζ cDNA, PCR was performed. The samples were then spliced into pcDNA 3.1 Amp Plasmid and transformed into E. coli. After incubation to allow replication, the DNA was extracted from the bacteria, purified, then analyzed using gel electrophoresis to verify the integrity of the plasmid. The samples were then sequenced to verify which bases were mutated. The sequencing showed that multiple base pair mutations occurred. Therefore, it is inconclusive as to which area was actually responsible for the faulty signaling.
Woodward Mentor: Ms. Chery Gibson (past faculty)
Project Advisor: Dr. Bhabadeb Chowdhury, NIH National Institute of Allergy and Infectious Diseases

Study of Synchronization of Metronomes

by Chris Simmons'07
This project investigates the synchronization of metronomes.  Spontaneous synchronization occurs in many places, such as heart cells and brain neurons.  The aim of this project is to precisely determine what initial conditions for coupled metronomes produce in phase vs. antiphase synchronization or no synchronization.  Two Wittner Super-Mini metronomes are placed on a Styrofoam platform floating on a fluid and tested under various conditions.  Preliminary results suggest that, when all variables besides frequency are held constant, there exists a certain frequency below which the metronomes will lock in phase and above which the metronomes will lock in antiphase.  This study aims to precisely determine those critical frequencies.
Woodward Mentor:  Dr. Jessica Bartling (past faculty)
Project Advisor:  Dr. Michael Schatz, Georgia Institute of Technology, School of Physics