Dr.

Websters Nanomedicine Lab, Brown University, 05/08-09/08 The objective of this research was to investigate whether rosette nanutobes (RNTs), a novel surface coating that had shown promise for orthopedic applications, could improve endothelial cell function on titanium vascular stents. My role was to conduct in vitro experiments to determine whether the coating enhanced adhesion and proliferation of the cells compared to bare titanium, the standard of care. After learning cell culture, fluorescence microscopy, cell staining, and surface coating techniques by shadowing a graduate student, I began running experiments independently. I designed a cell culture setup to test the effects of different concentrations of RNT coatings on titanium, including glass as a negative control, and ran fourhour adhesion and five-day proliferation experiments. In both sets of experiments, I found that RNT coatings significantly increased cell density compared to bare titanium in a dose-dependent manner. Since a healthy interaction between endothelial cells and the stent in situ is important in preventing side effects such as occlusion of the artery through thrombosis or restenosis, these results constitute an initial step in improving vascular stents to fight cardiovascular disease, the number one cause of death in the USA. While working in the lab with cryopreserved cells, I found that because there was such a large number of cell samples and types in the storage system, it was difficult to find empty space to store ones own cells. I came up with an idea for an online database and presented it at a group meeting. Following an enthusiastic response from my labmates, I implemented a system that allowed easy entry and editing of a samples location in storage, could be queried by desired cell type or owner, and would flag any samples that had been in storage more than a certain amount of time as candidates for removal to free up space. In September, I was awarded an internal funding grant from Brown that allowed me to travel to the BMES Annual Meeting to present my research.1 After returning from the conference I developed my findings into a paper.2 Since its publication in 2009, my research has been cited by eight articles, demonstrating its broader impact on the vascular stent field as a whole. 1. Fine E, et al., Using Helical Rosette Nanotubes to Enhance Endothelial Cell Adhesion and
Proliferation. Poster, Oct 2008. Biomedical Engineering Society Annual Meeting. St. Louis, MO. stents. Int J Nanomedicine 4, 91-97 (2009).

2. Fine E, et al., Enhanced endothelial cell functions on rosette nanotube-coated titanium vascular Dr. Kimias Medical Imaging Lab, Brown University, 10/08-05/09 The power of computers as a tool has always enticed me, so when Dr. Kimia told me he had a project involving analysis of MRI data that I could work on, I jumped at the opportunity. The goal was to quantitatively validate the effects of cervical traction (CT), a chiropractic technique to relieve back pain caused by herniated disks, a condition that affects millions of Americans. My role was to develop the software that could analyze a series of MR images and quantify, in a semi-automated manner, the total disk volume, the protrusion volume, and the protrusion distance. I would then work with a clinician to generate patient data from before and after treatment with CT and compare these images using my software to quantify the differences. Since segmentation was critical to the analyses I would perform, my first task was to create a segmentation package that would not only accomplish my needs but would also mesh with the existing image analysis software created by the lab and provide additional functionality so that it could be used for future projects involving segmentation. After planning the features of this package in a group meeting, I programmed it in C++ and incorporated it into my custom spine analysis software. Unfortunately, while Dr. Kimia and I were working with the IRB, the approval process stalled, and we realized there would not be a chance to conduct the clinical experiments to collect the data needed to turn this project into a senior thesis before I graduated.

My software package, complete with a manual, is ready to be used by another student when IRB approval is granted. Utilizing its capabilities to gain a better understanding of the effects of cervical traction could lead to more personalized treatments and widespread adoption of this low-cost therapy. By the time I left the lab, my segmentation package had already been included in another students project, thereby creating an impact on the research of the lab. Dr. Fairbrothers Molecular & Computational Biology Lab, Brown University, 06/09-05/10 I combined my interest in wet and dry experimentation in the molecular and computational biology laboratory of Dr. Fairbrother with the support of an NSF Interdisciplinary Undergraduates in Biology & Mathematics Fellowship. My initial assignment was fairly broad in that I was to use bioinformatic analysis to search for patterns in the exons of D. melanogaster. Using customized Perl scripts I coded to analyze sequences in the whole genome, I began to notice several factors that indicated the possibility that stop codon readthrough (SCR) could be taking place in a much more widespread manner than previously realized. SCR is a phenomenon where a stop codon is bypassed and translation continues into the 3 UTR creating an alternate protein with a C-terminal extension. If SCR was indeed a widespread occurrence, it could represent a mechanism to generate additional protein diversity from a limited genomic sequence, much as alternative splicing does. By the end of the summer, I had generated correlations across a variety of statistically significant datasets of factors relating to what I had learned from the literature about the mechanism of SCR as well as general signals for protein coding sequence. After I showed these results at a lab meeting, Dr. Fairbrother invited me to present them as a poster at the annual departmental graduate student retreat. As the year progressed, I continued to refine the analyses, and the project began to expand. An examination of the human genome found similar patterns supporting SCR, and through collaboration with a proteomics lab and comparisons with online mass spectrometry databases, I was able to find evidence of in vivo translation of several of the predicted downstream SCR regions. I acquired additional funding to begin in vivo validation of the predictions in HEK 293 cells when Brown awarded me one of the four Halpin Prizes for Interdisciplinary Senior Capstone Projects. A rotating graduate student, another undergraduate, and I used molecular cloning techniques to attempt to validate several of my predicted cases of SCR. Unfortunately, in the short time before graduation, no candidates were successfully validated, but a new student to the lab has picked up the effort. However, the computational results showed that SCR could be acting as a widespread mechanism to increase protein diversity in human and D. melanogaster genomes, and after graduation I presented my results as a poster at the RNA Society Annual Meeting.4 3. Fine E. Running Red Lights: A Search for Stop Codon Readthrough in Drosophila and Human
Genomes. Honors Thesis Defense, May 2010, Brown University, Providence, RI.

4. Fine E and Fairbrother WG, Running Red Lights: A Search For Stop Codon Readthrough in

Drosophila and Human Genomes. Poster, June 2010. RNA Society Annual Meeting. Seattle, WA.

As I am beginning graduate school, I feel that my previous research experiences at Brown have given me a diverse skillset, which allows me to address research topics from many different angles. Upon entering Georgia Tech I was awarded an institutional Presidents Fellowship to offer me further support while I perform my research, and now that I have joined Dr. Baos Nanomedicine Lab, I will be able to combine and apply my interests in in vivo and in silico experimentation to contribute to the future progress of genetic engineering and gene therapy.