|Spring 2013 Newsletter
On Saturday November 10, 2012 the Rochester Academy of Sciences met at St. John Fisher College, Shawna Henry, a biology major at RWC, presented her poster entitled “Gene Annotation of Hydrogenobacter Thermophilus DSM 6534” based on the research she completed at RWC. This research was done in conjunction with a research collaboration with the Department of Energy Joint Genome Institute in Walnut Creek, California. The research by Shawna was done under the direction of Dr. David Roll.
Aaron Van Dyne
Aaron Van Dyne, (mathematics, physics) is now working with Dr. Dave Mathews at the University of Rochester Medical Center in computational biophysics. He is working on a MonteCarlo algorithm for predicting the secondary structure of RNA from the nucleotide sequence. The algorithm generates possible low free energy structures by performing millions of steps where a pair is formed or broken at each step. The structure is read out to a file every so often, and the file of structures represents possible low free energy structures, which could be the actual secondary structure. The idea of the algorithm, however, is to generate a variety of low free energy structures, so that the pairing probabilities can be estimated by counting how many of the structures have a particular pairing. The variability of the structure is enhanced by a process called replica exchange where the algorithm is run for multiple structures with temperatures between physiological temperature, 310.15K, and some higher temperature. The structures can then be exchanged from a higher temperature to a lower temperature at regular intervals. The exchange does not always occur, but it always occurs if the higher temperature structure has a lower free energy, and it occurs only with some probability if the higher temperature structure has a higher free energy. The larger the difference in free energy the less likely the exchange is to occur.
Aaron has done a lot of the work of debugging and testing the code. The algorithm and replica exchange are both functioning correctly now. The algorithm with the replica exchange has successfully predicted the known structure of two different 74 nucleotide tRNAs as one of the possible structures. The match between the pairing probabilities predicted by the algorithm and the pairing probabilities found using the partition function is currently being investigated. We are also currently investigating the optimal parameters of the simulation including getting good exchange probabilities. In the future, the algorithm will be extended to longer sequences and eventually sequences with a structural feature known as a pseudoknot.
Olivia Pitts presented the beginning results of her DNA Barcoding research in her Senior Honors Presentation entitled Apple to Apples. DNA barcoding tools have been developed for undergraduate students to use in their own research by the DNA Learning Center located in Cold Spring Harbor New York.
Olivia has collected leaf samples from a number of unique apple varieties cultivated on a large apple farm managed by her father. She has processed the leaves to isolate chloroplast DNA and has amplified a specific Rubisco gene from each apple variety. These amplified genes have just been sequenced, and this data is being collected and analyzed with DNA Subway software for presentation Saturday, February 9. This research work will continue to look at other gene sequences that may allow one to uniquely identify particular apple cultivars that have economic value in the marketplace.
Last semester, Rebeckah Johnson worked with Dr. Amy Kovach on the enzymatic activity of ascorbate peroxidase extracted from the roots of rice plants. As soil salinity is becoming increasingly more prevalent, Rebeckah and Dr. Kovach examined the effect of salinity on enzymatic activity. It has been shown that higher salt concentrations in the soil of rice plants increases the enzymatic activity of ascorbate peroxidase. Dr. Kovach and Rebeckah worked to streamline an experimental process showing this increase in activity in order to use this experiment in an undergraduate laboratory setting. Pamela Harrisson is continuing the work with Dr. Kovach this semester.
During the fall semester, Seth Amidon and Rebecca Phelps worked with Dr. Jason Taylor optimizing the synthesis of gold nanoparticles ranging in size from 2-40 nm. Additionally, Rebecca Phelps worked on developing specific protocols for effectively linking modified protein molecules to the gold particle surface. Seth developed a method for synthesizing vancomycin conjugated gold nanoparticles for work in antibiotic resistance investigations on specific bacteria strains. Seth plans to continue his work in the spring semester in conjunction with his honors project examining additional nanoparticle probes such as silver, iron oxide, and superparamagnetic iron oxide nanoparticles (SPIONs).