Senior Abstracts 2011 - 2012

Elisabeth (Breezy) Dwyer
Faculty Mentor: Samantha Glazier
"Assay to Establish the Binding Affinity of Nogalamycin to Different DNA Motifs"

Many small molecules have structural characteristics like aromatic rings, allowing them to bind within the major and minor grooves of double stranded DNA. Such molecules serve many different purposes, including the ability to regulate transcription and stop cells from dividing. One such molecule is nogalamycin, a dumbbell-shaped anthracycline antibiotic drug, which threads itself between the base pairs of DNA strands (Bhuyan, 1970). Its low dissociation rate makes it a unique DNA binding drug worth studying as a class of anticancer therapeutics. Gel electrophoresis will be used to compare binding affinities of nogalamycin to circular plasmid DNA with the hope of perfecting the technique initiated by St. Lawrence University graduate Michelle Dumas, '10. The assay determines the amount of relaxation of the plasmid as a function of nogalamycin concentration. More nogalamycin introduces more negative supercoiling after being introduced to topoisomerase I, which is able to relax supercoiled DNA by causing breaks in the phosphodiester backbone (Webb, 2003). The more relaxed the plasmid is, the shorter distance it will travel in the agarose gel. The procedure has previously been successful for small molecules that bind to DNA via intercalation. If we can adapt the methodology for threading molecules, then our focus will be to expose nogalamycin to different DNA motifs, such as the helix-loop-helix, often present in leukemic patients, to determine the specificity of the drug (Chen, 1990).

Andrew Hayes
Faculty Mentor: Matthew Skeels
"Rational Design of a Stabilized GGBR Protein
"
The objective for my senior research is to design a stabilized Glucose-Galactose Binding Protein (GGBP) protein using computational methods. This involves manipulating the charged residues on the surface of the protein to decrease the folding energy of the protein relative to its unfolded form. We will use modeling software and the Tanford-Kirkwood model to evaluate interactions on the native protein as well as identify possible mutations. After developing these mutants we will produce them with mutagenesis and test them against denaturation curves of the wild type protein. So far we have determined preliminary denaturation curves for wild type GGBR bound and unbound to glucose in a urea environment. We hope that the mutant GGBP will be able to withstand more environmental stress than the native form.

Kiersten LaPorte
Faculty Mentor: Matthew Skeels
"Loading of elements and anions to the St. Lawrence River from tributaries in St. Lawrence County, New York
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A year-long sampling event (June 2011 to June 2012) is being conducted on four rivers belonging to the St. Lawrence River Basin—Oswegatchie, Grasse, Raquette, and St. Regis. Physical and chemical characteristics of water quality are being collected to: (1) establish a base line for water quality and the anthropogenic implications on the drinking water for local communities, as well as the habitat for aquatic life, and (2) determine the contribution of elements and anions to the St. Lawrence River from tributaries in St. Lawrence County, New York. Ion Chromatography is carried out for the quantification of seven anions—F-, Cl-, NO2-, Br-, SO42-, NO3-, and PO43-. ACME Analytical Laboratories analyze samples by inductive coupled plasma mass spectrometry (ICP-MS), which facilitates the quantification of 70 elements in each water sample. Acid neutralizing capacity and carbonate quantities are also being determined. The combination of physical and chemical characteristics of water quality, along with U.S. Geology Survey data, will be used to reveal weekly, monthly, and seasonal trends and correlations relating to each of the four rivers. Geological and anthropogenic factors will be used to explain the analyzed data.

Doug McWilliams
Faculty Mentor: Emily Dixon
"The recruitment of 14-3-3 proteins to DNA via histone H3 serine 28 phosphorylation
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Rapamycin is a small molecule that alters yeast gene expression in a way that mimics starvation. However, not much is known about how these transcriptional changes are mediated. 14-3-3 proteins are a highly conserved group of proteins that participate in a variety of biological functions and are known for their ability to interact with DNA to regulate gene expression. Preliminary data indicates that these proteins may play a role in mediating rapamycin-altered gene expression. One possible mechanism for this is that 14-3-3 proteins regulate transcription though the phosphorylation of serine-28 on H3. In order to test this hypothesis we have a mutant yeast strain with alanine in place of serine-28 (S28A) to prevent phosphorylation. We will use microarray analysis to compare gene expression upon rapamycin treatment in the wild-type yeast strain lacking 14-3-3 proteins and the S28A strain to see if this is a potential role for 14-3-3 proteins.

2010-2011 Abstracts