Department of Chemistry
Senior Year Experience 2007-2008
Scroll down to see pictures and research topics for:
Jen Achtyl, Kacey Anderson, Nicholas Calandra, Andrew Chapp, Derek Hansen, Shreya Kamath, Fraser Mackay,Kelly O'Connell, Mike Seaman, Stephanie Walter, and Jonathan Whicher.
Click on the title to see the abstract
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Jennifer Achtyl |
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Kacey Anderson |
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Synthesis of Simplified Salvinorin A Analogs for
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Chapp, Andrew Synthesis of Novel N-Cyanoguanidine Ligands Targeting the Transient Receptor Potential Vanilloid Type-1 Receptor Senior Research Project Dr. Larry French, advisor |
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Senior Research Project |
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Shreya Kamath Honors Thesis in Biochemistry
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Honors Thesis in Biochemistry
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Senior Research Project |
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Michael Seaman Honors Thesis is Biochemistry
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Stephanie Walter Ruthenium (II) Complexes and Intercalation Binding to DNA Honors Thesis in Chemistry
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Jonathan Whicher Honors Thesis in Biochemistry
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J Achtyl, K Anderson, N Calandra, A Chapp, D Hansen, S Kamath, F Mackay, K O'Connell, M Seaman, S Walter, and J Whicher.
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Achtyl, Jennifer.
Synthesis of a Ruthenium Polypyridyl Compound for Kinetic Studies
Honors Thesis in Chemistry -
Dr. Samantha Glazier, advisor
Abstract
The bis-intercalating ruthenium dimmer [m-C4(cpdppz)2(phen)4Ru2]4+ 1 developed by Lincoln et al. is of interest as a chemotherapeutic agent. Understanding how molecular structure affects binding mechanisms is essential for the development of more selective and effective anticancer drugs. The synthesis of this compound reported in the literature was spare with few diagnostics, reaction conditions, or reagent amounts. A synthetic pathway has been devised through extensive literature research, reaction optimization, and product characterization. The following intermediates were obtained: 1,4-bis(cyanoacetamido)butane (88%), 4,5-dimethyl-2,1,3-benzoselenadiazole (69%), 5,6-bix(bromomethyl)benzo-1,2,3-selenadiazole (46.6%), 1,10-phenanthroline-5,6-dione (24%), Ru(phen)2Cl2×H2O (70%), [Ru(phen)2phendione](PF6)2× 2H2O, “Product A” (56%), 6-cyano-6,7-dihydro-5H-1,2,5-selenadiazolo[3,4-f]indene-6-carboxylic acid methyl ester (55%). This leaves the synthesis complete up to the removal of selenium from “Product A” and addition of [Ru(phen)2phendione](PF6)×2H2O for formation of the final dimmer. With an optimization of a selenium deprotection synthesis, the target ruthenium dimer can be successfully complete. (top)
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Anderson, Kacey
Investigation of VOC Emission Sources for the Lake Champlain Basin
Honors Thesis in Chemistry -
Dr. Ning Gao, advisor
Abstract
Ambient VOCs measured in the Lake Champlain Basin in Vermont have been analyzed using the receptor model Positive Matrix Factorization (PMF). The ambient VOC monitoring took place at two sites: Burlington, an urban site, and Underhill, a more rural site. At Burlington and Underhill, fourteen sources were identified, with a good agreement between measured and predicted mass. At Burlington the following sources were identified: automobile sources (23 %), aircraft related sources (11 %), degreasing sources (4 %), and sources due to solvent utilization (29 %). At Underhill the following sources were identified: automobile sources (33 %), residential wood combustion (3 %), graphic arts coating source (2.5%), aircraft landing/takeoff source (9 %), and solvent utilization sources (25 %). Ten of the fourteen sources in Burlington and eleven of the fourteen sources in Underhill were identified. The receptor analyses produced source profiles that had distinctive, dominant species that were fairly consistent with wind speed data. The identified VOC emission sources were similar types to those reported in VOC studies for other regions (Jorquera, 2008; Brown, 2007; Buzcu, 2006). (top)
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Calandra, Nicholas
Synthesis of Simplified Salvinorin A Analogs for Potential Activity at the Kappa Opiate Receptor
Senior Research - Dr. Larry French, advisor
Abstract: Salvinorin A is the active ingredient found in the plant Salvia divinorum which has been used by the Mazetec Indians of Oaxaca, Mexico in various traditional rituals and also as a remedy for headaches and stomach ailments. Salvinorin A is the only known non-nitrogenous opiate agonist and is highly selective at the KOR receptor from which its potent antinociceptive properties derive. Previous work by others partially identified those molecular subunits responsible for target affinity. This project involves developing synthetic routes to simple Salvinorin A anologs. (top)
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Chapp, Andrew
Synthesis of Novel N-Cyanoguanidine Ligands Targeting the Transient Receptor Potential Vanilloid Type-1 Receptor
Senior Research - Dr. Larry French, advisor
Abstract: The vanilloid receptor (TRPV1) is a nociceptor capable of responding to thermal, chemical and protic stimuli. A number of compounds have been demonstrated to act agonistically or antagonistically at this ion channel which represents a novel target for the development of new analgesics. Our work has included successful bioisosteric replacement of the polar functional groups (cinnamide, amide and thiourea) in a series of of known ligands to produce N-cyanoguanidine anologs of compounds including capsaicin, capsazepine, SB 366791 and AMG 9810. Analogs are screened in transgenic C. elegans worms expressing rat TRPV1 channels. (top)
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Hansen, Derek
Does Rap1 recruit the histone deacetylase Rpd3 to the promoter of RPS11B, a rapamycin-repressible gene?
Abstract:
The small molecule rapamycin mimics nutrient deprivation in Saccharomyces cerevisiae. Rapamycin inhibits the nutrient sensitive TOR complex, which regulates cell growth. Rapamycin-dependent inhibition requires the histone deacetylase Rpd3, which is localized to the promoter region of rapamycin-repressible genes upon treatment only. We tested whether or not the transcription factor Rap1 was responsible for recruiting Rpd3 to the promoter of RPS11B, a rapamycin-repressible ribosomal protein gene. A mutant strain was created by transforming the plasmind YCplac 33, containing an RPS11B ∆ Rap1 insert, into a strain of Saccharomyces cerevisiae that had RPD3 Myc-tagged at the endogenous site. After treatment with rapamycin, a chromatin immunoprecipitation reaction was carried out to precipitate out DNA bound to Rpd3. Preliminary quantitative PCR analyses have found that Rap1p may recruit Rpd3p to the promoter of rapamycin repressible genes, but results thus far have been incomplete.
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Kamath, Shreya
Investigating Isoquinoline Alkaloid Content and Rhizosphere Leaching in Three Closely Related Medicinal Plant Species
Honors Thesis in Biochemistry - Dr. Matthew Skeels, advisor
Abstract
Coptis trifolia (American goldthread), Coptis chinensis (Chinese goldthread) and Hydrastis Canadensis (Goldenseal) are closely related species that are important to various ethnopharmacopeia. The commercial potential of C. trifolia rhizomes is yet to be realized, unlike C. chinensis and H. Canadensis, which are harvested extensively. A mixture of isoquinoline alkaloids present in the rhizomes of these species imbues them with anti-pathogenic activities. Leaching of plant compounds through the roots into surrounding soil has been observed in several plant species. I investigated the leaching of alkaloids in H. Canadensis and C. trifolia rhizospheres. I also compared the concentrations of individual isoquinoline alkaloids in the three species to determine which species might be most commercially desirable with respect to alkaloid content. I used microwave assisted extraction followed by HPLC analysis of the alkaloids on a reverse phase-C18 column to quantify alkaloid content in rhizome samples and check for alkaloid traces in soil samples. Non-parametric statistical tests of variance were used to determine significant differences in alkaloid content among the plant species. The berberine content analysis indicates that H. Canadensis is most suitable for commercial purposes, but the coptisine content analysis indicates that C. trifolia is a promising, ecologically-sustainable substitute for C. chinensis. Based on the HPLC chromatograms obtained, I conclude that alkaloid leaching does not occur in H. Canadensis and C. trifolia rhizospheres. (top)
Mackay, Fraser Colin
Characterizing the interactions in vitro between the amyloid protein HypF-N and liposomes composed of phosphotidylcholine and phosphotidylserine.
Honors Thesis in Biochemistry -
Dr. Nadia Marano, advisor
Abstract
Certain illnesses, including Parkinson’s and Alzheimer’s diseases, are characterized by the formation of toxic amyloid and pre-amyloid fibril protein aggregates within cells and tissues. On the cellular level, these aggregates can disrupt major cell processes and, on the organismal level, cause harmful protein deposits in joints and organs. Recent research has shown that certain cell membrane lipids with charged head groups affect and possibly catalyze the formation of amyloid fibrils in vitro from native protein. The mechanism by which this purported catalysis takes place is still unclear. HypF-N is the N-terminal fragment of the bacterial maturation factor HypF that can form amyloid fibrils similar in morphology to pathogenic fibrils found in human, amyloid-linked diseases. Expression of HypF-N was attempted in BL21-DE3 cells, but ultimately failed to produce usable protein. Analyses of intrinsic tryptophan fluorescence of HypF-N supplied by Monica Bucciantini after incubation with liposomes of varying phosphotidylserine (PS) and phosphatidylcholine (PC) compositions suggested that HypF-N is readily denatured by PS and liposomes containing both lipids. Comparisons between the intrinsic tryptophan fluorescence of HypF-N during liposome-mediated conformational changes and denaturation with guanidine hydrochloride (GnCl) further suggested that PS and PSPC liposomes caused HypF-N to aggregate or form a liposome- protein complex, respectively. (top)
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O'Connell, Kelly
Determining the effect of rpd3 on the expression of GAP1 and the mechanism of Rpd3 binding in S. cerevisiae upon starvation.
Abstract:
The small molecule rapamycin inhibits target of rapamycin (TOR) proteins which leads to several downstream effects reminiscent of nutrient depravation, or starvation. Because Saccharomyces cerevisiae are single-celled eukaryotes that are easy to manipulate genetically, they are an ideal model system for studying gene regulation in response to nutrient levels. Nutrient depravation leads to a dramatic change in the transcriptional program of S. cerevisiae. The gene that is most strongly activated following rapamycin treatment is GAP1. Also following rapamycin treatment, Rpd3, a histone deacetylase, becomes bound to the promoter of GAP1. It is widely known that histone deacteylases, HDACs, are required for the repression and, to a lesser extent, the activation of genes, but it is not known whether the rapamycin-induced regulation of GAP1 is dependent on the presence of Rpd3p. It has been suggested that the deletion of Rpd3 effects the recruitment of RNA polymerase II suggesting that ∆rpd3 may effect the expression of GAP1. Using quantitative reverse transcription PCR (qRT-PCR) data, we find that the deletion of Rpd3 increased the level of expression of GAP1. Due to these effects of Rpd3 on GAP1 transcription, research on the mechanism of binding of Rpd3 to the promoter of GAP1 under starvation conditions is currently in progress. (top)
Seaman, Michael
Utilizing Intrinsic Tryptophan Fluorescence in the Androgen Receptor to Characterize an Intermediate in the Ligand Binding Process.
Honors Thesis is Biochemistry -
Dr. Matthew Skeels, advisor
Abstract
Recent evidence suggests the process of ligand binding in nuclear steroid receptors involves large conformational changes. It has been demonstrated that nuclear steroid receptors can transiently access an intermediate state, one which aids in the process of ligand binding and unbinding. The discovery of this intermediate has implications in drug design and discovery. The overarching goal of our work was to use intrinsic tryptophan fluorescence of the human androgen receptor ligand binding domain (AR-LBD) to search for and characterize a molten globular intermediate in the ligand binding process. Our data suggests that the AR-LBD transiently accesses this intermediate state. Currently, focus is on using BSA as a model system to test fluorescence parameters so as to allow future research to replicate the results suggesting that the AR-LBD accesses an intermediate state. (top)
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Walter, Stephanie
Ruthenium (II) Complexes and Intercalation Binding to DNA
Honors Thesis in Chemistry -
Dr. Samantha Glazier, advisor
Abstract
The goal of this project was to find an adaptable and robust synthetic strategy to creating ruthenium complexes that would intercalate by threading through DNA. The ability of a molecule to thread through DNA is one strategy to prevent DNA replication and lead to cell death and is therefore significant for developing anticancer pharmaceuticals. Employing a series of reactions, our molecular design involved the monosubstitution of bipyridine ligands with an organic side chain and an aromatic end group, naphthalene. The ligands 4-(4-butyl ether-methylnaphthal)-4’-methyl-bpy and 4-methoxy methylnaphthal-4’-methyl-bpy, where bpy = 2,2’-bipyridine, were obtained and characterized by NMR and IR. The 4-(4-butyl ether-methylnaphthal)-4’-methyl-bpy was obtained in 7.4% yield, but the 4-methoxy methylnaphthal-4’-methyl-bpy was too wet to quantify a yield. The 4-methoxy methylnaphthal-4’methyl-bpy ligand was complexed to [Ru(phen)2]2+, where phen = 1,10-phenanthroline. Preliminary DNA binding studies were completed using a fluorescence titration. The results indicate a positive binding activity with CT DNA; the binding constant Kb was determined to be 1.64´106 M-1 and binding size, n, was 2.76 base pairs. The control [Ru(phen)3]2+ showed a lower binding constant of 5.77´105 M-1 and a smaller binding size of 1.84. (top)
Whicher, Jonathan
The role of 14-3-3 proteins, Bmh1p and Bmh2p, in Transcriptional Regulation of Saccharaomyces cerevisiae in a Limited-Nutrient Environment.
Honors Thesis in Biochemistry -
Dr. Emily Dixon, advisor
Abstract
The Tor pathway in yeast regulates gene expression in response to nutrient availability (Cardenas et al.,1999). Rpd3p is a histone deacetylase (HDAC) utilized by the Tor pathway to bind gene promoters and inhibit transcription during limited nutrient conditions (Rhode et al., 2003). However, the mechanism by which Rpd3p becomes localized at the promoters of repressed genes is unknown. Prior studies indicate that the 14-3-3 family of proteins binds to HDACs (Wang et al., 2000), (McKinsey et al., 2000), (Kao et al., 2001) and also binds to cruciform DNA, which is found in many gene promoters (Callejo et al., 2002). Therefore, the purpose of this study is to investigate the hypothesis that 14-3-3 proteins, Bmh1p and Bmh2p in Saccharomyces cerevisiae, bind to and transport Rpd3p to gene promoters in a cruciform DNA motif to regulate transcription in a limited-nutrient environment. For this study, the limited-nutrient environment was mimicked by rapamycin treatment. Chromatin immunoprecipitation with quantitative PCR analysis indicated that Bmh1p and Bhp2p bind to the promoter of the Rpd3p-regulated gene GAP1, which is thought to form a cruciform structure, to a greater extent during rapamycin treatment compared to a control treatment. However, a co-immunoprecipitation of Rpd3p and Bmh2p indicated that these proteins do not interact. The absence of an interaction between 14-3-3 proteins and Rpd3p disproved the proposed hypothesis. This is because 14-3-3 proteins do not bind to and hence cannot transfer Rpd3p to gene promoters in a cruciform DNA motif during limited nutrient conditions. However, this study determined that Bmh1p and Bmh2p bind to an Rpd3p-regulated promoter that may form a cruciform structure to a greater extent during rapamycin treatment. This indicates a possible functional interaction between the 14-3-3 proteins and Rpd3p during limited nutrient conditions.
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