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Past Trainees

2013

Will Birmingham (Mentor: Brian Bachmann, Biochemistry)

 

Publications for William Birmingham

Nannemann D.P., Birmingham W.R., Scism R.A., Bachmann B.O.. 2011, "Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis." Future Med Chem. 2011 3(7):809-19. PMCID: PMC3155183

Brown, D. W.; Schaab, M. R.; Birmingham, W. R.; Armstrong, R. N.. 2009, "Evolution of the antibiotic resistance protein, FosA, is linked to a catalytically promiscuous progenitor." Biochemistry, 2009 48(9):1847–1849. PMCID: PMC2756217.

 

Sean DeGuire (Mentor: Gary Sulikowski, Chemistry)

 

Awards
ACS Division of Organic Chemistry Travel Grant Fellowship to attend the 2013 National Organic Symposium.

Publications for Sean DeGuire

B. O. Bachmann, R. McNees, B. J. Melancon, V. P. Ghidu, R. Clark, B. C. Crews, S. M. DeGuire, L. J. Marnett, G. A. Sulikowski. 2010, “Light-Induced Isomerization of Apoptolidin A leads to Inversion of C2−C3 Double Bond Geometry”  Org. Lett. 2010, 12, 2944-2947. PMC3079550

Y. Du, D. K. Derewacz, S. M. Deguire, J. Teske, J. Ravel, G. A. Sulikowski, B. O. Bachmann. 2011, “Biosynthesis of the apoptolidins in Nocardiopsis sp. FU 40”  Tetrahedron 2011, 67, 35, 6568-6575. PMC31359176

S. M. DeGuire, S. Ma, G. A. Sulikowski. 2011, Synthesis of a Bicyclobutane Fatty Acid Identified from the Cyanobacterium Anabaena PCC 7120.” Angewandte Chemie Int. Ed. 2011, 50, in press. PMID: 21898738.

 

Adam Ketron (Mentor: Neil Osheroff, Biochemistry)

 

Publications for Adam Ketron

A.C. Ketron, W.A. Denny, D.E. Graves, and N. Osheroff (2011) Biochemistry, submitted. “Amsacrine as a Topoisomerase II Poison: Importance of Drug-DNA Interactions.”

lly promiscuous progenitor." Biochemistry, 2009 48(9):1847–1849. PMCID: PMC2756217.

 

Amy Russo (Mentor: Charles Hong, Cell & Developmental Biology)


2012

Rachel Crowder (Mentor: Walter Chazin, Biochemistry)

Dawn Makley (Mentor: Jeffrey Johnston, Chemistry)

 

Awards
2010-2011 ACS Organic Division Fellowship


Publications for Dawn Makley

Shen, B., Makley, D.M., Johnston, J.N. 2010, "Umpolung Reactivity in Amide and Peptide Synthesis, Nature, 465, 1027-1032. PMCID: PMC2945247

Shen, B., Makley, D.M., Johnston, J.N. 2010, "Umpolung Reactivity in Amide and Peptide Synthesis, Nature, 465, 1027-1032. PMCID: PMC2945247

 

 

 

2011

Kellen Harkness (Mentor: David Cliffel, Chemistry)
Current Position: Postdoc, David Cliffel, Vanderbilt University

 

Publications for Kellen Harkness

Harkness, Kellen M.; Balinski, Andrzej; McLean, John A.; Cliffel, David E. 2011, "Nanoscale Phase Segregation of Mixed Thiolates on Gold Nanoparticles." Angewandte Chemie, International Edition. ASAP on the web, DOI: 10.1002/anie.201102882

Carrie A. Simpson, Amanda C. Agrawal, Andrzej Balinski, Kellen M. Harkness, and David E. Cliffel. 2011, "Short-Chain PEG Mixed Monolayer Protected Gold Clusters Increase Clearance and Red Blood Cell Counts." ACS Nano, 2011, 5(5), 3577-3584, DOI: 10.1021/nn103148x

Simpson, Carrie; Farrow, Christopher; Tian, Peng; Billinge, Simon; Huffman, Brian; Harkness, Kellen; Cliffel, David. 2010, "Tiopronin Gold Nanoparticle Precursor Forms Aurophilic Ring Tetramer." Inorganic Chemistry, 2010, 49(23), 10858-10866. PMCID: PMC2993808

Kellen Harkness, Brian Hixson, Larissa Fenn, Brian Turner, Amanda Rape, Carrie A. Simpson, Brian Huffman, Tracy Okoli, John A. McLean, David E. Cliffel. 2010, "A Structural Mass Spectrometry Strategy for the Relative Quantitation of Ligands on Mixed Monolayer-Protected Gold Nanoparticles." Analytical Chemistry, 2010, 82(22), 9268-9274. PMCID: PMC2980554

Harkness, Kellen M.; Fenn, Larissa S.; Cliffel, David E.; McLean, John A. 2010, "Surface Fragmentation of Complexes from Thiolate Protected Gold Nanoparticles by Ion Mobility-Mass Spectrometry." Analytical Chemistry, 2010, 82(7), 3061-3066. PMCID: PMC2848286

K. M. Harkness, L. S. Fenn, D. E. Cliffel, J. A. McLean. 2010, "Analysis of capping structural motifs on thiolate-protected gold nanoparticles by ion mobility-mass spectrometry." Analytical Chemistry 82, 3061-3066 (2010)


Andrew Morin (Mentor: Jens Meiler, Chemistry)
Current Position: Postdoc, Piotr Sliz, Harvard

 

Publications for Andrew Morin

A. Morin, J. Meiler and L. S. Mizoue; 2011, "Computational design of protein-ligand interfaces: potential in therapeutic development"; Trends Biotechnol; Vol. 29 (4): p. 159-66. PMID: 21295366

A. Morin, K. W. Kaufmann, C. Fortenberry, J. M. Harp, L. S. Mizoue and J. Meiler; 2011, "Computational design of an endo-1,4-{beta}-xylanase ligand binding site"; Protein Eng Des Sel.PMCID: PMC3092692

 


Megan Wadington-Branch (Mentor: Richard Armstrong, Biochemistry)
Current Position: Postdoc, Richard Armstrong, Vanderbilt University

 

Publications for Megan Waddington-Branch

Stourman NV, Branch MC, Schaab MR, Harp JM, Ladner JE, and Armstrong RN, (2011) Structure and Function of YghU, a Nu-Class Glutathione Transferase Related to YfcG from Escherichia coli. Biochemistry 50: 1274-81. PMCID: PMC3040281

Wadington MC, Ladner JE, Stourman NV, Harp JM, Armstrong RN, (2009) Analysis of the Structure and Function of YfcG from Escherichia Coli Reveals an Efficient and Unique Disulfide Bond Reductase. Biochemistry 48: 6559-61. PMCID: PMC2996727

Stourman NV, Wadington MC, Schaab MR, Atkinson HJ, Babbitt PC and Armstrong RN (2007) Functional Genomics in Escherichia coli: Experimental Approaches for the Assignment of Enzyme Function. Proceedings of 3rd International ESCEC Symposium September 23rd - 26th, 2007, Ruedesheim, Germany




2010

Kevin Oliver (Masters in Chemistry, 2010 Advisor: Gary Sulikowki)
Current Position: Associate Chemist, Color Corporation of America, KY

 

Publications for Kevin Oliver

T. Pyburn, B. A. Bensing, Y. Q. Xiong, B. J. Melancon, T. M. Tomasiak, N. J. Ward, V. Yankovskaya, K. M. Oliver, G. Cecchini, G. A. Sulikowski, M. J. Tyska, P. M. Sullam, T. M. Iverson  2011, “A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors”, PLoS Pathogens 2011, 7, 7, e1002112. PMC3131266

 

Jonas Perez  (Advisor: David Wright)
Current Position: Research Scientist, Medical Neurogenetics

 

Publications for Jonas Perez

Perez, Jonas W.; Adams, Nicholas, M.; Zimmerman, Grant, R.; Haselton, Fredrick, R.; Wright, David W. 2011, "Detecting Respiratory Syncytial Virus Using Nanoparticle Amplified Immuno-PCR." NanoBiotechnology Protocols in Methods in Molecular Biology, S.J. Rosenthal and D.W. Wright, Eds. Humana Press:New Jersey, In Press

Jayagopal, Ashwath; Halfpenny, Kristin C.; Perez, Jonas W.; Wright, David W. 2010,“Hairpin DNA-functionalized gold colloids for the imaging of mRNA in live cells “ J. Am. Chem. Soc. 132(28), 9789-9796. PMCID: PMC2927968

Jonas W. Perez, Fredrick R. Haselton, and David W. Wright. 2009, “Viral detection using DNA functionalized gold filaments.” Analyst, 134, 1548–1553. Cross sighted in RSC Chemical Biology and listed as a Royal Society of Chemistry “Hot Paper” in analytical chemistry. PMCID: PMC2867084

 

Thomas Tomasiak ( Advisor: Tina Iverson)
Current Position: Postdoc, University of California-San Francisco

 

Publications for Thomas Tomasiak

Tomasiak, T.M., Maklashina, E., Cecchini, G., and Iverson, T.M. (2008) A Threonine on the Active Site Loop Controls Transition State Formation in Escherichia coli Respiratory Complex II. J. Biol. Chem. 283(22): 15460-15468. PMCID: PMC2397489

Pyburn, T.M., Bensing, B.A., Melancon, B.J., Tomasiak, T.M., Yankovskaya, V., Oliver, K., Ward, N.J., Sulikowski, G.A., Cecchini, G., Tyska, M.J., Sullam, P.M., and Iverson, T.M. (2011) A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors. PLos Pathogens. 7(7): e1002112. PMCID: PMC3131266

Cecchini, G., Maklashina, E., Tomasiak, T.M., and Iverson T.M., Conformational Changes at the Dicarboxylate Binding Site of Succinate Dehydrogenase (Complex II) and Fumarate Reductase, in S. Frago, C. Gómez-Moeno, and M. Medina (eds.) Flavins and Flavoproteins, Prensas Universitarias de Zaragoza (2008) pp. 17-26


 

2009

Chinessa Adkins Ph.D. in Chemistry (Advisor: Eva Harth)
Current Position: Postdoctoral Fellow, Howard Hughes Medical Institute, Chevy Chase, MD

  Publications for Chinessa Adkins

Adkins, C.T., Harth, E., 2008, “Synthesis of Star Polymer Architectures with Site-Isolated Chromophore Cores,” Macromolecules, 41(10); 3472-3480

Adkins, C.T., Muchalski, H., Harth, E., 2009, “Nanoparticles with Individual site-isolated Semiconducting Polymers from Intramolecular Chain Collapse Processes,” Macromolecules, 42 (15), 5786-5792

Croce, T. A.; Funk, M.; Adkins, C. T.; Harth, E., Strategies and synthesis of suitable precursors for the construction of 3-D bioactive scaffolds. Abstracts of Papers of the American Chemical Society 2005, 230, 337-PMSE.

Croce, T. A.; Muchalski, H.; Adkins, C. T.; Huang, K.; Hamilton, S. K.; van der Ende, A.; Harth, E., Approaches in the development of 3-D nanoscopic, multifunctional vectors. Abstracts of Papers of the American Chemical Society 2006, 231, 171-PMSE.

Somarajan, S.; Hasan, S.A.; Adkins, C.T.; Harth, E.; Dickerson, J.H. 2008, “Controlled Electrophoretic Deposition of Uniquely Nanostructured Star Polymer Films” Journal of Physical Chemistry B, 112(1), 23-28. PMID: 18069811


Amanda Kussrow Ph. D. in Chemistry (Advisor: Darryl Bornhop)
Current Position: Research Associate, Vanderbilt University

 

Publications for Amanda Kussrow

Bornhop, D. J.; Latham, J. C.; Kussrow, A.; Markov, D. A.; Jones, R. D.; Sorensen, H. S., Free-solution, label-free molecular interactions studied by back-scattering interferometry. Science 2007, 317 (5845), 1732-1736.

Kussrow, A.; Kaltgrad, E.; Wolfenden, M. L.; Cloninger, M. J.; Finn, M. G.; Bornhop, D. J., Measurement of Monovalent and Polyvalent Carbohydrate-Lectin Binding by Back-Scattering Interferometry. Analytical Chemistry 2009, 81 (12), 4889-4897.

 

2008

Almary Chacon Ph.D. in Chemistry (Advisor: Ned Porter)
Current Position: Research Scientist, Baxter Healthcare

 

Publications for Almary Chacon

Chacon A, Masterson DS, Yin H, Liebler DC, Porter NA (2006) N-Terminal amino acid side-chain cleavage of chemically modified peptides in the gas phase: a mass spectrometry technique for N-terminus identification. Bioorg Med Chem, 2006 Sep 15;14 (18):6213-22. PMID 16784867.

Chacon, A.; Masterson, D. S.; Yin, H. Y.; Liebler, D. C.; Porter, N. A., N-terminal amino acid side-chain cleavage of chemically modified peptides in the gas phase: A mass spectrometry technique for N-terminus identification. Bioorganic & Medicinal Chemistry 2006, 14 (18), 6213-6222.

Masterson DS, Yin H, Chacon A, Hachey DL, Norris JL, Porter NA (2004). Lysine peroxycarbamates: free radical-promoted peptide cleavage. J Am Chem Soc. 2004 Jan 28;126 (3):720-1. PMID: 14733538.

Yin, H.; Chacon, A.; Porter, N. A.; Yin, H. Y.; Masterson, D. S., Free radical-induced site-specific peptide cleavage in the gas phase: Low-energy collision-induced dissociation in ESI- and MALDI mass spectrometry. Journal of the American Society for Mass Spectrometry 2007, 18 (5), 807-816.


Andrew Felts Ph.D. in Chemistry (Advisor: Larry Marnett)
Current Position: Senior Research Specialist, Vanderbilt Center for Neuroscience Drug Discovery

 

Publications for Andrew Felts

Ansari, M. S.; Jones, C. K.; Felts, A. S.; Lindsley, C. W.; Alagille, D.; Tamagnan, G. D.; Kessler, R. M.; Baldwin, R. M., ONE POT SYNTHESIS OF 18F FPEB IN A SEMI-AUTOMATED MODULE. Journal of Labelled Compounds & Radiopharmaceuticals 2009, 52, S318-S318. Felts, A. S., Molecule of the month. Current Topics in Medicinal Chemistry 2008, 8 (14), 1310-1310.

Felts, A. S.; Ji, C.; Stafford, J. B.; Crews, B. C.; Kingsley, P. J.; Rouzer, C. A.; Washington, M. K.; Subbaramaiah, K.; Siegel, B. S.; Young, S. M.; Dannenberg, A. J.; Marnett, L. J., Desmethyl derivatives of indomethacin and sulindac as probes for cyclooxygenase-dependent biology. Acs Chemical Biology 2007, 2 (7), 479-483.

Felts, A. S.; Siegel, B. S.; Young, S. M.; Moth, C. W.; Lybrand, T. P.; Dannenberg, A. J.; Marnett, L. J.; Subbaramaiah, K., Sulindac derivatives that activate the peroxisome proliferator-activated receptor gamma but lack cyclooxygenase inhibition. Journal of Medicinal Chemistry 2008, 51 (16), 4911-4919.

Felts, A. S.; Siegel, B. S.; Young, S. M.; Moth, C. W.; Lybrand, T. P.; Dannenberg, A. J.; Marnett, L. J.; Subbaramaiah, K., Sulindac derivatives that activate the peroxisome proliferator-activated receptor gamma but lack cyclooxygenase inhibition. Journal of Medicinal Chemistry 2008, 51 (16), 4911-4919.

Felts, A.; Ji, C.; Prusakiewicz, J.; Mackenzie, B.; Crews, B.; Marnett, L. J. In Design and synthesis of indomethacin and sulindac derivatives that induce tumor cell apoptosis but do not inhibit cyclooxygenases, Elsevier Science Inc: 2006; pp 161-161.

Felts, A. S.; Ji, C.; Prusakiewicz, J. J.; Marnett, L. J., Structure-based design of novel NSAIDs that induce apoptosis in tumor cells but lack COX-2 inhibitory activity. Proceedings of the American Association for Cancer Research Annual Meeting 2005, 46, 595.

Marnett, L. J.; Prusakiewicz, J. J.; Felts, A. S.; Ji, C. Indoleacetic acid and indenacetic acid derivatives as therapeutic agents with reduced gastrointestinal toxicity. US 07491744, Feb 10 2009, 2009.

Walters, M. J.; Blobaum, A. L.; Kingsley, P. J.; Felts, A. S.; Sulikowski, G. A.; Marnett, L. J., The influence of double bond geometry in the inhibition of cyclooxygenases by sulindac derivatives. Bioorganic & Medicinal Chemistry Letters 2009, 19 (12), 3271-3274.


Craig Garmendia Masters in Chemistry (Advisor: Carmelo J. Rizzo)
Current Position:  FDA Investigator

 

Publications for Craig Garemendia

Christov PP, Chowdhury G, Garmendia CA, Wang F, Stover JS, Elmquist CE, Kozekova A, Angel KC, Turesky RJ, Stone MP, Guengerich FP, Rizzo CJ. 2010 Jun 21. "The C8-2'-deoxyguanosine adduct of 2-amino-3-methylimidazo[1,2-d]naphthalene, a carbocyclic analogue of the potent mutagen 2-amino-3-methylimidazo[4,5-f]quinoline, is a block to replication in vitro." Chem Res Toxicol. 2010 Jun 21;23(6):1076-88. PMCID: PMC2891123


Christopher Moth Ph.D. in Chemistry (Advisor: Terry Lybrand)
Current Position: Independent Software Consultant

 

Publications for Chris Moth

Moth, C. W.; Prusakiewicz, J. E. J.; Marnett, L. J.; Lybrand, T. P., Stereoselective binding of indomethacin ethanolamide derivatives to cyclooxygenase-1. Journal of Medicinal Chemistry 2005, 48 (10), 3613-3620.


 

 

 

 

 


 

 

 

 

 

 




 

 

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