Presentations and Publications
Examples of Recent Presentations and Publications by ECRP Staff
Beuning, P. J., "Critical Role of Processivity Clamp Proteins in the Cellular Response to DNA Damage", seminar, Department of Civil Environmental Engineering, Northeastern University, November 10, 2006.
Beuning P. J., "A Single Point Mutation in E. coli DNA Polymerase V Renders Cells Hypersensitive to UV Light", seminar, Institute of Biotechnology, Vilnius, Lithuania, September 21, 2007.
Beuning, P. J., Simon, S, M, Zemla, A., Barsky, D., Walker G. C. (2006) A Non-Cleavable UmuD Variant that Acts as a UmuD Mimic, J. Biol. Chem. 281, 9633-9640. Beuning P. J., Sawicka, D., Barsky, D., Walker, G. C. (2006) Two Processivity Clamp Interactions Differentially Alter the Dual Activities of UmuC, Molecular Microbiology 59 460-474.
Beuning, P. J., Simon, S. M., Godoy, V. G., Jarosz, D. F., Walker G. C. (2006) Characterization of E. coli translesion synthesis polymerases and their accessory factors, Methods in Enzymology 408, 318-340.
Beuning, P. J., Shurtleff, B., Sefcikova, J., Walker G. C., Steric Gate Variants in a Y family DNA Polymerase Confer UV-Hypersensitivity American Society for Biochemistry and Molecular Biology (Experimental Biology 2009), San Diego, CA, April 5-9, 2008.
Cruceanu, M., Stephen, A. G., Beuning, P.J., Gorelick, R. J., Fisher, R. J., Williams, R. J. (2006) Single DNA molecule stretching experiments provide an efficient method for determining the activity of drugs that target the HIV-1 nucleocapsid protein, Analytical Biochemistry 358 159-170.
Flarakos, J., Xiong, W., Glick, J., Vouros, P. (2005) Deoxynucleotide Derivatization Methodology for Improving LC-ESI-MS Detection, Anal Chem. 77, 2373-2380.
Giese, R. W., "Mass Specific Discovery of DNA Adducts", Lombardi Cancer Center, George Washington University, April 6, 2005; Capitol University of Medical Sciences, Beijing, China, Nov.1, 2005.
Giese, R. W., "Measurement and meaning of DNA Adducts", University of New Hampshire, Durham, NH, Sept. 28, 2006.
Giese, R., "Genotoxin Mass Profiling for Environmental Regulation", Department of Environmental Protection, Boston, January 22, 2008.
Giese, R. "Mass Tag Profiling of Chemical Damage to DNA", Pfizer, Groton, CT, April 16, 2008; Genotoxic Impurities Conference, Brussels, Belgium, June 17, 2008.
Godoy, V. G., Gizatullin, F. S. Fox, M. S. (2000) Some features of the mutability of bacteria during non-lethal selection. Genetics., vol. 154, 49-59.
Godoy, V. G., Fox, M. S. (2000) Transposon stability and a role for conjugational transfer in adaptive mutability. Proc Natl Acad Sci U S A. l.97, 7393-8.
Godoy, V. G., Beuning, P. J.,Walker, G. C., Lennarz, W. J., Lane, M. D. Eds. (2005) Gene Expression in Bacterial Systems: The LexA Regulatory System" in Encyclopedia of Biological Chemistry Vol 2., Academic Press/Elsevier Science, San Diego, CA. pp. 546-550 (encyclopedia chapter).
Godoy, V.G., Jarosz, D. F., Walker, F., Simmons, L., Walker, G. C. (2006) Y Family DNA polymerases respond to DNA damage-independent inhibition of replication fork progression, EMBO J. 25, 868-879.
Godoy, V. G., Jarosz, D. F., Simon, S. M., Abyzov, A., Ilyin, V., Walker, G. C. (2007) UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB., Molecular Cell 28, 1058-1070.
Jarosz, D. F., Beuning, P. J., Cohen, S. E., Walker, G. C. (2007) Y-Family DNA Polymerase in Escherichia coli, Trends in Microbiol. 15, 70-77.
Jarosz, D. F., Godoy, V. G., Walker, G. C. (2007) Proficient and accurate bypass of persistent DNA lesions by DinB DNA polymerases, Cell Cycle 6, 817-22.
Jarosz, D. F., Godoy, V. G., Delaney, J. C., Essigman, J. M., Walker, G. C. (2006) A single amino acid governs enhanced activity of DinB DNA polymerase on damaged templates, Nature 439, 225-228.
Kao, C-Y., Giese, R.W. (2005) Measurement of N7-(2'-Hydroxyethyl)guanine in Human DNA by Gas Chromatography Electron Capture Mass Spectrometry, Chem. Res. Toxicol. 18, 70-75.
Kautz, R. A., Goetzinger, W., and Karger, B.L. (2005) High-Throughput Microcoil NMR of Compound Libraries Using Zero-Dispersion Segmented Flow Analysis. J. Comb. Chem. 7, 14-20.
Kautz, R. A. "An Optimized LC-MS+NMR Strategy Using a Microcoil NMR Probe with Normal-bore LC," invited presentation, NIH/NIA Baltimore, MD, 23 April 2008.
Kautz, R. A., Karger, B.L. Method of Efficient Transport of Small Liquid Volumes To, From, or Within Microfluidic Devices, Patent App WO/2005/059512, PCT/US2004/041923.
Levin, D. S., Vouros, P., Miller, R. A., Nazarov, E. G., Morris, J. C. (2006) Characterization of gas phase interactions utilizing a novel nanoelectrospray ionization-differential mobility-mass spectrometer (nanoESI0DMS-MS) system, Anal. Chem. 78, 96-106.
Lewis, K., Epstein, S., Godoy, V. G., Hong, S-H. (2008) Intact DNA in ancient permafrost, Trends in Microbiology. 16, 92-94.
Liao Q. Chiu N. H. L., Shen C., Vouros, P. (2007) Investigation of the Enzymatic Behavior of Benzonase Alkaline Phosphatase in the Digestion of DNA and DNA Adducts by ESI-LC/MS, Anal. Chem. 79, 1907-1917.
Lin Y, Vouros P, Orjala J., Kautz R. A. (2007) An Ultrasensitive LC-MS-NMR Platform Utilizing Segmented-Flow Microcoil NMR, Nanospray ESI, and 4 mm LC Column, invited lecture, 48th Experimental NMR Conference, Daytona FL, 26 April 2007.
McCauley, M., Shokri, L., Venclovas, Beuning, P. J., Williams, M. C., "Double and Single Strand DNA Binding of Catalytic Alpha Subunit of E. Coli Replicative DNA Polymerase III", Biophysical Society of Annual Meeting, Long Beach, CA, February 2-6, 2008.
Murugaiah, V., Naim, A., Peng, S., Cui, G., Giese, R. W. (2006) 4-(4'-Methyltetrafluorophenyl)-2,3,5,6-tetrafluorobenzyl bromide: A new electrophoric derivatizing reagent, J. Chromatogr. A, 1134, 338-340.
Riciciki, E. M., Soglia, J. R., Teitel, C., Kane, R., Kadlubar, F., Vouros, P. (2005) Detection and Quantification of N-(deoxyguanosine-8-yl)-4-aminobiphenyl Adducts in Human Pancreas Tissue Using Capillary Liquid Chromatography-Microelectrospray Mass Spectrometry, Chem. Res. Toxicol. 18, 692-699.
Riciciki, E. M., Andrews, C. L., Schiavo, S., Vouros, P. (2006) Analysis of DNA Adducts, in Encyclopedia of Mass Spectrometry, vol 3, Biological Applications Part B: Carbohydrates, Nucleic Acids and other Biological compounds, Series editors: Caprioli, R., and Gross, M. Elsevier Ltd., Oxford, 61-85.
Riciciki, E.M., Luo, W., Zarbl, H., Vouros, P. (2006) "Quantification of N-(deoxyguanosin-8-yl)-4-aminobiphenyl Adducts in Human Lymphoblastoid TK6 Cells Dosed with N-hydroxy-4-aminobiphenyl and their Relationship to Mutation, Toxicity and Gene Expression Profiling, Anal. Chem.78, 6422-6432.
Sefcikova, J. Beuning, P. J., "Substrate specificity of DNA polymerases that Replicate Damaged DNA", American Chemical Society 2007 Fall Meeting, Boston, MA August 19-23, 2007.
Shao, G.,Giese. R. W. (2004) Trace Detection of Glycolic Acid by Electrophore Labeling Gas Chromatography-Electron Capture Mass Spectrometry, Anal. Chem. 76, 3049-3054.
Shao, G., Kautz, R. A., Peng, S., Cui,G., Giese, R.W. (2007) Calibration by NMR for quantitative analysis: p-Toluenesulfonic Acid as an Internal Standard, J. Chromatogr. A 1138, 305-308.
Shimelis, O., Zhou, X., Li, G., Giese, R. W. (2004) Phenolic extraction of DNA from mammalian tissues and conversion to deoxyribonucleoside-5'-monophosphates devoid of ribonucleotides, J. Chromatogr. A., 1053, 143-149.
Shimelis, O., Giese, R. W. (2006) Nuclease P1 digestion/high-performance liquid chromatography, a practical method for DNA quantitation, J. Chromatogr. A. 1117, 132-136.
Sutton, M. D., Smith, B. T., Godoy, V. G., Walker, G. C. (2000) The SOS response: recent insight s into umuDC-dependent mutagenesis and DNA damage tolerance, Annu. Rev. Genet. 34, 479-497.
Vorous, P., Greater Montreal Mass Spectrometry Discussion Group, "Monitoring DNA Damage from Environmental Carcinogens by Capillary LC-MS", Jan. 26, 2006.
Vouros, P., COSMOS: Conference on Small Molecule Science, Keynote Lecture, "Demonstrating Feasibility for Ultra-Rapid Quantitation with a Nanoelectrospray" "Differential Mobility Spectrometer" "Mass Spectrometer System", San Diego, CA, July 26, 2000.
Vouros, P., "Drug Metabolism Studies at the Trace Level Using HPLC- MS and microNMR", Department of Pharmacy, University of Athens, Greece, May 25, 2007.
Vouros, P., "In vitro and in vivo analysis of DNA Adducts by LC-MS", University of Crete in Heraklion, Tuesday May 8.
Vouros, P., James Glick, Robert C. Sullivan, Helmut Zarbl, Paul Vouros, Correlating DNA Adduct Levels and Gene Expression using LC-MS/MS and DNA Microarrays for a Foodborne Heterocyclic Aromatic Amine Procarcinogen, 55th ASMS Conference, Indianapolis, IN, June 3-7, 2007.
Xiong, W.; Glick, J.; Lin, Y., Vouros, P. (2007) Separation and Characterization of Isomeric Oligonucleotide Adducts Using Monolithic Columns by Ion-pair Reversed-Phase Nano- HPLC Coupled to Ion Trap Mass Spectrometry, Anal. Chem. 79, 5312-5321.
Yong. L. C., Schulte, P. A., Kao, C-K., Boeniger, M. F., Strauss, G. H.S., Petersen, M. R., Wiencke, J. K., Giese, R. W. (2007) DNA Adducts in Granulocytes of Hospital Workers Exposed to Ethylene Oxide, Am. J. Ind. Med., 50, 293-302.
Xiong, W., Glick, J., Lin, Y., Noronha, A.M., Wilds, C.J., and Vouros, P. “The Influence of Cytosine Methylation on the Chemoselectivity of Benzo[a]pyrene Diol Epoxide-Oligonucleotide Adducts Determined Using nano LC-MS/MS”,Journal of Mass Spectrom. 44, 1241-1248 (2009)
Randall, K. L., Argoti, D., Paonessa, J. D., Ding, Y., Oaks, Z., Zhang, Y., Vouros, P., “An Improved Liquid Chromatography-Tandem Mass Spectrometry Method for the Quantification of 4-Aminobiphenyl DNA Adducts in Urinary Bladder Cells and Tissues”, Journal of Chromatography A , 1217, 4135-4143 (2010) PMID: 19932483
Liao, Q., Shen, C., and Vouros, P., "GenoMass - A Computer Software for Automated Identification of Oligonucleotide DNA Adducts from LC-MS Analysis of DNA Digests", Journal of Mass Spectrom., 44, 549-560 (2009).
Zarbl, H.; Gallo, M. A.; Glick, J., Yeung, K. Y.; Vouros, P., “The Vanishing Zero Revisited: Thresholds in the Age of Genomics”, Chemico-Biological Interactions, 184, 273-278 (2010)
Liao, Q. And Vouros, P., “Oligonucleotide Adducts as Markers for Site Selective Carcinogen Adduction: Their analysis by Mass Spectrometry Coupled to Separation Methods”, Advances In Chromatography Series, Vol. 49, 187-249 (2010).
Ding, Y., Paonessa, J.D., Randall, K.L., Argoti, D., Chen, L., Vouros, P., Zhang, Y., Sulforaphane inhibits 4-Aminobiphenyl-induced DNA Damage in Bladder Cells and Tissues” Carcinogenesis, 31, 199-2003 (2010)
Vaneet K Sharma, Paul Vouros and James Glick, “Mass spectrometric based analysis, characterization and applications of circulating cell free DNA isolated from human body fluids”, Intern. Journal of Mass Spectrometry 304, 172-183 (2011).
Paonessa, J.D., Ding, Y., Randall, K.L., Munday, R., Argoti, D., Vouros, P., Zhang, Y., “An unintended consequence of Nrf2-directed cytoprotection against a major human bladder carcinogen and a counteracting solution”, Cancer Research, 71, 3904-3911 (2011).
Sharma, V., Glick, J., Liao, Q., Shen, C., Vouros, P., “GenoMass software: A tool based on electrospray ionization tandem mass spectrometry for characterization and sequencing of oligonucleotide adducts”, J. Mass Spectrom., [in press, 2012].
Microscale LC-MS-NMR platform applied to the identification of active cyanobacterial metabolites. Micah J. McCauley, Leila Shokri, Jana Sefcikova, Česlovas Venclovas, Penny J. Beuning, and Mark C. Williams (2008) “Distinct Double- and Single-Stranded DNA Binding of E. coli Replicative DNA Polymerase III Alpha Subunit” ACS Chemical Biology 3 577-587. Featured in journal Podcast, September 2008: http://community.acs.org/ChemBiol/Podcasts/2008/tabid/110/Default.aspx
Jing Fang, Kasper D. Rand, Michelle C. Silva, Thomas E. Wales, John R. Engen, and Penny J. Beuning (2010) “Conformational Dynamics of the Escherichia coli polymerase manager proteins UmuD and UmuD′ ” Journal of Molecular Biology 398 40-53.
Jaylene N. Ollivierre*, Jing Fang*, and Penny J. Beuning (2010) “The roles of UmuD in regulating mutagenesis” Journal of Nucleic Acids Article ID 947680, 12 pages, 2010. doi:10.4061/2010/947680.
Jason M. Walsh*, Lisa A. Hawver*, and Penny J. Beuning (2011) “Escherichia coli Y family DNA polymerases” Frontiers in Bioscience 16 3164-3182.
Jason M. Walsh, Imenne Bouamaied, Tom Brown, L. Marcus Wilhelmsson, Penny J. Beuning (2011) “Discrimination against the Cytosine Analog tC by Escherichia coli DNA Polymerase IV DinB” Journal of Molecular Biology 409 89-100.
Lisa A. Hawver and Penny J. Beuning “Chapter 486 UmuC D Lesion Bypass DNA Polymerase V” Encyclopedia of Biological Chemistry 2nd edition W. J. Lennarz and M. D. Lane, Eds., Elsevier Science, in press. (encyclopedia chapter).
Yong. L. C., Schulte, P. A., Kao, C-K., Giese, R. W., Boeniger, M. F., Strauss, G. H.S., Petersen, M. R., Wiencke, J. K. (2007) DNA Adducts in Granulocytes of Hospital Workers Exposed to Ethylene Oxide, Am. J. Ind. Med., 50, 293-302.09.
Bono, R., Romanazzi, V., Munnia, A., Piro, S., Allione, A., Ricceri, F., Guarrera, S., Pignata, C., Matullo, G., Wang, P. Giese, R. W., Peluso, M. (2010) Malondialdehyde-Deoxyguanosine Adduct Formation in Workers of Pathology Wards: The Role of Air Formaldehyde Exposure, Chem. Res. Toxicol. 23, 1342-1348.
Gao, H., Le, Y., Wu, X., Silberstein, L. E., Giese, R. W., Zhu, Z. (2010) VentX, a Novel Lymphoid-Enhancing Factor/T-Cell Factor-Associated Transcription Repressor, Is a Putative Tumor Suppressor, Cancer Res., 70, 202-211.
Peluso, M., Munnia, A., Risso, G. G., Catarzi, S., Piro, S., Ceppi, M., Giese, R. W., Brancato, B. (2011) Breast fine-needle aspiration malondialdehyde deoxyguanosine adduct in breast cancer, Free Radical Res. 45, 477-482.
Peluso, M., Munnia, A., Piro, S., Jedpiyawongse, A., Sangrajrang, S., giese, R. W., Ceppi, M., Boffetta, P. Srivatanakul, P. (2011) Fruit and vegetable and fried food consumption and 3-(2-deoxy-β-D-erythro-pentafuranosyl) pyrimido[1,2-α] purin-10(3H)-one deoxyguanosine adduct formation, Free Radical Res. 46, 85-92.
Wang, P., Fisher, D., Rao, A., Giese, R.W. (2012) Nontargeted Nucleotide Analysis Based on Benzoylhistamine Labeling-MALDI-TOF/TOF-MS: Discovery of Putative 6-Oxo-Thymine in DNA, Anal. Chem. March 12, 2012.