Michael J. Daly Lab: Deinococcus radiodurans

  1. Ajay Sharma, Elena K. Gaidamakova, Vera Y. Matrosova, Brian Bennett, MICHAEL J. DALY, Brian M. Hoffman (2013) Responses of Mn2+ speciation in Deinococcus radiodurans and Escherichia coli to γ-radiation by advanced paramagnetic resonance methods. Proc. Natl. Acad. Sci. USA, 110, 5945-5950.
     
  2. Valeria C. Culotta, MICHAEL J. DALY (2013) Manganese Complexes: Diverse Metabolic Routes to Oxidative Stress Resistance in Prokaryotes and Yeast. Antioxidants & Redox Signaling, 19(9), 933-944.
     
  3. Lawrence A. Klobutcher, Elena Gaidamakova, MICHAEL J. DALY, Barbara Setlow, Peter Setlow (2013) Effects of Mn2+ levels on the resistance properties of Bacillus cereus spores. Journal of Bacteriology Research, 5(1),9-12.
     
  4. E.K. Gaidamakova, I.A. Myles, D.P. McDaniel, C.J. Fowler, P.A. Valdez, S. Naik, M. Gayen, P. Gupta, A. Sharma, P.J. Glass, R.K. Maheshwari, S.K. Datta, MICHAEL J. DALY (2012) Preserving Immunogenicity of Lethally Irradiated Viral and Bacterial Vaccine Epitopes Using a Radio- Protective Mn(2+)-Peptide Complex from Deinococcus. Cell Host Microbe, 12(1),117-124. Supplemental Material.
     
  5. MICHAEL J. DALY (2012) Death by protein damage in irradiated cells. DNA Repair, 11(1), 12-21.
     
  6. MICHAEL J. DALY (2012) The Achilles' heel of radiation resistant prokaryotes. In Assessment of Planetary Protection Requirements for Spacecraft Missions to Icy Solar System Bodies (Sogin ML et al., eds). Division on Engineering and Physical Sciences, National Research Council of the National Academy of Sciences (In Press).
     
  7. S. Ghosh, A. Ramirez-Peralta, E. Gaidamakova, P. Zhang, Y.Q. Li, MICHAEL J. DALY, P. Setlow (2011) Effects of Mn levels on resistance of Bacillus megaterium spores to heat, radiation and hydrogen peroxide. J Appl Microbiol., 111(3),663-670.
     
  8. A.C. Granger, E.K. Gaidamakova, V.Y. Matrosova, MICHAEL J. DALY, P. Setlow (2011) Effects of Mn and Fe levels on Bacillus subtilis spore resistance and effects of Mn2+, other divalent cations, orthophosphate, and dipicolinic acid on protein resistance to ionizing radiation. Appl Environ Microbiol., 77(1),32-40.
     
  9. MICHAEL J. DALY, E.K. Gaidamakova, V. Y. Matrosova, J.G. Kiang, R. Fukumoto, D.Y. Lee, N.B. Wehr, G.A. Viteri, B.S. Berlett, R.L. Levine (2010) Small-molecule antioxidant proteome-shields in Deinococcus radiodurans. PLoS ONE, 5(9), e12570. Supplemental Material.
     
  10. K. S. Makarova, MICHAEL J. DALY (2010) Comparative genomics of stress response systems in Deinococcus bacteria. Storz G, Hennge R (Eds) In Bacterial Stress Responses, 27, 445-457.
     
  11. MICHAEL J. DALY (2010) Deinococcus radiodurans: revising the molecular basis for radiation effects on cells. Extremophiles Handbook. Horikoshi, K. (Ed.). Springer, Japan.
     
  12. MICHAEL J. DALY (2009) Deinococcus prospects. Nat. Rev. Microbiol., 7, 476.
     
  13. MICHAEL J. DALY (2009) A new perspective on radiation resistance based on Deinococcus radiodurans. Nat. Rev. Microbiol., 7, 237-245.
     
  14. J. K. Fredrickson, S. W. Li, E. K. Gaidamakova, V. Y. Matrosova, M. Zhai, H. M. Sulloway, J. C. Scholten, M. G. Brown, D. L. Balkwill, MICHAEL J. DALY (2008) Protein oxidation: Key to bacterial desiccation resistance. Nature Publishing Group: The ISME Journal, 2, 393-403. Supplemental Material.
     
  15. B. Lai, S. Vogt, J. Mase, B. Ravel, K. Kemner, MICHAEL J. DALY (2007) Applications and future prospects for x-ray fluorescence microprobe analysis. Microscopy and Microanalysis, 13, 1426-1427.
     
  16. Makarova K. S., M.V. Omelchenko, E.K. Gaidamakova, V.Y. Matrosova, A. Vasilenko, M. Zhai, A. Lapidus, A. Copeland, E. Kim, M. Land, K. Mavrommatis, S. Pitluck, P. Richardson, J.C. Detter, T. Brettin, E. Saunders, B. Lai, B. Ravel, K.M. Kemner, Y. I. Wolf, A. Sorokin, A. V. Gerasimova, M. S. Gelfand, J.K. Fredrickson, E. V. Koonin, MICHAEL J. DALY (2007) Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks, PLoS ONE, 9, e955. Supplemental Material.
     
  17. MICHAEL J. DALY, E.K. Gaidamakova, V.Y. Matrosova, A. Vasilenko, Min Zhai, R.D. Leapman, B. Lai, B. Ravel, Shu-Mei W. Li, K.M. Kemner, J.K. Fredrickson (2007) Protein oxidation implicated as the primary determinant of bacterial radioresistance. PLoS Biology, 5(4), e92. Supplemental Material.
     
  18. J. W. Szostak, R. E. Blake, MICHAEL J. DALY, D. H. Grinspoon, A. D. Keefe, G.J. Olsen (2006) Assessment of planetary protection requirements for Venus missions. The National Academies Press, Commission on Physical Sciences, Mathematics, and Applications. http://www.nap.edu/catalog.php?record_id=11584.
     
  19. J. Qin, L. Song, H. Brim, MICHAEL J. DALY, A. Summers (2006) Hg(II) sequestration and protection by the MerR metal-binding domain (MBD). Microbiology, 152, 709-719.
     
  20. H. Brim, J.P. Osborne, H.M. Konstandarithes, J.K. Fredrickson, L.P. Wackett, MICHAEL J. DALY (2006) Deinococcus radiodurans engineered for complete toluene degradation facilitates Cr(VI) reduction. Microbiology, 152(8), 2469-2477.
     
  21. MICHAEL J. DALY (2006) Modulating radiation resistance: Insights based on defenses against reactive oxygen species in the radioresistant bacterium Deinococcus radiodurans. Clin Lab Med, 26(2), 491-504.
     
  22. X. Qiu, MICHAEL J. DALY, A. Vasilenko, M.V. Omelchenko, E.K. Gaidamakova, L. Wu, J. Zhou, G.W. Sundin, J.M. Tiedje (2006) Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation. J. Bacteriology, 188(3), 1199-1204.
     
  23. M.V. Omelchenko, Yu.I. Wolf, E.K. Gaidamakova, V.Y. Matrosova, A. Vasilenko, Min Zhai, MICHAEL J. DALY, E.V. Koonin, K.S. Makarova. (2005) Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evolutionary Biology, 5, 57-80. Supplemental Material.
     
  24. D. Ghosal, M. V. Omelchenko, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, A. Venkateswaran, H. M. Kostandarithes, H. Brim, K. S. Makarova, L. P. Wackett, J. K. Fredrickson, MICHAEL J. DALY (2005) How Radiation Kills Cells: Survival of Deinococcus radiodurans and Shewanella oneidensis Under Oxidative Stress. FEMS Microbiology Reviews, 29, 361-375. Supplemental Material.
     
  25. J. Szostak, J. C. Wheeler, S. A. Benner, J. Berry, R. Blake, W. Calvin, MICHAL J. DALY, K. H. Freeman, J. P. Gogarten, J. F. Kasting, A. Keefe, M. Keller, S. Pizzarello, J. Siefert, R. Summons, N. Woolf, L. M. Ziurys (2005) The Astrophysical Context of Life. The National Academies Press, National Academy of Sciences, Washington, D.C.
     
  26. MICHAEL J. DALY, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. Zhai, A. Venkateswaran, M. Hess, M. V. Omelchenko, H. M. Kostandarithes, K. S. Makarova, L. P. Wackett, J. K. Fredrickson, D. Ghosal (2004) Accumulation of Mn(II) in Deinococcus radiodurans Facilitates Gamma-Radiation Resistance. Science 306, 1025-1028. Supplemental Material.
     
  27. J. K. Fredrickson, J. M. Zachara, D. L. Balkwill, D. Kennedy, S. W. Li, H. M. Kostandarithes, MICHAEL J. DALY, M. F. Romine, F. J. Brockman (2004) Geomicrobiology of high level nuclear waste contaminated vadose sediments at the Hanford Site, Washington state. Appl. Environ. Microbiol. 70, 4230-4241.
     
  28. M. Sandigursky, S. Sandigursky, P. Sonati, MICHAEL J. DALY, W. A. Franklin (2004) Multiple uracil-DNA glycosylase activities in D. radiodurans. DNA Repair, 3, 163-169.
     
  29. J. R. Battista, M. M. Cox, MICHAEL J. DALY, I. Narumi, M. Radman, S. Sommer (2003) The structure of Deinococcus radiodurans. Science, 302, 567-568.
     
  30. H. Brim, A. Venkateswaran, H. M. Kostandarithes, J. K. Fredrickson, MICHAEL J. DALY (2003) Engineering Deinococcus geothermalis for bioremediation of high-temperature radioactive waste environments. Appl. Environ. Microbiol., 69, 4575-4582.
     
  31. Y. Liu, J. Zhou, A. Beliaev, J. Stair, L. Wu, D.K. Thompson, D. Xu, A. Venkateswaran, M. Omelchenko, M. Zhai, E. K. Gaidamakova, K. S. Makarova, E. Koonin, MICHAEL J. DALY (2003) Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc. Natl. Acad. Sci. USA, 100, 4191-4196. Supplemental Material.
     
  32. M. S. Lipton, L. Pasa-Tolic, G. A. Anderson, D. J. Anderson, D. Auberry, J. R. Battista, MICHAEL J. DALY, J. K. Fredrickson, K. K. Hixson, H. Kostandarithes, T. Conrads, C. Masselon, M. Markille, R. J. Moore, M. F. Romine, Y. Shen, N. Tolic, H. R. Udseth, T. D.Veenstra, A. Venkateswaran , K. K Wong, R. Zhao, R. D. Smith (2002) Global analysis of the Deinococcus radiodurans R1 proteome using accurate mass tags. Proc. Natl. Acad. Sci. USA. 99, 11049-11054.
     
  33. J-I Kim, A. K. Sharma, S. N. Abbot, E. A Wood, D. Dwyer, A. Jambura, K. W. Minton, R B. Inman, MICHAEL J. DALY, M. M. Cox (2002) RecA protein from the extremely radioresistant bacterium Deinococcus radiodurans: Expression, purification, and characterization. J. Bacteriol. 184, 1649-1660.
     
  34. MICHAEL J. DALY (2002) The Quarantine and certification of martian samples: Appendix A: Deinococcus radiodurans as an analogue to extremophile organisms that may have survived on Mars. National Academy Press, Commission on Physical Sciences, Mathematics, and Applications, pp. 67-69 (http://www.nap.edu/openbook.php?isbn=0309075718&page=67).
     
  35. K. S. Makarova, L. Aravind, Y. I. Wolf, R. L.Tatusov, K. Minton, E. V. Koonin, MICHAEL J. DALY (2001) Genome of the extremely radiation resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiology and Molecular Biology Reviews 65, 44-79.
     
  36. MICHAEL J. DALY (2001) The emerging impact of genomics on the development of biological weapons: Threats and benefits posed by engineered extremophiles. Clinics in Laboratory Medicine 21, 619-629.
     
  37. J. Nolling, G. Breton, M. V. Omelchenko, K. S. Makarova, Q. Zeng, R. Gibson, H. M. Lee, J. Dubois., D. Qiu, J. Hitti, Y. I. Wolf, R. L. Tatusov, F. Sabathe, L. Doucette-Stamm, R. L. Tatusov, P. Soucaille, MICHAEL J. DALY, G. N. Bennett, E. V. Koonin, D. R. Smith (2001) Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol. 183, 4823-4838.
     
  38. A. F. Cheng, B. C. Clark, MICHAEL J. DALY, E. I. Friedman, B. M. Jakosky, R. Y Morita, A.-L. Reysenbach, D. A. Stahl, L. W. Esposito (2001) Planetary Protection for Europa, Space Studies Board, National Research Council, National Academy of Sciences, Washington, D.C. (http://sites.nationalacademies.org/SSB/index.htm).
     
  39. MICHAEL J. DALY (2000) Engineering radiation-resistant bacteria for environmental biotechnology. Current Opinion in Biotechnology 11, 280-285.
     
  40. H. Brim, S. McFarlan, L. Wackett, K. W. Minton, M. Zhai, J. Fredrickson, MICHAEL J. DALY (2000) Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments. Nature Biotechnology 18, 85-90.
     
  41. J. K. Fredrickson, H. M. Kostandarithes, A. W. Li, A. E. Pyle, MICHAEL J. DALY (2000) Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans. Appl. Environ. Microbiol. 66, 2006-2011.
     
  42. A.Venkateswaran, S. C. McFarlan, D. Ghosal, K. W. Minton, A. Vasilenko, K. Makarova, L. P. Wackett, MICHAEL J. DALY (2000) Physiologic determinants of radiation resistance in Deinococcus radiodurans. Appl. Environ. Mircobiol. 66, 2620-2626.
     
  43. K. S. Makarova, L. Aravind, MICHAEL J. DALY, E. V. Koonin (2000) Specific expansion of protein families in the radioresistant bacterium Deinococcus radiodurans. Genetica 108, 25-34.
     
  44. O. White, J. A. Eisen, J. F. Heidelberg, E. K. Hickey, J.D. Peterson, R. J. Dodson, C. Zalewski, K. S. Makarova, L. Aravind, MICHAEL J. DALY, K. W. Minton, R. D. Fleischmann, K. A. Ketchum, K. E. Nelson, S. Salzberg, H. O. Smith, J. C. Venter, C. M. Fraser et al. (1999) Sequencing and functional analysis of the Deinococcus radiodurans genome. Science 286, 1571-1577.
     
  45. J. Lin, R. Qi, C. Aston, J. Jing, T. S. Anantharaman, B. Mishra, O. White, K. W. Minton, MICHAEL J. DALY, J. C. Venter, D. C. Schwarzt (1999) Whole genome shotgun optical mapping of Deinococcus radiodurans using genomic DNA molecules. Science 285, 1558-1561.
     
  46. R. C. Richmond, R Sridhar, MICHAEL J. DALY (1999) Physicochemical survival pattern for the radiophile Deinococcus radiodurans: A polyextremophile model for life on Mars. SPIE, 3755, 210-222.
     
  47. K. S. Makarova, Y. I. Wolf, K. W. Minton, O. White, MICHAEL J. DALY (1999) Short repeats and insertional elements in Deinococcus radiodurans and comparison to other bacterial species. Res. Microbiol. 150, 711-724.
     
  48. C. Lange, L. P. Wackett, K. W. Minton, MICHAEL J. DALY (1998) Engineering a recombinant Deinococcus radiodurans for organopollutant degradation in radioactive mixed waste environments. Nature Biotechnology 16, 929-933.
     
  49. MICHAEL J. DALY, K. W. Minton (1997) Recombination between a resident plasmid and the chromosome following irradiation of the radioresistant bacterium Deinococcus radiodurans. Gene 187, 225-229.
     
  50. J. D. Carroll, MICHAEL J. DALY, K. W. Minton (1996) Expression of recA in Deinococcus radiodurans. J. Bacteriol. 178, 130-135.
     
  51. MICHAEL J. DALY, K. W. Minton (1996) An alternative pathway for recombination of chromosomal fragments precedes recA-dependent recombination in the radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 178, 4461-4471.
     
  52. MICHAEL J. DALY, K. W. Minton (1995) Resistance to radiation. Science 270, 1318.
     
  53. K. W. Minton, MICHAEL J. DALY (1995) A model for repair of radiation induced DNA DSB's in the extreme radiophile Deinococcus radiodurans. Bioessays 17, 457-464.
     
  54. MICHAEL J. DALY, K. W. Minton (1995) Interchromosomal recombination in the extremely radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 177, 5495-5505.
     
  55. MICHAEL J. DALY, L. Ouyang, K. W. Minton (1994) Interplasmidic recombination following irradiaition of the radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 176, 7506-7515.
     
  56. MICHAEL J. DALY, L. Ouyang, P. Fuchs, K. W. Minton (1994) In vivo damage and recA-dependent repair of plasmid and chromosomal DNA in the radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 176, 3508-3517.