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Microbiology Supergroup

 

Publications

259: Frank, D.N., L.M. Feazel, M.T. Bessesen, C.S. Price,  E.N. Janoff and N.R. Pace.  (2010) The human nasal microbiota and Staphylococcus aureus carriage.  PLoS ONE 5:e10598 (15 pp.).

258: Rodriguez, M., J.J. Walker, N.R. Pace and M. Hernandez. (2010) Molecular source tracking of bioaerosols in the quarantined Katrina flood zone.  Aerosol Science Technol.  44:236-245.

257: Frank, D.N., S.S. Wilson, A.L. St. Amand, and N.R. Pace. (2009) Culture-independent microbiological analysis of Foley urinary catheter biofilms.  PLoS ONE 4:e7811 (7 pp.).

256: Pace, N.R. (2009) Mapping the tree of life: progress and prospects. Microbiol. Mol. Biol. Rev. 73:564-576.

255: Baumgartner LK, Dupraz C, Buckley DH, Spear JR, Pace NR, and Visscher PT. (2009) Microbial species richness and metabolic activities in hypersaline microbial mats: Insight into biosignature formation through lithification. Astrobiology 9:861-874.

254: Feazel LM, Baumgartner LK, Peterson KL, Frank DN, Harris JK, and Pace NR. (2009) Opportunistic pathogens enriched in showerhead biofilms. PNAS 106: 16393-16399.


253: Baumgartner, LK, Spear, JR, Buckley, DH, Pace, NR, Reid, RP, Dupraz, C, and Visscher, PT (2009) Microbial diversity in modern marine stromatolites, Highborne Cay, Bahamas. Environ Microbiol. Published online July 6.

252: Frank, DN, Wysocki, A, Specht-Glick, DD, Rooney, A, Feldman, RA, St Amand, AL, Pace, NR, and Trent, JD (2009) Microbial diversity in chronic open wounds.
Wound Repair Regen 17(2):163-72.

251: Frank, DN (2008) XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data. BMC Bioinformatics 9: 420.

  • Download Xplorseq here

250: Kazantsev, AV, Krivenko, AA, and Pace, NR (2008) Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA.
RNA 15: 266-276.

249: Pace, NR (2009). Problems with "procaryote". J Bacteriol, 191(7): 2008-10; discussion 2011.

248: Pace, NR (2009) Rebuttal: the modern concept of the procaryote. J Bacteriol, 191(7): 2006-7.

247: Robertson, CE, Spear, JR, Harris, JK, and Pace, NR (2009) Diversity and stratification of Archaea in a hypersaline microbial mat.
Appl Environ Microbiol 75:(7) 1801-1810.

246: Frank, DN and Pace, NR (2008) Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol, 24(1):4-10.

245: Kunin, V, Raes, J, Harris, JK, Spear, JR, Walker, JJ, Ivanova, N, von Mering, C, Bebout, BM, Pace, NR, Bork, P, and Hugenholtz, P (2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 4:198.

244: Peterson, DA, Frank, DN, Pace, NR, and Gordon, JI (2008) Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases.
Cell Host Microbe 3(6):417-27.

243: Sahl, JW, Pace, NR, and Spear, JR. (2008) Comparative molecular analysis of endoevaporitic microbial communities. Appl Environ Microbiol 74(20):6444-6.

242: Feazel LM, Spear JR, Berger AB, Harris JK, Frank DN, Ley RE, Pace NR.(2008) Eucaryotic diversity in a hypersaline microbial mat. Appl Environ Microbiol. 74(1):329-32

241: Baumgartner L, Pace NR. (2007) Current taxonomy in classroom instruction: How to teach the new understanding of higher-level taxonomy. The Science Teacher 74:46-51.

240: Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, Penvari C, Kaess H, Deterding RR, Accurso FJ, Pace NR.(2007) Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis.Proc Natl Acad Sci 104(51):20529-33.

239: Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci;104(34):13780-5.

238: Spear JR, Barton HA, Robertson CE, Francis CA, Pace NR. (2007) Microbial community biofabrics in a geothermal mine adit. Appl Environ Microbiol. 73(19):6172-80.

237: Walker JJ, Pace NR. Endolithic microbial ecosystems.(2007) Annu Rev Microbiol. 2007;61:331-47. Review.

236: Walker JJ, Pace NR. Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems. (2007) Appl Environ Microbiol. 73(11):3497-504.


235: Marquez SM, Chen JL, Evans D, Pace NR. (2006) Structure and function of eukaryotic Ribonuclease P RNA. Mol Cell. 24(3):445-56.


234: De Groote MA, Pace NR, Fulton K, Falkinham JO 3rd. (2006) Relationships between Mycobacterium isolates from patients with pulmonary mycobacterial infection and potting soils. Appl Environ Microbiol.72(12):7602-6.


232: Frank DN, Pace NR. (2001) Molecular-phylogenetic analyses of human gastrointestinal microbiota. Curr Opin Gastroenterol. 17(1):52-7.

231: Dalby AB, Frank DN, St Amand AL, Bendele AM, Pace NR. (2006) Culture-independent analysis of indomethacin-induced alterations in the rat gastrointestinal microbiota. Appl Environ Microbiol. 72(10):6707-15.


230: Kazantsev AV, Pace NR.(2006) Bacterial RNase P: a new view of an ancient enzyme.
Nat Rev Microbiol. 4(10):729-40. Review.

229. Pace NR. (2006) Time for a change. Nature. 441(7091):289.

228. Evans D, Marquez SM, Pace NR. (2006) RNase P: interface of the RNA and protein worlds. Trends Biochem Sci. 31(6):333-41. Epub 2006 May 6. Review.

227. Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin ML, Pace NR. (2006) Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol. 72(5):3685-95.

226. Salmassi TM, Walker JJ, Newman DK, Leadbetter JR, Pace NR, Hering JG. (2006) Community and cultivation analysis of arsenite oxidizing biofilms at Hot Creek. Environ Microbiol;8(1):50-9.

225. Robertson CE, Harris JK, Spear JR, Pace NR. (2005) Phylogenetic diversity and ecology of environmental Archaea. Curr Opin Microbiol. 8(6):638-42. Review.

224. Buck AH, Kazantsev AV, Dalby AB, Pace NR. (2005) Structural perspective on the activation of RNAse P RNA by protein. Nat Struct Mol Biol. 12(11):958-64.

223. St Amand AL, Frank DN, De Groote MA, Basaraba RJ, Orme IM, Pace NR. (2005) Use of specific rRNA oligonucleotide probes for microscopic detection of Mycobacterium tuberculosis in culture and tissue specimens. J Clin Microbiol. 2005 Oct;43(10):5369-71.

222. Buck AH, Dalby AB, Poole AW, Kazantsev AV, Pace NR. (2005) Protein activation of a ribozyme: the role of bacterial RNase P protein. EMBO J. 24(19):3360-8.

221. Kazantsev AV, Krivenko AA, Harrington DJ, Holbrook SR, Adams PD, Pace NR. (2005) Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A. 102(38):13392-7.

220. Gardner EM, Burman WJ, DeGroote MA, Hildred G, Pace NR. (2005) Conventional and molecular epidemiology of macrolide resistance among new Mycobacterium avium complex isolates recovered from HIV-infected patients. Clin Infect Dis. 41(7):1041-4.

219. Papineau D, Walker JJ, Mojzsis SJ, Pace NR. (2005) Composition and structure of microbial communities from stromatolites of Hamelin Pool in Shark Bay, Western Australia. Appl Environ Microbiol. 71(8):4822-32.

218. Walker JJ, Spear JR, Pace NR. (2005) Geobiology of a microbial endolithic community in the Yellowstone geothermal environment.Nature. 434(7036):1011-4.

217. St Amand AL, Frank DN, De Groote MA, Pace NR.(2005) Use of specific rRNA oligonucleotide probes for microscopic detection of Mycobacterium avium complex organisms in tissue. J Clin Microbiol. 43(4):1505-14

216. Marquez SM, Harris JK, Kelley ST, Brown JW, Dawson SC, Roberts EC, Pace NR. (2005) Structural implications of novel diversity in eucaryal RNase P RNA. RNA. 11(5):739-51

215. Angenent LT, Kelley ST, St Amand A, Pace NR, Hernandez MT. (2005) Molecular identification of potential pathogens in water and air of a hospital therapy pool. Proc Natl Acad Sci U S A. 102(13):4860-5.

214. De Groote MA, Frank DN, Dowell E, Glode MP, Pace NR. (2005) Lactobacillus rhamnosus GG bacteremia associated with probiotic use in a child with short gut syndrome. Pediatr Infect Dis J. 24(3):278-80.

213. Spear JR, Walker JJ, McCollom TM, Pace NR.(2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc Natl Acad Sci U S A. 102(7):2555-60.


212. Kelley ST, Theisen U, Angenent LT, St Amand A, Pace NR. (2004) Molecular analysis of shower curtain biofilm microbes. Appl Environ Microbiol. 70(7):4187-92
.

211. Harris JK, Kelley ST, Pace NR. (2004) New perspective on uncultured bacterial phylogenetic division OP11. Appl Environ Microbiol. 70(2):845-9.


210. de la Torre JR, Goebel BM, Friedmann EI, Pace NR. (2003) Microbial diversity of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica. Appl Environ Microbiol. 69(7):3858-67.

209. Kazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams PD, Pace NR. (2003) High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci U S A. 100(13):7497-502

208. Spear JR, Ley RE, Berger AB, Pace NR. (2003) Complexity in natural microbial ecosystems: the Guerrero Negro experience. Biol Bull. 204(2):168-73.

207. Harris JK, Kelley ST, Spiegelman GB, Pace NR. (2003) The genetic core of the universal ancestor. Genome Res. 13(3):407-12.


206. Frank DN, Spiegelman GB, Davis W, Wagner E, Lyons E, Pace NR. (2003) Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. J Clin Microbiol. 41(1):295-303.

205. Blank CE, Cady SL, Pace NR. (2002) Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park. Appl Environ Microbiol. 68(10):5123-35.

204. McMahon KD, Dojka MA, Pace NR, Jenkins D, Keasling JD. (2002) Polyphosphate kinase from activated sludge performing enhanced biological phosphorus removal.Appl Environ Microbiol. 68(10):4971-8.


203. DeLong EF, Pace NR. (2001) Environmental diversity of bacteria and archaea.Syst Biol. 50(4):470-8. Review.


202. Krivenko AA, Kazantsev AV, Adamidi C, Harrington DJ, Pace NR. (2002) Expression, purification, crystallization and preliminary diffraction analysis of RNase P protein from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr. 58(Pt 7):1234-6.


201. Dawson SC, Pace NR. (2002) Novel kingdom-level eukaryotic diversity in anoxic environments.Proc Natl Acad Sci U S A. 99(12):8324-9.


200. Kelley ST, Harris JK, Pace NR. (2001) Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities.RNA. 7(9):1310-6.


199. de Souza MP, Amini A, Dojka MA, Pickering IJ, Dawson SC, Pace NR, Terry N. (2001) Identification and characterization of bacteria in a selenium-contaminated hypersaline evaporation pond. Appl Environ Microbiol. 67(9):3785-94.

198. Shukla SK, Vevea DN, Frank DN, Pace NR, Reed KD. (2001) Isolation and characterization of a black-pigmented Corynebacterium sp. from a woman with spontaneous abortion. J Clin Microbiol. 39(3):1109-13.


197. Pace NR. (2001) The universal nature of biochemistry. Proc Natl Acad Sci U S A. 98(3):805-8.


196. Frank DN, Adamidi C, Ehringer MA, Pitulle C, Pace NR. (2000) Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA. RNA. 6(12):1895-904.

195.Dojka MA, Harris JK, Pace NR. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol. 2000 Apr;66(4):1617-21.

194. Tanner MA, Shoskes D, Shahed A, Pace NR. Prevalence of corynebacterial 16S rRNA sequences in patients with bacterial and "nonbacterial" prostatitis. J Clin Microbiol. 1999 Jun;37(6):1863-70.

193. Thomas, B.C., A.V. Kazantsev, J.-L .Chen and N.R. Pace. (2000). Photoaffinity cross-linking and RNA structure analysis. Meth. Enzymol. 318:136-147. PubMed

192. Pace, N.R. (2000). Community interactions: toward a natural history of the microbial world. Environmental Microbiol. 2:7.

191. Dojka, M.A., J.K. Harris and N.R. Pace. (2000) Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl. Environ. Microbiol. 66:1617-1621. PubMed

190. Pace, N.R. (1999). Microbial Diversity and the Biosphere. Pp. 117-129, in "Nature and Human Society: The Quest for a sustainable World," P. Raven (ed), National Academy Press, Washington, D.C.

189. Edwards, K.J., B.M. Goebel, T.M. Rodgers, M.O. Schrenk, T.M. Gihring, M.M. Cardona, B.Hu, M.M. McGuire, R.J. Hamers, and N.R. Pace. (1999). Geomicrobiology of Pyrite Dissolution: Case Study at Iron Mountain, California. Geomicrobiol. J. 16:155-179.

188. Pace, N.R. (1999). Microbial Ecology and Diversity. Am. Soc. Microbiology News 65:328-333.

187. Tanner, M.A., D. Shoshes, A. Shahed, and N.R. Pace. (1999). Prevalence of corynebacterial 16s rRNA sequences in bacerial and "nonbacterial" prostatitis. J. Clin. Microbiol. 37"193-1870.

186. Pace, N.R., B.C. Thomas, and C.R. Woese. (1999). Probing RNA structure, function and history by comparative analysis. In "The RNA World, Second Edition," R.F. Gesteland, T.R. Cech and J.F. Atkins (eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 113-141

185. Pitulle, C, and N.R. Pace. (1999). T-cloning vector for plasmid-based 16s rDNA analysis. biotechniques 26:222-234.

184. Tanner, M.A., J.K. Harris, and N.R. Pace. (1999). Molecular phylogeny of Chlamydia and relatives. In "Chlamydia: Intracellular Biology, Pathenogenesis and Immunity," R.S. Stephens (ed.), American Society for Microbiology, Washington, D.C., pp. 1-8

183. Sandler, S.J., P. Hugenholtz, C. Schleper, E.F. Delong, N.R. Pace, and A.J. Clark. (1999). Diversity of radA genes from cultured and uncultured Archaea: comparative analysis of putative RadA proteins and their use as a phylogenetic marker. J. Bacteriol. 181:907-915.

182. Dojka, M.A., P. Hugenholtz, S.K. Haack, and N.R. Pace. (1998). Microbial diversity in a hydrocarbon and chlorinated solvent-contaminated aquifer undergoing intrinsic bioremediation., Appl. Environ. Microbiol. 64(10):3869-3877.

181. Hugenholtz, P., B.M. Goebel, and N.R. Pace. (1998). Impact of culture-independent studies on the emerging phylogenetic view of microbial diversity. J. Bacteriol. 180:4765-4774.

180. Tanner, M.A., B.M. Goebel, and N.R. Pace. (1998). Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl. Environ. Microbiol. 4(8):3110-3113.

179. Angert, E.R., D.E. Northup, A.-L. Reysenbach, A.S. Peek, B.M. Goebel, and N.R. Pace. (1998). Molecular phylogentic analysis of bacterial community in Sulfur River, Parker Cave, Kentucky. American Minerologist 83(11-12,pt 2):1583-1592.

178. Pitulle, C., M. Garcia-Paris, K.R. Zamudio, and N.R. Pace. (1998). Comparative structure analysis of vertebrate ribonuclease P RNA. Nucleic Acids Res. 26:3333-3339.

177. Kazantsev, A.V., and N.R. Pace. (1998). Identification by modification-interference of purine N-7 and ribose 2'-OH groups critical for catalysis by bacterial ribonuclease P. RNA 4:937-947.

176. Oh, B.-K., D.N. Frank, and N.R. Pace. (1998). Participation of the 3'-CCA of tRNA in the binding of catalytic Mg2+ ions by ribonuclease P. Biochemistry 37(20):7277-7283.

175. Chen, J.-L, J.M. Nolan, M.E. Harris, and N.R. Pace. (1998). Comparative photocross-linking analysis of the tertiary structure of Escherichia coli and Bacillus subtilis RNase P RNAs. EMBO J. 17:1515-1525.

174. Frank, D.N., and N.R. Pace. (1998). Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem. 67:153-180.

173. Hugenholtz, P., C. Pitulle, K.L. Hershberger and N.R. Pace. Novel division-level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366-376.

172. Harris, M.E., D.N. Frank, and N.R. Pace. (1998). Structure and catalytic function of the bacterial ribonuclease P ribozyme. In "RNA Structure and Function," R. Simons, and M. Grunberg-Manago (eds.), Cold Springs Harbor Press, pp. 309-337

171. Northup, D.E., A.-L. Reysenbach and N.R. Pace. (1997). Microorganisms and Speleothems. In "Cave Minerals of the World," C.Hill and P.Forti (eds.), National Speleological Society, Huntsville, Alabana, pp. 261-266.

170. Frank, D.N., and N.R. Pace.(1997). In vitro selection for altered divalent metal specificity in the RNase P RNA. Proc. Natl. Acad. Sci. USA 94:14355-14360

169. Pace, N.R. (1997) A molecular view of microbial diversity and the biosphere. Science 276:734-740.

168. Chen, J.-L. and N.R. Pace. (1997) Identification of the universally conserved core of ribonuclease P RNA. RNA 3:557-560.

167. Harris, M.E., A.V. Kazantsev, J.-L. Chen and N.R. Pace. (1997) Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by photoaffinity crosslinking. RNA 3:561-576.

166. Pace, N.R. (1997). Opening the door onto the natural microbial world: molecular microbial ecology. The Harvey Lectures, Series 91:59-78.

165 Barns,S.M., C.F. Delwich, J.D. Palmer, S.C. Dawson, K.L. Herschberger, and N.R. Pace. (1996). Phylogenetic perspective on microbial life in hydrothermal ecosystems, past and present. In "Evolution of Hydrothermal Ecosystems on Earth (and Mars?)," G.R. Bock, and J.A. Goode (eds.), Wiley Press, Chichester, pp. 24-32

164. Haas, E.S., A.B. Banta, J.K. Harris, N.R. Pace and J.W. Brown. (1996) Structure and evolution of ribonuclease P RNA in Gram-positive Bacteria. Nucleic Acids Res. 24:4790-4798.

163. Hershberger, K.L., Barns, S.M., Reysenbach,A.-L., Dawson,S.C. and Pace,N.R.(1996) Wild diversity of Crenarchaeota. Nature 384:420.

162. Frank, D.N., A.E. Ellington and N.R. Pace. (1996). RNase P RNA in vitro selection reveals catalytic role of Mg2+-binding core helix. RNA 2:1179-1188.

161. Pace, N.R. (1996) New perspective on the natural microbial world: molecular microbial ecology. ASM News 62:463-470.

160. Angert, E.R., A.E. Brooks and N.R. Pace. (1996) Phylogenetic analysis of Metabacterium polyspora: clues to the evolutionary origin of daughter cells in Epulopiscium species, the largest bacteria. J. Bacteriol. 178:1451-1456.

159. Rajan, J., K. Dudekula, R.E. Perkins, S. Sariaslani, S.M. Barns, A.-L. Reysenbach, S. Rehm, M. Ehringer and N.R. Pace. (1996) Mineralization of 2,4,6-trinitrophenol (picric acid): Characterization and phylogenetic identification of microbial strains. J. Industrial Microbiol. 16: 319-324.

158. Hugenholtz, P. and N.R. Pace. (1996) A molecular phylogenetic approach to the natural microbial world: the biotechnological potential. Trends Biotechnol. 14:190-197.

157. Siegel, R.W., A.B. Banta, E.S. Haas, J.W. Brown and N.R. Pace. (1996) RNase P RNA from Mycoplasma fermentans simplifies our view of the catalytic core of the ribozyme. RNA 2:452-462.

156. Barns, S.M., C.F. Delwiche, J.D. Palmer and N.R. Pace. (1996). Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193. (Published data available)

155. Brown, J.W., J.M. Nolan, E.S. Haas, M.A. Rubio, F. Major and N.R. Pace. (1996). Novel tertiary structure in ribonuclease P RNA detected by covariation in natural microbial populations. Proc. Natl. Acad. Sci. USA 93:3001-3006.

154. Harris, M.E. and N.R. Pace (1996). Analysis of the tertiary structure of bacterial RNase P RNA. Mol. Biol. Report 22:115-123.

153. Nolan, J. and N.R. Pace. (1996). Strucural analysis of the bacterial ribonuclease P RNA. Nucl. Acids and Mol. Biol. 10:109-128.

152. Pagan-Ramos, E., A.J. Tranguch, J.M. Nolan, N.R. Pace and D.R. Engelke. (1995) Analysis of conserved positions in nuclear RNase P RNA. Nucl. Acids Symp. Series 33:89-91.

151. Jeanthnon, C., A.-L. Reysenbach, S. Haridon, A. Gambacorta, N.R. Pace, P. Glenat and D. Prieur. (1995) Thermotoga subterranea sp. nov., a new thermophilic bacterium isolated from a continental oil reservoir. Arch. Microbiol. 164:91-97.

150. Harris, M.E. and N.R. Pace. (1995). Three-dimensional positions of phosphates involved in catalysis by the ribozyme RNase P RNA. RNA 1:210-218.

149. Pace, N.R. and J.W. Brown. (1995). Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J. Bacteriol. 177:1919-1928.

148. Reysenbach, A.-L. and N.R. Pace. (1994). Reliable amplification of hyperthermophilic archaeal 16S rRNA genes by the polymerase chain reaction. In, "Archaea - A Laboratory Manual: Thermophiles" (F.T. Robb et al., eds.) Cold Spring Harbor Laboratory Press, pp. 101-105.

147. Brown, J.W., E.S. Haas, D.G. Gilbert and N.R. Pace. (1994). The ribonuclease P database. Nucleic Acids Res. 22:3660-3662.

146. Frank, D.N., M.E. Harris and N.R. Pace. (1994). Remodeling active-site structure in a ribozyme: Rational design of self-cleaving pre-tRNA - ribonuclease P conjugates. Biochemistry 33:10800-10808.

145. Oh, B.-K. and N.R. Pace. (1994). Interaction of the 3'-end of tRNA with ribonuclease P RNA. Nucleic Acids Res. 22: 4087-4094.

144. LaGrandeur, T.E., Huttenhofer, A., Noller, H.F. and N.R. Pace. (1994). Phylogenetic- comparative chemical footprint analysis of the ribonuclease P RNA interaction with tRNA. EMBO J. 13:3945-3952.

143. Harris, M.E., J.M. Nolan, A. Malhotra, J.W. Brown, S.C. Harvey and N.R. Pace. (1994). Use of Photoaffinity crosslinking and molecular modeling to analyze the global architecture of ribonuclease P RNA. EMBO J. 13:3953-3963.

142. Reysenbach, A.-L., G.S. Wickham and N.R. Pace. (1994). Phylogenetic analysis of the hyperthermophilic "pink filament" community in Octopus Spring, Yellowstone National Park. Appl. Environ. Microbiol., 60:2113-2119.

141. Haas, E.S., J.W. Brown, C. Pitulle and N.R. Pace. (1994). Further perspective on the catalytic core and secondary structure of ribonuclease P RNA. Proc. Natl. Acad. Sci. USA 91:2527-2531.

140. Barns, S.M., R.E. Fundyga, M.W. Jeffries and N.R. Pace. (1994). Remarkable archaeal diversity in a Yellowstone Hot Spring Environment. Proc. Natl. Acad. Sci. USA 91:1609-1613.

139. Zito, K., A. Huttenhofer and N. R. Pace. (1993). Lead-catalyzed cleavage of ribonuclease P RNA as a probe for integrity of tertiary structure. Nucleic Acids Res. 21:5916-5920.

138. Pace, N.R., E.R. Angert, E.F. DeLong, T.M. Schmidt and G.S. Wickham. (1993). New perspective on the natural microbial world. In, "Industrial Microorganisms: Basic & Appl. Molec. Genetics" (R.H. Baltz, G. D. Hegeman and P.L. Skatrud, eds), pp. 77-83. American Society for Microbiology Press.

137. LaGrandeur, T., S. Darr, E. Haas and N.R. Pace. (1993). Structure of the ribonuclease P RNA of Sulfolobus acidocaldarius. J. Bacteriol. 175:5043-5948.

136. Erauso, Gaël, A.-L. Reysenbach, B. Crump, F. Partensky, J.A. Baross, V.T. Marteinsson, N.R. Pace and D. Prieur. (1993). Pyrococcus fijiensis sp. nov., a new hyperthermophilic archaeon isolated from a deep sea hydrothermal vent. Arch. Microbiol 160:338-349.

135. Nolan, J.M., D.H. Burke and N.R. Pace. (1993). Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P structure. Science 261:762-765.

134. Woese, C.R. and N.R. Pace. (1993). Probing RNA structure, function and history by comparative analysis. In "The RNA World," R. Gesteland and J. Atkins (eds.), pp. 91-117. Cold Spring Harbor Press.

133. Angert, E.R., K.D. Clements and N.R. Pace. (1993). The largest bacterium. Nature 362:239-241.

132. Brown, J.W., E.S. Haas and N.R. Pace. (1993). Characterization of ribonuclease P RNAs from thermophilic bacteria. Nucleic Acids Res. 21:671-679.

131. Durand, P., A.-L. Ryesenbach, D. Prieur and N.R. Pace. (1993). Isolation and characterization of Thiobacillus hydrothermalis sp. nov., a mesophilic obligately chemolithotrophic bacterium isolated from a deep sea hydrothermal vent in Fiji Basin. Arch. Microbiol. 159:39-44.

130. Waugh, D.S. and N.R. Pace. (1993). Gap-scan deletion analysis of Bacillus subtilis RNase P RNA. FASEB J. 7:188-195.

129. Smith, D. and N.R. Pace. (1993). Multiple magnesium ions in the ribonuclease P reaction mechanism. Biochemistry 32:5273-5281.

128. Reysenbach, A.-L., L.J. Giver, G.S. Wickham and N.R. Pace. (1992). Differential amplification of ribosomal RNA genes by PCR. Appl. Environ. Microbiol. 58:3417-3418.

127. Pace, N.R. (1992). New Horizons for RNA Catalysis. Science 256:1402-1403.

126. Darr, S.C., J. W. Brown and N.R. Pace. (1992). The varieties of ribonuclease P. Trends Biochem. Sci. 17:178-182.

125. Lane, D.J., A.P. Harrison, D. Stahl, B. Pace, S.J. Giovannoni, G.J. Olsen and N.R. Pace. (1992). Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. J. Bacteriol. 174:269-278.

124. Brown, J.W. and N. R. Pace. (1992) Ribonuclease P RNA and protein subunits from bacteria. Nucleic Acids Res. 20:1451-1456.

12. Banta, A.B., E.S. Haas, J.W. Brown and N.R. Pace. (1992). Sequence of the ribonuclease P RNA gene from the cyanobacterium Anacystis nidulans. Nucleic Acids Res. 20:911.

122. Wilmotte, A., S. Turner, Y. Van de Peer and N.R. Pace. (1992). Taxonomical study of marine oscillatorian strains (Cyanophyceae, cyanobacteria) with narrow trichomes. II. Nucleotide sequence analysis of the 16S ribosomal RNA. J. Phycol. 28:828-838.

121. Darr, S.C., K. Zitto, D. Smith and N.R. Pace. (1992). Contributions of phylogenetically variable structural elements to the function of the ribozyme ribonuclease P. Biochemistry 31:328-333.

120. Smith, D., A. Burgin, Elizabeth Haas and N.R. Pace. (1992). Influence of metal ions on the ribonuclease P reaction: Distinguishing catalytic effects from binding. J. Biol. Chem.267:2429-2436.

119. Haas, E.S., D. Morse, J. W. Brown, F.J. Schmidt and N.R. Pace. (1991). Sequence covariation reveals new long-range structure in ribonuclease P RNA. Science 254:853-856.

118. Pace, N.R. (1991). Origin of life--Facing up to the physical setting. Cell 65:531-533.

117. Schmidt, T.M., E.F. DeLong and N.R. Pace. (1991). Analysis of a marine picoplankton community using 16S rRNA gene cloning and sequencing. J. Bacteriol. 173:4371-4378.

116. Brown, J.W., E.S. Haas, B.D. James, D.A Hunt, J. Liu and N.R. Pace. (1991) Phylogenetic analysis of ribonuclease P RNA structure in proteobacteria. J. Bacteriol. 173:3855-3863.

115. Brown, J.W. and N.R. Pace. (1991). Structure and evolution of ribonuclease P RNA. Biochimie 73:689-697.

114. Schmidt, T.M., B. Pace and N.R. Pace. (1991). Detection of DNA contamination in Taq polymerase. BioTechniques 11:176-177.

113. Eden, P.A., T.M. Schmidt, R.P. Blakemore, and N.R. Pace. (1991). Phylogenetic analysis of Aquaspirillum magnetotacticum using PCR-amplified 16S ribosomal RNA-specific DNA. Internat. J. System. Bacteriol. 41:324-325.

112. Pace, N.R. and D.S. Waugh. (1991). The design of a simplified ribonuclease P RNA by phylogenetic comparison. Meth. Enzymol. 203:500-510.

111. Schmidt, T.M., E.F. DeLong and N.R Pace. (1991). Phylogenetic identification of uncultivated microorganisms in natural habitats. In "Rapid Methods and Automation in Microbiology and Immunology," A. Vaheri, R.C. Tilton, A. Balows (eds.). Springer-Verlag, pp. 37-46.

110. Burgin, A. and N.R. Pace. (1990). Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent. EMBO J. 9:4111-4118.

109.   Waugh, D.S. and N.R. Pace. (1990). Complementation of a thermoinducible RNase P RNA (rnpB) gene deletion in Escherichia coli by homologous genes from distantly related eubacteria. J. Bacteriol.172:6316-6322.

108. Brown, J.W., D.A. Hunt, and N.R. Pace. (1990). Nucleotide sequence of the 10Sa RNA gene of the b-purple eubacterium Alcaligenes eutrophus. Nucleic Acids Res. 18:2820.

107.   Darr, S.C., Pace, B., and N.R. Pace. (1990). Characterization of ribonuclease P from the archaebacterium Sulfolobus solfataricus. J. Biol. Chem. 265:12927-12932.

106. Giovannoni, S.J., E.F. DeLong, T.M. Schmidt and N.R. Pace. (1990). Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl. Environ. Microbiol. 56:2572-2575.

105. DeLong, E.F., T.M. Schmidt, and N.R. Pace. (1990). Analysis of single cells and oliogotrophic picoplankton populations using 16S ribosomal RNA sequences. In "Recent Advances in Microbial Ecology," T. Hatori, Y. Ishida, Y. Maruyama, R. Morita, and A. Uchida  (eds.). Japan Scientific Societies Press, pp. 697-701.

104. Pace, N.R. and A.B. Burgin. (1990). Processing and evolution of the ribosomal RNAs. In "The Structure, Function and Evolution of Ribosomes," W. E. Hill, A. Dahlberg, R.A. Garrett, P.B. Moore, D. Schlessinger and J.R. Warner (ed.). Am. Soc. Microbiol., pp. 417- 425.

103. Pace, N.R. and D. Smith. (1990). Ribonuclease P: function and variation. J. Biol. Chem. 265:3587-3590.

102. Burgin, A.B., K. Parodos, D.J. Lane, and N.R. Pace. (1990). The excision of intervening sequences from Salmonella 23S ribosomal RNA. Cell 60: 405-414.

101. Pace, N.R. and B. Pace. (1990). A ribosomal RNA terminal maturase: Ribonuclease M5 from Bacillus subtilis. Meth. Enzymol. 181:366-374.

100. Waugh, D.S., C.J. Green, and N.R. Pace. (1989). The design and catalytic properties of a simplified ribonuclease P RNA. Science 244:1569-1572.

99. DeLong, E.F., G.S. Wickham, and N.R. Pace. (1989). Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363.

98. Pace, N.R., D.K. Smith, G.J. Olsen, and B.D. James. (1989). Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA. Gene 82:65-75.

97. Turner, S., T. Burger-Wiersma, S.J. Giovannoni, L.R. Mur, and N.R. Pace. (1989). The relationship of a prochlorophyte, Prochlorothrix hollandica, to green chloroplasts. Nature 337:380-382.

96. Raff, R.A., K.G. Field, G.J. Olsen, S.J. Giovannoni, D.J. Lane, M.T. Ghiselin, N.R. Pace and E.C. Raff. (1989). Metazoan phylogeny based on analysis of 18S ribosomal RNA. In "The Heirarchy of Life," B. Fernholm, K. Bremer and H. Jörnvall (eds). Elsevier Science Publishers B.V., pp. 247-260.

95. James, B.D., G.J. Olsen, and N.R. Pace. (1989). Phylogenetic comparative analysis of RNA secondary structure. Meth. Enzymol. 180:227-239.

94. Giovannoni, S.J., S. Turner, G.J. Olsen, D.J. Lane, and N.R. Pace. (1988). Evolutionary relationships among cyanobacteria and green chloroplasts. J. Bacteriol. 170:3584-3592.

93. Distel, D.L., D.J. Lane, G.J. Olsen, S.J. Giovannoni, B. Pace, N.R. Pace, D.A. Stahl, and H. Felbeck. (1988). Sulfur-metabolizing bacterial endosymbionts: analysis of phylogeny, specificity and origins by 16S ribosomal RNA sequences. J. Bacteriol. 170:2506-2510.

92. Giovannoni, S.J., E.F. DeLong, G.J. Olsen, and N.R. Pace. (1988). Phylogenetic group-specific nucleic acid probes for identification of single microbial cells. J. Bacteriol. 170:720-726.

91. Turner, S., E.F. DeLong, S.J. Giovannoni, G.J. Olsen, and N.R. Pace. (1988). Phylogenetic analysis of microorganisms and natural populations using ribosomal RNA sequences. In, "Microbial Mats: Ecological Physiology of Benthic Microbial Communities," Y. Cohen and E. Rosenberg (eds.). Am. Soc. Microbiol. pp. 390-401.

90. Reich, C., G.J. Olsen, B. Pace, and N.R. Pace. (1988). The role of the protein moiety of ribonuclease P, a catalytic ribonucleoprotein. Science 239:178-181.

89. James, B.D., G.J. Olsen, J. Liu, and N.R. Pace. (1988). The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell 52:19-26.

88. Karl, D.M., G.T. Taylor, J.A. Novitsky, H.W. Jannasch, C.O. Wirsen, N.R. Pace, D.J. Lane, G.J. Olsen, and S.J. Giovannoni. (1988). A microbiological study of Guaymas Basin high temperature hydrothermal vents. Deep-Sea Research 35:777-791.

87. Field, K.G., G.J. Olsen, D.J. Lane, S.J. Giovannoni, M.T. Ghiselin, E.C. Raff, N.R. Pace, and R.A. Raff. (1988). Molecular phylogeny of the animal kingdom based on 18S ribosomal RNa sequences. Science 239:748-753.

86. Lane, D.J., K.G. Field, G.J. Olsen, and N.R. Pace. (1988). Reverse transcriptase sequencing of rRNA for phylogenetic analysis. Meth. Enzymol. 167:138-144.

85. Pace, N.R., C. Reich, B.D. James, G.J. Olsen, B . Pace, and D.S. Waugh. (1987). Structure and catalytic function in ribonuclease P. Cold Spring Harbor Symp. Quant. Biol. 52:239-248.

84. Romaniuk, P.J., B. Zoltowska, T.J. Trust, D.J. Lane, G.J. Olsen, N.R. Pace and D.J. Stahl. (1987). Campylobacter pylori, the spiral bacterium associated with human gastritis, is not a true Campylobacter sp. J. Bacteriol. 169:2137-2141.

83. Pace, N.R., B.D. James, C. Reich, D.S. Waugh, G.J. Olsen, and T.L. Marsh. (1987). Bacillus subtilis RNase P. In "Molecular Biology of RNA: New Perspectives," M. Inouye and B. Dudock (eds.). Academic Press, pp. 17-36.

82. Stahl, D.A., D.J. Lane, G.J. Olsen, D.J. Heller, T.M. Schmidt, and N.R. Pace. (1987). A phylogenetic analysis of certain sulfide-oxidizing and related morphologically conspicuous bacteria by 5S ribosomal RNA sequences. Internat. J. Syst. Bacteriol. 37:116-122.

81. Woese, C.R., N.R. Pace, and G.J. Olsen. 1986. Are arguments against archaebacteria valid? Nature 320:401-402.

80. Pace, N.R., D.J. Lane, G.J. Olsen, and D.A. Stahl. (1986). Phylogenetic analysis of organisms and populations using ribosomal RNA sequences. Proc. Fourth Internatl. Symp. on Microbial Ecology, pp. 117-122.

79. Pace, N.R., G.J. Olsen, and C.R. Woese. (1986). Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 45:325-326.

78. Reich, C., K. Gardiner, B. Pace, G.J. Olsen, T.L. Marsh and N.R. Pace. (1986). The RNA component of the Bacillus subtilis RNase P: sequence, activity and partial secondary structure. J. Biol. Chem. 261:7888-7893.

77. Leichtling, B.H., H.V. Rickenberg, R.J. Seely, D.E. Fahrney and N.R. Pace. (1986). The occurrence of cyclic AMP in archaebacteria. Biochem. Biophys. Res. Comm. 136:1078-1082.

76. Olsen, G.J., D.J. Lane, S.J. Giovannoni, D.A. Stahl and N.R. Pace. (1986). Microbial ecology and evolution: a ribosomal RNA approach. Ann. Rev. Microbiol. 40:337-365.

75. Waugh, D.S. and N.R. Pace. (1986). Catalysis by RNA. BioEssays 4:56-61.

74. Pace, N.R., D.A. Stahl, D.J. Lane, and G.J. Olsen. (1986). The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microbial Ecol. 9:1-55.

73. Pace, N.R. and T.L. Marsh. (1986). RNA catalysis and the origin of life. Origins of Life 16:97-116.

72. Marsh, T.L., B. Pace, C. Reich, K. Gardiner, and N.R. Pace. (1985). Processing of tRNA precursors by an RNA catalyst from Bacillus subtilis. In "Sequence Specificity in Transcription and Translation," R. Calender and L. Gold (eds.). Alan R. Liss, Inc. pp. 441-450.

71. Olsen, G.J., N.R. Pace, M. Nuell, B.P. Kaine, R. Gupta, and C.R. Woese. (1985). Sequence of the 16S rRNA gene from the thermoacidophilic archaebacterium Sulfolobus solfataricus and its evolutionary implications. J. Mol. Evol. 22:301-307.

70. Lane, D.J., B. Pace, G.J. Olsen, D.A. Stahl, M.L. Sogin, and N.R. Pace. (1985). Rapid determination of 16S ribosomal RNA sequences for phylogentic analyses. Proc. Natl. Acad. Sci. USA 82:6955-6959.

69. Stahl, D.A., D.J. Lane, G.J. Olsen, and N.R. Pace. (1985). Characterization of a Yellowstone hot spring microbial community by 5S ribosomal RNA sequences. Appl. Environ. Microbiol. 49:1379-1384.

68. Marsh, T.L. and N.R. Pace. (1985). RNase P catalysis differs from ribosomal RNA self-splicing. Science 229:79-81.

67. Lane, D.J., D.A. Stahl, G.J. Olsen, D.J. Heller, and N.R. Pace. (1985). A phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 5S ribosomal RNA sequences. J. Bacteriol. 163:75-81.

66. Gardiner, K.J., T.L. Marsh, and N.R. Pace. (1985). Ion dependence of the Bacillus subtilis RNase P reaction. J. Biol. Chem. 260:5415-5419.

65. Pace, N.R., D.A. Stahl, D.J. Lane, and G.J. Olsen. (1985). The analysis of natural microbial populations by ribosomal RNA sequences. Am. Soc. Microbiol. News 51:4-12.

64. Lane, D.J., D.A. Stahl, G.J. Olsen, and N.R. Pace. (1985). Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Proc. Biol. Soc. Wash. 6:389-400.

63. Pace, B., D.A. Stahl, and N.R. Pace. (1984). The catalytic element of a ribosomal RNA-processing complex. J. Biol. Chem. 259:11454-11458.

62. Stahl, D.A., B. Pace, T. Marsh, and N.R. Pace. (1984). The ribonucleoprotein substrate for a ribosomal RNA-processing nuclease. J. Biol. Chem. 259:11448-11453.

61. Stahl, D.A., D.J. Lane, G.J. Olsen, and N.R. Pace. (1984). The analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224:409-411.

60. Zagorska, L., J. Van Duin, H.F. Noller, B. Pace, K.D. Johnson, and N.R. Pace. (1984). The conserved 5S rRNA complement to tRNA is not required for translation of natural mRNA. J. Biol. Chem. 259:2798-2802.

59. Guerrier-Takada, C., K. Gardiner, T. Marsh, N.R. Pace, and S. Altman. (1983). The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849-857.

58. Walker, T.A. and N.R. Pace. (1983). 5.8S ribosomal RNA. Cell 33:320-322.

57. Pace, N.R. (1983). Protein-polynucleotide recognition and the RNA-processing nucleases in prokaryotes. In "Processing of RNA," D. Apirion (ed.), pp. 1-34. CRC Press.

A list of additional publications and abstracts is available upon request