pub

145. "Reconfiguring the Quorum-Sensing Regulator SdiA of Escherichia coli to Control Biofilm Formation via Indole and N-Acylhomoserine Lactones," J. Lee, T. Maeda, S. H. Hong, and T. K. Wood, Appl. Environ. Microbiol., 75: 1703-1716 (2009).

141. "Indole and 7-hydroxyindole diminish Pseudomonas aeruginosa virulence," J. Lee, C. Attila, S. L. G. Cirillo, J. D. Cirillo, and T. K. Wood, Microb. Biotechnol. 2: 75-90 (2009).

137. "Indole cell signaling occurs primarily at low temperatures in Escherichia coli," J. Lee, X.-S. Zhang, M. Hegde, W. E. Bentley, A. Jayaraman, and T. K. Wood, The ISME Journal. 2: 1007-1023 (2008). (featured article)

135. "Bacterial Quorum Sensing: Signals, Circuits, and Implications for Biofilms and Disease," A. Jayaraman and T. K. Wood, Annu. Rev. Biomed. Eng. 10: 145-167 (2008). (top 10 download)

123. "Structure and Function of the E. coli Protein YmgB: a Protein Critical for Biofilm Formation and Acid-resistance," J. Lee, R. Page, R. García-Contreras, J.-M. Palermino, X.-S. Zhang, O. Doshi, T. K. Wood, and W. Peti, J. Mol. Biol., 373: 11-26 (2007). (faculty of 1000)

119. “Differential Effects of Epinephrine, Norepinephrine, and Indole on Escherichia coli O157:H7 Chemotaxis, Colonization, and Gene Expression,” T. Bansal, D. Englert, J. Lee, M. Hegde, T. K. Wood, and A. Jayaraman, Infect. Immun., 75: 4597-4607 (2007).

115. "Indole is an inter-species biofilm signal mediated by SdiA," J. Lee, A. Jayaraman, and T. K. Wood, BMC Microbiology 7: 42 (2007). (highly accessed)

114. "Enterohemorrhagic Escherichia coli Biofilms Are Inhibited by 7-Hydroxyindole and Stimulated by Isatin," J. Lee, T. Bansal, A. Jayaraman, W. E. Bentley, and T. K. Wood, Appl. Environ. Microbiol., 73: 4100-4109 (2007).

62. “Stationary-Phase Quorum-Sensing Signals Affect Autoinducer-2 and Gene Expression in Escherichia Coli,” D. Ren, L. Bedzyk, R. W. Ye, S. Thomas, and T. K. Wood, Appl. Environ. Microbiol. 70: 2038-2043 (2004).

154. "Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli," Y. Kim and T. K. Wood, Biochem. Biophys. Res. Commun. (2009) online.

131. "Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)," X.-S. Zhang, R. Garcia Contreras, and T. K. Wood, The ISME Journal. 2: 615-631 (2008).

130. “Temporal regulation of enterohemorrhagic Escherichia coli virulence mediated by autoinducer-2,” T. Bansal, P. Jesudhasan, S. Pillai, T. K. Wood, and A. Jayaraman, Appl. Microbiol. Biotechnol. 78: 811-819 (2008).

117. “Quorum Sensing in E. coli is Signaled by AI-2/LsrR: Effects on sRNA and Biofilm Architecture,” J. Li, C. Attila, L. Wang, T. K. Wood, J. J. Valdes, and W. E. Bentley J. Bacteriol. 189: 6011-6020 (2007).

112. “Magnetic Nanofactories: Localized Synthesis and Delivery of Quorum-Sensing Signaling Molecule Autoinducer-2 to Bacterial Cell Surfaces," R. Fernandes, C.-H. Tsao, Y. Hashimoto, L. Wang, T. K. Wood, G. F. Payne, and W. E. Bentley, Metabolic Engineering 9: 228–239 (2007). (faculty of 1000)

111. “A Stochastic Model of E. coli AI-2 Quorum Signal Circuit Reveals Alternative Synthesis Pathways," J. Li, L. Wang, Y. Hashimoto, C.-H. Tsao, T. K. Wood, J. J. Valdez, E. Zafiriou, W. E. Bentley, Nature/EMBO Molecular Systems Biolog 2: 67 (2006).

96. "YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K12 Through Autoinducer 2 Transport," M. Herzberg, I. K. Kaye, W. Peti, and T. K. Wood, J. Bacteriol. 188: 587-598 (2006).

94. "Autoinducer 2 Controls Biofilm Formation in Escherichia coli K12 Through a Novel Motility Quorum Sensing Regulator (MqsR, B3022),” A. F. Gonzalez Barrios, R. Zuo, Y. Hashimoto, L. Yang, W. E. Bentley, and T. K. Wood, J. Bacteriol. 188: 305-316 (2006). (faculty of 1000)

150. "Connecting Quorum Sensing, c-di-GMP, Pel Polysaccharide, and Biofilm Formation in Pseudomonas aeruginosa through Tyrosine Phosphatase TpbA (PA3885)," A. Ueda and T. K. Wood, PLoS Pathogens 5: e1000483 (2009). (featured artwork)

149. "The neuroendocrine hormone norepinephrine increases Pseudomonas aeruginosa PA14 virulence through the las quorum-sensing pathway," M. Hegde, T. K. Wood, and A. Jayaraman, Appl. Microbiol. Biotechnol., online (2009).

140. "Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist," A. Ueda, C. Attila, M. Whiteley, and T. K. Wood, Microb. Biotechnol. 2: 62-74 (2009). (Editor’s choice)

128. “PA2663 (PpyR) increases biofilm formation in Pseudomonas aeruginosa PAO1 through the psl operon and stimulates virulence and quorum-sensing phenotypes,” C. Attila, A. Ueda, and T. K. Wood, Appl. Microbiol. Biotechnol. 78: 293-307 (2008).

124. "Pseudomonas aeruginosa PAO1 Virulence Factors and Poplar Tree Response in the Rhizosphere," C. Attila, A. Ueda, S. L. G. Cirillo, J. D. Cirillo, W. Chen, and T. K. Wood, Microb. Biotechnol. 1: 17-29 (2008). (top cited article)

155. "Identification of stress-related proteins in Escherichia coli using the pollutant cis-dichloroethylene," J. Lee, S. R. Hiibel, K. F. Reardon, and T. K. Wood, J. Appl. Microbiol., online (2009).

151. "OmpA influences Escherichia coli biofilm formation by repressing cellulose production through the CpxRA two-component system," Q. Ma, and T. K. Wood, Environ. Microbio l., 11:.2735-2746 (2009).

147. "Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms," X. Wang, Y. Kim, and T. K. Wood, The ISME Journal, 3: 1164-1179 (2009). (featured article)

146. "5-Fluorouracil reduces biofilm formation in Escherichia coli K-12 through global regulator AriR as an antivirulence compound," C. Attila, A. Ueda, and T. K. Wood, Appl. Microbiol. Biotechnol., 82: 525-533 (2009).

144. "Toxin-Antitoxin Systems in Escherichia coli Influence Biofilm Formation Through YjgK (TabA) and Fimbriae," Y. Kim, X. Wang, Q. Ma, X.-S. Zhang, and T. K. Wood, J. Bacteriol. 191: 1258-1267 (2009).

142. "Insights on Escherichia coli biofilm formation and inhibition from whole-transcriptome profiling," T. K. Wood, Environ. Microbiol., 11: 1-15 (2009).

139. "Protein Translation and Cell Death: The Role of Rare tRNAs in Biofilm Formation and in Activating Dormant Phage Killer Genes," R. Garcia-Contreras, X.-S. Zhang, Y. Kim, and T. K. Wood, PLoS ONE 3(6): e2394 (2008).

133. "The R1 Conjugative Plasmid Increases Escherichia coli Biofilm Formation through an Envelope Stress Response," X. Yang, Q. Ma, and T. K. Wood, Appl. Environ. Microbiol. 74: 2690-2699 (2008).

113. "YcfR (BhsA) Influences Escherichia coli Biofilm Formation Through Stress Response and Surface Hydrophobicity," X.-S. Zhang, R. Garcia Contreras, and T. K. Wood, J. Bacteriol. 189: 3051-3062 (2007).

109. "Temporal Gene-Expression in Escherichia coli K-12 Biofilms," J. Domka, J. Lee, T. Bansal, and T. K. Wood, Environ.Microbiol. 9: 332-346 (2007).

92. “Inhibition of Bacillus anthracis Growth and Virulence-Gene Expression by Inhibitors of Quorum-Sensing," M. B. Jones, R. Jani, D. Ren, T. K. Wood, and M. J. Blaser, J. Infect. Dis. 191: 1881-1888 (2005).

89. "Hha, YbaJ, and OmpA Regulate Escherichia coli K12 Biofilm Formation and Conjugation Plasmids Abolish Motility," A. Gonzalez, R. Zuo, D. Ren, and T. K. Wood, Biotechnol. Bioengr. 93: 188-200 (2006).

63. “Differential Gene Expression for Investigation of Escherichia coli Biofilm inhibition by Plant Extract Ursolic Acid," D. Ren, R. Zuo, A. F. Gonzalez Barrios, L. A. Bedzyk, G. R. Eldridge, M. E. Pasmore, and T. K. Wood, Appl. Environ. Microbiol. 71: 4022-4034 (2005). (faculty of 1000)

51. “Gene Expression in Bacillus subtilis Surface Biofilms with and without Sporulation and the Importance of yveR for Biofilm Maintenance,” D. Ren, L. Bedzyk, P. Setlow, R. W. Ye, S. Thomas, and T. K. Wood, Biotechnol. Bioeng. 86: 344-364 (2004).

153. “A Naturally Occurring Brominated Furanone Covalently Modifies and Inactivates LuxS,” T. Zang, B. W. K. Lee, L. M. Cannon, K. A. Ritter, S. Dai, D. Ren, T. K. Wood, and Z. S. Zhou, Bioorganic & Medicinal Chemistry Letters, 19:6200-6204 (2009).

118. “The Natural Furanone (5Z)-4-Bromo-5-(Bromomethylene)-3-Butyl-2(5H)-Furanone Disrupts Quorum Sensing-Regulated Gene Expression in Vibrio Harveyi by Decreasing the DNA-Binding Activity of the Transcriptional Regulator Protein LuxR,” T. Defoirdt, C. M. Miyamoto, T. K. Wood, E. A. Meighen, P. Sorgeloos, W. Verstraete, and P. Bossier, Environ. Microbiol. 9: 2486-2495 (2007).

110. “Interference with the Quorum Sensing Systems in Vibrio harveyi Strain Alters the Growth Rate of Gnotobiotically Cultured Rotifer Brachionus plicatilis,” N. T. N. Tinh, N. D. Linh, T. K. Wood, K. Dierckens, P. Sorgeloos, and P. Bossier, J. Appl. Microbiol. 103: 194-203 (2007).

108. "Quorum Sensing-Disrupting Brominated Furanones Protect the Gnotobiotic Brine Shrimp Artemia franciscana From Pathogenic Vibrio harveyi, Vibrio campbellii and Vibrio parahaemolyticus Isolates," T. Defoirdt, R. Crab, T. K. Wood, P. Sorgeloos, W. Verstraete and P. Bossier, Appl. Environ. Microbiol. 72: 6419-6423 (2006).

61. “Quorum-Sensing Antagonist (5Z)-4-Bromo-5-(Bromomethylene)-3-Butyl-2(5H)-Furanone Influences Siderophore Biosynthesis in Pseudomonas putida and Pseudomonas aeruginosa,” D. Ren, R. Zuo and T. K. Wood, Appl. Microbiol. Biotechnol. 66: 689-695 (2005).

56. “Differential Gene Expression Shows Natural Brominated Furanones Interfere with the Autoinducer-2 Bacterial Signaling System of Escherichia coli,” D. Ren, L. Bedzyk, R. W. Ye, S. Thomas, and T. K. Wood, Biotechnol. Bioeng. 88: 630-642 (2004). (faculty of 1000)

55. “(5Z)-4-Bromo-5-(Bromomethylene)-3-Butyl-2(5H)-Furanone Reduces Corrosion from Desulfotomaculum orientis,” D. Ren and T. K. Wood, Environ. Microbiol. 6: 535-540 (2004).

54. “Differential Gene Expression to Investigate the Effect of (5Z)-4-Bromo-5-(Bromomethylene)-3-Butyl-2(5H)-Furanone on Bacillus subtilis,” D. Ren, L. A. Bedzyk, P. Setlow, D. F. England, S. Kjelleberg, S. M. Thomas, R. W. Ye, and T. K. Wood, Appl. Environ. Microbiol. 70: 4941-4949 (2004).

43. "Inhibition of Biofilm Formation and Swarming of Bacillus subtilis by (5Z)-4-Bromo-5-(Bromomethylene)-3-Butyl-2(5H)-Furanone," D. Ren, J. J. Sims, and T. K. Wood, Lett. in Appl. Microbiol. 34: 293-299 (2002).

39. "Inhibition of Biofilm Formation and Swarming of Escherichia coli by (5Z)-4-Bromo-5-(Bromomethylene)-3-Butyl-2(5H)-Furanone," D. Ren, J. J. Sims, and T. K. Wood, Environ. Microbiol. 3: 731-736 (2001).

152. "Protein Engineering of the Transcriptional Activator FhlA to Enhance Escherichia coli Hydrogen Production," V. Sanchez-Torres, T. Maeda, and T. K. Wood, Appl. Environ. Microbiol., 75: 5639-5646 (2009).

134. "Formate detection by potassium permanganate for enhanced hydrogen production in Escherichia coli," T. Maeda and T. K. Wood, Int. J. Hyd. Ener., 33: 2409-2412 (2008).

132. "Protein engineering of hydrogenase 3 to enhance hydrogen production," T. Maeda, V. Sanchez-Torres, and T. K. Wood, Appl. Microbiol. Biotechnol., 79: 77-86 (2008).

127. "Metabolically engineered bacteria for producing hydrogen via fermentation," G. Vardar-Schara, T. Maeda, and T. K. Wood, Microb. Biotechnol., 1: 107-125 (2008).

126. "Enhanced Hydrogen Production from Glucose by Metabolically Engineered Escherichia coli," T. Maeda, V. Sanchez-Torres, and T. K. Wood, Appl. Microbiol. Biotechnol. 77: 879-890 (2007).

122. "Metabolic Engineering to Enhance Bacterial Hydrogen Production,” T. Maeda, V. Sanchez-Torres, and T. K. Wood, Microb. Biotechnol., 1: 30-39 (2008). (top cited article)

121. "Escherichia coli Hydrogenase 3 is a Reversible Enzyme Possessing Hydrogen Uptake and Synthesis Activities," T. Maeda, V. Sanchez-Torres, and T. K. Wood, Appl. Microbiol. Biotechnol. 76: 1035-1042 (2007).

116. “Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803,” T. Maeda, G. Vardar, W. T. Self, and T. K. Wood, BMC Biotechnology 7:25 (2007).

Evolved Enzymes for Remediation

105. "Protein Engineering of the 4-Methyl-5-Nitrocatechol Monooxygenase from Burkholderia sp. Strain DNT for Enhanced Degradation of Nitroaromatics," T. Leungsakul, G. R. Johnson, and T. K. Wood. Appl. Environ. Microbiol. 72: 3933-3939 (2006).

99. “Oxidation of Aminonitrotoluenes by 2,4-DNT Dioxygenase of Burkholderia sp. strain DNT,” T. Leungsakul, B. G. Keenan, M.-a. Mori, M. D. Morton, J. D. Stuart, B. F. Smets, and T. K. Wood, Biotechnology & Bioengineering 93: 231-237 (2006).

88. "Protein Engineering of the Archetypal Nitroarene Dioxygenase of Ralstonia sp. Strain U2 for Activity on Aminonitrotoluenes and Dinitrotoluenes through Alpha-Subunit Residues Leucine 225, Phenylalanine 350, and Glycine 407," B. G. Keenan, T. Leungsakul, B. F. Smets, M. -a. Mori, D. E. Henderson, and T. K. Wood, J. Bacteriol. 187: 3302-3310 (2005).

80. "Physiological Relevance of Successive Hydroxylations of Toluene by Toluene para-Monooxygenase of Ralstonia pickettii PKO1," A. Fishman, Y. Tao, and T. K. Wood, Biocatal. Biotransformation 22: 283-289 (2004).

77. "Protein Engineering of Toluene-o-Xylene Monooxygenase from Pseudomonas stutzeri OX1 for Enhanced Chlorinated Ethene Degradation and o-Xylene Oxidation," G. Vardar and T. K. Wood, Appl. Microbiol. Biotechnol. 68: 510-517 (2005).

76. "Saturation Mutagenesis of 2,4-DNT Dioxygenase of Burkholderia sp. strain DNT for Enhanced Dinitrotoluene Degradation," T. Leungsakul, B. G. Keenan, H. Yin, B. F. Smets, and T. K. Wood, Biotechnol. Bioeng. 92: 416-426 (2005),

71. "Toluene 3-Monooxygenase of Ralstonia pickettii PKO1 is a para-Hydroxylating Enzyme," A. Fishman, Y. Tao, and T. K. Wood, J. Bacteriol. 186: 3117-3123 (2004).

58. "Saturation Mutagenesis of Toluene ortho-Monooxygenase of Burkholderia cepacia G4 for Enhanced 1-Naphthol Synthesis and Chloroform Degradation," L. Rui, Y.-M. Kwon, A. Fishman, K. F. Reardon, and T. K. Wood, Appl. Environ. Microbiol. 70: 3246-3252 (2004).

44. "Directed Evolution of Toluene ortho-Monooxygenase for Enhanced 1-Naphthol Synthesis and Chlorinated Ethene Degradation," K. A. Canada, S. Iwashita, H. Shim, and T. K. Wood, J. Bacteriol. 184: 344-349 (2002).

Evolved Enzymes for Green Chemistry

148. "Rapid Methods for High-Throughput Detection of Sulfoxides," J. Shainsky, N. L. Derry, Y. Leichtmann, T. K. Wood, and A. Fishman, Appl. Environ. Microbiol., online (2009).

129. "Protein Engineering of Toluene Monooxygenases for Synthesizing Chiral Sulfoxides," R. Feingersch, J. Shainsky, T. K. Wood, and A. Fishman, Appl. Environ. Microbiol. 74: 1555-1566 (2008).

102. "Enantioconvergent Product of (R)-1-phenyl-1,2-Ethanediol From Styrene Oxide by Combining the Solanum tuberosum and an Evolved Agrobacterium radiobactor AD1 Epoxide Hydrolases,” L. Cao, J. Lee, W. Chen, T. K. Wood, Biotechnology & Bioengineering 94: 522-529 (2006).

95. "Alanine 101 and Alanine 101 of the Alpha Subunit of Pseudomonas stutzeri OX1 Toluene-o-Xylene Monooxygenase Influence the Regiospecific Oxidation of Aromatics," G. Vardar, Y. Tao, J. Lee, and T. K. Wood, Biotechnol. Bioengr. 92: 652-658 (2005).

83. "Phenol and 2-Naphthol Production by Toluene 4-Monooxygenases Using an Aqueous/Dioctyl Phthalate system," Y. Tao, W. E. Bentley, and T. K. Wood, Appl. Microbiol. Biotechnol. 68: 614-621 (2005).

82. "α-Subunit Positions Methionine 180 and Glutamate 214 of Pseudomonas stutzeri OX1 Toluene-o-Xylene Monooxygenase Influence Catalysis," G. Vardar and T. K. Wood, J. Bacteriol. 187: 1511-1514 (2005).

81. "Controlling the Regiospecific Oxidation of Aromatics via Active Site Engineering of Toluene para-Monooxygenase of Ralstonia pickettii PKO1," A. Fishman, Y. Tao, L. Rui and T. K. Wood, J. Biol. Chem. 280: 506-514 (2005).

79. "Regiospecific Oxidation of Naphthalene and Fluorene by Toluene Monooxygenase and Engineered Toluene 4-Monooxygenase of Pseudomonas mendocina KR1," Y. Tao, W. E. Bentley, and T. K. Wood, Biotechnol. Bioeng. 90: 85-94 (2005).

78. "Protein Engineering of Epoxide Hydrolase from Agrobacterium radiobacter AD1 for Enhanced Activity and Enantioselective Production of (R)-1-Phenylethane-1,2-Diol," L. Rui, L. Cao, W. Chen, K. F. Reardon, and T. K. Wood, Appl. Environ. Microbiol. 71: 3995-4003 (2005).

73. "Protein Engineering of Toluene-o-Xylene Monooxygenase from Pseudomonas stutzeri OX1 for Oxidizing Nitrobenzene to 3-Nitrocatechol, 4-Nitrocatechol, and Nitrohydroquinone," G. Vardar, K. Ryu, and T. K. Wood, J. Biotechnol. 115: 145-156 (2005).

70. "Protein engineering of Toluene ortho-Monooxygenase of Burkholderia cepacia G4 for Regiospecific Hydroxylation of Indole to Form Various Indigoid Compounds," L. Rui, K. Reardon, and T. K. Wood, Appl. Microbiol Biotechnol. 66: 422-429 (2005).

67. "Saturation Mutagenesis of Burkholderia cepacia R34 2,4-DNT Dioxygenase at DntAc Valine 350 for Synthesizing Nitrohydroquinone, Methylhydroquinone, and Methoxyhydroquinone," B. Keenan, T. Leungsakul, B. Smets, and T. K. Wood, Appl. Environ. Microbiol. 70: 3222-3231 (2004).

66. “Altering Toluene 4-monooxygenase by Active-Site Engineering for the synthesis of 3-Methoxycatechol, Methoxyhydroquinone, and Methylhydroquinone,” Y. Tao, A. Fishman, W. E. Bentley, and T. K. Wood, J. Bacteriol. 186: 4705-4713 (2004).

65. “Protein Engineering of Toluene 4-Monooxygenase of Pseudomonas mendocina KR1 for Synthesizing 4-Nitrocatechol from Nitrobenzene,” A. Fishman, Y. Tao, W. E. Bentley, and T. K. Wood, Biotechnol. Bioeng. 87: 779-790 (2004).

64. "Protein Engineering of Toluene-o-Xylene Monooxygenase from Pseudomonas stutzeri OX1 for Synthesizing 4-Methylresorcinol, Methylhydroquinone, and Pyrogallol," G. Vardar and T. K. Wood, Appl. Environ. Microbiol. 70: 3253-3262 (2004).

52. "Oxidation of Benzene to Phenol, Catechol and 1,2,3-Trihydroxybenzene by Toluene 4-Monooxygenase of Pseudomonas mendocina KR1 and Toluene 3-Monooxygenase of Ralstonia pickettii PKO1," Y. Tao, A. Fishman, W. E. Bentley, and T. K. Wood, Appl. Environ. Microbiol. 70: 3814-3820 (2004).

Metabolic Engineering

107. "Orthric Rieske dioxygenases for degrading mixtures of 2, 4-dinitrotoluene/naphthalene and 2-amino-4, 6-dinitrotoluene/4-amino-2, 6-dinitrotoluene," B. G. Keenan and T. K. Wood. Appl. Microbiol. Biotechnol. 73: 827-838 (2006).

103. "Proteome Changes after Metabolic Engineering to Enhance Aerobic Mineralization of cis-1,2-Dichloroethylene," J. Lee, L. Cao, S. Y. Ow, M. E. Barrios-Llerena, W. Chen, T. K. Wood, and P. C. Wright, J. Proteome Res. 5: 1388-1397 (2006).

75. "Active Site Engineering of the Epoxide Hydrolase from Agrobacterium radiobacter AD1 to Enhance Aerobic Mineralization of cis-1,2-Dichloroethylene in Cells Expressing an Evolved Toluene ortho-Monooxygenase," Lingyun Rui, Li Cao, Wifred Chen, Kenneth F. Reardon, and Thomas K. Wood, J. Biol. Chem. 279: 46810-46817 (2004).

68. “Metabolic Pathway Engineering to Enhance Aerobic Degradation of Chlorinated Ethenes and to Reduce Their Toxicity by Cloning a Novel Glutathione S-Transferase, an Evolved Toluene o-Monooxygenase, and γ-Glutamylcysteine Synthetase,” L. Rui, Y.-M. Kwon, K. F. Reardon, and T. K. Wood, Environ. Microbiol. 6: 491-500 (2004).

49. “Proteomic Changes in Escherichia coli TG1 After Metabolic Engineering for Enhanced Tricholorethylene Biodegradation,” V. A. Pferdeort, T. K. Wood, and K. F. Reardon, Proteomics 3: 1066-1069 (2003).

Rhizoremediation (word coined by Wood group in 1998 in ref. 25)

143. "Molecular approaches in bioremediation," T. K. Wood, Curr. Opin. Biotechnol. 19: 572-578 (2008).

138. "Detection of recombinant Pseudomonas putida in the wheat rhizosphere by fluorescence in situ hybridization targeting mRNA and rRNA," C. H. Wu, Y.-C. Hwang, W. Lee, A. Mulchandani, T. K. Wood, M. V. Yates, and W. Chen, Appl. Microbiol. Biotechnol. 79: 511-518 (2008).

120. "Transport and survival of GFP-tagged root-colonizing microbes: Implications for rhizodegradation." A. W. Gilbertson, M. W. Fitch, J. G. Burken, and T. K. Wood, European Journal of Soil Biology. 43: 224-232 (2007).

106. "Engineering TCE-Degrading Rhizobacteria for Heavy Metal Accumulation and Enhanced TCE Degradation," W. Lee, T. K. Wood, and W. Chen, Biotechnol. Bioengr. 95: 399-403 (2006).

100. "Engineering Plant-Microbe Symbiosis for Rhizoremediation of Heavy Metals," C. H. Wu, T. K. Wood, A. Mulchandani, and W. Chen, Appl. Environ. Microbiol. 72: 1129-1134 (2006).

35. "Rhizosphere Competitiveness of Trichloroethylene-Degrading, Poplar-Colonizing Recombinant Bacteria," H. Shim, S. Chauhan, D. Ryoo, K. Bowers, S. M. Thomas, K. A. Canada, J. G. Burken, and T. K. Wood, Appl. Environ. Microbiol. 66: 4673-4678 (2000).

25. "Rhizoremediation of Trichloroethylene by a Recombinant, Root-Colonizing Pseudomonas fluorescens Strain Expressing Toluene ortho-Monooxygenase Constitutively," D. C. Yee, J. A. Maynard, and T. K. Wood, Appl. Environ. Microbiol. 64: 112-118 (1998).

Inhibition of Biocorrosion via Beneficial Biofilms

91. “Aluminum- and Mild Steel-Binding Peptides from Phage Display,” R. Zuo, D. Örnek, and T. K. Wood, Appl. Microbiol. Biotechnol. 68: 505-509 (2005).

60. “Inhibiting Mild Steel Corrosion From Sulfate-Reducing and Iron-Oxidizing Bacteria Using Gramicidin-S-Producing Biofilms,” R. Zuo and T. K. Wood, Appl. Microbiol. Biotechnol. 65:747-753 (2004).

57. “The Importance of Live Biofilms in Corrosion Protection,” R. Zuo, E. Kus, F. Mansfield, and T. K. Wood, Corros. Sci. 47: 279-287 (2005).

53. “Inhibiting Mild Steel Corrosion from Sulfate-Reducing Bacteria Using Antimicrobial-Producing Biofilms in Three-Mile-Island Process Water,” R. Zuo, D. Ornek, B. C. Syrett, R. M. Green, C.-H. Hsu, F. B. Mansfeld, and T. K. Wood, Appl. Microbiol. Biotechnol. 64: 275-283 (2004).

48. "Corrosion Control of Mild Steel by Aerobic Bacteria Under Continuous Flow Conditions," K. M. Ismail, T. Gehrig, A. Jayaraman, T. K. Wood, K. Trandem, P. J. Arps, and J. C. Earthman, Corrosion 58: 417-423 (2002).

47. "Corrosion Control Using Regenerative Biofilms on Aluminum 2024 and Brass in Different Media," F. Mansfeld, H. Hsu, D. Ornek, T. K. Wood, and B. C. Syrett, Journal of the Electrochemical Society 149: B130-138 (2002).

46. "Pitting Corrosion Inhibition of Aluminum 2024 by Bacillus Biofilms Secreting Polyaspartate or γ-Polyglutamate," D. Ornek, A. Jayaraman, C.-H. Hsu, F. B. Mansfeld, and T. K. Wood, Appl. Microbiol. Biotechnol. 58: 651-657 (2002).

42. "Corrosion Control Using Regenerative Biofilms (CCURB) on Brass in Different Media," D. Ornek, T. K. Wood, C. H. Hsu, and F. Mansfeld, Corros. Sci. 44: 2291-2302 (2002).

41. "Ennoblement - A Common Phenomenon?" F. Mansfeld, C. H. Hsu, Z. Sun, D. Ornek, and T. K. Wood, Corrosion 58: 187-191 (2002).

40. "Pitting Corrosion Control Using of Aluminum 2024 Using Protective Biofilms That Secrete Corrosion Inhibitors," D. Ornek, T. K. Wood, C. H. Hsu, Z. Sun, and F. Mansfeld, Corrosion 58: 761-767 (2002).

38. "Pitting Corrosion Control Using Regenerative Biofilms on Aluminum 2024 in Artificial Seawater," D. Ornek, A. Jayaraman, Z. Sun, C. H. Hsu, T. K. Wood, and F. Mansfeld, Corros. Sci. 43: 2121-2133 (2001).

32. "The Influence of Bacteria on the Passive Film Stability of 304 Stainless Steel," K. M. Ismail, A. Jayaraman, T. K. Wood, and J. C. Earthman, Electrochimica Acta 44: 4685-4692 (1999).

30. "Axenic Aerobic Biofilms Inhibit Corrosion of Copper and Aluminum," A. Jayaraman, D. Ornek, D. A. Duarte, C.-C. Lee, F. B. Mansfeld, and T. K. Wood, Appl. Microbiol. Biotechnol. 52: 787-790 (1999).

29. "Inhibiting Sulfate-Reducing Bacteria in Biofilms by Expressing the Antimicrobial Peptides Indolicidin and Bactenecin," A. Jayaraman, F. B. Mansfeld, and T. K. Wood, J. Ind. Microbiol. Biotechnol. 22:167-175 (1999).

28. "Inhibiting Sulfate-Reducing Bacteria in Biofilms on Steel with Antimicrobial Peptides Generated in situ," A. Jayaraman, P. J. Hallock, R. M. Carson, C.-C. Lee, F. B. Mansfeld, and T. K. Wood, Appl. Microbiol. Biotechnol. 52: 267-275 (1999).

23. "Characterization of Axenic Pseudomonas fragi. and Escherichia. coli Biofilms That Inhibit Corrosion of SAE 1018 Steel," A. Jayaraman, A. K. Sun, and T. K. Wood, J. Appl. Microbiol. 84: 485-492 (1998).

21. "Axenic Aerobic Biofilms Inhibit Corrosion of SAE 1018 Steel Through Oxygen Depletion," A. Jayaraman, E. T. Cheng, J. C. Earthman, and T. K. Wood, Appl. Microbiol. Biotechnol. 48: 11-17 (1997).

20. "Importance of Biofilm Formation for Corrosion Inhibition of SAE 1018 Steel by Axenic Aerobic Biofilms," A. Jayaraman, E. T. Cheng, J. C. Earthman, and T. K. Wood, J. Ind. Microbiol. 18: 396-401 (1997).

15. "Corrosion Inhibition by Aerobic Biofilms on SAE1018 Steel," A. Jayaraman, J. C. Earthman, and T. K. Wood, Appl. Microbiol. Biotechnol. 47: 62-68 (1997).

Bioremediation

125. "An Inducible Propane Monooxygenase is Responsible for N-Nitrosodimethylamine Degradation by Rhodococcus sp. RHA1," J. O. Sharp, C. M. Sales, J. C. LeBlanc, J. Liu, T. K. Wood, L. D. Eltis, W. W. Mohn, and L. Alvarez-Cohen, Appl. Environ. Microbiol. 73: 6930-6938 (2007).

104. "Genotypic Characterization and Phylogenetic Relations of Pseudomonas sp. (Formerly P. stutzeri) OX1," F. Radice, V. Orlandi, V. Massa, L. Cavalca, A. Demarta, T. K. Wood, and P. Barbieri, Curr Microbiol. 52: 395-399 (2006).

101. “Reductive Transformation of TNT by Escherichia coli Resting Cells: Kinetic Analysis,” H. Yin, T. K. Wood, and B. F. Smets, Appl. Microbiol. Biotechnol. 69: 326-334 (2005).

85. "Aerobic Biodegradation of N-Nitrosodimethylamine" (NDMA) by Axenic Bacterial Strains," J. O. Sharp, T. K. Wood, and L. Alvarez-Cohen, Biotechnol. Bioengr. 89: 608-618 (2005).

84. "TNT and Nitroaromatic Compounds are Chemoattractants for Burkholderia cepacia R34 and Burkholderia sp. strain DNT," T. Leungsakul, B.G. Keenan, B. F. Smets, and T. K. Wood, Appl. Microbiol. Biotechnol. 69: 321-325 (2005).

74. "Reductive Transformation of TNT by Escherichia coli: Pathway Description, " H. Yin, T. K. Wood, B. F. Smets, Appl. Microbiol. Biotechnol. 67: 397-404 (2005).

59. “Chemotaxis of Pseudomonas stutzeri OX1 and Burkholderia cepacia G4 Toward Chlorinated Ethenes,” G. Vardar, P. Barbieri, and T. K. Wood, Appl. Microbiol. Biotechnol. 66: 696-701 (2005).

50. “Mesophilic Aerobic Degradation of a Metal Lubricant by a Biological Consortium,” S. Iwashita, T. P. Callahan, J. Haydu, and T. K. Wood, Appl. Microbiol. Biotechnol. 65: 620-626 (2004).

37. "Aerobic Degradation of Mixtures of Tetrachloroethylene, Trichloroethylene, Dichloroethtylenes, and Vinyl Chloride by Toluene-o-Xylene Monooxygenase of Pseudomonas stutzeri OX1," H. Shim, D. Ryoo, P. Barbieri, and T. K. Wood, Appl. Microbiol. Biotechnol. 56: 265-269 (2001).

36. "Tetrachloroethylene, Trichloroethylene, and chlorinated phenols induce toluene-o-xylene monooxygenase activity in Pseudomonas stutzeri OX1," D. Ryoo, H. Shim, F. L. G. Arenghi, P. Barbieri, and T. K. Wood, Appl. Microbiol. Biotechnol. 56: 545-549 (2001).

34. "Aerobic Degradation of Tetrachloroethylene by Toluene-o-Xylene Monooxygenase of Pseudomonas stutzeri OX1," D. Ryoo, H. Shim, P. Barbieri, and T. K. Wood, Nature Biotechnology 18: 775-778 (2000).

33. "Aerobic Degradation of Mixtures of Chlorinated Aliphatics by Cloned Toluene-o-Xylene-Monooxygenase and Toluene o-Monooxygenase in Resting Cells," H. Shim and T. K. Wood, Biotechnol. Bioeng. 70: 693-698 (2000).

31. "Degradation of 2,4,5-Trichlorophenol and 2,3,5,6-Tetrachlorophenol by Combining Pulse Electric Discharge with Bioremediation," S. Chauhan, E. Yankelevich, V. M. Bystritskii, and T. K. Wood, Appl. Microbiol. Biotechnol. 52: 261-266 (1999).

27. "Oxidation of Trichloroethylene, 1,1,-Dichloroethylene, and Chloroform by Toluene/o-Xylene-Monooxygenase from Pseudomonas stutzeri OX1," S. Chauhan, P. Barbieri, and T. K. Wood, Appl. Environ. Microbiol. 64: 3023-3024 (1998).

26. "Degradation of Perchloroethylene and Dichlorophenol by Pulsed-Electric Discharge and Bioremediation," D. C. Yee, S. Chauhan, E. Yankelevich, V. Bystritskii, and T. K. Wood, Biotechnol. Bioeng. 59: 438-444 (1998).

24. "Modeling Trichloroethylene Degradation by a Recombinant Pseudomonad Expressing Toluene ortho-Monooxygenase in a Fixed-Film Bioreactor," A. K. Sun, J. Hong, and T. K. Wood, Biotechnol. Bioeng. 59: 40-51 (1998).

17. "Trichloroethylene Mineralization in a Fixed-Film Bioreactor Using a Pure Culture Expressing Constitutively Toluene ortho-Monooxygenase," A. K. Sun and T. K. Wood, Biotechnol. Bioeng. 55: 674-685 (1997).

16. "2,4-Dichlorophenol Degradation Using Streptomyces viridosporus T7A Lignin Peroxidase," D. C. Yee and T. K. Wood, Biotechnol. Prog. 13: 53-59 (1997).

13. "Enhanced Expression and Hydrogen Peroxide Dependence of Lignin Peroxidase from Streptomyces viridosporus T7A", D. C. Yee, D. Jahng, and T. K. Wood, Biotechnol. Prog. 12: 40-46 (1996).

12. "Elicitation of Lignin Peroxidase in Streptomyces lividans," D. C. Yee and T. K. Wood, Applied Biochemistry & Biotechnology 60: 137-147 (1996).

11. "Trichloroethylene Degradation and Mineralization by Pseudomonads and Methylosinus trichosporium OB3b," A. K. Sun and T. K. Wood, Appl. Microbiol. Biotechnol. 45: 248-256 (1996).

10. "Optimization of Trichloroethylene Degradation Using Soluble Methane Monooxygenase of Methylosinus trichosporium OB3b Expressed in Recombinant Bacteria," D. Jahng, C. S. Kim, R. S. Hanson, and T. K. Wood, Biotechnol. Bioeng. 51: 349-359 (1996).

9. "Metal Ions and Chloramphenicol Inhibition of Soluble Methane Monooxygenase from Methylosinus trichosporium OB3b," D. Jahng and T. K. Wood, Appl. Microbiol. Biotechnol. 45: 744-749 (1996).

8. "Monitoring Trichloroethylene Mineralization by Pseudomonas cepacia G4 PR1," P. P. Luu, C. W. Yung, A. K. Sun, and T. K. Wood, Appl. Microbiol. & Biotechnol. 44: 259-264 (1995).

7. "Trichloroethylene and Chloroform Degradation by a Recombinant Pseudomonad Expressing Soluble Methane Monooxygenase from Methylosinus trichosporium OB3b," D. Jahng and T. K. Wood, Appl. Environ. Microbiol. 60: 2473-2482 (1994).

Plasmid Stability via Hok/Sok & Recombinant Protein Expression

45. "Antimicrobial Properties of the Escherichia coli R1 Plasmid Host Killing Peptide," D. C. Pecota, G. Osapay, M. E. Selsted, and T. K. Wood, J. Biotechnol. 100: 1-12 (2003).

18. "Combining the hok/sok, parDE, and pnd Post Segregational Killer Loci To Enhance Plasmid Stability," D. C. Pecota, C. S. Kim, K. Wu, K. Gerdes, and T. K. Wood, Appl. Environ Microbiol. 63: 1917-1924 (1997).

14. "Exclusion of T4 Phage by the hok/sok Locus of Plasmid R1," D. C. Pecota and T. K. Wood, J. Bacteriol. 178: 2044-2050 (1996).

6. "Temperature and Growth Rate Effects on the hok/sok Killer Locus for Enhanced Plasmid Stability," K. Wu, D. Jahng, and T. K. Wood, Biotechnol. Prog. 10: 621-629 (1994).

5. "Evaluation of the hok/sok Killer Locus for Enhanced Plasmid Stability," K. Wu and T. K. Wood, Biotechnol. Bioeng. 44: 912-921 (1994).

4. "Construction of a Specialized-Ribosome Vector for Cloned-Gene Expression in E. coli," T. K. Wood and S. W. Peretti, Biotechnol. Bioeng. 38: 891-906 (1991).

3. "Effect of Chemically-Induced, Cloned-Gene Expression on Protein Synthesis in E. coli," T. K. Wood and S. W. Peretti, Biotechnol. Bioeng. 38: 397-412 (1991).

2. "Enhanced Plasmid Stability Through Post-Segregational Killing of Plasmid-Free Cells," T. K. Wood, R. H. Kuhn, and S. W. Peretti, Biotechnology Techniques 4: 39-44 (1990).

1. "Depression of Protein Synthetic Capacity Due to Cloned-Gene Expression in E. coli," T. K. Wood and S. W. Peretti, Biotechnol. Bioeng. 36: 865-878 (1990).

Miscellany

22. "Electroporation of Pink-Pigmented Methylotrophic Bacteria," C. Kim and T. K. Wood, Appl. Biochem. Biotechnol. 73(#2/3): 81-88 (1998).

19. "Creating Auxotrophic Mutants in Methylophilus methylotrophus AS1 by Combining Electroporation and Chemical Mutagenesis," C. S. Kim and T. K. Wood, Appl. Microbiol. Biotechnol. 48: 105-108 (1997).

Editorials, Book Chapters, Peer-Reviewed Proceedings, & Technical Reports

11. “Controlling Regiospecific Oxidation of Aromatics and the Degradation of Chlorinated Aliphatics via Active Site Engineering of Toluene Monooxygenases,” A. Fishman, Y. Tao, G. Vardar, L. Rui, and T. K. Wood, Pseudomonas 4: Molecular Biology of Emerging Issues (2006).

10. “Field Evaluation of Corrosion Control Using Regenerative Biofilms (CCURB),” P. J. Arps, L.-C. Xu, T, K. Wood, F. Mansfeld, B. C. Syrett, and J. C. Earthman, NACE International Annual Conference, CORROSION/2003, San Diego, CA, March 16, 2003.

9. “Active Expression of Soluble Methane Monooxygenase from Methylosinus trichosporium OB3b in Heterologous Hosts,” T. K. Wood, Microbiology 148: 2-3, (2002) (reviewed editorial).

8. “Biofilms that Prevent Corrosion,” Barry C. Syrett, Peggy J. Arps, James C. Earthman, Florian Mansfeld, Thomas K. Wood, NACE Research Topical Symposium, Denver, CO, March 21, 2002.

7. “Consequences of Metabolic Engineering for Enhanced Trichloroethylene Biodegradation: A Proteomic Analysis,” V. A. Pferdeort, K. F. Reardon, X. Liu, and T. K. Wood. Topical Conference Proceedings of the 2002 Bioinformatics and Genomics Symposium and the 2001 Annual Meeting of the American Electrophoresis Society, 129-130 (2001).

6. “Corrosion Control Using Regenerative Biofilms (CCURB) on Aluminum 2024 and Brass in Different Media,” The Electrochemical Society Proceedings, vol. 2000-24, 99 (2001).

5. "Corrosion Control Using Regenerative Biofilms (CCURB) Laboratory Phase 2," D. Ornek and T. K. Wood, Electric Power Research Institute Report #L-1001421 (2001).

4. "Corrosion Control Using Regenerative Biofilms (CCURB) That Secrete Antimicrobials and Corrosion Inhibitors," D. Ornek and T. K. Wood, Electric Power Research Institute Report #TR-114824 (2000).

3. "Corrosion Prevention by Regenerative Biofilms," J. Earthman and T. Wood, Electric Power Research Institute Report #TR-110734 (1998).

2. "Application of Streamer Discharge for Polluted Water Cleanup," V. M. Bystritskii, Y. Yankelevich, F. Wessel, A. Gonzales, T. Olson, T. K. Wood, D. Yee, V. Puchkarev, and L. Rosocha, Environmental Applications of Ionizing Radiation (1997).

1. "Trichloroethylene Degradation Using Recombinant Bacteria Expressing Soluble Methane Monooxygenase from Methylosinus trichosporium OB3b," D. Jahng, A. K. Sun, C. S. Kim, and T. K. Wood, Molecular Biology of Pseudomonads, 280-288 (1996).

Patents

4. "Inhibition of the Bacillus Anthracis AI-2 Quorum-Sensing Molecule to Treat Bacillus Anthracis Infection" M. Blaser, M. Jones, T. K. Wood, and D. Ren, filed 11 April 2003.

3. "Reduction in Mild Steel and Brass Corrosion Using Beneficial Biofilms," T. K. Wood, D. Ornek, and F. B. Mansfeld, patent application filed 1 October 2000.

2. "Preventing Pitting Corrosion with Beneficial Biofilms," T. K. Wood, D. Ornek, and F. B. Mansfeld, patent application filed 9 May 2000.

1. U.S. patent no. 6,630,197 “Inhibition of Sulfate-Reducing-Bacteria-Mediated Degradation Using Bacteria Which Secrete Antimicrobials,” inventors: T. K. Wood, A. Jayaraman, and J. C. Earthman, patent application filed 6 May 1998, issued 7 October 2003 (also New Zealand patent 502111, 14 June 2001).