TY - JOUR AU - Johnson, J. M. AU - Coleman, M. D. AU - Gesch, R. AU - Jaradat, A. AU - Mitchell, R. AU - Reicosky, D. AU - Wilhelm, W. W. PY - 2007 DA - 2007// TI - Biomass, bioenergy crops in the United States: a changing paradigm JO - Am J Plant Sci Biotechnol VL - 1 ID - Johnson2007 ER - TY - JOUR AU - Hoffert, M. I. AU - Caldeira, K. AU - Benford, G. AU - Criswell, D. R. AU - Green, C. AU - Herzog, H. PY - 2002 DA - 2002// TI - Advanced technology paths to global climate stability: energy for a greenhouse planet JO - Science VL - 298 UR - https://doi.org/10.1126/science.1072357 DO - 10.1126/science.1072357 ID - Hoffert2002 ER - TY - JOUR AU - Moe, S. T. AU - Janga, K. K. AU - Hertzberg, T. AU - Hägg, M. B. AU - Øyaas, K. AU - Dyrset, N. PY - 2012 DA - 2012// TI - Saccharification of lignocellulosic biomass for biofuel and biorefinery applications A renaissance for the concentrated acid hydrolysis? JO - Energy Procedia. VL - 20 UR - https://doi.org/10.1016/j.egypro.2012.03.007 DO - 10.1016/j.egypro.2012.03.007 ID - Moe2012 ER - TY - JOUR AU - Jönsson, L. J. AU - Martín, C. PY - 2016 DA - 2016// TI - Pretreatment of lignocellulose: formation of inhibitory by-products and strategies for minimizing their effects JO - Bioresour Technol VL - 199 UR - https://doi.org/10.1016/j.biortech.2015.10.009 DO - 10.1016/j.biortech.2015.10.009 ID - Jönsson2016 ER - TY - STD TI - Sun N, Liu H, Sathitsuksanoh N, Stavila V, Sawant M, Bonito A, et al. Production and extraction of sugars from switchgrass hydrolyzed in ionic liquids. Biotechnol Biofuels. 2013;6:39. http://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/1754-6834-6-39. Accessed 13 Oct 2017. UR - http://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/1754-6834-6-39 ID - ref5 ER - TY - JOUR AU - Li, C. AU - Tanjore, D. AU - He, W. AU - Wong, J. AU - Gardner, J. L. AU - Sale, K. L. PY - 2013 DA - 2013// TI - Scale-up and evaluation of high solid ionic liquid pretreatment and enzymatic hydrolysis of switchgrass JO - Biotechnol Biofuels. VL - 6 UR - https://doi.org/10.1186/1754-6834-6-154 DO - 10.1186/1754-6834-6-154 ID - Li2013 ER - TY - JOUR AU - Li, C. AU - Knierim, B. AU - Manisseri, C. AU - Arora, R. AU - Scheller, H. V. AU - Auer, M. PY - 2010 DA - 2010// TI - Comparison of dilute acid and ionic liquid pretreatment of switchgrass: biomass recalcitrance, delignification and enzymatic saccharification JO - Bioresour Technol. VL - 101 UR - https://doi.org/10.1016/j.biortech.2009.10.066 DO - 10.1016/j.biortech.2009.10.066 ID - Li2010 ER - TY - JOUR AU - Ruegg, T. L. AU - Kim, E. -. M. AU - Simmons, B. A. AU - Keasling, J. D. AU - Singer, S. W. AU - Lee, T. S. PY - 2014 DA - 2014// TI - An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production JO - Nat Commun. VL - 5 UR - https://doi.org/10.1038/ncomms4490 DO - 10.1038/ncomms4490 ID - Ruegg2014 ER - TY - JOUR AU - Frederix, M. AU - Hütter, K. AU - Leu, J. AU - Batth, T. S. AU - Turner, W. J. AU - Rüegg, T. L. PY - 2014 DA - 2014// TI - Development of a native Escherichia coli induction system for ionic liquid tolerance JO - PLoS ONE VL - 9 UR - https://doi.org/10.1371/journal.pone.0101115 DO - 10.1371/journal.pone.0101115 ID - Frederix2014 ER - TY - JOUR AU - Reddy, A. P. AU - Simmons, C. W. AU - Claypool, J. AU - Jabusch, L. AU - Burd, H. AU - Hadi, M. Z. PY - 2012 DA - 2012// TI - Thermophilic enrichment of microbial communities in the presence of the ionic liquid 1-ethyl-3-methylimidazolium acetate JO - J Appl Microbiol VL - 113 UR - https://doi.org/10.1111/jam.12002 DO - 10.1111/jam.12002 ID - Reddy2012 ER - TY - JOUR AU - Qin, D. AU - Hu, Y. AU - Cheng, J. AU - Wang, N. AU - Li, S. AU - Wang, D. PY - 2016 DA - 2016// TI - An auto-inducible Escherichia coli strain obtained by adaptive laboratory evolution for fatty acid synthesis from ionic liquid-treated bamboo hydrolysate JO - Bioresour Technol. VL - 221 UR - https://doi.org/10.1016/j.biortech.2016.09.024 DO - 10.1016/j.biortech.2016.09.024 ID - Qin2016 ER - TY - JOUR AU - Frederix, M. AU - Mingardon, F. AU - Hu, M. AU - Sun, N. AU - Pray, T. AU - Singh, S. PY - 2016 DA - 2016// TI - Development of an E. coli strain for one-pot biofuel production from ionic liquid pretreated cellulose and switchgrass JO - Green Chem. VL - 18 UR - https://doi.org/10.1039/C6GC00642F DO - 10.1039/C6GC00642F ID - Frederix2016 ER - TY - JOUR AU - LaCroix, R. A. AU - Palsson, B. O. AU - Feist, A. M. PY - 2017 DA - 2017// TI - A model for designing adaptive laboratory evolution experiments JO - Appl Environ Microbiol. VL - 83 UR - https://doi.org/10.1128/AEM.03115-16 DO - 10.1128/AEM.03115-16 ID - LaCroix2017 ER - TY - JOUR AU - Deatherage, D. E. AU - Barrick, J. E. PY - 2014 DA - 2014// TI - Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq JO - Methods Mol Biol. VL - 1151 UR - https://doi.org/10.1007/978-1-4939-0554-6_12 DO - 10.1007/978-1-4939-0554-6_12 ID - Deatherage2014 ER - TY - JOUR AU - Baeshen, M. N. AU - Al-Hejin, A. M. AU - Bora, R. S. AU - Ahmed, M. M. M. AU - Ramadan, H. A. I. AU - Saini, K. S. PY - 2015 DA - 2015// TI - Production of biopharmaceuticals in E. Coli: current scenario and future perspectives JO - J Microbiol Biotechnol VL - 25 UR - https://doi.org/10.4014/jmb.1412.12079 DO - 10.4014/jmb.1412.12079 ID - Baeshen2015 ER - TY - JOUR AU - Monk, J. M. AU - Koza, A. AU - Campodonico, M. A. AU - Machado, D. AU - Seoane, J. M. AU - Palsson, B. O. PY - 2016 DA - 2016// TI - Multi-omics quantification of species variation of Escherichia coli links molecular features with strain phenotypes JO - Cell Syst. VL - 3 ID - Monk2016 ER - TY - JOUR AU - LaCroix, R. A. AU - Sandberg, T. E. AU - O’Brien, E. J. AU - Utrilla, J. AU - Ebrahim, A. AU - Guzman, G. I. PY - 2015 DA - 2015// TI - Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium JO - Appl Environ Microbiol. VL - 81 UR - https://doi.org/10.1128/AEM.02246-14 DO - 10.1128/AEM.02246-14 ID - LaCroix2015 ER - TY - JOUR AU - Lan, W. AU - Liu, C. F. AU - Sun, R. C. PY - 2011 DA - 2011// TI - Fractionation of bagasse into cellulose, hemicelluloses, and lignin with ionic liquid treatment followed by alkaline extraction JO - J Agric Food Chem. VL - 59 UR - https://doi.org/10.1021/jf201508g DO - 10.1021/jf201508g ID - Lan2011 ER - TY - JOUR AU - Lee, S. H. AU - Doherty, T. V. AU - Linhardt, R. J. AU - Dordick, J. S. PY - 2009 DA - 2009// TI - Ionic liquid-mediated selective extraction of lignin from wood leading to enhanced enzymatic cellulose hydrolysis JO - Biotechnol Bioeng. VL - 102 UR - https://doi.org/10.1002/bit.22179 DO - 10.1002/bit.22179 ID - Lee2009 ER - TY - JOUR AU - Lee, D. H. AU - Feist, A. M. AU - Barrett, C. L. AU - Palsson, B. PY - 2011 DA - 2011// TI - Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli JO - PLoS ONE. VL - 6 UR - https://doi.org/10.1371/journal.pone.0026172 DO - 10.1371/journal.pone.0026172 ID - Lee2011 ER - TY - JOUR AU - Lin, J. J. AU - Sancar, A. PY - 1989 DA - 1989// TI - A new mechanism for repairing oxidative damage to DNA: (A)BC excinuclease removes AP sites and thymine glycols from DNA JO - Biochemistry. VL - 28 UR - https://doi.org/10.1021/bi00446a002 DO - 10.1021/bi00446a002 ID - Lin1989 ER - TY - JOUR AU - Horst, J. P. AU - Wu, T. H. AU - Marinus, M. G. PY - 1999 DA - 1999// TI - Escherichia coli mutator genes JO - Trends Microbiol VL - 7 UR - https://doi.org/10.1016/S0966-842X(98)01424-3 DO - 10.1016/S0966-842X(98)01424-3 ID - Horst1999 ER - TY - STD TI - Minty JJ, Lesnefsky AA, Lin F, Chen Y, Zaroff TA, Veloso AB, et al. Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli. Microb Cell Fact. 2011;10:18. http://microbialcellfactories.biomedcentral.com/articles/10.1186/1475-2859-10-18. Accessed 22 Sept 2016. UR - http://microbialcellfactories.biomedcentral.com/articles/10.1186/1475-2859-10-18 ID - ref23 ER - TY - JOUR AU - Higashi, K. AU - Ishigure, H. AU - Demizu, R. AU - Uemura, T. AU - Nishino, K. AU - Yamaguchi, A. PY - 2008 DA - 2008// TI - Identification of a spermidine excretion protein complex (MdtJI) in Escherichia coli JO - J Bacteriol VL - 190 UR - https://doi.org/10.1128/JB.01505-07 DO - 10.1128/JB.01505-07 ID - Higashi2008 ER - TY - JOUR AU - Clarke, D. M. AU - Loo, T. W. AU - Gillam, S. AU - Bragg, P. D. PY - 1986 DA - 1986// TI - Nucleotide sequence of the pntA and pntB genes encoding the pyridine nucleotide transhydrogenase of Escherichia coli JO - Eur J Biochem. VL - 158 UR - https://doi.org/10.1111/j.1432-1033.1986.tb09802.x DO - 10.1111/j.1432-1033.1986.tb09802.x ID - Clarke1986 ER - TY - JOUR AU - Haverkorn van Rijsewijk, B. R. B. AU - Kochanowski, K. AU - Heinemann, M. AU - Sauer, U. PY - 2016 DA - 2016// TI - Distinct transcriptional regulation of the two Escherichia coli transhydrogenases PntAB and UdhA JO - Microbiology VL - 162 UR - https://doi.org/10.1099/mic.0.000346 DO - 10.1099/mic.0.000346 ID - Haverkorn van Rijsewijk2016 ER - TY - JOUR AU - Sauer, U. AU - Canonaco, F. AU - Heri, S. AU - Perrenoud, A. AU - Fischer, E. PY - 2004 DA - 2004// TI - The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli JO - J Biol Chem VL - 279 UR - https://doi.org/10.1074/jbc.M311657200 DO - 10.1074/jbc.M311657200 ID - Sauer2004 ER - TY - JOUR AU - Herzberg, M. AU - Kaye, I. K. AU - Peti, W. AU - Wood, T. K. PY - 2006 DA - 2006// TI - YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport JO - J Bacteriol. VL - 188 UR - https://doi.org/10.1128/JB.188.2.587-598.2006 DO - 10.1128/JB.188.2.587-598.2006 ID - Herzberg2006 ER - TY - JOUR AU - Köstner, M. AU - Schmidt, B. AU - Bertram, R. AU - Hillen, W. PY - 2006 DA - 2006// TI - Generating tetracycline-inducible auxotrophy in Escherichia coli and Salmonella enterica serovar typhimurium by using an insertion element and a hyperactive transposase JO - Appl Environ Microbiol VL - 72 UR - https://doi.org/10.1128/AEM.00492-06 DO - 10.1128/AEM.00492-06 ID - Köstner2006 ER - TY - JOUR AU - Conrad, T. M. AU - Frazier, M. AU - Joyce, A. R. AU - Cho, B. -. K. AU - Knight, E. M. AU - Lewis, N. E. PY - 2010 DA - 2010// TI - RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media JO - Proc Natl Acad Sci USA VL - 107 UR - https://doi.org/10.1073/pnas.0911253107 DO - 10.1073/pnas.0911253107 ID - Conrad2010 ER - TY - JOUR AU - Nedea, E. C. AU - Markov, D. AU - Naryshkina, T. AU - Severinov, K. PY - 1999 DA - 1999// TI - Localization of Escherichia coli rpoC mutations that affect RNA polymerase assembly and activity at high temperature JO - J Bacteriol. VL - 181 ID - Nedea1999 ER - TY - JOUR AU - Sandberg, T. E. AU - Pedersen, M. AU - Lacroix, R. A. AU - Ebrahim, A. AU - Bonde, M. AU - Herrgard, M. J. PY - 2014 DA - 2014// TI - Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations JO - Mol Biol Evol VL - 31 UR - https://doi.org/10.1093/molbev/msu209 DO - 10.1093/molbev/msu209 ID - Sandberg2014 ER - TY - JOUR AU - Phadtare, S. AU - Inouye, M. PY - 2001 DA - 2001// TI - Role of CspC and CspE in regulation of expression of RpoS and UspA, the stress response proteins in Escherichia coli JO - J Bacteriol. VL - 183 UR - https://doi.org/10.1128/JB.183.4.1205-1214.2001 DO - 10.1128/JB.183.4.1205-1214.2001 ID - Phadtare2001 ER - TY - JOUR AU - Bae, W. AU - Xia, B. AU - Inouye, M. AU - Severinov, K. PY - 2000 DA - 2000// TI - Escherichia coli CspA-family RNA chaperones are transcription antiterminators JO - Proc Natl Acad Sci USA VL - 97 UR - https://doi.org/10.1073/pnas.97.14.7784 DO - 10.1073/pnas.97.14.7784 ID - Bae2000 ER - TY - JOUR AU - Wu, X. AU - Altman, R. AU - Eiteman, M. A. AU - Altman, E. PY - 2014 DA - 2014// TI - Adaptation of Escherichia coli to elevated sodium concentrations increases cation tolerance and enables greater lactic acid production JO - Appl Environ Microbiol. VL - 80 UR - https://doi.org/10.1128/AEM.03804-13 DO - 10.1128/AEM.03804-13 ID - Wu2014 ER - TY - JOUR AU - Kelly, K. O. AU - Deutscher, M. P. PY - 1992 DA - 1992// TI - Characterization of Escherichia coli RNase PH JO - J Biol Chem. VL - 267 ID - Kelly1992 ER - TY - JOUR AU - Poulsen, P. AU - Bonekamp, F. AU - Jensen, K. F. PY - 1984 DA - 1984// TI - Structure of the Escherichia coli pyrE operon and control of pyrE expression by a UTP modulated intercistronic attentuation JO - Embo J. VL - 3 ID - Poulsen1984 ER - TY - JOUR AU - Jensen, K. F. PY - 1993 DA - 1993// TI - The Escherichia coli K-12 “wild types” W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels JO - J Bacteriol. VL - 175 UR - https://doi.org/10.1128/jb.175.11.3401-3407.1993 DO - 10.1128/jb.175.11.3401-3407.1993 ID - Jensen1993 ER - TY - STD TI - Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, et al. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol. 2009;10:R118. http://scholarscompass.vcu.edu/cmsc_pubs. Accessed 17 Oct 2016. UR - http://scholarscompass.vcu.edu/cmsc_pubs ID - ref39 ER - TY - JOUR AU - Roberts, J. W. PY - 1969 DA - 1969// TI - Termination factor for RNA synthesis JO - Nature. VL - 224 UR - https://doi.org/10.1038/2241168a0 DO - 10.1038/2241168a0 ID - Roberts1969 ER - TY - JOUR AU - Goodarzi, H. AU - Bennett, B. D. AU - Amini, S. AU - Reaves, M. L. AU - Hottes, A. K. AU - Rabinowitz, J. D. PY - 2010 DA - 2010// TI - Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli JO - Mol Syst Biol. VL - 6 UR - https://doi.org/10.1038/msb.2010.33 DO - 10.1038/msb.2010.33 ID - Goodarzi2010 ER - TY - JOUR AU - Haft, R. J. F. AU - Keating, D. H. AU - Schwaegler, T. AU - Schwalbach, M. S. AU - Vinokur, J. AU - Tremaine, M. PY - 2014 DA - 2014// TI - Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria JO - Proc Natl Acad Sci. VL - 111 UR - https://doi.org/10.1073/pnas.1401853111 DO - 10.1073/pnas.1401853111 ID - Haft2014 ER - TY - JOUR AU - Isik, M. AU - Sardon, H. AU - Mecerreyes, D. PY - 2014 DA - 2014// TI - Ionic liquids and cellulose: dissolution, chemical modification and preparation of new cellulosic materials JO - Int J Mol Sci VL - 15 UR - https://doi.org/10.3390/ijms150711922 DO - 10.3390/ijms150711922 ID - Isik2014 ER - TY - JOUR AU - He, B. AU - Smith, J. M. AU - Zalkin, H. PY - 1992 DA - 1992// TI - Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR JO - J Bacteriol. VL - 174 UR - https://doi.org/10.1128/jb.174.1.130-136.1992 DO - 10.1128/jb.174.1.130-136.1992 ID - He1992 ER - TY - JOUR AU - Yu, C. AU - Simmons, B. A. AU - Singer, S. W. AU - Thelen, M. P. AU - VanderGheynst, J. S. PY - 2016 DA - 2016// TI - Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts JO - Appl Microbiol Biotechnol. VL - 100 UR - https://doi.org/10.1007/s00253-016-7955-0 DO - 10.1007/s00253-016-7955-0 ID - Yu2016 ER - TY - JOUR AU - Bay, D. C. AU - Stremick, C. A. AU - Slipski, C. J. AU - Turner, R. J. PY - 2017 DA - 2017// TI - Secondary multidrug efflux pump mutants alter Escherichia coli biofilm growth in the presence of cationic antimicrobial compounds JO - Res Microbiol. VL - 168 UR - https://doi.org/10.1016/j.resmic.2016.11.003 DO - 10.1016/j.resmic.2016.11.003 ID - Bay2017 ER - TY - JOUR AU - Leuzzi, A. AU - Martino, M. L. AU - Campilongo, R. AU - Falconi, M. AU - Barbagallo, M. AU - Marcocci, L. PY - 2015 DA - 2015// TI - Multifactor regulation of the MdtJI polyamine transporter in Shigella JO - PLoS ONE VL - 10 UR - https://doi.org/10.1371/journal.pone.0136744 DO - 10.1371/journal.pone.0136744 ID - Leuzzi2015 ER - TY - JOUR AU - Yung, P. Y. AU - Lo, G. r. a. s. s. o. L. AU - Mohidin, A. F. AU - Acerbi, E. AU - Hinks, J. AU - Seviour, T. PY - 2016 DA - 2016// TI - Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds JO - Sci Rep. VL - 6 UR - https://doi.org/10.1038/srep19899 DO - 10.1038/srep19899 ID - Yung2016 ER - TY - JOUR AU - Herring, C. D. AU - Glasner, J. D. AU - Blattner, F. R. PY - 2003 DA - 2003// TI - Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli JO - Gene VL - 311 UR - https://doi.org/10.1016/S0378-1119(03)00585-7 DO - 10.1016/S0378-1119(03)00585-7 ID - Herring2003 ER - TY - JOUR AU - Utrilla, J. AU - O’Brien, E. J. AU - Chen, K. AU - McCloskey, D. AU - Cheung, J. AU - Wang, H. PY - 2016 DA - 2016// TI - Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution JO - Cell Syst. VL - 2 UR - https://doi.org/10.1016/j.cels.2016.04.003 DO - 10.1016/j.cels.2016.04.003 ID - Utrilla2016 ER -