Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli.
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Luis H. Reyes | Luis H Reyes | Katy C Kao | Katy C. Kao | James D. Winkler | James Winkler | Maria P Almario | Margarita M Orozco | Maria P. Almario | Margarita Orozco
[1] Jay D. Keasling,et al. Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli , 2010, Applied and Environmental Microbiology.
[2] D. Botstein,et al. Systematic changes in gene expression patterns following adaptive evolution in yeast. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[3] S. Adhya,et al. The pleiotropic ts15 mutation of E. coli is an IS1 insertion in the rho structural gene. , 1983, Genetics.
[4] Saeed Tavazoie,et al. Molecular Systems Biology 6; Article number 378; doi:10.1038/msb.2010.33 Citation: Molecular Systems Biology 6:378 , 2022 .
[5] T. Mizuno,et al. A Genome-Wide View of the Escherichia coli BasS–BasR Two-component System Implicated in Iron-responses , 2004, Bioscience, biotechnology, and biochemistry.
[6] Michael L. Bittner,et al. Microarrays: Optical Technologies and Informatics , 2001 .
[7] Bernhard Ø. Palsson,et al. Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, l-1,2-Propanediol , 2010, Applied and Environmental Microbiology.
[8] R. Gourse,et al. Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. , 1994, Journal of molecular biology.
[9] H. Mori,et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.
[10] J. Neilands,et al. Ferric uptake regulation protein acts as a repressor, employing iron (II) as a cofactor to bind the operator of an iron transport operon in Escherichia coli. , 1987, Biochemistry.
[11] D. Friedman,et al. Analysis of the Escherichia coli nusA10(Cs) allele: relating nucleotide changes to phenotypes , 1991, Journal of bacteriology.
[12] W. Umbreit,et al. EFFECT OF BIOTIN ON FATTY ACID DISTRIBUTION IN ESCHERICHIA COLI. , 1965, Journal of bacteriology.
[13] B. Rak,et al. IS5: a mobile enhancer of transcription in Escherichia coli. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[14] H. Saedler,et al. IS2, a genetic element for turn-off and turn-on of gene activity in E. coli , 2004, Molecular and General Genetics MGG.
[15] J. Liao,et al. Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. , 2008, Metabolic engineering.
[16] Xiaoming Yang,et al. Temperature-Sensitive Growth and Decreased Thermotolerance Associated with relA Mutations in Escherichia coli , 2003, Journal of bacteriology.
[17] Michael M. Desai,et al. Clonal Interference, Multiple Mutations and Adaptation in Large Asexual Populations , 2008, Genetics.
[18] Cong T. Trinh,et al. Redesigning Escherichia coli Metabolism for Anaerobic Production of Isobutanol , 2011, Applied and Environmental Microbiology.
[19] G. Stephanopoulos,et al. Selection and optimization of microbial hosts for biofuels production. , 2008, Metabolic engineering.
[20] James C Liao,et al. A Global Regulatory Role of Gluconeogenic Genes in Escherichia coli Revealed by Transcriptome Network Analysis* , 2005, Journal of Biological Chemistry.
[21] H. A. Orr,et al. Adaptation in Sexuals vs. Asexuals: Clonal Interference and the Fisher-Muller Model , 2005, Genetics.
[22] E. Papoutsakis,et al. Aldehyde–alcohol dehydrogenase and/or thiolase overexpression coupled with CoA transferase downregulation lead to higher alcohol titers and selectivity in Clostridium acetobutylicum fermentations , 2009, Biotechnology and bioengineering.
[23] Stephen S. Fong,et al. Laboratory Evolution and Multi-platform Genome Re-sequencing of the Cellulolytic Actinobacterium Thermobifida fusca , 2011, The Journal of Biological Chemistry.
[24] Katy C. Kao,et al. gNCA: a framework for determining transcription factor activity based on transcriptome: identifiability and numerical implementation. , 2005, Metabolic engineering.
[25] James C Liao,et al. Microbial production of advanced transportation fuels in non-natural hosts. , 2009, Current opinion in biotechnology.
[26] Manoj Agrawal,et al. Adaptation yields a highly efficient xylose‐fermenting Zymomonas mobilis strain , 2011, Biotechnology and bioengineering.
[27] E. Papoutsakis,et al. Dynamics of Genomic-Library Enrichment and Identification of Solvent Tolerance Genes for Clostridium acetobutylicum , 2007, Applied and Environmental Microbiology.
[28] A. May,et al. Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. An enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance. , 2005, Biochemistry.
[29] R. Lenski,et al. Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations , 2010, BMC Evolutionary Biology.
[30] B. Palsson,et al. Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. , 2005, Genome research.
[31] Katy C. Kao,et al. Global Expression Profiling of Acetate-grown Escherichia coli * , 2002, The Journal of Biological Chemistry.
[32] B. Wanner,et al. Conditional-Replication, Integration, Excision, and Retrieval Plasmid-Host Systems for Gene Structure-Function Studies of Bacteria , 2001, Journal of bacteriology.
[33] Kevin M. Smith,et al. Metabolic engineering of Escherichia coli for 1-butanol production. , 2008, Metabolic engineering.
[34] John Quackenbush. Microarray data normalization and transformation , 2002, Nature Genetics.
[35] Luis H. Reyes,et al. Genomic Library Screens for Genes Involved in n-Butanol Tolerance in Escherichia coli , 2011, PloS one.
[36] H. Mori,et al. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. , 2006, DNA research : an international journal for rapid publication of reports on genes and genomes.
[37] Terence P. Speed,et al. Normalization for cDNA microarry data , 2001, SPIE BiOS.
[38] Ryan T Gill,et al. Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides , 2010, Nature Biotechnology.
[39] M. Valvano,et al. Genetic analysis of the O-specific lipopolysaccharide biosynthesis region (rfb) of Escherichia coli K-12 W3110: identification of genes that confer group 6 specificity to Shigella flexneri serotypes Y and 4a , 1994, Journal of Bacteriology.
[40] A I Saeed,et al. TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.
[41] F. Hui,et al. Mesomorphic behaviour of some phospholipids with aliphatic alcohols and other non-ionic substances. , 1973, Biochimica et biophysica acta.
[42] R. Lenski,et al. The fate of competing beneficial mutations in an asexual population , 2004, Genetica.
[43] C. Grisham,et al. The effects of long-chain alcohols on membrane lipids and the (Na++K+)-ATPase. , 1973, Biochimica et biophysica acta.
[44] T. Ferenci,et al. Experimental analysis of molecular events during mutational periodic selections in bacterial evolution. , 2000, Genetics.
[45] Katy C. Kao,et al. Novel Escherichia coli hybrids with enhanced butanol tolerance , 2010, Biotechnology Letters.
[46] Michael M. Desai,et al. Beneficial Mutation–Selection Balance and the Effect of Linkage on Positive Selection , 2006, Genetics.
[47] Computational identification of adaptive mutants using the VERT system , 2012, Journal of biological engineering.
[48] E. Papoutsakis,et al. A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation. , 2010, Metabolic engineering.
[49] T Platt,et al. Transcription termination and the regulation of gene expression. , 1986, Annual review of biochemistry.
[50] J. Liao,et al. An evolutionary strategy for isobutanol production strain development in Escherichia coli. , 2011, Metabolic engineering.
[51] B. Poolman,et al. Mechanisms of membrane toxicity of hydrocarbons. , 1995, Microbiological reviews.
[52] C. Paquin,et al. Frequency of fixation of adaptive mutations is higher in evolving diploid than haploid yeast populations , 1983, Nature.
[53] Ryan T Gill,et al. Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli. , 2005, Metabolic engineering.
[54] Nathan E Lewis,et al. Microbial laboratory evolution in the era of genome-scale science , 2011, Molecular systems biology.
[55] J. Pronk,et al. Engineering topology and kinetics of sucrose metabolism in Saccharomyces cerevisiae for improved ethanol yield. , 2011, Metabolic engineering.
[56] Ryan T Gill,et al. SCALEs: multiscale analysis of library enrichment , 2007, Nature Methods.
[57] R. Gourse,et al. Growth rate-dependent control of the rrnB P1 core promoter in Escherichia coli , 1994, Journal of bacteriology.
[58] J. Cronan,et al. Cyclopropane fatty acid synthase of Escherichia coli. Stabilization, purification, and interaction with phospholipid vesicles. , 1979, Biochemistry.
[59] Chiara Sabatti,et al. Network component analysis: Reconstruction of regulatory signals in biological systems , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[60] J. Neilands,et al. Siderophores: Structure and Function of Microbial Iron Transport Compounds (*) , 1995, The Journal of Biological Chemistry.
[61] Transcript analysis of Escherichia coli K-12 insertion element IS5. , 2005, FEMS microbiology letters.
[62] Gavin Sherlock,et al. Molecular Characterization of Clonal Interference during Adaptive Evolution in Asexual Populations of Saccharomyces cerevisiae , 2008, Nature Genetics.
[63] H. Kobayashi,et al. Cell surface properties of organic solvent-tolerant mutants of Escherichia coli K-12 , 1997, Applied and environmental microbiology.
[64] Rainer Breitling,et al. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments , 2004, FEBS letters.
[65] Judith Berman,et al. Evolutionary Dynamics of Candida albicans during In Vitro Evolution , 2011, Eukaryotic Cell.
[66] C. Paquin,et al. Relative fitness can decrease in evolving asexual populations of S. cerevisiae , 1983, Nature.
[67] Jean-Marie Rouillard,et al. Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli , 2011, Microbial cell factories.
[68] M. Kahn,et al. The nucleotide sequence of IS5 from Escherichia coli. , 1981, Gene.