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Library2.bib file://localhost/Users/Barry/Library/texmf/bibtex/Library2.bib BibTeX Bibliography en Copyright 2006 Tue, 01 Aug 2006 14:23:23 -0400 Proteomic profiling of recombinant Escherichia coli in high-cell-density fermentations for improved production of an antibody fragment biopharmaceutical. Roles and applications of small heat shock proteins in the production of recombinant proteins in Escherichia coli. Stationary phase protein overproduction is a fundamental capability of Escherichia coli. Role of the general stress response during strong overexpression of a heterologous gene in Escherichia coli. Genomic analysis of high-cell-density recombinant Escherichia coli fermentation and "cell conditioning" for improved recombinant protein yield. Monitoring of genes that respond to overproduction of an insoluble recombinant protein in Escherichia coli glucose-limited fed-batch fermentations. DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli. Effects of plasmid presence on growth and enzyme activity of Escherichia coli DH5Î$\pm$ T7 RNA polymerase-dependent expression of COXII in yeast mitochondria. Plasmid presence changes the relative levels of many host cell proteins and ribosome components in recombinant <I>Escherichia coli</I> Effects of recombinant plasmid content on growth properties and cloned gene product formation in <I>Escherichia coli</I> Plasmid-encoded protein: The principal factor in the ?metabolic burden? associated with recombinant bacteria Host-vector interactions in Escherichia coli. Conversion of the Vibrio fischeri transcriptional activator, LuxR, to a repressor. Recombinant protein expression in high cell density fed-batch cultures of Escherichia coli. A fluctuation method to quantify in vivo fluorescence data Feedback control of ribosome synthesis in Escherichia coli is dependent on eight critical amino acids Tuning genetic control through promoter engineering An excitable gene regulatory circuit induces transient cellular differentiation. FACS-optimized mutants of the green fluorescent protein (GFP). New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Analogs of the autoinducer of bioluminescence in Vibrio fischeri. Detection, purification, and structural elucidation of the acylhomoserine lactone inducer of Vibrio fischeri luminescence and other related molecules. Quorum sensing in Vibrio fischeri: probing autoinducer-LuxR interactions with autoinducer analogs. N-acyl homoserinelactone-mediated gene regulation in gram-negative bacteria. gfp-based N-acyl homoserine-lactone sensor systems for detection of bacterial communication. Effect of sdiA on biosensors of N-acylhomoserine lactones. The LuxR receptor: the sites of interaction with quorum-sensing signals and inhibitors. N-acyl-L-homoserine lactone signal interception by Escherichia coli. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Emergent Properties of Reduced-Genome Escherichia coli. DNA uptake in bacteria. Intracellular compartmentation in planctomycetes. Linearly concatenated cyclobutane lipids form a dense bacterial membrane. Identification of organelles in bacteria similar to acidocalcisomes of unicellular eukaryotes. Bacterial growth inhibition by overproduction of protein. Characterization of stress and protein turnover from protein overexpression in fed-batch E. coli cultures. A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. Structured model to predict intracellular amino acid shortages during recombinant protein overexpression in E. coli Modeling of the controlled expression of a harmful protein by a three-plasmid harboring system. Reaction pathways in transcript elongation. Sequence-dependent kinetic model for transcription elongation by RNA polymerase. Mathematical modeling and analysis in biochemical engineering: past accomplishments and future opportunities. Improved cloning efficiency of polymerase chain reaction (PCR) products after proteinase K digestion. Preparation and storage of competent Escherichia coli cells Analysis of growth rate effects on productivity of recombinant Escherichia coli populations using molecular mechanism models. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Cellular logic with orthogonal ribosomes. Engineered riboregulators enable post-transcriptional control of gene expression. Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Transcribing of Escherichia coli genes with mutant T7 RNA polymerases: stability of lacZ mRNA inversely correlates with polymerase speed. A network of orthogonal ribosome[middot]mRNA pairs The efficiency of promoter clearance distinguishes T7 class II and class III promoters. Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA. Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Escherichia coli and Salmonella: Cellular and Molecular Biology Escherichia coli and Salmonella: Cellular and Molecular Biology A synthetic multicellular system for programmed pattern formation. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. Programmed population control by cell-cell communication and regulated killing PL of coliphage lambda: an alternative solution for an efficient promoter. Transcriptional response of Escherichia coli to temperature shift. Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. Compared tolerance to osmotic stress in various microorganisms: Towards a survival prediction test. Cell-to-cell signalling in Escherichia coli and Salmonella enterica. Reversible acyl-homoserine lactone binding to purified Vibrio fischeri LuxR protein. Quorum sensing in Vibrio fischeri: analysis of the LuxR DNA binding region by alanine-scanning mutagenesis. RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro. "Host shutoff" function of bacteriophage T7: involvement of T7 gene 2 and gene 0.7 in the inactivation of Escherichia coli RNA polymerase. Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators. Evidence that the N-terminal region of the Vibrio fischeri LuxR protein constitutes an autoinducer-binding domain. Active efflux and diffusion are involved in transport of Pseudomonas aeruginosa cell-to-cell signals. The Vibrio fischeri luminescence gene activator LuxR is a membrane-associated protein. Analysis of growth rate effects on productivity of recombinant Escherichia coli populations using molecular mechanism models. Reprinted from Biotechnology and Bioengineering, Vol. 26, Issue 1, Pages 66-73 (1984). Complex biology with no parameters. Real-time RNA profiling within a single bacterium. A regulatory trade-off as a source of strain variation in the species Escherichia coli. Fluorescence correlation spectrometry of the interaction kinetics of tetramethylrhodamin [alpha]-bungarotoxin with Torpedo californica acetylcholine receptor Long-term and homogeneous regulation of the Escherichia coli araBAD promoter by use of a lactose transporter of relaxed specificity. Quantitative analysis of ribosome binding sites in E.coli. Effects of carriage and expression of the Tn10 tetracycline-resistance operon on the fitness of Escherichia coli K12. Green fluorescent protein purification by organic extraction. Signal transduction: molecular monogamy. Is modification sufficient to protect a bacterial chromosome from a resident restriction endonuclease? Genetic analysis of the Shine-Dalgarno interaction: selection of alternative functional mRNA-rRNA combinations. Definition of the Escherichia coli MC4100 genome by use of a DNA array. Host specificity of DNA produced by Escherichia coli: bacterial mutations affecting the restriction and modification of DNA. Mutants of initiator tRNA that function both as initiators and elongators. Formation of the central pseudoknot in 16S rRNA is essential for initiation of translation. Construction and analysis of luxCDABE-based plasmid sensors for investigating N-acyl homoserine lactone-mediated quorum sensing. The specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance. Methylglyoxal, an endogenous aldehyde, crosslinks DNA polymerase and the substrate DNA Initiation factor IF 2 binds to the alpha-sarcin loop and helix 89 of Escherichia coli 23S ribosomal RNA. Binding of Escherichia coli initiation factor IF2 to 30S ribosomal subunits: a functional role for the N-terminus of the factor. Anticodon sequence mutants of Escherichia coli initiator tRNA: effects of overproduction of aminoacyl-tRNA synthetases, methionyl-tRNA formyltransferase, and initiation factor 2 on activity in initiation. Thin-layer chromatographic methods to isolate 32P-labeled 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP): determination of cellular PRPP pools and assay of PRPP synthetase activity. Measuring control of transcription initiation by changing concentrations of nucleotides and their derivatives. Interspecies communication in bacteria. The structure of the zinc finger domain from human splicing factor ZNF265 fold. Generation of an AraC-araBAD promoter-regulated T7 expression system. Culture medium for enterobacteria. Residual guanosine 3',5'-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. Analysis of sequence elements important for the synthesis and control of ribosomal RNA in E coli. Properties of a bacterial mutant lacking amino acid control of RNA synthesis. Regulated expression of foreign genes in mammalian cells under the control of coliphage T3 RNA polymerase and lac repressor. Eukaryotic transient-expression system based on recombinant vaccinia virus that synthesizes bacteriophage T7 RNA polymerase. Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes. Expression from reporter genes does not always reflect functional mRNA levels. Translation initiation in Escherichia coli: sequences within the ribosome-binding site. The use of a tRNA as a transcriptional reporter: the T7 late promoter is extremely efficient in Escherichia coli but its transcripts are poorly expressed. Hierarchies of base pair preferences in the P22 ant promoter. The effects of mutations in the ant promoter of phage P22 depend on context. Compilation and analysis of Escherichia coli promoter DNA sequences. Modulating substrate choice: the SspB adaptor delivers a regulator of the extracytoplasmic-stress response to the AAA+ protease ClpXP for degradation. Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Retroregulation of the synthesis of ribosomal proteins L14 and L24 by feedback repressor S8 in Escherichia coli. Recombineering: a powerful new tool for mouse functional genomics. Phage RNA polymerase vectors that allow efficient gene expression in both prokaryotic and eukaryotic cells. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Over-expression of Escherichia coli F1Fo-ATPase subunit a is inhibited by instability of the uncB gene transcript Effect of increased ppGpp concentration on DNA replication of different replicons in Escherichia coli. Monitoring of Stress Responses Molecular Components of Physiological Stress Responses in Escherichia coli Stress Induced by Recombinant Protein Production in Escherichia coli Co-overexpression of folding modulators improves the solubility of the recombinant guinea pig liver transglutaminase expressed in Escherichia coli. tRNA-assisted overproduction of eukaryotic ribosomal proteins. Directing ribosomes to a single mRNA species: a method to study ribosomal RNA mutations and their effects on translation of a single messenger in Escherichia coli. Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. Modulation of gene expression from the arabinose-inducible araBAD promoter. Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. Mechanism of inhibition of bacteriophage T7 RNA polymerase by T7 lysozyme. Recombinant expression systems in the pharmaceutical industry. Recombinant protein expression in Escherichia coli. Advanced genetic strategies for recombinant protein expression in Escherichia coli. Studies on polynucleotides. XCVI. Repair replications of short synthetic DNA's as catalyzed by DNA polymerases. Restriction endonucleases in the analysis and restructuring of dna molecules. In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 3. Influences of individual DNA elements within the promoter recognition region on abortive initiation and promoter escape. SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants. Interplay of SOS induction, recombinant gene expression, and multimerization of plasmid vectors in Escherichia coli. Protein production by auto-induction in high density shaking cultures. Cellular Computation and Communications using Engineered Genetic Regulatory Networks lambda Repressor and cro--components of an efficient molecular switch. Genetic regulatory mechanisms in the synthesis of proteins. Plasmid (1952-1997) Synthesis of the beta and beta' subunits of Escherichia coli RNA polymerase is autogenously regulated in vivo by both transcriptional and translational mechanisms. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Cytoplasmic RNA Polymerase in Escherichia coli. Characterization of RNA and DNA synthesis in Escherichia coli strains devoid of ppGpp. A vesicle bioreactor as a step toward an artificial cell assembly. Decay of rplN and lacZ mRNA in Escherichia coli. Expression of lacZ from the promoter of the Escherichia coli spc operon cloned into vectors carrying the W205 trp-lac fusion. Amino acid content of recombinant proteins influences the metabolic burden response. Pausing and termination by bacteriophage T7 RNA polymerase. Metabolic load and heterologous gene expression. Free RNA polymerase and modeling global transcription in Escherichia coli. A comparative study of global stress gene regulation in response to overexpression of recombinant proteins in Escherichia coli. Optimization of the host-plasmid interaction in the recombinant Escherichia coli strains overproducing penicillin G acylase Macromolecular composition during steady-state growth of Escherichia coli B-r. Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state. Use of T7 RNA polymerase to direct expression of cloned genes. Control of RNA synthesis in Escherichia coli after a shift to higher temperature. Modeling allosteric regulation of de novo pyrimidine biosynthesis in Escherichia coli Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate. An Integrated Model of the Transcription Complex in Elongation, Termination, and Editing Control of spoT-dependent ppGpp synthesis and degradation in Escherichia coli. Control of the Escherichia coli rrnB P1 promoter strength by ppGpp. mRNA composition and control of bacterial gene expression. Determination of synthesis rate and lifetime of bacterial mRNAs. Activities of constitutive promoters in Escherichia coli. Control of rRNA synthesis in Escherichia coli at increased rrn gene dosage. Role of guanosine tetraphosphate and ribosome feedback. Effects of Fis on ribosome synthesis and activity and on rRNA promoter activities in Escherichia coli. Efficient attenuation of stochasticity in gene expression through post-transcriptional control. Escherichia coli ppGpp synthetase II activity requires spoT. Gene Regulation at the Single-Cell Level Guanosine tetraphosphate (ppGpp) dependence of the growth rate control of rrnB P1 promoter activity in Escherichia coli. Guanosine tetraphosphate as a global regulator of bacterial RNA synthesis: a model involving RNA polymerase pausing and queuing. Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones. Sensing starvation: a homoserine lactone--dependent signaling pathway in Escherichia coli. Physiological characterization of Escherichia coli rpoB mutants with abnormal control of ribosome synthesis. rpoB mutation in Escherichia coli alters control of ribosome synthesis by guanosine tetraphosphate. Stringent and growth control of rRNA synthesis in Escherichia coli are both mediated by ppGpp. Editing of errors in selection of amino acids for protein synthesis. An efficient recombination system for chromosome engineering in Escherichia coli. Studies in vivo on Escherichia coli RNA polymerase mutants altered in the stringent response. The cell cycle in Escherichia coli B/r. Construction, purification, and characterization of Escherichia coli RNA polymerases tagged with different fluorescent proteins. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade Toxic effects of high levels of ppGpp in Escherichia coli are relieved by rpoB mutations. Kinetics of the AHL Regulatory System in a Model Biofilm System: How Many Bacteria Constitute a "Quorum"? Transcription in bacteria at different DNA concentrations. An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Transcription of ribosomal component genes and lac in a relA+/relA pair of Escherichia coli strains. Luminescence Control in Marine Bacterium \emph{Vibrio Fishceri}: An Analysis of the Dynamics of \emph{lux} regulation Variation of generation times in Escherichia coli populations: its cause and implications. Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea Cell-Cell Signaling in Bacteria Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. Bacterial Bioluminescence: isolation and genetic analysis of functions from \emph{Vibrio Fischeri} How Bacteria Talk to Each Other: Regulation of Gene Expression by Quorum Sensing Limitations of quantitative gene regulation models: a case study. Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution. A novel in vivo assay reveals inhibition of ribosomal nuclear export in ran-cycle and nucleoporin mutants. Metabolic engineering of a novel propionate-independent pathway for the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in recombinant Salmonella enterica serovar typhimurium. Products transcribed from rearranged rrn genes of Escherichia coli can assemble to form functional ribosomes. In situ localized amplification and contact replication of many individual DNA molecules. Common Location of Determinants in Initiator Transfer RNAs for Initiator-Elongator Discrimination in Bacteria and in Eukaryotes Detailed map of a cis-regulatory input function. Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Controlling basal expression in an inducible T7 expression system by blocking the target T7 promoter with lac repressor. Creation of a T7 autogene. Cloning and expression of the gene for bacteriophage T7 RNA polymerase under control of its cognate promoter. More surprises in translation: initiation without the initiator tRNA. Initiation of protein synthesis from a termination codon. Control of rRNA synthesis in Escherichia coli: a systems biology approach. Spatiotemporal control of gene expression with pulse-generating networks. In the Escherichia coli lacZ gene the spacing between the translating ribosomes is insensitive to the efficiency of translation initiation. Specialized ribosomes: highly specific translation in vivo of a single targetted mRNA species. The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues. Invariance of the nucleoside triphosphate pools of Escherichia coli with growth rate. Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria. Stochastic gene expression in a single cell. Kinetic properties of rrn promoters in Escherichia coli. Precision and functional specificity in mRNA decay. Synthesizing life. Intrinsic and extrinsic contributions to stochasticity in gene expression. Mechanisms of noise-resistance in genetic oscillators. Negative autoregulation speeds the response times of transcription networks. Summing up the noise in gene networks. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. Interdependence of translation, transcription and mRNA degradation in the lacZ gene. Engineering stability in gene networks by autoregulation. Engineered Communications for Microbial Robotics Genetic Circuit Building Blocks for Cellular Computation, Communications and Signal Processing Robustness in simple biochemical networks. A model of excitation and adaptation in bacterial chemotaxis. Construction of a genetic toggle switch in Escherichia coli. A mathematical model for quorum sensing in Pseudomonas aeruginosa. Synchronizing genetic relaxation oscillators by intercell signaling. Regulation of noise in the expression of a single gene. Engineering Signal Processing in Cells: Towards Molecular Concentration Band Detection Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Noise-based switches and amplifiers for gene expression Prediction and measurement of an autoregulatory genetic module. A synthetic oscillatory network of transcriptional regulators.

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