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Genes of the GadX-GadW Regulon in Escherichia coli. Don L. Tucker, 2003.Acid in the stomach is thought to be a barrier to bacterial colonization of the intestine . Escherichia coli, however, has three systems for acid resistance, which overcome this barrier . The most effective of these systems is dependent on transport and decarboxylation of glutamate . GadX regulates two genes that encode isoforms of glutamate decarboxylase critical to this system, but additional genes associated with the glutamate-dependent acid resistance system remained to be identified . The gadX gene and a second downstream araC-like transcription factor gene, gadW, were mutated separately and in combination, and the gene expression profiles of the mutants were compared to those of the wild-type strain grown in neutral and acidified media under conditions favoring induction of glutamate-dependent acid resistance . Cluster and principal-component analyses identified 15 GadX-regulated, acid-inducible genes . Reverse transcriptase mapping demonstrated that these genes are organized in 10 operons . Analysis of the strain lacking GadX but possessing GadW confirmed that GadX is a transcriptional activator under acidic growth conditions . Analysis of the strain lacking GadW but possessing GadX indicated that GadW exerts negative control over three GadX target genes . The strain lacking both GadX and GadW was defective in acid induction of most but not all GadX target genes, consistent with the roles of GadW as an inhibitor of GadX-dependent activation of some genes and an activator of other genes . Resistance to acid was decreased under certain conditions in a gadX mutant and even more so by combined mutation of gadX and gadW . However, there was no defect in colonization of the streptomycin-treated mouse model by the gadX mutant in competition with the wild type, and the gadX gadW mutant was a better colonizer than the wild type . Thus, E . coli colonization of the mouse does not appear to require glutamate-dependent acid resistance . Influence of Apple Cultivars on Inactivation of Different Strains of Escherichia coli O157:H7 in Apple Cider by UV Irradiation. N. Basaran, 2004.This study examined the effect of different apple cultivars upon the UV inactivation of Escherichia coli O157:H7 strains within unfiltered apple cider . Apple cider was prepared from eight different apple cultivars, inoculated with approximately 106 to 107 CFU of three strains of E . coli O157:H7 per ml (933, ATCC 43889, and ATCC 43895), and exposed to 14 mJ of UV irradiation per cm2 . Bacterial populations for treated and untreated samples were then enumerated by using nonselective media . E . coli O157:H7 ATCC 43889 showed the most sensitivity to this disinfection process with an average 6.63-log reduction compared to an average log reduction of 5.93 for both strains 933 and ATCC 43895 . The highest log reduction seen, 7.19, occurred for strain ATCC 43889 in Rome cider . The same cider produced the lowest log reductions: 5.33 and 5.25 for strains 933 and ATCC 43895, respectively . Among the apple cultivars, an average log reduction range of 5.78 (Red Delicious) to 6.74 (Empire) was observed, with two statistically significant ( 
 0.05) log reduction groups represented . Within the paired cultivar-strain analysis, five of eight ciders showed statistically significant (
0.05) differences in at least two of the E . coli strains used . Comparison of log reductions among the E . coli strains to the cider parameters of °Brix, pH, and malic acid content failed to show any statistically significant relationship (R2
 0.95) . However, the results of this study indicate that regardless of the apple cultivar used, a minimum 5-log reduction is achieved for all of the strains of E . coli O157:H7 tested .
Genome-Scale Metabolic Model of Helicobacter pylori 26695. Christophe H. Schilling, 2002.A genome-scale metabolic model of Helicobacter pylori 26695 was constructed from genome sequence annotation, biochemical, and physiological data . This represents an in silico model largely derived from genomic information for an organism for which there is substantially less biochemical information available relative to previously modeled organisms such as Escherichia coli . The reconstructed metabolic network contains 388 enzymatic and transport reactions and accounts for 291 open reading frames . Within the paradigm of constraint-based modeling, extreme-pathway analysis and flux balance analysis were used to explore the metabolic capabilities of the in silico model . General network properties were analyzed and compared to similar results previously generated for Haemophilus influenzae . A minimal medium required by the model to generate required biomass constituents was calculated, indicating the requirement of eight amino acids, six of which correspond to essential human amino acids . In addition a list of potential substrates capable of fulfilling the bulk carbon requirements of H . pylori were identified . A deletion study was performed wherein reactions and associated genes in central metabolism were deleted and their effects were simulated under a variety of substrate availability conditions, yielding a number of reactions that are deemed essential . Deletion results were compared to recently published in vitro essentiality determinations for 17 genes . The in silico model accurately predicted 10 of 17 deletion cases, with partial support for additional cases . Collectively, the results presented herein suggest an effective strategy of combining in silico modeling with experimental technologies to enhance biological discovery for less characterized organisms and their genomes .
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