Project description:We have estimated the fitness effects of horizontally transferred Salmonella genes to E.coli. To better understand the role of protein-protein interactions, we want to identify the expression levels of known interaction partners of the transferred genes.
Project description:DNA microarrays were carried out to compare the transcriptional profiles of P. putida KT2440 and its isogenic knock-out mutant in agmR gene (mut agmR) when grown in M9 medium with glucose as a sole carbon source and in absense of chloramphenicol or any other stressor compound.
Project description:E. coli BW25113 growth in a nutrient-rich medium supplemented with 20 proteinogenic amino acid medium was studied and compared to growth in minimal medium. Proteome data from these experiments revealed significant differences in amino acid synthesis and transport proteins that were reduced in the nutrient-rich meidum. Changes in energy production and conversion proteins were also observed as in nutrient-rich conditions pyruvate dehydrogenase complex and acetate producing proteins increased, while the TCA cycle proteins decreased.
Project description:Transcriptional profiling of E.coli SE15 comparing wild type E.coli SE15 with Autoindecur 2 synthesis gene LuxS mutnat E.coli SE15. E.coli SE15 is isolated from indwelling catheter of urinary tract infected patient. Examine change of quorum sensing related gene by deleting autoinducer 2 synthesis gene LuxS in E.coli
Project description:This experiment studied the effect of FPP accumulation on E. coli. E. coli cells transformed with pMBIS (the S. cerevisiae mevalonate pathway enzymes converting mevalonate to FPP) and fed mevalonate produce large amounts of FPP, which causes toxicity when it accumulates. When coupled with an active amorphadiene synthase (pADS) the cells produce amorphadiene, a non-toxic isoprenoid. To accumulate FPP, but maintain similar protein burden, an amorphadiene synthase with 3 mutations to render it inactive was used (pADSmut) to accumulate FPP. E. coli was transformed with pMBIS and pADS or pMBIS and pADSMut and grown in M9+glucose with varying magnesium concentrations and fed 20 mM mevalonate and induced with 0.5 mM IPTG, then sampled at subsequent time points.
Project description:Salmonella typhimurium 14028s Transposon library recovered after three consecutive rounds of growth to late log phase in M9 minimal medium (arabinose 0.4%) at 37°C with aeration, compared to an expansion of the initial library selected on Luria agar plates + kanamycin (50ug/ml), O/N at 37°C Keywords: Transposon tag analysis
Project description:Study of the possible existence of a replication fork trap in Vibrio cholerae. 1- FX85: EPV50(WT) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 2- FX86: EPV50(WT) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 3- FX288: EGV140 (oriL3) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 4- FX289:EGV140 (oriL3) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 5- FX290: EGV111 (oriR4) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 6- FX291:EGV111 (oriR4) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 7- FX355:EPV50 (WT) grown in LB medium to exponential phase (0.2 OD 650nm) 8- FX356:EPV50 (WT) grown in LB medium to stationary phase (overnight) 9- FX286:EGV140 (oriL3) grown in LB medium to exponential phase (0.2 OD 650nm) 10- FX287:EGV140 (oriL3) grown in LB medium to stationary phase (overnight) 11- FX292:EGV111 (oriR4) grown in LB medium to exponential phase (0.2 OD 650nm) 12- FX49: MCH1 (WT monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 13- FX48: MCH1 (WT monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 14- FX11: EGV369 (oriL3 monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 15- FX12: EGV366 (oriR4 monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 16- FX296 EPV50 M9 Exp 17- FX294 EPV50 M9 Stat 18-FX316 EGV140 M9 Exp 19- FX315 EGV111 M9 Exp 20-FX318 MCH1 M9 Exp 21- FX317 MCH1 M9 Stat 22- FX320 EGV369 M9 Exp 23- FX319 EGV366 M9 Exp Chromosomal DNA was extracted using the Sigma GenElute bacterial genomic DNA kit. 5 μg of DNA were used to generate a genomic library according to Illumina's protocol. The libraries and the sequencing were performed by the High-throughput Sequencing facility of the I2BC (http://www.i2bc.paris-saclay.fr/spip.php?article399〈=en,CNRS, Gif-sur-Yvette, France). Genomic DNA libraries were made with the ‘Nextera DNA library preparation kit’ (Illumina) following the manufacturer’s recommendations. Library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent technologies). Libraries were pooled in equimolar proportions. 75 bp single reads were generated on an Illumina MiSeq instrument, using a MiSeq Reagent kit V2 (500 cycles) (Illumina), with an expected depth of 217X. Reads were aligned on the in silico reconstituted genome of the cognate strain using BWA software. An in-lab written MATLAB-based script was used to perform marker frequency analysis. Data were normalized by dividing uniquely mapping sequence reads by the total number of reads. Enrichment of uniquely mapping sequence reads in 1 kb non-overlapping windows were calculated and plotted against the chromosomal coordinates.