Project description:Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days. 7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol. Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. coli (day 0) to a midpoint evolved strain (day 20) and evolutionary endpoints
Project description:We have performed adaptive laboratory evolution of E. coli pdhR gene deletion strain to examine the adaptive strategies of E. coli.
Project description:In this project we aim to construct a tyrosine-producing E. coli strain through iterative steps of genome engineering. High PEP availability through knockout of the PTS was combined with the precise, in-place genomic integration of several engineering interventions, known to increase L-tyrosine production yields, to create a tyrosine-overproducing E. coli strain that can function as a platform for further engineering and optimization. Utilizing a design-build-test-learn (DBTL) cycle, an evolved pts-knockout E. coli strain was equipped with optimizations of the aroG, aroB and tyrA genes and cultivated under batch and fed-batch conditions. Subsequently, metabolomics, transcriptomics and proteomics samples from the fed-batch experiments were analyzed to inform the design of new genomic interventions.
Project description:Strains of urinary tract associated E. coli both recent isolates and from the ECOR collection and non pathogenic E. coli strains were analyzed. Replicates were performed to establish the reproduciblity, then single experiments were performed there on.
Project description:To quantify the transcription level of genes for Escherichia coli DY330 in different growth phases a series of RNA-Seq experiments was performed.
Project description:Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days. 7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol. Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. coli (day 0) to a midpoint evolved strain (day 20) and evolutionary endpoints Biological replicate arrays were conducted for each of the time points tested for the different evolution strains
Project description:Chromosome conformation capture and sequencing experiments were carried out at 37℃ and 45℃ for E. coli in logarithmic phase and stable phase, respectively. Three-dimensional DNA interaction data of E. coli under four different growth conditions and control group were obtained
Project description:To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.