Comparative transcriptome analysis of a panel of Escherichia coli natural isolates
ABSTRACT: The link between phylogeny, gene expression and adaptation remains vague in bacteria. Here we compare the transcriptome of 16 E. coli stains isolated from various sources and spanning most common E. coli phylogroups (A, B1, B2, D, E and, F) and lifestyles. Total RNAs were extracted after growth of three biological replicates in lysogeny broth medium to exponential phase. After quality control on an Agilent 2100 Bioanalyzer. Samples were prepared for sequencing using the TruSeq® Stranded Total RNA Kit (Illumina) and sequenced on a NextSeq 500 benchtop sequencer (Illumina).
Project description:This SuperSeries is composed of the following subset Series: GSE12877: Transcriptional profiling of Escherichia coli after addition of CO-RMs to aerobically growing cells GSE12878: Transcriptional profiling of Escherichia coli after addition of CO-RMs to anaerobically growing cells Refer to individual Series
Project description:Citramalate is a chemical of potential industrial importance. Efficient fermentations have been developed using recombinant E. coli as the chassis. The experiments explore the transcriptional reprogramming that occurs upon induction of citramalate production.
Project description:Small non coding RNA molecules (sncRNAs) are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sncRNAs in the Gram positive opportunistic pathogen Enterococcus faecalis. Enterococcus faecalis. We characterized 11 sncRNAs by tiling microarray analysis, 5’ and 3’ RACE-PCR, and Northern blot analysis. Six sncRNAs were specifically expressed at exponential phase, two sncRNAs were observed at stationary phase, and three were detected during both phases. This is the first experimental genome-wide identification of sncRNAs in E. faecalis and provides impetus to the understanding of gene regulation in this important human pathogen. Identification of sncRNA candidates transcribed by E. faecalis V583 was undertaken with two samples of cells harvested in mid-log growth phase and stationary phase after 24h of incubation at 37°C in M17 glucose media.
Project description:Comparative study between the cervical lymph nodes and spleens of C57BL/6 mice. The focus of our study was the examination of the transcriptome profiles in the lymphoid organs of C57BL/6 mice (wild type and CD200-deficient).
Project description:A 13-(4-isopropylbenzyl)berberine derivative (named KR-72) was synthesized and examined for antifungal activities against various human pathogenic fungi. The synthesized compound exhibited remarkably enhanced antifungal activity than berberine and berberrubine. Regardless of the potent antifungal activity of KR-72, its mode of action and the physiological impacts of the drug on fungal metabolism remain elusive. In this study, we performed the DNA microarray-based transcriptome analysis to identify KR-72 responsive genes and employed reverse genetics approaches to characterize their functions in Cryptococcus neoformans, which causes fatal meningoencephalitis in humans. First, KR-72 treatment altered in remodeling of transcriptome profiles in C. neoformans. Genes involved in translation and transcription were mostly upregulated, while those involved in cytoskeleton, intracellular trafficking, lipid and carbohydrate metabolism and energy production were downregulated. Supporting this, KR-72 has a strong synergistic effect with a calcineurin inhibitor FK506, while it has an antagonistic effect with polyene drug. Finally, KR-72 treatment promoted expression of ECM16, NOP14, HSP10, and MGE1, which we proved to be essential for the growth of C. neoformans. Among them, KR-72 mediated induction of MGE1 also appeared to hamper the viability of C. neoformans, potentially through impaired cell cycle or DNA repair system. This study will proposed mode of action for KR-72. The six slides of Cryptococcus_neoformans 3X20K are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted under 2 conditions (with or without treatment of KR-72 with H99 (H99 Wild type strain (Cryptococcus neoformans var. grubii serotype A). We use the KR-72 non-treated RNAs from this experiment as a control RNA. We use Cy5 as Sample dye and Cy3 as a control dye.
Project description:OmpR is a DNA binding protein belonging to the OmpR/EnvZ two component system. This system is known to sense changes in osmolarity in Escherichia coli. Recently, OmpR in Salmonella enterica serovar Typhimurium was found to be activated by acidic pH and DNA relaxation. In this study, ChIP-on-chip was employed to ascertain the genome-wide distribution of OmpR in Salmonella Typhimurium and Escherichia coli in acidic and neutral pH. In addition we investigated the affect of DNA relaxation on OmpR binding in Salmonella Typhimurium. Analysis of OmpR binding at pH 7 and pH 4.5 in E-minimal medium in both SL1344 and CSH50. Three independent biological replicates at each pH 7 and pH 4.5 was performed. This was done in each strain background. DNA was immunopreciptated using an anti-FLAG anitbody which binds to flag-tagged OmpR in both strains. Two control ‘mock’ experiments were performed under the same culture condtions in each strain background; DNA was immunopreciptated using normal mouse IgG antibody. To analyse the effect of DNA relaxation onOmpR binding SL1344 was maintained in the exponential growth phase in LB broth with and without treatment with the drug novobiocin (25 μg/ml) for 40 min. This was peformed on two independent occasions. In all cases the experimental immunoprecipitated DNA was hybridised against the input DNA.
Project description:Transcriptional profiling of E. coli DH5alpha cells comparing control untreated cells with cells exposed to sublethal concentrations of reuterin (3-hydroxypropionaldehyde). Two-condition experiment, reuterin-treated vs. untreated control E. coli DH5alpha cells. 5 biological replicate sets of reuterin-treated vs. untreated cells which were independently grown and harvested. Each array is probed with 1 replicate set.
Project description:The overall objective of the heritage project is to study the role of the genotype in cardiovascular,metabolic and hormonal responses to aerobic exercise training and the contribution of regular exercise to changes in several cardiovascular disease and diabetes risk factors. The study cohort in this analysis consists of 473 Caucasian subjects (230 male and 243 female) from 99 nuclear families who completed ≥58 of the prescribed 60 exercise-training sessions.The phenotypic expression of each individual’s genotype is assessed under two well-defined environmental conditions, the pre- and post-training conditions. Here we have made the pre-training data available as used in the article Phillips BE, Williams JP, Gustafsson T, Bouchard C, Rankinen T, et al. (2013) Molecular Networks of Human Muscle Adaptation to Exercise and Age. PLoS Genet 9(3): e1003389. doi:10.1371/journal.pgen.1003389 52 U133+2 profiles (17–63 yr) generated from pre-exercise muscle biopsy samples from the HERITAGE Family Study. Heritage_pre dataset.
Project description:Here we report the construction of a absA2 mutant strain which exhibited the classic precocious hyper-production of antibiotics and its complementation by an N-terminal triple-FLAG tagged version of AbsA2. The complemented and non-complemented absA2 mutant strains were used in large-scale time-course experiments to investigate the effect of deleting absA2 on gene expression at multiple time points and identify AbsA2 DNA binding sites in ChIP-on-chip studies using high-density microarrays.
Project description:The widespread use of electricity raises the question of whether or not 50 Hz (power line frequency in Europe) magnetic fields (MFs) affect organisms. We investigated the transcription of Escherichia coli K-12 MG1655 in response to extremely low-frequency (ELF) MFs. Fields generated by three signal types (sinusoidal continuous, sinusoidal intermittent, and power line intermittent; all at 50 Hz, 1 mT), were applied and gene expression was monitored at the transcript level using an Affymetrix whole-genome microarray. Bacterial cells were grown continuously in a chemostat (dilution rate D = 0.4 h-1) fed with glucose-limited minimal medium and exposed to 50 Hz MFs with a homogenous flux density of 1 mT. For all three types of MFs investigated, neither bacterial growth (determined using optical density) nor culturable counts were affected. Likewise, no statistically significant change (fold-change > 2, P ≤ 0.01) in the expression of 4,358 genes and 714 intergenic regions represented on the gene chip was detected after MF exposure for 2.5 h (1.4 generations) or 15 h (8.7 generations). Moreover, short-term exposure (8 min) to the sinusoidal continuous and power line intermittent signal neither affected bacterial growth nor showed evidence for reliable changes in transcription. In conclusion, our experiments did not indicate that the different tested MFs (50 Hz, 1 mT) affected the transcription of E. coli. A total of 60 chips are included in this study. Each comparison (treated vs. sham-treated cultures; untreated negative control cultures) consists of three replicates. The three magnetic field test conditions include sinusoidal continous, sinusoidal intermittent (2 min on, 4 min off) and power line intermittent (2 min on, 4 min off). Exposure periods were 8 min, 2.5 h, or 15 h. The response control consists of E. coli cells treated for 10 min with 1 mM H2O2 or the equivalent water volume. The negative control comprises samples taken from cultures grown with the exposure chambers swiched off.