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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional analysis between Streptomyces clavuligerus ATCC 27064 and mutants altered in the antibiotics production

ABSTRACT: The objective is to analyze the differential expression between the wild strain and a ccaR-deleted and oppA2::aph mutants 6 biological conditions were used, three strains in two times (exponential and stationary growth phase; Streptomyces clavuligerus ATCC 27064, S. clavuligerus M-bM-^HM-^FccaR and S. clavuligerus oppA2::aph). Four biological replicates were made for each condition

ORGANISM(S): Streptomyces clavuligerus

SUBMITTER: Paloma Liras

PROVIDER: E-GEOD-51435 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional analysis between Streptomyces clavuligerus ATCC 27064 and a mutant altered in antibiotic production

Project description:The objective was to analyze the differential expression between the wild strain and the Streptomyces clavuligerus ΔclaR::aac mutant Six experimental conditions were assayed, two strains (Streptomyces clavuligerus ATCC 27064, S. clavuligerus ΔclaR::aac) in three culture times (22.5h, 46.5h and 60 h). Two biological replicates for each condition.

2015-08-05 | E-GEOD-66683 | biostudies-arrayexpress

Switching on antibiotic resistance in Staphylococcus aureus M-bM-^@M-^S Contribution of WalK and VraS histidine kinases in the development of vancomycin and daptomycin resistance

Project description:Staphylococcus aureus is a notorious bacterial pathogen that causes a broad range of human diseases, and isolates that are resistant to several antibiotic classes including last resort antibiotics like vancomycin and daptomycin complicate the situation. We characterized S. aureus VC40, a strain that shows full resistance to vancomycin (MIC of 64 M-BM-5g/ml) and daptomycin (MIC of 4 M-BM-5g/ml) as well as a decreased susceptibility to further cell wall active agents. Genome sequencing revealed mutations in genes encoding the histidine kinases WalK and VraS that control cell envelope related processes and gene expression profiling indicated the induction of the respective regulons in strain VC40. Reconstitution of the mutations in walK or vraS into the susceptible S. aureus NCTC 8325 background resulted in a considerably increased resistance to vancomycin and daptomycin with MICs surpassing the clinical breakpoints for these antibiotics, thereby generating vancomycin-intermediate S. aureus (VISA) strains. As observed for S. aureus VC40, the walKwalk and vraS mutations also led to an increased expression of the respective regulons in the NCTC 8325 background. Phenotypic studies showed that S. aureus VC40 as well as the walKwalk and vraS mutants of strain NCTC 8325 were characterized by a significantly thickened cell wall, a decreased growth rate, a reduced autolytic activity and an increased resistance to lysostaphin-induced lysis. These results demonstrate that the WalK and VraS histidine kinases act as major switches which allow S. aureus to rapidly develop vancomycin resistance up to the VISA level via mutation of one single gene locus and concomitantly contribute to cross-resistance to other antibiotics including the last resort antibiotic daptomycin. Microarray was used to evaluate alteration in the transcriptome of mutS mutant and compared to the parental strain VC40

2014-08-18 | E-GEOD-46887 | biostudies-arrayexpress

Molecular bases of virulence variability in Staphylococcus aureus mastitis isolates

Project description:Background: S. aureus is one of the main pathogen involved in ruminant mastitis worldwide. The severity of staphylococcal infection is highly variable and ranges from subclinical to gangrenous mastitis. Such variability implies host as well as staphylococcal factors. This work is an in-depth characterization of S. aureus mastitis isolates to identify factors involved in mastitis severity. Methods and findings: We combined three “omic” approaches to comprehensively compare two clonally related S. aureus strains that were isolated from and shown to reproducibly induce severe (strain O11) and milder (strain O46) mastitis in ewes. The genomes of O11 and O46 were sequenced (Illumina technology) to determine their respective gene content and comparative transcriptomic and proteomic analyses were carried out on both strains grown in conditions mimicking mastitis context. High differences were highlighted in mobile genetic elements, iron acquisition and metabolism, transcriptional regulation and exoprotein production. In particular, O11 overproduced exoproteins, including toxins and proteases when compared to O46. This was confirmed in 4 other S. aureus strains isolated from subclinical or clinical mastitis cases. Dose-dependant production of some staphylococcal factors seem to play a role in hypervirulence of strains isolated from severe mastitis. Mobile genetic elements, transcriptional regulators, exoproteins or strain ability to deal with iron starvation constitute good targets for further research to better define the underlying mechanisms of mastitis severity. Conclusions: Differences observed in mastitis severity likely result from the ability of the strains to adapt and to express virulence factors in the mastitis context rather than from deep variations in gene content. Expression of S. aureus O46 from subclinical mastitis and O11 from a lethal gangrenous mastitis were compared at two different times

2011-11-11 | E-GEOD-25084 | biostudies-arrayexpress

Chromatin immunopreciptiation of human lymphoblastoid untreated and treated with aphidicolin (APH), trichostatin A (TSA), or APH plus TSA cells to map the origins of DNA replication at common fragile sites

Project description:Map the origins of DNA replication in human cells at 7 common fragile sites and their flanking non-fragile sequences as well as a 200kb containing the rare fragile site FRAXA, and a 1,075kb non-fragile region on chr22 . The origins were mapped in untreated cells, as well as, in cells treated with aphidicolin (APH), trichostatin A (TSA), or APH plus TSA. The origin mapping experiment is based on the fact that during S phase, short newly replicated DNA fragments (300bp-1kb) are generated only at the origins of replication. By combining the nascent strand assay with a tiled microarray platform, we have previoulsy developed a rapid, non-PCR based, high-throughput approach to map active origins in asynchronous human cells (Lucas et al., 2007, AC 17668008).

2010-02-27 | E-TABM-348 | biostudies-arrayexpress

In vitro transcriptomic comparison of daptomycin-resistant Staphylococcus aureus

Project description:Mutants from SG511 and NCTC8325 (wild type isolates) resistant to daptomycin were obtained following serial passage experiments in vitro. Transcriptomic experiments showed alteration in the expression of genes involved in various pathways including general metabolism, cell wall regulon and lipid metabolism. Microarray was used to evaluate alteration in the transcriptome between wild type strains SG511 and NCTC8325 and their daptomycin resistant isolates, in antibiotic-free medium.

2015-11-01 | E-GEOD-50842 | biostudies-arrayexpress

Chromatin immunopreciptiation of human lymphoblastoid cells to identify histone H3K9/14 acetylation regions at common fragile sites

Project description:Map the histone H3K9/14 acetylation regions of in human cells at 7 common fragile sites and their flanking non-fragile sequences as well as a 200kb containing the rare fragile site FRAXA, a 1,075kb non-fragile region on chr22, a hyperacetylated region HALPHA44, and a heterochromatic region HET405. The acetylated regions were mapped in untreated, aphidicolin(APH)-treated, trichostatin(TSA)-treated, and TSA plus APH-treated cells by combining the chromatin-immunoprecipitation with a tiled microarray platform (ChIP-chip).

2009-10-07 | E-TABM-347 | biostudies-arrayexpress

A direct role for cohesin in genome-wide gene regulation and Ecdysone-response in Drosophila salivary gland

Project description:Developmental abnormalities observed in Cornelia de Lange Syndrome (CdLS) have been genetically linked to mutations in the cohesin machinery. These findings raise the possibility that cohesin, in addition to its canonical function of mediating sister chromatid cohesion, might also be involved in regulating gene expression. We report that cleavage of cohesin’s kleisin subunit in post-mitotic Drosophila salivary glands induces major changes (both up and down) in the transcript levels of many genes. Kinetic analyses of changes in transcript levels upon cohesin cleavage reveal that a subset of genes responds to cohesin cleavage within a few hours. In addition, cohesin binds to most of these loci, suggesting that cohesin is directly regulating their expression. Amongst these genes are several that are regulated by the steroid hormone Ecdysone. Transcripts at EcR and Eip74EF, which encode an Ecdysone Receptor and an Ecdysone-regulated transcription factor, respectively, decline ten-fold within four hours of cohesin cleavage. Cytological visualization of transcription at selected Ecdysone-responsive genes reveals that puffing at Eip74EF ceases within an hour or two of cohesin cleavage, long before any decline in EcR associated with this locus. We conclude that cohesin regulates expression of a distinct set of genes, including those mediating the Ecdysone response DamID experiments for Rad21 were performed on gDNA from drosophila salivary glands. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. The experiment was done in duplicate in the reverse dye orientation.

2011-03-22 | E-GEOD-21874 | biostudies-arrayexpress

Bacillithiol as Part of the Response of Staphylococcus aureus to Oxidative Stress

Project description:Overnight cultures of wild type COL or the bshA mutant were back-diluted to an O.D.650 of 0.1 in 30 mL of TSB. The cells were grown at 37C with shaking in a 300mL flask until they reached an O.D.650 of 1.1. The cells were then equally separated into 50mL Falcon tubes, so that each tube had 10mL of culture. One tube for each strain was induced with 1 mM diamide and one with 10 mM H2O2, which we did not send for analysis. All cultures were allowed to continue growing at 37C with shaking for another 20 minutes. RNA extractions were carried out as previously described in Tamber et al., Infect Imunn, 2010. Microarray was used to evaluate alteration in the transcriptome of COL and its bshA mutant strain in the presence/absence of bacillithiol

2013-11-12 | E-GEOD-46885 | biostudies-arrayexpress

A comprehensive microarray analysis of Enterococcus faecium in response to vancomycin in combination with the essential oil components carvacrol and cuminaldehyde

Project description:This study aims to determine the global gene expression in vancomycin resistant Enterococcus faecium (VRE) in response to a novel essential oil-vancomycin combination, and the individual components (vancomycin, carvacrol and cuminaldehyde) to help determine the mechanism of action of this antimicrobial formulation. This formulation increases the susceptibility of VRE to vancomycin and the array provides data on the synergistic mechanism of action. Five conditions (1. Control; 2. Carvacrol, 1.98 mM; 3. Cuminaldehyde, 4.20 mM; 4. Vancomycin, 0.031 mg/l; 5. Combination, 1.98 mM Carvacrol, 4.2 mM Cuminaldehyde, 0.031 mg/l vancomycin) all with 1% DMSO were tested in triplicate with a 60 minute exposure time before extraction.

2019-12-31 | E-MTAB-8072 | biostudies-arrayexpress

Effect of ppGpp on Salmonella Typhimurium gene expression

Project description:The expression profile of an S. Typhimurium mutant strain unable to synthesise ppGpp (relAspoT deletions) was compared to the wild-type strain. The effect of ppGpp on virulence gene expression was studied under 4 different growth conditions that induce virulence gene expression. Keywords: genetic modification Study comprised 4 separate experiments (with 2 strains and 4 replicates for each strain per growth condition). The experiments were indirect comparisons using Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

2010-06-11 | E-GEOD-4631 | biostudies-arrayexpress

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