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Y. pestis exposed to various concentrations of ciprofloxacin for various time points (treated/nontreated analysis in each array).

ABSTRACT: Cultures of Y. pestis Kimberley53 virulent strain were exposed to different concentrations of ciprofloxacin (including 0.016 µg/ml representing the strains' MIC value) for various time periods. Total RNA samples were extructed and used for cRNA synthesis and labelling (using Cy3-CTP for the treated samples and Cy5-CTP for the non-treated sample in one biological experiment and dye swap for the 2nd replicate of independent biological experiment). 8 Labeled cRNA samples were hybridized to custom made Agilent 8x15K slide (each slide represent 1 time point). Goal: Identifing alterations in gene expression profile which correlates with the ciprofloxacin induced growth inhibition. Those altered mRNA transcrips will be used as a markers for the development of rapid molecular Antibiotic Susceptibility Test.

ORGANISM(S): Yersinia pestis

PROVIDER: GSE79687 | GEO | 2016/03/30

SECONDARY ACCESSION(S): PRJNA316706

REPOSITORIES: GEO

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Y. pestis exposed to various concentrations of ciprofloxacin for various time points (treated/nontreated analysis in each array).

Project description:Cultures of Y. pestis Kimberley53 virulent strain were exposed to different concentrations of ciprofloxacin (including 0.016 Âµg/ml representing the strains' MIC value) for various time periods. Total RNA samples were extructed and used for cRNA synthesis and labelling (using Cy3-CTP for the treated samples and Cy5-CTP for the non-treated sample in one biological experiment and dye swap for the 2nd replicate of independent biological experiment). 8 Labeled cRNA samples were hybridized to custom made Agilent 8x15K slide (each slide represent 1 time point). Goal: Identifing alterations in gene expression profile which correlates with the ciprofloxacin induced growth inhibition. Those altered mRNA transcrips will be used as a markers for the development of rapid molecular Antibiotic Susceptibility Test. Y. perstis exposed to 0.001, 0.016, 0.5 and 4 Âµg/ml ciprofloxacin, compared to growth control (non treated) sample, for 3 time periods (45, 90 and 120 min.). Two independent biological replicates were performed. Extracted total RNA were used for cRNA synthesis and labeling with Cy3/Cy5-CTP, hybridized to Agilent custom-made 8x15K slide format.

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S. coelicolor, Control (untreated) Vs Ciprofloxacin treated

Project description:Transcriptional profiling of S. coelicolor comparing control untreated cells with ciprofloxacin treated cells. Two-condition experiment, Control Vs CIP treatment. Biological replicates: 3 control, One dye swap replicate. four samples and three biological replicate to study the response of S. coleicolor cells to ciprofloxacin

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Project description:Ciprofloxacin, an inhibitor of bacterial gyrase and topoisomerase IV, was shown to inhibit growth of C. glutamicum with concomitant excretion of L-glutamate. C. glutamicum strains overproducing L-lysine, L-arginine, L-ornithine, and putrescine, respectively, produced L-glutamate instead of the desired amino acid when exposed to ciprofloxacin. Even in the absence of the putative L-glutamate exporter gene yggB, ciprofloxacin effectively triggered L-glutamate production. When C. glutamicum wild type was cultivated under nitrogen-limiting conditions, 2-oxoglutarate rather than L-glutamate was produced as consequence of exposure to ciprofloxacin. Transcriptome analysis revealed that ciprofloxacin increased RNA levels of genes involved in DNA synthesis, repair and modification. Enzyme assays showed that 2-oxoglutarate dehydrogenase activity was decreased due to ciprofloxacin addition. Here, it was shown for the first time that production of L-glutamate by C. glutamicum may be triggered by an inhibitor of DNA synthesis and L-glutamate titers of up to 37 ± 1 mM and a substrate specific L-glutamate yield of 0.13 g/g were reached.

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Project description:Fresh MEC1 cells (chronic lymphocytic leukemia) (ACC-497, DSMZ) previously untreated and treated in cultures in vitro with glycodendrimers (nanoparticle with maltotriose on the surface). MEC1 cells were centrifuged after incubation with drugs or dendrimers. Agilent’s Low Input Quick Amp Labeling Kit was used to generate fluorescent cRNA (complimentary RNA) with a sample input 100ng of total RNA for two-color processing. The method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP. Amplification is typically at least a 100-fold from total RNA to cRNA with the use of this kit. cRNA quantification had been done using NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1. Arrays were placed onto the gaskets and than to the slide chamber in rotisserie in a hybridization oven set. Hybrydization was carried out at 65-Celsius degrees for 17 hours. Arrays were scanning using Agilent Scanner. Scan resolution was set up for 3μM.

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PAO1-Lon-ciprofloxacin

Project description:Microarray experiments were preformed comparing the effect of sub-inhibitory concentrations of ciprofloxacin on five independent cultures of PAO1 and the PAO1 Lon mutant

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Transcriptional profiling of Campylobacter jejuni wild-type 81-176 and its ciprofloxacin-resistant derivative (P3) in the presence and absence of ciprofloxacin

Project description:Campylobacter jejuni is one of the most important zoonotic enteric bacterial pathogens able to colonize the gastrointestinal tract of various animals. The number of campylobacteriosis cases has increased worldwide and the particular concern has been the high level of fluoroquinolone resistance observed in C. jejuni isolates. In this study, we explored the effect of ciprofloxacin in Campylobacter jejuni by gene expression microarray analysis. The comparisons of transcriptional responses were performed in the absence and presence of ciprofloxacin with the wild-type strain 81-176 and its intermediate-resistant variant (P3). The resistant variant contained a single-nucleotide mutation causing amino acid change Asp-90-Asn in the gyrA gene instead of the most common Thr-86-Ile, causing a high-level resistance to ciprofloxacin. After the short-term exposure to a relatively high concentration of ciprofloxacin, the viability of C. jejuni 81-176 wild-type cells remained notably high when compared with other gram-negative bacteria. The general responses of short-term ciprofloxacin exposure were determined from both genetic backgrounds and resulted in the expression variation of genes participating in general cellular processes, e.g. , in carbon and amino-acid metabolism and protein transport.

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