Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome profiling of E. coli under different naphthoquinone treatments

ABSTRACT: E. coli MG1655 was grown in the presence of either PL (Plumbagin)/JU (Juglone)/ME (Menadione) (50 micro molar) and DMSO (0.75%)as control, and subjected to microarray analysis. The aim of the work was to understand the structure-function relationship between plumbagin and its analogues.

ORGANISM(S): Escherichia coli

SUBMITTER: Arun Sharma

PROVIDER: E-MEXP-3765 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Antimutagenic and antioxidant properties of plumbagin and other naphthoquinones.

Kumar Sanjeev S Gautam Satyendra S Sharma Arun A

Mutation research 20130517 1

The structure-function relationships of the naphthoquinone phytochemicals, plumbagin, juglone, and menadione, have been studied with regard to antimutagenic and antioxidant activities. Antimutagenicity of these compounds was assessed by the Ames test and RNA polymerase B (rpoB)-based rifampicin resistance assay. Antioxidant potential was evaluated by radical scavenging assays and reducing power measurement. Protection of cells and DNA against gamma radiation-induced oxidative damage was assayed ...[more]

PMID: 23688616

Similar Datasets

Project description:Paracoccidioides brasiliensis is a thermodimorphic fungus associated with paracoccidioidomycosis (PCM), the most common systemic mycosis in Latin America. The infection is initiated by inhalation of environmental dispersed conidia produced by the saprophytic phase of the fungus. In the lungs, P. brasiliensis assumes the parasitic yeast form and must cope with the adverse conditions imposed by cells of the host immune system, which includes a harsh environment highly concentrated in reactive oxygen species (ROS). In this work, we used the ROS-generating agent paraquat to experimentally simulate oxidative stress conditions in order to evaluate the stress-induced modulation in gene expression of cultured P. brasiliensis yeast cells using a microarray hybridization approach. Microarray hybridizations were carried out with RNA obtained from cells treated with paraquat (0.5 or 5.0 mM) for 5 hours. The RNA obtained from cells unexposed to paraquat was taken as reference. Each treatment was analyzed with four independent hybridizations (two pairs of dye-swapped hybridizations), using RNA from two biological replicas. The data has been filtered, normalized and adjusted as described in the "data processing" box for each individual sample. Dye swap consistency checking has been performed between equivalent experimental pairs with the aid of the software TIGR MIDAS v2.19 and inconsistent spots have been flagged and excluded from further analyses. The values obtained from each dye swap pair have been averaged and consolidated into a single data file, generating a total of 8 hybridization files (four from each treatment concentration). These files have been loaded into the software TIGR Multi-Experiment Viewer, v.3.01. Experiments were then normalized and genes that displayed statistically significant modulation were identified by one-way ANOVA, considering p < 0.01 as a cutoff value. A list of statisticaly significant, modulated genes was created, showing the average log ratio for each one of these genes, within each time point

Project description:Phenothiazines are antipsychotic drugs used in the treatment of schizophrenia, which have been shown to present antimicrobial activity (in vitro and in vivo) against a great variety of pathogenic microorganisms, including bacteria, parasites (protozoa and helmints) and fungi. In this study, we used competitive microarray hybridization to evaluate the effects of increasing concentrations of the piperidinic phenothiazine derivative thioridazine (TR) on the transcriptome of Paracoccidioides brasiliensis, the causative agent of paracoccidioidomycosis (PCM) - the most common systemic mycosis in Latin America. These analyses showed that the presence of TR affected expression of more than 1,800 genes from this fungus, including genes related to cellular processes such as cell wall metabolism and drug resistance. Microarray hybridizations were carried out with amplified RNA (aRNA), which was produced starting with total RNA extracted from cells treated with thioridazine (15, 20 or 25 M-BM-5M) for 168 hours. The aRNA synthesized from cells unexposed to TR was taken as reference. Each treatment was analyzed with two independent hybridizations (a pair of hybridizations, with dye-swaps within each pair). Since each biochip carried two replicas of the arrayed genes, a total of four intensity readings were generated for each element in the microarray.The data has been filtered, normalized and adjusted as described in the "data processing" box for each individual sample. Dye swap consistency checking has been performed between equivalent experimental pairs with the aid of the software TIGR MIDAS v2.19 and inconsistent spots have been flagged and excluded from further analyses. The values obtained from each dye swap pair have been averaged and consolidated into a single data file, generating a total of 8 hybridization files (four from each treatment concentration). These files have been loaded into the software TIGR Multi-Experiment Viewer, v.3.1 Experiments were then normalized and genes that displayed statistically significant modulation were identified by one-way ANOVA, considering p < 0.01 as a cutoff value. A list of statisticaly significant, modulated genes was created, showing the average log ratio for each one of these genes, within each time point.

Project description:Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa, is an important citrus disease that produces chlorotic injuries on leaves and reduced fruit size. This bacterium colonizes plant xylem, thereby interrupting sap flow. Other disease symptoms depend on environmental factors, since asymptomatic and symptomatic CVC plants may be genetically similar. The endophytic microbiome comprises many microbial species that may interact with pathogens, reducing disease symptoms and improving plant growth. However, the genetic and physiological mechanisms that underlie this interaction are largely unknown. In this study, the citrus endophytic bacterium Methylobacterium mesophilicum SR1.6/6 was isolated from healthy plants. This bacterium was able to colonize citrus xylem and could be transferred from plant to plant by Bucephalogonia xanthopis (Insecta), suggesting that this endophytic bacterium may interact with X. fastidiosa in planta, as a result of co-transmission by the same insect vector. To better understand how X. fastidiosa genetic responds to the presence of M. mesophilicum in the same environment, we used microarrays to evaluate the transcriptional profile of X. fastidiosa, after in vitro co-cultivation with M. mesophilicum SR1.6/6. The results showed that during co-cultivation with M. mesophilicum, X. fastidiosa downregulated genes related to growth, while genes related to energy production (cellular respiration) and transport were upregulated. Moreover, X. fastidiosa modulates genes associated with molecular recognition, nutrient competition and the stress response, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium To evaluate and compare the Xylella fastidiosa 9a5c transcriptome profiles from bacteria cultured in PW and in co-cultive with Methylobacterium mesophilicum SR1.6/6, bacterial cultures were harvested for total RNA extraction after 24h of inoculation. Samples from the resulting RNAs were then used in competitive hybridizations against Xf microarrays. Replicated experiments were performed with RNA preparations from cells in each treatment and since each microarray carried two replicas of each spotted gene, we ended up with a series of 4 independent readings for each gene present in the microarrays. Images were analyzed with the TIGR Spotfinder program (v.2.2.4). All spots with median values lower than the median local background plus two Standard Deviations have been flagged and excluded from further analyses. Replicated experiments were performed with two independent RNA preparations from cells cultivated in each medium. For each pair of RNA preparations, two independent hybridizations were performed, with dye swaps within each pair. The results from each hybridization were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array. Finally, the results from each individual experiment were loaded into the software TIGR Multi-Experiment Viewer (TMEV), v.3.01. Experiments were then normalized and genes that displayed statistically significant modulation were identified with the aid of the one-class option of the Significance Analysis of Microarrays (SAM) test, described by Tusher et al. (2001). The Î´ factor of the SAM test was adjusted to guarantee a False Discovery Rate (FDR) < 1.

Dataset Information

Transcriptome profiling of E. coli under different naphthoquinone treatments

Publications

Antimutagenic and antioxidant properties of plumbagin and other naphthoquinones.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets