Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Effect of amphotericin B on Aspergillus fumigatus

ABSTRACT: Amphotericin B (AMB) is the most widely used polyene antifungal drug for the treatment of systemic fungal infections including invasive aspergillosis. We aimed to understand molecular targets of AMB in Aspergillus fumigatus (Afu) by genomic approaches. Amphotericin B (AMB) is the most widely used polyene antifungal drug for the treatment of systemic fungal infections including invasive aspergillosis. We aimed to understand molecular targets of AMB in Aspergillus fumigatus (Afu) by microarray and proteomic methods. Keywords: Aspergillus fumigatus treated with amphotericin B for 24 hours Experiment was performed in dye swap manner from two different biological replicates

ORGANISM(S): Aspergillus fumigatus

SUBMITTER: Puranam Sarma

PROVIDER: E-GEOD-10505 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Proteomic and transcriptomic analysis of Aspergillus fumigatus on exposure to amphotericin B.

Gautam Poonam P Shankar Jata J Madan Taruna T Sirdeshmukh Ravi R Sundaram Curam Sreenivasacharlu CS Gade Wasudev Namdeo WN Basir Seemi Farhat SF Sarma Puranam Usha PU

Antimicrobial agents and chemotherapy 20081006 12

Amphotericin B (AMB) is the most widely used polyene antifungal drug for the treatment of systemic fungal infections, including invasive aspergillosis. It has been our aim to understand the molecular targets of AMB in Aspergillus fumigatus by genomic and proteomic approaches. In transcriptomic analysis, a total of 295 genes were found to be differentially expressed (165 upregulated and 130 downregulated), including many involving the ergosterol pathway, cell stress proteins, cell wall proteins, ...[more]

PMID: 18838595

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Project description:We examined the antifungal activity of artemisinin against Aspergillus fumigatus (A. fumigatus), a pathogenic filamentous fungus responsible for allergic and invasive aspergillosis in humans and analyzed transcript profiles of the fungus on exposure to Artemisinin. A. fumigatus spores were cultured for 48 h and then treated with artemisinin (at MIC50 concentration) or solvent control (DMSO) for 3 h to study its transcriptomic profiles. Total RNA (7 M-BM-5g) from A. fumigatus treated with solvent control (DMSO) or artemisinin was reverse transcribed separately using fluorescein-labeled dCTP or biotin-labeled dCTP from Micromax TSA labeling kit (Cy3 or Cy5 dyes are differentially deposited to these labeled cDNAs, post-hybridization, using tyramide signal amplification (TSA) protocol). Labeled cDNAs from test and control sample were mixed in equal amount and hybridized to microarray slide(s). After hybridization, the slides were processed as per the protocol of the Micromax TSA labeling kit and scanned in both the Cy3 and the Cy5 channels with a model 4200 Axon Instruments scanner with a 10-M-BM-5m resolution. Each of the signals was converted into a resolution of 16 bits per pixel. A dye swap experiment with a biological replicate was performed to ensure the reproducibility of each gene expression pattern.TIFF images were analyzed using GenePix Pro 6.0 software. The signal intensity value of each spot was reduced by the local background level for each spot. Diagnosis and normalization of microarray data (DNMAD) program was used for print-tip loess normalization of microarray data and for merging the data from dye-swap experiments . M-values obtained from this program were converted to log ratio (test/reference) and fold modulation. Genes having less than 3 spots in 2 dye swap slides were discarded and only those having their all fold change values (from 3 or 4 replicates in 2 slides; as each target is spotted twice on the slide) within a coefficient of variation M-BM-1 0.5 were used for analysis. Gene expression ratios of M-bM-^IM-%2 (fold upregulation or downregulation) in both replicates (dye swap) were considered to be differentially expressed genes.

Dataset Information

Effect of amphotericin B on Aspergillus fumigatus

Publications

Proteomic and transcriptomic analysis of Aspergillus fumigatus on exposure to amphotericin B.

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