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Antimicrobial mechanism analysis of an oil-in-water micro-emulsion by DNA microarray-mediated transcriptional profiling of Escherichia coli

ABSTRACT: The DNA microarray was employed in this study to investigate the gene expression profiles of Escherichia coli treated by an oil-in-water (o/w) microemulsion, in order to better understand the antimicrobial mechanism of the microemulsion as a promising food-grade antimicrobial system. 5,440 open reading frames (ORFs) of E. coli were investigated.

ORGANISM(S): Escherichia coli

PROVIDER: GSE50556 | GEO | 2014/01/28

SECONDARY ACCESSION(S): PRJNA217935

REPOSITORIES: GEO

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Antimicrobial mechanism analysis of an oil-in-water micro-emulsion by DNA microarray-mediated transcriptional profiling of Escherichia coli

Project description:The DNA microarray was employed in this study to investigate the gene expression profiles of Escherichia coli treated by an oil-in-water (o/w) microemulsion, in order to better understand the antimicrobial mechanism of the microemulsion as a promising food-grade antimicrobial system. 5,440 open reading frames (ORFs) of E. coli were investigated. 5 ml bacterial cultures with a known inoculum of E. coli cells (1.0 M-CM-^W 109 cfu/ml) was added at 1:1 (v/v) to the microemulsion and incubated on a tube rotator at 200 rpm for 4 h at 37 M-BM-0C for the subsequent DNA microarray analysis.

2014-01-28 | E-GEOD-50556 | biostudies-arrayexpress

Time course expression data from E.coli cells induced with differential amounts of IPTG

2011-05-15 | GSE12411 | GEO

Changes in cellular microRNA expression induced by porcine circovirus type 2-encoded proteins.

Project description:We employed deep sequencing technology to uncover cellular miRNAs differentially regulated after expression of each of three PCV2-encoded open reading frames (ORFs) in porcine kidney epithelial PK15 cells.

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Project description:We employed a proteogenomics workflow to identify microproteins encoded by small Open Reading Frames (ORFs) in the genome of Mycobacterium smegmatis strain mc²155.

2022-04-21 | PXD025604 | JPOST Repository

Pervasive, non-functional translation in mycobacterium tuberculosis

Project description:Open reading frame (ORF) boundaries in bacterial genomes have largely been drawn by gene prediction algorithms. However, these algorithms often fail to predict ORFs with non-canonical features, including those that are short, overlapping, or lack 5’ UTRs. Recent developments in genome-scale mapping of translation have facilitated the empirical identification of open reading frames (ORFs). Here, we use ribosome profiling approaches to map initiating and elongating ribosomes in Mycobacterium tuberculosis. Thus, we identify over 1,000 novel ORFs, revealing that much of the M. tuberculosis genome encodes proteins in overlapping reading frames, and/or on both strands. Most of the novel ORFs are short (sORFs), impeding their identification by traditional methods. The strong codon bias that characterizes annotated mycobacterial ORFs is not evident in the aggregate novel sORFs, and hence most are unlikely to encode functional proteins. Thus, our data suggest that bacterial transcriptomes are subject to pervasive translation that occurs as a result of the relatively low specificity requirements of initiating ribosomes. We speculate that the inefficiency of expressing spurious sORFs may be offset by positive contributions to M. tuberculosis biology through cis and trans regulatory activities of a small subset.

2019-06-20 | E-MTAB-8039 | biostudies-arrayexpress

Rhesus macaque rhadinovirus (RRV) gene expression in vivo

Project description:Viral gene expression profiling in a rhesus macaque rhadinovirus positive B cell lymphoma obtained from a rhesus macaque experimentally infected with simian immunodeficiency virus and rhesus macaque rhadinovirus strain 17577. The experiment identified two viral open reading frames (ORFs) that were expressed in the lymphoma. Expression of these viral ORFs were confirmed by reverse transcriptase-PCR.

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Time course expression data from E.coli cells induced with differential amounts of IPTG

Project description:In this work expression of two rhsA elements, ext-a1 and daORF-a1, was differentially induced using IPTG. RhsA is a member of multigene rhs family and can code for five different open reading frames (ORFs), referred to as genetic elements. The functions of rhsA and the different ORFs it codes are not well understood. We used microarrays to study the effect of over-expression of two rhsA elements, ext-a1 and daORF-a1, on E. coli cells. Keywords: time course E. coli cells were harvested from biological replicate cultures at 0 hrs (0 mM IPTG) and at 1.5 and 3.5 hrs (0, 0.1, and 1 mM IPTG) after IPTG induction for RNA extraction and hybridization on Affymetrix arrays. A total of seven different conditions were analysed. Two biological replicates and two technical replicates were performed for each condition (a total of 28 microarray hybridizations).

2011-05-15 | E-GEOD-12411 | biostudies-arrayexpress

PMCDS000ABG - samples

Project description:This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.

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PMCDS000ABF - samples

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Sequencing of a human Orfeome in subcellular compartments of mouse primary cortical neurons (mPCN)

Project description:To study how the codon composition of the coding sequence affects subcellular localization of mRNA in an unbiased way, mouse primary cortical neurons were transfected with a collection of human open reading frames (ORFs) with identical untranslated regions, separated into soma and neurites, and subjected to RNA sequencing with specific amplification of the ORFs.

2023-07-12 | E-MTAB-11571 | biostudies-arrayexpress

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