Ontology highlight
ABSTRACT:
PROVIDER: PRJNA606529 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11080151_1.fastq.gz | Fastqsanger.gz | |||
| SRR11080151_2.fastq.gz | Fastqsanger.gz | |||
| SRR11080152_1.fastq.gz | Fastqsanger.gz | |||
| SRR11080152_2.fastq.gz | Fastqsanger.gz | |||
| SRR11080153_1.fastq.gz | Fastqsanger.gz |
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Project description:Sodium benzoate is a widely used food antimicrobial in drinks and fruit juices. A microarray study was conducted to determine the transcriptional response of Escherichia coli O157:H7 to 0.5% (w/v) sodium benzoate. Stationary phase E. coli O157:H7 grown in 150 ml Luria-Bertani broth (LB) was exposed to 0 (control) and 0.5% sodium benzoate. Each treatment was duplicated and sampled at 0 (immediately after exposure), 5, 15, 30, and 60 min. Total RNA was extracted and analyzed with E. coli 2.0 Gene Chips.
2009-10-05 | GSE17519 | GEO
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.
2014-01-28 | GSE50556 | GEO
Project description:Pathogenic biofilms have been associated with persistent infections due to their high resistance to antimicrobial agents. To identify non-toxic biofilm inhibitors for enterohemorrhagic Escherichia coli O157:H7, indole-3-acetaldehyde was used and reduced E. coli O157:H7 biofilm formation. Global transcriptome analyses revealed that indole-3-acetaldehyde most repressed two curli operons, csgBAC and csgDEFG, and induced tryptophanase (tnaAB) in E. coli O157:H7 biofilm cells. Electron microscopy showed that indole-3-acetaldehyde reduced curli production in E. coli O157:H7. Together, this study shows that Actinomycetales are an important resource of biofilm inhibitors as well as antibiotics.
2012-07-05 | GSE30424 | GEO
Project description:Sodium benzoate is a widely used food antimicrobial in drinks and fruit juices. A microarray study was conducted to determine the transcriptional response of Escherichia coli O157:H7 to 0.5% (w/v) sodium benzoate. Stationary phase E. coli O157:H7 grown in 150 ml Luria-Bertani broth (LB) was exposed to 0 (control) and 0.5% sodium benzoate. Each treatment was duplicated and sampled at 0 (immediately after exposure), 5, 15, 30, and 60 min. Total RNA was extracted and analyzed with E. coli 2.0 Gene Chips. Experiment Overall Design: Completely randomized design with 0% (control) and 0.5% (w/v) sodium benzoate treated cells were exposed for 0 (immediately after exposure), 5 min, 15 min, 30 min, and 60 min. Each experiment was replicated once and total RNA was extracted and Affymetrix prokaryotic protocol was followed to hybridize cDNA onto E. coli Genome 2.0 Arrays.
2009-10-09 | E-GEOD-17519 | biostudies-arrayexpress
Project description:An experiment to identify the downstream targets of PatE, a prophage encoded AraC-like transcriptional regulator, in transcriptional activation of acid-resistance pathways of enterohemorrhagic Escherichia coli strain EDL933 using deletion and complementation strains (Delta3 and Delta3_1, respectively). Incomplete 2 factor with dye swaps. Genotype: 3 levels (wt, detla3, delta3_1) Bicarbonate: 2 levels (pos, neg) on wt only. 4 biological replicates, 2 in each dye orientation. Microarrays processed at Australian Genome Research Facility.
2012-03-29 | E-GEOD-36922 | biostudies-arrayexpress
Project description:<p>The study of antimicrobial resistance (AMR) in infectious diarrhea has generally been limited to cultivation, antimicrobial susceptibility testing and targeted PCR assays. When individual strains of significance are identified, whole genome shotgun (WGS) sequencing of important clones and clades is performed. Genes that encode resistance to antibiotics have been detected in environmental, insect, human and animal metagenomes and are known as "resistomes". While metagenomic datasets have been mined to characterize the healthy human gut resistome in the Human Microbiome Project and MetaHIT and in a Yanomani Amerindian cohort, directed metagenomic sequencing has not been used to examine the epidemiology of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate antibiotic resistance elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple antibiotic resistance in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia. We propose to use deep metagenomic sequencing and genome level assembly to study the epidemiology of AMR in stools of children suffering from diarrhea. Here the epidemiology component will be surveillance and analysis of the microbial composition (to the bacterial species/strain level where possible) and its constituent antimicrobial resistance genetic elements (such as plasmids, integrons, transposons and other mobile genetic elements, or MGEs) in samples from a cohort where diarrhea is prevalent and antibiotic exposure is endemic. The goal will be to assess whether consortia of specific mobile antimicrobial resistance elements associate with species/strains and whether their presence is enhanced or amplified in diarrheal microbiomes and in the presence of antibiotic exposure. This work could potentially identify clonal complexes of organisms and MGEs with enhanced resistance and the potential to transfer this resistance to other enteric pathogens.</p> <p>We have performed WGS, metagenomic assembly and gene/protein mapping to examine and characterize the types of AMR genes and transfer elements (transposons, integrons, bacteriophage, plasmids) and their distribution in bacterial species and strains assembled from DNA isolated from diarrheal and non-diarrheal stools. The samples were acquired from a cohort of pediatric patients and controls from Colombia, South America where antibiotic use is prevalent. As a control, the distribution and abundance of AMR genes can be compared to published studies where resistome gene lists from healthy cohort sequences were compiled. Our approach is more epidemiologic in nature, as we plan to identify and catalogue antimicrobial elements on MGEs capable of spread through a local population and further we will, where possible, link mobile antimicrobial resistance elements with specific strains within the population.</p>
| phs001260 | dbGaP
Project description:Jamaican fruit bats (Artibeus jamaicensis) naturally harbor a wide range of viruses of human relevance. These infections are typically mild in bats, suggesting unique features of their immune system. To better understand the immune response to viral infections in bats, we infected Jamaican fruit bats with the bat-derived influenza A virus H18N11. Using comparative single-cell RNA sequencing, we generated a single-cell atlas of the Jamaican fruit bat intestine and mesentery, the target organs of infection. Gene expression profiling showed that H18N11 infection resulted in a moderate induction of interferon-stimulated genes and transcriptional activation of immune cells. H18N11 infection was prominent in various leukocytes, including macrophages, B cells, and NK/T cells. Confirming these findings, human leukocytes, particularly macrophages, were also susceptible to H18N11, highlighting the zoonotic potential of this virus. Our study provides insight into the virus-host relationship and thus serves as a fundamental resource for further characterization of bat immunology.
2024-05-06 | GSE243982 | GEO
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
Project description:Evolution of antibiotic resistance in microbes is frequently achieved by acquisition of spontaneous mutations during antimicrobial therapy. Here we demonstrate that inactivation of a central regulator of iron homeostasis (fur) facilitates laboratory evolution of ciprofloxacin resistance in Escherichia coli. To decipher the underlying molecular mechanisms, we first performed a global transcriptome analysis and demonstrated a substantial reorganization of the Fur regulon in response to antibiotic treatment. We hypothesized that the impact of Fur on evolvability under antibiotic pressure is due to the elevated intracellular concentration of free iron and the consequent enhancement of oxidative damage-induced mutagenesis. In agreement with expectations, over-expression of iron storage proteins, inhibition of iron transport, or anaerobic conditions drastically suppressed the evolution of resistance, while inhibition of the SOS response-mediated mutagenesis had no such effect in fur deficient population. In sum, our work revealed the central role of iron metabolism in de novo evolution of antibiotic resistance, a pattern that could influence the development of novel antimicrobial strategies. We used microarrays to identify genotype specific transcriptional changes under severe DNA damaging conditions (antibiotic ciprofloxacin). We treated Escherichia coli cells with a highly toxic level of ciprofloxacin (gyrase inhibitor) for RNA extraction and hybridization on Affymetrix microarrays. We planned to find genotype specific transcriptional responses using WT control (BW25113) and fur-knockout mutant (selected from the KEIO collection) strains during antibiotic treatments. For each treatment type we used two biological replicates.
2014-09-11 | E-GEOD-55662 | biostudies-arrayexpress