Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1139408 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mandarin fish (Siniperca chuatsi) has become one of the most commercially important freshwater aquaculture species in China because of its fast growth and high nutritional value. Here, the proteome of the spleen of pathogenetic and resistant mandarin fish on the 8th day after ISKNV infection were analyzed using Illumina NovaSeq 6000 and isobaric tag for relative and absolute quantitation. The spleen tissue of the control group (C), resistant group (K), and pathogenetic group (B) were collected at 8 dpc.
2021-07-09 | PXD027200 |
Project description:Treatment failures of antibiotic therapy are of major concern and can be caused by a misalignment of the antibiotic susceptibility determined in vitro with the behaviour of the pathogen in the patient. The aim of this study was to investigate the transcriptomic response of the uropathogenic strain E. coli CFT073 to antibiotic treatment in blood stream infection (BSI) models in order to understand and avoid antibiotic therapy failures in urosepsis treatments. Blood stream infection models were established by growing E. coli CFT073 in pooled human serum with and without ciprofloxacin and compared to Iso-sensitest medium. The antibiotic challenge was introduced at mid-logarithmic phase of growth of the organism to depict a clinical scenario . Global gene expression profiling of these conditions was examined using commercial DNA microarrays. The organismâs metabolic genes appeared to be regulated differently in each medium, this indicated that the bacterial growth regulation were different between the models. Bacterial growth in human serum mainly involved regulations of amino acid synthesis/utilisation such as glycine, arginine, thiamine, regulations of fimbrial proteins and bacteriophage genes. When comparing the responses to antibiotic challenge, bacteria grown in the respective medium displayed specific responses to the antibiotic challenge which were not seen in the other media. The common functions of genes that responded to the ciprofloxacin challenge were SOS response, DNA repair, DNA replication, fimbrial genes and bacteriophage initiation. A subset of the bacteriophage genes showed similar responses between the three models. From genes that were differentially regulated, responses observed in the serum model appeared to have the highest fold changes. In this study we established new models to investigate blood stream infections. They have been used to identify previously unknown differences in the molecular response to antibiotic treatment by the uropathogenic E. coli CFT073 depending on the media. These unique responses will help to unravel the complexity of bloodstream infection and can help to improve the antibiotic therapy that is used. A 20 array study using total RNA recovered from bacteria from bacteria that were either grown in human serum or Iso-Sensitest (IST) broth, with and without ciprofloxacin challenge. Arrays were performed in 5 biological replicates from each condition.Upon QC checks, certain biological repeats were excluded due to poor hybridisation results.
2016-04-01 | E-GEOD-68105 | biostudies-arrayexpress
Project description:One key concept in the evolution of new functions is the ability of enzymes to perform promiscuous side-reactions that serve as a source of novelty that may become beneficial under certain conditions. Here, we identify a mechanism where a bacteriophage-encoded enzyme introduces novelty by inducing expression of a promiscuous bacterial enzyme. By screening for bacteriophage DNA that rescued an auxotrophic E. coli mutant carrying a deletion of the ilvA gene, we show that bacteriophage-encoded S-adenosylmethionine (SAM) hydrolases reduce SAM levels. Via this perturbation of bacterial metabolism, expression of the promiscuous bacterial enzyme MetB is increased, which in turn complements the absence of IlvA. These results demonstrate how foreign DNA can increase the metabolic capacity of bacteria, not only by transfer of bona fide new genes, but also by bringing cryptic bacterial functions to light via perturbations of cellular physiology.
2018-04-11 | GSE92601 | GEO
Project description:Treatment failures of antibiotic therapy are of major concern and can be caused by a misalignment of the antibiotic susceptibility determined in vitro with the behaviour of the pathogen in the patient. The aim of this study was to investigate the transcriptomic response of the uropathogenic strain E. coli CFT073 to antibiotic treatment in blood stream infection (BSI) models in order to understand and avoid antibiotic therapy failures in urosepsis treatments. Blood stream infection models were established by growing E. coli CFT073 in pooled human blood with and without ciprofloxacin. The antibiotic challenge was introduced at mid-logarithmic phase of growth of the organism to depict a clinical scenario. The responses were quantified by comparing to the responses at a given time point without the challenge. Global gene expression profiling of these conditions was examined using commercial DNA microarrays. The organismâ??s metabolic genes appeared to be regulated differently in each medium, this indicated that the bacterial growth regulation were different between the models. Bacterial growth in human serum mainly involved regulations of amino acid synthesis/utilisation such as glycine, arginine, thiamine, regulations of fimbrial proteins and bacteriophage genes. When comparing the responses to antibiotic challenge, bacteria grown in the respective medium displayed specific responses to the antibiotic challenge which were not seen in the other media. The common functions of genes that responded to the ciprofloxacin challenge were SOS response, DNA repair, DNA replication, fimbrial genes and bacteriophage initiation. A subset of the bacteriophage genes showed similar responses between the three models. From genes that were differentially regulated, responses observed in the serum model appeared to have the highest fold changes. In this study we established new models to investigate blood stream infections. They have been used to identify previously unknown differences in the molecular response to antibiotic treatment by the uropathogenic E. coli CFT073 depending on the media. These unique responses will help to unravel the complexity of bloodstream infection and can help to improve the antibiotic therapy that is used. A 10 array study using total RNA recovered from bacteria that were grown in human whole blood, with and without ciprofloxacin challenge. Arrays were performed in 5 biological replicates from each condition.
2016-04-01 | E-GEOD-68106 | biostudies-arrayexpress
Project description:An important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S. aureus biofilms formed in the presence of a non-lethal dose of phage phiIPLA-RODI exhibit a unique physiological state that could potentially benefit both the host and the predator. Thus, biofilms formed under phage pressure are thicker and have a greater DNA content. Also, the virus-infected biofilm displayed major transcriptional differences compared to an untreated control. Significantly, RNA-seq data revealed activation of the stringent response, which could slow down the advance of the bacteriophage within the biofilm. The end result would be an equilibrium that would help bacterial cells to withstand environmental challenges, while maintaining a reservoir of sensitive bacterial cells available to the phage upon reactivation of the dormant carrier population.
2017-01-20 | GSE87706 | GEO