Ontology highlight
ABSTRACT:
PROVIDER: PRJNA507334 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8255530_1.fastq.gz | Fastqsanger.gz | |||
| SRR8255530_2.fastq.gz | Fastqsanger.gz | |||
| SRR8255540_1.fastq.gz | Fastqsanger.gz | |||
| SRR8255540_2.fastq.gz | Fastqsanger.gz | |||
| SRR8255550_1.fastq.gz | Fastqsanger.gz |
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Project description:We report here the release of a multi organ transcriptome developped for the Arctic char Salvelinus alpinus. This reference set was obtained using the 454 GS FLX+ technology. A pool of one-year-old, immature offspring of wild, anadromous Arctic charr originating from Lake Varflusjoen, Svalbard (79oN), including both lean and fat individuals, and three-years-old mature offspring of charr originating from Lake Vårflusjøen, North-Norway (70oN) was sampled. In order to maximize the diversity of expressed transcripts, we sampled a variety of organs and tissues; the whole brain, gill and head kidney and pieces of the liver, gonad, abdominal fat and muscle.
2016-08-18 | E-MTAB-3522 | biostudies-arrayexpress
Project description:Challenge of vaccinated and unvaccinated salmon with Aeromonas salmonicida
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Project description:Background Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Despite the identification of several virulence factors the pathogenesis is still poorly understood. We have used high-throughput proteomics to display the differences between in vitro secretome of A. salmonicida wild-type (wt, hypervirulent, JF5054) and T3SS-deficient (isogenic DeltaascV, extremely low-virulent, JF2747) strains in exponential (GP) and stationary (SP) phases of growth. Results Among the different experimental conditions we obtained semi-quantitative values for a total of 2136 A. salmonicida proteins. Proteins of specific A. salmonicida species were proportionally less detected than proteins common to the Aeromonas genus or those shared with other Aeromonas species, suggesting that in vitro growth did not induce the expression of these genes. Four detected proteins which are unidentified in the genome of reference strains of A. salmonicida were homologous to components of the conjugative T4SS of A. hydrophila pRA1 plasmid. Polypeptides of three proteins which are specific to the 01-B526 strain were also discovered. In supernatants (SNs), the number of detected proteins was higher in SP (326 for wt vs 329 for mutant) than in GP (275 for wt vs 263 for mutant). In pellets, the number of identified proteins (a total of 1536) was approximately the same between GP and SP. Numerous highly conserved cytoplasmic proteins were present in A. salmonicida SNs (mainly EF-Tu, EF-G, EF-P, EF-Ts, TypA, AlaS, ribosomal proteins, HtpG, DnaK, peptidyl-prolyl cis-trans isomerases, GAPDH, Enolase, FbaA, TpiA, Pgk, TktA, AckA, AcnB, Mdh, AhpC, Tpx, SodB and PNPase), and several evidences support the theory that their extracellular localization was not the result of cell lysis. According to the Cluster of Orthologous Groups classification, 29% of excreted proteins in A. salmonicida SNs were currently poorly characterized. Conclusions In this part of our work we elucidated the whole in vitro exoproteome of hypervirulent A. salmonicida subsp. salmonicida and showed the secretion of several highly conserved cytoplasmic proteins with putative moonlighting functions and roles in virulence. All together, our results offer new information about the pathogenesis of furunculosis and point out potential candidates for vaccine development.
2013-11-11 | PXD000429 | Pride
Project description:Aeromonas salmonicida is a fish pathogen that causes furunculosis. Virulent strains of this bacterium are able to infect salmonid macrophages and survive within them, although mechanisms favouring intracellular survival are not completely understood. It is known that A. salmonicida cultured in vivo in the peritoneal cavity of the host undergoes changes in gene expression and surface architecture compared with cultures grown in vitro in broth. Therefore, in this study, the macrophage responses to A. salmonicida grown in vivo and in vitro were compared. Enriched macrophages isolated from head kidney of Atlantic salmon (Salmo salar) were infected in vitro in 96-well microtitre dishes and changes in gene expression during the infection process were monitored using a custom Atlantic salmon cDNA microarray. A. salmonicida cultures grown in tryptic soy broth and in peritoneal implants were used to infect the macrophages. The macrophages were harvested at 0.5, 1.0 and 2.0 h after addition of the bacteria to the medium. Significant changes in gene expression were evident by microarray analysis at 2.0 h post-infection in macrophages infected with broth-grown and implant-grown bacteria; however, qPCR analysis revealed earlier up-regulation of JunB and TNF-alpha in macrophages exposed to the implant-grown bacteria. Up-regulation of those genes and others is consistent with the effects of extracellular products of aeromonad bacteria on macrophages and also suggests initiation of the innate immune response. Keywords: time course
2008-02-27 | GSE8526 | GEO
Project description:Aeromonas salmonicida is a fish pathogen that causes furunculosis. Virulent strains of this bacterium are able to infect salmonid macrophages and survive within them, although mechanisms favouring intracellular survival are not completely understood. It is known that A. salmonicida cultured in vivo in the peritoneal cavity of the host undergoes changes in gene expression and surface architecture compared with cultures grown in vitro in broth. Therefore, in this study, the macrophage responses to A. salmonicida grown in vivo and in vitro were compared. Enriched macrophages isolated from head kidney of Atlantic salmon (Salmo salar) were infected in vitro in 96-well microtitre dishes and changes in gene expression during the infection process were monitored using a custom Atlantic salmon cDNA microarray. A. salmonicida cultures grown in tryptic soy broth and in peritoneal implants were used to infect the macrophages. The macrophages were harvested at 0.5, 1.0 and 2.0 h after addition of the bacteria to the medium. Significant changes in gene expression were evident by microarray analysis at 2.0 h post-infection in macrophages infected with broth-grown and implant-grown bacteria; however, qPCR analysis revealed earlier up-regulation of JunB and TNF-alpha in macrophages exposed to the implant-grown bacteria. Up-regulation of those genes and others is consistent with the effects of extracellular products of aeromonad bacteria on macrophages and also suggests initiation of the innate immune response. Keywords: time course Enriched macrophages from 24 responder fish that showed positive respiratory burst in response to phorbol myristate acetate were plated in individual wells of 96-well flat-bottom polystyrene tissue culture plates. A. salmonicida were added to the macrophages, and incubated for 0.5, 1.0 or 2.0 h. Control wells received 10 ul of HBSS. Three replicate infections were performed for each type of bacteria. Hybridizations were carried out in duplicate, reversing the fluors for each sample on the second chip.
2010-05-26 | E-GEOD-8526 | biostudies-arrayexpress
Project description:Aeromonas salmonicida
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Project description:High-throughput proteomics was used to determine the role of the fish liver in defense responses to bacterial infection, done using a rainbow trout (Oncorhynchus mykiss) model following infection with Aeromonas salmonicida, the causative agent of furunculosis. The vertebrate liver has multifaceted roles in innate immunity, metabolism, and growth; we hypothesize this tissue serves a dual function in supporting host defense in parallel to metabolic adjustments that promote effective immune function. While past studies have reported mRNA responses to A. salmonicida in salmonids, the impact of bacterial infectionon the liver proteome remains uncharacterized in fish.
2018-10-08 | PXD010186 | Pride
Project description:Salmon Macrophage early response to Aeromonas salmonicida
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