NAuRA: Genomic tool to identify staphylococcal enterotoxins
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ABSTRACT:
PROVIDER: PRJEB36994 | ENA |
REPOSITORIES: ENA
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Project description:NAuRA: Genomic tool to identify staphylococcal enterotoxins in Staphylococcus aureus strains responsible for foodborne outbreaks
| PRJEB36867 | ENA
Project description:WGS Staphylococcal isolates from PJI and Wounds
| PRJNA765573 | ENA
Project description:Genome-wide analysis of translation has the potential to provide major contributions in understanding the pathophysiology of infection processes, given the complex interplay between pathogens and host cells. This study uncovers the reshaping undergoing in the translational control system of the host in response to staphylococcal α-hemolysin oligomers (rAHL). Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, staphylococcal α-hemolysin, pore forming toxins, PTF. The comparison between translatome and transcriptome profiling was used to discover mRNA-specific changes of the SH-SY5Y cells transcriptome and translatome in response to staphylococcal α-hemolysin oligomers (rAHL). To identify translationally regulated mRNAs, gene expression signals derived from the polysomal mRNA populations were compared by microarrays analysis to those obtained from total RNAs. Polysomal mRNA and total mRNA were isolated from SH-SY5Y cells treated with 3nM of extracted oligomers (rAHL) for 2 hours. Cells lysates were collected from untreated cells (control) and from treated cells. All experiments were run in biological triplicates.
2015-04-01 | E-GEOD-60543 | biostudies-arrayexpress
Project description:Genome-wide analysis of translation has the potential to provide major contributions in understanding the pathophysiology of infection processes, given the complex interplay between pathogens and host cells. This study uncovers the reshaping undergoing in the translational control system of the host in response to staphylococcal α-hemolysin oligomers (rAHL). Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, staphylococcal α-hemolysin, pore forming toxins, PTF.
2015-04-01 | GSE60543 | GEO
Project description:Genome-wide analysis of translation has the potential to provide major contributions in understanding the pathophysiology of infection processes, given the complex interplay between pathogens and host cells. Informations about the translational state of mRNAs or the activity of RNA binding proteins and ncRNAs after treatment with sublytic doses of pore forming toxins are completely missing. This study uncovers the reshaping undergoing in the translational control system of the host in response to sublytic doses of staphylococcal α-hemolysin (AHL). Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, staphylococcal α-hemolysin, pore forming toxins, PTF. The comparison between translatome and transcriptome profiling was used to discover mRNA-specific changes of the SH-SY5Y cells transcriptome and translatome in response to sublytic doses of staphylococcal α-hemolysin (AHL). To identify translationally regulated mRNAs, gene expression signals derived from the polysomal mRNA populations were compared by microarrays analysis to those obtained from total RNAs. Polysomal mRNA and total mRNA were isolated from SH-SY5Y cells treated with sublytic doses (3nM) of AHL for 2 hours. Cells lysates were collected from untreated cells (control) and from treated cells. All experiments were run in biological triplicates.
2015-04-01 | E-GEOD-50652 | biostudies-arrayexpress
Project description:Staphylococcus aureus, a gram-positive bacterium, causes food poisoning and toxic shock syndrome through the production of superantigenic toxins known as Staphylococcal enterotoxins serotypes A-J (SEA, SEB, etc.) and toxic shock syndrome toxin-1 (TSST-1). A subset of these toxins have been classified as potential biothreat agents. The chronology of molecular events that could potentially characterize superantigenic toxicity and early pathogenesis is not well understood. The focus of this study was to determine the distinct and shared mechanisms of response to three toxins of the superantigenic family, namely SEA, SEB and TSST-1. Since skin functions as the front line of the host’s defense mechanism, melanocytes were selected for the study and treated with 25 µg/mL of one of these three toxins. Cells were collected after treatment for six different time periods, ranging from 0.5 h to 48 h. Total RNA was investigated using gene expression microarrays containing approximately 50,000 probes, and a subset of the results were validated using NanoString assays. Transcriptomic expression data indicated that each of these three toxins had a unique longitudinal trajectory. In particular, the gene expression profiles of SEB post-exposure was very distinct from those for SEA and TSST-1 superantigens. All three superantigens showed enriched biological networks related to necrosis, skin disorders, and inflammation. The three superantigens share some similarities in acting on the mechanisms underlying apoptosis, innate immunity, and other biological processes. Pathways related to innate immunity, such as the patterns of cytokine production and acute-phase response, showed toxin-specific regulation. The differentially regulated networks can be logical targets for early therapeutic intervention and can potentially serve as early diagnostic markers for superantigen-induced toxicity.
2022-06-30 | GSE124756 | GEO
Project description:Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated-annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. Recently, our group catalogued and annotated all previously known and newly identified sRNAs in several Staphylococcus aureus strains. These complete annotation files now serve as tools to compare the sRNA content of S. aureus to other bacterial strains to investigate the conservation of their sRNomes. Accordingly, in this study we performed RNAseq on two staphylococcal species, S. epidermidis and S. carnosus, identifying 118 and 89 sRNAs in these organisms, respectively. The sRNA content of all three species were then compared to elucidate their common and species-specific sRNA content, identifying a core set between 53 and 36 sRNAs encoded in each organism. In addition, we determined that S. aureus has the largest set of unique sRNAs (137) while S. epidermidis has the fewest (25). Finally, we identify a highly conserved sequence and structural motif differentially represented within, yet common to, both S. aureus and S. epidermidis. Collectively, in this study, we uncover the sRNome common to three staphylococcal species, shedding light on sRNAs that are likely to be involved in basic physiological processes common to the genus. More significantly, we have identified species-specific sRNAs that are likely to influence the individual lifestyle and behavior of these diverse staphylococcal strains.
2016-04-25 | GSE77567 | GEO
Project description:Genome-wide analysis of translation has the potential to provide major contributions in understanding the pathophysiology of infection processes, given the complex interplay between pathogens and host cells. Informations about the translational state of mRNAs or the activity of RNA binding proteins and ncRNAs after treatment with sublytic doses of pore forming toxins are completely missing. This study uncovers the reshaping undergoing in the translational control system of the host in response to sublytic doses of staphylococcal α-hemolysin (AHL). Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, staphylococcal α-hemolysin, pore forming toxins, PTF.
2015-04-01 | GSE50652 | GEO
Project description:Dermal macrophages (Macs) are essential for the timely resolution of staphylococcal skin infections. However the cell intrinsic pathways and microenvironmental cues that mediate this are unclear. Here we analyzed a strictly intradermal ear infection model with Staphylococcus aureus (S. aureus) to explore immunometabolic regulation.
2024-05-01 | GSE174674 | GEO
Project description:Dermal macrophages (Macs) are essential for the timely resolution of staphylococcal skin infections. However the cell intrinsic pathways and microenvironmental cues that mediate this are unclear. Here we analyzed a strictly intradermal ear infection model with Staphylococcus aureus (S. aureus) to explore immunometabolic regulation.
2024-05-01 | GSE174675 | GEO