Ontology highlight
ABSTRACT:
PROVIDER: PRJNA830167 | ENA |
REPOSITORIES: ENA
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2021-07-05 | PXD020863 | Pride
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2021-07-05 | PXD020791 | Pride
Project description:The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pneumoniae and Streptococcus pyogenes, 5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. This submission contains the results from five Escherichia coli strains (B36, MS14384, MS14385, MS14386, MS14387) grown in either RPMI or pooled human sera. Six replicates of each condition were subjected to shotgun proteomics and label-free MS1-based quantitation.
2021-07-05 | PXD020545 | Pride
Project description:The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pneumoniae and Streptococcus pyogenes, 5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. This submission contains the results from five Streptococcus pneumoniae strains (4496, 947, 4559, 180-2, 180-15) grown under three conditions: RPMI supplemented with glucose, RPMI supplemented with galactose, or pooled human sera. Six replicates of each condition were subjected to shotgun proteomics and label-free MS1-based quantitation.
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Project description:We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over E. coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro display strong rotational positioning. Nucleosome arrays generated by the ACF assembly factor display fewer nucleosome-free regions, reduced rotational positioning, and less translational positioning than obtained by intrinsic histone-DNA interactions. Importantly, in vitro assembled nucleosomes display only a limited preference for specific translational positions and do not show the pattern observed in vivo. Our results argue against a genomic code for nucleosome positioning, and they suggest that the nucleosomal pattern in coding regions arises primarily from statistical positioning from a barrier near the promoter that involves some aspect of transcriptional initiation by RNA polymerase II.
2009-07-15 | GSE15188 | GEO
Project description:The genomic DNAs of strains JPCM5 and 263 of L. infantum, strains LV39 and Friedlin of L. major and strains Parrot-TarII and S125 of L. tarentolae were used in comparative genomic hybridizations to reveal the intra-species and inter-species gene content, and to validate L. tarentolae Parrot-TarII genome sequencing results. Leishmania (Sauroleishmania) tarentolae was first isolated in the lizard Tarentola mauritanica. This species is not known to be pathogenic to humans but is often used as a model organism for molecular analyses or protein overproduction. The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved by high-throughput sequencing technologies. The L. tarentolae genome was first assembled de novo and then aligned against the reference L. major Friedlin genome to facilitate contig positioning and annotation, providing a 23-fold coverage of the genome. This is the first non-pathogenic to humans kinetoplastid protozoan genome to be described, and it provides an opportunity for comparison with the completed genomes of the pathogenic Leishmania species. A high synteny was observed in de novo assembled contigs between all sequenced Leishmania species. A number of limited chromosomal regions diverged between L. tarentolae and L. infantum, while remaining syntenic with L. major. Globally, over 90% of the L. tarentolae gene content was shared with the other Leishmania species. There were 250 L. major genes absent from L. tarentolae, and interestingly these missing genes were primarily expressed in the intracellular amastigote stage of the pathogenic parasites. This implies that L. tarentolae may have impaired ability to survive as an intracellular parasite. In contrast to other Leishmania genomes, two gene families were expanded in L. tarentolae, namely the leishmanolysin (GP63) and a gene related to the promastigote surface antigen (PSA31C). Overall, L. tarentolae appears to have a gene content more adapted to the insect stage rather than the mammalian one. This may partly explain its inability to replicate within mammalian macrophages and its suspected preferred life style as promastigote in the lizards.
2011-10-21 | GSE27184 | GEO
Project description:Marine is one of the most important resources of microorganisms, including bacteria, actinomycetes, and fungi. As marine and terrestrial environments differ a lot in many aspects it is not surprising that the species and characteristics of microorganisms living there are very different. Interestingly, many marine microorganisms can find their congeners of the same species from terrestrial resources. The aim of this work is to evaluate the intraspecies differences between marine and terrestrial actinomycetes on metabolic level and to uncover the mechanism responsible for the differences. To address this, we carried out comparative metabolomics study on Nesterenkonia flava strains isolated from marine and terrestrial environments. The results showed that marine strains were clearly distinguished from their terrestrial congeners on the principal components analysis (PCA) scores plot of intracellular metabolites. The markers responsible for the discrimination of marine and terrestrial strains were figured out using loading plot from partial least squares discrimination analysis (PLS-DA). Pathway analysis based on PLS-DA, univariate analysis, and correlation analysis of metabolites showed that the major differential metabolites between the terrestrial N. flava and the marine ones were involved in osmotic regulation, redox balancing, and energy metabolism. Together, these insights provide clues as to how the previous living environment of microbes affect their current metabolic performances under laboratory cultivation conditions.
2017-08-12 | ST000875 | MetabolomicsWorkbench