Ontology highlight
ABSTRACT:
PROVIDER: PRJNA801099 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR18534252.fastq.gz | Fastqsanger.gz | |||
| SRR18534253.fastq.gz | Fastqsanger.gz | |||
| SRR18534254.fastq.gz | Fastqsanger.gz | |||
| SRR18534255.fastq.gz | Fastqsanger.gz |
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Project description:Bartonelloses are neglected emerging infectious diseases caused by facultatively intracellular bacteria transmitted between vertebrate hosts by various arthropod vectors. The highest diversity of Bartonella species has been identified in rodents. Within this study we focused on the edible dormouse (Glis glis), a rodent with unique life-history traits that often enters households and whose possible role in the epidemiology of Bartonella infections had been previously unknown. We identified and cultivated two distinct Bartonella sub(species) significantly diverging from previously described species, which were characterized using growth characteristics, biochemical tests, and various molecular techniques including also proteomics. Two novel (sub)species were described: Bartonella grahamii subsp. shimonis subsp. nov. and Bartonella gliris sp. nov.We sequenced two individual strains per each described (sub)species. During exploratory genomic analyses comparing two genotypes ultimately belonging to the same species, both factually and most importantly even spatiotemporally, we noticed unexpectedly significant structural variation between them. We found that most of the detected structural variants could be explained either by prophage excision or integration. Based on a detailed study of one such event, we argue that prophage deletion represents the most probable explanation of the observed phenomena.Moreover, in one strain of Bartonella grahamii subsp. shimonis subsp. nov. we identified a deletion related to Bartonella Adhesin A, a major pathogenicity factor that modulates bacteria-host interactions. Altogether, our results suggest that even a limited number of passages induced sufficient selective pressure to promote significant changes at the level of the genome.
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Project description:Genomic and proteomic characterization of novel Bartonella species/subspecies.
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Project description:The genomic diversity of 38 Bartonella henselae isolates was studied by comparative genomic hybridizations. In addition, the effect of growth time (5 or 10 days) was studied for 5 strains.
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Project description:Following the domestication of maize over the past 10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.
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Project description:Genomic plasticity helps adapt to extreme environmental conditions. We tested the hypothesis that exposure to space environment (ESE) impacts the epigenome as marked by DNA hypomethylation to induce genomic plasticity in responders. Murine skin samples from the Rodent Research Reference Mission-1 were procured from the International Space Station (ISS) National Lab. Targeted RNA sequencing to test differential gene expression between the skin of ESE versus ground controls revealed upregulation of VEGF mediated angiogenesis pathways secondary to promoter hypomethylation in responder ESE cohort. Methylome sequencing identified ESE-sensitive candidate hypomethylated genes including developmental angiogenic genes Araf, VegfbandVegfr1. Based on differentially expressed genes, the angiogenesis biofunction was enriched in responders compared to non-responders. The induction of genomic plasticity in response to ESE, as reported herein, may be viewed as a mark of biological resilience that is evident in a minority of organisms, responders but not in non-responders, exposed to the same stressor. Inducible genomic plasticity may be implicated in natural resilience to ESE.
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Project description:Genomic plasticity helps adapt to extreme environmental conditions. We tested the hypothesis that exposure to space environment (ESE) impacts the epigenome as marked by DNA hypomethylation to induce genomic plasticity in responders. Murine skin samples from the Rodent Research Reference Mission-1 were procured from the International Space Station (ISS) National Lab. Targeted RNA sequencing to test differential gene expression between the skin of ESE versus ground controls revealed upregulation of VEGF mediated angiogenesis pathways secondary to promoter hypomethylation in responder ESE cohort. Methylome sequencing identified ESE-sensitive candidate hypomethylated genes including developmental angiogenic genes Araf, VegfbandVegfr1. Based on differentially expressed genes, the angiogenesis biofunction was enriched in responders compared to non-responders. The induction of genomic plasticity in response to ESE, as reported herein, may be viewed as a mark of biological resilience that is evident in a minority of organisms, responders but not in non-responders, exposed to the same stressor. Inducible genomic plasticity may be implicated in natural resilience to ESE.
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Project description:As a result of increasing thermal fluctuations and mean temperature values, organisms will experience conditions beyond their physiological limits. In situ adaptation to thermal regimes is mediated via directional selection and phenotypic plasticity. The latter involves physiological and morphological adjustments realized by underlying molecular mechanisms. Understanding species' adaptive capacities requires investigating these adjustive processes. Yet, acclimation through phenotypic plasticity remains largely unexplored, especially at the molecular level; For example, whether cold-adapted species inhabiting freshwater spring ecosystems have evolved adaptive mechanisms to cope with warming of freshwater habitats has, to our knowledge, never been investigated. This work reports a comprehensive proteomics study of the stenotopic species Crunoecia irrorata (Curtis, 1834) (Trichoptera: Lepistomatidae) acclimated to 10, 15 and 20 °C for 168 h. A liquid chromatography tandem mass spectrometry (LC-MS/MS)-based shotgun proteomics approach identified molecular mechanisms underlying acclimation. We constructed a homology-based database by combining genomic and transcriptomic data from related species and quantified 1356 proteins, of which 186 were differentially expressed between temperature treatments. Through functional annotation, we identified candidate proteins facilitating, among others, trehalose accumulation, tracheal system alteration, and heat shock protein regulation, then discuss concomitant ecophysiological implications. These results provide new insights into the mechanisms of adaptive responses to warming of species inhabiting freshwater ecosystems sensitive to climate change. Further, identified candidate proteins will aid in developing targeted experiments to understand their compensatory physiology. To our knowledge, this is the first study utilizing this approach to investigate the nature of phenotypic plasticity of aquatic macroinvertebrates.
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