Crocodile skin microbiota
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB31501 | ENA |
REPOSITORIES: ENA
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Project description:MicroRNAs (miRNAs) are 18-24 nucleotide autonomous regulatory RNA molecules found in all eukaryotes. They are involved in the regulation of a multitude of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Previous data has suggested a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to its closest extant relatives, the birds. Understanding genome regulation, adaptive capabilities and physiological features in the saltwater crocodile in the context of relatively slow genomic change thus holds significant potential for the investigation of genomics, evolution and adaptive studies. Utilizing eleven different tissue types and sixteen small RNA libraries, we report a catalog of 644 miRNAs in the saltwater crocodile with > 78% of miRNAs being potentially novel to crocodilians. We also predicted and identified targets for the miRNAs as well as analyzed the relationship of the miRNA repertoire to transposable elements (TEs) in the saltwater crocodile that showed an increased association of DNA transposons with miRNA biogenesis when compared to retrotransposons. Phylogenetic analysis of C. porosus miRNA expectedly revealed highest number of miRNAs in sister crocodilian clades of the American Alligator and the Indian Gharial. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus for and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile as well as supporting the role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.
2020-08-24 | GSE150461 | GEO
Project description:In a reproductive strategy that is considered unique to the mammalian lineage, spermatozoa must undergo a series of physiological changes, termed capacitation, in the female reproductive tract prior to developing their capacity to fertilize an ovum. Here, we have employed a comparative proteomic strategy to explore the biological significance of this form of post-testicular maturation in the ancient reptilian species of the Australian saltwater crocodile (Crocodylus porosus).
2018-04-08 | MSV000082258 | MassIVE
Project description:Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus
| PRJNA632490 | ENA
Project description:Background: The skin harbors complex communities of resident microorganisms, yet little is known of their physiological roles and the molecular mechanisms that mediate cutaneous host-microbe interactions. Here, we profiled skin transcriptomes of mice reared in the presence and absence of microbiota to elucidate the range of pathways and functions modulated in the skin by the microbiota. Results: A total of 2820 genes were differentially regulated in response to microbial colonization and were enriched in gene ontology (GO) terms related to the host-immune response and epidermal differentiation. Innate immune response genes and genes involved in cytokine activity were generally upregulated in response to microbiota and included genes encoding toll-like receptors, antimicrobial peptides, the complement cascade, and genes involved in IL-1 family cytokine signaling and homing of T cells. Our results also reveal a role for the microbiota in modulating epidermal differentiation and development, with differential expression of genes in the epidermal differentiation complex (EDC). Genes with correlated co-expression patterns were enriched in binding sites for the transcription factors Klf4, AP-1, and SP-1, all implicated as regulators of epidermal differentiation. Finally, we identified transcriptional signatures of microbial regulation common to both the skin and the gastrointestinal tract. Conclusions: With this foundational approach, we establish a critical resource for understanding the genome-wide implications of microbially mediated gene expression in the skin and emphasize prospective ways in which the microbiome contributes to skin health and disease.
2018-01-24 | GSE98877 | GEO
Project description:We identified skin microbiota signatures related to different symptoms, i.e. pain, pruritus, in patients with Mycosis Fungoides.
2022-04-11 | GSE186083 | GEO
Project description:Essential to terrestrial life is the formation of a competent skin barrier that prevents desiccation and entry by harmful substances. A tightly orchestrated series of cellular changes is required for the proper formation of the epidermal permeability barrier. These changes occur in the context of the commensal skin microbiota. Using germ free mice and antibiotic depletion models, we demonstrate the microbiota is necessary for proper differentiation and repair of the barrier. These effects were mediated by keratinocyte signaling through the aryl hydrocarbon receptor (AHR), a xenobiotic receptor that also regulates epidermal differentiation. Murine skin lacking keratinocyte AHR was more susceptible to infection by S. aureus and increased pathology in a model of atopic dermatitis. Topical colonization with a defined consortium of human skin commensals restored barrier competence in germ free skin and during epicutaneous sensitization; these effects were dependent on keratinocyte AHR. We reveal a fundamental role for the commensal skin microbiota in directing skin barrier formation and repair through the AHR, with far-reaching implications for the numerous skin disorders characterized by disrupted epidermal differentiation and/or barrier competence.
2021-03-31 | GSE162925 | GEO
Project description:fish skin mucosal microbiota Raw sequence reads
| PRJNA792590 | ENA
Project description:Variations on the diversity of amphibian skin microbiota across forests fragments
| PRJEB22810 | ENA