Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA549962 | ENA |
REPOSITORIES: ENA
Similar Datasets
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Project description:Abrupt environment changes can elicit an array of genetic effects. However, many of these effects can be overlooked by functional genomic studies conducted in static laboratory conditions. We studied the transcriptomic responses of Caenorhabditis elegans under single generation exposures to drastically different culturing conditions. In our experimental scheme, P0 worms were maintained on terrestrial environments (agar plates), F1 in aquatic cultures, and F2 back to terrestrial environments. The laboratory N2 strain and the wild isolate AB1 strain were utilized to examine how the genotype contributes to the transcriptome dynamics. Significant variations were found in the gene expressions between the “domesticated” laboratory strain and the wild isolate in the different environments. The results showed that 20% - 27% of the transcriptional responses to the environment changes were transmitted to the subsequent generation. In aquatic conditions, the domesticated strain showed differential gene expression particularly for the genes functioning in the reproductive system and the cuticle development. In accordance with the transcriptomic responses, phenotypic abnormalities were detected in the germline and cuticle of the domesticated strain. Further studies showed that distinct groups of genes are exclusively expressed under specific environmental conditions, and many of these genes previously lacked supporting biochemical evidence.
2018-07-09 | GSE103776 | GEO
Project description:Methods currently available to estimate the post-mortem submerged interval (PMSI) of cadavers in water suffer from poor accuracy, being mostly based on morphological examination of the remains. Proteins present within bones have recently attracted more attention from researchers interested in the estimation of the post-mortem interval (PMI) in terrestrial environments. Despite the great potential of proteomic methods for PMI estimation, their application to aquatic environments has not yet been explored. In this study, we examined whether four different types of aquatic environment (tap water, saltwater, pond water and chlorinated water) affected the proteome of mice bones with increasing PMSIs (from zero to three weeks).
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Project description:Chemical modifications to the tails of histone proteins act as gene regulators that play a pivotal role in adaptive responses to environmental stress. Determining the short and long term kinetics of histone marks is essential for understanding their functions in adaptation. We used Caenorhabditis elegans as a model organism to study the histone modification kinetics in response to environmental stress, taking advantage of their ability to live in both terrestrial and aquatic environments. We investigated the multigenerational genome-wide dynamics of five histone marks (H3K4me3, H3K27me3, H4K20me1, H3K36me1, and H3K9me3) by maintaining P0 animals on terrestrial (agar plates), F1 in aquatic cultures, and F2 back on terrestrial environments. We determined the distributions of histone marks in the gene promoter regions and found that H4K20me1, H3K36me1, and H3K9me3 showed up to eleven-fold differences in density, whereas H3K4me3 and H3K27me3 remained highly constant during adaptation from terrestrial to aquatic environments. Furthermore, we predicted that up to five combinations of histone marks can co-occupy single gene promoters and confirmed the colocalization of these histone marks by structured illumination microscopy. The co-occupancy increases with environment changes and different co-occupancy patterns contribute to variances in gene expressions and thereby presents a supporting evidence for the histone code hypothesis.
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Project description:Imatinib mesylate (IM) a protein kinase inhibitor drug that selectively inhibits certain oncogenic mutant protein tyrosine kinases. After application, IM is via hospital and municipal waste water effluents released into the aquatic environment, where it can harm non-target organisms. The aim of this study was to evaluate changes in gene transcription in liver of adult F1 zebrafish (Danio rerio) continuously exposed to IM at environmentaly relevant concentrations of 0.01 µg/L and 1 µg/L.
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Project description:Complete genome sequencing of antimicrobial-resistant bacteria isolated from environment including aquatic animals and plants in Japan
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