Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA549962 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Isolation of novel species of prokaryotes from aquatic environments
| PRJDB17504 | ENA
Project description:Purpose: This study aimed to investigate the biological effects of PET microfibers and their underlying mechanisms in early-staged sheepshead minnows (Cyprinodon variegatus). Method: PET microfibers (about 13 μm diameter × 106 μm length) were prepared by cutting PET threads and treated to sheepshead minnow larvae at 10 and 100 mg/L for 10 days. mRNA was produced with a TruSeq Standed mRNA library kit, and sequencing using a NovaSeq6000 equipment. Results and Conclusions: Our study represents a detailed analysis of the transcriptome of sheepshead minnow larvae exposed to PET microfibers by RNA-seq technology. No acute toxicity was found in the minnow, but PET microfibers significantly produced reactive oxygen species and reduced behavioral responses of traveled distance and maximum velocity. The transcriptomic data suggested that Merkel cells (flow sensors) and corpuscles of Stannius (calcium regulator) are putative targets, which were derived from oxidative stress, sensory neuropathy, cognitive impairment, and movement disorders. These findings underscore that although PET microfibers are not directly lethal to sheepshead minnows, they could impact their survival by damaging swimming-related key genes. This study provides new insights into how PET microfibers are toxic to aquatic organisms and disrupt ecosystems beyond survival and pathological changes.
2024-10-01 | GSE181695 | GEO
Project description:Biodegradation of isoprene in the terrestrial and marine environment
| PRJNA272922 | ENA
Project description:Survey of the Distribution of Drug-Resistant Bacteria in Nursing Home Facility Environments
| PRJDB18029 | ENA
Project description:Polylactic acid (PLA) is a promising biodegradable material used in various fields, such as mulching films and disposable packaging materials. Biological approaches for completely degrading biodegradable polymers can provide environmentally friendly solutions. However, to our knowledge, no studies have performed transcriptome profiling to analyze PLA-degrading genes of PLA-degrading bacteria. Therefore, this study reports for the first time an RNA sequence approach for tracing genes involved in PLA biodegradation in the PLA-degrading bacterium Brevibacillus brevis. In the interpretation results of the differentially expressed genes, the hydrolase genes mhqD and nap and the serine protease gene besA were up-regulated by a fold change of 7.97, 4.89, and 4.09, respectively. This result suggests that hydrolases play a key role in PLA biodegradation by B. brevis. In addition, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that genes implicated in biofilm formation were upregulated. The biodegradation of PLA starts with bacteria attaching to the surface of PLA and forming a biofilm. Therefore, it could be confirmed that the above genes were up-regulated for access to PLA and biodegradation. Our results provide transcriptome-based insights into PLA biodegradation, which pitch a better understanding of microbial biodegradation of plastics.
2025-01-16 | GSE223668 | GEO
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).
2020-04-06 | PXD017386 | Pride
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.
2021-07-09 | GSE103775 | GEO
Project description:Whole genome sequencing of antimicrobial-resistant bacteria isolated from aquatic animals, plants, and environment in Asia
| PRJDB10427 | ENA