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ABSTRACT:
PROVIDER: PRJNA787012 | ENA |
REPOSITORIES: ENA
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Project description:Silver nanoparticles (NPs) are extensively used due to their antimicrobial activity and, therefore, their input into the ecosystem will increase. Silver can be bioaccumulated by low trophic level organisms and, then, incorporated into the food chain, reaching high level predators. The objectives of this study were to test the acute toxicity of N-vynil-2-pirrolidone/polyethylenimine (PVP-PEI) coated Ag NPs of 5 nm to brine shrimp (Artemia sp) larvae and to assess bioaccumulation and effects of silver transferred by the diet. For the later, brine shrimps were exposed to two different concentrations of Ag NPs, 100 ng/L as an environmentally relevant concentration and 100 µg/L as a likely effective concentration, in parallel with an unexposed control group and, then, used to feed zebrafish during 21 days in order to simulate two trophic levels of a simplified food web. For brine shrimp larvae, EC50 values ranged from 7.39 mg Ag/L (48 h post hatch larvae (hph) exposed for 48 h) to 19.63 mg Ag/L (24 hph larvae exposed for 24 h. Silver accumulation was measured in brine shrimps exposed to 0.1 and 1 mg/L of Ag NPs for 24 h. In zebrafish fed with brine shrimps exposed to Ag NPs, intestine showed higher metal accumulation than liver, although both organs presented the same pattern of dose and time-dependent metal accumulation as revealed by autometallography. Feeding of zebrafish for 3 days with brine shrimps exposed to 100 ng/L of Ag NPs was enough to impair fish health as reflected by the significant reduction of the lysosomal membrane stability and the presence of several histopathological conditions in the liver. Overall, results showed that Ag NPs were able to exert toxic effects on zebrafish through dietary exposure, even at an environmentally relevant concentration, which should act as concern of the need of studies in further detail about real impact of nanomaterials in the environment.
2017-03-21 | GSE90457 | GEO
Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard
2013-03-01 | GSE42286 | GEO
Project description:Halophilic microorganisms have long been known to survive within the brine inclusions of salt crystals, as evidenced by their pigmentation. However, the molecular mechanisms allowing this survival has remained an open question for decades. While protocols for the surface sterilization of halite (NaCl) have enabled isolation of cells and DNA from within halite brine inclusions, “-omics” based approaches have faced two main technical challenges: (1) removal of all contaminating organic biomolecules (including proteins) from halite surfaces, and (2) performing selective biomolecule extractions directly from cells contained within halite brine inclusions with sufficient speed to avoid modifications in gene expression during extraction. In this study, we present methods to resolve these two technical challenges. In addition, we apply these methods to perform the first examination of the early acclimation of a model haloarchaeon (Halobacterium salinarum NRC-1) to halite brine inclusions. Examinations of the proteome of Halobacterium cells two months post-evaporation revealed a high degree of similarity with stationary phase liquid cultures, but with a sharp down-regulation of ribosomal proteins. Low quantities of RNA from halite brine inclusions corroborate the hypothesis of low transcriptional and translational activities. While proteins for central metabolism were part of the shared proteome between liquid cultures and halite brine inclusions, proteins involved in cell mobility (archaellum, gas vesicles) were either absent or less abundant in halite samples. Proteins unique to cells within brine inclusions included transporters, suggesting modified interactions between cells and the surrounding brine inclusions microenvironment. The methods and hypotheses presented here enable future studies of the survival of halophiles in both culture model and natural halite systems.
2023-03-10 | PXD037167 | Pride
Project description:Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes. Despite increased interest in archaeal histones in recent years, the properties of archaeal chromatin have been little studied using genomic tools. Here, we adapt the ATAC-seq assay to the archaeal context and use it to map the accessible landscape of the genome of the euryarchaeote Haloferax volcanii. We integrate the resulting datasets with genome-wide maps of active transcription and single-stranded DNA (ssDNA), and find that while H. volcanii promoters exist in a preferentially accessible state, modulation of transcriptional activity is not associated with changes in promoter accessibility, unlike the typical situation in eukaryotes. Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection of H. volcanii, and find that archaeal nucleosomal chromatin is at its baseline comparably to slightly more open than that of eukaryotes. We also evaluate the degree of coordination of transcription within archaeal operons and make the unexpected observation that some CRISPR arrays are associated with highly prevalent ssDNA structures. These results provide a foundation for the future functional studies of archaeal chromatin.
2022-10-01 | GSE207470 | GEO
Project description:Barite mineral crust brine pool diversity
| PRJNA267505 | ENA
Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard Two color array (cy3 and cy5): the universal standard 20 bp oligo (fluoresced with cy5) is printed to the slide with a 70-mer. Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer will bind to it. Signal is the cy3/cy5. Up to four arrays per sample, with two biological replicates made into two targets, each run on duplicate arrays.
2013-03-01 | E-GEOD-42286 | biostudies-arrayexpress