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PROVIDER: PRJEB59515 | ENA |
REPOSITORIES: ENA
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Project description:Extracting the cell-free extracellular DNA from wastewater: a critical evaluation
| PRJEB64188 | ENA
Project description:Extracting extracellular DNA from wastewater
| PRJEB59524 | ENA
Project description:The kinetics and fragmentation of cell-free DNA from cancer cells are influenced by anticancer treatments
| PRJEB52377 | ENA
Project description:Metaproteomics can be used to study functionally active biofilm-based bacterial populations in reclaimed water distribution systems, which in turn result in bacterial regrowth that impacts the water quality. However, existing protein extraction methods have differences in their protein recovery and have not been evaluated for their efficacies in reclaimed water biofilm samples. In this study, we first evaluated six different protein extraction methods with diverse chemical and physical properties on a mixture of bacterial cell culture. Based on a weighting scores-based evaluation, the extraction protocols in order of decreasing performance are listed as B-PER > RIPA > PreOmics > SDS > AllPrep > Urea. The highest four optimal methods on cell culture were further tested against treated wastewater non-chlorinated and chlorinated effluent biofilms. In terms of protein yield, our findings showed that RIPA performed the best; however, the highest number of proteins were extracted from SDS and PreOmics. Furthermore, SDS and PreOmics worked best to rupture gram-positive and gram-negative bacterial cell walls. Considering the five evaluation factors, PreOmics obtained highest weighted score, indicating its potential effectiveness in extracting proteins from biofilms. This study provides the first insight into evaluating protein extraction methods to facilitate metaproteomics for complex reclaimed water matrices.
2023-08-04 | PXD042292 | Pride
Project description:Cell-free chromatin immunoprecipitation can determine tumor gene expression in lung cancer patients
| PRJEB56750 | ENA
Project description:Wastewater treatment plants (WWTPs) and Drinking water treatment plants (DWTPs) are critical points for public health for persistently remaining microorganisms after treatment may pose a risk. This study aimed to conduct microbial metagenomic analyses on waters from both DWTPs and WWTPs under the Istanbul Water and Sewerage Administration (ISKI). In this study a total of 52 samples were included, comprising 18 samples from DWTPs and 34 from WWTPs. All water samples underwent pre-isolation filtration. DNA isolation was conducted using filter material, followed by library preparation and sequencing on a NovaSeq 6000 instrument following the manufacturer's guidelines.
2025-01-09 | E-MTAB-14353 | biostudies-arrayexpress
Project description:The study of chromatin has mostly been restricted to defining its function in the nucleus, where histone proteins fulfil vital roles in packaging genomic DNA and regulating transcription. However, chromatin components are often released into the extracellular space, either intentionally via cellular secretion or during disease or damage-induced cell death. These extracellular chromatin components, depending on the context, can consist of free histones, free DNA, intact nucleosomes (histone octamers wrapped by DNA), or heterogeneous, higher order structures such as neutrophil extracellular traps (NETs). They have been associated with diverse pathologies such as inflammation, cancer, and sepsis, and distinct toxic effects, most notably the damaging effects of free histones over intact nucleosomes. Extracellular chromatin components are emerging, suggested biomarkers for various associated diseases, yet there is a widely acknowledged lack of methods that distinguish between them and their unique functions in circulation. Here, we explore the fate and effects of extracellular free histone H3 by utilizing FIRESCAPE ([18F]-Fluorine Isotopic Radiolabeling Enabling Scanning of Clearance After Proteolytic Events), a novel radiolabeling concept that leverages the unique, high-sensitivity properties of the radioisotope 18F and residue-specific protein editing chemistry. By installing true 18F-containing protein sidechain mimics site-specifically into histone H3, FIRESCAPE enabled in vivo scanning of the half-lives, proteolytic susceptibility, and clearance of single residues in a protein of interest, at microdoses far below toxic levels (low nanomole). This now precisely reveals the remarkably distinct distribution, half-lives, damage-inducing abilities, and accumulation of free extracellular histones in cellulo and in vivo, comparing them to other chromatin states such as intact nucleosomes where appropriate. Free extracellular histones are rapidly cleared from circulation, first mediated by proteolysis of the histone tail. However, direct injection of free histones versus nucleosomes into tissue (brain) that is unprotected by such proteolysis provokes a starkly different response: free histones exhibited limited diffusion and swiftly promoted damage both in cell culture and in vivo, in contrast to the largely passive and benign nature of intact nucleosomes. Synthetic extracellular histone H3 uptake was observed and characterized with biochemical, genomic, and proteomic methodologies, revealing apparent deposition into chromatin indistinguishable from native H3 in localization and post-translational modification (PTM) accumulation, yet paired with cellular and tissue damage. These exploratory studies now provide much-needed clarity to the distinct fates and effects of extracellular histones versus nucleosomes, in particular the strongly damaging effects of free histones, their rapid uptake into cells, and an associated histone-specific proteolysis pathway via the removal of the histone tail.
2025-11-02 | GSE276733 | GEO