Ontology highlight
ABSTRACT:
PROVIDER: PRJNA745382 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15096688_1.fastq.gz | Fastqsanger.gz | |||
| SRR15096688_2.fastq.gz | Fastqsanger.gz | |||
| SRR15096689_1.fastq.gz | Fastqsanger.gz | |||
| SRR15096689_2.fastq.gz | Fastqsanger.gz | |||
| SRR15096690_1.fastq.gz | Fastqsanger.gz |
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Project description:Despite significant advances in nanoengineering, developing a universal nanoparticle engineering strategy that enables tailored nanoparticle organ deposition post intravenous administration remains challenging. Here, we report a simple and modular strategy mediated by metal–organic network coatings composed of polyethylene glycol (PEG), proteins, phenolic ligands, and metal ions. The versatile binding affinity of phenolic ligands facilitates the formation of coatings on diverse nanoparticle platforms, including quantum dots, lipid, polymeric, inorganic, and metal–organic nanoparticles. The organ deposition selectivity of these coated nanoparticles is readily directed towards the kidney, lung, heart, and brain by varying the coating composition. Mechanistic studies reveal that the combined effect of PEG, phenolic ligands, and metal ions on the surface properties governs the overall biodistribution of the coated nanoparticles, while the protein component contributes to the coating integrity. This work provides a generalizable approach for developing an organ-targeting nanotechnology, with the potential to advance nanoparticle-mediated treatments and theranostics.
2026-06-26 | PXD077631 | Pride
Project description:Streptococcus pneumoniae D39 AdcR (adhesion competence repressor) is the first metal-sensing member of the MarR (multiple antibiotic resistance repressor) family to be characterized. Expression profiling of a ∆adcR strain grown in liquid culture under microaerobic conditions revealed that transcript amounts for 13 genes were up-regulated relative to the wild-type strain, among them adcR, adcCBA, encoding a high affinity ABC uptake system for zinc, and genes encoding cell-surface zinc-binding pneumococcal histidine triad (pht) and adcII (lmb, laminin binding) proteins. Down-regulated transcripts included those encoding two putative zinc-containing alcohol dehydrogenases.
2010-10-01 | GSE21506 | GEO
Project description:Tetrachloroauric acid has been explored as an FDA-approved alternative to treat antibiotic-resistant bacterial strains. Questions remain as it relates to the full-systems response elicited to counteract its toxic effects, especially in the context of a non-lethal exposure. We explored the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of tetrachloroauric acid (10 µM, 3.39 µg/mL). Our results yielded significant changes in gene expresson levels: 1028 genes were up-regulated, while 1025 were down-regulated in our tetrachloroauric acid treatment. Several biological processes became dysregulated to cope with the presence of this metal stressor, including iron metabolism, ribosome assembly, sulfur metabolism, cysteine biosynthesis, zinc uptake, and the copper homeostasis system Cue. Altogether, this work provides a valuable snapshot of how our indicator strain adapts to metal-induced stress. This is a significant step in understanding how bacteria can adjust their physiology to coexist with sublethal concentrations of metal-based antimicrobials.
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Project description:Heavy metal and antibiotic resistance plasmids
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Project description:Emerging antibiotic resistance among clinically relevant bacteria, paired with their ability to form biofilms on medical and technical devices, represents a serious problem in terms of effective and long-term decontamination in health care environments and gives rise to an urgent need for new antimicrobial materials. Here we present the first study of the impact of AGXX®, a novel broad-spectrum antimicrobial surface coating consisting of micro galvanic elements formed by silver and ruthenium, on the transcriptome of the nosocomial pathogen Enterococcus faecalis. E. faecalis was subjected to metal stress by growing it for different periods of time in the presence of AGXX® or silver-coated steel meshes. Subsequently, total RNA was isolated and next-generation RNA sequencing was performed to analyze variations in gene expression levels in the presence of the antimicrobial materials with focus on known stress genes. Exposure to AGXX® had a large impact on the transcriptome of E. faecalis. After 24 minutes almost 1/5 of the E. faecalis genome displayed differential expression. At each time-point the cop operon was strongly up-regulated, providing indirect evidence for the presence of free Ag+-ions. Moreover, exposure to AGXX® induced a broad general stress response in E. faecalis. Genes coding for the chaperones GroEL and GroES as well as the Clp proteases ClpE and ClpB were among the top up-regulated heat shock genes. Furthermore, differential expression of genes coding for thioredoxin, superoxide dismutase and glutathione synthetase indicates a high level of oxidative stress. We postulate a mechanism of action where the combination of Ag+-ions and reactive oxygen species generated by AGXX® results in a synergistic antimicrobial effect, which is superior to that of conventional silver coatings. Gene expression analysis of Enterococcus faecalis 12030 either subjected to metal stress by exposure to an antimicrobial AGXX®- or Ag-coated V2A steel mesh or exposed to an uncoated V2A steel mesh or left untreated performing RNA Sequencing with an Ion ProtonTM Sequencer and subsequent data analysis with a T-REx RNA-Sequencing expression analysis pipeline.
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Project description:Cells respond to changes in environment by shifting their gene expression profile to deal with the new conditions. The cellular response to changes in metal homeostasis is an important example of this. Transition metals such as iron, zinc, and copper are essential micronutrients but other metals such as cadmium are simply toxic. The cell must maintain metal concentrations in a window that supports efficient metabolic function but must also protect against the damaging effects of high concentrations of these metals. One way a cell regulates metal homeostasis is to control genes involved in metal mobilization and storage. Much of this regulation occurs at the level of transcription and the protein most responsible for this is the conserved metal responsive transcription factor, MTF-1. Interestingly, the nature of the changes in the gene expression profile depends on the type of exposure. The cell somehow senses the kind of metal challenge and responds appropriately. We have been using the Drosophila system to try to understand the mechanism of this metal discrimination. Using genome-wide mapping of MTF-1 binding under different metal stresses, we find that, surprisingly, MTF-1 chooses different DNA binding sites depending on the specific nature of the metal insult. We also find that the type of binding site chosen is an important component of the capability to induce the metal-specific transcription activation.
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Project description:Conventional human pluripotent stem cells (hPSCs) are widely used to study early embryonic development, generate somatic cells, and model diseases, with differentiation potential aligned to a post-implantation epiblast identity. In the past decade, naive hPSCs, representing a pre-implantation stage, have been derived, exhibiting broader differentiation potential, including embryonic and extraembryonic lineages such as trophectoderm, primitive endoderm, and extraembryonic mesoderm. Naive hPSCs can also self-organize into blastocyst-like structures called blastoids. However, their culture typically relies on mouse embryonic fibroblasts (MEFs), which are variable, resource-intensive, and can contaminate analyses. We report the long-term maintenance of naive hPSCs in a feeder-free, serum-coated system. Growth rate, clonogenicity, and gene expression profiles on serum coating were comparable to MEF-based cultures, but serum coating minimised fibroblast contamination. Naive hPSCs cultured on serum exhibited faster exit from pluripotency, more efficient germ layer specification, and retained trophectoderm potential with high blastoid formation efficiency. Exome sequencing revealed fewer mutations in serum-cultured cells, and mass spectrometry identified extracellular matrix proteins like vitronectin, fibronectin, and collagens in the serum coating. Overall, serum coating offers a scalable, cost-effective alternative for naive hPSC culture, maintaining developmental potential, reducing DNA mutations, and eliminating MEF-related confounding factors. We believe serum coating will expand the use of naive hPSCs to large-scale studies and mechanistic insights of developmental and disease modelling.
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Project description:Conventional human pluripotent stem cells (hPSCs) are widely used to study early embryonic development, generate somatic cells, and model diseases, with differentiation potential aligned to a post-implantation epiblast identity. In the past decade, naive hPSCs, representing a pre-implantation stage, have been derived, exhibiting broader differentiation potential, including embryonic and extraembryonic lineages such as trophectoderm, primitive endoderm, and extraembryonic mesoderm. Naive hPSCs can also self-organize into blastocyst-like structures called blastoids. However, their culture typically relies on mouse embryonic fibroblasts (MEFs), which are variable, resource-intensive, and can contaminate analyses. We report the long-term maintenance of naive hPSCs in a feeder-free, serum-coated system. Growth rate, clonogenicity, and gene expression profiles on serum coating were comparable to MEF-based cultures, but serum coating minimised fibroblast contamination. Naive hPSCs cultured on serum exhibited faster exit from pluripotency, more efficient germ layer specification, and retained trophectoderm potential with high blastoid formation efficiency. Exome sequencing revealed fewer mutations in serum-cultured cells, and mass spectrometry identified extracellular matrix proteins like vitronectin, fibronectin, and collagens in the serum coating. Overall, serum coating offers a scalable, cost-effective alternative for naive hPSC culture, maintaining developmental potential, reducing DNA mutations, and eliminating MEF-related confounding factors. We believe serum coating will expand the use of naive hPSCs to large-scale studies and mechanistic insights of developmental and disease modelling.
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