Bioactivity screening of sponge-associated bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB41620 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4902120_1.fastq.gz | Fastqsanger.gz | |||
| ERR4902120_2.fastq.gz | Fastqsanger.gz | |||
| ERR4901861_1.fastq.gz | Fastqsanger.gz | |||
| ERR4901861_2.fastq.gz | Fastqsanger.gz | |||
| ERR4901882_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 26 |
Similar Datasets
Project description:Marine sponges harbor diverse microbial communities that represent a significant source of natural products. In the present study, extracts of 21 sponge-associated bacteria were screened for their antimicrobial and anticancer activity, and their genomes were mined for secondary metabolite biosynthetic gene clusters (BGCs). Phylogenetic analysis assigned the strains to four major phyla in the sponge microbiome, namely Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Bioassays identified one extract with anti-methicillin-resistant Staphylococcus aureus (MRSA) activity, and more than 70% of the total extracts had a moderate to high cytotoxicity. The most active extracts were derived from the Proteobacteria and Actinobacteria, prominent for producing bioactive substances. The strong bioactivity potential of the aforementioned strains was also evident in the abundance of BGCs, which encoded mainly beta-lactones, bacteriocins, non-ribosomal peptide synthetases (NRPS), terpenes, and siderophores. Gene-trait matching was performed for the most active strains, aiming at linking their biosynthetic potential with the experimental results. Genetic associations were established for the anti-MRSA and cytotoxic phenotypes based on the similarity of the detected BGCs with BGCs encoding natural products with known bioactivity. Overall, our study highlights the significance of combining in vitro and in silico approaches in the search of novel natural products of pharmaceutical interest.
| S-EPMC7912018 | biostudies-literature
Project description:Bioactivity screening of antiparasitic drugs in vitro
| PRJEB98681 | ENA
Project description:Bioactivity screening of antiparasitic drugs in vitro
| PRJEB90302 | ENA
Project description:This dataset contains several sponge-derived bacteria, along with data from the sponges to enable the assignation of the biosynthetic source of detected metabolite features. Media controls and solvent blanks are also included. Please see metadata for the bacterial source sponge.
2022-10-28 | MSV000090609 | MassIVE
Project description:Comparative genomics of sponge-associated Alphaproteobacteria
| PRJEB18465 | ENA
Project description:We aimed to identify specific biomarkers of IFN-beta bioactivity in order to compare their gene expression induction by type I IFNs with the MxA, and to investigate their potential role in MS pathogenesis. Gene expression microarrays were performed in PBMC from MS patients who developed neutralizing antibodies (NAB) to IFN-beta. Nine genes followed patterns in gene expression over time similar to the MX1 and were selected for further experiments: IFI6, IFI27, IFI44L, IFIT1, HERC5, LY6E, RSAD2, SIGLEC1, and USP18. In vitro experiments revealed specific induction of selected biomarkers by IFN-beta but not IFN-gamma, and several markers, in particular USP18 and HERC5, were significantly induced at lower IFN-beta concentrations and more selective than the MX1 as biomarkers of IFN-beta bioactivity. In addition, USP18 expression was deficient in MS patients compared with healthy controls (p=0.0004). We propose specific biomarkers that may be considered in addition to the MxA to evaluate IFN-beta bioactivity, and to further explore their implication in MS pathogenesis. Number of samples: 32. We analyzed PBMC from 8 patients at baseline and after 3, 12 and 24 months of IFN-beta treatment
2010-12-18 | E-GEOD-26104 | biostudies-arrayexpress
Project description:High-throughput profiling assays such as high-throughput phenotypic profiling (HTPP) with Cell Painting and high-throughput transcriptomics (HTTr) with TempO-SeqTM are new approach methods that have been used to characterize the bioactivity and potential hazards of chemicals. To better account for potential in vivo hazards in screening, we previously coupled both assays to an in vitro metabolism platform, Alginate Immobilization of Metabolic Enzymes (AIME). In this study, we expanded upon our previous results in estrogenic reference chemicals by screening an additional 40 chemicals in VM7Luc4E2 breast cells anticipated to have varied activity and/or shifts in activity with metabolism in an estrogen receptor transactivation assay (ERTA) using the AIME platform. Our results demonstrate how HTTr could detect ER activity and the influence of metabolism on estrogenicity through the activation of ER high-confidence (ERHC) gene signatures and metabolism-induced shifts in ERHC signature enrichment. Additionally, HTPP could detect cases where metabolism impacted chemical cytotoxicity and detect generation of metabolites that were bioactive in a different way than their respective parent compounds when comparing the profiles of active features between AIME conditions. Notably, our findings highlighted examples of chemicals that had very different phenotypic and gene expression profiles between metabolic conditions that would not be observed in traditional chemical screening in most cell models. This study exhibited how high-throughput profiling assays could distinguish changes in bioactivity with metabolic competence using the AIME platform, which will ultimately better inform next generation risk assessment by providing more comprehensive hazard characterizations.
2025-06-10 | GSE296915 | GEO
Project description:Marine sponge-associated bacteria are known as bio-active compound produce. We have constructed metagenome libraries of the bacteria and developed a metagenomic screening approach. Activity-based screening successfully identified novel genes and novel enzymes; however, the efficiency was only in 1 out of 104 clones. Therefore, in this study, we thought that bioinformatics could help to reduce screening efforts, and combined activity-based screening with database search. Neutrophils play an important role for the immune system to recognize excreted bacterial by-products as chemotactic factors and are recruited to infection sites to kill pathogens via phagocytosis. These excreted by-products are considered critical triggers that engage the immune system to mount a defense against infection, and identifying these factors may guide developments in medicine and diagnostics. We focused on genes encoding amino acid ligase and peptide synthetase and selected from an in-house sponge metagenome database. Cell-free culture medium of each was used in a neutrophil chemiluminescence assay in luminol reaction. The clone showing maximum activity had a genomic sequence expected to produce a molecule like a phospho-N-acetylmuramyl pentapeptide by the metagenome fragment analysis.
| S-EPMC8402132 | biostudies-literature
Project description:Laparoscopic surgery of the distal colon and rectum requires surgery with an appropriate field of view. A commonly used technique to create a clear exposure is the steep Trendelenburg position in which the patient is positioned in an angle of 15 to 40 degrees with the head down using the effect of gravity to retract the small intestine. This method is associated with haemostatic changes caused by the cranial shift of abdominal organs and blood. Recently, a cellulose compressed sponge was developed as intraoperative retractor, with the aim to keep the small intestines aside while the patient remains in a horizontal position. The safety of the sponge is secured with CE marking. The retractor sponge ensures a clear surgical field and potentially prevents haemostatic instability by avoiding Trendelenburg position. A pilot study in the St Antonius Hospital Nieuwegein has shown that use of the sponge might be associated with shorter hospital stay.
| 2258291 | ecrin-mdr-crc
Project description:miRNA sponge, a special class of miRNA target, has been emerging as a pivotal player in miRNA mediated regulatory network. Currently, the identified miRNA sponge genes mostly act on sequestering conserved miRNAs (e.g. miR-7, miR-145), however, the existence, potential function and evolutionary process of miRNA sponge genes for species-specific miRNA, especially for human specific miRNA, are largely unknown. In this study, we conducted a systematic analysis including sponge gene identification and subsequent function and evolutionary analyses for an authentic human-specific miRNA, miR-941.
2019-01-01 | GSE93716 | GEO