Ontology highlight
ABSTRACT:
PROVIDER: PRJNA729229 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:oil pipeline community Genome sequencing
| PRJNA356928 | ENA
Project description:This bacterial MALDI-TOF dataset was used for the study "AMinimizing Taxonomic and Natural Product Redundancy in Microbial Libraries Using MALDI-TOF MS and the Bioinformatics Pipeline IDBac"
It consists of triplicate MALDI-TOF MS profiles (both reflectron and linear datasets) for >1,600 bacteria cultivated from a collection in Iceland.
2019-02-18 | MSV000083461 | MassIVE
Project description:Background. As current methods for antibiotic drug discovery are being outpaced by the rise of antimicrobial resistance, new methods and innovative technologies are necessary to replenish our dwindling arsenal of antimicrobial agents. To this end, we developed the PepSAVI-MS pipeline to expedite the search for natural product bioactive peptides. Results. Herein we demonstrate expansion of PepSAVI-MS for the discovery of bacterial-sourced bioactive peptides through identification of the bacteriocin Bac-21 from Enterococcus faecalis pPD1. Minor pipeline modifications including implementation of bacteria-infused agar diffusion assays and optional digestion of peptide libraries highlight the versatility and wide adaptability of the PepSAVI-MS pipeline. Additionally, we have experimentally validated the primary protein sequence of the active, mature Bac-21 peptide for the first time and have confirmed identity with respect to primary sequence and post-translational processing. Conclusions: Successful application of PepSAVI-MS to bacterial secretomes as demonstrated herein establishes proof-of-principle for use in novel microbial bioactive peptide discovery.
2018-07-23 | PXD009003 | Pride
Project description:After a 14-week feeding trial, Atlantic salmon fed a diet based on animal by-product meal and vegetable oil (ABP) showed lower growth rates compared to others fed an FM/FO-based diet (MAR). Interestingly, feeding a vegetable meal/oil-based diet (VEG) resulted in growth rates similar to the FM/FO-based diet. A 44K microarray experiment conducted on liver total RNA samples from these three dietary groups identified 46 genes related to metabolic and growth-relevant pathways, 25 immune-related, and 12 related to oxidation-reduction processes.
2018-10-16 | GSE106604 | GEO
Project description:In this study, we first analyzed the components of shochu oil and then investigated the effects of shochu oil on short-term memory, using a mouse model exhibiting spontaneous alternating behavior caused by the intracerebroventricular administration of Aß25-35. On the last day of the experiment, we examined gene expression in the mouse hippocampus using DNA microarrays. We confirmed the effect of the oil components derived from sweet potato shochu on impaired short-term memory in mice after amyloid ß25-35 injection. Sweet potato shochu oil is a by-product of shochu production. We investigated the effects of shochu oil on short-term memory using a murine model of spontaneous alternating behavior induced by the intracerebroventricular administration of amyloid β25-35 (Aß25-35). Mice were orally administered shochu oil for 15 days. Experiments with a Y-maze model revealed that the Aß25-35 caused a significant decrease in spontaneous alternation behavior, and supplementation with shochu oil significantly improved this behavior. DNA microarray analysis revealed that the administration of shochu oil downregulated the expression of S100a9 and Ptgs2, which reportedly exacerbate amyloid β deposition in Alzheimer’s disease. The administration of shochu oil upregulated the expression of Dnaja1 and PP2A, which is typically downregulated in Alzheimer’s disease. These data suggest that shochu oil ameliorates symptoms of amyloid β lesions, as indicated by its effects on improving spontaneous alternation behavior and modulating the expressions of related genes.
2022-07-15 | GSE208013 | GEO
Project description:Design: double blind controlled randomized trial with a parallel design and 3 treatment groups Description of subjects: Patients admitted in study centers for colorectal surgery under laporoscopy and/or laparotomy.
Product:
Product 1: BB536 and LA1 (10E9) Product 2: BB536 and LA1 (10E7) Placebo: Maltodextrin Number of patients: enrolled subjects: n=33, ITT data set: n=31, PP data set: n=30
Primary objective:
Colonization (biopsy+stools) of each bacteria for one of the dose at D0 (surgical procedure)
Secondary objectives:
* Influence of the probiotic bacteria on the gut microflora
* Modulation of the immune and inflammatory response
Additional objectives:
* Investigate dose effect on La1 colonization
* Investigate the effect of La1 colonization, treatment without La1 colonization, and absence of treatment and La1 colonization on other bacteria and on immunological parameters
| 2074940 | ecrin-mdr-crc
Project description:We have deep sequenced the small transcriptome of Escherichia coli growing in LB and in MOPS, in exponential and stationary phase, and analyzed the resulting reads by a novel pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 14,000 small transcripts enriched during both growth stages. RNA samples were collected from total RNA pools or from crude ribosome pools and then size selected by electrophoresis to limit the products to 20-300nt.
2020-11-21 | GSE161907 | GEO
Project description:RNA-seq was performed by infecting primary mammary epithelial cells (pMECs) with both gram negative (E.coli) and gram positive bacteria (S. aureus). Using stringent pipeline, a set of 1957 known and 1175 novel lncRNAs were identified, among which, 112 lncRNAs were found differentially expressed in bacteria challenged PMECs compared with the control.
2022-01-25 | GSE167591 | GEO
Project description:Several reports have described the involvement of miRNAs in abiotic stresses. However, their role in biotic stress or to beneficial microbes has not been fully explored. In order to understand on the epigenetic regulation in plant in response to nitrogen-fixing bacteria association, we analyzed the sRNA regulation in maize hybrids (Zea mays – UENF 506-8) inoculated with the beneficial diazotrophic bacteria (Herbaspirillum seropedicae). Deep sequencing analysis was carried out to identify the sRNAs regulated in maize during association with diazotrophic bacteria. For this analysis, maize plants were germinated in wet paper and put in hydroponic system with Hoagland’s solution and then inoculated with H. seropedicae for seven days. Mock and inoculated plants were collected and total RNA from a pool of samples was extracted with Trizol reagent. The two sRNA libraries were sequenced by Illumina. The sequences were filtered to remove adaptors and contaminants rRNA and tRNAs, and sequences with 18-28 nt in length were selected. To identify the miRNAs present in these libraries, we used two strategies using the same website (http://srna-tools.cmp.uea.ac.uk): one to identify novel miRNAs using the maize genome (verson 2) and miRCat pipeline; and other to identify conserved miRNAs using the miRBase database (release 13.0, http://microrna.sanger.ac.uk) and miRProf pipeline. We identified 17 novel putative miRNAs candidates and mapped the precursor of these miRNAs in the maize genome. Furthermore, we identified 25 conserved miRNAs families and the differential expressions were analyzed with miRProf pipeline. The bioinformatics analysis of four up-regulated miRNAs (miR397, miR398, miR408 and miR528) in inoculated plant was validated using stem–loop RT-PCR assay. Our findings contribute to increase the knowledge of the molecular relation between plants and endophytic bacteria.
2013-08-01 | GSE47886 | GEO