An OMIC approach to elaborate the antibacterial mechanisms of different alkaloids
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA414212 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In the current study, RNA sequencing was used to comparatively elaborate the activities and the effects of the alkaloids, boldine, bulbocapnine, and roemerine along with the well-known antibacterial alkaloid berberine on Bacillus subtilis cells.
2018-07-17 | GSE104946 | GEO
Project description:Purpose: The aim of this study was to explore the antibacterial effect and molecular mechanism of gallium nitrate [Ga(NO 3 ) 3 ] against Acinetobacter baumannii from bloodstream infection. Methods: A total of 40 A. baumannii with different antimicrobials susceptibility patterns were isolated from bloodstream infections. In vitro antibacterial effect of Ga(NO 3 ) 3 was analyzed by micro-dilution method and time-kill assay. The effect of ferric chloride/heme on the antibacterial effect of Ga(NO 3 ) 3 was evaluated. Transcriptome sequencing was performed to elucidate the antibacterial mechanism of gallium nitrate. Mouse infection model was conducted to explore the in vivo efficacy of gallium nitrate . Results: Ga(NO 3 ) 3 exhibited excellent antibacterial effect in RPMI 1 640 medium containing 10% human serum (MICs ranged from 0.06 μg/mL to 0.125 μg/mL), whereas its antibacterial effect was weakened by exogenous ferric chloride/heme. Ga(NO 3 ) 3 inhibited A. baumannii growth in a dose- and time- dependent manner. Ga(NO 3 ) 3 exerted antibacterial effect by up-regulating the expression of genes associated with biosynthesis and transport of siderophore and disrupting multiple iron dependent metabolism processes. Ga(NO 3 ) 3 significantly reduced bacterial load in the neutropenic mouse thigh infection model. Conclusions: This study revealed that Ga(NO 3 ) 3 had excellent antibacterial activity both in vivo and in vitro . It might be a potential drug for treating bloodstream infections of A. baumannii
2022-01-27 | GSE194255 | GEO
Project description:RNA-seq was employed to detect hepatic differential expression genes between pyrrolizidine alkaloids-induced liver injury mice and the untreated ones.
2021-04-13 | GSE171874 | GEO
Project description:Catharanthus roseus produces a variety of indole alkaloids with significant biological activities. The indole alkaloids including catharanthine, vindolinine, ajmalicine and the precursor strictosidine were dramatically induced in the leaves following binary stress. To profile the modification of indole alkaloids in C. roseus seedlings under the binary stress of ultraviolet-B irradiation and dark incubation, gel-free proteomic analysis was carried out to uncover the underlying molecular mechanism.
2015-08-24 | PXD001937 | Pride
Project description:To investigate of phenotypic effects of antibacterial synergy and gene expression analysis
2023-07-01 | GSE233610 | GEO
Project description:High throughput single-cell RNA sequencing (sc-RNAseq) has become a frequently used tool to assess immune cell function and heterogeneity. Recently, the combined measurement of RNA and protein expression by sequencing was developed, which is commonly known as CITE-Seq. Acquisition of protein expression data along with transcriptome data resolves some of the limitations inherent to only assessing transcript, but also nearly doubles the sequencing read depth required per single cell. Furthermore, there is still a paucity of analysis tools to visualize combined transcript-protein datasets. Here, we describe a novel targeted transcriptomics approach that combines analysis of over 400 genes with simultaneous measurement of over 40 proteins on more than 25,000 cells. This targeted approach requires only about 1/10 of the read depth compared to a whole transcriptome approach while retaining high sensitivity for low abundance transcripts. To analyze these multi-omic transcript-protein datasets, we adapted One-SENSE for intuitive visualization of the relationship of proteins and transcripts on a single-cell level.
2020-03-30 | GSE135325 | GEO
Project description:Poison frogs sequester chemical defenses from their diet of leaf litter arthropods for defense against predation. Little is known about the physiological adaptations that confer this unusual bioaccumulation ability. We conducted an alkaloid-feeding experiment with the Diablito poison frog (Oophaga sylvatica) to determine how quickly alkaloids are accumulated and how toxins modify frog physiology using quantitative proteomics. Diablito frogs rapidly accumulated the alkaloid decahydroquinoline within four days, and dietary alkaloid exposure modified protein abundance in the intestines, liver, and skin. Many proteins that increased in abundance with toxin accumulation are plasma glycoproteins, including the complement system and the toxin-binding protein saxiphilin. Other protein classes that change in abundance with toxin accumulation are membrane proteins involved in small molecule transport and metabolism. Overall, this work shows poison frogs can rapidly accumulate alkaloids, which alter carrier protein abundance, initiate an immune response, and alter small molecule transport and metabolism dynamics across tissues
2021-01-25 | PXD021216 | Pride
Project description:Pyrocystis lunula (Schutt) is a photoautotrophic unarmoured dinoflagellate, commonly found in marine environments. Today it exist several biotechnological applications derived from the bioluminescent system of this species. From a post-genomic perspective, and in order to study the whole proteome of P. lunula, a ¨omic¨ approach (transcriptomic-proteomic analysis) was initiated using fresh microalgae samples. A total of 80.875.390 reads were generated (400.000 conting, XXX pb) and 17.461 peptides were detected, getting 3.182 protein identification hits. The identified proteins were categorized according to functional description and gene ontology classification. In this study, it has been developed and described the first proteomic analysis of the microalgae P. lunula. In addition to shed light on a series of important factors involved with the processes of regulation of gene expression. The presence of the luciferin-binding protein (LBP), which had not been described so far in Pyrocystis, is highlighted.
2019-04-12 | PXD011555 | Pride
Project description:Type I interferons were discovered as the primary antiviral cytokines and are now known to serve critical functions in host defense against bacterial pathogens. Accordingly, established mediators of interferon antiviral activity may mediate previously unrecognized antibacterial functions. RNase-L is the terminal component of an RNA decay pathway that is an important mediator of interferon-induced antiviral activity. Here we identify a novel role for RNase-L in the host antibacterial response. RNase-L-/- mice exhibited a dramatic increase in mortality following challenge with Bacillus anthracis and Escherichia coli; this increased susceptibility was due to a compromised immune response resulting in increased bacterial load. Investigation of the mechanisms of RNase-L antibacterial activity indicated that RNase-L is required for the optimal induction of proinflammatory cytokines that play essential roles in host defense from bacterial pathogens. RNase-L also regulated the expression of the endolysosomal protease, cathepsin-E, and endosome-associated activities, that function to eliminate internalized bacteria and may contribute to RNase-L antimicrobial action. Our results reveal a unique role for RNase-L in the antibacterial response that is mediated through multiple mechanisms. As a regulator of fundamental components of the innate immune response, RNase-L represents a viable therapeutic target to augment host defense against diverse microbial pathogens. two strains: wildtype and knockout, three time points: untreated, 2hours, and 8hours. three replication for each group. Totally 18 samples.
2008-12-19 | E-GEOD-13530 | biostudies-arrayexpress