Bacteria
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ABSTRACT:
PROVIDER: PRJNA559375 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Analysis used total RNA samples of individual brains of low hygienic strain worker bees that were derived from experimental colonies combined of low hygienic genotypes (L pure colonies) resp. low and high hygienic genotypes (L/H mixed colonies). Four-condition experiment: individuals that did perform hygienic behavior (uncapping) vs individuals that did not perform hygienic behavior (non-hygienic); individuals from L pure colonies vs individuals from L/H mixed colonies. A total of 76 biological replicates was analyzed, subdivided into 24 individuals that did perform hygienic behavior in mixed colonies; 24 individuals that did perform hygienic behavior in pure colonies; 14 individuals that did not perform hygienic behavior in mixed colonies; 14 individuals that did not perform hygienic behavior in pure colonies. Each individual brain RNA sample was divided into two subsamples labeled with cy3 resp. cy5. Loop Design was applied so that each individual brain sample was directly compared to at least two other samples.
2012-09-24 | E-MTAB-801 | biostudies-arrayexpress
Project description:Probing epigenomic marks such as histone modifications at a single cell level in thousands of cells has been recently enabled by technologies such as scCUT&Tag. Here we developed a multimodal and optimized iteration of scCUT&Tag called nano-CT (for nano-CUT&Tag) that allows simultaneous probing of three epigenomic modalities at single-cell resolution, using nanobody-Tn5 fusion proteins. nano-CT is compatible with starting materials as low as 25 000 cells and has significantly higher resolution than scCUT&Tag, with a 16-fold increase in the number of fragments per cells. We used nano-CT to simultaneously profile chromatin accessibility, H3K27ac and H3K27me3 in a complex tissue - juvenile mouse brain. The obtained multimodal dataset allowed for discrimination of more cell types/states that scCUT&Tag, and inference of chromatin velocity between ATAC and H3K27ac in the oligodendrocyte (OL) lineage. In addition, we used nano-CT to deconvolute H3K27me3 repressive states and infer two sequential waves of H3K27me3 repression at distinct gene modules during OL lineage progression. Thus, given its high resolution, versatility, and multimodal features, nano-CT allows unique insights in epigenetic landscapes in different biological systems at single cell level.
2022-09-20 | GSE198467 | GEO
Project description:We performed gene expression studies in worker bees displaying quantitative genetic differences in hygienic behavior derived from backcrosses. We established hybrid queens and backcrossed to high and low performing hygienic behavioral sources and scored the hygienic behavior of single worker bees under same environmental conditions.
2016-03-31 | E-MTAB-4142 | biostudies-arrayexpress
Project description:Incomplete antibiotic removal in pharmaceutical wastewater treatment plants (PWWTPs) could lead to the development and spread of antibiotic-resistant bacteria (ARBs) and genes (ARGs) in the environment, posing a growing public health threat. In this study, two multiantibiotic-resistant bacteria, Ochrobactrum intermedium (N1) and Stenotrophomonas acidaminiphila (N2), were isolated from the sludge of a PWWTP in Guangzhou, China. The N1 strain was highly resistant to ampicillin, cefazolin, chloramphenicol, tetracycline, and norfloxacin, while the N2 strain exhibited high resistance to ampicillin, chloramphenicol, and cefazolin. Whole-genome sequencing revealed that N1 and N2 had genome sizes of 0.52 Mb and 0.37 Mb, respectively, and harbored 33 and 24 ARGs, respectively. The main resistance mechanism in the identified ARGs included efflux pumps, enzymatic degradation, and target bypass, with the N1 strain possessing more multidrug-resistant efflux pumps than the N2 strain (22 vs 12). This also accounts for the broader resistance spectrum of N1 than of N2 in antimicrobial susceptibility tests. Additionally, both genomes contain numerous mobile genetic elements (89 and 21 genes, respectively) and virulence factors (276 and 250 factors, respectively), suggesting their potential for horizontal transfer and pathogenicity. Overall, this research provides insights into the potential risks posed by ARBs in pharmaceutical wastewater and emphasizes the need for further studies on their impact and mitigation strategies.
2024-10-20 | E-MTAB-14497 | biostudies-arrayexpress
Project description:The exposure to nano-plastics affects mammalian neurotoxic hazard characterization remains to be determined. Our aim was to investigate the neurotoxicity of nano-plastics in rodents. Animals were randomly divided into two groups: a control group and 50 mg/kg body weight PS NPs treatment groups. Before treatment, animals were fasted overnight. PS NPs were suspended into waters, vigorously stirred. The PS NPs via oral gavage once per day and for 6 months. The mice were treated with water in control group. We found that exposure to PS NPs caused cognitive decline. PS NPs exposure influenced the prefrontal cortex cells with more pathological alteration with increasing dosage. High-throughput RNA sequencing was conducted to explore miRNA expression in prefrontal cortex. Twenty-nine differentially expressed miRNAs were detected, including 12 upregulated and 17 downregulated miRNAs. This finding provided a reference for further studies on the development mechanisms of ncRNA during cognitive dysfunction.
2023-10-01 | GSE159881 | GEO
Project description:The rapid global rise of antimicrobial resistance (AMR) that increasingly invalidates conventional antibiotics has become a huge threat to human health. Although nanosized antibacterial agents have been extensively explored, they cannot sufficiently discriminate between microbes and mammals, which necessitates the exploration of other antibiotic-like candidates for clinical uses. Herein, two-dimensional boron nitride (BN) nanosheets are reported to exhibit antibiotic-like activity to AMR bacteria. Interestingly, BN nanosheets had AMR-independent antibacterial activity without triggering secondary resistance in their long-term use and displayed excellent biocompatibility in mammals. Surface proteome analysis coupled with molecular dynamic simulations and Bio-Layer Interferometry revealed that BN nanosheets could rapidly interact with the key surface proteins of cell division including FtsP, EnvC, and TolB, resulting in a specific antibacterial mechanism by impairment of Z-ring constriction in cell division. Notably, BN nanosheets had a potent antibacterial effect in a lung infection model by P. aeruginosa (AMR), displaying a two-fold increment of survival rate. Overall, these results suggested that BN nanosheets could be a promising nano-antibiotic to combat resistant bacteria and prevent AMR evolution.
2023-04-15 | PXD033277 | JPOST Repository
Project description:Cationic antimicrobial peptides (CAPs) are promising novel alternatives to conventional antibacterial agents, but the overlap in resistance mechanisms between small-molecule antibiotics and CAPs is unknown. Does evolution of antibiotic resistance decrease (cross-resistance) or increase (collateral sensitivity) susceptibility to CAPs? We systematically addressed this issue by studying the susceptibilities of a comprehensive set of antibiotic resistant Escherichia coli strains towards 24 antimicrobial peptides. Strikingly, antibiotic resistant bacteria frequently showed collateral sensitivity to CAPs, while cross-resistance was relatively rare. We identified clinically relevant multidrug resistance mutations that simultaneously elevate susceptibility to certain CAPs. Transcriptome and chemogenomic analysis revealed that such mutations frequently alter the lipopolysaccharide composition of the outer cell membrane and thereby increase the killing efficiency of membrane-interacting antimicrobial peptides. Furthermore, we identified CAP-antibiotic combinations that rescue the activity of existing antibiotics and slow down the evolution of resistance to antibiotics. Our work provides a proof of principle for the development of peptide based antibiotic adjuvants that enhance antibiotic action and block evolution of resistance.
2018-03-29 | GSE96706 | GEO
Project description:DNA, RNA and protein were extracted from the culture and subjected to massive parallel sequencing and nano-LC-MS-MS respectively Combination of these methods enabled the reconstruction of the complete genome sequence of M oxyfera from the metagenome and identification of the functionally relevant enzymes and genes
2010-03-25 | E-GEOD-18535 | biostudies-arrayexpress
Project description:Effects of dietary porous and nano particles ZnO on the gut microbiota of pigs
| PRJNA1058595 | ENA