16S-23S-PrEP-microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB29019 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human gut microbiota from pre and post-PrEP specimens
| PRJEB29018 | ENA
Project description:Pseudomonas entomophila strain:23S Genome sequencing
| PRJNA669330 | ENA
Project description:Prep ChIP-seq on whole zebrafish embryos at 3.5 and 12 hours post fertilisation (hpf)
2018-06-25 | E-MTAB-5967 | biostudies-arrayexpress
Project description:Post-transcriptional modifications are added to ribosomal RNAs (rRNAs) to govern ribosome biogenesis and to fine-tune protein biosynthesis. RlhA, a dedicated modification enzyme, adds a unique 5-hydroxycytidine (ho5C) at 23S rRNA position 2501 in E. coli and related bacteria. However, the molecular and biological functions as well as the regulation of ho5C2501 remain unclear. We conducted extensive growth curves with the modification-deficient ∆rlhA strain and quantified the extent of the modification during different conditions by mass spectrometry and reverse transcription. The levels of ho5C2501 in E. coli ribosomes turned out to be highly dynamic and growth phase-dependent, with the most effective hydroxylation yields observed in the stationary phase. We demonstrated a direct effect of ho5C2501 on translation efficiencies in vitro and in vivo. High ho5C2501 levels reduced protein biosynthesis which however turned out to be beneficial for E. coli for adapting to oxidative stress. This functional advantage was small under optimal conditions or during heat or cold shock, but becomes pronounced in the presence of hydrogen peroxide. Taken together, these data provided first functional insights into the role of this unique 23S rRNA modification for ribosome functions and bacterial growth under oxidative stress.
2022-02-16 | PXD025875 | Pride
Project description:The use of antiretroviral therapy (ART) as pre-exposure prophylaxis (PrEP) is an effective strategy for preventing HIV acquisition. The cellular consequences of PrEP exposure, however, have not been sufficiently explored to determine potential effects on health in individuals without HIV. Peripheral blood mononuclear cells (PBMCs) from people without HIV were exposed to tenofovir disoproxil fumarate (TDF) or emtricitabine (FTC) overnight. Mitochondrial mass and function were measured by flow cytometry and Agilent XFp analyzer. Monocyte-derived macrophages (MDMs) were differentiated in 20% autologous serum for 5 days in the presence or absence of TDF or FTC, and surface markers, lipid uptake, and efferocytosis were measured by flow cytometry. MDM gene expression was measured using RNAseq. Serum lipids were measured using mass spectrometry. PBMCs exposed to TDF or FTC had decreased maximal oxygen consumption rate (OCR) and reduced mitochondrial mass. Exposure to PrEP also increased reactive oxygen species (ROS) production from monocyte subsets. Compared to MDMs cultured in medium alone, cells differentiated in the presence of TDF (829 genes) or FTC (888) genes had significant changes in gene expression. Further, PrEP-exposed MDMs had decreased mitochondrial mass, and displayed increased lipid uptake and reduced efferocytosis. Plasma biomarkers and lipid levels were also altered in vivo in individuals receiving a PrEP regimen. Exposure of leukocytes to TDF or FTC resulted in decreased mitochondrial function, and altered functional and transcriptional profiles. These findings may have important implications for the metabolic and immunologic consequences of PrEP in populations at risk for HIV acquisition.
2021-10-01 | GSE159339 | GEO
Project description:We performed miRNA microarray profiling on samples prepared from two different cell lines by three widely-used total RNA sample prep methods.
2008-08-19 | GSE11840 | GEO
Project description:The 120-nt long 5S rRNA, is an indispensable component of cytoplasmic ribosomes in all living organisms. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether maintaining 5S rRNA as an independent molecule is critical for ribosome function and cell survival. By fusing circularly permutated 5S rRNA (cp5S) with 23S rRNA and deleting all wild type 5S rRNA genes, we generated an Escherichia coli strain completely devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is not required for cell growth at 37°C and is unlikely to have essential functions outside the ribosome. The fully-assembled ribosomes carrying 23S-cp5S hybrid rRNA and lacking free 5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits that are unable to form stable 70S ribosomes. Cryo-EM analysis revealed a dramatically malformed peptidyl transferase center in the misassembled 50S subunits. The results of our experiments argue that the key evolutionary force preserving the autonomous nature of the smallest rRNA is its role in ribosome biogenesis.
2020-06-18 | PXD019058 | Pride
Project description: Not available
| S-EPMC8766866 | biostudies-literature
Project description:The growth rate (µ) of microbes is a fundamental property influencing its production capacity. To identify the transcriptomic changes of Corynebacterium glutamicum ATCC13032 with increasing growth rate, three transitions, induced by different pre-culture conditions, were sampled in triplicate at growth rates ranging from 0.02 to 0.4 h-1. The pre-culture conditions differed in limiting substrate (phosphate, nitrogen, carbon) and the length of the stationary phase. Samples of 2 mL were withdrawn from the bioreactor in biological triplicates and immediately centrifuged at 20000 g for 30 seconds at 4 °C. The supernatant was discarded and the remaining cell pellet was immediately flash frozen in liquid nitrogen. Total RNA was isolated from three biological replicates using RNeasy Mini Kit along with a DNase Kit (both from Qiagen). Initially RNA quality was checked by Trinean Xpose (Gentbrugge,Belgium) and Agilent RNA Nano 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Samples contaminated with DNA were treated with DNase (Qiagen), cleaned as described above and rechecked by Xpose and Agilent Bioanalyzer. Finally RNA was free of DNA with an RNA Integrity Number (RIN) > 9 and rRNA Ratio [23s / 16s] > 1.5. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). RNA was free of detectable rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was used to prepare cDNA libraries. The resulting cDNAs were sequenced paired end on an Illumina MiSeq system using 75 bp read length and on Illumina HiSeq 1500 system using 70 bp read length and 50 bp read length for one single sample. Through the comparison of these three datasets, each containing three biological replicates, the pre-condition independent gene expression changes could be deduced and the growth rate modulon was identified.
2019-04-01 | E-MTAB-7436 | biostudies-arrayexpress
Project description:This study applies targeted Cas9-based gene insertion strategies for the correction of full-length dystrophin in a pre-clinical humanized mouse model of Duchenne muscular dystrophy. Following intramuscular or intravenous delivery, full-length dystrophin is restored in skeletal and cardiac muscle.
2021-04-24 | GSE173224 | GEO