Streptococcus pneumoniae
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB14360 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR410690_1.fastq.gz | Fastqsanger.gz | |||
| DRR410690_2.fastq.gz | Fastqsanger.gz | |||
| DRR410691_1.fastq.gz | Fastqsanger.gz | |||
| DRR410691_2.fastq.gz | Fastqsanger.gz | |||
| DRR410692_1.fastq.gz | Fastqsanger.gz |
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Project description:We measured abundances of tRNAs by means of hydro-tRNA-seq (Gogakos et al., 2017), a method based on partial alkaline RNA hydrolysis that generates fragments suitable for sequencing, in the genome-reduced bacterium Mycoplasma pneumoniae.
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2023-01-13 | PXD036472 | Pride
Project description:In recent years, several small molecule cytotoxic drugs have been identified as potential inhibitors of ribosome biogenesis (Drygin et al., 2011; Peltonen et al., 2014a; Peltonen et al., 2014b). CX-5461 is one such drug that has also demonstrated anticancer potential for a wide range of malignancies (Bywater et al., 2012; Cornelison et al., 2017; Devlin et al., 2015; Drygin et al., 2011; Hald et al., 2019; Hein et al., 2017; Ismael et al., 2019; Lawrence et al., 2018; Lee et al., 2017; Negi and Brown, 2015; Taylor et al., 2019; Xu et al., 2017; Yan et al., 2017) (Haddach et al., 2012), and is presently under phase I trials for the treatment of both hematological cancers and solid tumours (Group, 2016; Khot et al., 2019). CX-5461 was initially characterized as an inhibitor of RNA Polymerase I (RPI/PolR1/PolI) that is responsible for the synthesis of the major ribosomal RNAs and the initial step in ribosome biogenesis (Drygin et al., 2011). Since RPI and its corresponding core transcription factors are dedicated to this task alone, they present ideal molecular targets by which to modulate ribosome biogenesis. However, the specificity of CX-5461 has been questioned and it has been suggested that this drug may also act by stabilizing DNA G-quadruplexes or by “poisoning” topoisomerase II (Topo II). Thus, the primary target of this drug and its mode of action are still in doubt. Here we used Deconvolution-ChIP-Seq in NIH3T3 and HEK293T cells treated for different times with CX-5461. The data show that the primary target of CX5461 is the initiation of ribosomal RNA gene (rDNA) transcription. CX-5461 blocks transcription initiation in vitro and in vivo by arresting RNA polymerase I (RPI/Pol1) within the preinitiation complex. In contrast to previous suggestions, CX-5461 does not effect recruitment of the TBP-TAF complex SL1 to the rDNA promoter, the recruitment of the initiation competent RPI-Rrn3 complex or ongoing transcription elongation, arguing against a role for G-quadruplex stabilization or topoisomerase II poisoning. Inhibition of transcription by CX-5461 is not reversible, the RPI-Rrn3 complex remains arrested in the preinitiation complex even after drug removal. This leads to nucleolar stress, extensive DNA damage and cell senescence. Our data show that the cytotoxicity of CX-5461 is the downstream result of the highly specific inhibition of rDNA transcription. The observation that this inhibition is irreversible will be important for the future design of chemotherapeutic strategies and the avoidance of drug resistance.
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Project description:RNA-sequencing data from human iPSC PGP1 cells (n=4) differentiated into mesoderm (day-2) (n=4) or cardiomyocytes (days 25-30) (n=4) through modulation of Wnt/β-catenin signaling as previously described (Cohn et al., 2019; Hinson et al., 2017; Hinson et al., 2015; Lian et al., 2012).
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Project description:Background Pediatric tuberculosis (TB) diagnosis is often challenging due to difficultly obtaining diagnostic respiratory specimens, which may contain low concentrations of Mycobacterium tuberculosis (Mtb) bacilli. However, we have reported that an immuno-affinity liquid chromatography-tandem mass spectrometry TB assay (ILM-TB) that detects a peptide derived from Mtb 10-kDa culture filtrate protein (CFP10pep) can diagnose TB regardless of patient age or infection site when analyzing trypsin-digested blood samples.
Methods Discovery and validation cohorts were respectively generated from children who consecutively presented at two hospitals in South Africa (SA) from April 2012 to August 2017 (157 children <13 years-of-age) or at two communities in the Dominican Republic (DR) from July 2019 to May 2023 (101 children <17 years-of-age). All children were evaluated for TB at enrollment and 6-months post-enrollment, and assigned confirmed, unconfirmed, or unlikely TB diagnoses based on the 2015 NIH criteria for pediatric TB. Serum samples were collected at and two and six months after SA/DR enrollment, and at two weeks DR post-enrollment (270 SA and 304 DR samples) to evaluate ILM-TB assay performance.
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Project description:In a previous study we applied a quantitative proximity-labeling technique called Biotin Identification (BioID, Roux et al., 2012) to analyze the microenvironment of the Gβ-like scaffold protein Asc1 (Opitz et al., 2017). The WD40-repeat protein Asc1 binds to the head region of the small 40S ribosomal (hr40S) subunit. In this study, we analyzed the hr40S from the perspective of Rps2, a ribosomal neighbor of Asc1. We intended to confirm proteins of the Asc1 proxiOME at the hr40S and to observe changes when Asc1 was absent. References: Roux K.J., Kim D.I., Raida M., Burke B. 2012. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol 196:801-810 Opitz N., Schmitt K., Hofer-Pretz V., Neumann B., Krebber H., Braus G.H., Valerius O. 2017. Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast. Mol Cell Proteomics 16:2199-2218
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