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265 results for “ribosomal RNA”
FIGURE 7 in Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene
FIGURE 7. Phylogeny of the Chinese Prionini based on combined sequences of 12S rRNA and 16S rRNA (excluding Priotyrannus closteroides). A: Bootstrap 50% majority-rule consensus tree of distance method by PAUP* with bootstrap values (%), Wtd. S.S. = 0.0251, APSD = 3.047, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; B: Bootstrap 50% majority-rule consensus tree of maximum likelihood method by PAUP* with bootstrap values (%), -Ln likelihood = 4077.7392, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; C: Bootstrap 50% majority-rule consensus tree of parsimony method by PAUP* with bootstrap values (%), tree length =682, CI = 0.7405, RI = 0.3723, the scale bar in the bottom left corner of the tree being in units appropriate to the tree; D: Bayesian tree by MrBayes with Bayesian posterior probabilities (%), the scale bar in the bottom left corner of the tree meaning 0.1 nucleotide substitutions per site.
Data from: Decrease in ribosomal RNA in Candida albicans induced by serum exposure
Candida albicans is an important polymorphic human pathogen. It can switch from a unicellular yeast form to germinating hypha, which may play a role in making it the successful pathogen it is. This hyphal transformation can be triggered by various extracellular stimuli, the most potent one being serum from any source. We have previously reported that Candida albicans transiently polyadenylates portions of both the large and small subunits of ribosomal RNA, shortly after serum exposure. Northern blots at the same time suggested that serum might induce a decrease in total ribosomal RNA. We have carried out a number of experiments to carefully assess this possibility and now report that serum significantly reduces ribosomal RNA in Candida albicans. Fluorometric measurements, Northern blotting and quantitative RT-PCR, have all confirmed this decrease. Timed experiments show that serum induces this decrease rapidly, as it was seen in as early as five minutes. Cell mass is not decreased as total cellular protein content remains the same and metabolic activity does not appear to slow, as assessed by XTT assay, and by the observation that cells form hyphal structures robustly. Another hyphal inducer, N-acetylglucosamine, also caused RNA decrease, but to a lesser extent. We also observed it in non-germinating yeast, such as Candida glabrata. The reason for this decrease is unknown and overall our data suggests that decrease in rRNA does not play a causal role in hyphal transformation. Rapid and significant decrease in a molecule so central to the yeast's biology is of some importance, and further studies, such as its effect on protein metabolism, will be required to better understand its purpose.
Data from: Delimitation of the Thoracosphaeraceae (Dinophyceae), including the calcareous dinoflagellates, based on large amounts of ribosomal RNA sequence data
The phylogenetic relationships of the Dinophyceae (Alveolata) are not sufficiently resolved at present. The Thoracosphaeraceae (Peridiniales) are the only group of the Alveolata that include members with calcareous coccoid stages; this trait is considered apomorphic. Although the coccoid stage apparently is not calcareous, Bysmatrum has been assigned to the Thoracosphaeraceae based on thecal morphology. We tested the monophyly of the Thoracosphaeraceae using large sets of ribosomal RNA sequence data of the Alveolata including the Dinophyceae. Phylogenetic analyses were performed using Maximum Likelihood and Bayesian approaches. The Thoracosphaeraceae were monophyletic, but included also a number of non-calcareous dinophytes (such as Ensiculifera and Pfiesteria) and even parasites (such as Duboscquodinium and Tintinnophagus). Bysmatrum had an isolated and uncertain phylogenetic position outside the Thoracosphaeraceae. The phylogenetic relationships among calcareous dinophytes appear complex, and the assumption of the single origin of the potential to produce calcareous structures is challenged. The application of concatenated ribosomal RNA sequence data may prove promising for phylogenetic reconstructions of the Dinophyceae in future.
Data from: Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage
The ribosomal RNA genes (rDNA) comprise a highly repetitive gene cluster. The copy number of genes at this locus can readily change and is therefore one of the most unstable regions of the genome. DNA damage in rDNA occurs after binding of the replication fork blocking protein Fob1 in S phase, which triggers unequal sister chromatid recombination. However, the precise mechanisms by which such DNA double-strand breaks (DSBs) are repaired is not well understood. Here, we demonstrate that the conserved protein kinase Tel1 maintains rDNA stability after replication fork arrest. We show that rDNA associates with nuclear pores, which is dependent on DNA damage checkpoint kinases Mec1/Tel1 and replisome component Tof1. These findings suggest that rDNA-nuclear pore association is due to a replication fork block and subsequent DSB. Indeed, quantitative microscopy revealed that rDNA is relocated to the nuclear periphery upon induction of a DSB. Finally, rDNA stability was reduced in strains where this association with the nuclear envelope was prevented, which suggests its importance for avoiding improper recombination repair that could induce repeat instability.
2'O-ribose methylation of ribosomal RNA (rRNA 2'Ome) in primary human T cells from septic shock and COVID-19 patients
<h2>Abstract</h2> <p>T cell exhaustion plays a central role in sepsis-induced immunosuppression. Deciphering the precise mechanism of this cellular dysfunction could lead to new therapies. In several pathophysiological contexts, the 2’O-ribose methylation of ribosomal RNA (rRNA 2’Ome) has emerged as a level of epitranscriptomic regulation. Here, we report for the first time site-specific alterations of rRNA 2’Ome epitranscriptomic marks in T cells after sepsis, associated with impaired functionality. Using primary human T cells from septic shock and COVID-19 patients, we identified a subset of sites with high inter-individual variability, the levels of which correlated with lymphocyte effector functions. This was recapitulated in an ex vivo model of stimulated T lymphocytes from healthy donors. Finally, 2’Ome signature discriminated samples from septic patients from those of healthy donors. We describe rRNA 2’Ome regulation as a new molecular mechanism that controls T lymphocyte effector function in sepsis with high potential as biomarker and therapeutic target. </p> <p>---------------------------------------------------</p> <h2>Description of the data and file structure</h2> <p>Each folder contains the read-end counts in the sub-directory <strong>RiboMethSeq_ReadEnd_Counts</strong> and the metadata file. The metadata file describe each file contained in this sub-directory.</p> <p></p> <p>The read-end count file structure:</p> <ol> <li> <p>The <strong>name of the RNA</strong> on which the read end counting was performed.</p> </li> <li> <p>The <strong>number of the position</strong> on the RNA.</p> </li> <li> <p>The <strong>value of the read end counts</strong> at the position.</p> </li> </ol> <h2>Code/Software</h2> <p>Using <a href="https://github.com/RibosomeCRCL/ribomethseq-nf">ribomethseq-nf</a> pipeline, fastq were used to align reads on the human rRNA sequence (NR_046235), compute 5’/3’-end read counts.</p> <p>These files can be the input of <a href="https://github.com/RibosomeCRCL/rRMSAnalyzer">rRMSAnalyzer package</a> to adjust batch effect (ComBat-seq method) and calculate C-score corresponding to the end read count at the genomic position of interest normalized to the median of end read counts of the local environment (6 upstream and 6 downstream nucleotides).</p>
Linked collectors and determiners for: Fungal 28S Ribosomal RNA (LSU) RefSeq Targeted Loci Project..
Natural history specimen data linked to collectors and determiners held within, "Fungal 28S Ribosomal RNA (LSU) RefSeq Targeted Loci Project.". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/bf3f09bd-3af6-45be-a2c4-bd5c285cab8a">https://bionomia.net/dataset/bf3f09bd-3af6-45be-a2c4-bd5c285cab8a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/bf3f09bd-3af6-45be-a2c4-bd5c285cab8a">https://gbif.org/dataset/bf3f09bd-3af6-45be-a2c4-bd5c285cab8a</a>. Formatted as a Frictionless Data package.
Data from: Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage
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Data from: Delimitation of the Thoracosphaeraceae (Dinophyceae), including the calcareous dinoflagellates, based on large amounts of ribosomal RNA sequence data
Open the record for dataset details and reuse information.
Data from: Decrease in ribosomal RNA in Candida albicans induced by serum exposure
Open the record for dataset details and reuse information.
FUS modulates the level of ribosomal RNA modifications by regulating a subset of snoRNA expression [HydraPsiSeq]
GEO Series GSE202524. Homo sapiens. 20 samples. Type: Other.
A non-canonical role for a small nucleolar RNA in ribosome biogenesis and senescence (CRISPRi screen)
GEO Series GSE232856. Homo sapiens. 4 samples. Type: Other.
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]
GEO Series GSE155649. Homo sapiens. 77 samples. Type: Other.
E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]
GEO Series GSE107327. Escherichia coli. 14 samples. Type: Expression profiling by high throughput sequencing.
An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation (CRISPRi screen) [786-O]
GEO Series GSE270847. Homo sapiens. 4 samples. Type: Other.
Hierarchical RNA processing is rate limiting for mitochondrial ribosome assembly
GEO Series GSE83471. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing; Other.
Heat shock-induced ribosomal intergenic spacer RNA
GEO Series GSE115731. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA polymerase I activators count and adjust ribosomal RNA gene copy number
GEO Series GSE116661. Saccharomyces cerevisiae BY4741. 25 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing.
Structural and molecular insights into specialized translation mediated by the ribosome mRNA-binding channel [RNA-Seq]
GEO Series GSE301926. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans.
GEO Series GSE65392. Homo sapiens. 6 samples. Type: Expression profiling by array.
RNA Sequencing and Ribosome profiling of TMA46, STM1 and YGR054W knockout yeast strains
GEO Series GSE185458. Saccharomyces cerevisiae. 32 samples. Type: Expression profiling by high throughput sequencing; Other.
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