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40 results for “large subunit”
Figure 5 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 5 ML tree of Sordariomycetes constructed from the reference sequence alignments and OTUs for both markers (clustering thresholds: 98% ITS2, 99% LSU D1-D2). Leotia lubrica (Leotiomycetes) was specified as the outgroup. The assignment of OTUs by each of the three classifiers (RDP, IDTAXA, Protax-fungi) is shown by coloured boxes. Terminals missing these boxes are the reference sequences. Coloured dots on the nodes of the tree indicate the hypothetical ancestor defining monophyletic groups corresponding to the various orders of Sordariomycetes. The extent of each order is indicated by the coloured inner ring. Note that the ancestor of an order is defined by the youngest node from which all reference sequences are descended; OTUs falling outside of the resulting clades appear as 'unassigned' by the phylogenetic analysis approach. The distribution of ITS2 (red squares) and LSU D1-D2 (blue bullets) relative to the reference set (yellow stars) on each of the tips of the tree. Note the limited presence of ITS sequences in the Ophiostomatales (in top right quadrant).
Figure 8 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 8 Proportion of OTUs assigned to each Order from metabarcoding with LSU (left panel) and ITS (right panel) markers based on the RDP classifier and the phylogenetic tree, under increasing threshold values.
Figure 4 in Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1
Figure 4. Phoronid phylogeny. Bayesian relaxed clock analysis of rDNA sequences. At each node is shown the relative node height, the 95% highest posterior density (HPD) limits, and the node label. Labels at brachiopod nodes are as used previously (Cohen & Weydmann, 2005). The 24tx alignment file was loaded into the utility BEAUTI to prepare an xml input file for BEAST and taxon groups corresponding to nodes B, D, F, M, N, and R were defined. The general time reversible + gamma + invariant sites model was selected, with four gamma categories and the mean substitution rate was fixed = 1.0 (the default). The uncorrelated lognormal clock rate variation model was selected, with all priors set to 'Uniform'. Operators that would change tree topology were switched off, and auto-optimize selected. The xml file was edited to include the maximum likelihood starting tree, which had been exported from PAUP*4 in Newick format with branch lengths. Multiple analyses were run with closely comparable results; the particular analysis shown was stopped after 1.3 ¥ 107 generations with default data-logging, when inspection of the log file in TRACER revealed that all parameter distributions had smooth, quasi-normal curves and the lowest effective sample size was> 450. The best resulting tree was selected in TreeAnnotator, with 10% discarded as burnin, displayed in FigTree as relative heights (root = 1.0) with 95% HPD node bars, and the graphics file exported for editing. Diagonal lines mark a truncated node bar.
Data from: Phylogenetic relationships of Agaric fungi based on nuclear large subunit ribosomal DNA sequences
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Data from: SiSTL1, encoding a large subunit of ribonucleotide reductase, is crucial for plant growth, chloroplast biogenesis, and cell cycle progression in Setaria italica
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Experimental upregulation of developmentally downregulated ribosomal protein large subunits 7 and 7A promotes axon regeneration after injury in vivo [bulk RNA-Seq]
GEO Series GSE240315. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
The nucleolar protein NOL12 is required for processing of large ribosomal subunit rRNA precursors in Arabidopsis
GEO Series GSE232067. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
RBM-5 modulates U2AF large subunit-dependent alternative splicing in C. elegans
GEO Series GSE115695. Caenorhabditis elegans. 18 samples. Type: Expression profiling by high throughput sequencing.
Experimental upregulation of developmentally downregulated ribosomal protein large subunits 7 and 7A promotes axon regeneration after injury in vivo [scRNA-Seq]
GEO Series GSE240316. Mus musculus. 0 samples. Type: Expression profiling by high throughput sequencing; Third-party reanalysis.
Small and large ribosomal subunit deficiencies lead to distinct gene expression signatures that reflect cellular growth rate
GEO Series GSE121189. Saccharomyces cerevisiae. 50 samples. Type: Expression profiling by high throughput sequencing; Other.
RNA Post-transcriptional Modifications in Two Large Subunit Intermediates Populated in E.coli Cells Expressing Helicase Inactive R331A DbpA
GEO Series GSE196821. Escherichia coli. 15 samples. Type: Other.
Modifying plant photosynthesis and growth via simultaneous chloroplast transformation of Rubisco large and small subunits
<p>Engineering improved Rubisco poses a crucial strategy for enhancing photosynthesis but is challenged by the alternate locations of the plastome rbcL gene and nuclear RbcS genes. Here we develop a RNAi-RbcS Nicotiana tabacum (tobacco) master-line, tobRrΔS, amenable to rbcL-rbcS co-engineering by chloroplast transformation. Four tobacco genotypes coding alternative rbcS genes and adjoining 5ˈ-intergenic sequences revealed Rubisco production was highest in the lines incorporating a rbcS gene whose codon use and 5ˈUTR matched rbcL. These lines produced up to 50% the wild-type Rubisco content. Additional tobacco lines coding potato rbcL-rbcS operons examined how the differing mesophyll made small subunits (pS1, pS2, pS3) or the trichome pST-25 subunit influenced Rubisco biogenesis, catalysis, leaf physiology and plant growth. Rubisco levels were ~15% lower in leaves expressing pS3 relative to those producing pS1, pS2, and pST. However, the pS3-subunit increased carboxylation rate (kcatC) by 13% and carboxylation efficiency (CE, kcatC divided by the Km for CO2) by 17% relative to the pS1 and pS2 subunits as a result of the βa-βb loop substitutions Asn-55-His and Lys-57-Ser. By contrast tobacco photosynthesis and growth were most impaired in lines producing the pST-subunit that reduced CE and CO2/O2 specificity of potato Rubisco by 40% and 15% respectively.<br> </p>
Modifying plant photosynthesis and growth via simultaneous chloroplast transformation of Rubisco large and small subunits
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RNA Post-transcriptional Modifications of an Early-Stage Large Subunit Ribosomal Intermediate
GEO Series GSE232539. Escherichia coli. 3 samples. Type: Other.
Pol5 is required for recycling of small subunit biogenesis factors and for formation of the polypeptide exit tunnel of the large ribosomal subunit
GEO Series GSE132973. Saccharomyces cerevisiae. 2 samples. Type: Other.
A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit
GEO Series GSE179085. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing; Other.
Structural transitions during yeast large ribosomal subunit maturation analyzed by tethered nuclease structure probing
GEO Series GSE97276. Saccharomyces cerevisiae. 8 samples. Type: Expression profiling by high throughput sequencing; Other.
Connections for binders csv (small and large subunit with nb Helices and proteins)
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Experimental upregulation of developmentally downregulated ribosomal protein large subunits 7 and 7A promotes axon regeneration after injury in vivo
GEO Series GSE240317. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing; Third-party reanalysis.
Ataxin-2 modulates mRNA levels of proteins in ribosomal large and small subunit and in translation initiation complex
GEO Series GSE57998. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
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