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1,344 results for “ribosome”
YBEY as a ribosome biogenesis factor
<p>The ultraconserved RNA-binding protein YbeY has been associated with ribosomal RNA processing in numerous bacteria. However, mechanistic understanding of its function is still lacking, in particular in the light of the generally poor conservation of rRNA processing pathways across the bacterial kingdom. By leveraging the fact that YbeY homologues are wide-spread not only in bacteria but also in most eukaryotes harbouring bacteria-derived organelles, we addressed the functional significance of this protein in the highly divergent genetic system of human mitochondria.</p> <p>Mammalian mitochondrial rRNAs are known to be fully processed by dedicated RNase P and RNase Z enzymes, making additional ribonucleases superfluous. Indeed, <em>YBEY</em> knockout mitochondria were found to process all their ribosomal RNAs normally. Nevertheless, in the absence of YBEY, the mitochondrial small subunit (SSU) rRNA showed significant destabilisation, associated with a late SSU assembly defect. Component analysis identified a significant depletion of the mitoribosomal protein uS11m and several other, structurally dependent SSU constituents forming the platform and the head of the subunit. Our biochemical and genetic data suggest that this assembly defect renders the mitochondrial SSU initiation-incompetent, leading to a nearly complete translational shutdown in the mitochondrial compartment. Consequently, <em>YBEY</em> KO cells completely lose the ability to carry out oxidative phosphorylation.</p> <p>Coimmunoprecipitation and FLIM-FRET <em>in situ</em> interactomics, further supported by analyses in a heterologous system, identified direct and tight interactions between YBEY, uS11m and p32, a deeply conserved RNA-binding protein involved in mitoribosome assembly in a variety of eukaryotes. The three proteins form together stable and stoichiometric complexes. We propose that YBEY, together with p32, helps to efficiently deliver and/or correctly position uS11m on the nascent mitochondrial SSU in order to complete the assembly of the platform. Based on existing data, this YBEY function appears to be broadly conserved.</p>
Fig. 3 in Relationships Of The Heteronchocleidids (Heteronchocleidus, Eutrianchoratus And Trianchoratus) As Inferred From Ribosomal Dna Nucleotide Sequence Data
Fig. 3. Bayesian consensus tree for the anabantoids, channids and catfishes (silurids, bagrids, clariids) obtained using partial Cytochrome b sequences with cyprinids as outgroup. The heteronchocleidids genera present on the anabantoids and channids are shown with their geographical areas. Values shown at each node refer to Bayesian posterior probabilities. (*refer to Table 3 for names used in GenBank).
Fig. 2. Bayesian consensus tree generated from partial 28S in Relationships Of The Heteronchocleidids (Heteronchocleidus, Eutrianchoratus And Trianchoratus) As Inferred From Ribosomal Dna Nucleotide Sequence Data
Fig. 2. Bayesian consensus tree generated from partial 28S rDNA sequences (D1 domain) with Diplectanum spp. and Gyrodactylus spp. as outgroups. Values shown at each node refer to Bayesian (BI) posterior probabilities/maximum likelihood (ML) percentages of the bootstrap values with 100 replicates. Bootstrap values lower than 50 are given as dashes (-).
Fig. 1 in Relationships Of The Heteronchocleidids (Heteronchocleidus, Eutrianchoratus And Trianchoratus) As Inferred From Ribosomal Dna Nucleotide Sequence Data
Fig. 1. Neighbour joining (NJ) tree constructed by PAUP* using partial 28S rDNA sequences (D1 domain) with Diplectanum spp. and Gyrodactylus spp. as outgroups. Percentages of the bootstrap values for neighbour joining (NJ)/maximum parsimony (MP) (NJ & MP=1,000 replicates) are shown along the branches. Bootstrap values lower than 50 are given as dashes (-).
Fig. 3 in Broad Taxon Sampling of Ciliates Using Mitochondrial Small Subunit Ribosomal DNA
Fig. 3. Concatenated mitochondrial and nuclear SSU-rDNA tree inferred from an alignment of 2333 included characters. Most likely ML tree is shown; the BI tree was the same for well-supported nodes. Node support is as in Fig 1.
Fig. 2 in Broad Taxon Sampling of Ciliates Using Mitochondrial Small Subunit Ribosomal DNA
Fig. 2. Nuclear SSU-rDNA tree inferred from an alignment of 1543 included characters. The most likely ML tree is shown; the BI tree was the same for well-supported nodes. Node support is as in Fig 1.
Fig. 1 in Broad Taxon Sampling of Ciliates Using Mitochondrial Small Subunit Ribosomal DNA
Fig. 1. Mitochondrial SSU-rDNA tree inferred from an alignment of 790 included characters. The most likely ML tree is shown; the BI tree was the same for well-supported nodes. Node support is shown as: ML bootstraps/BI posterior probability. Values ≤ 50 are shown as "-".
Fig. 2 in Karyotype characterization of Mugil incilis Hancock, 1830 (Mugiliformes: Mugilidae), including a description of an unusual co-localization of major and minor ribosomal genes in the family
Fig. 2. Metaphase plates of Mugil incilis after (a) C-banding and (b) AgNO -staining. Arrows indicate chromosome pair number 1.
Gene-guided discovery and ribosomal biosynthesis of anticancer moroidin peptides
<p>Moroidin is a bicyclic plant octapeptide with tryptophan side-chain crosslinks, originally isolated as a pain-causing agent from Australian stinging tree <em>Dendrocnide moroides</em>. Moroidin and its analog celogentin C, derived from <em>Celosia argentea</em>, are inhibitors of tubulin polymerization and, thus, lead structures for cancer therapy. However, low isolation yields from source plants and challenging organic synthesis hinder moroidin-based drug development. Here, we present biosynthesis as an alternative route to moroidin-type bicyclic peptides and report that they are ribosomally synthesized and posttranslationally modified peptides (RiPPs) derived from BURP-domain peptide cyclases in plants.</p> <p>This submission includes the 793 plant transcriptomes from the 1kp databases [1] of Table S2 which were assembled de novo by rnaSPAdes [2,3] and searched for moroidin peptide cyclases.</p> <ol> <li>Yan, Z., Carpenter, E.J., Wickett, N.J., Mirarab, S., Nguyen, N., Warnow, T., Ayyampalayam, S., Barker, M. and Burleigh, J.G., 2014. Data access for the 1,000 Plants (1KP) project. <em>Gigascience</em>, <em>3</em>(1), pp.2047-217X.</li> <li>Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D. and Pyshkin, A.V., 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. <em>Journal of computational biology</em>, <em>19</em>(5), pp.455-477.</li> <li>Bushmanova, E., Antipov, D., Lapidus, A. and Prjibelski, A.D., 2019. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. <em>GigaScience</em>, <em>8</em>(9), p.giz100.</li> </ol> <p> </p>
Figure 5 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 5. Ancestral area reconstruction produced by means of the RASP–Bayesian binary Markov Chain Monte Carlo method and based on the occurrence of Verbesina L. (Heliantheae–Asteraceae) species. Nodes with a predicted dispersal component are circled in blue, and those with a significant vicariance component are circled in green. The green bar indicates the consensus age of the closure of the Panama Isthmus (age based on Leigh et al., 2013; O'Dea et al., 2016). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NIC, Nicaragua; PER, Peru; USA, United States of America; VEN, Venezuela.
Figure 4 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 4. Time-calibrated Bayesian inference tree generated using concatenated internal and external transcribed spacer data. The values at the nodes indicate mean divergence dates, and the horizontal bars indicate 95% highest posterior density ranges for the age at each node. The green bar indicates the consensus age of the closure of the Panama Isthmus (age based on Leigh et al., 2013; O'Dea et al., 2016). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NIC, Nicaragua; PER, Peru; USA, United States of America; VEN, Venezuela.
Figure 3 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 3. Bayesian inference tree of combined internal and external transcribed spacer data. Posterior probabilities> 0.9 are given above the branches. The red text indicates South American species. Leaf figures indicate opposite and alternate phyllotaxy. Chromosome numbers are based on Moreira & Cavalcanti (2020) and Panero & Strother (2021). BOL, Bolivia; BRA, Brazil; CAR, Caribbean; COL, Colombia; CRC, Costa Rica; ECU, Ecuador; MEX, Mexico; NA, North America; NIC, Nicaragua; PER, Peru; SA, South America; VEN, Venezuela.
Figure 2 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 2. Total distribution of Verbesina in North America, Central America, the Caribbean, and South America. (Data accessed from GBIF, https://www.gbif.org/).
Figure 1 in A TIME-CALIBRATED PHYLOGENY OF VERBESINA (HELIANTHEAE - ASTERACEAE) BASED ON NUCLEAR RIBOSOMAL ITS AND ETS SEQUENCES
Figure 1. Morphological characters in Verbesina. A, Tree of Verbesina floribunda Gardner; B, subshrubby habit of V. bipinnatifida Baker; C, capitulum of V. luetzelburgii Mattf.; D, capitulum of V. bipinnatifida; E, cypsela of V. bipinnatifida; F, cypsela of V. floribunda; G, scanning electron micrograph (SEM) of the verrucous cypsela surface of V. macrophylla (Cass.) S.F.Blake; H, inflorescence of V. macrophylla; I, pinnatipartite leaf of V. macrophylla; J, SEM of the scalariform cypsela surface of V. glabrata Hook. & Arn.; K, inflorescence of V. glabrata; L, entire leaf of V. glabrata. Vouchers: C, G.L. Moreira et al. 118 (CEN); D–E, G.L. Moreira et al. 116 (CEN); F, G.L. Moreira et al. 101 (CEN). Scale bars: C, 8 mm; D, 4 mm; E, 2 mm; F, 4 mm; G and J, 200 μm. Photographs: G. L. Moreira.
Fig. 1 in Phylogenetic position of the freshwater fish trypanosome, Trypanosoma ophiocephali (Kinetoplastida) inferred from the complete small subunit ribosomal RNA gene sequence
Fig. 1 The neighbor-joining tree of aquatic trypanosomes constructed from complete small subunit ribosomal RNA (SSrRNA) sequences indicating the systematic position of T. ophiocephali and phylogenetic relationships among the aquatic trypanosomes whose sequences are available. T. lewisi, T. theileri, and T. avium are taken as the outgroup. Bootstrap values are shown for the maximum parsimony/neighborjoining/Bayes analyses
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 3. Maximum likelihood tree constructed from 38 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to the number of expected nucleotide substitutions per site.
Fig. 2 in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 2. Neighbor-joining tree inferred form the analysis of 39 nuclear rDNA ITS1 and ITS2 sequences from Apiaceae genus Daucus and its relatives using a transition/transversion rate ratio of 1.6. Branch lengths are proportional to distance estimated from the two parameter method of Kimura. Numbers at nodes indicate bootstrap values for 100 replicate analyses. On this tree, bootstrap values <20% are not indicated.
Fig. 1 in Molecular phylogeny of Daucus (Apiaceae): Evidence from nuclear ribosomal DNA ITS sequences
Fig. 1. Strict consensus of 11 parsimony trees derived from equally-weighted parsimony analysis of combined nuclear DNA ITS1 and ITS2 sequences from Daucus and its relatives using all unambiguously-aligned positions (CIs with and without uninformative characters= 0.6613 and 0.5817; RI=0.8387). From the left to the right, names of taxa, sections, and clades are given. Numbers above the nodes indicate the number of times a monophyletic group occurred in 100 bootstrap replicates; AutoDecay values are given below.
Fig. 1 in Taxonomic review of the umbelliferous taxa Heracleum moellendorffii complex in Korea based on molecular phylogenies of nuclear ribosomal ITS sequences
Fig. 1. Cladograms inferred from the analysis of 29 nuclear ribosomal DNA ITS1 and ITS2 sequences from the genus Heracleum and an outgroup. (A) The strict consensus of two minimal length 138-step trees derived from equally weighted maximum parsimony analysis of combined nuclear rDNA ITS and 5.8S sequences (CI's with and without uninformative characters=0.91 and 0.89, respectively; RI=0.95). Numbers above nodes indicate the number of times a monophyletic group occurred in 100 bootstrap replicates; decay values are presented below. (B) The Maximum likelihood tree using a transition/tranversion rate ratio of 1.5. Branch lengths are proportional to the number of expected nucleotide substitutions per site. Boxes A, B, and C indicate clades H. maximum-moellendorffii, H. subbipinnatum, and H. sphondylium, respectively.
Figure 6 in Genetic divergences of South and Southeast Asian frogs: a case study of several taxa based on 16S ribosomal RNA gene data with notes on the generic name Fejervarya
Figure 6. Maximum likelihood (ML) tree of bufonid frogs based on nucleotide sequences of the mitochondrial 16S rRNA gene with Leptophryne borbonica as an outgroup. The bootstrap support (>50%) is indicated at nodes in the order of ML (500) replicates. Asterisks represent Bayesian posterior probability (BPP; * ≥95%). Specimens examined in this study are indicated by boldface type.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.