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1,344 results for “ribosome”
Figure 2 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 2. Maximum likelihood (ML) tree based on nucleotide sequences of the mitochondrial 16S rRNA gene from 88 haplotypes of frogs (Table 1), with Xenopus laevis as an outgroup. Bootstrap support (>50%) is indicated at nodes in the order of ML (1000) replicates. Asterisks represent Bayesian posterior probability (BPP; * ≥95%).
Figure 3 in Diceratocephala boschmai (Platyhelminthes: Temnocephalida) from crayfish farms in Thailand: investigation of the topographic surface and analysis of 18S ribosomal DNA sequences
Figure 3. The neighbor-joining phylogenetic tree based on the 18S rDNA gene, showing the relationships of D. boschmai with 29 other turbellarian species.
Figure 2 in Diceratocephala boschmai (Platyhelminthes: Temnocephalida) from crayfish farms in Thailand: investigation of the topographic surface and analysis of 18S ribosomal DNA sequences
Figure 2. Surface topography of D. boschmai. A–C) Unhatched and hatched eggs; D) ventral view of a specimen; E) mouth with protruding pharynx; F) thread-like filaments adhered to the pharynx; G, H) a higher magnification of write-dot boxes in 2E; I, J) a higher magnification of write-dot boxes in 2D; K) ventral view of a specimen at posterior end; L) dorsal view of a specimen; M) a higher magnification of write-dot box in Figure L. ad, adhesive disc; af, adhered filaments; ci, ciliated cell; ds, double spines; fi, filament; gr, groove; gv, gravel-like units; in, intertentacular flange; mo, mouth; op, opercular plate; pe, peduncle; pi, pit; sp, single spine; tb, trabecular meshwork; tc, tentacle; th, thread-like filaments; tr, trunk; vi, villi..
Figure 1. A in Diceratocephala boschmai (Platyhelminthes: Temnocephalida) from crayfish farms in Thailand: investigation of the topographic surface and analysis of 18S ribosomal DNA sequences
Figure 1. A) C. destructor harboring adult D. boschmai and eggs of flatworm; B) dorsal view of an extending body; C) diagram of organ structures in dorsal view; D) diagram of reproductive complex; E, F) photomicrograph and diagram of penial stylet, respectively; G) unhatched and hatched eggs. ad, adhesive disc; at, atrium; cv, contractile vesicle; ds, dorsal side; es, ejaculatory sac; ey, eye; ev, excretory vesicle; fi, filament; in, intertentacular flange; ine, intestine; int, introvert; mo, mount; ov, ovary; pe, peduncle; pf, plane of fracture; ph, pharynx; pn, subepidermal pigment network; ps, penial stylet; rv, resorbens vesicle; s, stalk; se, seminal vesicle; sr, seminal receptacle; sp, sclerotized papillae; tc, tentacle; te, testis; tg, tentacular gland; ve, vasa efferentia; vg, vagina; vi, vitellaria; vs, ventral side.
Figure 1 in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)
Figure 1. The nucleotide and deduced amino acid sequences of the P. xylostella RpS27a gene coding region. The deduced amino acid sequence is presented below the nucleotide sequence in a single letter. The nuclear localization signal sequence is shaded. The initial and termination codon are underlined. The stop codon is denoted with an asterisk.
Figure 5. Phylogenetic relationship between P. xylostella RpS27a in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)
Figure 5. Phylogenetic relationship between P. xylostella RpS27a and some other species. Corresponding GenBank accession numbers are: M. sexta: ACY95367.1; P. dardanus: CAH04128.1; Bombyx mori: NP_001091826.1; P. polytes: BAM18943.1; P. xuthus: BAM17728.1; S. frugiperda: AAL62473.1; D. plexippus: EHJ77179.1; A. yamamai: BAD05031.1; P. xylostella: JX437934; T. rubida: AER92457.1; D. melanogaster: NP_476778.1; A. aegypti: AAS79344.1; C. quinquefasciatus: XP_001844485.1.
Figure 6 in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)
Figure 6. mRNA level of RpS27a in DS-strain and DR-strain of P. xylostella. All values are expressed as means ± SD. DS-strain: deltamethrin-susceptible strain; DR-strain: deltamethrinresistant strain. *P <0.01.
The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation
<p>Additional files, Scripts and Data related to the manuscript Papadopoulos et al, The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation. </p> <p>Additional file 1: contains supplemental figures and tables of the manuscript</p> <p>Additional file 2: contains the complete list of the 89 Ribo-Seq datasets (89 biological replicas).</p> <p>Papadopoulos_et_al_2024.tar.gz: contains the scripts, raw data, intermediate data and final (processed) data to reproduce the analyses, Figures, and Tables of the manuscript Papadopoulos et al, The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation. </p> <p>The archive contains 3 directories:</p> <p>*** input: contains the protocols, raw data, and the associated intermediate processed data that are used as inputs of the scripts that perform the subsequent analyses and generate the Figures and Tables</p> <p><br>*** scripts: all the scripts necessary to perform the analyses of the manuscript and generate the final data, Figures and Tables available in the ./output directory</p> <p>*** output: contains the final processed data including the final lists and tables resulting from MSMS analyses or RiboSeq analyses, the final Figures and Tables of the manuscript as well as the 3 final tables that integrate the processed data from Ribo-Seq, MSMS, evolutionary analyses, sequence and structural analyses, final analyses on codon propensities. These 3 tables, beyond being necessary for the anlayses performed for this study can also be useful for users to realize their own analyses. All the data, Figures and Tables contained in this directory can be directly generated from the scripts available in the directory ./scripts and the data contained in the directory ./input. Please see the README in the different directories to reproduce everything.</p> <p> </p>
BFR2: a curated benthic foraminifera ribosomal reference database
<p>The present data set provides a fasta file, a tab-separated text file, and an Excel file. The fasta file includes 5,324 18S rDNA reference sequences for benthic foraminifera. The tab-separated text file includes the following fields: BFR2 number = unique internal sequence accession number; length = sequence length; class = class to which each sequence is assigned; order/suborder/clade = order/suborder/clade to which each sequence is assigned; family = family to which each sequence is assigned; genus = genus to which each sequence is assigned; species = species to which each sequence is assigned; isolate number = unique DNA extraction number; clone/direct: indicates whether it has been directly sequenced or cloned; genbank_accession = NCBI sequence accession number; sampling site = biogeographic region where the specimen has been collected; latitude in decimal degrees, longitude in decimal degrees; collection date = year in which specimen was collected; collector = person who collected the specimen; publication = publication associated to the sequence; journal = journal associated to publication; first author = first author associated to publication/sequence; taxonomic remarks = additional taxonomic information/comment; sampling remarks = addional sampling information/comment.<br><br>List of added or updated:<br>- Clone/direct: indicates whether it has been directly sequenced or cloned.<br>- Latitude and longitude in decimal degrees.<br>- Genbank accession number of 1700 18S rRNA sequences added.</p>
Linked collectors and determiners for: Fungal 18S Ribosomal RNA (SSU) RefSeq Targeted Loci Project.
Natural history specimen data linked to collectors and determiners held within, "Fungal 18S Ribosomal RNA (SSU) RefSeq Targeted Loci Project". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad">https://bionomia.net/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad">https://gbif.org/dataset/3bfbda20-1a91-4cf9-992f-bc1e9e5b7dad</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project.
Natural history specimen data linked to collectors and determiners held within, "Bacterial 16S Ribosomal RNA RefSeq Targeted Loci Project". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0b0dc293-3b26-49db-b9f1-817b31ebf603">https://bionomia.net/dataset/0b0dc293-3b26-49db-b9f1-817b31ebf603</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0b0dc293-3b26-49db-b9f1-817b31ebf603">https://gbif.org/dataset/0b0dc293-3b26-49db-b9f1-817b31ebf603</a>. Formatted as a Frictionless Data package.
Figure S1 in Natural selection on various sites of ribosomal proteins: a cladistic view
Figure S1. Conserved sites of ribosomal protein 40S subunit labeling on crystal structure. The ribbons colored in red represent the synapomorphic s. str. sites of Eukaryota, the green ones represent the synapomorphic s. lat. sites of Eukaryota, and the blue ones represent the potential autapomorphic sites of clades lower than Eukaryota. The magenta ribbons represent the sites related to DBA, and the sites presented by sticks and balls are also synapomorphic sites. Because there are too many synapomorphic sites according to clades lower than Eukaryota in the RP, only the synapomorphic sites related to DBA are colored in this figure (shown in orange).
Figure S2 in Natural selection on various sites of ribosomal proteins: a cladistic view
Figure S2. Conserved sites of ribosomal protein 60S subunit labeling on crystal structure. The ribbons colored in red represent the synapomorphic s. str. sites of Eukaryota, the green ones represent the synapomorphic s. lat. sites of Eukaryota and the blue ones represent the potential autapomorphic sites of clades lower than Eukaryota. The magenta ribbons represent the sites related to DBA, and the sites shown by sticks and balls are also synapomorphic sites. Because there are too many synapomorphic sites according to clades lower than Eukaryota in the RP, only the synapomorphic sites related to DBA are colored in this figure (shown in orange).
Figure 1 in Natural selection on various sites of ribosomal proteins: a cladistic view
Figure 1. Summarized distribution of group-specific sites in the cladogram of eukaryotic diversification. The numerals shown above the line correspond to RPL, and the numerals shown below correspond to RPS. The Ecdysozoa-Neoptera and Chordata-Mammalia lineages are highlighted with blue and yellow, respectively. The amino acids with equivalent biochemical properties were not taken into account.
Figure 2 in Natural selection on various sites of ribosomal proteins: a cladistic view
Figure 2. Conserved sites in the tertiary structures of RPL11 (A) and RPS19 (B). The red ribbons represent the synapomorphic s. str. sites of Eukaryota, the green ones represent the synapomorphic sites s. lat. of Eukaryota, and the blue ones represent the potential autapomorphic sites of clades lower than Eukaryota. The ribbons with sticks and balls represent sites related to DBA. The synapomorphic sites related to DBA are shown in orange. The magenta ones represent the sites for which it is difficult to deduce the synapomorphy but appear to be related to DBA.
Fig. 2 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans
Fig. 2. Phylogenetic tree of the centipedes based on the combined analysis of Edgecombe et al. (1999). The arrow indicates where the insertion of ca. 300 bp at region V7 occurred during the evolution of centipedes.
Fig. 5 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans
Fig. 5. Phylogenetic analysis of the data from fig. 4 using the ''fixed character states'' method of Wheeler (1999) implemented in the computer program POY (Gladstein and Wheeler, 1997). Commands: poy fixedstates noleading norandomizeoutgroup gap 1 maxtrees 20 multibuild 10 seed‾1 slop 2 checkslop 5. The two circles illustrate the insertions of the Geophilomorpha (ca. 300 bp), and the Scolopendridae (ca. 25 bp).
Fig. 1 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans
Fig. 1. Schematic representation of the 18S rRNA locus. The gray squares represent the variable regions V2, V4, V7, and V9 with insertions (V2: Onychophora, Geophilomorpha, Cephalopoda, Archaeogastropoda; V4: Hexapoda, Crustacea, Pauropoda, Holothuroidea, Chaetognatha, Platyhelminthes, Cephalopoda; V7: Onychophora, Hexapoda, Crustacea, Pauropoda, Chilopoda, Platyhelminthes, Hirudinea, Cephalopoda, Gastropoda; V9: Onychophora, Crustacea, Cephalopoda). The black arrowheads represent particular insertions (10: Pauropoda; 11: Onychophora; E23–7: Onychophora and Pauropoda; E23–8: Pauropoda; 29: Pauropoda; 46: Protura). The black bar represents the 500 bp deletion of the Symphyla.
Fig. 3 in Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans
Fig. 3. Phylogenetic tree based on 18S rRNA sequence data indicating the position of two symphylans (box) with respect to other myriapods (underlined taxa) in a phylogenetic analysis of arthropods (from Giribet, 1997). The two symphylans appear related to other myriapods.
Figure 2 in Phylogenetic structure of the Sphaeriinae, a global clade of freshwater bivalve molluscs, inferred from nuclear (ITS-1) and mitochondrial (16S) ribosomal gene sequences
Figure 2. Strict consensus of the 1040 equally most parsimonious trees (L = 445; CI = 0.724; RI = 0.886) obtained from the phylogenetic analysis of sphaeriid nuclear ITS1 rDNA sequences. The inferred evolutionary gain and loss of a ~160 nt fragment are indicated. Two Eupera species, E. cubensis and E. platensis, were designated as outgroups and inferred sequence gaps were considered as missing data. Numbers above the branches represent bootstrap values and numbers below indicate decay index values.
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