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FIGURE 5. The secondary structures for 22 in A new species of the genus Xistra (Orthoptera: Tetrigoidea: Metrodorinae) with comments on the characters of mitochondrial genome
FIGURE 5. The secondary structures for 22 tRNA genes of the Xistra zhengi, sp. nov. Watson–Crick base pairings and mismatches are represented by dashes (-) and pluses (★).
Source data of Mirtronstructdb - A comprehensive database of mirtrons with predicted secondary structure
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FIGURE 2. Predicted secondary structures for 22 in The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae
FIGURE 2. Predicted secondary structures for 22 tRNA genes of the S. pieli mitogenome. The tRNAs are labeled with the abbreviations of their corresponding amino acids. The minus sign (-) indicates Watson-Crick base pairing and plus sign (.) indicates G-U base pairing.
Fig. 1 in Ultrastructural and immunocytochemical investigation of paramylon combined with new 18S rDNA-based secondary structure analysis clarifies phylogenetic affiliation of Entosiphon sulcatum (Euglenida: Euglenozoa)
Fig. 1 Phylograms obtained from maximum likelihood (ML) analyses of 182 euglenozoan taxa with new 18S rDNA sequences boxed and most ingroup taxa pruned to major groupings, sequences of Heterolobosea and Jakobida were used as outgroup. Congruent Bayesian inference (BI) posterior probability values>0.50 were mapped onto both ML trees and are
Fig. 4 in Ultrastructural and immunocytochemical investigation of paramylon combined with new 18S rDNA-based secondary structure analysis clarifies phylogenetic affiliation of Entosiphon sulcatum (Euglenida: Euglenozoa)
Fig. 4 Schematic phylogram combining molecular and morphological findings corroborating phylogenetic position of Entosiphon as sister group of Helicales within Euglenida. States of key characters are illustrated tabularly: black squares code presence and blanks absence, e.g., paramylon is present only in Entosiphon and Helicales. Unpaired base in 18S rDNA helix 44 is present in primordial petalomonads and kinetoplastids, but absent in more derived taxa within respective groups. White Roman numerals depict heterogeneous dispersal of different types of feeding apparatuses (FA) according to Triemer and Farmer (1991), white Arabic numerals count for number of rods in FA. Heterolobosea and Jakobida represent outgroup taxa
Fig. 2 in Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada)
Fig. 2 Phylogenetic tree topol- ogies and sampling locations. a Neighbor-joining tree obtained by ProfDistS and supporting bootstrap values (1,000 repli- cates) shown in black; CBC tree obtained by CBCanalyzer in dark grey; corresponding sampling locations indicated by arrows. b Numbers of CBCs distinguishing three species classified within Paramacrobiotus; grey ovals correspond to those in Fig. 2a and indicate the species groups that can be identified on the basis of CBCs
FIGURE 8. Secondary structure V3 in A phylogenetically distant clade of Nostoc-like (Cyanobacteria) taxa with the description of Reofilinostoc matlalcueyense gen. et sp. nov. from an extreme environment
FIGURE 8. Secondary structure V3 helix (16S-23S ITS) of Reofilinostoc matlalcueyense, Desikacharya nostocoides, and Minunostoc cylindricum.
Figure 2. Proposed general secondary structure model for the ITS1–5.8S rDNA–ITS2 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes
Figure 2. Proposed general secondary structure model for the ITS1–5.8S rDNA–ITS2–LSU rDNA of Opalinida* The expansion segments (ES#L) containing helices (in red) where there are important differences between genera are annotated. Colour code: yellow* ITS1 region; blue* 5.8S rRNA; magenta* ITS2 region; grey* LSU rRNA.
Apendices(Effect of Vegetation Structure on Secondary Wind Dispersal Distance of Diaspores)
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FIGURE 7. Secondary structures for the D1–D1 in Roholtiella, gen. nov. (Nostocales, Cyanobacteria)-a tapering and branching cyanobacteria of the family Nostocaceae
FIGURE 7. Secondary structures for the D1–D1' helix in the ITS regions for Roholtiella spp. and representative outgroup taxa, Calochaete cimrmanii and Nostoc indistinguendum. Arrows and a bold font style show bases variable among species, while the circled adenine residue is an alternate base in R. edaphica CCALA 1063 and circled cytosine is an alternate base in N. indistinguendum. A–B. Equally thermodynamically stable structures in R. edaphica are shown for the following strains: CCALA 1061 for the operon with no tRNA genes; CCALA 1055-56, 1060, 1062 for the no tRNA operon as well as the operon with both tRNA genes. C–D. Differences in operons are shown for R. mojaviensis. C. Operon with no tRNA for CCALA 1051 and 1052 as well as the operon with both tRNA for CCALA 1052. D. Variation of the operon with no tRNA of CCALA 1051. E. No sequence differences existed between operons with no or with both tRNAs for R. fluviatilis (CCALA 1058), and R. bashkiriorum (CCALA 1057, 1059). F. D1–D1' helix for C. cimrmanii (strain CCALA 1012) showing the operon with no tRNA. G. D1–D1' helix for recovered operons with and without both tRNAs for N. indistinguendum (strain CM1-VF10).
FIGURE 8. Secondary structures for the BoxB and V3 in Roholtiella, gen. nov. (Nostocales, Cyanobacteria)-a tapering and branching cyanobacteria of the family Nostocaceae
FIGURE 8. Secondary structures for the BoxB and V3 helices in the ITS regions for Roholtiella spp. and representative outgroup taxa, C. cimrmanii and N. indistinguendum. Arrows and a bold font style show bases variable among species. Helices are arranged by taxon in vertical columns, with taxon label next to the V3 helix. A–F. BoxB helices from operons with both tRNA genes. A. Roholtiella edaphica strains CCALA 1055-56, CCALA 1060-61. B. Roholtiella edaphica strain CCALA 1062. C. Roholtiella mojaviensis strains CCALA 1051- 52. D. Roholtiella bashkiriorum strains CCALA 1057 and 1059. E. Roholtiella fluviatilis strain CCALA 1058. F. Nostoc indistinguendum strain CM1-VF10. G–M. BoxB helices from operons with no tRNA genes. G. Roholtiella edaphica strains CCALA 1055 and 1060. H. Roholtiella edaphica strain CCALA 1062. I. Roholtiella mojaviensis strain CCALA 1052. J. Roholtiella bashkiriorum strain CCALA 1057. K. Roholtiella fluviatilis strain CCALA 1058. L. C. cimrmanii strain CCALA 1012. M. Nostoc indistinguendum strain CM1-VF10. N–T. V3 helices. Circled residues represent alternate bases in different strains, or in the case of R. fluviatilis, between different operons in the same strain. N. The structure without the circled bases was obtained for R. edaphica strains CCALA 1060 (no and both tRNA operons) and CCALA 1056 (no tRNA operon).The alternative structure with the circled bases was obtained for strains CCALA 1061 (no tRNA operon) and CCALA 1055 (no and both tRNA operons). O. Roholtiella edaphica strain CCALA 1062. P. Roholtiella mojaviensis strains CCALA 1051-52. Q. The structure without the circled bases was obtained for R. bashkiriorum strains CCALA 1057 (both tRNA operons) and CCALA 1059 (no tRNA operon). The alternative structure with the circled bases was obtained for strain CCALA 1057 (no tRNA operon). R. The structure without the circled bases was obtained for R. fluviatilis strain CCALA 1058 for the operon with both tRNA. The alternative structure with the circled bases was obtained for the operon with no tRNA. S. C. cimrmanii strain CCALA 1012 showing the
FIGURE 5. Secondary structures for the D1–D1 in Phylogenetic position reevaluation of Kyrtuthrix and description of a new species K. huatulcensis from Mexico´s Pacific coast
FIGURE 5. Secondary structures for the D1–D1', Box-B, V2 and V3 helices in the conserved regions of the 16S–23S ITS region: A, F, K, P: Kyrtuthrix huatulcensis; B, G, L, Q: Marine Rivulariaceae I (with variability in two operons shown); C, H, M, R: Marine Rivulariaceae II; D, I, N, S: Marine Rivulariaceae III; E, J, O, T: Microchaete grisea CCAP1445.
FIGURE 5. Estimated 16S-23S ITS secondary structures D1-D1 in Revealing hidden diversity among tropical cyanobacteria the new genus Onodrimia (Synechococcales, Cyanobacteria) described using the polyphasic approach
FIGURE 5. Estimated 16S-23S ITS secondary structures D1-D1´and Box-B helices of (A, J) Onodrimia javanensis E27, E28, E30, (B, K) Leptolyngbya appalachiana GSM-SFF-MF60 (EF429286), (C, L) Phormidesmis sp. WJT36-NPBG20 (KJ939034), (D, M) Phormidesmis sp. WJT67-NPBG4A (KJ939043), (E, N) Stenomitos rutilans HA7619-LM2 (KF417430), (F, O) Neosynechococcus sphagnicola sy1 (KJ469130), (G, P) Nodosilinea nodulosa UTEX 2910 (KF307598), (H, Q) Oculatella subterranea, (I, R) Leptolyngbya boryana UTEX B 485 (EF429291).
FIGURE 4. Predicted secondary structure for D1–D1 in Aliterella shaanxiensis (Aliterellaceae), a new coccoid cyanobacterial species from China
FIGURE 4. Predicted secondary structure for D1–D1′ helix of 16S–23S rRNA intergenic spacer of three Aliterella strains. (a) A. antarctica CENA408T; (b) A. atlantica CENA595T; (c) A. shaanxiensis FACHB–2293.
FIGURE 5. Predicted secondary structure for Box-B in Aliterella shaanxiensis (Aliterellaceae), a new coccoid cyanobacterial species from China
FIGURE 5. Predicted secondary structure for Box-B helix of 16S–23S rRNA intergenic spacer of three Aliterella strains. (a) A. antarctica CENA408T; (b) A. atlantica CENA595T; (c) A. shaanxiensis FACHB–2293.
Figure 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 1. Mitochondrial genome synteny in Cubaris murina and closely related species. A dash (-) before the gene name means that the gene is encoded on the light strand. NCR means a non-coding region that is longer than 100 bp. Cubaris murina is marked in bold black and shades of grey.
Figure 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 2. Secondary structure of each transfer RNA (tRNA) visualised in Forna (http://rna.tbi.univie.ac. at/forna).
Table 3 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 3.</b> Characteristic (AT content, repeat, number of predicted secondary structure, range of <i>ΔG</i> value (kcal/mol)) of control region of <i>Cubaris murina</i> by RNAstructure.</p><table><tbody><tr><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th>Number of predicted</th><th></th></tr></tbody><tbody><tr><th>Species [reference]</th><td>Name</td><td>Start</td><td>Stop</td><td>(bp)</td><td>Location</td><td>%AT</td><td>Repeat</td><td>secondary structures</td><td><i>ΔG</i> value (kcal/mol)</td></tr><tr><th><i>Cubaris murina</i></th><td>NCR1</td><td>5219</td><td>5360</td><td>142</td><td>Between <i>nad1</i> and <i>trnN</i></td><td>52.80%</td><td></td><td>7</td><td>−16.9 to −15.4</td></tr><tr><th>[present study]</th><td>NCR2</td><td>6297</td><td>6666</td><td>370</td><td>Between <i>trnS1</i> and <i>trnL1</i></td><td>59.70%</td><td>CT-rich & AT-loop</td><td>20</td><td>−103.7 to −101.0</td></tr><tr><th></th><td>NCR3</td><td>12,550</td><td>12,753</td><td>204</td><td>Between <i>rrnL</i> and <i>trnE</i></td><td>71.10%</td><td>poly-A</td><td>7</td><td>−17.5 to −17.1</td></tr><tr><th></th><td>NCR4</td><td>12,813</td><td>12,950</td><td>138</td><td>Between <i>trnE</i> and <i>trnV</i></td><td>71.70%</td><td>AG-rich</td><td>5</td><td>−13.4 to −12.3</td></tr><tr><th><i>Panulirus argus</i> [Baeza, 2018]</th><td>NCR</td><td>13,525</td><td>14,326</td><td>801</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>69.60%</td><td>AT-rich</td><td>7</td><td>−99.20 to −94.52</td></tr><tr><th><i>Synalpheus microneptunus</i> [Chak <i>et al.</i>, 2020]</th><td>NCR</td><td>13,365</td><td>14,198</td><td>834</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>79.50%</td><td>AT-rich</td><td>20</td><td>− 104 (lowest)</td></tr></tbody></table>
FIGURE 5. Secondary structures for the D1–D1 in Morphology and molecular description of Wilmottia koreana sp. nov. (Oscillatoriales, Cyanobacteria) isolated from the Republic of Korea
FIGURE 5. Secondary structures for the D1–D1', Box-B, and V3 helix in the conserved regions of the 16S–23S internal transcribed spacer region: A, F, K,: Wilmottia murrayi KGI28; B, G, L: W. murrayi FBCC-A402; C, H, M: W. murrayi FBCC-A401; D, I, N, S: W. stricta 16PC; and E, J, O: W. koreana FBCC-A812. These structures were drawn considering Machado-de-Lima et al. (2017).
Structural 3D domain reconstruction of the RNA genome from viruses from a secondary structure model
<p>Fragments and final models of reconstructed STMV genome from in virio and in vitro secondary structures reported in Larman et al. (2017).</p> <p>Simulation scripts for simulations of genome and fragments.</p> <p>Full code of SPQR package for performing simulations.</p>
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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.