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Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732). in A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732).
Fig. 2. The PCR products identified within the 18S in Usefulness of PCR-RFLP of 18S rRNA gene for rapid post-mortem diagnostics of highly pathogenic Eimeria spp. (Apicomplexa: Eimeriidae) of European bison, Bison bonasus L. with histopathological correlation
Fig. 2. The PCR products identified within the 18S rRNA of Eimeria bovis following digestion with two restriction endonucleases: AluI recognising AG∧CT and Hin1II recognising CATG∧. M1: GeneRuler 100 bp Plus DNA Ladder (Thermo Fisher Scientific); M2: GeneRuler 50bp DNA Ladder (Thermo Fisher Scientific); lane 1: European bison colon wall tissue; lane 2: European bison colon wall tissue after digestion; lane 3: E. bovis oocysts of European bison; lane 4: E. bovis oocysts of European bison after digestion.
Fig. 3 in Usefulness of PCR-RFLP of 18S rRNA gene for rapid post-mortem diagnostics of highly pathogenic Eimeria spp. (Apicomplexa: Eimeriidae) of European bison, Bison bonasus L. with histopathological correlation
Fig. 3. The virtual double digestion of the 18S rRNA gene of eimerians infecting the large intestine of the European bison with the restriction enzymes Mval (BstNI) recognising CC∧WGG, and KpnI recognising GGTAC∧C, simulated with SnapGene version 5.0.6 (GSL Biotech LLC); M: GeneRuler 50 bp DNA Ladder (Thermo Fisher Scientific). (A) A three-band pattern for E. bovis (20 bp, 210 bp, 343 bp). (B) A four-band pattern for E, zuernii (20 bp, 100 bp, 210 bp, 242 bp). (C) A two-band pattern for E. alabamensis (212 bp, 362 bp).
Fig. 1 in Usefulness of PCR-RFLP of 18S rRNA gene for rapid post-mortem diagnostics of highly pathogenic Eimeria spp. (Apicomplexa: Eimeriidae) of European bison, Bison bonasus L. with histopathological correlation
Fig. 1. Histopathological lesions associated with endogenous stages of Eimeria spp. in sections of the ileum and colon of European bison (H-E staining). (A) Shortening and blunting of the intestinal villi of the ileum with diffuse infiltration of mononuclear inflammatory cells within the lamina propria, edematous stroma, dilated crypt containing necrotic debris (arrow), and atrophy of submucosal lymphoid follicles (× 20 magnification). (B) Schizonts and degenerating merozoites in the crypt lumen of the colon (arrows); immature macrogamont with a central nucleus (arrowhead) (× 1000 magnification). (C) Immature microgamonts in the epithelial cells of the colon crypt (arrows) (× 400 magnification). (D) Mature microgamont in the epithelial cells of the colon crypt (arrow) (× 1000 magnification). (E) Gametogonic stages of Eimeria development in the epithelial cells of the colon. Microgamont with peripheral microgames (arrowhead), (a) nearly mature microgamonts, (b) macrogamont with eosinophilic wall-forming bodies, (c) early oocyst (× 400 magnification). (F) Mature macrogamont in the epithelial cells of the cecum (arrow) (× 1000 magnification).
Fig. 2 in Diversity of fecal parasitomes of wild carnivores inhabiting Korea, including zoonotic parasites and parasites of their prey animals, as revealed by 18S rRNA gene sequencing
Fig. 2. Relative abundance of all parasite genera detected from fecal samples of wild carnivores in Korea. The relative abundance of each parasite is defined as the ratio of the number of sequence reads assigned to that parasite to the total number of sequence reads assigned to all target parasites.
Fig. 1 in Diversity of fecal parasitomes of wild carnivores inhabiting Korea, including zoonotic parasites and parasites of their prey animals, as revealed by 18S rRNA gene sequencing
Fig. 1. Diversity of fecal parasitomes of wild carnivores in Korea. The results shown are based on the diversity of zero-radius operational taxonomic units (ZOTUs) that were taxonomically assigned to parasites. (a) Comparison of richness and diversity of parasite ZOTUs between host animals estimated by the Chao1 estimator and Shannon index, respectively. (b) Non-metric multidimensional scaling (NMDS) plots showing the structure and membership of parasite ZOTUs represented by the Bray–Curtis dissimilarity and Jaccard index, respectively. In the panel (a), one asterisk (*) and two asterisks (**) represent p <0.05 and p <0.01, respectively, by the post hoc Wilcoxon rank-sum test. The abbreviation "ns" represents no statistical difference.
Fig. 4. Phylogenetic relationships generated from the 16S rRNA gene for 16 in A survey of auchenorrhynchan insects for identification of potential vectors of the 16SrIV-D phytoplasma in Florida
Fig. 4. Phylogenetic relationships generated from the 16S rRNA gene for 16SrIV phytoplasmas by using maximum likelihood (1,000 replicates) methods in MEGA. The 16S partial sequence amplified from Haplaxius crudus (indicated by the black triangle) and unidentified Cicadellidae specimen (indicated by the white triangle) from this study were included in the analysis.
UMI SSU rRNA amplicon datasets
<p>Analysis of 721 SSU rRNA amplicon data from 58 stations in the Pacific Ocean. This item contains following files.</p> <p>abundance.csv</p> <p>- Read count of 155906 OTUs in UMI dataset</p> <p>centroid_seqs.fa</p> <p>- Centroid sequence of each OTU</p> <p>OTU_module_taxon.csv</p> <p>- Results of clustering by WGCNA analysis and assigned taxonomy using the SILVA database</p> <p>Thaumarchaeota.fasta</p> <p>- Sequenced used for phylogenetic analysis of Thaumarchaeota OTUs</p>
Figure 4. 18S rRNA strict consensus tree from 12 in Reconstructing the Anomalodesmata (Mollusca: Bivalvia): morphology and molecules
Figure 4. 18S rRNA strict consensus tree from 12 most parsimonious trees (3228 steps, CI = 0.4786, RC = 0.3076). Above branches are 'bootstrap proportion | decay index', below are 'Bayesian posterior probability | ML-puzzling proportion'. Arrows indicate the 'thraciid' (T) and 'lyonsiid' (L) lineages.
Figure 6 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 6. Secondary structure models of the highly variable proximal part of helix 43 (S6, Fig. 1) in Zygaeninae. All structures are based on thermodynamic folding by minimizing the free energy and have been calculated considering the entire nucleotide sequence of helix 43. The change in the Gibb's free energy (dG) refers to the S6 structure only. Applied ambiguity code: G/A = R, C/U = Y.
Figure 3 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 3. Consensus structure and base pair probability matrix of helix E23-5 (S3, Fig. 1) in Lepidoptera. Nucleotides in circles indicate consistent and/or compensatory substitutions. The size of squares in the grid is proportional to the probability of a base pairing. Note that the species Z. centaureae, Z. laeta and Z. huguenini have been omitted from this analysis because of their deviating secondary structure (compare with Fig. 4).
Figure 2 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 2. Distribution of pairwise tree edit distances between highly variable SSU rRNA secondary structure areas (S1–S6, Fig. 1) of Zygaenoidea excluding taxa of the subgenus Mesembrynus (top) and of Zygaena species belonging to the subgenus Mesembrynus only (bottom). The extreme values in the Zygaenoidea tree edit distance distribution on the right all involve Z. excelsa, a species showing a highly derived secondary structure in the area S6 (compare with Fig. 6).
Figure 1 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 1. Secondary structure model of the SSU (18S) rRNA gene sequence of Zygaena (Mesembrynus) sarpedon lusitanica Reiss, 1936 (Lepidoptera: Zygaenidae; accession no. AJ830858) and structure variation in the helices E10-1 and E23-12 among species of the subfamily Zygaeninae. Nucleotides in the model are continuously numbered beginning at the 5′-end of the molecule; tick marks identify every tenth base. Light shading indicate helices numbered according to Wuyts et al. (2002). S1–S6 (dark shades) denote areas with variable secondary structure in the subfamily Zygaeninae. Roman numerals specify the domains I, II, III and IV. The following ambiguity code has been applied: A/C = M, C/U = Y, G/A = R.
Figure 7 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 7. Neighbour-joining tree based on structural differences in the variable areas S1–S6 (compare with Fig. 1) of the small-subunit (18S) rRNA in taxa of the genus Zygaena. The topology is rooted with Reissita simonyi and Epizygaenella caschmirensis as outgroup. Taxa of the subgenus Mesembrynus are indicated by shading. Numbers in parentheses specify the number of species in a particular group.
Figure 5 in Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera)
Figure 5. Consensus structure and base pair probability matrix of the proximal part of helix 43 (S6, Fig. 1) in Lepidoptera. Nucleotides in circles indicate consistent and/or compensatory substitutions. The size of squares in the grid is proportional to the probability of a base pairing. Note that the unpaired nucleotides C and G in the helix will most likely bind in individual structures having this specific nucleotide combination, but non-Watson–Crick pairings are too frequent in the alignment for assuming a generally nucleotide interaction at this position in the consensus structure.
Figure 1 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
Figure 1. Morphology and infraciliature of Psammomitra retractilis (F–J, from Song & Warren, 1996). A, B, F, individuals in extended states to show the typical body shapes. Arrowheads in (A) mark the long, dominant membranelles. C, lateral view of a contracted specimen. D, posterior part, to demonstrate the long dorsal cilia. E, anterior part. Arrowheads indicate the long membranelles, whereas arrows mark the dorsal cilia. G, H, dorsal and lateral views of contracted cells. I, J, ventral and dorsal views to show the infraciliature and macronuclear nodules. Scale bars: A, C, D, F = 40 Mm; E = 30 Mm.
Figure 3 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
Figure 3. Maximum parsimony phylogeny of small subunit rRNA genes. Psammomitra is highlighted in black, and holostichids are enclosed in rectangles. Thick branches and arrows denote position of investigated species. Numbers on branches are values generated from 1000 bootstrap replicates.
Figure 2 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
Figure 2. Phylogenetic tree based on small subunit rRNA sequences showing the position of Psammomitra retractilis, by Bayesian inferences applying the GTR + G + I model. '-' reflects disagreement between a method and the reference Bayesian tree at a given node. The fully supported (1.00/100%/100%) branches are marked with solid circles. Psammomitra is shaded black, and holostichids are enclosed in rectangles. Thick branches and arrows denote position of investigated species. The scale bar corresponds to five substitutions per 100 nucleotide positions. Infraciliature of Oxytricha and Uroleptus (from Foissner et al., 2004), Amphisiella (from Li et al., 2007), Trachelostyla (from Gong et al., 2006), and Holosticha (from Hu & Song, 2001) are also shown.
Figure 4 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
Figure 4. Bayesian trees based on different data sets showing phylogenetic relationships amongst Spirotrichea. '-' reflects disagreement between the maximum likelihood/ maximum parsimony method and the reference Bayesian tree at a given node. The fully supported (1.00/100%/100%) branches are marked with solid circles. Species sequenced in the present study are shown in bold type. The scale bar corresponds to 10/2 substitutions per 100 nucleotide positions. A, phylogenetic analyses inferred from alpha-tubulin gene sequences data set. B, phylogenetic analyses inferred from alpha-tubulin amino acids data set.
Figure 5 in Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
Figure 5. Summary cladogram representing the relationships of the anomalodesmatan family-level taxa inferred from the 18S rRNA data. Asterisks indicate lacking support for the monophyly of the taxon.
ScienceDex guides
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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.