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206 results for “secondary structure”
FIGURE 5. The secondary structures for 22 in Comparative mitogenome analysis and phylogenetic inference of the genus Ultragryllacris (Orthoptera: Gryllacrididae)
FIGURE 5. The secondary structures for 22 tRNA genes of the Ultragryllacris pulchra rubricapitis XZ506.
The Utility of Radiotherapy in the Management of Haemoptysis Secondary to Aspergillomata and Structural Lung Diseases
ClinicalTrials.gov study NCT02878447. IPD Sharing: NO. Countries: 1. Publications: 5.
Secondary Prevention By Structured Semi-Interactive Stroke Prevention Package in INDIA (SPRINT INDIA) Study
ClinicalTrials.gov study NCT03228979. IPD Sharing: NO. Countries: 1. Publications: 7.
Data from: The 5S rDNA gene family in mollusks: characterization of transcriptional regulatory regions, prediction of secondary structures, and long-term evolution, with special attention to Mytilidae mussels
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Data from: Comparing forest structure and biodiversity on private and public land: secondary tropical dry forests in Costa Rica
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Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure
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Data from: An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models
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Data from: Stand structural diversity rather than species diversity enhances aboveground carbon storage in secondary subtropical forests in Eastern China
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Data from: Population genetic structure and secondary symbionts in host-associated populations of the pea aphid complex
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NGS Data from: Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage
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Data from: Genetic structuring and secondary contact in the white-chested Amazilia hummingbird species complex
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Data from: Secondary contact and changes in coastal hydrology influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)
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Annotation and analysis of the secondary structure elements in the Cytochrome P450 protein family
<p>We collected all currently available structures for proteins in the Cytochrome P450 family and annotated their secondary structure elements using SecStrAnnotator software (https://webchem.ncbr.muni.cz/Wiki/SecStrAnnotator). We used 2nnjA as the template domain for the annotation. Based on these annotations, we analysed the occurrence, length distribution, amino acid sequence, and presence of structural irregularities (β-bulges, 3<sub>10</sub>-helices, π-helices) of each secondary structure element class. We also statistically compared the bacterial vs eukaryotic structures. For the secondary structure element classes with sufficient sequence conservation, the most conserved residue is annotated as the reference residue.</p> <p>Main files:</p> <ul> <li><strong>set_ALL.json</strong> - Set-ALL: list of 1012 protein domains belonging to the Cytochrome P450 family (CATH accession 1.10.630.10 + Pfam accession PF00067, accessed on 7 July 2020, one domain per PDB entry)</li> <li><strong>set_NR.json</strong> - Set-NR: non-redundant list of 183 domains (one domain per UniProt ID)</li> <li><strong>domain_lists_table.tsv</strong> - Overview of Set-ALL and Set-NR and separation into subsets Set-NR-Bact (bacterial), Set-NR-Euka (eukaryotic), Set-NR-Arch (archaeal), Set-NR-Viru (viral)</li> <li><strong>structures/template_2NNJ-template.sses.json</strong> - Manually prepared annotation template (domain 2nnjA)</li> <li><strong>structures/template_2NNJ.cif</strong> - Structure of the template domain (2nnjA)</li> <li><strong>annotations_with_reference_residues_ALL.json, annotations_with_reference_residues_ALL.tsv</strong> - Annotation of secondary structure elements for Set-ALL</li> <li><strong>annotations_with_reference_residues_NR.json, annotations_with_reference_residues_NR.tsv</strong> - Annotation of secondary structure elements for Set-NR</li> <li><strong>aligments_NR</strong> - Multiple sequence alignments for each SSE class (Set-NR)</li> <li><strong>logos_NR</strong> - Sequence logos for each SSE class (Set-NR)</li> <li><strong>plots</strong> - Plots of SSE occurrence, length distribution, contained helix types and beta-bulge occurrence (Set-NR), some plots show the comparison between Set-NR-Bact and Set-NR-Euka</li> <li><strong>statistical_tests.ods</strong> - Comparison of SSE occurrence between Set-NR-Bact and Set-NR-Euka by the test of equal proportions and the Fisher test, comparision of the SSE length by the Kolmogorov-Smirnov test and the two-sample Wilcoxon test</li> </ul>
Data from: Compensatory evolution in RNA secondary structures increases substitution rate variation among sites
There is growing evidence that interactions between biological molecules (e.g., RNA-RNA, protein-protein, RNA-protein) place limits on the rate and trajectory of molecular evolution. Here, by extending Kimura's model of compensatory evolution at interacting sites, we show that the ratio of transition to transversion substitutions (κ) at interacting sites should be equal to the square of the ratio at independent sites. Because transition mutations generally occur at a higher rate than transversions, the model predicts that κ should be higher at interacting sites than at independent sites. We tested this prediction in 10 RNA secondary structures by comparing phylogenetically derived estimates of κ in paired sites within stems (κ(p)) and unpaired sites within loops (κ(u)). Eight of the 10 structures showed an excellent match to the quantitative predictions of the model, and 9 of the 10 structures matched the qualitative prediction κ(p) > κ(u). Only the Rev response element from the human immunovirus (HIV) genome showed the reverse pattern, with κ(p) < κ(u). Although a variety of evolutionary forces could produce quantitative deviations from the model predictions, the reversal in magnitude of κ(p) and κ(u) could be achieved only by violating the model assumption that the underlying transition (or transversion) mutation rates were identical in paired and unpaired regions of the molecule. We explore the ability of the APOBEC3 enzymes, host defense mechanisms against retroviruses, which induce transition mutations preferentially in single-stranded regions of the HIV genome, to explain this exception to the rule. Taken as a whole, our findings suggest that kappa may have utility as a simple diagnostic to evaluate proposed secondary structures.
Data from: Multiple sexual selection pressures drive the rapid evolution of complex morphology in a male secondary genital structure
The genitalia of internally fertilizing taxa represent a striking example of rapid morphological evolution. Although sexual selection can shape variation in genital morphology, it has been difficult to test whether multiple sexual selection pressures combine to drive the rapid evolution of individual genital structures. Here, we test the hypothesis that both pre- and postcopulatory sexual selection can act in concert to shape complex structural variation in secondary genital morphology. We genetically modified the size and shape of the posterior lobes of Drosophila melanogaster males and tested the consequences of morphological variation on several reproductive measures. We found that the posterior lobes are necessary for genital coupling and that they are also the targets of multiple postcopulatory processes that shape quantitative variation in morphology, even though these structures make no direct contact with the external female genitalia or internal reproductive organs during mating. We also found that males with smaller and less structurally complex posterior lobes suffer substantial fitness costs in competitive fertilization experiments. Our results show that sexual selection mechanisms can combine to shape the morphology of a single genital structure and that the posterior lobes of D. melanogaster are the targets of multiple postcopulatory selection pressures.
Data from: Secondary structure models of 18S and 28S rRNAs of the true bugs based on complete rDNA sequences of Eurydema maracandica Oshanin, 1871 (Heteroptera: Pentatomidae)
The sequences of 18S and 28S rDNAs have been used as molecular markers to resolve phylogenetic relationships of Heteroptera for two decades. The complete sequences of 18S rDNAs have been used in many studies, while in most studies only partial sequences of 28S rDNAs have been used due to technical difficulties of amplifying the complete lengths. In this study, we amplified the complete 18S and 28S rDNA sequences of Eurydema maracandica Oshanin, 1871, and reconstructed the secondary structure models of the corresponding rRNAs. In addition, and more importantly, all of the length variable regions of 18S rRNA were compared among 37 families of Heteroptera based on 140 sequences, and the D3 region of 28S rRNA was compared among 51 families based on 84 sequences. It was found that 8 length variable regions could potentially serve as molecular synapomorphies for some monophyletic groups. Therefore discoveries of more molecular synapomorphies for specific clades can be anticipated from amplification of complete 18S and 28S rDNAs of more representatives of Heteroptera.
Dataset and R code (Effect of Vegetation Structure on Secondary Wind Dispersal Distance of Diaspores)
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Expansion of the RNAStructuromeDB to include secondary structural data spanning the human protein-coding transcriptome
<p>This dataset includes the -2, -1, and no filter z-score dot bracket files from ScanFold for all protein coding transcript isoforms.</p>
FIGURE 38. The secondary structures for 22 in Contribution to the knowledge of Chinese Gryllacrididae (Orthoptera) V: Further study on the Chinese Capnogryllacris and comment on the phylogenetic relationships of the Gryllacrididae
FIGURE 38. The secondary structures for 22 tRNA genes of the Capnogryllacris spinosa.
FIGURE 37. The secondary structures for 22 in Contribution to the knowledge of Chinese Gryllacrididae (Orthoptera) V: Further study on the Chinese Capnogryllacris and comment on the phylogenetic relationships of the Gryllacrididae
FIGURE 37. The secondary structures for 22 tRNA genes of the Capnogryllacris rufonotata.
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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.