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206 results for “secondary structure”
The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"
<p>The datasets used in "RNA secondary structure prediction using deep learning with thermodynamic integration"</p>
Data from: Secondary contact and changes in coastal hydrology influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)
Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.
Data from: An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models
BACKGROUND: Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. RESULTS: Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea. CONCLUSION: An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.
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
Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.
Data from: Comparing forest structure and biodiversity on private and public land: secondary tropical dry forests in Costa Rica
Secondary forests constitute a substantial proportion of tropical forestlands. These forests occur on both public and private lands and different underlying environmental variables and management regimes may affect post‐abandonment successional processes and resultant forest structure and biodiversity. We examined whether differences in ownership led to differences in forest structure, tree diversity, and tree species composition across a gradient of soil fertility and forest age. We collected soil samples and surveyed all trees in 82 public and 66 private 0.1‐ha forest plots arrayed across forest age and soil gradients in Guanacaste, Costa Rica. We found that soil fertility appeared to drive the spatial structure of public vs. private ownership; public conservation lands appeared to be non‐randomly located on areas of lower soil fertility. On private lands, areas of crops/pasture appeared to be non‐randomly located on higher soil fertility areas while forests occupied areas of lower soil fertility. We found that forest structure and tree species diversity did not differ significantly between public and private ownership. However, public and private forests differed in tree species composition: 11 percent were more prevalent in public forest and 7 percent were more prevalent in private forest. Swietenia macrophylla, Cedrela odorata, and Astronium graveolens were more prevalent in public forests likely because public forests provide stronger protection for these highly prized timber species. Guazuma ulmifolia was the most abundant tree in private forests likely because this species is widely consumed and dispersed by cattle. Furthermore, some compositional differences appear to result from soil fertility differences due to non‐random placement of public and private land holdings with respect to soil fertility. Land ownership creates a distinctive species composition signature that is likely the result of differences in soil fertility and management between the ownership types. Both biophysical and social variables should be considered to advance understanding of tropical secondary forest structure and biodiversity.
Fig. 6. ITS2 secondary structures showing significant variations between our isolate A in Funiculosone, a substituted dihydroxanthene-1,9-dione with two of its analogues produced by an endolichenic fungus Talaromyces funiculosus and their antimicrobial activity
Fig. 6. ITS2 secondary structures showing significant variations between our isolate A. Talaromyces sp. (MF927596.1*) and B. T. funiculosus (consensus), incompatible base pairs are highlighted in pale red and yellow colour based on their degrees of incompatibility; * indicating own isolate. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Simulation Input Data for "Quantifying acetylation-induced changes in the plant secondary cell wall structure and dynamics"
<p>This is the reduced data behind an upcoming manuscript investigating impact of acetylation on plant secondary cell wall. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was: </p> <p> </p> <pre><code>tar -zcvf Acetylatedcellwall.tar.gz --exclude="*BAK" --exclude="*dcd" --exclude="*poster*" --exclude="*old" --exclude="*out" --exclude="*vel" --exclude="*ppm" --exclude="*mp4" --exclude="*txt" --exclude="*tga" --exclude="*vmd" --exclude="*log" --exclude="fixed*png" --exclude="frame*png" --exclude="nonacetylation*png" . </code></pre>
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined.
FIGURE 3. Secondary structures for the D1–D1 in New cyanobacterium Aliterella vladivostokensis sp. nov. (Aliterellaceae, Chroococcidiopsidales), isolated from temperate monsoon climate zone (Vladivostok, Russia)
FIGURE 3. Secondary structures for the D1–D1′ helices in the ITS regions for five Aliterella species and putative genus member Synechocystis sp. PCC 7509. Conservative nucleotides are grey colored.The unique marker mutations for the new species A. vladivostokensis are black colored. Arrowheads show compensatory (CBCs) and hemi-compensatory base changes (hCBCs). Homological base pairs among different species are indicated by dotted lines.
FIGURE 23. The secondary structures for 22 in Contribution to the knowledge of Chinese Gryllacrididae (Orthoptera) IV: New additions of Chinese Furcilarnaca Gorochov, 2004
FIGURE 23. The secondary structures for 22 tRNA genes of the Furcilarnaca mitogenomes. A. Furcilarnaca wufengensis; B. Furcilarnaca armata; C. Furcilarnaca chirurga.
NGS Data from: Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage
<p><span><span>We engineered gRNAs with highly stable hairpins in their constant parts and further enhanced their stability by chemical modifications. The 'Genome-editing Optimized Locked Design' (GOLD)-gRNA increases genome editing efficiency up to around 1000-fold (from 0.08% to 80.5%) with a mean increase across different other targets of 7.4-fold. The related NGS data is deposited </span></span>here.</p>
FIGURE 5. Secondary structures for the D1–D1 in Porphyrosiphon annulatus sp. nov. (Oscillatoriales, Cyanobacteria) isolated on moist soil in Suwon, Republic of Korea
FIGURE 5. Secondary structures for the D1–D1ʹ helix (A–G) and Box-B helix (H–N) in conserved regions of the 16S–23S ITS. (A, H) Microcoleus vaginatus, (B, I) M. autumnalis, (C, J) Kamptonema formosum, (D, K) Anagnostidinema carotinosum, (E, L), A. pseudacutissimum, (F, M) Geitlerinema splendidum, (G, N) Porphyrosiphon annulatus. Species in bold represents our studied organism.
FIGURE 36. 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 36. The secondary structures for 22 tRNA genes of the Capnogryllacris nigromarginata hainanensis ssp. nov..
FIGURE 35. 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 35. The secondary structures for 22 tRNA genes of the Capnogryllacris nigromarginata rectispina ssp. nov..
FIGURE 34. 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 34. The secondary structures for 22 tRNA genes of the Capnogryllacris nigromarginata nigromarginata.
FIGURE 32. 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 32. The secondary structures for 22 tRNA genes of the Capnogryllacris erythrocephala maculatis ssp. nov..
FIGURE 6. The secondary structures for 22 in Study on the Chinese Subfamily Anostostomatinae (Orthoptera: Anostostomatidae IV: One new recorded species Anabropsis (Apteranabropsis) tonkinensis Rehn, 1906
FIGURE 6. The secondary structures for 22 tRNA genes of Anabropsis (Apteranabropsis) tonkinensis (XZ262) mitogenome.
FIGURE 7. The secondary structures for 22 in Study on the Chinese Subfamily Anostostomatinae (Orthoptera: Anostostomatidae IV: One new recorded species Anabropsis (Apteranabropsis) tonkinensis Rehn, 1906
FIGURE 7. The secondary structures for 22 tRNA genes of Anabropsis (Apteranabropsis) tonkinensis (XZ335) mitogenome.
FIGURE 14. The secondary structures for 22 in Study of the Subfamily Anabropsinae (Orthoptera: Anostostomatidae) in China V Two new species of Anabropsis (Apteranabropsis) from Guangxi and phylogenetic analysis of the genus Anabropsis
FIGURE 14. The secondary structures for 22 tRNA genes of A. (Apteranabropsis) shii sp. nov. (XZ258).
FIGURE 13. The secondary structures for 22 in Study of the Subfamily Anabropsinae (Orthoptera: Anostostomatidae) in China V Two new species of Anabropsis (Apteranabropsis) from Guangxi and phylogenetic analysis of the genus Anabropsis
FIGURE 13. The secondary structures for 22 tRNA genes of A. (Apteranabropsis) multispinula sp. nov. (XZ24).
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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.