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573 results for “Structure analysis”
Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis
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Data and scripts from: Long term analysis of social structure: evidence of age-based consistent associations in male Alpine ibex
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Prognostic, biological, and structural implications of FLT3-JMD point mutations in acute myeloid leukemia: an analysis of Alliance studies
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Structure analysis of a p53 fusion protein
<p><span><span><span><span><span><span><span><span><span><span><span>The tumor suppressor p53 is a key target for cancer therapy, but its low expression levels, poor conformational stability, and high degree of disorder remain major challenges to its structural investigation. Here, we address these issues by fusing the N-terminal transactivation domain of p53 to an engineered spider silk domain termed NT*. Molecular dynamics simulations show that the disordered transactivation domain of p53 wraps around the NT* domain via a series of folding events, resulting in a globular structure.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: The effects of aging on neuropil structure in mouse somatosensory cortex—A 3D electron microscopy analysis of layer 1
This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region. The loss of excitatory synapses was balanced by an increase in their size such that the total amount of synaptic surface, per unit length of axon, and per unit volume of neuropil, stayed the same. There was also a greater reduction of inhibitory synapses than excitatory, particularly those found on dendritic spines, resulting in an increase in the excitatory/inhibitory balance. The close correlations, that exist in young and adult neurons, between spine volume, bouton volume, synaptic size, and docked vesicle numbers are all preserved during aging. These comparisons display features that indicate a reduced plasticity of cortical circuits, with fewer, more transient, connections, but nevertheless an enhancement of the remaining connectivity that compensates for a generalized synapse loss.
Data from: Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and phylogenetic analysis
This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ∼33 of the ∼36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/≃jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A–F, or 6A–C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly divergent cephalopod and urochordate sequences out of those clades. Unlikely to be correct, these refutations show for the first time that rRNA phylogeny can support some 'wrong' clades. Along with its weaknesses, the rRNA tree has strengths: It recovers many clades that are supported by independent evidence (e.g., Metazoa, Bilateria, Hexapoda, Nonoculata, Ambulacraria, Syndermata, and Thecostraca with Malacostraca) and shows good resolution within certain groups (e.g., in Platyhelminthes, Insecta, Cnidaria). As another strength, the newly added rRNA sequences yielded the first rRNA-based support for Carnivora and Cetartiodactyla (dolphin + llama) in Mammalia, for basic subdivisions of Bryozoa ('Gymnolaemata + Stenolaemata' versus Phylactolaemata), and for Oligostraca (ostracods + branchiurans + pentastomids + mystacocarids). Future improvement could come from better sequence-evolution models that account for base-compositional heterogeneity, and from combining rRNA with protein-coding genes in phylogenetic reconstruction.
Data from: Community structure of a Neotropical bat fauna as revealed by stable isotope analysis: Not all species fit neatly into predicted guilds
Neotropical bat communities are among the most diverse mammal communities in the world, and a better understanding of these assemblages may permit inferences about how so many species coexist. While broad trophic guilds (e.g., frugivore, insectivore) of bats are recognized, details of diet and similarities among species remain largely unknown. We used stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) to characterize the community structure of a diverse Neotropical bat fauna from Belize to test predictions of niche theory and the competitive exclusion principle. We predicted that (1) interspecific variation in isotopic overlap would be greater within guilds than between guilds, and (2) no two sympatric populations would have isotopic niches that overlap completely, unless there is variation along some other axis (e.g., temporal, spatial). We additionally tested body size as an explanatory metric of potential overlap, and predicted that larger-bodied animals would have greater niche breadths. Results suggest that while guild-level characterizations of communities is at least somewhat informative, there are multiple examples of intra- and inter-guild species pairs with significantly overlapping isotopic niches, suggesting that, counter to predictions, they may compete for resources. Understanding the trophic structure of animal communities is fundamental to conservation and management of endangered species and ecosystems and important for evolutionary studies, and stable isotope analyses can provide key insights as well as informing hypotheses of the diet of species that are not well known.
Data from: Comparative analysis indicates historical persistence and contrasting contemporary structure in sympatric woody perennials of semi-arid south-west Western Australia
We used a comparative approach to assess congruence of phylogeographic and genetic structure and diversity, demographic signals, and ratios of pollen to seed dispersal, in the context of species-specific life-history traits, for two widespread sympatric perennial plant species. We sampled Grevillea paradoxa and Melaleuca nematophylla across the species' ranges throughout the Transitional Rainfall Zone and extending slightly into the Arid Zone of south-west Western Australia. Both species exhibited range-wide phylogeographic and contemporary genetic structure. Moderate haplotype diversity centred in populations on Banded Ironstone Formation (BIF) outcrops and within the Murchison River gorge supports a hypothesis of historical persistence and evolution in these mesic refugia. These features are likely to play important roles in evolutionary persistence with ongoing climate change. There was little evidence of particularly complex demographic histories for the region. More limited haplotype diversity, as well as more limited nuclear genetic diversity and connectivity, in G. paradoxa was consistent with predictions from life-history traits of shorter lifespan, lower fecundity, more limited seed dispersal, and shorter plants, but inconsistent with a prediction of greater pollen dispersal by bird pollinators. Low pollen to seed dispersal ratios suggest seed dispersal plays a greater than expected role in maintaining connectivity in this semi-arid landscape. The study highlights a need for research that integrates aspects of seed ecology and seed and pollen dispersal as well as phylogeographic and genetic patterns in Gondwanan shrublands and other semi-arid landscapes globally.
Data from: Genome-wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep (Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia)
Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge–Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar-Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographical pattern. Pairwise FST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor-Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population–TIK, and maximum values were observed in the most southern population–SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the late Pleistocene glaciations of Verkhoyansk Range.
Data from: Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris
<p>This dataset contains genetic and landscape data of 19 <i>Primula veris</i> populations in Muhu and Saaremaa islands in Estonia. Genetic samples were collected in 2015 and 2016. Landscape data was extracted from maps dated 2016 and 2017 for current data and 1930s for historical data. Data is divided to node- and link-based data. Node-based data contains genetic diversity data of the <i>P. veris</i> populations and landscape data in circular buffers surrounding the populations. Link-based data contains genetic differentiation between population pairs and landscape data in buffers surrounding a straight line between population pairs.</p>
Data from: Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography
Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure, and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analyzed 10 microsatellite loci from over 1,900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation, and management.
Data from: Analysis of the karyotype structure in Ricolla quadrispinosa (Linneus, 1767): inferences about the chromosomal evolution of the tribes of Harpactorinae (Heteroptera, Reduviidae)
The subfamily Harpactorinae is composed of six tribes. Phylogenetic studies bring together some of Harpactorinae tribes, but by and large the data on evolutionary relationships of the subfamily are scarce. Chromosome studies are of great importance for understanding the systematics of different groups of insects. For Harpactorinae, these studies are restricted to some subfamilies and involved only conventional chromosome analysis. This work analyzed cytogenetically Ricolla quadrispinosa (Linneus, 1767). The chromosome number was determined as 2n = 24 + X1X2Y in males. In metaphase II the autosomal chromosomes were organized in a ring with the pseudo-trivalent of sex chromosomes in its center. After C-banding followed by staining with DAPI, AT-rich blocks in autosomes were observed and the negatively heteropycnotic sex chromosomes. The data obtained, together with existing data for other species of the group, indicated that different chromosomal rearrangements are involved in the evolution of the species. In addition, a proposal of karyotype evolution for the subfamily, based on existing phylogenetic studies for the group is presented.
Data from: Hierarchical analysis of genetic structure in the habitat-specialist Eastern Sand Darter (Ammocrypta pellucida)
Quantifying spatial genetic structure can reveal the relative influences of contemporary and historic factors underlying localized and regional patterns of genetic diversity and gene flow – important considerations for the development of effective conservation efforts. Using 10 polymorphic microsatellite loci, we characterize genetic variation among populations across the range of the Eastern Sand Darter (Ammocrypta pellucida), a small riverine percid that is highly dependent on sandy substrate microhabitats. We tested for fine scale, regional, and historic patterns of genetic structure. As expected, significant differentiation was detected among rivers within drainages and among drainages. At finer scales, an unexpected lack of within-river genetic structure among fragmented sandy microhabitats suggests that stratified dispersal resulting from unstable sand bar habitat degradation (natural and anthropogenic) may preclude substantial genetic differentiation within rivers. Among-drainage genetic structure indicates that postglacial (14 kya) drainage connectivity continues to influence contemporary genetic structure among Eastern Sand Darter populations in southern Ontario. These results provide an unexpected contrast to other benthic riverine fish in the Great Lakes drainage and suggest that habitat-specific fishes, such as the Eastern Sand Darter, can evolve dispersal strategies that overcome fragmented and temporally unstable habitats.
Data from: Extending RAD tag analysis to microbial ecology: a comparison between multi locus sequence typing (MLST) and 2b-RAD to investigate Listeria monocytogenes genetic structure
The advent of next-generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are quite laborious and time-consuming, especially for large-scale analyses. In this study, a genotyping approach based on restriction site-associated (RAD) tag sequencing, 2b-RAD, was applied to characterize Listeria monocytogenes strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico mlst analysis was conducted as well. Subsequently, 2b-RAD and mlst analyses were experimentally carried out on 58 isolates collected from food samples or food-processing sites. The obtained results demonstrate that 2b-RAD predicts mlst types and often provides more detailed information on population structure than mlst. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although mlst still represents a reliable typing method, large-scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b-RAD analysis proposed here.
Structure prediction analysis of huntingtin using Phyre2 (2016/03/07)
<p>Huntingtin structure-function open lab notebook project</p>
FIGURE 5 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure
FIGURE 5. Unrooted phylogenetic tree constructed with Freqpars (Swofford & Berlocher 1987) on the basis of allele frequencies.
FIGURE 4 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure
FIGURE 4. UPGMA dendrogram showing evolutionary relationships between populations based on genetic identity values (Nei 1978).
FIGURE 3 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure
FIGURE 3. Map of collecting sites. See Table 1 for abbreviations. Solid boxes are sites where only D. ornata was found; solid circles are sites where only D. saundersi was found; asterisks are sites where both species live sympatrically.
FIGURES 38–50. Abdomen structures. 38 in An analysis of speciesgroups of the genus Plinthisus Stephens (Hemiptera: Rhyparochromidae) in the Ethiopian Region with the description of eight new species
FIGURES 38–50. Abdomen structures. 38 (p. 48), lateral view, male, P. e r ic a e. 39–48, left dorsal view, male. 39, P. rudebecki. 40, P. hirsutus. 41, P. brachyoccus. 42, P. pulchellus. 43, P. e r i c a e. 44, P. fynbosi. 45, P. peninsularis. 46, P. lamprus. 47, P. zuurbergi. 48, P. drakensbergensis. 49–50, dorsal abdominal segments 5–8, female. 49, P. pulchellus. 50, P. fynbosi. Abbreviations: e—epipleurite of connexivum, h—hypopleurite of connexivum, oj— oblique juncture of hypopleurites 4&5, pl—plectrum on tergum one, sg—scent gland scar, sp–spiracle, spl—secondary plectrum, St3—sternum 3, St7— sternum 7, Tg2—tergum 2, Tg6—tergum 6, Tg7—tergum 7, tr—trichobothrium. Figures 44 to 50 on the next page.
FIGURE 6. Hyalessa maculaticollis. Echemes structure. A in Description of a new species of the genus Hyalessa China (Hemiptera: Cicadidae: Sonatini) from Yunnan, China, with a key to the species of Hyalessa and a calling song analysis for two Hyalessa species
FIGURE 6. Hyalessa maculaticollis. Echemes structure. A, Power frequency spectrum represented with overlay of 52 spectra computed from echemes with high amplitude oscillations showing a dominant frequency marked by F3. B, Detailed oscillogram showing the first echeme with low amplitude oscillations and the second echeme with high amplitude oscillations. C, Power frequency spectrum represented with overlay of 71 spectra computed from echemes with low amplitude oscillations showing dominant frequencies marked by F1 and F2.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.