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230 results for “structure determination”
Data from: Population structure and history of the Welsh sheep breeds determined by whole genome genotyping
Background: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project. Results: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise FST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825. Conclusions: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK.
Data from: Do intraspecific or interspecific interactions determine responses to predators feeding on a shared size-structured prey community?
1. Coexistence of predators that share the same prey is common. This is still the case in size structured predator communities where predators consume prey species of different sizes (interspecific prey responses) or consume different size classes of the same species of prey (intraspecific prey responses). 2. A mechanism has recently been proposed to explain coexistence between predators that differ in size but share the same prey species, emergent facilitation, which is dependent on strong intraspecific responses from one or more prey species. Under emergent facilitation predators can depend on each other for invasion, persistence or success in a size structured prey community. 3. Experimental evidence for intraspecific size-structured responses in prey populations remain rare and further questions remain about direct interactions between predators that could prevent or limit any positive effects between predators (e.g. intraguild predation). 4. Here we provide a community wide experiment on emergent facilitation including natural predators. We investigate both the direct interaction between two predators that differ in body size (fish vs. invertebrate predator) and the indirect interaction between them via their shared prey community (zooplankton). 5. Our evidence supports the most likely expectation of interactions between differently sized predators, that intraguild predation rates are high and interspecific interactions in the shared prey community dominate the response to predation (i.e. predator-mediated competition). The question of whether emergent facilitation occurs frequently in nature requires more empirical and theoretical attention, specifically to address the likelihood that its pre-conditions may co-occur with high rates of intraguild predation.
Data from: Determining population structure and hybridization for two iris species
Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up "species boundaries" can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping-by-sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species.
Data from: Seasonal dynamics and changing sea level as determinants of the community and trophic structure of oribatid mites in a salt marsh of the Wadden Sea
Global change processes affect seasonal dynamics of salt marshes and thereby their plant and animal communities. However, these changes have been little investigated for microarthropod communities. We studied the effect of seasonality and changes in sea level on oribatid mites in the natural salt marsh and on artificial islands in the back-barrier environment of the island Spiekeroog (Wadden Sea, Germany). Three zones of the artificial islands were filled with transplanted sods from the lower salt marsh zone and thereby exposed to three different inundation frequencies. We hypothesized that oribatid mite communities will differ along the natural salt marsh vegetation zones [upper salt marsh (USM), lower salt marsh (LSM), pioneer zone (PZ)], which are influenced by different tidal regimes. Accordingly, total oribatid mite densities declined from the USM and LSM to the PZ. Similarly, oribatid mite species compositions changed along the salt marsh transect and also responded to variations in inundation frequency in LSM on artificial islands with typical species of the USM, LSM and PZ being Multioppia neglecta (USM), Hermannia pulchella (LSM), Zachvatkinibates quadrivertex (LSM, PZ) and Ameronothrus schneideri (LSM, PZ). Oribatid mite density in the salt marsh and on the artificial islands was at a maximum in winter and spring; this was due in part to high density of juveniles, pointing to two reproductive periods. We hypothesized that oribatid mite trophic structure changes due to variations in abiotic (e.g., tidal dynamics, temperature) and biotic conditions (e.g., resource availability). Stable isotope (15N, 13C) and neutral lipid fatty acid analyses indicated that oribatid mite species have different diets with e.g., Z. quadrivertex feeding on macroalgae and fungi, A. schneideri feeding on microalgae and bacteria, and Scheloribates laevigatus and M. neglecta feeding on dead organic matter, bacteria and fungi. Overall, the results indicate that oribatid mite species in salt marshes are affected by changes in environmental factors such as inundation intensity, with the effects being most pronounced in species with narrow trophic niches and limited niche plasticity. The results also indicate that oribatid communities of the LSM respond little to short-term (one year) changes in inundation frequency.
Data from: Admixture of hybrid swarms of native and introduced lizards in cities is determined by the cityscape structure and invasion history
Introductions of non-native lineages increase opportunities for hybridization. Non-native lineages of the common wall lizard, Podarcis muralis, are frequently introduced in cities where they hybridize with native populations. We aimed at unravelling the invasion history and admixture of native and non-native wall lizards in four German cities using citywide, comprehensive sampling. We barcoded and genotyped 826 lizards and tested if gene flow in populations composed of admixed native and introduced lineages is facilitated by similar environmental factors as in native populations by comparing fine-scale landscape genetic patterns. In cities with non-native lineages, lizards commonly occurred in numerous clusters of hybrid swarms, which showed variable lineage composition, consisting of up to four distinct evolutionary lineages. Hybrid swarms held vast genetic diversity and showed recent admixture with other hybrid swarms. Landscape genetic analyses showed differential effects of cityscape structures across cities, but identified water bodies as strong barriers to gene flow in both native and admixed populations. In contrast, railway tracks facilitated gene flow of admixed populations only. Our study shows that cities represent unique settings for hybridization, caused by multiple introductions of non-native taxa. Cityscape structure and invasion histories of cities will determine future evolutionary pathways at these novel hybrid zones.
Data from: Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure
Predicting the outcome of interspecific interactions is a central goal in ecology. The diverse soil microbes that interact with plants are shaped by different aspects of plant identity, such as phylogenetic history and functional group. Species interactions may also be strongly shaped by abiotic environment, but there is mixed evidence on the relative importance of environment, plant identity, and their interactions in shaping soil microbial communities. Using a multi-factor, split-plot field experiment, we tested how hydrologic context, and three facets of Salicaceae plant identity - habitat specialization, phylogenetic distance, and species identity - influence soil microbial community structure. Analysis of microbial community sequencing data with generalized dissimilarity models showed that abiotic environment explained up to 25% of variation in community composition of soil bacteria, fungi, and archaea, while Salicaceae identity influenced less than 1% of the variation in community composition of soil microbial taxa. Multivariate linear models indicated that the influence of Salicaceae identity was small, but did contribute to differentiation of soil microbes within treatments. Moreover, results from a microbial niche breadth analysis show that soil microbes in wetlands have more specialized host associations than soil microbes in drier environments - showing that abiotic environment changed how plant identity correlated with soil microbial communities. This study demonstrates the predominance of major abiotic factors in shaping soil microbial community structure; the significance of abiotic context to biotic influence on soil microbes; and the utility of field experiments to disentangling the abiotic and biotic factors that are thought to be most essential for soil microbial communities.
Data from: Contrasting definitive hosts as determinants of the genetic structure in a parasite with complex life cycle along the Southeastern Pacific
The spatial genetic structure (and gene flow) of parasites with complex life cycles, such as digeneans, has been attributed mainly to the dispersion ability of the most mobile host, which most often corresponds to the definitive host (DH). In this study, we compared the genetic structure and diversity of adult Neolebouria georgenascimentoi in two fish species (DHs) that are extensively distributed along the Southeastern Pacific (SEP). The analysis was based on the cytochrome oxidase subunit I gene sequences of parasites collected between 23°S and 45°S. In total, 202 sequences of N. georgenascimentoi in Pinguipes chilensis isolated from 9 sites and 136 sequences of Prolatilus jugularis from 5 sites were analyzed. Our results showed that N. georgenascimentoi is a species complex that includes three different parasite species; however, in this study, only group 1 and 2 found in P. chilensis and P. jugularis, respectively, were studied because they are widely distributed along the coastline. Group 1 parasites had two common haplotypes with wide distribution and unique haplotypes in northern sites. Group 2 had only one common haplotype with wide distribution and a large number of unique haplotypes with greater genetic diversity. Both groups have experienced recent population expansion. Only group 1 exhibited a genetic structure that was mainly associated with a biogeographic break at approximately 30°S along the SEP. Our finding suggests that host access to different prey (=intermediate hosts) could affect the genetic structure of the parasite complex discovered here. Consequently, difference between these patterns suggests that factors other than DH dispersal are involved in the genetic structure of autogenic parasites.
Data for: The long-term impacts of deer herbivory in determining temperate forest stand and canopy structural complexity
<p>1. Ungulates place immense consumptive pressure on forest vegetation globally, leaving legacies of reduced biodiversity and simplified vegetative structure. However, what remains unresolved is whether browse-induced changes occurring early in succession ultimately manifest themselves in the developed forest canopy. Understanding the development and persistence of these legacies is critical as canopy structure is an important determinant of forest ecosystem functions like carbon sequestration and wildlife habitat.</p> <p>2. We measured how white-tailed deer (Odocoileus virginianus) browse during stand initiation affected canopy structure, tree species richness, diversity, stem density, and basal area on Pennsylvania's Allegheny Plateau using a portable canopy LiDAR system. We capitalized on an historic deer enclosure experiment where forests were subjected to four deer densities (4, 8, 15, and 25 deer/km2) for ten years following stand initiation.</p> <p>3. Deer browsing impacts on the forest canopy are apparent nearly four decades since stand initiation. The highest deer density treatment experienced a significant reduction in tree species diversity, density, and basal area with stands becoming dominated by black cherry (Prunus serotina). Reductions in overstory diversity and tree density resulted in a more open canopy with low leaf area and high horizontal leaf variability. Canopies were tallest at the lowest and highest deer densities.</p> <p><i>4. Synthesis and Applications</i>: Using a portable canopy LiDAR system and a former deer enclosure experiment, we show that high deer browsing pressure during stand initiation can have a decades-long impact on stand and canopy structure. High deer densities led to stands with lower species diversity and tree density, which resulted in canopies that were taller and less dense. Managers should consider the lasting legacy of ungulate herbivory on canopy structure, as canopy structure influences several important management goals, such as forest carbon sequestration, maintenance of diverse understory communities, and creation of wildlife habitat.</p>
Structural dynamics determine voltage and pH gating in human voltage-gated proton channel
<p>Voltage-gated ion channels are key players of electrical signaling in cells. As a unique subfamily, voltage-gated proton (Hv) channels are standalone voltage sensors without separate ion conductive pores. Hv channels are gated by both voltage and transmembrane proton gradient (i.e ∆pH), serving as acid extruders in most cells. Amongst their many functions, Hv channels are known for regulating the intracellular pH of human spermatozoa and compensating for the charge and pH imbalances caused by NADPH oxidases in phagocytes. Like the canonical voltage sensors, Hv channels are a bundle of 4 helices (named S1 through S4), with the S4 segment carrying 3 positively charged Arg residues. Extensive structural and electrophysiological studies on voltage-gated ion channels, in general, agree on an outwards movement of the S4 segment upon activating voltage, but the real-time conformational transitions are still unattainable. With purified human voltage-gated proton (hHv1) channels reconstituted in liposomes, we have examined its conformational dynamics, including the S4 segment at different voltage and pHs using single-molecule fluorescence resonance energy transfer (smFRET). Here, we provide the first glimpse of real-time conformational trajectories of the hHv1 voltage sensor and show that both voltage and pH gradient shift the conformational dynamics of the S4 segment to control channel gating. Our results indicate that the S4 segment transits among 3 major conformational states and kinetic analysis suggest that only the transitions between the inward and outward conformations are highly dependent on voltage and pH changes. Our smFRET studies uncover the stochastic conformational dynamics of S4 and demonstrate how voltage and pH shift its conformational distributions to regulate channel gating. Altogether, we propose a kinetic model that explains the mechanisms underlying voltage and pH gating in Hv channels, which may also serve as a general framework for understanding the voltage sensing and gating in other voltage-gated ion channels.</p>
A hybrid structure determination approach to investigate the druggability of the nucleocapsid protein of SARS-CoV-2
<p><span>The ongoing pandemic caused by SARS-CoV-2 has called for concerted efforts to generate new insights into the biology of betacoronaviruses to inform drug screening and development. Here, we establish a workflow to determine the RNA recognition and druggability of the nucleocapsid N-protein of SARS-CoV-2, a highly abundant protein crucial for the viral life cycle. We use a synergistic method that combines NMR spectroscopy and protein-RNA cross-linking coupled to mass spectrometry to quickly determine the RNA binding of two RNA recognition domains of the N-protein. Finally, we explore the druggability of these domains by performing an NMR fragment screening. This workflow identified small molecule chemotypes that bind to RNA binding interfaces and that have promising properties for further drug development.</span></p> <p><span>This deposition contains the NMR data acquired to determine the structural features of RBDs- RNA recognition as well as selected relevant data regarding the characterization of promising molecular fragments to disrupt protein-RNA interaction.</span></p> <p><span>Furthermore, we included the molecular docking files used to obtain the reported structural model.</span></p>
EMRNA: Accurate RNA structure determination from cryo-EM maps by deep learning and integrated modeling
<p>EMRNA: Accurate RNA structure determination from cryo-EM maps by deep learning and integrated modeling.</p><p>Here stores the input files and output structures of EMRNA and the reproduction result of auto-DRRAFTER.</p>
FIGURE 9 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 9. Paucumara falcata. Photomicrographs: (A) PLA-Pa002, testes; (B–C) PLA-Pa002, penis and musculoparenchymatic organ; (D) PLA-Pa002, female reproductive system; (E) PLA-Pa001, oviducts and bursal canal. Scale bar: 20 µm.
FIGURE 8 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 8. Paucumara falcata. Whole mounts. (A) PLA-N004, entire animal; (B) PLA-N004, testes and ovaries; (C) PLA- N006, penis and musculo-parenchymatic organ; (D) PLA-N005, musculo-parenchymatic organ. Scale bar: A–B = 200 µm, C– D = 50 µm.
FIGURE 6 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 6. Nerpa fistulata. (A) diagrammatic horizontal reconstruction of entire animal, based on examination of several specimens; (B) diagrammatic sagittal reconstruction of the copulatory apparatus, based on examination of several specimens.
FIGURE 5 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 5. Nerpa fistulata. Photomicrographs of sagittal sections. (A–B) PLA-N003, ovaries; (C) PLA-N003, copulatory apparatus; (D) PLA-N003, lateral bursa; (E) PLA-N001, oviduct. Scale bar: 20 µm.
FIGURE 4. Nerpa fistulata. PLA-N004 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 4. Nerpa fistulata. PLA-N004, photomicrographs of horizontal sections. (A) anterior end; (B–F) copulatory apparatus. Scale bar: 20 µm.
FIGURE 11 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 11. Paucumara falcata. (A) diagrammatic reconstruction of the copulatory apparatus, based on examination of several specimens; (B) two animals in copulation. Scale bar: 500 µm.
FIGURE 1 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 1. Bayesian inference phylogenetic tree topology based on 18S rDNA dataset. Numbers on branches indicate support values (posterior probability/bootstrap).
FIGURE 3 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 3. Nerpa fistulata. Whole mounts. (A) PLA-N005, whole animal; (B) PLA-N006, penis and oviduct; (C) PLA-N005, penis. Scale bar: A = 100 µm, B–C = 20 µm.
FIGURE 7 in Two new species of marine flatworm from southern China facilitate determination of the phylogenetic position of the genus Nerpa Marcus, 1948 and the histochemical structure of the nervous system in the genus Paucumara Sluys, 1989 (Platyhelminthes, Tricladida, Maricola)
FIGURE 7. Paucumara falcata. Live specimen: (A–B) entire animal; (C) testes and ovaries; (D) musculo-parenchymatic organ; (E) penis and vas deferentia. (F) cocoon. Scale bar: A–C, F = 200 µm; D–E = 20 µm;
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)
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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.