Find research datasets worth reusing

opencc-by-4.0Jan 2020View details →

Supplementary data files for: Huston, D.C., Cribb, T.H. and Smales, L.R. 20XX. Molecular characterisation of acanthocephalans from Australian marine teleosts: proposal of a new family, synonymy of another and transfer of taxa between orders. Systematic Parasitology, Jan 2020.

These are the supplementary data files for the manuscript "Molecular characterisation of acanthocephalans from Australian marine teleosts: proposal of a new family, synonymy of another and transfer of taxa between orders." Published in the Journal Systematic Parasitology on the 7 of January 2020. Included are the Nexus and Phylip alignment files used for the phylogenetic analyses, and the resulting tree files (in nexus format).

opencc-by-4.0Apr 2020View details →

Molecular dynamics simulation data of designed stapled α-helix

Raw simulations data (protein only) and simulation set-up files of designed stapled α-helix peptides. More details can be found in this paper:  Arusha Acharyya*, Yunhui Ge*, Haifan Wu*, William DeGrado, Vincent Voelz, Feng Gai. <a href="https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.8b12220">Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study.</a> J. Phys. Chem. B., 2019, 123 (8), pp 1797-1807 (* shared first author)

Molecular dynamics simulation data of designed cyclic peptide - ligand 4 (receptor-ligand bound)

Trajectories of receptor-ligand bound simulation and simulation set-up files of designed cyclic peptide as MDM2 binders. This dataset contains simulations of ligand 4. Due to the file size limitation, ligand 1-3 data and simulation set-up files can be found here: http://doi.org/10.5281/zenodo.3780463 The original paper of these designed cyclic peptide: Danelius, E., Pettersson, M., Bred, M., Min, J., Waddell, M. B., Guy, R. K., et al. (2016). Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins. Org. Biomol. Chem., 14(44), 10386–10393. http://doi.org/10.1039/C6OB01510G

Molecular dynamics simulation data of designed cyclic peptide - ligand 1-3 (receptor-ligand bound)

Trajectories of receptor-ligand bound simulation and simulation set-up files of designed cyclic peptide as MDM2 binders. This dataset contains simulations of ligand 1-3. Ligand 4 data can be found here: http://doi.org/10.5281/zenodo.3782629 The original paper of these designed cyclic peptide: Danelius, E., Pettersson, M., Bred, M., Min, J., Waddell, M. B., Guy, R. K., et al. (2016). Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins. Org. Biomol. Chem., 14(44), 10386–10393. http://doi.org/10.1039/C6OB01510G

Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH) (dimer only)

Raw data of molecular dynamics simulations of regulatory ACT domain dimer. Simulation starts from the crystal pose (PDB: 5FII) and is motivated by this paper: Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532">Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</a> J. Biol. Chem., 2018, 293(51), pp 19532-19543

Supporting data files for "Binding of Biologically Relevant Divalent Cations to Aqueous Carboxylates: Molecular Simulations Guided by Raman Spectroscopy"

Parameter files and typical simulation input files that allow replication of the computational work presented in the paper "Binding of Biologically Relevant Divalent Cations to Aqueous Carboxylates: Molecular Simulations Guided by Raman Spectroscopy", authored by Denilson Mendes de Oliveira, Samual R. Zukowski, Vladimir Palivec, Jérôme Hénin, Hector Martinez Seara, Dor Ben Amotz, Pavel Jungwirth and Elise Duboué-Dijon

opencc-zeroMay 2020View details →

Data from: Molecular evolutionary analysis of nematode Zona Pellucida (ZP) modules reveals disulfide-bond reshuffling and standalone ZP-C domains

Zona pellucida (ZP) modules mediate extracellular protein-protein interactions and contribute to important biological processes including syngamy and cellular morphogenesis. While some biomedically-relevant ZP modules are well-studied, little is known about the protein family's broad-scale diversity and evolution. The increasing availability of sequenced genomes from "non-model" systems provides a valuable opportunity to address this issue, and to use comparative approaches to gain new insights into ZP module biology. Here, through phylogenetic and structural exploration of ZP module diversity across the nematode phylum, I report evidence that speaks to two important aspects of ZP module biology. First, I show that ZP-C domains—which in some modules act as regulators of ZP-N domain-mediated polymerization activity, and which have never before been found in isolation—can indeed be found as standalone domains. These standalone ZP-C domain proteins originated in independent (paralogous) lineages prior to the diversification of extant nematodes, after which they evolved under strong stabilizing selection, suggesting the presence of ZP-N domain-independent functionality. Second, I provide a much-needed phylogenetic perspective on disulfide bond variability, uncovering evidence for both convergent evolution and disulfide-bond reshuffling. This result has implications for our evolutionary understanding and classification of ZP module structural diversity and highlights the usefulness of phylogenetics and diverse sampling for protein structural biology. All told, these findings set the stage for broad-scale (cross-phyla) evolutionary analysis of ZP modules and position Caenorhabditis elegans and other nematodes as important experimental systems for exploring the evolution of ZP modules and their constituent domains.

opencc-by-4.0Jul 2020View details →

Supplementary data for "Molecular dynamics study of confined water in the periclase-brucite system under conditions of reaction-induced fracturing"

In this dataset you can find sample data from periclase and brucite simulations and python scripts that can be used to confirm the plots in the paper. <ul> <li>"bruciteSimualtions" and "periclaseSimualtions" contains the simulations where the mineral in contact with water is either brucite or periclase. Within each of these two folders, there are two subfolders, "waterProperties" and "waterThickness".  <ul> <li>The data in "waterProperties" is used to calculate water properties. Each folder inside "simulations" represent one simulation.</li> <li>The data in "waterThickness" is used to calculate the change in water film thickness with time under different conditions. The simulations are run for either 3 ns or 10 ns. Each folder inside "simulations_Xns" represent one simulation.</li> </ul> </li> <li>For each folder containing one simulations, we provide: <ul> <li>NAME.run: The input script</li> <li>NAME.data: The input data</li> <li>job.sh: Script to run the simulation</li> <li>log.lammps: Thermodynamic output from the simulation</li> <li>Note that the pressures given in the folder names and in the simulations are in atm, not MPa.</li> </ul> </li> </ul>   <ul> <li>"bruciteSimulations" and "periclaseSimualtions" are in zip containers. In order to use them, please unzip them and leave the resulting folders in the same directory as this README file. </li> </ul>   <ul> <li>The python scripts shows how to extract the relevant data from the lammps log files, which enables reproduction of the figures in the paper. See instructions below to use the scripts.</li> </ul> Installation instructions to make the python plot scripts working, assuming you already have numpy and matplotlib: > pip3 install git+https://github.com/henriasv/regex-file-collector.git > pip3 install git+https://github.com/henriasv/lammps-logfile.git   If this does not work, please contact Marthe Grønlie Guren, m.g.guren@geo.uio.no

opencc-zeroJul 2020View details →

Data from: Using molecular and crowd-sourcing methods to assess breeding ground diet of a migratory brood parasite of conservation concern

Breeding ground food availability is critical to the survival and productivity of adult birds. The common cuckoo Cuculus canorus is a brood-parasitic Afro-Palearctic migrant bird exhibiting long-term (breeding) population declines in many European countries. Variation in population trend between regions and habitats suggests breeding ground drivers such as adult food supply. However, cuckoo diet has not been studied in detail since before the most significant population declines in Europe began in the mid-1980s. 20th century studies of cuckoo diet largely comprised field observations likely to carry bias towards larger prey taxa. Here we demonstrate the potential value of 1) using high-throughput DNA sequencing of invertebrate prey in faeces to determine cuckoo diet with minimal bias towards large prey taxa, and 2) using crowd-sourced digital photographs from across Britain to identify lepidopteran cuckoo prey taxa during recent years post-decline (2005-2016). DNA analysis found a high frequency of Lepidoptera, including moths of family Lasiocampidae, prominent within the past literature, but also grasshoppers (Orthoptera) and flies (Diptera) that may be overlooked by field observation methodologies. The range of larval lepidopteran prey identified from photographs largely agreed with those previously documented, with potential signs of reduced diversity, and identities of key adult prey taxa were supported by molecular results. Notably, many identified cuckoo prey taxa have shown severe declines due to agricultural intensification, suggesting this has driven spatial patterns of cuckoo loss. Landscape-scale, lowland rewilding interventions provide opportunities to understand the scale of reversal of previous agricultural intensification that may be necessary to restore prey populations sufficiently to permit recolonization by cuckoos.

opencc-zeroDec 2019View details →

Data from: Chemical structure predicts the effect of plant-derived low-molecular weight compounds on soil microbiome structure and pathogen suppression

1. Plant-derived low molecular weight compounds play a crucial role in shaping soil microbiome functionality. While various compounds have been demonstrated to affect soil microbes, most data are case-specific and do not provide generalizable predictions on their effects. Here we show that the chemical structural affiliation of low molecular weight compounds typically secreted by plant roots – sugars, amino acids, organic acids and phenolic acids – can predictably affect microbiome diversity, composition and functioning in terms of plant disease suppression. 2. We amended soil with single or mixtures of representative compounds, mimicking carbon deposition by plants. We then assessed how different classes of compounds, or their combinations, affected microbiome composition and the protection of tomato plants from the soil-borne Ralstonia solanacearum bacterial pathogen. 3. We found that chemical class predicted well the changes in microbiome composition and diversity. Organic and amino acids generally decreased the microbiome diversity compared to sugars and phenolic acids. These changes were also linked to disease incidence, with amino acids and nitrogen-containing compound mixtures inducing more severe disease symptoms connected with a reduction in bacterial community diversity. 4. Together, our results demonstrate that low molecular weight compounds can predictably steer rhizosphere microbiome functioning providing guidelines to engineer microbiomes based on root exudation patterns by specific plant cultivars or crop regimes.

opencc-by-4.0Aug 2020View details →

Experimental and DFT structural data for OPE3-Ph - Au molecular junctions

Experimental crystal structures (CIF), plane wave DFT relaxed structures (Quantum ESPRESSO) and DFTB transport geometries (CIF, GEN) for OPE3-Ph - Au molecular junctions. Data for article: "Electronic Conductance and Thermopower of Single-molecule Junctions of Oligo(phenyleneethynylene) Derivatives" by Hervé Dekkiche, Andrea Gemma, Fatemeh Tabatabatai,  Andrei S. Batsanov, Thomas Niehaus, Bernd Gotsmann, and Martin R. Bryce to appear in Nanoscale

opencc-by-4.0Sep 2020View details →

Molecular dynamics simulations data for "Bayesian unsupervised learning reveals hidden structure in concentrated electrolytes".

Molecular dynamics simulation data created and used in "Bayesian unsupervised learning reveals hidden structure in concentrated electrolytes".

opencc-zeroOct 2020View details →

Data from: A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

<div class="page"> <div class="layoutArea"> <div class="column"> Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras. </div> </div> </div>

opencc-by-4.0Jun 2021View details →

Data associated to the article "A semiclassical Thomas–Fermi model to tune the metallicity of electrodes in molecular simulations"

Contains input files and data used to generate the figures of the article: A semiclassical Thomas–Fermi model to tune the metallicity of electrodes in molecular simulations Laura Scalfi, Thomas Dufils, Kyle G. Reeves, Benjamin Rotenberg and Mathieu Salanne, J. Chem. Phys. 153, 174704 (2020) https://doi.org/10.1063/5.0028232 The folder typical_input_files contains typical MetalWalls input files used to perform the simulations. The folder DATA_FIGURES contains the processed data used to plot all the figures of the paper.

opencc-zeroDec 2018View details →

Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders

1. Adaptive radiations are typically characterized by niche partitioning among their constituent species. Trophic niche partitioning is particularly important in predatory animals, which rely on limited food resources for survival. 2. We test for trophic niche partitioning in an adaptive radiation of Hawaiian Tetragnatha spiders, which have diversified in situ on the Hawaiian Islands. We focus on a community of nine species belonging to two different clades, one web building and the other actively hunting, which co-occur in wet forest on East Maui. We hypothesize that trophic niches differ significantly both 1) among species within a clade, indicating food resource partitioning, and 2) between the two clades, corresponding with their differences in foraging strategy. 3. To assess niches of the spider species, we measure a) web architecture, the structure of the hunting tool, and b) site choice, the physical placement of the web in the habitat. We then test whether differences in these parameters translate into meaningful differences in trophic niche by measuring c) stable isotope signatures of carbon and nitrogen in the spiders' tissues, and d) gut content of spiders based on metabarcoding data. 4. We find significant interspecific differences in web architecture and site choice. Importantly, these differences are reflected in stable isotope signatures among the five web-building species, as well as significant isotopic differences between web-builders and active hunters. Gut content data also show interspecific and inter-clade differences. Pairwise overlaps of web architecture between species are positively correlated with overlaps of isotopic signature. 5. Our results reveal trophic niche partitioning among species within each clade, as well as between the web-building and actively hunting clades. Based on the correlation between web architecture and stable isotopes, it appears that the isotopic signatures of spiders' tissues are influenced by architectural differences among their webs. Our findings indicate an important link between web structure, microhabitat preference and diet in the Hawaiian Tetragnatha.

opencc-zeroDec 2017View details →

Data from: Molecular signatures of host specificity linked to habitat specialization in Exaiptasia sea anemones.

Rising ocean temperatures associated with global climate change induce breakdown of the symbiosis between coelenterates and photosynthetic microalgae of the genus Symbiodinium. Association with more thermotolerant partners could contribute to resilience, but the genetic mechanisms controlling specificity of hosts for particular Symbiodinium types are poorly known. Here we characterize wild populations of a sea anemone laboratory model system for anthozoan symbiosis, from contrasting environments in Caribbean Panama. Patterns of anemone abundance and symbiont diversity were consistent with specialization of holobionts for particular habitats, with Exaiptasia pallida/S. minutum (ITS2 type B1) abundant on vertical substrate in thermally stable, shaded environments but E. brasiliensis/Symbiodinium sp. (ITS2 clade A) more common in shallow areas subject to high temperature and irradiance. Population genomic sequencing revealed a novel E. pallida population from the Bocas del Toro Archipelago that only harbors S. minutum. Loci most strongly associated with divergence of the Bocas-specific population were enriched in genes with putative roles in cnidarian symbiosis, including activators of the complement pathway of the innate immune system, thrombospondin-type-1 repeat domain proteins, and coordinators of endocytic recycling. Our findings underscore the importance of unmasking cryptic diversity in natural populations and the role of long-term evolutionary history in mediating interactions with Symbiodinium.

opencc-zeroDec 2019View details →

Data from: Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)

Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the Black Mangrove (Avicennia germinans). Fifty-seven trees were sampled in seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation genetic differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought-tolerance or plant response to drought. Moreover, our results suggest the occurrence of rapid evolution of a population, likely in response to sudden and persistent limitation in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcripts expression levels associated with increased drought-tolerance, through accumulation of osmoprotectants and antioxidants, biosynthesis of plant cuticle, protection against stress-induced proteins degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.

opencc-zeroSep 2019View details →

Data from: The molecular phylogenetics of Trachymyrmex ants and their fungal cultivars provide insights into the origin and co-evolutionary history of 'higher-attine' ant agriculture

The fungus‐growing ants and their fungal cultivars constitute a classic example of a mutualism that has led to complex coevolutionary dynamics spanning c. 55–65 Ma. Of the five agricultural systems practised by fungus‐growing ants, higher‐attine agriculture, of which leaf‐cutter agriculture is a derived subset, remains poorly understood despite its relevance to ecosystem function and human agriculture across the Neotropics and parts of North America. Among the ants practising higher‐attine agriculture, the genus Trachymyrmex Forel, as currently defined, shares most‐recent common ancestors with both the leaf‐cutter ants and the higher‐attine genera Sericomyrmex Mayr and Xerolitor Sosa‐Calvo et al. Although previous molecular‐phylogenetic studies have suggested that Trachymyrmex is a paraphyletic grade, until now insufficient taxon sampling has prevented a full investigation of the evolutionary history of this group and limited the possibility of resolving its taxonomy. Here we describe the results of phylogenetic analyses of 38 Trachymyrmex species, including 27 of the 49 described species and at least 11 new species, using four nuclear markers, as well as phylogenetic analyses of the fungi cultivated by 23 species of Trachymyrmex using two markers. We generated new genetic data for 112 ants (402 new gene sequences) and 95 fungi (153 new gene sequences). Our results corroborate previous findings that Trachymyrmex, as currently defined, is paraphyletic. We propose recognizing two new genera, Mycetomoellerius gen.n. and Paratrachymyrmex gen.n., and restricting the continued use of Trachymyrmex to the clade of nine largely North American species that contains the type species [Trachymyrmex septentrionalis (McCook)] and that is the sister group of the leaf‐cutting ants. Our fungal cultivar phylogeny generally corroborates previously observed broad patterns of ant–fungus association, but it also reveals further violations of those patterns. Higher‐attine fungi are divided into two groups: (i) the single species Leucoagaricus gongylophorus (Möller); and (ii) its sister clade, consisting of multiple species, recently referred to as Leucoagaricus Singer 'clade B'. Our phylogeny indicates that, although most non‐leaf‐cutting higher‐attine ants typically cultivate species in clade B, some species cultivate L. gongylophorus, whereas still others cultivate fungi typically associated with lower‐attine agriculture. This indicates that the attine agricultural systems, which are currently defined by associations between ants and fungi, are not entirely congruent with ant and fungal phylogenies. They may, however, be correlated with as yet poorly understood biological traits of the ants and/or of their microbiomes.

opencc-zeroDec 2018View details →

Data from: The molecular biogeography of the Indo-Pacific: testing hypotheses with multispecies genetic patterns

Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo-Pacific Ocean. Time Period: Pliocene through the Holocene. Major Taxa Studied: 56 marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance vs. environmental or geographical barriers to pairwise ΦST with a distance-based redundancy analysis (dbRDA). Results: We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analyzed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographical or environmental barriers other than distance. Main Conclusions: Although there is support for three previously described barriers, phylogeographic discordance in the Indo-Pacific oceans indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo-Pacific species, even hard vicariance for tens of thousands of years can yield ΦST values that range from 0 to nearly 0.5.