Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
6,383
datasets available to search
ShareScore release 0.9.0
Dataset results
6,383 results for “isolates”
Data from: Mating environments mediate the evolution of behavioral isolation during ecological speciation
<p>The evolution of behavioral isolation is often the first step towards speciation. While past studies show that behavioral isolation will sometimes evolve as a by-product of divergent ecological selection, we lack a more nuanced understanding of factors that may promote or hamper its evolution. The environment in which mating occurs may be important in mediating whether behavioral isolation evolves for two reasons. Ecological speciation could occur as a direct outcome of different sexual interactions being favored in different mating environments. Alternatively, mating environments may vary in the constraint they impose on traits underlying mating interactions, such that populations evolving in a 'constraining' mating environment would be less likely to evolve behavioral isolation than populations evolving in a less constraining mating environment. In the latter, mating environment is not the direct cause of behavioral isolation but rather permits its evolution only if other drivers are present. We test these ideas with a set of 28 experimental fly populations, each of which evolved under one of two mating environments and one of two larval environments. Counter to the prediction of ecological speciation by mating environment, behavioral isolation was not maximal between populations evolved in different mating environments. Nonetheless, mating environment was an important factor as behavioral isolation evolved among populations from one mating environment but not among populations from the other. Though one mating environment was conducive to the evolution of behavioral isolation, it was not sufficient: assortative mating only evolved between populations adapting to different larval environments within that mating environment, indicating a role for ecological speciation. Intriguingly, the mating environment that promoted behavioral isolation is characterized by less sexual conflict compared to the other mating environment. Our results suggest that mating environments plays a key role in mediating ecological speciation via other axes of divergent selection.</p>
Metadata for Confocal Laser Scanning Microscopy Images of Monoculture and Mixed-Species Biofilms Formed by Bacterial Isolates of Dairy Origin
<p>In a project conducted by ILVO (Belgium), a wide variety of bacterial species were recovered from the surface of a dairy pasteurizer after cleaning and disinfection (C&D). The biofilm-forming ability of these bacteria was determined in both single-species and various mixed-culture combinations. Some work related to this study has been published in Frontiers: "Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries". Bacterial species were mixed in different combinations to assess the community biofilm mass and growth dynamics of individual species. ILVO and the University of Copenhagen conducted experiments aimed at revealing the structural characteristics and spatial organization of bacterial species within different mixed-species biofilms. In our research, we employed oligonucleotide FISH probes, each conjugated with a unique fluorescent dye: Cy5 for <em>Stenotrophomonas rhizophila</em> (B68), Cy3 for <em>Bacillus licheniformis</em> (B65), and FAM for <em>Microbacterium lacticum</em> (B30). C1 combination refers to a combination containing B68 and B30. </p> <p><span>Images of the biofilms formed on the coupons were captured using a confocal laser scanning microscope (LSM 800, Zeiss) with a Plan-Apochromat 63x/1.4 oil-immersion objective. Z-stacks were recorded to obtain three-dimensional (3D) images. Standard images were made with an image size of 1024 × 1024 pixels, corresponding to physical dimensions of 101.4 × 101.4 μm for each image. For each image, two separate channels were applied to detect any dual-species combination using a flexible detector (GaAsP-PMT) in the LSM 800 system. Representative 3D views of images were generated using the 3D model function in the ZEN system 3.7.</span></p> <p>Biofilms were grown in BHI for 24 h on plastic coupons. The samples were imaged at different time points: 6h, 12h, 18h and 24h. Each samples had three replicates and for each replicate imaging was performed from 3-6 different positions. </p> <p>Details of the oligonucleotide probes are given below:</p> <table> <tbody> <tr> <td> <p><strong><span>Name of the species</span></strong></p> </td> <td> <p><strong><span>Sequences</span></strong></p> </td> <td> <p><strong><span>Max. excitation</span></strong></p> </td> <td> <p><strong><span>Max. emission</span></strong></p> </td> <td> <p><strong><span>Fluorophores</span></strong></p> </td> </tr> <tr> <td> <p><em><span>S. rhizophila</span></em><span> B68<span> </span></span></p> </td> <td> <p><span>GGGCCTTTACCCCGCCA</span></p> </td> <td> <p><span>649 nm</span></p> </td> <td> <p><span>670 nm</span></p> </td> <td> <p><span>Cy5</span></p> </td> </tr> <tr> <td> <p><em><span>B. licheniformis</span></em><span> B65</span></p> </td> <td> <p><span>ACCGCCTGCGCGCGCTT</span></p> </td> <td> <p><span>550 nm</span></p> </td> <td> <p><span>570 nm</span></p> </td> <td> <p><span>Cy3</span></p> </td> </tr> <tr> <td> <p><em><span>M. lacticum</span></em><span> B30</span></p> </td> <td> <p><span>CCCCACCCTTTCGCTCC</span></p> </td> <td> <p><span>495 nm</span></p> </td> <td> <p><span>520 nm</span></p> </td> <td> <p><span>FAM</span></p> </td> </tr> </tbody> </table>
Fig. 2 in Besnoitia tarandi in Canadian woodland caribou - Isolation, characterization and suitability for serological tests
Fig. 2. Growth of Besnoitia besnoiti Bb-EvoraCl2 (triangles) and Besnoitia tarandi Bt-CA-Quebec1 (crosses) as assessed by real-time PCR on in-vitro cultivated MARC-145 cells 24, 48 or 72 h p.i. Linear regression revealed that B. tarandi BtCA-Quebec1 grew faster than B. besnoiti BbEvoraCl2.
PubMLST allele profiles and sequence alignments of 382 carbapenem-resistant Pseudomonas aeruginosa isolates collected from Japanese hospitals in 2019-2020
<p>This dataset provides PubMLST allele profiles, sequence alignments, and Mash distance data used in the study of "Nationwide genome surveillance of carbapenem-resistant Pseudomonas aeruginosa in Japan". </p>
Genome assemblies of 382 carbapenem-resistant Pseudomonas aeruginosa isolates collected from Japanese hospitals in 2019−2020
<p>This dataset provides genome assemblies used in the study of "Nationwide genome surveillance of carbapenem-resistant Pseudomonas aeruginosa in Japan".</p> <p> </p>
Data from: Do genetic loci that cause reproductive isolation in the lab inhibit gene flow in nature?
<p>The genetic dissection of reproductive barriers between diverging lineages provides enticing clues into the origin of species. One strategy uses linkage analysis in experimental crosses to identify genomic locations involved in phenotypes that mediate reproductive isolation. A second framework searches for genomic regions that show reduced rates of exchange across natural hybrid zones. It is often assumed that these approaches will point to the same loci, but this assumption is rarely tested. In this perspective, we discuss the factors that determine whether loci connected to postzygotic reproductive barriers in the laboratory are inferred to reduce gene flow in nature. We synthesize data on the genetics of postzygotic isolation in house mice, one of the most intensively studied systems in speciation genetics. In a rare empirical comparison, we measure the correspondence of loci tied to postzygotic barriers via genetic mapping in the laboratory and loci at which gene flow is inhibited across a natural hybrid zone. We find no evidence that the two sets of loci overlap beyond what is expected by chance. In light of these results, we recommend avenues for empirical and theoretical research to resolve the potential incongruence between the two predominant strategies for understanding the genetics of speciation.</p>
Data from: Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus
<p>Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model, and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish, <em>Gasterosteus doryssus</em>. This lineage appeared and, over ~8,000 generations, evolved significant reduction of twelve of sixteen traits related to armor, swimming, and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reproductively isolated, benthic-limnetic ecotypes of extant <em>Gasterosteus aculeatus</em>. Therefore, we infer that reproductive isolation was evolving. However, local extinction of low-armoured <em>G. doryssus</em> lineages shows how young isolate populations often disappear, supporting Darwin's explanation for missing evidence and revealing a mechanism behind morphological stasis. Exctinction may also account for limited sustained divergence within the stickleback species complex and help reconcile speciation rate variation observed across time scales.</p>
Fig. 10. Isolated tooth crown ZPAL V. 69 in The giant pliosaurid that wasn't-revising the marine reptiles from the Kimmeridgian, Upper Jurassic, of Krzyżanowice, Poland
Fig. 10. Isolated tooth crown ZPAL V. 69/1 ("ZPAL V-KRZ/33") from the Kimmeridgian of Krzyżanowice, pertaining to an indeterminate vertebrate, incorrectly identified as Machimosaurus sp. by Tyborowski and Błażejowski (2019a).
FIG. 2 in Morphological and molecular characterization of Goleter sp. (Nostocales, Nostocaceae) isolated from freshwater in Iran
FIG. 2. — Micrographs of the isolate Goleter sp. in culture: A, older filaments featuring end cells with two corner "spines"; B, "spines" absent in young filaments; trichomes appear branched due to the proliferation of hormogonia derived from the main filaments; C, granular cell contents; D, filament uniseriate, biseriate or multiseriate; E, necridium cells occasionally found in the main filaments. Reproduction occurs via uniseriate hormogonia with two corner "spines" and bristles. Akinetes very rare; F, long branching filaments with prostrate main axes; G, trichomes often aggregate into subspherical multiseriate clumps. Heterocytes bone, shaped and spherical.Monocyte reproductive cells observed. Abbreviations:aki, akinete;biser, biseriate;brch, branching;clum, clump;gran, granules;het b, bone shaped heterocytes; het s, spherical shaped heterocytes; hor, hormogonium; mono, monocyte; multis, multiseriate; nec, necridium; non spi, "spines" absent; relea, released granules; spi, two corner "spines"; unise, uniseriate. Scale bars: 10 µm.
FIG. 1. — A-C in Morphological and molecular characterization of Goleter sp. (Nostocales, Nostocaceae) isolated from freshwater in Iran
FIG. 1. — A-C, Nostocaceae cyanobacterium in the original sampled site; D, colonies on a Petri dish.
FIG. 4 in Morphological and molecular characterization of Goleter sp. (Nostocales, Nostocaceae) isolated from freshwater in Iran
FIG. 4. — Secondary structures of the 16S-23S ITS of the isolate Goleter sp. and related Goleter sequences.
FIG. 3 in Morphological and molecular characterization of Goleter sp. (Nostocales, Nostocaceae) isolated from freshwater in Iran
FIG. 3. — Maximum likelihood (ML) phylogenetic tree for the isolate (Goleter sp., in red) and reference strains, based on 16S rRNA gene sequences (1490 bp). Gloeobacter violaceus Rippka, J.B.Waterbury & Cohen-Bazire is the outgroup. Bootstrap values are shown near nodes. Scale indicates phylogenetic distance. GenBank accession numbers are indicated next to species names. For further details on sequences and BLAST results, see Appendix 3. For p-distances, see Appendix 4.
APPENDIX 2. — BLASTN results for the 16S in Morphological and molecular characterization of Goleter sp. (Nostocales, Nostocaceae) isolated from freshwater in Iran
APPENDIX 2. — BLASTN results for the 16S rRNA gene of the isolate Goleter sp. against the standard nucleotide database.
Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA
<p>Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study we consider three states of eDNA: 1) a membrane-bound state referring to DNA enveloped in a cellular or organellar membrane, 2) a dissolved state defined as the extracellular DNA molecule in the environment without any interaction with other particles, and 3) an adsorbed state defined as extracellular DNA adsorbed to a particle surface in the environment. Capturing, isolating, and analyzing a target state of eDNA provides utility for better interpretation of eDNA degradation rates and transport potential. While methods for separating different states of DNA have been developed, they remain poorly evaluated due to the lack of state-controlled experimentation. We evaluated the methods for separating states of eDNA from a single sample by spiking DNA from three different species to represent the three states of eDNA as state-specific controls. We used chicken DNA to represent the dissolved state, cultured mouse cells for the membrane-bound state, and salmon DNA adsorbed to clay particles as the adsorbed state. We performed the separation in three water matrices, two environmental and one synthetic, spiked with the three eDNA states. The membrane-bound state was the only state that was isolated with minimal contamination from non-target states. The membrane-bound state also had the highest recovery (54.11 ± 19.24 %), followed by the adsorbed state (5.08 ± 2.28 %), and the dissolved state had the lowest total recovery (2.21 ± 2.36 %). This study highlights the potential to sort the states of eDNA from a single sample and independently analyze them for more informed biodiversity assessments. However, further method development is needed to improve recovery and reduce cross-contamination.</p>
РИС. 2. ГлаЗ Monachoides incarnata. A. ФотографиЯ препарата иЗолированного глаЗа. B. ФотографиЯ продольного полутонкого среЗа глаЗа. СокраЩениЯ: c – роговица; ec – глаЗнаЯ капсула; r – сетчатка; p – краЯ Зрачка; l – хрусталик, окруженный слоем стекловидного тела. FIG. 2. The eye of Monachoides incarnata. A. Photograph of the preparation of the isolated eye. B. Photograph of the longitudinal semithin section of the eye. Abbreviation: c – cornea; ec – eye capsule; r – retina; p – edges of the pupil; l – lens, surrounded by a layer of the vitreous body. in Зрачок камерных глаЗ наЗемных брюхоногих моллюсков (Heterobranchia, Stylommatophora)
РИС. 2. ГлаЗ Monachoides incarnata. A. ФотографиЯ препарата иЗолированного глаЗа. B. ФотографиЯ продольного полутонкого среЗа глаЗа. СокраЩениЯ: c – роговица; ec – глаЗнаЯ капсула; r – сетчатка; p – краЯ Зрачка; l – хрусталик, окруженный слоем стекловидного тела. FIG. 2. The eye of Monachoides incarnata. A. Photograph of the preparation of the isolated eye. B. Photograph of the longitudinal semithin section of the eye. Abbreviation: c – cornea; ec – eye capsule; r – retina; p – edges of the pupil; l – lens, surrounded by a layer of the vitreous body.
BanglaWriting Words Dataset: A Collection of Isolated Word Images from the BanglaWriting multi-purpose Bangla offline-handwriting dataset (WoBW)
<p>The WoBW (Words from BanglaWriting) dataset is a curated collection of isolated word images, adapted from the original BanglaWriting dataset (url: https://data.mendeley.com/datasets/r43wkvdk4w/1).</p> <p>WoBW focuses on individual words extracted from handwritten Bangla text samples in the BanglaWriting corpus, making it a valuable resource for research in word-level Bangla handwriting recognition and related natural language processing tasks.</p> <p>Mridha, Dr. M. F.; Quwsar Ohi, Abu; Ali, M. Ameer; Emon, Mazedul Islam; Kabir, Md Mohsin (2020), “BanglaWriting: A multi-purpose offline Bangla handwriting dataset”, Mendeley Data, V1, doi: 10.17632/r43wkvdk4w.1</p>
Our predicted Crinkler (CRN) family effector proteins and the corresponding GFF3 files across 128 Phytophthora isolates
<p>These files contain predicted Crinkler (CRN) family effector proteins and the corresponding GFF3 files across 128 Phytophthora isolates.</p>
High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria
<p>Fastqs files for paper: "High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria"</p>
Improved genome annotation of Rhynchosporium commune isolate UK7 using Illumina short reads of in vitro and in plantae conditions
<p>Improved genome annotation of the <em>Rhynchosporium commune</em> isolate UK7 using Illumina short reads of <em>in vitro</em> and <em>in plantae</em> conditions. The short reads used for the annotation are available at <a href="https://doi.org/10.5281/zenodo.5729968">https://doi.org/10.5281/zenodo.5729968</a> and <a href="https://doi.org/10.5281/zenodo.5729863">https://doi.org/10.5281/zenodo.5729863</a>.To create the gene models, we used tophat v. 2.0.14 to align short reads to the UK7 reference genome (Trapnell et al., 2009). The Intron splice site hints were generated using bam2hints, included in the AUGUSTUS v. 3.2.1 software (Stanke et al., 2006). Due to the very high RNA-sequencing depth available, intron splice hints were filtered for a minimum coverage of 20 reads to avoid an impact of spurious splice signals on gene prediction. To produce <em>ab initio </em>gene models, the BRAKER v. 1.0 pipeline (Hoff et al., 2016) combining GeneMark-ET <em>ab initio </em>gene model predictions and AUGUSTUS v. 3.2.1. GeneMark-ET was trained using the RNA-seq-based splice information as hints. AUGUSTUS was automatically trained using <em>ab initio </em>gene models that were fully supported by splice information. Finally, AUGUSTUS was used to predict gene models using both RNA-seq splice information and coding sequence hints based on exonerate protein alignments as extrinsic evidence.</p>
Genomic signatures of isolation, hybridization, and selection during speciation of island finches
<p><strong>Data associated</strong> to the study <em>Genomic signatures of isolation, hybridization, and selection during speciation of island finches</em></p> <p><strong>Contents</strong></p> <ul> <li>Table_S9_samples_accession_nos.xlsx: Editable Excel matrix with sample names and accession numbers.</li> <li>RAD_SNPs_stacks_42424_loci.vcf.tar.gz: VCF file (gzip-compressed tarball) containing SNPs in 42,424 loci, based on analyses of restriction site-associated DNA (RAD) sequencing using Stacks.</li> <li>RAD_SNPs_standard_variant_calling.vcf.tar.gz: VCF file (gzip-compressed tarball) containing 131,661 SNPs from standard variant calling pipelines.</li> <li>mitochondrial_markers_full_data.nex: Nexus file containing mitochondrial (mt) sequences used for mt-phylogeny. Partitioned for COX2, tRNA-Lys, ATP8, and ATP6. </li> <li>sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz: Directory (gzip-compressed tarball) containing genotype sequence (heterozygous sites with IUPAC codes) alignments of nuclear markers in nexus files. In addition to the study species, the sequence for zebra finch <em>Taeniopygia guttata</em> is included with sample code TG.</li> <li>sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include only those individuals that match individuals sequenced for mitochondrial markers (also included here). In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>sequences_nuclear_phased_haplotypes_all.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include all individuals. In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>microsatellite_dataset.xlsx: Microsatellite datasets for the study species and additional outgroups. <ul> </ul> <p>Sequences and short read datasets available from NCBI; accession numbers in Table S9 (Table_S9_samples_accession_nos.xlsx).</p> </li> </ul> <p> </p> <p><strong>Study summary</strong></p> <p>Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.</p>
ScienceDex guides
Understand access before you commit
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.