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.
99
datasets available to search
ShareScore release 0.7.1
Dataset results
99 results for “Emerging pathogens”
Emerging fungal pathogen of an invasive grass: Implications for competition with native plant species
This data package includes data and code from an experiment testing the effects of a leaf spot fungal infection and competition from the invasive (to the U.S.) grass Microstegium vimineum on the performance of three native grass species: Dichanthelium clandestinum, Elymus virginicus, and Eragrostis spectabilis. The experiment was performed between June and September of 2019 in a greenhouse on the University of Florida campus in Gainesville, FL, USA. The leaf spot infection is caused by the fungal pathogen Bipolaris gigantea, which has recently emerged on populations of M. vimineum in the U.S. We tested the hypothesis that infection of B. gigantea would both directly and indirectly affect the native grass species by measuring the change in biomass of each species with and without pathogen inoculation (direct effects) and by measuring the effect of pathogen inoculation on M. vimineum competition through changes in native grass biomass across a density gradient of M. vimneum (indirect effects). The code includes statistical analyses and figures. The code was run using R (version 4.0.1).
Fig. 1 in Cryptosporidium viatorum from the native Australian swamp rat Rattus lutreolus - An emerging zoonotic pathogen?
Fig. 1. Phylogenetic relationships of small subunit of nuclear ribosomal RNA (SSU) gene nucleotide sequence data (aligned over 563 bp) of selected Cryptosporidium taxa in relation to the novel C. viatorum genotype using the neighbor joining distance method. Individual GenBank accession numbers precede species name, followed by host common name and locality descriptors. Bootstrap support values (based on 2000 iterations) are indicated next to supported branches. Cryptosporidium baileyi was chosen as the outgroup. The novel genotype from this study is in bold-type. Scale bar indicates the number of nucleotide substitutions per site.
Fig. 1 in Detection of Escherichia fergusonii - an emerging pathogen harbouring drug resistant genes from seafood samples of Tamil Nadu, India
Fig. 1 — Gene specific PCR amplification of Escherichia fergusonii (lane 1 – 100 bp DNA ladder, lane 2 – positive control (clinical E. fergusonii), lane 3 – negative control, lane 4 – E011, lane 5 – E060)
Fig. 7 in Description, life cycle, and development of the myxozoan Myxobolus rasmusseni n. sp. in fathead minnows, Pimephales promelas: A possible emerging pathogen in southern Alberta, Canada
Fig. 7. Coronal histological section of the anterior head region of a Myxobolus rasmusseni n. sp. infected fathead minnow. Approximately 8 myxospore-filled plasmodia are located between the two optic lobes in the anterior-dorsal region of the head cavity. Plasmodia demarcated from adjacent host tissue by a thin fibrocytic membrane that also encircles Ornithodiplostomum ptychocheilus metacercariae. 100X magnification. Op = Ornithodiplostomum ptychocheilus metacercariae, Olb: Optic lobe of the minnow brain, Ps: Plasmodia of Myxobolus rasmusseni n. sp. Inset demonstrates distribution of numerous stained and unstained myxospores located within plasmodia.
Fig. 8 in Description, life cycle, and development of the myxozoan Myxobolus rasmusseni n. sp. in fathead minnows, Pimephales promelas: A possible emerging pathogen in southern Alberta, Canada
Fig. 8. Size-frequency distributions of fathead minnows collected from two wetlands in southern Alberta. The left-hand triplet of graphs (A, B, C) indicates size distributions of the 2020 cohort of fathead minnows assessed in Sept. 2020, June 2021, and Sept. 2021 at McQuillan Reservoir. The right-hand triplet (D, E, F) indicates size distributions assessed at the same times for Coalhurst Stormwater Pond. Dark bars indicate minnows with M. rasmusseni n. sp. lesions.
Fig. 6 in Description, life cycle, and development of the myxozoan Myxobolus rasmusseni n. sp. in fathead minnows, Pimephales promelas: A possible emerging pathogen in southern Alberta, Canada
Fig. 6. Coronal histological section through the dorsal head region along the frontal plane of a fathead minnow that contained multiple, various-sized plasmodia of Myxobolus rasmusseni n. sp. 1.25X magnification. Rt - Retina of the eye, Ps - Plasmodia, Br - Brain, Ls - Lens of the eye, Ns - Nares, Of – Opercular flap.
Fig. 5 in Description, life cycle, and development of the myxozoan Myxobolus rasmusseni n. sp. in fathead minnows, Pimephales promelas: A possible emerging pathogen in southern Alberta, Canada
Fig. 5. Phylogenetic tree produced by Bayesian analysis of aligned partial 18S rDNA gene sequences of M. rasmusseni n. sp. and other Myxobolus spp. infecting cyprinid fishes in Canada, Europe, and Asia. The tree is rooted with Ceratonova shasta (AF001579.1). Nodes are denoted with bootstrap probabilities generated by Bayesian analyses. Species in taxa in groups I-III are highlighted in the pairwise percent identity matrix in Supplementary Table 1.
Fig. 4 in Description, life cycle, and development of the myxozoan Myxobolus rasmusseni n. sp. in fathead minnows, Pimephales promelas: A possible emerging pathogen in southern Alberta, Canada
Fig. 4. Transmission electron micrographs of plasmodia that contain M. rasmusseni n. sp. myxospores. Sections are from lesioned tissue (see inset in A) located in the circumorbital cavity of a fathead minnow. A. Side-on view of a couplet of Myxobolus rasmusseni n. sp. myxospores at 2500X magnification. Sp - Sporoplasm, Iv - Iodinophilous vacuole, Pc - Polar capsule, Pf - Polar filament; Black arrowheads indicate nuclei, orange arrowheads indicate sutural ridge along the midline of myxospore; blue arrowheads indicate posterior projections on the myxospore. B. Myxospores sectioned in various orientations with adjacent rodlet cells at 2000X magnification. Rc - Rodlet cell, Ms: myxospore.
Fig. 1 in Description, life cycle, and development of the myxozoan Myxobolus rasmusseni n. sp. in fathead minnows, Pimephales promelas: A possible emerging pathogen in southern Alberta, Canada
Fig. 1. Disfiguring lesions on the heads of 1-yr old fathead minnows infected with Myxobolus rasmusseni n. sp. Minnows were live-trapped from University Pond, Lethbridge, Ab in summer, 2022, placed into a single aquarium in the laboratory, then photographed with a digital camera. A) Unilateral exopthalmia of the right eye. B) Bilateral exopthalmia with additional lesions on dorsal surface of circumorbital cavity and on surface of left nares. C) Asymmetric exopthalmia of the left dorsal circumorbital cavity; hemorrhage within left vitreous humour, D) Severe hemorrhage of the right eye. E) Pathology of the epidermis of the left posterior circumorbital cavity and surface of left operculum.
Fig. 3. A in Description, life cycle, and development of the myxozoan Myxobolus rasmusseni n. sp. in fathead minnows, Pimephales promelas: A possible emerging pathogen in southern Alberta, Canada
Fig. 3. A. Myxospores of Myxobolus rasmusseni n. sp. prepared from a wet mount of a plasmodia-packed lesion located in the circumorbital cavity of an infected fathead minnow. A. Myxospores imaged with differential interference contrast microscope. Thin mucus coat envelopes posterior two thirds of myxospores. B. Composite line drawing of a Myxobolus rasmusseni n. sp. myxospore; PC – polar capsule; PF – polar filament; MC – mucus coat; SP – sporoplasm; IV – iodinophilous vacuole; N – nucleus.
Fig. 2 in Description, life cycle, and development of the myxozoan Myxobolus rasmusseni n. sp. in fathead minnows, Pimephales promelas: A possible emerging pathogen in southern Alberta, Canada
Fig. 2. In situ image of a school of surfacing 1-yr old fathead minnows in University Pond, Lethbridge, Ab. Each minnow has bilateral or unilateral exopthalmia associated with infection of myxospore-containing plasmodia of Myxobolus rasmusseni n. sp. Note additional large, whitish lesions located on the anterior epidermal surface of some minnows.
Continent-wide recent emergence of a global pathogen in African amphibians
<p>These datasets are associated with the study entitled, "Continent-wide recent emergence of a global pathogen in African amphibians." In this study we describe the historical and recent biogeographical spread of a fungal pathogen of amphibians, <em>Batrachochytrium dendrobatidis</em> (<em>Bd</em>) and assess its risk to amphibians across the continent of Africa.</p> <p>The larger combined file, "AfricaBd_CombinedFile_LitReview_BdMaps_GhoseData.xlsx", contains <em>Bd</em> occurrence records processed by the authors of the study (N=4,623) and previously published records (N=12,297). Of the previously published records, 12,234 records came from studies reporting both <em>Bd</em>-negative and <em>Bd</em>-positive records (i.e. prevalence) that we used along with our data (N=4,623) to assess emergence of <em>Bd</em> in African amphibians.</p> <p>The file "AfricaBd_Ghosedata_Hirschfelddata_ZimkusCameroondata.xlsx" contains all georeferenced <em>Bd </em>records collected by the authors of this study, data from Hirschfeld et al. 2016, and data for Cameroon from Zimkus et al. 2020. This file includes more metadata including amphibian species tested, and includes infection intensity data detected by qPCR for <em>Bd</em>-positive records.</p> <p>Using these datasets we document a pattern of <em>Bd </em>emergence beginning largely at the turn of the century (the year 2000). From 1852–1999, we found low <em>Bd</em> prevalence (3.2% overall) and limited geographic spread, but after 2000 we documented a sharp increase in prevalence (18.7% overall), wider geographic spread, and our genotyping revealed multiple <em>Bd </em>lineages with indications of hybridization. Our habitat suitability model showed that <em>Bd</em> risk to amphibians was highest in much of eastern, central, and western Africa. Our study documents a largely overlooked yet significant increase in a fungal pathogen that could pose a threat to amphibians across an entire continent. We emphasize the need to bridge historical and contemporary datasets to better describe and predict host-pathogen dynamics over larger temporal scales.</p> <p> </p>
Indirect pathogen transmission underlies an emerging infectious fungal disease outbreak in a wild reptile population
Open the record for dataset details and reuse information.
Data from: Incomplete host immunity favors the evolution of virulence in an emergent pathogen
Immune memory evolved to protect hosts from reinfection, but incomplete responses that allow future reinfection might inadvertently select for more harmful pathogens. We present empirical and modeling evidence that incomplete immunity promotes the evolution of higher virulence in a natural host-pathogen system. We performed sequential infections of house finches with Mycoplasma gallisepticum strains of varying virulence. Virulent bacterial strains generated stronger host protection against reinfection than less virulent strains, and thus excluded less virulent strains from infecting previously-exposed hosts. In a two-strain model, the resulting fitness advantage selected for an almost two-fold increase in pathogen virulence. Thus, the same immune systems that protect hosts from infection can concomitantly drive the evolution of more harmful pathogens in nature.
Virulence and antibiotic resistance plasticity of Arcobacter butzleri: insights on the genomic diversity of an emerging human pathogen (genome assembly, annotation dataset, core- and pan-genome loci)
<p>This dataset refers to the analysis of 49 <em>Arcobacter butzleri</em> genomes and includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the predicted transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files), the respective amino acid sequences of the translated CDS sequences (.faa files), the nucleotide alignments of all the 1165 core-genome loci, the nucleotide alignments of the genes <em>hecA</em>, <em>tetR </em>and <em>porA</em>, the categorized amino acid sequences of the six hypervariable regions of PorA, and the nucleotide sequences of the first allele of each of the 7474 pan-genome loci with the respective complete allelic profile matrix.</p> <p>All raw sequence reads used in this study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB34441).</p>
Data and code for "Mapping hotspots of zoonotic pathogen emergence: an integrated model- and participatory-based approach"
<p>Code for "Mapping hotspots of zoonotic pathogen emergence: an integrated model- and participatory-based approach". Note shapefiles will need to be downloaded from GADM (https://gadm.org/), or from the gadm package in R (https://rdrr.io/github/rspatial/geodata/man/gadm.html). </p> <p>Data are available in Version 1.0 of this record</p>
Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America
<p>Previously unrecognized diseases continue to threaten the health of forest ecosystems globally. Understanding processes leading to disease emergence is important for effective disease management and prevention of future epidemics. Utilizing whole genome sequencing, we studied the phylogenetic relationship and within diversity of two populations of the bacterial oak pathogen <em>Lonsdalea</em> <em>quercina</em> from western North America (Colorado and California) and compared these populations to other <em>Lonsdalea</em> species found worldwide. Phylogenetic analysis separated Colorado and California populations into two well-supported clades within the genus <em>Lonsdalea</em>, with an average nucleotide identity between them near species boundaries (95.31%) for bacteria, suggesting long isolation. Populations comprise distinct patterns in genetic structure and distribution. Genotypes collected from different host species and habitats were randomly distributed within the California cluster, while most Colorado isolates from introduced planted trees were distinct from isolates collected from a natural stand of CO native <em>Q. gambelii,</em> indicating the presence of cryptic population structure. The distribution of clones in California varied, while Colorado clones were always collected from neighboring trees. Despite its recent emergence, the Colorado population had higher nucleotide diversity, possibly due to migrants moving with nursery stock. Overall results suggest independent pathogen emergence in two states likely driven by changes in host-microbe interactions due to ecosystem conditions changing. To our knowledge, this is the first study on <em>L. quercina</em> population structure. Further studies are warranted to understand evolutionary relationships among <em>L. quercina</em> populations from different areas, including the native habitat of red oak in northeastern USA.</p>
Putative resistance and tolerance mechanisms have little impact on disease progression for an emerging salamander pathogen
Open the record for dataset details and reuse information.
Data from: Incomplete host immunity favors the evolution of virulence in an emergent pathogen
Open the record for dataset details and reuse information.
Eco-evolutionary responses of a cold-water fish (Salmo trutta) to the combined effects of an emerging pathogen and temperature
Open the record for dataset details and reuse information.
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.