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95 results for “host-pathogen”
Graphic Illustration of Kendra Phelp's Talk: A harmonized taxonomic resource is critical for accurately interpreting host-pathogen interactions
<p><a href="https://lib.ku.edu/people/courtney-foat" target="_blank" rel="noopener">Courtney Foat</a>, Advisor for Strategic Initiatives & Organizational Engagement at the University of Kansas, graphically recorded this invited talk by Kendra Phelps at an NSF-supported Workshop: Digital Collections Data and Tracking Disease.</p>
Host-pathogen interactions under pressure: a review and meta-analysis of stress-mediated effects on disease dynamics
<p>Human activities have increased the intensity and frequency of natural stressors and created novel stressors, altering host-pathogen interactions, and changing the risk of emerging infectious diseases. Despite the ubiquity of such anthropogenic impacts, predicting the directionality of outcomes has proven challenging. Here, we conduct a review and meta-analysis to determine the primary mechanisms through which stressors affect host-pathogen interactions and to evaluate the impacts stress has on host fitness (survival and fecundity) and pathogen infectivity (prevalence and intensity). We assessed 891 effect sizes from 71 host species (representing seven taxonomic groups) and 78 parasite taxa from 98 studies. We found that infected and uninfected hosts had similar sensitivity to stressors and that responses varied according to stressor type. Specifically, limited resources compromised host fecundity and decreased pathogen intensity, while abiotic environmental stressors (e.g., temperature and salinity) decreased host survivorship and increased pathogen intensity, and pollution increased mortality but decreased pathogen prevalence. We then used our meta-analysis results to develop Susceptible-Infected theoretical models to illustrate scenarios where infection rates are expected to increase or decrease in response to resource limitation or environmental stress gradients. Our results carry implications for conservation and disease emergence and reveal areas for future work. </p>
Host-pathogen interactions under pressure: a review and meta-analysis of stress-mediated effects on disease dynamics
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Data from: Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems
DataS1 <p>These files are Maple and Matlab scripts for analyzing the predator-prey and host-pathogen models in "Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems" and generating the figures in that study. </p>
Host-pathogen protein interactions predicted using structure
<p>This dataset accompanies a manuscript describing a method to predict host-pathogen protein interactions using structure:</p> <p>Host-pathogen protein interactions predicted by comparative modeling.<br /> Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. Protein Sci (2007) 16:2585-2596.<br /> http://www.proteinscience.org/cgi/doi/10.1110/ps.073228407</p> <p>The files contain predictions made for 10 human pathogens including species of Mycobacterium, Apicomplexa, and Kinetoplastida. The species.all.zip files contain all interactions predictions for each species along with the filter criteria that each interaction passed. The species.filter.zip files contains the same information, but only for the subset of interactions that passed the biological and network-level filters. These files can be viewed in any spreadsheet program, such as Excel.</p> <p> </p> <p>Predictions were made for interactions between human and </p> <ol> <li>Mycobacterium tuberculosis: mtuber</li> <li>Mycobacterium leprae: mleprae</li> <li>Leishmania major: lmajor</li> <li>Trypanosoma brucei: tbrucei</li> <li>Trypanosoma cruzi: tcruzi</li> <li>Cryptosporidium hominis: chominis</li> <li>Cryptosporidium parvum: cparvum</li> <li>Plasmodium falciparum: pfalciparum</li> <li>Plasmodium vivax: pvivax</li> <li>Toxoplasma gondii: tgondi</li> </ol>
Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells
<p>Single cell gene expression data for the paper "Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells" to appear in PLOS Pathogens.</p> <p>Package contains two single cell data sets, one consisting of single cells from PBMCs in three animals, and the other three tissues from one animal.</p> <p>The single-cells are grouped based on the SIV viral genes that they express.</p> <p> </p>
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
<p>Summary statistics for "Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation" </p><p>Files are organized in the following directory structure:</p><p><strong>G2G/</strong> - Summary statistics of G2G associations (SNPs, HLA, and gene-level analysis). </p><p><strong>HLA/ </strong>- Peptide binding prediction results</p><p><strong>preS1_haplotypes/ - </strong>Resolved intra-host haplotypes of the preS1 binding region. </p><p><strong>DnDs/</strong> - Calculation of intra-host positive selection, within the preS1 binding region. </p><p> </p>
Challenging a host-pathogen paradigm: Susceptibility to chytridiomycosis is decoupled from genetic erosion
<p>The putatively positive association between host genetic diversity and the ability to defend against pathogens has long attracted the attention of evolutionary biologists. Chytridiomycosis, a disease caused by the chytrid fungus <em>Batrachochytrium dendrobatidis</em> (<em>Bd</em>), has emerged in recent decades as a cause of dramatic declines and extinctions across the amphibian clade. Bd susceptibility can vary widely across populations of the same species, but the relationship between standing genetic diversity and susceptibility has remained notably underexplored so far. Here, we focus on a putatively <em>Bd</em>-naive system of two mainland and two island populations of the common toad (<em>Bufo bufo</em>) at the edge of the species' range, and use controlled infection experiments and dd-RAD sequencing of >10,000 SNPs across 95 individuals to characterise the role of host population identity, genetic variation and individual body mass in mediating host response to the pathogen. We found strong genetic differentiation between populations and marked variation in their susceptibility to Bd. This variation was not, however, governed by isolation-mediated genetic erosion, and individual heterozygosity was even found to be negatively correlated with survival. Individual survival during infection experiments was strongly positively related to body mass, which itself was unrelated to population of origin or heterozygosity. Our findings underscore the general importance of context-dependency when assessing the role of host genetic variation for the ability of defence against pathogens.</p>
Data from: Comparative host-pathogen associations of Snake Fungal Disease in sympatric species of water snakes (Nerodia)
<p>The ascomycete fungus <em>Ophidiomyces ophiodiicola</em> (<em>Oo</em>) is the causative agent of ophidiomycosis (Snake Fungal Disease), which has been detected globally. However, surveillance efforts in the central U.S., specifically Texas, have been minimal. The threatened and rare Brazos water snake (<em>Nerodia harteri harteri</em>) is one of the most range restricted snakes in the U.S. and is sympatric with two wide-ranging congeners, <em>N. erythrogaster transversa</em> and <em>N. rhombifer</em>, in north central Texas; thus, providing an opportunity to test comparative host-pathogen associations in this system. To accomplish this, we surveyed a portion of the Brazos river drainage (~400 river km) over 29 months and tested 150 Nerodia individuals for the presence of <em>Oo </em>via quantitative PCR and recorded any potential signs of <em>Oo </em>infection. We found <em>Oo </em>was distributed across the entire range of <em>N. h. harteri,</em> <em>Oo</em> prevalence was 46% overall, and there was a significant association between <em>Oo </em>occurrence and signs of infection in our sample. Models indicated adults had a higher probability of <em>Oo </em>infection than juveniles and subadults, and adult <em>N. h. harteri</em> had a higher probability of infection than adult <em>N. rhombifer</em> but not higher than adult <em>N. e. transversa</em>. High <em>Oo </em>prevalence estimates (94.4%) in adult <em>N. h. harteri </em>has implications for their conservation and management owing to their patchy distribution, comparatively low genetic diversity, and threats from anthropogenic habitat modification.</p>
Data from: Eco-evolutionary rescue promotes host-pathogen coexistence
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Challenging a host-pathogen paradigm: Susceptibility to chytridiomycosis is decoupled from genetic erosion
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Data from: Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems
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Data from: Combining in vivo and in vitro approaches to better understand host-pathogen nutritional interactions
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Data from: Comparative host-pathogen associations of Snake Fungal Disease in sympatric species of water snakes (Nerodia)
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Data: Canonical host-pathogen tradeoffs subverted by mutations with dual benefits
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Data from: Genetic variation in resistance and fecundity tolerance in a natural host-pathogen interaction
Individuals vary in their ability to defend against pathogens. Determining how natural selection maintains this variation is often difficult, in part because there are multiple ways that organisms defend themselves against pathogens. One important distinction is between mechanisms of resistance that fight off infection, and mechanisms of tolerance that limit the impact of infection on host fitness without influencing pathogen growth. Theory predicts variation among genotypes in resistance, but not necessarily in tolerance. Here, we study variation among pea aphid (Acyrthosiphon pisum) genotypes in defense against the fungal pathogen Pandora neoaphidis. It has been well established that pea aphids can harbor symbiotic bacteria that protect them from fungal pathogens. However, it is unclear whether aphid genotypes vary in defense against Pandora in the absence of protective symbionts. We therefore measured resistance and tolerance to fungal infection in aphid lines collected without symbionts, and found variation among lines in survival and in the percent of individuals that formed a sporulating cadaver. We also found evidence of variation in tolerance to the effects of pathogen infection on host fecundity, but no variation in tolerance of pathogen-induced mortality. We discuss these findings in light of theoretical predictions about host-pathogen coevolution.
Data from: Environmentally dependent host-pathogen and vector-pathogen interactions in the barley yellow dwarf virus pathosystem
1. Understanding environmentally dependent variation in interspecific interactions is needed for evaluating how agroecosystems respond to abiotic stressors, including climate change. Both biotic and abiotic conditions shape crop responses to stress events, but interactions between environmental conditions and insect borne plant pathogens remain poorly understood. 2. We tested the hypothesis that drought stress, as applied by experimental water deprivation, drives conditional outcomes in host–pathogen and host–vector interactions using a cereal–aphid–virus association and greenhouse experiments. 3. Under conditions of ample water supply, infection of wheat plants with Barley yellow dwarf virus (BYDV) resulted in reduced above-ground growth, seed set, seed yields and seed germination compared with plants exposed only to non-infected (non-viruliferous) aphids or control plants not subjected to aphid infestation. However, when water was chronically limiting, infection with Barley yellow dwarf virus did not significantly affect plant performance. 4. When wheat was subjected to acute drought stress, plants infected with Barley yellow dwarf virus surpassed both control plants and plants exposed to non-infected aphids in all measured performance traits. 5. Feeding experiments with aphid vectors (Rhopalosiphum padi) and subsequent life table analysis revealed that aphid fecundity improved by 47% when feeding on Barley yellow dwarf virus-infected plants when water inputs were chronically low. However, when plants received ample water, aphid fecundity was enhanced by only 23% from feeding on BYDV-infected plants. 6. Synthesis and applications. Collectively, our experiments suggest that wheat– Barley yellow dwarf virus interactions shift along gradients of water stress severity and duration. When Barley yellow dwarf virus infection preceded water deprivation, plant performance was not reduced from virus infection, and infected plants recovered from severe stress events more readily than non-infected plants. However, vector–pathogen mutualism resulting in enhanced reproduction of aphids on virus-infected plants is likely to amplify direct plant injury from herbivory in the field. Our findings indicate that during periods of drought, management of Barley yellow dwarf virus infection may not be needed and infection could benefit wheat under conditions of acute water stress.
Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution
<p>Dataset created in the study "A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration" </p><p><strong>Structure</strong></p><p><strong>ST_berghei_liver</strong></p><p>contains data generated during <i>stpipeline </i>analysis and imaging on 2k arrays Spatial Transcriptomics platform as well as data necessary for and from hepaquery analysis. These samples include 38 sections in total of which 8 are from mice (n=4) infected with sporozoites for 12h, 5 sections from control mice (n=3) at 12h, 7 sections from mice (n=4) infected with sporozoites for 24h and 4 sections from control mice (n=3) for 24 as well as 8 samples of mice (n=2) infected with sporozoites for 38h and control mice (n =2) for 38h. </p><ul><li><i><strong>count</strong></i> contains gene expression matrix output from stpipeline in .tsv format</li><li><i><strong>spotfiles</strong> </i>contains coordinate files for count matrices</li><li><i><strong>images </strong></i>contains scaled H&E, Fluorescence (FL) and annotated H&E images (from FL annotations) scaled to 10% of the original image size.</li><li><i><strong>masks </strong></i>contains image masks for hepaquery analysis</li><li><i><strong>distances </strong></i>contains distance measurements from original section sorted by timepoint as well as combined across timepoints</li><li><strong>cluster</strong> contains clustering information across spatial positions used in spatial enrichment analysis</li></ul><p><strong>STUtiility_mus_pb_ST.RDS </strong>describes seurat object generated using the STUtility package using ST data of the 38 liver sections of which the data is stored in <strong>ST_berghei_liver</strong></p><p><strong>h5ad</strong></p><p>contains anndata files of ST data (normalized read counts), spot information, distance measurements, images and masks generated using the hepaquery package. </p><p><strong>visium_berghei_liver</strong></p><p>contains data generated with the <i>spaceranger </i>pipeline and imaging using the Visium spatial transcriptomics platform. These samples include 8 sections in total, of which 1 was infected with sporozoites for 12h, 1 control section at 12h, 1 section infected with sporozoites for 24h and 1 control section at 24 as well as 2 sporozoite infected sections, and 2 control sections at 38h. </p><ul><li><i><strong>V10S29-135_A1</strong></i> contains spaceranger output for section 1 for infected and control sections at 38h post-infection</li><li><i><strong>V10S29-135_B1</strong></i> contains spaceranger output for section 1 for infected and control sections at 12h post-infection </li><li><i><strong>V10S29-135_C1 </strong></i>contains spaceranger output for section 1 for infected and control sections at 24h post-infection </li><li><i><strong>V10S29-135_D1 </strong></i>contains spaceranger output for section 2 for infected and control sections at 38h post-infection </li></ul><p><strong>se_visium.RDS </strong>describes seurat object generated using the STUtility package using ST data of the 38 liver sections of which the data is stored in <strong>visium_berghei_liver</strong></p><p><strong>snSeq_berghei_liver</strong></p><p>contains data generated with the <i>cellranger </i>pipeline and imaging using the Visium spatial transcriptomics platform. These samples include single nuclei of 2 infected and control mice after 12h, 2 infected and control mice after 24h, 2 infected and control mice after 38h, and 2 uninfected mice prior to a challenge.</p><p><i><strong>cellranger_cnt_out</strong> </i>contains feature count matrix information from cell ranger output</p><p><strong>final_merged_curated_annotations_270623.RDS </strong>describes seurat object generated using the STUtility package using ST data of the 38 liver sections of which the data is stored in <strong>snSeq_berghei_liver.tar.gz</strong></p><p><strong>raw images.zip </strong>contains raw images for supplementary figures 20-22</p><p><strong>adjusted images.zip </strong>contains brightness and contrast adjusted images for supplementary figures 20-22</p>
Experimental evidence that host species composition alters host-pathogen dynamics in a ranavirus-amphibian assemblage
<p>Losses in biodiversity can alter disease risk through changes in host species composition. Host species vary in pathogen susceptibility and competence. Yet how changes in diversity alter host-pathogen dynamics remains unclear in many systems, particularly with respect to generalist pathogens. Amphibians are experiencing worldwide population declines linked to generalist pathogens, such as ranavirus, and thus represent an ideal group to investigate how host species composition affects disease risk. We conducted experiments where individuals in the laboratory and assemblages of three amphibian species (Pacific tree frogs, Pseudacris regilla; Cascades frogs, Rana cascadae; and Western toads, Anaxyrus boreas) or just A. boreas alone in outdoor mesocosms were exposed to ranavirus as larvae. In laboratory experiment, we observed low survival and high viral loads in P. regilla compared to the other species suggesting that this species was highly susceptible to the pathogen. In the mesocosm experiment, we observed 41% A. boreas mortality when alone and 98% mortality when maintained with P. regilla and R. cascadae. Our results suggest that the presence of highly susceptible species can alter disease dynamics across multiple species, potentially increasing infection risk and mortality in co-occurring species.</p>
Comparative analyses of compatible and incompatible host-pathogen interactions provide insight into divergent host specialization of closely related pathogens
<p>The following animations accompany the manuscript "Comparative analyses of compatible and incompatible host-pathogen interactions provide insight into divergent host specialization of closely related pathogens". These animations are of confocal microscopy images of wheat leaves infected with isolates of <em>Zymoseptoria pseudodarliae </em>and <em>Z. ardabiliae, </em>at two infection stages (early and late), scrolling through different planes of focus into the wheat leaf. Two isolates of <em>Zymoseptoria pseudodarliae (</em>Zp13 and Zp72) and three isolates of <em>Zymoseptoria ardabiliae </em>(Za17, Za48, and Za94) on wheat, were screened in this study. Each isolate is expressing GFP in order to visualise hyphae. <em>Z. pseudodarliae </em>and <em>Z. ardabiliae </em>are avirulent on wheat, and infections do not pentrate beyond the stomata and into the wheat tissue. These differ from previously obtained images of <em>Z. tritici </em>(virulent on wheat), which penetrate into the wheat tissue (<a href="https://doi.org/10.1002/ece3.4724">https://doi.org/10.1002/ece3.4724</a>).</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.