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40 results for “host heterogeneity”
Data from: Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification
Colonization of novel hosts is thought to play an important role in parasite diversification, yet little consensus has been achieved about the macroevolutionary consequences of changes in host use. Here we offer a mechanistic basis for the origins of parasite diversity by simulating lineages evolved in silico. We describe an individual-based model in which (i) parasites undergo sexual reproduction limited by genetic proximity, (ii) hosts are uniformly distributed along a one-dimensional resource gradient, and (iii) host use is determined by the interaction between the phenotype of the parasite and a heterogeneous fitness landscape. We found two main effects of host use on the evolution of a parasite lineage. First, the colonization of a novel host allowed parasites to explore new areas of the resource space, increasing phenotypic and genotypic variation. Second, hosts produced heterogeneity in the parasite fitness landscape, which led to reproductive isolation and therefore, speciation. As a validation of the model, we analyzed empirical data from Nymphalidae butterflies and their host plants. We then assessed the number of hosts used by parasite lineages and the diversity of resources they encompass. In both simulated and empirical systems, host diversity emerged as the main predictor of parasite species richness.
Data from: Integrated molecular imaging reveals tissue heterogeneity driving host-pathogen interactions
All diseases are characterized by distinct changes in tissue molecular distribution. Molecular analysis of intact tissues traditionally requires pre-existing knowledge of, and reagents for, the targets of interest. Conversely, label-free discovery of disease-associated tissue analytes requires destructive processing for downstream identification platforms. Tissue-based analyses therefore sacrifice discovery to gain spatial distribution of known targets, or sacrifice tissue architecture for discovery of unknown targets. To overcome these obstacles, we developed a multi-modality imaging platform for discovery-based molecular histology. We apply this platform to a model of disseminated infection triggered by the important pathogen Staphylococcus aureus, leading to the discovery of infection-associated alterations in the distribution and abundance of proteins and elements in tissue. These data provide an unbiased, three-dimensional analysis of how disease impacts the molecular architecture of complex tissues, enable culture-free diagnosis of infection through imaging-based detection of bacterial and host analytes, and reveal molecular heterogeneity at the host-pathogen interface.
Data from: Spatial heterogeneity lowers rather than increases host-parasite specialization
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Data from: The genetic structure of a Venturia inaequalis population in a heterogeneous host population composed of different Malus species
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Data from: Evolution of virulence in heterogeneous host communities under multiple trade-offs
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Data from: Integrated molecular imaging reveals tissue heterogeneity driving host-pathogen interactions
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Data from: Habitat heterogeneity, host population structure and parasite local adaptation
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Data from: Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification
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Data from: Virulence evolution of a generalist plant virus in a heterogeneous host system
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Simultaneous transcriptional profiling of bacteria and their host cells by heterogeneous RNA-Seq (hRNA-Seq)
GEO Series GSE44253. Chlamydia trachomatis; Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Integration of M. tuberculosis phenotype with single cell RNA-seq to interrogate host macrophage heterogeneity in vivo.
GEO Series GSE167232. Mus musculus; Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
The Host Modulates Transcriptional Profile and Phenotypic Heterogeneity in Symbionts.
GEO Series GSE232120. Serratia marcescens. 9 samples. Type: Expression profiling by high throughput sequencing.
Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]
GEO Series GSE159787. Homo sapiens; Severe acute respiratory syndrome coronavirus 2. 363 samples. Type: Other; Expression profiling by high throughput sequencing.
Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [GeoMx human protein]
GEO Series GSE159785. Homo sapiens. 363 samples. Type: Other.
The Host Modulates Transcriptional Profile and Phenotypic Heterogeneity in Symbionts
GEO Series GSE232484. Serratia marcescens. 10 samples. Type: Expression profiling by high throughput sequencing.
Individual heterogeneity in ixodid tick infestation and prevalence of Borrelia burgdorferi sensu lato in a northern community of small mammalian hosts
<p>Dataset and scripts for our paper "Individual heterogeneity in ixodid tick infestation and prevalence of <i>Borrelia burgdorferi</i> sensu lato in a northern community of small mammalian hosts" in Oecologia</p>
Dual single-cell and bulk RNA sequencing reveal transcriptional profiles underlying heterogenous host-parasite interactions in human peripheral blood mononuclear cells
GEO Series GSE295224. Homo sapiens. 42 samples. Type: Expression profiling by high throughput sequencing.
Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection
GEO Series GSE159788. Homo sapiens; Severe acute respiratory syndrome coronavirus 2. 726 samples. Type: Other; Expression profiling by high throughput sequencing.
Vaccine-primed CAR T-cells reject antigen-heterogenous tumors via host immunity
GEO Series GSE212453. Mus musculus. 27 samples. Type: Expression profiling by high throughput sequencing; Other.
seurat objects for : "scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics"
<p><strong>Summary</strong></p> <p>Here, we utilize Dual-scSeq to parse out heterogeneous transcription of bone marrow-derived dendritic cells (BMDCs) infected with T. gondii type I, RH (LDM) or type II, ME49 (PTG) parasites, over multiple time points post-infection (3 and 12h post-infection).</p> <p><strong>Data</strong></p> <p>This repository contains two files, one for each organism investigated (mouse and tgondii), in ".RDS" format generated using Seurat v.4.3.: </p> <p><strong>1. BMDC_infected_mouse.RDS </strong>- object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs. </p> <p><strong> metadata columns </strong>describe: </p> <p> - orig.ident: <em>plate identity from smartSeq setup</em></p> <p> - nCount_RNA: <em>UMI count before normalization</em></p> <p> - nFeature_RNA: <em>Gene count before normalization</em></p> <p> - nCount_RNA: <em>UMI count before normalization</em></p> <p> - nUMI: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em></p> <p> - toxo_nUMI:<em> sum of reads per cell for t.gondii</em></p> <p> - mouse_nUMI: <em>sum of reads per cell for mouse</em></p> <p> - nGene: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em></p> <p> - toxo_nGene: <em>sum of genes per cell for t.gondii</em></p> <p> - mouse_nGene: <em>sum of genes per cell for mouse</em></p> <p> - cell_ID: <em>enumerated cells by well</em></p> <p> - well:<em> well_ID of plate used for smartSeq2</em></p> <p> - condition: <em>treatment of cell (one of 8: LDM infection for 3h, LDM infection for 12h, PTG infection for 3h, PTG infection for 12h, LDM Lysate control, PTG Lysate control, uninfected control or LPS control)</em></p> <p> - percent.mt: <em>percentage of transcript mapped to the mitochondrial genome</em></p> <p> - cell_ID: <em>enumerated cells by well</em></p> <p> - nFeature_SCT: <em>Gene count after normalization</em></p> <p> - nCount_SCT: <em>UMI count after normalization</em></p> <p> - nFeature_RNA: <em>Gene count before normalization</em></p> <p> - seurat_clusters: <em>Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering </em></p> <p> - toxo_clusters: <em>Clusters of t.gondii dataset of the corresponding infected cell </em></p> <p> - cell type: <em>Annotated subpopulation of infected cells</em></p> <p> - condition_celltype: <em>condition (see above) combined with celltype (see above)</em></p> <p> - cluster_celltype: <em>seurat_clusters (see above) combined with celltype (see above)</em></p> <p> - cluster_condition: <em>seurat_clusters (see above) combined with condition (see above)</em></p> <p> - UMAP_1: <em>Umap embedding coordinates x-axis</em></p> <p> - UMAP_2: <em>Umap embedding coordinates y-axis</em></p> <p> - cell_cycle_phase: <em>predicted cell cycle phase of murine host cells </em></p> <p> - cycle_phase_t.gondii: <em>predicted cycling phase of t.gondii in the corresponding infected host cell </em></p> <p><strong>2. BMDC_infected_tgondii.RDS </strong>- object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs. </p> <p><strong> metadata columns </strong>describe: </p> <p> - orig.ident: <em>plate identity from smartSeq setup</em></p> <p> - nCount_RNA: <em>UMI count before normalization</em></p> <p> - nFeature_RNA: <em>Gene count before normalization</em></p> <p> - nCount_RNA: <em>UMI count before normalization</em></p> <p> - nUMI: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em></p> <p> - toxo_nUMI:<em> sum of reads per cell for t.gondii</em></p> <p> - mouse_nUMI: <em>sum of reads per cell for mouse</em></p> <p> - nGene: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em></p> <p> - toxo_nGene: <em>sum of genes per cell for t.gondii</em></p> <p> - mouse_nGene: <em>sum of genes per cell for mouse</em></p> <p> - cell_ID: <em>enumerated cells by well</em></p> <p> - well:<em> well_ID of plate used for smartSeq2</em></p> <p> - condition: <em>treatment of cell (one of 8: LDM infection for 3h, LDM infection for 12h, PTG infection for 3h, PTG infection for 12h, LDM Lysate control, PTG Lysate control, uninfected control or LPS control)</em></p> <p> - percent.mt: <em>percentage of transcript mapped to the mitochondrial genome</em></p> <p> - cell_ID: <em>enumerated cells by well</em></p> <p> - nFeature_SCT: <em>Gene count after normalization</em></p> <p> - nCount_SCT: <em>UMI count after normalization</em></p> <p> - nFeature_RNA: <em>Gene count before normalization</em></p> <p> - seurat_clusters: <em>Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering </em></p> <p> - mouse_clusters: <em>Clusters of mouse dataset of the corresponding infected cell </em></p> <p> - mouse_celltype: <em>Annotated subpopulation if infected cells</em></p> <p> - condition_celltype: <em>condition (see above) combined with mouse_celltype (see above)</em></p> <p> - cluster_celltype: <em>seurat_clusters (see above) combined with mouse_celltype (see above)</em></p> <p> - cluster_condition: <em>seurat_clusters (see above) combined with condition (see above)</em></p> <p> - UMAP_1: <em>Umap embedding coordinates x-axis</em></p> <p> - UMAP_2: <em>Umap embedding coordinates y-axis</em></p> <p> - cell_cycle_phase_mouse: <em>predicted cell cycle phase of murine host cells </em></p> <p> - cycle_phase_t.gondii: <em>predicted cycling phase of t.gondii in the corresponding infected host cell </em></p>
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)
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.