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183 results for “infection dynamics”
Data for: Effects of habitat management on rodent diversity, abundance, and virus infection dynamics
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Data from: The stochastic dynamics of early epidemics: probability of establishment, initial growth rate, and infection cluster size at first detection
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Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies
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Data from: Estimating transmission dynamics and serial interval of the first wave of COVID-19 infections under different control measures: A statistical analysis in Tunisia from February 29 to May 5, 2020
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Data from: Coinfection with chytrid genotypes drives divergent infection dynamics reflecting regional distribution patterns
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Data from: Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin
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Data from: Dynamics of the CD9 interactome during bacterial infection of epithelial cells by proximity labelling proteomics
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Data for: Host infection dynamics and disease induced mortality modify species contributions to the environmental reservoir
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Data from: Negative interactions and virulence differences drive the dynamics in multispecies bacterial infections
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Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages
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Data from: Infection dynamics, dispersal, and adaptation: understanding the lack of recovery in a remnant frog population following a disease outbreak
Emerging infectious diseases can cause dramatic declines in wildlife populations. Sometimes these declines are followed by recovery, but many populations do not recover. Studying differential recovery patterns may yield important information for managing disease-afflicted populations and facilitating population recoveries. In the late1980s, a chytridiomycosis outbreak caused multiple frog species in Australia's Wet Tropics to decline. Populations of some species (e.g., Litoria nannotis) subsequently recovered, while others (e.g., Litoria dayi) did not. We examined the population genetics and current infection status of L. dayi, to test several hypotheses regarding the failure of its populations to recover: 1) a lack of individual dispersal abilities has prevented recolonization of previously occupied locations, 2) a loss of genetic variation has resulted in limited adaptive potential, and 3) L. dayi is currently adapting to chytridiomycosis. We found moderate to hig h levels of gene flow and diversity (Fst range: <0.01–0.15; minor allele frequency: 0.192–0.245), which were similar to previously published levels for recovered L. nannotis populations. This suggests that dispersal ability and genetic diversity do not limit the ability of L dayi to recolonize upland sites. Further, infection intensity and prevalence increased with elevation, suggesting that chytridiomycosis is still limiting the elevational range of L. dayi. Outlier tests comparing infected and uninfected individuals consistently identified 18 markers as putatively under selection, and several of those markers matched genes that were previously implicated in infection. This suggests that L. dayi has genetic variation for genes that affect infection dynamics and may be undergoing adaptation.
Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data
<p>This upload contains data and all the scripts required to reproduce the results of the artice entitled "Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data".</p> <p><strong>Code is located within Code.zip</strong> . It contains scripts in R and Bash and launchers. Some of the scripts require data files contained within Data.zip.</p> <p><strong>Data is located within Data.zip</strong> , such as the sequences, the inferred phylogeny and the Beast XML file.</p>
Data from: The hitchhiker's guide to Europe: the infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi
Wolbachia is a maternally inherited and ubiquitous endosymbiont of insects. It can hijack host reproduction by manipulations such as cytoplasmic incompatibility (CI) to enhance vertical transmission. Horizontal transmission of Wolbachia can also result in the colonization of new mitochondrial lineages. In this study, we present a 15-year-long survey of Wolbachia in the cherry fruit fly Rhagoletis cerasi across Europe and the spatiotemporal distribution of two prevalent strains, wCer1 and wCer2, and associated mitochondrial haplotypes in Germany. Across most of Europe, populations consisted of either 100% singly (wCer1) infected individuals with haplotype HT1, or 100% doubly (wCer1&2) infected individuals with haplotype HT2, differentiated only by a single nucleotide polymorphism. In central Germany, singly infected populations were surrounded by transitional populations, consisting of both singly and doubly infected individuals, sandwiched between populations fixed for wCer1&2. Populations with fixed infection status showed perfect association of infection and mitochondria, suggesting a recent CI-driven selective sweep of wCer2 linked with HT2. Spatial analysis revealed a range expansion for wCer2 and a large transition zone in which wCer2 splashes appeared to coalesce into doubly infected populations. Unexpectedly, the transition zone contained a large proportion (22%) of wCer1&2 individuals with HT1, suggesting frequent intraspecific horizontal transmission. However, this horizontal transmission did not break the strict association between infection types and haplotypes in populations outside the transition zone, suggesting that this horizontally acquired Wolbachia infection may be transient. Our study provides new insights into the rarely studied Wolbachia invasion dynamics in field populations.
Data from: Infection dynamics in coexisting sexual and asexual host populations: support for the Red Queen hypothesis
The persistence of sexual reproduction is a classic problem in evolutionary biology. The problem stems from the fact that, all else equal, asexual lineages should rapidly replace coexisting sexual individuals due to the cost of producing males in sexual populations. One possible countervailing advantage to sexual reproduction is that, on average, outcrossed offspring are more resistant than common clones to coevolving parasites, as predicted under the Red Queen hypothesis. In the present study, we evaluated the prevalence of infection by a sterilizing trematode (Microphallus sp.) in a natural population of freshwater snails that was composed of both sexual and asexual individuals (Potamopyrgus antipodarum). More specifically, we compared the frequency of infection in sexual and asexual individuals over a five-year period at four sites at a natural glacial lake (Lake Alexandrina, South Island, New Zealand). We found that at most sites and over most years, the sexual population was less infected than the coexisting asexual population. Moreover, the frequency of uninfected sexual females was periodically greater than two times the frequency of uninfected asexual females. These results give clear support for a fluctuating parasite-mediated advantage to sexual reproduction in a natural population.
Data from: Population structure of a microparasite infecting Daphnia: spatio-temporal dynamics
Background: Detailed knowledge of spatial and temporal variation in the genetic population structure of hosts and parasites is required for understanding of hostparasite coevolution. As hot-spots of contemporary coevolution in natural systems are difficult to detect and long-term studies are restricted to few systems additional population genetic data from various hostparasite systems may provide important insights into the topic. This is particularly true for parasites as these players have been under-investigated so far due to the lower availability of suitable molecular markers. Here we traced genetic variation (based on sequence variants in the internal transcribed spacer region ITS) among seven geographically isolated populations of the ichthyosporean Caullerya mesnili a common microparasite of the cladoceran Daphnia (here the D. longispina hybrid complex). At some sites we also studied parasite genetic variation over time. Then we tested for associations between parasite genotypes and host species. Results: Parasite (and host) populations were significantly structured across space indicating limited dispersal. Moreover the frequency of parasite genotypes varied significantly over time suggesting rapid evolutionary change in Caullerya. Finally the distribution of parasite genotypes was similar across different host species which might in turn have important consequences for parasite epidemiology. Conclusions: The approach proposed here can be applied to track spatial and temporal changes in the population structure of other microparasite species for which sequence variation in the ITS or other highly variable genome regions has been documented but other types of polymorphic markers are lacking. Screening of parasite sequence variants allows for reliable detection of cross-species infections and using advanced sequencing techniques in the near future for detailed studies of parasite evolution in natural hostparasite systems.
Data from: Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection
To understand the eco-evolutionary significance of plant viruses in nature, we must (i) quantify the effects of infection on plant fitness and (ii) recognize that native plants are increasingly exposed to crop-associated viruses. Studies of perennials are particularly needed: most of our knowledge of plant-virus interactions is from annuals, yet long-lived species dominate landscapes. Here we used aster models for life-history analysis and longitudinal measures of plant virus status to evaluate multi-year consequences of crop virus infection in a native perennial. We used Barley yellow dwarf virus acquired from wheat to inoculate seedlings of Panicum virgatum L. (switchgrass), a North American prairie grass. We grew inoculated and mock-inoculated individuals of two ecotypes for 3 years in the field. We measured plant size, infection status and fitness components. Aster modelling provided integrated multi-year measures of fitness. Crop virus inoculation reduced multi-year native plant fitness by 30% over 2 years despite generally asymptomatic infection and evidence of resistance. This reduction was greater than predicted from individual fitness components or most size measures. Ecotypes differed in response, with the lowland ecotype experiencing higher apparent recovery from infection. Virus treatment in the upland ecotype delayed flowering phenology and reduced seed filling. Synthesis. Our use of field experimentation, surveys of plant infection status and aster modelling demonstrates a rigorous and broadly applicable approach for quantifying the effects of viruses and other microbes on multi-year plant fitness. We found that a crop virus had negative multi-year effects on native plant fitness even after infection was no longer detected. Viruses may have substantial effects on native vegetation with domestication of landscapes and agricultural expansion.
Data from: The contribution of host cell-directed vs. parasite-directed immunity to the disease and dynamics of malaria infections
<p>Hosts defend themselves against pathogens by mounting an immune response. Fully understanding the immune response as a driver of host disease and pathogen evolution requires a quantitative account of its impact on parasite population dynamics. Here, we use a data-driven modeling approach to quantify the birth and death processes underlying the dynamics of infections of the rodent malaria parasite, <span>Plasmodium chabaudi</span>, and the red blood cells (RBCs) it targets. We decompose the immune response into 3 components, each with a distinct effect on parasite and RBC vital rates, and quantify the relative contribution of each component to host disease and parasite density. Our analysis suggest that these components are deployed in a coordinated fashion to realize distinct resource-directed defense strategies that complement the killing of parasitized cells. Early in the infection, the host deploys a strategy reminiscent of siege and scorched-earth tactics, in which it both destroys RBCs and restricts their supply. Late in the infection, a "juvenilization" strategy, in which turnover of RBCs is accelerated, allows the host to recover from anemia while holding parasite proliferation at bay. By quantifying the impact of immunity on both parasite fitness and host disease. we reveal that phenomena often interpreted as immunopathology may in fact be beneficial to the host. Finally, we show that, across mice, the components of the host response are consistently related to each other, even when infections take qualitatively different trajectories. This suggests the existence of simple rules that govern the immune system's deployment.</p>
Data Supporting The Paper 'Fine-tuned spatiotemporal dynamics of DNA replication during phage lambda infection'
<p>The dataset includes raw images, source code, raw vectors saved from MATLAB, and curated data used to generate figures and analyses in the paper <strong>'Fine-tuned spatiotemporal dynamics of DNA replication during phage lambda infection'</strong> by Z. Yu, et al.</p> <p>Additional information about the experiments will be available upon request. </p>
Dimerization the ACE-2 with Different RBD Mounts: A Dynamic Simulation Perspective on SARS-Cov-2 Infecting Details
<p>The system construction and dynamic simulation data of paper "Dimerization the ACE-2 with Different RBD Mounts: A Dynamic Simulation Perspective on SARS-Cov-2 Infecting Details"(manuscript, ci-2023-00041c) are prepared.</p>
IL-17 signalling is critical for controlling subcutaneous adipose tissue dynamics and parasite burden during chronic Trypanosoma brucei infection
<p>In the skin, <em>Trypanosoma brucei </em>colonises the subcutaneous white adipose tissue (WAT) and harbours a pool of parasites competent for forward transmission. The interaction between parasites, adipose tissue, and the local immune system is likely to drive adipose tissue wasting and weight loss observed in cattle and humans infected with <em>T. brucei</em>. However, mechanistically, this process is not fully understood. Here, using several complementary approaches including mass cytometry by time of flight, bulk and single cell transcriptomics, we found that <em>T. brucei</em> infection drives a local expansion of several IL-17A-producing cells in the murine WAT, including T<sub>H</sub>17 and Vg6<sup>+</sup> T cells. We also found that global IL-17 deficiency, or mice lacking IL-17 receptor expression specifically on adipocytes, were protected from infection-induced WAT wasting and weight loss. Unexpectedly, we found that abrogation of IL-17 signalling on adipocytes results in higher burden of extravascular parasites in the WAT. Taken together, our study highlights the central role of IL-17 signalling on adipocytes in controlling WAT responses to infection, suggesting that adipocytes are a critical coordinator of the tissue immune response to <em>T. brucei</em> infection. </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.