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1,737 results for “host data”
Data from: Symbiont infection and psyllid haplotype influence phenotypic plasticity during host switching events
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Raw data from: Dysregulation of host-control causes interspecific conflict over host investment into symbiotic organs
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Data from: Host response to conspecific brood parasitism in colonial Red-breasted Mergansers (Mergus serrator): Positioning of parasitic eggs within the clutch
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Data from: Pollinator community species richness dilutes prevalence of multiple viruses within multiple host species
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Data: Canonical host-pathogen tradeoffs subverted by mutations with dual benefits
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Data from Pliant pathogens: Estimating viral spread when confronted with new vector, host, and environmental conditions
To determine the effects of new conditions (host, vector, and nutrient) on pathogen spread rate, we introduced a vector-borne viral plant pathogen, Barley Yellow Dwarf Virus PAV (BYDV-PAV) into hosts, vectors, and host nutrient supplies that it had not encountered for thousands of viral generations. We quantified pathogen prevalence over the course of two serial inoculations under the new conditions.
Data from: A comparison of diversity estimators applied to a database of host-parasite associations
Understanding the drivers of biodiversity is important for forecasting changes in the distribution of life on earth. However, most studies of biodiversity are limited by uneven sampling effort, with some regions or taxa better sampled than others. Numerous methods have been developed to account for differences in sampling effort, but most methods were developed for systematic surveys in which all study units are sampled using the same design and assemblages are sampled randomly. Databases compiled from multiple sources, such as from the literature, often violate these assumptions because they are composed of studies that vary widely in their goals and methods. Here, we compared the performance of several popular methods for estimating parasite diversity based on a large and widely used parasite database, the Global Mammal Parasite Database (GMPD). We created artificial datasets of host-parasite interactions based on the structure of the GMPD, then used these datasets to evaluate which methods best control for differential sampling effort. We evaluated the precision and bias of seven methods, including species accumulation and nonparametric diversity estimators, compared to analyzing the raw data without controlling for sampling variation. We find that nonparametric estimators, and particularly the Chao2 and second-order jackknife estimators, perform better than other methods. However, these estimators still perform poorly relative to systematic sampling, and effect sizes should be interpreted with caution because they tend to be lower than actual effect sizes. Overall, using these estimators is more effective in comparative studies than for estimating true estimates of diversity. We make recommendations for future sampling strategies and statistical methods that would improve estimates of global parasite diversity.
A Large-scale Data Set and an Empirical Study of Docker Images Hosted on Docker Hub
<p>The data set schema, fields description, and analysis scripts are in the GitHub artifact repository.</p> <p>https://github.com/linncy/icsme2020-docker-study</p> <p> </p> <p>@inproceedings{LinICSME20,<br>author={Changyuan Lin and Sarah Nadi and Hamzeh Khazaei},<br>title={A Large-scale Data Set and an Empirical Study of Docker Images Hosted on Docker Hub},<br>booktitle={Proceedings of the 36th IEEE International Conference on Software Maintenance and Evolution (ICSME)},<br>year={2020},<br>url_Paper={https://www.dropbox.com/s/3bktcmdr7rlw1ic/LinICSME20.pdf}<br>}</p>
Data from: Reprograming of epigenetic mechanisms controlling host insect immunity and development in response to egg-laying by a parasitoid wasp
<p>Parasitoids are insects that use other insects as hosts. They sabotage host cellular and humoral defenses to promote the survival of their offspring by injecting viruses and venoms along with their eggs. Many pathogens and parasites disrupt host epigenetic mechanisms to overcome immune system defenses, and we hypothesized that parasitoids may utilize the same strategy. We used the ichneumon wasp Pimpla turionellae as a model idiobiont parasitoid to test this hypothesis, with pupae of the greater wax moth Galleria mellonella as the host. We found that parasitoid infestation involves the suppression of host immunity-related effector genes and the modulation of host genes involved in developmental hormone signaling. The transcriptional reprogramming of host genes following the injection of parasitoid eggs was associated with changes in host epigenetic mechanisms. The introduction of parasitoids resulted in a transient decrease in host global DNA methylation and the modulation of acetylation ratios for specific histones. Genes encoding regulators of histone acetylation and deacetylation were mostly downregulated in the parasitized pupae, suggesting that parasitoids can suppress host transcription. We also detected a strong parasitoid-specific effect on host microRNAs regulating gene expression at the post-transcriptional level. Our data therefore support the hypothesis that parasitoids may favor the survival of their offspring by interfering with host epigenetic mechanisms to suppress the immune system and disrupt development.</p>
Data from: Host-induced genome instability rapidly generates phenotypic variation across Candida albicans strains and ploidy states
<p>Candida albicans is an opportunistic fungal pathogen of humans that is typically diploid yet has a highly labile genome tolerant of large-scale perturbations including chromosomal aneuploidy and loss-of-heterozygosity events. The ability to rapidly generate genetic variation is crucial for C. albicans to adapt to changing or stressful environments, like those encountered in the host. Genetic variation occurs via stress-induced mutagenesis or can be generated through its parasexual cycle, in which tetraploids arise via diploid mating or stress-induced mitotic defects and undergo nonmeiotic ploidy reduction. However, it remains largely unknown how genetic background contributes to C. albicans genome instability in vitro or in the host environment. Here, we tested how genetic background, ploidy, and the host environment impacts C. albicans genome stability. We found that host association induced both loss-of-heterozygosity events and genome size changes, regardless of genetic background or ploidy. However, the magnitude and types of genome changes varied across C. albicans strain background and ploidy state. We then assessed if host-induced genomic changes resulted in fitness consequences on growth rate and nonlethal virulence phenotypes and found that many host-derived isolates significantly changed relative to their parental strain. Interestingly, diploid host-associated C. albicans predominantly decreased host reproductive fitness, whereas tetraploid host-associated C. albicans increased host reproductive fitness. Together, these results are important for understanding how host-induced genomic changes in C. albicans alter its relationship with the host.</p> <p>IMPORTANCE Candida albicans is an opportunistic fungal pathogen of humans. The ability to generate genetic variation is essential for adaptation and is a strategy that C. albicans and other fungal pathogens use to change their genome size. Stressful environments, including the host, induce C. albicans genome instability. Here, we investigated how C. albicans genetic background and ploidy state impact genome instability, both in vitro and in a host environment. We show that the host environment induces genome instability, but the magnitude depends on C. albicans genetic background. Furthermore, we show that tetraploid C. albicans is highly unstable in host environments and rapidly reduces in genome size. These reductions in genome size often resulted in reduced virulence. In contrast, diploid C. albicans displayed modest host-induced genome size changes, yet these frequently resulted in increased virulence. Such studies are essential for understanding how opportunistic pathogens respond and potentially adapt to the host environment.</p> <p> </p>
Data from: Distribution of the specialist aphid Uroleucon nigrotuberculatum (Homoptera: Aphididae) in response to host plant semiochemical induction by the gall fly Eurosta solidaginis (Diptera: Tephritidae)
Many plants use terpenoids and other volatile compounds as semiochemicals. Reception of plant volatiles by conspecifics may trigger a defensive phytochemical response. These same compounds can also function as host recognition signals for phytophagous insects. In this experiment we find that when the specialist gall-forming fly Eurosta solidaginis attacks its tall goldenrod (Solidago altissima) host plant, the fly indirectly induces a phytochemical response in nearby tall goldenrod plants. This phytochemical response may, in turn, act as a positive signal attracting the goldenrod specialist aphid Uroleucon nigrotuberculatum. Laboratory based experiments exposing ungalled tall goldenrod plants to the volatiles released by E. solidaginis galls demonstrated a consistent increase in foliar terpenoid concentrations in ungalled plants. Analysis of tall goldenrod stem and gall tissue chemistry revealed induction of terpenoids in gall tissue, with a simultaneous decrease in green leaf volatile concentrations. Field experiments demonstrated a consistent spatial relationship in tall goldenrod foliar terpenoid concentrations with distance from an E. solidaginis gall. Both laboratory and field experiments establish consistent induction of the terpene β-farnesene, and that this compound is a strong positive predictor of U. nigrotuberculatum aphid presence on goldenrod plants along with plant biomass and several other foliar terpenoids. These findings suggest E. solidaginis induced phytochemistry, especially β-farnesene, may be acting as a kairomone, driving aphid distribution in the field.
Data from: Different distribution of malaria parasite in left and right extremities of vertebrate hosts translates into differences in parasite transmission
<p class="Body"><span>Malaria, a vector-borne disease caused by <i>Plasmodium</i> <i>spp</i>., remains a major global cause of mortality. Optimization of disease control strategies requires a thorough understanding of the processes underlying parasite transmission. While the number of transmissible stages (gametocytes) of <i>Plasmodium</i> in blood is frequently used as an indicator of host-to-mosquito transmission potential, this relationship is not always clear. Significant effort has been made in developing molecular tools that improve gametocyte density estimation and therefore prediction of mosquito infection rates. However a significant level of uncertainty around estimates remains. The weakness in the relationship between gametocyte burden, measured from a blood sample, and the mosquito infection rate could be explained by a non-homogeneous distribution of gametocytes in the bloodstream. The estimated gametocyte density would then only be a single snapshot that does not reflect the host infectivity. This aspect of <i>Plasmodium</i> infection, however, remains largely neglected. In both humans and birds, we found here that the gametocyte densities differed depending on which side of the body the sample was taken, suggesting that gametocytes are not homogeneously distributed within the vertebrate host. We observed a fluctuating asymmetry, in other words, the extremity of the body with the highest density of parasites is not always the same from one individual to another. An estimation of gametocyte density from only one blood sample, as is commonly measured, could, therefore, over- or underestimated the infectivity of gametocyte carriers. This might have important consequences on the epidemiology of the disease since we show that this variation influences host-to-mosquito transmission. Vectors fed on the least infected body part had a lower parasite burden than those fed on the most infected part. The heterogeneous distribution of gametocytes in bloodstream should be considered to improve diagnosis and test new malaria control strategies.</span></p>
Data from: Contrasting effects of host identity, plant community, and local species pool on the composition and colonisation levels of arbuscular mycorrhizal fungal community in a temperate grassland
Arbuscular mycorrhizal fungi (AMF) are important plant symbionts, but we know little about the effects of plant taxonomic identity or functional group on the AMF community composition. To examine effects of the surrounding plant community, of host, and of the AMF pool on the AMF community in plant roots, we manipulated plant community composition in a long-term field experiment. Within four types of manipulated grassland plots, seedlings of eight grassland plant species were planted for 12 weeks, and AMF in their roots were quantified. Additionally, we characterised the AMF community of individual plots (as their AMF pool) and quantified plot abiotic conditions. The largest determinant of AMF community composition was the pool of available AMF, varying at metre scale due to changing soil conditions. The second strongest predictor was the host functional group. The differences between grasses and dicotyledonous forbs in AMF community variation and diversity were much larger than the differences among species within those groups. High cover of forbs in the surrounding plant community had a strong positive effect on AMF colonisation intensity in grass hosts. Using a manipulative field experiment enabled us to demonstrate direct causal effects of plant host and surrounding vegetation.
Data from: Intraspecific variation in host plant traits mediates taxonomic and functional composition of local insect herbivore communities
<p class="abstract_para">Host plant phenotypic traits affect the structure of the associated consumer community and mediate species interactions. We compare herbivore assemblages from the canopy of the phenotypically variable tree <em class="fi">Metrosideros polymorpha</em> on Hawai'i Island. Multiple distinct varieties of <em class="fi">M. polymorpha</em> frequently co‐occur, with variation in morphological traits. Using this system, we identify host and insect traits that underlie patterns of herbivore abundance and quantify the strength of host‐insect trait interactions.</p> <p class="abstract_para">The dataset includes host plant phenotypic traits (specific leaf area, leaf water content, foliar nutrients, trichome presence), as well as collection information. The dataset also contains the herbivorous insect community associated with this host plant, their abundances and life history traits. R code for analyses in this article is also included.</p>
Data from: Host-plant use of a polyphagous mirid, Apolygus lucorum: molecular evidence from migratory individuals
While the host-plant use of insect herbivores is important for understanding their interactions and coevolution, field evidence of these preferences is limited for generalist species. Molecular diet analysis provides an effective option for gaining such information, but data from field-sampled individuals are often greatly affected by the local composition of their host plants. The polyphagous mirid bug Apolygus lucorum (Meyer-Dür) seasonally migrates across the Bohai Sea, and molecular analysis of migrant bugs collected on crop-free islands can be used to estimate the host-plant use of A. lucorum across the large area (northern China) from where these individuals come. In this study, the host-plant use of A. lucorum adults was determined by identifying plant DNA using a three-locus DNA barcode (rbcL, trnH-psbA and ITS) in the gut of migrant individuals collected on Beihuang Island. We successfully identified the host plant families of A. lucorum adults, and the results indicated that captured bugs fed on at least 17 plant families. In addition, gut analyses revealed that 35.9% of A. lucorum individuals fed on multiple host plants but that most individuals (64.1%) fed on only one plant species. Cotton, Gossypium hirsutum L., DNA was found in 35.8% of the A. lucorum bugs examined, which was much higher than the percentage of bugs in which other host plants were found. Our work provides a new understanding of multiple host-plant use by A. lucorum under natural conditions, and these findings are available for developing effective management strategies against this polyphagous pest species.
Data from: Tandem host-parasite dispersal inferred from similarities in phylogeographic patterns among little penguins and their 'terrestrial' ectoparasites
Aim Organisms with poor intrinsic dispersal capacity, such as parasites, often rely entirely on transport with host species that have a greater dispersal capacity. Penguins, for example, are exploited by terrestrial ectoparasites when they come ashore to breed. Recent research indicates that little penguin (Eudyptula minor and E. novaehollandiae) hard ticks (Ixodes eudyptidis and I. kohlsi) may be capable of surviving short periods (days) at sea with their hosts, but their capacity to survive longer voyages (weeks) is not known. We here aimed to assess whether phylogeographic patterns in little penguins and their ticks indicate that the terrestrial ectoparasites are able to disperse long distances at sea with their swimming hosts. Location Southern Australia and New Zealand. Taxon Ixodes eudyptidis and I. kohlsi ticks. Methods We conducted a broad-scale genomic assessment of little penguin ticks from across their hosts' ranges in Australia and New Zealand. Using Genotyping by Sequencing (GBS), we generated SNP data sets from ticks from 14 penguin colonies, and analysed phylogeographic structure. We included ticks from some sympatric flighted seabirds to verify host-specificity. Results We resolved two distinct lineages of Ixodes from little penguins, with one restricted to Australia, and the other found throughout New Zealand and in low numbers at some eastern Australian sites. Both lineages exhibited phylogeographic structure consistent with patterns observed in their hosts, with some evidence of occasional oceanic dispersal, including across the Tasman Sea between Australia and New Zealand. Ticks from sympatric short-tailed shearwaters (Ardenna tenuirostris), which disperse aerially, were genetically distinct from those collected from little penguins, supporting prior evidence of host-specificity in seabird ticks. Main conclusions The most parsimonious explanation for our results is that ticks can travel at sea with little penguins. We infer that some terrestrial ectoparasites associated with aquatically-dispersing hosts have evolved the capacity to survive oceanic voyages.
Data from: Molecular biogeography and host relations of a parasitoid fly
Successful geographic range expansion by parasites and parasitoids may also require host range expansion. Thus the evolutionary advantages of host specialization may trade off against the ability to exploit new host species encountered in new geographic regions. Here we use molecular techniques and confirmed host records to examine biogeography, population divergence, and host flexibility of the parasitoid fly, Ormia ochracea (Bigot). Gravid females of this fly find their cricket hosts acoustically by eavesdropping on male cricket calling songs; these songs vary greatly among the known host species of crickets. Using both nuclear and mitochondrial genetic markers, we (1) describe the geographical distribution and sub-division of genetic variation in O. ochracea from across the continental United States, the Mexican states of Sonora and Oaxaca, and populations introduced to Hawaii; (2) demonstrate that the distribution of genetic variation among fly populations is consistent with a single widespread species with regional host specialization, rather than locally differentiated cryptic species, (3) identify the more-probable source populations for the flies introduced to the Hawaiian islands; (4) examine genetic variation and sub-structure within Hawaii; (5) show that among-population geographic, genetic, and host song distances are all correlated, and (6) discuss specialization and lability in host-finding behavior in light of the diversity of cricket songs serving as host cues in different geographically separate populations.
Data from: The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs
How can we explain morphological variations in a holobiont? The genetic determinism of phenotypes is not always obvious and could be circumstantial in complex organisms. In symbiotic cnidarians, it is known that morphology or colour can misrepresent a complex genetic and symbiotic diversity. Anemonia viridis is a symbiotic sea anemone from temperate seas. This species displays different colour morphs based on pigment content and lives in a wide geographical range. Here, we investigated whether colour morph differentiation correlated with host genetic diversity or associated symbiotic genetic diversity by using RAD-sequencing and symbiotic dinoflagellate typing of 140 sea anemones from the English Channel and the Mediterranean Sea. We did not observe genetic differentiation among colour morphs of A. viridis at the animal host or symbiont level, rejecting the hypothesis that A. viridis colour morphs correspond to species level differences. Interestingly, we however identified at least four independent animal host genetic lineages in A. viridis that differed in their associated symbiont populations. In conclusion, although the functional role of the different morphotypes of A. viridis remains to be determined, our approach provides new insights on the existence of cryptic species within A. viridis.
Data from: Fecundity compensation is dependent on the generalised stress response in a nematode host
Background: Fecundity compensation, increased offspring output following parasite exposure, is widely reported, but the underlying mechanisms remain unclear. General stress responses are linked to other indirect defences against parasites, and therefore may be responsible. We challenged strains of Caenorhabditis elegans (wild-type and mutants with compromised or strengthened stress responses) with Staphylococcus aureus. Results: In all strains except the compromised stress response mutant, we saw elevated offspring production if hosts survived initial parasite exposure. Conclusion: We infer that general stress responses are linked with fecundity compensation. These results may explain why trade-offs are not observed among parasite defence mechanisms.
Data from: Parasite infection leads to widespread glucocorticoid hormone increases in vertebrate hosts: a meta-analysis
1. Parasites and pathogens (hereafter parasites) commonly challenge organisms, but the extent to which their infections are physiologically stressful to hosts remains unclear. Importantly, vertebrate hormones, glucocorticoids (GCs), have been reported to increase, decrease, or show no alterations stemming from infections, challenging the generality of parasite-associated GC responses and motivating a search for important moderator variables. 2. We undertook the first meta-analysis of changes in vertebrate GCs following experimental infection with parasites, extracting 146 effect sizes from 42 studies involving 32 host and 32 parasite species to test for general patterns of GC following infection, as well as the influence of moderators. 3. Overall, infection increased GCs relative to preliminary or control levels when the single largest effect sizes from repeated measures studies were examined, suggesting that parasites of vertebrate hosts can be thought of generally as physiological stressors by elevating GCs. 4. When all effect sizes were included along with the moderator of sampling time post-infection (tPI), parasite infection still had a positive effect on host GCs. However, the strength of that effect did not relate consistently to tPI, illustrating temporal differences in GC changes during the course of infection among parasite taxa (e.g., arthropod versus bacterial infections). Other moderator variables examined did not influence GC responses. 5. Studies broadening the range of host and parasite taxa, and sampling during critical time windows, would aid in our understanding of variation in the host stress response and its consequences for fitness of both vertebrate hosts and their parasites. 25-Sep-2019
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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.