Find research datasets worth reusing

Identification of system-level features in HIV migration within a host

Objective: Identify system-level features in HIV migration within a host across body tissues. Evaluate heterogeneity in the presence and magnitude of these features across hosts. Method: Using HIV DNA deep sequencing data generated across multiple tissues from 8 people with HIV, we represent the complex dependencies of HIV migration among tissues as a network and model these networks using the family of exponential random graph models (ERGMs). ERGMs allow for the statistical assessment of whether network features occur more (or less) frequently in viral migration than might be expected by chance. The analysis investigates ve potential features of the viral migration network: (1) bi-directional ow between tissues; (2) preferential migration among tissues in the same biological system; (3) heterogeneity in the level of viral migration related to HIV reservoir size; (4) hierarchical structure of migration; and (5) cyclical migration among several tissues. We calculate the Cohran's Q statistic to assess heterogeneity in the magnitude of the presence of these features across hosts. The analysis adjusts for missing data on body tissues. Results: We observe strong evidence for bi-directional ow between tissues; migration among tissues in the same biological system; and hierarchical structure of the viral migration network. This analysis shows no evidence for differential level of viral migration with respect to the HIV reservoir size of a tissue. There is evidence that cyclical migration among three tissues occurs less frequently than expected given the amount of viral migration. The analysis also provides evidence for heterogeneity in the magnitude that these features are present across hosts. Adjusting for missing tissue data identifies system-level features within a host as well as heterogeneity in the presence of these features across hosts that are not detected when the analysis only considers the observed data. Discussion: Identification of common features in viral migration may increase the efficiency of HIV cure efforts as it enables targeting specific processes.

High physiological function for corals with thermally tolerant, host-adapted symbionts

The flexibility to associate with more than one symbiont may considerably expand a host's niche breadth. Coral animals and dinoflagellate micro-algae represent one of the most functionally integrated and widespread mutualisms between two eukaryotic partners. Symbiont identity greatly affects a coral's ability to cope with extremes in temperature and light. Over its broad distribution across the Eastern Pacific, the ecologically dominant branching coral, Pocillopora grandis, depends on mutualisms with the dinoflagellates Durusdinium glynnii and Cladocopium latusorum. Measurements of skeletal growth, calcification rates, total mass increase, calyx dimensions, reproductive output and response to thermal stress were used to assess the functional performance of these partner combinations. The results show both host–symbiont combinations displayed similar phenotypes; however, significant functional differences emerged when exposed to increased temperatures. Negligible physiological differences in colonies hosting the more thermally tolerant D. glynnii refute the prevailing view that these mutualisms have considerable growth tradeoffs. Well beyond the Eastern Pacific, pocilloporid colonies with D. glynnii are found across the Pacific in warm, environmentally variable, near-shore lagoonal habitats. While rising ocean temperatures threaten the persistence of contemporary coral reefs, lessons from the Eastern Pacific indicate that co-evolved thermally tolerant host–symbiont combinations are likely to expand ecologically and spread geographically to dominate reef ecosystems in the future.

Data from: When perfection isn't enough: host egg signatures are an effective defence against high-fidelity African cuckoo mimicry

Most mimicry systems involve imperfect mimicry, whereas perfect and high-fidelity mimicry are rare. When the fidelity of mimicry is high, mimics might be expected to have the upper hand against their antagonists. However, in coevolving systems, diversification of model phenotypes may provide an evolutionary escape, because mimics cannot simultaneously match all model individuals in the population. Here we investigate high-fidelity mimicry in a highly specialised, Afrotropical brood parasite-host system: the African cuckoo and fork-tailed drongo. Specifically, we test whether host egg polymorphisms are an effective defence against such mimicry. We show, using a combination of image analysis, field experiments, and simulations, that 1) egg colour and pattern mimicry of fork-tailed drongo eggs by African cuckoos is near-perfect on average; 2) drongos show fine-tuned rejection of foreign eggs, exploiting unpredictable pattern differences between parasitic eggs and their own; and 3) the high degree of interclutch variation (polymorphic egg 'signatures') exhibited by drongos gives them the upper hand in the arms race, with 93.7% of cuckoo eggs predicted to be rejected, despite cuckoos mimicking the full range of drongo egg phenotypes. These results demonstrate the effectiveness of model diversification as a defence against mimics, even when mimicry is highly accurate.

Variation among strains of Borrelia burgdorferi in host tissue abundance and lifetime transmission determine the population strain structure in nature

Pathogen life history theory assumes a positive relationship between pathogen load in host tissues and pathogen transmission. Empirical evidence for this relationship is surprisingly rare due to the difficulty of measuring transmission for many pathogens. The comparative method, where a common host is experimentally infected with a set of pathogen strains, is a powerful approach for investigating the relationships between pathogen load and transmission. The validity of such experimental estimates of strain-specific transmission is greatly enhanced if they can predict the pathogen population strain structure in nature. Borrelia burgdorferi is a multi-strain, tick-borne spirochete that causes Lyme disease in North America. This study used 11 field-collected strains of B. burgdorferi, a rodent host (Mus musculus, C3H/HeJ) and its tick vector (Ixodes scapularis) to determine the relationship between pathogen load in host tissues and lifetime host-to-tick transmission (HTT). Mice were experimentally infected via tick bite with 1 of 11 strains. Lifetime HTT was measured by infesting mice with I. scapularis larval ticks on 3 separate occasions. The prevalence and abundance of the strains in the mouse tissues and the ticks were determined by qPCR. We used published databases to obtain estimates of the frequencies of these strains in wild I. scapularis populations. Spirochete loads in ticks and lifetime HTT varied significantly among the 11 strains of B. burgdorferi. Strains with higher spirochete loads in the host tissues were more likely to infect feeding larvae, which molted into nymphs with a higher probability of B. burgdorferi infection (i.e., higher HTT). Our laboratory-based estimates of lifetime HTT were predictive of the frequencies of these strains in wild I. scapularis populations. For B. burgdorferi, the strains that establish high abundance in host tissues and that have high lifetime transmission are the strains that are most common in nature.

Data from: Dissecting molecular evolution of class 1 integron gene cassettes and their bacterial hosts in suburban creeks via epicPCR

Horizontal gene transfer (HGT) of class 1 integrons plays a key role in the dissemination of antimicrobial resistance (AMR) with clinical consequences worldwide. Class 1 integrons in clinical pathogens are commonly associated with AMR genes and embedded in mobile genetic elements. Over time, these mobile class 1 integrons have spread to diverse environmental bacterial hosts via HGT. We applied a single-cell fusion PCR-based technique to link class 1 integron gene cassette arrays to the phylogenetic markers in their bacterial hosts. Class 1 integrons and associated gene cassettes were detected in Alpha- and Gammaproteobacteria hosts from freshwater samples from two creeks in suburban Sydney. Molecular and bioinformatic characterisations of altered gene cassettes generated new insights into mechanisms that contribute to the evolution of class 1 integron gene cassettes. Here, we present experimental and bioinformatic evidence for key signatures of molecular evolution of gene cassettes, including the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an insertion sequence (IS) element. Notably, our experimental testing of a new variant of the aminoglycoside adenylyltransferase encoding aadA11 gene cassette demonstrated that the gain of 5'-UTR contributed to a 3-fold increase in the minimum inhibitory concentration of streptomycin relative to the ancestral reference gene cassette. Understanding these signatures of molecular evolution allows us to explain their effects on AMR phenotypes and offers the potential to better predict evolutionary trajectories of class 1 integrons.

opencc-by-4.0Apr 2023View details →

Understanding the impact of host networking elements on traffic bursts: Raw measurement data

This record contains the raw trace files gathered by the Valinor network traffic burst measurement framework in Redis dump (rdb) format. Please refer to the artifact repository for instructions on how to parse and use the datasets: <a href="https://github.com/hopnets/valinor-rawdata">hopnets/valinor-rawdata: Raw Redis datasets containing the measurement results of Valinor NSDI '23 paper (github.com)</a>

opencc-zeroAug 2023View details →

You are what your host eats: The trophic structure and food chain length of a symbiont community are coupled with the plastic diet of the host ant

Food chain length provides key information on the flow of nutrients and energy in ecosystems. Variation in food chain length has primarily been explained by environmental drivers such as ecosystem size and productivity. Most insights are obtained from theory or aquatic systems, but the importance of these drivers remains largely untested in terrestrial systems. We exploited red wood ant nests markedly differing in size as natural experiments to quantify the drivers of trophic structure and food chain length of their symbiont arthropod communities. Using stable isotopes, we explored the variation in the trophic positions of four symbiont species with the trophic position of the top predator as a proxy for food chain length of the symbiont community. Nest size did not affect food chain length, nor trophic distance between the symbionts. Instead, food chain length and the trophic positions of the symbionts were strongly affected by the host's foraging decisions. When the host diet shifted from predominantly herbivorous to more predacious, the trophic position of the symbionts and food chain length strongly increased. We show for the first time that a food web can be structured by biotic interactions with an engineering species rather than by abiotic environmental variable

opencc-zeroAug 2023View details →

Data from: Host plant height explains the effect of nitrogen enrichment on arbuscular mycorrhizal fungal communities

Nitrogen (N) enrichment is widely known to affect the root-associated arbuscular mycorrhizal fungal (AMF) community in different ways, for example, via altering soil properties and/or shifting host plant functional traits. However, empirical knowledge of their relative importance is still lacking. Using a long-term N addition experiment, we measured the AMF community taxonomic and phylogenetic diversity at the single plant species (roots of 15 plant species) and plant community (mixed roots) levels. We also measured four functional traits of 35 common plant species along the N addition gradient. We found divergent responses of AMF diversity to N addition for host plants with different innate heights (i.e., plant natural height under unfertilized treatment). Furthermore, our data showed that species-specific responses of AMF diversity to N addition were negatively related to the change in maximum plant height. When scaling up to the community level, N addition affected AMF diversity mainly by increasing the maximum plant height, rather than altering soil properties. Our results highlight that plant height drives the AMF community dynamics under nitrogen enrichment at both species and community levels, thus providing important implications for understanding the response of AMF diversity to anthropogenic nitrogen deposition.

opencc-by-4.0Aug 2023View details →

Data for Torppa et al. 2023 'Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety'

The dataset consists of the data that supports the findings of the article 'Soil compaction effects on arbuscular mycorrhizal symbiosis in wheat depend on host plant variety’ written by Torppa et al. and published in Plant and Soil in 2023. The data consists of arbuscular mycorrhizal colonization, fatty acid and community data, as well as soil and crop nutrient and yield data.

opencc-by-4.0Nov 2023View details →

Spatial metatranscriptomics resolves host-bacteria-fungi interactomes, Source Data

Source Data for a publication: Spatial metatranscriptomics resolves host-bacteria-fungi interactomes.  Includes the data sets to generate the results.  Contains five different experiment types: - Pst  bacterial infiltration experiment - Enrichment experiment with different array types - Comparison between SmT vs. Amp-seq - Outdoor-grown leaf experiments - Sterile leaf experiment For each of the experiments are included (if generated, see the README file): - Gene count matrices - Microbial taxa count matrices - Bright field images - Alignment files (Spot files) - Putative microbial reads and related probe information - Data for enrichment analysis - Fluorescent images and corresponding fluorescent values

opencc-zeroDec 2022View details →

Transcriptional patterns of sexual dimorphism and in host developmental programs in the model parasitic nematode Heligmosomoides bakeri

Background Heligmosomoides bakeri (often mistaken for Heligmosomoides polygyrus) is a promising model for parasitic nematodes with the key advantage of being amenable to study and manipulation within a controlled laboratory environment. While draft genome sequences are available for this worm, which allow for comparative genomic analyses between nematodes, there is a notable lack of information on its gene expression. Methods We generated biologically replicated RNA-seq datasets from samples taken throughout the parasitic life of H. bakeri. RNA from tissue-dwelling and lumen-dwelling worms, collected under a dissection microscope, was sequenced on an Illumina platform. Results We find extensive transcriptional sexual dimorphism throughout the fourth larval and adult stages of this parasite and identify alternative splicing, glycosylation, and ubiquitination as particularly important processes for establishing and/or maintaining sex-specific gene expression in this species. We find sex-linked differences in transcription related to aging and oxidative and osmotic stress responses. We observe a starvation-like signature among transcripts whose expression is consistently upregulated in males, which may reflect a higher energy expenditure by male worms. We detect evidence of increased importance for anaerobic respiration among the adult worms, which coincides with the parasite's migration into the physiologically hypoxic environment of the intestinal lumen. Furthermore, we hypothesize that oxygen concentration may be an important driver of the worms encysting in the intestinal mucosa as larvae, which not only fully exposes the worms to their host's immune system but also shapes many of the interactions between the host and parasite. We find stage- and sex-specific variation in the expression of immunomodulatory genes and in anthelmintic targets. Conclusions We examine how different the male and female worms are at the molecular level and describe major developmental events that occur in the worm, which extend our understanding of the interactions between this parasite and its host. In addition to generating new hypotheses for follow-up experiments into the worm's behavior, physiology, and metabolism, our datasets enable future more in-depth comparisons between nematodes to better define the utility of H. bakeri as a model for parasitic nematodes in general.

opencc-by-4.0Sep 2023View details →

SI_IV_3_Reverse chemical ecology to study the defense of the plant host Sextonia rubra and the chemical mediators of its endophyte Fusarium falciforme against phytopathogen Trametes versicolor

Ces travaux présentant les données supplémentaires générés lors de l'étude de la confrontation d'isolat identifiés comme des Fusarium falciforme contre Trametes versicolor.

opencc-zeroSep 2023View details →

Omnivore diet composition effects on parasite load and host weight

Diet composition modulates animals' ability to resist parasites and recover from stress. Broader diet breadths enable omnivores to mount dynamic responses to parasite attack, but little is known about how plant/prey mixing might influence responses to infection. Using omnivorous deer mice (Peromyscus maniculatus) as a model, we examine how varying plant and prey concentrations in blended diets influence resistance and body condition following infestation by Rocky Mountain wood ticks (Dermacentor andersoni). In two repeated experiments, deer mice fed for four weeks on controlled diets that varied in proportions of seeds and insects, were then challenged with 50 tick larvae in two sequential infestations. The numbers of ticks successfully feeding on mice declined by 25% and 66% after the first infestation (in the first and second experiments, respectively), reflecting a pattern of acquired resistance, and resistance was strongest when plant/prey ratios were more equally balanced in mouse diets, relative to seed-dominated diets. Diet also dramatically impacted the capacity of mice to cope with tick infestations. Mice fed insect-rich diets lost 15% of their body weight when parasitized by ticks, while mice fed seed-rich diets lost no weight at all. While mounting/maintaining an immune response may be energetically demanding, mice may compensate for parasitism with fat and carbohydrate-rich diets. Altogether, these results suggest that a diverse nutritional landscape may be key in enabling omnivores' resistance and resilience to infection and immune stressors in their environments.

opencc-by-4.0Sep 2023View details →

Fig. 6 in The Australian issid planthopper genus Orinda Kirkaldy, 1907: New subgenera, new species, host plant and identification key (Hemiptera: Fulgoromorpha: Issidae)

Fig. 6. Orinda spp., distribution map.

opencc-by-4.0Sep 2023View details →

Identifying viral and host genetic determinants of vaccine efficacy

This dataset includes summary statistics results from genetic analyses testing the hypothesis that germline genetic variants are associated with COVID-19 mRNA vaccine efficacy.    These genetic studies include GWAS, HLA-WAS and rare variant gene burden tests.

opencc-zeroOct 2023View details →

Field sampling and DNA-barcoding of fig pollinator wasps across host species and host developmental phase and on non-Ficus controls

To better understand factors that might contribute to this observed range of specificity, we used sticky traps to capture fig-pollinating wasp individuals at 13 Ficus species, sampling at different stages of the reproductive cycle of the host figs (e.g. trees with receptive inflorescences, or vegetative trees, bearing only leaves). We also sampled at other tree species, using them as non-Ficus controls. DNA barcoding allowed us to identify the wasps to species, and therefore assign their presence and abundance to host fig species and the developmental stage of that individual tree. Here we upload the data and the R scripts used to analyze these data.

opencc-zeroOct 2023View details →

A field experiment reveals reciprocal effects of host personality and parasitism in wild lizards

Host behavior and parasite infection reciprocally interact, but this dynamic is rarely studied experimentally in the field with multiple behaviors. Using the dataset provided here, we investigated the interplay between parasitism and host behavior via an in situ experimental tick infestation of a wild population of sleepy lizards, Tiliqua rugosa. Using Bayesian models, we assessed the relationship between experimental infestation and lizard aggression and boldness before and after infestation. First, we tested whether lizard aggression and boldness prior to infestation predicted the probability of tick attachment in the infestation experiment. Second, we evaluated whether experimental infestation affected subsequent lizard aggression and boldness. We found that aggression and boldness related interactively with infestation: for unaggressive lizards, higher boldness was associated with reduced experimental infestation success, but the opposite occurred for aggressive individuals. Second, increased tick infestation did not affect post-infestation aggression, but tended to increase boldness. Taken together, these results highlight the potential for feedbacks between parasites and multi-dimensional host behaviors.

opencc-by-4.0Feb 2015View details →

Figure 1 in Infection behavior, life history, and host parasitism rates of Emblemasoma erro (Diptera: Sarcophagidae), an acoustically hunting parasitoid of the cicada Tibicen dorsatus (Hemiptera: Cicadidae)

Figure 1 Male Tibicen dorsatus, Harvey Co., KS.

opencc-by-4.0Feb 2015View details →

Figure 2 in Infection behavior, life history, and host parasitism rates of Emblemasoma erro (Diptera: Sarcophagidae), an acoustically hunting parasitoid of the cicada Tibicen dorsatus (Hemiptera: Cicadidae)

Figure 2 Female Emblemasoma erro, Ellsworth Co., KS.