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openother-openFeb 2022View details →

Data and code for "Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis" by Park et al., iScience 2022

This repository is a part of the supplementary document in Park et al., "Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis" published in iScience 2022. Abstract: To date, there has been no multi-omic analysis characterizing the intricate relationships between the intragastric microbiome and gastric mucosal gene expression in gastric carcinogenesis. Using multi-omic approaches, we provide a comprehensive view of the connections between the microbiome and host gene expression in distinct stages of gastric carcinogenesis (i.e., healthy, gastritis, cancer). We uncover associations specific to disease states. For example, uniquely in gastritis, Helicobacteraceae is highly correlated with the expression of FAM3D, which has been previously implicated in gastrointestinal inflammation. Additionally, in gastric cancer but not in adjacent gastritis, Lachnospiraceae is highly correlated with the expression of UBD, which regulates mitosis and cell cycle time. Furthermore, lower abundances of B cells in gastric cancer compared to gastritis may suggest a previously unidentified immune evasion process in gastric carcinogenesis. Our integrative analysis provides the most comprehensive description of microbial, host transcriptomic, and immune cell factors of the gastric carcinogenesis pathway.

opencc-by-4.0Feb 2022View details →

Raw data for the article: Successful Use of Heterologous CMV-Reactive T Lymphocyte to Treat Severe Refractory Cytomegalovirus (CMV) Infection in a Liver Transplanted Patient: Correlation of the Host Antiviral Immune Reconstitution with CMV Viral Load and CMV miRNome

Cytomegalovirus (CMV) infection is the most significant viral infection in hosts with compromised immune systems as solid organ transplant patients. Despite significant progress being made in the prevention of CMV disease in these patients, further therapeutic strategies for CMV disease and for the CMV reactivation prevention are needed. Here, we describe the outcome of the infusion of in vitro expanded CMV-reactive T-cells, taken from a healthy CMV-seropositive donor, in a liver-transplanted recipient with a refractory recurrent CMV. In this particular case, adoptive transfer of allogenic CMV-reactive T-lymphocytes resulted in the clearance of CMV infection and resolution of the pathological manifestations of the patient. In the study we also investigated circulating miRNAs, both cellular and viral, as potential biomarkers during the course of CMV infection. The results indicate that the infusion of allogenic CMV-reactive T-cells can be an effective strategy to treat CMV infection recurrence when the generation of autologous virus specific T cell clones is not possible.

opencc-by-4.0Feb 2022View details →

Physiological host range of three Trissolcus parasitoids in New Zealand

This archive contains a 'data' folder holding an Excel workbook with the results of no-choice oviposition experiments conducted with Trissolcus basalis (Wollaston) & Trissolcus oenone (Dodd) (Scelionidae: Hymenoptera) and New Zealand species of Pentatomidae. Trissolcus basalis is a biological control agent released in New Zealand in 1949 against Nezara viridula L., and Trissolcus oenone is a native parasitoid also present in Australia. This is the first time the physiological host ranges of each parasitoid have been established quantitatively in New Zealand, and for Trissolcus basalis, this study provides a retrospective view of its physiological host range after 80 years in the country. This workbook also contains a second sheet holding a combined dataset - a combination of results from the previously mentioned study and those from: "Experimental assessment of the biosafety of Trissolcus japonicus in New Zealand, prior to the anticipated arrival of the invasive pest Halyomorpha halys" (DOI: 10.1007/s10526-019-09949-x). The archive also contains a 'src' folder containing an R markdown file with the R code used to perform analyses.

Dataset: "Generalized scaling of spin qubit coherence in over 12,000 host materials"

Accompanying data for the main text and supplemental materials of Generalized scaling of spin qubit coherence in over 12,000 host materials

Challenging a host-pathogen paradigm: Susceptibility to chytridiomycosis is decoupled from genetic erosion

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 Batrachochytrium dendrobatidis (Bd), 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 Bd-naive system of two mainland and two island populations of the common toad (Bufo bufo) 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.

TARA Pacific CDIV cnidarian host taxonomic annotation release version 1_1

This data is the result of the primary analysis of the 18SV9 sequencing data and photos associated with the Coral Diversity dataset collected from all islands as part of the Tara Pacific expedition. A full README is contained within the data upload.

SingleCellExperiment Object MIS-C data (Hoste et al., 2022)

Data from https://rupress.org/jem/article/219/2/e20211381/212918/TIM3-TRBV11-2-T-cells-and-IFN-signature-in

Host preferences inhibit transmission from potential superspreader host species

Host species that are particularly abundant, infectious, and/or infected tend to contribute disproportionately to symbiont (parasite or mutualist) maintenance in multi-host systems. Therefore, in a facultative multi-host system where two host species had high densities, high symbiont infestation intensities, and high infestation prevalence, we expected interspecific transmission rates to be high. Instead, we found that interspecific symbiont transmission rates to caged sentinel hosts were an order of magnitude lower than intraspecific transmission rates in the wild. Using laboratory experiments to decompose transmission rates, we found that opportunities for interspecific transmission were frequent, where interspecific and intraspecific contact rate functions were statistically indistinguishable. But most interspecific contacts did not lead to transmission events due to a previously unrecognized transmission barrier: strong host preferences. During laboratory choice experiments, the symbiont preferred staying on or dispersing to its current host species, even though the oligochaete symbiont is a globally distributed host generalist that can survive and reproduce on many snail species. These surprising results suggest that when managing symbiont transmission, identifying key host species is still important, but it may be equally important to identify and manage transmission barriers that keep potential superspreader host species in check.

Dose relationships can exacerbate, mute, or reverse the impact of heterospecific host density on infection prevalence

The likelihood an individual becomes infected depends on the community in which it is embedded. For environmentally transmitted parasites, host community composition can alter host density, the density of parasites that hosts encounter in the environment, and the dose to which hosts are subsequently exposed. While some multi-host theory incorporates some of these factors (e.g., competition among hosts), it does not currently consider the nonlinear relationships between parasite exposure dose and per-propagule infectivity (dose-infectivity relationships), between exposure dose and infected host mortality (dose-mortality relationships), and between exposure dose and parasite propagule excretion (dose-excretion relationships). This makes it difficult to predict the impact of host species on one another's likelihood of infection. To understand the implications of these non-linear dose relationships for multi-host communities, we first performed a meta-analysis on published dose-infectivity experiments to quantify the proportion of accelerating, linear, or decelerating dose-infectivity relationships; we found that most experiments demonstrated decelerating dose-infectivity relationships. We then explored how dose-infectivity, dose-mortality, and dose-excretion relationships might alter the impact of heterospecific host density on infectious propagule density, infection prevalence, and density of a focal host using two host, one parasite models. We found that dose relationships either decreased the magnitude of the impact of heterospecific host density on propagule density and infection prevalence via negative feedback loops (decelerating dose-infectivity relationships, positive dose-mortality relationships, and negative dose-excretion relationships), or increased the magnitude of the impact of heterospecific host density on infection prevalence via positive feedback loops (accelerating dose-infectivity relationships and positive dose-excretion relationships). Further, positive dose-mortality relationships resulted in hosts that traditionally decrease disease (e.g. low-competence, strong competitors) increasing infection prevalence, and vice versa. Finally, we found that dose-relationships can create positive feedback loops that facilitate friendly competition (i.e., increased heterospecific density has a positive effect on focal host density because the reduction in disease outweighs the negative effects of interspecific competition). This suggests that without taking dose relationships into account, we may incorrectly predict the effect of heterospecific host interactions, and thus host community composition, on environmentally transmitted parasites.

Data from: Parasite-driven cascades or hydra effects: susceptibility and foraging depression shape parasite-host-resource interactions

This contains data for the manuscript listed in the title. We measured the foraging rates of individual zooplankton hosts, Daphnia dentifera, on phytoplankton resources, Ankistrodesmus falcatus, in the presence of fungal parasites of zooplankton, Metschnikowia bicuspidata. Some of these data are previously published (Genotypes12_foraging.csv by Strauss, Alexander T., et al. "Genotypic variation in parasite avoidance behaviour and other mechanistic, nonlinear components of transmission." Proceedings of the Royal Society B 286.1915 (2019): 20192164.) and some are published now for the first time (Genotype3_foraging.csv). In addition, we present novel evidence from a mesocosm experiment (Mesocosm_data1.csv-Mesocosm_data20.csv) of populations of each genotype or each pair of genotypes with phytoplankton resources and fungal parasites present or absent; our last treatment was low or high nutrient supply for the phytoplankton. With data on infection prevalence, host density, and phytoplankton density, we show how host traits and nutrients control outcomes for prevalence, host density, and phytoplankton density. These data may be reused with appropriate citation.

Parasite resistance and parasite tolerance: insights into transgenerational immune priming in an invertebrate host

Parasites impose different selection regimes on their hosts, which respond by increasing their resistance and/or tolerance. Parental challenge with parasites can enhance the immune response of their offspring, a phenomenon documented in invertebrates and termed transgenerational immune priming. We exposed two parental generations of the model organism Daphnia magna to the horizontally-transmitted parasitic yeast Metschnikowia bicuspidata, and recorded resistance- and tolerance-related traits in the offspring generation. We hypothesized that parentally-primed offspring will increase either their resistance or their tolerance to the parasite. Our susceptibility assays revealed no impact of parental exposure on offspring resistance. Nonetheless, different fitness-related traits, which are indicative of tolerance, were altered. Specifically, maternal priming increased offspring production and decreased survival. Grandmaternal priming positively affected age at first reproduction and negatively affected brood size at first reproduction. Interestingly, both maternal and grandmaternal priming significantly reduced within-host parasite proliferation. Nevertheless, Daphnia primed for two consecutive generations had no competitive advantage in comparison to unprimed ones, implying additive maternal and grandmaternal effects. Our findings do not support evidence of transgenerational immune priming from bacterial infections in the same host species, thus emphasizing that transgenerational immune responses may not be consistent even within the same host species.

opencc-by-4.0Oct 2021View details →

Host Faults Database of central Italy

The “Q-host faults database” is an original compilation, on a GIS platform, of Quaternary faults hosting the Structural Sites (SS) of the QUIN 1.0 database and neighboring to them. It is supplementary to: QUaternary fault strain INdicators database - QUIN 1.0 - first release from the Apennines of central Italy by: Giusy Lavecchia1,2, Simone Bello1,2*, Carlo Andrenacci1,2, Daniele Cirillo1,2, Federica Ferrarini1,2, Noemi Vicentini1,2, Rita de Nardis1,2, Gerald Roberts3, Francesco Brozzetti1,2 1: DiSPuTer - Dipartimento di Scienze Psicologiche, della Salute e del Territorio, Università G. d’Annunzio Chieti-Pescara, Chieti, Italy. 2: CRUST - Centro inteRUniversitario per l’analisi Sismotettonica Tridimensionale, Chieti, Italy. 3: Department of Earth and Planetary Sciences, Birkbeck, University of London Corresponding author: Simone Bello (simone.bello@unich.it).

opencc-zeroApr 2022View details →

Host identity matters – up to a point: the community context of Batrachochytrium dendrobatidis transmission

The level of detail on host communities needed to understand multi-host parasite invasions is an unresolved issue in disease ecology. Coarse community metrics that ignore functional differences between hosts, like host species richness, can be good predictors of invasion outcomes. Yet, if host species vary in the extent to which they maintain and transmit infections, then explicitly accounting for those differences may be important. Through controlled mesocosm experiments and modelling, we show that interspecific differences between host species are important for community-wide infection dynamics of the multi-host fungal parasite of amphibians, Batrachochytrium dendrobatidis (Bd), but only up to a point. The most abundant host species in our system, fire salamander larvae (Salamandra salamandra), did not maintain or transmit infections. Rather, two less abundant 'auxiliary' host species, Iberian tree frog (Hyla molleri) and spiny toad (Bufo spinosus) larvae, maintained and transmitted Bd. Frogs had the highest mean rates of Bd shedding, giving them the highest contributions to R0. Toad contributions to R0 were substantial however, and when examining community-level patterns of infection and transmission, the effects of frogs and toads were similar. Specifying more than just host species richness to distinguish salamanders from auxiliary host species was critical for predicting community-level Bd prevalence and transmission. Distinguishing frogs from toads, however, did not improve predictions. These findings demonstrate limitations to the importance of host species identities in multi-host infection dynamics. Host species that exhibit different functional traits, like susceptibility and infectiousness, may play similar epidemiological roles in the broader community.

opencc-zeroApr 2022View details →

Effects of an alternative host on the prevalence and infection intensity of a bumble bee parasite

Several bee parasites are transmitted through flowers, and some of them can infect multiple host species. Given the shared use of flowers by bee species, parasites can potentially encounter multiple host species, which could affect the evolution of parasite virulence. We used the trypanosomatid parasite Crithidia bombi and its host, the common eastern bumble bee (Bombus impatiens), to explore the effect of infecting an alternative host, the alfalfa leaf-cutter bee (Megachile rotundata), on parasite infectivity and ability to replicate. We conducted a serial passage experiment on primary and alternative hosts, assessing infectivity and intensity of infection during five passes. Parasite cells from each pass through the alternative host were also used to infect a group of primary hosts. We found that serial passes through the alternative host increased infectivity, but there was no effect on intensity of infection. Interestingly, both the probability and intensity of infection on the primary host increased after serial passage through the alternative host. This increase in intensity of infection could be due to maladaptation after selection of new C. bombi strains has occurred in the alternative host. This study suggests that host switching has the potential to affect the adaptation of bee parasites to their hosts.

Beyond single host, single parasite interactions: quantifying competence for complete multi-host, multi-parasite communities

Understanding parasite transmission in communities requires knowledge of each species' capacity to support transmission. This property, "competence", is a critical currency for modeling transmission under community change and for testing diversity-disease theory. Despite the central role of competence in disease ecology, we lack a clear understanding of the factors that generate competence and drive its variation. We developed novel conceptual and quantitative approaches to systematically quantify competence for a multi-host, multi-parasite community. We applied our framework to an extensive dataset: five amphibian host species exposed to four parasitic trematode species across five ecologically realistic exposure doses. Together, this experimental design captured twenty host-parasite interactions while integrating important information on variation in parasite exposure. Using experimental infection assays, we measured multiple components of the infection process and combined them to produce competence estimates for each interaction. With directly estimated competence values, we asked which components of the infection process best explained variation in competence: barrier resistance (the initial fraction of administered parasites blocked from infecting a host), internal clearance (the fraction of established parasites lost over time) or pre-transmission mortality (the probability of host death prior to transmission). We found that variation in competence among the twenty interactions was best explained by differences in barrier resistance and pre-transmission mortality, underscoring the importance of host resistance and parasite pathogenicity in shaping competence. We also produced dose-integrated estimates of competence that incorporated natural variation in exposure to address questions on the basis and extent of variation in competence. We found strong signals that host species identity shaped competence variation (as opposed to parasite species identity). While variation in infection outcomes across hosts, parasites, individuals, and doses was considerable, individual heterogeneity was limited compared to among-species differences. This finding highlights the robustness of our competence estimates and suggests that species-level values may be strong predictors for community-level transmission in natural systems. Competence emerges from distinct underlying processes and can have strong species-level characteristics; thus, this property has great potential for linking mechanisms of infection to epidemiological patterns.

Microclimate and host body condition influence mite population growth in a wild bird-ectoparasite system

Parasite populations are never evenly distributed among the hosts they infect. Avian nest ectoparasites, such as mites, are no exception, as their distribution across the landscape is highly aggregated. It remains unclear if this pattern is driven by differences in transmission events alone, or if the environment that parasites inhabit after transmission also plays a role. Here, we experimentally examined the influence of the post-transmission microclimate, nest characteristics, and host condition on ectoparasite population growth in a bird-ectoparasite system. We infested barn swallow (Hirundo rustica erythrogaster) nests with a standardized number of Northern Fowl Mites (Ornithonyssus sylvarium) and analyzed both biotic (nestling mass, wing length, number of other arthropods present in the nest, and brood size) and abiotic (temperature, humidity, nest lining, nest dimensions, and substrate upon which the nest was built) predictors of mite population growth. Our results suggest that mite populations were most successful, in terms of growth, in nests with higher temperatures, lower humidity, few other arthropods, and hosts in good condition. We also found that nests built on wooden substrates support larger populations of mites than those constructed on metal or concrete. These findings lend insight into the factors that drive large-scale patterns of ectoparasite distributions.

opencc-by-4.0May 2022View details →

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages.

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages. preprint, bioRxiv, 2022. DOI: 10.1101/2022.05.06.490883 Each zip file contains the raw computational data (as a gzip compressed tarball), YAML input files, as well as Python plotting scripts. The Python plotting scripts have dependencies on the packages: tarfile, multiprocessing, numpy, scipy, and matplotlib. Note that the Python plotting scripts plot directly from the gzip compressed tarballs. The corresponding code can be found on GitHub: https://github.com/Ruth-Bowness-Group/CAModel

Figure 13 in Geographic variation in host selection in the spider wasps Entypus unifasciatus (Say) and Tachypompilus ferrugineus (Say) (Hymenoptera: Pompilidae), II

Figure 13. Host spider family distribution for Entypus unifasciatus.

Host-parasite interactions between a copepod (Pharodes tortugensis) and small reef-associated gobies (Coryphopterus) in the British Virgin Islands

The effects of parasitic copepods on free-living hosts are infrequently documented, and the copepod Pharodes tortugensis has remained virtually unstudied since described. For the first time, we document its host range in the British Virgin Islands (BVI), the prevalence and intensity of infections on wild hosts, and its impacts on host morphology and performance. Infections were observed on four benthic gobies in the BVI (Coryphopterus glaucofraenum, C. venezuelae, C. dicrus and C. eidolon) but not on other host species previously reported from other parts of the western Atlantic. Infected gobies were widespread in the BVI (detected at 33 of 52 sites, prevalence from 1–25%) but extremely rare elsewhere in the Caribbean (detected at 2 of 16 sites, prevalence <0.006%). As is typical of macroparasite infections, P. tortugensis was over-dispersed in BVI host populations (mean intensity = 4.7, range = 1–17). Infections were most common in juvenile and female hosts, and rarely found in larger male hosts. The copepods attach in the branchial chamber of the goby; female copepods show high attachment fidelity to the ventral surface of the chamber, while male copepods attached most often to the first two gill arches and in the branchial chamber adjacent to the female. Infections caused substantial damage to the host's branchial chamber and gill filaments. Parasitized gobies also had larger livers and smaller gonads than unparasitized individuals of similar length. The changes in organ mass of infected gobies were not sizeable enough to affect total body mass, and host condition (the body-length vs. body-mass relationship) was similar for gobies with and without infections. Parasitized gobies were, however, significantly smaller in body mass at a given age, reflecting slower overall growth. Effects of P. tortugensis on individual hosts were broadly similar to those of other parasitic copepods that infect fish gills and, for unknown reasons, the BVI appears to be a persistent hotspot of infections on these goby hosts.

Data from: A role for the local environment in driving species-specific parasitism in a multi-host parasite system

The extent and magnitude of parasitism often vary among closely related host species and across populations within species. Determining the ecological basis for this species and population-level variation in parasitism is critical for understanding infection dynamics in multi-host-parasite systems. To investigate such ecological underpinnings of variation in parasitism, we studied Enallagma damselflies host species and their water mite (Arrenurus spp.) ectoparasites in lakes. We first evaluated how host identity and density could shape parasitism. To test the effects of con- and heterospecific host density on parasitism, we used a field experiment with E. basidens and E. signatum. We found that parasitism did not vary with con- or heterospecific density and was determined by host identity alone, with no spillover effects. We also evaluated the potential role of local adaptation and resource availability in shaping parasitism. To do so, we used E. signatum in a reciprocal transplant experiment crossed with a prey resource level manipulation. This experiment revealed that parasitism declined sharply for one host population in its non-local lake, but not the other source population, with no effects of prey levels. This asymmetry implies that damselflies express enhanced defenses against parasitism that are not population specific nor dependent on resource abundance, or that mites developed heightened local host specificity. The results of multivariate modeling from an observational study generally supported these experimental findings: neither host density nor resource abundance strongly explained among population variation in parasitism. Instead, local abiotic conditions (pH) had the strongest relationship with parasitism, with minimal associations with predator density, temperature, and a measure of immune function. Collectively, our findings suggest a crucial role for the local environment in shaping host-parasite interactions within multi-host-parasite systems. More generally, these results show that research at the intersection of community ecology and disease ecology is critical for understanding host-parasite dynamics within natural communities.