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opencc-by-4.0Sep 2021View details →

SARS-CoV-2–host proteome interactions for antiviral drug discovery

Images and datasets used in Fig 6 and corresponding supplementary material Image analysis was performed with Harmony 4.9 software (PerkinElmer) with feature extraction and linear classification of N-protein positive cells from the total population as presented in the PlateResults file. Prism files (GraphPad Software) include the calculations for curve fits of drug testing data (4PL logistic regression) as well as area under the curve (AUC) of the fitted curves..

Data from: Predator performance and fitness Is dictated by herbivore prey type plus indirect effects of their host plant

Animals, including herbivores and predators, use diet-mixing to balance their macro- and micronutrient intake. Recent work demonstrated that lady beetles fed only pea aphids from fava beans had reduced fitness caused by a deficiency of dietary sterols. However, beetles redressed this deficit by eating fava bean leaves. In the current study we used Coccinella septempunctata as a model to test the hypotheses that pea aphids are a poor sterol resource independent of their host plant, and that fava beans produce low quality prey regardless of aphid species. Additionally, we tested the reproductive rescue capacity of alfalfa and barley foliage compared to fava, and profiled the sterols of phloem exudates, foliage, and aphids reared on these different hosts. Beetle fecundity and egg viability was significantly better when provided pea aphids reared on alfalfa (compared to fava beans) and green peach aphids reared on fava plants. Alfalfa and barley leaves were not consumed by beetles and did not support beetle reproduction. The sterol profile of aphids largely reflected their host plant phloem. However, green peach aphids from fava acquired 125-times more sterol than pea aphids from fava. Our findings show how the sterol content of different host-plants can affect the third trophic level. Our results suggest that 1) prey quality varies depending on prey species, even when they occur on the same plant, 2) plant species can mediate prey quality, 3) host plant-mediated effects on prey quality partially drive omnivory, and 4) diet-mixing benefits growth and reproduction by redressing micronutrient deficits.

Data from: Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)

Previous work, using morphological characters, identified a generalist copepod parasite (Pharodes tortugensis) at high prevalence on two common gobies (Coryphopterus glaucofraenum and C. dicrus) in the British Virgin Islands (BVI). DNA barcoding subsequently revealed C. glaucofraenum to be three morphologically similar species (C. glaucofraenum, C. venezuelae and C. tortugae), casting doubt on host identities in the BVI and the classification of the parasite as a single species. Mitochondrial cytochrome c oxidase subunit I (COI) data from 67 gobies in the BVI showed that, in addition to C. dicrus, host gobies were a mix of C. glaucofraenum and C. venezuelae, while C. tortugae was unexpectedly absent from the study area. COI data (n = 70) indicated that the copepod infecting all three hosts was a single species, almost certainly P. tortugensis. The pharodes–coryphopterus interaction has a strong impact on host dynamics in the BVI, and a revised understanding of these dynamics must account for any differences among the three newly confirmed hosts in transmission of, and susceptibility to, the shared parasite. No other infected hosts were discovered at our sites, but P. tortugensis is reportedly widespread and infects 12 additional host species elsewhere. Further DNA barcoding is thus needed to test whether P. tortugensis is truly a widespread generalist, or instead represents a group of more specialized cryptic species.

Data from: Endophytes shape the legacy left by the above- and below ground litter of the host affecting the establishment of a legume

Plant litter is a key component of plant-soil feedback (PSF), given its strong potential impacts on plant establishment and growth, through chemical and physical pathways. Although PSF of the layer of dead plant material on the soil surface (aboveground litter) has been widely studied little is known about the role of dead roots (belowground litter) and the impact of plant symbionts on host litter legacy. Here, we examined whether the fungal endophyte Epichloë occultans changed the effects of above and belowground litter of Lolium multiflorum plants on the establishment of Trifolium repens. We hypothesized that both types of litter deposited by the grass-endophyte symbiosis reduce the establishment of the legume due to the release of allelopathic compounds during the decomposition and leaching processes. To test this, we performed two experiments with different quantities of litter produced by plants of the same grass population, with high and low levels of endophyte infection (E+ and E-). Seeds of T. repens were exposed to the aboveground litter with or without the addition of belowground litter, or to their leachates, to separate the physical and chemical pathways. We found that the treatments with the combination of the above and belowground litter produced by E+ plants, increased the germination speed and seedling emergence of T. repens by 56% compared with both types of litter produced by E- plants. A similar effect was also observed with only the aboveground litter. However, the belowground litter of E+ plants reduced the germination speed, seedling emergence by 76% and establishment of T. repens by 73% compared with the belowground litter of E- plants. Besides, the belowground litter had positive effects on the root colonization by arbuscular mycorrhizal fungi and reduced the root nodulation of T. repens. The quantity of litter did not affect any of these responses. Our results suggest that these litter legacy effects could be due to the release of endophyte induced secondary metabolites, such as phenolic and flavonoid compounds. Changes in host plant litter inputs may have consequences for the prevalence of legume plants in grasslands and pastures, affecting their quality and dynamics.

Alternative developmental and transcriptomic responses to host plant water limitation in a butterfly metapopulation

The dataset is from a study examining the effects of host plant water stress on the developmental and transcriptomic responses of its specialist Lepidopteran herbivore. The study combines host plant metabolic profiling with development assays and full-transcriptome sequencing of herbivore larvae. First, we profiled metabolic differences between well-watered and water-limited ribwort plantain (Plantago lanceolata) using proton nuclear magnetic resonance spectroscopy (1H-NMR). Second, we tested how performance of developing Glanville fritillary (Melitaea cinxia) larvae was affected by host plant water limitation experienced at different larval developmental stages. Third, we examined larval gene regulatory responses to water limited host plants by sequencing full transcriptomes of 77 female larvae (RNA seq). Finally, to examine intrapopulation variation in the responses of the larvae, we compared the phenotypic and transcriptomic responses across full-sib families originating from different parts of the metapopulation. In this dataset, we provide data for the P. lanceolata metabolite responses to water limitation and developmental responses of the M. cinxia larvae to feeding on water limited P. lanceolata. The transcriptomic data are available from NCBI's Gene Expression Omnibus, with the accession number GSE159376.

A geographic mosaic of coevolution between Eurosta solidaginis (Fitch) and its host plant tall goldenrod Solidago altissima (L.)

A geographic mosaic of coevolution has produced local reciprocal adaptation in tall goldenrod, Solidago altissima (L.), and the goldenrod ball gall fly, Eurosta solidaginis (Fitch 1855). The fly is selected to induce gall diameters that minimize mortality from natural enemies, and the plant is selected to limit gall growth that reduces plant fitness. We conducted a double reciprocal transplant experiment where S. altissima and E. solidaginis from three sites were grown in gardens at each site to partition the gall morphology variation into fly genotype, plant genotype, and the environment components. The host plant gall diameter induced by each E. solidaginis population was adapted to inhibit local natural enemies from ovipositing on or consuming enclosed larvae. Reciprocally, increasing the gall size induced by the local fly population increased the resistance of the local plant host population to gall growth. Differences among sites in natural enemies produced a mosaic of hotspots of coevolutionary arms races between flies selecting for greater gall diameter and plants for smaller diameters, and coldspots where there is no selection on plant or fly for a change in gall diameter. In contrast, the geographic variations of gall length and gall shape were not due to coevolutionary interactions.

opencc-zeroOct 2022View details →

Gastrointestinal helminths increase Bordetella bronchiseptica shedding and host variation in supershedding

Co-infected hosts, individuals that carry more than one infectious agent at any one time, have been suggested to facilitate pathogen transmission, including the emergence of supershedding events. However, how the host immune response mediates the interactions between co-infecting pathogens and how these affect the dynamics of shedding remains largely unclear. We used laboratory experiments and a modeling approach to examine temporal changes in the shedding of the respiratory bacterium Bordetella bronchiseptica in rabbits with one or two gastrointestinal helminth species. Experimental data showed that rabbits co-infected with one or both helminths shed significantly more B. bronchiseptica, by direct contact with an agar petri dish than rabbits with bacteria alone. Co-infected hosts generated supershedding events of higher intensity and more frequently than hosts with no helminths. To explain this variation in shedding an infection-immune model was developed and fitted to rabbits of each group. Simulations suggested that differences in the magnitude and duration of shedding could be explained by the effect of the two helminths on the relative contribution of neutrophils and specific IgA and IgG to B. bronchiseptica neutralization in the respiratory tract. However, the interactions between infection and immune response at the scale of analysis that we used could not capture the rapid variation in the intensity of shedding of every rabbit. We suggest that fast and local changes at the level of respiratory tissue probably played a more important role. This study indicates that co-infected hosts are an important source of variation in shedding, and provides a quantitative explanation of the role of helminths in the dynamics of respiratory bacterial infections.

opencc-by-4.0Jan 2022View details →

Host phylogeny and elevation predict infection by avian haemosporidians in a diverse New Guinean bird community (R script for analyses, figures, and supplemental figures )

This script performs the glmm analysis of the elevation and infection prevalence data as well as the script required to generate the figures in the article.

opencc-zeroOct 2022View details →

Parasitism shapes selection by drastically reducing host fitness and increasing host fitness variation

Determining the effects of parasites on host reproduction is key to understanding how parasites affect the underpinnings of selection on hosts. Although infection is expected to be costly, reducing mean fitness, infection could also increase variation in fitness costs among hosts, both of which determine the potential for selection on hosts. To test these ideas, we used a phylogenetically informed meta-analysis of 118 studies to examine how changes in the mean and variance in the outcome of reproduction differed between parasitized and non-parasitized hosts. We found that parasites had severe negative effects on mean fitness, with parasitized hosts suffering reductions in fecundity, viability, and mating success. Parasite infection also increased variance in reproduction, particularly fecundity and offspring viability. Surprisingly, parasites had similar effects on viability when either the male or female was parasitized. These results not only provide the first synthetic, comparative, and quantitative summary of the strong deleterious effects of parasites on host reproductive fitness, but also reveal a consistent role for parasites in shaping the opportunity for selection.

Data from: Arbuscular mycorrhizal fungi communities shaped by host-plant affect the outcome of plant-soil feedback in dryland restoration

1. Plant inoculation with Arbuscular mycorrhizal fungi (AMF) can be a useful tool to overcome challenges in dry forest restoration. However, advances are still needed to guide choices regarding soil origin and inoculum production methods, since outcomes can vary due to plant-soil feedbacks (PSF). We evaluate how soil origin and host plant used for inoculum production affect AMF community and therefore the plant biomass accumulation and functional traits. 2. In the conditioning phase, we investigated whether soils originating from a recovered area (Quarry) and a vegetation fragment (Caatinga) would have their AMF communities modified due to the growth of Sorghum bicolor (used for inoculum production) and Senna uniflora (used in Brazilian semiarid restoration). In the feedback phase, we compared the performance of four plants species growing on a degraded soil and inoculated or not by a mixture of AMF isolates in comparison to soil inoculum prepared from the conditioning phase. 3. The inoculum from Caatinga presented seven times more AMF species compared to that from the Quarry, which presented ruderal and stress tolerant species. The soil inoculum conditioned by S. uniflora, regardless of origin, presented greater evenness compared to the soil inoculum produced with S. bicolor and promoted 33% more plant biomass compared to the control without inoculation. Root colonization by AMF increased PSF and decreased plant investment in functional traits such as specific root length (SRL) and specific leaf area (SLA). 4. Our results demonstrate the importance of adopting strategies that preserve local adaptation of inoculants produced. The use of native plant for propagation of native AMF in the conditioning phase provided more positive responses for Mesosphaerum suaveolens and Rhaphiodon echinus than inoculated with introduced AMF isolates. This is probably due to the interaction of inoculated plants with responsive AMF present in the soil. 5. Synthesis and applications: Our study shows that conditioning field-collected soil with S. uniflora and using it for inoculation can be a simple technique to promote biomass accumulation for other native herbaceous species. This preserves the compatibility between the soil inoculum produced with native AMF and native plants, representing an important tool for restoration programs.

Helminth-associated changes in host immune phenotype connect top-down and bottom-up interactions during co-infection

Within-host parasite interactions can be mediated by the host and changes in host phenotypes often serve as indicators of the presence or intensity of parasite interactions. Parasites like helminths induce a range of physiological, morphological, and immunological changes in hosts that can drive bottom-up (resource-mediated) or top-down (immune-mediated) interactions with co-infecting parasites. Although top-down and bottom-up interactions are typically studied in isolation, the diverse phenotypic changes induced by parasite infection may serve as a useful tool for understanding if, and when, these processes act in concert. Using an anthelmintic treatment study of African buffalo (Syncerus caffer), we tracked changes in host immunological and morphological phenotypes during helminth-coccidia co-infection to investigate their role in driving independent and combinatorial bottom-up and top-down parasite interactions. We also examined repercussions for host fitness. Clearance of a blood-sucking helminth, Haemonchus, from the host gastrointestinal tract induced a systemic Th2 immune phenotype, while clearance of a tissue-feeding helminth, Cooperia, induced a systemic Th1 phenotype. Furthermore, the Haemonchus-associated systemic Th2 immune phenotype drove simultaneous top-down and bottom-up effects that increased coccidia shedding by changing the immunological and morphological landscapes of the intestine. Higher coccidia shedding was associated with lower host body condition, a lower chance of pregnancy, and older age at first pregnancy, suggesting that coccidia infection imposed significant condition and reproductive costs on the host. Our findings suggest that top-down and bottom-up interactions may commonly co-occur and that tracking key host phenotypes that change in response to infection can help uncover complex pathways by which parasites interact.

opencc-by-4.0Nov 2022View details →

No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host - Phenotype dataset

The present dataset contains all the phenotype data (.csv files) and R scripts used for data analysis, and to generated the figures (Figures 2 to 5) present in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host". The uploaded archive (.zip) contains 4 folders corresponding to the 4 Figures present in the manuscript (Figure 2, Figure 3, Figure 4 and Figure 5). Each folder contains the phenotype data tables (.csv files), a R script used to analyze the data and to generate the Figures and a readme file, explaining how the phenotype data tables are organized.

Population-specific responses of an insect herbivore to variation in host-plant quality

Anthropogenic climate change poses a substantial challenge to many organisms, to which they need to respond to avoid fitness reductions. Investigating responses to environmental change is particularly interesting in herbivores, as they are potentially affected by indirect effects mediated via variation in host-plant quality. We here use the herbivorous insect Pieris napi to investigate geographic variation in the response to variation in food quality. We performed a common garden experiment using replicated populations from Germany and Italy, and manipulating host quality by growing host plants at different temperature and water regimes. We found that feeding on plants grown at a higher temperature generally diminished the performance of P. napi, evidenced by a prolonged development time and reduced larval growth rate, body mass, fat content, and phenoloxidase activity. Genotype by environment interactions (G x E) were present in several performance traits, indicating that Italian populations (1) respond more strongly to variation in host-plant quality and (2) are more sensitive to poor food quality than German ones. This may reflect a cost of the rapid lifestyle found in Italian populations. Consequently, German populations may be more resilient against environmental perturbations and may perhaps even benefit from warmer temperatures, while Italian populations will likely suffer from the concomitantly reduced host-plant quality. Our study thus exemplifies how investigating G x E may help to better understand the vulnerability of populations to climate change.

Data for: Polymorphism at the nestling stage and host-specific mimicry in an Australasian cuckoo-host arms race

Decades of research have shown that the coevolutionary arms race between avian brood parasites and their hosts can promote phenotypic diversification in hosts and brood parasites. However, relatively little is known about the role of brood parasitism in promoting phenotypic diversification of nestlings. We review field data collected over four decades in Australia, New Caledonia and New Zealand to assess potential for coevolutionary interactions between the shining bronze-cuckoo (Chalcites lucidus) and its hosts, and how diversification at the nestling stage may be generating different subspecies. The shining bronze-cuckoo is a specialist parasite of a few hosts in the family Acanthizidae. It has diversified into subspecies, of which the nestlings closely mimic the respective host nestlings in each region. Additionally, some cuckoo subspecies have polymorphic nestlings. The Acanthizidae hosts have similar breeding and nesting habits and only moderately effective frontline defences against parasitism at cuckoo egg laying or at the egg stages. However, some hosts have developed highly effective defences at the nestling stage by recognising and ejecting cuckoo nestlings from the nest. As with the cuckoo nestlings, some hosts have polymorphic nestlings. The coevolutionary interactions in each region suggest different evolutionary stages of the arms race in which either the parasite or the host is currently in the lead. The presence of moderately effective defences at the egg laying and egg stages might explain why some hosts do not have defences at the nestling stage. The south-Pacific cuckoo – host systems are excellent models to explore the evolutionary mechanisms driving the diversification at the nestling stage in the coevolutionary arms race between avian brood parasites and their hosts.

Data for: Ectoparasite population dynamics affected by host body size but not host density or water temperature in a 32-year long time series

Host density, host body size, and ambient temperature have all been positively associated with increases in parasite infection. However, the relative importance of these factors in shaping long-term parasite population dynamics in wild host populations is unknown due to the absence of long-term studies. Here, we examine long-term drivers of gill lice (Copepoda) infections in Arctic charr (Salmonidae) over 32 years. We predicted that host density and body size and water temperature would all positively affect parasite population size and population growth rate. Our results show that fish size was the main driver of gill lice infections in Arctic charr. In addition, Arctic charr became infected at smaller sizes and with more parasites in years of higher brown trout population size. Negative intraguild interactions between brown trout and Arctic charr appear to drive smaller Arctic charr to seek refuge in deeper areas of the lake, thus increasing infection risk. There was no effect of host density on the force of infection, and the relationship between Arctic charr density and parasite mean abundance was negative, possibly due to an encounter-dilution effect. The population densities of host and parasite fluctuated independently of one another. Water temperature had negligible effects on the temporal dynamics of the gill lice population. Understanding long-term drivers of parasite population dynamics is key for research and management. In fish farms, artificially high densities of hosts lead to vast increases in the transmission of parasitic copepods. However, in wild fish populations fluctuating at natural densities, the surface area available for copepodid attachment might be more important than the density of available hosts.

opencc-zeroDec 2022View details →

Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation and concatenation PCR) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR.

opencc-by-4.0May 2023View details →

[Data S2] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation

Data S2. GLIPH2 hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. For all TCRs within each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), GLIPH2 specificity groups are generated as described in methods.

opencc-by-4.0May 2023View details →

[Data S1] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation

Data S1. ALICE hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. For each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), all ALICE hits generated as described in methods.

opencc-by-4.0May 2023View details →

[Github Sample Dataset] Microbiota dictate T cell clonal selection to promote graft-vs-host disease after stem cell transplantation

[Github Sample Dataset]. This is an accompanying data set for the github repository "https://github.com/acyeh-lab/2023/tree/main/tcr-simulation" referred to in "Non-genetic determinants of clonotypic T cell expansion following stem cell transplantation" by Yeh AC et al.