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opencc-zeroApr 2024View details →

Data from: A theoretical model for host-controlled regulation of symbiont density

There is growing empirical evidence that hosts (such as insects and corals) actively control the density of their mutualistic symbionts according to their requirements. Such active regulation can be facilitated by compartmentalisation of symbionts within host tissues, which confers a high degree of control of the symbiosis to the host. Here, we build a general theoretical framework to predict the underlying ecological drivers and evolutionary consequences of host-controlled endosymbiont density regulation for a mutualistic association between a host and a compartmentalised, vertically transmitted symbiont. Building on the assumption that the costs and benefits of hosting a symbiont population increase with symbiont density, we use state-dependent dynamic programming to determine an optimal strategy for the host, i.e., that which maximises host fitness, when regulating the density of symbionts. Simulations of active host-controlled regulation governed by the optimal strategy predict that the density of the symbiont should converge to a constant level during host development, and following perturbation. However, a similar trend also emerges from alternative strategies of symbiont regulation. The strategy which maximises host fitness also promotes symbiont fitness compared to alternative strategies, suggesting that active host-controlled regulation of symbiont density could be adaptive for the symbiont as well as the host. Adaptation of the framework allowed the dynamics of symbiont density to be predicted for other host-symbiont ecologies, such as for non-essential symbionts, demonstrating the versatility of this modelling approach.

opencc-by-4.0Apr 2024View details →

Temperature modulates dominance of a superinfecting Arctic virus in its unicellular algal host - Nanopore sequencing reads

Nanopore sequencing reads of two Micromonas polaris viruses, MpoV-45T and MpoV-46T using R9 chemistry.

opencc-by-4.0Feb 2024View details →

Fig. 1 in The great gerbil (RhombomYS opimUS) as a host for tick species in Gurbantunggut Desert

Fig. 1 Sampling sites in Xinjiang Uygur Autonomous Region, northwestern China

opencc-by-4.0Apr 2024View details →

Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes - Identifying the host taxon of a previously undescribed plasmid

We investigated the taxonomic association of an unknown plasmid within a plaque biofilm of a patient diagnosed with stage 3 periodontitis. We combined long- and short- read sequencing to identify a complete plasmid with minimal homology to any sequence in the RefSeq database. The plasmid carried several predicted genes for mobilization and toxin-antitoxin systems. We designed MGE-FISH probes for the plasmid and combined this MGE-FISH stain with an 18-genera HiPR-FISH panel. Images are labeled by collection time such that the laser order for a given field of view (fov) is: 488nm Lambda, 514nm Lambda, 561nm Lambda, 633nm Airyscan, 405nm Lambda. We used Flye (https://github.com/fenderglass/Flye) to assemble the plasmid using long read Nanopore sequencing only and we used OPERA-MS (https://github.com/CSB5/OPERA-MS) to do hybrid assembly with Illumina short reads and Nanopore long reads. The assemblies are in the fasta files and the reads that map to the assemblies are in the fastq files.

opencc-by-4.0Apr 2024View details →

Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes - Combined MGE and taxonomic mapping

We used rRNA-FISH to stain five common oral genera, Veillonella, Streptococcus, Corynebacterium, Lautropia, and Neisseria, each with a different fluorophore, and we used MGE-FISH to stain the termL gene of the active prophage with a sixth fluorophore. We assembled contigs using combined long- and short-read sequencing and identified a highly abundant plasmid. Alignment of this contig to the plasmid database (PLSDB) showed that the plasmid had previously been observed in Prevotella nigrescens (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_018127865.1/). We selected two genes from the contig with metallo-β-lactamase (MBL) domains as targets for MGE-FISH (https://www.uniprot.org/uniprotkb/V8CNR4/entry, https://www.uniprot.org/uniprotkb/V8CNR9/entry). We stained both putative MBL genes (pMBL) with the same color using MGE-FISH. For taxonomic mapping, we broadened our target panel by employing HIPR-FISH. We selected a target panel of 18 genera that are highly abundant and prevalent in human plaque. We designed a HiPR-FISH spectral encoding using a 5-fluorophore combinatorial barcoding scheme, whereby each fluorophore represents a binary bit, providing 31 possible barcodes (2^5 - 1 = 31). The fluorophore for MGE-FISH was spectrally distinct from those of HiPR-FISH, enabling simultaneous implementation of both methods. Images are labeled by collection time such that the laser order for a given field of view (fov) is: 488nm Lambda, 514nm Lambda, 561nm Lambda, 633nm Airyscan, 405nm Lambda. We used OPERA-MS (https://github.com/CSB5/OPERA-MS) to do hybrid assembly with Illumina short reads and Nanopore long reads. The assemblies are in the fasta files and the reads that map to the assemblies are in the fastq files.

Quantifying intraspecific variation in host resistance and tolerance to a lethal pathogen

Testing for intraspecific variation for host tolerance or resistance in wild populations is important for informing conservation decisions about captive breeding, translocation, and disease treatment. Here, we test the importance of tolerance and resistance in multiple populations of boreal toads (Anaxyrus boreas boreas) against Batrachochytrium dendrobatidis (Bd), the amphibian fungal pathogen responsible for the greatest host biodiversity loss due to disease. Boreal toads have severely declined in Colorado (CO) due to Bd, but toad populations challenged with Bd in western Wyoming (WY) appear to be less affected. We used a common garden infection experiment to expose post-metamorphic toads sourced from four populations (2 in CO and 2 in WY) to Bd and monitored changes in mass, pathogen burden, and survival for eight weeks. We used a multi-state modeling approach to estimate weekly survival and transition probabilities between infected and cleared states, reflecting a dynamic infection process that traditional approaches fail to capture. We found that WY boreal toads are more tolerant to Bd infection with higher survival probabilities than those in CO when infected with identical pathogen burdens. WY toads also appeared more resistant to Bd with a higher probability of infection clearance and an average of five days longer to reach peak infection burdens. Our results demonstrate strong intraspecific differences in tolerance and resistance that likely contribute to why population declines vary regionally across this species. Our multi-state framework allowed us to gain inference on typically hidden disease processes when testing for host tolerance or resistance. Our findings demonstrate that describing an entire host species as 'tolerant' or 'resistant' (or lack thereof) is unwise without testing for intraspecific variation.

opencc-by-4.0May 2024View details →

Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought

Plants are colonized by distinct pathogenic and commensal microbiomes across different regions of the globe, but the factors driving their geographic variation are largely unknown. Using 16S rDNA and shotgun sequencing, we characterized the associations of the Arabidopsis thaliana leaf microbiome with host genetics and climate variables from 267 populations in the species’ native range across Europe. Comparing the distribution of the 575 major bacterial amplicon variants (phylotypes), we discovered that microbiome composition in A. thaliana segregates along a latitudinal gradient. The latitudinal clines in microbiome composition are predicted by metrics of drought, but also by the spatial genetics of the host. To validate the relative effects of drought and host genotype we conducted a common garden field study, finding 10% of the core bacteria to be affected directly by drought, and 20% to be affected by host genetic associations with drought. These data provide a valuable resource for the plant microbiome field, with the identified associations suggesting that drought can directly and indirectly shape genetic variation in A. thaliana via the leaf microbiome.

Forest structure and heterogeneity increase diversity and alter the composition of host-parasitoid networks

Antagonistic host-parasitoid interactions can be quantified using bipartite and meta networks, which have the potential to reveal how habitat structural elements relate to this important ecosystem function. Here, we analysed the host-parasitoid interactions of cavity-nesting bees and wasps, as well as their abundance, diversity, and species richness with forest structural elements from 127 forest research plots in southwestern Germany. We found that parasitoid abundance, diversity, and species richness all increase with host abundance, a potential mediator between parasitoids and forest structure. Both parasitoid abundance and diversity increased with stand structural complexity, possibly mediated by the abundance of hosts. Additionally, parasitoid abundance increased with increasing standing deadwood and herb cover. The bipartite networks of host-parasitoid interactions showed higher connectance with increasing standing deadwood, herb cover, and host abundance. Analyses of interactions within the host-parasitoid metanetwork revealed that increasing host abundance and decreasing canopy cover diversify the suites of interactions present at the plot level. These results demonstrate that forest structural elements can improve the stability and resilience of host-parasitoid networks by promoting parasitoids and diversifying interactions in ecological networks.

opencc-by-4.0May 2024View details →

Interfacial host–guest complexation for inverted perovskite solar cells

Characterisation dataset for “Interfacial host–guest complexation for inverted perovskite solar cells”, doi:10.1063/5.0202163, including data for main and supporting figures provided as image (*.png, *.tiff, and *.svg), Origin (*.opju) and *.txt files. NMR data is provided by the TopSpin software, which is available from Bruker.

Data from: Symbiont infection and psyllid haplotype influence phenotypic plasticity during host switching events

Many herbivorous insect species exhibit phenotypic plasticity when using multiple hosts, which facilitates survival in heterogeneous host environments. Physiological host acclimation is an important part of it, yet the effects of host acclimation on insect feeding behavior are not well studied, particularly for insect vectors of plant pathogens. We studied the combined effects of host acclimation and infection with a plant pathogenic symbiont on feeding behavior of Bactericera cockerelli, an oligophagous psyllid widespread in both crop and natural habitats that feeds primarily on Solanaceae and transmits an economically important plant pathogen, Candidatus Liberibacter solanacearum (CLso). We used a factorial design and the electrical penetration graphing technique to disentangle the effects of host acclimation, CLso infection, and psyllid haplotype on the within-plant feeding behavior of B. cockerelli during conspecific and heterospecific host switches. This approach allows to connect phenotypic plasticity with the role of B. cockerelli as a vector by quantifying the frequency and duration of behaviors involved in CLso transmission. We found significant reductions in multiple metrics of B. cockerelli feeding efficiency, exacerbated by infection with CLso, which could lead to reduced transmission of this pathogen. Psyllid genotype was also important; the Central haplotype exhibited less dramatic changes in feeding efficiency than the Western haplotype during heterospecific host switches. Our study shows that host acclimation and heterospecific host switching directly alter feeding behaviors underlying pathogen transmission, and that the magnitude of feeding efficiency reductions depends on both host genotype and infection status.

Data from: The basic-reproduction number of infectious diseases in spatially structured host populations

The spatial structure of a host population has a profound effect on the dynamics of infectious diseases. The basic reproduction number, a central quantity in the study of epidemic dynamics, is affected by host clustering as well as host density. Several authors have developed methods to quantify the basic reproduction number in a spatially structured host population. The methods used and the expressions derived are however difficult to apply to real life spatial host structures. In this paper we introduce an explicit expression for the basic reproduction number using the O-ring statistic, developed in spatial statistics, that quantifies the host density as a function of the distance from a randomly selected host individual. The O-ring statistic is frequently used in the study of the ecology of spatially structured plant populations, being a convenient summary of the properties of a landscape by way of a single function. The connection we develop between spatial statistics and epidemic dynamics can be used to study the effect of host spatial pattern on the basic reproduction number of infectious diseases. As well as showing how explicit expressions for the basic reproduction number can be derived for landscapes with standard structures, our expression for the basic reproduction number is tested against a simulation model. The model structure in our simulation is motivated by the spread of a plant disease epidemic, although it is applicable more broadly. The agreement between our analytic expression for the basic reproduction number and the corresponding numeric quantity extracted from simulations is close to perfect across a wide range of landscape structures and model parameterisations, and including cases in which more than one species of host is at risk of infection.

opencc-by-4.0Dec 2015View details →

Fig. 6 in Molecular characteristics of representatives of the genus Brachylecithum Shtrom, 1940 (Digenea, Dicrocoeliidae) with comments on life cycle and host specificity

Fig. 6 Possibilities of the B. lobatum life cycle

opencc-by-4.0Feb 2017View details →

Fig. 1 in Morphological and molecular description of Ixodes woyliei n. sp. (Ixodidae) with consideration for co-extinction with its critically endangered marsupial host

Fig. 1 Locatcons of Bettongia penicillata populatcons where samples were obtacned

opencc-zeroJun 2024View details →

Diverse host-parasite interactions mediate seasonal ecosystem linkages

Nematomorph parasites manipulate terrestrial arthropods, such as crickets and ground beetles, to enter streams where the parasites reproduce. These manipulated arthropods become a substantial prey subsidy for stream salmonids, causing cross-ecosystem energy flow. Diverse nematomorph-arthropod interactions are known to underlie the energy flow. However, whether and how they can mediate the magnitude and temporal attributes of energy flow remains largely unknown. Here, we investigated whether distinct species or phylogenetic groups of nematomorphs respectively manipulate different arthropod hosts, and how the diverse nematomorph-arthropod interactions, if any, mediate seasonal prey subsidy for stream salmonids. We found that distinct phylogenetic groups of Gordionus and Gordius nematomorphs infected ground beetle and orthopteran hosts, respectively. The Gordionus nematomorphs led their ground beetle hosts to enter streams in spring, subsidizing salmonid individuals during that season. By contrast, the Gordius nematomorphs manipulated orthopterans in autumn, causing the prey subsidy for salmonid individuals during that time. Maintaining the two distinct nematomorph-arthropod interactions, thus, resulted in the parasite-mediated prey subsidy in both spring and autumn in the study streams. Manipulative parasites are common, and they often associate with a range of host lineages, suggesting that similar effects of diverse host-parasite interactions on energy flow might be widespread in nature.

opencc-zeroJun 2024View details →

Data from: More evolvable bacteriophages better suppress their host

The number of multidrug-resistant strains of bacteria is increasing rapidly, while the number of new antibiotic discoveries has stagnated. This trend has caused a surge in interest in bacteriophages as anti-bacterial therapeutics, in part because there is near limitless diversity of phages to harness. While this diversity provides an opportunity, it also creates the dilemma of having to decide which criteria to use to select phages. Here we test whether a phage's ability to coevolve with its host (evolvability) should be considered and how this property compares to two previously proposed criteria: fast reproduction and thermostability. To do this, we compared the suppressiveness of three phages that vary by a single amino acid yet differ in these traits such that each strain maximized two of three characteristics. Our studies revealed that both evolvability and reproductive rate are independently important. The phage most able to suppress bacterial populations was the strain with high evolvability and reproductive rate, yet this phage was unstable. Phages varied due to differences in the types of resistance evolved against them and their ability to counteract resistance. When conditions were shifted to exaggerate the importance of thermostability, one of the stable phages was most suppressive in the short-term, but not over the long-term. Our results demonstrate the utility of biological therapeutics' capacities to evolve and adjust in action to resolve complications like resistance evolution. Furthermore, evolvability is a property that can be engineered into phage therapeutics to enhance their effectiveness.

opencc-by-4.0Jun 2024View details →

WiFeS observation of southern nearby Type Ia supernova host galaxies

This repository contains all the reduced and spatially-binned spectral data used in this work. Refer to the README for more detailed information.

opencc-by-4.0May 2024View details →

Figure 3 in Untangling the Derogenes varicus species complex in Scandinavian waters and the Arctic: description of Derogenes abba n. sp. (Trematoda, Derogenidae) from Hippoglossoides platessoides and new host records for D. varicus (Müller, 1784) sensu stricto

Figure 3. "Derogenes limula" ex Parablennius tentacularis. Unpublished line drawing by A. Looss.

opencc-by-4.0Feb 2024View details →

Fig. 5 in Taxonomic Notes and New Distribution and Host Plant Records for Sawflies and Woodwasps (Hymenoptera, Symphyta) of Japan IX

Fig. 5.ɹEmpria takeuchii, ovipositor (A) and serrulae 5–7 (B), Nakagawa. Photographed by H. Hara.

opencc-by-4.0Nov 2003View details →

Fig. 4. Transversotrema licinum MANTER, 1970 from Diplodus noct. Ventral view. Scale 1.00 in Digenetic Trematodes From Marine Fishes Off The Coast Of Kuwait, Arabian Gulf: Fellodistomidae And Some Smaller Families, New Host And Geographic Records

Fig. 4. Transversotrema licinum MANTER, 1970 from Diplodus noct. Ventral view. Scale 1.00 mm