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78 results for “host-specificity”
Dataset 2 for "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses"
<p>Dataset with 154 host species (min 45 sampled individuals sampled at 1+ sites) for the second part of the analysis in "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses". One file contains the data table. One file contains a table with descriptions of the columns in the data table.</p>
Fig. 2. Solenopsis invicta virus 3 in Solenopsis invicta virus 3: Further host-specificity tests with native Solenopsis ants (Hymenoptera: Formicidae)
Fig. 2. Solenopsis invicta virus 3 (SINV-3) infections are restricted to Solenopsis fire ants in the South American saevissima group (S. invicta, S. richteri, and their hybrid in the United States). North American fire ants in the geminata group, thief ants, two species of Monomorium (also tribe Solenopsidini), and 14 additional species of ants from 3 subfamilies and 12 genera were not infected in lab trials (this paper and Porter et al. 2013).
Part 1: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory.</p> <p>The file Data.One.Focb-2.tar contains 22 files of paired-end reads from F. oxysporum f.sp. cubense tropical race 1 isolate N2 (SRA accession: SRR550150, SRR550151), and F. oxysporum f.sp. cubense TR4 isolates Hainan.B2 (SRR550152), My-1 (SRR7226877), La-2 (SRR7226878), Vn-2 (SRR7226879), Leb1.2C (SRR7226880), JV11 (SRR7226881), Phi2.6C (SRR7226882), Pak1.1A (SRR7226883), UK0001 (SRR9733598).</p>
Part 2: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory.</p> <p>The file Data.One.Focb.tar contains 16 files of paired-end reads from F. oxysporum f.sp. cubense TR4 isolates II-5 (SRA accession: SRR10054446), S1B8 (SRR10054447), JV14 (SRR10054448), FOC.TR4-5 (SRR10054449), FOC.TR4-1 (SRR10054450), Col2 (SRR10103605), Col4 (SRR10125423), Col17 (SRR10747097).</p> <p> </p>
Part 4: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogen
<p>Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory.</p> <p>The file reads.tar contains 44 files of paired-end reads from <em>F. oxysporum </em>f.sp. <em>lycopersici</em> isolate Fol069 (SRA accession: SRR307106, SRR307107, SRR307113, SRR307115, SRR307123, SRR307257, SRR307266), isolate Fol072 (SRR307122, SRR307092, SRR307091, SRR307090, SRR307086, SRR307281, SRR307250), isolate Fol4287 (SRR7690004, SRR3139043), and F. oxysporum f.sp. radicis-cucumerinum isolate Forc016 (SRR3139027, SRR3139028), isolate Forc024 (SRR3139029, SRR3139030), isolate Forc031 (SRR3139031, SRR3139032).</p>
MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids
<p>This tar-Archives hold the complete collection of n=7,506 metagenome-assembled genomes presented in the preprint "Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids" by Rühlemann <em>et al., <a href="https://www.biorxiv.org/content/10.1101/2023.03.01.530589v1">bioRxiv</a>, </em>2023.</p> <p>Article Summary</p> <p>Characterizing trajectories of the composition and function of hominid gut microbiota across diverse environments and host species can help reveal specific properties of the human microbiota, with possible implications for host evolution and health. Using shotgun metagenomic sequencing, we investigated taxonomic and functional diversity in the gut microbiota of wild-living great apes, including two gorilla subspecies (<em>Gorilla gorilla gorilla, Gorilla beringei beringei</em>), three chimpanzee subspecies (<em>Pan troglodytes verus, P.t. troglodytes, P.t. schweinfurthii</em>), and bonobos (<em>Pan paniscus</em>), together with human samples from Africa and Europe. We identified microbial taxonomic and functional adaptations convergent with host phylogeny at both the community and microbial genomic levels. We could show that repeated horizontal gene transfer and gene loss are processes involved in these adaptations. We hypothesize, that these adaptation processes and changes in the microbiome predispose the host to chronic inflammatory disorders, such as type 2 diabetes via altered histidine metabolism and inflammatory bowel disease indicated by adaptation of microbes to aerobic conditions. Additionally, we find multiple lines of evidence suggesting a widespread loss of microbial diversity and evolutionary conserved clades in the human microbiota, especially in the European population. Lastly, we observed patterns consistent with codivergence of hosts and microbes, particularly for the bacterial family <em>Dialisteraceae</em>, though we find that overall, co-phylogeny patterns are frequently disrupted in humans.</p>
Dataset 1 for "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses"
<p>Dataset with 9 host species (min. 5 study sites and min 45 sampled individuals sampled per site) for the first part of the analysis in "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses". One file contains the data table. One file contains a table with descriptions of the columns in the data table.</p>
Patterns of genotype-specific interactions in an obligate host-specific insect pathogenic fungus
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Data from: The polygenic strategies of host-specific and general virulence of Botrytis cinerea across diverse eudicot hosts
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Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
<p class="Corps"><span><span><span><span><span><span><span><span><span><span>Sporocarps (fruit bodies) are the sexual reproductive stage in the life cycle of many fungi. They are highly nutritious and consequently vulnerable to grazing by birds and small mammals, and invertebrates, and can be infected by microbial and fungal parasites and pathogens. The complexity of communities thriving inside sporocarps is largely unknown. In this study, we revealed the diversity, taxonomic composition and host-preference of fungicolous fungi (i.e fungi that feed on other fungi) in sporocarps. We carried out DNA metabarcoding of the ITS2 region from 176 sporocarps of 11 wood-decay fungal host species, all collected within a forest in northeast Finland. We assessed the influence of sporocarp traits, such as lifespan, morphology and size, on the fungicolous fungal community. The level of colonisation by fungicolous fungi, measured as the proportion of non-host ITS2 reads, varied between 2.8-39.8% across the 11 host species and was largely dominated by Ascomycota. Host species was the major determinant of the community composition and diversity of fungicolous fungi, suggesting that host adaptation is important for many fungicolous fungi. Furthermore, the alpha-diversity was consistently higher in short-lived and resupinate sporocarps compared to long-lived and pileate ones, perhaps due to a more hostile environment for fungal growth in the latter too. The fungicolous fungi represented numerous lineages in the fungal tree of life, among which a significant portion was poorly represented with reference sequences in databases. </span></span></span></span></span></span></span></span></span></span></p>
Host-specificity in Scelionid parasitoids: Arrestment, competition, and egg electrophysiology results
<p>This archive contains the raw data from a series of experiments with Trissolcus basalis and Trissolcus oenone to better understand the chemical basis mediating differences in host-specificity between these parasitoids. First, we compared the searching behaviour of T. basalis and T. oenone in open arena arrestment bioassays contaminated with footprint compounds from Nezara viridula and Cuspicona simplex. Trissolcus basalis spent four times longer searching for N. viridula than C. simplex, while T. oenone spent four times longer searching for C. simplex than N. viridula. We then conducted competition experiments to assess factors important to determining the outcomes of extrinsic and intrinsic contests between these parasitoids when they are simultaneously exposed to C. simplex egg masses. Trissolcus oenone, was the superior competitor in extrinsic and intrinsic contests. Finally, we recorded the antennal responses of T. basalis to egg extracts of N. viridula to tentatively identify potential contact kairomones used by this parasitoid to recognise and accept hosts.</p>
Data for: Polymorphism at the nestling stage and host-specific mimicry in an Australasian cuckoo-host arms race
<p>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 (<em>Chalcites lucidus</em>) 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.</p>
Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
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Data for: Polymorphism at the nestling stage and host-specific mimicry in an Australasian cuckoo-host arms race
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Data from: AM fungal spore communities and networks demonstrate host-specific variation throughout the growing season
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Data from: Malagasy bats shelter a considerable genetic diversity of pathogenic Leptospira suggesting notable host-specificity patterns
Pathogenic Leptospira are the causative agents of leptospirosis, a disease of global concern with major impact in tropical regions. Despite the importance of this zoonosis for human health, the evolutionary and ecological drivers shaping bacterial communities in host reservoirs remain poorly investigated. Here, we describe Leptospira communities hosted by Malagasy bats, composed of mostly endemic species, in order to characterize host–pathogen associations and investigate their evolutionary histories. We screened 947 individual bats (representing 31 species, 18 genera and seven families) for Leptospira infection and subsequently genotyped positive samples using three different bacterial loci. Molecular identification showed that these Leptospira are notably diverse and include several distinct lineages mostly belonging to Leptospira borgpetersenii and L. kirschneri. The exploration of the most probable host-pathogen evolutionary scenarios suggests that bacterial genetic diversity results from a combination of events related to the ecology and the evolutionary history of their hosts. Importantly, based on the data set presented herein, the notable host-specificity we have uncovered, together with a lack of geographical structuration of bacterial genetic diversity, indicates that the Leptospira community at a given site depends on the co-occurring bat species assemblage. The implications of such tight host-specificity on the epidemiology of leptospirosis are discussed.
Data from: Host-specific effects of soil microbial filtrates prevail over those of arbuscular mycorrhizae in a fragmented landscape
Plant-soil interactions have been shown to determine plant community composition in a wide range of environments. However, how plants distinctly interact with beneficial and detrimental organisms across mosaic landscapes containing fragmented habitats is still poorly understood. We experimentally tested feedback responses between plants and soil microbial communities from adjacent habitats across a disturbance gradient within a human-modified tropical montane landscape. In a greenhouse experiment, two components of soil microbial communities were amplified; arbuscular mycorrhizal fungi (AMF) and a filtrate excluding AMF spores from the soils of pastures (high disturbance), coffee plantations (intermediate disturbance), and forest fragments (low disturbance), using potted seedlings of 11 plant species common in these habitats (pasture grass, coffee, and 9 native species). We then examined their effects on growth of these same 11 host species with reciprocal habitat inoculation. Most plant species received a similar benefit from AMF, but differed in their response to the filtrates from the three habitats. Soil filtrate from pastures had a net negative effect on plant growth, while filtrates from coffee plantations and forests had a net positive effect on plant growth. Pasture grass, coffee and five pioneer tree species performed better with the filtrate from "away" (where these species rarely occur) compared to "home" (where these species typically occur) habitat soils, while four shade tolerant tree species grew similarly with filtrates from different habitats. These results suggest that pastures accumulate species-specific soil enemies, while coffee plantations and forests accumulate beneficial soil microbes that benefit pioneer native plants and coffee, respectively. Thus, compared to AMF, soil filtrates exerted stronger habitat and host-specific effects on plants, being more important mediators of plant-soil feedbacks across contrasting habitats.
Data from: Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes
Background: The underlying strategies used by influenza A viruses (IAVs) to adapt to new hosts while crossing the species barrier are complex and yet to be understood completely. Several studies have been published identifying singular genomic signatures that indicate such a host switch. The complexity of the problem suggested that in addition to the singular signatures, there might be a combinatorial use of such genomic features, in nature, defining adaptation to hosts. Results: We used computational rule-based modeling to identify combinatorial sets of interacting amino acid (aa) residues in 12 proteins of IAVs of H1N1 and H3N2 subtypes. We built highly accurate rule-based models for each protein that could differentiate between viral aa sequences coming from avian and human hosts. We found 68 host-specific combinations of aa residues, potentially associated to host adaptation on HA, M1, M2, NP, NS1, NEP, PA, PA-X, PB1 and PB2 proteins of the H1N1 subtype and 24 on M1, M2, NEP, PB1 and PB2 proteins of the H3N2 subtypes. In addition to these combinations, we found 132 novel singular aa signatures distributed among all proteins, including the newly discovered PA-X protein, of both subtypes. We showed that HA, NA, NP, NS1, NEP, PA-X and PA proteins of the H1N1 subtype carry H1N1-specific and HA, NA, PA-X, PA, PB1-F2 and PB1 of the H3N2 subtype carry H3N2-specific signatures. M1, M2, PB1-F2, PB1 and PB2 of H1N1 subtype, in addition to H1N1 signatures, also carry H3N2 signatures. Similarly M1, M2, NP, NS1, NEP and PB2 of H3N2 subtype were shown to carry both H3N2 and H1N1 host-specific signatures (HSSs). Conclusions: To sum it up, we computationally constructed simple IF-THEN rule-based models that could distinguish between aa sequences of avian and human IAVs. From the rules we identified HSSs having a potential to affect the adaptation to specific hosts. The identification of combinatorial HSSs suggests that the process of adaptation of IAVs to a new host is more complex than previously suggested. The present study provides a basis for further detailed studies with the aim to elucidate the molecular mechanisms providing the foundation for the adaptation process.
FIGURE 1 in An updated concept and revised composition for Hamacreadium Linton, 1910 (Opecoelidae: Plagioporinae) clarifies a previously obscured pattern of host-specificity among species
FIGURE 1. Hamacreadium mutabile specimen SI NMNH IZ #1402929 collected by Dr M. J. Andres from Lutjanus griseus in the Gulf of Mexico. Ventral perspective of (a) adult worm, (b) terminal genitalia and (c) ovarian complex. Abbreviations: C, caecum; Cs, cirrus-sac; E, egg; Ep, excretory pore; Ev, excretory vesicle; Ga, genital atrium; Gp, genital pore; Lc, Laurer's canal; Mg, Mehlis' gland; Mp, male pore; O, ovary; Oes, oesophagus; Oo, ootype; Os, oral sucker; P, pharynx; Pp, pars prostatica; Sr, seminal receptacle; Sv, seminal vesicle; T, testis; U, uterus; Vd, vitelline duct; Vf, vitelline follicles; Vr, vitelline reservoir; Vs, ventral sucker. Scale: 1000 µm, 300 µm, 300 µm.
FIGURE 5 in An updated concept and revised composition for Hamacreadium Linton, 1910 (Opecoelidae: Plagioporinae) clarifies a previously obscured pattern of host-specificity among species
FIGURE 5. Reproduction with modification of type illustration for (a) Hamacreadium morgani Baz, 1946 and (b) Hamacreadium phyllorchis (Bilqees, 1976) Cribb, 2005. Abbreviations: C, caecum; Cs, cirrus-sac; Ep, excretory pore; Ev, excretory vesicle; Gp, genital pore; O, ovary; Oes, oesophagus; Os, oral sucker; P, pharynx; T, testis; U, uterus; Vf, vitelline follicles; Vs, ventral sucker. Scale: 1000 µm, 1000 µm.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.