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Figure 8 in Sleeping with the enemy: unravelling the symbiotic relationships between the scale worm Neopolynoe chondrocladiae (Annelida: Polynoidae) and its carnivorous sponge hosts
Figure 8. Stable isotopic values (mean and standard deviation of δ15N and δ13C) of the different hosts (Acanella arbuscula and Chondrocladia robertballardi) and annelids (Neopolynoe acanellae and N. chondrocladiae) collected in this study. Zooplankton values correspond to a mixture of species of crustaceans (copepods, ostracods, amphipods, and cumaceans) and chaetognaths.
Data Source file for manuscript: Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients
<p>ABSTRACT</p><p>Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) are associated with excess morbidity and mortality. Despite recognition of this immediate impact on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-producing <i>Klebsiella pneumoniae </i>species complex and ESBL-<i>Escherichia coli</i> in individual patients over time, we conducted performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-<i>K. pneumoniae</i> species complex and 284 ESBL-<i>E. coli</i> isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-<i>K. pneumoniae </i>species complex, and 83.6% of patients colonized with ES BL-<i>E. coli</i>. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at a prolonged risk of recurrent infection with colonizing strains.</p><p>DATA SOURCE FILE</p><p>In this Data Source file, you will find access to the raw data, metadata and results obtained during the study: "Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients". Data is organized following the structure of Figures/Tables of the manuscript and Supplementary Material. Additional figures not included in the main manuscript nor in the Supplementary Material are also available.</p><p>All sequencing and sample data from this study can be accessed at the NCBI database under the BioProject number PRJNA910977: <a href="http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977">http://dataview.ncbi.nlm.nih.gov/object/PRJNA910977. </a>No new software was developed during this study. Standard bioinformatics software was used and the commands used can be accessed at the Supplementary Information file.</p>
Active eosinophils regulate host defence and immune responses in colitis
<p>This repository contains processed R objects generated and used for this publication. </p><p>The code is available at: <a href="https://github.com/Moors-Code/Eosinophils_scRNASeq">https://github.com/Moors-Code/Eosinophils_scRNASeq</a>.</p><p>The publication can be accessed from here: <a href="https://www.nature.com/articles/s41586-022-05628-7">https://www.nature.com/articles/s41586-022-05628-7</a></p><p>The scRNAseq raw datasets are available here: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182001">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182001</a>.</p>
FIGURE 7. Host crinoid Metacrinus rotundus Carpenter, 1885 in A new genus and new species of palaemonid shrimp (Decapoda: Caridea), associated with the deep-sea crinoid Metacrinus rotundus (Echinodermata: Isocrinidae), from Suruga Bay, Japan
FIGURE 7. Host crinoid Metacrinus rotundus Carpenter, 1885 in situ. A, entire animal on the muddy bottom; B, holotype of Metacrimenes fenestra n. gen., n. sp. clinging to the arm of M. rotundus (blue arrow).
Spectrophotometrical raw data of viability and total sugar content included in the paper "Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts"
<p>Raw data of spectrophotometrical data included in the paper: "Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts" published in npj biofilms and Microbiomes. </p>
Targeting host-virus interactions: In silico analysis of the binding of human milk oligosaccharides to viral proteins involved in respiratory infections
<p><span>Respiratory viral infections, a major public health concern, necessitate the continuous development of novel antiviral strategies, particularly in the face of emerging and re-emerging pathogens. In this study, we </span><span>explored</span><span> the potential of human milk oligosaccharides (HMOs) as broad-spectrum antiviral agents against key respiratory viruses. </span><span>By examining the</span><span> structural mimicry of host cell receptors and </span><span>their </span><span>known biological functions, including antiviral activities, we assessed the </span><span>ability</span><span> of HMOs to bind and potentially inhibit viral proteins crucial for host</span><span> </span><span>cell entry. Our <em>in silico</em> analysis </span><span>focused</span><span> on viral proteins integral to host-virus interactions</span><span>, namely,</span><span> the hemagglutinin protein of influenza, fusion proteins of respiratory syncytial and human metapneumovirus, and the spike protein of SARS-CoV-2. Using molecular docking and simulation studies, we </span><span>demonstrated</span><span> that HMOs exhibit varying binding affinities to these viral proteins, suggesting their potential as viral entry inhibitors. </span><span>This</span><span> study </span><span>identified</span><span> several HMOs with promising binding profiles, highlighting their potential in antiviral drug development. This research provides a foundation for utilizing HMOs as a natural source for designing new therapeutics, offering a novel approach in the fight against respiratory viral infections.</span></p>
Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution
<p>Dataset created in the study "A Spatial Transcriptomics Atlas of the Malaria-infected Liver Indicates a Crucial Role for Lipid Metabolism and Hotspots of Inflammatory Cell Infiltration" </p><p><strong>Structure</strong></p><p><strong>ST_berghei_liver</strong></p><p>contains data generated during <i>stpipeline </i>analysis and imaging on 2k arrays Spatial Transcriptomics platform as well as data necessary for and from hepaquery analysis. These samples include 38 sections in total of which 8 are from mice (n=4) infected with sporozoites for 12h, 5 sections from control mice (n=3) at 12h, 7 sections from mice (n=4) infected with sporozoites for 24h and 4 sections from control mice (n=3) for 24 as well as 8 samples of mice (n=2) infected with sporozoites for 38h and control mice (n =2) for 38h. </p><ul><li><i><strong>count</strong></i> contains gene expression matrix output from stpipeline in .tsv format</li><li><i><strong>spotfiles</strong> </i>contains coordinate files for count matrices</li><li><i><strong>images </strong></i>contains scaled H&E, Fluorescence (FL) and annotated H&E images (from FL annotations) scaled to 10% of the original image size.</li><li><i><strong>masks </strong></i>contains image masks for hepaquery analysis</li><li><i><strong>distances </strong></i>contains distance measurements from original section sorted by timepoint as well as combined across timepoints</li><li><strong>cluster</strong> contains clustering information across spatial positions used in spatial enrichment analysis</li></ul><p><strong>STUtiility_mus_pb_ST.RDS </strong>describes seurat object generated using the STUtility package using ST data of the 38 liver sections of which the data is stored in <strong>ST_berghei_liver</strong></p><p><strong>h5ad</strong></p><p>contains anndata files of ST data (normalized read counts), spot information, distance measurements, images and masks generated using the hepaquery package. </p><p><strong>visium_berghei_liver</strong></p><p>contains data generated with the <i>spaceranger </i>pipeline and imaging using the Visium spatial transcriptomics platform. These samples include 8 sections in total, of which 1 was infected with sporozoites for 12h, 1 control section at 12h, 1 section infected with sporozoites for 24h and 1 control section at 24 as well as 2 sporozoite infected sections, and 2 control sections at 38h. </p><ul><li><i><strong>V10S29-135_A1</strong></i> contains spaceranger output for section 1 for infected and control sections at 38h post-infection</li><li><i><strong>V10S29-135_B1</strong></i> contains spaceranger output for section 1 for infected and control sections at 12h post-infection </li><li><i><strong>V10S29-135_C1 </strong></i>contains spaceranger output for section 1 for infected and control sections at 24h post-infection </li><li><i><strong>V10S29-135_D1 </strong></i>contains spaceranger output for section 2 for infected and control sections at 38h post-infection </li></ul><p><strong>se_visium.RDS </strong>describes seurat object generated using the STUtility package using ST data of the 38 liver sections of which the data is stored in <strong>visium_berghei_liver</strong></p><p><strong>snSeq_berghei_liver</strong></p><p>contains data generated with the <i>cellranger </i>pipeline and imaging using the Visium spatial transcriptomics platform. These samples include single nuclei of 2 infected and control mice after 12h, 2 infected and control mice after 24h, 2 infected and control mice after 38h, and 2 uninfected mice prior to a challenge.</p><p><i><strong>cellranger_cnt_out</strong> </i>contains feature count matrix information from cell ranger output</p><p><strong>final_merged_curated_annotations_270623.RDS </strong>describes seurat object generated using the STUtility package using ST data of the 38 liver sections of which the data is stored in <strong>snSeq_berghei_liver.tar.gz</strong></p><p><strong>raw images.zip </strong>contains raw images for supplementary figures 20-22</p><p><strong>adjusted images.zip </strong>contains brightness and contrast adjusted images for supplementary figures 20-22</p>
Aphid-induced phytochemicals in Brassica juncea (L.) Czern & Coss. afflicting host preference and bionomics of Lipaphis erysimi (Kaltenbach)
<p>Bionomics of an insect and metabolic flux of the host plant are important tools to decipher the status of plant resistance against insect species. This study illuminates vital information on aphid-induced levels of phytochemicals in the siliquae<em> </em>of <em>Brassica juncea</em> cultivars and their effect on host selection and population growth parameters of <em>Lipaphis erysimi</em>. The current study unveiled that the siliquae preference, intrinsic rate of increase (r), finite rate of increase (λ), gross reproductive rate (GRR) and net reproductive rate (R0) were significantly lower on Pusa Mustard 27, DRMR 150-35, RLC 3, NRCHB 101, Pusa Mustard 26 and Pusa Mustard 25. However, mean generation time (T) and doubling time (DT) of <em>L. erysimi</em> were significantly longer (P<0.001) in these genotypes. These cultivars were also found with elevated levels of aphid-induced phytochemicals and their associated enzymes, except in a few cases. Total antioxidants, FRAP, chlorophyll A, total chlorophyll, AO, catalase, PAL and myrosinase were found to contribute 49.18 to 85.30% variation for siliquae preference and bionomics of <em>L. erysimi</em> on the test <em>B. juncea</em> cultivars. The study revealed that phenols, antioxidants, chlorophyll A, chlorophyll B, total carotenoids, AO, APX, PAL, TAL and myrosinase had significant and negative direct consequences on the siliquae preference and bionomics, thus can be exploited as biochemical markers to identify sources of resistance against <em>L. erysimi</em>. Further, DRMR 150-35, NRCHB 101, RLC 3, Pusa mustard 26, RH 749, and Pusa Mustard 27 were found with greater aphid-induced defence phytochemicals and detrimental effects on the host selection and bionomics of <em>L. erysimi</em>, thus can be deployed in <em>Brassica</em> improvement program.</p>
Data from: Seasonal host community dynamics constrain the risk of parasite transmission between migrant and resident species
<p>Seasonal migration shapes the community dynamics that influence pathogen transmission between migrants and resident species. While theoretical and empirical evidence has accumulated, whether migration increases or decreases the risk of cross-species infection remains inconclusive. We studied how the seasonal arrival and departure of a single avian migrant species change the composition of local communities in breeding areas affecting the haemosporidian infection dynamics. The seasonal reordering of resident species abundances induced by migrants, minimizes the opportunities for contact between highly infected hosts and susceptible species, either migrants or residents, thereby limiting the transmission of parasites to occasional spillover events. The occurrence of spillover dynamics during the seasonal sympatry between migrants and residents provides a plausible explanation that reconciles empirical inconsistencies in the intersection of animal migration and infection risk at the host community level. Our findings underscore the critical role played by seasonality in shaping infection dynamics in migratory systems.</p>
Contribution of parasite and host genotype to immunopathology of schistosome infections
<p>The present dataset contains all the phenotype data (.csv files) and R scripts used for data analysis and generation of figures (Fig. 2-6) present in the manuscript entitled "Contribution of parasite and host genotype to immunopathology of schistosome infections."</p>
Effects of host essential oils and log length on bark beetle attack
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Figure 4 in Host plants and nymph morphology of an endemic treehopper, Pyrgonota bifoliata, in the Mount Makiling Forest Reserve, Luzon, Philippines
Figure 4. (a–f) Morphological characteristics of the last-instar nymph and (g–h) exuvia of Pyrgonota bifoliata. (a) Anterior view; (b) lateral view; (c) dorsal view; (d) lateral view; (e) dorsal view; (f) ventral view; (g) dorsal view; (h) lateral view.
Figure 3 in Host plants and nymph morphology of an endemic treehopper, Pyrgonota bifoliata, in the Mount Makiling Forest Reserve, Luzon, Philippines
Figure 3. Pyrgonota bifoliata and its associated host plants and ants in the Mount Makiling Forest Reserve. The white arrows indicate cryptically coloured nymphs of Pyrgonota bifoliata. (a) Adult pyrgonota bifoliata on Alangium longiflorum (Cornaceae). (b) Adult Pyrgonota bifoliata on Ficus ulmifolia (Moraceae). (c) Adult and a nymph Pyrgonota bifoliata with an attended ant (Pheidole sp.) on Piper umbellatum (Piperaceae). (d) Young adult Pyrgonota bifoliata on Piper umbellatum. (e) Two Pyrgonota bifoliata nymphs and a crab spider (Thomisidae) on Piper umbellatum. (f) Two Pyrgonota bifoliata nymphs and an ant (Technomyrmex sp.) on Piper umbellatum. (g) Nymph and an adult Pyrgonota bifoliata, three ants (one Pheidole sp. and two Crematogaster sp.) on Saurauia latibractea (Actinidiaceae). (h) Three Pyrgonota bifoliata nymphs and two ants (Crematogaster sp.) on Saurauia latibractea.
Figure 1 in Host plants and nymph morphology of an endemic treehopper, Pyrgonota bifoliata, in the Mount Makiling Forest Reserve, Luzon, Philippines
Figure 1. (a) Philippine archipelago and its major islands. The white circle indicates the study site (Mount Makiling Forest Reserve, Laguna Province, Luzon). (b) Adult Pyrgonota bifoliata collected in Mount Makiling, Luzon, 26 January 2019. (c) Type specimen of Pyrgonota bifoliata (Westwood 1837). Images obtained from the Oxford University Museum of Natural History (OUMNH) and used with permission.
Figure 2 in Host plants and nymph morphology of an endemic treehopper, Pyrgonota bifoliata, in the Mount Makiling Forest Reserve, Luzon, Philippines
Figure 2. Host plant records of Pyrgonota bifoliata in the Mount Makiling Forest Reserve. The numbers at the top of the bars represent the total numbers of treehoppers on each plant, whereas the numbers in parentheses represent the percentages of total treehoppers on each plant. The black and white bars represent the data for adults and nymphs, respectively.
Figure 3 in A novel host association of Idris Förster (Hymenoptera: Scelionidae) with description of a new species from India
Figure 3. Maximum likelihood tree for the species of Idris based on 493 bp of mt COI DNA gene sequence.
Figure 2 in A novel host association of Idris Förster (Hymenoptera: Scelionidae) with description of a new species from India
Figure 2. Idris hirsutus Sunita and Rajmohana sp. n. Female. (A) Lateral habitus. (B) Antenna. (C) Dorsal view of head. (D) Lateral view of mesosoma. (E) Dorsal view of head and mesosoma. (F) Dorsal view of metasoma. (G) Ventral view of metasoma. (H) Fore wing.
Phage-host co-evolution has led to distinct generalized transduction strategies
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Supplementary Data, Figures and Code - Europium in plagioclase-hosted melt inclusions reveals mantle melting modulates oxygen fugacity
<p>Electronic supplementary data, figures and code to the article Europium in plagioclase reveals mantle melting modulates oxygen fugacity. Data tables include major and trace element analyses, replicate analyses of secondary standards, which establish trace element data quality, a summary of new plagioclase-melt major and trace element data and data compiled from the literature, and recovered temperatures and oxygen fugacities, and spatial variations of plagioclase compositions around melt inclusions in phenocrysts extracted from sample D23-2 from the Juan de Fuca ridge, which were thermally homogenized over different periods of time (30 minutes, four hours, one day, and four days). The compressed archive contains Matlab scripts which may be used to recover temperatures from trivalent REE distributions in coexisting plagioclase crystals and melt inclusions or glasses.</p>
Integrating Metagenomic and Metabolomic Insights into Host-Microbe Connections for Gut-Lung Axis in Childhood Asthma
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ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.