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6,383 results for “isolates”
Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments
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Data for: Reproductive isolating mechanisms contributing to asymmetric hybridization in Killifishes (Fundulus spp.)
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Genomic analysis reveals close genetic similarity between ESBL-producing E. coli isolates from humans and dogs, suggesting potential for inter-species transmission
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Isolation controls reestablishment mechanisms and post-drying community structure in an intermittent stream
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Data from: Genome-wide epigenetic isolation by environment in a widespread Anolis lizard
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Parallel evolution of phenological isolation across the speciation continuum in serpentine-adapted annual wildflowers
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Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease
<p>Supplemental File 1: Main genome assemblies (Unpolished Flye assembly, Polished Flye assembly, Unicycler Hybrid Assembly and Unicycler Illumina-only assembly) generated in this study for comparison and their BUSCO output.</p> <p>Supplemental File 2: Phyre2 protein modelling output of the putative MVP1 TcdA toxin</p> <p>Supplemental File 3: Phyre2 protein modelling output of the putative MVP1 TcdB toxin</p> <p>Supplemental File 4: Phyre2 protein modelling output of the putative MVP1 TccC toxin</p> <p>Supplemental File 5: InterProScan output of the NCBI-predicted MVP1 proteome.</p> <p>Supplemental Table 1: NCBI BlastN output using the <em>fuc</em> genes of <em>Vibrio parahaemolyticus</em> MVP1 as the query to search against the Vibrio reference WGS database as of 21 Oct 2019</p>
Supporting Data for "A partial coupling method to isolate the roles of ocean and atmosphere in coupled climate simulations"
<p>Supporting data for "A partial coupling method to isolate the roles of the atmosphere and ocean in coupled climate simulations", submitted to Journal of Advances in modelling Earth system</p> <p>Monthly averaged variables for the 100 and 150 year fully coupled (b.e11.B1850C5CN.f09_g16.abrupt4xCO2.full.POP.100101_110012.nc) and partially coupled (b.e11.B1850C5CN.f09_g16.abrupt4xCO2.partial.POP.100101_115012.nc) abrupt CO2 quadrupling simulations and 40 yr ocean-driven partially coupled simulation (b.e11.B1850C5CN.f09_g16.prescribed.partial.POP.100101_115012.nc)</p> <p>Control simulation data is available on the NCAR HPSS /CCSM/csm/b.e11.B1850C5CN.f09_g16.005</p>
FIGURE 3. Pegomya cedrica Huckett. A. Isolated live 3 in Pegomya disticha Griffiths and P. cedrica Huckett (Diptera: Anthomyiidae) - first documented case of insects trespassing the silica barrier of Common scouringrush, Equisetum hyemale L.
FIGURE 3. Pegomya cedrica Huckett. A. Isolated live 3rd instar larva with dark gut contents showing through. B. Isolated live puparium. C. Stem with external signs of larval attack. D. Opened stem showing larval tunnel through two successive internodes and larva at base. E. Transect showing larval mine inside the wall. F, G. Basal remains of attacked shoot by early spring exposing a hibernating puparium. Scales in millimetres.
Extended Data Table 2 in Isolation of an archaeon at the prokaryote eukaryote interface
Extended Data Table 2 | Carbon isotope fractionation values in MK-D1 cultures after 120 days incubation with and without stable isotope labelled amino acids
Extended Data Table 1 in Isolation of an archaeon at the prokaryote eukaryote interface
Extended Data Table 1 | SSU rRNA gene clones obtained from the primary and six successive transferred enrichment cultures
Extended Data Fig. 6 in Isolation of an archaeon at the prokaryote eukaryote interface
Extended Data Fig. 6 | Maximum-likelihood tree of Asgard archaea urocanate hydratase.Urocanate hydratase (HutU) homologues were obtained by BLASTp analysis of the Asgard archaea sequences against the UniProt database (release 2019_06).Of homologues with sequence similarity ≥40% and overlap ≥70%,representative sequences were selected using CD-HIT with a clustering cut-off of 70% similarity (otherwise default settings were used). Additional homologues with verified biochemical activity, sequence similarity ≥30% and overlap ≥70% were obtained by BLASTp analysis of the Asgard archaea sequences against the UniProt/SwissProt database (2019_05). Sequences were aligned using MAFFT v.7 with default settings and trimmed using trimAl v.1.2 with default settings.The maximum-likelihood tree was constructed using RAxML-NG using fixed empirical substitution matrix (LG), 4 discrete GAMMA categories,empirical amino acid frequencies from the alignment and 100 bootstrap replicates.In total, 876 sites of the alignment were used for tree construction.
Fig. 3 in Isolation of an archaeon at the prokaryote eukaryote interface
Fig. 3 | Microscopy characterization and lipid composition of MK-D1. a–c, SEM images of MK-D1.Single cell (a), aggregated cells covered with EPS-like materials (b) and a dividing cell with polar chains of blebs (c). d, Cryo-electron tomography image of MK-D1.The top-right inset image shows a magnification of the boxed area to show the cell envelope structure.e, Cryo-EM image of large membrane vesicles attached to and surrounding MK-D1 cells.f, Ultrathin section of an MK-D1 cell and a membrane vesicle.The bottom-right inset image shows a magnified view of the membrane vesicle.g, h, SEM images of MK-D1 cells producing long branching (g) and straight (h) membrane protrusions. i, Ultrathin section of a MK-D1 cell with protrusions.j, A total ion chromatogram of gas chromatography–mass spectrometry (GC–MS) for lipids extracted from a highly purified MK-D1 culture.The chemical structures of isoprenoids and their relative compositions are also shown (Supplementary Fig.2).Scale bars, 1 µm (b, c, g, h), 500 nm (a, d, e, i) and 200 nm (f). a–c, g, h, SEM images are representative of n = 122 recorded images that were obtained from four independent observations from four culture samples.d, e, Cryo-EM images are representative of n = 14 recorded images that were taken from two independent observations from two culture samples.f, i, The ultrathin section images are representative of n = 131 recorded images that were obtained from six independent observations from six culture samples.White arrows in the images indicate large membrane vesicles.The lipid composition experiments were repeated twice and gave similar results.Detailed iTAG-based community compositions of the cultures are shown in Supplementary Table 1.
Extended Data Fig. 3 in Isolation of an archaeon at the prokaryote eukaryote interface
Extended Data Fig. 3 | Other representative photomicrographs of MK-D1 cultures and Methanobacterium sp.strain MO-MB1. a, b, Fluorescence images of cells from enrichment cultures after 8 (a) and 11 (b) transfers stained with DAPI (violet) and hybridized with nucleotide probes that target MK-D1 (green) and Bacteria (red).The images are different fields of view to those shown in Fig.1b, c, which were taken at the same time.c, A fluorescence image of cells in the enrichments after 11 transfers hybridized with nucleotide probes that target MK-D1 (green) and Archaea (but with one mismatch against MK-D1; red).Large and irregular coccoid-shaped cells stained by only ARC915 are probably Methanogenium. d, e, Dividing cells of MK-D1 with a bleb.The topright inset image in e shows a magnification of the bleb. f, g, Cryo-EM images of MK-D1 cells and large membrane vesicles (white arrows).h, i, Ultrathin sections of MK-D1 cells with a membrane vesicle.The image i shows a magnified image of h. j, k, SEM images of MK-D1 cells with protrusions.l, Ultrathin section of a MK-D1 cell with a protrusion.m, n, Photomicrographs of pure culture of Methanobacterium sp.strain MO-MB1 cells stained with SYBR Green I. Phasecontrast (m) and fluorescence (n) images of the same field are shown. a, b, The FISH experiments were performed three times with similar results.d, e, j, k, The SEM images are representative of n = 122 recorded images that were obtained from four independent observations from four culture samples.The lipid composition experiments were repeated twice and gave similar results. f, g, The cryo-EM images are representative of n = 14 recorded images that were taken from two independent observations from two culture samples.h, i, l, The ultrathin-section images are representative of n = 131 recorded images that were obtained from six independent observations from six culture samples. m, n, The SYBR Green I staining experiment was performed once,but all 10 recorded images showed similar results.Detailed iTAG analyses of cultures are shown in Supplementary Table 1.
Extended Data Fig. 1 in Isolation of an archaeon at the prokaryote eukaryote interface
Extended Data Fig. 1 | Growth of MK-D1. a, Effect of temperature on growth of MK-D1.Data are mean ± s.d. of triplicate determinations.Each data point is shown as a dot.The temperature range test was performed twice with similar results.b, c, The amino acid concentrations and growth curves of MK-D1 in pure cocultures at 20 °C.Results from cultures 1 (b) and 2 (c) are shown.Please note that the initial concentrations of amino acids were normalized to 100%.Total amino acids and several representative amino acids (Val,valine;Leu,leucine; Ile, isoleucine) are independently shown for the duplicate culture samples. Detailed iTAG-based community compositions of the cultures are shown in Supplementary Table 1.
A dash indicates that data were not taken for that sample. a in Isolation of an archaeon at the prokaryote eukaryote interface
A dash indicates that data were not taken for that sample. a The iTAG analysis was performed for samples in which an increase of about 10 times or more in 16S rRNA gene copy numbers of MK-D1 was observed after incubation;data were analysed by qPCR assay.Detailed results are shown in Supplementary Table 1. b Final concentration of casamino acids was 0.05% (w/v). c Final concentration of each amino acid was 0.1 mM. d Powdered milk for baby (Hohoemi, Meiji) was used at a final concentration of 0.1% (w/v). e The concentration of hydrogen gas was in the head space of the culture bottle. f2-BES was added to inhibit methanogens. g Addition of nitrate completely suppressed the growth of MK-D1.This is probably because nitrate inhibits formate dehydrogenase activity of MK-D1 95. h Archaeal cell membrane components were a mixture of phytol,intact polar lipid–glycerol-dialkyl-glycerol tetraethers and core lipid– glycerol-dialkyl-glycerol tetraethers (each at a final concentration 50 ng ml −1). We used the archaeal membrane components as these have a positive effect on the growth of some archaeal species:(i) archaeal cell extract including membrane lipids stimulates the growth of the extremely thermophilic archaeon Thermocaldium modestius 96, and (ii) the hyperthermophilic archaeon Thermofilum pendes requires the polar lipids for growth,which was obtained from the archaeal species Thermoproteus tenax 97.
Extended Data Fig. 7 in Isolation of an archaeon at the prokaryote eukaryote interface
Extended Data Fig. 7 | Maximum-likelihood tree of Asgard archaea Lthreonine/L-serine dehydratase. a, Tree calculated for target Asgard archaea L-threonine/L-serine dehydratase (TdcB) and homologues.TdcB homologues were obtained by BLASTp analysis of the Asgard archaea sequences against the UniProt reference proteome and SwissProt database (release 2019_06).Of homologues with sequence similarity ≥40%,overlap ≥70% and predicted prosite domain PS00165 (serine/threonine dehydratases pyridoxal-phosphate attachment site), representative sequences were selected using CD-HIT with a clustering cut-off of 70% similarity (otherwise default settings were used). Additional homologues with verified biochemical activity, sequence similarity ≥30% and overlap ≥70% were obtained by BLASTp analysis of the Asgard archaea sequences against the UniProt/SwissProt database (2019_05). Sequences were aligned using MAFFT v.7 with default settings.Positions with gaps in more than 10% of the sequences were excluded from the alignment using trimAl v.1.2 (-gt 0.9; and otherwise default settings were used).The maximum-likelihood tree was constructed using PhyML using a fixed empirical substitution matrix (LG),4 discrete GAMMA categories,empirical amino acid frequencies from the alignment and 100 bootstrap replicates (-b 100 -d aa -m LG -v e). In total,308 sites of the alignment were used for tree construction. b, Tree calculated for a subset of sequences contained in a section of the original tree (branches that are coloured blue).Sequences were realigned and trimmed as described for a. In total,308 sites of the alignment were used for tree construction.
Extended Data Fig. 4 in Isolation of an archaeon at the prokaryote eukaryote interface
Extended Data Fig. 4 | Ribosomal protein- and 16S rRNA gene-based phylogeny of MK-D1. a, Phylogenomic tree of MK-D1 and select cultured archaea,eukaryotes and bacteria based on 31 ribosomal proteins conserved across the three domains (Supplementary Table 7). Ribosomal protein sequences of MK-D1,the organisms shown in the tree and MAGs of uncultured archaeal lineages (Supplementary Table 8) were aligned individually using MAFFT.MAG-derived sequences (except for Ca. Korarchaeum) were then removed for tree construction.After removing all-gap positions and concatenation,the maximum-likelihood tree was constructed using RAxML- NG.Bootstrap values around critical branching points are also shown.In total, 14,875 sites of the alignment were used for tree construction. b, A ribosomal protein-based phylogenomic tree constructed using MrBayes.Bayesian inference phylogenies were calculated using MrBayes 3.2.7a and a ribosomal protein concatenated alignment used for Fig.4a. c, Phylogenetic tree of MK-D1 and related archaea based on 16S rRNA genes.The 16S rRNA gene sequences were aligned using SINA against the Silva v.132 alignment and the maximumlikelihood tree was calculated using RAxML.
Extended Data Fig. 2 in Isolation of an archaeon at the prokaryote eukaryote interface
Extended Data Fig. 2 | Circular representation of MK-D1 genome.From the outside to the centre:the distribution of the coding sequences based on the conserved (orange) or non-conserved (grey) genes in the first circle,noncoding RNAs in the second circle,GC content showing deviation from average (40.7%) in the third circle,and GC skew in the fourth circle.The GC content and GC skew were calculated using a sliding window of 2 kb in step of 10 kb. The coding sequences and RNA genes illustrate the findings for plus and minus strands.
Fig. 5 in Isolation of an archaeon at the prokaryote eukaryote interface
Fig. 5 | Proposed hypothetical model for eukaryogenesis. a, The syntrophic/ fermentative host archaeon is suggested to degrade amino acids to short-chain fatty acids and H2, possibly by interacting with H2-scavenging (and indirectly O2-scavenging) SRB (orange; see Supplementary Note 6). b, The host may have further interacted with a facultatively aerobic organotrophic partner that could scavenge toxic O2 (the future mitochondrion;red).Continued interaction with SRB could have been beneficial but not necessarily essential; dotted arrows indicate the interaction;see Supplementary Note 7.c, Host external structures could have interacted (for example,mechanical or biological fusion50) with the aerobic partner to enhance physical interaction and further engulf the partner for simultaneous development of endosymbiosis and a primitive nucleoid-bounding membrane.d, After engulfment,the host and symbiont could have continued the interaction shown in b as a primitive type of endosymbiosis.e, Development of ADP/ATP carrier (AAC) by the endosymbiont (initial direction of ATP transport remains unclear; see Supplementary Note 9). f, Endogenization of partner symbiosis by the host through delegation of catabolism and ATP generation to the endosymbiont and establishment of a symbiont-to-host ATP channel.
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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)
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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.