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Molecular reshaping of phage-displayed Interleukin-2 at beta chain receptor interface to obtain potent super-agonists with improved developability profiles-primary dataset
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Data from: A multiscale biophysical model for the recruitment of actin nucleating proteins at the membrane interface
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Replicate analysis from: tinyVAST: R package with an expressive interface to specify lagged and simultaneous effects in multivariate spatio-temporal models
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Resource selection by New York City deer reveals the effective interface between wildlife, zoonotic hazards, and humans
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Data from: Emergent Rashba spin-orbit coupling in bulk gold with buried network of nanoscale interfaces
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Data from: Advancing neural interfaces: A framework for the fabrication and characterization of freestanding micro-nanodevices
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Rapid, DNA-induced interface swapping by DNA gyrase
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Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation
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Landscape heterogeneity shapes bird phylogenetic responses at forest-matrix interfaces in Atlantic Forest, Brazil
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Spatiotemporal study of iron oxide nanoparticle monolayer formation at liquid/liquid interfaces by using in situ small-angle x‐ray scattering
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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.
dataset for experimental study of 'Role of the calcite-water interface in wettability alteration during low salinity waterflooding '
<p>In order to understand the pore- and mineral-surface-scale processes that underpin improved oil recovery during controlled salinity waterflooding, the streaming potential measurements. The two carbonate samples tested, Carbonate-I and Carbonate-II, have the same mineralogy, but the zeta potential of Carbonate-II is anomalously negative in highly saline, natural formation brine compared to the conventionally conventional positive value for Carbonate-I. After aging with same crude oil and using the same coreflooding protocol, improved oil recovery was observed in the oil-brine-Carbonate-II system during low salinity waterflooding, but not in the Carbonate-I system. We suggest that textural differences cause calcite crystal edges in Carbonate-II to be preferentially exposed to the brine in the pore-space, yielding different calcite-brine interfacial behaviour compared to the calcite crystal faces exposed in Carbonate-I.</p>
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.
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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
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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
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