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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.
Extended Data Fig. 5 in Isolation of an archaeon at the prokaryote eukaryote interface
Extended Data Fig. 5 | Amino acid, cofactor and nucleotide biosynthesis capacities of MK-D1 and other Asgard archaea. Genomes that encode proteins for the synthesis of amino acids,cofactors and nucleotides from pyruvate or acetyl-CoA (dark blue) and synthesis from other intermediates (light blue) are indicated. Those without complete pathways from pyruvate and/or acetyl-CoA are indicated in white.Halodesulfovibrio sp.strain MK-HDV and Methanogenium sp.strain MK-MG isolated in this study are also shown.
Fig. 2 in Isolation of an archaeon at the prokaryote eukaryote interface
Fig. 2 | Syntrophic amino acid utilization of MK-D1. a, Genome-based metabolic reconstruction of MK-D1.Metabolic pathways identified (coloured or black) and not identified (grey) are shown.For identified pathways,each step (solid line) or process (dotted) is marked by whether it is oxidative (red), reductive (blue),ATP-yielding (orange) or ATP-consuming (purple).Wavy arrows indicate exchange of compounds:formate,H2, amino acids,vitamin B12, biotin, lipoate and thiamine pyrophosphate (TPP),which are predicted to be metabolized or synthesized by the partnering Halodesulfovibrio and/or Methanogenium. Biosynthetic pathways are indicated with a yellow background.Metatranscriptomics-detected amino-acid-catabolizing pathways are indicated (black dots above amino acids).DHDH,4,5-dihydroxy- 2,6-dioxohexanoate;DHDG,2-dehydro-3-deoxy-d-gluconate;DHDG6P, 3-dehydro-3-deoxy-d-gluconate 6-phosphate;Ac-CoA,acetyl-CoA;uro, urocanate;Fo-Glu,formyl glutamate;CH3=H4F,methylene-tetrahydrofolate; CH≡H4F,methenyl-tetrahydrofolate;Fo-H4F,formyl-tetrahydrofolate;2OB, 2-oxobutyrate;Prop-CoA,propionyl-CoA;ACAC,acetoacetate; GB-CoA, γ-amino-butyryl-CoA;But-CoA,butyryl-CoA;Fd,ferredoxin;XSH/X-S-S-X, thiol/disulfide pair; TCA,tricarboxylic acid cycle;PPP,pentose-phosphate pathway.b–e, NanoSIMS analysis of a highly purified MK-D1 culture incubated with a mixture of 13C- and 15N-labelled amino acids.b, Green fluorescent micrograph of SYBR Green I-stained cells.Aggregates are MK-D1,and filamentous cells are Methanobacterium sp. strain MO-MB1 (fluorescence can be weak owing to the high rigidity and low permeability of the cell membrane (Extended Data Fig.2m,n; see also ref.49). c, NanoSIMS ion image of 12C (cyan). d, NanoSIMS ion image of 12C15N/12C14N (magenta).e, Overlay image of b–d. d, The colour bar indicates the relative abundance of 15N expressed as 15N/14N. Scale bars 5 µm.The NanoSIMS analysis was performed without replicates due to its slow growth rate and low cell density.However,to ensure the reproducibility,we used two different types of highly purified cultures of MK-D1 (see Methods).Representative of n = 8 recorded images.The iTAG analysis of the imaged culture is shown in Supplementary Table 1.
Fig. 4 in Isolation of an archaeon at the prokaryote eukaryote interface
Fig. 4 | Phylogeny of MK-D1 and catabolic features of Asgard archaea. a, Maximum-likelihood tree (100 bootstrap replicates) of MK-D1 and select cultured archaea,eukaryotes and bacteria based on 31 ribosomal proteins that are conserved across the three domains (Supplementary Tables 7,8). Bootstrap values around critical branching points are also shown.We used 14,024 sites of the alignment for tree construction.b, The presence or absence of amino acid degradation,electron metabolism,fermentation,C1 metabolism,sulfur metabolism and aerobic respiration in individual genomes are shown (complete pathway,full circle; mostly complete pathway,half circle).For amino acid metabolism,pathways that are exclusively used for catabolism or degradation are in bold.Glycine metabolism through pyruvate (top) or formate (bottom). Butyrate metabolism is reversible (fermentation or β-oxidation); however,butyryl-CoA dehydrogenases tend to be associated with EtfAB in the genomes,suggesting formation of an electron-confurcating complex for butyrate fermentation.Propionate was determined by the presence of methylmalonyl-CoA decarboxylase,biotin carboxyl carrier protein and pyruvate carboxylase.Propionate metabolism is also reversible;however,no member of the Asgard archaea encodes the full gene set for syntrophic degradation.Alcohol dehydrogenases can have diverse substrate specificities. See Supplementary Note 5 for abbreviations.
Fig. 1 in Isolation of an archaeon at the prokaryote eukaryote interface
Fig. 1 | Growth curves and photomicrographs of the cultured Lokiarchaeota strain MK-D1. a, Growth curves of MK-D1 in anaerobic medium supplemented with casamino acids (CA) alone; casamino acids with 20 amino acids (AAs) and powdered milk (PM); or peptone with powdered milk. Results are also shown for cultures fed with 10- and 100-fold dilution of casamino acids,20 amino acids and powdered milk.b, c, Fluorescence images of cells from enrichment cultures after 8 (b) and 11 (c) transfers stained with DAPI (violet) and hybridized with nucleotide probes that target MK-D1 (green) and Bacteria (red). Pie charts show the relative abundance of microbial populations based on SSU rRNA gene-tag sequencing (iTAG) analysis.d, A fluorescence image of cells from enrichment cultures after 11 transfers hybridized with nucleotide probes that target MK-D1 (green) and Methanogenium (red).The FISH experiments were performed three times with similar results.e, SEM image of a highly purified co-culture of MK-D1 and Methanogenium. White arrows indicate Methanogenium cells.We observed four different co-cultures with Methanogenium. Representative of n = 40 recorded images.The detailed iTAG-based community compositions of cultures corresponding to each of the images are shown in Supplementary Table 1. Scale bars,10 µm (b, c) and 5 µm (d, e).
Development of a neural interface for high-definition, long-term recording in rodents and nonhuman primates
<p>Data set and code used to generate figures in "Development of a neural interface for high-definition, long-term recording in rodents and nonhuman primates".</p> <p> </p>
Test of the haptic knob using a pilot software interface
<p>Additional material related to the paper "<em>A LOW-COST ENDLESS KNOB CONTROLLER WITH PROGRAMMABLE RESISTIVE FORCE FEEDBACK FOR MULTIMEDIA PRODUCTION</em>"</p> <p>This video contains an example of a hapitc knob device used for supporting basic audio editing operations in a pilot software environment developed in Processing. In particular, the five effects shown are amplitude transient detection, time window navigation, volume control, multiple choice selector and variable resistance.</p>
Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces
<p>These are data corresponding to the paper '<a href="https://doi.org/10.1093/bioinformatics/btaa263">Learning Context-aware Structural Representations to Predict Antigen and Antibody Binding Interfaces</a>', published in Bioinformatics 2020. The code to run the experiments can be found on github <a href="https://github.com/vamships/PECAN">here</a>.</p>
Simulations of the air-water interface at the presence of salt, Dang ions + SPCE water model
<p>Simulations of a water–air interface. There are ~20000 water molecules with various concentrations of NaCl or CaCl_2 in a simulation box of 12*12*22 nm^3. The SPCE water and the ions by Dang et al. are used. The numbering in file names corresponds to the different concentrations, and data for a pure water–air interface "NOION" is also provided. GROMACS-compatible inputs are provided: simulation parameters (md.mdp), topologies (top), and index (ndx) files. Initial structure can be extracted from the tpr file using gmx editconf. The run input (tpr) is provided, as are the outputs: energy file (edr), trajectory (xtc), and final structure (gro). Surface tensions can be extracted by gmx energy.</p> <p>These values are reported in DOI: [ADD].</p> <p>Data for scaled ions based on the electronic continuum correction (ECC) with two different water models are provided in DOI: 10.5281/zenodo.3888383 (SPCE) and DOI: 10.5281/zenodo.3888369 (OPC).</p> <p> </p>
Simulations of the air-water interface at the presence of salt, ECC ions + SPCE water model
<p>Simulations of a water–air interface. There are ~20000 water molecules with various concentrations of NaCl or CaCl_2 in a simulation box of 12*12*22 nm^3. The SPCE water and the ions with scaled charges based on the electronic continuum correction (ECC) are used. The numbering in file names corresponds to the different concentrations, and data for a pure water–air interface "NOION" is also provided. GROMACS-compatible inputs are provided: simulation parameters (md.mdp), topologies (top), and index (ndx) files. Initial structure can be extracted from the tpr file using gmx editconf. The run input (tpr) is provided, as are the outputs: energy file (edr), trajectory (xtc), and final structure (gro). Surface tensions can be extracted by gmx energy.</p> <p>These values are reported in DOI: [ADD].</p> <p>Data for these ECC ions with OPC water is provided at DOI: 10.5281/zenodo.3888369 and for the full charge ions by Dang et al. in SPCE water at DOI: 10.5281/zenodo.3888436.</p>
Processes at the soil-root interface determine the different responses of nutrient limitation and metal toxicity in forbs and grasses to nitrogen enrichment
<ol> <li>Nutrient limitation and metal toxicity have been implicated in changes of grassland communities by nitrogen (N) deposition. Belowground processes, especially those at the soil-root interface, play important roles in determining variation in nutrient concentrations in plants. However, few studies have specifically focused on the roles of these processes in mineral-element acquisition in grassland plants in response to N enrichment.</li> <li>Here we investigated the contributions of belowground processes at the soil-root interface to the differential acquisition of phosphorus (P), calcium (Ca) and manganese (Mn) by forbs and grasses of a temperate steppe in response to N addition by combining field and glasshouse experiments.</li> <li>Nitrogen addition increased the concentrations of both leaf P ([P]) and Mn ([Mn]) and decreased leaf [Ca] of forbs, while it had little effects on leaf concentrations of these elements in grasses. Nitrogen addition led to a higher activity of acid phosphatase in the rhizosphere of forb, and greater release of protons and carboxylates from forb roots than grass roots, contributing to the differential [P], [Ca] and [Mn] in leaves of forbs and grasses. Applying oxalate to soil to simulate the release of carboxylates by N enrichment enhanced [P] and [Mn], and decreased [Ca] in the soil solution. However, addition of hydrogen-ion increased [P], [Mn] and [Ca] in the soil solution. Lime addition mitigated the N addition-induced soil acidification, while it did not abolish the stimulatory effect of short-term N addition on leaf [P] and [Mn] of forbs. Therefore, we conclude that differences in the ecophysiological processes at the soil-root interface account for changes in leaf [P], [Ca] and [Mn] under short-term N addition, and that soil acidification aggravates the responses of these elements, especially [Ca] and [Mn], to long-term N enrichment.</li> <li><span>Synthesis: Our results highlight the contribution of belowground processes, especially those at the soil-root interface, to variation in plant element concentrations between dominant forbs and grasses in the temperate steppe. These findings greatly enhance our mechanistic understanding of the effects of N deposition on grassland communities.</span></li> </ol>
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
<p>A dye-sensitized solar cell was solvated by RTILs; using optimized empirical potentials, a molecular dynamics simulation was applied to compute vibrational properties. The obtained vibrational spectra were compared with experiment and ab initio molecular dynamics; various empirical potential spectra show how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction.</p>
Thermal regime and petrologic metamorphism in Alaska: Implications for subduction interface and wedge earthquakes
<p>Characterized by repeated large earthquakes, slow slips, and tectonic tremors with their simultaneous release of large amounts of energy, the unstable subduction interface beneath Alaska presents a chance to understand the composite dynamic transition from deep to shallow subduction channel where these enigmatic fault slips and seismic events occur. The complex subducted slab morphology associated with the frequent occurrence of various types of faulting behaviors in Alaska is poorly understood. Our result shows that the subduction of the Pacific plate and the subsequent release of large amounts of fluid likely contribute to the repeated fast and slow earthquakes there, as evidenced by the petrological metamorphic transition in the incoming plate. The offshore Alaska seismogenic zone, as well as the slow earthquakes identified near the Upper Cook Inlet, compare well with the distribution of slab dehydration slivers, including large destructive earthquakes that have occurred in Alaska. The fluid upwelling from dewatered oceanic crust and the continental wedge serpentinizing is probably related to various transportation pathways controlled by dip angle and upwell in the predominant direction following the subduction channel or veins in the overriding lithosphere.</p>
Social representations and interface layout: a new way of enhancing persuasive technology applied to organ donation
<p>Although campaigns promoting organ donation have proved their effectiveness, increasing the number of people who explicitly agree to become donors is still difficult. Based on the social marketing notion of persuasive technology, we reasoned that it was timely to focus on the design of this persuasive technology and to analyze its contribution in particularly challenging contexts such as organ donation. More specifically, the originality of the present study lay in the way we linked the field of persuasive technology to the theory of social representations, and combined them with an analysis of the ergonomic aspects of interface layout. This study had two complementary goals. The first was to determine whether the sociocognitive salience of the central elements of social representations (i.e., the most frequent and important themes related to the subject—here, organ donation—for individuals), can be used to achieve persuasive outcomes. The second was to determine whether interface layout, in terms of information location and background characteristics (color and contrast), can strengthen the persuasive impact. University students (<em>N</em> > 200) were exposed to a computer screen displaying a message involving either central or peripheral elements of the social representations of organ donation (status), placed either in the middle or on one side of the screen (location), and shown against either a white or a blue background (background). Eye-tracking data were recorded, in addition to self-reported data. In line with the elaboration likelihood model, results showed that participants who were exposed to central (vs. peripheral) elements of the social representations of organ donation followed the central route in processing information. Moreover, they had stronger attitudes, and more of them stated that they were <em>actual</em> organ donors. Importantly, however, at least for some variables, these status-related effects were not independent of the interface layout. More specifically, the persuasive impact of the central elements was enhanced when the information was displayed in the middle (vs. the side) of the screen and when it was displayed on a white (vs. blue) background. We discuss the theoretical and practical issues raised by these results.</p> <p> </p>
Brewster angle optical reflection observation of self-limiting nanoparticle monolayer self-assembly at a liquid/liquid interface
<p>Real-time optical reflection of incident <i>p</i>-polarized light near Brewster's angle shows that after drop-casting iron oxide nanoparticles (NPs) in heptane on top of a diethylene glycol (DEG) liquid substrate, an iron oxide NP layer forms at the DEG/heptane interface, and it self-limits to a monolayer even when there are excess NPs dispersed in the upper heptane phase. Most modes of NP self-assembly do not self-limit growth after the formation of a single monolayer. Observations are compared to a reflection model incorporating the reflectances expected at each interface. An effective medium model of the dielectric constant is used to model the reflectance of the NP layer at the DEG/heptane interface.</p>
Slab metamorphism and interface earthquakes in Peru: implications for along-strike fluid content and seismotectonic variation
<p>Evidenced by a typically shallow subducted thick mid-ocean ridge basalt (MORB) layer that dominates the subducting Nazca plate and a significant lack of arc magmatism, the Peruvian megathrust remain enigmatic in thermal regime and petrological metamorphism. Thermally controlled slab dehydration in the incoming plate may facilitate fluids release and migration which possibly causes fault instability and seismic and aseismic slips. We find that (1) the eclogitization of the MORB layer and the harzburgitization of the ultramafic layer, and the subsequent dehydration embrittlement probably affect interface seismicity in Peru; (2) the subduction of the Nazca Ridge separates southern Peru from north-central Peru, leading to a MORB-dominant oceanic lithosphere beneath Peru associated with an aseismic interface at depth and a lack of arc magmatism; (3) slab dehydration of >0.01 wt%/km accompanied by temperatures of 300-600°C possibly affect the occurrence of earthquakes and slips distributed on the hydrated interface. The along-strike fluid content variation possibly interprets the forearc seismotectonic segmentation associated with pore fluid pressure variation on megathrusts.</p>
Cumulative impacts of land cover change and dams on the land-water interface of the Tocantins River
<p>This dataset accompanies the manuscript entitled "Cumulative impacts of land cover change and dams on the land-water interface of the Tocantins River". It contains shapefiles and geoTIFF files.</p>
Data from: Biomechanics of shear-sensitive adhesion in climbing animals: peeling, pre-tension and sliding-induced changes in interface strength
Many arthropods and small vertebrates use adhesive pads for climbing. These biological adhesives have to meet conflicting demands: attachment must be strong and reliable, yet detachment should be fast and effortless. Climbing animals can rapidly and reversibly control their pads' adhesive strength by shear forces, but the mechanisms underlying this coupling have remained unclear. Here, we show that adhesive forces of stick insect pads closely followed the predictions from tape peeling models when shear forces were small, but strongly exceeded them when shear forces were large, resulting in an approximately linear increase of adhesion with friction. Adhesion sharply increased at peel angles less than ca 30°, allowing a rapid switch between attachment and detachment. The departure from classic peeling theory coincided with the appearance of pad sliding, which dramatically increased the peel force via a combination of two mechanisms. First, partial sliding pre-stretched the pads, so that they were effectively stiffer upon detachment and peeled increasingly like inextensible tape. Second, pad sliding reduces the thickness of the fluid layer in the contact zone, thereby increasing the stress levels required for peeling. In combination, these effects can explain the coupling between adhesion and friction that is fundamental to adhesion control across all climbing animals. Our results highlight that control of adhesion is not solely achieved by direction-dependence and morphological anisotropy, suggesting promising new routes for the development of controllable bio-inspired adhesives.
Data from: Hunger mediates apex predator's risk avoidance response in wildland-urban interface
1. Conflicts between large mammalian predators and humans present a challenge to conservation efforts, as these events drive human attitudes and policies concerning predator species. Unfortunately, generalities portrayed in many empirical carnivore landscape selection studies do not provide an explanation for a predator's occasional use of residential development preceding a carnivore-human conflict event. In some cases, predators may perceive residential development as a risk-reward tradeoff. 2. We examine whether state dependent mortality-risk sensitive foraging can explain an apex carnivore's (Puma concolor) occasional utilization of residential areas. We assess whether puma balance the risk and rewards in a system characterized by a gradient of housing densities ranging from wildland to suburban. Puma GPS location data, characterized as hunting and feeding locations, were used to assess landscape variables governing hunting success and hunting site selection. Hunting site selection behavior was then analyzed conditional on indicators of hunger state. 3. Residential development had a high energetic reward for puma, based on increases in prey availability and hunting success rates associated with increased housing density. Despite a higher energetic reward, hunting site selection analysis indicated that pumas generally avoided residential development, a landscape type attributed with higher puma mortality risk. However, when a puma experienced periods of extended hunger, risk avoidance behavior toward housing waned. 4. This study demonstrates that an apex carnivore faces a tradeoff between acquiring energetic rewards and avoiding risks associated with human housing. Periods of hunger can help explain an apex predator's occasional use of developed landscapes and thus the rare conflicts in the wildland-urban interface. Apex carnivore movement behaviors in relation to human conflicts are best understood as a three-player community level interaction incorporating wild prey distribution.
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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.
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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.