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3,169 results for “bat”
Plant pathogens provide clues to the origin of bat white-nose syndrome Pseudogymnoascus destructans
<p>Phylogenomic analyses of P. destructans.</p> <p>This is a snapshot of the GitLab repository available at https://gitlab.gwdg.de/molsysevol/pseudogymnoascus-destructans-phylogeny/.</p>
Acoustic lures increase tropical forest understorey bat captures
<p>Data used in the publication "Effectiveness of acoustic lures for increasing tropical forest understorey bat captures".</p>
The location and vegetation physiognomy of ecological infrastructures determine bat activity in Mediterranean floodplain landscapes
<p>Ecological infrastructures (EI), defined as natural or semi-natural structural elements, are important to support biodiversity and could play a crucial role in counteracting the well-known impacts of intensive agriculture. Yet, the importance of EI remains largely unexplored in Mediterranean agricultural landscapes and for species providing essential ecosystem services such as bats. Here, we evaluated the role of different EI types – in terms of location (riparian vs terrestrial) and vegetation physiognomy (woody vs non-woody) – in shaping bat guild activity in crop fields located in the floodplains of the Iberian Peninsula. We recorded 60,732 bat sequences in 96 crop fields and characterized 106 EI patches via an adaptation of the Biodiversity Potential Index (BPI). We found that the activity of mid-range echolocators (MRE) and long-range echolocators (LRE) was twofold higher when the nearest EI patch was riparian (i.e., contiguous to a watercourse) than when it was terrestrial. When assessing changes in bat activity in crop fields in relation to a gradient distance from EI types, our results revealed both distinct and similar effects of the location and vegetation physiognomy of the EI on bat guilds. For instance, while only the LRE guild positively responded to the proximity of woody EI, both MRE and LRE showed a marked increase of activity when increasing distances to non-woody EI, thus suggesting low bat activity levels near these features. Our habitat quality assessment also revealed that woody EI and riparian EI had higher biodiversity potential and related habitat quality, thus contributing to our understanding of bat responses to EI type in crop fields. As riparian areas are rarely targeted in biodiversity-friendly measures in farmland, we strongly recommend including riparian EI (especially the woody type) in conservation planning as they are crucial for both biodiversity conservation and ecosystem functioning.</p>
Data: Physical constraints on thermoregulation and flight drive morphological evolution in bats
<p>Body size and shape fundamentally determine organismal energy requirements by modulating heat and mass exchange with the environment and the costs of locomotion, thermoregulation, and maintenance. Ecologists have long used the physical linkage between morphology and energy balance to explain why the body size and shape of many organisms vary across climatic gradients, e.g., why larger endotherms are more common in colder regions. However, few modeling exercises have aimed at investigating this link from first principles. Body size evolution in bats contrasts with the patterns observed in other endotherms, probably because physical constraints on flight limit morphological adaptations. Here, we develop a biophysical model based on heat transfer and aerodynamic principles to investigate energy constraints on morphological evolution in bats. Our biophysical model predicts that the energy costs of thermoregulation and flight, respectively, impose upper and lower limits on the relationship of wing surface area to body mass (S-MR), giving rise to an optimal S-MR at which both energy costs are minimized. A comparative analysis of 278 species of bats supports the model’s prediction that S-MR evolves toward an optimal shape and that the strength of selection is higher among species experiencing greater energy demands for thermoregulation in cold climates. Our study suggests that energy costs modulate the mode of morphological evolution in bats—hence shedding light on a long-standing debate over bats’ conformity to ecogeographical patterns observed in other mammals—and offers a procedure for investigating complex macroecological patterns from first principles.</p>
Fig. 1 in Preliminary Study Of Habitat-Related Bat Fauna Of Mastouta-Bishshouk Region (Northwest Tunisia)
Fig. 1. Bat sampling sites in the Mastouta-Bishshouk region (Beja, Northwest Tunisia). 1 — Bridge of Beja Wadi, 2 — Artificial basin, 3 — Crop fields, 4 — Tunnel of water channel, 5 — Train abandoned tunnel.
Extended Data Fig. 7 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 7 | Analysis of the inter-subunitshydrogen bondsat the interfaceof RBDandhACE2. Frequencyofformationofhydrogenbondsat theinterface of RBDandhACE2 intheknob (A), base (B), andtipregions (C). Theanalysisisperformedfor 9 different MDsimulations:3 replicatesof the SARS-CoV-2 (shadesof green),BANAL-236 (shadesof red), and BANAL-52/103 (shadesofblue) RBD–hACE2 complexes.
Extended Data Fig. 3 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 3 | Nucleotideandamino-acidalignmentsof thefurin cleavagesiteregion. Completenucleotideandamino-acidspikesequencesof representativebat SARS-CoV-2-likecoronavirusesweredownloadedfrom GenBankand GISAIDandaligned with MAFFT (G-INS-I parameter) (A & C). Alignmentsweremanuallyeditedas proposedby Zhou2 andLytras47 with CLC Main Workbench (Qiagen) (B & D). Alignmentsof thefurincleavageregionare presentedatthenucleotide (A & B) andtheamino-acid (C & D) level, respectively.
Extended Data Fig. 1 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 1 | Spike identity matricesatthe genus level of representativesarbecoviruses. Amino-acid (lower) andnucleotide (upper) identitymatricesof Laotianandrepresentativehuman,bat, andpangolin sarbecoviruses.Spike N-terminal (NTD), Receptor-binding (RBD) and S2 nucleotideandamino-acidsequenceswerealigned with MAFFT, andidentity matriceswereconstructedusing CLCMain Workbench 21.0.4 (Qiagen). Matriceswerecoloredaccordingtotheidentityscale,from 25% (red) to 100% (green) of nucleotideoramino-acididentity.
Extended Data Fig. 2 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 2 | Alignmentofthespike RBDdomain. Protein alignmentof the Receptor Binding Domain (RBD) of Laotianandrepresentative human, batandpangolinsarbecoviruses.Sequenceswerealignedwith MAFFT in G-iNS-Imode. Residuesinteractingwithhuman ACE2 receptorare highlighted ingrey.Thedomainusedforinteractionsmodeling,basedonthe X-raystructure 6M0J (residues T333 to G526), ishighlightedbyablackline.
Fig. 2 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Fig. 2 | Recombinationevents in the evolutionaryhistoryof sarbecoviruses. Representationof the 15 recombinant fragmentsof relevant Sarbecovirus genomescomparedtothe SARS-CoV-2 humanprototypestrain (NC_045512). Thecoordinatesof thebreakpointsrefertothenucleotide positioninthealignment.Wherepossible,theclosestviralsequenceis indicatedforeachfragment.Inothercases,MULTindicatesagroupof multiple sequences.Theasteriskmarksunresolvedfragment phylogeny (fragment 13, from positions 27,344 to 27,800 inthealignment).Sequencesarecolouredas in Fig. 1. Thecomplete phylogeneticanalysesarepresentedin Supplementary Fig.2.
Fig. 1 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Fig. 1 | Genomicdescriptionofbat-bornesarbecovirusesidentifiedin Laos. a, Mapof samplingsites.All BANALisolateswerecollectedfromthesamesite (site 1). Themapwasdownloadedfrom DIVA-GIS (https://www.diva-gis.org/ gdata). b, Phylogeneticanalysisof theproteinsequenceof the RBDof Laotian andrepresentativehuman,bat,andpangolinsarbecoviruses.Sequenceswere alignedwith MAFFT (ref.49) inautomode, andmaximum-likelihood phylogeneticreconstructionwasperformedwith PhyMLimplemented throughthe NGPhylogenyportal50 withthe LG + Gsubstitutionmodel.Branch supportwasevaluatedwiththeaBayes parameter.Batspeciesarespecifiedin thename of thesequences.Sequencesarecolouredaccordingto Fig. 1c. c, Similarityplotanalysisof Laotianandrepresentativebatandpangolin sarbecovirusesbasedonthefull-lengthgenomesequenceof the SARS-CoV-2 humanprototypestrain (NC_045512, Wuhan-Hu-1) usedasareference. Theanalysiswasperformedwiththe SimPlotprogramversion 3.5.1 (ref.51) with the Kimuratwo-parametermodel, awindowsizeof 1,000 basepairs,astepsize of 100 basepairs,a transition/transversionrate (T/t) of 2.0, anda Gap/Strip parameter: on51. nsp,non-structural protein;RdRP, RNA-dependent RNA polymerase.d, Heatmapof identitiesattheproteinlevelof representative human,batandpangolinsarbecovirusescomparedtohuman SARS-CoV-2 lineage B (NC_045512). Spikeproteinhasbeendividedintofunctionaldomains, andthesequencesareorderedaccordingtopercentageof identityof the RBD domain.Theasteriskmarkstheabsenceof afunctional ORF10 in Thaibat RacCS203 (accessionnumber MW251308). Theheatmapwascreatedusingthe gplotspackagein R (version 3.6.3). AA, aminoacid.
Extended Data Fig. 5 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 5 | Additionalanalysisof the MDsimulationsof the BANAL-52/103 RBD–hACE2 complex. Comparisonof thetimeseriesof interface RMSDduringthecourseof two MDsimulationsof the BANAL-52/103 RBD–hACE2 complexwithshort (BANAL-52/103-CoV.1) andlong (BANAL- 52/103-CoV.1*) equilibrationphase.Thelargefluctuationsof theinterface RMSDareduetotheflexibilityof the RBDloopbetweenresidues S443 and Y449 (insets, inyellow).Whentheseresidueswerenotincludedinthe calculationof theinterface RMSD, thetimeseriesdisplayedamorestable behavior (BANAL-52/103-CoV.1-Land BANAL-52/103-CoV.1*-L).
Fig. 4 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Fig. 4 | BANAL-236 entryandpropagationinhumancells. a, Resultsof spike-pseudotyped BANAL-236 (squares) and SARS-CoV-2 (strain BetaCoV/ France/IDF0372/2020, GISAIDaccessionnumber EPI_ISL_406596,diamonds) pseudovirusentryassayin HEK-293T cellsexpressing (purple lines) ornot (grey lines) thehACE2 receptor,showninrelativeluminescenceunits (RLUs) producedbythefireflyluciferasepresentinthelentiviralbackbone andthe Bright-Gloluciferasesubstrate.Asingleexperimentperformedintriplicate representativeof twoexperiments isshown.Centrevaluesrepresentthe averageof thethreereplicatesanderrorbarsindicates.d. b, Resultsof spike-pseudotyped BANAL-236 (black) and SARS-CoV-2 (strain BetaCoV/ France/IDF0372/2020, grey) neutralizationassayexpressedas apercentageof neutralizationofluciferaseactivityintheabsenceof serum.Seraneutralizing SARS-CoV-2 werefrompatientswithconfirmedinfectionswhereas non-neutralizingserasampleswerecollectedbeforethespreadof SARS-CoV-2 Laos.Thedashedlinemarkstheneutralizationthreshold.Asingleexperiment representativeof threeindependentexperimentsisshown. c, Humancelllines expressingendogenous ACE2,Calu-3 (blue lines) and Caco-2 (green lines),were infectedatan MOIof 0.01 withthe BANAL-236 virus (squares) andthevirusfirst detectedin Wuhan (diamonds).VeroE6 cellswereinfectedatan MOI of 0.0001 with BANAL-236 virus (squares) and SARS-CoV-2 (strain BetaCoV/France/ IDF0372/2020, diamonds) pre-incubatedwith (grey lines) orwithout (pink lines) solublehACE2 (sACE2) at 25 Μgml−1 for 30 min. Genomecopynumberwas determinedbyquantitative RT-PCRinthesupernatantsrecovered 3 and 4 days post-infection. Asingleexperimentperformedintriplicateisshown.Centre valuesrepresenttheaverageof thethreereplicatesanderrorbarsindicates.d.
Fig. 3 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Fig. 3 | Dynamicsof thebindingof hACE2 to bat-sarbecovirus-borne RBDs andinsightintothestructureofthecomplex. a, Biolayerinterferometry (BLI) bindinganalysis of thehACE2 peptidasedomaintoimmobilized BANAL-52/103,BANAL-236 or SARS-CoV-2 RBDs.Black linescorrespondto aglobalfitof thedatausinga 1:1 bindingmodel.b, Frequencyofformationof saltbridgesclosetothe RBD–ACE2 interface (fromlefttoright:D30/K417, E35/ K493, D38/K493, K31/E35 and D38/K353) duringthecourseof the MD simulations.Theanalysiswasperformedforninedifferent MDsimulations (threereplicatesforeachcomplex) ofhACE2 incomplexwith RBDs from SARS-CoV-2 (SARS-CoV-2.1,SARS-CoV-2.2 and SARS-CoV-2.3, shadesof green), BANAL-236 (BANAL 236-CoV.1, BANAL 236-CoV.2 and BANAL 236-CoV.3,shadesof red) and BANAL-52/103 (BANAL 52/103-CoV.1, BANAL 52/103-CoV.2 and BANAL 52/103-CoV.3, shadesofblue). c, Ribbon representationsof thecrystalstructuresof thehACE2 peptidase domain (cyan) incomplexwith SARS-CoV-2 (PDB 6M0J) or BANAL-236 (this study,PDB 7PKI) RBDs (pink). Blackarrowsintheoverallstructuresindicatethestructural differencebetweenthetwocomplexesatthelevelofhelix H4. The magnificationsshowthemaininteractionsinthe ACE2–RBD interfaces. Residuesinthereceptor-bindingmotif alteredbetween SARS-CoV-2 and BANAL-236 arehighlighted withcolouredoutlines.Numbers 1, 2 and 3 indicate thethreemainclustersof interactionsbetweenhACE2 and RBDs.
Extended Data Fig. 4 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 4 | Analysisof thestability and conformational heterogeneityofRBD–hACE2 complexes. Timeseries (leftcolumn) and violinplots (rightcolumn) ofbackbone Root Mean Square Deviation (RMSD) fromtheinitial,energy-minimizedmodelcalculatedontheresiduesin RBD (A), hACE2 (B), attheinterface of RBDandhACE2 (C), andontheentirecomplex (D). Intheviolinplots,thewhitecirclecorrespondstothemedianvalue,the blackrectangleextendsfromthefirsttothethirdquantiles,andthethinblack linerepresentsthe 95% confidenceintervals.Populationof the 3 most significantclustersvisitedduringthecourseof the MDsimulations (E). Theanalysisisperformedfor 9 different MDsimulations:3 replicatesof the SARS-CoV-2 (shadesof green),BANAL-236 (shadesof red), and BANAL-52/103 (shadesofblue) RBD–hACE2 complexes.
Extended Data Fig. 8 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 8 | Stick representation. Stick representation of segments D364-S375 of BANAL-236 (left panel) and SARS-CoV-2 (right panel) RBDs.A 2Fo-Fc composite omit map (contoured at 3σ) is shown for this region in BANAL-236 RBD.
Extended Data Fig. 6 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 6 | Estimationof RBD–hACE2 bindingenergy. Time series (leftcolumn) andviolinplots (rightcolumn) of the RBD–hACE2 binding energyestimatedusing ROSETTA (A) and FoldX (B). Intheviolinplots,the whitecirclecorresponds tothemedianvalue,theblackrectangleextendsfrom thefirsttothethirdquantiles,andthethinblacklinerepresentsthe 95% confidenceintervals.Theanalysisisperformedfor 9 different MDsimulations: 3 replicatesof the SARS-CoV-2 (shadesof green), BANAL-236 (shadesof red), and BANAL-52/103 (shadesofblue) RBD–hACE2 complexes.
Extended Data Fig. 9 in Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
Extended Data Fig. 9 | Isolationof BANAL-236 on VeroE6 cells. (A) CPE observedon VeroE64 daysafterinoculationatan MOIof 10-4 fromthe C1. (B) Uninfected VeroE6 cellslayer.(C) Plaqueassayperformedfromthe C2 stock on VeroE6 cells.(D) Comparative CPEobservedon VeroE6 cellsinfectedwith SARS-CoV-2 ('Wuhan', toppanel) or BANAL-236 (bottom panel) inabsence (left) orinpresence (right) of soluble ACE2. Photosweretakenwitha EVOSXLCore microscopeatx10. Asingleexperimentperformedintriplicateisshownfor eachcellline.
Fig. 4 in Regional Recaptures Of Bats (Chiroptera, Vespertilionidae) Ringed In Eastern Ukraine
Fig. 4. Map of recaptures of N. noctula in Kharkiv Region (recaptures N 24 and 51), and the farthest recapture (N 50) from Kharkiv Region to Luhansk Region (research polygon N 3 according to fig. 1).
Fig. 1 in Regional Recaptures Of Bats (Chiroptera, Vespertilionidae) Ringed In Eastern Ukraine
Fig. 1. Map of Kharkiv Region with territories of main recaptures: 1 — recaptures within Kharkiv City and surroundings; 2 — recaptures in NNP "Homilsha Forest"; 3 — recaptures outside of Kharkiv Region.
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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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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.
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