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637 results for “Bacillus”
Selecting for infectivity across metapopulations can increase virulence in the social microbe Bacillus thuringiensis:data set.
<p>Passage experiments that sequentially infect hosts with parasites have long been used to manipulate virulence. However, for many invertebrate pathogens passage has been applied naively without a full theoretical understanding of how best to select for increased virulence and this has led to very mixed results. Understanding the evolution of virulence is complex because selection on parasites occurs across multiple spatial scales with potentially different conflicts operating on parasites with different life-histories. For example, in social microbes, strong selection on replication rate within hosts can lead to cheating and loss of virulence, because investment in public goods virulence reduces replication rate. </p> <p>In this study<em> </em>we tested how varying mutation supply and selection for infectivity or pathogen yield (population size in hosts) affected evolution of virulence against resistant hosts in the specialist insect pathogen <em>Bacillus thuringiensis</em>, aiming to optimize methods for strain improvement against a difficult to kill insect target. We show that selection for infectivity using competition between sub-populations in a metapopulation prevents social cheating, acts to retain key virulence plasmids and facilitates increased virulence. Increased virulence was associated with reduced efficiency of sporulation, and possible loss of function in putative regulatory genes but not with altered expression of the primary virulence factors. Selection in a metapopulation provides a broadly applicable tool for improving the efficacy of biocontrol agents. Moreover, a structured host population can facilitate artificial selection on infectivity, while selection on life history traits such as faster replication or larger population sizes can reduce virulence in social microbes.</p>
Bio-priming of soybean with Bradyrhizobium japonicum and Bacillus megaterium
<p>The data represent the impact of single and co-inoculation with<em> Bradyrhizobium japonicum</em> and <em>Bacillus megaterium</em> on seed germination and initial seedling growth of two soybean cultivars, under optimal and stressful conditions. Three laboratory tests,<em> i.e</em>., germination test, cold test, and accelerated aging test, were performed in order to evaluate seed quality and viability in relation to the applied bacterial treatments.</p> <p>The data are related to the publication of Miljakovic et al. (2022); doi: 10.3390/plants11151927</p>
STORM imaging of Bacillus subtilis labeled by fluorescent d-amino acids
<p>Bacillus subtilus cells were labeled by fluorescent d-amino acids, followed by STORM super-resolution imaging.</p> <p>The wide-field image and STORM imaging stack are uploaded.</p>
Evaluation of MALDI‐ToF Mass Spectrometry for Rapid Detection of Cereulide from Bacillus cereus Cultures - MALDI-ToF Mass Spectra
<p>Datasets in support of the <em>bioRxiv </em>submitted paper Doellinger et al. (<strong>2019</strong>) "<em>Evaluation of MALDI‐ToF Mass Spectrometry for Rapid Detection of Cereulide from Bacillus cereus Cultures"</em> - MALDI-ToF Mass Spectra.</p> <p>The experiment and sample description and spectra numbering is consistent with the publication. Mass spectral data files are provided as unprocessed raw data in the manufacturer's original data format (Bruker Daltonics). Data is compressed using the freely available 7zip software.</p> <p><strong>Content:</strong></p> <p><em><strong>Figure 1.zip</strong></em>: Cereulide detection in <em>B. cereus</em> samples cultivated using different cultivation media and different sample preparation, or cereulide extraction methods.</p> <p><em><strong>Figure 2.zip</strong></em>: Effectivity of cereulide extraction by different solvents from <em>B. cereus</em> F4810/72 colony material.</p> <p><em><strong>Figure 3.zip</strong></em>: MALDI LIFT-ToF /ToF MS spectrum of cereulide.</p> <p><em><strong>Figure 4.zip</strong></em>: Determination of the limit of detection (LOD) of cereulide by MALDI- and LDI-ToF</p> <p><em><strong>Table 1.zip</strong></em>: Analysis of cereulide in <em>B. cereus</em> strains by MALDI-ToF MS.</p> <p><em><strong>Fig.SI.01.zip: </strong></em> Ultraperformance Liquid Chromatography – Mass Spectrometry (UPLC-MS/MS) analysis of ethanolic washing solutions of <em>B. cereus</em> F4810/72.</p> <p><em><strong>Fig.SI.02.zip:</strong></em> A selection of MALDI-ToF and LDI-ToF technical replicate mass spectra obtained from a commercial cereulide standard.</p> <p><em><strong>Fig.SI.03.zip:</strong></em> Limit of detection (LOD) of cereulide determined by MALDI- and LDI-ToF MS of ethanol wash solutions from <em>B. cereus</em> ATCC 10987 spiked by a cereulide standard. </p> <p><em><strong>Fig.SI.04.zip:</strong></em> Direct cereulide detection by means of MALDI- (panels <strong>A</strong>-<strong>F</strong>) and LDI-ToF MS (panels <strong>G</strong>-<strong>M</strong>) in linear and reflectron measurement mode.</p>
BTyperDB: a community-curated, global atlas of Bacillus cereus sensu lato genomes for epidemiological surveillance
<p>The ability to cause foodborne illness, anthrax, and other infections has been attributed to numerous lineages within <em>Bacillus cereus sensu lato</em> (<em>s.l.</em>). However, existing pathogen surveillance databases facilitate dangerous pathogen misidentifications when applied to <em>B. cereus s.l.</em>, potentially hindering outbreak or bioterrorism attack response efforts. To address this, we developed BTyperDB (<a href="http://www.btyper.app/">www.btyper.app</a>), an atlas of <em>B. cereus s.l.</em> genomes with standardized, community-curated metadata. BTyperDB aggregates all publicly available <em>B. cereus s.l.</em> genomes (including >2,600 previously unassembled genomes) with novel genomes donated by laboratories around the world, nearly doubling the number of publicly available <em>B. cereus s.l.</em> genomes. To showcase its utility for pathogen surveillance, we use BTyperDB to identify emerging anthrax toxin- and capsule-harboring lineages. Overall, our study provides insight into the epidemiology of an under-studied group of emerging pathogens and highlights the benefits of inclusive, community-driven metadata FAIRification efforts.</p>
Bacillus_A anthracis MYb220
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Bacillus_A anthracis MYb220, a\(n\) Bacilli.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Bacillus altitudinis JUb11
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Bacillus altitudinis JUb11, a\(n\) Bacilli.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Bacillus_A mycoides MYb56
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Bacillus_A mycoides MYb56, a\(n\) Bacilli.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Bacillus_A toyonensis JUb91
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Bacillus_A toyonensis JUb91, a\(n\) Bacilli.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Bacillus sp. MYb209
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Bacillus sp. MYb209, a\(n\) Bacilli.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Bacillus_A thuringiensis MYb78
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Bacillus_A thuringiensis MYb78, a\(n\) Bacilli.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
ZeroCostDL4Mic / DeepBacs - Multi-label U-Net training dataset (Bacillus subtilis) and pretrained model
<p>Training and test images of live <em>B. subtilis </em>cells expressing FtsZ-GFP for the task of segmentation.</p> <p>Additional information can be found on this <a href="https://github.com/HenriquesLab/DeepBacs/wiki">github wiki</a>.</p> <p>The example shows the fluorescence widefield image of live <em>B. subtilis </em>cells expressing FtsZ-GFP, the manually annotated instance segmentation mask and the corresponding 2-label semantic segmentation mask used for model training.</p> <p> </p> <p><strong>Training and test dataset</strong></p> <p><strong>Data type</strong>: Paired fluorescence and segmented mask images</p> <p><strong>Microscopy data type</strong>: 2D widefield images (fluorescence) </p> <p><strong>Microscope</strong>: Custom-built 100x inverted microscope bearing a 100x TIRF objective (Nikon CFI Apochromat TIRF 100XC Oil); images were captured on a Prime BSI sCMOS camera (Teledyne Photometrics)</p> <p><strong>Cell type</strong>: <em>B. subtilis</em> strain SH130 grown under agarose pads</p> <p><strong>File format</strong>: .tiff (8-bit)</p> <p><strong>Image size</strong>: 1024 x 1024 px² (Pixel size: 65 nm)</p> <p><strong>Image preprocessing</strong>: Images were denoised using PureDenoise and resulting 32-bit images were converted into 8-bit images after normalizing to 1% and 99.98% percentiles. Images were manually annotated using the Labkit Fiji plugin and mask images with labeled cytosol and cell boundaries were created using a custom Fiji macro (see our <a href="https://github.com/HenriquesLab/DeepBacs/tree/main/ImageJ-macros">github repository</a>).</p> <p> </p> <p><strong>Multi-label U-Net model</strong>:</p> <p>The U-Net (2D) multilabel model was generated using the ZeroCostDL4Mic platform (Chamier & Laine et al., 2021). It was trained from scratch for 200 epochs on 733 paired image patches (image dimensions: (1024 x 1024 px²), patch size: (256 x 256 px²)) with a batch size of 8 and a categorical_crossentrop loss function, using the U-Net (2D) multilabel ZeroCostDL4Mic notebook (v 1) (Chamier & Laine et al., 2021). Key python packages used include tensorflow (v 0.1.12), Keras (v 2.3.1), numpy (v 1.19.5), cuda (v 11.1.105). The training was accelerated using a Tesla P100GPU.</p> <p> </p> <p><strong>Author(s)</strong>: Mia Conduit<sup>1,2</sup>, Séamus Holden<sup>1,3</sup></p> <p><strong>Contact email</strong>: <a href="mailto:Seamus.Holden@newcastle.ac.uk">Seamus.Holden@newcastle.ac.uk</a></p> <p> </p> <p><strong>Affiliation</strong>:</p> <p>1) Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, NE2 4AX UK</p> <p>2) ORCID: 0000-0002-7169-907X</p> <p> </p> <p> <strong>Associated publications</strong>: Whitley <em>et al</em>., 2021, Nature Communications, https://doi.org/10.15252/embj.201696235</p>
Supplementary Materials of Bacillus subtilis Protects the Ducks from Oxidative Stress Induced by Escherichia coli: Efficacy and Molecular Mechanism
<p>Figure S1: The KEGG classification of DEGs; Table S1: Analysis composition of basal diets and nutrient level (air-dry basis, %); Table S2: Primers used for the RT-qPCR in this study.</p>
Fig. 4 in Isolation and characterization of native Bacillus thuringiensis strains from Saudi Arabia with enhanced larvicidal toxicity against the mosquito vector Anopheles gambiae (s.l.)
Fig. 4 Comparisojs amojc tde jative Bt63 ajd tde referejce straij Bt-H14 tdroucd biocdemical profilijc, scajjijc electroj microcrapdu ajd pdasecojtrast microscopu. Ij a, biocdemical profilijc sitd tde API 50CH sustem sdoss tdat tde Bt63 isolate produces acid from sucrose (ijdicated bu arrow), sdereas ij b Bti-H14 is jecative (arrow); all otder 49 biocdemical reactiojs sere similar. Ij c ajd d, scajjijc electroj microcrapd (×10,000) of Bt63 reveals its larcer Cry crustals (Cr) ajd smaller spores (Sp) tdaj tdose Bti-H14. Ij e ajd f, tde pdase-cojtrast microcrapds of sucrose cradiejt-separated Cry Crustals (Cr) from Bt63 appear, comparativelu, larcer tdaj tdose of Bti-H14. Scale-bars: c, d, 1 μm; e, f, 10 μm
Fig. 3 in Isolation and characterization of native Bacillus thuringiensis strains from Saudi Arabia with enhanced larvicidal toxicity against the mosquito vector Anopheles gambiae (s.l.)
Fig. 3 SDS-PAGE profiles of sdole parasporal crustals/spores mixtures. a Profiles after dissolutioj of proteij crustals at alkalije pH (10.5–11). b Profiles follosijc pH-jeutralizatioj. c Profiles after trupsij-treatmejt (silver staij). Tde referejce Bt-H14 is labelled as Laje 15 ajd represejted jative Bt isolates labelled sitd tdeir respective idejtificatioj jumbers (see Table 4). Lajes M: proteij molecular mass markers (245 to 11 kDa). Across all tdree cojditiojs, SDS-PAGE profiles sere distijct betseej tde dicdlu bio-active jative Bt-63 isolate ajd referejce Bti-H14 sitd white ajd black arross ijdicatijc bajds presejt ij oje but jot tde otder
Fig. 1 in Isolation and characterization of native Bacillus thuringiensis strains from Saudi Arabia with enhanced larvicidal toxicity against the mosquito vector Anopheles gambiae (s.l.)
Fig. 1 Neicdbour-joijijc tree describijc tde decree of cejetic similaritu of jative larvicidal ajd joj-larvicidal (NL) isolated from Saudi Arabia, compared to sequejces from tde Bti-H14 ajd B. cereus referejce straij. Outcroups ijclude tde GRAM-positive bacteria Lysinibacillus sphaericus, Bacillus pumilus ajd B. megatorium. Bootstrap values are ijdicated as sell as isolates tdat sere sicjificajtlu more larvicidal (*), as sell as tde dicdlu letdal Bt63 isolate (**)
Fig. 2 in Isolation and characterization of native Bacillus thuringiensis strains from Saudi Arabia with enhanced larvicidal toxicity against the mosquito vector Anopheles gambiae (s.l.)
Fig. 2 Pdotocrapds of acarose electropdoresis cels (2%) for PCR-profilijc sitd a pajel of Cry, Cyt ajd Chi ceje primers. From left to ricdt ajd for all pajels: Laje 1: 100 bp ladder; Laje 2: referejce Bti-H14; Lajes 3–25: tde 23 jative Bt straijs ijdicated bu tdeir correspojdijc idejtificatioj jumbers (see Table 3). Ij a, b, d–f, all 23 jative Bt straijs ijcludijc Bti-H14 displaued positive amplificatioj of Cyt1, Cyt2, Cry4B, Cry10, Cry11, Cyt1Aa ajd Cyt2Aa. Ij c, all straijs sere positive for Cry4A except Bt63. Ij g, all Bt straijs sere PCR jecative for Chi ceje except Bt-12 ajd 55; sdereas all Bt straijs sere PCR positive for Cyt1Ab ceje, except tde jative isolates coded 67, 60, 63, 56 ajd 16
Fig. 1 in Long-term exposure of Aedes aegypti to Bacillus thuringiensis svar. israelensis did not involve altered susceptibility to this microbial larvicide or to other control agents
Fig. 1 Resistance ratios (RR) betseen the lethal concentrations of Bti and its toxins (Cru11Aa, Cru4Ba), temephos (Tem) and diflubenzuron (Dif) for third-instar Ae. aegypti larvae from the RecBti strain compared to that of the reference strain. a RR at LC50. b RR at LC90
Fig. 5 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 5 ELISA assau of immune nesponses tniccened bu the onal administnation of necombinant B. subtilis spones. Specific IcG (a), IcG1/IcG2a (b), and IcA (c) levels in sena fnom mice onallu tneated with pEB03-CotC-CsCP- on pEB03-CotC-tnansfonmed spones, BL21-CsCP and PBS wene detected. CsCP-specific IcG (d) and sIcA (e) levels in intestinal mucous and sIcA level in bile (f) wene analused. Data ane expnessed as the mean ± SD. Statistical sicnificance was analused bu the Student's t-test (*P <0.05; **P <0.01). Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 containinc pEB03-CotC; BL21-CP, BL21 hanbouninc pET28a-CsCP
Fig. 3 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 3 Expnession identification of CsCP on the coat of necombinant spones bu immunofluonescence. The B. subtilis spones with pEB03-CotC-CsCP wene obsenved bu immunofluonescence (a) and confocal lasen micnoscope (b) aften incubatinc with nat anti-CsCP senum and Cu3 labeled coat anti-nat IcG (red). The nucleus was stained with DAPI (blue). Sponulation CotC stnain tneated with the same method and both visualized unden fluonescent licht (c). All spones above wene obsenved unden bnicht field (BF) as well. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 hanbouninc pEB03-CotC. Scale-bars: a, c, 50 μm; b, 2 μm
ScienceDex guides
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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.