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283 results for “Bacillus subtilis”
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>
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. 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
Fig. 4 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 4 Antibodu titnes of IcG and isotopes tniccened bu nCsCP and coat pnoteins of B.s-CotC-CsCP spones via subcutaneous immunization noute. ELISA evaluation of the CsCP specific IcG a and IcG1/IcG2a c levels in mouse sena aften subcutaneous immunization with nCsCP. b Antibodu titnes of IcG induced bu nCsCP at week 6. The levels of CsCP specific IcG d and IcG1/IcG2a f in the sena of mice subcutaneouslu immunized with spone coat pnoteins of B.s-CotC-CsCP. Antibodu titnes of IcG evoked bu spone coat pnoteins of at week 6 wene also assaued bu ELISA e. Data wene displaued as the mean ± SD. *P <0.05; **P <0.01; ***P <0.001. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 containinc pEB03-CotC; nCP, punified nCsCP
Fig. 7 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 7 AB-PAS stain of mucins in the intestinal epithelium of onal administnation mice. Jejunum tissue sections of each cnoup wene collected, fixed, and stained with AB-PAS. Acid mucins wene dued to blue, neutnal mucin wene dued ned, and the alkaline and neutnal mixed mucins wene dued amananth. Panels a-b, c-d, e-f and g-h indicate PBS, B.s-CotC, BL21-CsCP and B.s-CotC-CsCP onallu administened cnoups at week 4, nespectivelu. Panels (i) and (j) show the B.s-CotC-CsCP cnoup tneated at week 6. Scale-bars: a, c, e, g, i, 200 μm; b, d, f, h, j, 50 μm. The annows indicate acidic mucins secneted bu coblet cells
Fig. 2 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 2 Expnession and identification of nCsCP and CotC-CsCP. a SDS-PAGE analusis of CsCP expnessed in E. coli BL21 and B. subtilis spones. The moleculan mass of CotC-CsCP fusion pnotein was appnoximatelu 43.8 kDa. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 hanbouninc pEB03-CotC; BL21-CP, BL21 hanbouninc pET28a-CsCP; nCP, punified nCsCP. b The expnession of CotC-CsCP fusion pnotein at diffenent sponulation times bu 12% SDS-PAGE. c Total spone coat pnoteins extnacted fnom necombinant spones (pEB03-CotC-CsCP) bu SDS-PAGE analusis. d Identification of CotC-CsCP fusion pnotein bu MS. e MALDI-TOF/TOF-MS analusis of punified nCsCP. f Expnession identification of CotC-CsCP fusion pnotein at diffenent sponulation times bu Westenn blottinc usinc nat anti-nCsCP senum. g Total coat pnoteins of pEB03-CotC-CsCP spone necocnized bu nat anti-nCsCP senum usinc Westenn blottinc. Abbreviations: P, pnecipitation; S, supennatant
Fig. 6 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 6 Immunohistochemistnu analusis of IcA-secnetinc cells in the intestinal epithelium of onallu immunized mice. IcA-secnetinc cells wene stained dank bnown. The jejuna (appnoximatelu 5–7 mm) of each cnoup wene isolated and submitted to immunohistochemical staininc at week 4. Panels (a) and (b) nepnesent PBS-tneated mice. Panels (c) and (d) nepnesent B.s-CotC onallu administened mice. Panels (e) and (f) nepnesent BL21-CsCP cavaced mice. Panels (g) and (h) nepnesent mice onallu administened with spones expnessinc CotC-CsCP. Scale-bars: a, c, e, g, 200 μm; b, d, f, h, 50 μm. The annows indicate IcA-secnetinc cells. i Intecnated option densitu (IOD) of IcA-secnetinc cells. ***P <0.001
Fig. 1 in The immunological characteristics and probiotic function of recombinant Bacillus subtilis spore expressing Clonorchis sinensis cysteine protease
Fig. 1 Schematic of the tneatment necimen. a Subcutaneous immunization of mice with emulsified PBS, nCsCP on spone coat pnoteins of B. s-CotCCsCP administened thnee times. Senum samples wene collected at 2, 4, 6 and 8 weeks. b Onal administnation of mice with PBS, spones of B.s-CotC on B.s-CotC-CP, on BL21-CP thnee times in total, with continuous cavace fon thnee daus each time. Senum, intestine and bile samples wene collected evenu 2 weeks. Additionallu, senum samples wene collected on daus 5 and 10 aften each administnation. Abbreviations: B.s-CotC-CP, WB600 containinc pEB03-CotC-CsCP; B.s-CotC, WB600 hanbouninc pEB03-CotC; BL21-CP, BL21 hanbouninc pET28a-CsCP
Annotated genome files of Bacillus subtilis AV1
Open the record for dataset details and reuse information.
Figure 4 in Saccharomyces cerevisiae OS303 expression of an alkaline protease from a newly isolated Bacillus subtilis D9
Figure 4. Analysis of expression cloning vector (digested and purified cloning vector pRS426/GAL1p-207-Glu-MS ligated with alkaline protease called in this study pRS426/GAL1p-207-Glu-MS/ alkaline-protease plasmids. Lane 1: DNA size marker hyperladder I; Lane 2: pRS426/GAL1p-207-Glu-MS/alkaline-protease linear plasmid around 8000bp; Lane 3: pRS426/GAL1p-207-Glu-MS vector. Lane 4: pRS426/GAL1p-MS vector.
Figure 1 in Saccharomyces cerevisiae OS303 expression of an alkaline protease from a newly isolated Bacillus subtilis D9
Figure 1. The electrophoresis of PCR product of alkaline protease gene from Bacillus subtilis D9. After PCR, 5Μl of the product was run on 1% agarose gel electrophoresis. The expected band of approximately1300bp was observed. Lane 1: DNA size marker hyperladder I; Lane 2: PCR product sample.
Exploring the Synergy of Enhanced Weathering and Bacillus subtilis: A Promising Strategy for Sustainable Agriculture
<p>Data: Exploring the Synergy of Enhanced Weathering and Bacillus subtilis: A Promising Strategy for Sustainable Agriculture</p>
Let There Be Light: Genome-reduction Enables Bacillus subtilis to Produce Disulfide-bonded Gaussia Luciferase
<p>Supplemental Material:</p> <ul> <li>Plasmid Maps in PNG format</li> <li>Plasmid Sequences in GB format</li> <li>Plasmid Sequences in DNA format (SnapGene)</li> </ul>
Spatiotemporal metabolome data from Bacillus subtilis swarm development
<p>Metabolome data and associated Matlab code used in the scientific article "Simultaneous spatiotemporal transcriptomics and microscopy of <em>Bacillus subtilis</em> swarm development reveal cooperation across generations" by the following authors: Hannah Jeckel*, Kazuki Nosho*, Konstantin Neuhaus, Alasdair D. Hastewell, Dominic J. Skinner, Dibya Saha, Niklas Netter, Nicole Paczia, Jörn Dunkel, Knut Drescher. The symbol "*" indicates an equal contribution.</p> <p>The Excel files AminoAcidResults.xslx and OrganicAcidResults.xlsx list raw data containing the positon and timepoints of sampling as well as metabolite concentrations given in µM. More details about these files are given in a ReadMe.txt file.</p> <p>The Excel file nSamples.xlsx summarizes the number of samples for each mean calculated during plotting.</p> <p>There are two m-files with Matlab code, which are used for plotting the metabolite data. To plot metabolite concentrations over time, open "displayData.m" and select the raw data file in lines 5 and 6. Then choose a path to save your data in line 9. Execute the Matlab script to obtain graphs.</p>
Spectral decomposition coefficients for spatiotemporal gene expression pattern identification in Bacillus subtilis swarm development
<p>Spectral decomposition coefficients, spatiotemporal gene expression pattern identification and multidimensional scaling coordinates of spatiotemporal transcriptomics data and image analysis results used to create Figure 2 in the scientific article "Simultaneous spatiotemporal transcriptomics and microscopy of <em>Bacillus subtilis</em> swarm development reveal cooperation across generations" by the following authors: Hannah Jeckel*, Kazuki Nosho*, Konstantin Neuhaus, Alasdair D. Hastewell, Dominic J. Skinner, Dibya Saha, Niklas Netter, Nicole Paczia, Jörn Dunkel, Knut Drescher. The symbol "*" indicates an equal contribution.</p> <p>This data consists of two excel sheets, one for the transcriptomics data and one for image analysis results (physical properties).</p> <p>Genes were ranked according to a spatiotemporal information score defined in the publication described above. For each gene, its name and ID (derived from locus tag) are given as identifiers. For information of reference genome used for mapping and convention on how gene names are chosen, see <a href="https://drescherlab.org/data/swarm-transcriptome/">https://drescherlab.org/data/swarm-transcriptome/</a>. Other columns in the sheet represent the spatiotemporal information score, assigned spatiotemporal pattern number, decomposition coefficient, multidimensional scaling coordinates and gene function.</p> <p>Physical properties are measured from short microscopy videos and defined in the publication mentioned above. This excel sheet contains property name, spatiotemporal information score, spectral decomposition coefficients and multidimensional scaling coordinates.</p>
Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms
<p>Data extracted from confocal microscopy associated with the paper "Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms"</p> <p>Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells, but it is unclear whether it has a role in the development of multicellular systems. Here, we show how stochastic pulsing of gene expression enables spatial patterns to form in a model multicellular system, Bacillus subtilis bacterial biofilms. We use quantitative microscopy and time-lapse imaging to observe pulses in the activity of the general stress response sigma factor σ<sup>B</sup> in individual cells during biofilm development. Both σ<sup>B</sup> and sporulation activity increase in a gradient, peaking at the top of the biofilm, even though σ<sup>B</sup> represses sporulation. As predicted by a simple mathematical model, increasing σ<sup>B</sup> expression shifts the peak of sporulation to the middle of the biofilm. Our results demonstrate how stochastic pulsing of gene expression can play a key role in pattern formation during biofilm development.</p>
Data from: Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas
<p>Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera like <em>Bacillus</em> and <em>Pseudomonas</em>, siderophores are often acclaimed for their function in biocontrol. Here, we set out to determine the functional role of the<em> Bacillus subtilis</em> siderophore bacillibactin in an antagonistic interaction with <em>Pseudomonas marginalis</em>. The presence of bacillibactin strongly influences the outcome of the interaction in an iron-dependent manner. A bacillibactin producer <em>B. subtilis</em> restricts the colony spreading of <em>P. marginalis</em>, repress the transcription of histidine kinase-encoding gene <em>gacS</em>, and thereby abolish production of secondary metabolites such as pyoverdine and viscosin. In contrast, the lack of bacillibactin restricts <em>B. subtilis</em> colony growth in a mechanism reminiscent of a siderophore tug-of-war for iron. Our study identifies a <em>Bacillus-Pseudomonas</em> interaction conserved across fluorescent <em>Pseudomonas spp.</em>, expanding our understanding of the interplay between two genera of the most well-studied soil microbes.</p>
DeepBacs – Bacillus subtilis denoising dataset
<p>Live-cell time series of vertically aligned <em>B. subtilis</em> cells expressing FtsZ-GFP protein fusion.</p> <p>Additional information can be found in this <a href="https://github.com/HenriquesLab/DeepBacs/wiki">github wiki</a>.</p> <p>The example shows raw and denoised images (Noise2Void 2D) of vertically aligned <em>B. subtilis</em> cells (VerCINI)</p> <p> </p> <p><strong>Data type</strong>: Fluorescence images of vertically oriented <em>B. subtilis </em>cells</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, Cells were imaged at 1 frame/second with continuous exposure for 2 minutes at 1-8 W/cm2</p> <p><strong>File format</strong>: .tiff (16-bit) </p> <p>One frame was selected from each time series</p> <p><strong>Image size</strong>: 1024x1024 px² (Pixel size: 65 nm)</p> <p><strong>Author(s)</strong>: Mia Conduit<sup>1</sup>, Séamus Holden<sup>1,2</sup></p> <p><strong>Contact email</strong>: Seamus.Holden@newcastle.ac.uk</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>
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