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283 results for “Bacillus subtilis”
Reconciliation of regulatory data: the regulatory networks of Escherichia coli and Bacillus subtilis
<p>The dataset hereby uploaded, presents state-of-art, reconciled transcriptional regulatory networks of <em>Escherichia coli </em>K12 MG1655<em> </em>and <em>Bacillus subtilis </em>str 168<em>. </em>The networks were reconciled through the retrieval and integration of relevant regulatory data from multiple resources, including databases, such as <em>RegulonDB </em>and <em>DBTBS</em> as well as available literature.</p>
DeepBacs – Bacillus subtilis fluorescence segmentation dataset
<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 and the manually annotated segmentation mask.</p> <p> </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) or .png (8-bit)</p> <p>For segmented masks, binary masks are used for training of CARE/U-Net models, 8-bit .tif ROI maps for training of StarDist models and .png images for training of pix2pix models</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</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>
Raw holograms frames of Bacillus Subtilis at different temperatures
<p class="MsoNormal">We describe a system for high-temperature investigations of bacterial motility using a digital holographic microscope completely submerged in heated water. Temperatures above 90 ºC could be achieved, with a constant 5 ºC offset between the sample temperature and the surrounding water bath. Using this system, we observed active motility in <em>Bacillus subtilis</em> up to 66 ºC. As temperatures rose, most cells became immobilized on the surface, but a fraction of cells remained highly motile at distances of > 100 µm above the surface. Suspended non-motile cells showed Brownian motion that scaled consistently with temperature and viscosity. A novel open-source automated tracking package was used to obtain 2D tracks of motile cells and quantify motility parameters, showing that swimming speed increased with temperature until ~40 ºC, then plateaued. These findings are consistent with the observed heterogeneity of <em>B. subtilis</em> populations, and represent the highest reported temperature for swimming in this species. This technique is a simple, low-cost method for quantifying motility at high temperatures and could be useful for investigation of many different cell types, including thermophilic archaea.</p>
Figure 2 in Saccharomyces cerevisiae OS303 expression of an alkaline protease from a newly isolated Bacillus subtilis D9
Figure 2. Analysis cloning vector construction containing alkaline protease gene with restriction enzymes to confirm the integrity of the PCR product of alkaline protease gene and to design the appropriate primers to construct the expression vector. By the enzyme combination of NheI- NdeI- BamHI restriction enzymes showed two bands of approximately 3000bp and ~1300bp must be shown as alkaline protease gene. Lane 1: DNA size marker hyperladder I; Lane 2, 3, 4, and 5: Digested sample of TA Cloning vector construction containing alkaline protease with enzyme SpeI, EcoRI, XbaI, and NheI- NdeI- BamHI respectively.
Figure 3 in Saccharomyces cerevisiae OS303 expression of an alkaline protease from a newly isolated Bacillus subtilis D9
Figure 3. 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. To screen the recombinant plasmids, the plasmids prepared from colonies were digested with double restriction enzymes and then were run on 0.8% agarose gel electrophoresis. Lane 1: DNA size marker hyperladder I; Lane 2, 3: pRS426/GAL1p-207-Glu-MS/alkaline-protease plasmid digested with BamHI and SpeI, after digestion, two bands of>6000bp and <1500bp observed.
Data from: Use of a microfluidic platform to uncover basic features of energy and environmental stress responses in individual cells of Bacillus subtilis
Bacteria use a variety of stress-sensing systems to sense and respond to diverse stressors and to ensure their survival under adverse conditions. The gram-positive bacterium Bacillus subtilis responds to energy stress (ATP depletion) and to environmental stressors using two distinct stress-sensing pathways that converge on the alternative sigma factor σB to provoke a general stress response. Past efforts to study the σB stress response in bulk culture and on agarose pads were unable to visualize the responses of individual cells under tightly controlled conditions for extended periods of time. Here we use a microfluidics-based strategy to discern the basic features of σB activation in single cells in response to energy and environmental stress, both immediately upon stressor exposure and for tens of generations thereafter. Upon energy stress at various levels of stressor, cells exhibited fast, transient, and amplitude-modulated responses but not frequency modulation as previously reported. Upon environmental stress, which is mediated by the stressosome complex, wild-type cells primarily exhibited a transient and amplitude-modulated response. However, mutant cells producing only one of the four paralogous RsbR stressosome proteins showed striking and previously unseen differences. Whereas RsbRA-only cells mimicked the wild type, RsbRC-only cells displayed a slower but sustained overall response composed of repeated activation events in single cells.
The Development of a COVID19 Oral Vaccine Consisting of Bacillus Subtilis Spores
ClinicalTrials.gov study NCT05057923. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Preliminary Clinical Study on the Effect of Bacillus Subtilis on the Efficacy of Infliximab in Patients With Crohn's Disease
ClinicalTrials.gov study NCT07123207. IPD Sharing: NO. Countries: 1. Publications: 0.
Safety and Tolerability of Bacillus Subtilis MB40 in Healthy Adult Volunteers
ClinicalTrials.gov study NCT04655352. IPD Sharing: NO. Countries: 0. Publications: 1.
Data from: The effects of Bacillus subtilis on Caenorhabditis elegans fitness after heat stress
Open the record for dataset details and reuse information.
Raw holograms frames of Bacillus Subtilis at different temperatures
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Data from: Use of a microfluidic platform to uncover basic features of energy and environmental stress responses in individual cells of Bacillus subtilis
Open the record for dataset details and reuse information.
Bacillus subtilis spores PROTECT experiment Space-exposed and Mars-exposed vs. Earth-control
Because of their ubiquity and resistance to spacecraft decontamination bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return spores were germinated total RNA extracted and fluorescently labeled and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response SP-beta prophage induction) protein damage (CtsR/Clp system) oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars. Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.
HARV replication of the BRIC-23 Bacillus subtilis spaceflight
Previous spaceflight experiments using Bacillus subtilis have reported altered transcriptome profiles during spaceflight compared to matching ground samples. This study tried to replicate those transcriptome changes using High Aspect Ratio Vessels (HARVs). B. subtilis spores were grown in HARVs using the same protocol and growth conditions as the BRIC-23 spaceflight mission. RNA was extracted from the HARV samples and sequenced for differential expression analysis. HARV differentially expressed genes were then compared to the genes identified as differentially expressed in the BRIC-23 mission to access the accuracy of HARVs as a model for spaceflight experiments.
HARV replication of the BRIC-21 Bacillus subtilis spaceflight samples
Previous spaceflight experiments using Bacillus subtilis have reported altered transcriptome profiles during spaceflight compared to matching ground samples. This study tried to replicate those transcriptome changes using High Aspect Ratio Vessels (HARVs). B. subtilis spores were grown in HARVs using the same protocol and growth conditions as the BRIC-21 spaceflight mission. RNA was extracted from the HARV samples and sequenced for differential expression analysis. HARV differentially expressed genes were then compared to the genes identified as differentially expressed in the BRIC-21 mission to access the accuracy of HARVs as a model for spaceflight experiments.
Analysis of the messenger RNAs in Spores of Bacillus subtilis
GEO Series GSE125530. Bacillus subtilis. 9 samples. Type: Expression profiling by high throughput sequencing.
An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.
GEO Series GSE67023. Bacillus subtilis. 268 samples. Type: Expression profiling by array.
Undomesticated Bacillus subtilis RemA regulon
GEO Series GSE47409. Bacillus subtilis. 3 samples. Type: Expression profiling by array.
Tn-seq of hydroxyurea treated Bacillus subtilis cells
GEO Series GSE169564. Bacillus subtilis. 22 samples. Type: Other.
Transcriptional profiling of Bacillus subtilis WT (ABS2005) and ydcH mutant (ASEC56)
GEO Series GSE104816. Bacillus subtilis. 12 samples. Type: Expression profiling by high throughput sequencing.
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