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871 results for “escherichia coli”
Processed mass spectrometry data - systematic identification of allosteric effectors in Escherichia coli metabolism
<p>MATLAB files of processed mass spectrometry data, i.e. full data table after peak picking, annotation and quantification. Additionally, for each of the tested enzymes, the relevant ion traces of substrates and products are extracted, sorted by timepoint and replicate and saved in separate tables.</p>
DeepBacs – Escherichia coli MreB denoising dataset and CARE model
<p>Training and test images of MreB-sfGFP<sup>sw</sup> expressing <em>E. coli </em>cells for image denoising, as well as a trained CARE model.</p> <p>Additional information can be found on our <a href="https://github.com/HenriquesLab/DeepBacs/wiki">github wiki</a>.</p> <p>The example images show confocal images of labelled <em>E. coli</em> MreB filaments at low and high SNR.</p> <p> </p> <p><strong>Training and test dataset:</strong></p> <p> </p> <p><strong>Data type</strong>: Paired microscopy images (fluorescence)</p> <p><strong>Microscopy data type</strong>: Confocal fluorescence images</p> <p><strong>Microscope</strong>: Leica SP8 confocal microscope with a 1.40 NA 63x oil immersion objective </p> <p><strong>Cell type</strong>: <em>E. coli</em> strain NO34 expressing MreB-sfGFPsw fusion protein (kindly provided by Zemer Gitai) </p> <p><strong>File format</strong>: .tif (16-bit)</p> <p><strong>Image size</strong>: 512x512 (Pixel size: 45 nm)</p> <p> </p> <p>The CARE 2D model was generated using the ZeroCostDL4Mic platform (Chamier et al., 2021). It was trained from scratch for 100 epochs (600 steps/epoch) on 1500 paired image patches (image dimensions: (512 x 512 px²), patch size: (64 x 64 px²), 50 patches/image) with a batch size of 8 and a laplace loss function, using the CARE 2D ZeroCostDL4Mic notebook (v 1). Key python packages used include tensorflow (v 0.1.12), Keras (v2.3.1), csbdeep (v 0.6.3), numpy (v 1.21.5), cuda (v 11.1.105). The training was accelerated using a Tesla K80 GPU and data was augmented by a factor of 4 using rotation and flipping.</p> <p>The model weights can be used with the ZeroCostDL4Mic CARE 2D notebook and the CSBDeep Fiji plugin.</p> <p> </p> <p><strong>Author(s)</strong>: Christoph Spahn<sup>1,2</sup>, Mike Heilemann<sup>1,3</sup></p> <p><strong>Contact email</strong>: christoph.spahn@mpi-marburg.mpg.de</p> <p> </p> <p><strong>Affiliation(s)</strong>: </p> <p>1) Institute of Physical and Theoretical Chemistry, Max-von-Laue Str. 7, Goethe-University Frankfurt, 60439 Frankfurt, Germany</p> <p>2) ORCID: 0000-0001-9886-2263 </p> <p>3) ORCID: 0000-0002-9821-3578</p>
Wildtype Escherichia coli and Enterococcus lactis isolated from HK WWTP
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Data from: Escherichia coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity
There is considerable understanding about how laboratory populations respond to predictable (constant or deteriorating environment) selection for single environmental variables such as temperature or pH. However, such insights may not apply when selection environments comprise multiple variables that fluctuate unpredictably, as is common in nature. To address this issue, we grew replicate laboratory populations of Escherichia coli in nutrient broth whose pH and concentrations of salt (NaCl) and hydrogen peroxide (H2O2) were randomly changed daily. After ~170 generations, the fitness of the selected populations had not increased in any of the three selection environments. However, these selected populations had significantly greater fitness in four novel environments which have no known fitness-correlation with tolerance to pH, NaCl or H2O2. Interestingly, contrary to expectations, hypermutators did not evolve. Instead, the selected populations evolved an increased ability for energy-dependent efflux activity that might enable them to throw out toxins, including antibiotics, from the cell at a faster rate. This provides an alternate mechanism for how evolvability can evolve in bacteria and potentially lead to broad-spectrum antibiotic resistance, even in the absence of prior antibiotic exposure. Given that environmental variability is increasing in nature, this might have serious consequences for public health.
Data from: Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size
In vitro and in vivo evolution experiments on Escherichia coli revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of E. coli in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant E. coli clone ED1a belonging to B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed amutation rate of 6.90x10-7 per base per year of the chromosome for E. coli ED1a in healthy human gut. We observed a very limited genomic diversity, and could not detect any evidence of selection contrary to what is observed in experimental evolution over similar length of time. We therefore suggest that ED1a being well adapted to the healthy human gut evolves mostly neutrally with a low effective population size (Ne ≈ 500 – 1700).
Data for "A massively parallel double selection workflow for the evolution of molecular switches based on surface-display in Escherichia coli" by Givelet, et al., 2023
<p>Data related to a publication on "A massively parallel double selection workflow for the evolution of molecular switches based on surface-display in Escherichia coli"</p> <p> </p> <p>The data contains</p> <p>- FACS data for the images (organized in folders)<br> - images (tiff and jpg)<br> - sequence data (fasta)<br> - one video (mov)</p>
Dose Escalating Study of a Prototype CS6 Subunit Vaccine With a Modified Heat-labile Enterotoxin From Enterotoxigenic Escherichia Coli (ETEC)
ClinicalTrials.gov study NCT03404674. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Resistance Profile of Escherichia Coli in Infections of Community Origin: The Importance of Antimicrobial Stewardship
ClinicalTrials.gov study NCT06305455. IPD Sharing: NO. Countries: 0. Publications: 5.
A Phase Ⅳ Clinical Trial of the Recombinant Hepatitis E Vaccine (Escherichia Coli)(the Chronic Hepatitis B Patients )
ClinicalTrials.gov study NCT02964910. IPD Sharing: YES. Countries: 1. Publications: 0.
Characteristics of Lower Respiratory Tract Escherichia Coli Isolates in Mechanically Ventilated Intensive Care Patients
ClinicalTrials.gov study NCT03303937. IPD Sharing: UNDECIDED. Countries: 0. Publications: 5.
A Study of 9-valent Extraintestinal Pathogenic Escherichia Coli Vaccine (ExPEC9V) and High-dose Quadrivalent Influenza Vaccine, With and Without Co-administration, in Adults Aged 65 Years or Older
ClinicalTrials.gov study NCT06134804. IPD Sharing: YES. Countries: 4. Publications: 0.
Data from: Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli
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Data from: Adaptation of Escherichia coli to glucose promotes evolvability in lactose
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Data from: Homeostasis of metabolites in Escherichia coli on transition from anaerobic to aerobic conditions and the transient secretion of pyruvate
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Data from: Parallelism in adaptive radiations of experimental Escherichia coli populations
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Data from: Synonymous genetic variation in natural isolates of Escherichia coli does not predict where synonymous substitutions occur in a long-term experiment
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Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli
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Data from: Escherichia coli populations adapt to complex, unpredictable fluctuations by minimizing trade-offs across environments
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Data from: Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity
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Data from: Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli
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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.
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.