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    • naei  (New England Biolabs)
    94
    New England Biolabs naei
    (a) Diagram of the main steps in sample preparation, detection, and classification: PCR fragments from isolated pathogens are subjected to a restriction digest, which recognizes and cuts only one genomic variant. Nanopore translocations are used to classify the pathogen according to the combination of fragment lengths detected. (b) <t>The</t> <t>mazG</t> gene of the avirulent M . tuberculosis strain H37Ra is not cut by <t>NaeI</t> (942 bp), while the same gene in the closely related virulent strain H37Rv, which differs by only a single A-to-C mutation, is cut by NaeI (621bp + 321 bp). (c) Gaussian mixture model (one component) fit to translocations of mazG fragments from H37Ra. (d) Gaussian mixture model (two components) fit to translocations of mazG fragments from H37Rv. (e) Posterior probabilities for correctly identifying the H37Ra and H37Rv strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data. (f) The parC gene of the multi-drug-resistant MRSA strain FPR3757 is not cut by BseRI (886 bp) due to a single C-to-A mutation, while the closely related and less resistant strain HOU-MR is cut by BseRI (640bp + 245 bp). (g) Gaussian mixture model (one component) fit to translocations of parC fragments from FPR3757. (h) Gaussian mixture model (two components) fit to translocations of parC fragments from HOU-MR. (i) Posterior probabilities for correctly identifying the FPR3757 and HOU-MR strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data.
    Naei, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    (a) Diagram of the main steps in sample preparation, detection, and classification: PCR fragments from isolated pathogens are subjected to a restriction digest, which recognizes and cuts only one genomic variant. Nanopore translocations are used to classify the pathogen according to the combination of fragment lengths detected. (b) The mazG gene of the avirulent M . tuberculosis strain H37Ra is not cut by NaeI (942 bp), while the same gene in the closely related virulent strain H37Rv, which differs by only a single A-to-C mutation, is cut by NaeI (621bp + 321 bp). (c) Gaussian mixture model (one component) fit to translocations of mazG fragments from H37Ra. (d) Gaussian mixture model (two components) fit to translocations of mazG fragments from H37Rv. (e) Posterior probabilities for correctly identifying the H37Ra and H37Rv strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data. (f) The parC gene of the multi-drug-resistant MRSA strain FPR3757 is not cut by BseRI (886 bp) due to a single C-to-A mutation, while the closely related and less resistant strain HOU-MR is cut by BseRI (640bp + 245 bp). (g) Gaussian mixture model (one component) fit to translocations of parC fragments from FPR3757. (h) Gaussian mixture model (two components) fit to translocations of parC fragments from HOU-MR. (i) Posterior probabilities for correctly identifying the FPR3757 and HOU-MR strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data.

    Journal: PLoS ONE

    Article Title: Genomic Pathogen Typing Using Solid-State Nanopores

    doi: 10.1371/journal.pone.0142944

    Figure Lengend Snippet: (a) Diagram of the main steps in sample preparation, detection, and classification: PCR fragments from isolated pathogens are subjected to a restriction digest, which recognizes and cuts only one genomic variant. Nanopore translocations are used to classify the pathogen according to the combination of fragment lengths detected. (b) The mazG gene of the avirulent M . tuberculosis strain H37Ra is not cut by NaeI (942 bp), while the same gene in the closely related virulent strain H37Rv, which differs by only a single A-to-C mutation, is cut by NaeI (621bp + 321 bp). (c) Gaussian mixture model (one component) fit to translocations of mazG fragments from H37Ra. (d) Gaussian mixture model (two components) fit to translocations of mazG fragments from H37Rv. (e) Posterior probabilities for correctly identifying the H37Ra and H37Rv strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data. (f) The parC gene of the multi-drug-resistant MRSA strain FPR3757 is not cut by BseRI (886 bp) due to a single C-to-A mutation, while the closely related and less resistant strain HOU-MR is cut by BseRI (640bp + 245 bp). (g) Gaussian mixture model (one component) fit to translocations of parC fragments from FPR3757. (h) Gaussian mixture model (two components) fit to translocations of parC fragments from HOU-MR. (i) Posterior probabilities for correctly identifying the FPR3757 and HOU-MR strains as a function of number of translocation events collected from an unknown sample, simulated using bootstrap sampling from nanopore translocation data.

    Article Snippet: We chose a restriction enzyme specific to the single nucleotide variation: for the mazG gene in H37Rv, NaeI (New England Biolabs) will cut the amplicon into two pieces of 321 and 621 bp, whereas the mazG gene from H37Ra will not be digested with this enzyme (942 bp).

    Techniques: Sample Prep, Isolation, Variant Assay, Mutagenesis, Translocation Assay, Sampling