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Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.

Nilsson AN, Emilsson G, Nyberg LK, Noble C, Stadler LS, Fritzsche J, Moore ER, Tegenfeldt JO, Ambjörnsson T, Westerlund F - Nucleic Acids Res. (2014)

Bottom Line: Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold.The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains.The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.

View Article: PubMed Central - PubMed

Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.

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Related in: MedlinePlus

P-value for all 36 fragments (squares) fitted to the correct strain CCUG 10979 (x-axis) and the reference strain P12b (y-axis). The 12 fragments with an IS above 100 are shown as full symbols. The dashed line corresponds to equal values for both strains.
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Figure 9: P-value for all 36 fragments (squares) fitted to the correct strain CCUG 10979 (x-axis) and the reference strain P12b (y-axis). The 12 fragments with an IS above 100 are shown as full symbols. The dashed line corresponds to equal values for both strains.

Mentions: Figure 9 shows the P-values for all 36 fragments matched to the barcodes of strains CCUG 10979 and P12b. While there is a slight trend that the P-values are lower for the correct strain, the resolution in separating the two is poor. However, when using the IS threshold introduced above, a vast majority of the DNA fragments have a significantly lower P-value than for strain P12b; there is only one significant false positive.


Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.

Nilsson AN, Emilsson G, Nyberg LK, Noble C, Stadler LS, Fritzsche J, Moore ER, Tegenfeldt JO, Ambjörnsson T, Westerlund F - Nucleic Acids Res. (2014)

P-value for all 36 fragments (squares) fitted to the correct strain CCUG 10979 (x-axis) and the reference strain P12b (y-axis). The 12 fragments with an IS above 100 are shown as full symbols. The dashed line corresponds to equal values for both strains.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150756&req=5

Figure 9: P-value for all 36 fragments (squares) fitted to the correct strain CCUG 10979 (x-axis) and the reference strain P12b (y-axis). The 12 fragments with an IS above 100 are shown as full symbols. The dashed line corresponds to equal values for both strains.
Mentions: Figure 9 shows the P-values for all 36 fragments matched to the barcodes of strains CCUG 10979 and P12b. While there is a slight trend that the P-values are lower for the correct strain, the resolution in separating the two is poor. However, when using the IS threshold introduced above, a vast majority of the DNA fragments have a significantly lower P-value than for strain P12b; there is only one significant false positive.

Bottom Line: Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold.The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains.The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.

View Article: PubMed Central - PubMed

Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.

Show MeSH
Related in: MedlinePlus