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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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(A) Histogram (gray) of P-values obtained when fitting 36 experimental fragments from the E. coli strain CCUG 10979 to its theoretical barcode, and the 12 fragments with an IS above 100 (black). (B) Plot of the IS versus the P-value for the 36 fragments.
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Figure 7: (A) Histogram (gray) of P-values obtained when fitting 36 experimental fragments from the E. coli strain CCUG 10979 to its theoretical barcode, and the 12 fragments with an IS above 100 (black). (B) Plot of the IS versus the P-value for the 36 fragments.

Mentions: We henceforth use P-values to quantify agreement between experiments and theory and use the phrase ‘reliable match’, for scenarios when the experiment-theory match is significantly better than what we would expect by chance, i.e. when P < Pthreshold. Using Pthreshold = 10% we find that 12 of the 36 fragments have a P-value that is below the threshold, although there is also a significant fraction with larger P's (see Figure 7A). By investigating the horizontal bars in Figure 6A, where IS and P-values are indicated, we note that fragments with P-values larger than 10% are typically short and have a small IS.


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)

(A) Histogram (gray) of P-values obtained when fitting 36 experimental fragments from the E. coli strain CCUG 10979 to its theoretical barcode, and the 12 fragments with an IS above 100 (black). (B) Plot of the IS versus the P-value for the 36 fragments.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 7: (A) Histogram (gray) of P-values obtained when fitting 36 experimental fragments from the E. coli strain CCUG 10979 to its theoretical barcode, and the 12 fragments with an IS above 100 (black). (B) Plot of the IS versus the P-value for the 36 fragments.
Mentions: We henceforth use P-values to quantify agreement between experiments and theory and use the phrase ‘reliable match’, for scenarios when the experiment-theory match is significantly better than what we would expect by chance, i.e. when P < Pthreshold. Using Pthreshold = 10% we find that 12 of the 36 fragments have a P-value that is below the threshold, although there is also a significant fraction with larger P's (see Figure 7A). By investigating the horizontal bars in Figure 6A, where IS and P-values are indicated, we note that fragments with P-values larger than 10% are typically short and have a small IS.

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