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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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Fragments fitted to the theoretical genomes of CCUG 10979 and P12b, respectively. (A and B) A fragment with a good fit to both the correct strain CCUG 10979 and the P12b strain. (A) Location of one fragment (cyan curve) on the genome of the correct strain CCUG 10979 (black curve) with a P-value of 0.04% and a best cross correlation value of . (B) The same fragment as in (A) (cyan) located on strain P12b (black) with a P-value of 0.12% and . (C and D) A fragment with a good fit to CCUG 10979 and a bad fit to P12b. (C) Location of one fragment (magenta) on the genome of the correct strain CCUG 10979 (black curve) with a P-value of 0.13% and . (D) The same fragment as in (C) (magenta) located on strain P12b (black) with a P-value of 23% and .
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Figure 8: Fragments fitted to the theoretical genomes of CCUG 10979 and P12b, respectively. (A and B) A fragment with a good fit to both the correct strain CCUG 10979 and the P12b strain. (A) Location of one fragment (cyan curve) on the genome of the correct strain CCUG 10979 (black curve) with a P-value of 0.04% and a best cross correlation value of . (B) The same fragment as in (A) (cyan) located on strain P12b (black) with a P-value of 0.12% and . (C and D) A fragment with a good fit to CCUG 10979 and a bad fit to P12b. (C) Location of one fragment (magenta) on the genome of the correct strain CCUG 10979 (black curve) with a P-value of 0.13% and . (D) The same fragment as in (C) (magenta) located on strain P12b (black) with a P-value of 23% and .

Mentions: (A) The theoretical probability ptheory(i) for YOYO binding to the full genome of E. coli strain CCUG 10979, calculated using the transfer matrix approach discussed in the Materials and Methods section. Horizontal lines represent the location of the best fits of 36 experimental E. coli fragments; the associated IS values are also displayed. Solid horizontal lines correspond to a P-value below 10% and dashed lines have a P-value above 10%. The five colored horizontal lines correspond to traces which are detailed in panels B–D, see also Figure 8. The best fit (colored curves) of three experimental fragments matched to the theoretical trace (black curves): (B) a representative fragment with a large best cross-correlation value (0.771) and a small P-value (0.09 %); (C) a representative fragment with a small (0.670) and a large P-value (37.1%); (D) a representative fragment with a large (0.877) and a large P-value (33.3%). The colors of the fits correspond to the colors of the horizontal lines in (A).


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)

Fragments fitted to the theoretical genomes of CCUG 10979 and P12b, respectively. (A and B) A fragment with a good fit to both the correct strain CCUG 10979 and the P12b strain. (A) Location of one fragment (cyan curve) on the genome of the correct strain CCUG 10979 (black curve) with a P-value of 0.04% and a best cross correlation value of . (B) The same fragment as in (A) (cyan) located on strain P12b (black) with a P-value of 0.12% and . (C and D) A fragment with a good fit to CCUG 10979 and a bad fit to P12b. (C) Location of one fragment (magenta) on the genome of the correct strain CCUG 10979 (black curve) with a P-value of 0.13% and . (D) The same fragment as in (C) (magenta) located on strain P12b (black) with a P-value of 23% and .
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Figure 8: Fragments fitted to the theoretical genomes of CCUG 10979 and P12b, respectively. (A and B) A fragment with a good fit to both the correct strain CCUG 10979 and the P12b strain. (A) Location of one fragment (cyan curve) on the genome of the correct strain CCUG 10979 (black curve) with a P-value of 0.04% and a best cross correlation value of . (B) The same fragment as in (A) (cyan) located on strain P12b (black) with a P-value of 0.12% and . (C and D) A fragment with a good fit to CCUG 10979 and a bad fit to P12b. (C) Location of one fragment (magenta) on the genome of the correct strain CCUG 10979 (black curve) with a P-value of 0.13% and . (D) The same fragment as in (C) (magenta) located on strain P12b (black) with a P-value of 23% and .
Mentions: (A) The theoretical probability ptheory(i) for YOYO binding to the full genome of E. coli strain CCUG 10979, calculated using the transfer matrix approach discussed in the Materials and Methods section. Horizontal lines represent the location of the best fits of 36 experimental E. coli fragments; the associated IS values are also displayed. Solid horizontal lines correspond to a P-value below 10% and dashed lines have a P-value above 10%. The five colored horizontal lines correspond to traces which are detailed in panels B–D, see also Figure 8. The best fit (colored curves) of three experimental fragments matched to the theoretical trace (black curves): (B) a representative fragment with a large best cross-correlation value (0.771) and a small P-value (0.09 %); (C) a representative fragment with a small (0.670) and a large P-value (37.1%); (D) a representative fragment with a large (0.877) and a large P-value (33.3%). The colors of the fits correspond to the colors of the horizontal lines in (A).

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