Limits...
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.

Show MeSH

Related in: MedlinePlus

(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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4150756&req=5

Figure 6: (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).

Mentions: One potential application of optical mapping is the characterization and identification of bacterial species and strains. We extracted DNA from the E. coli strain CCUG 10979 (= ATCC 8739), using conventional methods (see the Materials and Methods section). During the extraction protocol the DNA is fragmented, and barcodes for 36 such DNA fragments, with lengths ranging from 51.7 kb to 153.4 kb, were matched to the theoretical barcode of CCUG 10979, derived from the genome sequence (RefSeq, Acc. No. NC_010468.1). Figure 6A shows the full theoretical barcode of CCUG 10979 calculated using the transfer matrix approach (see the Materials and Methods section for details and input parameters). Figure 6A also shows the location of the best fits and the associated IS for each of the 36 fragments along the genome.


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) 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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: (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).
Mentions: One potential application of optical mapping is the characterization and identification of bacterial species and strains. We extracted DNA from the E. coli strain CCUG 10979 (= ATCC 8739), using conventional methods (see the Materials and Methods section). During the extraction protocol the DNA is fragmented, and barcodes for 36 such DNA fragments, with lengths ranging from 51.7 kb to 153.4 kb, were matched to the theoretical barcode of CCUG 10979, derived from the genome sequence (RefSeq, Acc. No. NC_010468.1). Figure 6A shows the full theoretical barcode of CCUG 10979 calculated using the transfer matrix approach (see the Materials and Methods section for details and input parameters). Figure 6A also shows the location of the best fits and the associated IS for each of the 36 fragments along the genome.

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