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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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Explicit transfer matrix elements for site i in a multi-ligand setting. Conditioned that site i + 1 is in one of its allowed states (see Figure S4 in the Supplementary Information) site i can be in one of the states listed. Associated with each such pair of states (at sites i + 1 and site i) is a transfer matrix element value as given in the figure, and further detailed in Equations (2)–(7) in the Supplementary Information. These results are valid for arbitrary numbers of ligand types, even though we in this figure limit ourselves to three types of ligands (S = 3), for illustrative purposes.
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Figure 3: Explicit transfer matrix elements for site i in a multi-ligand setting. Conditioned that site i + 1 is in one of its allowed states (see Figure S4 in the Supplementary Information) site i can be in one of the states listed. Associated with each such pair of states (at sites i + 1 and site i) is a transfer matrix element value as given in the figure, and further detailed in Equations (2)–(7) in the Supplementary Information. These results are valid for arbitrary numbers of ligand types, even though we in this figure limit ourselves to three types of ligands (S = 3), for illustrative purposes.

Mentions: We are now in a position to introduce the transfer matrices (27,28). Briefly, for each base pair we introduce an M × M transfer matrix with elements T(i; m, m′). These matrix elements give the statistical weight for site i to be in state m provided that site i + 1 is in state m′. Most of the elements in the transfer matrix are zero since, for example, if site i + 1 is occupied by the last monomer of a type 1 ligand, then site i cannot also be occupied by the last monomer of another type 1 ligand (if λ1 ≥ 2). With the statistical weights presented in Figure 2 and our choice of enumeration in mind, it is straightforward to provide expressions for the elements of the transfer matrix . Explicit results are given in Figure 3. In the Supplementary Information, we provide explicit forms for T(i:m, m′) which allow straightforward automated computation of these transfer matrices for arbitrary S and λi (see Equations (2)–(7) in the Supplementary Information).


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)

Explicit transfer matrix elements for site i in a multi-ligand setting. Conditioned that site i + 1 is in one of its allowed states (see Figure S4 in the Supplementary Information) site i can be in one of the states listed. Associated with each such pair of states (at sites i + 1 and site i) is a transfer matrix element value as given in the figure, and further detailed in Equations (2)–(7) in the Supplementary Information. These results are valid for arbitrary numbers of ligand types, even though we in this figure limit ourselves to three types of ligands (S = 3), for illustrative purposes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Explicit transfer matrix elements for site i in a multi-ligand setting. Conditioned that site i + 1 is in one of its allowed states (see Figure S4 in the Supplementary Information) site i can be in one of the states listed. Associated with each such pair of states (at sites i + 1 and site i) is a transfer matrix element value as given in the figure, and further detailed in Equations (2)–(7) in the Supplementary Information. These results are valid for arbitrary numbers of ligand types, even though we in this figure limit ourselves to three types of ligands (S = 3), for illustrative purposes.
Mentions: We are now in a position to introduce the transfer matrices (27,28). Briefly, for each base pair we introduce an M × M transfer matrix with elements T(i; m, m′). These matrix elements give the statistical weight for site i to be in state m provided that site i + 1 is in state m′. Most of the elements in the transfer matrix are zero since, for example, if site i + 1 is occupied by the last monomer of a type 1 ligand, then site i cannot also be occupied by the last monomer of another type 1 ligand (if λ1 ≥ 2). With the statistical weights presented in Figure 2 and our choice of enumeration in mind, it is straightforward to provide expressions for the elements of the transfer matrix . Explicit results are given in Figure 3. In the Supplementary Information, we provide explicit forms for T(i:m, m′) which allow straightforward automated computation of these transfer matrices for arbitrary S and λi (see Equations (2)–(7) in the Supplementary Information).

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