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Food borne bacterial models for detection of benzo[a]pyrene-DNA adducts formation using RAPD-PCR.

Lanzone V, Tofalo R, Fasoli G, Perpetuini G, Suzzi G, Sergi M, Corrado F, Compagnone D - Microb Biotechnol (2016)

Bottom Line: Some extra bands were detected for L. plantarum and E. faecium, while in E. coli and S. cerevisiae DNAs BPDE and DEB treatments did not result in new extra bands.Besides qualitatively analysis, cluster analysis based on Unweighted Pair-Group Method with Average algorithm was performed to compare DNA fingerprints before and after treatments.This analysis confirmed the absence of significant differences between negative controls and treated DNA in S. cerevisiae and E. coli however the disappearance of some bands can be detected.

View Article: PubMed Central - PubMed

Affiliation: Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Mosciano Sant'Angelo (TE), 64023, Italy.

No MeSH data available.


Related in: MedlinePlus

Dendrogram showing the similarity among RAPD‐PCR patterns of Lactobacillus plantarum ATCC 14917T (A), Enterococcus faecium DSMZ 20477T (B), (C) Saccharomyces cerevisiae S441 and Escherichia coli PQ37 (D) after exposure to toxic compounds tested. Similarities were calculated using UPGMA. Arbitrary threshold 90% was used to identify new adducted biotypes. n.c.: negative control.
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mbt212355-fig-0002: Dendrogram showing the similarity among RAPD‐PCR patterns of Lactobacillus plantarum ATCC 14917T (A), Enterococcus faecium DSMZ 20477T (B), (C) Saccharomyces cerevisiae S441 and Escherichia coli PQ37 (D) after exposure to toxic compounds tested. Similarities were calculated using UPGMA. Arbitrary threshold 90% was used to identify new adducted biotypes. n.c.: negative control.

Mentions: To better highlight these differences in signal intensity besides qualitatively analysis, based on disappearance and/or appearance of RAPD bands, Pearson correlation coefficient was used to construct dendrograms since this index does not consider just the presence/absence of the bands to evaluate the strain's differences, as the Dice or Jaccard indexes, but depends on the variance between two fluorescence density values at each point in the curve pattern and does not suffer from typical peak/shoulder mismatches (Seward et al., 1997). In fact, the band‐based Dice coefficient method is based on the comparison of designated band positions and divides the number of matching bands between patterns by the total number of bands, thereby emphasizing the matching bands (Dice, 1945). The Pearson correlation coefficient method compares the whole densitometric curves of patterns and is independent of band definition (Pearson, 1926). This approach resulted to be an effective method to establish the relationships among samples (Atienzar and Jha, 2006; Tofalo et al., 2014). DNA fingerprints before and after treatments were compared. Cluster analysis for E. faecium, L. plantarum, S. cerevisiae and E. coli is reported in Fig. 2.


Food borne bacterial models for detection of benzo[a]pyrene-DNA adducts formation using RAPD-PCR.

Lanzone V, Tofalo R, Fasoli G, Perpetuini G, Suzzi G, Sergi M, Corrado F, Compagnone D - Microb Biotechnol (2016)

Dendrogram showing the similarity among RAPD‐PCR patterns of Lactobacillus plantarum ATCC 14917T (A), Enterococcus faecium DSMZ 20477T (B), (C) Saccharomyces cerevisiae S441 and Escherichia coli PQ37 (D) after exposure to toxic compounds tested. Similarities were calculated using UPGMA. Arbitrary threshold 90% was used to identify new adducted biotypes. n.c.: negative control.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4835576&req=5

mbt212355-fig-0002: Dendrogram showing the similarity among RAPD‐PCR patterns of Lactobacillus plantarum ATCC 14917T (A), Enterococcus faecium DSMZ 20477T (B), (C) Saccharomyces cerevisiae S441 and Escherichia coli PQ37 (D) after exposure to toxic compounds tested. Similarities were calculated using UPGMA. Arbitrary threshold 90% was used to identify new adducted biotypes. n.c.: negative control.
Mentions: To better highlight these differences in signal intensity besides qualitatively analysis, based on disappearance and/or appearance of RAPD bands, Pearson correlation coefficient was used to construct dendrograms since this index does not consider just the presence/absence of the bands to evaluate the strain's differences, as the Dice or Jaccard indexes, but depends on the variance between two fluorescence density values at each point in the curve pattern and does not suffer from typical peak/shoulder mismatches (Seward et al., 1997). In fact, the band‐based Dice coefficient method is based on the comparison of designated band positions and divides the number of matching bands between patterns by the total number of bands, thereby emphasizing the matching bands (Dice, 1945). The Pearson correlation coefficient method compares the whole densitometric curves of patterns and is independent of band definition (Pearson, 1926). This approach resulted to be an effective method to establish the relationships among samples (Atienzar and Jha, 2006; Tofalo et al., 2014). DNA fingerprints before and after treatments were compared. Cluster analysis for E. faecium, L. plantarum, S. cerevisiae and E. coli is reported in Fig. 2.

Bottom Line: Some extra bands were detected for L. plantarum and E. faecium, while in E. coli and S. cerevisiae DNAs BPDE and DEB treatments did not result in new extra bands.Besides qualitatively analysis, cluster analysis based on Unweighted Pair-Group Method with Average algorithm was performed to compare DNA fingerprints before and after treatments.This analysis confirmed the absence of significant differences between negative controls and treated DNA in S. cerevisiae and E. coli however the disappearance of some bands can be detected.

View Article: PubMed Central - PubMed

Affiliation: Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Mosciano Sant'Angelo (TE), 64023, Italy.

No MeSH data available.


Related in: MedlinePlus