Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics
Identifieur interne : 002736 ( Main/Merge ); précédent : 002735; suivant : 002737Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics
Auteurs : Ricardo Franco-Duarte [Portugal] ; Inês Mendes [Portugal] ; Ana Catarina Gomes [Portugal] ; Manuel A. S. Santos [Portugal] ; Bruno De Sousa [Portugal] ; Dorit Schuller [Portugal]Source :
- ELECTROPHORESIS [ 0173-0835 ] ; 2011-06.
English descriptors
- Teeft :
- Absolute values, Annealing temperature, Appl, Biodiversity conservation, Biorad, Biorad mycycler, Caliper labchips, Capillary electrophoresis, Careful standardization, Cerevisiae, Cerevisiae strains, Concentration values, Cycler, Cyclers, Delimitation, Delta elements, Delta sequences, Different laboratories, Discriminatory power, Distinct numbers, Electrophoresis, Electrophoresis system, Experimental condition, Experimental conditions, Experimental variation, Fems microbiol, Food microbiol, Fragment, Fragment size, Fragment sizes, Genetic resources, Genotypic data, Ghost bands, Gmbh, Gray squares, Group medians, High number, High reproducibility, Interdelta, Interdelta fragments, Interdelta method, Interdelta regions, Interdelta sequence typing, Interdelta sequences, Interlaboratory reproducibility, Internal markers, Kgaa, Labchips, Labchips system, Large strain collections, Median, Median values, Microbiol, Microsatellite analysis, Mtdna rflp, Multi locus sequence typing, Multiple pairwise comparisons, Numerous factors, Optimization approaches, Overall percentages, Polymerase, Present work, Primer, Reaction mixture, Relative concentration, Relative concentration values, Relative concentrations, Relative values, Replicates, Reproducibility, Saccharomyces cerevisiae strains, Similar results, Statistical analysis, Statistical differences, Strain delimitation, Sustainable development, Technical differences, Thermal cycler, Thermal cyclers, Typing method, Variance, Verlag, Verlag gmbh, Weinheim, Weinheim electrophoresis, Yeast, Yeast strains.
Abstract
Amplification of genomic sequences flanked by delta elements of retrotransposons TY1 and TY2 is a reliable method for characterization of Saccharomyces cerevisiae strains. The aim of this study is to evaluate the usefulness of microfluidic electrophoresis (Caliper LabChip®) to assess the factors that affect interlaboratory reproducibility of interdelta sequence typing for S. cerevisiae strain delimitation. We carried out experiments in two laboratories, using varying combinations of Taq DNA polymerases and thermal cyclers. The reproducibility of the technique is evaluated using non‐parametric statistical tests and we show that the source of Taq DNA polymerase and technical differences between laboratories have the highest impact on reproducibility, whereas thermal cyclers have little impact. We also show that the comparative analysis of interdelta patterns is more reliable when fragment sizes are compared than when absolute and relative DNA concentrations of each band are considered. Interdelta analysis based on a smaller fraction of bands with intermediate sizes between 100 and 1000 bp yields the highest reproducibility.
Url:
DOI: 10.1002/elps.201000640
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The aim of this study is to evaluate the usefulness of microfluidic electrophoresis (Caliper LabChip®) to assess the factors that affect interlaboratory reproducibility of interdelta sequence typing for S. cerevisiae strain delimitation. We carried out experiments in two laboratories, using varying combinations of Taq DNA polymerases and thermal cyclers. The reproducibility of the technique is evaluated using non‐parametric statistical tests and we show that the source of Taq DNA polymerase and technical differences between laboratories have the highest impact on reproducibility, whereas thermal cyclers have little impact. We also show that the comparative analysis of interdelta patterns is more reliable when fragment sizes are compared than when absolute and relative DNA concentrations of each band are considered. Interdelta analysis based on a smaller fraction of bands with intermediate sizes between 100 and 1000 bp yields the highest reproducibility.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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