Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics
Autor(a) principal: | |
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Data de Publicação: | 2011 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/13514 |
Resumo: | 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 yield the highest reproducibility. |
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Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidicsCapillary electrophoresisInterdelta sequencesNon-parametric methodsSaccharomyces cerevisiaeScience & TechnologyAmplification 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 yield the highest reproducibility.Fundação para a Ciência e TecnologiaWileyUniversidade do MinhoDuarte, Ricardo FrancoGomes, Ana CatarinaSantos, Manuel A. S.Sousa, BrunoSchuller, Dorit ElisabethMendes, Inês20112011-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/13514eng0173-083510.1002/elps.20100064021630290info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:21:15Zoai:repositorium.sdum.uminho.pt:1822/13514Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:14:28.584240Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics |
title |
Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics |
spellingShingle |
Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics Duarte, Ricardo Franco Capillary electrophoresis Interdelta sequences Non-parametric methods Saccharomyces cerevisiae Science & Technology |
title_short |
Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics |
title_full |
Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics |
title_fullStr |
Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics |
title_full_unstemmed |
Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics |
title_sort |
Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics |
author |
Duarte, Ricardo Franco |
author_facet |
Duarte, Ricardo Franco Gomes, Ana Catarina Santos, Manuel A. S. Sousa, Bruno Schuller, Dorit Elisabeth Mendes, Inês |
author_role |
author |
author2 |
Gomes, Ana Catarina Santos, Manuel A. S. Sousa, Bruno Schuller, Dorit Elisabeth Mendes, Inês |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Duarte, Ricardo Franco Gomes, Ana Catarina Santos, Manuel A. S. Sousa, Bruno Schuller, Dorit Elisabeth Mendes, Inês |
dc.subject.por.fl_str_mv |
Capillary electrophoresis Interdelta sequences Non-parametric methods Saccharomyces cerevisiae Science & Technology |
topic |
Capillary electrophoresis Interdelta sequences Non-parametric methods Saccharomyces cerevisiae Science & Technology |
description |
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 yield the highest reproducibility. |
publishDate |
2011 |
dc.date.none.fl_str_mv |
2011 2011-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/13514 |
url |
http://hdl.handle.net/1822/13514 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
0173-0835 10.1002/elps.201000640 21630290 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Wiley |
publisher.none.fl_str_mv |
Wiley |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799132587956895744 |