Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://hdl.handle.net/1822/80634 |
Resumo: | Assessment of genomic DNA (gDNA) extraction efficiency is required for accurate bacterial quantification by qPCR. Exogenous DNA molecules are often added after bacterial cultures are lysed, but before DNA purification steps, to determine extraction efficiency. Herein we found that different exogenous DNA controls have different recovery rates, suggesting distinct DNA extraction efficiencies. Recovery rates are also affected by the gDNA extraction method being more affected in silica-based columns than in phenol-chloroform extraction. Overall, we determined that the use of long DNA fragments, such as gDNA, as exogenous controls have a higher recovery rate than use of smaller size DNA molecules. |
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Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractionsgDNA extraction efficiencygDNA qPCR bacterial quantificationExogenous controlsScience & TechnologyAssessment of genomic DNA (gDNA) extraction efficiency is required for accurate bacterial quantification by qPCR. Exogenous DNA molecules are often added after bacterial cultures are lysed, but before DNA purification steps, to determine extraction efficiency. Herein we found that different exogenous DNA controls have different recovery rates, suggesting distinct DNA extraction efficiencies. Recovery rates are also affected by the gDNA extraction method being more affected in silica-based columns than in phenol-chloroform extraction. Overall, we determined that the use of long DNA fragments, such as gDNA, as exogenous controls have a higher recovery rate than use of smaller size DNA molecules.This work was partially funded by the Portuguese Foundation for Science and Technology (FCT), with the strategic funding of the unit (UIDB/04469/2020). It was also partially funded by the National Institute of Allergy and Infectious Diseases (R01AI146065-01A1 to CAM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation.info:eu-repo/semantics/publishedVersionElsevierUniversidade do MinhoLima, Ângela MartinsSousa, Lúcia Filipa Guimarães VieiraMacedo, FilipaMuzny, Christina A.Cerca, Nuno2022-122022-12-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/1822/80634engLima, Â.; Sousa, Lúcia; Macedo, Filipa; Muzny, Christina A.; Cerca, Nuno, Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions. Journal of Microbiological Methods, 203(106607), 20220167701210.1016/j.mimet.2022.10660736343770106607http://www.journals.elsevier.com/journal-of-microbiological-methods/info: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:RCAAP2023-07-21T12:00:13Zoai:repositorium.sdum.uminho.pt:1822/80634Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:50:04.705795Repositório 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 |
Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions |
title |
Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions |
spellingShingle |
Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions Lima, Ângela Martins gDNA extraction efficiency gDNA qPCR bacterial quantification Exogenous controls Science & Technology |
title_short |
Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions |
title_full |
Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions |
title_fullStr |
Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions |
title_full_unstemmed |
Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions |
title_sort |
Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions |
author |
Lima, Ângela Martins |
author_facet |
Lima, Ângela Martins Sousa, Lúcia Filipa Guimarães Vieira Macedo, Filipa Muzny, Christina A. Cerca, Nuno |
author_role |
author |
author2 |
Sousa, Lúcia Filipa Guimarães Vieira Macedo, Filipa Muzny, Christina A. Cerca, Nuno |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Lima, Ângela Martins Sousa, Lúcia Filipa Guimarães Vieira Macedo, Filipa Muzny, Christina A. Cerca, Nuno |
dc.subject.por.fl_str_mv |
gDNA extraction efficiency gDNA qPCR bacterial quantification Exogenous controls Science & Technology |
topic |
gDNA extraction efficiency gDNA qPCR bacterial quantification Exogenous controls Science & Technology |
description |
Assessment of genomic DNA (gDNA) extraction efficiency is required for accurate bacterial quantification by qPCR. Exogenous DNA molecules are often added after bacterial cultures are lysed, but before DNA purification steps, to determine extraction efficiency. Herein we found that different exogenous DNA controls have different recovery rates, suggesting distinct DNA extraction efficiencies. Recovery rates are also affected by the gDNA extraction method being more affected in silica-based columns than in phenol-chloroform extraction. Overall, we determined that the use of long DNA fragments, such as gDNA, as exogenous controls have a higher recovery rate than use of smaller size DNA molecules. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-12 2022-12-01T00:00:00Z |
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 |
https://hdl.handle.net/1822/80634 |
url |
https://hdl.handle.net/1822/80634 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Lima, Â.; Sousa, Lúcia; Macedo, Filipa; Muzny, Christina A.; Cerca, Nuno, Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions. Journal of Microbiological Methods, 203(106607), 2022 01677012 10.1016/j.mimet.2022.106607 36343770 106607 http://www.journals.elsevier.com/journal-of-microbiological-methods/ |
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 |
Elsevier |
publisher.none.fl_str_mv |
Elsevier |
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 |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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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 |
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1799132268246073344 |