In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus spp
Autor(a) principal: | |
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Data de Publicação: | 2012 |
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/1822/23396 |
Resumo: | Bacterial vaginosis (BV) is a common pathology of women in reproductive age that can lead to serious health complications, and is associated with shifts in the normal microflora from predominance of Lactobacillus spp. to a proliferation of other anaerobes such as G. vaginalis and A vaginae, which can be detected by PCR. The optimal PCR pathogen detection assay relies mainly on the specificity and sensitivity of the primers used. Findings Here we demonstrate that in silico analytical testing of primer specificity is not a synonym to in vitro analytical specificity by testing a range of published and newly designed primers with both techniques for the detection of BV-associated microorganisms. Conclusions By testing primer in vitro specificity with a sufficient range of bacterial strains, we were able to design primers with higher specificity and sensitivity. Also by comparing the results obtained for the newly designed primers with other previously published primers, we confirmed that in silico analysis is not sufficient to predict in vitro specificity. As such care must be taken when choosing the primers for a detection assay. |
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In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus sppA. vaginaeG. vaginalisIn silico primer testingIn vitro primer testingLactobacillus spp.Primer sensitivityPrimer specificityBacterial vaginosis (BV) is a common pathology of women in reproductive age that can lead to serious health complications, and is associated with shifts in the normal microflora from predominance of Lactobacillus spp. to a proliferation of other anaerobes such as G. vaginalis and A vaginae, which can be detected by PCR. The optimal PCR pathogen detection assay relies mainly on the specificity and sensitivity of the primers used. Findings Here we demonstrate that in silico analytical testing of primer specificity is not a synonym to in vitro analytical specificity by testing a range of published and newly designed primers with both techniques for the detection of BV-associated microorganisms. Conclusions By testing primer in vitro specificity with a sufficient range of bacterial strains, we were able to design primers with higher specificity and sensitivity. Also by comparing the results obtained for the newly designed primers with other previously published primers, we confirmed that in silico analysis is not sufficient to predict in vitro specificity. As such care must be taken when choosing the primers for a detection assay.(undefined)BioMed Central (BMC)BioMed CentralUniversidade do MinhoHenriques, Ana Filipa Frutuoso MendesCereija, Tatiana Barros ReisMachado, AntónioCerca, Nuno20122012-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/23396eng1756-050010.1186/1756-0500-5-63723153093info: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:RCAAP2023-07-21T12:17:50Zoai:repositorium.sdum.uminho.pt:1822/23396Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:10:31.838597Repositório 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 |
In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus spp |
title |
In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus spp |
spellingShingle |
In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus spp Henriques, Ana Filipa Frutuoso Mendes A. vaginae G. vaginalis In silico primer testing In vitro primer testing Lactobacillus spp. Primer sensitivity Primer specificity |
title_short |
In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus spp |
title_full |
In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus spp |
title_fullStr |
In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus spp |
title_full_unstemmed |
In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus spp |
title_sort |
In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, atopobium vaginae and lactobacillus spp |
author |
Henriques, Ana Filipa Frutuoso Mendes |
author_facet |
Henriques, Ana Filipa Frutuoso Mendes Cereija, Tatiana Barros Reis Machado, António Cerca, Nuno |
author_role |
author |
author2 |
Cereija, Tatiana Barros Reis Machado, António Cerca, Nuno |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Henriques, Ana Filipa Frutuoso Mendes Cereija, Tatiana Barros Reis Machado, António Cerca, Nuno |
dc.subject.por.fl_str_mv |
A. vaginae G. vaginalis In silico primer testing In vitro primer testing Lactobacillus spp. Primer sensitivity Primer specificity |
topic |
A. vaginae G. vaginalis In silico primer testing In vitro primer testing Lactobacillus spp. Primer sensitivity Primer specificity |
description |
Bacterial vaginosis (BV) is a common pathology of women in reproductive age that can lead to serious health complications, and is associated with shifts in the normal microflora from predominance of Lactobacillus spp. to a proliferation of other anaerobes such as G. vaginalis and A vaginae, which can be detected by PCR. The optimal PCR pathogen detection assay relies mainly on the specificity and sensitivity of the primers used. Findings Here we demonstrate that in silico analytical testing of primer specificity is not a synonym to in vitro analytical specificity by testing a range of published and newly designed primers with both techniques for the detection of BV-associated microorganisms. Conclusions By testing primer in vitro specificity with a sufficient range of bacterial strains, we were able to design primers with higher specificity and sensitivity. Also by comparing the results obtained for the newly designed primers with other previously published primers, we confirmed that in silico analysis is not sufficient to predict in vitro specificity. As such care must be taken when choosing the primers for a detection assay. |
publishDate |
2012 |
dc.date.none.fl_str_mv |
2012 2012-01-01T00:00:00Z |
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/1822/23396 |
url |
http://hdl.handle.net/1822/23396 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
1756-0500 10.1186/1756-0500-5-637 23153093 |
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 |
BioMed Central (BMC) BioMed Central |
publisher.none.fl_str_mv |
BioMed Central (BMC) BioMed Central |
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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1799132534734323712 |