Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L.
- Autores
- Lukaszewicz, Germán; Amé, María Valeria; Menone, Mirta Lujan
- Año de publicación
- 2018
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- The RT-qPCR has been the method used to analyze gene expression in plants but its benefits have not been completely exploited in the field of plants ecotoxicology when used as molecular biomarkers. The correct use of RT-qPCR demands to establish a certain number of reference genes (RG) which are expected to be invariable in their expression although it does not always happen. The main goals of this work were to: (1) analyze the stability of six potential RG, (2) establish the optimum number of RG, (3) select the most suitable RG to be applied in Bidens laevis under different test conditions and tissues and (4) confirm its convenience by normalizing the expression of one gene of interest under three different challenges. When all data were pooled together, the geNorm algorithm pointed out beta-actin and beta-tubulin (TUB) as the optimal RG pair while NormFinder algorithm selected nicotinamide adenine dinucleotide dehydrogenase (NADHD) and histone 3 (H3) as possessing the most invariable levels of expression. On the other hand, when data were grouped by tissues, ANOVA test selected H3 and TUB, while data grouped by conditions indicated that H3 and NADHD were the most stable RG under this analysis. Therefore, for a general-purpose set of RG, the overall analysis showed that a set of three RG would be optimum, and H3, TUB and NADHD were the selected ones. On the other hand, as RG can vary depending on the tissues or conditions, results achieved with ANOVA would be more reliable. Thus, appropriate normalization process would clearly need more than one RG.
Fil: Lukaszewicz, Germán. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina
Fil: Amé, María Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina
Fil: Menone, Mirta Lujan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina - Materia
-
AQUATIC MACROPHYTE
ECOTOXICOLOGY
MOLECULAR BIOMARKERS
REFERENCE GENES
RT-QPCR
XENOBIOTICS - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/95931
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Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L.Lukaszewicz, GermánAmé, María ValeriaMenone, Mirta LujanAQUATIC MACROPHYTEECOTOXICOLOGYMOLECULAR BIOMARKERSREFERENCE GENESRT-QPCRXENOBIOTICShttps://purl.org/becyt/ford/1.5https://purl.org/becyt/ford/1The RT-qPCR has been the method used to analyze gene expression in plants but its benefits have not been completely exploited in the field of plants ecotoxicology when used as molecular biomarkers. The correct use of RT-qPCR demands to establish a certain number of reference genes (RG) which are expected to be invariable in their expression although it does not always happen. The main goals of this work were to: (1) analyze the stability of six potential RG, (2) establish the optimum number of RG, (3) select the most suitable RG to be applied in Bidens laevis under different test conditions and tissues and (4) confirm its convenience by normalizing the expression of one gene of interest under three different challenges. When all data were pooled together, the geNorm algorithm pointed out beta-actin and beta-tubulin (TUB) as the optimal RG pair while NormFinder algorithm selected nicotinamide adenine dinucleotide dehydrogenase (NADHD) and histone 3 (H3) as possessing the most invariable levels of expression. On the other hand, when data were grouped by tissues, ANOVA test selected H3 and TUB, while data grouped by conditions indicated that H3 and NADHD were the most stable RG under this analysis. Therefore, for a general-purpose set of RG, the overall analysis showed that a set of three RG would be optimum, and H3, TUB and NADHD were the selected ones. On the other hand, as RG can vary depending on the tissues or conditions, results achieved with ANOVA would be more reliable. Thus, appropriate normalization process would clearly need more than one RG.Fil: Lukaszewicz, Germán. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Amé, María Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Menone, Mirta Lujan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaSpringer2018-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/95931Lukaszewicz, Germán; Amé, María Valeria; Menone, Mirta Lujan; Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L.; Springer; Physiology and Molecular Biology of Plants; 24; 5; 9-2018; 781-7920971-5894CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1007/s12298-018-0534-3info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs12298-018-0534-3#Abs1info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103946/info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:53:26Zoai:ri.conicet.gov.ar:11336/95931instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:53:26.683CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L. |
title |
Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L. |
spellingShingle |
Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L. Lukaszewicz, Germán AQUATIC MACROPHYTE ECOTOXICOLOGY MOLECULAR BIOMARKERS REFERENCE GENES RT-QPCR XENOBIOTICS |
title_short |
Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L. |
title_full |
Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L. |
title_fullStr |
Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L. |
title_full_unstemmed |
Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L. |
title_sort |
Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L. |
dc.creator.none.fl_str_mv |
Lukaszewicz, Germán Amé, María Valeria Menone, Mirta Lujan |
author |
Lukaszewicz, Germán |
author_facet |
Lukaszewicz, Germán Amé, María Valeria Menone, Mirta Lujan |
author_role |
author |
author2 |
Amé, María Valeria Menone, Mirta Lujan |
author2_role |
author author |
dc.subject.none.fl_str_mv |
AQUATIC MACROPHYTE ECOTOXICOLOGY MOLECULAR BIOMARKERS REFERENCE GENES RT-QPCR XENOBIOTICS |
topic |
AQUATIC MACROPHYTE ECOTOXICOLOGY MOLECULAR BIOMARKERS REFERENCE GENES RT-QPCR XENOBIOTICS |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.5 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
The RT-qPCR has been the method used to analyze gene expression in plants but its benefits have not been completely exploited in the field of plants ecotoxicology when used as molecular biomarkers. The correct use of RT-qPCR demands to establish a certain number of reference genes (RG) which are expected to be invariable in their expression although it does not always happen. The main goals of this work were to: (1) analyze the stability of six potential RG, (2) establish the optimum number of RG, (3) select the most suitable RG to be applied in Bidens laevis under different test conditions and tissues and (4) confirm its convenience by normalizing the expression of one gene of interest under three different challenges. When all data were pooled together, the geNorm algorithm pointed out beta-actin and beta-tubulin (TUB) as the optimal RG pair while NormFinder algorithm selected nicotinamide adenine dinucleotide dehydrogenase (NADHD) and histone 3 (H3) as possessing the most invariable levels of expression. On the other hand, when data were grouped by tissues, ANOVA test selected H3 and TUB, while data grouped by conditions indicated that H3 and NADHD were the most stable RG under this analysis. Therefore, for a general-purpose set of RG, the overall analysis showed that a set of three RG would be optimum, and H3, TUB and NADHD were the selected ones. On the other hand, as RG can vary depending on the tissues or conditions, results achieved with ANOVA would be more reliable. Thus, appropriate normalization process would clearly need more than one RG. Fil: Lukaszewicz, Germán. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina Fil: Amé, María Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina Fil: Menone, Mirta Lujan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina |
description |
The RT-qPCR has been the method used to analyze gene expression in plants but its benefits have not been completely exploited in the field of plants ecotoxicology when used as molecular biomarkers. The correct use of RT-qPCR demands to establish a certain number of reference genes (RG) which are expected to be invariable in their expression although it does not always happen. The main goals of this work were to: (1) analyze the stability of six potential RG, (2) establish the optimum number of RG, (3) select the most suitable RG to be applied in Bidens laevis under different test conditions and tissues and (4) confirm its convenience by normalizing the expression of one gene of interest under three different challenges. When all data were pooled together, the geNorm algorithm pointed out beta-actin and beta-tubulin (TUB) as the optimal RG pair while NormFinder algorithm selected nicotinamide adenine dinucleotide dehydrogenase (NADHD) and histone 3 (H3) as possessing the most invariable levels of expression. On the other hand, when data were grouped by tissues, ANOVA test selected H3 and TUB, while data grouped by conditions indicated that H3 and NADHD were the most stable RG under this analysis. Therefore, for a general-purpose set of RG, the overall analysis showed that a set of three RG would be optimum, and H3, TUB and NADHD were the selected ones. On the other hand, as RG can vary depending on the tissues or conditions, results achieved with ANOVA would be more reliable. Thus, appropriate normalization process would clearly need more than one RG. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-09 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/95931 Lukaszewicz, Germán; Amé, María Valeria; Menone, Mirta Lujan; Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L.; Springer; Physiology and Molecular Biology of Plants; 24; 5; 9-2018; 781-792 0971-5894 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/95931 |
identifier_str_mv |
Lukaszewicz, Germán; Amé, María Valeria; Menone, Mirta Lujan; Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L.; Springer; Physiology and Molecular Biology of Plants; 24; 5; 9-2018; 781-792 0971-5894 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/doi/10.1007/s12298-018-0534-3 info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs12298-018-0534-3#Abs1 info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6103946/ |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
Springer |
publisher.none.fl_str_mv |
Springer |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
reponame_str |
CONICET Digital (CONICET) |
collection |
CONICET Digital (CONICET) |
instname_str |
Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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13.13397 |