In silico and experimental evaluation of DNA-based detection methods for the ability to discriminate almond from other Prunus spp.
Identifieur interne : 000139 ( Main/Exploration ); précédent : 000138; suivant : 000140In silico and experimental evaluation of DNA-based detection methods for the ability to discriminate almond from other Prunus spp.
Auteurs : Barbara Brežná [Slovaquie] ; Ji Šmíd [République tchèque] ; Joana Costa [Portugal] ; Jan Radvanszky [Slovaquie] ; Isabel Mafra [Portugal] ; Tomáš Kuchta [Slovaquie]Source :
- Molecular and cellular probes [ 1096-1194 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Protéines végétales, Prunus.
- métabolisme : Sondes d'ADN.
- méthodes : Réaction de polymérisation en chaîne.
- Feuilles de plante, Simulation numérique.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Plant Proteins.
- chemical , metabolism : DNA Probes.
- classification : Prunus.
- methods : Polymerase Chain Reaction.
- Computer Simulation, Plant Leaves.
Abstract
Ten published DNA-based analytical methods aiming at detecting material of almond (Prunus dulcis) were in silico evaluated for potential cross-reactivity with other stone fruits (Prunus spp.), including peach, apricot, plum, cherry, sour cherry and Sargent cherry. For most assays, the analysis of nucleotide databases suggested none or insufficient discrimination of at least some stone fruits. On the other hand, the assay targeting non-specific lipid transfer protein (Röder et al., 2011, Anal Chim Acta 685:74-83) was sufficiently discriminative, judging from nucleotide alignments. Empirical evaluation was performed for three of the published methods, one modification of a commercial kit (SureFood allergen almond) and one attempted novel method targeting thaumatin-like protein gene. Samples of leaves and kernels were used in the experiments. The empirical results were favourable for the method from Röder et al. (2011) and a modification of SureFood allergen almond kit, both showing cross-reactivity <10(-3) compared to the model almond.
DOI: 10.1016/j.mcp.2014.11.006
PubMed: 25483259
Affiliations:
Links toward previous steps (curation, corpus...)
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Box 25, 824 75 Bratislava 26, Slovakia.</nlm:affiliation><country xml:lang="fr">Slovaquie</country><wicri:regionArea>Department of Microbiology and Molecular Biology, Food Research Institute, Priemyselná 4, P.O. 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Box 25, 824 75 Bratislava 26, Slovakia. Electronic address: brezna@vup.sk.</nlm:affiliation><country xml:lang="fr">Slovaquie</country><wicri:regionArea>Department of Microbiology and Molecular Biology, Food Research Institute, Priemyselná 4, P.O. Box 25, 824 75 Bratislava 26</wicri:regionArea><wicri:noRegion>824 75 Bratislava 26</wicri:noRegion></affiliation></author><author><name sortKey="Smid, Ji" sort="Smid, Ji" uniqKey="Smid J" first="Ji" last="Šmíd">Ji Šmíd</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology and Molecular Biology, Food Research Institute, Priemyselná 4, P.O. Box 25, 824 75 Bratislava 26, Slovakia; Institute of Food Chemistry and Biotechnolgy, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Department of Microbiology and Molecular Biology, Food Research Institute, Priemyselná 4, P.O. Box 25, 824 75 Bratislava 26, Slovakia; Institute of Food Chemistry and Biotechnolgy, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno</wicri:regionArea><wicri:noRegion>612 00 Brno</wicri:noRegion></affiliation></author><author><name sortKey="Costa, Joana" sort="Costa, Joana" uniqKey="Costa J" first="Joana" last="Costa">Joana Costa</name><affiliation wicri:level="1"><nlm:affiliation>REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto</wicri:regionArea><wicri:noRegion>4050-313 Porto</wicri:noRegion></affiliation></author><author><name sortKey="Radvanszky, Jan" sort="Radvanszky, Jan" uniqKey="Radvanszky J" first="Jan" last="Radvanszky">Jan Radvanszky</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Vlárska 5, 83334 Bratislava, Slovakia.</nlm:affiliation><country xml:lang="fr">Slovaquie</country><wicri:regionArea>Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Vlárska 5, 83334 Bratislava</wicri:regionArea><wicri:noRegion>83334 Bratislava</wicri:noRegion></affiliation></author><author><name sortKey="Mafra, Isabel" sort="Mafra, Isabel" uniqKey="Mafra I" first="Isabel" last="Mafra">Isabel Mafra</name><affiliation wicri:level="1"><nlm:affiliation>REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto</wicri:regionArea><wicri:noRegion>4050-313 Porto</wicri:noRegion></affiliation></author><author><name sortKey="Kuchta, Tomas" sort="Kuchta, Tomas" uniqKey="Kuchta T" first="Tomáš" last="Kuchta">Tomáš Kuchta</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology and Molecular Biology, Food Research Institute, Priemyselná 4, P.O. Box 25, 824 75 Bratislava 26, Slovakia.</nlm:affiliation><country xml:lang="fr">Slovaquie</country><wicri:regionArea>Department of Microbiology and Molecular Biology, Food Research Institute, Priemyselná 4, P.O. Box 25, 824 75 Bratislava 26</wicri:regionArea><wicri:noRegion>824 75 Bratislava 26</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular and cellular probes</title><idno type="eISSN">1096-1194</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computer Simulation (MeSH)</term><term>DNA Probes (metabolism)</term><term>Plant Leaves (MeSH)</term><term>Plant Proteins (genetics)</term><term>Polymerase Chain Reaction (methods)</term><term>Prunus (classification)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Feuilles de plante (MeSH)</term><term>Protéines végétales (génétique)</term><term>Prunus (classification)</term><term>Réaction de polymérisation en chaîne (méthodes)</term><term>Simulation numérique (MeSH)</term><term>Sondes d'ADN (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA Probes</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Prunus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéines végétales</term><term>Prunus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Sondes d'ADN</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Réaction de polymérisation en chaîne</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term><term>Plant Leaves</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Feuilles de plante</term><term>Simulation numérique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Ten published DNA-based analytical methods aiming at detecting material of almond (Prunus dulcis) were in silico evaluated for potential cross-reactivity with other stone fruits (Prunus spp.), including peach, apricot, plum, cherry, sour cherry and Sargent cherry. For most assays, the analysis of nucleotide databases suggested none or insufficient discrimination of at least some stone fruits. On the other hand, the assay targeting non-specific lipid transfer protein (Röder et al., 2011, Anal Chim Acta 685:74-83) was sufficiently discriminative, judging from nucleotide alignments. Empirical evaluation was performed for three of the published methods, one modification of a commercial kit (SureFood allergen almond) and one attempted novel method targeting thaumatin-like protein gene. Samples of leaves and kernels were used in the experiments. The empirical results were favourable for the method from Röder et al. (2011) and a modification of SureFood allergen almond kit, both showing cross-reactivity <10(-3) compared to the model almond.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25483259</PMID><DateCompleted><Year>2015</Year><Month>11</Month><Day>02</Day></DateCompleted><DateRevised><Year>2015</Year><Month>03</Month><Day>17</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-1194</ISSN><JournalIssue CitedMedium="Internet"><Volume>29</Volume><Issue>2</Issue><PubDate><Year>2015</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Molecular and cellular probes</Title><ISOAbbreviation>Mol Cell Probes</ISOAbbreviation></Journal><ArticleTitle>In silico and experimental evaluation of DNA-based detection methods for the ability to discriminate almond from other Prunus spp.</ArticleTitle><Pagination><MedlinePgn>99-115</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.mcp.2014.11.006</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0890-8508(14)00064-4</ELocationID><Abstract><AbstractText>Ten published DNA-based analytical methods aiming at detecting material of almond (Prunus dulcis) were in silico evaluated for potential cross-reactivity with other stone fruits (Prunus spp.), including peach, apricot, plum, cherry, sour cherry and Sargent cherry. For most assays, the analysis of nucleotide databases suggested none or insufficient discrimination of at least some stone fruits. On the other hand, the assay targeting non-specific lipid transfer protein (Röder et al., 2011, Anal Chim Acta 685:74-83) was sufficiently discriminative, judging from nucleotide alignments. Empirical evaluation was performed for three of the published methods, one modification of a commercial kit (SureFood allergen almond) and one attempted novel method targeting thaumatin-like protein gene. Samples of leaves and kernels were used in the experiments. The empirical results were favourable for the method from Röder et al. (2011) and a modification of SureFood allergen almond kit, both showing cross-reactivity <10(-3) compared to the model almond.</AbstractText><CopyrightInformation>Copyright © 2014 Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Brežná</LastName><ForeName>Barbara</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Molecular Biology, Food Research Institute, Priemyselná 4, P.O. Box 25, 824 75 Bratislava 26, Slovakia. Electronic address: brezna@vup.sk.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Šmíd</LastName><ForeName>Jiří</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Molecular Biology, Food Research Institute, Priemyselná 4, P.O. Box 25, 824 75 Bratislava 26, Slovakia; Institute of Food Chemistry and Biotechnolgy, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Costa</LastName><ForeName>Joana</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Radvanszky</LastName><ForeName>Jan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Vlárska 5, 83334 Bratislava, Slovakia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mafra</LastName><ForeName>Isabel</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kuchta</LastName><ForeName>Tomáš</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Molecular Biology, Food Research Institute, Priemyselná 4, P.O. Box 25, 824 75 Bratislava 26, Slovakia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>12</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Cell Probes</MedlineTA><NlmUniqueID>8709751</NlmUniqueID><ISSNLinking>0890-8508</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015342">DNA Probes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>53850-34-3</RegistryNumber><NameOfSubstance UI="C003427">thaumatin protein, plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015342" MajorTopicYN="N">DNA Probes</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018515" MajorTopicYN="N">Plant Leaves</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D027861" MajorTopicYN="N">Prunus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Allergen</Keyword><Keyword MajorTopicYN="N">Almond</Keyword><Keyword MajorTopicYN="N">DNA</Keyword><Keyword MajorTopicYN="N">Food</Keyword><Keyword MajorTopicYN="N">Real-time PCR</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>03</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2014</Year><Month>11</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>11</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>12</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>12</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>11</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25483259</ArticleId><ArticleId IdType="pii">S0890-8508(14)00064-4</ArticleId><ArticleId IdType="doi">10.1016/j.mcp.2014.11.006</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Portugal</li><li>République tchèque</li><li>Slovaquie</li></country></list><tree><country name="Slovaquie"><noRegion><name sortKey="Brezna, Barbara" sort="Brezna, Barbara" uniqKey="Brezna B" first="Barbara" last="Brežná">Barbara Brežná</name></noRegion><name sortKey="Kuchta, Tomas" sort="Kuchta, Tomas" uniqKey="Kuchta T" first="Tomáš" last="Kuchta">Tomáš Kuchta</name><name sortKey="Radvanszky, Jan" sort="Radvanszky, Jan" uniqKey="Radvanszky J" first="Jan" last="Radvanszky">Jan Radvanszky</name></country><country name="République tchèque"><noRegion><name sortKey="Smid, Ji" sort="Smid, Ji" uniqKey="Smid J" first="Ji" last="Šmíd">Ji Šmíd</name></noRegion></country><country name="Portugal"><noRegion><name sortKey="Costa, Joana" sort="Costa, Joana" uniqKey="Costa J" first="Joana" last="Costa">Joana Costa</name></noRegion><name sortKey="Mafra, Isabel" sort="Mafra, Isabel" uniqKey="Mafra I" first="Isabel" last="Mafra">Isabel Mafra</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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