PhytophthoraV1, Main, Exploration, bibRecord, 000077

RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors.

Identifieur interne : 000077 ( Main/Exploration ); précédent : 000076; suivant : 000078

RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors.

Auteurs : Mustafa Ahmad Munawar [Finlande] ; Frank Martin [États-Unis] ; Anna Toljamo [Finlande] ; Harri Kokko [Finlande] ; Elina Oksanen [Finlande]

Source :

BioTechniques [ 1940-9818 ] ; 2020.

RBID : pubmed:32815734

Abstract

DNA extraction can be lengthy and sometimes ends up with amplification inhibitors. We present the potential of recombinase polymerase amplification (RPA) to replace plant DNA extraction. In our rapid 'RPA-PCR couple' concept, RPA is tuned to slower reaction kinetics to promote amplification of long targets. RPA primers amplify target and some flanking regions directly from simple plant macerates. Then PCR primers exponentially amplify the target directly from the RPA reaction. We present the coupling of RPA with conventional, TaqMan and SYBR Green PCR assays. We applied the concept to strawberry Phytophthora pathogens and the Phytophthora identification marker atp9-nad9. We found RPA-PCR couple specific, sensitive and reliable. The approach may also benefit other difficult samples such as food, feces and ancient samples.

DOI: 10.2144/btn-2020-0065
PubMed: 32815734

Affiliations:

Links toward previous steps (curation, corpus...)

to stream Main, to step Corpus: 000091
to stream Main, to step Curation: 000091

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors.</title>
<author><name sortKey="Munawar, Mustafa Ahmad" sort="Munawar, Mustafa Ahmad" uniqKey="Munawar M" first="Mustafa Ahmad" last="Munawar">Mustafa Ahmad Munawar</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211</wicri:regionArea>
<wicri:noRegion>Kuopio 70211</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Martin, Frank" sort="Martin, Frank" uniqKey="Martin F" first="Frank" last="Martin">Frank Martin</name>
<affiliation wicri:level="2"><nlm:affiliation>US Department of Agriculture, ARS, Salinas, CA 93905, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>US Department of Agriculture, ARS, Salinas, CA 93905</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Toljamo, Anna" sort="Toljamo, Anna" uniqKey="Toljamo A" first="Anna" last="Toljamo">Anna Toljamo</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211</wicri:regionArea>
<wicri:noRegion>Kuopio 70211</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kokko, Harri" sort="Kokko, Harri" uniqKey="Kokko H" first="Harri" last="Kokko">Harri Kokko</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211</wicri:regionArea>
<wicri:noRegion>Kuopio 70211</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Oksanen, Elina" sort="Oksanen, Elina" uniqKey="Oksanen E" first="Elina" last="Oksanen">Elina Oksanen</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211</wicri:regionArea>
<wicri:noRegion>Kuopio 70211</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2020">2020</date>
<idno type="RBID">pubmed:32815734</idno>
<idno type="pmid">32815734</idno>
<idno type="doi">10.2144/btn-2020-0065</idno>
<idno type="wicri:Area/Main/Corpus">000091</idno>
<idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000091</idno>
<idno type="wicri:Area/Main/Curation">000091</idno>
<idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000091</idno>
<idno type="wicri:Area/Main/Exploration">000091</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors.</title>
<author><name sortKey="Munawar, Mustafa Ahmad" sort="Munawar, Mustafa Ahmad" uniqKey="Munawar M" first="Mustafa Ahmad" last="Munawar">Mustafa Ahmad Munawar</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211</wicri:regionArea>
<wicri:noRegion>Kuopio 70211</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Martin, Frank" sort="Martin, Frank" uniqKey="Martin F" first="Frank" last="Martin">Frank Martin</name>
<affiliation wicri:level="2"><nlm:affiliation>US Department of Agriculture, ARS, Salinas, CA 93905, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>US Department of Agriculture, ARS, Salinas, CA 93905</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Toljamo, Anna" sort="Toljamo, Anna" uniqKey="Toljamo A" first="Anna" last="Toljamo">Anna Toljamo</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211</wicri:regionArea>
<wicri:noRegion>Kuopio 70211</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kokko, Harri" sort="Kokko, Harri" uniqKey="Kokko H" first="Harri" last="Kokko">Harri Kokko</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211</wicri:regionArea>
<wicri:noRegion>Kuopio 70211</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Oksanen, Elina" sort="Oksanen, Elina" uniqKey="Oksanen E" first="Elina" last="Oksanen">Elina Oksanen</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</nlm:affiliation>
<country xml:lang="fr">Finlande</country>
<wicri:regionArea>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211</wicri:regionArea>
<wicri:noRegion>Kuopio 70211</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">BioTechniques</title>
<idno type="eISSN">1940-9818</idno>
<imprint><date when="2020" type="published">2020</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">DNA extraction can be lengthy and sometimes ends up with amplification inhibitors. We present the potential of recombinase polymerase amplification (RPA) to replace plant DNA extraction. In our rapid 'RPA-PCR couple' concept, RPA is tuned to slower reaction kinetics to promote amplification of long targets. RPA primers amplify target and some flanking regions directly from simple plant macerates. Then PCR primers exponentially amplify the target directly from the RPA reaction. We present the coupling of RPA with conventional, TaqMan and SYBR Green PCR assays. We applied the concept to strawberry <i>Phytophthora</i>
 pathogens and the <i>Phytophthora</i>
 identification marker <i>atp9-nad9</i>
. We found RPA-PCR couple specific, sensitive and reliable. The approach may also benefit other difficult samples such as food, feces and ancient samples.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32815734</PMID>
<DateRevised><Year>2020</Year>
<Month>11</Month>
<Day>03</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1940-9818</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>69</Volume>
<Issue>4</Issue>
<PubDate><Year>2020</Year>
<Month>10</Month>
</PubDate>
</JournalIssue>
<Title>BioTechniques</Title>
<ISOAbbreviation>Biotechniques</ISOAbbreviation>
</Journal>
<ArticleTitle>RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors.</ArticleTitle>
<Pagination><MedlinePgn>270-280</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.2144/btn-2020-0065</ELocationID>
<Abstract><AbstractText>DNA extraction can be lengthy and sometimes ends up with amplification inhibitors. We present the potential of recombinase polymerase amplification (RPA) to replace plant DNA extraction. In our rapid 'RPA-PCR couple' concept, RPA is tuned to slower reaction kinetics to promote amplification of long targets. RPA primers amplify target and some flanking regions directly from simple plant macerates. Then PCR primers exponentially amplify the target directly from the RPA reaction. We present the coupling of RPA with conventional, TaqMan and SYBR Green PCR assays. We applied the concept to strawberry <i>Phytophthora</i>
 pathogens and the <i>Phytophthora</i>
 identification marker <i>atp9-nad9</i>
. We found RPA-PCR couple specific, sensitive and reliable. The approach may also benefit other difficult samples such as food, feces and ancient samples.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Munawar</LastName>
<ForeName>Mustafa Ahmad</ForeName>
<Initials>MA</Initials>
<Identifier Source="ORCID">0000-0002-2604-850X</Identifier>
<AffiliationInfo><Affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Martin</LastName>
<ForeName>Frank</ForeName>
<Initials>F</Initials>
<AffiliationInfo><Affiliation>US Department of Agriculture, ARS, Salinas, CA 93905, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Toljamo</LastName>
<ForeName>Anna</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Kokko</LastName>
<ForeName>Harri</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Oksanen</LastName>
<ForeName>Elina</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>Department of Environmental & Biological Sciences, University of Eastern Finland, Kuopio 70211, Finland.</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>2020</Year>
<Month>08</Month>
<Day>20</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Biotechniques</MedlineTA>
<NlmUniqueID>8306785</NlmUniqueID>
<ISSNLinking>0736-6205</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">PCR inhibitors</Keyword>
<Keyword MajorTopicYN="Y">Phytophthora</Keyword>
<Keyword MajorTopicYN="Y">Phytophthora cactorum</Keyword>
<Keyword MajorTopicYN="Y">Phytophthora fragariae</Keyword>
<Keyword MajorTopicYN="Y">atp9-nad9</Keyword>
<Keyword MajorTopicYN="Y">plant DNA extraction</Keyword>
<Keyword MajorTopicYN="Y">recombinase polymerase amplification</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2020</Year>
<Month>8</Month>
<Day>21</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2020</Year>
<Month>8</Month>
<Day>21</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2020</Year>
<Month>8</Month>
<Day>21</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">32815734</ArticleId>
<ArticleId IdType="doi">10.2144/btn-2020-0065</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>Finlande</li>
<li>États-Unis</li>
</country>
<region><li>Californie</li>
</region>
</list>
<tree><country name="Finlande"><noRegion><name sortKey="Munawar, Mustafa Ahmad" sort="Munawar, Mustafa Ahmad" uniqKey="Munawar M" first="Mustafa Ahmad" last="Munawar">Mustafa Ahmad Munawar</name>
</noRegion>
<name sortKey="Kokko, Harri" sort="Kokko, Harri" uniqKey="Kokko H" first="Harri" last="Kokko">Harri Kokko</name>
<name sortKey="Oksanen, Elina" sort="Oksanen, Elina" uniqKey="Oksanen E" first="Elina" last="Oksanen">Elina Oksanen</name>
<name sortKey="Toljamo, Anna" sort="Toljamo, Anna" uniqKey="Toljamo A" first="Anna" last="Toljamo">Anna Toljamo</name>
</country>
<country name="États-Unis"><region name="Californie"><name sortKey="Martin, Frank" sort="Martin, Frank" uniqKey="Martin F" first="Frank" last="Martin">Frank Martin</name>
</region>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PhytophthoraV1/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000077 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000077 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Bois
   |area=    PhytophthoraV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     pubmed:32815734
   |texte=   RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:32815734" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a PhytophthoraV1

This area was generated with Dilib version V0.6.38.
Data generation: Fri Nov 20 11:20:57 2020. Site generation: Wed Mar 6 16:48:20 2024

	Serveur d'exploration Phytophthora
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration Phytophthora

RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors.

RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors.

Source :

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki