Total RNA extraction method and Prunus species influence the detection of Plum pox potyvirus by real-time RT-PCR
Identifieur interne : 000884 ( Istex/Corpus ); précédent : 000883; suivant : 000885Total RNA extraction method and Prunus species influence the detection of Plum pox potyvirus by real-time RT-PCR
Auteurs : Irena Pleško ; Mojca Marn ; Nataša ToplakSource :
- Acta agriculturae Slovenica [ 1581-9175 ] ; 2011-05-01.
English descriptors
- KwdEn :
- 18S rRNA, MGB, PCR inhibition, PPV.
Abstract
Successful total RNA (totRNA) extraction is a prerequisite for a successful real-time PCR. In the present work we compared one manual and one automated totRNA extraction method for detection of Plum pox potyvirus (PPV) in leaves of different Prunus sp. using developed real-time RT-PCR assay. Advantages and disadvantages of compared methods are described in the view of sensitivity, reproducibility and in terms of laboratory use. The results suggest that the column based totRNA extraction method is more effective for apricot, plum and peach. In the case of damson the differences in real-time PCR results between both extraction methods were negligible. In case of negative results obtained with automated method, manual column based extraction method should be used additionally.
Url:
DOI: 10.2478/v10014-011-0006-8
Links to Exploration step
ISTEX:F1C2005AFDA3632544156D35D0EE39111235DB6FLe document en format XML
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In the present work we compared one manual and one automated totRNA extraction method for detection of Plum pox potyvirus (PPV) in leaves of different Prunus sp. using developed real-time RT-PCR assay. Advantages and disadvantages of compared methods are described in the view of sensitivity, reproducibility and in terms of laboratory use. The results suggest that the column based totRNA extraction method is more effective for apricot, plum and peach. In the case of damson the differences in real-time PCR results between both extraction methods were negligible. In case of negative results obtained with automated method, manual column based extraction method should be used additionally.</div></front></TEI><istex><corpusName>degruyter-journals</corpusName><author><json:item><name>Irena Pleško</name><affiliations><json:string>Agricultural Institute of Slovenia, Hacquetova 17, SI-1000 Ljubljana, Slovenia</json:string></affiliations></json:item><json:item><name>Mojca Marn</name><affiliations><json:string>Agricultural Institute of Slovenia, Hacquetova 17, SI-1000 Ljubljana, Slovenia</json:string></affiliations></json:item><json:item><name>Nataša Toplak</name><affiliations><json:string>Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>18S rRNA</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MGB</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>PCR inhibition</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>PPV</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>18S rRNA</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MGB</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>inhibicija PCR</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>PPV</value></json:item></subject><articleId><json:string>v10014-011-0006-8</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>research-article</json:string></originalGenre><abstract>Successful total RNA (totRNA) extraction is a prerequisite for a successful real-time PCR. In the present work we compared one manual and one automated totRNA extraction method for detection of Plum pox potyvirus (PPV) in leaves of different Prunus sp. using developed real-time RT-PCR assay. Advantages and disadvantages of compared methods are described in the view of sensitivity, reproducibility and in terms of laboratory use. The results suggest that the column based totRNA extraction method is more effective for apricot, plum and peach. In the case of damson the differences in real-time PCR results between both extraction methods were negligible. 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In the present work we compared one manual and one automated totRNA extraction method for detection of Plum pox potyvirus (PPV) in leaves of different Prunus sp. using developed real-time RT-PCR assay. Advantages and disadvantages of compared methods are described in the view of sensitivity, reproducibility and in terms of laboratory use. The results suggest that the column based totRNA extraction method is more effective for apricot, plum and peach. In the case of damson the differences in real-time PCR results between both extraction methods were negligible. In case of negative results obtained with automated method, manual column based extraction method should be used additionally.</p></abstract><abstract xml:lang="sl"><p>Uspešnost izolacije RNA je osnova za uspešno izvedbo reakcije PCR v realnem času (qPCR). V svojem delu smo primerjali ročno in avtomatsko metodo izolacije celokupne RNA (totRNA) iz listov različnih rastlinskih vrst iz rodu Prunus. Uspešnost izolacije totRNA smo preverjali z uvedeno metodo qPCR za detekcijo virusa šarke (Plum pox potyvirus - PPV). Prednosti in slabosti uporabljenih metod smo ugotavljali s primerjavo občutljivosti detekcije, ponovljivosti in intenzivnosti laboratorijskega dela. Rezultati raziskave so pokazali, da je ročna metoda izolacije totRNA učinkovitejša pri marelicah, breskvah in slivah, medtem ko so bile razlike med obema metodama pri ciborah zanemarljive. Pri uporabi preizkušene avtomatske metode izolacije totRNA je priporočljivo, da v primeru negativnih rezultatov le-te še dodatno preverimo z uporabo ročne metode izolacije.</p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Keywords</head><item><term>18S rRNA</term></item><item><term>MGB</term></item><item><term>PCR inhibition</term></item><item><term>PPV</term></item></list></keywords></textClass><textClass xml:lang="sl"><keywords scheme="keyword"><list><head>Keywords</head><item><term>18S rRNA</term></item><item><term>MGB</term></item><item><term>inhibicija PCR</term></item><item><term>PPV</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2011-06-13">Created</change><change when="2011-05-01">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/document/F1C2005AFDA3632544156D35D0EE39111235DB6F/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus degruyter-journals" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//NLM//DTD Journal Publishing DTD v3.0 20080202//EN" URI="journalpublishing3.dtd" name="istex:docType"></istex:docType><istex:document><article article-type="research-article" dtd-version="3.0" xml:lang="en"><front><journal-meta><journal-id journal-id-type="publisher-id">ACAS</journal-id><journal-title-group><abbrev-journal-title abbrev-type="full">Acta agriculturae Slovenica</abbrev-journal-title></journal-title-group><issn pub-type="epub">1854-1941</issn><issn pub-type="ppub">1581-9175</issn><publisher><publisher-name>Versita</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">v10014-011-0006-8</article-id><article-id pub-id-type="doi">10.2478/v10014-011-0006-8</article-id><title-group><article-title>Total RNA extraction method and <italic>Prunus</italic> species influence the detection of <italic>Plum pox potyvirus</italic> by real-time RT-PCR</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Pleško</surname><given-names>Irena</given-names></name><xref ref-type="aff" rid="A1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Marn</surname><given-names>Mojca</given-names></name><xref ref-type="aff" rid="A1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Toplak</surname><given-names>Nataša</given-names></name><xref ref-type="aff" rid="A2"><sup>1</sup></xref></contrib><aff id="A1">Agricultural Institute of Slovenia, Hacquetova 17, SI-1000 Ljubljana, Slovenia<sup>1</sup></aff><aff id="A2">Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia<sup>2</sup></aff></contrib-group><author-notes><corresp></corresp></author-notes><pub-date pub-type="ppub"><day>1</day><month>5</month><year>2011</year></pub-date><pub-date pub-type="epub"><day>13</day><month>6</month><year>2011</year></pub-date><volume>97</volume><issue>2</issue><fpage>105</fpage><lpage>113</lpage><permissions><license license-type="open-access"><license-p>This content is open access.</license-p></license></permissions><related-article related-article-type="pdf" xlink:href="v10014-011-0006-8.pdf"></related-article><abstract xml:lang="en"><title>Total RNA extraction method and <italic>Prunus</italic> species influence the detection of <italic>Plum pox potyvirus</italic> by real-time RT-PCR</title><p>Successful total RNA (totRNA) extraction is a prerequisite for a successful real-time PCR. In the present work we compared one manual and one automated totRNA extraction method for detection of <italic>Plum pox potyvirus</italic> (PPV) in leaves of different Prunus sp. using developed real-time RT-PCR assay. Advantages and disadvantages of compared methods are described in the view of sensitivity, reproducibility and in terms of laboratory use. The results suggest that the column based totRNA extraction method is more effective for apricot, plum and peach. In the case of damson the differences in real-time PCR results between both extraction methods were negligible. In case of negative results obtained with automated method, manual column based extraction method should be used additionally.</p></abstract><abstract xml:lang="sl"><title>Rastlinska Vrsta in Metoda Izolacije Celokupne RNA Vplivata na Uspešnost Detekcije Virusa Šarke s PCR v Realnem Času</title><p>Uspešnost izolacije RNA je osnova za uspešno izvedbo reakcije PCR v realnem času (qPCR). V svojem delu smo primerjali ročno in avtomatsko metodo izolacije celokupne RNA (totRNA) iz listov različnih rastlinskih vrst iz rodu Prunus. Uspešnost izolacije totRNA smo preverjali z uvedeno metodo qPCR za detekcijo virusa šarke (<italic>Plum pox potyvirus</italic> - PPV). Prednosti in slabosti uporabljenih metod smo ugotavljali s primerjavo občutljivosti detekcije, ponovljivosti in intenzivnosti laboratorijskega dela. Rezultati raziskave so pokazali, da je ročna metoda izolacije totRNA učinkovitejša pri marelicah, breskvah in slivah, medtem ko so bile razlike med obema metodama pri ciborah zanemarljive. Pri uporabi preizkušene avtomatske metode izolacije totRNA je priporočljivo, da v primeru negativnih rezultatov le-te še dodatno preverimo z uporabo ročne metode izolacije.</p></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>18S rRNA</kwd><kwd>MGB</kwd><kwd>PCR inhibition</kwd><kwd>PPV</kwd></kwd-group><kwd-group xml:lang="sl"><title>Keywords</title><kwd>18S rRNA</kwd><kwd>MGB</kwd><kwd>inhibicija PCR</kwd><kwd>PPV</kwd></kwd-group></article-meta></front></article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Total RNA extraction method and Prunus species influence the detection of Plum pox potyvirus by real-time RT-PCR</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>Total RNA extraction method and Prunus species influence the detection of Plum pox potyvirus by real-time RT-PCR</title></titleInfo><name type="personal"><namePart type="given">Irena</namePart><namePart type="family">Pleško</namePart><affiliation>Agricultural Institute of Slovenia, Hacquetova 17, SI-1000 Ljubljana, Slovenia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Mojca</namePart><namePart type="family">Marn</namePart><affiliation>Agricultural Institute of Slovenia, Hacquetova 17, SI-1000 Ljubljana, Slovenia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Nataša</namePart><namePart type="family">Toplak</namePart><affiliation>Omega d.o.o., Dolinškova 8, SI-1000 Ljubljana, Slovenia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="research-article"></genre><originInfo><publisher>Versita</publisher><dateIssued encoding="w3cdtf">2011-05-01</dateIssued><dateCreated encoding="w3cdtf">2011-06-13</dateCreated><copyrightDate encoding="w3cdtf">2011</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract lang="en">Successful total RNA (totRNA) extraction is a prerequisite for a successful real-time PCR. In the present work we compared one manual and one automated totRNA extraction method for detection of Plum pox potyvirus (PPV) in leaves of different Prunus sp. using developed real-time RT-PCR assay. Advantages and disadvantages of compared methods are described in the view of sensitivity, reproducibility and in terms of laboratory use. The results suggest that the column based totRNA extraction method is more effective for apricot, plum and peach. In the case of damson the differences in real-time PCR results between both extraction methods were negligible. In case of negative results obtained with automated method, manual column based extraction method should be used additionally.</abstract><abstract lang="sl">Uspešnost izolacije RNA je osnova za uspešno izvedbo reakcije PCR v realnem času (qPCR). V svojem delu smo primerjali ročno in avtomatsko metodo izolacije celokupne RNA (totRNA) iz listov različnih rastlinskih vrst iz rodu Prunus. Uspešnost izolacije totRNA smo preverjali z uvedeno metodo qPCR za detekcijo virusa šarke (Plum pox potyvirus - PPV). Prednosti in slabosti uporabljenih metod smo ugotavljali s primerjavo občutljivosti detekcije, ponovljivosti in intenzivnosti laboratorijskega dela. Rezultati raziskave so pokazali, da je ročna metoda izolacije totRNA učinkovitejša pri marelicah, breskvah in slivah, medtem ko so bile razlike med obema metodama pri ciborah zanemarljive. Pri uporabi preizkušene avtomatske metode izolacije totRNA je priporočljivo, da v primeru negativnih rezultatov le-te še dodatno preverimo z uporabo ročne metode izolacije.</abstract><subject lang="en"><genre>Keywords</genre><topic>18S rRNA</topic><topic>MGB</topic><topic>PCR inhibition</topic><topic>PPV</topic></subject><subject lang="sl"><genre>Keywords</genre><topic>18S rRNA</topic><topic>MGB</topic><topic>inhibicija PCR</topic><topic>PPV</topic></subject><relatedItem type="host"><titleInfo><title>Acta agriculturae Slovenica</title></titleInfo><genre type="journal">journal</genre><identifier type="ISSN">1581-9175</identifier><identifier type="eISSN">1854-1941</identifier><identifier type="PublisherID">ACAS</identifier><part><date>2011</date><detail type="volume"><caption>vol.</caption><number>97</number></detail><detail type="issue"><caption>no.</caption><number>2</number></detail><extent unit="pages"><start>105</start><end>113</end></extent></part></relatedItem><identifier type="istex">F1C2005AFDA3632544156D35D0EE39111235DB6F</identifier><identifier type="DOI">10.2478/v10014-011-0006-8</identifier><identifier type="ArticleID">v10014-011-0006-8</identifier><identifier type="pdf">v10014-011-0006-8.pdf</identifier><accessCondition type="use and reproduction" contentType="open-access">This content is open access.</accessCondition><recordInfo><recordContentSource>De Gruyter</recordContentSource></recordInfo></mods></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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