Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription.
Identifieur interne : 002801 ( PubMed/Corpus ); précédent : 002800; suivant : 002802Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription.
Auteurs : Daiji Endoh ; Tetsuya Mizutani ; Rikio Kirisawa ; Yoshiyuki Maki ; Hidetoshi Saito ; Yasuhiro Kon ; Shigeru Morikawa ; Masanobu HayashiSource :
- Nucleic acids research [ 1362-4962 ] ; 2005.
English descriptors
- KwdEn :
- Animals, Base Sequence, Cattle, Cell Line, DNA, Complementary (biosynthesis), DNA, Complementary (chemistry), Genome, Viral, Nucleotides (analysis), Parainfluenza Virus 3, Bovine (genetics), Parainfluenza Virus 3, Bovine (isolation & purification), Polymerase Chain Reaction (methods), RNA Viruses (genetics), RNA Viruses (isolation & purification), RNA, Ribosomal (chemistry), RNA, Viral (analysis), RNA, Viral (chemistry), Rats, Reverse Transcription, SARS Virus (genetics), SARS Virus (isolation & purification), Sequence Analysis, RNA.
- MESH :
- chemical , analysis : Nucleotides, RNA, Viral.
- chemical , biosynthesis : DNA, Complementary.
- chemical , chemistry : DNA, Complementary, RNA, Ribosomal, RNA, Viral.
- genetics : Parainfluenza Virus 3, Bovine, RNA Viruses, SARS Virus.
- isolation & purification : Parainfluenza Virus 3, Bovine, RNA Viruses, SARS Virus.
- methods : Polymerase Chain Reaction.
- Animals, Base Sequence, Cattle, Cell Line, Genome, Viral, Rats, Reverse Transcription, Sequence Analysis, RNA.
Abstract
A method for the isolation of genomic fragments of RNA virus based on cDNA representational difference analysis (cDNA RDA) was developed. cDNA RDA has been applied for the subtraction of poly(A)(+) RNAs but not for poly(A)(-) RNAs, such as RNA virus genomes, owing to the vast quantity of ribosomal RNAs. We constructed primers for inefficient reverse transcription of ribosomal sequences based on the distribution analysis of hexanucleotide patterns in ribosomal RNA. The analysis revealed that distributions of hexanucleotide patterns in ribosomal RNA and virus genome were different. We constructed 96 hexanucleotides (non-ribosomal hexanucleotides) and used them as mixed primers for reverse transcription of cDNA RDA. A synchronous analysis of hexanucleotide patterns in known viral sequences showed that all the known genomic-size viral sequences include non-ribosomal hexanucleotides. In a model experiment, when non-ribosomal hexanucleotides were used as primers, in vitro transcribed plasmid RNA was efficiently reverse transcribed when compared with ribosomal RNA of rat cells. Using non-ribosomal primers, the cDNA fragments of severe acute respiratory syndrome coronavirus and bovine parainfluenza virus 3 were efficiently amplified by subtracting the cDNA amplicons derived from uninfected cells from those that were derived from virus-infected cells. The results suggest that cDNA RDA with non-ribosomal primers can be used for species-independent detection of viruses, including new viruses.
DOI: 10.1093/nar/gni064
PubMed: 15817564
Links to Exploration step
pubmed:15817564Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription.</title><author><name sortKey="Endoh, Daiji" sort="Endoh, Daiji" uniqKey="Endoh D" first="Daiji" last="Endoh">Daiji Endoh</name><affiliation><nlm:affiliation>Laboratory of Veterinary Radiology, School of Veterinary Medicine, Rakuno Gakuen University Ebetsu 069-8501, Japan. dendoh@rakuno.ac.jp</nlm:affiliation></affiliation></author><author><name sortKey="Mizutani, Tetsuya" sort="Mizutani, Tetsuya" uniqKey="Mizutani T" first="Tetsuya" last="Mizutani">Tetsuya Mizutani</name></author><author><name sortKey="Kirisawa, Rikio" sort="Kirisawa, Rikio" uniqKey="Kirisawa R" first="Rikio" last="Kirisawa">Rikio Kirisawa</name></author><author><name sortKey="Maki, Yoshiyuki" sort="Maki, Yoshiyuki" uniqKey="Maki Y" first="Yoshiyuki" last="Maki">Yoshiyuki Maki</name></author><author><name sortKey="Saito, Hidetoshi" sort="Saito, Hidetoshi" uniqKey="Saito H" first="Hidetoshi" last="Saito">Hidetoshi Saito</name></author><author><name sortKey="Kon, Yasuhiro" sort="Kon, Yasuhiro" uniqKey="Kon Y" first="Yasuhiro" last="Kon">Yasuhiro Kon</name></author><author><name sortKey="Morikawa, Shigeru" sort="Morikawa, Shigeru" uniqKey="Morikawa S" first="Shigeru" last="Morikawa">Shigeru Morikawa</name></author><author><name sortKey="Hayashi, Masanobu" sort="Hayashi, Masanobu" uniqKey="Hayashi M" first="Masanobu" last="Hayashi">Masanobu Hayashi</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:15817564</idno><idno type="pmid">15817564</idno><idno type="doi">10.1093/nar/gni064</idno><idno type="wicri:Area/PubMed/Corpus">002801</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002801</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription.</title><author><name sortKey="Endoh, Daiji" sort="Endoh, Daiji" uniqKey="Endoh D" first="Daiji" last="Endoh">Daiji Endoh</name><affiliation><nlm:affiliation>Laboratory of Veterinary Radiology, School of Veterinary Medicine, Rakuno Gakuen University Ebetsu 069-8501, Japan. dendoh@rakuno.ac.jp</nlm:affiliation></affiliation></author><author><name sortKey="Mizutani, Tetsuya" sort="Mizutani, Tetsuya" uniqKey="Mizutani T" first="Tetsuya" last="Mizutani">Tetsuya Mizutani</name></author><author><name sortKey="Kirisawa, Rikio" sort="Kirisawa, Rikio" uniqKey="Kirisawa R" first="Rikio" last="Kirisawa">Rikio Kirisawa</name></author><author><name sortKey="Maki, Yoshiyuki" sort="Maki, Yoshiyuki" uniqKey="Maki Y" first="Yoshiyuki" last="Maki">Yoshiyuki Maki</name></author><author><name sortKey="Saito, Hidetoshi" sort="Saito, Hidetoshi" uniqKey="Saito H" first="Hidetoshi" last="Saito">Hidetoshi Saito</name></author><author><name sortKey="Kon, Yasuhiro" sort="Kon, Yasuhiro" uniqKey="Kon Y" first="Yasuhiro" last="Kon">Yasuhiro Kon</name></author><author><name sortKey="Morikawa, Shigeru" sort="Morikawa, Shigeru" uniqKey="Morikawa S" first="Shigeru" last="Morikawa">Shigeru Morikawa</name></author><author><name sortKey="Hayashi, Masanobu" sort="Hayashi, Masanobu" uniqKey="Hayashi M" first="Masanobu" last="Hayashi">Masanobu Hayashi</name></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Cattle</term><term>Cell Line</term><term>DNA, Complementary (biosynthesis)</term><term>DNA, Complementary (chemistry)</term><term>Genome, Viral</term><term>Nucleotides (analysis)</term><term>Parainfluenza Virus 3, Bovine (genetics)</term><term>Parainfluenza Virus 3, Bovine (isolation & purification)</term><term>Polymerase Chain Reaction (methods)</term><term>RNA Viruses (genetics)</term><term>RNA Viruses (isolation & purification)</term><term>RNA, Ribosomal (chemistry)</term><term>RNA, Viral (analysis)</term><term>RNA, Viral (chemistry)</term><term>Rats</term><term>Reverse Transcription</term><term>SARS Virus (genetics)</term><term>SARS Virus (isolation & purification)</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Nucleotides</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>DNA, Complementary</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Complementary</term><term>RNA, Ribosomal</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Parainfluenza Virus 3, Bovine</term><term>RNA Viruses</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Parainfluenza Virus 3, Bovine</term><term>RNA Viruses</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Cattle</term><term>Cell Line</term><term>Genome, Viral</term><term>Rats</term><term>Reverse Transcription</term><term>Sequence Analysis, RNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A method for the isolation of genomic fragments of RNA virus based on cDNA representational difference analysis (cDNA RDA) was developed. cDNA RDA has been applied for the subtraction of poly(A)(+) RNAs but not for poly(A)(-) RNAs, such as RNA virus genomes, owing to the vast quantity of ribosomal RNAs. We constructed primers for inefficient reverse transcription of ribosomal sequences based on the distribution analysis of hexanucleotide patterns in ribosomal RNA. The analysis revealed that distributions of hexanucleotide patterns in ribosomal RNA and virus genome were different. We constructed 96 hexanucleotides (non-ribosomal hexanucleotides) and used them as mixed primers for reverse transcription of cDNA RDA. A synchronous analysis of hexanucleotide patterns in known viral sequences showed that all the known genomic-size viral sequences include non-ribosomal hexanucleotides. In a model experiment, when non-ribosomal hexanucleotides were used as primers, in vitro transcribed plasmid RNA was efficiently reverse transcribed when compared with ribosomal RNA of rat cells. Using non-ribosomal primers, the cDNA fragments of severe acute respiratory syndrome coronavirus and bovine parainfluenza virus 3 were efficiently amplified by subtracting the cDNA amplicons derived from uninfected cells from those that were derived from virus-infected cells. The results suggest that cDNA RDA with non-ribosomal primers can be used for species-independent detection of viruses, including new viruses.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15817564</PMID><DateCompleted><Year>2005</Year><Month>04</Month><Day>25</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>33</Volume><Issue>6</Issue><PubDate><Year>2005</Year><Month>Apr</Month><Day>07</Day></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation></Journal><ArticleTitle>Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription.</ArticleTitle><Pagination><MedlinePgn>e65</MedlinePgn></Pagination><Abstract><AbstractText>A method for the isolation of genomic fragments of RNA virus based on cDNA representational difference analysis (cDNA RDA) was developed. cDNA RDA has been applied for the subtraction of poly(A)(+) RNAs but not for poly(A)(-) RNAs, such as RNA virus genomes, owing to the vast quantity of ribosomal RNAs. We constructed primers for inefficient reverse transcription of ribosomal sequences based on the distribution analysis of hexanucleotide patterns in ribosomal RNA. The analysis revealed that distributions of hexanucleotide patterns in ribosomal RNA and virus genome were different. We constructed 96 hexanucleotides (non-ribosomal hexanucleotides) and used them as mixed primers for reverse transcription of cDNA RDA. A synchronous analysis of hexanucleotide patterns in known viral sequences showed that all the known genomic-size viral sequences include non-ribosomal hexanucleotides. In a model experiment, when non-ribosomal hexanucleotides were used as primers, in vitro transcribed plasmid RNA was efficiently reverse transcribed when compared with ribosomal RNA of rat cells. Using non-ribosomal primers, the cDNA fragments of severe acute respiratory syndrome coronavirus and bovine parainfluenza virus 3 were efficiently amplified by subtracting the cDNA amplicons derived from uninfected cells from those that were derived from virus-infected cells. The results suggest that cDNA RDA with non-ribosomal primers can be used for species-independent detection of viruses, including new viruses.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Endoh</LastName><ForeName>Daiji</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Laboratory of Veterinary Radiology, School of Veterinary Medicine, Rakuno Gakuen University Ebetsu 069-8501, Japan. dendoh@rakuno.ac.jp</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mizutani</LastName><ForeName>Tetsuya</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Kirisawa</LastName><ForeName>Rikio</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Maki</LastName><ForeName>Yoshiyuki</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Saito</LastName><ForeName>Hidetoshi</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Kon</LastName><ForeName>Yasuhiro</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Morikawa</LastName><ForeName>Shigeru</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Hayashi</LastName><ForeName>Masanobu</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2005</Year><Month>04</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nucleic Acids Res</MedlineTA><NlmUniqueID>0411011</NlmUniqueID><ISSNLinking>0305-1048</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018076">DNA, 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MajorTopicYN="N">biosynthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009711" MajorTopicYN="N">Nucleotides</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029101" MajorTopicYN="N">Parainfluenza Virus 3, Bovine</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012328" MajorTopicYN="N">RNA Viruses</DescriptorName><QualifierName UI="Q000235" 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purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2005</Year><Month>4</Month><Day>9</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2005</Year><Month>4</Month><Day>26</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2005</Year><Month>4</Month><Day>9</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15817564</ArticleId><ArticleId IdType="pii">33/6/e65</ArticleId><ArticleId IdType="doi">10.1093/nar/gni064</ArticleId><ArticleId IdType="pmc">PMC1074749</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Virus Genes. 2000;20(2):173-82</Citation><ArticleIdList><ArticleId 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