Fast protocols for the 5S rDNA and ITS-2 based identification of Oenococcus oeni
To identify specific marker sequences for the rapid identification of Oenococcus oeni, we sequenced the 23S-5S internal transcribed spacer (ITS-2) region and the 5S rDNA of five different O. oeni strains and three phylogenetically related lactic acid bacteria (LAB). Comparative analysis revealed 100...
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| Veröffentlicht in: | FEMS microbiology letters 2005-03, Vol.244 (1), p.165-171 |
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| creator | Hirschhäuser, Steffen Fröhlich, Jürgen Gneipel, Armin Schönig, Inge König, Helmut |
| description | To identify specific marker sequences for the rapid identification of
Oenococcus oeni, we sequenced the 23S-5S internal transcribed spacer (ITS-2) region and the 5S rDNA of five different
O. oeni strains and three phylogenetically related lactic acid bacteria (LAB). Comparative analysis revealed 100% identity among the ITS-2 region of the
O. oeni strains and remarkable differences in length and sequence compared to related LAB. These results enabled us to develop a primer set for a rapid PCR-identification of
O. oeni within three hours. Moreover, the comparison of the 5S rDNA sequences and the highly conserved secondary structure provided the template for the design of three fluorescence-labeled specific oligonucleotides for fluorescence in situ hybridization (FISH). These probes are partial complementary to each other. This feature promotes the accessibility to the target sequence within the ribosome and enhances the fluorescence signal. For the rapid identification of Oenococci both the 5S rRNA gene and the ITS-2 region are useful targets. |
| doi_str_mv | 10.1016/j.femsle.2005.01.033 |
| format | Article |
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Oenococcus oeni, we sequenced the 23S-5S internal transcribed spacer (ITS-2) region and the 5S rDNA of five different
O. oeni strains and three phylogenetically related lactic acid bacteria (LAB). Comparative analysis revealed 100% identity among the ITS-2 region of the
O. oeni strains and remarkable differences in length and sequence compared to related LAB. These results enabled us to develop a primer set for a rapid PCR-identification of
O. oeni within three hours. Moreover, the comparison of the 5S rDNA sequences and the highly conserved secondary structure provided the template for the design of three fluorescence-labeled specific oligonucleotides for fluorescence in situ hybridization (FISH). These probes are partial complementary to each other. This feature promotes the accessibility to the target sequence within the ribosome and enhances the fluorescence signal. For the rapid identification of Oenococci both the 5S rRNA gene and the ITS-2 region are useful targets.</description><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1016/j.femsle.2005.01.033</identifier><identifier>PMID: 15727836</identifier><identifier>CODEN: FMLED7</identifier><language>eng</language><publisher>Oxford, UK: Elsevier B.V</publisher><subject>5S rDNA ; Bacteria ; Bacteriological methods and techniques used in bacteriology ; Bacteriology ; Base Sequence ; Biological and medical sciences ; Comparative analysis ; DNA, Bacterial - genetics ; DNA, Ribosomal - genetics ; DNA, Ribosomal Spacer - genetics ; Fluorescence ; Fluorescence in situ hybridization ; Fundamental and applied biological sciences. Psychology ; Genes, Bacterial ; Genetics ; Gram-Positive Cocci - classification ; Gram-Positive Cocci - genetics ; Gram-Positive Cocci - isolation & purification ; Identification ; In Situ Hybridization, Fluorescence ; Internal transcribed spacer ; Lactic acid ; Lactic acid bacteria ; Leuconostoc - classification ; Leuconostoc - genetics ; Leuconostoc - isolation & purification ; Microbiology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oenococcus oeni ; Oligonucleotides ; PCR ; Phylogeny ; Polymerase Chain Reaction - methods ; Protein structure ; RNA, Bacterial - chemistry ; RNA, Bacterial - genetics ; RNA, Ribosomal, 5S - chemistry ; RNA, Ribosomal, 5S - genetics ; rRNA 5S ; Secondary structure ; Sequence Homology, Nucleic Acid ; Strains (organisms)</subject><ispartof>FEMS microbiology letters, 2005-03, Vol.244 (1), p.165-171</ispartof><rights>2005 Federation of European Microbiological Societies</rights><rights>2005 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved. 2005</rights><rights>2005 INIST-CNRS</rights><rights>2005 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5385-577ae8db867e9579a3eca399e4e100b5aacb58c1ab3ae0b3a7ad9118a594a8c03</citedby><cites>FETCH-LOGICAL-c5385-577ae8db867e9579a3eca399e4e100b5aacb58c1ab3ae0b3a7ad9118a594a8c03</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1016%2Fj.femsle.2005.01.033$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1016%2Fj.femsle.2005.01.033$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27923,27924,45573,45574</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=16551823$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15727836$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hirschhäuser, Steffen</creatorcontrib><creatorcontrib>Fröhlich, Jürgen</creatorcontrib><creatorcontrib>Gneipel, Armin</creatorcontrib><creatorcontrib>Schönig, Inge</creatorcontrib><creatorcontrib>König, Helmut</creatorcontrib><title>Fast protocols for the 5S rDNA and ITS-2 based identification of Oenococcus oeni</title><title>FEMS microbiology letters</title><addtitle>FEMS Microbiol Lett</addtitle><description>To identify specific marker sequences for the rapid identification of
Oenococcus oeni, we sequenced the 23S-5S internal transcribed spacer (ITS-2) region and the 5S rDNA of five different
O. oeni strains and three phylogenetically related lactic acid bacteria (LAB). Comparative analysis revealed 100% identity among the ITS-2 region of the
O. oeni strains and remarkable differences in length and sequence compared to related LAB. These results enabled us to develop a primer set for a rapid PCR-identification of
O. oeni within three hours. Moreover, the comparison of the 5S rDNA sequences and the highly conserved secondary structure provided the template for the design of three fluorescence-labeled specific oligonucleotides for fluorescence in situ hybridization (FISH). These probes are partial complementary to each other. This feature promotes the accessibility to the target sequence within the ribosome and enhances the fluorescence signal. For the rapid identification of Oenococci both the 5S rRNA gene and the ITS-2 region are useful targets.</description><subject>5S rDNA</subject><subject>Bacteria</subject><subject>Bacteriological methods and techniques used in bacteriology</subject><subject>Bacteriology</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>Comparative analysis</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Ribosomal - genetics</subject><subject>DNA, Ribosomal Spacer - genetics</subject><subject>Fluorescence</subject><subject>Fluorescence in situ hybridization</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes, Bacterial</subject><subject>Genetics</subject><subject>Gram-Positive Cocci - classification</subject><subject>Gram-Positive Cocci - genetics</subject><subject>Gram-Positive Cocci - isolation & purification</subject><subject>Identification</subject><subject>In Situ Hybridization, Fluorescence</subject><subject>Internal transcribed spacer</subject><subject>Lactic acid</subject><subject>Lactic acid bacteria</subject><subject>Leuconostoc - classification</subject><subject>Leuconostoc - genetics</subject><subject>Leuconostoc - isolation & purification</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Nucleic Acid Conformation</subject><subject>Oenococcus oeni</subject><subject>Oligonucleotides</subject><subject>PCR</subject><subject>Phylogeny</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Protein structure</subject><subject>RNA, Bacterial - chemistry</subject><subject>RNA, Bacterial - genetics</subject><subject>RNA, Ribosomal, 5S - chemistry</subject><subject>RNA, Ribosomal, 5S - genetics</subject><subject>rRNA 5S</subject><subject>Secondary structure</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Strains (organisms)</subject><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkdFqFDEUhoModq2-gUhA6t1Mk8lkktwIpbptYbVC63U4kzmDWWYnazKj9O3NMgsFL7Q3yc33_eccfkLeclZyxpvzbdnjLg1YVozJkvGSCfGMrLhUddGYRj8nKyaULjgz6oS8SmnLGKsr1rwkJxmqlBbNinxbQ5roPoYpuDAk2odIpx9I5R2Nn75eUBg7enN_V1S0hYQd9R2Ok--9g8mHkYae3uKYVefmRAOO_jV50cOQ8M3xPyXf15_vL6-Lze3VzeXFpnBSaFlIpQB11-pGoZHKgEAHwhiskTPWSgDXSu04tAKQ5UdBZzjXIE0N2jFxSj4suXn3nzOmye58cjgMMGKYk21ULUVl_g9ypTk3SmTw_V_gNsxxzEfYSrBG5i0Vz1S9UC6GlCL2dh_9DuKD5cweirFbuxRjD8VYxm0uJmvvjuFzu8PuUTo2kYGzIwDJwdBHGJ1Pj1yez3V1CNIL99sP-PCk4Xb9ZZP9rJ4vapj3T93642JgbvKXx2iT8zg67HxEN9ku-H8H_AGdhMwo</recordid><startdate>200503</startdate><enddate>200503</enddate><creator>Hirschhäuser, Steffen</creator><creator>Fröhlich, Jürgen</creator><creator>Gneipel, Armin</creator><creator>Schönig, Inge</creator><creator>König, Helmut</creator><general>Elsevier B.V</general><general>Blackwell Publishing Ltd</general><general>Blackwell</general><general>Oxford University Press</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>200503</creationdate><title>Fast protocols for the 5S rDNA and ITS-2 based identification of Oenococcus oeni</title><author>Hirschhäuser, Steffen ; Fröhlich, Jürgen ; Gneipel, Armin ; Schönig, Inge ; König, Helmut</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5385-577ae8db867e9579a3eca399e4e100b5aacb58c1ab3ae0b3a7ad9118a594a8c03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>5S rDNA</topic><topic>Bacteria</topic><topic>Bacteriological methods and techniques used in bacteriology</topic><topic>Bacteriology</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>Comparative analysis</topic><topic>DNA, Bacterial - genetics</topic><topic>DNA, Ribosomal - genetics</topic><topic>DNA, Ribosomal Spacer - genetics</topic><topic>Fluorescence</topic><topic>Fluorescence in situ hybridization</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes, Bacterial</topic><topic>Genetics</topic><topic>Gram-Positive Cocci - classification</topic><topic>Gram-Positive Cocci - genetics</topic><topic>Gram-Positive Cocci - isolation & purification</topic><topic>Identification</topic><topic>In Situ Hybridization, Fluorescence</topic><topic>Internal transcribed spacer</topic><topic>Lactic acid</topic><topic>Lactic acid bacteria</topic><topic>Leuconostoc - classification</topic><topic>Leuconostoc - genetics</topic><topic>Leuconostoc - isolation & purification</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Nucleic Acid Conformation</topic><topic>Oenococcus oeni</topic><topic>Oligonucleotides</topic><topic>PCR</topic><topic>Phylogeny</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Protein structure</topic><topic>RNA, Bacterial - chemistry</topic><topic>RNA, Bacterial - genetics</topic><topic>RNA, Ribosomal, 5S - chemistry</topic><topic>RNA, Ribosomal, 5S - genetics</topic><topic>rRNA 5S</topic><topic>Secondary structure</topic><topic>Sequence Homology, Nucleic Acid</topic><topic>Strains (organisms)</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hirschhäuser, Steffen</creatorcontrib><creatorcontrib>Fröhlich, Jürgen</creatorcontrib><creatorcontrib>Gneipel, Armin</creatorcontrib><creatorcontrib>Schönig, Inge</creatorcontrib><creatorcontrib>König, Helmut</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS microbiology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hirschhäuser, Steffen</au><au>Fröhlich, Jürgen</au><au>Gneipel, Armin</au><au>Schönig, Inge</au><au>König, Helmut</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Fast protocols for the 5S rDNA and ITS-2 based identification of Oenococcus oeni</atitle><jtitle>FEMS microbiology letters</jtitle><addtitle>FEMS Microbiol Lett</addtitle><date>2005-03</date><risdate>2005</risdate><volume>244</volume><issue>1</issue><spage>165</spage><epage>171</epage><pages>165-171</pages><issn>0378-1097</issn><eissn>1574-6968</eissn><coden>FMLED7</coden><abstract>To identify specific marker sequences for the rapid identification of
Oenococcus oeni, we sequenced the 23S-5S internal transcribed spacer (ITS-2) region and the 5S rDNA of five different
O. oeni strains and three phylogenetically related lactic acid bacteria (LAB). Comparative analysis revealed 100% identity among the ITS-2 region of the
O. oeni strains and remarkable differences in length and sequence compared to related LAB. These results enabled us to develop a primer set for a rapid PCR-identification of
O. oeni within three hours. Moreover, the comparison of the 5S rDNA sequences and the highly conserved secondary structure provided the template for the design of three fluorescence-labeled specific oligonucleotides for fluorescence in situ hybridization (FISH). These probes are partial complementary to each other. This feature promotes the accessibility to the target sequence within the ribosome and enhances the fluorescence signal. For the rapid identification of Oenococci both the 5S rRNA gene and the ITS-2 region are useful targets.</abstract><cop>Oxford, UK</cop><pub>Elsevier B.V</pub><pmid>15727836</pmid><doi>10.1016/j.femsle.2005.01.033</doi><tpages>7</tpages></addata></record> |
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| ispartof | FEMS microbiology letters, 2005-03, Vol.244 (1), p.165-171 |
| issn | 0378-1097 1574-6968 |
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| subjects | 5S rDNA Bacteria Bacteriological methods and techniques used in bacteriology Bacteriology Base Sequence Biological and medical sciences Comparative analysis DNA, Bacterial - genetics DNA, Ribosomal - genetics DNA, Ribosomal Spacer - genetics Fluorescence Fluorescence in situ hybridization Fundamental and applied biological sciences. Psychology Genes, Bacterial Genetics Gram-Positive Cocci - classification Gram-Positive Cocci - genetics Gram-Positive Cocci - isolation & purification Identification In Situ Hybridization, Fluorescence Internal transcribed spacer Lactic acid Lactic acid bacteria Leuconostoc - classification Leuconostoc - genetics Leuconostoc - isolation & purification Microbiology Molecular Sequence Data Nucleic Acid Conformation Oenococcus oeni Oligonucleotides PCR Phylogeny Polymerase Chain Reaction - methods Protein structure RNA, Bacterial - chemistry RNA, Bacterial - genetics RNA, Ribosomal, 5S - chemistry RNA, Ribosomal, 5S - genetics rRNA 5S Secondary structure Sequence Homology, Nucleic Acid Strains (organisms) |
| title | Fast protocols for the 5S rDNA and ITS-2 based identification of Oenococcus oeni |
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