The microbial signature of drinking waters: myth or reality?
This paper presents a new software developed for analyzing single strand conformation polymorphism (SSCP) electrophoresis patterns delivered by the genetic analyzer ABI310 (Applied Biosystems). SSCP is a molecular typing technique based on the PCR amplification of microbial 16S rDNA and used for the...
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| Veröffentlicht in: | Water science and technology 2006, Vol.53 (1), p.259-266 |
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| creator | Harmand, J Paulou, L Desmoutiers, J Garrelly, L Dabert, P Godon, J J |
| description | This paper presents a new software developed for analyzing single strand conformation polymorphism (SSCP) electrophoresis patterns delivered by the genetic analyzer ABI310 (Applied Biosystems). SSCP is a molecular typing technique based on the PCR amplification of microbial 16S rDNA and used for the monitoring of complex microbial ecosystems dynamics. The software--a home-made MATLAB toolbox called MODIMECO--developed for the analysis of SSCP patterns is presented. MODIMECO includes a number of basic signal processing abilities as well as largely used statistical tools such as the well known principal component analysis. The use of the SSCP for assessing the hypothesis of the existence of a microbial signature of drinking waters illustrates the typical advantages of using such software tools. Results are discussed and conclusions drawn. |
| doi_str_mv | 10.2166/wst.2006.028 |
| format | Article |
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Results are discussed and conclusions drawn.</description><identifier>ISSN: 0273-1223</identifier><identifier>ISBN: 1843395541</identifier><identifier>ISBN: 9781843395546</identifier><identifier>EISSN: 1996-9732</identifier><identifier>DOI: 10.2166/wst.2006.028</identifier><identifier>PMID: 16532756</identifier><language>eng</language><publisher>England: IWA Publishing</publisher><subject>Analytical methods ; Computer programs ; Conformation ; Data processing ; DNA ; DNA, Bacterial - analysis ; Dynamics ; Earth Sciences ; Ecological monitoring ; Ecosystem ; Ecosystems ; Environmental Monitoring ; Gene polymorphism ; Hydrology ; Hypotheses ; Information processing ; Microorganisms ; Nucleotide sequence ; PCR ; Polymerase Chain Reaction ; Polymorphism ; Polymorphism, Single-Stranded Conformational ; Principal components analysis ; Reference Values ; rRNA 16S ; Sciences of the Universe ; Signal processing ; Software ; Software development tools ; Standard deviation ; Typing ; Water Microbiology ; Water Supply</subject><ispartof>Water science and technology, 2006, Vol.53 (1), p.259-266</ispartof><rights>Copyright IWA Publishing Jan 2006</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c382t-7083ca30cdd327dbe10c7cd814734fb76f3b482f8de4ab868caa4efef777b98d3</citedby><orcidid>0000-0002-6124-2316 ; 0000-0002-8653-3582 ; 0000-0002-4922-4617</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,309,310,314,776,780,785,786,881,4010,23909,23910,25118,27900,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16532756$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.inrae.fr/hal-02657637$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Beck, MB (eds)</contributor><contributor>Chen, J</contributor><creatorcontrib>Harmand, J</creatorcontrib><creatorcontrib>Paulou, L</creatorcontrib><creatorcontrib>Desmoutiers, J</creatorcontrib><creatorcontrib>Garrelly, L</creatorcontrib><creatorcontrib>Dabert, P</creatorcontrib><creatorcontrib>Godon, J J</creatorcontrib><title>The microbial signature of drinking waters: myth or reality?</title><title>Water science and technology</title><addtitle>Water Sci Technol</addtitle><description>This paper presents a new software developed for analyzing single strand conformation polymorphism (SSCP) electrophoresis patterns delivered by the genetic analyzer ABI310 (Applied Biosystems). 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| ispartof | Water science and technology, 2006, Vol.53 (1), p.259-266 |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals |
| subjects | Analytical methods Computer programs Conformation Data processing DNA DNA, Bacterial - analysis Dynamics Earth Sciences Ecological monitoring Ecosystem Ecosystems Environmental Monitoring Gene polymorphism Hydrology Hypotheses Information processing Microorganisms Nucleotide sequence PCR Polymerase Chain Reaction Polymorphism Polymorphism, Single-Stranded Conformational Principal components analysis Reference Values rRNA 16S Sciences of the Universe Signal processing Software Software development tools Standard deviation Typing Water Microbiology Water Supply |
| title | The microbial signature of drinking waters: myth or reality? |
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