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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Size Does Matter: Application-driven Approaches for Soil Metagenomics</title><author><name sortKey="Kakirde, Kavita S" sort="Kakirde, Kavita S" uniqKey="Kakirde K" first="Kavita S." last="Kakirde">Kavita S. Kakirde</name></author><author><name sortKey="Parsley, Larissa C" sort="Parsley, Larissa C" uniqKey="Parsley L" first="Larissa C." last="Parsley">Larissa C. Parsley</name></author><author><name sortKey="Liles, Mark R" sort="Liles, Mark R" uniqKey="Liles M" first="Mark R." last="Liles">Mark R. Liles</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21076656</idno><idno type="pmc">2976544</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976544</idno><idno type="RBID">PMC:2976544</idno><idno type="doi">10.1016/j.soilbio.2010.07.021</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000283</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Size Does Matter: Application-driven Approaches for Soil Metagenomics</title><author><name sortKey="Kakirde, Kavita S" sort="Kakirde, Kavita S" uniqKey="Kakirde K" first="Kavita S." last="Kakirde">Kavita S. Kakirde</name></author><author><name sortKey="Parsley, Larissa C" sort="Parsley, Larissa C" uniqKey="Parsley L" first="Larissa C." last="Parsley">Larissa C. Parsley</name></author><author><name sortKey="Liles, Mark R" sort="Liles, Mark R" uniqKey="Liles M" first="Mark R." last="Liles">Mark R. Liles</name></author></analytic><series><title level="j">Soil biology & biochemistry</title><idno type="ISSN">0038-0717</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Metagenomic analyses can provide extensive information on the structure, composition, and predicted gene functions of diverse environmental microbial assemblages. Each environment presents its own unique challenges to metagenomic investigation and requires a specifically designed approach to accommodate physicochemical and biotic factors unique to each environment that can pose technical hurdles and/or bias the metagenomic analyses. In particular, soils harbor an exceptional diversity of prokaryotes that are largely undescribed beyond the level of ribotype and are a potentially vast resource for natural product discovery. The successful application of a soil metagenomic approach depends on selecting the appropriate DNA extraction, purification, and if necessary, cloning methods for the intended downstream analyses. The most important technical considerations in a metagenomic study include obtaining a sufficient yield of high-purity DNA representing the targeted microorganisms within an environmental sample or enrichment and (if required) constructing a metagenomic library in a suitable vector and host. Size does matter in the context of the average insert size within a clone library or the sequence read length for a high-throughput sequencing approach. It is also imperative to select the appropriate metagenomic screening strategy to address the specific question(s) of interest, which should drive the selection of methods used in the earlier stages of a metagenomic project (e.g., DNA size, to clone or not to clone). Here, we present both the promising and problematic nature of soil metagenomics and discuss the factors that should be considered when selecting soil sampling, DNA extraction, purification, and cloning methods to implement based on the ultimate study objectives.</p></div></front></TEI><pmc article-type="research-article" xml:lang="EN"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">0244736</journal-id><journal-id journal-id-type="pubmed-jr-id">21709</journal-id><journal-id journal-id-type="nlm-ta">Soil Biol Biochem</journal-id><journal-title>Soil biology & biochemistry</journal-title><issn pub-type="ppub">0038-0717</issn></journal-meta><article-meta><article-id pub-id-type="pmid">21076656</article-id><article-id pub-id-type="pmc">2976544</article-id><article-id pub-id-type="doi">10.1016/j.soilbio.2010.07.021</article-id><article-id pub-id-type="manuscript">NIHMS230220</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Size Does Matter: Application-driven Approaches for Soil Metagenomics</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kakirde</surname><given-names>Kavita S.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Parsley</surname><given-names>Larissa C.</given-names></name></contrib><contrib contrib-type="author"><name><surname>Liles</surname><given-names>Mark R.</given-names></name></contrib><aff id="A1">Department of Biological Sciences, Auburn University, Auburn, AL 36849</aff></contrib-group><pub-date pub-type="nihms-submitted"><day>23</day><month>8</month><year>2010</year></pub-date><pub-date pub-type="ppub"><day>1</day><month>11</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>1</day><month>11</month><year>2011</year></pub-date><volume>42</volume><issue>11</issue><fpage>1911</fpage><lpage>1923</lpage><permissions><copyright-statement>© 2010 Elsevier Ltd. All rights reserved.</copyright-statement><copyright-year>2010</copyright-year></permissions><abstract><p id="P1">Metagenomic analyses can provide extensive information on the structure, composition, and predicted gene functions of diverse environmental microbial assemblages. Each environment presents its own unique challenges to metagenomic investigation and requires a specifically designed approach to accommodate physicochemical and biotic factors unique to each environment that can pose technical hurdles and/or bias the metagenomic analyses. In particular, soils harbor an exceptional diversity of prokaryotes that are largely undescribed beyond the level of ribotype and are a potentially vast resource for natural product discovery. The successful application of a soil metagenomic approach depends on selecting the appropriate DNA extraction, purification, and if necessary, cloning methods for the intended downstream analyses. The most important technical considerations in a metagenomic study include obtaining a sufficient yield of high-purity DNA representing the targeted microorganisms within an environmental sample or enrichment and (if required) constructing a metagenomic library in a suitable vector and host. Size does matter in the context of the average insert size within a clone library or the sequence read length for a high-throughput sequencing approach. It is also imperative to select the appropriate metagenomic screening strategy to address the specific question(s) of interest, which should drive the selection of methods used in the earlier stages of a metagenomic project (e.g., DNA size, to clone or not to clone). Here, we present both the promising and problematic nature of soil metagenomics and discuss the factors that should be considered when selecting soil sampling, DNA extraction, purification, and cloning methods to implement based on the ultimate study objectives.</p></abstract><kwd-group><kwd>soil</kwd><kwd>metagenomics</kwd><kwd>metagenomic library construction</kwd><kwd>PCR</kwd><kwd>pyrosequencing</kwd><kwd>16S rRNA</kwd><kwd>high molecular weight DNA</kwd><kwd>cosmid</kwd><kwd>fosmid</kwd><kwd>BAC</kwd></kwd-group><contract-num rid="AI1">R21 AI083852-02
||AI</contract-num><contract-num rid="AI1">R21 AI083852-01
||AI</contract-num><contract-sponsor id="AI1">National Institute of Allergy and Infectious Diseases Extramural Activities : NIAID</contract-sponsor></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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