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000009598 0247_ $$2DOI$$a10.1038/ismej.2010.46
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000009598 084__ $$2WoS$$aEcology
000009598 084__ $$2WoS$$aMicrobiology
000009598 1001_ $$0P:(DE-HGF)0$$aHe, Z.$$b0
000009598 245__ $$aGeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity
000009598 260__ $$aBasingstoke$$bNature Publishing Group$$c2010
000009598 300__ $$a1167 - 1179
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000009598 440_0 $$022241$$aThe ISME Journal: Multidisciplinary Journal of Microbial Ecology$$v4$$y9
000009598 500__ $$aThis work is supported by the Genomics: GTL program through the Virtual Institute of Microbial Stress and Survival (VIMSS; http://vimss.lbl.gov) as part of contract no. DE-AC02-05CH11231 between the US Department of Energy and Lawrence Berkeley National Laboratory, the United States Department of Agriculture (Project 2007-35319-18305) through NSF-USDA Microbial Observatories Program, the Environmental Remediation Science Program, the Oklahoma Bioengery Center (OBC) of State of Oklahoma, and the Oklahoma Applied Research Support (OARS), Oklahoma Center for the Advancement of Science and Technology (OCAST), the State of Oklahoma.
000009598 520__ $$aA new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with approximately 28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.
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000009598 65320 $$2Author$$amicroarray
000009598 65320 $$2Author$$afunctional genes
000009598 65320 $$2Author$$amicrobial community
000009598 65320 $$2Author$$aplant diversity
000009598 650_2 $$2MeSH$$aBacteria: classification
000009598 650_2 $$2MeSH$$aBacteria: genetics
000009598 650_2 $$2MeSH$$aBiota
000009598 650_2 $$2MeSH$$aComputational Biology: methods
000009598 650_2 $$2MeSH$$aDNA Gyrase: genetics
000009598 650_2 $$2MeSH$$aDrug Resistance, Bacterial
000009598 650_2 $$2MeSH$$aEnvironmental Microbiology
000009598 650_2 $$2MeSH$$aMetabolic Networks and Pathways: genetics
000009598 650_2 $$2MeSH$$aMetagenomics: methods
000009598 650_2 $$2MeSH$$aMicroarray Analysis: methods
000009598 650_2 $$2MeSH$$aOligonucleotide Array Sequence Analysis: methods
000009598 650_2 $$2MeSH$$aOligonucleotide Probes: genetics
000009598 650_2 $$2MeSH$$aPhylogeny
000009598 650_2 $$2MeSH$$aSensitivity and Specificity
000009598 650_2 $$2MeSH$$aSoftware
000009598 650_7 $$00$$2NLM Chemicals$$aOligonucleotide Probes
000009598 650_7 $$0EC 5.99.1.-$$2NLM Chemicals$$aDNA Gyrase
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000009598 7001_ $$0P:(DE-HGF)0$$aDeng, Y.$$b1
000009598 7001_ $$0P:(DE-HGF)0$$aVan Nostrand, J.D.$$b2
000009598 7001_ $$0P:(DE-HGF)0$$aTu, Q.$$b3
000009598 7001_ $$0P:(DE-HGF)0$$aXu, M.$$b4
000009598 7001_ $$0P:(DE-HGF)0$$aHemme, C.L.$$b5
000009598 7001_ $$0P:(DE-HGF)0$$aLi, X.$$b6
000009598 7001_ $$0P:(DE-HGF)0$$aWu, L.$$b7
000009598 7001_ $$0P:(DE-HGF)0$$aGentry, T.J.$$b8
000009598 7001_ $$0P:(DE-HGF)0$$aYin, Y.$$b9
000009598 7001_ $$0P:(DE-Juel1)VDB940$$aLiebich, J.$$b10$$uFZJ
000009598 7001_ $$0P:(DE-HGF)0$$aHazen, T.C.$$b11
000009598 7001_ $$0P:(DE-HGF)0$$aZhou, J.$$b12
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000009598 8567_ $$uhttp://dx.doi.org/10.1038/ismej.2010.46
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