title: Discrimination of shifts in a soil microbial community associated with TNT-contamination using a functional ANOVA of 16S rRNA hybridized to oligonucleotide microarrays.
abstract: A functional ANOVA analysis of the thermal dissociation of RNA hybridized to DNA microarrays was used to improve discrimination between two soil microbial communities. Following hybridization of in vitro transcribed 16S rRNA derived from uncontaminated and 2,4,6-trinitrotoluene contaminated soils to an oligonucleotide microarray containing group- and species-specific perfect match (PM) probes and mismatch (MM) variants, thermal dissociation was used to analyze the nucleic acid bound to each PM-MM probe set. Functional ANOVA of the dissociation curves generally discriminated PM-MM probe sets when Td values (temperature at 50% probe-target dissociation) could not. Maximum discrimination for many PM and MM probes often occurred at temperatures greaterthan the Td. Comparison of signal intensities measured prior to dissociation analysis from hybridizations of the two soil samples revealed significant differences in domain-, group-, and species-specific probes. Functional ANOVA showed significantly different dissociation curves for 11 PM probes when hybridizations from the two soil samples were compared, even though initial signal intensities for 3 of the 11 did not vary.
authors.affiliation: Unit of Bioengineering and Institute of Statistics, University of Louvain, Belgium.
authors.forename: Laurent
authors.initials: L
authors.lastname: Eyers
authors.forename: James C
authors.initials: JC
authors.lastname: Smoot
authors.forename: Laura M
authors.initials: LM
authors.lastname: Smoot
authors.forename: Céline
authors.initials: C
authors.lastname: Bugli
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Urakawa
authors.forename: Zack
authors.initials: Z
authors.lastname: McMurry
authors.forename: Slil
authors.initials: S
authors.lastname: Siripong
authors.forename: Said
authors.initials: S
authors.lastname: El-Fantroussi
authors.forename: Philippe
authors.initials: P
authors.lastname: Lambert
authors.forename: Spiros N
authors.initials: SN
authors.lastname: Agathos
authors.forename: David A
authors.initials: DA
authors.lastname: Stahl
mesh_terms: D000704:Analysis of Variance; D020411:Oligonucleotide Array Sequence Analysis; D016958:Pseudomonas putida / Q000235:genetics*; D012329:RNA, Bacterial / Q000032:analysis; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D012988:Soil Microbiology; D012989:Soil Pollutants; D014303:Trinitrotoluene
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants; D014303:Trinitrotoluene