Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies

Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519–539, E969–983, E1063–1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies

Mother and Adolescent Reports of Associations Between Child Behavior Problems and Mother-Child Relationship Qualities: Separating Shared Variance from Individual Variance

This study contrasts results from different correlational methods for examining links between mother and child (N = 72 dyads) reports of early adolescent (M = 11.5 years) behavior problems and relationship negativity and support. Simple (Pearson) correlations revealed a consistent pattern of statistically significant associations, regardless of whether scores came from the same reporter or from different reporters. When correlations between behavior problems and relationship quality differed, within-reporter correlations were always greater in magnitude than between-reporter correlations. Dyadic (common fate) analyses designed for interdependent data decomposed within-reporter correlations into variance shared across reporters (dyadic correlations) and variance unique to specific reporters (individual correlations). Dyadic correlations were responsible for most associations between adolescent behavior problems and relationship negativity; after partitioning variance shared across reporters, no individual correlations emerged as statistically significant. In contrast, adolescent behavior problems were linked to relationship support via both shared variance and variance unique to maternal perceptions. Dyadic analyses provide a parsimonious alternative to multiple contrasts in instances when identical measures have been collected from multiple reporters. Findings from these analyses indicate that same-reporter variance bias should not be assumed in the absence of dyadic statistical analyses