An extended dynamic range scan was then accomplished by performing a primary scan at 100% laser power and a secondary scan at 10% power; the former used to calculate intensities for non-saturating features, and the latter used to calculate intensities for saturating features.
The primary scan forms the basis of the analysis, whereas the secondary scan is used to correct the intensities of spots with saturation in the primary scan.
Main QTL and corresponding mean trait values from the primary scans were used to obtain estimates of residual empirical thresholds to search for additional QTL via secondary scans [ 46].
This secondary scan procedure was equivalent to installing the a priori QTL as covariates, thereby attributing a large portion of the overall variation to these QTL and allowing for detection of additional loci controlling the remaining variation.
We therefore propose a procedure where two scans are obtained for each of the red and green channel; a primary scan with the lowest intensities within the usable range of the scanner and a secondary scan with the intensities of the brightest spots just below the level of saturation.
For RDP4, we use the RDP (Martin and Rybicki 2000), Geneconv (Padidam et al. 1999), BootScan (Martin et al. 2005), MaxChi (Smith 1992), Chimaera (Posada and Crandall 2001), SiSscan (Gibbs et al. 2000), and 3Seq (Boni et al. 2007) methods with the default settings during both the primary scan (identification of recombination) and secondary scan (verification) phases.
Consequently, the remaining unassigned fraction of CT variation was analyzed using secondary scans of the residual variation after statistically removing the effect from the chromosome 12 locus; subsequent genome-wide scans identified markers C14M96 and C14M68 on chromosome 14 (LOD scores of 2.388 and 2.392 respectively).
When we considered only strains homozygous for the N2 allele at the marker closest to ppw-1 (4,175,488), or when we included this marker as a covariate and repeated the linkage mapping (see Figure 1B), no significant QTL were recovered from the secondary scan.
Both unadjusted and adjusted models were adjusted for baseline age, diabetes duration, sex, and DCCT baseline retinopathy cohort (primary vs. secondary) with scanning site as a random effect.
Capacity is increased by synthesis of ribosomal subunits and other translational components, whereas efficiency is regulated by the rate of translational initiation (assembly of initiation factors, "unwinding" of RNA secondary structures, scanning and recognition of the initiation codon), and the rate of peptide chain elongation.
