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For fluorescent labeling of the S6C mutant, we applied minor modifications to a published protocol as described.
To detect genes differentially expressed in the wild type and the Δ mpkA mutant, we applied the R package baySeq [ 32] which takes advantage of the three biological replicates for each condition.
To determine the BR sensitivity of the cp3 mutant, we applied 1 μM of brassinolide (BL), the most bioactive BR, to the mutant plants on the region where the plants were exhibiting growth.
However, in view of the fact that morpholinos can sometimes elicit off-target effects that are not recapitulated by a corresponding mutant, we applied an additional exclusion criterion to eliminate probes that exhibited less than a 1.2-fold change in expression (of the same polarity) in 27 hpf hdac1 mutants, as compared to wild-type embryos (Additional file 3).
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In order to determine basal levels of oxidative stress in fibroblasts from Parkin mutants, we applied an OxyBlot.
To assess the overall lengths of telomere tracts in somatic cells of the tert/nbs1 mutants, we applied the TRF method (terminal restriction fragment analysis) to DNAs isolated from individual plants of various generations and from both lines, K12 and L2.
To complement the screening of the mutant library, we applied laboratory evolution and analysis of the resulting evolved strains [ 35, 39- 41].
With the estimated total number of alleles and the number of mutant observed, we applied the GLM to examine the effects of age, smoking and case status on mutation frequencies.
To begin to understand the basis for the different activities of these mutant enzymes, we applied a 3-D structural model of 11β-HSD2 (Arnold et al. 2003; Atanasov et al. 2003) to investigate the structure surrounding each of these cysteines.
To demonstrate and reproduce these studies in a larger variety of embryos and to include the mutant in the analysis, we applied a different functional test.
Because of the availability of both time-course and mutant steady-state data we applied the MOO-Sens procedure.
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