Dose escalation was performed with an accelerated design (Supplementary Data, Appendix 2) and continued until the MTD was determined.
Estimation of gains and losses under the ACCTRAN (accelerated transformation) algorithm (supplementary table S3, Supplementary Material online) and using a gain/loss penalty of 1 (supplementary table S4, Supplementary Material online) gave very similar results for the 83 known sRNAs.
Conversely, when isolating cardiac myocytes from mouse hearts that were irradiated in vivo, we observed a conserved positive inotropic stress response with increased Ca transients and accelerated relaxation (see supplementary Fig. 1a c).
From our filtered set of noncoding blocks, 661 blocks are within 5 kb of one of those accelerated peptides (12 peptides; supplementary table S1, Supplementary Material online).
Next, we tracked individual plus ends and found that ectopic NAV3 decreased catastrophe rates, as well as accelerated MT rescue rates (Supplementary Fig S6C).
We find minimal correlation between LRTs in parents and daughters on average (supplementary fig. S4, Supplementary Material online), suggesting that accelerated substitutions happened independently in one or both copies after duplication (supplementary results SR4, Supplementary Material online).
In addition to SUMO-2 N-terminal conjugation, we found that Ube2W ubiquitylates its own N-terminus in the absence of RNF4 (Supplementary Figures 2A and 2B at http://www.biochemj.org/bj/453/bj4530137add.htm), although RNF4 does modestly accelerate the process (Supplementary Figure 2A).
However, disproportionately long branches are observed in the gene tree after the common ancestor of gastric Helicobacter (compare branches #2 and #3 in fig. 3 and supplementary fig. S9, Supplementary Material online), suggesting accelerated evolution in this lineage.
However, we found that overexpression of γ-taxilin accelerated apoptosis of normoxic cells (Supplementary Figure S3a).
