We therefore examined the seven closest relatives of BceB, which formed a well defined branch in the MSD tree (i.e. proteins from B. subtilis, B. licheniformis, B. amyloliquefaciens, B. halodurans, B. pumilus, G. kaustophilus, B. clausii and O. iheyensis, Figure 2) with a view to characterizing their large extra-cytoplasmic loops.
For this we used a branch-sites method [ 42] and a Bayes Empirical Bayes approach [ 43] to predict sites that evolved under positive selection (those with a posterior probability > 95% of falling in a site class where d N /d S = ω >1 along a defined branch; Figure 4a).
It still uses arboreal forms, but they now mesh with other overtly defined branching systems: a vascular network of arteries and veins with two plump kidneys, mushroom colonies and their germinating mycelia, neuron bundles and taxonomic diagrams, and raw pipelines connected to steel tanks and industrial valves.
The polymerization proceeds with degenerative chain transfer and leads to well defined branched polymers with functional primary and secondary iodomethyl groups as revealed by NMR studies.
Because the analytical expressions for the full molecular weight distribution (MWD) as well as the fractional MWDs containing 0, 1, 2, etc., branch points can be determined, such polymer molecules are regarded as polymers with a well defined branched structure.
This dendrogram defines two vertically defined branches that discriminate absolutely between the non-proliferating Rasless cells and proliferating, control K-Raslox and the BRAF- or MEK1-rescued cells.
While the different actin isoforms of H. sapiens and D. melanogaster, respectively, build defined branches, most P. tetraurelia actins are isolated and scattered throughout the tree.
Furthermore, the emergence of the repeat protein PGRS and MPTR subfamilies is a recent evolutionary event, occurring at defined branching points in the evolution of the genus Mycobacterium.
Hierarchical clustering defined branches of the cluster dendrogram in 13 color-coded modules (Fig. 3a) ranging in size from 35 to 339 genes (average size of 127 genes).
Their model notably differs from the BSM (Zhang et al., 2005) in that putative positive selection is not optimized on a priori defined branches, but over a subset of branches which are determined by the software.
Thus, geometric parameters, such as vessel simple tortuosity (ST), which reflects the undulation of a vessel along its course, and length/diameter ratio (LDR), which uses the axial length between two defined branching points divided by the vessel's diameter, may be more robust predictors of diabetic microvascular and macrovascular complications.
