Phylogenetic similarity

If a phylogenetic comparison is made of the 16S-Iike rRNAs from an archae-bacterium Halobacterium volcanii), a eubacterium E. coli), and a eukaryote (the yeast Saccharomyces cerevisiae), a striking similarity in secondary structure emerges (Figure 12.40). Remarkably, these secondary structures are similar despite the fact that the nucleotide sequences of these rRNAs themselves exhibit a low degree of similarity. Apparently, evolution is acting at the level of rRNA secondary structure, not rRNA nucleotide sequence. Similar conserved folding patterns are seen for the 23S-Iike and 5S-Iike rRNAs that reside in the... 

Kolb S, S Seeliger, N Springer, W Ludwig, B Schink (1998) The fermenting bacterium Malonomonas rubra is phylogenetically related to sulfur-reducing bacteria and contains a c-type cytochrome similar to those of sulfur and sulfate reducers. SystAppl Microbiol 21 340-345. 

Figure 6.1. Phylogenetic profile method. Four genomes are shown, each containing a subset of proteins (PI, .P7). The presence or absence of a protein is given by 1 or 0 in the phylogenetic profile shown at lower left. Identical profiles are shown clustered on the right. In this example, the P2 and P7 are functionally linked because they exhibit the same phylogenetic profile. The P3 and P6 protein are similarly linked. Figure adapted from Pellegrini et al. (1999).

The amino acid sequence similarities of all 36 PHA synthases were pairwise revealed, and the results of this comparison are compiled in Table 2. The data correspond well with phylogenetic tree shown in Fig. 1, and the similarities va-... 

Chlorophycean species [Proeschold et al., 2001], the HydA proteins of C. moewusii, C. reinhardtii and S. obliquus form 3 different branches which possess, one to the other, a rather similar evolutionary distance. The three different HydA branches reflect the membership to three distinct phylogenetic clades ( Moewusii -clade, Reinhardtii -clade, Scenedesmus -clade) which can be found in completely different regions of the chlorophycean phylogenetic tree. 

The physiological similarity and phylogenetic proximity of nonhuman primates to humans are often cited as rationale for primate selection for safety studies especially when mechanisms of toxicity or pharmacologic action are expected to be closely related to potential physiological reactions in humans. Likewise, species selection is often based on the demonstration of pharmacologic activity of the test article. Many biopharmaceuticals do not exhibit their intended activity in nonprimate species, whereas small molecules may have activity across all species. 

Advantages and Disadvantages. Advantages of using monkeys in safety assessment studies include their phylogenetic proximity, as well as their physiological, behavioral, and, often, metabolic similarities, to humans (Table 16.13). An example is the similarity between the ovarian cycle of female monkeys and women (Mazue and Richez, 1982), which makes the monkey the ideal animal model for reproductive studies. Another advantage associated with most species of monkeys used in safety assessment studies is that they are much smaller than nonrodents such as the dog and, thus like the ferret, require less test compound. 

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