Massimo Di Giulio

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The level reached by the optimization of the polarity distances during the evolution of the genetic code was investigated. The results, although not conclusive, indicate that this optimization level is higher than the data reported in the literature. The results seem compatible with the reaching of an evolutionary minimum, with respect to the optimization(More)
In order to establish the statistical significance between the biosynthetic pathways of amino acids and the organization of the genetic code, Amirnovin (1997) generates random codes of amino acid permutation (Di Giulio 1989), i.e., codes that maintain the relative position of the blocks of synonymous codons constant, as in the genetic code, but also allow(More)
A logical-evolutionary analysis is conducted to clarify whether or not pathways of type Glu-tRNAGln \rightarrow Gln-tRNAGln are molecular fossils of the mechanism that gave rise to the evolutionary organization of the genetic code. The result of this analysis is that these pathways are most likely a manifestation of this mechanism. This provides strong(More)
Ronneberg et al. (Proc Natl Acad Sci USA 97:13690–13695, 2000) recently suggested abandoning the coevolution theory of genetic code origin on the basis of two pieces of evidence. They (1) criticize the use of several pairs of amino acids in a precursor–product relationship to support this theory and (2) suggest a new set of codes in which to investigate the(More)
In order to establish whether the first lines of divergence in the Bacteria domain were the mesophilic or the hyperthermophilic organisms, we have performed a phylogenetic analysis on a concatenamer obtained from the fusion of 20 different proteins. The phylogenetic analysis carried out using five different methods has shown that, contrary to what is(More)
In this paper, I define a measure of the relative position of each amino acid in the genetic code by means of a 21-dimensional vector describing its potential for mutation, in a single step, to each of the other amino acids, or to a chain termination codon. This measure allows us to make a systematic investigation of the type and number of the(More)
We have assumed that the coevolution theory of genetic code origin (Wong JT, Proc Natl Acad Sci USA 72:1909–1912, 1975) is essentially correct. This theory makes it possible to identify at least 10 evolutionary stages through which genetic code organization might have passed prior to reaching its current form. The calculation of the minimization level of(More)
A comparison is made among all the models proposed to explain the origin of the tRNA molecule. The conclusion reached is that, for the model predicting that the tRNA molecule originated after the assembly of two hairpin-like structures, molecular fossils have been found in the half-genes of the tRNAs of Nanoarchaeum equitans. These might be the witnesses of(More)
Many studies have suggested that the modern cloverleaf structure of tRNA may have arisen through duplication of a primordial hairpin, but the timing of this duplication event has been unclear. Here we measure the level of sequence identity between the two halves of each of a large sample of tRNAs and compare this level to that of chimeric tRNAs constructed(More)
Two forces are in general, hypothesized to have influenced the origin of the organization of the genetic code: the physicochemical properties of amino acids and their biosynthetic relationships. In view of this, we have considered a model incorporating these two forces. In particular, we have studied the optimization level of the physicochemical properties(More)