Biomedical subjects

J P Fallot

Publications and source records attributed to J P Fallot.

4 recordsLinked to original sources

PubMed1999

An evolutionary analytical model of a complementary circular code.

The subset X0=[AAC,AAT,ACC,ATC,ATT,CAG,CTC,CTG, GAA,GAC,GAG,GAT,GCC,GGC,GGT,GTA,GTC,GTT,TAC,TTC] of 20 trinucleotides has a preferential occurrence in the frame 0 (reading frame established by the ATG start trinucleotide) of protein (coding) genes of both prokaryotes and eukaryotes. This subset X0 is a complementary maximal circular code with two permutated maximal circular codes X1 and X2 in the frames 1 and 2 respectively (frame 0 shifted by one and two nucleotides respectively in the 5'-3' direction). X0 is called a C3 code (Arquès and Michel, 1997, J. Biosyst 44, 107-134). A quantitative study of these three subsets X0, X1 and X2 in the three frames 0, 1 and 2 of eukaryotic protein genes shows that their occurrence frequencies are constant functions of the trinucleotide positions in the sequences. The frequencies of X0, X1 and X2 in the frame 0 of eukaryotic protein genes are 48.5%, 29% and 22.5% respectively. These properties are not observed in the 5' and 3' regions of eukaryotes where X0, X1 and X2 occur with variable frequencies around the random value (1/3). Several frequency asymmetries unexpectedly observed, e.g. the frequency difference between X1 and X2 in the frame 0, are related to a new property of the C3 code X0 involving substitutions. An evolutionary analytical model at three parameters (p, q, t) based on an independent mixing of the 20 codons (trinucleotides in the frame 0) of X0 with equiprobability (1/20) followed by t approximately 4 substitutions per codon according to the proportions p approximately 0.1, q approximately 0.1 and r = 1 - p - q approximately 0.8 in the three codon sites respectively, retrieves the frequencies of X0, X1 and X2 observed in the three frames of protein genes and explains these asymmetries. The complex behaviour of these analytical curves is totally unexpected and a priori difficult to imagine. Finally, the evolutionary analytical method developed could be applied to the phylogenetic tree reconstruction and the DNA sequence alignment.

Animals↗

PubMed1998

An evolutionary analytical model of a complementary circular code simulating the protein coding genes, the 5' and 3' regions.

The self-complementary subset T0 = X0 [symbol: see text] ¿AAA, TTT¿ with X0 = ¿AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC¿ of 22 trinucleotides has a preferential occurrence in the frame 0 (reading frame established by the ATG start trinucleotide) of protein (coding) genes of both prokaryotes and eukaryotes. The subsets T1 = X1 [symbol: see text] ¿CCC¿ and T2 = X2 [symbol: see text] ¿GGG¿ of 21 trinucleotides have a preferential occurrence in the shifted frames 1 and 2 respectively (frame 0 shifted by one and two nucleotides respectively in the 5'-3' direction). T1 and T2 are complementary to each other. The subset T0 contains the subset X0 which has the rarity property (6 x 10(-8) to be a complementary maximal circular code with two permutated maximal circular codes X1 and X2 in the frames 1 and 2 respectively. X0 is called a C3 code. A quantitative study of these three subsets T0, T1, T2 in the three frames 0, 1, 2 of protein genes, and the 5' and 3' regions of eukaryotes, shows that their occurrence frequencies are constant functions of the trinucleotide positions in the sequences. The frequencies of T0, T1, T2 in the frame 0 of protein genes are 49, 28.5 and 22.5% respectively. In contrast, the frequencies of T0, T1, T2 in the 5' and 3' regions of eukaryotes, are independent of the frame. Indeed, the frequency of T0 in the three frames of 5' (respectively 3') regions is equal to 35.5% (respectively 38%) and is greater than the frequencies T1 and T2, both equal to 32.25% (respectively 31%) in the three frames. Several frequency asymmetries unexpectedly observed (e.g. the frequency difference between T1 and T2 in the frame 0), are related to a new property of the subset T0 involving substitutions. An evolutionary analytical model at three parameters (p, q, t) based on an independent mixing of the 22 codons (trinucleotides in frame 0) of T0 with equiprobability (1/22) followed by t approximately 4 substitutions per codon according to the proportions p approximately 0.1, q approximately 0.1 and r = 1 - p - q approximately 0.8 in the three codon sites respectively, retrieves the frequencies of T0, T1, T2 observed in the three frames of protein genes and explains these asymmetries. Furthermore, the same model (0.1, 0.1, t) after t approximately 22 substitutions per codon, retrieves the statistical properties observed in the three frames of the 5' and 3' regions. The complex behaviour of these analytical curves is totally unexpected and a priori difficult to imagine.

Animals↗

PubMed1997

An evolutionary model of a complementary circular code.

The subset X0 = [sequence: see text] of 20 trinucleotides has a preferential occurrence in frame 0 (a reading frame established by the ATG start trinucleotide) of protein (coding) genes of both prokaryotes and eukaryotes. This subset X0++ has the rarity property (6 x 10(-8)) to be a complementary maximal circular code with two permutated maximal circular codes X1 and X2 in frames 1 and 2 respectively (frame 0 shifted by one and two nucleotides respectively in the 5'-3' direction). X0 is called a C3 code. A quantitative study of these three subsets X0, X1 and X2 in the three frames 0, 1 and 2 of eukaryotic protein genes shows that their occurrence frequencies are constant functions of the trinucleotide positions in the sequences. The frequencies of X0, X1 and X2 in frame 0 of the eukaryotic protein genes are 48.5%, 29% and 22.5% respectively. These properties are not observed in the 5' and 3' regions of eukaryotes where X0, X1 and X2 occur with variable frequencies around the random value (1/3). Several frequency asymmetries unexpectedly observed, e.g. the frequency difference between X1 and X2 in the frame 0, are related to a new property of the C3 code X0 involving substitutions. An evolutionary model at three parameters (p, q, k) based on an independent mixing of the 20 codons (trinucleotides in frame 0) of X0 with equiprobability (1/20) followed by k approximately 5 substitutions per codon in the three codon sites in proportions p approximately 0.1, q approximately 0.1 and r = 1-p-q approximately 0.8 respectively, retrieves the frequencies of X0, X1 and X2 observed in the three frames of protein genes and explains these asymmetries.

Animals↗

PubMed1996

Identification of several types of periodicities in the collagens and their simulation.

The collagens constitute an important population of proteins providing the structural support in vertebrate tissues A collagen is mainly based on a series of tripeptides of the type GX1X2 (G = Glycine, X1 and X2 being any residues). The nine amino acids occurring with significant frequencies in the X1 and X2 residue sites and G form the reduced protein alphabet Q = [A,D,E,G,K,L,P,Q,R,S] (A = Alanine, D = Aspartic acid, E = Glutamic acid, K = Lysine, L = Leucine, P = Proline, Q = Glutamine, R = Arginine, S = Serine). Surprisingly, the method based on the autocorrelation function w(X)iw' analysing the probability that an amino acid w' in Q occurs any i residues X after an amino acid w in Q (called i-motif w(X)iw'), identifies six types of modulo 3 periodicities in collagens: three basic types 0, 1 and 2 modulo 3 and three combined types 0,1, 0,2 and 1,2 modulo 3. Furthermore, the classification of these 100 i-motifs according to the types of periodicities shows several strong relations between four sub-sets of Q [G], [A,D,P,S], [E,L] and [K,Q,R]. Then, these relations allow the construction of a simple automaton for the generation of model collagen sequences. Indeed, this automaton can simulate the six types of periodicities and it retrieves the types of periodicities for almost all i-motifs. Finally, the autocorrelation function based on the sub-set [K,Q,R] identifies segments of 18 amino acids in collagens which may correspond to the exons (segments of genes of 54 nucleotides) coding for those collagens.

Algorithms↗