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Biomedical subjects

M A Soto

Publications and source records attributed to M A Soto.

17 recordsLinked to original sources
PubMed1990

Pattern recognition of the secondary structure of proteins (alpha-helix and beta-structure).

In this paper, an algorithm for the pattern recognition of secondary structure of proteins is proposed. The procedure simultaneously evaluates the contribution of all the residues of a given peptide to its conformation. By means of the algorithm it is possible to select from a universe of well known proteins the most representative alpha-helix and beta-structure peptides, and to use these peptides, as screening matrices to define the unknown structure of any peptide.

Algorithms↗
PubMed1990

Phylogenetic tree of tRNAs using a simple algorithm.

A simple method for phylogenetic tree construction is described. In this method each node is calculated considering the distance between the elements and the difference between these elements and an average element, allowing the selection of the most probable node. Two examples of tRNA phylogenies (E. coli set and Phe family) are analyzed, giving both reliable trees. Data from these dendrograms give support to the idea of an early cloverleaf arising.

Algorithms↗
PubMed1986

A simple algorithm for assisting medical diagnosis.

This is a description of an algorithm to assist in the selection of the most probable diagnosis of a given patient. This algorithm is based on the comparison of a scaled column vector of the symptoms displayed by the patient, and of each column of symptoms appearing in a disease matrix. Moreover, the same algorithm gives the degree of similarity of the diseases compared by the differential diagnosis, as well as the hierarchic order of the symptoms that characterise any disease.

Algorithms↗
PubMed1985

Conservation of the secondary structure of protein during evolution and the role of the genetic code.

In this communication we demonstrate, in a group of modern proteins, following an algorithm described by Argyle (1980), that the ordination of the amino acids in terms of the most frequent substitutions agrees with the conservation of the alpha-helix, beta-sheet, and beta-turn formation tendencies during evolution. The same correspondence has been demonstrated for the conservation of the physico-chemical properties in the amino acid substitutions. Both parameters are similar in showing higher correlation with the most frequent amino acid substitutions than with the feasibility of changes at the level of the respective codons. Some kind of restrictions for the expression of the genomic changes, due to the conservation of the secondary structure of proteins and/or the physicochemical properties of the substituted amino acids, could account for the differences found between the distribution of the amino acid substitutions and the most probable codon changes.

Amino Acids↗
PubMed1985

A hardware interpretation of the evolution of the genetic code.

A quantitative rationale for the evolution of the genetic code is developed considering the principle of minimal hardware. This principle defines an optimal code as one that minimizes for a given amount of information encoded, the product of the number of physical devices used by the average complexity of each device. By identifying the number of different amino acids, number of nucleotide positions per codon and number of base types that can occupy each such position with, respectively, the amount of information, number of devices and the complexity, we show that optimal codes occur for 3, 7 and 20 amino acids with codons having a single, two and three base positions per codon, respectively. The advantage of a code of exactly 4 symbols is deduced, as well as a plausible evolutionary pathway from a code of doublets to triplets. The present day code of 20 amino acids encoded by 64 codons is shown to be the most optimal in an absolute sense. Using a tetraplet code further evolution to a code in which there would be 55 amino acids is in principle possible, but such a code would deviate slightly more than the present day code from the minimal hardware configuration. The change from a triplet code to a tetraplet code would occur at about 32 amino acids. Our conclusions are independent of, but consistent with, the observed physico-chemical properties of the amino acids and codon structures. These correlations could have evolved within the constrains imposed by the minimal hardware principle.

Amino Acids↗
PubMed1984

Dissimilar rates in molecular evolution.

In this work we present an evolutionary tree based on the differences in the physico-chemical properties involved in amino acid substitutions, instead of considering, for its construction, only the number of changes between species. Phylogenetic trees were constructed from the differences in bulkiness, refractivity index, hydrophobicity, polarity and optical rotation of 9 vertebrate calcitonins. A correlation of the form y = a xb was found between the number of changes (x) and the differences in any given physico-chemical property (y). This correlation implies that the evolutionary time can not be evaluated directly from the number of changes between species.

Amino Acid Sequence↗
PubMed1984

Sexual dimorphism in the motor mounting pattern of the New Zealand white rabbit: steroid regulation of vigor and rhythmicity of pelvic thrusting.

The motor mounting patterns of male and female New Zealand white rabbits were analyzed by means of an accelerometric technique and frequency analysis. Clear behavioral dimorphism was noted in the motor mounting pattern. Pelvic thrusting by males was periodic while that performed by females lacked rhythmicity. Thrusting in males was more vigorous than in females. Ovariectomy markedly decreased the incidence of mounting behavior. Testosterone propionate (TP, 5 mg daily for 1 month), restored mounting in all ovariectomized rabbits. TP stimulated the vigor of thrusting and induced a rhythmic mounting pattern in many cases similar to that displayed by intact male rabbits, i.e., thrusting frequency 13-16 per second. Estradiol benzoate (10 micrograms daily for 1 month), elicited mounting in three of the seven rabbits tested. Pelvic thrusting in these rabbits was often highly synchronous showing a frequency higher (18 to 21 thrusts per second) than that displayed by male rabbits. The results suggest the following conclusions: (a) the behavioral dimorphism in mounting observed in rabbits is due to variations in the secretion of sex steroids by the adult gonads rather than to differences in the organization of the neural substrate of mounting; (b) gonadal steroids influence directly or indirectly the neural structures involved in some characteristics of pelvic thrusting, i.e., rhythmicity and vigor.

Animals↗
PubMed1983

Conservation of physico-chemical amino acid properties during the evolution of proteins.

Based on a similarity ring constructed from a substitution probability matrix, we have analyzed the conservation of some amino acid properties in the evolution of proteins. Refractive index and bulkiness are highly conserved, hydrophobicity and polarity are fairly well conserved while optical rotation appears to be a less relevant property. On the other hand, the analysis of the correspondence between phenotype and genotype shows that the most frequent amino acid substitutions in proteins do not always correspond to the most feasible codon changes. The apparent disagreement between amino acid substitutions in modern proteins and the primordial amino acid-codon assignment is discussed.

Amino Acids↗
PubMed1979

II. On the construction of a phylogenetic tree.

For the construction of a phylogenetic tree in algorithm is described. This, allows the correction of the original data and the proper selection, in each step of the process, of the nearest neighbours of a common ancestor.

Animals↗
PubMedDate not supplied

Genetic information analysis of bacteriophage phiX 174.

The genetic information of phix 174 genome (genes and intermediate segments) is analyzed in terms of its independent (D1 index) and dependent information (D2 and D3 Markovian indexes), as well as of its ability to generate secondary structure. Genes B and E, enclosed in A and D respectively, have: 1) values of D1 and D3 indexes closer to the theoretical random distribution curves than those of (A-B) and (D-E) gene fractions, and 2) in the ability for secondary structure generation minor differences with genes A and D. F leads to G and mRNA start leads to A intermediate segments differ from randomness in their D1 and D2 indexes, but not so much in the D3 values. All these data point out the use of code degeneracy for increasing the genetic information density of the virus.

Coliphages↗
PubMedDate not supplied

Algorithm for construction of phylogenetic trees.

An algorithm is described for the construction of phylogenetic trees. The algorithm is based on the progressive correction of data along the tree construction. For the correction, the average value of the difference between each pair of neighbour elements to the rest of the table is considered.

Algorithms↗