arXiv subjects

Robersy Sanchez

Publications and source records attributed to Robersy Sanchez.

10 recordsLinked to original sources

arXiv2008

An algebraic hypothesis about the primeval genetic code

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with unspecific pairing. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvements of a primitive DNA repair system could make possible the transition from the ancient to the modern genetic code. Our results suggest that the Watson-Crick base pairing and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the later. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment.Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences.

q-bio.GN↗

arXiv2006

Biophysical analysis of electric current mediated nucleoprotein inactivation process

Motivation: Its well known the use of electric current in the cleaning of viral diseases in plants instead a deep knowledge of this phenomenas theoretical basis is not yet available. The description of the real causes of nucleoprotein inactivation, will contribute to the optimization of further experiments in order to obtain more and more efficient cleaning methodologies for starting material supplies of vegetal species micropropagation process. The dissipated energy as heat will depend on the specific treatment applied and on the physical properties of the vegetal tissue and viral nucleoprotein. Results: A hyperbolic dependence between the absorbance output values, obtained during a diagnostic micro-ELISA experiment, and the electrical power (in watts) applied to each explant was found. The former, demonstrate the cleaning process nature is essentially the effect over viral nucleoprotein denaturation, by means of the heat, to which they were exposed in the thermal bath that the vegetal tissue constitutes. Our results are consistent with mathematical developed from theoretical frame of harmonic oscillators in which molecular machine (viral nucleoproteins) are redefined.

q-bio.QM↗

arXiv2005

Abelian Finite Group of DNA Genomic Sequences

The Z_64-algebra of the genetic code and DNA sequences of length N was recently stated. In order to beat the limits of this structure such as the impossibility of non-coding region analysis in genomes and the impossibility of the insertions and deletions analysis (indel mutations), we have develop a cycle group structure over the of extended base triplets of DNA X_1X_2X_3, X_i belong to {O, A, C, G, U}, where the letter O denote the base omission (deletion) in the codon. The obtained group is isomorphic to the abelian 5-group Z_125 of integer module 125. Next, it is defined the abelian finite group S over a set of DNA alignment sequences of length N. The group S could be represented as the direct sum of homocyclic groups: 2-group and 5-group. In particular, DNA subsequences without indel mutation could be considered building block of genes represented by homocyclic 2-groups (described in the previous Z_64-algebra). While those DNA subsequences affected by indel mutations are described by means of homocyclic 5-groups. This representation suggests identify genome block structures by way of a regular grammar capable of recognize it. In addition, this novel structure allows us a general analysis of the mutational pathways follow by genes and isofunctional genome regions by means of the automorphism group on S.

q-bio.QM↗

arXiv2005

The energy cost of protein messages lead to a new protein information law

By considering the energy cost of messages carried by proteins as proportional to their information content we found experimental proof that proteins from all living organisms tend to have their estimated semantic content of information per unit mass, statistically, close to a constant. Thus, in the message carried by proteins -to achieve minimum energy waste- the rate of information content per unit mass tends to be optimized in living organisms. The experimental evidence of this new information law resembles a marathon where highly optimized proteins correspond to advanced runners followed by a main bunch and the stragglers -lowly optimized proteins. Our results suggest the existence of a continuous optimization process that living organisms had to face, in which a compromise between biological functionality, economic feasibility and the survival requirements is established.

q-bio.BM↗

arXiv2005

Vector space of DNA genomic sequences on a Genetic Code Galois Field

A new N-dimensional vector space of DNA sequences over the Galois field of the 64 codons (GF(64)) was recently presented. Now, in order to include deletions and insertions (indel mutations), we have defined a new Galois field over the set of elements X1X2X3 (C125), where Xi belong to {O, A, C, G, C}. We have called this set, the extended triplet set and the elements X1X2X3, the extended triplets. The order of the bases is derived from the Z64-algebra of the genetic code -recently published-. Starting from the natural bijection phi: GF(5^3)-> C125 between the polynomial representation of elements from GF(5^3) and the elements X1X2X3, a novel Galois field over the set of elements X1X2X3 is defined. Taking the polynomial coefficients a0, a1, a2 belong to GF(5) and the bijective function f: GF(5) ->{O, A, C, G, C}, where f(0) = O, f(1) = A, f(2) = C, f(3) = G, f(4) = U, bijection phi is induced such that phi(a0 + a1x + a2x^2) = (f(a1), f(a2), f(a0)) = (X1X2X3). Next, by means of the bijection phi we define sum "+" and product "*" operations in the set of codons C125, in such a way that the resultant field (C125, +, *) turns isomorphic to the Galois Field GF(5^3). This field allows the definition of a novel N-dimensional vector space (S) over the field GF (5^3) on the set of all 125^N sequences of extended triplets in which all possible DNA sequence alignments of length N are included. Here the "classical gap" produced by alignment algorithms corresponds to the neutral element "O". It is verified that the homologous (generalized) recombination between two homologous DNA duplexes involving a reciprocal exchange of DNA sequences -e.g. between two chromosomes that carry the same genetic loci- algebraically corresponds to the action of two automorphism pairs (or two translation pairs) over two paired DNA duplexes.

q-bio.GN↗

arXiv2005

A Novel Lie Algebra of the Genetic Code over the Galois Field of Four DNA Bases

By starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient subspaces of the genetic code vector space over the Galois field of the four DNA bases. The new algebraic structure shows strong connections among algebraic relationships, codon assignment and physicochemical properties of amino acids. Moreover, a distance function defined between codons in the Lie algebra was demonstrated to have a linear behavior respect to physical variables such as the mean of amino acids energy in proteins. It was also noticed that the distance between wild type and mutant codons approach smaller values in mutational variants of four genes, i.e, human phenylalanine hydroxylase, human beta-globin, HIV-1 protease and HIV-1 reverse transcriptase. These results strongly suggest that deterministic rules in genetic code origin must be involved.

q-bio.QM↗

arXiv2005

The genetic signature of (astronomically induced) life extinctions

The current understanding of supernova and gamma-ray burst events suggests important effects on the biosphere if one of more of them happened to strike the earth in the past. In this paper we evaluate the possibility that life extinctions which probably occurred due to excess of radiation occurring in the geologic past might have left a genetic signature on surviving species. We emphasize the signatures of these extinctions, proposing a quantitative model to evaluate the surviving probability of the species, based on kinetic aspects of the frequency of mutations and the DNA repair rate.

q-bio.PE↗

arXiv2004

The Genetic Code Boolean Lattice

The algebraic structures of the genetic code are most important to obtain additional information about the semantic code and its applications. In this paper we define two dual Boolean codon lattices of the genetic code using hydrogen bond numbers and the chemical types of bases: purines and pyrimidines. The Boolean lattices reflect the role of hydrophobicity in the distribution of codon assignments to each amino acid. Particularly, the symmetric images of codons with adenine as second base coding to hydrophilic amino acids are always codons with uracil as second base coding to hydrophobic amino acids as they represented in the Hasse diagrams. The Hamming distance between two codons in the Hasse diagram reflects the different hydrophobicities between their respective coded amino acids. Our experiments have demonstrated a small Hamming distance to the wild type HXB2 of almost all the drug-resistant reported mutations in HIV protease gene. The human beta-globin mutant genes have also exhibited similar results. Our research suggests that the Hamming distance between two genes in the molecular evolution process have a minimal value.

q-bio.QM↗

arXiv2004

Gene Algebra from a Genetic Code Algebraic Structure

The biological distinction between the base positions in the codon, the chemical types of bases (purine and pyrimidine) and their hydrogen bond number have been the most relevant codon properties used in the genetic code analysis. Now, these properties have allowed us to build a Genetic Code ring isomorphic to the ring (Z64, +,*) of the integer module 64. On the Z64-algebra of the set of 64^N codon sequences of length N, gene mutations are described by means of endomorphisms F: (Z64)^N->(Z64)^N. Endomorphisms and automorphisms helped us describe the gene mutation pathways. For instance, 77.7% mutations in 749 HIV protease gene sequences correspond to unique diagonal endomorphisms of the wild type strain HXB2. In particular, most of the reported mutations that confer drug resistance to the HIV protease gene correspond to diagonal automorphisms of the wild type. What is more, in the human beta-globin gene a similar situation appears where most of the single codon mutations correspond to automorphisms. Hence, in the analyses of molecular evolution process on the DNA sequence set of length N, the Z64-algebra will help us explain the quantitative relationships between genes.

q-bio.QM↗

arXiv2004

A New DNA Sequences Vector Space on a Genetic Code Galois Field

A new n-dimensional vector space of the DNA sequences on the Galois field of the 64 codons (GF(64)) is proposed. In this vector space gene mutations can be considered linear transformations or translations of the wild type gene. In particular, the set of translations that preserve the chemical type of the third base position in the codon is a subgroup which describes the most frequent mutations observed in mutational variants of four genes: human phenylalanine hydroxylase (PAH), human beta globin (HBG), HIV-1 Protease (HIVP) and HIV-1 Reverse transcriptase (HIVRT). Furthermore, an inner pseudo-product defined between codons tends to have a positive value when the codons code to similar amino acids and a negative value when the codons code to amino acids with extreme hydrophobic properties. Consequently, it is found that the inner pseudo-product between the wild type and the mutant codons tends to have a positive value in the mutational variants of the genes: PAH, HBG, HIVP, HIVRT.

q-bio.QM↗