Related papers: GC3 Biology in Eukaryotes and Prokaryotes
This work analyzed genome-wide nucleotide distribution patterns in ten insect genomes. Two internal measures were applied: (i) GC variation and (ii) third codon nucleotide preference. Although the genome size and overall GC level did not…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
The GC content of prokaryotic genomes is species-specific and takes values from 16 to 77 percent. There are currently no accepted explanations for this diversity of selection for GC content. We analyzed the known correlations between GC…
The origin and early evolution of eukaryotes are one of the major transitions in the evolution of life on earth. One of its most interesting aspects is the emergence of cellular organelles, their dynamics, their functions, and their…
In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains…
Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A…
Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Genomes in living organisms consist of the nucleotides adenine (A), guanine (G), cytosine (C) and thymine (T). All prokaryotes have genomes consisting of double-stranded DNA, where the A's and G's (purines) of one strand bind respectively…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
Background: Prior to the current genomic era it was suggested that the number of protein-coding genes that an organism made use of was a valid measure of its complexity. It is now clear, however, that major incongruities exist and that…
The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two…
The present article is an invited contribution to the Encyclopedia of Complexity and System Science, Robert A. Meyers Ed., Springer New York (2009). It is a review of the biophysical mechanisms that underly cell motility. It mainly focuses…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…
A discrete symmetry S3 easily explains all neutrino data. However it is not obvious the embedding of S3 in GUT where all fermions live in the same representation. We show that embedding S3 in E6 it is possible to make distinction between…
Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our…