The modified base 5-methylcytosine ((m)C) plays an important functional role in the biology of mammals as an epigenetic modification and appears to exert a striking impact on the molecular evolution of mammal genomes. The collective epigenetic functions of (m)C revolve around its effect on gene transcription, while the influence of this modified base on the evolution of mammal genomes derives f...

Synonymous rare codons are considered to be sub-optimal for gene expression because they are translated more slowly than common codons. Yet surprisingly, many protein coding sequences include large clusters of synonymous rare codons. Rare codons at the 5' terminus of coding sequences have been shown to increase translational efficiency. Although a general functional role for synonymous rare cod...

The effective number of codons (N(c)) is a widely used index for characterizing codon usage bias because it does not require a set of reference genes as does codon adaptation index (CAI) and because of the freely available computational tools such as CodonW. However, N(c), as originally formulated has many problems. For example, it can have values far greater than the number of sense codons; it...

BACKGROUND In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking. Because most amino acids allow synonymous GC content changing substitutions in the third codon position, the overall GC bias of a genome or genomic region is highly correlated with GC3, a measure of third position GC conte...

Non-random usage of synonymous codons, known as “codon bias”, has been described in many organisms, from bacteria to Drosophila, but little is about it phytoplankton. This phenomenon thought be driven by selection for translational efficiency. As the efficacy proportional effective population size, species with large sizes, such phytoplankton, are expected have strong codon bias. To test this, ...

Medullary thyroid cancer accounts for 5-10% of thyroid carcinomas. RET proto-oncogene mutations occur in all of the hereditary MTCs and about 66% of the sporadic MTCs. So, the detection of the RET mutations is necessary for rapid and proper diagnosis and treatment. This systematic review seeks to find a comprehensive list of RET gene mutations in the diagnosis of medullary thyroid cancer. The ...

Most amino acids are encoded by multiple codons, and codon choice has strong effects on protein expression. Rare codons are enriched at the N terminus of genes in most organisms, although the causes and effects of this bias are unclear. Here, we measure expression from >14,000 synthetic reporters in Escherichia coli and show that using N-terminal rare codons instead of common ones increases exp...

Papillomaviruses use rare codons relative to their hosts. Recent studies have demonstrated that synonymous codon changes in viral genes can lead to increased protein production when the codons are matched to those of cells in which the protein is being expressed. We theorized that the immunogenicity of the virus would be enhanced by matching codons of selected viral genes to those of the host. ...

Degeneracy of the genetic code is a biological way to minimize effects of the undesirable mutation changes. Degeneration has a natural description on the 5-adic space of 64 codons C5(64) = {n0 + n1 5 + n2 5 2 : ni = 1, 2, 3, 4} , where ni are digits related to nucleotides as follows: C = 1, A = 2, T = U = 3, G = 4. The smallest 5-adic distance between codons joins them into 16 quadruplets, whic...