The transfer RNA gene complement of Saccharomyces cerevisiae was utilized for a whole-genome analysis of the deviation from a neutral usage of pyrimidine-ending cognate codons, that is, codons read by a single tRNA species having either inosine or guanosine as the first anticodon base. Mutational pressure at the wobble position was estimated from the base composition of the noncoding portion of...

Robustness to destabilizing effects of mutations is thought of as a key factor of protein evolution. The connections between two measures of robustness, the relative core size and the computationally estimated effect of mutations on protein stability (ΔΔG), protein abundance and the selection pressure on protein-coding genes (dN/dS) were analyzed for the organisms with a large number of availab...

Objective: This study aimed to determine the relationship between polymorphisms of C893T gene of platelet membrane receptor P2Y1 and cerebral infarction (CI) in Han population of North Shandong Province of China. Methods: A case-control study of 162 healthy people (the normal contrast group) and 185 CI patients confirmed by computed tomography or magnetic resonance imaging (CI group) was conduc...

The genome of a cancer cell carries somatic mutations that are the cumulative consequences of the DNA damage and repair processes operative during the cellular lineage between the fertilized egg and the cancer cell. Remarkably, these mutational processes are poorly characterized. Global sequencing initiatives are yielding catalogs of somatic mutations from thousands of cancers, thus providing t...

BACKGROUND Mutational signatures have been identified by the broad sequencing of cancer genomes and reflect underlying processes of mutagenesis. The clinical application of mutational signatures is not well defined. Here we aim to assess the prognostic utility of mutational signatures in ovarian high-grade serous carcinoma. METHODS Open access data of 15,439 somatic mutations of 310 ovarian h...

UNLABELLED Codon usage bias (CUB) is an omnipresent phenomenon, which occurs in nearly all organisms. Previous studies of codon bias in Plasmodium species were based on a limited dataset. This study uses whole genome datasets for comparative genome analysis of six Plasmodium species using CUB and other related methods for the first time. Codon usage bias, compositional variation in translated a...

Preface How can we stop cancer progression? Current strategies depend on modeling progression as the balanced outcome of mutations in, and expression of, tumor suppressor genes and oncogenes. New treatments emerge from successful attempts to tip that balance, but secondary mutational escape from those treatments has become a major impediment because it leads to resistance. In this Opinion artic...

The paper describes a mutational equilibrium model of genome size evolution. This model is different from both adaptive and junk DNA models of genome size evolution in that it does not assume that genome size is maintained either by positive or stabilizing selection for the optimum genome size (as in adaptive theories) or by purifying selection against too much junk DNA (as in junk DNA theories...

We have elaborated a new method of recognizing protein coding sequences in genomic sequences. The method is exploiting a specific way of genetic code degeneration and relations between mutational pressure and selection pressure shaping the amino acid usage in the proteomes. It is based on analyses of correlations in nucleotide occurrence separately in the first, the second and the third putativ...