BLOSUM and PAM series of protein substitution matrices are popular tools for scoring protein pairwise and multiple alignments. For protein multiple alignments there exists another representation of an evolving column, based on a set of predefined frequency profile patterns. For conserved sites, these profile patterns represent stationary points in a 20-dimensional profile space. There are 20 su...

Rates of molecular evolution at some loci are more irregular than described by simple Poisson processes. Three situations under which molecular evolution would not follow simple Poisson processes are reevaluated from the viewpoint of the neutrality hypothesis: concomitant or multiple substitutions in a gene, fluctuating substitution rates in time caused by coupled effects of deleterious mutatio...

Determining the extent of adaptive evolution at the genomic level is central to our understanding of molecular evolution. A suitable observation for this purpose would consist of polymorphic data on a large and unbiased collection of genes from two closely related species, each having a large and stable population. In this study, we sequenced 419 genes from 24 lines of Drosophila melanogaster a...

Despite the intense efforts of the last decades to understand the thermal stability of proteins, the mechanisms responsible for its modulation still remain debated. In this investigation, we tackle this issue by showing how a multiscale perspective can yield new insights. With the help of temperature-dependent statistical potentials, we analysed some amino acid interactions at the molecular lev...

The effect of two levels of fishmeal substitution (50 (FM1) and 150 (FM2) g/kg) of a grass silage control diet (C) on the rumen digestion of organic matter and nitrogen, and the small intestinal disappearance of amino acids was examined in young growing cattle each equipped with simple PVC cannulas in the dorsal sac of the reticulo-rumen, the proximal duodenum and the terminal ileum. The silage...

Every protein has a biosynthetic cost to the cell based on the synthesis of its constituent amino acids. In order to optimise growth and reproduction, natural selection is expected, where possible, to favour the use of proteins whose constituents are cheaper to produce, as reduced biosynthetic cost may confer a fitness advantage to the organism. Quantifying the cost of amino acid biosynthesis p...

Fermented maize product, ogi, is a popular weaning and breakfast cereal in west coasts of Africa. In the study proximate, mineral and amino acid compositions of ogi from a composite mixture of white maize (Zea mays L.) and scarlet runner bean (Phaseolus coccineus L.) flours were evaluated using standard processing techniques. Maize ogi was substituted with scarlet runner bean flour at ratios of...

phenylketonuria (pku) is an inborn error of amino acid metabolism with an autosomal recessive inheritance caused in most cases by mutations in the phenylalanine hydroxylase (pah) gene. pku has wide allelic heterogeneity. here we report a novel heterozygous substitution (c.1223g>t (p.arg408leu)) in the pah gene in an iranian pku family. the patient was 19-yr-old female with diagnosis of moderate...

Somatic hypermutation (SHM) plays a critical role in the maturation of antibodies, optimizing recognition initiated by recombination of V(D)J genes. Previous studies have shown that the propensity to mutate is modulated by the context of surrounding nucleotides and that SHM machinery generates biased substitutions. To investigate the intrinsic mutation frequency and substitution bias of SHMs at...