Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming

The aim of this study was to show that amino acid sequences have a latent periodicity with insertions and deletions of amino acids in unknown positions of the analyzed sequence. Genetic algorithm, dynamic programming and random weight matrices were used to develop a new mathematical algorithm for latent periodicity search. A multiple alignment of periods was calculated with help of the direct optimization of the position-weight matrix without using pairwise alignments. The developed algorithm was applied to analyze amino acid sequences of a small number of proteins. This study showed the presence of latent periodicity with insertions and deletions in the amino acid sequences of such proteins, for which the presence of latent periodicity was not previously known. The origin of latent periodicity with insertions and deletions is discussed.

A new method to reconstruct fish diet and movement patterns from δ13C values in otolith amino acids

Fish ecologists have used geochemical values in otoliths to examine habitat use, migration, and population connectivity for decades. However, it remains difficult to determine an unambiguous dietary δ13C signature from bulk analysis of otolith. Studies to date have focused on the aragonite component of otoliths with less attention paid to the organic fraction. We describe the application of compound-specific stable isotope analysis (SIA) to analyze amino acid (AA) δ13C values from small amounts (<1 mg) of otolith powder. We examined δ13C values of otolith and muscle AAs from a reef-associated snapper (Lutjanus ehrenbergii (Peters, 1869)) collected along a carbon isotope gradient (isoscape) from seagrass beds to coral reefs. Carbon isotope values in otolith and muscle samples were highly correlated within and among coastal habitats. Moreover, δ13C values of otolith AAs provided a purely dietary record that avoided dilution from dissolved inorganic carbon. Otolith AAs served as a robust tracer of δ13C values at the base of the food web, making compound-specific SIA a powerful tool for dietary reconstructions and tracking the movement of fishes across isoscapes.

An analysis of amino acid composition of a few oxidoreductases by different methods

1. All methods used to analyze amino acid composition of different enzymes agree well with each other. 2. They lead to a relationship between amino acid composition and function of proteins. 3. Cytochrome oxidase is in a class by itself; copper-containing oxidases are closely related as expected.