A genetic programming method for protein motif discovery and protein classification

Proteins can be grouped into families according to some features such as hydrophobicity, composition or structure, aiming to establish common biological functions. This paper presents MAHATMA—memetic algorithm-based highly adapted tool for motif ascertainment—a system that was conceived to discover features (particular sequences of amino acids, or motifs) that occur very often in proteins of a given family but rarely occur in proteins of other families. These features can be used for the classification of unknown proteins, that is, to predict their function by analyzing their primary structure. Experiments were done with a set of enzymes extracted from the Protein Data Bank. The heuristic method used was based on genetic programming using operators specially tailored for the target problem. The final performance was measured using sensitivity, specificity and hit rate. The best results obtained for the enzyme dataset suggest that the proposed evolutionary computation method is effective in finding predictive features (motifs) for protein classification.     

Microstructure Study at Different Thicknesses of Disc-Shaped YBa2Cu3O7?x Prepared by FQMG Method

The flame-quench-melt-growth (FQMG) method was used for the preparation of bulk YBa₂Cu₃O_7?x (Y123). Both the superconducting and nonsuperconducting regions changing with thickness of superconducting sample were determined by X-ray diffraction (XRD) patterns and also observed at micrographs taken by the polarized optical microscope. It was observed that superconducting forming ratio which was examined for different thicknesses of the sample ranging from 6.54 to 1.58 mm strongly enhanced. This means that a region near the top surface of the sample contains more superconducting phase than the other regions. These observations would be helpful in designing and manufacturing the practical applications of YBCO systems.     

Trehalose Metabolism: From Osmoprotection to Signaling

Trehalose is a non-reducing disaccharide formed by two glucose molecules. It is widely distributed in Nature and has been isolated from certain species of bacteria, fungi, invertebrates and plants, which are capable of surviving in a dehydrated state for months or years and subsequently being revived after a few hours of being in contact with water. This disaccharide has many biotechnological applications, as its physicochemical properties allow it to be used to preserve foods, enzymes, vaccines, cells etc., in a dehydrated state at room temperature. One of the most striking findings a decade ago was the discovery of the genes involved in trehalose biosynthesis, present in a great number of organisms that do not accumulate trehalose to significant levels. In plants, this disaccharide has diverse functions and plays an essential role in various stages of development, for example in the formation of the embryo and in flowering. Trehalose also appears to be involved in the regulation of carbon metabolism and photosynthesis. Recently it has been discovered that this sugar plays an important role in plant-microorganism interactions.     

RNA Relics and Origin of Life

A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells.