Representation of a protein molecule as a tree and application to modular computer programs which calculate and modify atomic coordinates

The concept and representation of a logical tree as defined in computer science is applied to obtain a suitable representation of protein molecules in computer programs which handle or calculate atomic coordinates of protein molecules. On the basis of this analysis and of the analysis of the calculation and modification of the structure of a protein from bond lengths, bond angles, and dihedral angles, which is reproduced in an appendix, program modules which accomplish the various required computations are described. Three such modules are given in Iverson notation; in fact, it is hoped that this article will serve as a reasonably complete basis for the preparation of machine programs by moderately proficient programmers.     

Sequence similarity is more relevant than species specificity in probabilistic backtranslation

Background  

Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes backtranslation potentially ambiguous since most amino acids are encoded by multiple codons. The common approach to overcome this difficulty is based on imitation of codon usage within the target species.     

The Brazilian experience of sugarcane ethanol industry

Biomass has gained prominence in the last few years as one of the most important renewable energy sources. In Brazil, a sugarcane ethanol program called ProAlcohol was designed to supply the liquid gasoline substitution and has been running for the last 30 yr. The federal government’s establishment of ProAlcohol in 1975 created the grounds for the development of a sugarcane industry that currently is one of the most efficient systems for the conversion of photosynthate into different forms of energy. Improvement of industrial processes along with strong sugarcane breeding programs brought technologies that currently support a cropland of 7 million hectares of sugarcane with an average yield of 75 tons/ha. From the beginning of ProAlcohol to the present time, ethanol yield has grown from 2,500 to around 7,000 l/ha. New technologies for energy production from crushed sugarcane stalk are currently supplying 15% of the electricity needs of the country. Projections show that sugarcane could supply over 30% of Brazil’s energy needs by 2020. In this review, we briefly describe some historic facts of the ethanol industry, the role of sugarcane breeding, and the prospects of sugarcane biotechnology