Narrow Results

We have developed a simple scheme to visualize the string composition of long DNA sequences and applied it to all available prokaryote complete genomes. Each species has a specific "portrait" and most clearly seen patterns in these portraits are determined by short avoided and under-represented strings. The "spatial" patterns in the space of short strings might reflect some "temporal" events in the evolutionary history.

We examine the short-term effects that a galactic Gamma Ray Burst would cause on a planetary biosphere. The immediate environmental perturbation would arise due to the emission of an aurora like spectrum in the middle and low atmosphere, delivering at planet's surface a brief but intense ultraviolet flash. We calculated potential damages to both the photosynthetic and DNA apparatuses of unicellular organisms. We conclude that if the progenitor is 1-2 kiloparsec distant in the Milky Way, its main short-term bio-effect will be radiation damage in the photosynthetic machinery rather than in the genome.

We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic potentials [23], we analyze the behavior of lattices built from real DNA sequences obtained from human genome data. We confirm the existence of threshold forces, already found in Fibonacci sequences, and of stop positions highly dependent on the specific sequence. Another relevant conclusion is that the effective potential, a collective coordinate formalism introduced by Salerno and Kivshar [21] is a useful tool to identify key regions that control the behaviour of a larger sequence. We then study how the fluctuations can assist the propagation process by helping the excitations to escape the stop positions. Our conclusions point out to improvements of the model which look promising to describe mechanical denaturation of DNA. Finally, we also consider how randomly distributed energy focus on the chain as a function of the sequence.