Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications

One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist; some, if not all, of these features would be relics of the primary genetic information. Based on this assumption, we analyzed the pattern of frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides of the whole-genome sequences from 458 species (including archaea, bacteria, and eukaryotes). Also, we studied the phenomenon of strand symmetry in these genomes. The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon that may contribute to frequency conservation. We propose a new hypothesis for the origin of strand symmetry and frequency conservation as well as for the constitution of early genomes. We conclude that the phenomena of strand symmetry and the pattern of frequency conservation would be original features of the primary genetic information

Characteristics of profiles of gamma-ray burst pulses associated with the Doppler effect of fireballs

In this paper, we derive in a much detail the formula of count rates, in terms of the integral of time, of gamma-ray bursts in the framework of fireballs, where the Doppler effect of the expanding fireball surface is the key factor to be concerned. Effects arising from the limit of the time delay due to the limited regions of the emitting areas in the fireball surface and other factors are investigated. Our analysis shows that the formula of the count rate of fireballs can be expressed as a function of $\tau$ which is the observation time scale relative to the dynamical time scale of the fireball. The profile of light curves of fireballs depends only on the relative time scale, entirely independent of the real time scale and the real size of the objects. It displays in detail how a cutoff tail, or a turn over, feature (called a cutoff tail problem) in the decay phase of a light curve can be formed. This feature is a consequence of a hot spot in the fireball surface, moving towards the observer, and was observed in a few cases previously. By performing fits to the count rate light curves of six sample sources, we show how to obtain some physical parameters from the observed profile of the count rate of GRBs. In addition, the analysis reveals that the Doppler effect of fireballs could lead to a power law relationship between the $FWHM$ of pulses and energy, which were observed previously by many authors.Comment: 38 pages, 10 figures; accepted for publication in ApJ (10 December 2004, v617