Highlights d DSB repair, but not NER, coevolves with maximum lifespan (MLS) in rodents d The activity of SIRT6 in stimulating DSB repair coevolves with MLS in rodent species d Five amino acids determine the differential activities of mouse and beaver SIRT6 d Stronger SIRT6 leads to a longer lifespan

Discriminating cell wall lytic enzymes from non lytic enzymes is a very important task for curing bacterial infections. In this paper, based on Chou's amphiphilic pseudo amino acid composition, we develop fisher-discriminant based classifier to predict cell wall lytic enzymes. Experiments show that 66.7% sensitivity with 88.6% specificity is obtained. The method is further able to predict endolysin and autolysin with an overall accuracy of 92.9%. Results demonstrated that our method can provide highly useful information for further bacterial control research.

The entropy production rate of cancer cell is always higher than healthy cell under the case of no external field applied. Different entropy production between two kinds of cells determines the direction of entropy flow among cells. The entropy flow is the carrier of information flow. The entropy flow from cancer to healthy cell takes along the harmful information of cancerous cell, propagating its toxic action to healthy tissues. We demonstrate that a low-frequency and low-intensity electromagnetic field or ultrasound irradiation may increase the entropy production rate of a cell in normal tissue than that in cancer, consequently reverse the direction of entropy current between two kinds of cells. The modification of PH value of cells may also cause the reversal of the direction of entropy flow between healthy and cancerous cells. So, the biological tissue under the irradiation of electromagnetic field or ultrasound or under the appropriate change of cell acidity can avoid the propagation of harmful information from cancer cells. We suggest that this entropy mechanism possibly provides a basis for a novel approach to anticancer therapy. Thermodynamic entropy is expressed by(1)where W is the number of microscopic states which are related to a given macroscopic thermodynamic state and k B is the Boltzmann constant. Entropy is a measure of disorder. From general physical principles, Schrodinger first indicated that life should remain in a low-entropy state or "an organism feeds with negative entropy" [1]. This means that entropy production in an organism is canceled by the outward entropy flow so that the system remains in a highly ordered state of low entropy. However, following our point of view, negative entropy (or negentropy) is only the first half of the story. The living organism is a chemical engine in which a series of chemical reactions take place one by one in an appropriate sequence. Accordingly, the energy transfer in an organism in the normal state is so efficient that the entropy production is minimized. Minimal entropy production in a healthy cell is the second half of the story [2]. We shall compare qualitatively and demonstrate that the entropy production rate (or "entropy production" for short) of a healthy cell is lower than that of a cancerous cell if no external energy input [3][4][5]. However, when the appropriate external energy is applied to tissues, the rate of entropy production of normal cells may exceed that of cancerous cells. As an example, we shall discuss the entropy production of cells under irradiation of ultrasound and alternative electromagnetic fields. We shall prove the

We review methods in the study of nucleotide correlation in DNA sequence, and demonstrate two basic properties of the correlation through statistical analysis, namely, the short-range dominance of nucleotide correlation in most DNA sequences and the coarse-grained evolutionary dependence of the short-range correlation in coding sequences. A corresponding evolutionary mechanism is suggested. By the use of spectral analysis a large inhomogeneity in long-range base correlations for different sequences is indicated. Some results on three-dimensional DNA walks are reported. The linguistic differences between coding and noncoding sequences are also indicated.

Based on the conservation of nucleotides at splicing sites and the features of base composition and base correlation around these sites we use the method of increment of diversity combined with quadratic discriminant analysis (IDQD) to study the dependence structure of splicing sites and predict the exons/introns and their boundaries for four model genomes: Caenorhabditis elegans, Arabidopsis thaliana, Drosophila melanogaster and human. The comparison of compositional features between two sequences and the comparison of base dependencies at adjacent or non-adjacent positions of two sequences can be integrated automatically in the increment of diversity (ID). Eight feature variables around a potential splice site are defined in terms of ID. They are integrated in a single formal framework given by IDQD. In our calculations 7 (8) base region around the donor (acceptor) sites have been considered in studying the conservation of nucleotides and sequences of 48 bp on either side of splice sites have been used in studying the compositional and base-correlating features. The windows are enlarged to 16 (donor), 29 (acceptor) and 80 bp (either side) to improve the prediction for human splice sites. The prediction capability of the present method is comparable with the leading splice site detector--GeneSplicer.

Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random mutation but primarily grows by random segmental duplication. That genomes grew mostly by duplication is consistent with the observation that repeat sequences in all genomes are widespread and intragenomic and intergenomic homologous genes are preponderant across all life forms.

No abstract

The occupancy of nucleosomes along chromosome is a key factor for gene regulation. However, except promoter regions, genome-wide properties and functions of nucleosome organization remain unclear in mammalian genomes. Using the computational model of Increment of Diversity with Quadratic Discriminant (IDQD) trained from the microarray data, the nucleosome occupancy score (NOScore) was defined and applied to splice junction regions of constitutive, cassette exon, alternative 3′ and 5′ splicing events in the human genome. We found an interesting relation between NOScore and RNA splicing: exon regions have higher NOScores compared with their flanking intron sequences in both constitutive and alternative splicing events, indicating the stronger nucleosome occupation potential of exon regions. In addition, NOScore valleys present at ∼25 bp upstream of the acceptor site in all splicing events. By defining folding diversity-to-energy ratio to describe RNA structural flexibility, we demonstrated that primary RNA transcripts from nucleosome occupancy regions are relatively rigid and those from nucleosome depleted regions are relatively flexible. The negative correlation between nucleosome occupation/depletion of DNA sequence and structural flexibility/rigidity of its primary transcript around splice junctions may provide clues to the deeper understanding of the unexpected role for nucleosome organization in the regulation of RNA splicing.