Biomedical subjects

B Borstnik

Publications and source records attributed to B Borstnik.

8 recordsLinked to original sources

PubMed1999

Criticality of D=2 and D=3 Ising models: cluster structure versus populations.

The energy and the specific heat of two- and three-dimensional Ising systems are analyzed in terms of cluster properties. The energy and the specific heat are decomposed into two components, which are defined by quantities pertaining to cluster populations and cluster structure expressed in terms of average cluster perimeters. It is shown that the structural component of the energy as well as of the specific heat represents the dominant contribution. Indications are presented that the critical exponent of structural and populational components of specific heat matches the exponent of the entire specific heat.

Journal Article↗

PubMed1994

Tandemly repeated pentanucleotides in DNA sequences of eucaryotes.

Genetic sequence data banks were scanned in order to retrieve tandemly repeated pentanucleotides (pnts). It was found that among 102 (=(1024-4)/2/5) possible distinct pnts roughly each fourth is involved in tandem repeats. It is shown that tandemly repeated pnts are composed of frequently occurring di- and trinucleotides and that those pnts which occur frequently in the form of mono- or di-pnts form also tandem repeats either in the form of satellites or in the form of shorter tandem repeats. Human satellite III is taken as a specific example. It is shown that the first guanine within GG-AAT pnt exhibits the highest mutability. Sequential distribution of base changes gives evidence that the mutations do not occur at random positions but in a correlated fashion so that long stretches of original pnts remain intact. It is found that pnts related to the satellite III are present in introns and flanking regions of some structural genes, but are not preserved between orthologous genes of related species. The results corroborate the most plausible mechanism of their evolution--rapid amplification followed by successive divergence of repeat units by various mutational processes.

Animals↗

PubMed1992

Detection of satellite DNA in Palorus ratzeburgii: analysis of curvature profiles and comparison with Tenebrio molitor satellite DNA.

Very abundant and homogenous satellite DNA has been found in the flour beetle Palorus ratzeburgii, representing 40% of its genome. Sequencing of 14 randomly cloned satellite monomers revealed a conserved monomer length of 142 bp and an average A+T content of 68%. Sequence variation analysis showed that base substitutions, appearing with a frequency of 2.3%, are predominant differences among satellite monomers. The satellite sequence is unique without significant direct repeats and with only two potentially stable inverted repeats. After electrophoresis of satellite monomers on native polyacrylamide gel retarded mobilities characteristic for curved DNA molecules are observed. The curvature profiles and DNA helix axis trajectory are calculated on the basis of three different algorithms. These calculations predict that P ratzeburgii satellite DNA forms a left-handed solenoid superstructure. Comparison of described features with other satellite DNAs reveals some striking similarities with satellite DNA from related species Tenebrio molitor, which belongs to the same family of Tenebrionidae. Both satellites are very abundant and homogenous with the same, highly conserved monomer length, although there is no homology at the nucleotide level. Their monomers, as well as multimers, exhibit very similar retarded electrophoretic mobilities. The calculated curvature profiles predict two bend centers in monomers of each satellite, resulting in a model of left-handed solenoid superstructures of similar appearance.

Animals↗

PubMed1992

Evidence for random distribution of sequence variants in Tenebrio molitor satellite DNA.

Tenebrio molitor satellite DNA has been analysed in order to study sequential organization of tandemly repeated monomers, i.e. to see whether different monomer variants are distributed randomly over the whole satellite, or clustered locally. Analysed sequence variants are products of single base substitutions in a consensus satellite sequence, producing additional restriction sites. The ladder of satellite multimers obtained after digestion with restriction enzymes was compared with theoretical calculations and revealed the distribution pattern of particular monomer variants within the satellite. A defined higher order repeating structure, indicating the existence of satellite subfamilies, could not be observed. Our results show that some sequence variants are very abundant, being present in nearly 50% of the monomers, while others are very rare (0-1% of monomers). However, the distribution of either very frequent, or very rare sequence variants in T. molitor satellite DNA is always random. Monomer variants are randomly distributed in the total satellite DNA and thus spread across all chromosomes, indicating a relatively high rate of sequence homogenization among different chromosomes. Such a distribution of monomer variants represents a transient stage in the process of sequence homogenization, indicating the high rate of spreading in comparison with the rate of sequence variant amplification.

Animals↗

PubMed1990

Stochastic traits of molecular evolution--acceptance of point mutations in native actin genes.

A stochastic matrix of nucleotide mutation probabilities is derived by counting differences and identities in alignments of native actin genes, with the aim of obtaining a more reliable data base for regular modes of molecular evolution. The evolution of DNA sequences is thereby considered as a Markov process consisting of events (point mutations) characterized by a stochastic matrix for codon-codon interchanges. The genetic distance is set to 1 PAM (percentage of accepted point mutations). The results can be reproduced by Monte Carlo simulations which are subjected to selective constraints. The latter are observed as nonrandom codon usage and ratios of silent to recognizable point mutations. Specific patterns within the matrix of mutation probabilities attest to preferences of natural selection in the evolution of a specific protein.

Actins↗

PubMed1990

An ESS-analysis for ensembles of prisoner's dilemma strategies.

The ESS (Evolutionary Stable Strategy) concept of Maynard Smith can be applied in its weak form to ensembles of competing PD ("Prisoner's Dilemma") strategies memorizing two to three of one's own and one's opponent's moves. The format of our study is: (1) games have very long duration; (2) Taylor-Jonker dynamics applies; (3) Effects of finite population size can be ignored. It is shown that in the case R greater than (T + S)/2 a set of strategies can be singled out which do not lose against any other strategy while co-operating with themselves. Such a set is uninvadable by other PD strategies if it constitutes more than half of the total population.

Biological Evolution↗

PubMed1990

Sequence-induced curvature of Tenebrio molitor satellite DNA.

Single satellite DNA constitutes about 50% of the Tenebrio molitor genome. Electrophoresis of 142 base pair long satellite monomers on nondenaturating polyacrylamide gel shows retarded mobility, a characteristic of fragments with sequence-induced DNA curvature. Migrational analysis of circularly permuted satellite monomers revealed the existence of 2 bend centers in the monomer sequence. We calculated the trajectory of DNA helix axis according to the algorithm of De Santis et al. This model predicts that T molitor naked satellite DNA forms a solenoid structure with left-handed superhelix. One turn of the superhelix has approximately 310 base pairs and a 33 nm pitch. Point mutations found in the satellite DNA (1.8%) influence bending characteristics, but do not distort the general geometry of satellite superhelix.

Animals↗

PubMed1987

Point mutations as an optimal search process in biological evolution.

Point mutations are pictured as jumps in a phase space representing the sequences of amino acids or nucleotides as discrete points. It is shown that this space can be given a natural metric by quantifying common physical and chemical properties of amino acid constituents in terms of a natural measure. Evolution through point mutations is simulated by the search for points in the phase space representing amino acid sequences of high survival fitness. Due to the local compactness of the distribution of these functionally allowed points in phase space any successful search procedure has characteristics qualitatively different from those in the case of a random distribution. This is demonstrated by model calculations. A specified distribution of allowed points is generated with subsequent evaluation of the success of the retrieval process as a function of the jump probabilities between lattice sites. The results of such simulations are compared with data obtained from the analysis of the DNA or mRNA sequences coding related proteins. By counting silent and expressed nucleotide replacement frequencies one can draw conclusions as to the efficacy of the natural evolutionary search processes in the phase space of amino acid sequences. There are cases, where the highest possible information gain of one bit per accepted point mutation is achieved. In general the information gain is found to be somewhat sub-maximal due to functional requirements.

Amino Acid Sequence↗