High correlation between the turnover of nucleotides under mutational pressure and the DNA composition

BACKGROUND: Any DNA sequence is a result of compromise between the selection and mutation pressures exerted on it during evolution. It is difficult to estimate the relative influence of each of these pressures on the rate of accumulation of substitutions. However, it is important to discriminate between the effect of mutations, and the effect of selection, when studying the phylogenic relations between taxa. RESULTS: We have tested in computer simulations, and analytically, the available substitution matrices for many genomes, and we have found that DNA strands in equilibrium under mutational pressure have unique feature: the fraction of each type of nucleotide is linearly dependent on the time needed for substitution of half of nucleotides of a given type, with a correlation coefficient close to 1. Substitution matrices found for sequences under selection pressure do not have this property. A substitution matrix for the leading strand of the Borrelia burgdorferi genome, having reached equilibrium in computer simulation, gives a DNA sequence with nucleotide composition and asymmetry corresponding precisely to the third positions in codons of protein coding genes located on the leading strand. CONCLUSIONS: Parameters of mutational pressure allow us to count DNA composition in equilibrium with this mutational pressure. Comparing any real DNA sequence with the sequence in equilibrium it is possible to estimate the distance between these sequences, which could be used as a measure of the selection pressure. Furthermore, the parameters of the mutational pressure enable direct estimation of the relative mutation rates in any DNA sequence in the studied genome

The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms

<p>Abstract</p> <p>Background</p> <p>The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.</p> <p>Results</p> <p>We have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes – positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.</p> <p>Conclusion</p> <p>The distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.</p

Phase Transition in Sexual Reproduction and Biological Evolution

Using Monte Carlo model of biological evolution we have discovered that populations can switch between two different strategies of their genomes' evolution; Darwinian purifying selection and complementing the haplotypes. The first one is exploited in the large panmictic populations while the second one in the small highly inbred populations. The choice depends on the crossover frequency. There is a power law relation between the critical value of crossover frequency and the size of panmictic population. Under the constant inbreeding this critical value of crossover does not depend on the population size and has a character of phase transition. Close to this value sympatric speciation is observed.Comment: 13 pages, 8 figure

Peculiarity of hybrid entrepreneurs – revisiting Lazear’s theory of entrepreneurship

The aim of this study is to explore and elaborate the concept of hybrid entrepreneurship, i.e., a simultaneous mix of self-employment (entrepreneurship) and salary employment. Lazear’s theory of entrepreneurship is assessed in terms whether it can explain the phenomenon of being a hybrid entrepreneur. The hypothesis is that the probability of linking a salary job with one’s own business increases with the variety and level of education gained, the broadness of professional and management experience but also the level of entrepreneurial self-efficacy. The hypotheses are tested with multivariate logistic regression, using survey data gathered from 1600 entrepreneurs. In light of the results, Lazear’s theory cannot be unambiguously extended to the case of hybrid entrepreneurs. Although the probability of being a hybrid entrepreneur increases with broader professional and managerial experience, at the same time it diminishes as the level and diversity of education increase. The results suggest that hybrid entrepreneurs are an importantly discrete population and therefore need to be treated separately. The theoretical and practical implications of the results are discussed

MEDIAEVAL HOUSES ON POTS IN THE LIGHT OF ARCHAEOLOGICAL EXCAVATIONS IN NIDZICA

The expectations associated with the archaeological supervision initiated in September 1999 in the eastern row of houses in the Old Town of Nidzica concerned relics connected with old settlements and town development. Already the exploration of the first metres unearthed strata dating from the Hallstatt D/La Tene A period, associated with the settlement of the western Balt barrow culture and the Przeworsk culture. The significance of this discovery made it possible to change the very nature of the excavation from supervision to archaeological research. The five basic stratigraphic layers distinguished in the course of the investigations include: I level – contemporary and nineteenth-century surfaces, II level – late mediaeval and modern layers, III level – late mediaeval traces of half-timber buildings in the southern row of houses in the market square, IV level – mediaeval strata containing relics of pottery, V level – ancient. The most interesting element registered in the course of the excavations was the longitudinal insulation of the mediaeval buildings made of pots fashioned on a potter’s wheel. A stone pavement on a sand bed, certainly comprising the cellar floor, was found at a depth not exceeding 2 metres. A layer of vessels was discovered after the removal of the pavement. Compactly arranged and turned upside down, the empty pots, covered with clay, provided excellent insulation against dampness and, at the same time, created a stable sleeper for the whole building, as evidenced by the remnants of partition walls built directly on the “pot” insulation. The excavations registered more than 200 whole “insulation” vessels and almost the same number of their fragments. The dendrochronological examination of the wooden construction on the pavement above the insulation was performed by M. Krąpiec, who established the time span of the construction as 1372-1407. In view of the fact that the town’s locatio took place in 1381, we may narrow down the origin of the construction to the post-1381 and pre-1408 period. The described insulation remains unique on a Polish and European scale. The exposition of the findings posed a different problem. Thanks to an agreement between the Voivodeship Conservator of Historical Monuments for Varmia and Mazuria and the museum at Nidzica Castle as well as the assistance of the staff of the Voivodeship Office for the Protection of Historical Monuments in Olsztyn it was possible to recreate a small fragment of this example of mediaeval technology