Biological modelling / Biomodélisation Effect of variable surrounding on species creation

Abstract We constructed a model of speciation from evolution in an ecosystem consisting of a limited amount of energy recources. The species possesses genetic information, which is inherited according to the rules of the Penna model of genetic evolution. The increase in the number of the individuals of each species depends on the quality of their genotypes and the available energy resources. The decrease in number of the individuals results from genetic death or maximum-age reaching by the individual. The amount of energy resources is represented by a solution of the differential logistic equation, where the growth rate of the amount of the energy resources has been modified to include the number of individuals from all species in the ecosystem under consideration. The fluctuating surrounding is modelled with the help of the function V (x, t) = 1 4 x 4 + 1 2 b(t)x 2 , where x represents phenotype and the coefficient b(t) shows the cos(ωt) time dependence. The closer the value x of an individual to the minimum of V (x, t), the better adapted its genotype to the surrounding. We observed that the life span of the organisms strongly depends on the value of the frequency ω. It becomes shorter the more frequent the changes of the surrounding. However, there is a tendency for the species that have a higher value of the reproduction age a R to win the competition with the other species. Another observation is that small evolutionary changes of the inherited genetic information lead to spontaneous bursts of the evolutionary activity when many new species may appear in a short period. Résumé Effet d'un milieu variable sur l'apparition des espèces. Un modèle de spéciation issu de l'évolution dans un écosystème aux ressources énergétiques limitées a été créé. Les espèces possédent des informations génétiques qui sont héritées selon les règles du modèle de Penna d'evolution génétique. L'augmentation du nombre d'individus de chaque espèce dépend de la qualité de leur génotype et de l'accessibilité des ressources énergétiques. La diminution du nombre d'individus résulte de la mort génétique ou de l'arrivée de l'un d'entre eux à l'âge maximum. La quantité des ressources énergétiques est donnée par la résolution de l'équation différentielle logique, où le taux de renouvellement de la quantité de ressources énergétiques a été modifié pour tenir compte de la quantité d'individus de toutes les espèces de l'écosystème analysé. . Nowicka et al. / C. R. Biologies 327 (2004) 283-292 Les fluctuations du milieu sont modélisées par la fonction V (x, t) = 1 4 x 4 + 1 2 b(t)x 2 , où x représente un phénotype et le coefficient b(t) désigne cos(ωt), la dépendance temporelle. Plus la valeur x d'un individu est proche du minimum V (x, t), mieux son génotype est adapté au milieu. Il a été constaté que la durée de vie des organismes dépend fortement de la valeur de la fréquence ω. Plus les changements du milieu sont fréquents, plus celle-ci devient faible. Cependant, les espèces dont la valeur a R de l'âge de reproduction est élevée ont tendance à remporter la compétition avec les autres espèces. L'autre observation est que les petits changements évolutifs des informations génétiques héritées conduisent à des explosions spontanées de l'activité évolutive, et de nombreuses nouvelles espèces peuvent alors apparaître, dans un laps de temps court

Food-chain competition influences gene's size

We have analysed an effect of the Bak-Sneppen predator-prey food-chain self-organization on nucleotide content of evolving species. In our model, genomes of the species under consideration have been represented by their nucleotide genomic fraction and we have applied two-parameter Kimura model of substitutions to include the changes of the fraction in time. The initial nucleotide fraction and substitution rates were decided with the help of random number generator. Deviation of the genomic nucleotide fraction from its equilibrium value was playing the role of the fitness parameter, $B$, in Bak-Sneppen model. Our finding is, that the higher is the value of the threshold fitness, during the evolution course, the more frequent are large fluctuations in number of species with strongly differentiated nucleotide content; and it is more often the case that the oldest species, which survive the food-chain competition, might have specific nucleotide fraction making possible generating long genesComment: 11 pages including 7 figure

On the dynamics and control of mechanical properties of hierarchical rotating rigid unit auxetics

In this work, we investigate the deformation mechanism of auxetic hierarchical rotating square systems through a dynamics approach. We show how their deformation behaviour, hence their mechanical properties and final configuration for a given applied load, can be manipulated solely by altering the resistance to rotational motion of the hinges within the system. This provides enhanced tunability without necessarily changing the geometry of the system, a phenomenon which is not typically observed in other non-hierarchical unimode auxetic systems. This gives this hierarchical system increased versatility and tunability thus making it more amenable to be employed in practical application which may range from smart filtration to smart dressings.peer-reviewe

The role of the genetic code in generating new codings sequences inside existing genes

Abstract The genetic code has a very interesting property-it generates an open reading frame (ORF) inside a coding sequence, in a specific phase of the antisense strand with much higher probability than in the random DNA sequences. Furthermore, these antisense ORFs (A-ORFs) possess the same features as real genes -the asymmetry in the nucleotide composition at the first and second positions in codons. About two thirds of the 2997 overlapping ORFs in the yeast genome possess this feature. Thus, the question arises: has this feature of the genetic code been exploited in the evolution of genes? We have searched the FASTA data bases for homologies with the antisense translation products of a specific class of genes and we have found some sequences with relatively high homology. Many of them have scores which could be randomly found in the searched data bases with a probability lower than 10 − 6 . We conclude that some genes could arise by positioning a copy of the original gene under a promoter in the opposite direction in such a way that both, the original gene and its copy initially use the same nucleotides in the third, degenerated positions in codons

Effect of Magnetic Heating on Stability of Magnetic Colloids

Stable aqueous suspension of magnetic nanoparticles is essential for effective magnetic hyperthermia and other applications of magnetic heating in an alternating magnetic field. However, the alternating magnetic field causes strong agglomeration of magnetic nanoparticles, and this can lead to undesirable phenomena that deteriorate the bulk magnetic properties of the material. It has been shown how this magnetic field influences the distribution of magnetic agglomerates in the suspension. When investigating the influence of the sonication treatment on magnetic colloids, it turned out that the hydrodynamic diameter as a function of sonication time appeared to have a power-law character. The effect of magnetic colloid ageing on magnetic heating was discussed as well. It was shown how properly applied ultrasonic treatment could significantly improve the stability of the colloid of magnetic nanoparticles, ultimately leading to an increase in heating efficiency. The optimal sonication time for the preparation of the magnetic suspension turned out to be time-limited, and increasing it did not improve the stability of the colloid. The obtained results are important for the development of new materials where magnetic colloids are used and in biomedical applications

Modelling of the interactions between magnetic nanoparticles in aqueous solutions

The ability of magnetic nanoparticles and their aggregates to form larger structures or new materials is primarily based on the interactions between individual particles. The article analyzes the behavior of spherical nanoparticles Fe3O4 placed in an aqueous base solution as a result of their mutual interactions, i.e. repulsive (electrostatic forces) and attractive (van der Waals forces and dipolar magnetic forces) for the full range of parameter values. Considering the application of magnetic aqueous suspensions in industry or environmental research, the presented method allows for a preliminary selection of the parameters of the dispersed material and the solution so as to obtain a suspension with the desired properties

Where does bacterial replication start? Rules for predicting the oriC region

Three methods, based on DNA asymmetry, the distribution of DnaA boxes and dnaA gene location, were applied to identify the putative replication origins in 120 chromosomes. The chromosomes were classified according to the agreement of these methods and the applicability of these methods was evaluated. DNA asymmetry is the most universal method of putative oriC identification in bacterial chromosomes, but it should be applied together with other methods to achieve better prediction. The three methods identify the same region as a putative origin in all Bacilli and Clostridia, many Actinobacteria and γ Proteobacteria. The organization of clusters of DnaA boxes was analysed in detail. For 76 chromosomes, a DNA fragment containing multiple DnaA boxes was identified as a putative origin region. Most bacterial chromosomes exhibit an overrepresentation of DnaA boxes; many of them contain at least two clusters of DnaA boxes in the vicinity of the oriC region. The additional clusters of DnaA boxes are probably involved in controlling replication initiation. Surprisingly, the characteristic features of the initiation of replication, i.e. a cluster of DnaA boxes, a dnaA gene and a switch in asymmetry, were not found in some of the analysed chromosomes, particularly those of obligatory intracellular parasites or endosymbionts. This is presumably connected with many mechanisms disturbing DNA asymmetry, translocation or disappearance of the dnaA gene and decay of the Escherichia coli perfect DnaA box pattern

Filtration of Nanoparticle Agglomerates in Aqueous Colloidal Suspensions Exposed to an External Radio-Frequency Magnetic Field

The study investigated the phenomenon of the fast aggregation of single-domain magnetic iron oxide nanoparticles in stable aqueous colloidal suspensions due to the presence of a radio-frequency (RF) magnetic field. Single-domain nanoparticles have specific magnetic properties, especially the unique property of absorbing the energy of such a field and releasing it in the form of heat. The localized heating causes the colloid to become unstable, leading to faster agglomeration of nanoparticles and, consequently, to rapid sedimentation. It has been shown that the destabilization of a stable magnetic nanoparticle colloid by the RF magnetic field can be used for the controlled filtration of larger agglomerates of the colloid solution. Two particular cases of stable colloidal suspensions were considered: a suspension of the bare nanoparticles in an alkaline solution and the silica-stabilized nanoparticles in a neutral solution. The obtained results are important primarily for biomedical applications and wastewater treatment

The Concept of Using 2D Self-Assembly of Magnetic Nanoparticles for Bioassays

It can be observed that magnetic iron-oxide nanoparticles are increasingly used in bioassay methods. This is due to their stability in aqueous solutions, ease of functionalization, biocompatibility and very low toxicity. Here, we show that the recent discovery of the ability of magnetic nanoparticles to self-assemble into 2D structures of ordered chains may be exploited for bioassays. This would open up the possibility of controlled immobilization of proteins, enzymes, DNA or RNA and other molecular systems on spatially ordered nanostructures. In this work, fluorescein was used as an example. Also shown is the possibility of using Raman spectroscopy to analyze material accumulated on such structures. The observed formation of regularly spaced chains of magnetic nanoparticles takes place during the drying process of a thin layer of magnetic liquid placed on an appropriately prepared low-density polyethylene (LDPE) film