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.

Extremely Non-Auxetic Behavior of a Typical Auxetic Microstructure Due to Its Material Properties.

The re-entrant honeycomb microstructure is one of the most famous, typical examples of an auxetic structure. The re-entrant geometries also include other members as, among others, the star re-entrant geometries with various symmetries. In this paper, we focus on one of them, having a 6-fold symmetry axis. The investigated systems consist of binary hard discs (two-dimensional particles with two slightly different sizes, interacting through infinitely repulsive pairwise potential), from which different structures, based on the mentioned geometry, were formed. To study the elastic properties of the systems, computer simulations using the Monte Carlo method in isobaric-isothermal ensemble with varying shape of the periodic box were performed. The results show that all the considered systems are isotropic and not auxetic-their Poisson's ratio is positive in each case. Moreover, Poisson's ratios of the majority of examined structures tend to +1 with increasing pressure, which is the upper limit for two-dimensional isotropic media, thus they can be recognized as the ideal non-auxetics in appropriate thermodynamic conditions. The results obtained contradict the common belief that the unique properties of metamaterials result solely from their microstructure and indicate that the material itself can be crucial.

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.

Controllable Hierarchical Mechanical Metamaterials Guided by the Hinge Design.

In this work, we use computer simulations (Molecular Dynamics) to analyse the behaviour of a specific auxetic hierarchical mechanical metamaterial composed of square-like elements. We show that, depending on the design of hinges connecting structural elements, the system can exhibit a controllable behaviour where different hierarchical levels can deform to the desired extent. We also show that the use of different hinges within the same structure can enhance the control over its deformation and mechanical properties, whose results can be applied to other mechanical metamaterials. In addition, we analyse the effect of the size of the system as well as the variation in the stiffness of its hinges on the range of the exhibited auxetic behaviour (negative Poisson's ratio). Finally, it is discussed that the concept presented in this work can be used amongst others in the design of highly efficient protective devices capable of adjusting their response to a specific application.

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.

The Effect of Fe3O4 Nanoparticles on Survival of Probiotic Bacteria Lactobacillus acidophilus PCM2499 at Lower pH.

This paper presents a description of an experiment in which the survival rate of the probiotic bacteria Lactobacillus acidophilus PCM2499 was increased only due to the presence of Fe3O4 magnetic nanoparticles. The survival rate increased from 1.3 to 10 times compare to the control. It has been shown that the minimum concentration of NPs with a positive effect equals 8 mg/ml and the maximum concentration of the NPs equals 24 mg/ml.

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

BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.

Higher mutation rate helps to rescue genes from the elimination by selection.

Directional mutation pressure associated with replication processes is the main cause of the asymmetry between the leading and lagging DNA strands in bacterial genomes. On the other hand, the asymmetry between sense and antisense strands of protein coding sequences is a result of both mutation and selection pressures. Thus, there are two different ways of superposition of the sense strand, on the leading or lagging strand. Besides many other implications of these two possible situations, one seems to be very important - because of the asymmetric replication-associated mutation pressure, the mutation rate of genes depends on their location. Using Monte Carlo methods, we have simulated, under experimentally determined directional mutation pressure, the divergence rate and the elimination rate of genes depending on their location in respect to the leading/lagging DNA strands in the asymmetric prokaryotic genome. We have found that the best survival strategy for the majority of genes is to sometimes switch between DNA strands. Paradoxically, this strategy results in higher substitution rates but remains in agreement with observations in bacterial genomes that such inversions are very frequent and divergence rate between homologs lying on different DNA strands is very high.

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 gamma 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.

Effect of variable surrounding on species creation.

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 x4 + 1/2 b(t)x2, where x represents phenotype and the coefficient b(t) shows the cos(omega t) 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 omega. 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 aR 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.

Representation of mutation pressure and selection pressure by PAM matrices.

This paper analyses the relationship between the mutation data matrix 1PAM/PET91, representing the effect of both mutation and selection pressures exerted on 16130 homologous proteins of different organisms, and a mutation probability matrix (1PAM/MPM) representing the effect of pure mutation pressure on protein coding of the Borrelia burgdorferi genome. The 1PAM/PMP matrix was derived with the help of computer simulations, which used empirical nucleotide substitution rates found for the B. burgdorferi genome. Here, it is shown that the frequency of amino acid occurrence is strongly related to their effective survival time. We found that the shorter the turnover time of an amino acid under pure mutation pressure, the lower its fraction in the proteins coded by the genome and the more protected by selection pressure is its position in proteins. Results of analyses suggest that during evolution the mutational pressure has been optimised to some extent to the selection requirements.

High divergence rate of sequences located on different DNA strands in closely related bacterial genomes.

One of the common features of bacterial genomes is a strong compositional asymmetry between differently replicating DNA strands (leading and lagging). The main cause of the observed bias is the mutational pressure associated with replication. This suggests that genes translocated between differently replicating DNA strands are subjected to a higher mutational pressure, which may influence their composition and divergence rate. Analyses of groups of completely sequenced bacterial genomes have revealed that the highest divergence rate is observed for the DNA sequences that in closely related genomes are located on different DNA strands in respect to their role in replication. Paradoxically, for this group of sequences the absolute values of divergence rate are higher for closely related species than for more diverged ones. Since this effect concerns only the specific group of orthologs, there must be a specific mechanism introducing bias into the structure of chromosome by enriching the set of homologs in trans position in newly diverged species in relatively highly diverged sequences. These highly diverged sequences may be of varied nature: (1) paralogs or other fast-evolving genes under weak selection; or (2) pseudogenes that will probably be eliminated from the genome during further evolution; or (3) genes whose history after divergence is longer than the history of the genomes in which they are found. The use of these highly diverged sequences for phylogenetic analyses may influence the topology and branch length of phylogenetic trees. The changing mutational pressure may contribute to arising of genes with new functions as well.

Rearrangements between differently replicating DNA strands in asymmetric bacterial genomes.

Many bacterial genomes are under asymmetric mutational pressure which introduces compositional asymmetry into DNA molecule resulting in many biases in coding structure of chromosomes. One of the processes affected by the asymmetry is translocation changing the position of the coding sequence on chromosome in respect to the orientation on the leading and lagging DNA strand. When analysing sets of paralogs in 50 genomes, we found that the number of observed genes which switched their positions on DNA strand is lowest for genomes with the highest DNA asymmetry. However, the number of orthologs which changed DNA strand increases with the phylogenetic distance between the compared genomes. Nevertheless, there is a fraction of coding sequences that stay on the leading strand in all analysed genomes, whereas there are no sequences that stay always on the lagging strand. Since sequences diverge very fast after switching the DNA strand, this bias in mobility of sequences is responsible, in part, for higher divergence rates among some of coding sequences located on the lagging DNA strand.

How many protein-coding genes are there in the Saccharomyces cerevisiae genome?

We have compared the results of estimations of the total number of protein-coding genes in the Saccharomyces cerevisiae genome, which have been obtained by many laboratories since the yeast genome sequence was published in 1996. We propose that there are 5300-5400 genes in the genome. This makes the first estimation of the number of intronless ORFs longer than 100 codons, based on the features of the set of genes with phenotypes known in 1997 to be correct. This estimation assumed that the set of the first 2300 genes with known phenotypes was representative for the whole set of protein-coding genes in the genome. The same method used in this paper for the approximation of the total number of protein-coding sequences among more than 40 000 ORFs longer than 20 codons gives a result that is only slightly higher. This suggests that there are still some non-coding ORFs in the databases and a few dozen small ORFs, not yet annotated, which probably code for proteins.