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.

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.

Auxetic and other mechanical metamaterials are typically studied in situations where they are subjected solely to mechanical forces or displacements even though they may be designed to exhibit additional anomalous behaviour or tunability when subjected to other disturbances such as changes in temperature or magnetic fields. It is shown that externally applied magnetic fields can tune the geometry and macroscopic properties of known auxetics that incorporate magnetic component/s, thus resulting in a change of their macroscopic properties. Anomalous properties which are observed in such novel magneto-mechanical systems include tunable Poisson's ratios, bi-stability or multi-stability, depending on the applied magnetic fields, and other electromagnetic-mechanical effects such as strain dependent induced electric currents and magnetic fields. The properties exhibited depend, amongst other things, on the relative position and orientation of the magnetic insertion/s within the structure, the geometry of the system and the magnetic strength of the magnetic components, including that of the external magnetic field.

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.

In a recent paper we have estimated the total number of protein coding open reading frames (ORFs) in the Saccharomyces cerevisiae genome, based on their properties, at about 4800. This number is much smaller than the 5800-6000 which is widely accepted. In this paper we analyse differences between the set of ORFs with known phenotypes annotated in the Munich Information Centre for Protein Sequences (MIPS) database and ORFs for which the probability of coding, counted by us, is very low. We have found that many of the latter ORFs have properties of antisense sequences of coding ORFs, which suggests that they could have been generated by duplication of coding sequences. Since coding sequences generate ORFs inside themselves, with especially high frequency in the antisense sequences, we have looked for homology between known proteins and hypothetical polypeptides generated by ORFs under consideration in all the six phases. For many ORFs we have found paralogues and orthologues in phases different than the phase which had been assumed in the MIPS database as coding.

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This work discusses the concept of allowing the control of the stiffness of a particular class of re-entrant auxetic magneto-mechanical metamaterials through the introduction of magnets to the system. It is shown, through experimental testing backed up by a theoretical model, that the appropriate insertion of magnets in such a system will alter its stiffness, possibly even making it exhibit ‘negative stiffness’. This leads to a completely different behaviour of the structure in terms of stability. It is also reported that the investigated mechanical metamaterials may exhibit both negative stiffness and negative Poisson's ratio at the same time. Moreover, it is shown that the effect which magnets have on the stiffness of the system may be fine-tuned upon replacing magnets with electromagnets. Such systems have the potential to be used in a wide range of practical applications such as vibration damping devices where achieving a negative stiffness is of fundamental importance.

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