Self-organization in biological systems

Biological systems are considered that are capable of dynamic self-organization, i.e., spontaneous emergence of spatio-temporal order with the formation of various spatio-temporal patterns. A cell is involved in the organization of ontogenesis of all stages. Embryonic cells exhibit coordinated social behavior and generate ordered morphological patterns displaying variability and equifinality of development. Physical and topological patterns are essential for biological systems as an imperative that restricts and directs biological morphogenesis. Biological self-organization is directed and fixed by natural selection during which selection of the most sustainable, flexible, modular systems capable of adaptive self-organization occurs.     

Taking the example of computer systems engineering for the analysis of biological cell systems

In this paper, we discuss the potential for the use of engineering methods that were originally developed for the design of embedded computer systems, to analyse biological cell systems. For embedded systems as well as for biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. In contrast to the biology domain, the computer engineering domain has the opportunity to quickly evaluate design options and consequences of its systems by methods for computer aided design and in particular design space exploration. We argue that there are enough concrete similarities between the two systems to assume that the engineering methodology from the computer systems domain, and in particular that related to embedded systems, can be applied to the domain of cellular systems. This will help to understand the myriad of different design options cellular systems have. First we compare computer systems with cellular systems. Then, we discuss exactly what features of engineering methods could aid researchers with the analysis of cellular systems, and what benefits could be gained.     

Taking the example of computer systems engineering for the analysis of biological cell systems

In this paper, we discuss the potential for the use of engineering methods that were originally developed for the design of embedded computer systems, to analyse biological cell systems. For embedded systems as well as for biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. In contrast to the biology domain, the computer engineering domain has the opportunity to quickly evaluate design options and consequences of its systems by methods for computer aided design and in particular design space exploration. We argue that there are enough concrete similarities between the two systems to assume that the engineering methodology from the computer systems domain, and in particular that related to embedded systems, can be applied to the domain of cellular systems. This will help to understand the myriad of different design options cellular systems have. First we compare computer systems with cellular systems. Then, we discuss exactly what features of engineering methods could aid researchers with the analysis of cellular systems, and what benefits could be gained.     

Human identity testing with PCR-based systems

Large numbers of repetitive stretches of DNA are present within the human genome that are associated with human individuality due to their polymorphic character. Approximately one-third of these repeat sequences is arranged as microsatellites or short tandem repeats (STRs) whose valuable application as state-of-the-art technique in human identity testing will be briefly summarized in this review. Prerequisties for successful DNA typing using STRs amplified by polymerase chain reaction (PCR) are outlined and particular attention is paid to the molecular structure of STRs from autosomes as well as from the Y chromosome. A comprehensive overview about current and emerging methods of STR analysis is given as well.     

Maxwell's demon in biological systems

Summary Boltzmann's gas model representing the second law of thermodynamics is based on the improbability of certain molecular distributions in space. Maxwell argued that a hypothetical being with the faculty of seeing individual molecules (Maxwell's Demon) could bring about such improbable distributions, thus violating the law of entropy. However, it appears that to render the molecules visible for any observer would increase the entropy more than the demon could decrease it, hence Maxwell's Demon cannot operate (Brillouin, 1951). In the study presented here Maxwell's Demon is interpreted in a general way as a biological observer system within (possibly closed) systems which can upset thermodynamic probabilities provided that the relative magnitudes between observer system and observed system are appropriate.Maxwell's Demon within Boltzmann's Gas Model thus appears only as a special case of inappropriate, relative magnitude between the two systems.     

Histidine phosphorylation in biological systems

Histidine phosphorylation is important in prokaryotes and occurs to the extent of 6% of total phosphorylation in eukaryotes. Nevertheless phosphohistidine residues are not normally observed in proteins due to rapid hydrolysis of the phosphoryl group under acidic conditions. Many rapid processes employ phosphohistidines, including the bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS), the bacterial two-component systems and reactions catalyzed by enzymes such as nucleoside diphosphate kinase and succinyl-CoA synthetase. In the PTS, the NMR structure of the phosphohistidine moiety of the phosphohistidine-containing protein was determined but no X-ray structures of phosphohistidine forms of PTS proteins have been elucidated. There have been crystal structures of a few phosphohistidine-containing proteins determined: nucleoside diphosphate kinase, succinyl-CoA synthetase, a cofactor-dependent phosphoglycerate mutase and the protein PAE2307 from the hyperthermophilic archaeon Pyrobaculum aerophilum. A common theme for these stable phosphohistidines is the occurrence of ion-pair hydrogen bonds (salt bridges) involving the non-phosphorylated nitrogen atom of the histidine imidazole ring with an acidic amino acid side chain.     

Information compression in biological systems

In biological systems a high coordination between their individual parts occurs. The concept of coordination can be given a rigorous mathematical basis by the concept of order parameters and the slaving principle. We calculate the information of the total system in terms of order parameters and slaved subsystems. When qualitative changes of a system happen, the information change is given by that of the order parameter alone and may amount to few bits only.     

Thermodynamic calculations in biological systems

The ability to compute intra- and inter-molecular interactions provides the opportunity to gain a deeper understanding of previously intractable problems in biochemistry and biophysics. This review presents three examples in which molecular dynamics calculations were used to gain insight into the atomic detail underlying important experimental observations. The three examples are the following: (1) Entropic contribution to rate acceleration that results from conformational constraints imposed on the reactants; (2) Mechanism of force unfolding of a small protein molecule by the application of a force that separates its N- and C-terminals; and (3) Loss of translational entropy experienced by small molecules when they bind to proteins.     

Heme-based sensors in biological systems

The past several years have been witness to a staggering rate of advancement in the understanding of how organisms respond to changes in the availability of diatomic molecules that are toxic and/or crucial to survival. Heme-based sensors presently constitute the majority of the proteins known to sense NO, O2 and CO and to initiate the chemistry required to adapt to changes in their availabilities. Knowledge of the three characterized members of this class, soluble guanylate cyclase, FixL and CooA, has grown substantially during the past year. The major advances have resulted from a broad range of approaches to elucidation of both function and mechanism. They include growth in the understanding of the interplay between the heme and protein in soluble guanylate cyclase, as well as alternate means for its stimulation. Insight into the O2-induced structural changes in FixL has been supplied by the single crystal structure of the heme domain of Bradyrhizobium japonicum. Finally, the ligation environment and ligand interchange that facilitates CO sensing by CooA has been established by spectroscopic and mutagenesis techniques.     

Redox processes in biological systems

General principles of organization and distinctive features of the redox processes of biological systems are discussed. We paid special attention to the most examined parts of redox biology. As one of the approaches to the generalization of accumulated knowledge about redox processes, the so-called redox hypothesis of oxidative stress was examined. Extrapolation of this hypothesis on the processes taking place in plant cells, formulated on the basis of thiol-disulfide metabolism of animal cells, may help to systematize the available knowledge about redox processes in plants.