Autopoiesis: The organization of living systems,its characterization and a model

We formulate the organization of living organisms through the characterization of the class of autopoietic systems to which living things belong. This general characterization is seen at work in a computer simulated model of a minimal case satisfying the conditions for autopoietic organization.     

Functional organization of cotransmission systems: Lessons from small nervous systems

Small invertebrate nervous systems allow one to ask a series of questions concerning the functional roles of cotransmitters. This review outlines some of the implications of cotransmission for target selectivity in complex neuropils. We suggest the possibility that a unique constellation of cotransmitters in individual identified modulatory neurons allows a specificity of action even when peptides may act over an extended distance, and when individual modulatory substances may be released from several modulatory neurons.     

Chemistry in living systems

Dissecting complex cellular processes requires the ability to track biomolecules as they function within their native habitat. Although genetically encoded tags such as GFP are widely used to monitor discrete proteins, they can cause significant perturbations to a protein's structure and have no direct extension to other classes of biomolecules such as glycans, lipids, nucleic acids and secondary metabolites. In recent years, an alternative tool for tagging biomolecules has emerged from the chemical biology community--the bioorthogonal chemical reporter. In a prototypical experiment, a unique chemical motif, often as small as a single functional group, is incorporated into the target biomolecule using the cell's own biosynthetic machinery. The chemical reporter is then covalently modified in a highly selective fashion with an exogenously delivered probe. This review highlights the development of bioorthogonal chemical reporters and reactions and their application in living systems.     

Biostructural theory of the living systems

Eugen Macovschi is among the few scientists who tried, and partly succeeded, to explain the differences between "dead" and "living" in biological sciences. He discovered and characterized the so-called biostructure of the living bodies and worked out a biostructural theory, which is the first supramolecular conception in biology. Nevertheless, complex biological systems are currently considered only from the molecular point of view, although they may be regarded as specific phenomena on highly structured bodies within the four-dimensional Universe. According to Macovschi, the biostructure provides organisms with life properties and controls their life processes and chemical changes. Nevertheless, plant cells or bacterial ones differ much from the animal or human cells. In fact, there are various biostructures which are related with cell properties. Hence, this theory creates confusions and cannot be easily used to explain all the properties of the biosystems. Consequently, it is our goal to highlight the principles, advantages, limitations, and applications of the biostructural theory, which might support new ideas and theories in modern life sciences.     

15N-NMR studies of living systems

15N-NMR spectroscopy has been applied to the study in vivo of nitrogen uptake during primary and secondary metabolism in Streptomyces parvulus. The nitrogen metabolism of Saccharomyces cerevisiae has been studied in a series of experiments in an effort to elucidate the flow of nitrogen along the various competing pathways as well as its dependence on culture conditions. The low NMR sensitivity of the 15N nucleus required, in spite of high isotopic enrichment, quite long acquisition times (10-20 min). Therefore, an indirect detection method using double quantum 1H-NMR spectroscopy was introduced allowing the selective detection of 15N-bound protons with excellent S/N-ratio in less than a minute.     

The first living systems: a bioenergetic perspective.

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.     

Levels of biological organization and the origin of novelty

The concept of novelty in evolutionary biology pertains to multiple tiers of biological organization from behavioral and morphological changes to changes at the molecular level. Identifying novel features requires assessments of similarity (homology and homoplasy) of relationships (phylogenetic history) and of shared developmental and genetic pathways or networks. After a brief discussion of how novelty is used in recent literature, we discuss whether the evolutionary approach to homology and homoplasy initially formulated by Lankester in the 19th century informs our understanding of novelty today. We then discuss six examples of morphological features described in the recent literature as novelties, and assess the basis upon which they are regarded as novel. The six are: origin of the turtle shell, transition from fish fins to tetrapod limbs, origination of the neural crest and neural crest cells, cement glands in frogs and casquettes in fish, whale bone-eating tubeworms, and the digestion of plant proteins by nematodes. The article concludes with a discussion of means of acquiring novel genetic information that can account for novelty recognized at higher levels. These are co-options of existing genetic circuitry, gene duplication followed by neofunctionalization, gene rearrangements through mobile genetic elements, and lateral gene transfer. We conclude that on the molecular level only the latter category provides novel genetic information, in that there is no homologous precursor. However, novel phenotypes can be generated through both neofunctionalization and gene rearrangements. Therefore, assigning phenotypic or genotypic "novelty" is contingent on the level of biological organization addressed.     

Levels of organization and repetition phenomena in seed plants

Each plant can be recognized by its general shape. Nevertheless, this physiognomy is the result of a very precise structure that expresses the existence of a strong organization. The architecture of a plant depends on the nature and relative arrangement of each of its parts; it is at any given time the result of an equilibrium between endogenous growth processes and the constraints exerted by the environment. Architectural studies have been carried out for some twenty years and have led to the definition of several concepts that provide a powerful tool for studying plant form. The results obtained in this field show that the architecture of a plant can be summarized by a small number of elementary structures: internode, growth unit, axis, architectural model,... In the course of ontogenesis, these structures are repeated and reveal several levels of organization that seem to be only different stages of a common process of growth and transformation.

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Résumé Toute espèce végétale peut être reconnue par sa forme générale. Toutefois, au-delà de cet aspect physionomique, la forme d'une plante repose sur une structure très précise qui traduit l'existence d'une grande organisation. L'architecture d'une plante dépend de la nature et de la position relative de ses différentes parties; elle est à tout instant, l'expression d'un èquilibre entre des processus endogénes de croissance et des contraintes extérieures exercées par le milieu. D'origine assez récente, les études en architecture végétale ont permis de dégager quelques concepts qui rendent compte du développement des végétaux. Les résultats obtenus dans ce domaine montrent que l'architecture d'une plante peut être résumée par un petit nombre de structures élémentaires: entre-noeud, unité de croissance, axe, modèle architectural,... Au cours du développement, ces structures élémentaires se répètent et dérivent les unes des autres traduisant l'existence de plusieurs niveaux d'organisation au sein de l'organisme végétal. L'analyse architecturale permet de révéler et de caractériser ces différents niveaux qui apparaissent alors comme les étapes d'un même processus dans une séquence précise et ordonnée d'événements.

     

Genetic systems of biodegradation: organization and regulation of expression

The review discusses the current state of genetic analysis of degradative processes. Attention is mainly given to the structural and functional organization of the plasmid systems of degradation of organic compounds in gram-negative bacteria. The data available on the regulation mechanisms of D plasmids' metabolic operons, based on the most studied models of xyl and nah operons, are critically analyzed. The problems of evolution of plasmid D systems are considered conceptually as well as the principles of the experimental strategy of developing new metabolic pathways under laboratory conditions. The prospects of constructing the strains capable of efficient degradation of xenobiotics are considered in brief.     

The systems organization of human functions: the theoretical aspects

On the basis of the theory of functional systems, suggested by P. K. Anokhin, leading principals of system organization of human functions are regarded. General characteristics of functional systems are stated. Some peculiarities of intrasystem and intersystem organization of functional systems of human organism are discovered. The role of functional systems in organization of normal human live activity as well as under psychoemotional stress and pathology is shown. System principals of compensation of disordered functions during rehabilitation of persons undergone stresses and ecologically unfavorable loads are considered.     

Nanoscale organization of multiple GPI-anchored proteins in living cell membranes

Cholesterol and sphingolipid-enriched "rafts" have long been proposed as platforms for the sorting of specific membrane components including glycosyl-phosphatidylinositol-anchored proteins (GPI-APs), however, their existence and physical properties have been controversial. Here, we investigate the size of lipid-dependent organization of GPI-APs in live cells, using homo and hetero-FRET-based experiments, combined with theoretical modeling. These studies reveal an unexpected organization wherein cell surface GPI-APs are present as monomers and a smaller fraction (20%-40%) as nanoscale (<5 nm) cholesterol-sensitive clusters. These clusters are composed of at most four molecules and accommodate diverse GPI-AP species; crosslinking GPI-APs segregates them from preexisting GPI-AP clusters and prevents endocytosis of the crosslinked species via a GPI-AP-selective pinocytic pathway. In conjunction with an analysis of the statistical distribution of the clusters, these observations suggest a mechanism for functional lipid-dependent clustering of GPI-APs.     

Some order-disorder considerations in living systems

Order and disorder in biological systems are considered quantitatively in terms of information and entropy. After discussing the factors contributing to the information content of a living cell, a calculation is made of this parameter. The value for a typical bacterial cell is 4.6×10¹⁰ bits. This value is compared with an experimental value of the heat of growth and entropy production ofE. Coli. A discussion of methods of improving the calculation is also presented.