Entity grammar systems: A grammatical tool for studying the hierarchal structures of biological systems

The hierarchal structures of biological systems are the typical complex hierarchal dynamical structures in the physical world, the effective investigations on which could not be performed with the existing formal grammar systems. To meet the needs of the investigation on these kinds of systems, especially the emerging field of system biology, a grammatical tool was proposed in the present article. Because the grammatical toolmainly deals with the systems composed of structured entities, they are called entity grammar systems (EGSs). The structure of entities in EGSs have the general form of the objects in the physical world, which means EGSs could be used as a tool to study the complex system composed of many objects with different structures, just like the biological systems. The article contains the formal definition of EGSs and the hierarchy of EGSs, which is congruent with the Chomsky hierarchy. The relationship between EGSs and array grammar systems, graph grammar systems, tree grammar systems, multi-set grammar systems are discussed to show the generative power of EGSs. At the end of the present article, the steps to define new grammar systems with the form of EGS are provided and the possible applicable fields of EGSs are discussed.     

A model for switch-like phenomena in biological systems.

We present a model for the activity of protein clusters based on a simultaneous desorption of an activator (agonist, substrate molecule, etc.) and an inactivator (antagonist, inhibitor, etc.) caused by the collision or interaction between two effector molecules (e.g. receptors, enzymes). This model gives rise to switch-like dose-response curves, which are difficult to explain by ordinary co-operativity. It fits with recent experimental results obtained on single cells. Some other interesting aspects of the model are also pointed out. The model is similar to the model used to explain steep 'dose-response curves' in heterogeneous catalysis, caused by the reaction between two different molecules or atoms on the surface of the catalyst.     

Catecholamine systems of retina: a model for studying synaptic mechanisms

The retina contains three catecholamine neurotransmitters: dopamine (DA); norepinephrine (NE); and epinephrine (EPI). DA and EPI appear to be associated with separate amacrine neurons that directly participate in the visual process. NE, in contrast, appears to be associated primarily with the sympathetic nerves that innervate the blood vessels of the retina. We present a synopsis of the anatomy, physiology, biochemistry and pharmacology of these retinal neurons. We also suggest that some diseases usually associated with catecholamines of brain may have their counterpart in retina.     

New trends in studying structure and function of biological membranes

Thirty years ago Singer and Nicolson constructed the "fluid mosaic model" of the membrane, which described the structural and functional characteristics of the plasma membrane of non-polarized cells like circulating blood lymphocytes as a fluid lipid phase accommodating proteins with a relatively free mobility. It is a rare phenomenon in biology that such a model could survive 30 years and even today it has a high degree of validity. However, in the light of new data it demands some modifications. In this minireview we present a new concept, which revives the SN model, by shifting the emphasis from fluidity to mosaicism, i.e. to lipid microdomains and rafts. A concise summary of data and key methods is given, proving the existence of non-random co-distribution patterns of different receptor kinds in the microdomain system of the plasma membrane. Furthermore we present evidence that proteins are not only accommodated by the lipid phase, but they are integral structural elements of it. Novel suggestions to the SN model help to develop a modernized version of the old paradigm in the light of new data.     

Cholesterol modulates maculosin's orientation in model systems of biological membranes. Relevance towards putative molecular recognition

Fluorescence techniques were used to study (1) the extent of insertion of the bioactive cyclic dipeptide cyclo(l-tyrosyl-l-prolyl), maculosin, in model systems of membranes of 1, 2-palmitoyl-sn-glycero-3-phosphatidyl choline (DPPC) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl choline (POPC), (2) its in-depth location in those lipidic membranes, and (3) the influence of cholesterol on the dipeptides's location and orientation. Partition into lipidic bilayers is extensive, mainly for liquid crystalline phase membranes (K(p)=1.3x10(4)). Maculosin locates at the lipid head groups level regardless of the membrane system. Nevertheless, its orientation is lipid phase dependent. When maculosin was inserted in liquid crystalline phase bilayers, its phenolic ring was perpendicular to the membrane surface, whereas it changed orientation when inserted in gel phase membranes. Cholesterol was able to reverse the lipid phase influence on maculosin's orientation.     

New model systems for studying the evolutionary biology of aging: Crustacea

Progress in any area of biology has generally required work on a variety of organisms. This is true because particular species often have characteristics that make them especially useful for addressing specific questions. Recent progress in studying the evolutionary biology of senescence has been made through the use of new species, such asCaenorhabditis elegans andDrosophila melanogaster, because of the ease of working with them in the laboratory and because investigators have used theories for the evolution of aging as a basis for discovering the underlying mechanisms.I describe ways of finding new model systems for studying the evolutionary mechanisms of aging by combining the predictions of theory with existing information about the natural history of organisms that are well-suited to laboratory studies. Properties that make organisms favorable for laboratory studies include having a short generation time, high fecundity, small body size, and being easily cultured in a laboratory environment. It is also desirable to begin with natural populations that differ in their rate of aging. I present three scenarios and four groups of organisms which fulfill these requirements. The first two scenarios apply to well-documented differences in age/size specific predation among populations of guppies and microcrustacea. The third is differences among populations of fairy shrimp (anostraca) in habitat permanence. In all cases, there is an environmentla factor that is likely to select for changes in the life history, including aging, plus a target organism which is well-suited for laboratory studies of aging.     

A systems theoretical approach to biological membranes

Zusammenfassung In der vorliegenden Arbeit wird die Eindeutigkeit der Beschreibung erregbarer Membranen mit Hilfe von Ersatzschaltungen untersucht. Bei Voraussetzung der Existenz verschiedener Membrankanäle für den Ionentransport läßt sich unter Berücksichtigung nichtlinearer Eigenschaften eine weitgehend eindeutige Ersatzschaltung für einen Kanal angeben. Als wesentliches Kriterium erweist sich dabei das Vorhandensein eines konstanten Gleichgewichts-potentials für jeden Kanal. Der lonentransport durch die Membran wird durch ein einfaches Elektrodiffusionsmodell beschrieben. Hierin ist der Potentialverlauf in der Membran durch physiko-chemische Eigenschaften der Membran und nicht durch die transportierten Ionen bestimmt. Die Leitfähigkeit eines bestimmten Kanals verändert eine Steuervariable, deren Wert sich mit Hilfe einer algebraischen Beziehung aus den Zustandsvariablen eines linearen Differentialgleichungssystems ergibt (dessen Koeffizienten vom Potential über der Zellmembran abhängen). Die Zusammenfassung mehrerer Kanäle (passives Transportsystem) und die Einführung von Stromgeneratoren für den aktiven Transport (deren Effektivität von der chemischen Zusammensetzung der an die Membran angrenzenden Lösungen abhängt) führt zu einer allgemeinen Ersatzschaltung für die erregbare Membran. Die so gewonnene Beschreibung ist hinreichend allgemeingültig, um als Grundlage für die Analyse von Problemen der Informationsverarbeitung im Nervensystem bzw. für die weitere Aufklärung der in der erregbaren Membran ablaufenden physikalisch-chemischen Prozesse zu dienen.

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Presented in part at the IV. Intern. Biophysics Congress, Moscow, August 1972.     

An osmotic model for the fusion of biological membranes

A molecular model for fusion-fission reactions in membranes is proposed that is based on data from studies on artificially induced cell fusion and on the behaviour of phospholipid bilayers: it is put forward as a framework for further investigations into this fundamental property of biological systems.     

Sphingomyelin-cholesterol interactions in biological and model membranes

Cholesterol and sphingomyelin are both important plasma membrane constituents in cells. It is now becoming evident that these two lipid classes affect each other's metabolism in the cell to an extent that was not previously appreciated. It is the aim of this review to present recent data in the literature concerning both molecular and membrane properties of the two lipid classes, how they interact in membranes (both biological and model), and the consequences their mutual interaction have on different functional and metabolic processes in cells and lipoproteins.     

Relay model of lipid peroxidation in biological membranes

The present study examines the evidence for the important role of free radicals, localized on carbon atoms of the hydrocarbon chains, in lipid peroxidation. These radicals show a great inter- and intramolecular mobility in membranes by the way of relay-transfer (isomerisation). The sequence of intermediate steps of shift of free radicals in membranes with correction for molecular organization of the hydrocarbon zone of membranes, the intramembrane localization of unsaturated links and the gradient of mobility of the hydrocarbon chains are described. The effect of inhibitors in lipid peroxidation are interpreted in terms of decay of hydrocarbon free radicals as a result of its interaction with the antioxidant molecules. The natural antioxidants having a side chain (such as tocopherols) may be regarded as a some kind of "channel" through which free radicals leave the hydrocarbon moiety of the membrane. The processes of lipid peroxidation in membranes are subjected to a great extent to the requirements of the theory of oxidation of solid polymers and hydrocarbons.     

A model for phase transitions in lipid bilayers and biological membranes

We wish to present an order-disorder model for the observed phase transitions in lipid bilayers and biological membranes. We show that the model may, under certain circumstances, exhibit two phase transitions, one corresponding to positional disordering of entire lipid molecules, and the other corresponding to orientational disordering in the hydrocarbon chains. We then give results of our numerical analysis of the model and compare them with experimental data. Shortcomings of the model and future directions for analyses of this type are also discussed.     

Phospholipid spherules (liposomes) as a model for biological membranes

This review describes the properties of artificial spherules composed of phospholipids and various long-chain anions or cations. The lipids, which are in the liquid-crystal state, trap aqueous solutes such as cations, anions, glucose, or glycine in aqueous compartments between a series of lipid bilayers. The diffusion of these solutes from the spherules can be studied in the same way that diffusion across biological membranes is studied. The spherules exhibit many of the properties of natural membrane-bounded structures: they are capable of ion-discrimination, osmotic swelling, and response to a variety of physiologic and pharmacologic agents. These agents (steroids, drugs, toxins, antibiotics) accelerate or retard diffusion of ions or molecules from the spherules in a way that qualitatively mimics their action on erythrocytes, lysosomes, or mitochondria. Thus the spherules constitute a valuable model system with which to study the properties of biological membranes that may be dependent on their lipid components.     

Stochastic model of domain kinetics in biological membranes

A stochastic storage model based on the behavior of macroscopic variables of the system is used to describe the kinetics of raft-like domains in biological membranes. For a simple output model, we examine the features of the system behavior corresponding to the noise-induced nonequilibrium phase transitions. Characteristics of the behavior of the statistical system are obtained: an explicit form of the stationary distribution of the number of domains; ratios for the phase transition points; the expression for the first two moments of the random domain concentration, and the expression for the lifetime of membrane domains in the stationary state.