Self-Organization in Living Cells: Networks of Protein Machines and Nonequilibrium Soft Matter

Microscopic self-organization phenomena inside a living cell should not represent merely a reduced copy of self-organization in macroscopic systems. A cell is populated by active protein machines that communicate via small molecules diffusing through the cytoplasm. Mutual synchronization of machine cycles can spontaneously develop in such networks – an effect which is similar to coherent laser generation. On the other hand, an interplay between reactions, diffusion and phase transitions in biological soft matter may lead to the formation of stationary or traveling nonequilibrium nanoscale structures.     

Instability of bacteriophage lambda initiator O and P proteins in DNA replication

Lambda dv plasmids having an amber mutation in an initiator gene, O or P, were constructed from mutant lambda phages by recombinant DNA techniques and several properties of such derivatives were investigated. These plasmids are perpetuated in suppressor-plus (amber-permissive) cells, but not in non-suppressor cells. The plasmid copy number in the suppressor-plus cells was low as compared to that of the plasmid without the amber mutation. In cells carrying a thermosensitive suppressor 2, raising the temperature is expected to block new production of amber proteins, but should not affect conservation of the protein made prior to heating. It was observed, however, that replication of the plasmids carrying an amber mutation in the O or P gene was abolished soon after raising the temperature, suggesting that neither of the initiator proteins can continue functioning unless replenished. Pulse-chase experiments demonstrated that O protein decays with a half-life of 8 min. Several lines of evidence suggest that this degradation occurs independently of the protein function. On the other hand, P protein was not degraded under the same experimental conditions. These observations are discussed in connection with functional instability of the initiator molecules. It appears that they do not work catalytically.     

Extracellular ion transport

It is a misconception to think that extracellular electric currents of biologic origin are carried by all of the ions in the extracellular medium. It is established that, for certain reasonable boundary conditions, only those ion species that are transported across the plasma membranes of the biological system, or that chemically derive from or contribute to these species, can contribute to the extracellular electric current at steady state. In the absence of convection, the extracellular current will be carried largely by diffusion of the transported ion species, at steady state. Extracellular electric potential gradients are shown to arise in a secondary manner, as a result of the electroneutrality condition. The effect of non-turbulent convection is included in the derivations and discussion.     

The topology of circular DNA]

A non-orientable structure, said M?bius stripe, is proposed for certain types of circular DNA. This structure could account for particular forms, such as dimers, double length molecules, or catenans which are molecules topologically interwomen. On the other hand, it is suggested that a second structure derived from the same principal of non-orientability could have gendered the dynamics of DNA replication at the origin of life: this is hypothesis of archetype M?bius strip.     

Unsteady Convection Flow and Heat Transfer over a Vertical Stretching Surface

This paper investigates the effect of thermal radiation on unsteady convection flow and heat transfer over a vertical permeable stretching surface in porous medium, where the effects of temperature dependent viscosity and thermal conductivity are also considered. By using a similarity transformation, the governing time-dependent boundary layer equations for momentum and thermal energy are first transformed into coupled, non-linear ordinary differential equations with variable coefficients. Numerical solutions to these equations subject to appropriate boundary conditions are obtained by the numerical shooting technique with fourth-fifth order Runge-Kutta scheme. Numerical results show that as viscosity variation parameter increases both the absolute value of the surface friction coefficient and the absolute value of the surface temperature gradient increase whereas the temperature decreases slightly. With the increase of viscosity variation parameter, the velocity decreases near the sheet surface but increases far away from the surface of the sheet in the boundary layer. The increase in permeability parameter leads to the decrease in both the temperature and the absolute value of the surface friction coefficient, and the increase in both the velocity and the absolute value of the surface temperature gradient.     

Absorption and magnetic circular dichroism spectra of hemoproteins in nonequilibrium states. V. Cytochrome P450 and its substrate complex

It was shown that ferrocytochrome P450 forms a nonequilibrium state if ferrocytochrome P450 and its complexes are reduced in freezed water-glycerol solutions by thermolysed electrons, arising during gamma-radiolysis of the matrix at 77 degrees K. Unlike the equilibrium form of ferrocytochrome P450 with the heme iron at the high-spin state the reduced nonequilibrium form of the protein contains the heme iron at a low-spin state. The absorption spectrum of ferrocytochrome P450 in the nonequilibrium state is characterized by alpha and beta-bands at 562 and 534 nm, respectively, whereas the magnetic circular dichroism spectra exhibit type A effect at 562 nm. Upon temperature increasing the nonequilibrium state is relaxed to the equilibrium one. Type 1 substrates had practically no influence on the spectral characteristic of the nonequilibrium form of ferrocytochrome P450. Binding of type 2 substrates results in an essential decrease of the intensity ratio of the alpha- and beta-bands (A alpha/A beta) and is accompanied by a red-shift of the alpha-band and corresponding magnetic circular dichroism effect. It was shown that mercaptoethanol complex of hemoglobin, formed by reduction at 77 degrees K is spectrally similar to the nonequilibrium ferrocytochrome P450 complex with type 2 substrates. From analysis of experimental data one can conclude that (i) the ligand environment of heme iron in oxidased and reduced cytochrome P450 are different; (ii) the sixth axial ligand of the heme iron in the oxidised protein is probably a water molecule (OH-) attached by a hydrogen bond to the neighbouring histidine. It is assumed that a similar nonequilibrium form of cytochrome P450 can be formed in physiological conditions.     

Conjugate Effects of Heat and Mass Transfer on MHD Free Convection Flow over an Inclined Plate Embedded in a Porous Medium

The aim of this study is to present an exact analysis of combined effects of radiation and chemical reaction on the magnetohydrodynamic (MHD) free convection flow of an electrically conducting incompressible viscous fluid over an inclined plate embedded in a porous medium. The impulsively started plate with variable temperature and mass diffusion is considered. The dimensionless momentum equation coupled with the energy and mass diffusion equations are analytically solved using the Laplace transform method. Expressions for velocity, temperature and concentration fields are obtained. They satisfy all imposed initial and boundary conditions and can be reduced, as special cases, to some known solutions from the literature. Expressions for skin friction, Nusselt number and Sherwood number are also obtained. Finally, the effects of pertinent parameters on velocity, temperature and concentration profiles are graphically displayed whereas the variations in skin friction, Nusselt number and Sherwood number are shown through tables.     

Equations of heat distribution within the body

A vector integral equation describing heat distribution within the body has been derived. The factors considered are heat conduction, forced convection via the circulatory system, environmental exchange, metabolic heat production, and change in heat content. The vector partial differential equation and alternative forms incorporating boundary conditions were also developed. A difference equation based on a first-order approximation to the fundamental equations was derived to form the basis of a model for heat distribution within the body. It has been shown that factors involving conduction and convection must be considered independently unless the temperature of the blood flowing from a region of the body is equal to the average temperature of the tissue in that region. If this relation between tissue and blood temperature does exist, only a single temperature from each eleeent is needed to describe the heat distribution. In this latter case, models which ascribe all heat transfer to “equivalent” conduction or to convection can give valid predictions.     

Surface of the Pacific Ocean and physical mechanisms of prebiological evolution

The hypothesis about the spontaneous generation of living cell predecessors on the ocean surface during prebiological evolution is further developed. Data obtained in experiments and observations are given that support our point of view. It is shown that the physicochemical properties of the nonequilibrium ocean-atmosphere boundary including ionic asymmetry, fractionation of enantiomers of amino and nucleic acids, and the formation of sealed vesicles provide conditions under which the spontaneous generation seems quite possible.     

Boundary Layer Flow Past a Stretching Surface in a Porous Medium Saturated by a Nanofluid: Brinkman-Forchheimer Model

In this study, the steady forced convection flow and heat transfer due to an impermeable stretching surface in a porous medium saturated with a nanofluid are investigated numerically. The Brinkman-Forchheimer model is used for the momentum equations (porous medium), whereas, Bongiorno’s model is used for the nanofluid. Uniform temperature and nanofluid volume fraction are assumed at the surface. The boundary layer equations are transformed to ordinary differential equations in terms of the governing parameters including Prandtl and Lewis numbers, viscosity ratio, porous medium, Brownian motion and thermophoresis parameters. Numerical results for the velocity, temperature and concentration profiles, as well as for the reduced Nusselt and Sherwood numbers are obtained and presented graphically.     

外泌体：病毒与宿主博弈的另一“角斗场”

外泌体是一类小型的细胞外囊泡,可以包裹蛋白质、核酸等生物活性分子随体液循环到达机体各处,具有广泛的信息传递作用。研究发现,外泌体在病毒感染宿主的过程中也扮演着重要的角色。病毒需要在宿主细胞内完成复制周期并释放子代病毒,而这一过程与外泌体的产生及分泌途径有共通的部分。一方面,病毒可以"挟持"外泌体并将自身成分装入其中,逃避宿主的免疫应答,促进其在细胞间的传播。另一方面,宿主细胞也可利用外泌体传递抗病毒因子以抑制病毒感染。文中旨在从病毒与宿主两方面阐述外泌体在病毒感染宿主过程中的作用,以期为该领域的研究提供新的思路。     

Replication in the phloem is not necessary for efficient vascular transport of tobacco mosaic tobamovirus

Plant viruses move systemically from one leaf to another via phloem. However, the viral functions needed for systemic movement are not fully elucidated. An experimental system was designed to study the effects of low temperature on the vascular transport of the tobacco mosaic tobamovirus (TMV). Vascular transport of TMV from lower inoculated leaves to upper non-inoculated leaves via a stem segment kept at low temperature (4 degrees C) was not affected. On the other hand, several experiments were performed on tobacco leaves to demonstrate that virus replication did not occur at the same temperature. The data suggest that replication of TMV in the phloem of wild-type tobacco plants is not necessary for the vascular transport of TMV, and that the virus moves with photoassimilates as suggested previously.     

Mesoscopic biochemical basis of isogenetic inheritance and canalization: stochasticity, nonlinearity, and emergent landscape

Biochemical reaction systems in mesoscopic volume, under sustained environmental chemical gradient(s), can have multiple stochastic attractors. Two distinct mechanisms are known for their origins: (a) Stochastic single-molecule events, such as gene expression, with slow gene on-off dynamics; and (b) nonlinear networks with feedbacks. These two mechanisms yield different volume dependence for the sojourn time of an attractor. As in the classic Arrhenius theory for temperature dependent transition rates, a landscape perspective provides a natural framework for the system's behavior. However, due to the nonequilibrium nature of the open chemical systems, the landscape, and the attractors it represents, are all themselves emergent properties of complex, mesoscopic dynamics. In terms of the landscape, we show a generalization of Kramers' approach is possible to provide a rate theory. The emergence of attractors is a form of self-organization in the mesoscopic system; stochastic attractors in biochemical systems such as gene regulation and cellular signaling are naturally inheritable via cell division. Delbrück-Gillespie's mesoscopic reaction system theory, therefore, provides a biochemical basis for spontaneous isogenetic switching and canalization.     

An optimal degree of physical and chemical heterogeneity for the origin of life?

The accumulation of pure, concentrated chemical building blocks, from which the essential components of protocells could be assembled, has long been viewed as a necessary, but extremely difficult step on the pathway to the origin of life. However, recent experiments have shown that moderately increasing the complexity of a set of chemical inputs can in some cases lead to a dramatic simplification of the resulting reaction products. Similarly, model protocell membranes composed of certain mixtures of amphiphilic molecules have superior physical properties than membranes composed of single amphiphiles. Moreover, membrane self-assembly under simple and natural conditions gives rise to heterogeneous mixtures of large multi-lamellar vesicles, which are predisposed to a robust pathway of growth and division that simpler and more homogeneous small unilamellar vesicles cannot undergo. Might a similar relaxation of the constraints on building block purity and homogeneity actually facilitate the difficult process of nucleic acid replication? Several arguments suggest that mixtures of monomers and short oligonucleotides may enable the chemical copying of polynucleotides of sufficient length and sequence complexity to allow for the emergence of the first nucleic acid catalysts. The question of the origin of life may become less daunting once the constraints of overly well-defined laboratory experiments are appropriately relaxed.     

Some factors affecting oxygen uptake by red blood cells in the pulmonary capillaries

In this study we investigate the equations governing the transport of oxygen in pulmonary capillaries. We use a mathematical model consisting of a red blood cell completely surrounded by plasma within a cylindrical pulmonary capillary. This model takes account of convection and diffusion of oxygen through plasma, diffusion of oxygen through the red blood cell, and the reaction between oxygen and haemoglobin molecules. The velocity field within the plasma is calculated by solving the slow flow equations. We investigate the effect on the solution of the governing equations of: (i) mixed-venous blood oxygen partial pressure (the initial conditions); (ii) alveolar gas oxygen partial pressure (the boundary conditions); (iii) neglecting the convection term; and (iv) assuming an instantaneous reaction between the oxygen and haemoglobin molecules. It is found that: (a) equilibrium is reached much more rapidly for high values of mixed-venous blood and alveolar gas oxygen partial pressure; (b) the convection term has a negligible effect on the time taken to reach a prescribed degree of equilibrium; and (c) an instantaneous reaction may be assumed. Explanations are given for each of these results.     

The effects of chemical kinetics on oxygen delivery to tissue.

A mathematical model has been formulated to analyze the effect of nonequilibrium kinetics on oxygen delivery to tissue. The model takes into account molecular diffusion, facilitated diffusion in the capillary blood, convection, chemical kinetics of O2 with hemoglobin, and the rate of metabolic consumption. A line iterative technique is described to solve numerically the resulting coupled system of nonlinear partial differential equations with physiologically relevant boundary and entrance conditions. With nonequilibrium kinetics the end-capillary PO2 is found to be lower than that in the venous blood. The effect is more pronounced during hypoxia and anemia. It is found that the tissue PO2 at the lethal corner decreases with the decrease in blood velocity, arterial PO2, hemoglobin concentration, P50, and increase in COHb concentration or metabolic rate, while the difference between end-capillary PO2 and venous PO2 increases, which reflects the effect of nonequilibrium kinetics on the delivery of O2 to tissue. Thus, the consideration of venous PO2 as an indicator of tissue PO2 in clinical and experimental studies may be questionable.     

Effects of synthetic bioactive lipids on the activity of D-beta-hydroxybutyrate dehydrogenase, a membrane enzyme

The structural requirements of lecithins analogs for purified D-beta-hydroxybutyrate dehydrogenase activation have been studied with chemically defined phospholipids. It appears that the trimethylamine group of choline can be changed by a pyridinium group. On the other hand, the decrease of density of the positive charges on the liposomes surface obtained by dilution of such bearing molecules with negative or non charged phospholipids increases the enzyme reactivation. Finally, the PAF acether, a lipid mediator, is able to reactivate the enzyme in similar conditions as these obtained with mitochondrial phosphatidylcholines.     

Hetero-alpha-helical, two-chain, coiled coils: alpha beta hybrid tropomyosin

The nature of the interhelix interaction in two-chain, α-helical, coiled coils is studied by experiments on the formation of hydrid molecules in which one helical chain is an α-tropomyosin and the other a β-tropomoysin. By means of a recently developed assay, the population of heterohelical (i.e., αβ hybrid) molecules relative to their homohelical (αα and ββ) parent species is determined under a variety of conditions, both equilibrium and nonequilibrium. It is found that mixed intact αα and ββ molecules do not form hybrid species in detectible amounts even after incubation at room temperature (or below) for periods of over one week. That the lack of αβ species in this “native-exchange” system is a result of a kinetic barrier is evident from experiments involving a thermal denaturation–renaturation cycle in which the largely dissociated, unfolded chains at higher temperature are annealed to benign temperatures over a period of 6 h, thus assuring an equilibrium population of two-chain species. In the resulting equilibrium state, the αβ population is one-half the total, indicating that recombination is random. Furthermore, this same (equilibrium) state is reached if the separated, mostly unfolded chains are renatured by a rapid (～ 40 s) quench to benign temperatures. Some implications of these results for the thermodynamics of interhelix interation, for kinetics of chain dissociation and recombination, and for in vivo genesis of two-chain coiled coils are discussed.