Characterization of hydroxyl free radical mediated damage to plasmid pBR322 DNA

We have investigated hydroxyl free radical mediated damage to pBR322 DNA produced by ascorbate/iron and oxygen in a phosphate-buffered in vitro system. An observed lag phase in DNA nicking suggests a multi-target model of hydroxyl free radical attack on DNA. In the present report we further examine the model system and show that there is a "heat labile" component of the ascorbate/iron system which can be completely restored by the readdition of ascorbate. These observations have allowed us to rule out the possibility that intermediates build up in the reaction and act independently of ascorbate to increase the reaction rate. We have investigated the initial rate of OH production with two OH trapping agents, salicylate and deoxyguanosine, and find that the lag in DNA nicking is not due to a corresponding lag in the production of OH as assessed by formation of the products, dihydroxybenzoic acids and 8-hydroxydeoxyguanosine, respectively. We have found that the energy of activation for DNA supercoiled nicking is 13.9 kcal/mole and for OH trapping by salicylate is 21.1 kcal/nmole. These two activation energies are sufficiently different to suggest that the rate-limiting steps of these two reactions are different. Investigation of the rate of oxygen consumption during the ascorbate/iron-mediated DNA damage showed that oxygen was not a limiting component at any point in the reaction. The addition of catalase slowed down oxygen consumption by 31% and this data taken together with our previous observations on the model implicate hydrogen peroxide as a key intermediate in DNA damage caused by hydroxyl free radical.     

Urocanic acid as an efficient hydroxyl radical scavenger: a quantum theoretical study

The photoisomerization of urocanic acid (UCA)—which is present in human skin epidermis, where it acts as a sunscreen—from its trans isomer to its cis isomer upon exposure to UV-B radiation is known to cause immunosuppression. In recent years, the antioxidant properties of UCA (it acts as a hydroxyl radical scavenger) have also been recognized. In view of this, the mechanisms of stepwise reactions of trans-UCA with up to four hydroxyl radicals were investigated. The molecular geometries of the different species and complexes involved in the reactions (reactant, intermediate and product complexes, as well as transition states) were optimized via density functional theory in the gas phase. Solvation in aqueous media was treated with single point energy calculations using DFT and the polarizable continuum model. Single point energy calculations in the gas phase and aqueous media were also carried out using second-order Møller–Plesset perturbation theory (MP2). The AUG-cc-pVDZ basis set was employed in all calculations. Corrections for basis set superposition error (BSSE) were applied. Vibrational frequency analysis was performed for each optimized structure to ensure the validity of the optimized transition states. It was found that the binding of the first OH· radical to UCA involves a positive energy barrier, while subsequent reactions of OH· radicals are exergonic. Transition states were successfully located, even in those cases where the barrier energies were found to be negative. The cis–trans isomerization barrier energy of UCA and that of the first OH· radical addition to UCA are comparable, meaning that both processes can occur simultaneously. It was found that UCA could serve as an antioxidant in the form of an efficient OH· radical scavenger.     

Synchrotron X-ray and neutron small-angle scattering of lyotropic lipid mesophases, model biomembranes and proteins in solution at high pressure

In this review we discuss the use of X-ray and neutron diffraction methods for investigating the temperature- and pressure-dependent structure and phase behaviour of lipid and model biomembrane systems. Hydrostatic pressure has been used as a physical parameter for studying the stability and energetics of lipid mesophases, but also because high pressure is an important feature of certain natural membrane environments and because the high pressure phase behaviour of biomolecules is of importance for several biotechnological processes. Using the pressure jump relaxation technique in combination with time-resolved synchrotron X-ray diffraction, the kinetics of different lipid phase transformations was investigated. The techniques can also be applied to the study of other soft matter and biomolecular phase transformations, such as surfactant phase transitions and protein un/refolding reactions. Several examples are given. In particular, we present data on the pressure-induced unfolding and refolding of small proteins, such as Snase. The data are compared with the corresponding results obtained using other trigger mechanisms and are discussed in the light of recent theoretical approaches.     

Synthesis and purification of fluorinated benzimidazole and benzene nucleoside-5'-triphosphates

The expression "universal base" is very often used to express hybridization properties and recognition patterns of nucleosides. Their behaviour in biological applications, however, is of great interest regarding, e.g.,' their incorporation by polymerases. The 4,6-difluorobenzimidazole and the 2,4-difluorobenzene nucleoside analogues have proven to be universal bases that do not discriminate between the four natural nucleobases in RNA duplexes. Therefore, we synthesized the corresponding triphosphates to evaluate their behavior in polymerase catalyzed reactions and to investigate their ability to serve as substrates for the T7 RNA polymerase.     

Age structure effects in predator-prey interactions

A mathematical model of predator-prey interactions is proposed which incorporates both age structure in the predators and density dependence in the prey. The properties of the model are investigated by a linearized analysis, which enables the conditions for stability to be formulated. The analysis indicates that for a substantial domain of parameter space, a stable equilibrium is possible with the prey well below its carrying capacity. The effect of violating the stability conditions on the behaviour of the model was investigated by computer simulation. Two further types of behaviour are noted in which coexistence is possible. The first is a two point limit cycle in which young and old predators occur in alternate time periods. The second involves a limit cycle in which the component population trajectories lie on closed curves in phase space.     

A first formal link between the price equation and an optimization program

The Darwin unification project is pursued. A meta-model encompassing an important class of population genetic models is formed by adding an abstract model of the number of successful gametes to the Price equation under uncertainty. A class of optimization programs are defined to represent the "individual-as-maximizing-agent analogy" in a general way. It is then shown that for each population genetic model there is a corresponding optimization program with which formal links can be established. These links provide a secure logical foundation for the commonplace biological principle that natural selection leads organisms to act as if maximizing their "fitness", provides a definition of "fitness", and clarifies the limitations of that principle. The situations covered do not include frequency dependence or social behaviour, but the approach is capable of extension.     

Cell cycles and growth laws: the CCC model

In the cell-cycle-with-control model (CCC model), cells have to satisfy a condition before they are allowed to pass a control point during G1. Different cycle durations within a cell population are explained by individual time spans needed to satisfy the passing condition. If the distribution of cycle durations is time invariant, the population will grow exponentially. However, if the average cycle duration becomes longer, while the population grows, non-exponential population growth results. Simple functions for the lengthening of the average cycle duration, like linear or exponential ones, yield the well-known growth laws found in the biological literature. The same functions can be represented by an "S-system" differential equation that was derived earlier as an approximation for biochemical systems with many fast reactions (metabolism) and one slow process (e.g. ageing).     

Functional significance of high-frequency components of brain electrical activity in the processes of gestalt formation

A review. Current views of the so-called binding problem, which considers hypothetical mechanisms of perception of sensory stimuli and formation of their corresponding Gestalts (internal images) are discussed. The mechanism of intensification of synchronized reactions of cortical electrical activity in the gamma band frequency (30-80 Hz) is the basis of the most popular point of view of "binding". The article considers the evidence for the functional significance of the high-frequency components exceeding the gamma-range (to 200 Hz) obtained by the author, the origin of these oscillations, and conditions of their focal derivation. The problem of "binding" and stages of instrumental conditioning (a stimulus, perception of the stimulus, and its transformation into a signal) as well as significance of the context in learning and formation of tonic states ensuring the realization of phasic reactions is discussed. Forms of "binding" at the final stage of conditioning (selective attention) are considered. The question is posed as to whether "binding" is exhausted only by the mechanisms of synchronization of activities of large neuronal populations and only in the frequencies of the gamma range.     

Studies on griseolic acid derivatives. III. Synthesis and biological activities of the adducts of griseolic acid and their base exchanged derivatives

Addition reactions across the double bond of griseolic acid were investigated. Dihydrogriseolic acid was obtained by a reduction of the adduct having halogen at 4' position. The ring juncture of the two five membered rings of the dihydro derivatives was all "cis" configuration. An acetolysis of the protected dihydro derivative gave corresponding 1'-acetoxy sugar. A glycosidation of this sugar derivative with silylated bases gave base exchanged derivatives of the dihydrogriseolic acid. The influence of the base moiety and the double bond to the PDE inhibitory activity was investigated. As a result, we found that this type of compounds had a weaker inhibitory activity than the corresponding compounds which had an original double bond or a dihydro bond that made the ring juncture of the two five membered ring "trans".     

Nonequilibrium linear behavior of biological systems. Existence of enzyme-mediated multidimensional inflection points.

The linear phenomenological equations of nonequilibrium thermodynamics are limited theoretically to near equilibrium although a number of biological systems have been shown to exhibit a "linear" relationship between steady-state flows and conjugate thermodynamic forces outside the range of equilibrium. We have found a multidimensional inflection point which can exist well outside the range of equilibrium around with enzyme-catalyzed reactions exhibit "linear" behavior between the logarithm of reactant concentrations and enzyme catalyzed flows. A set of sufficient conditions has been derived which can be applied to any enzyme mechanism to determine whether a multidimensional inflection point exists. The conditions do not appear overly restrictive and may be satisfied by a large variety of coupled enzyme reactions. It is thus possible that the linearity observed in some biological systems may be explained in terms of enzyme operating near this multidimensional point.     

Changes in innate forms of motor behavior in rats during long-term hypokinesia

The structure of motor behaviour in response to environmental tests--"open field" and "with-a-partner" situation (according to P. V. Simonov)--was studied in rats after 1, 3 and 6 weeks of hypokinesis, (to K. Hecht), as compared to the control. In control animals a relatively low level of orienting-investigation reactions and of grooming was observed as well as a low alimentary activity, which is considered as a manifestation of innate passive defensive reactions in the above situations. Disappearance of these reactions in the course of hypokinesia has two stages: predominant increase in orienting-investigating reactions (1-3 weeks); their subsequent decrease and an increase in the grooming (after 6 weeks). The relation between innate and conditioned behavioural changes is discussed as well as stability of alimentary behaviour in rats.     

Rate theory models for ion transport through rigid pores. I. Time-dependent analysis in the case of vanishing interactions

In this first of a series of papers concerning the theoretical analysis of rate theory models for ion transport through rigid pores, the case of vanishing interactions is investigated. "Rigidity" means that ions crossing membranes through pores see a fixed structure of the pores, not changing in time. A single pore is considered to be a sequence of (n + 1) activation barriers separated by n energy minima. The explicit analytical treatment is restricted to pores with regular internal barrier structure, including the nonequilibrium situation of an applied electric field. In this case the connection with continuum diffusion models is demonstrated by performing in the limit n leads to infinity (n = number of binding sites within the pores) the transition to continuum. Thus, from diffusion equations describing a discrete number of jumps, the corresponding diffusion-like partial differential equations and boundary conditions are generated. For regular pores, from the time dependent solutions of the discrete equations, the corresponding solutions of the continuum equations are explicitly generated. The time-dependent relaxation behaviour of the discrete model is in good agreement with the continuum model if one assumes more than two binding sites in the pores.     

Multi-criteria optimization of regulation in metabolic networks

Determining the regulation of metabolic networks at genome scale is a hard task. It has been hypothesized that biochemical pathways and metabolic networks might have undergone an evolutionary process of optimization with respect to several criteria over time. In this contribution, a multi-criteria approach has been used to optimize parameters for the allosteric regulation of enzymes in a model of a metabolic substrate-cycle. This has been carried out by calculating the Pareto set of optimal solutions according to two objectives: the proper direction of flux in a metabolic cycle and the energetic cost of applying the set of parameters. Different Pareto fronts have been calculated for eight different "environments" (specific time courses of end product concentrations). For each resulting front the so-called knee point is identified, which can be considered a preferred trade-off solution. Interestingly, the optimal control parameters corresponding to each of these points also lead to optimal behaviour in all the other environments. By calculating the average of the different parameter sets for the knee solutions more frequently found, a final and optimal consensus set of parameters can be obtained, which is an indication on the existence of a universal regulation mechanism for this system.The implications from such a universal regulatory switch are discussed in the framework of large metabolic networks.     

Nonlinear viscoelastic characterization of bovine trabecular bone

The time-independent elastic properties of trabecular bone have been extensively investigated, and several stiffness–density relations have been proposed. Although it is recognized that trabecular bone exhibits time-dependent mechanical behaviour, a property of viscoelastic materials, the characterization of this behaviour has received limited attention. The objective of the present study was to investigate the time-dependent behaviour of bovine trabecular bone through a series of compressive creep–recovery experiments and to identify its nonlinear constitutive viscoelastic material parameters. Uniaxial compressive creep and recovery experiments at multiple loads were performed on cylindrical bovine trabecular bone samples (\(n = 19\)). Creep response was found to be significant and always comprised of recoverable and irrecoverable strains, even at low stress/strain levels. This response was also found to vary nonlinearly with applied stress. A systematic methodology was developed to separate recoverable (nonlinear viscoelastic) and irrecoverable (permanent) strains from the total experimental strain response. We found that Schapery’s nonlinear viscoelastic constitutive model describes the viscoelastic response of the trabecular bone, and parameters associated with this model were estimated from the multiple load creep–recovery (MLCR) experiments. Nonlinear viscoelastic recovery compliance was found to have a decreasing and then increasing trend with increasing stress level, indicating possible stiffening and softening behaviour of trabecular bone due to creep. The obtained parameters from MLCR tests, expressed as second-order polynomial functions of stress, showed a similar trend for all the samples, and also demonstrate stiffening–softening behaviour with increasing stress.     

Non-equilibrium thermodynamics of temporally oscillating chemical reactions.

Two thermodynamic quantities are introduced: the entropy change due to a variation of chemical affinity from a steady, state. to some other state and the corresponding entropy production. The entropy change is always negative definite except at the steady state and is capable of being a Liapunov function. The phase-plane behaviour of the entropy production along the trajectory generated by kinetic equations is investigated in connection with the stability of steady state. The examples taken on that occasion are the Volterra-Lotka and Prigogine-Lefever models. The non-equilibrium thermodynamic properties common to the oscillating reactions in two-variable system are in general considered with an emphasis on the thermodynamic analysis for the direction of rotation of the trajectory generated by the two-variable kinetic equations.     

Linear viscoelasticity - bone volume fraction relationships of bovine trabecular bone

Trabecular bone has been previously recognized as time-dependent (viscoelastic) material, but the relationships of its viscoelastic behaviour with bone volume fraction (BV/TV) have not been investigated so far. Therefore, the aim of the present study was to quantify the time-dependent viscoelastic behaviour of trabecular bone and relate it to BV/TV. Uniaxial compressive creep experiments were performed on cylindrical bovine trabecular bone samples (\(\textit{n}\,{=}\,13\)) at loads corresponding to physiological strain level of 2000 \({\upmu }{\upvarepsilon }\). We assumed that the bone behaves in a linear viscoelastic manner at this low strain level and the corresponding linear viscoelastic parameters were estimated by fitting a generalized Kelvin–Voigt rheological model to the experimental creep strain response. Strong and significant power law relationships (\(r^2\,{=}\,0.73,\ p\,{<}\,0.001\)) were found between time-dependent creep compliance function and BV/TV of the bone. These BV/TV-based material properties can be used in finite element models involving trabecular bone to predict time-dependent response. For users’ convenience, the creep compliance functions were also converted to relaxation functions by using numerical interconversion methods and similar power law relationships were reported between time-dependent relaxation modulus function and BV/TV.     

Simulation model for gynecologic specimen classification in a high-resolution prescreening system

Presentation is made of the design of a statistical model for the generation of "artificial specimens" to be used in the development and testing of a high-resolution prescreening system for gynecologic specimen classification. The model is based on two considerations: (1) the nature of the biologic material to be examined and (2) the system to be studied, which in this case is the FAZYTAN cervical prescreening system. Since gynecologic specimens that belong to the same clinical class (Papanicolaou group) have similar compositions of the different cytologic cell types, the simulation model presented is based on the close relationship between the degree of cancer suspiciousness expressed in the clinical diagnostic group and the composition of the cellular samples on a specimen. Statistically, the model considered here is based on an analysis of the single-cell classification (SCC) output process, taking the inherent system properties into account. The statistical information obtained by evaluating large sets of labelled cells is then used to produce artificially generated point distributions in the SCC decision space ("artificial specimens"), which can be used for examination of system reactions under controlled conditions. False-positive and false-negative error rates and system operation characteristics can be measured, and the effects of varying cell compositions as well as the relative performance of different specimen classifiers can be investigated. Although the "artificial specimens" thus created allow the investigation of system reactions with respect to a great variety of input processes, they cannot replace experiments on thousands of original specimens in order to measure system quality under realistic conditions.     

Modelling of pyrolysis of large wood particles

A fully transient mathematical model has been developed to describe the pyrolysis of large biomass particles. The kinetic model consists of both primary and secondary reactions. The heat transfer model includes conductive and internal convection within the particle and convective and radiative heat transfer between the external surface and the bulk. An implicit Finite Volume Method (FVM) with Tridiagonal Matrix Algorithm (TDMA) is employed to solve the energy conservation equation. Experimental investigations are carried out for wood fines and large wood cylinder and sphere in an electrically heated furnace under inert atmosphere. The model predictions for temperature and mass loss histories are in excellent agreement with experimental results. The effect of internal convection and particle shrinkage on pyrolysis behaviour is investigated and found to be significant. Finally, simulation studies are carried out to analyze the effect of bulk temperature and particle size on total pyrolysis time and the final yield of char.     

Estimation of long-time effects of Chernobyl AES accident on behavior markers in a small rodent population

Differences in behaviour reactions in "open field" and glycemia under conditions of immobilisation stress of vole (Microtus oeconomus, Pallas) from two groups ("Yanov" and "Lelev") were investigated. Rodents were ensnared from two populations reproduced for a long time (11 years) in the areas of ChNPP Exclusion Zone with different level of radioactive contamination. The radiation absorbed dose for animals of "Yanov" group (external and internal irradiation) was 11-20 times higher than that of "Lelev" group. Males and females from the area with worse radioecological condition had higher vertical and horizontal locomotion. The level of emotional reactions of "Yanov" males was lower than the "Lelev" one. Statistically significant variation in female emotional reaction was found, but it had not the same directions. In both groups higher locomotion activity and lower emotionality were associated with male sex. The males of both groups showed similar fasting glucose level and glycemic response after 30-min. immobilisation. Our data provide the additional evidence of existence of long-time genetic effects in small rodent populations permanently reproduced on radiation contaminated areas.