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The dual biological identity of human beings and the naturalization of morality.

The last two centuries have been the centuries of the discovery of the cell evolution: in the XIX century of the germinal cells and in the XX century of two groups of somatic cells, namely those of the brain-mind and of the immune systems. Since most cells do not behave in this way, the evolutionary character of the brain-mind and of the immune systems renders human beings formed by t wo different groups of somatic cells, one with a deterministic and another with an indeterministic (say Darwinian) behavior. An inherent consequence is that of the generation, during ontogenesis, of a dual biological identity. The concept of the dual biological identity may be used to explain the Kantian concept of the two metaphysical worlds, namely of the causal necessity and of the free will (Azzone, 2001). Two concepts, namely those of complex adaptive systems (CAS) and of emergence (Holland, 2002), are useful tools for understanding the mechanisms of adaptation and of evolution. The concept of complex adaptive systems indicates that living organisms contain series of stratified components, denoted as building blocks, forming stratified layers of increasing complexity. The concept of emergence implies the use of repeating patterns and of building blocks for the generation of structures of increasing levels of complexity, structures capable of exchanging communications both in the top-down and in the bottom-up direction. Against the concept of emergence it has been argued that nothing can produce something which is really new and endowed of causal efficacy. The defence of the concept of emergence is based on two arguments. The first is the interpretation of the variation-selection mechanism as a process of generation of information and of optimization of free energy dissipation in accord with the second principle of thermodynamics. The second is the objective evidence of the cosmological evolution from the Big Bang to the human mind and its products. Darwin has defended the concept of the continuity of evolution. However evolution should be considered as continuous when there is no increase of information and as discontinuous when there is generation of new information. Examples of such generation of information are the acquisition of the innate structures for language and the transition from absence to presence of morality. There are several discontinuity thresholds during both phylogenesis and ontogenesis. Morality is a relational property dependent on the interactions of human beings with the environment. Piaget and Kohlberg have shown that the generation of morality during childhood occurs through several stages and is accompanied by reorganization of the child mental organization. The children respect the conventions in the first stage and gradually generate their autonomous morality. The transition from absence to presence of morality, a major adaptive process, then, not only has occurred during phylogenesis but it occurs again in every human being during ontogenesis. The religious faith does not provide a logical justification of the moral rules (Ayala, 1987) but rather a psychological and anthropological justification of two fundamental needs of human beings: that of rendering Nature an understandable entity, and that of increasing the cooperation among members of the human societies. The positive effects of the altruistic genes in the animal societies are in accord with the positive effects of morality for the survival and development of the human societies.

Adaptation, Biological↗

Characterization of an indigenous iron-oxidizing bacterium and its effectiveness in bioleaching heavy metals from anaerobically digested sewage sludge.

The objective of the present study was to isolate the indigenous iron-oxidizing bacterium and compare its effectiveness in bioleaching of heavy metals from fresh anaerobically digested sludge and aged sludge which had undergone a storage period in a sludge holding tank. An acidophilic iron-oxidizing bacterium Acidithiobacillus ferrooxidans strain ANYL-1 was successfully isolated from the sludge collected from a wastewater treatment plant at Yuen Long district in Hong Kong. It was a Gram negative, non-motile rod shaped bacterium which used ferrous iron, elemental sulfur or thiosulfate as energy source, but did not utilize tetrathionate or glucose as energy source. The optimal temperature and pH for its growth and iron oxidation were 30-35 degrees C and pH 2.0-2.5, respectively. When it was used in the bioleaching of anaerobically digested sewage sludge, an inhibition on metal solubilization was observed in fresh sludge except for Zn whose dissolution was solely a chemical process. Compared to the 3 and 4 days required for solubilization of Cu and Cr respectively from the sludge sample collected after the sludge holding tank (Sludge SHT), 6 days were required to bioleach Cu and Cr from fresh sludge (Sludge AD). The fresh sewage sludge posed an unfavorable condition for bioleaching of heavy metals from anaerobically digested sludge as reflected by the prolonged bioleaching time. Therefore, further studies were needed to understand the inhibitory effects in the fresh anaerobically digested sludge and develop measures to remove it in order to improve the heavy metal bioleaching efficiency.

Acidithiobacillus↗

An ab initio investigation of 2-amino-2-imidazoline: a key moiety in chemical and biochemical processes.

The 2-amino-2-imidazoline moiety is currently used not only in drugs, but also in insecticides, and fungicides. Ab initio calculations are performed to evaluate the molecular properties of the two tautomeric forms and the protonated form with extended basis sets ranging from 6-31G* to 6-311++G** at Hartree-Fock and density functional (BLYP and B3LYP) levels. Møller-Plesset perturbation is tested at the MP2/6-31G* level only. Optimized geometry structures, energies and thermochemical properties are generated. Basis set and correlation effects on geometries, tautomer equilibrium constant and protonation enthalpy are carefully analysed. Although observed for the isolated molecule, these results may be extrapolated to chemical and biochemical systems of interest.

Fungicides, Industrial↗

A multi-ion permeation mechanism in neuronal background chloride channels.

Unitary current/voltage relationships of background Cl channels of rat hippocampal neurons were determined for varied gradients and absolute concentrations of NaCl. The channels revealed permeabilities for both Cl and Na ions. A hyperlinear increase of unitary conductance, observed for a symmetrical increase of salt concentration from 300 and 600 mM, indicated a multi-ion permeation mechanism. A variety of kinetic models of permeation were tested against the experimental current/voltage relationships. Models involving a pore occupied by mixed complexes of up to five ions were necessary to reproduce all measurements. A minimal model included four equilibrium states and four rate-limiting transitions, such that the empty pore accepts first an anion and then can acquire one or two cation/anion pairs. Three transport cycles are formed: a slow anion cycle (between the empty and single-anion states), a slow cation cycle (between the one- and three-ion states), and a fast anion cycle (between the three- and five-ion states). Thus, permeant anions are required for cation permeation, and several bound anions and cations promote a high rate of anion permeation. The optimized free-energy and electrical charge parameters yielded a self-consistent molecular interpretation, which can account for the particular order in which the pore accepts ions from the solutions. Although the model describes the mixed anion/cation permeability of the channel observed at elevated concentrations, it predicts a high selectivity for Cl anion at physiological ionic conditions.

Animals↗

Optimization of protein structure on lattices using a self-consistent field approach.

Lattice modeling of proteins is commonly used to study the protein folding problem. The reduced number of possible conformations of lattice models enormously facilitates exploration of the conformational space. In this work, we suggest a method to search for the optimal lattice models that reproduced the off-lattice structures with minimal errors in geometry and energetics. The method is based on the self-consistent field optimization of a combined pseudoenergy function that includes two force fields: an "interaction field," that drives the residues to optimize the chain energy, and a "geometrical field," that attracts the residues towards their native positions. By varying the contributions of these force fields in the combined pseudoenergy, one can also test the accuracy of potentials: the better the potentials, i.e., the more accurate the "interaction field," and the smaller the contribution of the "geometrical field" required for building accurate lattice models.

Models, Chemical↗

MESHI: a new library of Java classes for molecular modeling.

UNLABELLED: Adapting a modular and object-oriented approach in the design of molecular modeling packages may reduce the software development barrier between ideas and their programed applications. Towards this goal we developed MESHI, a new, strictly object-oriented, molecular modeling suite written in Java. MESHI provides a comprehensive library of extendable classes for all the essential components of molecular modeling: molecular and geometry elements, energy functions and optimization methods. AVAILABILITY: MESHI and its related documentation are freely available at http://www.cs.bgu.ac.il/~meshi; the MESHI API is available at http://www.cs.bgu.ac.il/~meshi/API CONTACT: keasar@cs.bgu.ac.il SUPPLEMENTARY INFORMATION: The Supplementary information includes (1) a detailed description of several key packages and classes, and (2) a brief presentation of results achieved by using the MESHI application--Beautify--in the CASP6 experiment.

Computer Simulation↗

A history of boron neutron capture therapy of brain tumours. Postulation of a brain radiation dose tolerance limit.

Boron neutron capture therapy (BNCT) is a form of radiation therapy mediated by the short-range (less than 10 microns) energetic alpha (4He) and lithium-7 (7Li) ionizing particles that result from the prompt disintegration by slow neutrons of the stable (nonradioactive) nucleus boron-10 (10B). Recent advances in radiobiological and toxicological evaluation of tumour-affinitive boron-containing drugs and in optimization of the energies of neutrons in the incident beam have spurred interest in BNCT. This article presents a history of BNCT that emphasizes studies in the USA. A new dosimetric analysis of the 1959-1961 clinical trials of BNCT at Brookhaven National Laboratory is also presented. This analysis yields an acute radiation dose tolerance limit estimate of approximately 10 Gy-Eq to the capillary endothelium of human basal ganglia from BNCT. (Gy-Eq: Gray-equivalent, or relative biological effectiveness of a radiation component multiplied by the physical dose of the component (Gy), summed over the component kinds of radiation.)

Boron↗

Yeast mitochondrial F1F0-ATP synthase exists as a dimer: identification of three dimer-specific subunits.

Using the technique of blue native gel electrophoresis, the oligomeric state of the yeast mitochondrial F1F0-ATP synthase was analysed. Solubilization of mitochondrial membranes with low detergent to protein ratios led to the identification of the dimeric state of the ATP synthase. Analysis of the subunit composition of the dimer, in comparison with the monomer, revealed the presence of three additional small proteins. These dimer-specific subunits of the ATP synthase were identified as the recently described subunit e/Tim11 (Su e/Tim11), the putative subunit g homolog (Su g) and a new component termed subunit k (Su k). Although, as shown here, these three proteins are not required for the formation of enzymatically active ATP synthase, Su e/Tim11 and Su g are essential for the formation of the dimeric state. Su e/Tim11 appears to play a central role in this dimerization process. The dimer-specific subunits are associated with the membrane bound F0-sector. The F0-sector may thereby be involved in the dimerization of two monomeric F1F0-ATP synthase complexes. We speculate that the F1F0-ATP synthase of yeast, like the other complexes of oxidative phosphorylation, form supracomplexes to optimize transduction of energy and to enhance the stability of the complex in the membrane.

Amino Acid Sequence↗

Hypoenergetic high-carbohydrate or high-fat parenteral nutrition induces a similar metabolic response with differential effects on hepatic IGF-I mRNA in dexamethasone-treated rats.

The optimal level of energy for critically ill patients who require parenteral nutrition (PN) is unclear. Our objective was to determine whether 50% energy (50%E) restriction due to a reduction in carbohydrate or fat, with provision of adequate protein and micronutrients, ameliorates the detrimental effects of dexamethasone (Dex) on body protein catabolism, insulin resistance, and insulin-like growth factor-I (IGF-I) responses in rats administered PN. The experiment included 6 PN groups, adequate energy (AE) +/- Dex, 50% AE with high carbohydrate (50%E CHO) +/- Dex and 50% AE with high fat (50%E FAT) +/- Dex. There was a significant interaction between energy level and Dex such that the increase in body catabolism due to 50%E from CHO or FAT was reduced by approximately 50%, although the amount of body weight and nitrogen lost over 7 d was significantly greater with 50%E than with AE. AE+Dex induced a 60% increase in liver mass, whereas 50%E+Dex reduced the increase to 26%. AE+Dex induced a 5-fold increase in serum insulin level, whereas 50%E+Dex normalized the insulin to glucose ratio. Serum IGF-I levels were reduced 14-18% by Dex and 30% by 50%E. Hepatic immunoreactive IGF-I was significantly correlated with serum IGF-I and nitrogen balance. 50%E CHO and 50%E FAT had differential effects on hepatic IGF-I mRNA with a 40% decrease in IGF-I mRNA due to 50%E FAT+Dex. In summary,CHO or FAT hypoenergetic PN with adequate protein had similar effects in normalizing hyperinsulinemia, attenuating hepatomegaly, and reducing the increment, but not the total amount of body protein catabolism, induced by glucocorticoid excess.

Animals↗

A theoretical study of anthracene and phenanthrene derivatives acting as A-T specific intercalators.

Theoretical computations are performed on the comparative A-T versus G-C binding selectivities of two DNA intercalating molecules recently synthesized by Wilson et al. These are derivatives of phenanthrene and anthracene with side chains containing an hydroxy group bound to its C alpha carbon and a cationic amino group bound to its C beta carbon. We have optimized the binding energies of these phenanthrene and anthracene derivatives (1 and 2, respectively) to the double-stranded tetramers d(ATAT)2 and d(GCGC)2, the intercalation occurring in the central pyrimidine (3'-5') purine sequence. The sum of the intercalator-oligonucleotide intermolecular interaction energy plus the conformational energy variation of the intercalator upon binding were computed by the SIBFA procedures, which use empirical formulas based on ab initio SCF computations. Both compounds are found to bind more favourably to the AT sequence than to the GC one. Moreover, the affinity of 1 for the AT oligomer is computed to be larger than that of 2, whereas conversely that of 2 is larger than that of 1 for the GC oligomer. The AT versus GC binding selectivity of 1 is significantly larger than that of 2. These results are in excellent agreement with the experimental findings of Wilson et al. However, contrary to the suggestion of these authors the alpha-hydroxy group of the side chain of the intercalators does not seem to play a decisive role in determining the A-T specificity.

Adenine↗

High sensitivity RNA pseudoknot prediction.

Most ab initio pseudoknot predicting methods provide very few folding scenarios for a given RNA sequence and have low sensitivities. RNA researchers, in many cases, would rather sacrifice the specificity for a much higher sensitivity for pseudoknot detection. In this study, we introduce the Pseudoknot Local Motif Model and Dynamic Partner Sequence Stacking (PLMM_DPSS) algorithm which predicts all PLM model pseudoknots within an RNA sequence in a neighboring-region-interference-free fashion. The PLM model is derived from the existing Pseudobase entries. The innovative DPSS approach calculates the optimally lowest stacking energy between two partner sequences. Combined with the Mfold, PLMM_DPSS can also be used in predicting complicated pseudoknots. The test results of PLMM_DPSS, PKNOTS, iterated loop matching, pknotsRG and HotKnots with Pseudobase sequences have shown that PLMM_DPSS is the most sensitive among the five methods. PLMM_DPSS also provides manageable pseudoknot folding scenarios for further structure determination.

Algorithms↗

New strategies for the determination of macromolecular structure in solution.

Non-crystallographic approaches to the determination of protein structure must solve the problem of insufficient and low information content experimental data. Most successful methods augment experimentation with theoretical constraints (for example, potential energy functions or optimization error metrics). We believe it is important to separate the contributions of experimentation and theory in the construction of protein structure. The PROTEAN system defines protein topology on the basis of experimental data alone. Its performance on three data sets, derived from the lac-repressor headpiece of E. coli, sperm whale myoglobin, and domain 1 of bacteriophage T4 lysozyme, indicates that there may be families of related conformations that are consistent with the experimental data. These conformations provide insight into the strengths and weaknesses in the data sets. They also provide a set of structures with which to begin theoretical refinements. We outline here a strategy which maintains a clear distinction between refinements based on theory and those based on experiment, and thus allows a careful analysis of the properties of such refinement methods.

Expert Systems↗

A decision-support system for off-site nuclear emergencies.

In the case of a nuclear emergency, quick, well-founded decisions must be made about the type of protective action, its region of application, and initiation time. These typically are tasks for computer-based systems. Even with emergency-preparedness, exercises, and training, the decision-support system is one of great importance. This paper describes a decision-support system recently developed by the China Institute of Atomic Energy; it can optimally rank actions during the early phase of an accident using multiattribute utility analysis, and for the intermediate and later phases by cost-benefit analysis. This system runs both on MICRO VAX II and PC systems.

China↗

Qigong practice: a pathway to health and healing.

Qigong is a therapeutic Chinese practice that has been used for thousands of years to optimize and restore energy (Qi) to the body, mind, and spirit. Elements of Taoist and Buddhist philosophies form the foundation of Qigong, which promotes health and vitality through gentle exercises for the breath, body, mind, and the voice. One component of Qigong is T'ai Chi, an exercise modality that uses gentle movements. Research has demonstrated that Qigong and T'ai Chi have beneficial effects on the body and that these are becoming popular holistic modalities in the United States. Nurses should understand the philosophy, concepts, and elements of Qigong and T'ai Chi so that they can guide patients to the benefits of this ancient art and science.

Breathing Exercises↗

Method for efficient shape parametrization of fluid membranes and vesicles.

In this paper we describe a method for the parametrization of the shapes adopted by fluid membranes and vesicles. The method is based upon a boundary-value approach to geometry description in which smooth surfaces are produced as the solution to an elliptic partial differential equations. Shape parameters are introduced through the boundary conditions, which control the shape of the vesicle models. In combination with a model for the surface energy and a method for numerical minimization, it is shown how the method can accurately approximate the shapes of both axisymmetric and nonaxisymmetric vesicles over a wide range of control parameters. The particular value of the method lies in its ability to parametrize complicated shapes efficiently, a feature that becomes especially valuable when seeking shapes of minimal energy using direct optimization techniques.

Animals↗

Influence of the laser prepulse on proton acceleration in thin-foil experiments.

We investigate the influence of the laser prepulse due to amplified spontaneous emission on the acceleration of protons in thin-foil experiments. We show that changing the prepulse duration has a profound effect on the maximum proton energy. We find an optimal value for the target thickness, which strongly depends on the prepulse duration. At this optimal thickness, the rear side acceleration process leads to the highest proton energies, while this mechanism is rendered ineffective for thinner targets due to a prepulse-induced plasma formation at the rear side. In this case, the protons are primarily accelerated by the front side mechanism leading to lower cutoff energies.

Journal Article↗

Analytical model for ion acceleration by high-intensity laser pulses.

We present a general expression for the maximum ion energy observed in experiments with thin foils irradiated by high-intensity laser pulses. The analytical model is based on a radially confined surface charge set up by laser accelerated electrons on the target rear side. The only input parameters are the properties of the laser pulse and the target thickness. The predicted maximum ion energy and the optimal laser pulse duration are supported by dedicated experiments for a broad range of different ions.

Journal Article↗

Kinetic Characterization of Nitrite Uptake and Reduction by Chlamydomonas reinhardtii.

Kinetics of nitrite uptake and reduction by Chlamydomonas reinhardtii cells growing phototrophically has been studied by means of progress curves and the Michaelis-Menten integrated equation. Both uptake and reduction processes exhibited hyperbolic saturation kinetics, the nitrite uptake system lacking a diffusion component. Nitrite uptake and reduction showed significant differences in K(s) for nitrite at pH 7.5 (1.6 versus 20 micromolar, respectively), optimal pH, activation energy values, and sensitivity toward reagents of sulfhydryl groups. K(s) values for nitrite uptake were halved in cells subjected to darkness or to nitrogen-starvation. Nitrate inhibited nitrite uptake by a partially competitive mechanism. The same inhibition pattern was found for nitrite uptake by C. reinhardtii mutant 305 cells incapable of nitrate assimilation. The results demonstrate that C. reinhardtii cells take up nitrite via a highly specific carrier, probably energy-dependent, kinetically responsive to environmental changes, distinguishable from the enzymic nitrite reduction and endowed with an active site for nitrite not usable for nitrate transport.

Journal Article↗