Electroweak Parity-Violating Energy Shifts of Amino Acids: The “Conformation Problem”

The preceding paper described our coupled-perturbed Hartree-Fock (CPHF) and density functional theory (DFT) methods of computing the parity-violating energy shift (PVES). This paper addresses the “conformation problem”—the difficulty determining which hand of amino acids in solution is favoured by the weak force due to the difficulty determining the solution conformation. We attempt to resolve this by using the methods of the preceding paper to compute the PVES of solution and gas-phase amino acid structures determined by other groups from high level optimizations that include solvation. We conclude that the conformational hypersensitivity of the PVES still precludes a definite conclusion as to the sign of the PVES of L-alanine in solution, but that there is no problem in the gas phase: the PVES of gas-phase L-alanine is decisively negative. We show that the PVES is very sensitive to certain torsion angles, but is not hypersensitive to bondlengths or bond angles. In determining structures for PVES computations, there is therefore no need for expensive full optimizations: one can just optimize the crucial torsion angles. We present new computations of gas-phase amino acids PVESs, using partial optimizations with small basis sets, and the results agree well with those from higher level techniques. In the following paper we apply these less costly techniques to larger amino acids. The “conformation problem” has led some to dismiss the PVES as the source of life’s handedness, but we believe this is premature: we show here that amino acids are a special case because their favoured conformations are almost achiral.     

Kinetics of the Multistep Rupture of Fibrin ‘A-a’ Polymerization Interactions Measured Using Atomic Force Microscopy

Fibrin, the structural scaffold of blood clots, spontaneously polymerizes through the formation of ‘A-a’ knob-hole bonds. When subjected to external force, the dissociation of this bond is accompanied by two to four abrupt changes in molecular dimension observable as rupture events in a force curve. Herein, the configuration, molecular extension, and kinetic parameters of each rupture event are examined. The increases in contour length indicate that the D region of fibrinogen can lengthen by ∼50% of the length of a fibrin monomer before rupture of the ‘A-a’ interaction. The dependence of the dissociation rate on applied force was obtained using probability distributions of rupture forces collected at different pull-off velocities. These distributions were fit using a model in which the effects of the shape of the binding potential are used to quantify the kinetic parameters of forced dissociation. We found that the weak initial rupture (i.e., event 1) was not well approximated by these models. The ruptured bonds comprising the strongest ruptures, events 2 and 3, had kinetic parameters similar to those commonly found for the mechanical unfolding of globular proteins. The bonds ruptured in event 4 were well described by these analyses, but were more loosely bound than the bonds in events 2 and 3. We propose that the first event represents the rupture of an unknown interaction parallel to the ‘A-a’ bond, events 2 and 3 represent unfolding of structures in the D region of fibrinogen, and event 4 is the rupture of the ‘A-a’ knob-hole bond weakened by prior structural unfolding. Comparison of the activation energy obtained via force spectroscopy measurements with the thermodynamic free energy of ‘A-a’ bond dissociation indicates that the ‘A-a’ bond may be more resistant to rupture by applied force than to rupture by thermal dissociation.     

Variable optimization for the formation of three-dimensional self-organized heart muscle

Cardiac tissue-engineering research is focused on the development of functional three-dimensional (3D) heart muscle in vitro. These models allow the detailed study of critical events in organogenesis, such as the establishment of cell–cell communication and construction and modification of the extracellular matrix. We have previously described a model for 3D heart muscle, termed cardioids, formed by the spontaneous delamination of a cohesive monolayer of primary cells in the absence of any synthetic scaffolding material. In an earlier publication, we have shown that, upon electrical stimulation, cardioids generate a twitch force in the range of 200–300 μN, generate a specific force (twitch force normalized to total cross-sectional area) of 2–4 kN/m², and can be electrically paced at frequencies of up to 10 Hz without any notable fatigue. We have two objectives for the current study: model development and model optimization. Our model development efforts are focused on providing additional characterization of the cardioid model. In this study, we show for the first time that cardioids show a pattern of gene expression comparable to that of cells cultured in two dimensions on tissue culture plastic and normal mammalian heart muscle. Compared with primary cardiac cells cultured on tissue culture plastic, the expression of α-myosin heavy chain (MHC), β-MHC, SERCA2, and phospholamban was significantly higher in cardioids. Our second objective, model optimization, is focused on evaluating the effect of several cell culture variables on cardioid formation and function. Specifically, we looked at the effect of plating density (1.0–4.0 × 10⁶ cells per cardioid), concentration of two adhesion proteins (laminin at 0.2–2.0 μg/cm² and fibronectin at 1–10 μg/cm²), myocyte purity (using preplating times of 15 and 60 min), and ascorbic acid stimulation (1–100 μl/ml). For our optimization studies, we utilized twitch force in response to electrical stimulation as our endpoint metric. Based on these studies, we found that cardioids formed with a plating density in the range 3–4 × 10⁶ cells per cardioid generated the maximum twitch force, whereas increasing the surface adhesion protein (using either laminin or fibronectin) and increasing the myocyte purity both resulted in a decrease in twitch force. In addition, increasing the ascorbic acid concentration resulted in an increase in the baseline force of cardioids, which was recorded in the absence of electrical stimulation. Based on the model development studies, we have shown that cardioids do indeed exhibit a gene expression pattern similar to normal mammalian heart muscle. This provides further validity for the cardioid model. Based on the model optimization studies, we have identified specific cell culture regimes which support cardioid formation and function. These results are specific to the cardioid model; however, they may be translated and applied to other tissue-engineering models. Collectively, the work described in this study provides insight into the formation of functional 3D heart muscle and the effect of several cell culture variables on tissue formation and function.     

Muscle contraction history: modified Hill versus an exponential decay model

In recent years, it has been recognised that improvements to classic models of muscle mechanical behaviour are often necessary for properly modelling co-ordinated multi-joint actions. In this respect, the purpose of the present study was to improve on modelling stretch-induced force enhancement and shortening-induced force depression of muscle contraction. For this purpose, two models were used: a modified Hill model and a model based loosely on mechano-chemistry of the cross-bridge cycle (exponential decay model). The models were compared with a classic Hill model and experimental data. Parameter values were based, as much as possible, on experimental findings in the literature, and tested with new experiments on the gastrocnemius of the rat. Both models describe many features of slow-ramp movements well during short contractions (300–500 ms), but long-duration behaviour is described only partly. The exponential decay model does not incorporate a force–velocity curve. Therefore, its good performance indicates that the status of the classic force–velocity characteristic may have to be reconsidered. Like movement-induced force depression and enhancement, it seems a particular manifestation of time-dependent force behaviour of muscle, rather than a fundamental property of muscle (like the length–tension curve). It is argued that a combination of the exponential decay model (or other models based on the mechano-chemistry of contraction) and structurally based models may be fruitful in explaining this time-dependent contraction behaviour. Furthermore, not in the least because of its relative simplicity, the exponential decay model may prove more suitable for modelling multi-joint movements than the Hill model. Received: 19 March 1999 / Accepted in revised form: 9 June 2000     

Nonlinear EEG analysis based on a neural mass model

The well-known neural mass model described by Lopes da Silva et al. (1976) and Zetterberg et al. (1978) is fitted to actual EEG data. This is achieved by reformulating the original set of integral equations as a continuous-discrete state space model. The local linearization approach is then used to discretize the state equation and to construct a nonlinear Kalman filter. On this basis, a maximum likelihood procedure is used for estimating the model parameters for several EEG recordings. The analysis of the noise-free differential equations of the estimated models suggests that there are two different types of alpha rhythms: those with a point attractor and others with a limit cycle attractor. These attractors are also found by means of a nonlinear time series analysis of the EEG recordings. We conclude that the Hopf bifurcation described by Zetterberg et al. (1978) is present in actual brain dynamics. Received: 11 August 1997 / Accepted in revised form: 20 April 1999     

Force field based conformational analysis of RNA structural motifs: GNRA tetraloops and their pyrimidine relatives

The protocol of conformational analysis applied here to ribonucleotide oligomers combines conformational search in the space of torsion angles and energy minimization using the AMBER4.1 force field with a continuum treatment of electrostatic solute-solvent interactions. RNA fragments with 5′-GGGCGNNAGCCU-3′ sequences commonly fold into hairpins with four-membered loops. The combinatorial search for acceptable conformations using the MC-SYM program was restricted to loop nucleotides and yielded roughly 1500 structures being compatible with a double-stranded stem. After energy minimization by the JUMNA program (without applying any experimental constraints), these structures converged into an ensemble of 74 different conformers including 26 structures which contained the sheared G-A base pair observed in experimental studies of GNRA tetraloops. Energetic analysis shows that inclusion of solvent electrostatic effects is critically important for the selection of conformers that agree with experimentally determined structures. The continuum model accounts for solvent polarization by means of the electrostatic reaction field. In the case of GNRA loop sequences, the contributions of the reaction field shift relative stabilities towards conformations showing most of the structural features derived from NMR studies. The agreement of computed conformations with the experimental structures of GAAA, GCAA, and GAGA tetraloops suggests that the continuum treatment of the solvent represents a definitive improvement over methods using simple damping models in electrostatic energy calculations. Application of the procedure described here to the evaluation of the relative stabilities of conformers resulting from searching the conformational space of RNA structural motifs provides some progress in (non-homology based) RNA 3D-structure prediction. Received: 20 January 1999 / Revised version: 4 June 1999 / Accepted: 10 June 1999     

A model for steady isometric muscle activation

The present model of the motoneuronal (MN) pool – muscle complex (MNPMC) is deterministic and designed for steady isometric muscle activation. Time-dependent quantities are treated as time-averages. The character of the model is continuous in the sense that the motor unit (MU) population is described by a continuous density function. In contrast to most already published models, the wiring (synaptic weight) between the input fibers to the MNPMC and the MNs (about which no detailed data are known) is deduced, whereas the input–force relation is given. As suggested by experimental data, this relation is assumed to be linear during MU recruitment, but the model allows other, nonlinear relations. The input to the MN pool is defined as the number of action potentials per second in all input fibers, and the excitatory postsynaptic potential (EPSP) conductance in MNs evoked by the input is assumed to be proportional to the input. A single compartment model with a homogeneous membrane is used for a MN. The MNs start firing after passing a constant voltage threshold. The synaptic current–frequency relation is described by a linear function and the frequency–force transformation of a MU by an exponential function. The sum of the MU contraction forces is the muscle force, and the activation of the MUs obeys the size principle. The model parameters were determined a priori, i.e., the model was not used for their estimation. The analysis of the model reveals special features of the activation curve which we define as the relation between the input normalized by the threshold input of the MN pool and the force normalized by the maximal muscle force. This curve for any muscle turned out to be completely determined by the activation factor, the slope of the linear part of the activation curve (during MU recruitment). This factor determines quantitatively the relation between MU recruitment and rate modulation. This property of the model (the only known model with this property) allows a quantification of the recruitment gain (Kernell and Hultborn 1990). The interest of the activation factor is illustrated using two human muscles, namely the first dorsal interosseus muscle, a small muscle with a relatively small force at the end of recruitment, and the medial gastrocnemius muscle, a strong muscle with a relatively large force at the end of recruitment. It is concluded that the present model allows us to reproduce the main features of muscle activation in the steady state. Its analytical character facilitates a deeper understanding of these features. Received: 24 November 1997 / Accepted in revised form: 30 November 1998     

The creation of specific hominid names: Gloria in excelsis deo? or ego? or praxis?

The recent recommendation that it is preferable to recognize too many rather than too few species in the fossil record has led to a growing proliferation of specific names. Single specimens are being referred to different species by different authors, and new species are being proposed based on the juxtaposition of specimens from different sites and time levels representing different anatomical parts. In part this may represent the continuity of the Medieval assertion that a multitude of species is a better demonstration of the goodness of a divinely created world than a multitude of individuals in a single species. This has apparently accompanied the resurgence of the Medieval faith that species relationship are best demonstrated by the application of hierarchical Aristotelean logic. On the other hand, the suspicion remains that the vanity of the namer is frequently involved in the creation of new nomina. In general, anthropologists do not exhibit the “wide experience” and consequent “sound judgment” that Darwin recommended as necessary for those giving specific names. If the same criteria used to assign specific fossil names were applied to modern Homo sapiens, the different regional human populations would have to be recognized as specifically distinct. In opposition to the recommendation that we should recognize ever more specific names, there should be a moratorium called and no new species names should be proposed at all. The continuation of patterns of trivial trait configurations associated with the various inhabited regions of the world clearly indicates genetic continuity through time but, unless it can be shown that there is no reproductive continuity between one region and another, these differences do not warrant taxonomic recognition. Major adaptive changes such as significant increases in relative brain size do warrant formal named recognition.     

Modelling the potential geographic distribution of invasive ant species in New Zealand

Despite their economic and environmental impacts, there have been relatively few attempts to model the distribution of invasive ant species. In this study, the potential distribution of six invasive ant species in New Zealand are modelled using three fundamentally different methods (BIOCLIM, DOMAIN, MAXENT). Species records were obtained from museum collections in New Zealand. There was a significant relationship between the length of time an exotic species had been present in New Zealand and its geographic range. This is the first time such a time lag has been described for exotic ant species, and shows there is a considerable time lag in their spread. For example, it has taken many species several decades (40–60 years) to obtain a distribution of 17–25% of New Zealand regions. For all six species, BIOCLIM performed poorly compared to the other two modelling methods. BIOCLIM had lower AUC scores and higher omission error, suggesting BIOCLIM models under-predicted the potential distribution of each species. Omission error was significantly higher between models fitted with all 19 climate variables compared to those models with fewer climate variables for BIOCLIM, but not DOMAIN or MAXENT. Widespread species had a greater commission error. A number of regions in New Zealand are predicted to be climatically suitable for the six species modelled, particularly coastal and lowland areas of both the North and South Islands.     

Primary charge separation in Photosystem II

In this Minireview, we discuss a number of issues on the primary photosynthetic reactions of the green plant Photosystem II. We discuss the origin of the 683 and 679 nm absorption bands of the PS II RC complex and suggest that these forms may reflect the single-site spectrum with dominant contributions from the zero-phonon line and a pronounced ∼80 cm⁻¹ phonon side band, respectively. The couplings between the six central RC chlorins are probably very similar and, therefore, a `multimer' model arises in which there is no `special pair' and in which for each realization of the disorder the excitation may be dynamically localized on basically any combination of neighbouring chlorins. The key features of our model for the primary reactions in PS II include ultrafast (<500 fs) energy transfer processes within the multimer, `slow' (∼20 ps) energy transfer processes from peripheral RC chlorophylls to the RC multimer, ultrafast charge separation (<500 fs) with a low yield starting from the singlet-excited `accessory' chlorophyll of the active branch, cation transfer from this `accessory' chlorophyll to a `special pair' chlorophyll and/or charge separation starting from this `special pair' chlorophyll (∼8 ps), and slow relaxation (∼50 ps) of the radical pair by conformational changes of the protein. The charge separation in the PS II RC can probably not be described as a simple trap-limited or diffusion-limited process, while for the PS II core and larger complexes the transfer of the excitation energy to the PS II RC may be rate limiting. This revised version was published online in June 2006 with corrections to the Cover Date.     

An Overview of the Introns-First Theory

We review the introns-first hypothesis a decade after it was first proposed. It is that exons emerged from non-coding regions interspersed between RNA genes in an early RNA world, and is a subcomponent of a more general ‘RNA-continuity’ hypothesis. The latter is that some RNA-based systems, especially in RNA processing, are ‘relics’ that can be traced back either to the RNA world that preceded both DNA and encoded protein synthesis or to the later ribonucleoprotein (RNP) world (before DNA took over the main coding role). RNA-continuity is based on independent evidence—in particular, the relative inefficiency of RNA catalysis compared with protein catalysis—and leads to a wide range of predictions, ranging from the origin of the ribosome, the spliceosome, small nucleolar RNAs, RNases P and MRP, and mRNA, and it is consistent with the wide involvement of RNA-processing and regulation of RNA in modern eukaryotes. While there may still be cause to withhold judgement on intron origins, there is strong evidence against introns being uncommon in the last eukaryotic common ancestor (LECA), and expanding only within extant eukaryotic groups—the ‘very-late’ intron invasion model. Similarly, it is clear that there are selective forces on numbers and positions of introns; their existence may not always be neutral. There is still a range of viable alternatives, including introns first, early, and ‘latish’ (i.e. well established in LECA), and regardless of which is ultimately correct, it pays to separate out various questions and to focus on testing the predictions of sub-theories.     

A Dynamic Energy Budget model based on partitioning of net production

We formulate a Dynamic Energy Budget (DEB) model for the growth and reproduction of individual organisms based on partitioning of net production (i.e. energy acquisition rate minus maintenance rate) between growth and energy reserves. Reproduction uses energy from reserves. The model describes both feeding and non-feeding stages, and hence is applicable to embryos (which neither feed nor reproduce), juveniles (which feed but do not reproduce), and adults (which commonly both feed and reproduce). Embryonic growth can have two forms depending on the assumptions for acquisition of energy from yolk. By default, when the energy acquisition rate exceeds the maintenance rate, a fixed proportion of the resulting net production is spent on growth (increase in structural biomass), and the remaining portion is channelled to the reserves. Feeding organisms, however, modulate their allocation of net production energy in response to their total energy content (energy in the reserves plus energy bounded to structural biomass). In variable food environment an organism alternates between periods of growth, no-growth, and balanced-growth. In the latter case the organism adopts an allocation strategy that keeps its total energy constant. Under constant environmental conditions, the growth of a juvenile is always of von Bertalanffy type. Depending on the values of model parameters there are two long-time possibilities for adults: (a) von Bertalanffy growth accompanied by reproduction at a rate that approaches zero as the organism approaches asymptotic size, or (b) abrupt cessation of growth at some finite time, following which, the rate of reproduction is constant. We illustrate the model's applicability in life history theory by studying the optimum values of the energy allocation parameters for constant environment and for each of the dynamic regimes described above. Received: 11 May 1998 / Revised version: 18 February 2000 / Published online: 4 October 2000     

Probing elasticity and adhesion of live cells by atomic force microscopy indentation

Atomic force microscopy (AFM) indentation has become an important technique for quantifying the mechanical properties of live cells at nanoscale. However, determination of cell elasticity modulus from the force–displacement curves measured in the AFM indentations is not a trivial task. The present work shows that these force–displacement curves are affected by indenter-cell adhesion force, while the use of an appropriate indentation model may provide information on the cell elasticity and the work of adhesion of the cell membrane to the surface of the AFM probes. A recently proposed indentation model (Sirghi, Rossi in Appl Phys Lett 89:243118, 2006), which accounts for the effect of the adhesion force in nanoscale indentation, is applied to the AFM indentation experiments performed on live cells with pyramidal indenters. The model considers that the indentation force equilibrates the elastic force of the cell cytoskeleton and the adhesion force of the cell membrane. It is assumed that the indenter-cell contact area and the adhesion force decrease continuously during the unloading part of the indentation (peeling model). Force–displacement curves measured in indentation experiments performed with silicon nitride AFM probes with pyramidal tips on live cells (mouse fibroblast Balb/c3T3 clone A31-1-1) in physiological medium at 37°C agree well with the theoretical prediction and are used to determine the cell elasticity modulus and indenter-cell work of adhesion. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Impalement of marine turtles (Reptitia,Chelonia: Cheloniidae and Dermochelyidae) by billfishes (Osteichthyes,Perciformes: Istiophoridae and Xiphiidae)

Synopsis Billfishes have long been known to impale a great variety of objects, but there are only two brief, obscure records of marine turtles being speared. Details are presented on these two, as well as on two other confirmed records; data from two additional unconfirmed records are also presented. In total, three species of marine turtles are known to have been impaled by three species of billfishes; a fourth species of fish and a fourth species turtle are listed in an unconfirmed case. Records come from the eastern and western Pacific as well as the eastern Atlantic. Of the four confirmed cases, the turtles survived in two, and apparently died as an effect of the spearing in the other two. In three confirmed cases only the impaled rostrum was encountered, and in one confirmed case the entire fish was found, with its rostrum piercing the turtle. There is no obvious advantage — or clear disadvantage — involved in impaling turtles. It is argued that these attacks are accidental, and the result of attempts made by the billfish to capture prey that are near the turtle. These spearings indicate that the chelonians serve as shelters for prey animals on the high seas, and thus, are further evidence of the pelagic existence of marine turtles. The impalings are evidence of a singular ecological role of the turtles — as live fish aggregation devices.     

Explanations in search of observations

The paper explores how, in economics and biology, theoretical models are used as explanatory devices. It focuses on a modelling strategy by which, instead of starting with an unexplained regularity in the world, the modeller begins by creating a credible model world. The model world exhibits a regularity, induced by a mechanism in that world. The modeller concludes that there may be a part of the real world in which a similar regularity occurs and that, were that the case, the model would offer an explanation. Little concrete guidance is given about where such a regularity might be found. Three modelling exercises in evolutionary game theory—one from economics and two from biology—are used as case studies. Two of these (one from each discipline) exemplify ‘explanation in search of observation’. The third goes a step further, analysing a regularity in a model world and treating it as informative about the real world, but without saying anything about real phenomena. The paper argues that if the relation between the model and real worlds is understood in terms of similarity, and if modelling is understood as an ongoing discovery process rather than as the demonstration of empirical truths, there can be value in creating explanations before finding the regularities that are to be explained.     

Energetics and dynamics of global integrals modeling interaction between stiff filaments

The attractive and spacing interaction between pairs of filaments via cross-linkers, e.g. myosin oligomers connecting actin filaments, is modeled by global integral kernels for negative binding energies between two intersecting stiff and long rods in a (projected) two-dimensional situation, for simplicity. Whereas maxima of the global energy functional represent intersection angles of ‘minimal contact’ between the filaments, minima are approached for energy values tending to −∞, representing the two degenerate states of parallel and anti-parallel filament alignment. Standard differential equations of negative gradient flow for such energy functionals show convergence of solutions to one of these degenerate equilibria in finite time, thus called ‘super-stable’ states. By considering energy variations under virtual rotation or translation of one filament with respect to the other, integral kernels for the resulting local forces parallel and orthogonal to the filament are obtained. For the special modeling situation that these variations only activate ‘spring forces’ in direction of the cross-links, explicit formulas for total torque and translational forces are given and calculated for typical examples. Again, the two degenerate alignment states are locally ‘super-stable’ equilibria of the assumed over-damped dynamics, but also other stable states of orthogonal arrangement and different asymptotic behavior can occur. These phenomena become apparent if stochastic perturbations of the local force kernels are implemented as additive Gaussian noise induced by the cross-link binding process with appropriate scaling. Then global filament dynamics is described by a certain type of degenerate stochastic differential equations yielding asymptotic stationary processes around the alignment states, which have generalized, namely bimodal Gaussian distributions. Moreover, stochastic simulations reveal characteristic sliding behavior as it is observed for myosin-mediated interaction between actin filaments. Finally, the forgoing explicit and asymptotic analysis as well as numerical simulations are extended to the more realistic modeling situation with filaments of finite length.

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Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.      

Physico-chemical model of a voltage-gated sodium channel

A permeant ion is known to create in the channel pore a local electrical field, the intensity of which exceeds the intensity of an electrical field produced by the membrane potential. In our study, we consider a sodium channel model, in which the effects of a permeant ion, an inactivating particle, and pharmacological agents on mobile charged groups of the channel are semi-phenomenologically taken into account by using motion equations for a generalized structural variable. Stationary solutions for the equation correspond to “open,” “closed,” and “inactivated” channel states. Because of this, the channel free energy profile, as a function of the structural variable, has three local minima. The three energy values of these states depend both on the electrical field applied externally and on the near-membrane concentrations of permeant ions and acting pharmacological agents. Sodium channel activation and inactivation kinetics are considered resulting from relative changes of the free energy typical of the above three states of the channel. The results we obtained in the course of channel activation and inactivation modeling and their voltage dependence are qualitatively consistent with the commonly known experimental data. The proposed model allows one to qualitatively predict the dependence of the sodium channel kinetic characteristics on the concentrations of permeant ions and pharmacological agents.     

On the reciprocal interaction between believing and feeling: an adaptive agent modelling perspective

An agent’s beliefs usually depend on informational or cognitive factors such as observation or received communication or reasoning, but also affective factors may play a role. In this paper, by adopting neurological theories on the role of emotions and feelings, an agent model is introduced incorporating the interaction between cognitive and affective factors in believing. The model describes how the strength of a belief may not only depend on information obtained, but also on the emotional responses on the belief. For feeling emotions a recursive body loop between preparations for emotional responses and feelings is assumed. The model introduces a second feedback loop for the interaction between feeling and belief. The strength of a belief and of the feeling both result from the converging dynamic pattern modelled by the combination of the two loops. For some specific cases it is described, for example, how for certain personal characteristics an optimistic world view is generated in the agent’s beliefs, or, for other characteristics, a pessimistic world view. Moreover, the paper shows how such affective effects on beliefs can emerge and become stronger over time due to experiences obtained. It is shown how based on Hebbian learning a connection from feeling to belief can develop. As these connections affect the strenghts of future beliefs, in this way an effect of judgment ‘by experience built up in the past’ or ‘by gut feeling’ can be obtained. Some example simulation results and a mathematical analysis of the equilibria are presented.     

In silico approach to cisplatin toxicity. Quantum chemical studies on platinum(II)–cysteine systems

The behaviour of cisplatin in serum, and the drastic differences between the properties of this drug and its trans-isomer were the main motivations for this work. In a search for model “thiol–platin(II)” interactions, the first steps of the following reaction systems were evaluated: (1) cisplatin–thiomethanol; (2) transplatin–thiomethanol; (3) cisplatin–cysteine; and (4) transplatin–cysteine. In each case, calculations for the associative mode of reactions were performed. The electronic structure of these molecular systems was studied at the non-empirical all-electron level using density functional theory (DFT) within the Huzinaga and WTBS basis sets including polarisation Gaussian functions and full geometry optimisation. B3LYP or EPBO density functionals were applied throughout. The calculated molecular electrostatic potentials are presented graphically. Assuming that electrostatic effects are dominant, cisplatin should interact more strongly with the sulfur atom of CH₃S⁻ and deprotonated CYS-S⁻ than transplatin. This fact has been documented in the supermolecule model of the relevant interaction energies in both gas phase as well as within the solvent polarisable continuum model. The opposite relationship was observed when we compared values of energy differences between products and substrates for both isomers. The data obtained here could be applied to search for correlation between the biological activity of platinum complexes and their properties as estimated by various physico-chemical and in silico methodologies.     

Assessing extinction-risk of endangered plants using species distribution models: a case study of habitat depletion caused by the spread of greenhouses

The species distribution models (SDMs) are useful tools for investigating rare and endangered species as well as the environmental variables affecting them. In this paper, we propose the application of SDMs to assess the extinction-risk of plant species in relation to the spread of greenhouses in a Mediterranean landscape, where habitat depletion is one of the main causes of biodiversity loss. For this purpose, presence records of the model species (Linaria nigricans, a endemic and threatened species) and the greenhouses, a dataset of environmental variables, and different only presence-based modelling algorithms (Bioclim, Domain, GARP, MaxEnt and ENFA) were used to build SDMs for L. nigricans as well as for greenhouses. To evaluate the models a modified approach of the area-under-curve ROC was applied. Combining the most accurate models, we generated an extinction-risk model of L. nigricans populations, which enabled us to assess the sustainability of the most threatened populations. Our results show that is possible to model greenhouses spreading as a “biological invasion”. The procedure explained and used in this work is quite novel, and offers an objective spatial criterion intended for the management of natural resources and for the conservation of the biodiversity in areas threatened by habitat depletion processes as particular as greenhouses expansion.