Hydrogen bonding in DNA base complexes.

Experimental intermolecular frequencies in the DNA base complexes 1-methylthymine (1-MT) and cytosine monohydrate (CMH) are analyzed in terms of simple analytic interatomic potentials. Calculations with two different values for the constants of the nonbonded interactions are considered, and the hydrogen bond potentials are determined for each of these models. The observed frequencies in 1-MT are reasonably well described, although corresponding potentials are very different in the two models. The observed frequencies in CMH are less well described, although corresponding hydrogen bond potentials are similar in the two models. Hydration interactions are found to be important in CMH and the role of the water molecule is discussed. Possible reasons for the shortcomings of this simple analysis are considered.     

Evaluation of short-range interactions as secondary structure energies for protein fold and sequence recognition.

Short-range interactions for secondary structures of proteins are evaluated as potentials of mean force from the observed frequencies of secondary structures in known protein structures which are assumed to have an equilibrium distribution with the Boltzmann factor of secondary structure energies. A secondary conformation at each residue position in a protein is described by a tripeptide, including one nearest neighbor on each side. The secondary structure potentials are approximated as additive contributions from neighboring residues along the sequence. These are part of an empirical potential to provide a crude estimate of protein conformational energy at a residue level. Unlike previous works, interactions are decoupled into intrinsic potentials of residues, potentials of backbone-backbone interactions, and of side chain-backbone interactions. Also interactions are decoupled into one-body, two-body, and higher order interactions between peptide backbone and side chain and between backbones. These decouplings are essential to correctly evaluate the total secondary structure energy of a protein structure without overcounting interactions. Each interaction potential is evaluated separately by taking account of the correlation in the amino acid order of protein sequences. Interactions among side chains are neglected, because of the relatively limited number of protein structures. Proteins 1999;36:347-356. Published 1999 Wiley-Liss, Inc.     

A new comparison theorem on Hellmann potential

Using some basic inequalities, the spherical Hellmann potential is assigned its place in the hierarchy of relative ordering, within the set of standard screened Coulomb potentials at all radial distances. The previously known comparison theorem applicable to the screened Coulomb potentials is thereby expanded to ascertain the relative ordering of energy levels for n?-states of Hellmann potential vis-a-vis those corresponding to the screened Coulomb potentials. The analytic results are supported by numerical calculation.     

Comparison of hard-cylinder and screened coulomb interactions in the modeling of supercoiled DNAs

A 1000 base pair (bp) model supercoiled DNA is simulated using spherical screened Coulomb interactions between subunits on one hand and equivalent hard-cylinder interactions on the other. The amplitudes, or effective charges, of the spherical screened Coulomb electrostatic potentials are chosen so that the electrostatic potential surrounding the middle of a linear array of 2001 subunits (31.8 Å diameter) closely matches the solution of the nonlinear Poisson-Boltzmann equation for a cylinder with 12 Å radius and the full linear charge density of DNA at all distances beyond the 24 Å hard-core diameter. This superposition of spherical screened Coulomb potentials is practically identical to the particular solution of the cylindrical linearized Poisson-Boltzmann equation that matches the solution of the nonlinear Poisson-Boltzmann equation at large distances. The interaction energy between subunits is reckoned from the effective charges according to the standard DLVO expression. The equivalent hard-cylinder diameter is chosen following Stigter's protocol for matching second virial coefficients, but for the full linear charge density of DNA. The electrostatic persistence length of the model with screened Coulomb interactions is extremely sensitive to the (arbitrarily) chosen subunit length at the higher salt concentrations. The persistence length of the hard-cylinder model is adjusted to match that of the screened Coulomb model for each ionic condition. Simulations for a superhelix density σ = -0.05 using a spherical screened Coulomb interaction plus a 24 Å hard-cylinder core (SCPHC) potential indicate that the radius of gyration of this 1000 bp DNA actually undergoes a slight increase as the NaCl concentration is raised from 0.01 to 1.0M. Thus, merely softening the potential from hard-cylinder to screened Coulomb form does not produce a large decrease in radius of gyration with increasing NaCl concentration for DNAs of this size. Radii of gyration, static structure factors, and diffusion coefficients obtained using the equivalent hard-cylinder (EHC) potential agree well with those obtained using the SCPHC potential in 1.0M NaCl, but in 0.1M NaCl the agreement is not as good, and in 0.01M NaCl the agreement is definitely unsatisfactory. These conclusions differ in significant respects from those obtained in previous studies. © 1997 John Wiley & Sons, Inc. Biopoly 42: 455–470, 1997     

Relation of unit spike discharges and evoked potentials in the auditory cortex of cats.

Extracellular microelectrode recordings were made from the auditory cortex of anaesthetized cats during acoustic click stimulation. The microelectrode of low resistance allowed to record evoked field potentials and unit discharges simultaneously. In distant extracellular leads the relation of unit discharges and field potentials was equivocal. Near extracellular leads revealed that the antidromic invasion of the somadendritic membrane by excitation is a frequency dependent process (just as evoked field potentials) while spike potentials can reliably be elicited from the initial segment at high frequencies. It is assumed that the excitation spreading from the initial segment to the soma-dendritic membrane represents an important component of the evoked potentials, and their frequency dependence may be traced back to inhibitions activated by afferent impulses.     

Analyses on hydrophobicity and attractiveness of all‐atom distance‐dependent potentials

Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states, have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this study, we examined seven all‐atom distance‐dependent potentials with different reference states. As results, we observed that the variations of atom pair composition and those of distance distributions in the reference states produced systematic changes in the hydrophobic and attractive characteristics of the potentials. The performance evaluations with the CASP7 structures indicated that the preference of hydrophobic interactions improved the correlation between the energy and the GDT‐TS score, but decreased the Z‐score of the native structure. The attractiveness of potential improved both the correlation and Z‐score for template‐based modeling targets, but the benefit was smaller in free modeling targets. These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states.     

Atom–atom force field for simulation of zirconia bulk,nanosheets and nanotubes

The set of three pair atom–atom potentials for zirconia crystals and nano objects was developed. Besides Buckingham potential and Coulomb interaction, these force fields employ the additional functional forms: Fermi-Dirac, Inverse Gaussian or Morse potential. The developed force fields are capable to reproduce the structural, mechanical and thermodynamic properties of five zirconia phases: monoclinic, tetragonal, cubic, brookite and cotunnite with acceptable accuracy. The proposed force fields give monoclinic phase as a ground state structure and predict the correct energy ordering of the phases. The Raman and IR phonon frequencies, temperature dependencies of the thermodynamic properties of monoclinic and tetragonal zirconia are predicted in good and moderate agreement with the experimentally observed data and results of first-principles calculations. To test the transferability of proposed potentials, the zirconia-based nanosheets and nanotubes were simulated. Results of structure optimisation and calculation of the nanotubes’ strain energies are well compared with the corresponding data of the first-principles calculations.     

Auditory responses in the torus semicircularis of the cane toad, Bufo marinus. I. Field potential studies

Field potentials have been recorded in the torus semicircularis of the toad, Bufo marinus, in response to brief tones presented in the free field. The amplitude of the potentials varied with the frequency of the stimulus and location of the electrode along the rostro-caudal axis of the torus. All frequencies in the auditory range evoked largest potentials when the stimulus was located in the contralateral auditory field. Potentials evoked by low to mid frequencies were largest when the stimulus was located near the line orthogonal to the long axis of the animal. For progressively higher frequencies, the optimal stimulus position was progressively more anterior in the contralateral field. In animals in which one eighth nerve had been sectioned, field potentials evoked by tones of low to mid frequency were less sensitive to changes in stimulus direction than in normal animals. However, the directional sensitivity of field potentials evoked by mid to high frequencies was similar in monaural and normal animals. These observations suggest that binaural neural integration is important in determining the directional sensitivity of field potentials in the torus evoked by low to mid frequencies but not for potentials evoked by mid to high frequencies.     

Identifying sequence-structure pairs undetected by sequence alignments

We examine how effectively simple potential functions previously developed can identify compatibilities between sequences and structures of proteins for database searches. The potential function consists of pairwise contact energies, repulsive packing potentials of residues for overly dense arrangement and short-range potentials for secondary structures, all of which were estimated from statistical preferences observed in known protein structures. Each potential energy term was modified to represent compatibilities between sequences and structures for globular proteins. Pairwise contact interactions in a sequence-structure alignment are evaluated in a mean field approximation on the basis of probabilities of site pairs to be aligned. Gap penalties are assumed to be proportional to the number of contacts at each residue position, and as a result gaps will be more frequently placed on protein surfaces than in cores. In addition to minimum energy alignments, we use probability alignments made by successively aligning site pairs in order by pairwise alignment probabilities. The results show that the present energy function and alignment method can detect well both folds compatible with a given sequence and, inversely, sequences compatible with a given fold, and yield mostly similar alignments for these two types of sequence and structure pairs. Probability alignments consisting of most reliable site pairs only can yield extremely small root mean square deviations, and including less reliable pairs increases the deviations. Also, it is observed that secondary structure potentials are usefully complementary to yield improved alignments with this method. Remarkably, by this method some individual sequence-structure pairs are detected having only 5-20% sequence identity.     

High frequency of drill holes in brachiopods from the Pliocene of Algeria and its ecological implications

The fossil record holds a wealth of ecological data, including data on biotic interactions. For example, holes in the skeletons of invertebrates produced by drilling activities of their enemies are widely used for exploring the intensity of such interactions through time because they are common and easily distinguished from non-biotic holes or holes produced by other types of interactions. Such drill holes have been described in numerous studies of Palaeozoic brachiopods but rarely in those focusing on brachiopods of the post-Palaeozoic, a striking pattern given that in the late Mesozoic and Cenozoic drilling gastropods diversified and frequencies of drilled molluscs increased dramatically. During the past several years, however, drilled brachiopods were reported in several studies of the Mesozoic and Cenozoic, suggesting that this phenomenon may be more common than has been previously assumed. Here we report on drilled brachiopods from a Pliocene locality in Algeria where 90 of 261 (34.5%) specimens of Megerlia truncata show evidence of predatory drilling. These data confirm that Cenozoic drilling frequencies of brachiopods may be locally high and, when taken together with other published data, that drilling frequencies are highly heterogeneous in space and time.     

Red Queen Dynamics with Non-Standard Fitness Interactions

Antagonistic coevolution between hosts and parasites can involve rapid fluctuations of genotype frequencies that are known as Red Queen dynamics. Under such dynamics, recombination in the hosts may be advantageous because genetic shuffling can quickly produce disproportionately fit offspring (the Red Queen hypothesis). Previous models investigating these dynamics have assumed rather simple models of genetic interactions between hosts and parasites. Here, we assess the robustness of earlier theoretical predictions about the Red Queen with respect to the underlying host-parasite interactions. To this end, we created large numbers of random interaction matrices, analysed the resulting dynamics through simulation, and ascertained whether recombination was favoured or disfavoured. We observed Red Queen dynamics in many of our simulations provided the interaction matrices exhibited sufficient ‘antagonicity’. In agreement with previous studies, strong selection on either hosts or parasites favours selection for increased recombination. However, fast changes in the sign of linkage disequilibrium or epistasis were only infrequently observed and do not appear to be a necessary condition for the Red Queen hypothesis to work. Indeed, recombination was often favoured even though the linkage disequilibrium remained of constant sign throughout the simulations. We conclude that Red Queen-type dynamics involving persistent fluctuations in host and parasite genotype frequencies appear to not be an artefact of specific assumptions about host-parasite fitness interactions, but emerge readily with the general interactions studied here. Our results also indicate that although recombination is often favoured, some of the factors previously thought to be important in this process such as linkage disequilibrium fluctuations need to be reassessed when fitness interactions between hosts and parasites are complex.     

F 2-defect-based model for latent image formation and interactions of O, O– and O2– adsorbates at AgCl and AgBr (001) surfaces: DFT calculations

In an attempt to look for defect-based models for latent image formation, we have examined the reduction and mobility of silver clusters over the F₂-defect-containing surfaces of AgBr and AgCl crystals as well as the interactions of O, O^- and O^2- external adsorbates using an embedded cluster model and density functional theory calculations with effective core potentials. The alkali halide clusters were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces. The most energetically preferred orientations of silver clusters were associated with the rotational angle Š=30° with an uncertainty of DŽ°, 0.05 Å above each surface, internuclear separations of ca. 2.72 and 2.77 Å and activation energy barriers for rotational diffusion of ca. 0.36 and 0.364 eV for AgBr and AgCl, respectively. About 80-83% of the reduction of silver clusters was attributed to the internal structure of the lattice, leaving ca. 17-20% for reduction from external sources such as adsorbates, chemical reducing agents or developers. The contributions to adsorbate-substrate interactions were explainable in terms of surface electrostatic potentials. O, O^- and O^2- species adsorb chemically on the defect-containing surfaces. Charge transfer takes place from the surface to oxygen atoms and from the oxygen anions to the surface, confirming the donor-acceptor properties of the title adsorbates in the course of the adsorbate-substrate interactions.     

Encoding of Naturalistic Stimuli by Local Field Potential Spectra in Networks of Excitatory and Inhibitory Neurons

Recordings of local field potentials (LFPs) reveal that the sensory cortex displays rhythmic activity and fluctuations over a wide range of frequencies and amplitudes. Yet, the role of this kind of activity in encoding sensory information remains largely unknown. To understand the rules of translation between the structure of sensory stimuli and the fluctuations of cortical responses, we simulated a sparsely connected network of excitatory and inhibitory neurons modeling a local cortical population, and we determined how the LFPs generated by the network encode information about input stimuli. We first considered simple static and periodic stimuli and then naturalistic input stimuli based on electrophysiological recordings from the thalamus of anesthetized monkeys watching natural movie scenes. We found that the simulated network produced stimulus-related LFP changes that were in striking agreement with the LFPs obtained from the primary visual cortex. Moreover, our results demonstrate that the network encoded static input spike rates into gamma-range oscillations generated by inhibitory–excitatory neural interactions and encoded slow dynamic features of the input into slow LFP fluctuations mediated by stimulus–neural interactions. The model cortical network processed dynamic stimuli with naturalistic temporal structure by using low and high response frequencies as independent communication channels, again in agreement with recent reports from visual cortex responses to naturalistic movies. One potential function of this frequency decomposition into independent information channels operated by the cortical network may be that of enhancing the capacity of the cortical column to encode our complex sensory environment.     

RNA base-amino acid interaction strengths derived from structures and sequences.

We investigate RNA base-amino acid interactions by counting their contacts in structures and their implicit contacts in various functional sequences where the structures can be assumed to be preserved. These frequencies are cast into equations to extract relative interaction energetics. Previously we used this approach in considering the major groove interactions of DNA, and here we apply it to the more diverse interactions observed in RNA. Structures considered are the three different tRNA synthetase complexes, the U1A spliceosomal protein with an RNA hairpin and the BIV TAR-Tat complex. We use binding data for the base frequencies for the seryl, aspartyl and glutaminyl tRNA-synthetase and U1 RNA-protein complexes. We compare with the previously reported DNA major groove peptide contacts the results for atoms of RNA bases, usually in the major groove. There are strong similarities between the rank orders of interacting bases in the DNA and the RNA cases. The apparent strongest RNA interaction observed is between arginine and guanine which was also one of the strongest DNA interactions. The similar data for base atomic interactions, whether base paired or not, support the importance of strong atomic interactions over local structure considerations, such as groove width and alpha-helicity.     

Calculation of parameters of neuronal network model on the basis of analysis of power spectra of rat brain biopotentials

On the basis of neuronal network a linearized model of power spectrum of the network stable activity was calculated with the approximation of external input by "white" noise. The power spectrum function obtained was used for approximation of the power spectra of the rats motor cortex potentials by the least squares method. As a result the network parameters modelling excitatory and inhibitory cellular and synaptic mechanisms were calculated for two rat strains differing in seizure readiness. As a result of calculations genetically predisposed to seizures KM rats were assumed to differ from unpredisposed to seizures Wistar rats in the increase of efficacy of neuronal interactions (excitatory and inhibitory) as a consequence of the enhanced neuronal "reactivity".     

Spontaneous periodical arrhythmia in the rabbit isolated right atrium

Spontaneous periodical changes in the action potentials of myocytes occurring upon alternating of two types of frequencies were registered under the conditions of oxygenated perfusion of an isolated rabbit atrium. Spontaneous changes of the rhythm were elicited by doubling the duration of action potential, and arrhythmia arose upon passing from one frequency to the other. The rhythmicity was interrupted by spontaneous bigeminy and other minicycles. It was shown that spontaneous bigeminy of the atrium being studied is similar to the artificial bigeminy elicited by electrical impulses. These data indicate that the atrium can be considered as a determined nonlinear system. It was assumed that, from the parameters of spontaneous arrhythmia under stable conditions, it is possible to calculate the frequency of spontaneous rhythmical action potential.     

Non-linear cortico-cortical interactions modulated by cholinergic afferences from the rat basal forebrain

In the adult rat most of basal forebrain cholinergic neurons (BFCN) express the low-affinity p75 nerve growth factor recceptor (NGFr). The immunotoxin 192 IgG-saporin (SAP) provokes a selective loss of NGFr-positive BFCN, somewhat similar to the loss of integrity of BFCN associated with human senile dementia of Alzheimer's type, whereas NGF exerts a trophic action on BFCN. Cortico-cortical interactions are modulated by cholinergic projections of BFCN and it is proposed that alterations of these projections by SAP and by NGF produce opposite effects. This hypothesis was tested by recording multiple local field potentials (LFPs) in the rat temporal cortex and applying bispectral analysis to measure phase-coupled frequencies, somewhat analogous to frequencies of resonance. Choline acetyltransferase (ChAT) activity was measured in the septal area in order to assess the effects of the treatments. NGF-treatment increased ChAT activity by 45% and frequencies of non-linear coupling were shifted towards frequencies higher than 70 Hz, thus suggesting the presence of increased functional interactions in the short range. By contrast, SAP provoked a decrease of nearly 40% in ChAT activity and an increase of phase-coupling in the low frequencies (< 50 Hz), being interpreted as a decreased functional cortico-cortical interaction. Bispectral analysis revealed features of the effect of BFCN on cortical activity that could not be observed by other means and offers as a valuable tool of study that could be extended to the EEG of Alzheimer's patients.