Insight on the interaction of polychlorobiphenyl with nucleic acid–base

The interaction between one polychlorobiphenyl (3,3′,4,4′,-tetrachlorobiphenyl, coded PCB77) and the four DNA nucleic acid–base is studied by means of quantum mechanics calculations in stacked conformations. It is shown that even if the intermolecular dispersion energy is the largest component of the total interaction energy, some other contributions play a non negligible role. In particular the electrostatic dipole-dipole interaction and the charge transfer from the nucleobase to the PCB are responsible for the relative orientation of the monomers in the complexes. In addition, the charge transfer tends to flatten the PCB, which could therefore intercalate more easily between DNA base pairs. From these seminal results, we predict that PCB could intercalate completely between two base pairs, preferably between Guanine:Cytosine pairs.

Direct and indirect effects of ant–trophobiont interactions on the reproduction of a hummingbird-pollinated mistletoe

Plant Ecology - Fluid-feeding herbivores directly affect host plants through sap consumption. Moreover, they establish mutualistic relationships with ants, which might generate additional...     

Splitting of the spectra of MHD waves and the structure of a satellite alfvén resonance in a cold plasma in a strong axial magnetic field and a weak helical field

The possibility is demonstrated of splitting the eigenfrequencies of MHD plasma waves in a stellarator with a weakly rippled helical confining magnetic field. The distribution of the fields of an Alfvén wave in the satellite Alfvén resonance region is investigated when the influence of the helical ripple in a confining magnetic field on the resonance structure is comparable with the effects of the finite ion Larmor radius, electron inertia, and collisions between plasma particles.     

Comment on ‘Thermodynamic database supports deciphering protein–nucleic acid interactions’

Mei and colleagues reported a thermodynamic database, PNATDB for protein-nucleic acid interactions, which contains 12 635 experimentally determined thermodynamic parameters. They claimed that extracting data from existing databases is difficult. ProNAB, which has more than 20 000 experimental data points for binding affinities of protein–nucleic acid complexes and other information, was not discussed.     

Consumer–resource dynamics of indirect interactions in a mutualism–parasitism food web module

Food web dynamics are well known to vary with indirect interactions, classic examples including apparent competition, intraguild predation, exploitative competition, and trophic cascades of food chains. Such food web modules entailing predation and competition have been the focus of much theory, whereas modules involving mutualism have received far less attention. We examined an empirically common food web module involving mutualistic (N ₂) and parasitic (N ₃) consumers exploiting a resource of a basal mutualist (N ₁), as illustrated by plants, pollinators, and nectar robbers. This mutualism–parasitism food web module is structurally similar to exploitative competition, suggesting that the module of two consumers exploiting a resource is unstable. Rather than parasitic consumers destabilizing the module through (?,?) indirect interactions, two mechanisms associated with the mutualism can actually enhance the persistence of the module. First, the positive feedback of mutualism favors coexistence in stable limit cycles, whereby (+,?) indirect interactions emerge in which increases in N ₂ have positive effects on N ₃ and increases in N ₃ have negative effects on N ₂. This (+,?) indirect interaction arising from the saturating positive feedback of mutualism has broad feasibility across many types of food web modules entailing mutualism. Second, optimization of resource exploitation by the mutualistic consumer can lead to persistence of the food web module in a stable equilibrium. The mutualism–parasitism food web module is a basic unit of food webs in which mutualism favors its persistence simply through density-dependent population dynamics, rather than parasitism destabilizing the module.     

Impact of external forces on cyanophage–host interactions in aquatic ecosystems

Cyanobacterial (algal) blooms have by convention been attributed to the excessive level of nutrients from pollution and runoff, which promotes the rapid growth and multiplication of cyanobacteria or algae. The cyanophage (virus) is the natural predator of cyanobacteria (the host). The aim of this review is to unveil certain pressures that disrupt cyanophage–host interactions and the formation of cyanobacterial blooms. This review focuses principally on the impact of greenhouse gases, ozone depletion, solar ultraviolet radiation (SUR) and the role of recently discovered virophages, which coexist with and in turn are the natural predator of phages. The key findings are that the increase in SUR, the mutation of cyanophages and cyanobacteria, along with changing nutrient levels, have combined with virophages to impede cyanophage–host interactions and the resultant viral infection and killing of the cyanobacterial cell, which is a necessary step in controlling cyanobacterial blooms. Consider this a ‘call to action’ for researchers interested in corrective action aimed at evolving aquatic ecosystems.     

Nonlinear dynamics of beam–plasma instability in a finite magnetic field

The nonlinear dynamics of beam–plasma instability in a finite magnetic field is investigated numerically. In particular, it is shown that decay instability can develop. Special attention is paid to the influence of the beam?plasma coupling factor on the spectral characteristics of a plasma relativistic microwave accelerator (PRMA) at different values of the magnetic field. It is shown that two qualitatively different physical regimes take place at two values of the external magnetic field: B ₀ = 4.5 kG (Ω ~ ωB _p ) and 20 kG (Ω _B ? ω_p). For B ₀ = 4.5 kG, close to the actual experimental value, there exists an optimal value of the gap length between the relativistic electron beam and the plasma (and, accordingly, an optimal value of the coupling factor) at which the PRMA output power increases appreciably, while the noise level decreases.     

Electron spin resonance in membrane research: protein–lipid interactions from challenging beginnings to state of the art

Conventional electron paramagnetic resonance (EPR) spectra of lipids that are spin-labelled close to the terminal methyl end of the acyl chains are able to resolve the lipids directly contacting the protein from those in the fluid bilayer regions of the membrane. This allows determination of both the stoichiometry of lipid–protein interaction (i.e., number of lipid sites at the protein perimeter) and the selectivity of the protein for different lipid species (i.e., association constants relative to the background lipid). Spin-label EPR data are summarised for 20 or more different transmembrane peptides and proteins, and 7 distinct species of lipids. Lineshape simulations of the two-component conventional spin-label EPR spectra allow estimation of the rate at which protein-associated lipids exchange with those in the bulk fluid regions of the membrane. For lipids that do not display a selectivity for the protein, the intrinsic off-rates for exchange are in the region of 10 MHz: less than 10× slower than the rates of diffusive exchange in fluid lipid membranes. Lipids with an affinity for the protein, relative to the background lipid, have off-rates for leaving the protein that are correspondingly slower. Non-linear EPR, which depends on saturation of the spectrum at high radiation intensities, is optimally sensitive to dynamics on the timescale of spin-lattice relaxation, i.e., the microsecond regime. Both progressive saturation and saturation transfer EPR experiments provide definitive evidence that lipids at the protein interface are exchanging on this timescale. The sensitivity of non-linear EPR to low frequencies of spin exchange also allows the location of spin-labelled membrane protein residues relative to those of spin-labelled lipids, in double-labelling experiments.     

Natal imprinting to the Earth’s magnetic field in a pelagic seabird

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Theoretical studies on the interaction of proteins and nucleic acid: II. The binding of α-helix to B-DNA

Interactions between B-DNA and homopolymeric α-helices of glycine, alanine, serine, asparagine and aspartic acid have been studied theoretically. The complexation energy has been minimised taking into account the interactions between DNA and the polypeptides as well as the internal energy of the α-helix and the interaction energy of counterions with the complex. The results obtained indicate the important role of strong hydrogen bonds between the peptide side chains and nucleic acid phosphate groups, these bonds being much stronger than specific interactions with the base-pairs. The formation of these structural bonds depends on the size of the α-helix, which in turn determines whether bridging across the major groove is possible. The steric role of the methyl group of thymine in orienting the peptide helix and the role of DNA screening cations in complex stabilization are also significant.     

Effect of the periodic ripple in an axial confining magnetic field on the Alfvén heating of a cylindrical plasma

In a uniform axial magnetic field, the structure of local Alfvén resonance and the resonant absorption of RF power are governed by collisions, finite ion Larmor radius effects, and electron inertia. It is shown that, in a cylindrical plasma in a constant, periodically rippled, axial magnetic field, the structure of Alfvén resonance and the absorption of RF power can strongly depend on the ripple amplitude. The conditions under which the effect in question is dominant are intrinsic, e.g., to the modular Wendelstein stellarators.     

Nuclear magnetic resonance chromatography: applications of pulse field gradient diffusion NMR to mixture analysis and ligand–receptor interactions

Pulse field gradient (PFG) diffusion NMR spectroscopy is a non-invasive method for the spectroscopic separation and identification of compounds of interest from a mixture. Because it relies on differences in translational diffusion rates to resolve NMR signals from individual components, pulse field gradient NMR is a unique method for analyzing complex mixtures and for detecting intermolecular interactions. A number of multidimensional pulse field gradient NMR experiments have been developed to alleviate the overlap of NMR signals arising from a complex mixture and facilitate component identification. The applications of pulse field gradient NMR for mixture analysis and for the direct identification of high affinity ligands are reviewed.     

The role of intramolecular hydrogen bonding on nucleobase acidification following metal coordination: possible implications of an “indirect” role of metals in acid–base catalysis of nucleic acids

The acidifying effect of Pt^II on nucleobase –NH and –NH₂ groups depends both on the site of metal coordination and on the efficiency of stabilization of the deprotonated nucleobase via intracomplex hydrogen bonding. Weakly acidic nucleobase protons with pK _a values between 9 and 17 can be acidified by a single Pt^II to have pK _a values which are well within the physiological pH range. This could open the possibility of an acid–base catalysis occurring at pH 7, with the metal–nucleobase entity functioning either as an acid or a base. Examples of Pt^II complexes studied here include, among others, mixed nucleobase systems of 1-methylcytosine and 1,9-dimethyladenine as well as a complex of the rare iminooxo tautomer of 1-methylcytosine having the metal bonded at N4.     

Erratum to: An in silico biomechanical analysis of the stent–esophagus interaction

Biomechanics and Modeling in Mechanobiology - In the original publication of the article, Tables 2 and 3 were published with error. The correct tables are provided below (Tables 2, 3). The...