Torque-induced deformations of charged elastic DNA rods: thin helices,loops, and precursors of DNA supercoiling

We study the deformations of charged elastic rods under applied end forces and torques. For neutral filaments, we analyze the energetics of initial helical deformations and loop formation. We supplement this elastic approach with electrostatic energies of bent filaments and find critical conditions for buckling depending on the ionic strength of the solution. We also study force-induced loop opening, for parameters relevant for DNA. Finally, some applications of this nano-mechanical DNA model to salt-dependent onset of the DNA supercoiling are discussed.     

First-principles investigation on structural,elastic, electronic and thermodynamic properties of filled skutterudite PrFe4P12 compound for thermoelectric applications

Filled skutterudite compound PrFe₄P₁₂ is studied using the full potential linear muffin-tin orbital method with the local density approximation for the exchange correlation potential to investigate the systematic trends for structural and elastic properties of the cubic PrFe₄P₁₂ skutterudite. The calculated ground state quantities such as the lattice constant and internal free parameters are in fairly good agreement with the available experimental data. The elastic constants and their pressure dependence are obtained by calculating the total energy versus volume-conserving strains using the Mehl model. Pressure and temperature effects on the lattice constant, bulk modulus, thermal expansion coefficient, Debye temperature and heat capacity are obtained in the range of 0–30 GPa and 0–1000 K. Reduction of bulk modulus and Debye temperature with temperature essentially indicates the thermal softening of the rare earth-filled skutterudites lattice.     

Buckling of a growing tissue and the emergence of two-dimensional patterns

The process of biological growth and the associated generation of residual stress has previously been considered as a driving mechanism for tissue buckling and pattern selection in numerous areas of biology. Here, we develop a two-dimensional thin plate theory to simulate the growth of cultured intestinal epithelial cells on a deformable substrate, with the goal of elucidating how a tissue engineer might best recreate the regular array of invaginations (crypts of Lieberkühn) found in the wall of the mammalian intestine. We extend the standard von Kármán equations to incorporate inhomogeneity in the plate’s mechanical properties and surface stresses applied to the substrate by cell proliferation. We determine numerically the configurations of a homogeneous plate under uniform cell growth, and show how tethering to an underlying elastic foundation can be used to promote higher-order buckled configurations. We then examine the independent effects of localised softening of the substrate and spatial patterning of cellular growth, demonstrating that (within a two-dimensional framework, and contrary to the predictions of one-dimensional models) growth patterning constitutes a more viable mechanism for control of crypt distribution than does material inhomogeneity.     

Cheaters must prosper: reconciling theoretical and empirical perspectives on cheating in mutualism

Cheating is a focal concept in the study of mutualism, with the majority of researchers considering cheating to be both prevalent and highly damaging. However, current definitions of cheating do not reliably capture the evolutionary threat that has been a central motivation for the study of cheating. We describe the development of the cheating concept and distill a relative‐fitness‐based definition of cheating that encapsulates the evolutionary threat posed by cheating, i.e. that cheaters will spread and erode the benefits of mutualism. We then describe experiments required to conclude that cheating is occurring and to quantify fitness conflict more generally. Next, we discuss how our definition and methods can generate comparability and integration of theory and experiments, which are currently divided by their respective prioritisations of fitness consequences and traits. To evaluate the current empirical evidence for cheating, we review the literature on several of the best‐studied mutualisms. We find that although there are numerous observations of low‐quality partners, there is currently very little support from fitness data that any of these meet our criteria to be considered cheaters. Finally, we highlight future directions for research on conflict in mutualisms, including novel research avenues opened by a relative‐fitness‐based definition of cheating.     

Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutation

We examine properties of adaptive walks on uncorrelated (i.e. random) fitness landscapes starting from moderately fit genotypes under strong selection weak mutation. As an extension of Orr's model for a single step in an adaptive walk under these conditions, we show that the fitness rank of the dominant genotype in a population after the fixation of a beneficial mutation is, on average, (i+6)/4, where i is the fitness rank of the starting genotype. This accounts for the change in rank due to acquiring a new set of single-mutation neighbors after fixing a new allele through natural selection. Under this scenario, adaptive walks can be modeled as a simple Markov chain on the space of possible fitness ranks with an absorbing state at i = 1, from which no beneficial mutations are accessible. We find that these walks are typically short and are often completed in a single step when starting from a moderately fit genotype. As in Orr's original model, these results are insensitive to both the distribution of fitness effects and most biological details of the system under consideration.     

Buckling and postbuckling of radially loaded microtubules by nonlocal shear deformable shell model

This paper presents an investigation on the buckling and postbuckling of microtubules (MTs) subjected to a uniform external radial pressure in thermal environments. The microtubule is modeled as a nonlocal shear deformable cylindrical shell which contains small scale effects. The governing equations are based on higher order shear deformation shell theory with a von Kármán-Donnell-type of kinematic nonlinearity and include the extension-twist and flexural-twist couplings. The thermal effects are also included and the material properties are assumed to be temperature-dependent. A singular perturbation technique is employed to determine the buckling pressure and postbuckling equilibrium paths. The small scale parameter e₀a is estimated by matching the buckling pressure of MTs measured from the experiments with the numerical results obtained from the nonlocal shear deformable shell model. The numerical results show that buckling pressure and postbuckling behavior of MTs are very sensitive to the small scale parameter e₀a. The results reveal that the 13_3 microtubule has a stable postbuckling path, whereas the 13_2 microtubule has an unstable postbuckling behavior due to the presence of skew angles.     

DNA conformation and energy in nucleosome core: a theoretical approach

DNA conformation in complex with proteins is far from its canonical B-form. The affinity of complex formation and structure of DNA depend on its attachment configuration and sequence. In this article, we develop a mechanical model to address the problem of DNA structure and energy under deformation. DNA in nucleosome core particle is described as an example. The structure and energy of nucleosomal DNA is calculated based on its sequence and positioning state. The inferred structure has remarkable similarity with X-ray data. Although there is no sequence-specific interaction of bases and the histone core, we found considerable sequence dependency for the nucleosomal DNA positioning. The affinity of nucleosome formation for several sequences is examined and the differences are compatible with observations. We argue that structural energy determines the natural state of nucleosomal DNA and is the main reason for affinity differences in vitro. This theory can be utilized for the DNA structure and energy determination in protein–DNA complexes in general.

An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:17     

A unified framework for diversity gradients: the adaptive trait continuum

Aim Adaptive trait continua are axes of covariation observed in multivariate trait data for a given taxonomic group. These continua quantify and summarize life‐history variation at the inter‐specific level in multi‐specific assemblages. Here we examine whether trait continua can provide a useful framework to link life‐history variation with demographic and evolutionary processes in species richness gradients. Taking an altitudinal species richness gradient for Mediterranean butterflies as a study case, we examined a suite of traits (larval diet breadth, adult phenology, dispersal capacity and wing length) and species‐specific habitat measures (temperature and aridity breadth). We tested whether traits and species‐specific habitat measures tend to co‐vary, whether they are phylogenetically conserved, and whether they are able to explain species distributions and spatial genetic variation in a large number of butterfly assemblages. Location Catalonia, Spain. Methods We formulated predictions associated with species richness gradients and adaptive trait continua. We applied principal components analyses (PCAs), structural equation modelling and phylogenetic generalized least squares models. Results We found that traits and species‐specific habitat measures covaried along a main PCA axis, ranging from multivoltine trophic generalists with high dispersal capacity to univoltine (i.e. one generation per year), trophic specialist species with low dispersal capacity. This trait continuum was closely associated with the observed distributions along the altitudinal gradient and predicted inter‐specific differences in patterns of spatial genetic variability (F_ST and genetic distances), population responses to the impacts of global change and local turnover dynamics. Main conclusions The adaptive trait continuum of Mediterranean butterflies provides an integrative and mechanistic framework to: (1) analyse geographical gradients in species richness, (2) explain inter‐specific differences in population abundances, spatial distributions and demographic trends, (3) explain inter‐specific differences in patterns of genetic variation (F_ST and genetic distances), and (4) study specialist–generalist life‐history transitions frequently involved in butterfly diversification processes.     

Behavioral and neural Darwinism: Selectionist function and mechanism in adaptive behavior dynamics

An evolutionary theory of behavior dynamics and a theory of neuronal group selection share a common selectionist framework. The theory of behavior dynamics instantiates abstractly the idea that behavior is selected by its consequences. It implements Darwinian principles of selection, reproduction, and mutation to generate adaptive behavior in virtual organisms. The behavior generated by the theory has been shown to be quantitatively indistinguishable from that of live organisms. The theory of neuronal group selection suggests a mechanism whereby the abstract principles of the evolutionary theory may be implemented in the nervous systems of biological organisms. According to this theory, groups of neurons subserving behavior may be selected by synaptic modifications that occur when the consequences of behavior activate value systems in the brain. Together, these theories constitute a framework for a comprehensive account of adaptive behavior that extends from brain function to the behavior of whole organisms in quantitative detail.     

The evolutionary consequences of niche construction: a theoretical investigation using two-locus theory

This paper addresses the joint evolution of environment-altering (niche constructing) traits, and traits whose fitness depends on alterable sources of natural selection in environments. We explore the evolutionary consequences of this niche construction using a two-locus population genetic model. The novel conclusions are that niche construction can (1) cause evolutionary inertia and momentum, (2) lead to the fixation of otherwise deleterious alleles, (3) support stable polymorphisms where none are expected, (4) eliminate what would otherwise be stable polymorphisms, and (5) influence disequilibrium. The results suggest that the changes that organisms bring about in their niche can themselves be an important source of natural selection pressures, and imply that evolution may proceed in cycles of selection and niche construction.     

Buckling of inner cell wall layers after manipulations to reduce tensile stress: observations and interpretations for stress transmission

The inner layer of the cell wall in tissues that are under tensile stress in situ, e.g. epidermis and collenchyma of etiolated sunflower hypocotyls, shows a pattern of transverse folds when the tissues are detached and plasmolysed. This can be observed by Nomarski imaging of inner surfaces of the outer cell walls and electron microscopy of longitudinal sections after peeling the epidermis and bathing it in plasmolysing solutions. The folds are apparently caused by buckling of the inner layer due to the longitudinal compressive force exerted on this layer by the outer wall layer, when it shrinks after the removal of the longitudinal tensile stresses. In these stresses, two components can be distinguished: the tissue stress, disappearing on peeling, and that caused directly by turgor pressure, disappearing in hyperosmotic solution. Investigation of the buckling indicates that the outer layer of the cell wall transmits in situ most of the longitudinal tensile stress in the wall. The common concept that the inner layer of the wall is the region bearing most stress and therefore regulating growth can still be valid with respect to the transverse stress component.     

Roles of parasitic fungi in aquatic food webs: a theoretical approach

1. Parasites are ubiquitous in ecosystems, but their roles in material transfer are poorly understood. Fungal parasites in freshwater ecosystems are of major importance to small heterotrophic eukaryotes and consume large phytoplankton that are resistant to zooplankton grazing. 2. To evaluate their ecosystem‐level effects, we developed a simple food web model that incorporates competition between small and large phytoplankton for nutrients, zooplankton grazing on small phytoplankton, fungal parasitism on large phytoplankton and includes a newly discovered trophic link from fungal zoospores to zooplankton (F‐Z link). 3. Our model demonstrates the likely occurrence of an indirect mutualism between fungi and zooplankton, in which fungal parasitism increases zooplankton production by reducing the biomass of inedible large phytoplankton. Contradicting the expectation from a previous short‐term experiment that the F‐Z link may benefit zooplankton, the presence of the F‐Z link can reduce material transfer from phytoplankton to zooplankton because of the negative effect of the indirect mutualism. The model indicates that high growth efficiency of fungi on host tissue and their high nutrient status for zooplankton are crucial for the F‐Z link to increase zooplankton production. 4. The model also indicates that the contribution of material transfer via F‐Z link to zooplankton increases with nutrient availability. Our results suggest that parasitic fungi may be a key player in material transfer, especially in eutrophic ecosystems.     

Numerical Simulation of Bone Plate with Fatigue Crack and Investigation of Attraction Hole for Retarding Crack Growth

Premature fracture of the bone plate caused by fatigue crack is the main failure mode in treating femoral shaft fracture. In order to improve the durability of the plate, this study proposed a crack attraction hole (CAH) to retard the crack propagation based on the fracture mechanics. In this paper, a numerical model of the femoral fracture internal fixation system was constructed, in which the femur was developed using a validated simplified model. First, the fatigue crack initiation location was defined at the stress concentration through static analysis. Next, with the joint simulation method of Franc3D and ABAQUS, the fatigue crack path in the bone plate was predicted. Meanwhile, the Paris parameters of Ti-6Al-4V obtained through experiments were encoded into Franc3D to calculate the crack propagation life. Finally, we considered the influence of CAH designs with different relative vertical distances (2.0, 3.0, and 4.0 mm) and diameters (1.5, 2.0, and 2.5 mm) on the crack propagation path and life of the bone plate. Additionally, the effects of all CAH configurations on the biomechanical performance of the bone plate fixation system were evaluated. The results indicated that the fatigue crack growth path in the bone plate is comparable to a straight line, and the crack growth rate significantly increases when the crack tip reaches the outer boundary of the plate. The findings suggest that the addition of CAH in the bone plate will lead to the deflection of the crack path and increase the fatigue life. Equally important, the improvement of the fatigue life was positively correlated with the diameter of CAH and negatively correlated with the relative vertical distance. In addition, the biomechanical properties of the bone plate system were slightly affected by CAH, substantiating the feasibility of this method. Finally, the comparative analysis verified that a CAH with a relative vertical distance of 3 mm and a diameter of 2 mm exhibited superior improvement in the comprehensive performance on the bone plate.     

Arginine pathways and the inflammatory response: Interregulation of nitric oxide and polyamines: Review article

Summary. An early response to an acute inflammatory insult, such as wound healing or experimental glomerulonephritis, is the conversion of arginine to the cytostatic molecule nitric oxide (NO). This anti-bacterial phase is followed by the conversion of arginine to ornithine, which is the precursor for the pro-proliferative polyamines as well as proline for the production of extracellular matrix. This latter, pro-growth phase constitutes a repair phase response. The temporal switch of arginine as a substrate for the cytostatic iNOS/NO axis to the pro-growth arginase/ ornithine/polyamine and proline axis is subject to regulation by inflammatory cytokines as well as interregulation by the arginine metabolites themselves. Arginine is also the precursor for another biogenic amine, agmatine. Here we describe the capacity of these three arginine pathways to interregulate, and propose a model whereby agmatine has the potential to serve in the coordination of the early and repair phase pathways of arginine in the inflammatory response by acting as a gating mechanism at the transition from the iNOS/NO axis to the arginase/ODC/polyamine axis. Due to the pathophysiologic and therapeutic potential, we will further examine the antiproliferative effects of agmatine on the polyamine pathway.     

Structure and distribution of floral trichomes in Lycaste and Sudamerlycaste (Orchidaceae: Maxillariinae s.l.)

Phylogenetic analysis indicates that Lycastinae should be incorporated into a more broadly defined Maxillariinae. This is supported by several anatomical features, including the presence of sunken, glandular trichomes in both Lycastinae and Maxillariinae s.s. Until recently, these were known only from vegetative organs, but have since been reported from flowers of Maxillaria dichroma. One character currently used to distinguish between Lycaste and Sudamerlycaste is the distribution of floral trichomes. In this article, we test the reliability of this character, describe the floral micromorphology of Lycaste and Sudamerlycaste and investigate whether their flowers bear sunken hairs. Their floral micromorphology is compared with that of other genera currently assigned to Maxillariinae s.l. Flowers of Lycaste and Sudamerlycaste bear conical or obpyriform papillae and unbranched and unequally branched multicellular trichomes. Contrary to previous reports that trichomes are confined to the column in Sudamerlycaste, they also occur in the tepal axils. Labellar trichomes, although often present in Lycaste, are lacking in Sudamerlycaste. In Lycaste sections Lycaste and Aromaticae, floral trichomes tend to be unbranched, whereas section Intermediae has both unbranched and branched hairs. Branched hairs are more common in Sudamerlycaste. Some hairs are tracheoidal, pitted and lignified. These mainly occur in section Lycaste and, to a degree, in section Intermediae, but are absent from section Aromaticae and most species of Sudamerlycaste. Branched column hairs, present in Sudamerlycaste, are absent from all sections of Lycaste, and tracheoidal column hairs occur only in Sudamerlycaste. Sunken floral hairs are absent from both genera. Trichome structure and distribution may prove useful in distinguishing between these taxa and in elucidating the intergeneric relationships of Maxillariinae s.l.© 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 409–421.     

Phylogenetics and biogeography of the Balkan ‘sand gobies’ (Teleostei: Gobiidae): vulnerable species in need of taxonomic revision

Within the Atlantic–Mediterranean region, the ‘sand gobies’ are abundant and widespread, and play an important role in marine, brackish, and freshwater ecosystems. They include the smallest European freshwater fish, Economidichthys trichonis, which is threatened by habitat loss and pollution, as are several other sand gobies. Key to good conservation management is an accurate account of the number of evolutionary significant units. Nevertheless, many taxonomic and evolutionary questions remain unresolved within the clade, and molecular studies are lacking, especially in the Balkans. Using partial 12S and 16S mitochondrial ribosomal DNA sequences of 96 specimens of at least eight nominal species (both freshwater and marine populations), we assess species relationships and compare molecular and morphological data. The results obtained do not support the monophyly of Economidichthys, suggesting the perianal organ to be a shared adaptation to hole‐brooding rather than a synapomorphy, and urge for a taxonomic revision of Knipowitschia. The recently described Knipowitschia montenegrina seems to belong to a separate South‐East Adriatic lineage. Knipowitschia milleri, an alleged endemic of the Acheron River, and Knipowitschia cf. panizzae, are shown to be very closely related to other western Greek Knipowitschia populations, and appear conspecific. A distinct Macedonian–Thessalian lineage is formed by Knipowitschia thessala, whereas Knipowitschia caucasica appears as an eastern lineage, with populations in Thrace and the Aegean. The present study combines the phylogeny of a goby radiation with insights on the historical biogeography of the eastern Mediterranean, and identifies evolutionary units meriting conservation attention. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 73–91.     

Excitotoxic and post-ischemic neurodegeneration: Involvement of transglutaminases

Summary. Neurodegeneration induced by excitotoxicity is a common feature in various neurological disorders. This pathological condition is caused by prolonged stimulation of glutamate receptor subtypes, followed by both intracellular Ca²⁺ overload and activation of specific genes, resulting in synthesis of enzymes involved in cell stress response.Using experimental in vitro models of excitotoxicity, we demonstrated that glutamate exposure up-regulated tissue transglutaminase in primary cultures of both cerebellar granule cells and astrocytes. These changes were consequent to receptor-mediated Ca²⁺ influx, as demonstrated by the inhibition with selective antagonists, MK-801 and GYKI 52466. Early increases in different transglutaminase isoforms were also observed in global cerebral ischemia, which closely resembles neuronal damage caused by NMDA receptor activation.These findings agree with a postulated role for transglutaminases in molecular mechanisms of several neurodegenerative diseases. Indeed, increased cross-linking reactions could be of pathologic relevance, as part of biochemical changes observed in neurological disorders.     

Calorimetric and spectroscopic investigation of the interaction between the C‐terminal domain of Enzyme I and its ligands

Enzyme I initiates a series of phosphotransfer reactions during sugar uptake in the bacterial phosphotransferase system. Here, we have isolated a stable recombinant C-terminal domain of Enzyme I (EIC) of Escherichia coli and characterized its interaction with the N-terminal domain of Enzyme I (EIN) and also with various ligands. EIC can phosphorylate EIN, but their binding is transient regardless of the presence of phosphoenolpyruvate (PEP). Circular dichroism and NMR indicate that ligand binding to EIC induces changes near aromatic groups but not in the secondary structure of EIC. Binding of PEP to EIC is an endothermic reaction with the equilibrium dissociation constant (K_D) of 0.28 mM, whereas binding of the inhibitor oxalate is an exothermic reaction with K_D of 0.66 mM from calorimetry. The binding thermodynamics of EIC and PEP compared to that of Enzyme I (EI) and PEP reveals that domain–domain motion in EI can contribute as large as ∼−3.2 kcal/mol toward PEP binding.