Joint evolution of differential seed dispersal and self‐fertilization

Differential seed dispersal, in which selfed and outcrossed seeds possess different dispersal propensities, represents a potentially important individual‐level association. A variety of traits can mediate differential seed dispersal, including inflorescence and seed size variation. However, how natural selection shapes such associations is poorly known. Here, we developed theoretical models for the evolution of mating system and differential seed dispersal in metapopulations, incorporating heterogeneous pollination, dispersal cost, cost of outcrossing and environment‐dependent inbreeding depression. We considered three models. In the ‘fixed dispersal model’, only selfing rate is allowed to evolve. In the ‘fixed selfing model’, in which selfing is fixed but differential seed dispersal can evolve, we showed that natural selection favours a higher, equal or lower dispersal rate for selfed seeds to that for outcrossed seeds. However, in the ‘joint evolution model’, in which selfing and dispersal can evolve together, evolution necessarily leads to higher or equal dispersal rate for selfed seeds compared to that for outcrossed. Further comparison revealed that outcrossed seed dispersal is selected against by the evolution of mixed mating or selfing, whereas the evolution of selfed seed dispersal undergoes independent processes. We discuss the adaptive significance and constraints for mating system/dispersal association.     

RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials

A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Baker's minimisation. We show example applications of RASPA in computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, reaction systems and visualisation. The software is released under the GNU General Public License.     

A biomechanical study of the relationship between running velocity and three-dimensional lumbosacral kinetics

Faster running is not performed with proportional increase in all joint torque/work exertions. Although previous studies have investigated lumbopelvic kinetics for a single velocity, it is unclear whether each lumbopelvic torque should increase for faster running. We examined the relationship between running velocity and lumbopelvic kinetics. We calculated the three-dimensional lumbosacral kinetics of 10 male sprinters during steady-state running on a temporary indoor running track at five target velocities: 3.0 (3.20 ± 0.16), 4.5 (4.38 ± 0.18), 6.0 (5.69 ± 0.47), 7.5 (7.30 ± 0.41), and maximal sprinting (9.27 ± 0.36 m/s). The lumbosacral axial rotation torque increased more markedly (from 0.37 ± 0.06 to 1.99 ± 0.46 Nm/kg) than the extension and lateral flexion torques. The increase in the axial rotation torque was larger above 7.30 m/s. Conversely, the extension and lateral flexion torques plateaued when running velocity increased above 7.30 m/s. Similar results were observed for mechanical work. The results indicate that faster running required larger lumbosacral axial rotation torque. Conversely, the extension and lateral flexion torques were relatively invariant to running velocity above 7 m/s, implying that faster running below 7 m/s might increase the biomechanical loads causing excessive pelvic posterior tilt and excessive pelvic drop which has the potential to cause pain/injury related to lumbopelvic extensors and lateral flexors, whereas these biomechanical loads might not relate with running velocity above 7 m/s.     

Vegetation,fire and soil feedbacks of dynamic boundaries between rainforest,savanna and grassland

At fine spatial scales, savanna‐rainforest‐grassland boundary dynamics are thought to be mediated by the interplay between fire, vegetation and soil feedbacks. These processes were investigated by quantifying tree species composition, the light environment, quantities and flammability of fuels, bark thickness, and soil conditions across stable and dynamic rainforest boundaries that adjoin grassland and eucalypt savanna in the highlands of the Bunya Mountains, southeast Queensland, Australia. The size class distribution of savanna and rainforest stems was indicative of the encroachment of rainforest species into savanna and grassland. Increasing dominance of rainforest trees corresponds to an increase in woody canopy cover, the dominance of litter fuels (woody debris and leaf), and decline in grass occurrence. There is marked difference in litter and grass fuel flammability and this result is largely an influence of strongly dissimilar fuel bulk densities. Relative bark thickness, a measure of stem fire resistance, was found to be generally greater in savanna species when compared to that of rainforest species, with notable exceptions being the conifers Araucaria bidwillii and Araucaria cunninghamii. A transect study of soil nutrients across one dynamic rainforest – grassland boundary indicated the mass of carbon and nitrogen, but not phosphorus, increased across the successional gradient. Soil carbon turnover time is shortest in stable rainforest, intermediate in dynamic rainforest and longest in grassland highlighting nutrient cycling differentiation. We conclude that the general absence of fire in the Bunya Mountains, due to a divergence from traditional Aboriginal burning practices, has allowed for the encroachment of fire‐sensitive rainforest species into the flammable biomes of this landscape. Rainforest invasion is likely to have reduced fire risk via changes to fuel composition and microclimatic conditions, and this feedback will be reinforced by altered nutrient cycling. The mechanics of the feedbacks here identified are discussed in terms of landscape change theory.     

Conformational stability of the epidermal growth factor (EGF) receptor as influenced by glycosylation,dimerization and EGF hormone binding

The epidermal growth factor receptor (EGFR) is an important transmembrane glycoprotein kinase involved the initiation or perpetuation of signal transduction cascades within cells. These processes occur after EGFR binds to a ligand [epidermal growth factor (EGF)], thus inducing its dimerization and tyrosine autophosphorylation. Previous publications have highlighted the importance of glycosylation and dimerization for promoting proper function of the receptor and conformation in membranes; however, the effects of these associations on the protein conformational stability have not yet been described. Molecular dynamics simulations were performed to characterize the conformational preferences of the monomeric and dimeric forms of the EGFR extracellular domain upon binding to EGF in the presence and absence of N‐glycan moieties. Structural stability analyses revealed that EGF provides the most conformational stability to EGFR, followed by glycosylation and dimerization, respectively. The findings also support that EGF–EGFR binding takes place through a large‐scale induced‐fitting mechanism. Proteins 2017; 85:561–570. © 2016 Wiley Periodicals, Inc.     

桃江县毛竹林生态系统碳储量及其空间分布

采用标准地调查和生物量实测方法,研究了湖南省桃江县毛竹林生态系统生物量、碳含量、碳储量及空间分布格局。结果表明,不同年龄毛竹林生态系统总生物量分别为:28.147、30.889 t/hm~2和57.763 t/hm~2,其中竹林层生物量为20.254、25.036、55.685 t/hm~2,各器官生物量均以竹竿最高,占器官生物量的63.0%以上。不同年龄毛竹各器官碳平均含量为0.466—0.483 g C/g;灌木层碳含量为0.474—0.489 g C/g;草本层为0.472—0.490 g C/g;死地被物层为0.213—0.276 g C/g;土壤层有机碳含量为14.790—34.503 g C/g。各年龄毛竹林生态系统总碳储量分别为131.273、139.089 t/hm~2和167.817 t/hm~2,其中植被层碳储量为13.627—28.419 t/hm~2,占系统总碳储量的9.935%—16.935%;死地被物为0.307—0.420 t/hm~2,占0.234%—0.265%;土壤层为117.339—138.978 t/hm~2,占82.815%—89.799%。毛竹林生态系统碳储量分布格局为:土壤层植被层死地被物层。研究结果可为深入研究毛竹林的碳平衡提供基础数据。     

Efficient tuning of potential parameters for liquid–solid interactions

Spherical and cylindrical water droplets on silicon surface are studied to tune the silicon–oxygen interaction. We use molecular dynamics simulations to estimate the contact angle of two different shaped droplets. We found that the cylindrical droplets are independent of the line tension as their three phases curvature is equal zero. Additionally, we compare an analytical model, taking into account or not the Tolman length and we show that for spherical small size droplets, this length is important to be included, in contrast to cylindrical droplets in which the influence of the Tolman length is negligible. We demonstrate that the usual convenient way to exclude linear tension in the general case can give wrong results. Here, we consider cylindrical droplets, since their contact angle does not depend on the droplet size in the range of few to 10ths of nanometres. The droplets are stabilised due to the periodic boundary conditions. This allows us to propose a new parameterisation for nanoscale droplets, which is independent the size of the droplets or its shape, minimising at the same time the calculation procedure. With the proposed methodology, we can extract the epsilon parameter of the interaction potential between a liquid and a solid from the nanoscaled molecular simulation with only as input the macrosized experimental wetting angle for a given temperature.     

Substrate docking and molecular dynamic simulation for prediction of fungal enzymes from Trichoderma species-assisted extraction of nanocellulose from oil palm leaves

Abstract

Fungi of the Trichoderma species are valued industrial enzymes in support of the ‘zero-waste’ technology to convert agro-industrial biomass into valuable products, i.e. nanocellulose (NC). In this study, an in silico approach using substrate docking and molecular dynamic (MD) simulation was used to predict the order of which the multilayers of cellulosic polymers, i.e. lignin, hemicellulose and cellulose in oil palm leaves (OPL) are degraded by fungal enzymes, endocellulase and exocellulase. The study aimed to establish the catalytic tendencies of the enzymes to optimally degrade the cellulosic components of OPL for high yield production of NC. Energy minimized endocellulase and exocellulase models revealed satisfactory scores of PROCHECK (90.0% and 91.2%), Verify3D (97.23% and 98.85%) and ERRAT (95.24% and 91.00%) assessments. Active site prediction by blind docking, COACH meta-server and multiple sequence alignment indicated the catalytic triads for endocellulase and exocellulase were Ser116–His205–Glu249 and Ser382–Arg124–Asp385, respectively. Binding energy of endocellulase docked with hemicellulose (?6.0 ? kcal mol^?1) was the most favourable followed by lignin (?5.6 ? kcal mol^?1) and cellulose (?4.4 ? kcal mol^?1). Exocellulase, contrarily, bonded favorably with lignin (?8.7 ? kcal mol^?1), closely followed by cellulose (?8.5 ? kcal mol^?1) and hemicellulose (?8.4 ? kcal mol^?1). MDs simulations showed that interactions of complexes, endocellulase–hemicellulose and the exocellulase–cellulose being the most stable. Thus, the findings of the study successfully identified the specific actions of sugar-acting enzymes for NC production.

Communicated by Ramaswamy H. Sarma     

Endocytosis and Exocytosis Events Regulate Vesicle Traffic in Endothelial Cells

We used water-soluble styryl pyridinium dyes that fluoresce at the membrane-water interface to study vesicle traffic in endothelial cells. Cultured endothelial cells derived from bovine and human pulmonary microvessels were incubated in styryl probes, washed to remove dye from the plasmalemmal outer face, and observed by digital fluorescence microscopy. Vesicles that derived from plasmalemma by endocytosis were filled with the styryl dye. These vesicles were distributed throughout the cytosol as numerous particles of heterogeneous diameter and brightness. Vesicle formation was activated 2-fold following addition of extracellular albumin whereas a control protein, immunoglobulin G, had no effect. Dye uptake was abrogated by labeling at low temperatures and inhibitors of phosphoinositide-3-kinase (PI 3-kinase). Tyrosine kinase inhibitors (genistein and herbimycin A) prevented the albumin-induced vesicle formation. Cytochalasin B prevented vesicle redistribution indicating involvement of actin filaments in translocation of endosomes away from sites of vesicle formation. Styryl dye was lost from cells by exocytosis as evident by the disappearance of discrete fluorescent particles. N-ethylmaleimide and botulinum toxin types A and B caused cells to accumulate increased number of vesicles suggesting that exocytosis was regulated by NSF-dependent SNARE mechanism. The results suggest that phosphoinositide metabolism regulates endocytosis in endothelial cells and that extracellular albumin activates endocytosis by a mechanism involving tyrosine phosphorylation, whereas exocytosis is a distinct process regulated by the SNARE machinery. The results support the hypothesis that albumin regulates its internalization and release in vascular endothelial cells via activation of specific endocytic and exocytic pathways.