A multiscale theoretical model for diffusive mass transfer in cellular biological media

An integrated methodology is developed for the theoretical analysis of solute transport and reaction in cellular biological media, such as tissues, microbial flocs, and biofilms. First, the method of local spatial averaging with a weight function is used to establish the equation which describes solute conservation at the cellular biological medium scale, starting with a continuum-based formulation of solute transport at finer spatial scales. Second, an effective-medium model is developed for the self-consistent calculation of the local diffusion coefficient in the cellular biological medium, including the effects of the structural heterogeneity of the extra-cellular space and the reversible adsorption to extra-cellular polymers. The final expression for the local effective diffusion coefficient is: D(Abeta)=lambda(beta)D(Aupsilon), where D(Aupsilon) is the diffusion coefficient in water, and lambda(beta) is a function of the composition and fundamental geometric and physicochemical system properties, including the size of solute molecules, the size of extra-cellular polymer fibers, and the mass permeability of the cell membrane. Furthermore, the analysis sheds some light on the function of the extra-cellular hydrogel as a diffusive barrier to solute molecules approaching the cell membrane, and its implications on the transport of chemotherapeutic agents within a cellular biological medium. Finally, the model predicts the qualitative trend as well as the quantitative variability of a large number of published experimental data on the diffusion coefficient of oxygen in cell-entrapping gels, microbial flocs, biofilms, and mammalian tissues.     

Melittin: a Membrane-active Peptide with Diverse Functions

Melittin is the principal toxic component in the venom of the European honey bee Apis mellifera and is a cationic, hemolytic peptide. It is a small linear peptide composed of 26 amino acid residues in which the amino-terminal region is predominantly hydrophobic whereas the carboxy-terminal region is hydrophilic due to the presence of a stretch of positively charged amino acids. This amphiphilic property of melittin has resulted in melittin being used as a suitable model peptide for monitoring lipid–protein interactions in membranes. In this review, the solution and membrane properties of melittin are highlighted, with an emphasis on melittin–membrane interaction using biophysical approaches. The recent applications of melittin in various cellular processes are discussed.     

Ion channels of various types induced in lipid membranes by gramicidin a derivatives carrying a cationic sequence at their C-termini

The channel-forming activity of gramicidin A derivatives carrying positively charged amino acid sequences at their C-termini was studied on planar bilayer lipid membranes and liposomes. We showed previously (FEBS Lett., 2005, vol. 579, pp. 5247–5252) that, at low concentrations, these peptides form classical cation-selective pores typical of gramicidin A, whereas, at high concentrations, they form large nonselective pores. The ability of the peptides to form nonselective pores, which was determined by the efflux of carboxyfluorescein, an organic dye, from liposomes, decreased substantially as the length of the gramicidin fragment in the series of cationic analogues was truncated. CD spectra showed that large pores are formed by peptides having both β^6.3 single-stranded and β^5.6 double-stranded helical conformations of the gramicidin fragment, with the C-terminal cationic sequence being extended. The dimerization of the peptides by the oxidation of the terminal cysteine promoted the formation of nonselective pores. It was shown that nonselective pores are not formed in membranes of erythrocytes, which may indicate a dependence of the channel-forming ability on the membrane type. The results may be of interest for the directed synthesis of peptides with antibacterial activity.     

Pore and Heteroatom Engineered Carbon Foams for Supercapacitors

Carbonaceous materials are attractive supercapacitor electrode materials due to their high electronic conductivity, large specific surface area, and low cost. Here, a unique hierarchical porous N,O,S‐enriched carbon foam (KNOSC) with high level of structural complexity for supercapacitors is reported. It is fabricated via a combination of a soft‐template method, freeze‐drying, and chemical etching. The carbon foam is a macroporous structure containing a network of mesoporous channels filled with micropores. It has an extremely large specific surface area of 2685 m² g^?1. The pore engineered carbon structure is also uniformly doped with N, O, and S. The KNOSC electrode achieves an outstanding capacitance of 402.5 F g^?1 at 1 A g^?1 and superior rate capability of 308.5 F g^?1 at 100 A g^?1. The KNOSC exhibits a Bode frequency at the phase angle of ?45° of 18.5 Hz, which corresponds to a time constant of 0.054 s only. A symmetric supercapacitor device using KNOSC as electrodes can be charged/discharged within 1.52 s to deliver a specific energy density of 15.2 W h kg^?1 at a power density of 36 kW kg^?1. These results suggest that the pore and heteroatom engineered structures are promising electrode materials for ultrafast charging.     

Actin‐spectrin scaffold supports open fenestrae in liver sinusoidal endothelial cells

Fenestrae are open transmembrane pores that are a structural hallmark of healthy liver sinusoidal endothelial cells (LSECs). Their key role is the transport of solutes and macromolecular complexes between the sinusoidal lumen and the space of Disse. To date, the biochemical nature of the cytoskeleton elements that surround the fenestrae and sieve plates in LSECs remain largely elusive. Herein, we took advantage of the latest developments in atomic force imaging and super‐resolution fluorescence nanoscopy to define the organization of the supramolecular complex(es) that surround the fenestrae. Our data revealed that spectrin, together with actin, lines the inner cell membrane and provided direct structural support to the membrane‐bound pores. We conclusively demonstrated that diamide and iodoacetic acid (IAA) affect fenestrae number by destabilizing the LSEC actin‐spectrin scaffold. Furthermore, IAA induces rapid and repeatable switching between the open vs closed state of the fenestrae, indicating that the spectrin‐actin complex could play an important role in controlling the pore number. Our results suggest that spectrin functions as a key regulator in the structural preservation of the fenestrae, and as such, it might serve as a molecular target for altering transendothelial permeability.     

Bongkrekic acid facilitates glycolysis in cultured cells and induces cell death under low glucose conditions

Bongkrekic acid (BKA) inhibits adenine nucleotide translocator (ANT) and suppresses ADP/ATP exchange in the mitochondrial inner membrane. Previously, we demonstrated that BKA exhibited cytotoxic effects on 4T1 tumor cells, depending on the cell number in the culture, but not on NIH3T3 cells. However, the cause of this differential sensitivity was unelucidated. Here we demonstrate that BKA reduced the O₂ consumption in both cell lines and increased the mitochondrial membrane potential, thereby facilitating glucose consumption. BKA reduced cellular ATP in 4T1 cells in a dose-dependent manner but not in NIH3T3 cells. The cellular ATP of 4T1 cells was decreased with a reduced glucose concentration in the media, but that of NIH3T3 cells remained constant. We also demonstrated that BKA-induced cell death in both cell lines in low glucose media; however, the susceptibility to the reduced glucose concentration was slightly higher in 4T1 cells, which may be attributed to the difference in the dependency on glycolysis as their energy source. These results indicate that 4T1 tumor cells rely heavily on glucose for energy production. Our data demonstrate that BKA disturbs ATP production in mitochondria and increases the susceptibility to a low glucose condition.     

Large shrubs partly compensate negative effects of grazing on hydrological function in a semi-arid savanna

Semiarid woodlands and savannas are globally important biomes that provide ecosystem goods and services such as habitat for biota and sinks for carbon, support millions of people that rely primarily on pastoralism, and supply livelihoods for about a third of the global human population. Savannas, however, are prone to degradation by overgrazing, and encroachment by woody plants, reducing their capacity to produce forage that pastoral enterprises depend on. We examined the impacts of livestock grazing and woody encroachment on soil hydrological processes, hypothesizing that heavy grazing by livestock would reduce hydrological function, whereas woody plants would increase hydrological function, therefore, partially offsetting any negative effects of overgrazing by livestock. Understanding the major drivers of soil hydrology in savanna ecosystems is important because water is a critical, yet limited resource in savannas. We found that livestock grazing reduced the early (sorptivity) and late (steady-state infiltration) stages of infiltration under both ponding and tension, and attributed this to a reduction in porosity caused by livestock trampling. Steady-state infiltration and sorptivity under ponding were greater under the canopies of woody shrubs than in open areas, partly compensating for any negative effect of grazing. Structural equation modeling revealed a direct positive effect of shrub height on hydrological functions, and an indirect effect via increases in litter cover. Our results suggest that woody plants can play important roles in driving hydrological function in savannas, counteracting the suppressive effect of livestock overgrazing on infiltration processes. Management strategies in semiarid savannas should aim to reduce trampling by livestock and retain large woody plants in order to maintain hydrological function.     

A modelling framework to simulate foliar fungal epidemics using functional–structural plant models

Background and Aims

Sustainable agriculture requires the identification of new, environmentally responsible strategies of crop protection. Modelling of pathosystems can allow a better understanding of the major interactions inside these dynamic systems and may lead to innovative protection strategies. In particular, functional–structural plant models (FSPMs) have been identified as a means to optimize the use of architecture-related traits. A current limitation lies in the inherent complexity of this type of modelling, and thus the purpose of this paper is to provide a framework to both extend and simplify the modelling of pathosystems using FSPMs.

Methods

Different entities and interactions occurring in pathosystems were formalized in a conceptual model. A framework based on these concepts was then implemented within the open-source OpenAlea modelling platform, using the platform''s general strategy of modelling plant–environment interactions and extending it to handle plant interactions with pathogens. New developments include a generic data structure for representing lesions and dispersal units, and a series of generic protocols to communicate with objects representing the canopy and its microenvironment in the OpenAlea platform. Another development is the addition of a library of elementary models involved in pathosystem modelling. Several plant and physical models are already available in OpenAlea and can be combined in models of pathosystems using this framework approach.

Key Results

Two contrasting pathosystems are implemented using the framework and illustrate its generic utility. Simulations demonstrate the framework''s ability to simulate multiscaled interactions within pathosystems, and also show that models are modular components within the framework and can be extended. This is illustrated by testing the impact of canopy architectural traits on fungal dispersal.

Conclusions

This study provides a framework for modelling a large number of pathosystems using FSPMs. This structure can accommodate both previously developed models for individual aspects of pathosystems and new ones. Complex models are deconstructed into separate ‘knowledge sources’ originating from different specialist areas of expertise and these can be shared and reassembled into multidisciplinary models. The framework thus provides a beneficial tool for a potential diverse and dynamic research community.     

Reconciliation of different simulation methods in the determination of the equilibrium branch for adsorption in pores

The recently proposed mid-density scheme [Liu Z, Herrera L, Nguyen VT, Do DD, Nicholson D. A Monte Carlo scheme based on mid-density in a hysteresis loop to determine equilibrium phase transition. Mol Simul. 2011; 37(11):932–939, Liu Z, Do DD, Nicholson D. A thermodynamic study of the mid-density scheme to determine the equilibrium phase transition in cylindrical pores. Mol Simul. 2012; 38(3):189–199] is tested against a method 2V-NVT (similar to the well-established gauge cell method) and the canonical ensemble (CE) method, using argon adsorption at 87 K in graphitic slit pores of infinite and finite length. In infinitely long pores, the equilibrium transition is vertical that is expected for an infinite system to have a first-order transition and this vertical transition was found to lie at the middle of the hysteresis loop and satisfies the well-known Maxwell rule of equal area. For pores of finite length, the equilibrium transitions are steep and are close to, but not exactly identical to, the desorption branch. This lends support to the conventional view that the desorption branch is nearest to equilibrium, although both adsorption and desorption branches are strictly speaking metastable; a view proposed originally by Everett [Everett DH. Capillary condensation and adsorption hysteresis. Berichte Der Bunsen-Gesellschaft [Phys Chem Chem Phys]. 1975; 79(9):732–734]. As a consequence, the Maxwell rule of equal area does not apply to finite systems. As the widely accepted CE and gauge cell methods do not falsify the mid-density scheme, this study lends strong support to the validity of this technique for the study of equilibria.     

Local vs. landscape controls on diversity: a test using surface-dwelling soil macroinvertebrates of differing mobility

Aim A better understanding of the processes driving local species richness and of the scales at which they operate is crucial for conserving biodiversity in cultivated landscapes. Local species richness may be controlled by ecological processes acting at larger spatial scales. Very little is known about the effect of landscape variables on soil biota. The aim of our study was to partly fill this gap by relating the local variation of surface‐dwelling macroarthropod species richness to factors operating at the habitat scale (i.e. land use and habitat characteristics) and the landscape scale (i.e. composition of the surrounding matrix). Location An agricultural landscape with a low‐input farming system in Central Hesse, Germany. Methods We focused on five taxa significantly differing in mobility and ecological requirements: ants, ground beetles, rove beetles, woodlice, and millipedes. Animals were caught with pitfall traps in fields of different land use (arable land, grassland, fallow land) and different habitat conditions (insolation, soil humidity). Composition of the surrounding landscape was analysed within a radius of 250 m around the fields. Results Factors from both scales together explained a large amount of the local variation in species richness, but the explanatory strength of the factors differed significantly among taxa. Land use particularly affected ground beetles and woodlice, whereas ants and rove beetles were more strongly affected by habitat characteristics, namely by insolation and soil characteristics. Local species richness of diplopods depended almost entirely on the surrounding landscape. In general, the composition of the neighbouring landscape had a lower impact on the species richness of most soil macroarthropod taxa than did land use and habitat characteristics. Main conclusions We conclude that agri‐environment schemes for the conservation of biodiversity in cultivated landscapes have to secure management for both habitat quality and heterogeneous landscape mosaics.