Modelling of the mechanical and mass transport properties of auxetic molecular sieves: an idealised inorganic (zeolitic) host–guest system

Force field based simulations have been employed to model the structure, and mechanical and mass transport properties of the all-silica zeolite MFI (ZSM5—Si₉₆O₁₉₂). Undeformed and deformed MFI subject to uniaxial loading in each of the three principal directions were investigated. The mechanical properties are predicted to include negative on-axis Poisson's ratios (auxetic behaviour) in the x ₁–x ₃ plane of the undeformed structure, and are strain-dependent. Transformation from positive-to-negative Poisson's ratio behaviour, and vice versa, is predicted for most on-axis Poisson's ratios at critical loading strains. Simulations of the simultaneous sorption of neopentane and benzene guest molecules onto the undeformed host MFI framework indicate a low neopentane-to-benzene loading ratio, consistent with experimental observation. The sorption of these two molecular species onto deformed MFI is Poisson's ratio- and strain-dependent. Uniaxial tensile loading along a direction containing a negative on-axis Poisson's ratio leads to an increase in the loading of the larger neopentane molecules with respect to benzene, strongly correlated with the increase in volume associated with auxetic behaviour.     

Arabinoxylan-degrading enzyme system of the fungusAspergillus awamori: purification and properties of an α-l-arabinofuranosidase

An -l-arabinofuranosidase produced by the fungusAspergillus awamori had molecular mass of approximately 64 kDa on sodium dodecyl sulphate/polyacrylamide gel electrophoresis (SDS-PAGE) and was optimally active at pH 4.6 and 50°C. The enzyme, which chromatographed as a single component on SDS-PAGE, appeared to consist of two iso-enzymes of pI 3.6 and 3.2. Acting in isolation, the -l-arabinofuranosidase had only a very limited capacity to releasel-arabinose (less than 11%) directly from arabinoxylans that had been extracted from a number of plant cell wall preparations using 18% alkali, but a much higher proportion of thel-arabinose (46%) was released from a wheat straw arabinoxylan that had been isolated by steam treatment. There was a marked synergistic effect between the -l-arabinofuranosidase and an endo-(1 4)--d-xylanase produced byA. awamori in both the rate and extent of the release ofl-arabinose from both oat straw and wheat straw arabinoxylans, suggesting thatl-arabinose-substituted oligosaccharides generated by the endoxylanase action were better substrates for enzyme action. A novel property of the -l-arabinofurasidase was its capacity to release a substantial proportion (42%) of feruloyll-arabinose from intact wheat straw arabinoxylan. The concerted action of the -l-arabinofuranosidase and endoxylanase released 71% of the feruloyll-arabinose and 69% of thep-coumaroyll-arabinose substituents from the wheat straw arabinoxylan.     

Out of the ESCPE room: Emerging roles of endosomal SNX-BARs in receptor transport and host–pathogen interaction

Several functions of the human cell, such as sensing nutrients, cell movement and interaction with the surrounding environment, depend on a myriad of transmembrane proteins and their associated proteins and lipids (collectively termed “cargoes”). To successfully perform their tasks, cargo must be sorted and delivered to the right place, at the right time, and in the right amount. To achieve this, eukaryotic cells have evolved a highly organized sorting platform, the endosomal network. Here, a variety of specialized multiprotein complexes sort cargo into itineraries leading to either their degradation or their recycling to various organelles for further rounds of reuse. A key sorting complex is the Endosomal SNX-BAR Sorting Complex for Promoting Exit (ESCPE-1) that promotes the recycling of an array of cargos to the plasma membrane and/or the trans-Golgi network. ESCPE-1 recognizes a hydrophobic-based sorting motif in numerous cargoes and orchestrates their packaging into tubular carriers that pinch off from the endosome and travel to the target organelle. A wide range of pathogens mimic this sorting motif to hijack ESCPE-1 transport to promote their invasion and survival within infected cells. In other instances, ESCPE-1 exerts restrictive functions against pathogens by limiting their replication and infection. In this review, we discuss ESCPE-1 assembly and functions, with a particular focus on recent advances in the understanding of its role in membrane trafficking, cellular homeostasis and host–pathogen interaction.     

Effect of collagenase–gelatinase ratio on the mechanical properties of a collagen fibril: a combined Monte Carlo–molecular dynamics study

Loading in cartilage is supported primarily by fibrillar collagen, and damage will impair the function of the tissue, leading to pathologies such as osteoarthritis. Damage is initiated by two types of matrix metalloproteinases, collagenase and gelatinase, that cleave and denature the collagen fibrils in the tissue. Experimental and modeling studies have revealed insights into the individual contributions of these two types of MMPs, as well as the mechanical response of intact fibrils and fibrils that have experienced random surface degradation. However, no research has comprehensively examined the combined influences of collagenases and gelatinases on collagen degradation nor studied the mechanical consequences of biological degradation of collagen fibrils. Such preclinical examinations are required to gain insights into understanding, treating, and preventing degradation-related cartilage pathology. To develop these insights, we use sequential Monte Carlo and molecular dynamics simulations to probe the effect of enzymatic degradation on the structure and mechanics of a single collagen fibril. We find that the mechanical response depends on the ratio of collagenase to gelatinase—not just the amount of lost fibril mass—and we provide a possible mechanism underlying this phenomenon. Overall, by characterizing the combined influences of collagenases and gelatinases on fibril degradation and mechanics at the preclinical research stage, we gain insights that may facilitate the development of targeted interventions to prevent the damage and loss of mechanical integrity that can lead to cartilage pathology.

     

The dynamics of the lynx–hare system: an application of the Lotka–Volterra model

The Lotka–Volterra model of predator–prey dynamics was used for approximation of the wellknown empirical time series on the lynx–hare system in Canada that was collected by the Hudson Bay Company in 1845–1935. The model was assumed to demonstrate satisfactory data approximation if the sets of deviations of the model and empirical data for both time series satisfied a number of statistical criteria (for the selected significance level). The frequency distributions of deviations between the theoretical (model) trajectories and empirical datasets were tested for symmetry (with respect to the Y-axis; the Kolmogorov–Smirnov and Lehmann–Rosenblatt tests) and the presence or absence of serial correlation (the Swed–Eisenhart and “jumps up–jumps down” tests). The numerical calculations show that the set of points of the space of model parameters, when the deviations satisfy the statistical criteria, is not empty and, consequently, the model is suitable for describing empirical data.     

Blood-to-brain influx transport of nicotine at the rat blood–brain barrier: Involvement of a pyrilamine-sensitive organic cation transport process

Nicotine is the most potent neural pharmacological alkaloid in tobacco, and the modulation of nicotine concentration in the brain is important for smoking cessation therapy. The purpose of this study was to elucidate the net flux of nicotine transport across the blood–brain barrier (BBB) and the major contributor to nicotine transport in the BBB. The in vivo brain-to-blood clearance was determined by a combination of the rat brain efflux index method and a rat brain slice uptake study, and the blood-to-brain transport of nicotine was evaluated by in vivo vascular injection in rats and a conditionally immortalized rat brain capillary endothelial cell line (TR-BBB13 cells) as an in vitro model of the rat BBB. The blood-to-brain nicotine influx clearance was obtained by integration plot analysis as 272 μL/(min g brain), and this value was twofold greater than the brain-to-blood efflux clearance (137 μL/(min g brain)). Thus, it is suggested that the net flux of nicotine transport across the BBB is dominated by blood-to-brain influx transport. In vivo blood-to-brain nicotine transport was inhibited by pyrilamine. [³H]Nicotine uptake by TR-BBB13 cells exhibited time-, temperature-, and concentration-dependence with a K_m value of 92 μM. Pyrilamine competitively inhibited nicotine uptake by TR-BBB13 cells with a K_i value of 15 μM, whereas substrates and inhibitors of organic cation transporters had little effect. These results suggest that pyrilamine-sensitive organic cation transport process(es) mediate blood-to-brain influx transport of nicotine at the BBB, and this is expected to play an important role in regulating nicotine-induced neural responses.     

The study of lysogeny at the Pasteur Institute (1950–1960): an epistemologically open system

Many historical studies have been devoted to the French school of molecular biology, in particular to the work of Jacques Monod on adaptive enzymes. By focusing on François Jacob’s studies on lysogeny between 1950 and 1960, we intend to redress the imbalance of historiography, as well as proposing a more fruitful point of view for understanding the relative importance of international contacts and local traditions in the genesis of the operon model.Elie Wollman and Jacob’s work on temperate bacteriophages rendered respectable a system that had been considered an artefact for more than two decades. They did this firstly by modelling their studies on those of the US phage group and secondly by basing these studies on a complex vision of the relations between bacteria and bacteriophages. The interaction between bacteria and temperate bacteriophages was considered ab initio as a biochemical process, the mechanisms of which would eventually be characterized. It was also considered as a “normal” phenomenon that could be used as a model to understand the process of differentiation, as well as the role of viruses in diseases and cancer. The temperate bacteriophage was a model system that was far more epistemologically open and, for this reason, in a sense more productive than the virulent phage studied by the US phage group.     

National politics and international trends: EMBO and the making of molecular biology in Spain (1960–1975)

From the mid-1960s onwards, a set of Spanish molecular biology research groups emerged in Spain. The factors contributing to this included: the return of a group of molecular biologists from their postdoctoral period abroad, the negotiations for the return of Spanish-born Nobel prize winner Severo Ochoa from New York, the negotiations for Spanish membership in the European Conference of Molecular Biology, and national policy towards university reform. As a result, the early molecular biologists’ research groups began to be recognised as research schools by Spanish authorities and postgraduate courses and new research centres for molecular biology were set up. Foreign influence in the whole process was crucial.     

Parasitoid-mediated effects: apparent competition and the persistence of host–parasitoid assemblages

Indirect effects such as apparent competition (in which two hosts that do not compete for resources interact via a shared natural enemy) are increasingly being shown to be prevalent in the structure and function of ecological assemblages. Here, we review the empirical and theoretical evidence for these enemy-mediated effects in host–parasitoid assemblages. We first address questions about the design of experiments to test for apparent competition. Second, we consider factors likely to affect the coexistence of host species that share a parasitoid and are involved in apparent competition. We show that parasitoid aggregation, and the switching effect that this can generate when hosts occur in separate patches, not only promotes persistence but is also strongly stabilizing. The broader consequences of these effects are discussed. Received: November 6, 1998 / Accepted: January 13, 1999     

Parasites of Perccottus glenii Dybowski, 1877 (Actinopterygii: Odontobutidae) in the native and the introduced host range: Abundance–occupancy and abundance–variance relationships

The Chinese sleeper Perccottus glenii Dybowski, 1877 is an invasive fish species rapidly expanding in Siberia and Europe. Its native range encompasses the Far East region of Russia, northeastern China and northern North Korea. We studied species composition, prevalence, mean abundance and variance of mean abundance of macroparasites of the Chinese sleeper in the native and the introduced range. The species composition of the parasite component communities differed considerably in the native and the introduced range. The frequency distributions of prevalence, mean abundance and variance of mean abundance of the parasites did not demonstrate any significant differentiation between the two parts of the host range. However, an analysis of the abundance–occupancy and the abundance–variance relationships revealed that the parasite component communities in the two parts of the host range were quite distinct. In the native range, prevalence increased faster and variance increased more slowly with the increasing abundance of the parasites than in the introduced range. These features are mostly associated with considerably increased prevalence, abundance and aggregation of the host-specific cestode Nippotaenia mogurndae in recipient water bodies as compared with the native habitats.     

Conformation of an immunoreactive undecapeptide fragment (10–20) of Asp f 1 by NMR and molecular modeling

Allergic bronchopulmonary aspergillosis (ABPA), caused by Aspergillus fumigatus, is a complication of allergic asthma. Asp f 1 secreted by A. fumigatus is reported to be a major allergen/antigen involved in pathogenesis of aspergillosis. A 11-mer immunodominant epitope (Leu-Asn-Pro-Lys-Thr⁵-Asn-Lys-Trp-Glu-Asp¹⁰-Lys) of Asp f 1 has shown immunoreactivity with specific IgG and IgE antibodies in the sera of patients with ABPA in ELISA inhibitionassay. Various studies have suggested that the peptide has a potential use in the development of ELISA based diagnostic kit for early diagnosis of infections caused by A. fumigatus.In view of these interesting properties of the undecapeptide wehave embarked on an investigation of its conformation to understand the relationship between structure and immunoreactivity. NMR and molecular modeling studies of the peptide suggest a structure with a -turn spanning residuesAsn⁶ – Glu⁹ in water at pH 4.0, a -pleated sheet in DMSO and a -helix in 40% HFA.     

A historical perspective of the biophysics of the thrombin–heparin system: an example of nonspecific binding and the consequent parking problem in action

Difficulties are encountered in the thermodynamic characterization of interactions between a protein ligand and a linear acceptor, such as a polynucleotide or a polysaccharide, because of the involvement of more than one unit of the polymer chain in each attachment of a protein molecule. Complications arise from the fact that random attachment of ligand to the polymer chain, each unit of which is a potential binding site, initially leads to suboptimal location of protein molecules along the polymer chain—a situation that has to be rectified before the attainment of thermodynamic equilibrium can be realized. Kinetic as well as thermodynamic consequences of such nonspecific binding, termed the parking problem, therefore need to be considered in any quantitative characterization of the interaction between a large ligand and a linear polymer acceptor chain. Results for the thrombin–heparin interaction have been used to illustrate a thermodynamic characterization of nonspecific binding that takes into account these consequences of the parking problem.     

Conformation of an immunoreactive undecapeptide fragment (10–20) of Asp f 1 by NMR and molecular modeling

Summary Allergic bronchopulmonary aspergillosis (ABPA), caused byAspergillus fumigatus, is a complication of allergic asthma. Asp f 1 secreted byA. fumigatus is reported to be a major allergen/antigen involved in pathogenesis of aspergillosis. A 11-mer immunodominant epitope (Leu-Asn-Pro-Lys-Thr⁵-Asn-Lys-Trp-Glu-Asp¹⁰-Lys) of Asp f 1 has shown immunoreactivity with specific IgG and IgE antibodies in the sera of patients with ABPA in ELISA inhibition assay. Various studies have suggested that the peptide has a potential use in the development of ELISA based diagnostic kit for early diagnosis of infections caused byA. fumigatus. In view of these interesting properties of the undecapeptide we have embarked on an investigation of its conformation to understand the relationship between structure and immunoreactivity. NMR and molecular modeling studies of the peptide suggest a structure with a β-turn spanning residues Asn⁶-Glu⁹ in water at pH 4.0, a β-pleated sheet in DMSO and α-helix in 40% HFA.     

Anti-diuresis in the blood-feeding insect Rhodnius prolixus Stål: antagonistic actions of cAMP and cGMP and the role of organic acid transport

Secretion of primary urine by upper Malpighian tubules of the blood-sucking insect Rhodnius prolixus has recently been shown to be inhibited by cyclic GMP (cGMP). In the present work, we have demonstrated that cGMP has effects antagonistic to those of cAMP in Rhodnius tubules and have further characterized the effects of cGMP on tubular secretion. Cyclic GMP inhibited secretion at all concentrations from 5x10(-6) to 10(-3)M, though this inhibition was partially or wholly reversed by large (2mM) doses of cAMP. While sub-maximal concentrations of cGMP did not significantly alter [K(+)] and [Na(+)] of secreted fluid, high external [cGMP] reduced secretion to minimal levels and caused [K(+)] and [Na(+)] to approach pre-stimulation levels. Cyclic GMP does not appear to affect the permeability of the lower Malpighian tubule to water. Both cAMP and cGMP likely enter tubule cells by way of an organic acid transporter whose activity is induced by feeding. Sensitivity of the tubules to exogenous cGMP and cAMP, which is assumed to be a function of transport activity, reaches a peak approximately 5 days after the blood meal and declines rapidly thereafter. Transport of anions into upper tubules involves at least two different transporters: one for acylamides (e.g., p-aminohippuric acid) and another for sulphonates (e.g., amaranth, phenol red). Amaranth and phenol red blocked the actions of both cGMP and cAMP, whereas p-aminohippuric acid was without effect. This suggests that cyclic nucleotides enter by way of the sulphonate transporter.     

Finite element analysis of the Poisson–Boltzmann equation coupled with chemical equilibriums: redistribution and transport of protons in nanophase separated polymeric acid–base proton exchange membranes

Abstract

The finite element analysis is applied to the study of the redistribution and transport of protons in model nanophase separated polymeric acid–base composite membranes by the Poisson–Boltzmann equation coupled with the acid and base dissociation equilibriums for the first time. Space charge redistribution in terms of proton and hydroxide redistributions is observed at the interfaces of acidic and basic domains. The space charge redistribution causes internal electrostatic potential, and thus, promotes the macroscopic transport of protons in the acid–base composite membranes.