Effect of arabinose substitution on the material properties of arabinoxylan films

This study was undertaken to investigate the effect of arabinose content on film properties. The substrate used was a rye arabinoxylan that had an Ara/Xyl ratio of 0.52 and an average number molecular weight of 305 kDa. Oxalic acid was used to attempt selective removal of the arabinose substituents on the xylan main chain. The debranching of the polymer was coupled with a decrease in molecular weight. The effect of reaction conditions on the decrease in arabinose content and loss of molecular weight was investigated. Optimal conditions were selected using an experimental design. Treatment at lower temperature for longer period of times resulted in debranching with less degradation of the main chain. As the Ara/Xyl ratio was lowered, aggregates began to form in an interval of the Ara/Xyl ratio between 0.31 and 0.23 in a water solution. Precipitation occurred below an Ara/Xyl ratio of 0.1. Thus, removal of arabinose substituents results in a gradual association of unsubstituted chains. There is a linear correlation between arabinose substitution and the moisture content of arabinoxylan at 98% RH. A decrease in arabinose content resulted in the loss of a plasticizing effect, as determined by dynamic mechanical analysis, which is correlated to water binding capacity.     

Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: a Bayesian Monte Carlo approach

The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue substitutions from amino acid sequences is also important because the rate matrix can be used to develop scoring matrices for sequence alignment. Here we use a continuous time Markov process to model the substitution rates of residues and develop a Bayesian Markov chain Monte Carlo method for rate estimation. We validate our method using simulated artificial protein sequences. Because different local regions such as binding surfaces and the protein interior core experience different selection pressures due to functional or stability constraints, we use our method to estimate the substitution rates of local regions. Our results show that the substitution rates are very different for residues in the buried core and residues on the solvent-exposed surfaces. In addition, the rest of the proteins on the binding surfaces also have very different substitution rates from residues. Based on these findings, we further develop a method for protein function prediction by surface matching using scoring matrices derived from estimated substitution rates for residues located on the binding surfaces. We show with examples that our method is effective in identifying functionally related proteins that have overall low sequence identity, a task known to be very challenging.     

Adsorption of cellulase on cellulose: Effect of physicochemical properties of cellulose on adsorption and rate of hydrolysis

In the cellulase-cellulose reaction system, the adsorption of cellulase on the solid cellulose substrate was found to be one of the important parameters that govern the enzymatic hydrolysis rate of cellulose. The adsorption of cellulase usually parallels the rate of hydrolysis of cellulose. The affinity for cellulase varies depending on the structural properties of cellulose. Adsorption parameters such as the half-saturation constant, the maximum adsorption constant, and the distribution coefficient for both the cellulase and cellulsoe have been experimentally determined for several substrates. These adsorption parameters vary with the source of cellulose and the pretreatment methods and are correlated with the crystallinity and the specific surface area of cellulose substrates. The changing pattern of adsorption profile of cellulase during the hydrolysis reaction has also been elucidated. For practical utilization of cellulosic materials, the cellulose structural properties and their effects on cellulase adsorption, and the rate of hydrolysis must be taken into consideration.     

Fish meal replacement by plant protein substitution and guar gum addition in trout feed. Part II: Effects on faeces stability and rheology

In the explosively growing aquaculture industry, the challenge of sustainability includes a requirement to produce more fish than are consumed by stock. A promising avenue of research is the substitution of the fish meal in feeds with plant protein. However, there are inherent risks in the development of such feeds, and serious consideration should be given not only to nutritional content, but also to the mechanical quality of resulting faecal wastes. The present study uses a plate on plate rheometer running in different flow modes (creep, oscillation) to assess the rheological properties of wastes resulting from different diets.All faeces were shown to be thixotropic in nature, independent of diet composition. Details of dietary composition influence the consistency and the characteristic stresses at which faecal structure changes from a viscoelastic solid into a viscoelastic liquid. Furthermore, in linking active food components with mechanical properties of chyme faeces, rheological studies may be used to understand and counteract some problematic properties. Substituting 100% of fish meal with plant proteins leads to faeces that rapidly disintegrate into very fine solids which threaten the viability of aquacultural operations. Adding just 0.3% of the rapidly hydrating non-starch polysaccharide, guar gum (GG), significantly increased the viscosity and elastic modulus of the faeces. These mechanical improvements increase the size of the resulting particles and the effectiveness with which they can be removed, thereby leading to optimized water quality. GG addition was sufficiently effective to counter the stability and particle size effects of a 50% substitution of fish meal, but could not mitigate those of a 100% substitution, wherein dissolution effects of an unknown emulsifier are suspected.     

Fluorine-free mixed amphiphilic polymers based on PDMS and PEG side chains for fouling release applications

Fluorine-free mixed amphiphilic block copolymers with mixtures of short side groups of polydimethyl siloxane (PDMS) and polyethylene glycol (PEG) were synthesized and studied for their ability to influence the surface properties and control the adhesion of marine organisms to coated surfaces. The settlement (attachment) and strength of adhesion of two different marine algae, the green seaweed Ulva and the diatom Navicula, were evaluated against the surfaces. It is known that hydrophobic coatings based on polydimethyl siloxane elastomers (PDMSe) are prone to protein adsorption and accumulation of strongly adherent diatom slimes, in contrast to PEG-based hydrophilic surfaces that inhibit protein adsorption and moderate only weak adhesion of diatoms. By incorporating both PDMS and PEG side chains into the polymers, the effect of incorporating both polar and non-polar groups on fouling-release could be studied. The dry surfaces were characterized by X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). The ability of these mixed amphiphilic polymers to reconstruct in water was examined using underwater bubble contact angle and dynamic water contact angle experiments. To understand more about surface reconstruction behavior, protein adsorption experiments were carried out with fluorescein isothiocyanate-labeled bovine serum albumin (BSA-FITC) on both dry and pre-soaked surfaces.     

Adsorption from saliva to silica and hydroxyapatite surfaces and elution of salivary films by SDS and delmopinol

The adsorption of proteins from human whole saliva (HWS) onto silica and hydroxyapatite surfaces (HA) was followed by quartz crystal microbalance with dissipation (QCM-D) and ellipsometry. The influence of different surface properties and adsorption media (water and PBS) on the adsorption from saliva was studied. The viscoelastic properties of the salivary films formed on the solid surfaces were estimated by the use of the Voigt-based viscoelastic film model. Furthermore, the efficiency of SDS and delmopinol to elute the adsorbed salivary film from the surfaces was investigated at different surfactant concentrations. A biphasic kinetic regime for the adsorption from saliva on the silica and HA surfaces was observed, indicating the formation of a rigidly coupled first layer corresponding to an initial adsorption of small proteins and a more loosely bound second layer. The results further showed a higher adsorption from HWS onto the HA surfaces compared to the silica surfaces in both adsorption media (PBS and water). The adsorption in PBS led to higher adsorbed amounts on both surfaces as compared to water. SDS was found to be more efficient in removing the salivary film from both surfaces than delmopinol. The salivary film was found to be less tightly bound onto the silica surfaces since more of the salivary film could be removed with both SDS and delmopinol compared to that from the HA surface. When adsorption took place from PBS the salivary layer formed at both surfaces seemed to have a similar structure, with a high energy dissipation implying that a softer salivary layer is built up in PBS as opposed to that in water. Furthermore, the salivary layers adsorbed from water solutions onto the HA were found to be softer than those on silica.     

Self-assembled monolayers of rigid thiols

The preparation, structure, properties and applications of self-assembled monolayers (SAMs) of rigid 4-mercapto-biphenyls are briefly reviewed. The rigid character of the biphenyl moiety results in a molecular dipole moment that affects both the adsorption kinetics on gold surfaces, as well as the equilibrium structure of mixed SAMs. Due to repulsive intermolecular interaction, the Langmuir isotherm model does not fit the adsorption kinetics of these biphenyl thiols, and a new Ising model was developed to fit the kinetics data. The equilibrium structures of SAMs and mixed SAMs depend on the polarity of the solution from which they were assembled. Infrared spectroscopy suggests that biphenyl moieties in SAMs on gold have small tilt angles with respect to the surfaces normal. Wetting studies shows that surfaces of these SAMs are stable for months, thus providing stable model surfaces that can be engineered at the molecular level. Such molecular engineering is important for nucleation and growth studies. The morphology of glycine crystals grown on SAM surfaces depends on the structure of the nucleating glycine layer, which, in turn, depends on the H-bonding of these molecules with the SAM surface. Finally, the adhesion of PDMS cross-linked networks to SAM surfaces depends on the concentration of interfacial H-bonding. This non-linear relationship suggests that the polymeric nature of the elastomer results in a collective H-bonding effect.     

Temporal and spatial changes in cell wall composition in developing grains of wheat cv. Hereward

A combination of enzyme mapping, FT-IR microscopy and NMR spectroscopy was used to study temporal and spatial aspects of endosperm cell wall synthesis and deposition in developing grain of bread wheat cv. Hereward. This confirmed previous reports that changes in the proportions of the two major groups of cell wall polysaccharides occur, with β-glucan accumulating earlier in development than arabinoxylan. Changes in the structure of the arabinoxylan occurred, with decreased proportions of disubstituted xylose residues and increased proportions of monosubstituted xylose residues. These are likely to result, at least in part, from arabinoxylan restructuring catalysed by enzymes such as arabinoxylan arabinofurano hydrolase and lead to changes in cell wall mechanical properties which may be required to withstand stresses during grain maturation and desiccation.     

Fluorine-free mixed amphiphilic polymers based on PDMS and PEG side chains for fouling release applications

Fluorine-free mixed amphiphilic block copolymers with mixtures of short side groups of polydimethyl siloxane (PDMS) and polyethylene glycol (PEG) were synthesized and studied for their ability to influence the surface properties and control the adhesion of marine organisms to coated surfaces. The settlement (attachment) and strength of adhesion of two different marine algae, the green seaweed Ulva and the diatom Navicula, were evaluated against the surfaces. It is known that hydrophobic coatings based on polydimethyl siloxane elastomers (PDMSe) are prone to protein adsorption and accumulation of strongly adherent diatom slimes, in contrast to PEG-based hydrophilic surfaces that inhibit protein adsorption and moderate only weak adhesion of diatoms. By incorporating both PDMS and PEG side chains into the polymers, the effect of incorporating both polar and non-polar groups on fouling-release could be studied. The dry surfaces were characterized by X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). The ability of these mixed amphiphilic polymers to reconstruct in water was examined using underwater bubble contact angle and dynamic water contact angle experiments. To understand more about surface reconstruction behavior, protein adsorption experiments were carried out with fluorescein isothiocyanate-labeled bovine serum albumin (BSA-FITC) on both dry and pre-soaked surfaces.     

Dynamic changes in cell wall polysaccharides during wheat seedling development

Changes in arabinoxylan content and composition during development of wheat seedlings were investigated. The cell walls isolated from the seedlings showed an increasing content of arabinoxylan during development, which could be correlated to increased activity of xylan synthase and arabinoxylan arabinosyltransferase. Arabinoxylan changed from initially having a high degree of arabinose substitution to a much lower degree of substitution. beta-Glucan was present in the walls at the early stages of development, but was actively degraded after day 4. Increased deposition of arabinoxylan did not take place until beta-glucan had been fully degraded. Ferulic and p-coumaric acid esters were present at all points but increased significantly from day 3 to 6, where lignification began. Ferulic acid dimers did not appear in the cell wall until day three and the different ferulic acid dimers varied in the course of accumulation. The ratio of ferulic acid dimers to free ferulic acid was maximal at the time when the wall had been depleted for beta-glucan, which had not yet been fully replaced by arabinoxylan. This pattern suggests a role for ferulic acid dimers in stabilizing the wall during the transition from a flexible to a more rigid structure. To investigate if the same changes could be observed within a single seedling, 7 day old seedlings were divided into four sections and the walls were analyzed. Some of the changes observed during the seedling development could also be observed within a single seedling, when analyzing the segments from the elongation zone at the base to the top of the leaf. However, the expanding region of older seedlings was much richer in hydroxycinnamates than the expanding region of younger seedlings. Diferulic acids are stabilizing the wall in the transition phase from an expanding to a mature wall. This transition can take place in different manners depending on the cell and tissue type.     

Strong regional biases in nucleotide substitution in the chicken genome

Interspersed repeats have emerged as a valuable tool for studying neutral patterns of molecular evolution. Here we analyze variation in the rate and pattern of nucleotide substitution across all autosomes in the chicken genome by comparing the present-day CR1 repeat sequences with their ancestral copies and reconstructing nucleotide substitutions with a maximum likelihood model. The results shed light on the origin and evolution of large-scale heterogeneity in GC content found in the genomes of birds and mammals--the isochore structure. In contrast to mammals, where GC content is becoming homogenized, heterogeneity in GC content is being reinforced in the chicken genome. This is also supported by patterns of substitution inferred from alignments of introns in chicken, turkey, and quail. Analysis of individual substitution frequencies is consistent with the biased gene conversion (BGC) model of isochore evolution, and it is likely that patterns of evolution in the chicken genome closely resemble those in the ancestral amniote genome, when it is inferred that isochores originated. Microchromosomes and distal regions of macrochromosomes are found to have elevated substitution rates and a more GC-biased pattern of nucleotide substitution. This can largely be accounted for by a strong correlation between GC content and the rate and pattern of substitution. The results suggest that an interaction between increased mutability at CpG motifs and fixation biases due to BGC could explain increased levels of divergence in GC-rich regions.     

Cellulose-based virus-retentive filters: a review

Viral filtration is a critical step in the purification of biologics and in the monitoring of microbiological water quality. Viral filters are also essential protection elements against airborne viral particles. The present review first focuses on cellulose-based filter media currently used for size-exclusion and/or adsorptive filtration of viruses from biopharmaceutical and environmental water samples. Data from spiking studies quantifying the viral filtration performance of cellulosic filters are detailed, i.e., first, the virus reduction capacity of regenerated cellulose hollow fiber filters in the manufacturing process of blood products and, second, the efficiency of virus recovery/concentration from water samples by the viradel (virus adsorption–elution) method using charge modified, electropositive cellulosic filters or conventional electronegative cellulose ester microfilters. Viral analysis of field water samples by the viradel technique is also surveyed. This review then describes cellulose-based filter media used in individual protection equipment against airborne viral pathogens, presenting innovative filtration media with virucidal properties. Some pros and cons of cellulosic viral filters and perspectives for cellulose-based materials in viral filtration are underlined in the review.     

Atomistic Simulation of Mineral Surfaces

Abstract

Atomistic simulation techniques are now able to model the structure of mineral surfaces at the atomic level. In this paper we begin to address the question of whether surface reactivity can be studied reliably by modelling the surface reactivity of calcite, fluorite and forsterite under aqueous conditions. We first used energy minimisation techniques to investigate the interaction between the minerals calcite and fluorite with water and methanoic acid. The relative adsorption energies suggest that methanoic acid preferentially adsorbs onto fluorite surfaces, while water adsorbs preferentially onto calcite as inferred from experiments on mineral separation. Molecular Dynamics simulations were also used to model the effect of temperature on the adsorption of water on the calcite {1014} and fluorite {111} surfaces. Furthermore we used these techniques to model point defect formation at surfaces. We are also interested in modelling the competition between associative and dissociative adsorption on mineral surfaces. Simulations of adsorption of water on the low-index forsterite surfaces have predicted the adsorption energies and equilibrium morphology. The calculated equilibrium morphology adequately reproduces the experimental morphology of forsterite suggesting that the relative stabilities of the surfaces, both unhydrated and hydroxylated, are calculated correctly.     

Effect of nonindependent substitution on phylogenetic accuracy

All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption of independent substitution is examined. A compound Poisson process is used to model DNA substitution. This model assumes that substitution events are Poisson-distributed in time and that the number of substitutions associated with each event is geometrically distributed. The asymptotic properties of phylogenetic methods do not appear to change under a compound Poisson process of DNA substitution. Moreover, the rank order of the performance of different methods does not change. However, all phylogenetic methods become less efficient when substitution follows a compound Poisson process.     

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

Nucleotide substitution in both coding and noncoding regions is context-dependent, in the sense that substitution rates depend on the identity of neighboring bases. Context-dependent substitution has been modeled in the case of two sequences and an unrooted phylogenetic tree, but it has only been accommodated in limited ways with more general phylogenies. In this article, extensions are presented to standard phylogenetic models that allow for better handling of context-dependent substitution, yet still permit exact inference at reasonable computational cost. The new models improve goodness of fit substantially for both coding and noncoding data. Considering context dependence leads to much larger improvements than does using a richer substitution model or allowing for rate variation across sites, under the assumption of site independence. The observed improvements appear to derive from three separate properties of the models: their explicit characterization of context-dependent substitution within N-tuples of adjacent sites, their ability to accommodate overlapping N-tuples, and their rich parameterization of the substitution process. Parameter estimation is accomplished using an expectation maximization algorithm, with a quasi-Newton algorithm for the maximization step; this approach is shown to be preferable to ordinary Newton methods for parameter-rich models. Overlapping tuples are efficiently handled by assuming Markov dependence of the observed bases at each site on those at the N - 1 preceding sites, and the required conditional probabilities are computed with an extension of Felsenstein's algorithm. Estimated substitution rates based on a data set of about 160,000 noncoding sites in mammalian genomes indicate a pronounced CpG effect, but they also suggest a complex overall pattern of context-dependent substitution, comprising a variety of subtle effects. Estimates based on about 3 million sites in coding regions demonstrate that amino acid substitution rates can be learned at the nucleotide level, and suggest that context effects across codon boundaries are significant.     

Preparation of cellulase concoction using differential adsorption phenomenon

Controlled depolymerization of cellulose is essential for the production of valuable cellooligosaccharides and cellobiose from lignocellulosic biomass. However, enzymatic cellulose hydrolysis involves multiple synergistically acting enzymes, making difficult to control the depolymerization process and generate desired product. This work exploits the varying adsorption properties of the cellulase components to the cellulosic substrate and aims to control the enzyme activity. Cellulase adsorption was favored on pretreated cellulosic biomass as compared to synthetic cellulose. Preferential adsorption of exocellulases was observed over endocellulase, while β-glucosidases remained unadsorbed. Adsorbed enzyme fraction with bound exocellulases when used for hydrolysis generated cellobiose predominantly, while the unadsorbed enzymes in the liquid fraction produced cellooligosaccharides majorly, owing to its high endocellulases activity. Thus, the differential adsorption phenomenon of the cellulase components can be used for the controlling cellulose hydrolysis for the production of an array of sugars.     

Modulating short tryptophan- and arginine-rich peptides activity by substitution with histidine

BackgroundHigh antimicrobial efficacy of short tryptophan-and arginine-rich peptides makes them good candidates in the fight against pathogens. Substitution of tryptophan and arginine by histidine could be used to modulate the peptides efficacy by optimizing their structures.MethodsThe peptide (RRWWRWWRR), reported to showed good antimicrobial efficacy, was used as template, seven new analogs being designed substituting tryptophan or arginine with histidine. The peptides' efficacy was tested against E. coli, B. subtilis and S. aureus. The cytotoxicity and hemolytic effect were evaluated and the therapeutic index was inferred for each peptide. Atomic force microscopy and molecular simulation were used to analyze the effects of peptides on bacterial membrane.ResultsThe substitution of tryptophan by histidine proved to strongly modulate the antimicrobial activity, mainly by changing the peptide-to-membrane binding energy. The substitution of arginine has low effect on the antimicrobial efficacy. The presence of histidine residue reduced the cytotoxic and hemolytic activity of the peptides in some cases maintaining the same efficacy against bacteria. The peptides' antimicrobial activity was correlated to the 3D-hydrophobic moment and to a simple structure-based packing parameter.ConclusionThe results show that some of these peptides have the potential to become good candidates to fight against bacteria. The substitution by histidine proved to fine tune the therapeutic index allowing the optimization of the peptide structure mainly by changing its binding energy and 3D-hydrophobic moment.General significanceThe short tryptophan reach peptides therapeutic index can be maximized using the histidine substitution to optimize their structure.     

Reconstruction of surfaces from mixed hydrocarbon and PEG components in water: responsive surfaces aid fouling release

Coatings derived from surface active block copolymers (SABCs) having a combination of hydrophobic aliphatic (linear hydrocarbon or propylene oxide-derived groups) and hydrophilic poly(ethlyene glycol) (PEG) side chains have been developed. The coatings demonstrate superior performance against protein adsorption as well as resistance to biofouling, providing an alternative to coatings containing fluorinated side chains as the hydrophobe, thus reducing the potential environmental impact. The surfaces were examined using dynamic water contact angle, captive air-bubble contact angle, atomic force microscopy, X-ray photoelectron spectroscopy, and near-edge X-ray absorption fine structure analysis. The PS(8K)-b-P(E/B)(25K)-b-PI(10K) triblock copolymer precursor (K3) initially dominated the dry surface. In contrast to previous studies with mixed fluorinated/PEG surfaces, these new materials displayed significant surface changes after exposure to water that allowed fouling resistant behavior. PEG groups buried several nanometers below the surface in the dry state were able to occupy the coating surface after placement in water. The resulting surface exhibits a very low contact angle and good antifouling properties that are very different from those of K3. The surfaces are strongly resistant to protein adsorption using bovine serum albumin as a standard protein challenge. Biofouling assays with sporelings of the green alga Ulva and cells of the diatom Navicula showed the level of adhesion was significantly reduced relative to that of a PDMS standard and that of the triblock copolymer precursor of the SABCs.     

Studies on the mechanism of enzymatic hydrolysis of cellulosic substances.

Most cellulosic substances contain appreciable amounts of cellulose and hemicellulose, which on enzymatic hydrolysis mainly yield a mixture of glucose, cellobiose, and xylose. In this paper, studies on the mechanisms of hydrolysis of bagasse (a complex native cellulosic waste left after extraction of juice from cane sugar) by the cellulase enzyme components are described in light of their adsorption characteristics. Simultaneous adsorption of exo- and endoglucanases on hydrolyzable cellulosics is the causative factor of the hydrolysis that follows immediately after. It supports the postulate of synergistic enzyme action proposed by Eriksson. Xylanase pretreatment enhanced the hydrolysis of bagasse owing to the creation of more accessible cellulosic regions that are readily acted upon by exo- and endoglucanases. The synergistic action of the purified exoglucanase, endoglucanase, and xylanse has been found to be most effective for hydrolysis of bagasse but not for pure cellulose. Significant quantities of glucose are produced in beta-glucosidase-free cellulase action on bagasse. Individual and combined action of the purified cellulase components on hydrolysis of native and delignified bagasse are discussed in respect to the release of sugars in the hydrolysate.     

Characterization of chemical substitution of hydroxypropyl cellulose using enzymatic degradation

The distribution of substituents along the polymer backbone will have a strong influence on the properties of modified cellulose. Endoglucanases were used to degrade a series of hydroxypropyl cellulose (HPC) derivatives with a high degree of substitution. The HPCs were characterized with cloud-point analysis prior to degradation. The extent of enzymatic degradation was determined with size-exclusion chromatography with online multi-angle light scattering and refractive index detection and also with high-pH anion exchange chromatography with pulsed amperometric detection. To further characterize the formed products, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was employed for analysis of short-chained oligosaccharides. The different endoglucanases showed varying degradation capability depending on structure of the active site. The highly substituted HPCs had different susceptibility to degradation by the endoglucanases. The results show a difference in substituent distribution between HPCs, which would explain the differing cloud-point behaviors. Increased number of regions with low substitution could be correlated with lower polymer cloud point. The study shows the usefulness of enzymatic degradation to study the distribution of substituents in soluble biopolymer derivates.