Mapping of serotype-specific, immunodominant epitopes in the NS-4 region of hepatitis C virus (HCV):use of type-specific peptides to serologically differentiate infections with HCV types 1, 2, and 3

The effect of sequence variability between different types of hepatitis C virus (HCV) on the antigenicity of the NS-4 protein was investigated by epitope mapping and by enzyme-linked immunosorbent assay with branched oligopeptides. Epitope mapping of the region between amino acid residues 1679 and 1768 in the HCV polyprotein revealed two major antigenic regions (1961 to 1708 and 1710 to 1728) that were recognized by antibody elicited upon natural infection of HCV. The antigenic regions were highly variable between variants of HCV, with only 50 to 60% amino acid sequence similarity between types 1, 2, and 3. Although limited serological cross-reactivity between HCV types was detected between peptides, particularly in the first antigenic region of NS-4, type-specific reactivity formed the principal component of the natural humoral immune response to NS-4. Type-specific antibody to particular HCV types was detected in 89% of the samples from anti-HCV-positive blood donors and correlated almost exactly with genotypic analysis of HCV sequences amplified from the samples by polymerase chain reaction. Whereas almost all blood donors appeared to be infected with a single virus type (97%), a higher proportion of samples (40%) from hemophiliacs infected from transfusion of non-heat-inactivated clotting factor contained antibody to two or even all three HCV types, providing evidence that long-term exposure may lead to multiple infection with different variants of HCV

Contact inhibition of locomotion and mechanical cross-talk between cell-cell and cell-substrate adhesion determines the pattern of junctional tension in epithelial cell aggregates

We generated a computational approach to analyze the biomechanics of epithelial cell aggregates, either island or stripes or entire monolayers, that combines both vertex and contact-inhibition-of-locomotion models to include both cell-cell and cell-substrate adhesion. Examination of the distribution of cell protrusions (adhesion to the substrate) in the model predicted high order profiles of cell organization that agree with those previously seen experimentally. Cells acquired an asymmetric distribution of basal protrusions, traction forces and apical aspect ratios that decreased when moving from the edge to the island center. Our in silico analysis also showed that tension on cell-cell junctions and apical stress is not homogeneous across the island. Instead, these parameters are higher at the island center and scales up with island size, which we confirmed experimentally using laser ablation assays and immunofluorescence. Without formally being a 3-dimensional model, our approach has the minimal elements necessary to reproduce the distribution of cellular forces and mechanical crosstalk as well as distribution of principal stress in cells within epithelial cell aggregates. By making experimental testable predictions, our approach would benefit the mechanical analysis of epithelial tissues, especially when local changes in cell-cell and/or cell-substrate adhesion drive collective cell behavior.Comment: 39 pages, 8 Figures. Supplementary Information is include

Artificial Immune System based on Hybrid and External Memory for Mathematical Function Optimization

Artificial immune system (AIS) is one of the natureinspired algorithm for optimization problem. In AIS, clonal selection algorithm (CSA) is able to improve global searching ability. However, the CSA convergence and accuracy can be further improved because the hypermutation in CSA itself cannot always guarantee a better solution. Alternatively, Genetic Algorithms (GAs) and Particle Swarm Optimization (PSO) have been used efficiently in solving complex optimization problems, but they have a tendency to converge prematurely. Thus, a hybrid PSO-AIS and a new external memory CSA based scheme called EMCSA are proposed. In hybrid PSO-AIS, the good features of PSO and AIS are combined in order to reduce any limitation. Alternatively, EMCSA captures all the best antibodies into the memory in order to enhance global searching capability. In this preliminary study, the results show that the performance of hybrid PSO-AIS compares favourably with other algorithms while EMCSA produced moderate results in most of the simulations

Artificial Immune System Based Remainder Method for Multimodal Mathematical Function Optimization

Artificial immune system (AIS) is one of the nature-inspired algorithm for solving optimization problems. In AIS, clonal selection algorithm (CSA) is able to improve global searching ability compare to other meta-heuristic methods. However, the CSA rate of convergence and accuracy can be further improved as the hypermutation in CSA itself cannot always guarantee a better solution. Conversely, Genetic Algorithms (GAs) and Particle Swarm Optimization (PSO) have been used efficiently in solving complex optimization problems, but they have an inclination to converge prematurely. In this work, the CSA is modified using the best solutions for each exposure (iteration) namely Single Best Remainder (SBR) - CSA. Simulation results show that the proposed algorithm is able to enhance the performance of the conventional CSA in terms of accuracy and stability for single objective functions

Antibody Remainder Method Based Artificial Immune System for Mathematical Function Optimization

Artificial immune system (AIS) is one of the natureinspired algorithm for solving optimization problem. In AIS, clonal selection algorithm (CSA) is able to improve global searching ability. However, the CSA convergence and accuracy can be improved further because the hypermutation in CSA itself cannot always guarantee a better solution. Alternatively,Genetic Algorithms (GAs) and Particle Swarm Optimization(PSO) have been used efficiently in solving complex optimization problems, but they have a tendency to converge prematurely. In this study, the CSA is modified using the best solution for each exposure (iteration) namely Single Best Remainder (SBR) CSA. In this study, the results show that the performance of the proposed algorithm (SBR-CSA) compares favourably with other algorithms while Half Best Insertion (HBI) CSA produced moderate results in most of the simulations

Engineering Dehydrated Amino Acid Residues in the Antimicrobial Peptide Nisin

The small antimicrobial peptide nisin, produced by Lactococcus lactis, contains the uncommon amino acid residues dehydroalanine and dehydrobutyrine and five thio ether bridges. Since these structures are posttranslationally formed from Ser, Thr, and Cys residues, it is feasible to study their role in nisin function and biosynthesis by protein engineering. Here we report the development of an expression system for mutated nisin Z (nisZ) genes, using nisin A producing L. lactis as a host. Replacement by site-directed mutagenesis of the Ser-5 codon in nisZ by a Thr codon, led to a mutant with a dehydrobutyrine instead of a dehydroalanine residue at position 5, as shown by NMR. Its antimicrobial activity was 2-10-fold lower relative to wild-type nisin Z, depending on the indicator strain used. In another mutagenesis study a double mutation was introduced in the nisZ gene by replacing the codons for Met-17 and Gly-18 by codons for Gln and Thr, respectively, as in the third lanthionine ring of the related antimicrobial peptide subtilin from Bacillus subtilis. This resulted in the simultaneous production of two mutant species, one containing a Thr residue and the other containing a dehydrobutyrine residue at position 18, both having different bacteriocidal properties.

(In Press) Rheological characterisation of municipal sludge: A review

Sustainable sludge management is becoming a major issue for wastewater treatment plants due to increasing urban populations and tightening environmental regulations for conventional sludge disposal methods. To address this problem, a good understanding of sludge behaviour is vital to improve and optimize the current state of wastewater treatment operations. This paper provides a review of the recent experimental works in order for researchers to be able to develop a reliable characterization technique for measuring the important properties of sludge such as viscosity, yield stress, thixotropy, and viscoelasticity and to better understand the impact of solids concentrations, temperature, and water content on these properties. In this context, choosing the appropriate rheological model and rheometer is also important

Myosin VI and vinculin cooperate during the morphogenesis of cadherin cell–cell contacts in mammalian epithelial cells

Cooperation between cadherins and the actin cytoskeleton controls many aspects of epithelial biogenesis. We report here that myosin VI critically regulates the morphogenesis of epithelial cell–cell contacts. As epithelial monolayers mature in culture, discontinuous cell–cell contacts are initially replaced by continuous (cohesive) contacts. Myosin VI is recruited to cell contacts as they become linear and cohesive, where it forms a biochemical complex with epithelial cadherin (E-cadherin). Myosin VI is necessary for strong cadherin adhesion, for cells to form cohesive linear contacts, and for the integrity of the apical junctional complex. We find that vinculin mediates this effect of myosin VI. Myosin VI is necessary for vinculin and E-cadherin to interact. A combination of gain and loss of function approaches identifies vinculin as a downstream effector of myosin VI that is necessary for the integrity of intercellular contacts. We propose that myosin VI and vinculin form a molecular apparatus that generates cohesive cell–cell contacts in cultured mammalian epithelia

Clear model fluids for peculiar rheological properties of thickened digested sludge

Optimising flow processes in wastewater treatment plants requires that designers and operators take into account the flow properties of the sludge. Moreover, due to increasingly more stringent conditions on final disposal avenues such as landfill, composting, incineration etc., practitioners need to produce safer sludge in smaller quantities. Anaerobic digestion is a key treatment process for solids treatment and pathogen reduction. Due to the inherent opacity of sludge, it is impossible to visualise the mixing and flow patterns inside an anaerobic digester. Therefore, choosing an appropriate transparent model fluid which can mimic the rheological behaviour of sludge is imperative for visualisation of the hydrodynamic functioning of an anaerobic digester. Digested sludge is a complex material with time dependent non-Newtonian thixotropic characteristics. In steady state, it can be modelled by a basic power-law. However, for short-time processes the HerscheleBulkley model can be used to model liquid-like properties. The objective of this study was to identify transparent model fluids which will mimic the behaviour of real sludge. A comparison of three model fluids, Carboxymethyl Cellulose (CMC), Carbopol gel and Laponite clay revealed that these fluids could each model certain aspects of sludge behaviour. It is concluded that the rheological behaviour of sludge can be modelled using CMC in steady state flow at high shear rates, Carbopol gel for short-time flow processes and Laponite clay suspension where time dependence is dominant