Characterization of Selective Antibacterial Peptides by Polarity Index

In the recent decades, antibacterial peptides have occupied a strategic position for pharmaceutical drug applications and became subject of intense research activities since they are used to strengthen the immune system of all living organisms by protecting them from pathogenic bacteria. This work proposes a simple and easy statistical/computational method through a peptide polarity index measure by which an antibacterial peptide subgroup can be efficiently identified, that is, characterized by a high toxicity to bacterial membranes but presents a low toxicity to mammal cells. These peptides also have the feature not to adopt to an alpha-helicoidal structure in aqueous solution. The double-blind test carried out to the whole Antimicrobial Peptide Database (November 2011) showed an accuracy of 90% applying the polarity index method for the identification of such antibacterial peptide groups

Stochastic Approach to Enantiomeric Excess Amplification and Chiral Symmetry Breaking

Stochastic aspects of chemical reaction models related to the Soai reactions as well as to the homochirality in life are studied analytically and numerically by the use of the master equation and random walk model. For systems with a recycling process, a unique final probability distribution is obtained by means of detailed balance conditions. With a nonlinear autocatalysis the distribution has a double-peak structure, indicating the chiral symmetry breaking. This problem is further analyzed by examining eigenvalues and eigenfunctions of the master equation. In the case without recycling process, final probability distributions depend on the initial conditions. In the nonlinear autocatalytic case, time-evolution starting from a complete achiral state leads to a final distribution which differs from that deduced from the nonzero recycling result. This is due to the absence of the detailed balance, and a directed random walk model is shown to give the correct final profile. When the nonlinear autocatalysis is sufficiently strong and the initial state is achiral, the final probability distribution has a double-peak structure, related to the enantiomeric excess amplification. It is argued that with autocatalyses and a very small but nonzero spontaneous production, a single mother scenario could be a main mechanism to produce the homochirality.Comment: 25 pages, 6 figure

Exploiting the effect of noise on a chemical system to obtain logic gates

Small added noise has been predicted to direct certain classes of chemical systems towards a specific enantiomeric direction, with the dependence of product asymmetry on noise levels being non-monotonic and nonlinear. Associating the product selection in such chemical reactions with different outputs, and varying noise levels to encode the inputs, we observe that the response of the system mirrors the input-output relations of different fundamental logic operations. So the complex enantioselection, under the influence of noise, allows the chemical system to effectively behave as a logic gate. This observation may have potential applications in the design of chemical gates, as well as provide understanding of the information processing capacity of naturally occurring chiral symmetry-breaking chemical systems, with noise acting as the logic pattern selector. Copyright (C) EPLA, 200

Endogenous CO2 may inhibit bacterial growth and induce virulence gene expression in enteropathogenic Escherichia coli

Analysis of the growth kinetics of enteropathogenic Escherichia coil (EPEC) revealed that growth was directly proportional to the ratio between the exposed surface area and the liquid culture volume (SA/V). It was hypothesized that this bacterial behavior was caused by the accumulation of an endogenous volatile growth inhibitor metabolite whose escape from the medium directly depended on the SA/V. The results of this work support the theory that an inhibitor is produced and indicate that it is CO2. We also report that concomitant to the accumulation of CO2, there is secretion of the virulence-related EspB and EspC proteins from EPEC. We therefore postulate that endogenous CO2 may have an effect on both bacterial growth and virulence. (C) 2012 Elsevier Ltd. All rights reserved

Effect of the Volume-to-Surface Ratio of Cultures on Escherichia coli Growth: An Experimental and Theoretical Analysis

The growth dynamics of bacterial populations are usually represented by the classical S-shaped profiles composed of lag, exponential and stationary growth phases. Although exceptions to this classical behavior occur, they are normally produced under non-standard conditions such as supply of two carbohydrates as sole carbon source. However, we here report variations in the classic S-shaped growth profiles of Escherichia coli under standard culturing conditions; explicitly, we found growth during transition to the stationary phase wherein the bacterial growth rate inversely depended on the volume-to-surface ratio of cultures (V/S); the reasons for this behavior were experimentally explored. To complement our experimental analysis, a theoretical model that rationalizes the bacterial response was developed; simulations based on the developed model essentially reproduced experimental growth curves. We consequently conclude that the effect of V/S on E. coli growth reflects an interplay between auto-catalytic bacterial growth, bacterial growth auto-inhibition, and, the relief of that inhibition