Efficient method for identification of Escherichia coli strains isolated from various chicken (Gallus gallus domesticus) organs

Tracing of transmission routes and identification of pathogen sources are important issues in preventive measures aimed at controlling human and animal infectious diseases. A fast and accurate method for bacterial strain identification (genotyping) allows scientifically sound planning of preventive schemes. Despite the existence of numerous bacterium genotyping techniques, there is still room for developing a unified typing approach that would be applicable to a variety of bacterial species. The aim is to develop a genotyping method allowing identification of E. coli strains circulating at Russian chicken farms. The method is based on the earlier proposed idea of double digestion and selective labeling of DNA restriction fragments (DDSL). Bacterial genomic DNA is simultaneously digested with two restriction enzymes and labeled with biotinylated deoxynucleoside triphosphates with the presence of DNA polymerase. The enzymes are chosen in silico for each bacterial species so that a limited number of DNA fragments be generated for subsequent separation in conventional agarose gel. After implementation of the study with E. coli isolates, adequate reproducibility and high discriminatory power of the technique were demonstrated. This approach was previously applied to genotyping other pathogenic bacterial species. The advantages of the proposed technique are the short turn-around time of analysis and easy availability of reagents and equipment. Transmission of a pathogen among chicken within one farm and existence of slightly different E. coli genotypes in various organs of the same individual were observed. Bacterial isolates obtained from any organ except the intestine were suitable for genotyping. Chicken intestine contains endogenous E. coli strains, which hamper the interpretation of genotyping data obtained for a set of isolates. Thus, our work demonstrates the potential of the DDSL method for genotyping field E. coli isolates in the context of molecular epizootology

Liquid-Liquid Phase Transitions for Soft-Core Attractive Potentials

Using event driven molecular dynamics simulations, we study a three dimensional one-component system of spherical particles interacting via a discontinuous potential combining a repulsive square soft core and an attractive square well. In the case of a narrow attractive well, it has been shown that this potential has two metastable gas-liquid critical points. Here we systematically investigate how the changes of the parameters of this potential affect the phase diagram of the system. We find a broad range of potential parameters for which the system has both a gas-liquid critical point and a liquid-liquid critical point. For the liquid-gas critical point we find that the derivatives of the critical temperature and pressure, with respect to the parameters of the potential, have the same signs: they are positive for increasing width of the attractive well and negative for increasing width and repulsive energy of the soft core. This result resembles the behavior of the liquid-gas critical point for standard liquids. In contrast, for the liquid-liquid critical point the critical pressure decreases as the critical temperature increases. As a consequence, the liquid-liquid critical point exists at positive pressures only in a finite range of parameters. We present a modified van der Waals equation which qualitatively reproduces the behavior of both critical points within some range of parameters, and give us insight on the mechanisms ruling the dependence of the two critical points on the potential's parameters. The soft core potential studied here resembles model potentials used for colloids, proteins, and potentials that have been related to liquid metals, raising an interesting possibility that a liquid-liquid phase transition may be present in some systems where it has not yet been observed.Comment: 29 pages, 15 figure