Optimum DNA curvature using a hybrid approach involving an artificial neural network and genetic algorithm

Detection of cell-free DNA nanoparticles in insulator based dielectrophoresis systems

In this paper, a semi-analytical investigation was performed to study the effect of the geometrical parameters of insulator-based dielectrophoresis (iDEP) systems for cell free DNA (cfDNA) trapping. For this purpose, first electrical potential and fluid flow fields were calculated by solving the governing equations including Poisson and Navier-stokes equations with appropriate boundary conditions (BCs) and then a Lagrangian approach was utilized to analyze the motion of cfDNA under the most important forces affected on it including Brownian, Drag, electrophoresis and dielectrophoresis (DEP) forces. The effect of the different parameters such as the electrical conductivity of the medium, shape and geometrical parameters of the insulators on the dielectrophoretic behavior of cfDNA was studied and the optimal value of these parameters was presented. Finally, in order to predict the minimum voltage required for cfDNA trapping, artificial neural network (ANN) was utilized and a relation between input and output parameters was introduced.

EMILINs interact with anthrax protective antigen and inhibit toxin action in vitro

The informational spectrum method (ISM) is a virtual spectroscopy method for the fast analysis of potential protein-protein relationships. By applying the ISM approach to the GeneBank protein database the vascular proteins EMILIN1 (Elastin Microfibril Interface Located ProteIN), EMILIN2, MMN1, and MMN2 were identified as additional anthrax PA antigen interacting molecules. This virtual molecular interaction was formally proven by solid phase assays using recombinant proteins. The interaction is independent of the presence of divalent cations and does not involve PA aspartic residue at 683, a critical residue in receptor binding. In fact, the D683A point mutation fully prevented the cell intoxication ability of PA in the presence of Lethal Factor, but it was fully ineffective on the binding of mutated PA to EMILIN1 and EMILIN2. The ISM approach also led to the identification of the potential interaction sites between PA and EMILINs. A PA mutant with a deletion at residue D425 and solid phase protein-protein interaction studies as well as deletion mutant of EMILIN2 confirmed the hypothesized interaction site. Our findings imply that the PA-cell surface receptor interaction is not likely to provide the full explanation for the vascular lesions and prominent hemorrhages that follow Bacillus anthracis infection and spreading and call into play vascular associated proteins such as EMILINs as potential inhibitory proteins.