Showing papers by "Alexander M. Samsonov published in 2011"

Mechanisms of gap gene expression canalization in the Drosophila blastoderm

Abstract: Extensive variation in early gap gene expression in the Drosophila blastoderm is reduced over time because of gap gene cross regulation. This phenomenon is a manifestation of canalization, the ability of an organism to produce a consistent phenotype despite variations in genotype or environment. The canalization of gap gene expression can be understood as arising from the actions of attractors in the gap gene dynamical system. In order to better understand the processes of developmental robustness and canalization in the early Drosophila embryo, we investigated the dynamical effects of varying spatial profiles of Bicoid protein concentration on the formation of the expression border of the gap gene hunchback. At several positions on the anterior-posterior axis of the embryo, we analyzed attractors and their basins of attraction in a dynamical model describing expression of four gap genes with the Bicoid concentration profile accounted as a given input in the model equations. This model was tested against a family of Bicoid gradients obtained from individual embryos. These gradients were normalized by two independent methods, which are based on distinct biological hypotheses and provide different magnitudes for Bicoid spatial variability. We showed how the border formation is dictated by the biological initial conditions (the concentration gradient of maternal Hunchback protein) being attracted to specific attracting sets in a local vicinity of the border. Different types of these attracting sets (point attractors or one dimensional attracting manifolds) define several possible mechanisms of border formation. The hunchback border formation is associated with intersection of the spatial gradient of the maternal Hunchback protein and a boundary between the attraction basins of two different point attractors. We demonstrated how the positional variability for hunchback is related to the corresponding variability of the basin boundaries. The observed reduction in variability of the hunchback gene expression can be accounted for by specific geometrical properties of the basin boundaries. We clarified the mechanisms of gap gene expression canalization in early Drosophila embryos. These mechanisms were specified in the case of hunchback in well defined terms of the dynamical system theory.

DEEP--differential evolution entirely parallel method for gene regulatory networks

Abstract: The Differential Evolution Entirely Parallel (DEEP) method is applied to the biological data fitting problem. We introduce a new migration scheme, in which the best member of the branch substitutes the oldest member of the next branch that provides a high speed of the algorithm convergence. We analyze the performance and efficiency of the developed algorithm on a test problem of finding the regulatory interactions within the network of gap genes that control the development of early Drosophila embryo. The parameters of a set of nonlinear differential equations are determined by minimizing the total error between the model behavior and experimental observations. The age of the individuum is defined by the number of iterations this individuum survived without changes. We used a ring topology for the network of computational nodes. The computer codes are available upon request.

Bulk elastic strain solitons in polycarbonate

Abstract: The excitation and propagation of bulk elastic strain solitons in a polycarbonate waveguide (bar) has been studied. The anomalously low damping of this nonlinear solitary wave is evaluated

Observation of a radiating bulk strain soliton in a solid-state waveguide

Abstract: The appearance and propagation of a radiating bulk elastic strain soliton is experimentally detected for the first time in layered nonlinearly elastic waveguides with nonideal contact between the layers. The nature of such waves is explained in terms of a model using coupled Boussinesq equations.

Strain solitary waves in polymeric nanocomposites

Abstract: Our recent theoretical and experimental investigations demonstrated the physical possibility of generation and further propagation of bulk strain solitary waves in waveguides made of nonlinearly elastic materials, namely glassy polymers: polystyrene and polymethylmethacrylate. These materials are widely used as matrices for polymeric nanocomposite materials, with an addition of a wide range of fillers that can drastically change the resulting elastic characteristics of a nanocomposite. Mechanical properties of nanocomposites depend, among other parameters, upon the filler content as well as upon an adhesion of its particles to the matrix. Here we present first experimental results on bulk strain soliton generation in a waveguide made of polymeric nanocomposite.