title: Pattern selection in a cooperative biochemical in vitro amplification system: the role of parasites.
abstract: Previously, numerical simulations have shown that evolving systems can be stabilized against emerging parasites by pattern formation in spatially extended flow reactors. Hence, it can be argued that pattern formation is a prerequisite for any experimental investigation of the biochemical evolution of cooperative function. Here, we study a model of an experimental biochemical system for the cooperative in vitro amplification of DNA strands and show that emerging parasites can induce a complex pattern formation even when no pattern formation occurs without parasites. In an adiabatic approximation where the cooperative amplification reaction is assumed to adapt fast to slowly emerging parasites, the parasite concentration itself acts as a Steuer parameter for the selection of various complex patterns. Without such an adiabatic approximation only transient patterns emerge. As any species can grow for very low concentrations, the parasite is able to infect the entire reactor and the system is finally diluted out. In the experimental biochemical system, however, the species are individual molecules and the growth of spatially separated, non-infected regions becomes feasible. Hence a cutoff threshold for the minimal concentration is applied. In these simulations the otherwise lethal infection by parasites induces the formation of spatiotemporal spirals, and this spatial structure help the host and parasitoid species to survive together. These theoretical results describe an inherent property of cooperative reactions and have an important impact on experimental investigations on the molecular evolution and complex function in spatially extended reactors. Since the formation of the complex pattern is restricted either to a rather large cutoff value or a special choice of the kinetic parameters, we, however, conclude that the persistence of evolving cooperative amplification is not possible in a simple reaction-diffusion reactor. Experimental set-ups with patchy environments, e.g. biomolecular amplification in coupled microstructured flow chambers or in microemulsion, are eligible candidates for the observation of such a self-organized pattern selection.
authors.affiliation: Fraunhofer Gesellschaft, Biomolecular Information Processing, Schloss Birlinghoven, D-53754 Sankt Augustin, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Kirner
authors.forename: J
authors.initials: J
authors.lastname: Ackermann
mesh_terms: D000818:Animals; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D019143:Evolution, Molecular; D006790:Host-Parasite Interactions; D008957:Models, Genetic; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D009693:Nucleic Acid Hybridization / Q000379:methods; D010271:Parasites / Q000254:growth & development*; D012641:Selection, Genetic
chemical_list: D012321:DNA-Directed RNA Polymerases