Mathematical modeling of microRNA-mediated mechanisms of translation repression

MicroRNAs can affect the protein translation using nine mechanistically different mechanisms, including repression of initiation and degradation of the transcript. There is a hot debate in the current literature about which mechanism and in which situations has a dominant role in living cells. The worst, same experimental systems dealing with the same pairs of mRNA and miRNA can provide ambiguous evidences about which is the actual mechanism of translation repression observed in the experiment. We start with reviewing the current knowledge of various mechanisms of miRNA action and suggest that mathematical modeling can help resolving some of the controversial interpretations. We describe three simple mathematical models of miRNA translation that can be used as tools in interpreting the experimental data on the dynamics of protein synthesis. The most complex model developed by us includes all known mechanisms of miRNA action. It allowed us to study possible dynamical patterns corresponding to different miRNA-mediated mechanisms of translation repression and to suggest concrete recipes on determining the dominant mechanism of miRNA action in the form of kinetic signatures. Using computational experiments and systematizing existing evidences from the literature, we justify a hypothesis about co-existence of distinct miRNA-mediated mechanisms of translation repression. The actually observed mechanism will be that acting on or changing the limiting "place" of the translation process. The limiting place can vary from one experimental setting to another. This model explains the majority of existing controversies reported.Comment: 40 pages, 9 figures, 4 tables, 91 cited reference. The analysis of kinetic signatures is updated according to the new model of coupled transcription, translation and degradation, and of miRNA-based regulation of this process published recently (arXiv:1204.5941). arXiv admin note: text overlap with arXiv:0911.179

Role of Temperature in the Growth of Silver Nanoparticles Through a Synergetic Reduction Approach

This study presents the role of reaction temperature in the formation and growth of silver nanoparticles through a synergetic reduction approach using two or three reducing agents simultaneously. By this approach, the shape-/size-controlled silver nanoparticles (plates and spheres) can be generated under mild conditions. It was found that the reaction temperature could play a key role in particle growth and shape/size control, especially for silver nanoplates. These nanoplates could exhibit an intensive surface plasmon resonance in the wavelength range of 700–1,400 nm in the UV–vis spectrum depending upon their shapes and sizes, which make them useful for optical applications, such as optical probes, ionic sensing, and biochemical sensors. A detailed analysis conducted in this study clearly shows that the reaction temperature can greatly influence reaction rate, and hence the particle characteristics. The findings would be useful for optimization of experimental parameters for shape-controlled synthesis of other metallic nanoparticles (e.g., Au, Cu, Pt, and Pd) with desirable functional properties