Title |
Quasi-cellular systems: stochastic simulation analysis at nanoscale range
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Published in |
BMC Bioinformatics, April 2013
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DOI | 10.1186/1471-2105-14-s7-s7 |
Pubmed ID | |
Authors |
Lorenzo Calviello, Pasquale Stano, Fabio Mavelli, Pier Luigi Luisi, Roberto Marangoni |
Abstract |
The wet-lab synthesis of the simplest forms of life (minimal cells) is a challenging aspect in modern synthetic biology. Quasi-cellular systems able to produce proteins directly from DNA can be obtained by encapsulating the cell-free transcription/translation system PURESYSTEM(PS) in liposomes. It is possible to detect the intra-vesicle protein production using DNA encoding for GFP and monitoring the fluorescence emission over time. The entrapment of solutes in small-volume liposomes is a fundamental open problem. Stochastic simulation is a valuable tool in the study of biochemical reaction at nanoscale range. QDC (Quick Direct-Method Controlled), a stochastic simulation software based on the well-known Gillespie's SSA algorithm, was used. A suitable model formally describing the PS reactions network was developed, to predict, from inner species concentrations (very difficult to measure in small-volumes), the resulting fluorescence signal (experimentally observable). |
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Mendeley readers
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