Stepping Stones to Synthetic Biology by Sergio Carrà

Author:Sergio Carrà
Language: eng
Format: epub, pdf
ISBN: 9783319954592
Publisher: Springer International Publishing

Regular: where local groups of interconnected nodes are present.

Casual: where groups of interconnected nodes are absent and the net can be easily crossed.

Scale-free: if interconnected nodes are present, the net is also easily crossed.

Actually, hierarchical structures can also arise through originating systems that combine modularity and scale–free topology. The corresponding hierarchical models are based on the replication of small clusters linked to the central node of the original cluster. The resulting network is scale–free because it has a power–law distribution.

As mentioned, any model of cellular phenomena takes the form of interaction diagrams whose components are small molecules, macromolecules, or molecular motors. Their interactions include a range of processes, such as chemical binding or unbinding, catalytic reactions, and regulation of activities. These processes result in the production, interconversion, transport, or consumption of the species present in the network.

Therefore, in a cell, the processes characterized by mass, energy and information transfer are connected through a complex network of cellular constituents and reactions. Any cell is built on thousands of interconnected enzymatic reactions, which control the energy fluxes and the production of cellular components involved in metabolism. The afore-mentioned exponential relation, obtained from experimental data, indicates the presence of a scale-free network. A pioneering investigation from this perspective was performed some years ago by A.L. Barabasi and coworkers, on the metabolism of Escherichia coli, a bacterium that, thanks to its versatility, is the most intensively studied and best understood organism on the planet. It is, in fact, a highly diverse organism with a number of complex, multi-faceted aspects. From the investigations, an elevated dishomogeneity in the distribution of the fluxes of the various components emerged, revealing a network whose composition mirrors that of a cell described just above, and therefore also indicating the presence of a scale-free network. On the whole, a “high flux backbone” of metabolism emerges, in which the various reactions are reciprocally connected to a topological structure similar to a star.

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