31 May 2010. A new system using bacterial communities to autonomously solve complex problems was developed at the Universidad Politécnica de Madrid’s Facultad de Informática. This system is a step forward in the formation of a new scientific discipline called synthetic biology.
The designed algorithms help to synchronize different bacteria according to the bacteria’s natural capabilities and mechanisms of communication, like bacterial conjugation and quorum sensing.
Bacterial conjugation is the process of transferring genetic information from a donor cell to a receptor cell. Quorum sensing is a mechanism for controlling genetic expression depending on cell density.
Manipulating bacterial communication
The new system developed as part of this research modifies and manipulates these mechanisms of communication among bacteria to achieve computations with rudimentary decision-making systems.
The newly designed architectures have been used in computational applications like autonomous complex problem solving by bacterial communities or the design of a population oscillator modelled after the likeness of a client/server architecture. The client/server architecture is a major model in computer science for developing information systems where the transactions are divided into independent processes that cooperate with each other to exchange information, services or resources.
Medical and ecological applications
The applications of the system, which has been validated both at the biological (expertise) and computational (simulation) levels, cover scientific fields as far apart as medicine or ecology.
Research has focused on their development to design communications architectures for multi-strain bacterial communities. On the one hand, a heterogeneous community using bacterial conjugation as a key communications protocol was designed. This heterogeneous community is based on the idea of differentiating computational instructions stored in the bacterial chromosome of the data sets stored in plasmid vectors. Plasmids or vectors are extrachromosomal circular or linear DNA molecules that are replicated and transcribed independently of chromosomal DNA.
On the other hand, using quorum sensing in the communications protocol, the research realized an emerging behaviour by mixing several functionally different strains of the same community. This led to the design of hardware devices using non-electric molecular technology based on biology as instead of electronics as is usual practice in computing.
Another step towards synthetic biology
The methodology developed in this research has led to the design of a bacterium that can perform a specific purpose independently of the rest of the system, thereby enhancing component reusability.
This research is another step forward in the development of an interdisciplinary science, synthetic biology and bacterial computing, a product of the marriage between biology and computer science.
This new discipline has led to the construction of molecular devices acting as rudimentary computers and performing defined logical calculation tasks. Engineering is an aid for undertaking the design of these biosystems as a formalized component configuration task. The underlying idea is to build living systems with functionalities that are not found in nature.
This research was developed by informatics engineer Ángel Goñi Moreno as his PhD thesis defended at the Facultad de Informática in May 2010. The PhD thesis was supervised by Facultad de Informática professor Juan Castellanos Peñuela, PhD.
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