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From 2011.igem.org

Logic gates in our project

Logic gates are the basic bricks to build electronic circuits. These operate with logic values (true or false, 1 or 0, open or closed, etc.) represented by different electric tensions, according to the rules of the Boolean algebra. High tension represents 1 (true) and low tension means 0 (false)

Each kind of logic gate (there are eight) performs a specific logic function, and they have a different number of inputs and outputs. By combining many logic gates we can build circuits that can carry out more complex functions.

We intend to transfer the concept of logic gate from electronics to biology, using strains of bacteria as logic gates and chemical substances instead of electric tension. This substances, that we call bbits, will activate the expresion of a gene, and this will result into the secretion of another chemical substance, the output information that will become the input information for the next strain.

But for this, it is an essential requirement that we find a specific chemical substance for each couple of bacteria that have to communicate, for there are no “wires” that can transmit information from one point to another in an ordered, isolated way: all the substances are secreted into the same medium but they must not interfere in other couple’s communication circuit, each couple needs to have a unique substance for communication.

To create logic gates it’s necessary that biobits generate a genetic response only under a specific condition (the presence of two signals, the presence of one but not the other, etc.). Besides, the “receptor half-wires” must have a threshold level for activation so that they’re only activated when their specific biobit reaches a high concentration. This would prevent the module from failure in case of one bacterium’s failure in its response. The great majority of the bacteria will work properly and the erroneus activity of a single bacterium won’treach the threshold level, the “genetic noise” will be silenced (this is one of the main problems when building biological circuits)

Quorum sensing in our project

 Quorum sensing, or bacterial auto-induction, is the way in which bacteria measure the density of the colony, exchanging chemical substances among the ones of its kind. It allows bacteria to know how many they are and how to act coordinately. This phenomenom is mediated by autoinducers, substances characteristic of each species. Bacteria are both emitters and receptors of this signal, but the receptor is only activated when a threshold level of signal is reached (this is, when the population is big enough to produce such amount of substance), then leading to a differential gene expression through a signalling cascade.

Quorum sensing fulfills all the requirements we need to create solid logic gates. Each species produces and senses a specific autoinducer, so there’s a wide range of these substances we can use as bbits. All we have to do is insert an output gene in the target gene of the regulatory cascade. The fact that receptors answer only when the signal reaches a threshold is a key to avoid genetic background, and this will give sturdiness to our system.