1. Distributed computation: the new wave of synthetic biology devices
Javier Macía, Francesc Posas, Ricard V. Solé 
Trends in Biotechnology 
Volume 30, Issue 6, Pages (June 2012)
DOI: /j.tibtech
Copyright © 2012 Elsevier Ltd Terms and Conditions

2. Figure 1
Different logic gates and switches can be engineered from cellular and/or molecular systems. A gate defines a minimal logic unit and is fully defined by a ‘truth table’ indicating the output associated to each possible input. In our context, 0 and 1 indicate absence or presence of the molecular signal, respectively. Here, we show how to combine two of these elements, namely (a) the AND and (b) the NOT gates, in a sequential fashion in order to obtain a NAND gate (c) or a N-IMPLIES gate (d). In this example, a, b and g indicate the (molecular) input signals. By simply connecting different gates in different ways, we can obtain the desired result. In (e) and (f) we illustrate these two examples through a hypothetical gene regulatory system (the inset pictures are the compact representation of the gates). Here, Pz indicates the promoter of gene Z. In (e) the NAND gate is obtained by using a heterodimer formed by two proteins, which repress the expression of a reporter gene (green fluorescent protein, GFP). The two input signals repress the genes that express the two components of the heterodimer and only if they are both present will the two monomers assemble and repress the reporter. Otherwise, GFP will be produced. Although the basic idea of combining gates is successful within electronics, the wiring among different parts of a synthetic circuit can be a rather difficult problem. This is illustrated by the so-called multiplexer, a standard element in electronics, schematically indicated in (g). This is a three-input one-output system where a given signal ‘selects’ one of the two inputs. In (h), a possible regulatory network implementing this function is shown. Such circuits can be constructed with a single cell [71] but are difficult to construct. Complex circuits in single cells are time consuming and cannot be re-used to build further circuits.
Trends in Biotechnology  , DOI: ( /j.tibtech )
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3. Figure 2
Examples of complex decision-making synthetic designs, based on engineering a single cell complex. A population of cells on a Petri dish receives light (a) on a given area as defined by a mask (here a start). After the light is applied (b, c), cells respond to light and can detect the boundaries. The genetic circuit implements a simple function (d), which codes a specific response associated with the synthesis of a dark pigment. In (e), we show a synthetic cellular device, where Escherichia coli acts as an edge detector [60] where the engineered cells identify light-dark edges from a projected image. The circuit essentially executes two instructions: ‘IF NOT light, produce signal’ and ‘IF signal AND NOT (NOT light), produce pigment’. Cells can detect light using a light-sensitive protein, Cph8, which is a chimera sensor kinase bearing the photoreceptor domain of the Synechocystis phytochrome Cph1 and the kinase domain of E. coli EnvZ. In the presence of red light, the kinase activity of Cph8 is inhibited, activating the transcription of two different genes, namely LuxI and cI. LuxI is an enzyme that produces the quorum sensing signal 3-oxohexanoyl-homoserine lactone (AHL), whereas CI is the transcriptional repressor protein from λ-phage. AHL binds to the constitutively expressed transcription factor LuxR activating the expression of lacZ under the promoter Plux-λ whereas CI dominantly represses this promoter. If light is not detected, AHL signal is produced, spreading locally and affecting neighboring cells. Moreover, if a cell is receiving this signal AND light (something to expect at the edges of the image), it produces dark pigment by cleaving a substrate in the media using the product of lacZ (β-galactosidase). Adapted from [60]. Here, X, Y and Z indicate AHL, CI and the dark pigment, respectively.
Trends in Biotechnology  , DOI: ( /j.tibtech )
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4. Figure 3
Implementing complex circuits using logic division of labor. One possible scenario involves the use of spatially segregated colonies of engineered strains, connected through quorum wiring molecules (here, acyl homoserine lactones). By combining orthogonal NOR gates, it is possible to build all two-input one-output logic gates. The last component on the right is the output colony, expressing a reporter (here, the yellow fluorescent protein, YFP) if a non-zero input is detected. The basic units (a) are constructed on Escherichia coli, using promoters PBAD and PTet, which are activated under the presence of arabinose (Ara) and anhydroteracycline (aTc), respectively. This approach has been developed by implementing the NOR gates with two tandem promoters as inputs, driving the transcription of a repressor (b). In electronics, the spatially-extended combination of NOR gates is widely used to obtain chips, such as the one shown in (c). Using a fixed spatial arrangement of the colonies (d) and using Ara and aTc as input molecules, the conventional combinatorial logic used in electronics is used in order to construct all the two-input one-output logic gates.
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5. Figure 4
A simple example of distributed computational design of a MUX circuit. Here, we combine two engineered cells (C1 and C2) that are not connected and both express the same reporter (GFP) as output molecule. Each cell type implements a simple logic gate (here, we have (a) AND and (b) N-IMPLIES, respectively), but they are not connected through chemical signals. The use of a consortium along with the distributed output allows strong reduction of wiring requirements. Compare with the equivalent single-cell design in Figure 1g,h.
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6. Figure 5
A non-standard alternative to synthetic design of cellular devices involves the use of a library of engineered cells (a) where several cell types can produce the output signal, here indicated as R or r. The different engineered cell types are indicated by different colors, a indicates a diffusible communicating signal used as our wire. These cells can have receptors for external signals as well as for cell–cell communication wires. The key difference here is that the output is distributed over different engineered cells. This makes possible a proper isolation of computational modules with a dramatic reduction of wiring costs. In (b–e), we show several examples of consortia implementing simple logic functions (N implies and NOR) but also complex ones, as is the case for the multiplexer (MUX) or a comparator (COMP) where two reporters (R and r) are used to indicate which entry is larger than the other. This approach was successfully implemented using yeast strains [70]. The potential of this approach compared to standard designs is illustrated in (f) and (g). Here, we have computed, for different numbers of cells (f) and wires (g), the number of possible computational devices (functions) that can be implemented using distributed computation (blue bars) and NOR-based systems (yellow bars) where only NOR gates have been used according with standard design rules. As we can see, in the distributed scenario, a small number of cell types or wires allow construction of a large number of functional devices.
Trends in Biotechnology  , DOI: ( /j.tibtech )
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