Fan-out in Gene Regulatory Networks. J Biol Eng 4:16

Department of Bioengineering, University of Washington, William H, Foege Building, Box 355061, Seattle, WA 98195-5061, USA. .
Journal of Biological Engineering (Impact Factor: 2.48). 12/2010; 4(1):16. DOI: 10.1186/1754-1611-4-16
Source: PubMed

ABSTRACT In synthetic biology, gene regulatory circuits are often constructed by combining smaller circuit components. Connections between components are achieved by transcription factors acting on promoters. If the individual components behave as true modules and certain module interface conditions are satisfied, the function of the composite circuits can in principle be predicted.
In this paper, we investigate one of the interface conditions: fan-out. We quantify the fan-out, a concept widely used in electrical engineering, to indicate the maximum number of the downstream inputs that an upstream output transcription factor can regulate. The fan-out is shown to be closely related to retroactivity studied by Del Vecchio, et al. An efficient operational method for measuring the fan-out is proposed and shown to be applied to various types of module interfaces. The fan-out is also shown to be enhanced by self-inhibitory regulation on the output. The potential role of an inhibitory regulation is discussed.
The proposed estimation method for fan-out not only provides an experimentally efficient way for quantifying the level of modularity in gene regulatory circuits but also helps characterize and design module interfaces, enabling the modular construction of gene circuits.

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Available from: Herbert M Sauro, May 20, 2015
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    • "A precise gate wiring needs a more detailed promoter characterization with a better estimation of operator positional effects and leakage. Furthermore, the fan-out[37] of every gate has to be determined properly. Distributed output architecture, in contrast, demands that basic gates have similar performance–namely comparable output fluorescence levels–such that one can predict and clearly distinguish the 0 and 1 output of the circuit realized via gates’ composition. "
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    ABSTRACT: In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with the Karnaugh map method and, then, the translation of the Boolean formulas into circuit schemes organized into layers of Boolean gates and Pools of signal carriers. In our framework, gene digital circuits that take up to three different input signals (chemicals) arise from the composition of three kinds of basic Boolean gates, namely YES, NOT, and AND. Here we present a library of YES, NOT, and AND gates realized via plasmidic DNA integration into the yeast genome. Boolean behavior is reproduced via the transcriptional control of a synthetic bipartite promoter that contains sequences of the yeast VPH1 and minimal CYC1 promoters together with operator binding sites for bacterial (i.e. orthogonal) repressor proteins. Moreover, model-driven considerations permitted us to pinpoint a strategy for re-designing gates when a better digital performance is required. Our library of well-characterized Boolean gates is the basis for the assembly of more complex gene digital circuits. As a proof of concepts, we engineered two 2-input OR gates, designed by our software, by combining YES and NOT gates present in our library.
    Journal of Biological Engineering 02/2014; 8(1):6. DOI:10.1186/1754-1611-8-6 · 2.48 Impact Factor
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    • "● Approximate knowledge of RNA folding and cis-/transinteraction of multiple regulators [13] [16]. ● Functional composition of devices that leads to unexpected circuit failure [20] [21] [22] [23]. "
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    ABSTRACT: Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues.
    Biotechnology Journal 07/2012; 7(7):856-66. DOI:10.1002/biot.201200085 · 3.49 Impact Factor
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    ABSTRACT: Modularity is a concept that is widely used in biological science with various interpretations. In this chapter we will first give a general overview of modularity in biology, and later focus on modularity in synthetic biology. In engineering, a module is a component whose intrinsic functionality is independent of its surrounding milieu. In biology, however, modularity is less clear-cut; for example, modules can be classified by network interactions or by functional distinctiveness such as the reuse of protein domains. In synthetic biology the question of modularity is more closely related to engineering where functional independence is important. One way of defining synthetic modules is by specifying a generic pattern of regulations that results in desired functionalities, which we term a design pattern. In this perspective, connections between modules are described by the regulatory links, which are represented by molecular reactions. Under these reactions, the output of an upstream module – the concentration of regulating molecules – is sequestered by the input of the downstream module. This sequestration can cause changes in the upstream module function. We quantify the maximally tolerable load from the downstream input, which we term gene circuit fan-out. We provide an efficient and practical way of estimating the fan-out by experiment.
    Design and Analysis of Biomolecular Circuits, 01/2011: pages 117-138; , ISBN: 978-1-4419-6765-7
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