Papers by Mario Andrea Marchisio
Bioinformatics, 2008
Motivation: In principle, novel genetic circuits can be engineered using standard parts with well... more Motivation: In principle, novel genetic circuits can be engineered using standard parts with well-understood functionalities. However, no model based on the simple composition of these parts has become a standard, mainly because it is difficult to define signal exchanges between biological units as unambiguously as in electrical engineering. Corresponding concepts and computational tools for easy circuit design in biology are missing. Results: Taking inspiration from (and slightly modifying) ideas in the 'MIT Registry of Standard Biological Parts', we developed a method for the design of genetic circuits with composable parts. Gene expression requires four kinds of signal carriers: RNA polymerases, ribosomes, transcription factors and environmental 'messages' (inducers or corepressors). The flux of each of these types of molecules is a quantifiable biological signal exchanged between parts. Here, each part is modeled independently by the ordinary differential equations (ODE) formalism and integrated into the software ProMoT (Process Modeling Tool). In this way, we realized a 'drag and drop' tool, where genetic circuits are built just by placing biological parts on a canvas and by connecting them through 'wires' that enable flow of signal carriers, as it happens in electrical engineering. Our simulations of well-known synthetic circuits agree well with published computational and experimental results.
2009 IEEE International Symposium on Circuits and Systems (ISCAS), 2009
Concepts and tools at the basis of electrical engineering can be borrowed to assemble genetic cir... more Concepts and tools at the basis of electrical engineering can be borrowed to assemble genetic circuits in silico. As electrical components talk to each other by means of the electron current, standard biological parts exchange information through the fluxes of functional molecules, referred to as common signal carriers. Hence, synthetic circuits can be designed by connecting biological parts with wires where signal carriers flow. In this paper we present new features and applications of our model to computationally design synthetic gene circuits. In particular, we show a new design for polycistronic transcription units and a possible implementation of an enzyme-dependent pulsegenerating network.
Current Opinion in Biotechnology, 2009
Computer-aided design, pervasive in other engineering disciplines, is currently developing in syn... more Computer-aided design, pervasive in other engineering disciplines, is currently developing in synthetic biology. Concepts for standardization and hierarchies of parts, devices and systems provide a basis for efficient engineering in biology. Recently developed computational tools, for instance, enable rational (and graphical) composition of genetic circuits from standard parts, and subsequent simulation for testing the predicted functions in silico. The computational design of DNA and proteins with predetermined quantitative functions has made similar advances. The biggest challenge, however, is the integration of tools and methods into powerful and intuitively usable workflows-and the field is only starting to address it.
PLoS Computational Biology, 2011
De novo computational design of synthetic gene circuits that achieve well-defined target function... more De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology and a corresponding tool for in silico automatic design. For a given truth table that specifies a circuit's input-output relations, our algorithm generates and ranks several possible circuit schemes without the need for any optimization. Logic behavior is reproduced by the action of regulatory factors and chemicals on the promoters and on the ribosome binding sites of biological Boolean gates. Simulations of circuits with up to four inputs show a faithful and unequivocal truth table representation, even under parametric perturbations and stochastic noise. A comparison with already implemented circuits, in addition, reveals the potential for simpler designs with the same function. Therefore, we expect the method to help both in devising new circuits and in simplifying existing solutions.
The International Journal of Biochemistry & Cell Biology, 2011
An essential feature of synthetic biology devices is the conversion of signals from the exterior ... more An essential feature of synthetic biology devices is the conversion of signals from the exterior of the cell into specific cellular events such as the synthesis of a fluorescent protein. In the first synthetic gene circuits, signal transduction was accomplished via inducible or repressible transcription factors. Today, these rather simple transcription networks are the basis for the construction of more sophisticated devices that, for instance, couple artificial gene circuits with cellular pathways to create a biosensing moiety. In the future, completely artificial signaling pathways will give us the possibility to control cellular processes in a direct, precise and reliable way. At present, numerous pathway components such as receptors, adapters, scaffolds and their interactions with ligands and other signaling proteins have been already characterized and, in some cases, reengineered. In addition, important results have been obtained by rewiring pathways and building more complex gene networks-such as "cell phones" and ecosystems-based on synthetically induced cell-cell communication mechanisms. Furthermore, RNA-interference and lightdependent control of transcription factors have become new instruments to integrate different signals and better regulate protein synthesis. Overall, synthetic biology of sensing systems appears to be in continuous evolution. Nevertheless, rapid improvements on the available DNA-recombinant technology are essential to achieve, within few years, a full engineering of cell transduction pathways.
BMC Systems Biology, 2013
Background: The modular design of synthetic gene circuits via composable parts (DNA segments) and... more Background: The modular design of synthetic gene circuits via composable parts (DNA segments) and pools of signal carriers (molecules such as RNA polymerases and ribosomes) has been successfully applied to bacterial systems. However, eukaryotic cells are becoming a preferential host for new synthetic biology applications. Therefore, an accurate description of the intricate network of reactions that take place inside eukaryotic parts and pools is necessary. Rule-based modeling approaches are increasingly used to obtain compact representations of reaction networks in biological systems. However, this approach is intrinsically non-modular and not suitable per se for the description of composable genetic modules. In contrast, the Model Description Language (MDL) adopted by the modeling tool ProMoT is highly modular and it enables a faithful representation of biological parts and pools. Results: We developed a computational framework for the design of complex (eukaryotic) gene circuits by generating dynamic models of parts and pools via the joint usage of the BioNetGen rule-based modeling approach and MDL. The framework converts the specification of a part (or pool) structure into rules that serve as inputs for BioNetGen to calculate the part's species and reactions. The BioNetGen output is translated into an MDL file that gives a complete description of all the reactions that take place inside the part (or pool) together with a proper interface to connect it to other modules in the circuit. In proof-of-principle applications to eukaryotic Boolean circuits with more than ten genes and more than one thousand reactions, our framework yielded proper representations of the circuits' truth tables. Conclusions: For the model-based design of increasingly complex gene circuits, it is critical to achieve exact and systematic representations of the biological processes with minimal effort. Our computational framework provides such a detailed and intuitive way to design new and complex synthetic gene circuits.
Journal of Biological Engineering, 2014
In our previous computational work, we showed that gene digital circuits can be automatically des... more 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 redesigning 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.
Frontiers in Bioengineering and Biotechnology, 2014
Pools represents one of the first attempts to conceptualize the modular design of bacterial synth... more Pools represents one of the first attempts to conceptualize the modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNA segments) and Pools of molecules referred to as common signal carriers (e.g., RNA polymerases and ribosomes). The original framework for modeling bacterial components and designing prokaryotic circuits evolved over the last years and brought, first, to the development of an algorithm for the automatic design of Boolean gene circuits. This is a remarkable achievement since gene digital circuits have a broad range of applications that goes from biosensors for health and environment care to computational devices. More recently, Parts & Pools was enabled to give a proper formal description of eukaryotic biological circuit components.This was possible by employing a rule-based modeling approach, a technique that permits a faithful calculation of all the species and reactions involved in complex systems such as eukaryotic cells and compartments. In this way, Parts & Pools is currently suitable for the visual and modular design of synthetic gene circuits in yeast and mammalian cells too.
Journal of Biological Engineering, 2016
Background: In bacteria, transcription units can be insulated by placing a terminator in front of... more 
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Papers by Mario Andrea Marchisio