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Okumura S, Gines G, Lobato-Dauzier N, Baccouche A, Deteix R, Fujii T, Rondelez Y, Genot AJ. Nonlinear decision-making with enzymatic neural networks. Nature 2022; 610:496-501. [PMID: 36261553 DOI: 10.1038/s41586-022-05218-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 08/09/2022] [Indexed: 12/22/2022]
Abstract
Artificial neural networks have revolutionized electronic computing. Similarly, molecular networks with neuromorphic architectures may enable molecular decision-making on a level comparable to gene regulatory networks1,2. Non-enzymatic networks could in principle support neuromorphic architectures, and seminal proofs-of-principle have been reported3,4. However, leakages (that is, the unwanted release of species), as well as issues with sensitivity, speed, preparation and the lack of strong nonlinear responses, make the composition of layers delicate, and molecular classifications equivalent to a multilayer neural network remain elusive (for example, the partitioning of a concentration space into regions that cannot be linearly separated). Here we introduce DNA-encoded enzymatic neurons with tuneable weights and biases, and which are assembled in multilayer architectures to classify nonlinearly separable regions. We first leverage the sharp decision margin of a neuron to compute various majority functions on 10 bits. We then compose neurons into a two-layer network and synthetize a parametric family of rectangular functions on a microRNA input. Finally, we connect neural and logical computations into a hybrid circuit that recursively partitions a concentration plane according to a decision tree in cell-sized droplets. This computational power and extreme miniaturization open avenues to query and manage molecular systems with complex contents, such as liquid biopsies or DNA databases.
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Affiliation(s)
- S Okumura
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - G Gines
- Laboratoire Gulliver, PSL Research University, Paris, France
| | - N Lobato-Dauzier
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - A Baccouche
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - R Deteix
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - T Fujii
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Y Rondelez
- Laboratoire Gulliver, PSL Research University, Paris, France
| | - A J Genot
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan.
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2
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Gines G, Zadorin AS, Galas JC, Fujii T, Estevez-Torres A, Rondelez Y. Microscopic agents programmed by DNA circuits. Nat Nanotechnol 2017; 12:351-359. [PMID: 28135261 DOI: 10.1038/nnano.2016.299] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 12/14/2016] [Indexed: 05/03/2023]
Abstract
Information stored in synthetic nucleic acids sequences can be used in vitro to create complex reaction networks with precisely programmed chemical dynamics. Here, we scale up this approach to program networks of microscopic particles (agents) dispersed in an enzymatic solution. Agents may possess multiple stable states, thus maintaining a memory and communicate by emitting various orthogonal chemical signals, while also sensing the behaviour of neighbouring agents. Using this approach, we can produce collective behaviours involving thousands of agents, for example retrieving information over long distances or creating spatial patterns. Our systems recapitulate some fundamental mechanisms of distributed decision making and morphogenesis among living organisms and could find applications in cases where many individual clues need to be combined to reach a decision, for example in molecular diagnostics.
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Affiliation(s)
- G Gines
- LIMMS, CNRS, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - A S Zadorin
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- Laboratoire Jean Perrin, CNRS, Université Pierre et Marie Curie, UMR 8237, 4 place Jussieu, 75005 Paris, France
| | - J-C Galas
- Laboratoire Jean Perrin, CNRS, Université Pierre et Marie Curie, UMR 8237, 4 place Jussieu, 75005 Paris, France
| | - T Fujii
- LIMMS, CNRS, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
| | - A Estevez-Torres
- Laboratoire Jean Perrin, CNRS, Université Pierre et Marie Curie, UMR 8237, 4 place Jussieu, 75005 Paris, France
| | - Y Rondelez
- LIMMS, CNRS, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
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3
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Genot AJ, Baccouche A, Sieskind R, Aubert-Kato N, Bredeche N, Bartolo JF, Taly V, Fujii T, Rondelez Y. High-resolution mapping of bifurcations in nonlinear biochemical circuits. Nat Chem 2016; 8:760-7. [PMID: 27442281 DOI: 10.1038/nchem.2544] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/05/2016] [Indexed: 11/09/2022]
Abstract
Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.
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Affiliation(s)
- A J Genot
- LAAS, CNRS, UPR 8001, 7 av. Col. Roche, 31400 Toulouse, France.,LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan
| | - A Baccouche
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan.,LCBPT, CNRS, UMR 8601, Université Paris Descartes, 45 rue des Saints Pères, 75006 Paris, France
| | - R Sieskind
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan.,Electrical Engineering and Applied Physics department (EEA), Ecole Normale Superieure of Cachan, 61 avenue du Président Wilson, 94230 Cachan, France.,Laboratoire Gulliver, CNRS, UMR 7083, ESPCI, 10 rue Vauquelin, 75005 Paris, France
| | - N Aubert-Kato
- Ochanomizu University, 112-8610 Tokyo, Japan.,Earth- Life Science Institute (ELSI), Tokyo Institute of Technology, 152-8550 Tokyo, Japan
| | - N Bredeche
- Sorbonne Universités, UPMC Université Paris 06, CNRS, ISIR, F-75005 Paris, France
| | - J F Bartolo
- LCAMB, UMR 7199, CNRS/Université de Strasbourg, F-67400 Illkirch, France.,Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - V Taly
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - T Fujii
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan
| | - Y Rondelez
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan.,Laboratoire Gulliver, CNRS, UMR 7083, ESPCI, 10 rue Vauquelin, 75005 Paris, France
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Zambrano A, Zadorin AS, Rondelez Y, Estévez-Torres A, Galas JC. Pursuit-and-Evasion Reaction-Diffusion Waves in Microreactors with Tailored Geometry. J Phys Chem B 2015; 119:5349-55. [DOI: 10.1021/jp509474w] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- A. Zambrano
- Laboratoire
de Photonique et de Nanostructures, CNRS-UPR20, Marcoussis 91460, France
| | - A. S. Zadorin
- Laboratoire
de Photonique et de Nanostructures, CNRS-UPR20, Marcoussis 91460, France
| | - Y. Rondelez
- LIMMS/CNRS-IIS, University of Tokyo, Komaba 4-6-2 Meguro-ku, Tokyo 113-8654, Japan
| | - A. Estévez-Torres
- Laboratoire
de Photonique et de Nanostructures, CNRS-UPR20, Marcoussis 91460, France
| | - J.-C. Galas
- Laboratoire
de Photonique et de Nanostructures, CNRS-UPR20, Marcoussis 91460, France
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Abstract
Four novel calix[6]arene-based cuprous complexes are described. They present a biomimetic tris(imidazole) coordination core associated with a hydrophobic cavity that wraps the apical binding site. Each differs from the other by the methyl or ethyl substituents present on the phenoxyl groups (OR1) and on the imidazole arms (NR2) of the calix[6]arene structure. In solution, stable CO complexes were obtained. We have investigated their geometrical and dynamic properties with respect to the steric demand. IR and NMR studies revealed that, in solution, these complexes adopted two distinct conformations. The preferred conformation was dictated only by the size of the OR1 group. When R1 was an ethyl group, the complex preferentially adopted a flattened C3-symmetrical structure. The corresponding helical enantiomers were in conformational equilibrium, which, however, was slow on the 1H NMR time scale at -80 degrees C. When R1 was a methyl group, the low-temperature NMR spectra revealed the partial inclusion of one tBu group. The complex wobbled between three dissymmetric but equivalent conformations. Hence, small differences in the steric demand of the calixarene's skeleton changed the geometry and dynamics of the system. Indeed, this supramolecular control was promoted by the strong conformational coupling between the metal center and the host structure. Interestingly, this was not only the result of a covalent preorganization, but also stemmed from weak interactions within the hydrophobic pocket. The vibrational spectra of the bound CO were revealed to be a sensitive gauge of this supramolecular behavior, similar to copper proteins in which allosteric effects are common.
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Affiliation(s)
- Y Rondelez
- Laboratoire de Chimie et Biochimie des Complexes Moléculaires, UMR, CNRS 7576, Ecole Nationale Supérieure de Chimie de Paris, France
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