Artificial multicellularity and pattern formation

En aquesta tesi hem intentat atacar preguntes relacionades amb els orígens de la vida multicel•lular i dels comportaments cooperatius a la nostra biosfera. Particularment hem fet ús de mètodes “no naturals”: la vida artificial i la biologia sintètica. A diferencia dels enfocs més tradicionals com la caracterització filogenètica i la biologia teòrica, aquests mètodes permeten observar les transicions en individualitat i complexitat a mesura que tenen lloc. Més concretament, en aquest projecte hem proposat noves regles per aconseguir sistemes de trencament de simetria espacial i com la multicel•lularitat amb diferenciació pot ser seleccionada des de genotips unicel•lulars amb les pressions selectives apropiades.This project has tackled unanswered questions regarding the origins of multicellular life and cooperation using artificial approaches, namely: artificial evolution and synthetic biology. These offer unique opportunities to watch the evolution of complexity unfold and complement the extensively used methods of characterization of extant multicellular systems and theoretical biology. In particular we have proposed new mechanisms to create periodical structures in synthetic systems and how differentiated multicellularity might arise from Darwinian entities

Synthetic circuit designs for earth terraformation

Background. Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, among others. None of these scenarios seems powerful enough to achieve the desired restoration of safe boundaries./nPresentation of the hypothesis. We hypothesize that synthetic organisms with the appropriate engineering design could be used to safely prevent declines in some stressed ecosystems and help improving carbon sequestration. Such schemes would include engineering mutualistic dependencies preventing undesired evolutionary processes. We hypothesize that some particular design principles introduce unescapable constraints to the engineered organisms that act as effective firewalls./nTesting the hypothesis. Testing this designed organisms can be achieved by using controlled bioreactor models, with single and heterogeneous populations, and accurate computational models including different scales (from genetic constructs and metabolic pathways to population dynamics)./nImplications of the hypothesis. Our hypothesis heads towards a future anthropogenic action that should effectively act as Terraforming processes. It also implies a major challenge in the existing biosafety policies, since we suggest release of modified organisms as potentially necessary strategy for success./nReviewers. This article was reviewed by This article was reviewed by Eugene V. Koonin, Tom Ellis (nominated by Purificación Lopez-Garcia) and Eörs Szathmary.This study was supported by an ERC Advanced Grant Number 294294 from the EU seventh framework program (SYNCOM), the Botin Foundation, by Banco Santander through its Santander Universities Global Division and by the Santa Fe Institute, where most of the work was done

Synthetic circuit designs for earth terraformation

Background. Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, among others. None of these scenarios seems powerful enough to achieve the desired restoration of safe boundaries./nPresentation of the hypothesis. We hypothesize that synthetic organisms with the appropriate engineering design could be used to safely prevent declines in some stressed ecosystems and help improving carbon sequestration. Such schemes would include engineering mutualistic dependencies preventing undesired evolutionary processes. We hypothesize that some particular design principles introduce unescapable constraints to the engineered organisms that act as effective firewalls./nTesting the hypothesis. Testing this designed organisms can be achieved by using controlled bioreactor models, with single and heterogeneous populations, and accurate computational models including different scales (from genetic constructs and metabolic pathways to population dynamics)./nImplications of the hypothesis. Our hypothesis heads towards a future anthropogenic action that should effectively act as Terraforming processes. It also implies a major challenge in the existing biosafety policies, since we suggest release of modified organisms as potentially necessary strategy for success./nReviewers. This article was reviewed by This article was reviewed by Eugene V. Koonin, Tom Ellis (nominated by Purificación Lopez-Garcia) and Eörs Szathmary.This study was supported by an ERC Advanced Grant Number 294294 from the EU seventh framework program (SYNCOM), the Botin Foundation, by Banco Santander through its Santander Universities Global Division and by the Santa Fe Institute, where most of the work was done

Spatial self-organization in hybrid models of multicellular adhesion

Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically cellular automata or reaction-diffusion systems. A different class of dynamical processes involves the correlated movement of agents over space, which can be mediated through chemotactic movement or minimization of cell-cell interaction energy. A classic example of the latter is given by the formation of spatially segregated assemblies when cells display differential adhesion. Here, we consider a new class of dynamical models, involving cell adhesion among two stochastically exchangeable cell states as a minimal model capable of exhibiting well-defined, ordered spatial patterns. Our results suggest that a whole space of pattern-forming rules is hosted by the combination of physical differential adhesion and the value of probabilities modulating cell phenotypic switching, showing that Turing-like patterns can be obtained without resorting to reaction-diffusion processes. If the model is expanded allowing cells to proliferate and die in an environment where diffusible nutrient and toxic waste are at play, different phases are observed, characterized by regularly spaced patterns. The analysis of the parameter space reveals that certain phases reach higher population levels than other modes of organization. A detailed exploration of the mean-field theory is also presented. Finally, we let populations of cells with different adhesion matrices compete for reproduction, showing that, in our model, structural organization can improve the fitness of a given cell population. The implications of these results for ecological and evolutionary models of pattern formation and the emergence of multicellularity are outlined.This work has been supported by the Botín Foundation by Banco Santander through its Santander Universities Global Division, a MINECO fellowship and by the Santa Fe Institut

Spatial dynamics of synthetic microbial mutualists and their parasites

A major force contributing to the emergence of novelty in nature is the presence of cooperative interactions, where two or more components of a system act in synergy, sometimes leading to higher-order, emergent phenomena. Within molecular evolution, the so called hypercycle defines the simplest model of an autocatalytic cycle, providing major theoretical insights on the evolution of cooperation in the early biosphere. These closed cooperative loops have also inspired our understanding of how catalytic loops appear in ecological systems. In both cases, hypercycle and ecological cooperative loops, the role played by space seems to be crucial for their stability and resilience against parasites. However, it is difficult to test these ideas in natural ecosystems, where time and spatial scales introduce considerable limitations. Here, we use engineered bacteria as a model system to a variety of environmental scenarios identifying trends that transcend the specific model system, such an enhanced genetic diversity in environments requiring mutualistic interactions. Interestingly, we show that improved environments can slow down mutualistic range expansions as a result of genetic drift effects preceding local resource depletion. Moreover, we show that a parasitic strain is excluded from the population during range expansions (which acknowledges a classical prediction). Nevertheless, environmental deterioration can reshape population interactions, this same strain becoming part of a three-species mutualistic web in scenarios in which the two-strain mutualism becomes non functional. The evolutionary and ecological implications for the design of synthetic ecosystems are outlined.This study was supported by an European Research Council Advanced Grant (SYNCOM, grant number 294294), a MINECO grant FIS2015-67616-P, by Banco Santander through its Santander Universities Global Division, the Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya and by the Santa Fe Institute

Synthetic lateral inhibition in periodic pattern forming microbial colonies

Multicellular entities are characterized by intricate spatial patterns, intimately related to the functions they perform. These patterns are often created from isotropic embryonic structures, without external information cues guiding the symmetry breaking process. Mature biological structures also display characteristic scales with repeating distributions of signals or chemical species across space. Many candidate patterning modules have been used to explain processes during development and typically include a set of interacting and diffusing chemicals or agents known as morphogens. Great effort has been put forward to better understand the conditions in which pattern-forming processes can occur in the biological domain. However, evidence and practical knowledge allowing us to engineer symmetry-breaking is still lacking. Here we follow a different approach by designing a synthetic gene circuit in E. coli that implements a local activation long-range inhibition mechanism. The synthetic gene network implements an artificial differentiation process that changes the physicochemical properties of the agents. Using both experimental results and modeling, we show that the proposed system is capable of symmetry-breaking leading to regular spatial patterns during colony growth. Studying how these patterns emerge is fundamental to further our understanding of the evolution of biocomplexity and the role played by self-organization. The artificial system studied here and the engineering perspective on embryogenic processes can help validate developmental theories and identify universal properties underpinning biological pattern formation, with special interest for the area of synthetic developmental biology.This study was supported by a European Research Council Advanced Grant (SYNCOM), the Botin Foundation, by Banco Santander through its Santander Universities Global Division and by a MINECO Grant FIS2015-67616-P. This work has also received support by the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya and by the Santa Fe Institute

A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology

Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses-the so-called transfer function-and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined.Fundacion Botín, Banco de Santander through its Santander Universities Global Division [BES-2010-038940 to/nR.M., C.R.C.]; ERC SYNCOM [291294 to M.C.B.]; FPI MINECO fellowship [to S.D.N.]. Funding for open access charge: ERC SYNCOM [291294]

Population dynamics of synthetic terraformation motifs

Ecosystems are complex systems, currently experiencing several threats associated with global warming, intensive exploitation and human-driven habitat degradation. Because of a general presence of multiple stable states, including states involving population extinction, and due to the intrinsic nonlinearities associated with feedback loops, collapse in ecosystems could occur in a catastrophic manner. It has been recently suggested that a potential path to prevent or modify the outcome of these transitions would involve designing synthetic organisms and synthetic ecological interactions that could push these endangered systems out of the critical boundaries. In this paper, we investigate the dynamics of the simplest mathematical models associated with four classes of ecological engineering designs, named Terraformation motifs (TMs). These TMs put in a nutshell different ecological strategies. In this context, some fundamental types of bifurcations pervade the systems' dynamics. Mutualistic interactions can enhance persistence of the systems by means of saddle-node bifurcations. The models without cooperative interactions show that ecosystems achieve restoration through transcritical bifurcations. Thus, our analysis of the models allows us to define the stability conditions and parameter domains where these TMs must work.This study was supported by a European Research Council Advanced Grant (SYNCOM), by the Botin Foundation, by Banco Santander through its Santander Universities Global Division, by grant FIS2015-67616-P, by the PR01018-EC-H2020-FET-Open MADONNA project and by the Santa Fe Institute. This work has also counted with the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya. J.S. has been also partially funded by a ‘Ramón y Cajal’ Fellowship (RYC-2017-22243) and by the CERCA Programme of the Generalitat de Catalunya. The research leading to these results has received funding from ‘la Caixa’ Foundatio