Nuria Conde-Pueyo

Multicellularity is one of the major evolutionary transitions, and its rise provided the ingredients for the emergence of a biosphere inhabited by complex organisms. Over the last decades, the potential for bioengineering multicellular systems has been instrumental in interrogating nature and exploring novel paths to regeneration and disease, as well as cognition and behaviour. Here, we provide a list of open problems that encapsulate many of the ongoing and future challenges in the field, and we suggest conceptual approaches that may facilitate progress.

The study of ecosystems, both natural and artificial, has historically been mediated by population dynamics theories. In this framework, quantifying population numbers and related variables (associated with metabolism or biological-environmental interactions) plays a central role in measuring and predicting system-level properties. As we move towards advanced technological engineering of cells and organisms, the possibility of bioengineering ecosystems (from the gut microbiome to wildlands) opens several questions that will require quantitative models to find answers. Here, we present a comprehensive survey of quantitative modelling approaches for managing three kinds of synthetic ecosystems, sharing the presence of engineered strains. These include test tube examples of ecosystems hosting a relatively low number of interacting species, mesoscale closed ecosystems (or ecospheres), and macro-scale, engineered ecosystems. The potential outcomes of synthetic ecosystem designs and their limits will be relevant to different disciplines, including biomedical engineering, astrobiology, space exploration and fighting climate change impacts on endangered ecosystems. We propose a space of possible ecosystems that captures this broad range of scenarios and a tentative road map for open problems and further exploration.

Complex dynamical fluctuations, from intracellular noise, brain dynamics or computer traffic display bursting dynamics consistent with a critical state between order and disorder. Living close to the critical point has adaptive advantages and it has been conjectured that evolution could select these critical states. Is this the case of living cells? A system can poise itself close to the critical point by means of the so-called self-organized criticality (SOC). In this paper we present an engineered gene network displaying SOC behaviour. This is achieved by exploiting the saturation of the proteolytic degradation machinery in E. coli cells by means of a negative feedback loop that reduces congestion. Our critical motif is built from a two-gene circuit, where SOC can be successfully implemented. The potential implications for both cellular dynamics and behaviour are discussed.

Complex dynamical fluctuations, from molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display noisy behaviour consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and it has been conjectured that evolution could select (and even tend to) these critical states. One way of approaching such state is by means of so called self-organized criticality (SOC) where the system poises itself close to the critical point. Is this the case of living cells? It is difficult to test this idea given the enormous dimensionality associated with gene and metabolic webs. In this paper we present an alternative approach: to engineer synthetic gene networks displaying SOC behaviour. This is achieved by exploiting the presence of a saturation (congestion) phenomenon of the ClpXP protein degradation machinery in E. coli cells. Using a feedback design that detects and then reduces ClpXP congestion, a critical motif is built from a two-gene network system, where SOC can be successfully implemented. Both deterministic and stochastic models are used, consistently supporting the presence of criticality in intracellular traffic. The potential implications for both cellular dynamics and designed intracellular noise are discussed.

Multicellular entities are characterized by exquisite spatial patterns, intimately related to the functions they perform. Oftentimes these patterns emerge as periodic structures with a well-defined characteristic scale. A candidate mechanism to explain their origins was early introduced by Alan Turing through the interaction and diffusion of two so called morphogens . Unfortunately, most available evidence for Turing patterns in biology is usually obscured by the tangled nature of regulatory phenomena, making difficult to validate Turing’s proposal in developmental processes. Here we follow a different approach, by designing synthetic genetic circuits in engineered E. coli strains that implement the essential activator-inhibitor motif (AIM) using a two-cell consortium. The two diffusible compartments are one cell type (activator, small-diffusion component) and a small signal molecule (a homoserine lactone, acting as the fast-diffusing inhibitor). Using both experimental results, we show that the AIM is capable of generating diffusion-induced instabilities leading to regular spatial patterns. The artificial construction taken here can help validate developmental theories and identify universal properties underpinning biological pattern formation. The implications of the work for the area of synthetic developmental biology are outlined.

What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems capable of persisting in closed environments? Can synthetic communities be created to thrive on planets different from ours? These and other questions pervade major future developments within synthetic biology. The goal of engineering ecosystems is plagued with all kinds of technological, scientific and ethic problems. In this paper, we consider the requirements for terraformation, i.e., for changing a given environment to make it hospitable to some given class of life forms. Although the standard use of this term involved strategies for planetary terraformation, it has been recently suggested that this approach could be applied to a very different context: ecological communities within our own planet. As discussed here, this includes multiple scales, from the gut microbiome to the entire biosphere.

Photobioelectrochemical systems are an emerging possibility for renewable energy. By exploiting photosynthesis, they transform the energy of light into electricity. This study evaluates a simple, scalable bioelectrochemical system built from recycled plastic bottles, equipped with an anode made from recycled aluminum, and operated with the green alga Chlorella sorokiniana. We tested whether such a system, referred to as a bio-bottle-voltaic (BBV) device, could operate outdoors for a prolonged time period of 35 days. Electrochemical characterisation was conducted by measuring the drop in potential between the anode and the cathode, and this value was used to calculate the rate of charge accumulation. The BBV systems were initially able to deliver ~500 mC·bottle⁻¹·day⁻¹, which increased throughout the experimental run to a maximum of ~2000 mC·bottle⁻¹·day⁻¹. The electrical output was consistently and significantly higher than that of the abiotic BBV system operated without algal cells (~100 mC·bottle⁻¹·day⁻¹). The analysis of the rate of algal biomass accumulation supported the hypothesis that harvesting a proportion of electrons from the algal cells does not significantly perturb the rate of algal growth. Our finding demonstrates that bioelectrochemical systems can be built using recycled components. Prototypes of these systems have been displayed in public events; they could serve as educational toolkits in schools and could also offer a solution for powering low-energy devices off-grid.

Background: Cells are subjected to dramatic changes of gene expression upon environmental changes. Stress causes a general down-regulation of gene expression together with the induction of a set of stress-responsive genes. The p38-related stress-activated protein kinase Hog1 is an important regulator of transcription upon osmostress in yeast. Results: Genome-wide localization studies of RNA polymerase II (RNA Pol II) and Hog1 showed that stress induced major changes in RNA Pol II localization, with a shift toward stress-responsive genes relative to housekeeping genes. RNA Pol II relocalization required Hog1, which was also localized to stress-responsive loci. In addition to RNA Pol II-bound genes, Hog1 also localized to RNA polymerase III-bound genes, pointing to a wider role for Hog1 in transcriptional control than initially expected. Interestingly, an increasing association of Hog1 with stress-responsive genes was strongly correlated with chromatin remodeling and increased gene expression. Remarkably, MNase-Seq analysis showed that although chromatin structure was not significantly altered at a genome-wide level in response to stress, there was pronounced chromatin remodeling for those genes that displayed Hog1 association. Conclusion: Hog1 serves to bypass the general down-regulation of gene expression that occurs in response to osmostress, and does so both by targeting RNA Pol II machinery and by inducing chromatin remodeling at stress-responsive loci.