Multicellularity & Pattern Formation
Multicellularity is a crucial biological innovation that has been invented more than a dozen times over the course of the evolution of our biosphere. From the first one (more than 2 billion years ago) to the last one (that of green algae), these transitions have created a myriad of complex creatures and greatly impacted ecosystems. The evolutionary process from single to multiple cells and development is plagued with uncertainties and challenges to cooperation: cheaters, cancer and the efficient construction of form. Using wet-lab and dry-lab approaches, I have been trying to offer some insights into potentially general features of multicellular systems: from the rules used to build structures and patterns in the developing embryo to the selective pressures that can force this Major Transition in Evolution.
Duran-Nebreda S. and Solé R. (2015) Emergence of multicellularity in a computational model of cell growth, death and aggregation under size-dependent selection. Royal Society Interface.
Ollé-Vila A., Duran-Nebreda S., Conde-Pueyo N., Montañez R. and Solé R. (2016) A morphospace for synthetic organs and organoids: the possible and the actual. Integrative Biology.
Tissue Architecture & Cellular Computation
Underlying biological function at the organ level lyes the physical organization of the cellular components. Who is connected to whom and what metabolic functions (i.e. the cell type identity) is everybody carrying out. Whitin this context, my research has tried to address the connection between structure and function by digitizing multiple tissues in confocal stacks, capturing their physical configurations and using a network science framework to characterize statistical properties of ensembles of annotated cells. By performing such analyses in diverging environments (from different plant species with different designs to all the adult organs of Arabidopsis) I hope to provide a solid quantitative framework to undestand organ design as well as provide new avenues to quantify disease and promote tissue bioengineering.
Duran-Nebreda S. and Bassel G.W. (2017). Bridging scales in plant biology using network science. Trends in plant science.
Jackson, M.D., Duran-Nebreda, S., et al. (2019). Global topological order emerges through local mechanical control of cell divisions in the Arabidopsis shoot apical meristem. Cell systems.
Duran-Nebreda S. and Bassel G.W. (2019). Plant behaviour in response to the environment: information processing in the solid state. Phil Trans of the Royal Society B.
Collective Behavior & Cooperation
A remarkable property of multicellular organisms (but also widely present in social systems) is the appearance of higher order features by means of communication and functional integration. This is readily observable in the astonishing behavior of birds and ants, where minimal interaction rules and cognitive capabilities of the individual are in place yet the group is able to display complex emergent and adaptive properties. More recently, due to the advent of synthetic biology, the possibility of engineering collective phenomena has become a reality. My work in this area includes modeling efforts of potential genetic devices as well as characterization of engineered systems.
Solé, R., Amor, D. R., Duran-Nebreda, S., Conde-Pueyo, N., Carbonell-Ballestero, M., and Montañez, R. (2016). Synthetic collective intelligence. Biosystems.
Amor, D. R., Montañez, R., Duran-Nebreda, S., and Solé, R. (2017). Spatial dynamics of synthetic microbial mutualists and their parasites. PLoS computational biology.
Synthetic Biology & Earth Terraformation
Our world is sadly experiencing a massive, world-wide transformation in terms of climate stability due to human intervention. It is likely to involve several possitive feedback and runaway dynamics, where the disapearance of key species may trigger massive extinctions and non-linear effects, ensuring a difficult recovery of collapsed ecosystems. On the other hand, we know that most of our biosphere in not wild, i.e. it has incorporated new species due to the effects of globalization, sometimes with positive results (like increased efficiency or growth rates). We think that this realization, that artificial ecosystems can be constructed and synthetic organisms can play an important part in them, will help aleviate the pressure on the endangered ecosystems as well regenerate the lost ones.
Solé, R. V., Montañez, R., and Duran-Nebreda, S. (2015). Synthetic circuit designs for earth terraformation. Biology direct.
Solé, R. V., Montañez, R., Duran-Nebreda, S. et al. (2018). Population dynamics of synthetic terraformation motifs. Royal Society open science.