Biology subjects

Vidiella Rocamora, B.

Publications and source records attributed to Vidiella Rocamora, B..

4 recordsLinked to original sources

bioRxiv2020

Engineering self-organized criticality in living cells

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.

bioengineering↗

bioRxiv2020

Synthetic Turing patterns in engineered microbial consortia

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.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗

bioRxiv2020

Habitat loss causes long transients in small trophic chains

Transients in ecology are extremely important since they determine how equilibria are approached. The debate on the dynamic stability of ecosystems has been largely focused on equilibrium states. However, since ecosystems are constantly changing due to climate conditions or to perturbations such as the climate crisis or anthropogenic actions (habitat destruction, deforestation, or defaunation), it is important to study how dynamics can proceed till equilibria. In this contribution we investigate dynamics and transient phenomena in small food chains using mathematical models. We are interested in the impact of habitat loss in ecosystems with vegetation undergoing facilitation. We provide a thorough dynamical study of a small food chain system given by three trophic levels: vegetation, herbivores, and predators. The dynamics of the vegetation alone suffers a saddle-node bifurcation, causing extremely long transients. The addition of a herbivore introduces a remarkable number of new phenomena. Specifically, we show that, apart from the saddle node involving the extinction of the full system, a transcritical and a supercritical Hopf-Andronov bifurcation allow for the coexistence of vegetation and herbivores via non-oscillatory and oscillatory dynamics, respectively. Furthermore, a global transition given by a heteroclinic bifurcation is also shown to cause a full extinction. The addition of a predator species to the previous systems introduces further complexity and dynamics, also allowing for the coupling of different transient phenomena such as ghost transients and transient oscillations after the heteroclinic bifurcation. Our study shows how the increase of ecological complexity via addition of new trophic levels and their associated nonlinear interactions may modify dynamics, bifurcations, and transient phenomena.

ecology↗

bioRxiv2019

Synthetic soil crusts against green-desert transitions: a spatial model

Semiarid ecosystems are threatened by global warming due to longer dehydration times and increasing soil degradation. Mounting evidences indicate that, given the current trends, drylands are likely to expand and possibly experience catastrophic shifts from vegetated to desert states. Here we explore a recent suggestion based on the concept of ecosystem terraformation, where a synthetic organism is used to counterbalance some of the nonlinear effects causing the presence of such tipping points. Using an explicit spatial model incorporating facilitation and considering a simplification of states found in semiarid ecosystems i.e., vegetation, fertile and desert soil, we investigate how engineered microorganisms can shape the fate of these ecosystems. Specifically, two different, but complementary, terraformation strategies are proposed: Cooperation-based: C-terraformation; and Dispersion-based: D-terraformation. The first strategy involves the use of soil synthetic microorganisms to introduce cooperative loops (facilitation) with the vegetation. The second one involves the introduction of engineered microorganisms improving their dispersal capacity, thus facilitating the transition from desert to fertile soil. We show that small modifications enhancing cooperative loops can effectively change the location of the critical transition found at increasing soil degradation rates, also identifying a stronger protection against soil degradation by using the D-terraformation strategy. The same results are found in a mean field model providing insights into the transitions and dynamics tied to these terraformation strategies. The potential consequences and extensions of these models are discussed.

bioengineering↗