Essential plasticity and redundancy of metabolism unveiled by synthetic lethality analysis

We unravel how functional plasticity and redundancy are essential mechanisms underlying the ability to survive of metabolic networks. We perform an exhaustive computational screening of synthetic lethal reaction pairs in Escherichia coli in a minimal medium and we find that synthetic lethal pairs divide in two different groups depending on whether the synthetic lethal interaction works as a backup or as a parallel use mechanism, the first corresponding to essential plasticity and the second to essential redundancy. In E. coli, the analysis of pathways entanglement through essential redundancy supports the view that synthetic lethality affects preferentially a single function or pathway. In contrast, essential plasticity, the dominant class, tends to be inter-pathway but strongly localized and unveils Cell Envelope Biosynthesis as an essential backup for Membrane Lipid Metabolism. When comparing E. coli and Mycoplasma pneumoniae, we find that the metabolic networks of the two organisms exhibit a large difference in the relative importance of plasticity and redundancy which is consistent with the conjecture that plasticity is a sophisticated mechanism that requires a complex organization. Finally, coessential reaction pairs are explored in different environmental conditions to uncover the interplay between the two mechanisms. We find that synthetic lethal interactions and their classification in plasticity and redundancy are basically insensitive to medium composition, and are highly conserved even when the environment is enriched with nonessential compounds or overconstrained to decrease maximum biomass formation.Comment: 22 pages, 4 figure

Differential susceptibility to noise of mixed Turing and Hopf modes in a photosensitive chemical medium

We report on experiments with the photosensitive chlorine dioxide-iodine-malonic acid reaction (CDIMA) when forced with a random (spatiotemporally) distributed illumination. Acting on a mixed mode consisting of oscillating spots, close enough to the Hopf and Turing codimension-two bifurcation, we observe attenuation of oscillations while the spatial pattern is preserved. Numerical simulations confirm and extend these results. All together these observations point out to a larger vulnerability of the Hopf with respect to the Turing mode when facing noise of intermediate intensity and small correlation parameters.Peer ReviewedPostprint (published version

Proposta d'aplicació de la micromorfologia a l'estudi dels materials de construcció protohistòrics

Jornadas de Jóvenes en Investigación Arqueológica, JIA (3as : 5-7 de mayo 2010 : Universitat Autònoma de Barcelona). Sesión 6. La arquitectura en Arqueología : nuevas perspectivas para una vieja disciplina.Con este articulo presentamos una metodologia para estudiar unos materiales poco tratados en la investigacion del poblamiento protohistorico del nordeste peninsular. Nos referimos a los elementos elaborados con una argamasa de tierra (arcillas, limos y arenas), con componentes minerales y/o vegetales, y secados al sol. Este material, muy usado en la arquitectura protohistorica, es de una fragilidad extrema, y en consecuencia es realmente reducido el numero de restos recuperados. Queremos anadir al estudio tipologico la perspectiva del analisis micromorfologico. Esta tecnica consiste en analizar el sedimento a escala microscopica. Esto nos permite determinar la composicion y elaboracion de los distintos materiales de construccion; asi como distinguir los procesos edafosedimentarios postdeposicionales que afectan a la preservacion y conservacion de los mismos. Como punto de inicio nos centramos en los materiales recuperados en el asentamiento de Sant Jaume-Mas d'en Serra (Alcanar, Montsia), fechado en la transicion de los siglos VII al VI ane.With this article we present a methodology to study some materials little treated in the research, made until the present, of the protohistoric settlement of the peninsular northeast. We refer to the elements made from a mortar of soil (clay, slime, sand), mineral and vegetal components, without firing. This material, a lot used in the protohistoric architecture, is extremely fragile, and the number of retrieved rests is consequently really reduced. We want to add the perspective of the micromorphological analysis to the typological study. This technique consists on analyzing the sediment at scale microscopic. In this way we can gauge the composition and elaboration to the different building materials, as well as to distinguish the pedosedimentary post-depositional processes that they affect to the preservation and conservation of the same ones. As a starting point we focus on the materials retrieved in the site of Sant Jaume-Mas d'en Serra (Alcanar, Montsia), dated in the transition of the 7th centuries to 6th BC.Del poblament protohistoric del nord-est peninsular. Ens referim als elements fets a partir d'una argamassa de terra (argiles, llims, sorres), amb components minerals (gravetes i graves) i/o vegetals, i assecats al sol. Aquest material, molt usat en l'arquitectura protohistorica, es d'una gran fragilitat, i en consequencia es realment reduit el nombre de restes recuperades. Volem afegir a l'estudi tipologic la perspectiva de l'analisi micromorfologica. Aquesta tecnica consisteix en analitzar el sediment a escala microscopica. Aixo ens permet determinar la composicio i elaboracio dels diferents materials de construccio, aixi com distingir els processos edafosedimentaris postdeposicionals que afecten a la preservacio i conservacio dels mateixos. Com a punt de partida ens centrem en els materials recuperats a l'assentament de Sant Jaume-Mas d'en Serra (Alcanar, Montsia), datat a la transicio dels segles VII a VI ane

Synthetizing hydrodynamic turbulence from noise: formalism and applications to plankton dynamics

We present an analytical scheme, easily implemented numerically, to generate synthetic Gaussian 2D turbulent flows by using linear stochastic partial differential equations, where the noise term acts as a random force of well-prescribed statistics. This methodology leads to a divergence-free, isotropic, stationary and homogeneous velocity field, whose characteristic parameters are well reproduced, in particular the kinematic viscosity and energy spectrum. This practical approach to tailor a turbulent flow is justified by its versatility when analizing different physical processes occurring in advectely mixed systems. Here, we focuss on an application to study the dynamics of Planktonic populations in the ocean