Biomedical subjects

Ricard V Solé

Publications and source records attributed to Ricard V Solé.

8 recordsLinked to original sources

PubMed2003

Evolving protein interaction networks through gene duplication.

The topology of the proteome map revealed by recent large-scale hybridization methods has shown that the distribution of protein-protein interactions is highly heterogeneous, with many proteins having few edges while a few of them are heavily connected. This particular topology is shared by other cellular networks, such as metabolic pathways, and it has been suggested to be responsible for the high mutational homeostasis displayed by the genome of some organisms. In this paper we explore a recent model of proteome evolution that has been shown to reproduce many of the features displayed by its real counterparts. The model is based on gene duplication plus re-wiring of the newly created genes. The statistical features displayed by the proteome of well-known organisms are reproduced and suggest that the overall topology of the protein maps naturally emerges from the two leading mechanisms considered by the model.

Animals↗

PubMed2003

Coinfection and superinfection in RNA virus populations: a selection-mutation model.

In this paper, we present a general selection-mutation model of evolution on a one-dimensional continuous fitness space. The formulation of our model includes both the classical diffusion approach to mutation process as well as an alternative approach based on an integral operator with a mutation kernel. We show that both approaches produce fundamentally equivalent results. To illustrate the suitability of our model, we focus its analytical study into its application to recent experimental studies of in vitro viral evolution. More specifically, these experiments were designed to test previous theoretical predictions regarding the effects of multiple infection dynamics (i.e., coinfection and superinfection) on the virulence of evolving viral populations. The results of these experiments, however, did not match with previous theory. By contrast, the model we present here helps to understand the underlying viral dynamics on these experiments and makes new testable predictions about the role of parameters such the time between successive infections and the growth rates of resident and invading populations.

Evolution, Molecular↗

PubMed2002

Metapopulation dynamics and spatial heterogeneity in cancer.

With the advent of drugs targeting specific molecular defects in cancerous cells [Gorre, M. E., et al. (2001) Science 293, 876-880], it is important to understand the degree of genetic heterogeneity present in tumor cell populations and the rules that govern microdiversity in human cancer. Here, we first show that populations with different genotypes in genes influencing cell growth and programmed cell death coexist in advanced malignant tumors of the colon, exhibiting microsatellite instability. Detailed, physical mapping of the diverse populations shows them to be arranged in small, intermingling areas, resulting in a variegated pattern of diversity. Using computational modeling of the experimental data, we find that the coexistence between similar competitors is enhanced, instead of deterred, by spatial dynamics [Hanski, I. (1999) Metapopulation Dynamics (Oxford Univ. Press, New York)]. The model suggests a simple and plausible scenario for the generation of spatial heterogeneity during tumor progression. The emergence and persistence of the patterns of diversity encountered in the tumors can be generated without a need to invoke differences in mutation rates, neutrality of interactions, or separated time scales. We posit that the rules that apply to spatial ecology and explain the maintenance of diversity are also at work in tumors and may underlie tumor microheterogeneity.

Adenocarcinoma↗

PubMed2002

Spatial patterns in ant colonies.

The origins of large-scale spatial patterns in biology have been an important source of theoretical speculation since the pioneering work by Turing (1952) on the chemical basis of morphogenesis. Knowing how these patterns emerge and their functional role is important to our understanding of the evolution of biocomplexity and the role played by self organization. However, so far, conclusive evidence for local activation-long-range inhibition mechanisms in real biological systems has been elusive. Here a well-defined experimental and theoretical analysis of the pattern formation dynamics exhibited by clustering behavior in ant colonies is presented. These experiments and a simple mathematical model show that these colonies do indeed use this type of mechanism. All microscopic variables have been measured and provide the first evidence, to our knowledge, for this type of self-organized behavior in complex biological systems, supporting early conjectures about its role in the organization of insect societies.

Animals↗

PubMed2002

Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics.

Biotic recoveries following mass extinctions are characterized by a process in which whole ecologies are reconstructed from low-diversity systems, often characterized by opportunistic groups. The recovery process provides an unexpected window to ecosystem dynamics. In many aspects, recovery is very similar to ecological succession, but important differences are also apparently linked to the innovative patterns of niche construction observed in the fossil record. In this paper, we analyse the similarities and differences between ecological succession and evolutionary recovery to provide a preliminary ecological theory of recoveries. A simple evolutionary model with three trophic levels is presented, and its properties (closely resembling those observed in the fossil record) are compared with characteristic patterns of ecological response to disturbances in continuous models of three-level ecosystems.

Animals↗

PubMed2002

Self-organized instability in complex ecosystems.

Why are some ecosystems so rich, yet contain so many rare species? High species diversity, together with rarity, is a general trend in neotropical forests and coral reefs. However, the origin of such diversity and the consequences of food web complexity in both species abundances and temporal fluctuations are not well understood. Several regularities are observed in complex, multispecies ecosystems that suggest that these ecologies might be organized close to points of instability. We explore, in greater depth, a recent stochastic model of population dynamics that is shown to reproduce: (i) the scaling law linking species number and connectivity; (ii) the observed distributions of species abundance reported from field studies (showing long tails and thus a predominance of rare species); (iii) the complex fluctuations displayed by natural communities (including chaotic dynamics); and (iv) the species-area relations displayed by rainforest plots. It is conjectured that the conflict between the natural tendency towards higher diversity due to immigration, and the ecosystem level constraints derived from an increasing number of links, leaves the system poised at a critical boundary separating stable from unstable communities, where large fluctuations are expected to occur. We suggest that the patterns displayed by species-rich communities, including rarity, would result from such a spontaneous tendency towards instability.

Animals↗

PubMed2002

Controlling chaos in unidimensional maps using macroevolutionary algorithms.

We introduce a simple search algorithm that explores the parameter of periodically perturbed discrete maps in order to find desired orbits through chaos control. The method has been applied to one-dimensional maps but is easily extendable to higher-dimensional systems. Here, we consider two types of chaos control involving proportional pulses in the system variables [Phys. Rev. Lett. 72, 1455 (1994)] and constant feedback [Phys. Rev. E 51, 6239 (1995)], the first case being presented in detail. It is shown that our method allows a rapid exploration of parameter space and the finding of high-fitness (i.e., controlled) solutions close to the target orbits, even when high periodicities are required.

Journal Article↗

PubMed2002

Complex discrete dynamics from simple continuous population models.

Nonoverlapping generations have been classically modelled as difference equations in order to account for the discrete nature of reproductive events. However, other events such as resource consumption or mortality are continuous and take place in the within-generation time. We have realistically assumed a hybrid ODE bidimensional model of resources and consumers with discrete events for reproduction. Numerical and analytical approaches showed that the resulting dynamics resembles a Ricker map, including the doubling route to chaos. Stochastic simulations with a handling-time parameter for indirect competition of juveniles may affect the qualitative behaviour of the model.

Animals↗