Dataset Information

A cellular solution to an information-processing problem.

ABSTRACT: Signaling receptors on the cell surface are mobile and have evolved to efficiently sense and process mechanical or chemical information. We pose the problem of identifying the optimal strategy for placing a collection of distributed and mobile sensors to faithfully estimate a signal that varies in space and time. The optimal strategy has to balance two opposing objectives: the need to locally assemble sensors to reduce estimation noise and the need to spread them to reduce spatial error. This results in a phase transition in the space of strategies as a function of sensor density and efficiency. We show that these optimal strategies have been arrived at multiple times in diverse cell biology contexts, including the stationary lattice architecture of receptors on the bacterial cell surface and the active clustering of cell-surface signaling receptors in metazoan cells.

SUBMITTER: Iyengar G

PROVIDER: S-EPMC4151762 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A cellular solution to an information-processing problem.

Iyengar Garud G Rao Madan M

Proceedings of the National Academy of Sciences of the United States of America 20140811 34

Signaling receptors on the cell surface are mobile and have evolved to efficiently sense and process mechanical or chemical information. We pose the problem of identifying the optimal strategy for placing a collection of distributed and mobile sensors to faithfully estimate a signal that varies in space and time. The optimal strategy has to balance two opposing objectives: the need to locally assemble sensors to reduce estimation noise and the need to spread them to reduce spatial error. This re ...[more]

PMID: 25114246

Similar Datasets

Project description:One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.

Project description:The investigation of genetic clusters in natural populations is an ubiquitous problem in a range of fields relying on the analysis of genetic data, such as molecular ecology, conservation biology and microbiology. Typically, genetic clusters are defined as distinct panmictic populations, or parental groups in the context of hybridisation. Two types of methods have been developed for identifying such clusters: model-based methods, which are usually computer-intensive but yield results which can be interpreted in the light of an explicit population genetic model, and geometric approaches, which are less interpretable but remarkably faster.Here, we introduce snapclust, a fast maximum-likelihood solution to the genetic clustering problem, which allies the advantages of both model-based and geometric approaches. Our method relies on maximising the likelihood of a fixed number of panmictic populations, using a combination of geometric approach and fast likelihood optimisation, using the Expectation-Maximisation (EM) algorithm. It can be used for assigning genotypes to populations and optionally identify various types of hybrids between two parental populations. Several goodness-of-fit statistics can also be used to guide the choice of the retained number of clusters.Using extensive simulations, we show that snapclust performs comparably to current gold standards for genetic clustering as well as hybrid detection, with some advantages for identifying hybrids after several backcrosses, while being orders of magnitude faster than other model-based methods. We also illustrate how snapclust can be used for identifying the optimal number of clusters, and subsequently assign individuals to various hybrid classes simulated from an empirical microsatellite dataset. snapclust is implemented in the package adegenet for the free software R, and is therefore easily integrated into existing pipelines for genetic data analysis. It can be applied to any kind of co-dominant markers, and can easily be extended to more complex models including, for instance, varying ploidy levels. Given its flexibility and computer-efficiency, it provides a useful complement to the existing toolbox for the study of genetic diversity in natural populations.

Dataset Information

A cellular solution to an information-processing problem.

Publications

A cellular solution to an information-processing problem.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets