RNA-based regulation: dynamics and response to perturbations of competing RNAs

The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that RNAs can regulate each other in extended 'cross-talk' networks. Such an ability might play a major role in post-transcriptional regulation (PTR) in shaping a cell's protein repertoire. Recent work focusing on the emergent properties of the cross-talk networks has emphasized the high flexibility and selectivity that may be achieved at stationarity. On the other hand, dynamical aspects, possibly crucial on the relevant time scales, are far less clear. We have carried out a dynamical study of the ceRNA hypothesis on a model of PTR. Sensitivity analysis shows that ceRNA cross-talk is dynamically extended, i.e. it may take place on time scales shorter than those required to achieve stationairity even in cases where no cross-talk occurs in the steady state, and is possibly amplified. Besides, in case of large, transfection-like perturbations the system may develop strongly non-linear, threshold response. Finally, we show that the ceRNA effect provides a very efficient way for a cell to achieve fast positive shifts in the level of a ceRNA when necessary. These results indicate that competition for miRNAs may indeed provide an elementary mechanism to achieve system-level regulatory effects on the transcriptome over physiologically relevant time scales.Comment: Main text: 10 pages, 13 figures. Supporting Text: 3 pages, 6 figure

MicroRNAs as a selective channel of communication between competing RNAs: a steady-state theory

It has recently been suggested that the competition for a finite pool of microRNAs (miRNA) gives rise to effective interactions among their common targets (competing endogenous RNAs or ceRNAs) that could prove to be crucial for post-transcriptional regulation (PTR). We have studied a minimal model of PTR where the emergence and the nature of such interactions can be characterized in detail at steady state. Sensitivity analysis shows that binding free energies and repression mechanisms are the key ingredients for the cross-talk between ceRNAs to arise. Interactions emerge in specific ranges of repression values, can be symmetrical (one ceRNA influences another and vice-versa) or asymmetrical (one ceRNA influences another but not the reverse) and may be highly selective, while possibly limited by noise. In addition, we show that non-trivial correlations among ceRNAs can emerge in experimental readouts due to transcriptional fluctuations even in absence of miRNA-mediated cross-talk.Comment: 15 pages, 10 figures, to appear in Biophys

Probing the limits to microRNA-mediated control of gene expression

According to the `ceRNA hypothesis', microRNAs (miRNAs) may act as mediators of an effective positive interaction between long coding or non-coding RNA molecules, carrying significant potential implications for a variety of biological processes. Here, inspired by recent work providing a quantitative description of small regulatory elements as information-conveying channels, we characterize the effectiveness of miRNA-mediated regulation in terms of the optimal information flow achievable between modulator (transcription factors) and target nodes (long RNAs). Our findings show that, while a sufficiently large degree of target derepression is needed to activate miRNA-mediated transmission, (a) in case of differential mechanisms of complex processing and/or transcriptional capabilities, regulation by a post-transcriptional miRNA-channel can outperform that achieved through direct transcriptional control; moreover, (b) in the presence of large populations of weakly interacting miRNA molecules the extra noise coming from titration disappears, allowing the miRNA-channel to process information as effectively as the direct channel. These observations establish the limits of miRNA-mediated post-transcriptional cross-talk and suggest that, besides providing a degree of noise buffering, this type of control may be effectively employed in cells both as a failsafe mechanism and as a preferential fine tuner of gene expression, pointing to the specific situations in which each of these functionalities is maximized.Comment: 16 page

Inverse Statistical Physics of Protein Sequences: A Key Issues Review

In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques, sequence data accumulate at unprecedented pace. This provides large sets of so-called homologous, i.e.~evolutionarily related protein sequences, to which methods of inverse statistical physics can be applied. Using sequence data as the basis for the inference of Boltzmann distributions from samples of microscopic configurations or observables, it is possible to extract information about evolutionary constraints and thus protein function and structure. Here we give an overview over some biologically important questions, and how statistical-mechanics inspired modeling approaches can help to answer them. Finally, we discuss some open questions, which we expect to be addressed over the next years.Comment: 18 pages, 7 figure

EIKONAL-BASED MODELS OF RANDOM TESSELLATIONS

In this article, we propose a novel, efficient method for computing a random tessellation from its vectorial representation at each voxel of a discretized domain. This method is based upon the resolution of the Eikonal equation and has a complexity in O(N log N), N being the number of voxels used to discretize the domain. By contrast, evaluating the implicit functions of the vectorial representation at each voxel location has a complexity of O(N²) in the general case. The method also enables us to consider the generation of tessellations with rough interfaces between cells by simulating the growth of the germs on a domain where the velocity varies locally. This aspect constitutes the main contribution of the article. A final contribution is the development of an algorithm for estimating the multi-scale tortuosity of the boundaries of the tessellation cells. The algorithm computes the tortuosity of the boundary at several scales by iteratively deforming the boundary until it becomes a straight line. Using this algorithm, we demonstrate that depending on the local velocity model, it is possible to control the roughness amplitude of the cells boundaries

Effect of micro- and macroencapsulation on oxygen consumption by pancreatic islets.

Immunoisolation of pancreatic islets is extensively investigated for glycemic control in diabetic experimental animals. We previously reported that subcutaneous xenotransplantation of bovine islets protected by a selective polysulfone membrane successfully controlled glycemia in diabetic rats for up to 20 days. We then wondered whether immunoisolated islets have adequate oxygen supply in this device, where only diffusive transport allows cell function and survival. Here we set up an experimental technique to measure oxygen consumption rate (OCR) using a Clark's electrode inserted in a glass thermostated chamber connected to a data recorder and acquisition system. Bovine islets were isolated from 6-month-old calves, encapsulated in sodium alginate microcapsules or inserted in polysulfone hollow fibers. After 1 and 2 days in culture a series of measurements was performed using free islets (at normal or high-glucose concentration), islets encapsulated in microcapsules, or in hollow fibers. In free islets OCR averaged from 2.0 ± 0.8 pmol/IEQ/min at low-glucose concentration and from 2.5 ± 1.0 pmol/IEQ/min at high-glucose concentration ( p < 0.01). OCR in islets encapsulated in microcapsules and in hollow fibers was comparable, and not significantly different from that measured in free islets. Two days after isolation OCR averaged 2.3 ± 0.6 in free islets, 2.3 ± 0.9 in alginate microcapsules, and 2.2 ± 0.7 pmol/IEQ/min in hollow fibers. These results show that OCR by bovine islets is comparable to that previously reported for other species. OCR increases in islets stimulated with high glucose and may be considered as a functional index. Moreover, islet encapsulation in alginate microcapsule, as well as in hollow fiber membranes, did not significantly affect in vitro OCR, suggesting adequate islet oxygenation in these conditions

Inteligência artificial: um novo paradigma tecnológico?

A proposta do presente trabalho consiste em caracterizar o conceito de Inteligência Artificial como um Paradigma Tecnológico. Com base numa análise histórico-analítica, serão apresentados e esclarecidos três conceitos-chave: revoluções tecnológicas, paradigmas tecnológicos, desemprego tecnológico. A relação destes três conceitos, auxiliados por outros paralelos (como: destruição criativa, ondas de desenvolvimento, forging ahead e falling behind) trarão à luz uma discussão corriqueira no campo acadêmico

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

The quantitative characterization of mutational landscapes is a task of outstanding importance in evolutionary and medical biology: It is, for example, of central importance for our understanding of the phenotypic effect of mutations related to disease and antibiotic drug resistance. Here we develop a novel inference scheme for mutational landscapes, which is based on the statistical analysis of large alignments of homologs of the protein of interest. Our method is able to capture epistatic couplings between residues, and therefore to assess the dependence of mutational effects on the sequence context where they appear. Compared with recent large-scale mutagenesis data of the beta-lactamase TEM-1, a protein providing resistance against beta-lactam antibiotics, our method leads to an increase of about 40% in explicative power as compared with approaches neglecting epistasis. We find that the informative sequence context extends to residues at native distances of about 20 Å from the mutated site, reaching thus far beyond residues in direct physical contact