Stochastic simulations of minimal cells: the Ribocell model

<p>Abstract</p> <p>Background</p> <p>Over the last two decades, lipid compartments (liposomes, lipid-coated droplets) have been extensively used as in vitro "minimal" cell models. In particular, simple and complex biomolecular reactions have been carried out inside these self-assembled micro- and nano-sized compartments, leading to the synthesis of RNA and functional proteins inside liposomes. Despite this experimental progress, a detailed physical understanding of the underlying dynamics is missing. In particular, the combination of solute compartmentalization, reactivity and stochastic effects has not yet been clarified. A combination of experimental and computational approaches can reveal interesting mechanisms governing the behavior of micro compartmentalized systems, in particular by highlighting the intrinsic stochastic diversity within a population of "synthetic cells".</p> <p>Methods</p> <p>In this context, we have developed a computational platform called ENVIRONMENT suitable for studying the stochastic time evolution of reacting lipid compartments. This software - which implements a Gillespie Algorithm - is an improvement over a previous program that simulated the stochastic time evolution of homogeneous, fixed-volume, chemically reacting systems, extending it to more general conditions in which a collection of similar such systems interact and change over the course of time. In particular, our approach is focused on elucidating the role of randomness in the time behavior of chemically reacting lipid compartments, such as micelles, vesicles or micro emulsions, in regimes where random fluctuations due to the stochastic nature of reacting events can lead an open system towards unexpected time evolutions.</p> <p>Results</p> <p>This paper analyses the so-called Ribocell (RNA-based cell) model. It consists in a hypothetical minimal cell based on a self-replicating minimum RNA genome coupled with a self-reproducing lipid vesicle compartment. This model assumes the existence of two ribozymes, one able to catalyze the conversion of molecular precursors into lipids and the second able to replicate RNA strands. The aim of this contribution is to explore the feasibility of this hypothetical minimal cell. By deterministic kinetic analysis, the best external conditions to observe synchronization between genome self-replication and vesicle membrane reproduction are determined, while its robustness to random fluctuations is investigated using stochastic simulations, and then discussed.</p

Exploiting the photoactivity of bacterial reaction center to investigate liposome dynamics

Charge recombination kinetics of bacterial photosynthetic protein&nbsp;Reaction Center displays an exquisite sensitivity to the actual occupancy of ubiquinone-10 in its QB-binding site. Here, we have exploited such phenomenon for assessing the growth and the aggregation/fusion of phosphocholine vesicles embedding RC in their membrane, when treated with sodium oleate

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics

The BITS2011 meeting, held in Pisa on June 20-22, 2011, brought together more than 120 Italian researchers working in the field of Bioinformatics, as well as students in Bioinformatics, Computational Biology, Biology, Computer Sciences, and Engineering, representing a landscape of Italian bioinformatics research

Selection for Replicases in Protocells

PMCID: PMC3649988This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Governing Uncertainty in a Secular Age: Rationalities of Violence, Theodicy and Torture

This article explores the problem of governing uncertainty in a secular age by focusing on the theological notion of ‘theodicy’ as the underlying rationale for the use of torture in the so-called ‘war on terror’. With God’s departure from the world, the problem of uncertainty acquires new salience as human beings can no longer explain tragic events as part of a transcendent order and must find immanent causes for the ‘evils’ that surround them. Taking a cue from Max Weber, I discuss how the problem of theodicy – how to reconcile the existence of God with the presence of evil in the world – does not disappear in the secular age but is mobilized through a Foucauldian biopolitical logic. Secular theodicy governs uncertainty through the production of economies of knowledge that rationalize processes of criminalization and securitization of entire groups and justify the use of violence. This process is particularly striking when analysing the use of torture in the so-called ‘war on terror’. Through a comparison with medieval practices and focusing on the cases of Guantanamo and Abu Ghraib, the article shows how secular torture is the product of a biopolitical theodicy aimed at governing uncertainty through the construction of the tortured as immanent evils who threaten our ‘good life’ and ‘deserve’ their treatment. Secular theodicy turns torture into an extreme form of governmentality of uncertainty in which the disciplining of conduct becomes the construction of subjectivities based on essentialist, stereotypical and racist – and for these very reasons, reassuring – economies of knowledge

Identification and Structural Characterization of a New Three-Finger Toxin Hemachatoxin from Hemachatus haemachatus Venom

10.1371/journal.pone.0048112PLoS ONE710

Theoretical approaches to ribocell modeling

The so-called Ribocell (ribozymes-based cell) is a theoretical cellular model that has been proposed some years ago as a possible minimal cell prototype. It consists in a self-replicating minimum RNA genome coupled with a self-reproducing lipid vesicle compartment. This model assumes the existence of two hypothetical ribozymes one able to catalyze the conversion of molecular precursors into lipids and the second one able to replicate RNA strands. Therefore, in an environment rich both of lipid precursors and activated nucleotides, the ribocell can self-reproduce if the genome self-replication and the compartment self-reproduction mechanisms are somehow synchronized. The aim of this contribution is to explore the feasibility of this model with in silico simulations using kinetic parameters available in literature