1,721,006 research outputs found
Extrinsic stochastic factors (solute partition) in gene expression inside lipid vesicles and lipid-stabilized water-in-oil droplets: a review
Full text linkThe encapsulation of transcription-translation (TX-TL) machinery inside lipid vesicles and water-in-oil droplets leads to the construction of cytomimetic systems (often called 'synthetic cells') for synthetic biology and origins-of-life research. A number of recent reports have shown that protein synthesis inside these microcompartments is highly diverse in terms of rate and amount of synthesized protein. Here, we discuss the role of extrinsic stochastic effects (i.e. solute partition phenomena) as relevant factors contributing to this pattern. We evidence and discuss cases where between-compartment diversity seems to exceed the expected theoretical values. The need of accurate determination of solute content inside individual vesicles or droplets is emphasized, aiming at validating or rejecting the predictions calculated from the standard fluctuations theory. At the same time, we promote the integration of experiments and stochastic modeling to reveal the details of solute encapsulation and intra-compartment reactions
Measurement and Numerical Modeling of Cell-Free Protein Synthesis: Combinatorial Block-Variants of the PURE System
No full textProtein synthesis is at the core of bottom-up construction of artificial cellular mimics. Intriguingly, several reports have revealed that when a transcription-translation (TX-TL) kit is encapsulated inside lipid vesicles (or water-in-oil droplets), high between-vesicles diversity is observed in terms of protein synthesis rate and yield. Stochastic solute partition can be a major determinant of these observations. In order to verify that the variation of TX-TL components concentration brings about a variation of produced protein rate and yield, here we directly measure the performances of the PURE system' TX-TL kit variants. We report and share the kinetic traces of the enhanced Green Fluorescent Protein (eGFP) synthesis in bulk aqueous phase, for 27 combinatorial block-variants. The eGFP production is a sensitive function of TX-TL components concentration in the explored concentration range. Providing direct evidence that protein synthesis yield and rate actually mirror the TX-TL composition, this study supports the above-mentioned hypothesis on stochastic solute partition, without excluding, however, the contribution of other factors (e.g., inactivation of components)
The impact of alkanes on the structure of Triton X100 micelles
No full textHere we investigate the structural evolution of TX100 micelles upon loading with several linear and cyclic alkanes by DLS, PGSE-NMR, 2D NOESY NMR, viscosity measurements, and molecular dynamic simulations. Our results confirm that TX100 alone forms spherical, onion-like micelles made of several partially interpenetrating surfactant layers where the polyethylene glycol chains are in contact with the tetramethyl-butyl-phenyl moieties. Loading with non-penetrating oils larger than decane induces a decrease in micellar size and hydration because the alkane molecules compete with both water and tetramethyl-butyl-phenyl groups for the polyethylene glycol chains. This results in the partial peeling of the "onion" and in the dehydration of polyethylene glycol chains so that the micelles increase in number and decrease in size upon alkane loading. In contrast, small and penetrable oils (mainly cyclo-alkanes) first swell the onion-like micelles (inducing an increase in size) and only above a critical oil/surfactant ratio does the oil induce the weakening of the multilayer structure and the dehydration of polyethylene glycol chains found in long linear alkanes
Exploiting the photoactivity of bacterial reaction center to investigate liposome dynamics
Full text linkCharge recombination kinetics of bacterial photosynthetic protein 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
Stochastic simulations of homogeneous chemically reacting systems
No full textAn object oriented computational environment for the stochastic simulation of homogeneous chemically reacting systems is presented and its theoretical background discussed. Some simple examples of applications will be presented to validate the code and to clarify the main features of this approach. A WIN32 executable is available for academic purposes upon request to the authors.An object oriented computational environment for the stochastic simulation of homogeneous chemically reacting systems is presented and its theoretical background discussed. Some simple examples of applications will be presented to validate the code and to clarify the main features of this approach. A WIN32 executable is available for academic purposes upon request to the authors
Emergent properties arising from the assembly of amphiphiles. Artificial vesicle membranes as reaction promoters and regulators
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