1,721,030 research outputs found
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)
STOCHASTIC SIMULATIONS OF MINIMAL CELL MODEL SYSTEMS
No full textThe construction of artificial cells based on the encapsulation of chemical reacting systems inside lipid vesicles is
rapidly progressing in recent years. Several groups are currently interested in synthesizing such simple cell models for
biotechnological purposes or for investigating origin of life scenarios. Within this context, the properties of lipid vesicles (e.g.,
their stability, permeability, growth dynamics, potential to host reactions or undergo division processes...) play a central role,
in combination with the dynamics of the encapsulated chemical or biochemical networks. Thus, from a theoretical standpoint,
it is very important to develop deterministic equations in order to explore first - and specify later - the conditions that allow the
robust implementation of these complex chemically reacting systems, as well as their controlled reproduction. Due to their
intrinsic compartmentalized nature, the population of reacting molecules can be very low in terms of number of molecules so
that their behaviour can be highly affected by stochastic effects both in the time course of their reactions and in their
occupancy distribution among the vesicle population. In this contribution we report our mathematical approaches to model
artificial cell systems in this complex scenario, with emphasis on the issue of primitive cell (protocell) systems
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
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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