Information-theoretic analysis of the directional influence between cellular processes

Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback. We re-analyze the experimental data from Kiviet et al. (2014) where fluctuations in gene expression of metabolic enzymes and growth rate have been measured in single cells of E. coli. We confirm the formerly detected modes between growth and gene expression, while prescribing more stringent conditions on the structure of noise sources. We furthermore point out practical requirements in terms of length of time series and sampling time which must be satisfied in order to infer optimally transfer entropy from times series of fluctuations.Comment: 24 pages, 7 figure

Universal motifs and the diversity of autocatalytic systems

Autocatalysis is essential for the origin of life and chemical evolution. However, the lack of a unified framework so far prevents a systematic study of autocatalysis. Here, we derive, from basic principles, general stoichiometric conditions for catalysis and autocatalysis in chemical reaction networks. This allows for a classification of minimal autocatalytic motifs called cores. While all known autocatalytic systems indeed contain minimal motifs, the classification also reveals hitherto unidentified motifs.We further examine conditions for kinetic viability of such networks, which depends on the autocatalytic motifs they contain and is notably increased by internal catalytic cycles. Finally, we show how this framework extends the range of conceivable autocatalytic systems, by applying our stoichiometric and kinetic analysis to autocatalysis emerging from coupled compartments. The unified approach to autocatalysis presented in this work lays a foundation toward the building of a systems-level theory of chemical evolution

Dynamic mechanical properties of oral mucosa: comparison with polymeric soft denture liners.

The purpose of this work was to characterize the viscoelastic behaviour of oral mucosa and compare it with the dynamic mechanical properties of different soft liners. For this purpose, a sample of pig oral mucosa and six commercialized soft liner samples have been investigated. A comparison was also carried with the first suitable hard rubber for dental prosthetics: vulcanite. Creep recovery (CR) and dynamic mechanical analysis (DMA)have been used to determine the mechanical modulus of oral mucosa and soft liners respectively. The Poisson ratio is used to compare mucosa bulk modulus and soft liner shear modulus. The biomechanical concept of conventional complete dentures needs a good adjustment of dynamic mechanical impedance between the base and oral mucosa. The viscoelastic mechanical property of the oral mucosa as a referent biopolymer has been confirmed in vitro. The modulus value, adjusted for old patients in physiological conditions, is in the order of 3 MPa. This study underlines the plasticization effect of absorbed water on the mechanical properties of the underlying tissue. This study allows us to define some characteristics of the most adapted biomaterial according to the clinical exigency. The required biomaterial must display the following properties: compatibility and chemical resistance with biological environment perpetuated mechanical properties during physiological conditions and clinical use, good adjustment of dynamic mechanical impedance with supporting mucosa and easy sample processing

Selection dynamics in transient compartmentalization

Transient compartments have been recently shown to be able to maintain functional replicators in the context of prebiotic studies. Motivated by this experiment, we show that a broad class of selection dynamics is able to achieve this goal. We identify two key parameters, the relative amplification of non-active replicators (parasites) and the size of compartments. Since the basic ingredients of our model are the competition between a host and its parasite, and the diversity generated by small size compartments, our results are relevant to various phage-bacteria or virus-host ecology problems.Comment: 11 pages, 10 figure

Application of inductive heating to granular media: temperature distribution in a granular bed.

Inductive heating aims at creating eddy currents in a conductor material by means of a periodic electromagnetic field : these currents generate heat by the Joule effect. This method and its applications, especially in surface treatment for metallurgy. have been studied for a long time, since it provides ;a fast and efficient way of heating items [I. 21. Another quality of this process is that it is all-electric, which makes it reliable. Clean and easy to automate

Reemergence of Dengue Virus Type 4, French Antilles and French Guiana, 2004–2005

After 10 years of absence, dengue virus type 4 (DENV-4) has recently reemerged in Martinique, Guadeloupe, and French Guiana. Phylogenetic analyses of strains isolated from 2004 to 2005 showed that they belong to DENV-4 genotype II, but to a different cluster than strains isolated from 1993 to 1995

A New Marker on Chicken Hematopoietic Cells is Defined by a Monoclonal Antibody Raised Against a V ß Chain of the Human TCR

In this paper, we show that a mouse monoclonal antibody, 111-427, specific for the V ß 5.3 chain of the human T-cell receptor (TCR) for antigen, also reacts with chicken hematopoietic cells. Our data indicate that the majority of 111-427 positive cells among peripheral blood leucocytes (PBL) are thrombocytes. This antibody also recognizes two in vitro cell lines, III-C5, an IL-2-dependent T-cell-line and HD11, a macrophage cell line. In addition, erythrocytes and a minor subpopulation of thymus and spleen cells are also stained by the monoclonal antibody (mAb). No specific immunoprecipitation could be detected from 125I radiolabeled cell lysates. By Western blotting techniques, the 111- 427 mAb identifies a single band of apparent molecular weight 91 kD, unaffected by reduction, from III-C5 and HD11 cell lysates. This band is absent in negative cell control lysates. On thrombocytes, the apparent molecular weight of the band is shifted to 87 kD. These results indicate that the mAb does not recognize the chicken T-cell receptor for antigen, but a cell surface marker shared primarily between thrombocytes and erythrocytes. This new chicken cell marker is compared to other cell surface markers in avian or mammalian species that present some analogies in their tissue distribution