Petri net modelling of biological regulatory networks

The complexity of biological regulatory networks often defies the intuition of the biologist and calls for the development of proper mathematical methods to model their structures and to delineate their dynamical properties. One qualitative approach consists in modelling regulatory networks in terms of logical equations (using either Boolean or multi-level discretisations). The Petri Net (PN) formalism offers a complementary framework to analyse the dynamical behaviour of large systems, either from a qualitative or from a quantitative point of view.

Our proposal consists in articulating the logical approach with the PN formalism. In a previous work, we have already defined a systematic re-writing of Boolean regulatory models into a standard PN formalism. In this paper, we propose a rigorous and systematic mapping of multi-level logical regulatory models into specific standard Petri nets, called Multi-level Regulatory Petri Nets (MRPNs). We further propose some reduction strategies. Consequently, the resulting models become amenable to the algebraic and computational analyses used by the PN community.

To illustrate our approach, we apply it to a multi-level logical model of the genetic switch controlling the lysis-lysogeny decision in the lambda bacteriophage.     

Improved transparency--nonlinearity trade-off with boroxine-based octupolar molecules

A series of octupolar molecules derived from the boroxine framework were designed and their optical nonlinearities were investigated by performing harmonic light scattering experiments in solution; the molecules were found to combine excellent transparency in the near UV-visible region (lambdamax < or = 280 nm) and significant first-order hyperpolarisabilities (up to beta(0) = 56 x 10(-30) esu).     

A cyclometallated iridium(III) dimethylphenylphosphine complex

[Ir(cod)Cl]₂ (cod = 1,5-cyclooctadiene) reacts with PMe₂Ph in CH₃CN to give the red cation [Ir(PMe₂Ph)₄]⁺. This complex in CH₃CN reacts with H₂ to give cis-[IrH₂(PMe₂Ph)₄]⁺, but on reflux for 6 h in the absence of H₂, it gives the first example of a cyclometallated PMe₂Ph complex fac-[IrH(PMe₂C₆H₄)(PMe₂Ph)₃]⁺, as shown by PMR spectroscopy and preliminary X-ray crystallographic data.     

The saddle point property for focusing selfsimilar solutions in a free boundary problem

We establish the saddle point property of the focusing selfsimilar solution of a free boundary problem for the heat equation with free boundary conditions given by and .

     

Activation of the Normal Human Skin Cells by a Portable Dielectric Barrier Discharge-Based Reaction-Discharge System of a Defined Gas Temperature

Skin injury leading to chronic wounds is of high interest due to the increasing number of patients suffering from this symptom. Proliferation, migration, and angiogenesis are key factors in the wound healing processes. For that reason, controlled promotion of these processes is required. In this work, we present the portable helium-dielectric barrier discharge (He-DBD)-based reaction-discharge system of controlled gas temperature for biological activities. To make this He-DBD-based reaction-discharge system safe for biological purposes, a multivariate optimization of the operating parameters was performed. To evaluate the effect of the He-DBD operating parameters on the rotational gas temperature T_rot(OH), a design of experiment followed by a Response Surface Methodology was applied. Based on the suggested statistical model, the optimal operating conditions under which the T_rot(OH) is less than 37 °C (310 K) were estimated. Then, the resulted model was validated in order to confirm its accuracy. After estimation the optical operating conditions of He-DBD operation, the spectroscopic characteristic of the He-DBD-based reaction-discharge system in relevance to the several optical temperatures in addition to electron number density has been carried out. Additionally, the qualitative and quantitative analyses of the reactive oxygen species and reactive nitrogen species were performed in order to investigate of reactions and processes running in the He-DBD-gaseous phase and in the He-DBD-treated liquid. Next, the developed portable He-DBD-based reaction-discharge system, working under the optimal operating conditions, was used to stimulate the wound healing process. It was found that a 30 s He-DBD treatment significantly increased the proliferation, migration, and angiogenesis of keratinocytes (HaCaT) and fibroblasts (MSU-1.1) cell lines, as well as human skin microvascular endothelial cells (HSkMEC.2). Hence, the application of the cold atmospheric pressure plasma generated in this He-DBD-based reaction-discharge system might be an alternative therapy for patient suffering from chronic wounds.

     

Conformational transition of DNA bound to Hfq probed by infrared spectroscopy

Hfq is a bacterial protein involved in RNA metabolism. Besides this, Hfq's role in DNA restructuring has also been suggested. Since this mechanism remains unclear, we examined the DNA conformation upon Hfq binding by combining vibrational spectroscopy and neutron scattering. Our analysis reveals that Hfq, which preferentially interacts with deoxyadenosine rich sequences, induces partial opening of dA-dT sequences accompanied by sugar repuckering of the dA strand and hence results in a heteronomous A/B duplex. Sugar repuckering is probably correlated with a global dehydration of the complex. By taking into account Hfq's preferential binding to A-tracts, which are commonly found in promoters, potential biological implications of Hfq binding to DNA are discussed.     

ChemInform Abstract: Equilibrium Structure and Torsional Barrier of BH3NH3.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.