Directed evolution of a gatekeeper domain in nonribosomal peptide synthesis

Modular natural products are biosynthesized by series of enzymes that activate, assemble, and process a nascent chain of building blocks. Adenylation domains are gatekeepers in nonribosomal peptide biosynthesis, providing the entry point for assembly of typical peptide-based natural products. We report the directed evolution of an adenylation domain based on a strategy of using a weak, promiscuous activity as a springboard for reprogramming the biosynthetic assembly line. Randomization of residues invoked in a "specificity-conferring code" and selection for a non-native substrate lead to mutant G2.1, favoring smaller amino acids with a specificity change of 10(5): a 170-fold improvement for L-alanine corresponds to a 10(3)-fold decrease for its original substrate (L-phenylalanine). These results establish directed evolution as a method to change gatekeeper domain specificity and suggest that adaptation of modules in combinatorial biosynthesis is achievable with few mutations during evolution.     

Tuning the spin-transition properties of pyrene-decorated 2,6-bispyrazolylpyridine based Fe(II) complexes

Two 2,6-bispyrazolylpyridine ligands (bpp) were functionalized with pyrene moieties through linkers of different lengths. In the ligand 2,6-di(1H-pyrazol-1-yl)-4-(pyren-1-yl)pyridine (L1) the pyrene group is directly connected to the bpp moiety via a C-C single bond, while in the ligand 4-(2,6-di(1H-pyrazol-1-yl)pyridin-4-yl)benzyl-4-(pyren-1-yl)butanoate (L2) it is separated by a benzyl ester group involving a flexible butanoic chain. Subsequent complexation of Fe(II) salts revealed dramatic the influence of the nature of the pyrene substitution on the spin-transition behaviour of the resulting complexes. Thus, compound [Fe(L1)(2)](ClO(4))(2) (1) is blocked in its high spin state due to constraints caused by a strong intermolecular π-π stacking in its structure. On the other hand, the flexible chain of ligand L2 in compounds [Fe(L2)(2)](ClO(4))(2) (2) and [Fe(L2)(2)](BF(4))(2)·CH(3)CN·H(2)O (3) prevents structural constraints allowing for reversible spin transitions. Temperature-dependent studies of the photophysical properties of compound 3 do not reveal any obvious correlation between the fluorescence of the pyrene group and the spin state of the spin transition core.     

Modelling of synchrotron SAXS patterns of silicalite-1 zeolite during crystallization

Synchrotron small angle X-ray scattering (SAXS) was used to characterize silicalite-1 zeolite crystallization from TEOS/TPAOH/water clear sol. SAXS patterns were recorded over a broad range of length scales, enabling the simultaneous monitoring of nanoparticles and crystals occurring at various stages of the synthesis. A simple two-population model accurately described the patterns. Nanoparticles were modeled by polydisperse core-shell spheres and crystals by monodisperse oblate ellipsoids. These models were consistent with TEM images. The SAXS results, in conjunction with in situ light scattering, showed that nucleation of crystals occurred in a short period of time. Crystals were uniform in size and shape and became increasingly anisotropic during growth. In the presence of nanoparticles, crystal growth was fast. During crystal growth, the number of nanoparticles decreased gradually but their size was constant. These observations suggested that the nanoparticles were growth units in an aggregative crystal growth mechanism. Crystals grown in the presence of nanoparticles developed a faceted habit and intergrowths. In the final stages of growth, nanoparticles were depleted. Concurrently, the crystal growth rate decreased significantly.     

Large Eddy Simulation of a Motored Single-Cylinder Piston Engine: Numerical Strategies and Validation

This paper describes a compressible Large Eddy Simulation (LES) used to investigate cyclic variations for nonreacting flow in an optical single cylinder engine setup. The simulated operating point is part of a large experimental database designed to validate LES for cycle-to-cycle prediction, and constitutes a first step towards the realization of fired operating points. The computational domain covers almost the whole experimental setup (intake and exhaust plenums, intake and exhaust ducts, cylinder) to account for acoustic phenomena. The assessment of the computation is performed in two regions of the domain: the intake and exhaust duct predictions are compared to the results of a Helmholtz solver and the experiment (pressure transducers and Particle Image Velocimetry (PIV)) while the in-cylinder dynamics are compared to PIV measurements. The ability of the developed methodology to capture the correct level of cycle-to-cycle variations is demonstrated considering in-cylinder pressure and velocity fields predictions. Cycle-to-cycle variations in velocity are highlighted and localized using a proper orthogonal decomposition analysis.     

A homogenization approach to flashing ratchets

The paper continues the program of the authors to develop a mathematical framework to understand and characterize the notion of “asymmetric” potentials, which has been introduced to explain how molecular motors work, considering flashing ratchets, i.e., molecules diffusing in a potential with periodic switches. The mathematical model is a Fokker–Planck equation with a space–time periodic potential and diffusion of order of magnitude compatible with the period of the potential. After performing a homogenization analysis of the problem the “asymmetric” potentials are characterized by the property that the solution, which models the molecule density, concentrates on one end of the domain. Finally explicit examples are presented exhibiting that the concentration phenomena (motor effect) takes place are presented. The proof uses techniques from the theory of viscosity solutions for the Hamilton–Jacobi equation which, in the homogenization limit, defines the effective hamiltonian.     

On the Global Regularity for a Wave-Klein—Gordon Coupled System

In this paper we consider a coupled Wave-Klein—Gordon system in 3D, and prove global regularity and modified scattering for small and smooth initial data with suitable decay at infinity. This...     

Structures de Poisson sur une intersection complète à singularités isoléesPoisson structures over a complete intersection with isolated singularities

We study Poisson structures over singular varieties. For this purpose, we consider the Koszul complex associated to the equations of a complete intersection. This complex forms a differential graded algebra which is equivalent to the algebra of the variety. We show that a Poisson structure is equivalent to a sequence of multiderivations over the Koszul complex. If the variety has isolated singularities, then we can construct a sequence of multiderivations of reduced form. To cite this article: B. Fresse, C. R. Acad. Sci. Paris, Ser. I 335 (2002) 5–10.     

Influence of columnar defects on the thermodynamic properties of BSCCO

Amorphous columnar defects strongly affect the reversible magnetization of Bi₂Sr₂CaCu₂O_8+δ single crystals both in the vortex solid, where the change reflects the change in vortex energy due to pinning, and in the vortex liquid, where the randomly positioned columns disrupt the interaction between superconducting fluctuations.     

Exponential decay for the fragmentation or cell-division equation

We consider a classical integro-differential equation that arises in various applications as a model for cell-division or fragmentation. In biology, it describes the evolution of the density of cells that grow and divide. We prove the existence of a stable steady distribution (first positive eigenvector) under general assumptions in the variable coefficients case. We also prove the exponential convergence, for large times, of solutions toward such a steady state.