Making E. coli an erythromycin production plant

The production of bioactive compounds in heterologous hosts has become a valuable tool for the investigation of biosynthetic pathways and their rational engineering. In this issue of Chemistry & Biology, Zhang et?al. (2010) report the manipulation of E. coli for the production of erythromycin A.     

Spectral structure of stratified turbulence: direct numerical simulations and predictions by large eddy simulation

Density stratification has a strong impact on turbulence in geophysical flows. Stratification changes the spatial turbulence spectrum and the energy transport and conversion within the spectrum. We analyze these effects based on a series of direct numerical simulations (DNS) of stratified turbulence. To facilitate simulations of real-world problems, which are usually beyond the reach of DNS, we propose a subgrid-scale turbulence model for large eddy simulations of stratified flows based on the Adaptive Local Deconvolution Method (ALDM). Flow spectra and integral quantities predicted by ALDM are in excellent agreement with direct numerical simulation. ALDM automatically adapts to strongly anisotropic turbulence and is thus a suitable tool for studying turbulent flow phenomena in atmosphere and ocean.     

Wall modeling for implicit large-eddy simulation and immersed-interface methods

We propose and analyze a wall model based on the turbulent boundary layer equations (TBLE) for implicit large-eddy simulation (LES) of high Reynolds number wall-bounded flows in conjunction with a conservative immersed-interface method for mapping complex boundaries onto Cartesian meshes. Both implicit subgrid-scale model and immersed-interface treatment of boundaries offer high computational efficiency for complex flow configurations. The wall model operates directly on the Cartesian computational mesh without the need for a dual boundary-conforming mesh. The combination of wall model and implicit LES is investigated in detail for turbulent channel flow at friction Reynolds numbers from Re _τ  = 395 up to Re _τ =100,000 on very coarse meshes. The TBLE wall model with implicit LES gives results of better quality than current explicit LES based on eddy viscosity subgrid-scale models with similar wall models. A straightforward formulation of the wall model performs well at moderately large Reynolds numbers. A logarithmic-layer mismatch, observed only at very large Reynolds numbers, is removed by introducing a new structure-based damping function. The performance of the overall approach is assessed for two generic configurations with flow separation: the backward-facing step at Re _h = 5,000 and the periodic hill at Re _H = 10,595 and Re _H = 37,000 on very coarse meshes. The results confirm the observations made for the channel flow with respect to the good prediction quality and indicate that the combination of implicit LES, immersed-interface method, and TBLE-based wall modeling is a viable approach for simulating complex aerodynamic flows at high Reynolds numbers. They also reflect the limitations of TBLE-based wall models.     

Über die relative Brauer-Gruppe der maximalen p-Erweiterung eines Körpers ohne p-te Einheitswurzeln

Ohne Zusammenfassung     

Molecular analysis of the kirromycin biosynthetic gene cluster revealed beta-alanine as precursor of the pyridone moiety

Kirromycin is a complex linear polyketide that acts as a protein biosynthesis inhibitor by binding to the bacterial elongation factor Tu. The kirromycin biosynthetic gene cluster was isolated from the producer, Streptomyces collinus Tü 365, and confirmed by targeted disruption of essential biosynthesis genes. Kirromycin is synthesized by a large hybrid polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) encoded by the genes kirAI-kirAVI. This complex involves some very unusual features, including the absence of internal acyltransferase (AT) domains in KirAI-KirAV, multiple split-ups of PKS modules on separate genes, and swapping in the domain organization. Interestingly, one PKS enzyme, KirAVI, contains internal AT domains. Based on in silico analysis, a route to pyridone formation involving PKS and NRPS steps was postulated. This hypothesis was experimentally proven by feeding studies with [U-13C3(15)N]beta-alanine and NMR and MS analyses of the isolated pure kirromycin.     

FT-IR Mapping—A New Tool for Spatially Resolved Characterization of Polymer-Bound Combinatorial Compound Libraries with IR Microscopy

In the search for selective receptors , a promising approach is provided by immobilization of cyclopeptides on sensor surfaces (see picture) and subsequent detection of low molecular weight analytes with reflectometric interference spectroscopy (RIfS). Together with combinatorial chemistry, this innovative method offers a great potential for applications as sensors.     

Transparent Boundary Conditions for Split-Step Padé Approximations of the One-Way Helmholtz Equation

In this paper, we generalize the nonlocal discrete transparent boundary condition introduced by F. Schmidt and P. Deuflhard (1995, Comput. Math. Appl.29, 53–76) and by F. Schmidt and D. Yevick (1997, J. Comput. Phys.134, 96–107) to propagation methods based on arbitrary Padé approximations of the two-dimensional one-way Helmholtz equation. Our approach leads to a recursive formula for the coefficients appearing in the nonlocal condition, which then yields an unconditionally stable propagation method.     

Synchronization of chaotic semiconductor laser systems: a vectorial coupling-dependent scenario

We demonstrate the influence of vectorial coupling on the synchronization behavior of complex systems. We study two semiconductor lasers subject to delayed optical feedback which are unidirectionally coherently coupled via their optical fields. Our experimental and numerical results demonstrate a characteristic synchronization scenario in dependence on the relative feedback phase leading cyclically from chaos synchronization to almost uncorrelated states, and back to chaos synchronization. Finally, we reveal the influence of the feedback phase on the dynamics of the solitary delay system.