PLoS Genet.

Our understanding of basic evolutionary processes in bacteria is still very limited. For example, multiple recent dating estimates are based on a universal inter-species molecular clock rate, but that rate was calibrated using estimates of geological dates that are no longer accepted. We therefore estimated the short-term rates of mutation and recombination in Helicobacter pylori by sequencing an average of 39,300 bp in 78 gene fragments from 97 isolates. These isolates included 34 pairs of sequential samples, which were sampled at intervals of 0.25 to 10.2 years. They also included single isolates from 29 individuals (average age: 45 years) from 10 families. The accumulation of sequence diversity increased with time of separation in a clock-like manner in the sequential isolates. We used Approximate Bayesian Computation to estimate the rates of mutation, recombination, mean length of recombination tracts, and average diversity in those tracts. The estimates indicate that the short-term mutation rate is 1.4x10(-6) (serial isolates) to 4.5x10(-6) (family isolates) per nucleotide per year and that three times as many substitutions are introduced by recombination as by mutation. The long-term mutation rate over millennia is 5-17-fold lower, partly due to the removal of non-synonymous mutations due to purifying selection. Comparisons with the recent literature show that short-term mutation rates vary dramatically in different bacterial species and can span a range of several orders of magnitude

Structural and mechanistic insights into Helicobacter pylori NikR activation

NikR is a transcriptional metalloregulator central in the mandatory response to acidity of Helicobacter pylori that controls the expression of numerous genes by binding to specific promoter regions. NikR/DNA interactions were proposed to rely on protein activation by Ni(II) binding to high-affinity (HA) and possibly secondary external (X) sites. We describe a biochemical characterization of HpNikR mutants that shows that the HA sites are essential but not sufficient for DNA binding, while the secondary external (X) sites and residues from the HpNikR dimer–dimer interface are important for DNA binding. We show that a second metal is necessary for HpNikR/DNA binding, but only to some promoters. Small-angle X-ray scattering shows that HpNikR adopts a defined conformation in solution, resembling the cis-conformation and suggests that nickel does not trigger large conformational changes in HpNikR. The crystal structures of selected mutants identify the effects of each mutation on HpNikR structure. This study unravels key structural features from which we derive a model for HpNikR activation where: (i) HA sites and an hydrogen bond network are required for DNA binding and (ii) metallation of a unique secondary external site (X) modulates HpNikR DNA binding to low-affinity promoters by disruption of a salt bridge

Recent progress and perspectives of space electric propulsion systems based on smart nanomaterials

Miniaturized spacecraft built from advanced nanomaterials are poised for unmanned space exploration. In this review, the authors examine the integration of nanotechnology in electric propulsion systems and propose the concept of self-healing and adaptive thrusters

Broadband characterization of congruent lithium niobate from mHz to optical frequencies

Lithium niobate (LiNbO3) is a well known uniaxial ferroelectric material. Using impedance measurement, quasi-optical free-space characterization, THz time domain spectroscopy (THz-TDS) and ellipsometry, its dielectric permittivity/refractive index was characterized depending on the crystal orientation over a broad frequency range: 1 mHz to 1 PHz (lambda = 300 nm). Three different frequency ranges, separated by well identified resonances, are observed: low frequency \u27free-piezoelectric\u27 response, intermediate frequency \u27clamped-ionic\u27 response and high frequency \u27electronic\u27 response. These features are discussed with an emphasis on the role of the crystallographic structure and piezoelectric response

Atomic layer deposition of vanadium oxides: process and application review

Atomic layer deposition (ALD)is a method of choice for the growth of highly conformal thin films with accurately controlled thickness on planar and nanostructured surfaces. These advantages make it pivotal for emerging nanotechnology applications. This review sheds light on the current developments on the ALD of vanadium oxide, which, with proper postdeposition treatment yields a variety of functional and smart oxide phases. The application of vanadium oxide coatings in electrochemical energy storage, microelectronics and smart windows are emphasized