Application of Surface Roughness Data for the Evaluation of Depth Profile Measurements of Nanoscale Multilayers

A secondary neutral mass spectrometric (SNMS) depth profile study of electrodeposited Co/Cu multilayers was performed. Depth profile measurements were performed both in the conventional way (i.e., starting the sputtering from the final deposit surface) and in the reverse manner (i.e., detaching the multilayers from the substrate and starting the analysis from the substrate side, which was very smooth as compared to the final deposit surface). The latter method could yield significantly larger intensity fluctuations in the SNMS spectra. Surface roughness data were measured with atomic force microscopy (AFM) for multilayers with different bilayer numbers but otherwise exhibiting the same layer structure as those used for the depth profiling. The experimental AFM surface roughness evolution was used to calculate the result of the depth profile measurements quantitatively. An excellent agreement was obtained between this calculation and the SNMS measurements. It was shown that the decrease in the intensity fluctuations during the depth profile analysis stems mainly from the increase in surface roughness of the samples studied, especially in the conventional sputtering mode. It was also concluded that the thickness fluctuation of the entire multilayer deposit and that of each layer are strongly correlated

dUTPase based switch controls transfer of virulence genes in order to preserve integrity of the transferred mobile genetic elements

dUTPases ubiquitously regulate cellular dUTP levels to preserve genome integrity. Recently, several other cellular processes were reported to be controlled by dUTPases including the horizontal transfer of Staphylococcus aureus pathogenicity islands (SaPI). SaPIs are mobil genetic elements that encode virulence enhancing factors e.g. toxins. Here, phage dUTPases were proposed to counteract the repressor protein (Stl) and promote SaPI excision and transfer. A G protein-like mechanism was proposed which is unexpected in light of the kinetic mechanism of dUTPase. Here we investigate the molecular mechanism of SaPI transfer regulation, using numerous dUTPase variants and a wide range of in vitro methods (steady-state and transient kinetics, VIS and fluorescence spectroscopy, EMSA, quartz crystal microbalance, X-ray crystallography). Our results unambiguously show that Stl inhibits the enzymatic activity of dUTPase in the nM concentration range and dUTP strongly inhibits the dUTPase: Stl complexation. These results identify Stl as a highly potent dUTPase inhibitor protein and disprove the G protein-like mechanism. Importantly, our results clearly show that the dUTPase:dUTP complex is inaccessible to the Stl repressor. Unlike in small GTPases, hydrolysis of the substrate nucleoside triphosphate (dUTP in this case) is required prior to the interaction with the partner (Stl repressor in this case). We propose that dUTPase can efficiently interact with Stl and induce SaPI excision only if the cellular dUTP level is low (i.e. when dUTPase resides mainly in the apo enzyme form) while high dUTP levels would inhibit SaPI transfer. This mechanism may serve the preservation of the integrity of the transferred SaPI genes and links the well-known metabolic role of dUTPases to their newly revealed regulatory function in spread of virulence factors

Structure and enzymatic mechanism of a moonlighting dUTPase

Genome integrity requires well controlled cellular pools of nucleotides. dUTPases are responsible for regulating cellular dUTP levels and providing dUMP for dTTP biosynthesis. In Staphylococcus, phage dUTPases are also suggested to be involved in a moonlighting function regulating the expression of pathogenicity-island genes. Staphylococcal phage trimeric dUTPase sequences include a specific insertion that is not found in other organisms. Here, a 2.1 Å resolution three-dimensional structure of a [varphi]11 phage dUTPase trimer with complete localization of the phage-specific insert, which folds into a small [beta]-pleated mini-domain reaching out from the dUTPase core surface, is presented. The insert mini-domains jointly coordinate a single Mg2+ ion per trimer at the entrance to the threefold inner channel. Structural results provide an explanation for the role of Asp95, which is suggested to have functional significance in the moonlighting activity, as the metal-ion-coordinating moiety potentially involved in correct positioning of the insert. Enzyme-kinetics studies of wild-type and mutant constructs show that the insert has no major role in dUTP binding or cleavage and provide a description of the elementary steps (fast binding of substrate and release of products). In conclusion, the structural and kinetic data allow insights into both the phage-specific characteristics and the generally conserved traits of [varphi]11 phage dUTPase

Spontaneous near-substrate composition modulation in electrodeposited Fe-Co-Ni alloys

Conventional and reverse depth profile analysis of electrodeposited Fe–Co–Ni alloys was performed by secondary neutral mass spectrometry (SNMS). It was found that the reverse sputtering method gave a much better depth resolution at the vicinity of the substrate. The reverse SNMS spectra showed that the deposition of Fe–Co–Ni alloys starts with the formation of an Fe-rich zone followed by an increase in Co concentration, then the nickel content increases and a steady-state alloy composition is achieved. At high current density, the initial depth pattern reproduces itself twice before the composition becomes stable. It was concluded that the varying depth profile is a consequence of the anomalous nature of the codeposition of the alloy components, the depletion of the electrolyte with respect to the metal salts, and the dependence of the intensity of the hydrogen evolution on the deposit surface composition

Influence of the core material polishing on the Fluxset sensor's operation

Mechanical, chemical and electrochemical polishing of the sensor core material was investigated on the operation of the Fluxset magnetic field sensor. A significant improvement of the sensitivity was found after proper polishing. The phenomenon was interpreted, taking into account chemical changes in the surface region, the effect of surface roughness on domain wall motion, volume changes in the core material, and the skin effect