The proton iron-sulfur cluster environment of the [FeFe]-hydrogenase maturation protein HydF from Thermotoga neapolitana

[FeFe]-hydrogenases contain a complex [4Fe–4S]-2Fe cluster (H-cluster) and are able to efficiently reduce protons to H₂. Due to their potential exploitation for renewable energy production biotechnologies, significant efforts have been put into understanding the mechanisms driving the H-cluster assembly, which involves three conserved proteins. Among them, HydF works as scaffold upon which the H-cluster precursor is synthesized and carrier to deliver it to the hydrogenase, resulting in its activation. A FeS cluster binding sequence (CxHx₄₆-₅₃HCxxC) is conserved in all HydF proteins and should in principle provide four ligands to coordinate the Fe atom. However, we found that alternative metal coordination may exist in different HydF proteins and that only the three cysteines are strictly required, whereas the fourth ligand may vary and is, in any case, readily exchangeable. In this work we analyzed by EPR/HYSCORE the FeS cluster proton environment of HydF from Thermotoga neapolitana to determine the possible role of surrounding residues in the non-cysteinyl iron ligation of the protein.     

Partial replacement of sodium chloride with potassium chloride in marinated rabbit meat

This study was aimed at evaluating the consequences of sodium chloride reduction by potassium chloride up to 50% on technological, sensorial and microbiological traits of marinated rabbit meat. In total, 226 rabbit loin meat samples were obtained and subjected to vacuum tumbling using solutions with different NaCl/KCl ratios. Replacing of sodium chloride up to 30% by potassium chloride did not change microbiological traits (total aerobic mesophilic and lactic acid bacteria maximum cell loads), sensorial acceptability (perceived saltiness and overall liking) and technological traits (pH, colour, texture, cooking loss and yield). Otherwise, reduction in sodium chloride to 50% significantly decreased perceived saltiness (4.15 vs. 4.73; P < 0.05) and reduced microbial shelf life by 1 day when compared to control, even if there was still no effect on technological traits. In conclusion, it is feasible imparting an added value for processed rabbit meat products by reduction in sodium content that could increase market interest.     

Biomechanics of fibrous proteins of the extracellular matrix studied by Brillouin scattering

Brillouin light scattering (BLS) spectroscopy is a technique that is able to detect thermally excited phonons within a material. The speed of propagation of these phonons can be determined from the magnitude of the Brillouin frequency shift between incident and scattered light, thereby providing a measure of the mechanical properties of the material in the gigahertz range. The mechanical properties of the extracellular matrices of biological tissues and their constituent biopolymers are important for normal tissue function and disturbances in these properties are widely implicated in disease. BLS offers the prospect of measuring mechanical properties on a microscopic scale in living tissues, thereby providing insights into structure–function relationships under normal and pathological conditions. In this study, we investigated BLS in collagen and elastin—the fibrous proteins of the extracellular matrix (ECM). Measurements were made on type I collagen in rat tail tendon, type II collagen in articular cartilage and nuchal ligament elastin. The dependence of the BLS spectrum on fibre orientation was investigated in a backscattering geometry using a reflective substrate. Two peaks, a bulk mode arising from phonon propagation along a quasi-radial direction to the fibre axis and a mode parallel to the surface, depending on sample orientation relative to the fibre axis, could be distinguished. The latter peak was fitted to a model of wave propagation through a hexagonally symmetric elastic solid, and the five components of the elasticity tensor were combined to give axial and transverse Young''s, shear and bulk moduli of the fibres. These were 10.2, 8.3, 3.2 and 10.9 GPa, and 6.1, 5.3, 1.9 and 8 GPa for dehydrated type I collagen and elastin, respectively. The former values are close to those previously reported. A microfocused BLS approach was also applied providing selection of single fibres. The moduli of collagen and elastin are much higher than those measured at lower frequency using macroscopic strains, and the difference between them is much less. We therefore believe, like previous investigators, that molecular-scale viscoelastic effects are responsible for the frequency dependence of the fibre biomechanics. Combining BLS with larger-scale mechanical testing methods therefore should, in the future, provide a means of following the evolution of mechanical properties in the formation of the complex structures found in the ECM.     

Absence of allergenic residues in experimental and commercial wines fined with caseinates

The possible presence of allergenic residues in wines treated with one of the potassium caseinates used as fining agents has been investigated.     

Temperature and electric field dependent hole mobility in a polyfluorene copolymer

Transport of holes in thin films of a low-bandgap alternating polyfluorene copolymer, APFO-Green5, was investigated by means of admittance spectroscopy as a function of field and temperature. The values of hole mobility were evaluated from the position of the maxima in the plots of the negative differential susceptance as a function of frequency. Hole mobility was found to be strongly field- and temperature-dependent. The charge transport parameters were extracted by analyzing the mobility data by the uncorrelated and the correlated Gaussian Disorder Models.     

A tool for design pattern detection and software architecture reconstruction

It is well known that software maintenance and evolution are expensive activities, both in terms of invested time and money. Reverse engineering activities support the obtainment of abstractions and views from a target system that should help the engineers to maintain, evolve and eventually re-engineer it. Two important tasks pursued by reverse engineering are design pattern detection and software architecture reconstruction, whose main objectives are the identification of the design patterns that have been used in the implementation of a system as well as the generation of views placed at different levels of abstractions, which let the practitioners focus on the overall architecture of the system without worrying about the programming details it has been implemented with.In this context we propose an Eclipse plug-in called MARPLE (Metrics and Architecture Reconstruction Plug-in for Eclipse), which supports both the detection of design patterns and software architecture reconstruction activities through the use of basic elements and metrics that are mechanically extracted from the source code. The development of this platform is mainly based on the exploitation of the Eclipse framework and plug-ins as well as of different Java libraries for data access and graph management and visualization. In this paper we focus our attention on the design pattern detection process.