The Finely Coordinated Action of SSB and NurA/HerA Complex Strictly Regulates the DNA End Resection Process in Saccharolobus solfataricus

Generation of the 3′ overhang is a critical step during homologous recombination (HR) and replication fork rescue processes. This event is usually performed by a series of DNA nucleases and/or helicases. The nuclease NurA and the ATPase HerA, together with the highly conserved MRE11/RAD50 proteins, play an important role in generating 3′ single-stranded DNA during archaeal HR. Little is known, however, about HerA-NurA function and activation of this fundamental and complicated DNA repair process. Herein, we analyze the functional relationship among NurA, HerA and the single-strand binding protein SSB from Saccharolubus solfataricus. We demonstrate that SSB clearly inhibits NurA endonuclease activity and its exonuclease activities also when in combination with HerA. Moreover, we show that SSB binding to DNA is greatly stimulated by the presence of either NurA or NurA/HerA. In addition, if on the one hand NurA binding is not influenced, on the other hand, HerA binding is reduced when SSB is present in the reaction. In accordance with what has been observed, we have shown that HerA helicase activity is not stimulated by SSB. These data suggest that, in archaea, the DNA end resection process is governed by the strictly combined action of NurA, HerA and SSB.     

Wall effects for the pressure drop in fixed beds

A very simple model is presented for the effect of the container wall on the pressure drop in a fluid flowing through a bed of spheres. It is based on the application of the Ergun equation to the bulk region of the bed, unaffected by the wall. Pressure loss predictions are found to correspond well to the opposing trends reported in the literature for the viscous- and inertial-flow regimes.     

Verification Approach of Metropolis Design Framework for Embedded Systems

In this paper, we focus on the verification approach of Metropolis, an integrated design framework for heterogeneous embedded systems. The verification approach is based on the formal properties specified in Linear Temporal Logic (LTL) or Logic of Constraints (LOC). Designs may be refined due to synthesis or be abstracted for verification. An automatic abstraction propagation algorithm is used to simplify the design for specific properties. A user-defined starting point may also be used with automatic propagation. Two main verification techniques are implemented in Metropolis the formal verification utilizing the model checker Spin and the simulation trace checking with automatic generated checkers. Translation algorithms from specification models to verification models, as well as algorithms of generated checkers are discussed. We use several case studies to demonstrate our approach for verification of system level designs at multiple levels of abstraction.     

Impact of SGLT2 Inhibitors on Heart Failure: From Pathophysiology to Clinical Effects

Heart failure (HF) affects up to over 20% of patients with type 2 diabetes (T2DM), even more in the elderly. Although, in T2DM, both hyperglycemia and the proinflammatory status induced by insulin resistance are crucial in cardiac function impairment, SGLT2i cardioprotective mechanisms against HF are several. In particular, these beneficial effects seem attributable to the significant reduction of intracellular sodium levels, well-known to exert a cardioprotective role in the prevention of oxidative stress and consequent cardiomyocyte death. From a molecular perspective, patients’ exposure to gliflozins’ treatment mimics nutrient and oxygen deprivation, with consequent autophagy stimulation. This allows to maintain the cellular homeostasis through different degradative pathways. Thus, since their introduction in the clinical practice, the hypotheses on SGLT2i mechanisms of action have changed: from simple glycosuric drugs, with consequent glucose lowering, erythropoiesis enhancing and ketogenesis stimulating, to intracellular sodium-lowering molecules. This provides their consequent cardioprotective effect, which justifies its significant reduction in CV events, especially in populations at higher risk. Finally, the updated clinical evidence of SGLT2i benefits on HF was summarized. Thus, this review aimed to analyze the cardioprotective mechanisms of sodium glucose transporter 2 inhibitors (SGLT2i) in patients with HF, as well as their clinical impact on cardiovascular events.     

Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future

Among the different aquaporins (AQPs), human aquaporin-4 (hAQP4) has attracted the greatest interest in recent years as a new promising therapeutic target. Such a membrane protein is, in fact, involved in a multiple sclerosis-like immunopathology called Neuromyelitis Optica (NMO) and in several disorders resulting from imbalanced water homeostasis such as deafness and cerebral edema. The gap of knowledge in its functioning and dynamics at the atomistic level of detail has hindered the development of rational strategies for designing hAQP4 modulators. The application, lately, of molecular modeling has proved able to fill this gap providing a breeding ground to rationally address compounds targeting hAQP4. In this review, we give an overview of the important advances obtained in this field through the application of Molecular Dynamics (MD) and other complementary modeling techniques. The case studies presented herein are discussed with the aim of providing important clues for computational chemists and biophysicists interested in this field and looking for new challenges.     

Effects of carbonaceous nanoparticles from low-emission and older diesel engines on human skin cells

Diesel exhaust particles (DEP) are major constituents of ambient air pollution and are associated with respiratory and cardiovascular diseases as well skin cell alterations in vitro. The epidermal cells are among the first cell populations exposed to chemical pollutants, including DEP, and are an important source of pro-inflammatory mediators. We evaluated the effects of carbonaceous soot particles from current low-emission (Euro IV) diesel engines on the oxidative and inflammatory response of normal human skin cells and compared the results with those induced by carbonaceous soot particles from an older diesel engine (BS) operating under black smoke conditions. We observed that both soot nanoparticles were spontaneously internalised by keratinocytes and distributed mostly around the cell nucleus. Moreover, at the same mass concentration, Euro IV soot particles exhibited a much higher oxidative, pro-fibrotic and toxic potential on these cell types than soot particles from the older diesel engine. These results are in agreement with and confirm our previous findings on human macrophage cells and strengthen the assumption that, at the same mass concentration, soot particles produced under low emission conditions are more cytotoxic than particles from the older diesel engine. This effect could be assigned to the defective surface structure of Euro IV diesel soot, rendering it highly active. Our findings highlight that the reduction of soot emission in terms of mass does not automatically lead to a reduction of the dangerous effects and show that soot particles from different diesel engines possess different biological behaviour towards human cells.     

Oxygen permeation in PET bottles with passive and active walls

The aim of this paper is to provide a framework, whereby gas permeation rates through plastic packaging walls, and hence, food shelf life may be estimated. Although the approach is quite general, specific attention is given to the case of liquid‐filled polyethylene terephthalate (PET) bottles with oxygen as the permeating gas. Two situations are considered: when the walls simply provide a passive resistance to the flux (as is the case for standard PET or PET blended with some other low permeability material) and when an active gas scavenger is incorporated within the boundary material. For the passive wall, permeability data relative to oxygen have been collected from literature sources and also measured using specific oxygen transmission rate experiments. For the active walls, scavenger kinetic constants were estimated from data obtained using test bottles prepared with varying scavenger concentrations. Numerical predictions in both cases have been verified by comparison with data on gas concentration in water‐filled bottles maintained under controlled conditions for periods of up to 6 months. Copyright © 2008 John Wiley & Sons, Ltd.     

Medium and interface components in impedance microbiology

Classic impedance microbiology (CIM) is based on the measurement of the impedance components that appear between a pair of electrodes submerged in a cell containing inoculated broth. Either a bipolar or a tetrapolar technique can be applied, requiring about 1 x 10(3) to 3 x 10(7) cells/ml to produce detectable changes in the impedance curves. Theoretical analysis of the electrode-electrolyte interface during bacterial growth is lacking, with no generally accepted measuring standards. Besides, there is considerable disagreement. We separated out the interface and medium components using the frequency variation technique (FVT) and also analyzed the interface reactance-resistance diagram, both before and after bacterial growth. Medium resistance Rm, interface reactance Xi, and interface resistance Ri, were quantified as time functions growth curves, from the complex bipolar impedance seen between two electrodes. We took into account the electrical current density, the temperature and the associated circuitry, also explaining the theoretical and experimental bases that justify the proposed dissecting procedure. It was found that, within the working frequency range, Rm, Ri, and Xi percental growth curves are frequency-independent, i.e., neither Rm(f), nor Xi(f) nor Ri(f) changed their slopes before, during and after bacterial growth. Besides, no alpha-dispersion effect in Rm curves was detected. It is concluded that impedance microbiology could become a fertile area for interdisciplinary knowledge; its development might offer new avenues for basic and applied research.     

Black curves and creep behaviour of crumb rubber modified binders containing warm mix asphalt additives

Warm mix asphalt (WMA) is a new research topic in the field of road pavement materials. This technology allows lower energy consumption and greenhouse gas (GHG) emissions by reducing compaction and placement temperatures of the asphalt mixtures. However, this technology is still under study, and the influence of the WMA additives has yet to be investigated thoroughly and clearly identified, especially in the case of crumb rubber modified (CRM) binders.In order to study the effect that different types and quantities of organic waxes have on the high and intermediate temperature properties of 15 % and 20 % CRM binders, a dynamic shear rheometer (DSR) was used. Using Black diagrams, the rheological behaviour of the binders for the defined range of test temperature and frequency are summarised in a single diagram. In this way, a preliminary evaluation of the rheological behaviour in the extended domain of time and temperature can be attained as well as the effectiveness of the time–temperature superposition principle (TTSP) on the materials under study. Creep tests were also performed in order to evaluate the differences regarding mechanical response due to the addition of rubber and WMA additives, and particularly the ability to recover the strain at high temperatures.The results of this study reveal that these binders do not conform to the Time Temperature Superposition Principle (TTSP) and their rheological behaviour is strongly affected by the interaction of waxes and bituminous matrix and thus generally exhibited a higher elasticity compared to the corresponding control binder. The creep test results carried out proved the enhancement of elasticity and the resistance to permanent deformation produced by the addition of waxes. The WMA additives significantly lower the maximum deformation when compared to the control binders and slightly increased their elastic recovery.     

Topological invariants for lines

A set of topological invariants for relations between lines embedded in the 2-dimensional Euclidean space is given. The set of invariants is proven to be necessary and sufficient to characterize topological equivalence classes of binary relations between simple lines. The topology of arbitrarily complex geometric scenes is described with a variation of the same set of invariants. Polynomial time algorithms are given to assess topological equivalence of two scenes. Invariants and efficient algorithms is due to application areas of spatial database systems where a model for describing topological relations between planar features is sought