Leonardo da Vinci: Cause, effect, linearity, and memory.

In this contribution, some textual portions of the Leonardo da Vinci's work were analyzed with the aim to highlight how, moving from Aristotle and going beyond him, he combines the intermediate positions that, from the Greek philosopher, passing through Buridan, arrive to Newton. This has been performed following a path that passes through the formulation of the principle of causality, the use of the concept of linear relationship (pyramidal law) between cause and effect and the introduction of a duration of the impression (memory) of mechanical systems. In the framework of the studies aimed to a valorization of Leonardo as a scientist, which is a crucial aspect in the analysis of the Leonardo genius, the present work sheds a new light on his intuitions about some fundamental physics concepts as well as about the conceptual model that, several centuries later, will be formalized in the modern linear response theory.

Biochemical and biophysical methodologies open the road for effective schistosomiasis therapy and vaccination.

BACKGROUND: Schistosomiasis caused by blood-dwelling flukes, namely Schistosoma mansoni and Schistosoma haematobium is a severe debilitating disease, widespread in sub-Saharan Africa, the Middle East, and South America. Developing and adult worms are unscathed by the surrounding immune effectors and antibodies because the parasite is protected by a double lipid bilayer armor which allows access of nutrients, while binding of specific antibodies is denied. SCOPE OF REVIEW: Fluorescence recovery after bleaching, extraction of surface membrane cholesterol by methyl-ß-cyclodextrin, inhibition and activation of sphingomyelin biosynthesis and hydrolysis, and elastic incoherent and quasi-elastic neutron scattering approaches have helped to clarify the basic mechanism of this immune evasion, and showed that sphingomyelin (SM) molecules in the worm apical lipid bilayer form with surrounding water molecules a tight hydrogen bond barrier. Viability of the parasite and permeability of the outer shield are controlled by equilibrium between SM biosynthesis and activity of a tegument-associated neutral sphingomyelinase (nSMase). MAJOR CONCLUSIONS: Excessive nSMase activation by polyunsaturated fatty acids (PUFA), such as arachidonic acid (ARA) leads to disruption of the SM molecules and associated hydrogen bond network, with subsequent access of host antibodies and immune effectors to the outer membrane and eventual parasite death. GENERAL SIGNIFICANCE: ARA was predicted and shown to be a potent schistosomicide in vitro and in vivo in experimental animals and in children. Additionally, it was advocated that schistosomiasis vaccine candidates should be selected uniquely among excretory-secretory products of developing worms, as contrary to cytosolic and surface membrane antigens, they are able to activate the effector functions of the host antibodies and toxic molecules. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".

Mobility and temperature resistance of trehalose mycolates as key characteristics of the outer membrane of Mycobacterium tuberculosis.

Trehalose mycolates are fundamental characteristics of the outer membrane (mycomembrane) of Mycobacterium tuberculosis and they are supposed to play a key role in the low permeability and high resistance of mycobacteria to many antibiotics; however, still, the molecular characteristics making mycolates so effective in their biological function are not fully understood. This work aims to investigate by quasi-elastic neutron scattering the diffusive dynamical properties of trehalose mycolates in water mixtures as a function of temperature, energy and exchanged wavevector Q in order to elucidate the dynamics-function relation in the mycomembrane. A comparison with lecithin lipids in water mixtures is performed since they are considered among the most rigid and resistant lipids. From the analysis of the data collected as a function of temperature, a lower temperature dependence of the mobility as well as a higher rigidity of trehalose mycolates in comparison with lecithin lipids are highlighted. The present findings provide detailed molecular information which allows to go ahead in the understanding at a molecular level of the resistance to stress and antibiotics by corynebacteria and mycobacteria.

Dynamical properties of α-synuclein in soluble and fibrillar forms by Quasi Elastic Neutron Scattering.

In the present paper, Quasi Elastic Neutron Scattering (QENS) results, gathered at different energy resolution values at the ISIS Facility (RAL, UK), on α-synuclein in soluble and fibrillar forms as a function of temperature and exchanged wave-vector Q are shown. The measurements reveal a different dynamic behavior of the soluble and fibrillar forms of α-synuclein as a function of thermal stress. In more detail, the dynamics of each protein form reflects its own complex conformational heterogeneity. Furthermore, the effect of a well known bioprotectant, trehalose, that influences α-synuclein fibrillation, on both soluble and fibrillar forms of α-synuclein is discussed.

Rigidity and resistance of larval- and adult schistosomes-medium interface.

Schistosomiasis is second only to malaria in prevalence and severity, and is still a major health problem in many tropical countries worldwide with about 200-300 million cases and with more than 800 million people at risk of infection. Based on these data, the World Health Organization recommends fostering research efforts for understanding at any level the mechanisms of the infection and then decreasing the social and economical impact of schistosomiasis. A key role is played by the parasite apical lipid membrane, which is entirely impervious to the surrounding elements of the immune system. We have previously demonstrated that the interaction between schistosomes and surrounding medium is governed by a parasite surface membrane sphingomyelin-based hydrogen barrier. In the present article, the elastic contribution to the total motion as a function of the exchanged wave-vector Q and the mean square displacement values for Schistosoma mansoni larvae and worms and Schistosomahaematobium worms have been evaluated by quasi elastic neutron scattering (QENS). The results point out that S. mansoni larvae show a smaller mean square displacement in comparison to S. mansoni and S. haematobium worms. These values increased by repeating the measurements after one day. These differences, which are analogous to those observed for the diffusion coefficient we previously evaluated, are interpreted in terms of rigidity of the parasite-medium interaction. S. mansoni larvae are the most rigid systems, while S. haematobium worms are the most flexible. In addition, temperature and hypoxia induce a weakening of the schistosome-medium interaction. These evidences are related to the strength of the hydrogen-bonded interaction between parasites and environment that we previously determined. We have shown that S. mansoni worms are characterized by a weakened interaction in respect to the larvae, while the S. haematobium worms more weakly interact with the surrounding medium than S. mansoni. The present QENS analysis allowed us to characterize the rigidity of larval- and adult S. mansoni and S. haematobium-host interface and to relate it to the parasite resistance to the hostile elements of the surrounding medium and to the immune effectors attack.

Is there a sphingomyelin-based hydrogen bond barrier at the mammalian host-schistosome parasite interface?

Schistosomes develop, mature, copulate, lay eggs, and live for years in the mammalian host bloodstream, importing nutrients across the tegument, but entirely impervious to the surrounding elements of the immune system. We have hypothesized that sphingomyelin (SM) in the parasite apical lipid bilayer is responsible for these sieving properties via formation of a tight hydrogen bond network with the surrounding water. Here we have used quasi-elastic neutron scattering for characterizing the diffusion of larval and adult Schistosoma mansoni and adult Schistosoma haematobium in the surrounding medium, under various environmental conditions. The results documented the presence of a hydrogen bond barrier around larvae and adult schistosomes. The hydrogen bond network readily collapses if worms are subjected to hypoxic conditions, likely via activation of the parasite tegument-associated neutral sphingomyelinase, and consequent excessive SM hydrolysis. The slower dynamics of lung-stage larvae as compared to adult worms has been related to the existence of hydrogen-bonded networks of different strength and then to their differential resistance to immune attacks.

Molecular mechanisms of survival strategies in extreme conditions.

Today, one of the major challenges in biophysics is to disclose the molecular mechanisms underlying biological processes. In such a frame, the understanding of the survival strategies in extreme conditions received a lot of attention both from the scientific and applicative points of view. Since nature provides precious suggestions to be applied for improving the quality of life, extremophiles are considered as useful model-systems. The main goal of this review is to present an overview of some systems, with a particular emphasis on trehalose playing a key role in several extremophile organisms. The attention is focused on the relation among the structural and dynamic properties of biomolecules and bioprotective mechanisms, as investigated by complementary spectroscopic techniques at low- and high-temperature values.

Elastic incoherent neutron scattering operating by varying instrumental energy resolution: principle, simulations, and experiments of the resolution elastic neutron scattering (RENS).

The main aim of this paper is to present the scientific case of the resolution elastic neutron scattering (RENS) method that is based on the collection of elastic neutron scattering intensity as a function of the instrumental energy resolution and that is able to extract information on the system dynamical properties from an elastic signal. In this framework, it is shown that in the measured elastic scattering law, as a function of the instrumental energy resolution, an inflection point occurs when the instrumental energy resolution intersects the system relaxation time, and in an equivalent way, a transition in the temperature behavior of the measured elastic scattering law occurs when the characteristic system relaxation time crosses the instrumental energy resolution time. With regard to the latter, an operative protocol to determine the system characteristic time by different elastic incoherent neutron scattering (EINS) thermal scans at different instrumental energy resolutions is also proposed. The proposed method, hence, is not primarily addressed to collect the measured elastic scattering intensity with a great accuracy, but rather relies on determining an inflection point in the measured elastic scattering law versus instrumental energy resolution. The RENS method is tested both numerically and experimentally. As far as numerical simulations are concerned, a simple model system for which the temperature behavior of the relaxation time follows an Arrhenius law, while its scattering law follows a Gaussian behavior, is considered. It is shown that the system relaxation time used as an input for the simulations coincides with the one obtained by the RENS approach. Regarding the experimental findings, due to the fact that a neutron scattering spectrometer working following the RENS method has not been constructed yet, different EINS experiments with different instrumental energy resolutions were carried out on a complex model system, i.e., dry and D(2)O hydrated lysozyme, in an extended temperature range. The resulting temperature behavior of the system relaxation time, obtained with RENS method, agrees very well with the one obtained in literature, for the same system, following the quasi-elastic neutron scattering (QENS) approach. The proposed scientific case puts into evidence the challenges of an RENS spectrometer working by varying the instrumental energy resolution; in particular, in comparison with QENS, the proposed RENS method requires a smaller amount of sample, which is an important point in dealing with biological and exotic systems; it is not affected by the use of model functions for fitting spectra as in QENS, but furnishes a direct access to relevant information.

Vibrational properties of bioprotectant mixtures of trehalose and glycerol.

In this work vibrational spectra of mixtures of two glass-forming bioprotectant systems, i.e., trehalose and glycerol, are collected at very low temperature by using the indirect geometry time-of-flight (t.o.f.) TOSCA spectrometer at the ISIS Pulse Neutron Facility (Rutherford Appleton Laboratory, Oxford, U.K.). The main aim of this work is to investigate, through inelastic neutron scattering (INS), the vibrational behavior of trehalose and its mixtures with glycerol at different concentration values in order to characterize the changes induced by glycerol on the trehalose hydrogen bonded network. The obtained experimental findings, which are discussed and interpreted in the framework of previous INS, quasi elastic neutron scattering (QENS) and molecular simulation data obtained on trehalose/glycerol mixtures at different concentration and temperature values, will be linked to the different mixtures bioprotectant effectiveness.

Puzzle of protein dynamical transition.

Despite recent extensive efforts, the nature of the dynamics of biological macromolecules still remains unclear. In particular, contradicting models have been proposed for explaining the temperature behavior of the mean square displacement, MSD, and of the system relaxation time, τ. To solve this puzzle, different neutron scattering experiments with different instrumental energy resolutions were performed on dry and hydrated lysozyme. The obtained results show that the so called dynamical transition: (i) is a finite instrumental energy resolution effect, and more specifically, it appears when the characteristic system relaxation time intersects the resolution time, (ii) it does not imply any transition in the dynamical properties of the systems, (iii) it is not due to the fragile-to-strong dynamical crossover (FSC) in the temperature behavior of the system relaxation time, differently to what S. H. Chen et al. proposed [Proc. Natl. Acad. Sci. U.S.A.2006, 103, 9012]. Furthermore, the obtained results confirm the change in the τ-temperature dependence at T = 220 K of S. H. Chen et al., and show that it is not due to finite instrumental energy resolution effects and it is not connected to numerical errors in the data analysis protocol, differently to what W. Doster et al. proposed [Phys. Rev. Lett.2010, 104, 098101].

Mean square displacements from elastic incoherent neutron scattering evaluated by spectrometers working with different energy resolution on dry and hydrated (H2O and D2O) lysozyme.

The main aim of the present paper is the evaluation of the effects of the instrumental energy resolution on the mean square displacement (MSD) obtained by elastic incoherent neutron scattering (EINS). In particular, this study is performed in the time domain, through the time-Fourier transform of the elastically scattered neutron intensity, and is mainly focused on the connection between the system MSD and the measured MSD. It is shown how in the case of EINS, the instrumental energy resolution gives rise to the time integration of the time-dependent system MSD function weighted in time by the resolution function. The formulated approach is applied to the data collected on dry and hydrated (H(2)O and D(2)O with h = 0.4) lysozyme samples by two spectrometers working with a different instrumental resolution (the IN10 and IN13 spectrometers of the Institute Laue-Langevin). As a result, the procedure furnishes an excellent agreement for the system MSD evaluated in the low temperature range up to T = 40 K.

Motion characterization by self-distribution-function procedure.

In the present paper a procedure for the biomolecular motion characterization based on the evaluation of the Mean Square Displacement (MSD), through the Self Distribution Function (SDF), is presented. In particular it will be shown how the MSD, which represents a good observable for the characterization of the dynamical properties in disordered systems, can be decomposed into partial contributions associated to the system dynamical processes within a specific spatial scale. It will be shown how the SDF procedure allows to evaluate both the total MSD and the partial MSDs through the total SFD and the partial SDFs. As a result, the total MSD is the weighed sum of the partial MSD contributions in which the weights are obtained by the fitting procedure of measured EINS intensity data. We apply the SDF procedure at EINS data collected, by the IN13 backscattering spectrometer at the Institute Laue-Langevin, Grenoble, on aqueous mixtures of two homologous disaccharides (sucrose and trehalose) and on dry myoglobin in trehalose environment. It emerges that the hydrogen bond imposed network of the water-trehalose mixture appears to be stronger with respect to that of the water-sucrose mixture and this result can justify the highest bioprotectant effectiveness of trehalose in comparison with sucrose. Furthermore it emerges that, the partial MSD behaviours of sucrose and trehalose are equivalent in the low Q domain (0-1.7) A(-1) whereas they are different in the high Q domain (1.7-4) A(-)(1). This circumstance suggests that the higher structure sensitivity of sucrose in respect to trehalose should be related to the small spatial observation windows.

Biomolecular motion characterization by a self-distribution-function procedure in elastic incoherent neutron scattering.

In the present paper we first focus on the role of the instrumental resolution in elastic incoherent neutron scattering (EINS) where the connection between the self-distribution function (SDF) and the measured EINS intensity profile is highlighted. Second we show how the SDF procedure, previously introduced, allows both the total and the partial mean-square displacement evaluations through the total and the partial SDFs. Finally, we compare the SDF and the Gaussian procedures, by applying the two approaches to EINS data collected, by the IN13 backscattering spectrometer (Institute Laue-Langevin, Grenoble), on aqueous mixtures of two homologous disaccharides, i.e., sucrose and trehalose, and on myoglobin.

Characterization of molecular motions in biomolecular systems by elastic incoherent neutron scattering.

In the present work the role played by the instrumental resolution function in elastic incoherent neutron scattering (EINS) experiment is discussed. An important result consists in the definition of an equivalent time t(*), which depends both on the characteristic system time and on the resolution time, for which the spatial Fourier transform of EINS intensity profile and the self-distribution function (SDF) evaluated at t=t(*) are proportional. Then the equivalent time t(*) is introduced in the SDF procedure, an operational recipe for the mean square displacement determination. The new revised procedure is applied on data of myoglobin in trehalose dry environment and of hydrated homologous disaccharides (sucrose and trehalose).

Influences of temperature and threshold effect of NaCl concentration on Alpias vulpinus OCT.

Thermodynamic, circular dichroism (CD), and activity measurements have been used to characterize the different conformational states and the effects of NaCl concentrations (0.0-3.0 M) on thermal unfolding of ornithine carbamoyltransferase (OCT) from Alopias vulpinus. Furthermore conformational changes in whole enzyme structure have been monitored by titration of SH-groups. OCT unfolding process follows an irreversible two-state mechanism with a first-order kinetic of denaturation, without breaking-point. NaCl shows very little stabilization effects at low concentration and its action become very important over 1.5 M concentration. The presence of 3.0 M NaCl completely avoids OCT unfolding at 60, 64 and 66 degrees C. Kinetic and thermodynamic parameters are strongly influenced by the presence of high NaCl concentration. Our experiments showed that NaCl stabilization process involved changes in preferential binding, in electrostatic and van der Waals interactions and exposure of buried site and SH-groups. During thermal denaturation, UV-vis and CD spectroscopy show that high salts concentration preserves OCT activity, avoiding exposure of hydrophobic site and destruction of secondary and tertiary structure elements.

Elastic incoherent neutron scattering on systems of biophysical interest: mean square displacement evaluation from self-distribution function.

In the present work an operational recipe for the mean square displacement (MSD) determination, highlighting the connection between the self-distribution function and average statistical values, is presented. The determination of the MSD and of its contributions associated with different mechanisms, together with their thermal behavior, is performed by evaluating the self-distribution function derived by elastic incoherent neutron scattering (EINS). The approach is tested on EINS data collected by the backscattering spectrometer IN13 (ILL, Grenoble, France) on two model systems such as dry myoglobin in trehalose and poly(ethylene glycol) with mean molecular weight M(w) = 400 (PEG 400).

Mean square displacement evaluation by elastic neutron scattering self-distribution function.

In the present work an operational recipe for the mean square displacement (MSD) determination, highlighting the connection between elastic incoherent neutron scattering (EINS) intensity profiles and the associated self-distribution function, is presented. The determination of the thermal behavior of the total MSD and of its partial contributions is tested on EINS data collected by the backscattering spectrometer IN13 (ILL, Grenoble) on a model system such as PolyEthylene Glycol with a mean molecular weight of 400 Dalton (PEG 400).

Trehalose: a biophysics approach to modulate the inflammatory response during endotoxic shock.

We evaluated the effects of trehalose against endotoxic shock, a condition in which the loss of bio-membrane integrity plays a pivotal role. In addition we performed a biophysics experiment by quasi elastic neutron scattering (QENS) study, to investigate whether the membrane stability effect of trehalose might be correlated with its high capability to switch-off the water diffusive dynamics and, hence, the kinetic mechanisms of interaction. Endotoxic shock was induced in male rats by a single injection of Salmonella enteritidis lipopolysaccharide (LPS; 20 mg/kg/i.p.). Thirty minutes before and 2 h after LPS injection, the animals were randomized to receive vehicle (1 ml/kg/i.p. 0.9%NaCl), sucrose (1 g/kg/i.p.) or trehalose (1 g/kg/i.p.). Mean arterial blood pressure, nuclear factor-kappaB (NF-kappaB) binding activity, Ikappa-Balpha and toll-like receptor-4 (TLR-4) activation were evaluated in both liver and lung. Plasmatic tumor necrosis factor-alpha (TNF-alpha), interleukin-1 (IL-1), interleukin-6 (IL-6) and malondialdehyde (MDA) were also investigated. We studied liver injury by means of blood alanine aminotransferase activity (ALT); inducible nitric oxide synthase (iNOS) expression, myeloperoxidase (MPO) activity and tissue edema evaluation. Lung injury was investigated by means of tissue monocyte chemoattractant protein-1 (MCP-1) levels, MPO activity, iNOS expression and edema formation. Trehalose reduced hypotension, NF-kappaB binding activity, IkappaBalpha protein loss and TLR-4 activation. In addition trehalose reduced TNF-alpha, IL-1, IL-6 and MDA levels. Trehalose also blunted liver and lung injury. QENS measurements showed also that trehalose possesses a high "switching off" capability. Sucrose did not modify endotoxic shock-induced sequelae. Trehalose blocked the inflammatory cascade triggered by endotoxin shock, stabilizing the bio-membranes and switching off the water diffusive dynamics.

Theoretical and experimental models on viscosity: I. Glycerol.

The main aim of the present work is to show, for the case of glycerol, the connection between the macroscopic fragility parameter, defined as m = (d log eta)/(d(Tg/T))|T=Tg+, and the average number of H-bonds per molecule. Furthermore, the relation between the macroscopic and microscopic definitions of fragility, which takes into account the temperature dependence of the atomic mean square displacement, is discussed.