Phase diagram of the fully frustrated transverse-field Ising model on the honeycomb lattice

Motivated by the current interest in the quantum dimer model on the triangular lattice, we investigate the phase diagram of the closely related fully-frustrated transverse field Ising model on the honeycomb lattice using classical and semi-classical approximations. We show that, in addition to the fully polarized phase at large field, the classical model possesses a multitude of phases that break the translational symmetry which in the dimer language, correspond to a plaquette phase and a columnar phase separated by an infinite cascade of mixed phases. The modification of the phase diagram by quantum fluctuations has been investigated in the context of linear spin-wave theory. The extrapolation of the semiclassical energies suggests that the plaquette phase extends down to zero field for spin 1/2, in agreement with the $\sqrt{12}\times\sqrt{12}$ phase of the quantum dimer model on the triangular lattice with only kinetic energy.Comment: 15 Pages, 11 Figures, Accepted for PR

Dynamical structure factors and excitation modes of the bilayer Heisenberg model

Using quantum Monte Carlo simulations along with higher-order spin-wave theory, bond-operator and strong-coupling expansions, we analyse the dynamical spin structure factor of the spin-half Heisenberg model on the square-lattice bilayer. We identify distinct contributions from the low-energy Goldstone modes in the magnetically ordered phase and the gapped triplon modes in the quantum disordered phase. In the antisymmetric (with respect to layer inversion) channel, the dynamical spin structure factor exhibits a continuous evolution of spectral features across the quantum phase transition, connecting the two types of modes. Instead, in the symmetric channel we find a depletion of the spectral weight when moving from the ordered to the disordered phase. While the dynamical spin structure factor does not exhibit a well-defined distinct contribution from the amplitude (or Higgs) mode in the ordered phase, we identify an only marginally-damped amplitude mode in the dynamical singlet structure factor, obtained from interlayer bond correlations, in the vicinity of the quantum critical point. These findings provide quantitative information in direct relation to possible neutron or light scattering experiments in a fundamental two-dimensional quantum-critical spin system.Comment: 19 pages, 15 figure

‘Malvasia nera di Brindisi/Lecce’ grapevine cultivar (Vitis vinifera L.) originated from ‘Negroamaro’ and ‘Malvasia bianca lunga’

‘Malvasia nera di Brindisi’ and ‘Malvasia nera di Lecce’ are two of the few Malvasias with black berries and belong to the Apulian ampelographic assortment (South Italy). Their presumed synonymy has been recently ascertained with SSR markers and therefore these two black 'Malvasias' can be considered as an unique variety. We discovered that this cultivar is the cross between ‘Malvasia bianca lunga’ alias ‘Malvasia del Chianti’ and ‘Negroamaro’ by using 42 nuclear SSR. Both parents belong to the Apulian varietal resources, since centuries. So far, ‘Malvasia nera di Brindisi/Lecce’ origin has been obscure; now we may assert that this cultivar was born right in Apulia. Three sets of chloroplast SSR loci were used to determine the female and the male parent: 6 ccmp loci, already used in previous pedigree studies, 15 ccSSR loci and 2 NTCP loci, derived from tobacco. The second set of loci was sequenced in order to compare the length of the markers with the reference species where they were originally obtained: in 4 cases no microsatellite motives were detected and in other 4 cases the perfect repetition found in tobacco was not maintained in grape. Unfortunately, the three sets of markers failed to show any polymorphism. A detailed comparison of the black Malvasia morphology with its two parents showed a closer similarity to ‘Negroamaro’. Also the anthocyanin profile is in agreement with that of the black parent; its varietal aroma presents interesting levels of free and bound 2-phenylethanol, responsible for rose flavor, and of bound linalool compounds.

Effects of a natural extract from Mangifera indica L, and its active compound, mangiferin, on energy state and lipid peroxidation of red blood cells

Following oxidative stress, modifications of several biologically important macromolecules have been demonstrated. In this study we investigated the effect of a natural extract from Mangifera indica L (Vimang), its main ingredient mangiferin and epigallocatechin gallate (EGCG) on energy metabolism, energy state and malondialdehyde (MDA) production in a red blood cell system. Analysis of NIDA, high energy phosphates and ascorbate was carried out by high performance liquid chromatography (HPLC). Under the experimental conditions, concentrations of NIDA and ATP catabolites were affected in a dose-dependent way by H2O2. Incubation with Vimang (0.1, 1, 10, 50 and 100 mu g/mL), mangiferin (1, 10, 100 mu g/mL) and EGCG (0.01, 0.1, 1, 10 mu M) significantly enhances erythrocyte resistance to H2O2-induced reactive oxygen species production. In particular, we demonstrate the protective activity of these compounds on ATP, GTP and total nucleotides (NT) depletion after H2O2-induced damage and a reduction of NAD and ADP, which both increase because of the energy consumption following H2O2 addition. Energy charge potential, decreased in H2O2-treated erythrocytes, was also restored in a dose-dependent way by these substances. Their protective effects might be related to the strong free radical scavenging ability described for polyphenols. (c) 2006 Elsevier B.V All rights reserved

Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative Novel Viruses.

Citrus sudden death (CSD) has caused the death of approximately four million orange trees in a very important citrus region in Brazil. Although its etiology is still not completely clear, symptoms and distribution of affected plants indicate a viral disease. In a search for viruses associated with CSD, we have performed a comparative high-throughput sequencing analysis of the transcriptome and small RNAs from CSD-symptomatic and -asymptomatic plants using the Illumina platform. The data revealed mixed infections that included Citrus tristeza virus (CTV) as the most predominant virus, followed by the Citrus sudden death-associated virus (CSDaV), Citrus endogenous pararetrovirus (CitPRV) and two putative novel viruses tentatively named Citrus jingmen-like virus (CJLV), and Citrus virga-like virus (CVLV). The deep sequencing analyses were sensitive enough to differentiate two genotypes of both viruses previously associated with CSD-affected plants: CTV and CSDaV. Our data also showed a putative association of the CSD-symptomatic plants with a specific CSDaV genotype and a likely association with CitPRV as well, whereas the two putative novel viruses showed to be more associated with CSD-asymptomatic plants. This is the first high-throughput sequencing-based study of the viral sequences present in CSD-affected citrus plants, and generated valuable information for further CSD studies

Modulation of the proteolytic activity of matrix metalloproteinase-2 (gelatinase A) on fibrinogen

The proteolytic processing of bovine fibrinogen by MMP-2 (gelatinase A), which brings about the formation of a product unable to form fibrin clots, has been studied at 37 degrees C. Catalytic parameters, although showing a somewhat lower catalytic efficiency with respect to thrombin and plasmin, indeed display values indicating a pathophysiological significance of this process. A parallel molecular modelling study predicts preferential binding of MMP-2 to the beta-chain of fibrinogen through its haemopexin-like domain, which has been directly demonstrated by the inhibitory effect in the presence of the exogenous haemopexin-like domain. However, the removal of this domain does not impair the interaction between MMP-2 and fibrinogen, but it dramatically alters the proteolytic mechanism, producing different fragmentation inter-mediates. The investigation at various pH values between 6.0 and 9.3 indicates a proton-linked behaviour, which is relevant for interpreting the influence on the process by environmental conditions occurring at the site of an injury. Furthermore, the action of MMP-2 on peroxynitrite-treated fibrinogen has been investigated, a situation possibly occurring under oxidative stress. The chemical alteration of fibrinogen, which has been shown to abolish its clotting activity, brings about only limited modifications of the catalytic parameters without altering the main enzymatic mechanism

The Collagen Binding Domain of Gelatinase A Modulates Degradation of Collagen IV by Gelatinase B

Type IV collagen remodeling plays a critical role in inflammatory responses, angiogenesis and metastasis. Its remodeling is executed by a family of matrix metalloproteinases (MMPs), of which the constitutive gelatinase A (MMP2) and the inducible gelatinase B (MMP9) are key examples. Thus, in many pathological conditions, both gelatinases act together. Kinetic data are reported for the enzymatic processing at 37 degrees C of type IV collagen from human placenta by MMP9 and its modulation by the fibronectin-like collagen binding domain (CBD) of MMP2. The alpha l and alpha 2 chain components of type IV collagen were cleaved by gelatinases and identified by mass spectrometry as well as Edman sequencing. Surface plasmon resonance interaction assays showed that CBD bound type IV collagen at two topologically distinct sites. On the basis of linked-function analysis, we demonstrated that CBD of MMP2 tuned the cleavage of collagen IV by MMP9, presumably by inducing a ligand-linked structural change on the type IV collagen. At low, concentrations, the CBD bound the first site and thereby allosterically modulated the binding of MMP9 to collagen IV, thus enhancing the collagenolytic activity of MMP9. At high concentrations, CBD binding to the second site interfered with MMP9 binding to collagen IV, acting as a competitive inhibitor. Interestingly, modulation of collagen IV degradation by inactive forms of MMP2 also occurred in a cell-based system, revealing that this interrelationship affected neutrophil migration across a collagen IV membrane. The regulation of the proteolytic processing by a catalytically inactive domain (i.e., CBD) suggests that the two gelatinases might cooperate in degrading substrates even when either one is inactive. This observation reinforces the idea of exosite targets for MMP inhibitors, which should include all macromolecular substrate recognition site

Folding mechanisms steer the amyloid fibril formation propensity of highly homologous proteins

Significant advances in the understanding of the molecular determinants of fibrillogenesis can be expected from comparative studies of the aggregation propensities of proteins with highly homologous structures but different folding pathways. Here, we fully characterize, by means of stopped-flow, T-jump, CD and DSC experiments, the unfolding mechanisms of three highly homologous proteins, zinc binding Ros87 and Ml153-149 and zinc-lacking Ml452-151. The results indicate that the three proteins significantly differ in terms of stability and (un)folding mechanisms. Particularly, Ros87 and Ml153-149 appear to be much more stable to guanidine denaturation and are characterized by folding mechanisms including the presence of an intermediate. On the other hand, metal lacking Ml452-151 folds according to a classic two-state model. Successively, we have monitored the capabilities of Ros87, Ml452-151 and Ml153-149 to form amyloid fibrils under native conditions. Particularly, we show, by CD, fluorescence, DLS, TEM and SEM experiments, that after 168 hours, amyloid formation of Ros87 has started, while Ml153-149 has formed only amorphous aggregates and Ml452-151 is still monomeric in solution. This study shows how metal binding can influence protein folding pathways and thereby control conformational accessibility to aggregation-prone states, which in turn changes aggregation kinetics, shedding light on the role of metal ions in the development of protein deposition diseases

Characterization of a globin-coupled oxygen sensor with a gene-regulating function

Globin-coupled sensors (GCSs) are multiple-domain transducers, consisting of a regulatory globin-like heme-binding domain and a linked transducer domain(s). GCSs have been described in both Archaea and bacteria. They are generally assumed to bind O2 (and perhaps other gaseous ligands) and to transmit a conformational change signal through the transducer domain in response to fluctuating O2 levels. In this study, the heme-binding domain, AvGReg178, and the full protein, AvGReg of the Azotobacter vinelandii GCS, were cloned, expressed, and purified. After purification, the heme iron of AvGReg178 was found to bind O2. This form was stable over many hours. In contrast, the predominant presence of a bis-histidine coordinate heme in ferric AvGReg was revealed. Differences in the heme pocket structure were also observed for the deoxygenated ferrous state of these proteins. The spectra showed that the deoxygenated ferrous derivatives of AvGReg178 and AvGReg are characterized by a penta-coordinate and hexa-coordinate heme iron, respectively. O2 binding isotherms indicate that AvGReg178 and AvGReg show a high affinity for O2 with P50 values at 20 °C of 0.04 and 0.15 torr, respectively. Kinetics of CO binding indicate that AvGReg178 carbonylation conforms to a monophasic process, comparable with that of myoglobin, whereas AvGReg carbonylation conforms to a three-phasic reaction, as observed for several proteins with bis-histidine heme iron coordination. Besides sensing ligands, in vitro data suggest that AvGReg(178) may have a role in O2-mediated NO-detoxification, yielding metAvGReg(178) and nitrate. © 2007 by The American Society for Biochemistry and Molecular Biology, Inc