Conformational studies of RGDechi peptide by natural‐abundance NMR spectroscopy

Integrins are heterodimeric cell‐surface proteins that play important roles during developmental and pathological processes. Diverse human pathologies involve integrin adhesion including thrombotic diseases, inflammation, tumour progression, fibrosis, and infectious diseases. Although in the past decade, novel integrin‐inhibitor drugs have been developed for integrin‐based medical applications, the structural determinants modulating integrin‐ligands recognition mechanisms are still poorly understood, reducing the number of integrin subtype exclusive antagonists. In this scenario, we have very recently showed, by means of chemical and biological assays, that a chimeric peptide (named RGDechi), containing a cyclic RGD motif linked to an echistatin C‐terminal fragment, is able to interact with the components of integrin family with variable affinities, the highest for α_vβ3. Here, in order to understand the mechanistic details driving the molecular recognition mechanism of α_vβ₃ by RGDechi, we have performed a detailed structural and dynamics characterization of the free peptide by natural abundance nuclear magnetic resonance (NMR) spectroscopy. Our data indicate that RGDechi presents in solution an heterogeneous conformational ensemble characterized by a more constrained and rigid pentacyclic ring and a largely unstructured acyclic region. Moreover, we propose that the molecular recognition of α_vβ₃ integrin by RGDechi occurs by a combination of conformational selection and induced fit mechanisms. Finally, our study indicates that a detailed NMR characterization, by means of natural abundance ¹⁵N and ¹³C, of a mostly unstructured bioactive peptide may provide the molecular basis to get essential structural insights into the binding mechanism to the biological partner.     

Brain dynamics underlying the nonlinear threshold for access to consciousness

When a flashed stimulus is followed by a backward mask, subjects fail to perceive it unless the target-mask interval exceeds a threshold duration of about 50 ms. Models of conscious access postulate that this threshold is associated with the time needed to establish sustained activity in recurrent cortical loops, but the brain areas involved and their timing remain debated. We used high-density recordings of event-related potentials (ERPs) and cortical source reconstruction to assess the time course of human brain activity evoked by masked stimuli and to determine neural events during which brain activity correlates with conscious reports. Target-mask stimulus onset asynchrony (SOA) was varied in small steps, allowing us to ask which ERP events show the characteristic nonlinear dependence with SOA seen in subjective and objective reports. The results separate distinct stages in mask-target interactions, indicating that a considerable amount of subliminal processing can occur early on in the occipito-temporal pathway (<250 ms) and pointing to a late (>270 ms) and highly distributed fronto-parieto-temporal activation as a correlate of conscious reportability.     

Grape seed procyanidins inhibit the expression of metallothione in genes in human HepG2 cells

Procyanidins are the most abundant polyphenols in red wine and are also found in cereals, fruits, chocolate and tea. They exert many beneficial health effects, especially on the cardiovascular system (Bagchi et al. in Mutat Res 523-524:87-97, 2003; Williams et al. in Free Radic Biol Med 36:838-849, 2004; Dell'Agli et al. in Cardiovasc Res 63(4):593-602, 2004; Del Bas et al. FASEB J 19:479-480, 2005). Here, we show that oral administration of a grape seed procyanidins extract (GSPE) to healthy rats results, 5 h after treatment, in a 70% inhibition of metallothionein (MT) gene expression in the liver, as determined by oligonucleotide microarray hybridization. Similarly, in cultured human hepatocytes HepG2, GSPE downregulate the expression of MT genes at the mRNA level, as evaluated by quantitative RTPCR. Thus, mRNA levels of six functional MT genes, MT1A, 1E, 1F, 1G, 1X and MT2A, are diminished between 50 and 80% when HepG2 cells are treated during 12 h with GSPE. Only the expression of two human MT genes, MT1G and MT1E, is transiently increased during the first 2 h of treatment. GSPE-induced inhibition of MT genes expression is dose dependent, at concentrations that are not toxic for the cells. Our findings demonstrate that metallothionein genes are direct targets of procyanidins action, both in vivo and in vitro, in hepatic cells. Thus, this study will help to elucidate the mechanisms by which procyanidin exert their beneficial actions.     

Genetic structure in Brazilian breeding colonies of the Roseate Spoonbill (Platalea ajaja, Aves: Threskiornithidae)

Roseate Spoonbills (Platalea ajaja, Linnaeus) are wading birds present in two of the most important Brazilian wetlands: the Pantanal wetlands and Rio Grande do Sul marshes. Natural populations of these species have not been previously studied with variable nuclear molecular markers. In order to support decision making regarding the management and conservation of these populations, we estimated and characterized the distribution of genetic variability among five Brazilian breeding colonies. The average observed heterozygosity in Brazilian Roseate Spoonbill populations (Ho = 0.575) did not differ significantly from the value determined in a U.S. wild-caught sample of 15 individuals, using data generated by the same set of microsatellite loci. Considering that the U.S. population underwent a recent reduction in size, we discuss this result supposing that the U.S. population was not genetically affected or that both populations had suffered a bottleneck. Global F(ST) indicated the lack of genetic differentiation among colonies, indicating the occurrence of past and/or present gene flow among them. Analysis of molecular variance revealed that most of the genetic variation is distributed within the colonies. Results are explained by a recent origin of colonies or by high levels of gene flow. Management decisions should take into consideration the fact that, even in the presence of high genetic exchange, ecological adaptations to different environments are important for species survival.     

LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise

Background  

Mass spectrometry protein profiling is a promising tool for biomarker discovery in clinical proteomics. However, the development of a reliable approach for the separation of protein signals from noise is required. In this paper, LIMPIC, a computational method for the detection of protein peaks from linear-mode MALDI-TOF data is proposed. LIMPIC is based on novel techniques for background noise reduction and baseline removal. Peak detection is performed considering the presence of a non-homogeneous noise level in the mass spectrum. A comparison of the peaks collected from multiple spectra is used to classify them on the basis of a detection rate parameter, and hence to separate the protein signals from other disturbances.     

Predominance of Th2 cytokines, CXC chemokines and innate immunity mediators at the mucosal level during severe respiratory syncytial virus infection in children

Profiling of immune mediators in both nasal and plasma samples is a common approach to the study of pathogenesis in respiratory viral infections. Nevertheless, mucosal immunity functions essentially independently from peripheral immunity. In our study, 27 immune mediators were profiled in parallel, in nasopharyngeal aspirates (NPAs) and plasma from 22 < 2 year-old children with a severe respiratory syncytial virus infection involving the lower respiratory tract, using a multiplex assay. NPAs from 22 children with innocent heart murmurs were used as controls. Differences in mediator concentrations between NPAs from patients and controls were assessed using the Mann-Whitney test. Ratios of innate/adaptive-immunity mediators, Th2/Th1-cytokines and CXC/CC-chemokines were calculated for NPAs and plasmas and differences were assessed using the Wilcoxon test. Associations mediators, severity and leukocyte counts were studied using the Spearman-Karber test. Results: increased levels of Th1 cytokines (IL-1beta, IL-2, IL-12p70, IFNgamma, TNFalpha), Th2 cytokines (IL-13, IL-4, IL-6, IL-10), chemokines (IP-10, IL-8, MIP1alpha, MIP-1beta), growth factors (FGFb, PDGFbb, GCSF) and IL-1RA, IL-17 were observed in patient NPAs in comparison to controls. In the relative comparisons between patient NPAs and plasmas, a predominance of innate immunity mediators, Th2 cytokines and CXC chemokines was found at the mucosal level. No association between the level of each mediator in NPAs and plasma was found. In plasma, PDGFbb, VEGF, MIP-1alpha, IL-8 correlated with severity; RANTES and IL-6 correlated with leukocyte counts. Conclusions: acute respiratory syncytial virus infection induces a relative predominance of innate-immunity mediators, Th2 cytokines and CXC chemokines in the mucosal compartment in infected children.     

Burkholderia cepacia complex infection in a cohort of Italian patients with cystic fibrosis

The aims of this study were to detect Burkholderia cepacia complex (Bcc) strains in a cohort of Cystic Fibrosis patients (n=276) and to characterize Bcc isolates by molecular techniques. The results showed that 11.23% of patients were infected by Bcc. Burkholderia cenocepacia lineage III-A was the most prevalent species (64.3%) and, of these, 10% was cblA positive and 50% esmR positive. Less than half of the strains were sensitive to ceftazidime, meropenem, piperacillin tazobactam, and trimethoprim-sulfamethoxazole. About half of the strains (41%) had homogeneous profiles, suggesting cross-transmission. The infection by B. cenocepacia was associated to a high rate of mortality (p=0.01).