Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase

SMYD3 is a multifunctional epigenetic enzyme with lysine methyltransferase activity and various interaction partners. It is implicated in the pathophysiology of cancers but with an unclear mechanism. To discover tool compounds for clarifying its biochemistry and potential as a therapeutic target, a set of drug-like compounds was screened in a biosensor-based competition assay. Diperodon was identified as an allosteric ligand; its R and S enantiomers were isolated, and their affinities to SMYD3 were determined (K_D=42 and 84 μM, respectively). Co-crystallization revealed that both enantiomers bind to a previously unidentified allosteric site in the C-terminal protein binding domain, consistent with its weak inhibitory effect. No competition between diperodon and HSP90 (a known SMYD3 interaction partner) was observed although SMYD3–HSP90 binding was confirmed (K_D=13 μM). Diperodon clearly represents a novel starting point for the design of tool compounds interacting with a druggable allosteric site, suitable for the exploration of noncatalytic SMYD3 functions and therapeutics with new mechanisms of action.     

Strategies to Apply Water-Deficit Stress: Similarities and Disparities at the Whole Plant Metabolism Level in Medicago truncatula

Water-deficit stresses such as drought and salinity are the most important factors limiting crop productivity. Hence, understanding the plant responses to these stresses is key for the improvement of their tolerance and yield. In this study M. truncatula plants were subjected to 250 mM NaCl as well as reduced irrigation (No-W) and 250 g/L polyethylene glycol (PEG)-6000 to induce salinity and drought stress, respectively, provoking a drop to −1.7 MPa in leaf water potential. The whole plant physiology and metabolism was explored by characterizing the stress responses at root, phloem sap and leaf organ level. PEG treatment led to some typical responses of plants to drought stress, but in addition to PEG uptake, an important impairment of nutrient uptake and a different regulation of carbon metabolism could be observed compared to No-W plants. No-W plants showed an important redistribution of antioxidants and assimilates to the root tissue, with a distinctive increase in root proline degradation and alkaline invertase activity. On the contrary, salinity provoked an increase in leaf starch and isocitrate dehydrogenase activity, suggesting key roles in the plant response to this stress. Overall, results suggest higher protection of salt-stressed shoots and non-irrigated roots through different mechanisms, including the regulation of proline and carbon metabolism, while discarding PEG as safe mimicker of drought. This raises the need to understand the effect at the whole plant level of the different strategies employed to apply water-deficit stress.     

The Role of Circulating Biomarkers in Peripheral Arterial Disease

Peripheral arterial disease (PAD) of the lower extremities is a chronic illness predominantly of atherosclerotic aetiology, associated to traditional cardiovascular (CV) risk factors. It is one of the most prevalent CV conditions worldwide in subjects >65 years, estimated to increase greatly with the aging of the population, becoming a severe socioeconomic problem in the future. The narrowing and thrombotic occlusion of the lower limb arteries impairs the walking function as the disease progresses, increasing the risk of CV events (myocardial infarction and stroke), amputation and death. Despite its poor prognosis, PAD patients are scarcely identified until the disease is advanced, highlighting the need for reliable biomarkers for PAD patient stratification, that might also contribute to define more personalized medical treatments. In this review, we will discuss the usefulness of inflammatory molecules, matrix metalloproteinases (MMPs), and cardiac damage markers, as well as novel components of the liquid biopsy, extracellular vesicles (EVs), and non-coding RNAs for lower limb PAD identification, stratification, and outcome assessment. We will also explore the potential of machine learning methods to build prediction models to refine PAD assessment. In this line, the usefulness of multimarker approaches to evaluate this complex multifactorial disease will be also discussed.     

Influence of the co-firing on the leaching of trace pollutants from coal fly ash

The (co)-firing of low-cost alternative fuels is expected to increase in the forthcoming years in the EU because of the economic and environmental benefits provided by this technology. This study deals with the impact of the different coal/waste fuel ratio of the feed blend on the mineralogy, the chemical composition and especially on the leaching properties of fly ash. Different blends of coal, petroleum coke, sewage sludge, wood pellets, coal tailings and other minor biomass fuels were tested in PCC (pulverised coal combustion) and FBC (fluidized bed combustion) power plants. The co-firing of the studied blends did not drastically modify the mineralogy, bulk composition or the overall leaching of the fly ash obtained. This suggests that the co-firing process using the alternative fuels studied does not entail significant limitations in the re-use or management strategies of fly ash.     

Phase field simulations of ferroelectrics domain structures in PbZrxTi1−xO3 bilayers

Domain stability and structures in Pb(Zr_0.3Ti_0.7)O₃/Pb(Zr_0.7Ti_0.3)O₃ bilayer films under different substrate strains are studied using the phase field method. It is demonstrated that the domain structure of the bilayer film is very different from those of the corresponding single layer films grown on the same silicon substrate with an incoherent interface. Moreover, the predicted rhombohedral domains in the Pb(Zr_0.7Ti_0.3)O₃ layer of the bilayer film have smaller sizes than those in the single layer case. These results are compared with experimental observations and previous thermodynamic analyses. The polarization distributions of the ferroelectric–paraelectric bilayer are analyzed as a function of the thickness of the bilayer film, where there is a “ferroelectric proximity effect” due to dipole–dipole interactions. The phase diagrams for both the bilayer and single layer films as a function of temperature and effective in-plane substrate strain are constructed.     

Cellular Integrin α5β1 and Exosomal ADAM17 Mediate the Binding and Uptake of Exosomes Produced by Colorectal Carcinoma Cells

Approximately 25% of colorectal cancer (CRC) patients develop peritoneal metastasis, a condition associated with a bleak prognosis. The CRC peritoneal dissemination cascade involves the shedding of cancer cells from the primary tumor, their transport through the peritoneal cavity, their adhesion to the peritoneal mesothelial cells (PMCs) that line all peritoneal organs, and invasion of cancer cells through this mesothelial cell barrier and underlying stroma to establish new metastatic foci. Exosomes produced by cancer cells have been shown to influence many processes related to cancer progression and metastasis. In epithelial ovarian cancer these extracellular vesicles (EVs) have been shown to favor different steps of the peritoneal dissemination cascade by changing the functional phenotype of cancer cells and PMCs. Little is currently known, however, about the roles played by exosomes in the pathogenesis and peritoneal metastasis cascade of CRC and especially about the molecules that mediate their interaction and uptake by target PMCs and tumor cells. We isolated exosomes by size−exclusion chromatography from CRC cells and performed cell-adhesion assays to immobilized exosomes in the presence of blocking antibodies against surface proteins and measured the uptake of fluorescently-labelled exosomes. We report here that the interaction between integrin α5β1 on CRC cells (and PMCs) and its ligand ADAM17 on exosomes mediated the binding and uptake of CRC-derived exosomes. Furthermore, this process was negatively regulated by the expression of tetraspanin CD9 on exosomes.     

Transcriptomic Profiles of CD47 in Breast Tumors Predict Outcome and Are Associated with Immune Activation

Targeting the innate immune system has attracted attention with the development of anti- CD47 antibodies. Anti-CD47 antibodies block the inhibition of the phagocytic activity of macrophages caused by the up-regulation of CD47 on tumor cells. In this study, public genomic data was used to identify genes highly expressed in breast tumors with elevated CD47 expression and analyzed the association between the presence of tumor immune infiltrates and the expression of the selected genes. We found that 142 genes positively correlated with CD47, of which 83 predicted favorable and 32 detrimental relapse-free survival (RFS). From those associated with favorable RFS, we selected the genes with immunologic biological functions and defined a CD47-immune signature composed of PTPRC, HLA-E, TGFBR2, PTGER4, ETS1, and OPTN. In the basal-like and HER2+ breast cancer subtypes, the expression of the CD47-immune signature predicted favorable outcome, correlated with the presence of tumor immune infiltrates, and with gene expression signatures of T cell activation. Moreover, CD47 up-regulated genes associated with favorable survival correlated with pro-tumoral macrophages. In summary, we described a CD47-immune gene signature composed of 6 genes associated with favorable prognosis, T cell activation, and pro-tumoral macrophages in breast cancer tumors expressing high levels of CD47.     

Gauging of Cytochrome c Structural Fluctuation by Time-Resolved Proton Pulse

A brief proton pulse technique, based on photo-excitation of pyranine, was employed for measuring the protonation dynamics of cytochrome c in aqueous solutions. Time-resolved monitoring of the protonation state of the pyranine anion yielded detailed information from which the temporal state protonation of the surface carboxylates and histidine residues were deduced. The surface groups were found to be coupled by electrostatic interaction where the state of protonation of one affects the pK of the others. In the same sense, altering the charge distribution of a protein by a redox reaction affects the reactivity of the surface groups with protons in the bulk. The surface groups can exchange protons among themselves at a very high rate. The velocities of these reactions are functions of the connectivity between the proton binding sites. A single proton exchange reaction between the surface groups could be identified as the proton exchange between H26 and E44. The reaction is fast and affected by the redox state of the protein. It is proposed that the enhanced rate of this reaction is coupled with transient conformational changes that are not noticeable in time-averaging measurements such as X-ray diffraction or NMR.     

Evaluation of a screening method for classifying virgin and recycled paper and board samples

This paper deals with the study of volatile compounds released by recycled paper and board. The aim of the study was to demonstrate the feasibility of headspace procedure coupled to gas chromatography/mass spectrometry (GC/MS) applied to complex paper‐based samples together with a chemometric procedure as a powerful method for screening potential volatile contaminants released by the recycled and virgin paper samples. Using this procedure, the identification of virgin or recycled paper could be achieved based on the identification on specific markers of the recycled pulp. Fifteen different samples within virgin and recycled paper were studied. After equilibration, the vapour phase of the samples was analysed by automatic headspace coupled online to GC/MS. The analytical approach for volatile compounds, their identification and the selection of some compounds as markers for recycled pulp are shown and discussed. A discriminate analysis applied to the set of results obtained allows classification of the samples into four different groups according to the content of recycled pulp (0, 10–30 and > 80% of recycled pulp), the surface treatment of the paper (no surface treatment, clay coating and plastic coating), the grammage (from < 100 to > 300 g/m²) and the sample thickness (from < 300 to > 600 µm). The matrix effect on the volatilization of some compounds from the paper samples and the analytical behaviour are also discussed. Copyright © 2009 John Wiley & Sons, Ltd.     

Bootstrap prediction intervals in state–space models

Abstract.  Prediction intervals in state–space models can be obtained by assuming Gaussian innovations and using the prediction equations of the Kalman filter, with the true parameters substituted by consistent estimates. This approach has two limitations. First, it does not incorporate the uncertainty caused by parameter estimation. Second, the Gaussianity of future innovations assumption may be inaccurate. To overcome these drawbacks, Wall and Stoffer [ Journal of Time Series Analysis (2002) Vol. 23, pp. 733–751] propose a bootstrap procedure for evaluating conditional forecast errors that requires the backward representation of the model. Obtaining this representation increases the complexity of the procedure and limits its implementation to models for which it exists. In this article, we propose a bootstrap procedure for constructing prediction intervals directly for the observations, which does not need the backward representation of the model. Consequently, its application is much simpler, without losing the good behaviour of bootstrap prediction intervals. We study its finite-sample properties and compare them with those of the standard and the Wall and Stoffer procedures for the local level model. Finally, we illustrate the results by implementing the new procedure to obtain prediction intervals for future values of a real time series.