Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase

Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ΔΔG_b values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme.     

A semantic role labelling-based framework for learning ontologies from Spanish documents

Currently, most of the information available in the Web is adapted primarily for human consumption, but there is so much information that can no longer be processed by a person in a reasonable time, either in digital or physical formats. To solve this problem, the idea of the Semantic Web arose. The Semantic Web deals with adding machine-readable information to Web pages. Ontologies represent a very important element of this web, as they provide a valid and robust structure to represent knowledge based on concepts, relations, axioms, etc. The need for overcoming the bottleneck provoked by the manual construction of ontologies has generated several studies and research on obtaining semiautomatic methods to learn ontologies. In this sense, this paper proposes a new ontology learning methodology based on semantic role labeling from digital Spanish documents. The method makes it possible to represent multiple semantic relations specially taxonomic and partonomic ones in the standardized OWL 2.0. A set of experiments has been performed with the approach implemented in educational domain that show promising results.     

Control of attendance applied in higher education through mobile NFC technologies

This paper presents an improved attendance control system, required for continuous evaluation which has become compulsory following the Bologna Process. It provides a solution based on NFC technology and is based on a real project developed and pilot tested at the “Universidad Pontificia de Salamanca, Campus Madrid”.     

Capillary self-alignment of polygonal chips: a generalization for the shift-restoring force

Capillary-driven self-alignment using droplets is currently extensively investigated for self-assembly and microassembly technology. In this technique, surface tension forces associated to capillary pinning create restoring forces and torques that tend to bring the moving part into the alignment. So far, most studies have addressed the problem of square chip alignment on a dedicated patch of a wafer, aiming to achieve 3D microelectronics. In this study, we investigate the shift-restoring forces for more complex moving parts such as regular—convex and non-convex—polygons and regular polygons with regular polygonal cavities. A closed-form approximate expression is derived for each of these polygonal geometries; this expression agrees with the numerical results obtained with the Surface Evolver software. For small shifts, it is found that the restoring force does not depend on the shift direction or on the polygonal shape. In order to tackle the problem of microsystem packaging, an extension of the theory is done for polygonal shapes pierced with connection vias (channels), and a closed form of the shift-restoring force is derived for these geometries and again checked against the numerical model. In this case, the restoring force depends on the shift direction. Finally, a non-dimensional number, the shift number, is proposed that indicates the isotropic or anisotropic behavior of the chip according to the shift direction.     

DATA ANALYSIS PRIOR TO A CIRCULATION MODEL IN GRAN CANARIA

The use of numerical models in physical oceanography, with the aim of reproducing and predicting water movements, is a common practice, especially for coastal areas. Nevertheless, results will be accurate only if the assumptions are appropriate and include all significant characteristics of the domain under modeling. Two-dimensional models are often used for shallow-water areas, but the implicit assumptions of conservation of a characteristic vertical profile for the horizontal velocities all over the domain and negligible vertical circulation must be exhaustively checked. Here a case is presented in which two-dimensionality would have led to inaccurate results, as the analysis of the field data showed a three-layer behavior. This case concerns the eastern coast of Gran Canaria island (Canary Islands) and illustrates how mathematical models will describe the phenomena they try to represent correctly only if all assumptions are right.     

Applicability assessment of a real-time PCR assay for the specific detection of bovine,ovine and caprine material in feedstuffs

A TaqMan real-time polymerase chain reaction (PCR) method was developed for specific detection of bovine, ovine and caprine processed animal protein (PAP) in industrial feedstuffs. The method uses species-specific primers and probes targeting short mitochondrial D-loop sequences, and a positive amplification control based on 18S rRNA gene. The applicability of the real-time PCR protocol was assessed through analysis of 126 industrial feed samples that were manufactured to reproduce rendering processes of commercial feeds destined for farmed animals. The assay successfully classified samples as positive or negative according to the ruminant composition, enabling qualitative detection of banned material in feeds at levels as low as 0.1%. Although the method provides quantitative potential, results suggest that the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing treatments of the feeds, which affect the amount and quality of amplifiable DNA.     

Analysis of the gate current as a suitable indicator for FET degradation under nonlinear dynamic regime

Electron device degradation, although not directly accounted for, represents a key issue in microwave circuit design. This is especially true when the particular applications involved (e.g., satellite, military, consumer) do not allow or strongly discourage any kind of maintenance. As a matter of fact, in order to account for device degradation in circuit design, a suitable electron device model is needed which is able to predict the performance degradation as a function of the actual electrical regime involved in the device operation. Such a kind of model is not available in literature. In this paper, quantitative results are provided for device degradation indicators which correlate DC and RF stress experiments. These results can be considered an important step toward the definition of a nonlinear model accounting for device degradation.     

Optimized allylamine deposition for improved pluripotential cell culture

Deposition of allylamine (ALL) by plasma enhanced chemical vapor deposition has been optimized on silicon based models. Simultaneous energy recoil detection analysis and Rutherford backscattering spectra show that 100 W deposition is ideal in terms of polymerized film formation and H content while, lower or higher power induce reduced film retention or excessive cross linking, respectively. Surface composition of the ALL film was further probed by X-ray photoelectron spectroscopy revealing a monocomponent N 1s spectrum compatible with the presence of primary amines. Optimized ALL films were applied to polycaprolactone (PCL) surfaces after Ar plasma activation with implications in the chemistry and wettability of this biocompatible polymer. Human mesenchymal stem cells (hMSCs) were cultured on ALL coated PCL surface and controls. ALL functionalized PCL was found to be especially attractive for the formation of confluent monolayers of hMSCs after 72 h of culture.