Influence of the nonprotein amino acid mimosine in peptide conformational propensities from novel amber force field parameters

Mimosine is a nonprotein amino acid derived from plantsknown for its ability to bind to divalent and trivalent metal cations suchas Zn2+, Ni2+, Fe2+, orAl3+. This results in interesting antimicrobial andanticancer properties, which make mimosine a promising candidate fortherapeutic applications. One possibility is to incorporate mimosine intosynthetic short peptide drugs. However, how this amino acid affects thepeptide structure is not well understood, reducing our ability to designeffective therapeutic compounds. In this work, we used computersimulations to understand this question. Wefirst built parameters for themimosine residue to be used in combination with two classical forcefields of the Amber family. Then, we used atomistic molecular dynamicssimulations with the resulting parameter sets to evaluate the influence ofmimosine in the structural propensities for this amino acid. We comparedthe results of these simulations with homologous peptides, wheremimosine is replaced by either phenylalanine or tyrosine. We found that the strong dipole in mimosine induces a preference forconformations where the amino acid rings are stacked over more extended conformations. We validated our results using quantummechanical calculations, which provide a robust foundation for the outcome of our classical simulation

The challenge of a joint cartography of the Pyrenean landscapes: Hautes-Pyrénées and Aragon

Con la presente investigación se está trabajando por alcanzar uno de los retos pendientes del Pirineo: una cartografía conjunta de paisajes fronterizos que facilite el conocimiento, la coordinación, la gestión y la planificación de los aspectos relacionados con el paisaje a ambos lados de la frontera. La zona de estudio es el Pirineo central en su sector fronterizo de Aragón y las regiones francesas de Nouvelle-Aquitaine y Occitanie. En una primera fase se ha recopilado y revisado la información tanto digital como analógica relativa al paisaje, así como las bases cartográficas disponibles de toda la zona de estudio. A escala de grandes dominios de paisaje en Aragón se cuenta con cartografía de todo el territorio mientras que en Francia se cuenta únicamente con cartografía del Departamento de Ariège que no es fronterizo con Aragón, pero si es paisaje pirenaico. Ello ha permitido contrastar ambas cartografías y elaborar una leyenda común que facilite la interpretación conjunta de ambas cartografías. La aportación de esta investigación ha consistido en elaborar un mapa del pirineo franco-español fronterizo con Aragón sobre la base topográfica del Global Digital Elevation Model y un primer borrador del mapa de dominios de paisaje que abarca todo el territorio aragonés y de Hautes-Pyrénées. Cette recherche vise à atteindre un des enjeux majeurs des Pyrénées: une cartographie des paysages frontaliers qui fournirait l’accés aux connaissances, et faciliterait la coordination, la gestion et la planification du paysage des deux côtés de la frontière. La zone d’étude serait les Pyrénées centrales au niveau de la frontière entre l’Aragon et les régions françaises de Nouvelle-Aquitaine et de l’Occitanie. Dans la première phase, l’information numérique et analogique sur le paysage et les bases cartographiques dans toute la zone d’étude disponible ont été récoltés et examinés. En Aragon la cartographie à l’échelle des grands domaines de paysage est disponible pour l’ensemble du territoire, alors qu’en France la seule cartographie disponible est celle du Département d’Ariège, qui n’est pas frontalier avec l’Aragon mais elle est de paysage pyrénéen. Cela a permis de comparer les deux cartes et développer une légende commune qui facilite l’interprétation conjointe des deux cartes. Cette recherche contribue à développer une carte de la frontière franco-espagnole Pyrénées avec Aragon sur la base topographique Global Digital Elevation Model et d’élaborer un premier projet de la carte des domaines du paysage qui couvre le territoire aragonais et des Hautes-Pyrénées.The main goal of this research is to address one of the open challenges about the Pyrenees: a joint cartography of cross-border landscape that will give access to the knowledge and facilitate the coordination, management, and planning of the different aspects related to the landscape of both sides of the border. The area of study is the central Pyrenees where Aragon and the French region of Nouvelle-Aquitaine and Occitanie are frontier. In the first stage, digital and analogue information about landscape and the available cartographic basis of the whole area of study have been collected and revised. In Aragon, the cartography on the scale of large landscape domains is available for the whole territory, whereas in France the only available mapping is the one from the Department of Ariège, which is not frontier with Aragon but is Pyrenean landscape. This has allowed to contrast the two cartographies and to elaborate a common legend that facilitates the joint interpretation of both mappings. This research contributes to the production of a map of the French-Spanish Pyrenees (around Aragon and its frontier counterpart) using the topographic basis of the Global Digital Elevation Model, and to the elaboration of a preliminary map of the landscape domains covering the entire territory of Aragon and Hautes-Pyrénées

Compounding process optimization for recycled materials using machine learning algorithms

The sustainable manufacturing of goods is one of the factors to minimize natural resource depletion and CO2 emissions. In the last decade a big effort has been done to transition from linear economy to circular economy. This transition requires to implement re-manufacturing processes into the current industrial manufacturing framework, replacing the sourcing of raw materials by re-manufacturing technologies. However, this transition is very challenging since it requires the transformation of the companies and more specially their processes, from traditional to circular. To speed up this transformation, the use of tools provided by the 4th industrial revolution are crucial. In particular, the use of artificial intelligence techniques enables the optimization of the re-manufacturing processes and make those optimizations available to all the stakeholders. This paper presents an optimization system for re-manufacturing of recycled fiber through compounding processes with materials that come from composite waste or end of life of products. The proposed approach has been trained with the data collected from several experiments carried out with a compounding machine under different specifications, fiber reinforcement grades, and output material properties. The system will allow to set up a compounding machine for different types of reinforced plastics needless of setting point experiments. The algorithms have been tested with previously unseen scenarios and they have proved to be efficient for giving the optimal material characteristics.This work has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 873111 (DIGIPRIME)

Raytracing optical analysis of a solar funnel cooker

Funnel type solar cookers rely on a multifaceted reflector to concentrate solar radiation on a cooking pot that is placed inside a transparent enclosure to create a greenhouse effect. This work aims to analyze the optical performance of this type of solar cooker using raytracing techniques. The open source Soltrace software tool is used to create an optical model of a solar funnel cooker. Numerous raytracing simulations are conducted in order to complete a parametric analysis of the optical performance against a set of influence variables, such as the elevation angle, sun tracking errors, optical quality of the different elements involved ( reflectors, greenhouse, cooking pot), etc.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Computational Study of Overtopping Phenomenon over Cylindrical Structures Including Mitigation Structures

Wave overtopping occurring in offshore wind renewable energy structures such as tension leg platforms (TLPs) or semi-submersible platforms is a phenomenon that is worth studying and preventing in order to extend the remaining useful life of the corresponding facilities. The behaviour of this phenomenon has been extensively reported for linear coastal defences like seawalls. However, no referenced study has treated the case of cylindrical structures typical of these applications to a similar extent. The aim of the present study is to define an empirical expression that portrays the relative overtopping rate over a vertical cylinder including a variety of bull-nose type mitigation structures to reduce the overtopping rate in the same fashion as for the linear structures characteristic of shoreline defences. Hydrodynamic interaction was studied by means of an experimentally validated numerical model applied to a non-impulsive regular wave regime and the results were compared with the case of a plain cylinder to evaluate the expected improvement in the overtopping performance. Four different types of parapets were added to the crest of the base cylinder, with different parapet height and horizontal extension, to see the influence of the geometry on the mitigation efficiency. Computational results confirmed the effectivity of the proposed solution in the overtopping reduction, though the singularity of each parapet geometry did not lead to an outstanding difference between the analysed options. Consequently, the resulting overtopping decrease in all the proposed geometries could be modelled by a unique specific Weibull-type function of the relative freeboard, which governed the phenomenon, showing a net reduction in comparison with the cylinder without the geometric modifications. In addition, the relationship between the reduced relative overtopping rate and the mean flow thickness over the vertical cylinder crest was studied as an alternative methodology to assess the potential damage caused by overtopping in real structures without complex volumetric measurements. The collection of computational results was fitted to a useful function, allowing for the definition of the overtopping discharge once the mean flow thickness was known.This work was carried out within the framework of the ITSAS-REM Research Group (IT-1514-22) funded by the Basque Government

Atualização da informação geológica e estratigráfica das jazidas de dinossáurios de La Rioja. Paleodiversidade do Cretácico Inferior do Grupo Enciso em Peña Cárcena (Igea, Espanha)

ABSTRACT: The discovery of new vertebrate fossil sites with skeletal remains in the Enciso Group of Igea (La Rioja) is showing the relevance of the area to study the palaeobiodiversity of Early Cretaceous vertebrate faunas from the Iberian Peninsula. At Peña Cárcena hill two sedimentary environments have been inferred: a mixed siliciclastic-carbonate lacustrine environment that is dominant at the outcrops, overlaid by a splay delta in an avulsion-belt. The vertebrate remains are especially abundant in the mixed siliciclastic-carbonate lacustrine deposits with two partially articulated skeletons (a theropod and a large-sized dinosaur), teeth and a fragment of a left maxilla of baryonychines, a pterosaur tooth that differs from those of Prejanopterus, a Goniopholis tooth, chelonian shell fragments that might belong to Camerochelys, a fairly complete lepisosteiform, teeth and dorsal fin spines of hybodontiforms. At the delta deposits, vertebrate fossils are rather scarce, with a single lepisosteiform skeleton and indeterminate bone fragments.RESUMO: A descoberta de novas jazidas com restos osteológicos de vertebrados no Grupo Enciso em Igea (La Rioja) comprova a importância da região para o estudo da paleobiodiversidade das faunas de vertebrados do Cretácico Inferior da Península Ibérica. Na colina de Peña-Cárcena, tem-se inferido dois ambientes sedimentares: o predominante nos afloramentos corresponde a um ambiente lacustre, siliciclástico-carbonatado misto, que se encontra sobreposto por depósitos de transbordo deltaico em cinturão abandonado. Restos de vertebrados são abundantes nos depósitos lacustres, incluindo dois esqueletos parciais articulados (de um terópode e de outro dinossáurio de grande porte), dentes e um fragmento de maxila esquerda de barionicinos, um dente de pterossáurio distinto de Prejanopterus, um dente de Goniopholis, fragmentos da carapaça de quelónios que poderão pertencer a Camerochelys, um lepisosteiforme praticamente completo, dentes e espinhos de barbatanas de hybodontiformes. Fósseis de vertebrados são escassos nos depósitos deltaicos, com apenas um esqueleto de lepisosteiforme e fragmentos indeterminados.info:eu-repo/semantics/publishedVersio

Aluminum's preferential binding site in proteins: sidechain of amino acids versus backbone interactions

The interaction of aluminum ion Al(III) with polypeptides is a subject of paramount importance, since it is a central feature to understand its deleterious effects in biological systems. Various drastic effects have been attributed to aluminum in its interaction with polypeptides and proteins. These interactions are thought to be established mainly through the binding of aluminum to phosphorylated and non-phosphorylated amino acid sidechains. However, a new structural paradigm has recently been proposed, in which aluminum interacts directly with the backbone of the proteins, provoking drastic changes in their secondary structure and leading ultimately to their denaturation. In the present paper, we use computational methods to discuss the possibility of aluminum to interact with the backbone of peptides and compare it with the known ability of aluminum to interact with amino acid sidechains. To do so, we compare the thermodynamics of formation of prototype aluminum-backbone structures with prototype aluminum-sidechain structures, and compare these results with previous data generated in our group in which aluminum interacts with various types of polypeptides and known aluminum biochelators. Our results clearly points to a preference of aluminum towards amino acid sidechains, rather than towards the peptide backbone. Thus, structures in which aluminum is interacting with the carbonyl group are only slightly exothermic, and they become even less favorable if the interaction implies additionally the peptide nitrogen. However, structures in which aluminum is interacting with negatively-charged sidechains like aspartic acid, or phosphorylated serines are highly favored thermodynamically.Technical and human support was provided by SGI/IZO (SGIker) of UPV/EHU and European funding (ERDF and ESF). Financial support comes from UPV/EHU (PES14/35), Eusko Jaurlaritza (IT588-13) and the Spanish Ministerio de Ciencia e Innovación (MINECO/FEDER) (CTQ2015-67608-P). GdT thanks the European Union for a Ph.D. grant inside the ITN-TCCM-642294 program