Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal Frustration" when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14249-14255). Similarly, repeats and structural mosaics may be fundamentally related to landscapes with multiple embedded funnels. Here we present analytical tools to detect and compare structural repetitions in protein molecules. By an exhaustive analysis of the distribution of structural repeats using a robust metric we define those portions of a protein molecule that best describe the overall structure as a tessellation of basic units. The patterns produced by such tessellations provide intuitive representations of the repeating regions and their association towards higher order arrangements. We find that some protein architectures can be described as nearly periodic, while in others clear separations between repetitions exist. Since the method is independent of amino acid sequence information we can identify structural units that can be encoded by a variety of distinct amino acid sequences

Thermodynamics of Cooperative DNA Recognition at a Replication Origin and Transcription Regulatory Site

Binding cooperativity guides the formation of protein-nucleic acid complexes, in particular those that are highly regulated such as replication origins and transcription sites. Using the DNA binding domain of the origin binding and transcriptional regulator protein E2 from human papillomavirus type 16 as model, and through isothermal titration calorimetry analysis, we determined a positive, entropy-driven cooperativity upon binding of the protein to its cognate tandem double E2 site. This cooperativity is associated with a change in DNA structure, where the overall B conformation is maintained. Two homologous E2 domains, those of HPV18 and HPV11, showed that the enthalpic-entropic components of the reaction and DNA deformation can diverge. Because the DNA binding helix is almost identical in the three domains, the differences must lie dispersed throughout this unique dimeric β-barrel fold. This is in surprising agreement with previous results for this domain, which revealed a strong coupling between global dynamics and DNA recognition.Fil: Dellarole, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. Fundación Instituto Leloir; ArgentinaFil: Sánchez Miguel, Ignacio Enrique. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. Fundación Instituto Leloir; ArgentinaFil: de Prat Gay, Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina. Fundación Instituto Leloir; Argentin

Molecular Modeling of Adsorption of 5-Aminosalicylic Acid in the Halloysite Nanotube

Halloysite nanotubes are becoming interesting materials for drug delivery. The knowledge of surface interactions is important for optimizing this application. The aim of this work is to perform a computational study of the interaction between 5-aminosalicylic acid (5-ASA) drug and halloysite nanotubes for the development of modified drug delivery systems. The optimization of this nanotube and the adsorption of different conformers of the 5-ASA drug on the internal surface of halloysite in the presence and absence of water were performed using quantum mechanical calculations by using Density Functional Theory (DFT) and methods based on atomistic force fields for molecular modeling, respectively.This work is funded by the Andalusian Government projects (RNM1897) and the MINECO project FIS2016-77692-C2-2P. It also supported by the Egyptian Cultural Affairs and Missions Sector (Plan 2013-2014), Ministry of Higher Education

Detector set up for the measurements of the neutron-induced fission cross section of 235U relative to n-p scattering up to 150 MeV at CERN-n_TOF

A new measurement of the U-235(n,f) fission cross section was carried out at n_TOF. The experiment covered the neutron energy range from 10 MeV up to 500 MeV, and it used the H-1(n,n) cross section as normalization for the neutron fluence measurement. In this contribution, the measurements and the characterization of the detectors covering the incident energy range up to 150 MeV are discussed

Conventional Space-Vector Modulation Techniques versus the Single-Phase Modulator for Multilevel Converters

Space-vector modulation is a well-suited technique to be applied to multilevel converters and is an important research focus in the last 25 years. Recently, a single-phase multilevel modulator has been introduced showing its conceptual simplicity and its very low computational cost. In this paper, some of the most conventional multilevel space-vector modulation techniques have been chosen to compare their results with those obtained with single-phase multilevel modulators. The obtained results demonstrate that the single-phase multilevel modulators applied to each phase are equivalent with the chosen wellknown multilevel space-vector modulation techniques. In this way, single-phase multilevel modulators can be applied to a converter with any number of levels and phases avoiding the use of conceptually and mathematically complex space-vector modulation strategies. Analytical calculations and experimental results are shown validating the proposed concepts

Percepción de los riesgos asociados a la pérdida auditiva inducida por ruido. Estado del arte y diseño de herramientas interactivas para formación y concienciación

La exposición al ruido en el puesto de trabajo y la pérdida auditiva inducida por ruido se encuentran estrechamente relacionadas con las actitudes que tienen de los trabajadores sobre el uso de los dispositivos de protección auditiva. En estudios previos se ha demostrado que los trabajadores son reacios a su utilización por diferentes motivos: desconocimiento de los efectos que produce el ruido sobre la salud auditiva, dificultades para utilizarlos de forma correcta, incomodidad, etc. Con el objetivo de mejorar las actitudes de los trabajadores ante el uso de dispositivos de protección auditiva se llevó a cabo un estudio bibliográfico sobre los factores que influyen en la conducta de los trabajadores ante el uso de protectores auditivos, así como su conocimiento sobre los riesgos asociados. Una vez analizados los antecedentes y las actuales necesidades, se desarrollaron herramientas interactivas de fácil utilización para mejorar la concienciación de los trabajadores sobre este aspecto. Se presenta la revisión bibliográfica sobre el uso de protectores auditivos, un análisis de los diferentes enfoques comúnmente utilizados para formación y concienciación de trabajadores sobre los riesgos derivados de la pérdida auditiva inducida por ruido y finalmente las herramientas desarrolladas como propuesta para mejorar la percepción de dicho riesgo entre los trabajadores

Improving the monitoring of corn phenology in large agricultural areas using remote sensing data series

Aim of study: Mexico's large irrigation areas demand non-structural actions to improve the irrigation service, such as monitoring crop phenology; however, its application has been limited by the large volumes of field information generated, diversity of crop management and climatic variability. The objective of this study was to generate and validate a methodology to monitor corn (Zea mays L.) phenology from the historical relationship of the vegetation indexes (VIs), EVI and NDVI, with the phenological development (PD) of corn grown in large irrigation zones.Area of study: Irrigation District (ID) 075 “Valle del Fuerte”, northern Sinaloa, Mexico.Material and methods: We used a database of 20 years of climate, field crop growth and crop phenology data, and Landsat satellite images. A methodology was proposed on a large scale supported with GIS and remote sensing data series.Main results: The methodology was validated in 19 plots with an acceptable correlation between observed PD and estimated PD for the two VIs, with slightly better values for EVI than for NDVI. NDVI and EVI models agreed with experimental PD observations in 92.1% of the farms used to validate the methodology, in 2.5% only the NDVI model coincided with the real, in 3.1% only the EVI model coincided, and in 2.3% both models disagreed with observation, generated a stage out of phase with respect to the real phenological stage.Research highlights: is possible to generalize the methodology applied to large irrigation zones with remote sensing data and GIS

Integral field spectroscopy of the central regions of 3C 120: Evidence of a past merging event

Optical integral field spectroscopy (IFS), combined with Hubble Space Telescope (HST ) WFPC imaging, was used to characterize the central regions of the Seyfert 1 radio galaxy 3C 120. We carried out the analysis of the data, deriving intensity maps of different emission lines and the continua at different wavelengths from the observed spectra. Applying a two-dimensional modeling to the HST images, we decoupled the nucleus and the host galaxy and analyzed the host morphology. The host is a highly distorted bulge-dominated galaxy, rich in substructures. We developed a new technique to model the IFS data extending the two-dimensional modeling (hereafter threedimensional modeling). Using this technique, we separated the Seyfert nucleus and the host galaxy spectra and derived a residual data cube with spectral and spatial information of the different structures in 3C 120. Three continuum-dominated structures (named A, B, and C) and three other extended emission-line regions (EELRs, named E1, E2, and E3) are found in 3C 120, which does not follow the general behavior of a bulge-dominated galaxy. We also found shells in the central kiloparsec that may be remnants of a past merging event in this galaxy. The origin of E1 is most probably due to the interaction of the radio jet of 3C 120 with the intergalactic medium (Axon et al. 1989; Sa´nchez et al. 2004a). Structures A, B, and the shell at the southeast of the nucleus seem to correspond to a larger morphological clumpy structure that may be a tidal tail, a consequence of the past merging event. We found a bright EELR (E2) in the innermost part of this tidal tail, nearby the nucleus, which shows a high ionization level. The kinematics of the E2 region and its connection to the tidal tail suggest that the tail has channeled gas from the outer regions to the cente

Overview of the dissemination of n_TOF experimental data and resonance parameters

The n_TOF neutron time-of-flight facility at CERN is used for nuclear data measurements. The n_TOF Collaboration works closely with the Nuclear Reaction Data Centres (NRDC) network to disseminate the experimental data through the international EXFOR library. In addition, the Collaboration helps integrate the results in the evaluated library projects. The present contribution describes the dissemination status of n_TOF results, their impact on evaluated libraries and ongoing efforts to provide n_TOF resonance parameters in ENDF-6 format for further use by evaluation projects