RNAiFold2T: Constraint Programming design of thermo-IRES switches

Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation. Results: Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allow- ing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site (thermo-IRES) elements, whose normalized cap-independent transla- tion efficiency is approximately 50% greater at 42?C than 30?C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements. Availability: RNAiFold2T is publicly available as as part of the new re- lease RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http: //bioinformatics.bc.edu/clotelab/RNAiFold, which latter has a web server as well. The software is written in C++ and uses OR-Tools CP search engine.Comment: 24 pages, 5 figures, Intelligent Systems for Molecular Biology (ISMB 2016), to appear in journal Bioinformatics 201

Size matters: Physiological sensitivity of the scallop Argopecten purpuratus to seasonal cooling and deoxygenation upwelling-driven events

Environment imposes physiological constraints which are life-stage specific as growth-maintenance and/or growth-reproduction energetic requirements are size and volume-dependent. The scallop Argopecten purpuratus, one of the most important bivalve species subjected to fishery and aquaculture along the Humboldt Current System, inhabits spaces affected by continuous changes in temperature, pH, oxygen, and food availability driven by remote and local oceanographic processes. Specifically, in Chile, this species is mainly cultured in central-north Chile where is permanently affected by upwelling events of dissimilar intensity and duration which generate local conditions of acidification, deoxygenation, and cooling with different magnitudes. However, to date, it remains unknown how this economic valuable resource is physiologically affected throughout its life cycle by the continuous environmental changes driven by upwelling events of different intensities and duration along the year. Here, for the first time, A. purpuratus life-stage physiological sensitivity was assessed at a seasonal scale through a year-field experiment where growth, calcification, and survivorship were evaluated. Our study shows how seasonal differences in the upwelling phenology (here measured as changes in temperature, dissolved oxygen, pH, and primary productivity, but also as the number, duration, and intensity of cooling and de-oxygenation events) notably impacted the A. purpuratus physiological performance from juvenile to adult life-stages. This was especially noticeable during the spring season which showed the most intense cooling and deoxygenation events driven by stronger favorable-upwelling winds and the lowest growth and gross calcification rates (the highest decalcification rates) where adult stages showed the lowest performance. On the other hand, A. purpuratus survivorship was not significantly affected by upwelling intensity which would be providing evidence of the high physiological flexibility and well-locally adapted is this species to fluctuating and occasional stressful environmental conditions. Our results are significantly relevant in the climate change context as some upwelling systems are at risk to change shortly (i.e., an upwelling intensification in frequency and intensity) as a consequence of changes in the atmospheric pressures that modulate favourable-upwelling winds. These changes may certainly increase the climate related-risks of the entire socio-ecological systems related to the fishery and aquaculture of A. purpuratus along the Humboldt Current System

Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation

The internal ribosome entry site (IRES) element located at the 5’untranslated genomic region of various RNA viruses mediates cap-independent initiation of translation. Picornavirus IRES activity is highly dependent on both its structural organization and its interaction with host factors. Small molecules able to interfere with RNA function are valuable candidates for antiviral agents. Here we show that a small molecule based on benzimidazole (IRAB) inhibited foot-andmouth disease virus (FMDV) IRES-dependent protein synthesis in cells transfected with infectious RNA leading to a decrease of the virus titer, which was higher than that induced by a structurally related benzimidazole derivative. Interestingly, IRAB preferentially inhibited IRES-dependent translation in cell free systems in a dose-dependent manner. RNA structural analysis by SHAPE demonstrated an increased local flexibility of the IRES structure upon incubation with IRAB, which affected 3 stem-loops (SL) of domain 3. Fluorescence binding assays conducted with individual aminopurinelabeled oligoribonucleotides indicated that the SL3A binds IRAB (EC 18 μM). Taken together, the results derived from SHAPE reactivity and fluorescence binding assays suggested that the target site of IRAB within the FMDV IRES might be a folded RNA structure that involves the entire apical region of domain 3. Our data suggest that the conformational changes induced by this compound on a specific region of the IRES structure which is essential for its activity is, at least in part, responsible for the reduced IRES efficiency observed in cell free lysates and, particularly, in RNA-transfected cells.Ministerio de Economia y Competitividad (MINECO), and by an Institutional grant from Fundación Ramón ArecesPeer Reviewe

Influence of the BaTiO3 addition to K0.5Na0.5NbO3 lead-free ceramics on the vacancy-like defect structure and dielectric properties

A study on the induced changes in the vacancy-like defect structure and the dielectric properties of K0.5Na0.5NbO3 ceramics by the addition of different amounts, between 0% and 7%, of BaTiO3 is presented. The samples were prepared by a mechanochemically activated solid-state reaction method. The structural evolution due to the orthorhombic to the tetragonal phase transition of the KNN doped samples was followed using X-ray diffraction and Raman spectroscopy. The use of positron annihilation lifetime spectroscopy allowed to identify the defect structure at sub-nanometric scale and the nature of the vacancy-like defects generated by the phase transition. The obtained results are discussed considering the lattice symmetry change and the defects structure formed due to the replacement of alkaline and niobium ions by barium and titanium ones. Additionally, changes in the dielectric properties are discussed in terms of the structural modifications of the different KNN-based ceramics involving different kinds of vacancy-like defects.Fil: Prado Espinosa, Fabiola Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Ciencia y Tecnología de Materiales. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones en Ciencia y Tecnología de Materiales; ArgentinaFil: Ramajo, Leandro Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Ciencia y Tecnología de Materiales. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones en Ciencia y Tecnología de Materiales; ArgentinaFil: Rubio Marcos, Fernando. Instituto de Cerámica y Vidrio de Madrid; EspañaFil: Macchi, Carlos Jorge. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Instituto de Física de Materiales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Somoza, A.. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Instituto de Física de Materiales; ArgentinaFil: Castro, Miriam Susana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Ciencia y Tecnología de Materiales. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones en Ciencia y Tecnología de Materiales; Argentin

Recursos para la inclusión educativa del alumnado con enfermedades minoritarias

En este trabajo se presenta un estudio cuyo objetivo fue caracterizar los recursos formativos, humanos, físicos y comunitarios que configuran las buenas prácticas educativas para la inclusión escolar del alumnado que padece alguna enfermedad poco frecuente, así como detectar las necesidades sentidas por profesionales y familias en cuanto a estos recursos. Para ello, se desarrolló un estudio transversal y cualitativo en el que participaron profesionales educativos y sanitarios, familias y estudiantes con este tipo de patologías. Los resultados sugieren que los recursos considerados clave son los formativos, humanos y comunitarios y que su orientación debería focalizarse en dotar a los docentes de estrategias de intervención más que en informar sobre estas enfermedades. Además, los recursos humanos y físicos existentes se valoran positivamente, aunque se señala la necesidad de ampliarlos, especialmente mediante la figura de auxiliares técnicos educativos. Los recursos y materiales físicos se consideran suficientes y se destaca el papel de los recursos tradicionales como complemento de las TIC. Otro elemento central que destacaron los participantes fue la coordinación y la interdisciplinariedad en el abordaje de las necesidades de este alumnado. Finalmente se discuten las implicaciones de estos resultados para el desarrollo de prácticas inclusivas, se presentan las principales limitaciones del estudio, así como se esbozan líneas futuras de intervención y de investigación para seguir avanzando en la inclusión educativa y social de estos estudiantes

Resources for the educational inclusion of students with rare diseases

En este trabajo se presenta un estudio cuyo objetivo fue caracterizar los recursos formativos, humanos, físicos y comunitarios que configuran las buenas prácticas educativas para la inclusión escolar del alumnado que padece alguna enfermedad poco frecuente, así como detectar las necesidades sentidas por profesionales y familias en cuanto a estos recursos. Para ello, se desarrolló un estudio transversal y cualitativo en el que participaron profesionales educativos y sanitarios, familias y estudiantes con este tipo de patologías. Los resultados sugieren que los recursos considerados clave son los formativos, humanos y comunitarios y que su orientación debería focalizarse en dotar a los docentes de estrategias de intervención más que en informar sobre estas enfermedades. Además, los recursos humanos y físicos existentes se valoran positivamente, aunque se señala la necesidad de ampliarlos, especialmente mediante la figura de auxiliares técnicos educativos. Los re-cursos y materiales físicos se consideran suficientes y se destaca el papel de los recursos tradicionales como complemento de las Tecnologías de la información y las comunicaciones (TIC). Otro elemento central que destacaron los participantes fue la coordinación y la interdisciplinariedad en el abordaje de las necesidades de este alumnado. Finalmente se discuten las implicaciones de estos resultados para el desarrollo de prácticas inclusivas, se presentan las principales limitaciones del estudio, así como se esbozan líneas futuras de intervención y de investigación para seguir avanzando en la inclusión educativa y social de estos estudiantes.This paper presents a study whose objective was to characterize the formative, human, physical and community resources that make up good educational practices for the educational inclusion of students who suffer from a rare disease, as well as to detect the needs experienced by professionals and families regarding these resources. To this end, a crosssectional and qualitative study was developed in which educational and health professionals, families and students with this type of pathology participated. The results suggest that educational, human, and community resources are considered key, and their orientation should focus on providing teachers with intervention strategies rather than on informing about these diseases. In addition, the existing human and physical resources are valued positively, although the need to expand them is pointed out, especially through the figure of educational technical assistants. Physical resources and materials are considered sufficient, highlighting the role of traditional resources as a complement to ICT. Another central element mentioned by the participants is the coordination and interdisciplinarity involved in addressing the needs of these students. Finally, the implications of these results for the development of inclusive practices are discussed. Besides, the main limitations of the study are presented, as well as futures lines of intervention and research which support the educational and social inclusion of these students.Cet article présente une étude dont l’objectif était de caractériser les ressources formati-ves, humaines, physiques et communautaires qui composent les bonnes pratiques éduca-tives pour l’inclusion scolaire des élèves atteints d’une maladie rare, ainsi que de détecter les besoins ressentis par les professionnels et les familles à propos de ces ressources. Pour cela, une étude transversale et qualitative a été élaborée et à laquelle ont participé des professionnels de l’éducation et de la santé, des familles et des étudiants atteints de ce type de pathologie. Les résultats suggèrent que les ressources considérées comme clés sont les ressources formatives, humaines et communautaires, et que leur orientation de-vrait viser à fournir aux enseignants des stratégies d’intervention plutôt qu’à informer sur ces maladies. De plus, les ressources humaines et physiques existantes sont valorisées positivement, bien que la nécessité de les développer soit soulignée, notamment à travers la figure des assistants techniques éducatifs. Les ressources physiques et matérielles sont considérées comme suffisantes et le rôle des ressources traditionnelles en complément des TIC est mis en évidence. Un autre élément central souligné par les participants était la coordination et l’interdisciplinarité pour répondre aux besoins de ces étudiants. En-fin, les implications de ces résultats pour le développement de pratiques inclusives sont discutées, les principales limites de l’étude sont présentées, ainsi que les futures lignes d’intervention et de recherche sont esquissées pour continuer à avancer dans l’inclusion scolaire et sociale de ces étudiants

Role of TGF-β1 and MAP Kinases in the Antiproliferative Effect of Aspirin in Human Vascular Smooth Muscle Cells

We aimed to test the antiproliferative effect of acetylsalicylic acid (ASA) on vascular smooth muscle cells (VSMC) from bypass surgery patients and the role of transforming growth factor beta 1 (TGF-beta1).VSMC were isolated from remaining internal mammary artery from patients who underwent bypass surgery. Cell proliferation and DNA fragmentation were assessed by ELISA. Protein expression was assessed by Western blot. ASA inhibited BrdU incorporation at 2 mM. Anti-TGF-beta1 was able to reverse this effect. ASA (2 mM) induced TGF-beta1 secretion; however it was unable to induce Smad activation. ASA increased p38(MAPK) phosphorylation in a TGF-beta1-independent manner. Anti-CD105 (endoglin) was unable to reverse the antiproliferative effect of ASA. Pre-surgical serum levels of TGF-beta1 in patients who took at antiplatelet doses ASA were assessed by ELISA and remained unchanged.In vitro antiproliferative effects of aspirin (at antiinflammatory concentration) on human VSMC obtained from bypass patients are mediated by TGF-beta1 and p38(MAPK). Pre-surgical serum levels of TGF- beta1 from bypass patients who took aspirin at antiplatelet doses did not change

Age-dependent defective TGF-beta1 signaling in patients undergoing coronary artery bypass grafting

Background: Transforming growth factor beta (TGF-beta 1) is a pleiotropic cytokine, which is deregulated in atherosclerosis; however the role of age in this process is unknown. We aimed to assess whether TGF-beta 1 signaling is affected by age. Methods: Vascular smooth muscle cells (VSMC) were obtained from patients undergoing abdominal surgery. Levels of TGF-beta 1 were measured by ELISA in sera from 169 patients undergoing coronary artery bypass grafting (CABG). The p27 expression was determined by Western blot from internal mammary arteries (IMA) obtained from CABG patients (n = 13). In VSMC from these patients undergoing abdominal surgery, secretion of TGF-beta 1 was determined by ELISA of cell-conditioned media. Results: In VSMC from aged patients we observed a lower TGF-beta 1 secretion, measured as TGF-beta 1 concentration in cell conditioned medium (p < 0.001). This effect was correlated to an age-dependent decrease of p27 expression in IMA from aged CABG patients. In a similar manner, there was an age-dependent decrease of serum TGF-beta 1 levels in CABG patients (p = 0.0195). Conclusions: VSMC from aged patients showed a higher degree of cellular senescence and it was associated to a lower TGF-beta 1 secretion and signaling.S

Decreased pre-surgical CD34+/CD144+ cell number in patients undergoing coronary artery bypass grafting compared to coronary artery disease-free valvular patients

<p>Abstract</p> <p>Background</p> <p>Cardiovascular disease has been linked to endothelial progenitor cell (EPC) depletion and functional impairment in atherosclerosis and aortic stenosis. EPCs may play a pivotal role in vascular grafting. However, the EPC depletion in coronary artery bypass grafting (CABG) patients has not been compared to coronary artery disease-free valvular replacement patients with aortic stenosis.</p> <p>Methods</p> <p>We aimed to assess the basal number of CD34⁺/KDR⁺and CD34⁺/CD144⁺cells in CABG patients, compared to aortic stenosis valvular replacement patients. 100 patients (51 CABG and 49 valvular surgery ones) were included in the present study. All CABG or valvular patients had angiographic demonstration of the presence or the absence of coronary artery disease, respectively. Numbers of CD34⁺/KDR⁺and CD34⁺/CD144⁺were assessed by flow cytometry of pre-surgical blood samples.</p> <p>Results</p> <p>We found a lower number of CD34⁺/CD144⁺cells in CABG patients compared to valvular patients (0.21 ± 0.03% vs. 0.47 ± 0.08%), and this difference remained statistically significant after the <it>P </it>was adjusted for multiple comparisons (<it>P </it>= 0.01428). Both groups had more EPCs than healthy controls.</p> <p>Conclusions</p> <p>Pre-surgical CD34⁺/CD144⁺numbers are decreased in CABG patients, compared to valvular patients with absence of coronary disease.</p

Cartografía indirecta de residuos industriales del barrio de La Almozara (Zaragoza) por medio de la susceptibilidad magnética

En el subsuelo del barrio de La Almozara (Zaragoza) persisten residuos de la tostación de sulfuros de una antigua planta industrial que finalizó su actividad en la década de 1970. Los residuos generados no fueron retirados y es habitual su aparición en obras y en zonas de parque del barrio. Su aparición en superficie produce la dispersión eólica y la exposición aérea a dichos residuos con altos contenidos en As, Sb, Be, Cd, Co, Cr. Mo, Ni, Ag, Pb, Se, Hg y Zn. La susceptibilidad magnética de estos residuos presenta valores entre los 5000 y 50000 x 10-6 (SI) que contrasta con los valores de fondo natural local que presenta valores entre 10 y 100 x 10-6. Los valores de susceptibilidad magnética exhiben una gradación prácticamente continua entre los suelos naturales tipo y los residuos que define la presencia de procesos de mezcla entre los materiales naturales, antrópicos y los residuos existentes de las zonas de parque del barrio. Se define así la cartografía de susceptibilidad magnética como herramienta para la cartografía de la distribución de los residuos y de los materiales de mezcla con los materiales naturales de la zona de estudio