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

Análisis económico, financiero y social de una entidad no lucrativa: el caso de estudio de Acufade

The growing interest of the citizenship in the specific impact of non-profit organisations on society means that they are increasingly interested in trying to quantify this effect. In this end-of-degree work, the specific case of the Acufade entity is studied, focusing especially on its economic-financial analysis. In order to cover this objective, a set of indicators adapted to the evaluation of non-profit entities has been used, highlighting the possibility of facing new projects with the economic remnant resulting from the activity itself.El creciente interés por parte de la ciudadanía sobre el impacto concreto de las entidades sin ánimo de lucro en la sociedad provoca que estas tengan cada vez más interés en tratar de cuantificar dicho efecto. En este trabajo de fin de grado se estudia el caso concreto de la entidad Acufade, poniendo el foco especialmente en el análisis económico-financiero de la misma. Para cubrir este objetivo se han utilizado un conjunto de indicadores adaptados a la evaluación de entidades sin fines de lucro, destacando la posibilidad de hacer frente a nuevos proyectos con el remanente económico resultante de la propia actividad

Structure-function mapping of a heptameric module in the nuclear pore complex.

The nuclear pore complex (NPC) is a multiprotein assembly that serves as the sole mediator of nucleocytoplasmic exchange in eukaryotic cells. In this paper, we use an integrative approach to determine the structure of an essential component of the yeast NPC, the ~600-kD heptameric Nup84 complex, to a precision of ~1.5 nm. The configuration of the subunit structures was determined by satisfaction of spatial restraints derived from a diverse set of negative-stain electron microscopy and protein domain-mapping data. Phenotypic data were mapped onto the complex, allowing us to identify regions that stabilize the NPC's interaction with the nuclear envelope membrane and connect the complex to the rest of the NPC. Our data allow us to suggest how the Nup84 complex is assembled into the NPC and propose a scenario for the evolution of the Nup84 complex through a series of gene duplication and loss events. This work demonstrates that integrative approaches based on low-resolution data of sufficient quality can generate functionally informative structures at intermediate resolution

NDT to identify biological damage in wood

Nondestructive techniques are widely used to assess existing timber structures. The models proposed for these methods are usually performed in the laboratory using small clear wood specimens. But in real situations many anomalies, defects and biological damage are found in wood. In these cases the existing models only indicate that the values are outside normality without providing any other information. To solve this problem, a study of non-destructive probing methods for wood was performed, testing the behaviour of four different techniques (penetration resistance, pullout resistance, drill resistance and chip drill extraction) on wood samples with different biological damage, simulating an in-situ test. The wood samples were obtained from existing Spanish timber structures with biotic damage caused by borer insects, termites, brown rot and white rot. The study concludes that all of the methods offer more or less detailed information about the degree of deterioration of wood, but that the first two methods (penetration and pullout resistance) cannot distinguish between pathologies. On the other hand, drill resistance and chip drill extraction make it possible to differentiate pathologies and even to identify species or damage location. Finally, the techniques used were compared to characterize their advantages and disadvantages

Functional relationships between wood structure and vulnerability to xylem cavitation in races of Eucalyptus globulus differing in wood density

Wood density can be considered as a measure of the internal wood structure, and it is usually used as a proxy measure of other mechanical and functional traits. Eucalyptus is one of the most important commercial forestry genera worldwide, but the relationship between wood density and vulnerability to cavitation in this genus has been little studied. The analysis is hampered by, among other things, its anatomical complexity, so it becomes necessary to address more complex techniques and analyses to elucidate the way in which the different anatomical elements are functionally integrated. In this study, vulnerability to cavitation in two races of Eucalyptus globulus Labill. with different wood density was evaluated through Path analysis, a multivariate method that allows evaluation of descriptive models of causal relationship between variables. A model relating anatomical variables with wood properties and functional parameters was proposed and tested. We found significant differences in wood basic density and vulnerability to cavitation between races. The main exogenous variables predicting vulnerability to cavitation were vessel hydraulic diameter and fibre wall fraction. Fibre wall fraction showed a direct impact on wood basic density and the slope of vulnerability curve, and an indirect and negative effect over the pressure imposing 50% of conductivity loss (P50) through them. Hydraulic diameter showed a direct negative effect on P50, but an indirect and positive influence over this variable through wood density on one hand, and through maximum hydraulic conductivity (ks max) and slope on the other. Our results highlight the complexity of the relationship between xylem efficiency and safety in species with solitary vessels such as Eucalyptus spp., with no evident compromise at the intraspecific level.Estación Experimental Agropecuaria BarilocheFil: Barotto, Antonio José. Universidad Nacional de La Plata. Facultad de Ciencias Agrarias y Forestales. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Monteoliva, Silvia Estela. Universidad Nacional de La Plata. Facultad de Ciencias Agrarias y Forestales. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gyenge, Javier. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce. Agencia de Extensión Rural Tandil. Consejo Nacional de Investigaciones Cientificas y Técnicas; ArgentinaFil: Martinez Meier, Alejandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Área de Recursos Forestales. Grupo de Ecología Forestal; ArgentinaFil: Fernandez, Maria Elena. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce. Agencia de Extensión Rural Tandil. Consejo Nacional de Investigaciones Cientificas y Técnicas; Argentin

Retinal and choroidal thickness in myopic young adults

The retinal and the choroidal thickness were measured at four locations along the horizontal direction (foveola, one nasal to the fovea and two temporal) in a group of 43 young adults (mean age: 27.1 ± 3.9 years), with ocular refraction ranging from emmetropia to high myopia (0 to −10D). Thickness values were obtained from OCT images centered at the foveal depression. The retinal thickness exhibited a correlation with refraction at all eccentricities but not at the fovea. When different subgroups of refraction were considered, the analysis of such correlations indicated that only the retinal thickness in the group of high myopia (refraction ≤ −6D) was statistically different from the other two groups (emmetropes: [−0.5, 0] D, and myopes: (−6, −0.5) D). No significant differences were found between emmetropic and myopic groups. In contrast to the retina, the choroidal thickness exhibited a significant correlation with refraction at the fovea, although such dependency only stood for high myopes (the choroid of myopes and emmetropes exhibited similar thickness). Correlation with refraction was also found at the nasal location, arising between emmetropic and high myopia groups. Other choroidal locations among groups did not exhibit relationship with the refraction. It is concluded that the differences in the choroid and retina thickness along the horizontal meridian as a function of refraction do not characterize the onset and progression of myopia at early stages, since they only manifest in the group of high myopia