Dissecting the role of low-complexity regions in the evolution of vertebrate proteins

Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few aminoacids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution. We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance. We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.

El mapa y el territorio: una aproximación histórico-bibliográfica a la emergencia de las Humanidades Digitales en España

Este artículo consta de tres partes: en la primera me ocupo de algunas analogías y paralelismos históricos, tales como el libro y la imprenta, que han moldeado la reflexión en torno a la tecnología digital, al hipertexto y a la interactividad. En la segunda parte mi objetivo es trazar una panorámica ordenada cronológicamente sobre los principales proyectos de digitalización (bibliotecas, archivos, corpus y ediciones de obras literarias medievales y áureas) aparecidos en el ámbito académico hispánico desde 1986 hasta 2005; por supuesto, el recuento es incompleto pero aspira a ser representativo. Por último, la tercera parte se centra en cómo ha evolucionado la relación entre estudios literarios y la tecnología digital desde 2006 hasta la celebración del primer congreso oficial sobre Humanidades Digitales en 2013.

En busca de la lengua perfecta: pasado, presente y futuro

Análisis de las lenguas artificiales más importantes que se han creado a lo largo de la historia con el objetivo de encontrar una lengua perfecta común para todos y presentación del Rodinio, una nueva lengua artificial basada en una serie de criterios en busca de esa perfección.

Generation and nonlinear evolution of shore-oblique/transverse sand bars

The coupling between topography, waves and currents in the surf zone may selforganize to produce the formation of shore-transverse or shore-oblique sand bars on an otherwise alongshore uniform beach. In the absence of shore-parallel bars, this has been shown by previous studies of linear stability analysis, but is now extended to the finite-amplitude regime. To this end, a nonlinear model coupling wave transformation and breaking, a shallow-water equations solver, sediment transport and bed updating is developed. The sediment flux consists of a stirring factor multiplied by the depthaveraged current plus a downslope correction. It is found that the cross-shore profile of the ratio of stirring factor to water depth together with the wave incidence angle primarily determine the shape and the type of bars, either transverse or oblique to the shore. In the latter case, they can open an acute angle against the current (upcurrent oriented) or with the current (down-current oriented). At the initial stages of development, both the intensity of the instability which is responsible for the formation of the bars and the damping due to downslope transport grow at a similar rate with bar amplitude, the former being somewhat stronger. As bars keep on growing, their finite-amplitude shape either enhances downslope transport or weakens the instability mechanism so that an equilibrium between both opposing tendencies occurs, leading to a final saturated amplitude. The overall shape of the saturated bars in plan view is similar to that of the small-amplitude ones. However, the final spacings may be up to a factor of 2 larger and final celerities can also be about a factor of 2 smaller or larger. In the case of alongshore migrating bars, the asymmetry of the longshore sections, the lee being steeper than the stoss, is well reproduced. Complex dynamics with merging and splitting of individual bars sometimes occur. Finally, in the case of shore-normal incidence the rip currents in the troughs between the bars are jet-like while the onshore return flow is wider and weaker as is observed in nature.

Creation and Validation of Chronojump-Boscosystem: A Free Tool to Measure Vertical Jumps

Measuring the height of the vertical jump is an indicator of the strength and power of the lower body. The technological tools available to measure the vertical jump are black boxes and are not open to third-party verification or adaptation. We propose the creation of a measurement system called Chronojump-Boscosystem, consisting of open hardware and free software. Methods: A microcontroller was created and validated using a square wave generator and an oscilloscope. Two types of contact platforms were developed using different materials. These platforms were validated by the minimum pressure required for activation at different points by a strain gauge, together with the on/off time of our platforms in respect of the Ergojump-Boscosystem platform by a sample of 8 subjects performing submaximal jumps with one foot on each platform. Agile methodologies were used to develop and validate the software. Results: All the tools fall under the free software / open hardware guidelines and are, in that sense, free. The microcontroller margin of error is 0.1%. The validity of the fiberglass platform is 0.95 (ICC). The management software contains nearly 113.000 lines of code and is available in 7 languages.

Gene Promoter Evolution Targets the Center of the Human Protein Interaction Network

Assessing the contribution of promoters and coding sequences to gene evolution is an important step toward discovering the major genetic determinants of human evolution. Many specific examples have revealed the evolutionary importance of cis-regulatory regions. However, the relative contribution of regulatory and coding regions to the evolutionary process and whether systemic factors differentially influence their evolution remains unclear. To address these questions, we carried out an analysis at the genome scale to identify signatures of positive selection in human proximal promoters. Next, we examined whether genes with positively selected promoters (Prom+ genes) show systemic differences with respect to a set of genes with positively selected protein-coding regions (Cod+ genes). We found that the number of genes in each set was not significantly different (8.1% and 8.5%, respectively). Furthermore, a functional analysis showed that, in both cases, positive selection affects almost all biological processes and only a few genes of each group are located in enriched categories, indicating that promoters and coding regions are not evolutionarily specialized with respect to gene function. On the other hand, we show that the topology of the human protein network has a different influence on the molecular evolution of proximal promoters and coding regions. Notably, Prom+ genes have an unexpectedly high centrality when compared with a reference distribution (P = 0.008, for Eigenvalue centrality). Moreover, the frequency of Prom+ genes increases from the periphery to the center of the protein network (P = 0.02, for the logistic regression coefficient). This means that gene centrality does not constrain the evolution of proximal promoters, unlike the case with coding regions, and further indicates that the evolution of proximal promoters is more efficient in the center of the protein network than in the periphery. These results show that proximal promoters have had a systemic contribution to human evolution by increasing the participation of central genes in the evolutionary process.

Influence on present-day coastal dynamics and evolution of a relict subaqueous delta lobe: Sol de Riu lobe, Ebro Delta. Continental Shelf Research, 74: 94-104. doi:10.1016/j.csr.2013.11.021

We used high-resolution swath-bathymetry data to characterise the morphology of the abandoned subaqueous Sol de Riu delta lobe in the Ebro Delta, Western Mediterranean Sea. This study aims to assess the influence of an abandoned delta lobe on present-day coastal dynamics in a micro-tidal environment. Detailed mapping of the relict Sol de Riu lobe also showed a set of bedforms interpreted as footprints of human activities: seasonal V-shaped depressions on the middle shoreface due to boat anchoring and old trawling marks between 16 and 18 m water depth. Estimations of the mobility of bottom sediment showed that the shallowest shoreface (i.e. less than 7 m depth) is the most dynamic part of the relict lobe, while the middle shoreface experienced significant morphological changes since the lobe was abandoned. The deepest shoreface (i.e. water depth in excess of 15 m), which corresponds to the front of the lobe, is defined by a very small potential for morphological change. Simulations showed that while the relict lobe does not significantly affect the typical short period waves (Tp ≈4 s) in the study area, it does interfere with the most energetic wave conditions (Tp ≥ 7 s) acting as a shoal leading to the concentration of wave energy along the shoreline northwest of the lobe. The consequence of such modification of the high-energy wave propagation pattern by the relict lobe is an alteration of the wave-induced littoral sediment dynamics with respect to a situation without the lobe.

Microstructural evolution of primary crystallization in diffusion-controlled grain growth

A model has been developed for evaluating grain size distributions in primary crystallizations where the grain growth is diffusion controlled. The body of the model is grounded in a recently presented mean-field integration of the nucleation and growth kinetic equations, modified conveniently in order to take into account a radius-dependent growth rate, as occurs in diffusion-controlled growth. The classical diffusion theory is considered, and a modification of this is proposed to take into account interference of the diffusion profiles between neighbor grains. The potentiality of the mean-field model to give detailed information on the grain size distribution and transformed volume fraction for transformations driven by nucleation and either interface- or diffusion-controlled growth processes is demonstrated. The model is evaluated for the primary crystallization of an amorphous alloy, giving an excellent agreement with experimental data. Grain size distributions are computed, and their properties are discussed.

Eficacia e ineficacia de la comunicación horizontal en los movimientos sociales. Caso análisis: Oposiciones justas en Cataluña 2011

Las redes sociales están generando un amplio entramado de comunicaciones, a distintos niveles y con distintos objetivos. En este artículo analizamos un caso concreto, fruto de la observación y el seguimiento de un grupo creado para la defensa de unas oposiciones justas para el acceso a la función pública de docentes para educación secundaria. Se trata de un grupo creado como reacción a una serie de posibles irregularidades. Interesa observar tanto la creación del grupo, como las distintas fases que sigue la evolución, muy ligada a la efectividad de los procesos de comunicación, y la vinculación de estos últimos a las posibilidades de acción y resolución del conflicto que existe en la base del grupo

Writing for the contemporany naturalistic stage: a personal process of creation

El objetivo principal de este proyecto es desarrollar más a fondo y consolidar los objetivos formativos y competencias del grado en Estudios Ingleses a través de un trabajo de escritura creativa, en concreto, la creación de una obra teatral original. Este trabajo consiste en, por un lado, una introducción al Naturalismo, como género literario en un marco cultural y metodológico, y por otro lado, la creación personal de una obra naturalista que incluye la primera parte del manuscrito. Este proyecto incluye un proceso completo de creatividad justificado gracias a las principales teorías de algunos escritores naturalistas, como: Émile Zola – como precursor del Naturalismo – y August Strindberg como uno de los mayores mentores de este género literario. Los resultados obtenidos en este trabajo son: la creación de una obra teatral original, una especialización en el movimiento Naturalista aplicado al teatro contemporáneo, y un profundo conocimiento de la lengua inglesa a través de la perspectiva de un dramaturgo.