Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: A possible advantage of DNA over RNA as genomic material

Heteroduplex joints are general intermediates of homologous genetic recombination in DNA genomes. A heteroduplex joint is formed between a single-stranded region (or tail), derived from a cleaved parental double-stranded DNA, and homologous regions in another parental double-stranded DNA, in a reaction mediated by the RecA/Rad51-family of proteins. In this reaction, a RecA/Rad51-family protein first forms a filamentous complex with the single-stranded DNA, and then interacts with the double-stranded DNA in a search for homology. Studies of the three-dimensional structures of single-stranded DNA bound either to Escherichia coli RecA or Saccharomyces cerevisiae Rad51 have revealed a novel extended DNA structure. This structure contains a hydrophobic interaction between the 2′ methylene moiety of each deoxyribose and the aromatic ring of the following base, which allows bases to rotate horizontally through the interconversion of sugar puckers. This base rotation explains the mechanism of the homology search and base-pair switch between double-stranded and single-stranded DNA during the formation of heteroduplex joints. The pivotal role of the 2′ methylene-base interaction in the heteroduplex joint formation is supported by comparing the recombination of RNA genomes with that of DNA genomes. Some simple organisms with DNA genomes induce homologous recombination when they encounter conditions that are unfavorable for their survival. The extended DNA structure confers a dynamic property on the otherwise chemically and genetically stable double-stranded DNA, enabling gene segment rearrangements without disturbing the coding frame (i.e., protein-segment shuffling). These properties may give an extensive evolutionary advantage to DNA.

LR property of non-well-formed scales

This article studies generated scales having exactly three different step sizes within the language of algebraic combinatorics on words. These scales and their corresponding step-patterns are called non well formed. We prove that they can be naturally inserted in the Christoffel tree of well-formed words. Our primary focus in this study is on the left- and right-Lyndon factorization of these words. We will characterize the non-well-formed words for which both factorizations coincide. We say that these words satisfy the LR property and show that the LR property is satisfied exactly for half of the non-well-formed words. These are symmetrically distributed in the extended Christoffel tree. Moreover, we find a surprising connection between the LR property and the Christoffel duality. Finally, we prove that there are infinitely many Christoffel–Lyndon words among the set of non-well-formed words and thus there are infinitely many generated scales having as step-pattern a Christoffel–Lyndon word.

Generadores ScalaCheck para property-based testing de programas Spark y Spark Streaming

En los últimos años hemos sido testigos de la expansión del paradigma big data a una velocidad vertiginosa. Los cambios en este campo, nos permiten ampliar las áreas a tratar; lo que a su vez implica una mayor complejidad de los sistemas software asociados a estas tareas, como sucede en sistemas de monitorización o en el Internet de las Cosas (Internet of Things). Asimismo, la necesidad de implementar programas cada vez robustos y eficientes, es decir, que permitan el cómputo de datos a mayor velocidad y de los se obtengan información relevante, ahorrando costes y tiempo, ha propiciado la necesidad cada vez mayor de herramientas que permitan evaluar estos programas. En este contexto, el presente proyecto se centra en extender la herramienta sscheck. Sscheck permite la generación de casos de prueba basados en propiedades de programas escritos en Spark y Spark Streaming. Estos lenguajes forman parte de un mismo marco de código abierto para la computación distribuida en clúster. Dado que las pruebas basadas en propiedades generan datos aleatorios, es difícil reproducir los problemas encontrados en una cierta sesion; por ello, la extensión se centrará en cargar y guardar casos de test en disco mediante el muestreo de datos desde colecciones mayores.