Uncovering Proximity of Chromosome Territories using Classical Algebraic Statistics

Exchange type chromosome aberrations (ETCAs) are rearrangements of the genome that occur when chromosomes break and the resulting fragments rejoin with other fragments from other chromosomes. ETCAs are commonly observed in cancer cells and in cells exposed to radiation. The frequency of these chromosome rearrangements is correlated with their spatial proximity, therefore it can be used to infer the three dimensional organization of the genome. Extracting statistical significance of spatial proximity from cancer and radiation data has remained somewhat elusive because of the sparsity of the data. We here propose a new approach to study the three dimensional organization of the genome using algebraic statistics. We test our method on a published data set of irradiated human blood lymphocyte cells. We provide a rigorous method for testing the overall organization of the genome, and in agreement with previous results we find a random relative positioning of chromosomes with the exception of the chromosome pairs \{1,22\} and \{13,14\} that have a significantly larger number of ETCAs than the rest of the chromosome pairs suggesting their spatial proximity. We conclude that algebraic methods can successfully be used to analyze genetic data and have potential applications to larger and more complex data sets

A Liquid Crystal Model of Viral DNA Encapsidation

A liquid crystal continuum modeling framework for icosahedra bacteriophage viruses is developed and tested. The main assumptions of the model are the chromonic columnar hexagonal structure of confined DNA, the high resistance to bending and the phase transition from solid to fluid-like states as the concentration of DNA in the capsid decreases during infection. The model predicts osmotic pressure inside the capsid and the ejection force of the DNA as well as the size of the isotropic volume at the center of the capsid. Extensions of the model are discussed

Problemática del txistu

El txistu, nuestro típico y ancestral instrumento, símbolo del sentir musical del pueblo vasco, íntimamente unido a su desarrollo, ha adquirido gran popularidad a través de las melodías ejecutadas por txistularis en romerías, danzas populares pero existe un escaso conocimiento del txistu de concierto. Actualmente se está llevando a cabo un movimiento de renovación del ambiente txistulari (mejora técnica de los instrumentos, aumento de la familia instrumental del txistu). El aspecto pedagógico del txistu necesita una estructuración urgente en sus sistemas y enseñanzas. El txistu puede servir a nuestra música de muy diversas formas. El rústico txistu se adentra en el terreno experimental con una doble problemática: técnica y emocional (adaptando nuestra mentalidad ante los aires renovadores del instrumento). Ha llegado la hora de apreciar nuevas sonoridades, técnicas nuevas, concertar el txistu con otros instrumentos, componer partituras originales, perfeccionar a los alumnos txistularis. El mantenimiento y progreso del txistu compete a todo

Quantitation of anti-Pythium insidiosum antibodies before and after immunotherapy in healthy dogs

Pythium insidiosum is an aquatic oomycete that causes invasive, progressive granulomatous lesions of the skin in dogs, horses, and cats, and of the gastrointestinal tract in dogs. Quantitation of anti-P. insidiosum IgG antibodies can be used in dogs to both confirm a suspected diagnosis and to monitor response to therapy. Recently, an immunotherapeutic product (IP) has been marketed for the treatment of pythiosis in dogs, horses, and people. The aim of this study was to evaluate the effect of administration of this product on anti-P. insidiosum IgG concentrations in dogs. The IP was administered to seven, healthy hound mixes on days zero, seven and 21. Serum was collected on days zero, seven, 14, 21, 28, 35, 42, 49, and 56. Anti-P. insidiosum antibody concentrations were measured using a previously-described ELISA that utilizes a soluble mycelial-based antigen, with results reported as percent positivity (PP) in comparison to a strong positive control serum. Prior to immunotherapy administration, average PP was 7.45% +/- 3.02%. Following immunotherapy administration, there was no significant change in anti-P. insidiosum antibody concentrations, with PP values in all dogs remaining within the range expected for healthy dogs (3% - 15%) for the entire study period. In conclusion, the IP did not produce a significant change in anti-P. insidiosum IgG concentrations when administered to healthy dogs using the protocol suggested by the manufacturers. Further investigation will be required to determine whether a similar effect is observed in naturally infected dogs

Fine Structure of Viral dsDNA Encapsidation

In vivo configurations of dsDNA of bacteriophage viruses in a capsid are known to form hexagonal chromonic liquid crystal phases. This article studies the liquid crystal ordering of viral dsDNA in an icosahedral capsid, combining the chromonic model with that of liquid crystals with variable degree of orientation. The scalar order parameter of the latter allows us to distinguish regions of the capsid with well-ordered DNA from the disordered central core. We employ a state-of-the-art numerical algorithm based on the finite element method to find equilibrium states of the encapsidated DNA and calculate the corresponding pressure. With a data-oriented parameter selection strategy, the method yields phase spaces of the pressure and the radius of the disordered core, in terms of relevant dimensionless parameters, rendering the proposed algorithm into a preliminary bacteriophage designing tool. The presence of the order parameter also has the unique role of allowing for non-smooth capsid domains as well as accounting for knot locations of the DNA

The Rabl configuration limits topological entanglement of chromosomes in budding yeast.

The three dimensional organization of genomes remains mostly unknown due to their high degree of condensation. Biophysical studies predict that condensation promotes the topological entanglement of chromatin fibers and the inhibition of function. How organisms balance between functionally active genomes and a high degree of condensation remains to be determined. Here we hypothesize that the Rabl configuration, characterized by the attachment of centromeres and telomeres to the nuclear envelope, helps to reduce the topological entanglement of chromosomes. To test this hypothesis we developed a novel method to quantify chromosome entanglement complexity in 3D reconstructions obtained from Chromosome Conformation Capture (CCC) data. Applying this method to published data of the yeast genome, we show that computational models implementing the attachment of telomeres or centromeres alone are not sufficient to obtain the reduced entanglement complexity observed in 3D reconstructions. It is only when the centromeres and telomeres are attached to the nuclear envelope (i.e. the Rabl configuration) that the complexity of entanglement of the genome is comparable to that of the 3D reconstructions. We therefore suggest that the Rabl configuration is an essential player in the simplification of the entanglement of chromatin fibers

Hermanos y cofrades en la aljama de Toledo a principios del siglo XV

Between 1402 and 1414, the activity of the members of a confraternity related to the mosque of Tornerías, in Toledo, was registered by their leaders in Arabic proceedings. These records prove that Arabic was still currently used by Muslims in Castile at the beginning of the fifteenth century. This is the first Mudejar confraternity known to us. Lacking knowledge about their statutes, the records of their meetings provide interesting clues to their development. This article focuses on the linguistic features of the records, and will describe the confraternity members, functions, and their capacities to manage Toledan Muslims’ alms.Entre 1402 y 1414, la actividad de los miembros de una cofradía vinculada a la mezquita aljama de las Tornerías, en Toledo, quedó registrada por sus autoridades en actas escritas en árabe, demostrando así que éste no había sido olvidado en Castilla a principios del siglo XV. Es la primera cofradía estrictamente mudéjar que conocemos y, a falta de sus estatutos, las actas de sus reuniones facilitan interesantes datos para conocer su funcionamiento. Este artículo abordará las características lingüísticas de la fuente, y caracterizará la cofradía a partir de sus miembros, sus funciones,  y su capacidad para gestionar la limosna de los mudéjares toledanos

The Sima de los Huesos cervical spine

Information regarding the evolution of the neck in genus Homo is hampered owing to a limited fossil record. Neandertals display significant metric and/or morphological differences in all the cervical vertebrae, when compared to Homo sapiens. Thus, the important fossil record from the Middle Pleistocene site of Sima de los Huesos (SH) not only offers important information about the evolution of this anatomical region within the Neandertal lineage, but also provides important clues to understand the evolution of this region at the genus level. We present the current knowledge of the anatomy of the cervical spine of the hominins found in SH compared to that of Neandertals and modern humans, and, when possible, to Homo erectus and Homo antecessor. The current SH fossil record comprises 172 cervical specimens (after refittings) belonging to a minimum of 11 atlases, 13 axes, and 52 subaxial cervical vertebrae. The SH hominins exhibit a morphological pattern in their cervical spine more similar to that of Neandertals than that of H. sapiens, which is consistent with the phylogenetic position of these hominins. However, there are some differences between the SH hominins and Neandertals in this anatomical region, primarily in the length and robusticity, and to a lesser extent in the orientation of the spinous processes of the lowermost cervical vertebrae. We hypothesize that these differences in the lowermost subaxial cervical vertebrae could be related to the increase in the brain size and/or changes in the morphology of the skull that occurred in the Neandertal lineage.Depto. de Geodinámica, Estratigrafía y PaleontologíaFac. de Ciencias GeológicasTRUEMinisterio de Ciencia e InnovaciónJunta de Castilla y LeónFundación Atapuercapu