Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Background Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. Results In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function. Conclusions We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.

La utilización del concepto de ADN en nuestra sociedad: tecnociencia, frases hechas y errores científicos

La tecnología científica relacionada con el ADN y sus aplicaciones ha revolucionado nuestra sociedad. La información respecto a estos progresos se ha extendido rápidamente mediante los medios de comunicación. A su vez, las personas han incorporado conceptos de las tecnologías relacionadas con el ADN en su cosmovisión. La utilización de frases hechas basadas en el ADN ha tenido un gran éxito mediático, pero algunas de ellas contienen errores científicos graves. En este artículo se pretende mostrar dichos errores y posibles vías de actuación para corregirlos. Palabras clave: ADN, cosmovisión, frases hechas, selección natural, darwinismo, herencia de caracteres adquiridos, lamarckismo.

Evolución: de la especie humana al cyborg

Resumen: Gracias a la evolución biológica y cultural el ser humano ha sido capaz de adaptarse al ambiente. Una opción para mejorar las prestaciones humanas podría ser la obtención de un cyborg o ser humano biónico en el cual la parte inorgánica fuese un chip computacional conectado directamente al cerebro. Esta y otras posibilidades se debaten en el presente artículo. Palabras clave: Evolución biológica, selección natural, evolución cultural, cyborg, biónico, inteligencia.

Changes in chromosomal polymorphism and global warming: The case of Drosophila subobscura from Apatin (Serbia)

Abstract In this study, chromosomal inversion polymorphism data for a natural population of Drosophila subobscura from a swampy region near the town of Apatin (Serbia) were compared with data for the same population collected approximately 15 years earlier. The pattern of chromosomal inversion polymorphism changed over time. There were significant increases in the frequency of characteristic southern latitude ("warm" adapted) chromosomal arrangements and significant decreases in the frequency of characteristic northern latitude ("cold" adapted) chromosomal arrangements in the O and U chromosomes. The chromosomal arrangements O3+4 and O3+4+22 (derived from the O3+4 arrangement)showed significant increases in 2008 and 2009 with regard to the 1994 sample. There was also a significant increase (~50%) in the U1+2 arrangement, while U1+8+2 (a typical southern arrangement) was detected for the first time. Since the Apatin swampy population ofD. subobscura has existed for a long time in a stable habitat with high humidity that has not been changed by man our results indicate that natural selection has produced chromosomal changes in response to the increase in temperature that has occurred in the Balkan Peninsula of central southeastern European. Key words: chromosomal inversions, Drosophila subobscura, global warming, karyotypes.

Molecular evidence to suggest the origin of a colonization: Drosophila subobscura in America

Abstract The recent colonization of America by Drosophila subobscura represents a great opportunity for evolutionary biology studies. Knowledge of the populations from which the colonization started would provide an understanding of how genetic composition changed during adaptation to the new environment. Thus, a 793 nucleotide fragment of the Odh (Octanol dehydrogenase) gene was sequenced in 66 chromosomal lines from Barcelona (western Mediterranean) and in 66 from Mt. Parnes (Greece, eastern Mediterranean). No sequence of Odh fragment in Barcelona or Mt. Parnes was identical to any of those previously detected in America. However, an Odh sequence from Barcelona differed in only one nucleotide from another found in American populations. In both cases, the chromosomal lines presented the same inversion: O7, and the Odh gene was located within this inversion. This evidence suggests a possible western Mediterranean origin for the colonization. Finally, the molecular and inversion data indicate that the colonization was not characterized by multiple reintroductions.

O-chromosome lethal frequencies in Serbian and Montenegrin Drosophila subobscura populations

Lethal chromosomal frequencies were obtained from three Drosophila subobscura samples from the Mt. Avala (Serbia) population in September 2003 (0.218), June 2004 (0.204) and September 2004 (0.250). These values and those from other Balkan populations studied previously (Petnica, Kamariste, Zanjic and Djerdap) were used to analyze the possible effect of population, year, month and altitude above sea level on lethal chromosomal frequencies. According to ANOVAS no effect were observed. Furthermore, the lethal frequencies of the Balkan populations did not vary according to latitude. This is probably due to the relative proximity and high gene flow between these populations. From a joint study of all the Palearctic D. subobscura populations so far analyzed, it can be deduced that the Balkan populations are located in the central area of the species distribution. Finally, it seems that lethal chromosomal frequencies are a consequence of the genetic structure of the populations.

La convivencia con los cyborgs y los robots: Consideraciones filosóficas, ético-morales y sociopolíticas

In this work, we present the cultural evolution that has allowed to overcome many problems derived from the limitations of the human body. These limitations have been solved by a"cyborization" process that began since early anthropogenesis. Originally, it was envisioned to deal with some diseases, accidents or body malfunctions. Nowadays, augmentations improve common human capabilities; one of the most notable is the increase of brain efficiency by using connections with a computer. A basic social question also addressed is which people will and should have access to these augmentations. Advanced humanoid robots (with human external aspect, artificial intelligence and even emotions) already exist and consequently a number of questions arise. For instance, will robots be considered living organisms? Could they be considered as persons? Will we confer the human status to robots? These questions are discussed. Our conclusions are that the advanced humanoid robots display some actions that may be considered as life-like, yet different to the life associated with living organisms, also, to some extend they could be considered as persons-like, but not humans.

Reflexiones sobre los cyborgs y los robots: evolucion humana y aumentacion

The human being has changed in time due to both, biological and cultural evolution. In a first step, biological evolution was the cornerstone of the changes in our species. However, cultural evolution was also a key element producing adaptations that allowed the evolution of modern human being. These adaptations include aspects as different as clothing, tools, reading and writing, calculation and some forms of rudimentary prosthesis. Technoscience has enhanced these adaptations that conduce to the concept of broad-sense cyborg. Present human society includes a huge proportion of these latter individuals. In this article we discuss this reality and the future of our society based on the interconnections between humans, cyborgs and robots.

Precisiones interdisciplinares y conceptuales de los términos cyborg, clon humnao y robot

La palabra cyborg (del cyborg: cyber, cibernético y organism, organismo), designa una criatura compuesta de elementos orgánicos y mecánicos que mejoran las capacidades biológicas a través de la tecnología: es un individuo en parte hombre y en parte máquina.

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

La ontología del espíritu: principio de epistemología de G. de Ockham

El principio radical de toda la filosofía de Ockham no es ni una metafísica del singular, ni una actitud logicista, teologal oescéptica. El Inceptor es la culminación de una tendencia neoplatónica, también central en el Eriúgena: aun para la creatura humanalo "inteligente" es anterior y ontológicamente superior a lo "inteligible" o "sensible".Heredado de Agustín de Hipona, pero transformado en el análisis hasta ser inmediato precedente de la Modernidad o comienzo de ella, el "yo pienso" es el quicio del sistema de Ockman. De la exacta acotación moderna de "espíritu" arranca todo el sistema; a partir de él se justifican incluso los rasgos que más sorprende hallar en un filósofo del siglo XIV: la centralidad de las nociones opuestas "intuición/evidencia", la plena actividad cognoscitiva del espíritu junto a la pasividad del intelecto, la nula causalidad próxima de las cosas sensibles en el conocimiento humano, e! paradigma perfectamente lingüístico del conocer. El nacimiento de una moderna "teoría del conocimiento", se da a partir de la constatación de que el acto más perfecto y paradigmáticode la vida del espíritu es la intuición de los "intellectualia" que radican en él mismo, y no la captación de los externos "sensibilia" aristotélicos.

The international competitiveness of cava : success of a particular firm or the district?

[spa] En primer lugar el autor se pregunta qué es lo que exactamente significa la palabra éxito aplicada al caso de la evolución reciente de la industria catalana del cava. La comparación de las trayectorias seguidas por la industria italiana del spumante y la del más reputado vino espumoso del mundo, el champagne, muestran una trayectoria muy positiva del volumen de producción y de las exportaciones. En segundo lugar el papel se pregunta por el agente responsable de este éxito. ¿Se debe a una empresa en particular o, por el contrario, al distrito en su conjunto, atendiendo que nos hallamos ante un sector muy concentrado geográficamente en torno a Sant Sadurní d’Anoia? La concentración de las exportaciones en más de dos tercios en manos de una sola empresa justificaría atribuir a dicha empresa el éxito. Sin embargo el análisis histórico de la formación del distrito industrial del cava en la zona del Penedés muestra como los productores se han podido beneficiar de las economías externas marshallianas inherentes a este tipo de concentraciones. El papel muestra que el éxito de la empresa exportadora líder se explica por la existencia de este tipo de ventajas invisibles derivadas de la concentración.

Connections between signal processing and complex analysis

We describe one of the research lines of the Grup de Teoria de Funcions de la UAB UB, which deals with sampling and interpolation problems in signal analysis and their connections with complex function theory.

A Geometric Characterization of Interpolation in $\hat{\E}^\prime(\R)$

We give a geometric description of the interpolating varieties for the algebra of Fourier transforms of distributions (or Beurling ultradistributions) with compact support on the real line.