Transformation rules form OntoProcED to OntoOKI

This file contains the transformtion rules in SWRL to translate formal specifications of two lower ontology levels (patterns and organization) to the upper level (implementation according to the OKI specification).

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.

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.

Thermal evolution of gene expression profiles in Drosophila subobscura

Background: Despite its pervasiveness, the genetic basis of adaptation resulting in variation directly or indirectly related to temperature (climatic) gradients is poorly understood. By using 3-fold replicated laboratory thermal stocks covering much of the physiologically tolerable temperature range for the temperate (i.e., cold tolerant) species Drosophila subobscura we have assessed whole-genome transcriptional responses after three years of thermal adaptation, when the populations had already diverged for inversion frequencies, pre-adult life history components, and morphological traits. Total mRNA from each population was compared to a reference pool mRNA in a standard, highly replicated two-colour competitive hybridization experiment using cDNA microarrays.Results: A total of 306 (6.6%) cDNA clones were identified as 'differentially expressed' (following a false discovery rate correction) after contrasting the two furthest apart thermal selection regimes (i.e., 13°C vs . 22°C), also including four previously reported candidate genes for thermotolerance in Drosophila (Hsp26, Hsp68, Fst, and Treh). On the other hand, correlated patterns of gene expression were similar in cold- and warm-adapted populations. Analysis of functional categories defined by the Gene Ontology project point to an overrepresentation of genes involved in carbohydrate metabolism, nucleic acids metabolism and regulation of transcription among other categories. Although the location of differently expressed genes was approximately at random with respect to chromosomes, a physical mapping of 88 probes to the polytene chromosomes of D. subobscura has shown that a larger than expected number mapped inside inverted chromosomal segments.Conclusion: Our data suggest that a sizeable number of genes appear to be involved in thermal adaptation in Drosophila, with a substantial fraction implicated in metabolism. This apparently illustrates the formidable challenge to understanding the adaptive evolution of complex trait variation. Furthermore, some clustering of genes within inverted chromosomal sections was detected. Disentangling the effects of inversions will be obviously required in any future approach if we want to identify the relevant candidate genes.

Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions

Background: The trithorax group (trxG) genes absent, small or homeotic discs 1 (ash1) and 2 (ash2) were isolated in a screen for mutants with abnormal imaginal discs. Mutations in either gene cause homeotic transformations but Hox genes are not their only targets. Although analysis of double mutants revealed that ash2 and ash1 mutations enhance each other's phenotypes, suggesting they are functionally related, it was shown that these proteins are subunits of distinct complexes.Results: The analysis of wing imaginal disc transcriptomes from ash2 and ash1 mutants showed that they are highly similar. Functional annotation of regulated genes using Gene Ontology allowed identification of severely affected groups of genes that could be correlated to the wing phenotypes observed. Comparison of the differentially expressed genes with those from other genome-wide analyses revealed similarities between ASH2 and Sin3A, suggesting a putative functional relationship. Coimmunoprecipitation studies and immunolocalization on polytene chromosomes demonstrated that ASH2 and Sin3A interact with HCF (host-cell factor). The results of nucleosome western blots and clonal analysis indicated that ASH2 is necessary for trimethylation of the Lys4 on histone 3 (H3K4).Conclusion: The similarity between the transcriptomes of ash2 and ash1 mutants supports a model in which the two genes act together to maintain stable states of transcription. Like in humans, both ASH2 and Sin3A bind HCF. Finally, the reduction of H3K4 trimethylation in ash2 mutants is the first evidence in Drosophila regarding the molecular function of this trxG gene.

Demócrito y Epicuro: el átomo como elemento y como límite onto-lógico

El presente artículo ofrece una interpretación parcialmente heterodoxa del atomismogriego que interpreta aquella revolucionaria teoría como: 1) Un salto adelante respecto de la ontología eleática que suministra una nueva base más sólida al principio básico de ésta,a saber, "El ser no puede generarse a partir del no-ser" (tesis más bien convencional y ya clásica). 2) Una respuesta, tímidamente formulada, a la pregunta pitagórica por una universalismensura de cada cosa, a saber, la hipótesis, claramente avanzada por Demócrito, de que las piezas constitutivas de la materia, las partículas atómicas, poseen infinitos tamañosdiferentes a fin de eludir las dificultades planteadas por el programa pitagórico y ejemplificadas en la inconmensurabilidad de la diagonal y el lado del cuadrado; dicha hipótesis (yaquí radica el aspecto innovador del artículo) podría considerarse como una anticipación implícita de la moderna noción de fluxión o infinitésimo; la refutación de dicha soluciónpor la teoría aristotélica del continuo forzará a la segunda generación de atomistas, encabezada por Epicuro, a intentar un nuevo enfoque del problema con la formulación de la teoríade las rninirnaepartes, que, según nuestra interpretación, habría que identificar con los límites geométricos de las figuras atómicas.

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.

Ontología y conocimiento en M. Merleau-Ponty

Se ofrece aquí una revisión de la filosofía de Merleau-Ponty atendiendo a la estructura básica desde la que se conforma tanto temporal como sistemáticamente: La coimplicación radical entre la vertiente metafísica y ontológica con la gnoseológica y crítica, en cuyo seno aparece una singular filosofía antropológica de la ambigüedad». El hilo conductor es el análisis del binomio conducta humana-existencia humana» del hombre-mundo como fenómeno unitario, lo que lleva a su autor a proyectar un monismo integrador que se desarrolla bajo el postulado de una síntesis inacabada de corte fluido y ambiguo.

La inversión ontológica de la crítica en Spinoza

El presente trabajo pretende poner de relieve los rasgos esenciales que configuran la sistematización spinozista del racionalismo heredado de Descartes, analizando las diferencias abismales que separan la actitud subjetual y antropológica de la crítica cartesiana, defensora de la categoría de "individualidad", frente a la de "totalidad" preconizada por Spinoza. La tarea se lleva a cabo, concretamente, contraponiendo las nociones de "método","razón" e "ideas", tal como se entienden en uno y otro sistema.

M.Merleau-Ponty: El hombre como unidad ontológica proyectiva

Este trabajo es un intento de retomar sistemáticamente el problema de la estructuraontológica unitaria del hombre, con su dinamicidad propia, partiendo de la temáticaexpuesta en la "Estructura del comportamiento ", con lo que se pone de relieve su unidad significativa para responder de forma nueva al clásico problema de las relaciones entre el alma y el cuerpo. La respuesta merleau-pontyana implica un monismo superador de exclusivismosreductivistas por los que se habían decantado soluciones históricas a las que hay que responder, sin recaer ni en el idealismo ni en el empirismo que desconocen el significado exacto del problema, y no ofrecen ninguna respuesta aceptable al problema de la percepción.En conclusión, lo que se pretende es llevar a cabo una reconstrucción de la antropologíafenomenológica del autor, con miras a mostrar la estructura ontológica que le sirve de fundamento.

Comparativa entre dues BD semàntiques : OWLIM-Lite i Virtuoso

L'objectiu fonamental d'aquest treball és estudiar els conceptes bàsics de la web semàntica mitjançant l'estudi de dos sistemes de gestió de bases de dades (SGBD) utilitzats en el context de la web semàntica, OWLIM-Lite i Virtuoso, que ens permetran dissenyar i implementar una ontologia.

Implicaciones de derechos humanos en el tratado de libre comercio entre Colombia y la Unión Europea

[spa] Tras largas y complejas negociaciones, la Unión Europea celebró un acuerdo comercial con Colombia en 2010 que ha empezado a aplicarse provisionalmente el 1 de agosto de 2013. El artículo se centra en las relaciones entre Colombia y la Unión y analiza el impacto que dicho acuerdo pueda tener en el marco de las obligaciones de las partes de respetar los derechos humanos universalmente reconocidos, incluyendo derechos sociales y los derechos de los pueblos indígenas. De dicho análisis se deriva que la presencia de cláusulas democráticas o de derechos humanos en el Acuerdo es insuficiente, habida cuenta los antecedentes del SGP+ vigente hasta la entrada en vigor del nuevo acuerdo, mientras que algunos aspectos sustantivos del Acuerdo permiten augurar consecuencias negativas respecto de los sectores sociales más desfavorecidos en la República de Colombia.

Enhanced Botrytis cinerea resistance of Arabidopsis plants grown in compost may be explained by increased expression of defense-related genes, as revealed by microarray analysis

Composts are the products obtained after the aerobic degradation of different types of organic matter waste and can be used as substrates or substrate/soil amendments for plant cultivation. There is a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost, rather than standard substrates, as growing medium. The purpose of this study was to examine the gene expression alteration produced by the compost to gain knowledge of the mechanisms involved in compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis, unlike the standard substrate, perlite. Microarray analyses revealed that 178 genes were differently expressed, with a fold change cut-off of 1, of which 155 were up-regulated and 23 were down-regulated in compost-grown, as against perlite-grown plants. A functional enrichment study of up-regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched, as were immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA-dependent/independent abiotic stress responses.

Implicaciones de derechos humanos en el tratado de libre comercio entre Colombia y la Unión Europea

[spa] Tras largas y complejas negociaciones, la Unión Europea celebró un acuerdo comercial con Colombia en 2010 que ha empezado a aplicarse provisionalmente el 1 de agosto de 2013. El artículo se centra en las relaciones entre Colombia y la Unión y analiza el impacto que dicho acuerdo pueda tener en el marco de las obligaciones de las partes de respetar los derechos humanos universalmente reconocidos, incluyendo derechos sociales y los derechos de los pueblos indígenas. De dicho análisis se deriva que la presencia de cláusulas democráticas o de derechos humanos en el Acuerdo es insuficiente, habida cuenta los antecedentes del SGP+ vigente hasta la entrada en vigor del nuevo acuerdo, mientras que algunos aspectos sustantivos del Acuerdo permiten augurar consecuencias negativas respecto de los sectores sociales más desfavorecidos en la República de Colombia.