DEL FESTIVAL A LA ACADEMIA. Informe sobre la institucionalización de una disciplina híbrida (arte digital)

Aquest document és un esborrany. Amb l'objectiu d'aprofundir en el procés d'institucionalització, vam dissenyar una investigació empírica que permetés visualitzar les tendències discursives i àmbits d'activitats de les pràctiques relacionades amb les interseccions entre l'art, la ciència i la tecnologia. La metodologia va consistir en la implementació de tres bases de dades que recullen l'activitat dels últims anys en relació a: 1) els congressos (i festivals associats) realitzats a nivell internacional 2) les publicacions acadèmiques i divulgatives centrades en aquest àmbit interdisciplinar 3) els programes acadèmics.

Transcription factor map alignment of promoter regions

We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed genes do not show discernible sequence conservation. In our approach, thus, we have not directly compared the nucleotide sequence of promoters. Instead, we have obtained predictions of transcription factor binding sites, annotated the predicted sites with the labels of the corresponding binding factors, and aligned the resulting sequences of labels—to which we refer here as transcription factor maps (TF-maps). To obtain the global pairwise alignment of two TF-maps, we have adapted an algorithm initially developed to align restriction enzyme maps. We have optimized the parameters of the algorithm in a small, but well-curated, collection of human–mouse orthologous gene pairs. Results in this dataset, as well as in an independent much larger dataset from the CISRED database, indicate that TF-map alignments are able to uncover conserved regulatory elements, which cannot be detected by the typical sequence alignments.

A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations

Studies of large sets of SNP data have proven to be a powerful tool in the analysis of the genetic structure of human populations. In this work, we analyze genotyping data for 2,841 SNPs in 12 Sub-Saharan African populations, including a previously unsampled region of south-eastern Africa (Mozambique). We show that robust results in a world-wide perspective can be obtained when analyzing only 1,000 SNPs. Our main results both confirm the results of previous studies, and show new and interesting features in Sub-Saharan African genetic complexity. There is a strong differentiation of Nilo-Saharans, much beyond what would be expected by geography. Hunter-gatherer populations (Khoisan and Pygmies) show a clear distinctiveness with very intrinsic Pygmy (and not only Khoisan) genetic features. Populations of the West Africa present an unexpected similarity among them, possibly the result of a population expansion. Finally, we find a strong differentiation of the south-eastern Bantu population from Mozambique, which suggests an assimilation of a pre-Bantu substrate by Bantu speakers in the region.

La Renovación de la atención primaria desde la consulta

Texto y contexto que responden claramente al título bajo la batuta dedos médicos de familia, Josep Casajuana y Juan Gérvas, que aman suprofesión pero que, sobre todo, llevan décadas impulsando iniciativasclínicas, gestoras y de investigación para mejorar la atención a lospacientes. De ellos (y Mercedes Pérez) son los dos capítulos inicialesque sitúan el tema: qué cambios pueden impulsar los profesionalespara recuperar el protagonismo y liberarse de ataduras y complejos ycómo, de manera muy práctica, se combina ciencia y tecnología paraobtener lo mejor de los valores y tiempo del profesional comprometido.Para acabar de tener consciencia de la situación y organización de laatención primaria en España, analizan en los dos capítulos siguientes(junto con Marc Casajuana y Roberto Sánchez) qué supone ser médicode familia en Europa y cómo en un día cualquiera se resuelven hasta17 problemas distintos de atención y seguimiento.El contexto de la consulta –en la segunda mitad del libro– plantea larenovación como exigencia social aportando investigación originalsobre: 1) cómo lo que vamos aprendiendo acerca de la elección deespecialidad médica puede ayudar a refundar la Medicina de Familia yComunitaria (Patricia Barber y Beatriz González); 2) las formas dereasignar recursos (Francisco Hernansanz); 3) cómo renovar los servicios sanitarios en su conjunto en época de crisis (Vicente Ortún y MaríaCallejón); y 4) un panorama muy documentado sobre los campos demanifiesta necesidad de mejora en atención primaria (Ricard Meneu ySalvador Peiró),cuyo abordaje da sentido y complementa la renovaciónplanteada en la primera parte del libro.

Exploring the rate-limiting steps in visual phototransduction recovery by bottom-up kinetic modeling

Phototransduction in vertebrate photoreceptor cells represents a paradigm of signaling pathways mediated by G-protein-coupled receptors (GPCRs), which share common modules linking the initiation of the cascade to the final response of the cell. In this work, we focused on the recovery phase of the visual photoresponse, which is comprised of several interacting mechanisms. We employed current biochemical knowledge to investigate the response mechanisms of a comprehensive model of the visual phototransduction pathway. In particular, we have improved the model by implementing a more detailed representation of the recoverin (Rec)-mediated calcium feedback on rhodopsin kinase and including a dynamic arrestin (Arr) oligomerization mechanism. The model was successfully employed to investigate the rate limiting steps in the recovery of the rod photoreceptor cell after illumination. Simulation of experimental conditions in which the expression levels of rhodospin kinase (RK), of the regulator of the G-protein signaling (RGS), of Arr and of Rec were altered individually or in combination revealed severe kinetic constraints to the dynamics of the overall network. Our simulations confirm that RGS-mediated effector shutdown is the rate-limiting step in the recovery of the photoreceptor and show that the dynamic formation and dissociation of Arr homodimers and homotetramers at different light intensities significantly affect the timing of rhodopsin shutdown. The transition of Arr from its oligomeric storage forms to its monomeric form serves to temper its availability in the functional state. Our results may explain the puzzling evidence that overexpressing RK does not influence the saturation time of rod cells at bright light stimuli. The approach presented here could be extended to the study of other GPCR signaling pathways.

A system-level, molecular evolutionary analysis of mammalian phototransduction

Visual perception is initiated in the photoreceptor cells of the retina via the phototransduction system.This system has shown marked evolution during mammalian divergence in such complex attributes as activation time and recovery time. We have performed a molecular evolutionary analysis of proteins involved in mammalianphototransduction in order to unravel how the action of natural selection has been distributed throughout thesystem to evolve such traits. We found selective pressures to be non-randomly distributed according to both a simple protein classification scheme and a protein-interaction network representation of the signaling pathway. Proteins which are topologically central in the signaling pathway, such as the G proteins, as well as retinoid cycle chaperones and proteins involved in photoreceptor cell-type determination, were found to be more constrained in their evolution. Proteins peripheral to the pathway, such as ion channels and exchangers, as well as the retinoid cycle enzymes, have experienced a relaxation of selective pressures. Furthermore, signals of positive selection were detected in two genes: the short-wave (blue) opsin (OPN1SW) in hominids and the rod-specific Na+/Ca2+,K+ ion exchanger (SLC24A1) in rodents. The functions of the proteins involved in phototransduction and the topology of the interactions between them have imposed non-random constraints on their evolution. Thus, in shaping or conserving system-level phototransduction traits, natural selection has targeted the underlying proteins in a concerted manner.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

Mutation patterns of amino acid tandem repeats in the human proteome

Background: Amino acid tandem repeats are found in nearly one-fifth of human proteins. Abnormal expansion of these regions is associated with several human disorders. To gain further insight into the mutational mechanisms that operate in this type of sequence, we have analyzed a large number of mutation variants derived from human expressed sequence tags (ESTs).Results: We identified 137 polymorphic variants in 115 different amino acid tandem repeats. Of these, 77 contained amino acid substitutions and 60 contained gaps (expansions or contractions of the repeat unit). The analysis showed that at least about 21% of the repeats might be polymorphic in humans. We compared the mutations found in different types of amino acid repeats and in adjacent regions. Overall, repeats showed a five-fold increase in the number of gap mutations compared to adjacent regions, reflecting the action of slippage within the repetitive structures. Gap and substitution mutations were very differently distributed between different amino acid repeat types. Among repeats containing gap variants we identified several disease and candidate disease genes.Conclusion: This is the first report at a genome-wide scale of the types of mutations occurring in the amino acid repeat component of the human proteome. We show that the mutational dynamics of different amino acid repeat types are very diverse. We provide a list of loci with highly variable repeat structures, some of which may be potentially involved in disease.

Les pintures murals negres del monestir de Pedralbes: problemes de conservació-restauració causats per l’envelliment de l’acetat de polivinil

Aquesta tesi s’inicia com un treball de recerca i posteriorment passa a formar part delprojecte de recerca BHA2002-02411 fi nançat pel Ministerio de Ciencia y Tecnología, dins elPlan Nacional de I+D+I (2000-2003).La idea principal, però, s’origina a partir d’un encàrrec professional del Museu-Monestir dePedralbes i del Museu d’Història de la Ciutat l’any 2000.Les pintures murals negres (Figura 1) són una de les obres menys vistoses, de les que tenenmenys protagonisme, d’entre les que integren la col·lecció del Museu-Monestir de Pedralbes.No semblen, a priori, l’obra més interessant des del punt de vista d’un encàrrec professionalper a un conservador-restaurador. Però el poc que es coneix de les pintures negres i la sevararesa (es desconeixen altres pintures similars que s’hagin pogut conservar), així com lespatologies derivades del seu arrencament i traspàs l’any 1974, aconsellaven aprofundir en el seu estudi, que, mica en mica, va acabar resultant absorbent.

Les pintures murals negres del monestir de Pedralbes: problemes de conservació-restauració causats per l’envelliment de l’acetat de polivinil

Aquesta tesi s’inicia com un treball de recerca i posteriorment passa a formar part delprojecte de recerca BHA2002-02411 fi nançat pel Ministerio de Ciencia y Tecnología, dins elPlan Nacional de I+D+I (2000-2003).La idea principal, però, s’origina a partir d’un encàrrec professional del Museu-Monestir dePedralbes i del Museu d’Història de la Ciutat l’any 2000.Les pintures murals negres (Figura 1) són una de les obres menys vistoses, de les que tenenmenys protagonisme, d’entre les que integren la col·lecció del Museu-Monestir de Pedralbes.No semblen, a priori, l’obra més interessant des del punt de vista d’un encàrrec professionalper a un conservador-restaurador. Però el poc que es coneix de les pintures negres i la sevararesa (es desconeixen altres pintures similars que s’hagin pogut conservar), així com lespatologies derivades del seu arrencament i traspàs l’any 1974, aconsellaven aprofundir en el seu estudi, que, mica en mica, va acabar resultant absorbent.

Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.

Anàlisi dels indicadors de la gestió per processos de la docència pràctica a la Unitat de Laboratoris Docents (ULD) de la Facultat de Farmàcia

[eng] In the Unitat de Laboratoris Docents (ULD) of the Faculty of Pharmacy a Quality System has been implemented to improve the management of the training laboratories and to introduce practical aspects of this system in the formation of the students. In the last years, we have designed the process map, and the flowcharts with the corresponding key point tables from which the indicators have been identified. The main objective of this work was to found a system that allows the evaluation of the ULD service, the teaching innovation introduced as well as the grade of implication of the lecturers who teach practical training and thus are directly responsible for the formation of the students. The values obtained for the operating ULD procedures correspond to the data from obligatory courses, with practical teaching in the ULD laboratories, of Pharmacy and Food Science and Technology degrees for the 2005-06 academic year. [spa] En la Unidad de Laboratorios Docentes (ULD) de la Facultad de Farmacia, se ha implantado un sistema de gestión de la calidad con el objetivo de mejorar la gestión de la docencia práctica y a su vez introducir aspectos prácticos de la gestión de la calidad en la formación de los estudiantes. En los últimos años se ha elaborado el mapa de procesos, el diagrama de flujo y la ficha de cada proceso a partir de la cual ha sido posible la identificación de los indicadores. El Prat, J. et al. Edusfarm, revista d"educació superior en Farmàcia. Núm. 2. 2007 2 principal objetivo del presente trabajo es buscar un sistema que permita evaluar el propio funcionamiento de la ULD, la innovación realizada así como el grado de implicación de los profesores que imparten la docencia práctica y que son responsables directos de la formación de los estudiantes. Los valores obtenidos para los procesos operativos de la ULD provienen de los datos generados en el curso académico 2005-2006 en las asignaturas troncales de las Licenciaturas de Farmacia y de Ciencia y Tecnología de los Alimentos.

Anàlisi dels indicadors de la gestió per processos de la docència pràctica a la Unitat de Laboratoris Docents (ULD) de la Facultat de Farmàcia

[eng] In the Unitat de Laboratoris Docents (ULD) of the Faculty of Pharmacy a Quality System has been implemented to improve the management of the training laboratories and to introduce practical aspects of this system in the formation of the students. In the last years, we have designed the process map, and the flowcharts with the corresponding key point tables from which the indicators have been identified. The main objective of this work was to found a system that allows the evaluation of the ULD service, the teaching innovation introduced as well as the grade of implication of the lecturers who teach practical training and thus are directly responsible for the formation of the students. The values obtained for the operating ULD procedures correspond to the data from obligatory courses, with practical teaching in the ULD laboratories, of Pharmacy and Food Science and Technology degrees for the 2005-06 academic year. [spa] En la Unidad de Laboratorios Docentes (ULD) de la Facultad de Farmacia, se ha implantado un sistema de gestión de la calidad con el objetivo de mejorar la gestión de la docencia práctica y a su vez introducir aspectos prácticos de la gestión de la calidad en la formación de los estudiantes. En los últimos años se ha elaborado el mapa de procesos, el diagrama de flujo y la ficha de cada proceso a partir de la cual ha sido posible la identificación de los indicadores. El Prat, J. et al. Edusfarm, revista d"educació superior en Farmàcia. Núm. 2. 2007 2 principal objetivo del presente trabajo es buscar un sistema que permita evaluar el propio funcionamiento de la ULD, la innovación realizada así como el grado de implicación de los profesores que imparten la docencia práctica y que son responsables directos de la formación de los estudiantes. Los valores obtenidos para los procesos operativos de la ULD provienen de los datos generados en el curso académico 2005-2006 en las asignaturas troncales de las Licenciaturas de Farmacia y de Ciencia y Tecnología de los Alimentos.

Anàlisi dels indicadors de la gestió per processos de la docència pràctica a la Unitat de Laboratoris Docents (ULD) de la Facultat de Farmàcia

[eng] In the Unitat de Laboratoris Docents (ULD) of the Faculty of Pharmacy a Quality System has been implemented to improve the management of the training laboratories and to introduce practical aspects of this system in the formation of the students. In the last years, we have designed the process map, and the flowcharts with the corresponding key point tables from which the indicators have been identified. The main objective of this work was to found a system that allows the evaluation of the ULD service, the teaching innovation introduced as well as the grade of implication of the lecturers who teach practical training and thus are directly responsible for the formation of the students. The values obtained for the operating ULD procedures correspond to the data from obligatory courses, with practical teaching in the ULD laboratories, of Pharmacy and Food Science and Technology degrees for the 2005-06 academic year. [spa] En la Unidad de Laboratorios Docentes (ULD) de la Facultad de Farmacia, se ha implantado un sistema de gestión de la calidad con el objetivo de mejorar la gestión de la docencia práctica y a su vez introducir aspectos prácticos de la gestión de la calidad en la formación de los estudiantes. En los últimos años se ha elaborado el mapa de procesos, el diagrama de flujo y la ficha de cada proceso a partir de la cual ha sido posible la identificación de los indicadores. El Prat, J. et al. Edusfarm, revista d"educació superior en Farmàcia. Núm. 2. 2007 2 principal objetivo del presente trabajo es buscar un sistema que permita evaluar el propio funcionamiento de la ULD, la innovación realizada así como el grado de implicación de los profesores que imparten la docencia práctica y que son responsables directos de la formación de los estudiantes. Los valores obtenidos para los procesos operativos de la ULD provienen de los datos generados en el curso académico 2005-2006 en las asignaturas troncales de las Licenciaturas de Farmacia y de Ciencia y Tecnología de los Alimentos.