Bioinformática aplicada a biología integrativa y de sistemas en cáncer

Máster Universitario en Biología y Clínica del Cáncer: Programa, Objetivos y Metodología.Peer Reviewe

Ciudades en busca de riquezas, ¿competitividad, calidad o quimera?

In Europe, the urban plan is changing into a more complex legal document, and is loosing its initial purpose of "giving shape" to the city; in that way, new intervention proposals are appearing, as for example the Strategic Plans. In that way, in the present article, it is questioned if the urban planification tries to get a better quality of life, or if it tries to be useful for the economic development, being the quality of life the final consecuence. It is not answered but it deals about sorne ideas of the relation between cities and richness. So there are comments to sorne texts chosen because all of them respond to the same concept: "the cities are richer and more successful, when they are more creative"

Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License.Mapping and understanding of the protein interaction networks with their key modules and hubs can provide deeper insights into the molecular machinery underlying complex phenotypes. In this article, we present the basic characteristics and definitions of protein networks, starting with a distinction of the different types of associations between proteins. We focus the review on protein-protein interactions (PPIs), a subset of associations defined as physical contacts between proteins that occur by selective molecular docking in a particular biological context. We present such definition as opposed to other types of protein associations derived from regulatory, genetic, structural or functional relations. To determine PPIs, a variety of binary and co-complex methods exist; however, not all the technologies provide the same information and data quality. A way of increasing confidence in a given protein interaction is to integrate orthogonal experimental evidences. The use of several complementary methods testing each single interaction assesses the accuracy of PPI data and tries to minimize the occurrence of false interactions. Following this approach there have been important efforts to unify primary databases of experimentally proven PPIs into integrated databases. These meta-databases provide a measure of the confidence of interactions based on the number of experimental proofs that report them. As a conclusion, we can state that integrated information allows the building of more reliable interaction networks. Identification of communities, cliques, modules and hubs by analysing the topological parameters and graph properties of the protein networks allows the discovery of central/critical nodes, which are candidates to regulate cellular flux and dynamics.This work was supported by the Consejo Superior de Investigaciones Cientificas (CSIC) [project iLINK0398]; the Spanish Government (ISCiii) [project PS09/00843]; and the European Commission [project FP7-HEALTH-2007-223411].Peer Reviewe

APID: Agile Protein Interaction DataAnalyzer

Agile Protein Interaction DataAnalyzer (APID) is an interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform main currently known information about protein–protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore >35 000 different proteins and 111 000 different proven interactions. The web includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Such parameters are for the ‘proteins’: connectivity, cluster coefficient, Gene Ontology (GO) functional environment, GO environment enrichment; and for the ‘interactions’: number of methods, GO overlapping, iPfam domain–domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network. The application is available open access at

Interactome Data and Databases: Different Types of Protein Interaction

In recent years, the biomolecular sciences have been driven forward by overwhelming advances in new biotechnological high-throughput experimental methods and bioinformatic genome-wide computational methods. Such breakthroughs are producing huge amounts of new data that need to be carefully analysed to obtain correct and useful scientific knowledge. One of the fields where this advance has become more intense is the study of the network of ‘protein–protein interactions’, i.e. the ‘interactome’. In this short review we comment on the main data and databases produced in this field in last 5 years. We also present a rationalized scheme of biological definitions that will be useful for a better understanding and interpretation of ‘what a protein–protein interaction is’ and ‘which types of protein–protein interactions are found in a living cell’. Finally, we comment on some assignments of interactome data to defined types of protein interaction and we present a new bioinformatic tool called APIN (Agile Protein Interaction Network browser), which is in development and will be applied to browsing protein interaction databases

Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains

Lactobacillus plantarum is a species of considerable industrial and medical interest. To date, the lack of reliable molecular methods for definite identification at strain level has hindered studies of the population biology of this organism. Here, a multilocus sequence typing (MLST) system for this organism is described, which exploits the genetic variation present in six housekeeping loci to determine the genetic relationship among isolates. The MLST system was established using 16 L. plantarum strains that were also characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S–23S rDNA intergenic spacer region (ISR). Ribotyping grouped the strains into four groups; however, RFLP analysis of the ISRs showed no differences in the strains analysed. In contrast, MLST had a good discriminatory ability. The sequence analysis of the six genes showed 14 different allelic combinations, with 12 of them represented by only one strain. By using this MLST approach we were able to confirm the identity of two strains deposited in the Spanish Type Culture Collection as different strains. Phylogenetic analysis indicated a panmictic population structure of L. plantarum and split decomposition analysis indicated that recombination plays a role in creating genetic heterogeneity in L. plantarum. As MLST allows precise identification, and easy comparison and exchange of results obtained in different laboratories, the future application of this new molecular method could be useful for the identification of valuable L. plantarum strainsThis work has been supported by grants AGL2005-00470 and RM03- 002. We thank R. Gonza´lez and E. Garcı´a for their critical reading of the manuscript. The technical assistance of M. V. Santamarı´a is greatly appreciated. We also thank A. Hexter for correcting the English version. B. de las Rivas is a recipient of a postdoctoral fellowship and A. Marcobal of a predoctoral fellowship both from the Comunidad de Madrid.Peer reviewe

Strengthening the territorial position of Valladolid through planning strategies: Networks, patterns and centralities

The urban condition of the European territory requires new approaches to explain the current development of cities and to propose new planning tools. The aim of this paper is to demonstrate that we can support an innovative perspective based on intermediate geographical scales, more useful for outlining the specific features of territory. While we analyze the territory, we should overcome the strictly local scale of the administrative boundaries and create new relationship between contemporary urban concepts (metropolization of territory and metapolis) and the regional ecological patterns. In the case of Valladolid (E) urban/metropolitan area, we focus on both causes and process of city growth. We have understood that it could be inefficient for planning forgetting the real spatial configuration (the city is located in an intersection between two territorial corridors) and misunderstanding the territorial role of the city at different scales (the double centrality in the emerging urban area and in the region). The significance of this case is to reveal the inter-scalar condition of places as generators of constraints in the contemporary urban fabric and, at the same time, to show the quality and the potential of places in the future urban real

El urbanismo en las escuelas de arquitectura, tensiones en una disciplina

Introduction of Ciudades 2nd.Introducción del nº2 de Ciudades