“Unmixing” Tissue Gene Expression Signatures from Tumor Biopsies

Emergent molecular measurement methods, such as DNA microarray, qRTPCR, and many others, offer tremendous promise for the personalized treatment of cancer. These technologies measure the amount of specific proteins, RNA, DNA or other molecular targets from tumor specimens with the goal of “fingerprinting” individual cancers. Tumor specimens are heterogeneous; an individual specimen typically contains unknown amounts of multiple tissues types. Thus, the measured molecular concentrations result from an unknown mixture of tissue types, and must be normalized to account for the composition of the mixture. For example, a breast tumor biopsy may contain normal, dysplastic and cancerous epithelial cells, as well as stromal components (fatty and connective tissue) and blood and lymphatic vessels. Our diagnostic interest focuses solely on the dysplastic and cancerous epithelial cells. The remaining tissue components serve to “contaminate” the signal of interest. The proportion of each of the tissue components changes as a function of patient characteristics (e.g., age), and varies spatially across the tumor region. Because each of the tissue components produces a different molecular signature, and the amount of each tissue type is specimen dependent, we must estimate the tissue composition of the specimen, and adjust the molecular signal for this composition. Using the idea of a chemical mass balance, we consider the total measured concentrations to be a weighted sum of the individual tissue signatures, where weights are determined by the relative amounts of the different tissue types. We develop a compositional source apportionment model to estimate the relative amounts of tissue components in a tumor specimen. We then use these estimates to infer the tissuespecific concentrations of key molecular targets for sub-typing individual tumors. We anticipate these specific measurements will greatly improve our ability to discriminate between different classes of tumors, and allow more precise matching of each patient to the appropriate treatment

Multi-isotopic and compositional exploration of factors controlling nitrate pollution

In Catalonia, according to the nitrate directive (91/676/EU), nine areas have been declared as vulnerable to nitrate pollution from agricultural sources (Decret 283/1998 and Decret 479/2004). Five of these areas have been studied coupling hydro chemical data with a multi-isotopic approach (Vitòria et al. 2005, Otero et al. 2007, Puig et al. 2007), in an ongoing research project looking for an integrated application of classical hydrochemistry data, with a comprehensive isotopic characterisation (δ15N and δ18O of dissolved nitrate, δ34S and δ18O of dissolved sulphate, δ13C of dissolved inorganic carbon, and δD and δ18O of water). Within this general frame, the contribution presented explores compositional ways of: (i) distinguish agrochemicals and manure N pollution, (ii) quantify natural attenuation of nitrate (denitrification), and identify possible controlling factors. To achieve this two-fold goal, the following techniques have been used. Separate biplots of each suite of data show that each studied region has a distinct δ34S and pH signatures, but they are homogeneous with regard to NO3- related variables. Also, the geochemical variables were projected onto the compositional directions associated with the possible denitrification reactions in each region. The resulting balances can be plot together with some isotopes, to assess their likelihood of occurrence

Nuevas funcionalidades de LocalGIS-DOS

LocalGIS-DOS es la nueva versión oficial de LocalGIS, el Sistema de Información Territorial Software Libre para Entidades Locales que surgió a iniciativa del Ministerio de Industria, Turismo y Comercio y que está englobado dentro del Plan Avanza. La nueva versión LocalGIS-DOS, que estará disponible en marzo de 2010 coincidiendo con las IV Jornadas de SIG Libre de Girona, va a contar con nuevos módulos que dotarán a LocalGIS de importantes mejoras tecnológicas y funcionales de Gestión Municipal. LocalGIS-DOS incluye un nuevo módulo de Enrutamiento y Cálculo de rutas, tanto en el Módulo de Editor GIS como en la Guía Urbana, que permitirá calcular caminos óptimos y zonas de influencia. El nuevo módulo de Movilidad facilitará la gestión de información municipal desde dispositivos móviles, con herramientas para la edición y visualización de la misma y para su correcta replicación con la base de datos central. LocalGIS-DOS permitirá gestionar varios municipios con intereses comunes de forma simultánea, creando el concepto de Entidad Supramunicipal, pudiendo así gestionar de forma conjunta capas, estilos y usuarios. Esta nueva versión incorpora también la Variable Temporal a las capas de información, permitiendo a los usuarios seleccionar por fechas la información que desean visualizar, facilitando así la elaboración de estudios temporales georreferenciados y el versionado histórico de mapas. También incluye un nuevo Módulo de Gestión de la Ciudad, desde donde se gestionarán avisos, mantenimientos y obras ubicadas en el suelo público. Finalmente indicar que a nivel tecnológico LocalGIS-DOS contará, entre otras, con mejoras relativas al acceso a bases de datos externas, al canal cifrado de comunicación, firma digital de documentos y mejoras en la generación de informes

Selenium cycling in volcanic environments: the role of soils as reactive interfaces

Selenium (Se) is an element with important health implications that is emitted in significant amounts from volcanoes. Attracted by the fertility of volcanic soils, around 10% of the world population lives within 100 km of an active volcano. Nevertheless, the behaviour of Se in volcanic environments is poorly understood. Therefore, the main aim of this thesis is to investigate the role of soils in the Se cycling in volcanic environments. Prior to the geochemical studies, precise and accurate methods for the determination of Se contents, speciation and isotopic signatures were developed. Afterwards, a combination of field studies and lab controlled experiments were performed with soils from two contrasting European volcanic settings: Mount Etna in Sicily (Italy) and Mount Teide in Tenerife (Spain). The results showed a strong link between Se behaviour and soil development, indicating that Se mobility in volcanic soils is controlled by sorption processes and soil mineralogy.