A user's guide to the Encyclopedia of DNA elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome

Comparison of the long-term outcome of two therapeutic strategies for the management of abdominal abscess complicating Crohn's disease: percutaneous drainage or immediate surgical treatment

AimThe management of abdominal abscesses complicating Crohn's disease is complex and involves a difficult choice between medical, radiological and surgical procedures. The long-term outcome was compared for two strategies for the management of abdominal abscess: percutaneous drainage (PD) followed by rescue surgery in the case of failure vs direct immediate surgery (IS). We also compared the results of IS with surgery performed after PD failure. MethodsWe retrospectively identified 44 patients with Crohn's disease with an abdominal abscess from January 2000 to December 2009. Therapeutic success was defined as abscess resolution and no reappearance within 1year of follow-up. ResultsThe first therapeutic approach was PD in 22 cases and IS in the other 22 cases. IS had a higher therapeutic success rate than PD (95.5% vs 27.2% respectively; P<0.001). PD was the only independent variable related to treatment failure in the multivariate analysis after adjustment for possible confounders such as abscess size, multilocularity, presence of fistula and corticosteroid use (OR 88.26, 95% CI 7.38-1055.36; P<0.001). Surgery after failure of PD (n=16) was associated with longer total hospitalization (56.1235.89 vs 27.52 +/- 15.11days; P=0.017) and longer postoperative stay (44.0 +/- 83.7 vs 14.3 +/- 30days; P=0.179) and needed a second operation more often (5/16, 31% vs 1/22, 4.5%; P=0.065) than IS. ConclusionsPercutaneous drainage provided durable abscess resolution in only one-third of the patients compared with more than 90% of those treated with IS. In addition, surgery performed after PD failure results in a poorer outcome than IS

Anales de Edafología y Agrobiología Tomo 47 Número 9-10

l. Suelos. La evaporación y evapotranspiración en el campo de Cartagena y vega media del Segura. Primeros resultados. Por, M. I . Sánchez-Toribio, F. López-Bermudez, F. del Amor y A . Torrecillas.-- Estudio mediante un simulador de lluvia del comportamiento de suelos de Valencia (España) frente a los procesos de erosión por escorrentía y salpicadura. Por, P. Sanroque, J. L. Rubio y L. Izquierdo.-- Química Adsorción de clorprofan (CIPC) por suelos. Por, G. Dios Cancela, J. A . Guillén Alfaro y S. González García.-- Relations betweeri B (total available) and severa! constituents of cultivated soils. Por, A. Ruiz-Nieto, E. Barahona, S. Jaime y A. Aguilar.-- Aplicación de disolución no tamponadas para la extracción de aluminio "activo" ligado a la materia orgánica en suelos ácidos de Galicia. Por, M. Urrutia Mera, E. García-Rodeja Gayoso y F. Macías Vázquez.-- Caracterización química y mineralógica de las formas de hierro en suelos sobre sustrato calizo de Galicia (NW de España). Por, M. T. Barral Silva, M. T. Taboada Castro y F. Guitián Ojea.—Biología. Estructura y variabilidad de las nematocenosis en relación con diversos factores bióticos y abióticos del medio en una vaguada adehesada del Oeste español. Por, J. J. Ibáñez, A. Blanco, A. Bello y J. L. Revuelta.-- Génesis, Clasificación y Cartografía. Suelos de la Isla de Gomera (l. Canarias). III. Meseta central. Ecología, características morfológicas, físico-químicas, mineralógicas, micromorfológicas, clasificación e interpretación. Po r, A . Rodríguez Rodríguez, M. L. Tejedor Salguero y C. Jiménez Mendoza.-- Mosaicos heterocrónicos, heterogénicos y heterolíticos en el macizo de Ayllón (Sistema Central). Repercusiones sobre la tipología de los suelos. Por, J. J. Ibáñez, A. López Lafuente, A. García Alvarez y R. García Giménez.-- Fraccionamiento y distribución de óxidos de hierro en superficies de tipo Raña y altas terrazas al sur del macizo de Ayllón y Somosierra (Sistema Central). Por, R. Jiménez Ballesta, J. J. Ibáñez, F. Monturiol, L. Alcalá y M. L. Palomar.-- Fertilidad. Dinámica de la fracción ligera de la materia orgánica en relación a la producción de nitratos a campo. Por, P. Hashimoto, J. Sierra y L. Barberis.-- II. Biología Vegetal.-Nutrición.-- Absorción del nitrógeno contenido en el agua residual depurada y su influencia en el rendimiento. Por, V. Pérez García, D. González de Chavez Rojo y E. Iglesias Gimenez.-- La nutrición N -NH4 durante el estado vegetativo de Nicotiana Rústica L.: Su efecto sobre el crecimiento. Por, M. D. Saco y M. S. Martín.-- Influencia de nutrientes y polifenoles en la descomposición de la hojarasca de especies autóctonas e introducidas en el sureste español. Por, M. T. Domínguez de Juan, E. González Esparcia y F. Penalva Rodríguez.-- Fisiología Fitotoxicidad por zinc : efectos sobre el crecimiento y contencido de pigmentos fotosintéticos en Phaseolus vulgar1s L. a Jo largo del ciclo de desarrollo . Por, A. Ruano, J. Barceló y Ch. Poschenrieder.-- Efectos del pH ácido y del aluminio sobre Pueraria phaseoloides en simbiosis con Bradyrhizobium SP. Por, C. R. Morales, M. J. Delgado y E. J. BedmarPeer reviewe

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen. Its conidia production is prolific, and so human respiratory tract exposure is almost constant. A. fumigatus is isolated from human habitats and vegetable compost heaps. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus

From Genes to Networks: The Regulatory Circuitry Controlling Candida albicans Morphogenesis

Online first chapterInternational audienceCandida albicans is a commensal yeast of most healthy individuals, but also one of the most prevalent human fungal pathogens. During adaptation to the mammalian host, C. albicans encounters different niches where it is exposed to several types of stress, including oxidative, nitrosative (e.g., immune system), osmotic (e.g., kidney and oral cavity) stresses and pH variation (e.g., gastrointestinal (GI) tract and vagina). C. albicans has developed the capacity to respond to the environmental changes by modifying its morphology, which comprises the yeast-to-hypha transition, white-opaque switching, and chlamydospore formation. The yeast-to-hypha transition has been very well characterized and was shown to be modulated by several external stimuli that mimic the host environment. For instance, temperature above 37 ℃, serum, alkaline pH, and CO2 concentration are all reported to enhance filamentation. The transition is characterized by the activation of an intricate regulatory network of signaling pathways, involving many transcription factors. The regulatory pathways that control either the stress response or morphogenesis are required for full virulence and promote survival of C. albicans in the host. Many of these transcriptional circuitries have been characterized, highlighting the complexity and the interconnections between the different pathways. Here, we present the major signaling pathways and the main transcription factors involved in the yeast-to-hypha transition. Furthermore, we describe the role of heat shock transcription factors in the morphogenetic transition, providing an edifying example of the complex cross talk between pathways involved in morphogenesis and stress response