eggNOG v4.0: nested orthology inference across 3686 organisms

With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.

Insertion of a malE B-Galactosidase fusion protein into the envelope of Escherichia coli disrupts biogenesis of outer membrane proteins and processing of inner membrane proteins

The synthesis of a membrane-bound MalE ,B-galactosidase hybrid protein, when induced by growth of Escherichia coli on maltose, leads to inhibition of cell division and eventually a reduced rate of mass increase. In addition, the relative rate of synthesis of outer membrane proteins, but not that of inner membrane proteins, was reduced by about 50%o. Kinetic experiments demonstrated that this reduction coincided with the period of maximum synthesis of the hybrid protein (and another maltose-inducible protein, LamB). The accumulation of this abnormal protein in the envelope therefore appeared specifically to inhibit the synthesis, the assembly of outer membrane proteins, or both, indicating that the hybrid protein blocks some export site or causes the sequestration of some limiting factor(s) involved in the export process. Since the MalE protein is normally located in the periplasm, the results also suggest that the synthesis of periplasmic and outer membrane proteins may involve some steps in common. The reduced rate of synthesis of outer membrane proteins was also accompanied by the accumulation in the envelope of at least one outer membrane protein and at least two inner membrane proteins as higher-molecular-weight forms, indicating that processing (removal of the N-terminal signal sequence) was also disrupted by the presence of the hybrid protein. These results may indicate that the assembly of these membrane proteins is blocked at a relatively late step rather than at the level of primary recognition of some site by the signal sequence. In addition, the results suggest that some step common to the biogenesis of quite different kinds of envelope protein is blocked by the presence of the hybrid protein.

Caracterización geológica de la región de enlace entre la Cuenca de Bransfield y la Dorsal Sur de Scotia (Antártida)

La Dorsal Sur de Scotia (DSS) constituye une frontera de placas transformante con sentido senestral, que limita las placas de Scotia, al norte, y Antártica, al sur. Durante la campaña de geología y geofísica marinas 'Scotia 92', realizada en Febrero de 1992 a bordo del BIO Hespérides, se ha estudiado su extremo occidental y sectores próximos a la Cuenca de Bransfield, entre el margen nor-occidental de la Península Antártica y las islas Shetland del Sur, Elefante y Orcadas del Sur. Al norte y sur de la DSS se desarrollan las cuencas de Scotia y de Powell, respectivamente. Los datos de sísmica de multicanal, magnetismo y gravimetna obtenidos muestran caracteristicas diferenciales entre ambas cuencas. La morfoestructura de la DSS, formada por dos crestas paralelas separadas por una profunda depresión axial, ha sido recubierta mediante perfilaje de multihaz con el sistema SIMRAD EM-12 en una área de 50 x 100 km. La batimetría resultante ha permitido reconocer en detalle las caracteristicas de una depresión de más de 5.300 m de profundidad y de 10 a 30 km de anchura, bautizada como Fosa Hespérides. En ella se aprecia la existencia de dos famílias de lineaciones, la primera de dirección E-W y paralela al límite de placas, y la segunda de dirección NW-SE. La primera acomodaría el movimiento cizallante regional mientras que la segunda estaría asociada con una componente extensional probablemente relacionada con la dirección de la Cuenca de Bransfield. La forma romboédrica de la fosa está determinada por la interacción de ambas famílias de lineaciones. Teniendo en cuenta que el límite de placas transcurre entre las dos crestas, interpretamos la Fosa Hespérides como una cuenca de pull-apart desarrollada como consecuencia del movimiento de cizalla a lo largo de la DSS.

Exploring the link between flexible working and organizational performance

The expansion of flexible work experienced since the 1980s in developed economies is consistent with a more generic trend towards organizational flexibility, which many authors see as essential in order to compete in the dynamic global environment (Volberda, 1998). From this point of view, the changing demands of the environment have forced organizations to seek the ability to adapt rapidly and effectively as a means to be successful or even to survive. In the quest for flexibility, every area of the organization has been scrutinized in order to render it as ¿agile¿ as possible. In the human resources arena, this analysis has led to the definition of diverse ¿flexible working practices¿ (FWP) that describe a wide range of employment practices, which differ from the traditional full-time job with a fixed salary and a permanent contract. These practices have been described using other terms, such as ¿alternative¿ (Polivka, 1996; Powell & Mainiero, 1999), ¿non-standard¿ (Kalleberg, 2000), or ¿atypical¿ (De Grip, Hoevenberg, &m Willems, 1997), which coincide in denoting their divergence from the most traditional forms of employment. This article will show that quite different practices have been embraced by the common term ¿flexible working practices.¿ Subsequently, the results of empirical research regarding the implications for organizational performance of a number of flexible practices will be commented on.