Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships

in Nucleic Acids Research (2004), 32(11), 3418-3426

Transcription factors (TFs) of bacterial helix-turn-helix superfamilies exhibit different effector-binding domains (EBDs) fused to a DNA-binding domain with a common feature. In a previous study of the ... [more ▼]

Transcription factors (TFs) of bacterial helix-turn-helix superfamilies exhibit different effector-binding domains (EBDs) fused to a DNA-binding domain with a common feature. In a previous study of the GntR superfamily, we demonstrated that classifying members into subfamilies according to the EBD heterogeneity highlighted unsuspected and accurate TF-binding site signatures. In this work, we present how such in silico analysis can provide prediction tools to discover new cis/trans relationships. The TF-binding site consensus of the HutC/GntR subfamily was used to (i) predict target sites within the Streptomyces coelicolor genome, (ii) discover a new HutC/GntR regulon and (iii) discover its specific TF. By scanning the S.coelicolor genome we identified a presumed new HutC regulon that comprises genes of the phosphotransferase system (PTS) specific for the uptake of N-acetylglucosamine (PTSNag). A weight matrix was derived from the compilation of the predicted cis-acting elements upstream of each gene of the presumed regulon. Under the assumption that TFs are often subject to autoregulation, we used this matrix to scan the upstream region of the 24 HutC-like members of S.coelicolor. orf SCO5231 (dasR) was selected as the best candidate according to the high score of a 16 bp sequence identified in its upstream region. Our prediction that DasR regulates the PTSNag regulon was confirmed by in vivo and in vitro experiments. In conclusion, our in silico approach permitted to highlight the specific TF of a regulon out of the 673 orfs annotated as 'regulatory proteins' within the genome of S.coelicolor. [less ▲]

Extending the job Demands-Resources Model : safety behaviour and perceived safety climate.

Conference (2009, May 16)

Extending the theory of planned behavior as a model of cognitive and motivational influences on academic performance

in Dubois, Daniel (Ed.) Computing anticipatory systems : Casys 4th international conference, Liège, Belgium, 7-12 August (2001)

Extension du domaine de la littérature

in Toussaint, Jean-Philippe (Ed.) La Mélancolie de Zidane (2009)

En se penchant sur la finale de la Coupe du monde de foot, Jean-Philippe Toussaint élargit le domaine de la littérature légitime.

Extension du patrimoine commun

in Leleu, Yves-Henri; Verbeke, Alain; Taymans, Jean-François (Eds.) et al Manuel de planification patrimoniale. Le couple, vie commune (2009)

Extension du réseau des rivières modélisées aux très petites masses d’eau et mise à jour des masses d’eau, application du modèle Pégase pour l'Agence de l'Eau Loire-Bretagne

Report (2010)

Dans le cadre de la caractérisation des cours d’eau du milieu naturel, l’Agence de l’Eau Loire- Bretagne a confié à l’Aquapôle la tâche d’étendre la sélection des rivières modélisées par le modèle PEGASE ... [more ▼]

Dans le cadre de la caractérisation des cours d’eau du milieu naturel, l’Agence de l’Eau Loire- Bretagne a confié à l’Aquapôle la tâche d’étendre la sélection des rivières modélisées par le modèle PEGASE aux très petites masses d’eau, permettant de représenter finement l’état de la qualité de l’ensemble des masses d’eau de surface du bassin Loire-Bretagne. [less ▲]

Extension et modulation des usages des outils médiateurs en design industriel. Impact sur les processus de conception.

Master of advanced studies dissertation (2009)

L'observation via une approche ergonomique compréhensive de l'extension et la modulation de l'utilisation des outils médiateurs en design industriel depuis l'avènement de la CAO nous a permis : (i) d ... [more ▼]

L'observation via une approche ergonomique compréhensive de l'extension et la modulation de l'utilisation des outils médiateurs en design industriel depuis l'avènement de la CAO nous a permis : (i) d'élargir les frontières du domaine de la pré-conception telles que généralement présentées : y sont désormais inclues, en plus des dessins à main levée, les représentations externes générées par les outils de CAO, dont le potentiel de soutien aux phases conceptuelles sera révélé lorsque l'on aura extrait des catachrèses, genèses instrumentales et schèmes d'utilisation l'essence des spécifications qui les rendront tout à fait adaptées; (ii) de moduler les niveaux de compréhension des métiers de la conception en design industriel, en soulignant l'importante part de co-conception et de "conception en cohabitation" qui apparaît avec le nouveau métier de dessinateur et l'usage des outils médiateurs. L'intervention sur le terrain est nourrie de ces apports plus conceptuels qui nous aident à comprendre dans quelle mesure l'amélioration des conditions de travail en conception industrielle pourrait concourir à l'atteinte des objectifs ergonomiques pour les autres métiers et les utilisateurs finaux. [less ▲]

Extension of Bayesian procedures to integrate and to blend multiple external information into genetic evaluations

Conference (2012, July 18)

Current genetic evaluations are mostly based on local data, potentially followed by an international second step, as it is performed by INTERBULL (Uppsala, Sweden) for dairy breeds. However, reliability ... [more ▼]

Current genetic evaluations are mostly based on local data, potentially followed by an international second step, as it is performed by INTERBULL (Uppsala, Sweden) for dairy breeds. However, reliability of estimated breeding values (EBV) for animals with few local data may be limited. Furthermore, the current development of genomic selection makes this issue more important and the blending of those multiple sources more necessary. Current methods are based on selection index and Bayesian procedures were proposed for a single external source. The aim of this research was to extend these methods to integrate information from multiple sources outside a given evaluation system, i.e. external information, into this genetic evaluation, i.e. internal evaluation, and to assess its potential to blend multiple sources of information when only external information is available. To allow simplifications of the computational burden and the propagation of all external information through the whole pedigree, all animals were considered as animals associated to external information thanks to the prediction of external information from available one for internal animals, i.e. animals with no external information. Multiple considerations of contributions due to relationships among animals were also taken into account. Two dairy cattle populations were simulated across 5 generations. Internal females were randomly mated with internal and 50 external males. Milk production for the first lactation for each female was simulated in both populations. Results for 100 replicates showed that average rank correlations among Bayesian EBV and EBV based on the joint use of external and internal data were close to 1 for both external and internal animals. The respective correlations for the internal evaluation were equal to 0.54 and 0.95. Mean squared error, expressed as a percentage of the internal mean squared error, was close to 0% for both external and internal animals. Thereby, the Bayesian procedure has the potential to integrate and to blend multiple sources of external information to evaluate animals more reliably. [less ▲]

Extension of INCL4 between 2 and 15 GeV

in Advances in Space Research (2009), 44(8),

The intranuclear cascade model INCL4 has been shown to be very successful for describing, without adjustable parameters, a whole set of data for p-induced reactions in the 40 MeV–2 GeV energy range. In ... [more ▼]

The intranuclear cascade model INCL4 has been shown to be very successful for describing, without adjustable parameters, a whole set of data for p-induced reactions in the 40 MeV–2 GeV energy range. In view of its possible application to cosmic ray interactions, the INCL4 code has been extended to the 2–15 GeV energy range, so covering a large part of the spectrum of the incident energy of the cosmic rays. In this paper, the changes brought into the INCL4 code are discussed and some illustrative comparisons between the results given by the modified version of the code and experimental data are presented. [less ▲]

Extension of the component method to joints in tubular construction

in Puthli, R.; Herion, S. (Eds.) Proceedings of the Ninth International Symposium and Euroconference on Tubular Structures (2001)