Publications

Ever since the observation that collinearity, that is, the sequential activity of Hox genes based on their relative positions within their gene clusters, is conserved throughout most of the animal kingdom, the question has been raised as to what are the underlying molecular mechanisms. In recent years, technological advances have allowed to uncover changes in chromatin organization that accompany collinearity at Hox gene clusters. Here, we discuss insights in the dynamics of histone modifications and 3D organization in Drosophila and mammals and relate these findings to genomic organization of Hox gene clusters. Using these findings, we propose a framework for collinearity, based on five components: clustering, coating, compaction, compartmentalization, and contacts. We argue that these five components may be sufficient to provide a mechanistic ground for the readout of collinearity in Drosophila and vertebrates.

In insects, products of the male reproductive tract are essential for initiating and maintaining the female post-mating response (PMR). The PMR includes changes in egg laying, receptivity to courting males, and sperm storage. In Drosophila, previous studies have determined that the main cells of the male accessory gland produce some of the products required for these processes. However, nothing was known about the contribution of the gland's other secretory cell type, the secondary cells. In the course of investigating the late functions of the homeotic gene, Abdominal-B (Abd-B), we discovered that Abd-B is specifically expressed in the secondary cells of the Drosophila male accessory gland. Using an Abd-B BAC reporter coupled with a collection of genetic deletions, we discovered an enhancer from the iab-6 regulatory domain that is responsible for Abd-B expression in these cells and that apparently works independently from the segmentally regulated chromatin domains of the bithorax complex. Removal of this enhancer results in visible morphological defects in the secondary cells. We determined that mates of iab-6 mutant males show defects in long-term egg laying and suppression of receptivity, and that products of the secondary cells are influential during sperm competition. Many of these phenotypes seem to be caused by a defect in the storage and gradual release of sex peptide in female mates of iab-6 mutant males. We also found that Abd-B expression in the secondary cells contributes to glycosylation of at least three accessory gland proteins: ovulin (Acp26Aa), CG1656, and CG1652. Our results demonstrate that long-term post-mating changes observed in mated females are not solely induced by main cell secretions, as previously believed, but that secondary cells also play an important role in male fertility by extending the female PMR. Overall, these discoveries provide new insights into how these two cell types cooperate to produce and maintain a robust female PMR.

The limitations of a traditional morphology-based classification of Foraminifera have been demonstrated by molecular phylogenetic studies for several years now. Despite the accumulation of molecular data, no alternative higher-level taxonomic system incorporating these data has been proposed yet. Here, we present a new supraordinal classification of Foraminifera based on an updated SSU rDNA phylogeny completed with the description of major morphological trends in the evolution of this group. According to the new system, multi-chambered orders are grouped in two new classes: Tubothalamea and Globothalamea. Naked and single-chambered Foraminifera possessing agglutinated or organic-walled tests are arranged into a paraphyletic assemblage of “monothalamids”. The new system maintains some multi-chambered calcareous orders, such as Rotaliida, Miliolida, Robertinida and Spirillinida, although their definitions have been modified in some cases to include agglutinated taxa. The representatives of the planktonic order Globigerinida are tentatively included in the order Rotaliida. The agglutinated Textulariida are probably paraphyletic. The position of the order Lagenida is uncertain because reliable molecular data are only available for one species. The new classification system separates orders or families, which differ in basic chamber shapes, prevailing mode of coiling and distance between successive apertures. It appears that these features correspond better to the main evolutionary trends in Foraminifera than wall composition and structure, both used in traditional classification.

Persons infected with human immunodeficiency virus (HIV) have increased rates of coronary artery disease (CAD). The relative contribution of genetic background, HIV-related factors, antiretroviral medications, and traditional risk factors to CAD has not been fully evaluated in the setting of HIV infection.

Evolutionary studies benefit from deep sequencing technologies that generate genomic and transcriptomic sequences from a variety of organisms. Genome sequencing and RNAseq have complementary strengths. In this study, we present the assembly of the most complete Hydra transcriptome to date along with a comparative analysis of the specific features of RNAseq and genome-predicted transcriptomes currently available in the freshwater hydrozoan Hydra vulgaris.

The arylamine N-acetyltransferases (NATs) are a unique family of enzymes widely distributed in nature that play a crucial role in the detoxification of aromatic amine xenobiotics. Considering the temporal changes in the levels and toxicity of environmentally available chemicals, the metabolic function of NATs is likely to be under adaptive evolution to broaden or change substrate specificity over time, making NATs a promising subject for evolutionary analyses. In this study, we trace the molecular evolutionary history of the NAT gene family during the last ~450 million years of vertebrate evolution and define the likely role of gene duplication, gene conversion and positive selection in the evolutionary dynamics of this family.

The vertebrate body plan is characterized by an increased complexity relative to that of all other chordates and large-scale gene amplifications have been associated with key morphological innovations leading to their remarkable evolutionary success. Here, we use compound full Hox clusters deletions to investigate how Hox genes duplications may have contributed to the emergence of vertebrate-specific innovations. We show that the combined deletion of HoxA and HoxB leads to an atavistic heart phenotype, suggesting that the ancestral HoxA/B cluster was co-opted to help in diversifying the complex organ in vertebrates. Other phenotypic effects observed seem to illustrate the resurgence of ancestral (plesiomorphic) features. This indicates that the duplications of Hox clusters were associated with the recruitment or formation of novel cis-regulatory controls, which were key to the evolution of many vertebrate features and hence to the evolutionary radiation of this group.

Recent archaeological survey conducted in Mali in the Guringin Valley, located in the Séno Plain, as well as at the top of the nearby Bandiagara Escarpment, has produced evidence allowing the characterisation of numerous settlement sites and locations at which prehistoric metallurgy was practised. The latter have abundant surface material, mainly consisting of ceramics that show a considerable diversity of decoration. Analysis of the surface pottery assemblages, complemented by that of stratified assemblages from a test pit at one of the sites, indicates important inter-site differences. The results suggest that water, a rare and precious resource in this sandy Sudano-Sahelian plain, attracted the settlement of different populations from Neolithic times to the present, with a particular density of occupation during the first and early second millennia AD. Groups of sites of similar modest size evoke the rural settlements of the Méma area of Mali more than the settlement clusters of the Inland Niger Delta, which are defined by large sites surrounded by satellite settlements in a context of proto-urbanisation. Les prospections archéologiques menées au Mali dans la vallée du Guringin, située dans la plaine du Séno, et sur le sommet de la Falaise de Bandiagara toute proche, ont permis de mettre en évidence et de caractériser de nombreux sites d'habitat ainsi que des lieux d'activités métallurgiques. Ces derniers livrent en surface un matériel abondant, constitué majoritairement de fragments de céramiques aux décors très variés. L'analyse des assemblages céramiques de surface, complétée d'assemblages stratifiés issus d'un sondage sur l'un des sites, nous indique des différences intersites significatives. Les résultats suggèrent une occupation de diverses populations attirées par l'eau, rare et précieuse dans cette plaine sableuse soudano-sahlienne, et ceci du Néolithique à la période actuelle, avec une densité particulière durant le premier et le début du second millénaire ap. J.C. Les ensembles de sites de tailles modestes et équivalentes se rapprochent plus des regroupements de sites ruraux du Méma que des clusters du Delta intérieur du Niger, définis par un site principal entouré de satellites, caractéristiques d'un contexte de proto-urbanisation.

A species of Galápagos tortoise endemic to Española Island was reduced to just 12 females and three males that have been bred in captivity since 1971 and have produced over 1700 offspring now repatriated to the island. Our molecular genetic analyses of juveniles repatriated to and surviving on the island indicate that none of the tortoises sampled in 1994 had hatched on the island versus 3% in 2004 and 24% in 2007, which demonstrates substantial and increasing reproduction in situ once again. This recovery occurred despite the parental population having an estimated effective population size