Tracking a genetic signal of extinction-recolonization events in a neotropical tree species: Voucapoua americana Aublet in French Guiana

Drier periods from the late Pleistocene and early Holocene have been hypothesized to have caused the disappearance of various rainforest species over large geographical areas in South America and restricted the extant populations to mesic sites. Subsequent improvement in climatic conditions has been associated with recolonization. Changes in population size associated with these extinction‐recolonization events should have affected genetic diversity within species. However, these historical hypotheses and their genetic consequences have rarely been tested in South America. Here, we examine the diversity of the chloroplast and nuclear genomes in a Neotropical rainforest tree species, Vouacapoua americana (Leguminosae, Caesalpinioideae) in French Guiana. The chloroplast diversity was analyzed using a polymerase chain reaction‐restriction fragment length polymorphism method (six pairs of primers) in 29 populations distributed over most of French Guiana, and a subset of 17 populations was also analyzed at nine polymorphic microsatellite loci. To determine whether this species has experienced extinction‐recolonization, we sampled populations in areas supposedly not or only slightly affected by climatic changes, where the populations would not have experienced frequent extinction, and in areas that appear to have been recently recolonized. In the putatively recolonized areas, we found patches of several thousands of hectares homogeneous for chloroplast variation that can be interpreted as the effect of recolonization processes from several geographical origins. In addition, we observed that, for both chloroplast and nuclear genomes, the populations in newly recolonized areas exhibited a significantly smaller allelic richness than others. Controlling for geographic distance, we also detected a significant correlation between chloroplast and nuclear population differentiation. This result indicates a cytonuclear disequilibrium that can be interpreted as a historical signal of a genetic divergence between fragmented populations. In conclusion, the spatial genetic structure of contemporary V. americana populations shows evidence that this species has experienced large extinction‐recolonization events, which were possibly caused by past climatic change

La fouille de puits. Contraintes, protocoles et perspectives de recherche

En archéologie, la fouille des puits a pendant longtemps été soit incomplète et hâtive, soit mécanisée et imprécise, et parfois réalisée selon des procédures risquées. En raison de la complexité de leur exploration, et malgré certaines découvertes exceptionnelles, les résultats ainsi obtenus sont restés fragmentaires, hétérogènes, et ont relégué ce type de structures au rang de faits archéologiques anecdotiques, voire secondaires. Ces dernières années, de nouvelles approches méthodologiques d..

Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae.

Mycoplasma feriruminatoris is a fast-growing Mycoplasma species isolated from wild Caprinae and first described in 2013. M. feriruminatoris isolates have been associated with arthritis, kerato conjunctivitis, pneumonia and septicemia, but were also recovered from apparently healthy animals. To better understand what defines this species, we performed a genomic survey on 14 strains collected from free-ranging or zoo-housed animals between 1987 and 2017, mostly in Europe. The average chromosome size of the M. feriruminatoris strains was 1,040±0,024 kbp, with 24 % G+C and 852±31 CDS. The core genome and pan-genome of the M. feriruminatoris species contained 628 and 1312 protein families, respectively. The M. feriruminatoris strains displayed a relatively closed pan-genome, with many features and putative virulence factors shared with species from the M. mycoides cluster, including the MIB-MIP Ig cleavage system, a repertoire of DUF285 surface proteins and a complete biosynthetic pathway for galactan. M. feriruminatoris genomes were found to be mostly syntenic, although repertoires of mobile genetic elements, including Mycoplasma Integrative and Conjugative Elements, insertion sequences, and a single plasmid varied. Phylogenetic- and gene content analyses confirmed that M. feriruminatoris was closer to the M. mycoides cluster than to the ruminant species M. yeatsii and M. putrefaciens. Ancestral genome reconstruction showed that the emergence of the M. feriruminatoris species was associated with the gain of 17 gene families, some of which encode defence enzymes and surface proteins, and the loss of 25 others, some of which are involved in sugar transport and metabolism. This comparative study suggests that the M. mycoides cluster could be extended to include M. feriruminatoris. We also find evidence that the specific organization and structure of the DnaA boxes around the oriC of M. feriruminatoris may contribute to drive the remarkable fast growth of this minimal bacterium

Sensitivity of Five Rapid HIV Tests on Oral Fluid or Finger-Stick Whole Blood: A Real-Time Comparison in a Healthcare Setting

BACKGROUND: Health authorities in several countries recently recommended the expansion of human immunodeficiency virus (HIV) antibody testing, including the use of rapid tests. Several HIV rapid tests are now licensed in Europe but their sensitivity on total blood and/or oral fluid in routine healthcare settings is not known. METHODS AND FINDINGS: 200 adults with documented HIV-1 (n=194) or HIV-2 infection (n=6) were prospectively screened with five HIV rapid tests using either oral fluid (OF) or finger-stick whole blood (FSB). The OraQuick Advance rapid HIV1/2 was first applied to OF and then to FSB, while the other tests were applied to FSB, in the following order: Vikia HIV 1/2, Determine HIV 1-2, Determine HIV-1/2 Ag/Ab Combo and INSTI HIV-1/HIV-2. Tests negative on FSB were repeated on paired serum samples. Twenty randomly selected HIV-seronegative subjects served as controls, and the results were read blindly. Most patients had HIV-1 subtype B infection (63.3%) and most were on antiretroviral therapy (68.5%). Sensitivity was 86.5%, 94.5%, 98.5%, 94.9%, 95.8% and 99% respectively, with OraQuick OF, OraQuick FSB, Vikia, Determine, Determine Ag/Ab Combo and INSTI (p<0.0001). OraQuick was less sensitive on OF than on FSB (p=0.008). Among the six patients with three or more negative tests, two had recent HIV infection and four patients on antiretroviral therapy had undetectable plasma viral load. When patients positive in all the tests were compared with patients who had at least one negative test, only a plasma HIV RNA level<200 cp/ml was significantly associated with a false-negative result (p=0.009). When the 33 rapid tests negative on FSB were repeated on serum, all but six (5 negative with OraQuick, 1 with INSTI) were positive. The sensitivity of OraQuick, Determine and Determine Ag/Ab Combo was significantly better on serum than on FSB (97.5%, p=0.04; 100%, p=0.004; and 100%, p=0.02, respectively). CONCLUSION: When evaluated in a healthcare setting, rapid HIV tests were less sensitive on oral fluid than on finger-stick whole blood and less sensitive on finger-stick whole blood than on serum

Paléofeux naturels et anthropiques - dynamique des écosystèmes de Guyane française

International audienceLes analyses anthracologiques menées en contexte de forêt dense sempervirente de Guyane française ont permis de réaliser une synthèse paléoécologique et d'étudier les dynamiques de végétation sur 13 000 ans, du Tardiglaciaire à l'Holocène récent, sous l'impact des fluctuations climatiques et des activités humaines. Les recherches anthracologiques s'inscrivent selon trois problématiques distinctes : paléoclimatique, paléoethnologique et paléoécologique : les charbons sont considérés à la fois en qualité de révélateurs de phases sèches, marqueurs d'anthropisation du milieu naturel et indicateurs des anciennes couvertures végétales. L'omniprésence de niveaux de charbons qui a été constatée dans les sols forestiers de cette région, et qui est attestée dans toute la zone amazonienne, nous a mené à nous interroger sur la signification de ces macrorestes, leur taphonomie et l'origine des feux dont ils sont issus

Un site d'habitat de hauteur sur le Mont Grand Matoury, Île de Cayenne, Guyane française

International audienc

Recherches sur les mécanismes du concrétionnement. Coefficients d'activité des ions, solubilité des sels et de la silice dans les pores de petite taille

Variation of salt or silica solubility as a function of water activity, capillarity pressure or pore size, is discussed as a probable origine of matter migration, concentration, and finally concretioning.La variation de la solubilité des sels et de la silice en fonction de l'activité de l'eau, de la pression capillaire ou de la taille des pores est considérée comme une cause probable de migration ou de concentration de matière. Le mécanisme du concrétionnement est discuté.Tardy Yves, Monnin Christophe. Recherches sur les mécanismes du concrétionnement. Coefficients d'activité des ions, solubilité des sels et de la silice dans les pores de petite taille. In: Bulletin de Minéralogie, volume 106, 3, 1983. pp. 321-328

CISAP : Une équipe de l'INRAP spécialisée dans les interventions au sein des structures profondes

International audienceArchaeological excavations frequently lead archaeologists to the discovery of complex deep structures such as wells, undergrounds, aqueducts or even mines or sinkholes during field research. These articular remains are generally difficult to access and expose a number of risks that archaeologists must deal with to carry out the study. The INRAP (French National Institute for Preventive Archaeologica Research) made the choice, in 2016, to set up a specialized unit in intervention on these unique remains (Cisap). This communication aims to present the protocol implemented to excavate these cavities, whether vertical or horizontal. It will insist on the specific technical aspects of securing deep excavation, taking into account the particular risks associated with working at height and in confined spaces.L'activité de fouille archéologique amène fréquemment les archéologues à la découverte de structures profondes complexes telles que des puits, des souterrains, des aqueducs voire des mines ou des avens lors de leurs opérations. Ces structures particulières sont généralement difficiles d'accès et présentent un certain nombre de risques qu'il convient de prendre en compte avant d'en réaliser l'étude. L'INRAP (Institut National de Recherches Archéologiques Préventives) a fait le choix, en 2016, de se doter d'une cellule spécialisée dans l'intervention sur ces vestiges singuliers (CISAP). Cette communication a pour objectif de présenter le protocole mis en oeuvre pour fouiller ces cavités, qu'elles soient verticales ou horizontales. Elle insistera sur les aspects techniques spécifiques à la sécurisation de la fouille en profondeur, en prenant en compte des risques particuliers liés au travail en hauteur et en espace confiné

Les apports de la plate-forme Archéopuits

Les moyens utilisés jusqu’à la fin des années 1990 ne pouvaient assurer les garanties suffisantes de sécurité dans les actions de descente dans les excavations, de remontée des déblais issus du remplissage et d’évacuation des eaux de pompage. Lors des campagnes de fouille entamées en 1999 au Moulin du Fâ (Charente-Maritime), sous la direction d’Alain Bouet, Jean-Marc Féménias, archéologue amateur et marin-pompier, attire l’attention sur l’impérieuse nécessité d’établir des règles propres à la..