Response of the human gut and saliva microbiome to urbanization in Cameroon.

Urban populations from highly industrialized countries are characterized by a lower gut bacterial diversity as well as by changes in composition compared to rural populations from less industrialized countries. To unveil the mechanisms and factors leading to this diversity loss, it is necessary to identify the factors associated with urbanization-induced shifts at a smaller geographical scale, especially in less industrialized countries. To do so, we investigated potential associations between a variety of dietary, medical, parasitological and socio-cultural factors and the gut and saliva microbiomes of 147 individuals from three populations along an urbanization gradient in Cameroon. We found that the presence of Entamoeba sp., a commensal gut protozoan, followed by stool consistency, were major determinants of the gut microbiome diversity and composition. Interestingly, urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas, suggesting that the loss of bacterial microbiome diversity observed in industrialized areas is likely associated with medication. Finally, we observed a weak positive correlation between the gut and the saliva microbiome diversity and composition, even though the saliva microbiome is mainly shaped by habitat-related factors

Spatial and phylogenetical closeness between chimpanzees and humans and health consequences. Study case of Kibale national park, Uganda

Chimpanzee, our closest relative, is today severely threatened by habitat fragmentation. As a consequence, people and chimpanzees live in increasing proximity. In order to estimate the risks for both species due to such changes, we aim at understanding if chimpanzees avoid the interface and limit occasions of contact with human beings. Fifteen years of research on two chimpanzee communities at Kibale National Park (Uganda) demonstrate that chimpanzees do not avoid forest boundaries, cross tarmac road and that human activities are frequent in the protected area. Direct consequences on chimpanzee health include severe mutilations due to poaching. The diagnosis of similar parasites in both species underlines the potential risk of interspecific transmission and the necessity to expand such study for public health and conservation issuesLe Chimpanzé, espèce vivante la plus proche phylogénétiquement de l’homme, est aujourd’hui menacée de disparition en particulier par la fragmentation des forêts tropicales. Afin d’évaluer les risques pour les deux espèces de cette proximité spatiale en potentielle augmentation, notre objectif est d’étudier si les chimpanzés évitent les interfaces et si leur santé témoignent de ces éventuels contacts. Quinze années de recherche sur deux communautés de chimpanzés sauvages du parc national de Kibale (Ouganda) montrent que les chimpanzés n’évitent pas les lisières, traversent une route à fort trafic et que les activités humaines en forêt sont fréquentes. Nos observations révèlent des conséquences sévères sur leur santé: mutilations dues au braconnage et détection d’agents pathogènes similaires, impliquant probablement des transmissions interspécifiques. Dans un contexte où les maladies émergentes peuvent entraîner des conséquences fatales sur la santé des hommes et des chimpanzés, il est primordial d’approfondir ces travaux pour la santé publique et la conservatio

beDNA : un projet visant à la collection systématique d’échantillons humains archéologiques à vocation paléogénétique – une première expérimentation

La paléogénétique occupe désormais une place importante dans les problématiques archéologiques. Toutefois, les analyses d’ADN ancien peuvent être desservies, voire empêchées, par l’état de préservation des échantillons en raison de contamination par de l’ADN moderne ou de mauvaises conditions de stockage. Le projet beDNA, "banque d’échantillons et de Données Nationale Archéogénétique", souhaite donner les moyens d’analyses paléogénétiques futures, en proposant le stockage systématique d’échantillons des squelettes humains tenant compte des contraintes inhérentes à la préservation de l’ADN ancien. Le projet implique (1) un protocole systématique d’échantillonnage "propre" des restes humains sur le terrain commun à toutes les opérations archéologiques, (2) un espace de stockage dédié à ces échantillons adapté à la conservation de l’ADN ancien, (3) une base de données faisant le lien entre les sites et les échantillons conservés dans la banque, (4) l’approbation par l’État des demandes d’analyse d’échantillons après expertise. La phase de test du projet, initiée en septembre 2020 sur la région Île-de-France, nous a permis d’évaluer et d’ajuster le protocole d’échantillonnage sur le terrain et les dispositifs de transfert vers la banque. Cette note présente les étapes envisagées pour chaque échantillon, depuis les terrains jusqu’aux laboratoires d’analyse génétique, ainsi que le déroulement de sa phase test, en cours, et les premiers retours d’expérience.Palaeogenetics is becoming increasingly important in tackling archaeological issues. However, analyses of ancient DNA can be hampered or even prevented by the state of preservation of samples due to poor storage conditions, and because of contamination by modern DNA. The beDNA project for a national archaeological genetic data and sample bank (banque d’échantillons et de Données Nationale Archéogénétique) is developing the means to enable future palaeogenetic analyses by systematically storing human skeletal samples, with the constraints inherent to the preservation of ancient DNA taken into account. This project comprises (1) a systematic protocol for "clean" sampling of human remains to be common to all archaeological operations, (2) a dedicated storage space for samples, suited to aDNA preservation, (3) a database linking sites with the samples stored in the bank, (4) approval of sample analysis requests by authorities, after expert review. The test phase of the project, which began in September 2020 in the Île-de-France region, enabled us to evaluate and adjust both the sampling protocol in the field and the transfer process to the beDNA bank. This note describes the different stages envisaged for each sample, from the archaeological field to the genetics laboratory, as well as the development of the experimental phase and initial feedback from it

Nodular Worm Infection in Wild Chimpanzees in Western Uganda: A Risk for Human Health?

This study focused on Oeosophagostomum sp., and more especially on O. bifurcum, as a parasite that can be lethal to humans and is widespread among humans and monkeys in endemic regions, but has not yet been documented in apes. Its epidemiology and the role played by non-human primates in its transmission are still poorly understood. O. stephanostomum was the only species diagnosed so far in chimpanzees. Until recently, O. bifurcum was assumed to have a high zoonotic potential, but recent findings tend to demonstrate that O. bifurcum of non-human primates and humans might be genetically distinct. As the closest relative to human beings, and a species living in spatial proximity to humans in the field site studied, Pan troglodytes is thus an interesting host to investigate. Recently, a role for chimpanzees in the emergence of HIV and malaria in humans has been documented. In the framework of our long-term health monitoring of wild chimpanzees from Kibale National Park in Western Uganda, we analysed 311 samples of faeces. Coproscopy revealed that high-ranking males are more infected than other individuals. These chimpanzees are also the more frequent crop-raiders. Results from PCR assays conducted on larvae and dried faeces also revealed that O. stephanostomum as well as O. bifurcum are infecting chimpanzees, both species co-existing in the same individuals. Because contacts between humans and great apes are increasing with ecotourism and forest fragmentation in areas of high population density, this paper emphasizes that the presence of potential zoonotic parasites should be viewed as a major concern for public health. Investigations of the parasite status of people living around the park or working inside as well as sympatric non-human primates should be planned, and further research might reveal this as a promising aspect of efforts to reinforce measures against crop-raiding

Elevated rates of horizontal gene transfer in the industrialized human microbiome

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.Peer reviewe

Rad51 Polymerization Reveals a New Chromatin Remodeling Mechanism

Rad51 protein is a well known protagonist of homologous recombination in eukaryotic cells. Rad51 polymerization on single-stranded DNA and its role in presynaptic filament formation have been extensively documented. Rad51 polymerizes also on double-stranded DNA but the significance of this filament formation remains unclear. We explored the behavior of Saccharomyces cerevisiae Rad51 on dsDNA and the influence of nucleosomes on Rad51 polymerization mechanism to investigate its putative role in chromatin accessibility to recombination machinery. We combined biochemical approaches, transmission electron microscopy (TEM) and atomic force microscopy (AFM) for analysis of the effects of the Rad51 filament on chromatinized templates. Quantitative analyses clearly demonstrated the occurrence of chromatin remodeling during nucleoprotein filament formation. During Rad51 polymerization, recombinase proteins moved all the nucleosomal arrays in front of the progressing filament. This polymerization process had a powerful remodeling effect, as Rad51 destabilized the nucleosomes along considerable stretches of DNA. Similar behavior was observed with RecA. Thus, recombinase polymerization is a powerful mechanism of chromatin remodeling. These remarkable features open up new possibilities for understanding DNA recombination and reveal new types of ATP-dependent chromatin dynamics

HIV-1 Protease and Reverse Transcriptase Control the Architecture of Their Nucleocapsid Partner

The HIV-1 nucleocapsid is formed during protease (PR)-directed viral maturation, and is transformed into pre-integration complexes following reverse transcription in the cytoplasm of the infected cell. Here, we report a detailed transmission electron microscopy analysis of the impact of HIV-1 PR and reverse transcriptase (RT) on nucleocapsid plasticity, using in vitro reconstitutions. After binding to nucleic acids, NCp15, a proteolytic intermediate of nucleocapsid protein (NC), was processed at its C-terminus by PR, yielding premature NC (NCp9) followed by mature NC (NCp7), through the consecutive removal of p6 and p1. This allowed NC co-aggregation with its single-stranded nucleic-acid substrate. Examination of these co-aggregates for the ability of RT to catalyse reverse transcription showed an effective synthesis of double-stranded DNA that, remarkably, escaped from the aggregates more efficiently with NCp7 than with NCp9. These data offer a compelling explanation for results from previous virological studies that focused on i) Gag processing leading to nucleocapsid condensation, and ii) the disappearance of NCp7 from the HIV-1 pre-integration complexes. We propose that HIV-1 PR and RT, by controlling the nucleocapsid architecture during the steps of condensation and dismantling, engage in a successive nucleoprotein-remodelling process that spatiotemporally coordinates the pre-integration steps of HIV-1. Finally we suggest that nucleoprotein remodelling mechanisms are common features developed by mobile genetic elements to ensure successful replication

Flemish Normative Data for the Buschke Selective Reminding Test

The purpose of this study was to provide normative data for a Flemish version of the Buschke Selective Reminding Test (SRT). The SRT allows for the simultaneous analysis of several components of verbal memory, such as short and long term retrieval. The Flemish SRT was administered to 3257 neurologically healthy adults (1627 men and 1630 women, age range = 18–94 years). Effects of age, sex and education on SRT performance were assessed. Results indicate that SRT performance decreased with age and that this decline accelerated in men compared to women. Furthermore, an effect of education was found favoring participants who completed a higher education. Normative data quantified through percentile ranks and stratified by age, sex and education level are provided.status: publishe