Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum

The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (～ 1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome.     

Changes in the termite assemblage across a sequence of land-use systems in the rural area around Lamto Reserve in central Côte d’Ivoire

Termites are major decomposers in tropical regions and play an important role in soil processes. This study investigated the termite assemblage structure across a sequence of differing land-use systems. With a standardized method, data were collected on termites from the following habitats: semi-deciduous forest, teak plantation, cocoa plantation, Jatropha plantation, food crop field and 4-years old fallow. Termite species richness declined from the semi-deciduous forest to 4-years old fallow through teak plantation, food crop field, cocoa plantation and Jatropha plantation. The relative abundance of fungus-growers was the highest in all land-use types while that of soil-feeders steeply declined in all man-modified sites. The wood-feeding species showed clear responses to disturbance, with low abundances in monospecific- and modified sites without high trees. Comparisons with other studies suggest that changes in the termite assemblage structure result from forest conversion to agricultural systems. To help mitigate the loss of termites when forests are disturbed or cleared, we recommend to: (1) promote the association of cropping and silvicultural systems that reduces changes in microclimate and maintains the original termite assemblage with the associated ecosystem services; (2) leave dead wood on the ground after forest disturbance to accelerate the recovery of the termite assemblage; and (3) increase forest and silvicultural patch size and reduce length of forest edges to sustain the survival of forest-dependent species.     

Aedes species in treeholes and fruit husks between dry and wet seasons in southeastern Senegal

During the dry season in February, 2010 and the wet season in September, 2011 we sampled mosquito larvae and eggs from treeholes of seven native hardwood species and the husks of Saba senegalensis in 18 sites in the PK‐10 forest in southeastern Senegal. Larvae were reared to adults for species identification. In the dry season, we recovered 408 Aedes mosquitoes belonging to seven species. Aedes aegypti s.l. comprised 42.4% of the collection, followed by Ae. unilineatus (39%). In contrast to reports from East Africa, both Ae. aegypti aegypti and Ae. aegypti formosus were recovered, suggesting that both subspecies survive the dry season in natural larval habitats in West Africa. In the wet season, 455 mosquitoes were collected but 310 (68.1%) were the facultatively predaceous mosquito Eretmapodites chrysogaster. The remaining 145 mosquitoes consisted of ten Aedes species. Aedes aegypti s.l. comprised 55.1% of these, followed by Ae. apicoargenteus (15.2%) and Ae. cozi (11.7%). Similar to East Africa, most (90%) of Ae. aegypti s.l. in the wet season were subspecies formosus.     

Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal

Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically identical parasite strains, coincident with increased deployment of malaria control interventions and decreased malaria deaths. Parasite genotypes in some cases persisted clonally across dry seasons. The increase in frequency of genetically identical parasite strains corresponded with decrease in the probability of multiple infections. Further, these observations support evidence of both clonal and epidemic population structures. These data provide the first evidence of a temporal correlation between the appearance of identical parasite types and increased malaria control efforts in Africa, which here included distribution of insecticide treated nets (ITNs), use of rapid diagnostic tests (RDTs) for malaria detection, and deployment of artemisinin combination therapy (ACT). Our results imply that genetic surveillance can be used to evaluate the effectiveness of disease control strategies and assist a rational global malaria eradication campaign.     

Laboratory and Field Evaluation of the Partec CyFlow MiniPOC for Absolute and Relative CD4 T-Cell Enumeration

BackgroundA new CD4 point-of-care instrument, the CyFlow miniPOC, which provides absolute and percentage CD4 T-cells, used for screening and monitoring of HIV-infected patients in resource-limited settings, was introduced recently. We assessed the performance of this novel instrument in a reference laboratory and in a field setting in Senegal.MethodologyA total of 321 blood samples were obtained from 297 adults and 24 children, all HIV-patients attending university hospitals in Dakar, or health centers in Ziguinchor. Samples were analyzed in parallel on CyFlow miniPOC, FACSCount CD4 and FACSCalibur to assess CyFlow miniPOC precision and accuracy.ResultsAt the reference lab, CyFlow miniPOC, compared to FACSCalibur, showed an absolute mean bias of -12.6 cells/mm³ and a corresponding relative mean bias of -2.3% for absolute CD4 counts. For CD4 percentages, the absolute mean bias was -0.1%. Compared to FACSCount CD4, the absolute and relative mean biases were -31.2 cells/mm³ and -4.7%, respectively, for CD4 counts, whereas the absolute mean bias for CD4 percentages was 1.3%. The CyFlow miniPOC was able to classify HIV-patients eligible for ART with a sensitivity of ≥ 95% at the different ART-initiation thresholds (200, 350 and 500 CD4 cells/mm3). In the field lab, the room temperature ranged from 30 to 35°C during the working hours. At those temperatures, the CyFlow miniPOC, compared to FACSCount CD4, had an absolute and relative mean bias of 7.6 cells/mm³ and 2.8%, respectively, for absolute CD4 counts, and an absolute mean bias of 0.4% for CD4 percentages. The CyFlow miniPOC showed sensitivity equal or greater than 94%.ConclusionThe CyFlow miniPOC showed high agreement with FACSCalibur and FACSCount CD4. The CyFlow miniPOC provides both reliable absolute CD4 counts and CD4 percentages even under the field conditions, and is suitable for monitoring HIV-infected patients in resource-limited settings.     

Arbuscular mycorrhizal soil infectivity and spores distribution across plantations of tropical,subtropical and exotic tree species: a case study from the forest reserve of Bandia,Senegal

Several fast‐growing and multipurpose trees such as exotic and valuable native species have been widely used in West Africa to reverse the tendency of massive degradation of plant cover and restore soil productivity. Although benefic effects have been reported on soil stabilization, a lack of information about their impact on soil symbiotic microorganisms still remains. This investigation has been carried out in field trees of 28 years old in a forest reserve at Bandia. To determine the mycorrhizal inoculum potential (MIP) of soils, a mycorrhizal bioassay was conducted using seedlings of Zea mays L. Spores concentration, arbuscular mycorrhizal (AM) fungi morphotypes and mycorrhizal colonization of field plants were examined. Results showed that fungal communities were dominated in all samples by the genus Glomus. Nevertheless, the others genera Gigaspora and Scutellospora occurred preferentially out of the plantations. The number and richness of spores as well as the MIP of soils were decreased in the tree plantations. Accordingly, the amount of annual herbaceous plants kept out of the tree plantations was much greater than those under the tree plantations. The colonization was higher in field root systems of herb plants in comparison with that of the tree plants. Comparisons allowed us to conclude that vegetation type modifies the AM fungal communities, and the results suggest further adoption of management practices that could improve or sustain the development of herbaceous layers and thus promote the AM fungal communities.     

Changes in soil diversity and global activities following invasions of the exotic invasive plant, Amaranthus viridis L., decrease the growth of native sahelian Acacia species

The objectives of this study were to determine whether the invasive plant Amaranthus viridis influenced soil microbial and chemical properties and to assess the consequences of these modifications on native plant growth. The experiment was conducted in Senegal at two sites: one invaded by A. viridis and the other covered by other plant species. Soil nutrient contents as well as microbial community density, diversity and functions were measured. Additionally, five sahelian Acacia species were grown in (1) soil disinfected or not collected from both sites, (2) uninvaded soil exposed to an A. viridis plant aqueous extract and (3) soil collected from invaded and uninvaded sites and inoculated or not with the arbuscular mycorrhizal (AM) fungus Glomus intraradices . The results showed that the invasion of A. viridis increased soil nutrient availability, bacterial abundance and microbial activities. In contrast, AM fungi and rhizobial development and the growth of Acacia species were severely reduced in A. viridis -invaded soil. Amaranthus viridis aqueous extract also exhibited an inhibitory effect on rhizobial growth, indicating an antibacterial activity of this plant extract. However, the inoculation of G. intraradices was highly beneficial to the growth and nodulation of Acacia species. These results highlight the role of AM symbiosis in the processes involved in plant coexistence and in ecosystem management programs that target preservation of native plant diversity.