Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum. Results: Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, interpopulation differentiation, and the degree to which allele frequencies are correlated between populations. Conclusions: The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits.

Protective effect of different tetrafluorides on erosion of pellicle-free and pellicle-covered enamel and dentine

The aim was to analyze the protective effects of titanium, zirconium and hafnium tetrafluorides on erosion of pellicle-free and pellicle-covered enamel and dentine in vitro. Eight groups of 20 specimens each of bovine enamel and bovine dentine were prepared. Half the specimens in each group were immersed in human saliva for 2 h for pellicle formation. Specimens were then left untreated (controls) or were treated for 120 s with TiF(4), ZrF(4) or HfF(4) solutions (0.4 or 1%) or 1.25% AmF/NaF gel. All specimens were eroded by exposure to hydrochloric acid, pH 2.6, for 25 min. Cumulative calcium release into the acid was monitored in consecutive 30-second intervals for 5 min, then at 2-min intervals up to a total erosion time of 25 min using the Arsenazo III procedure. Data were analyzed by ANOVA. 1% TiF(4) solution offered the best protective effect, especially in dentine (reduction of calcium loss about 50% at 25 min). 1% ZrF 4, 1% HfF 4 and 0.4% TiF(4) also reduced calcium loss, but to a lesser extent. Long-term effects were limited to dentine, while reduction of enamel erosion (about 25%) was restricted to 1-min erosion. The fluoride gel had a protective effect only in dentine. The efficacy of the tetrafluorides was influenced by the presence of the pellicle layer, in that the protection against dentine erosion by TiF(4) and ZrF(4) was greater on pellicle-covered specimens. Tetrafluoride solutions, especially 1% TiF(4), could decrease dental erosion, but were more effective on dentine than on enamel. Copyright (C) 2008 S. Karger AG, Basel.