Biomedical subjects
Patrick Durand
Publications and source records attributed to Patrick Durand.
Integration of data and methods for genome analysis.
The development of genomic and post-genomic technologies has created an explosion in the quantity, diversity and availability of both biological data and methods of analysis. Biologists are currently facing the problem of using all these resources to convert raw data into new valuable knowledge. This review presents software platforms designed to handle data and/or methods in the context of genome analysis.
Genetic diversity and population structure of Plasmodium falciparum isolates from Dakar, Senegal, investigated from microsatellite and antigen determinant loci.
We investigated the genetic diversity and the population structure of 32 Plasmodium falciparum blood sample isolates (25 from Dakar city and suburbs and seven from other localities in Senegal) with two different types of molecular markers, 19 microsatellite and four antigenic determinant loci. Under the same technical procedure, microsatellite loci showed a mean number of alleles greater than that of antigenic loci. Both markers revealed that 15.6% of blood samples were multi-infected. Mean expected heterozygosity calculated from microsatellites and antigens was similar, 0.74 and 0.70, respectively. Significant linkage disequilibrium was observed from microsatellite loci and antigenic determinant loci. This suggests a non-panmictic structure for this sample that could be explained by two non-exclusive hypotheses: (i) a particular mating system (i.e. clonality), and/or (ii) a population structure in P. falciparum (i.e. Wahlund effect). Urban samples could have been drawn from a heterogeneous set of foci with different level of parasitic transmission. Moreover, no relationship was found between multilocus genotypes and different parameters (i.e. age, sex and blood group of parasitized patients; number of trophozoites per microliter of blood). The results are discussed taking into account recently published studies on malaria population biology.
Morphometric and genetic variability of Rodentolepis asymmetrica (Hymenolepididae) from the Pyrenean mountains.
Rodentolepis asymmetrica (Janicki, 1904), is a common hymenolepidid cestode recorded in several vole species (rodents) in the Palearctic. Here, we report a detailed analysis of this species, which includes metrical features and multilocus enzyme electrophoresis. Worms isolated from 4 species of arvicolid hosts in 3 localities in Spain and France from 1994 to 1997 were studied. All the worms used in the morphological study ranged between I and 5 individuals per host. Furthermore, all individuals were analyzed electrophoretically. Statistical analysis of metrical features in scolex, sexual segments, and eggs was carried out, and significant differences were detected only in sexual structures of mature segments. These differences were found in worms from each host species in different localities and in the same host species in 2 localities. Multivariate statistical analysis shows correct classification of worms in all cases. Surprisingly, we observed a lack of genetic variability at the 11 enzymatic loci analyzed, which could be explained by 2 nonexclusive hypotheses: (1) a preferential selfing mode of reproduction for these parasites, and (2) a weak effective size of parasite populations.
[The active site of human glucocerebrosidase: structural predictions and experimental validations].
Gaucher disease is a lysosomal storage disorder caused by a deficiency in glucocerebrosidase which cleaves the beta-glucosidic linkage of glucosylceramide, a normal intermediate in glycolipid metabolism. Glucocerebrosidase belongs to the clan GH-A of glycoside hydrolases, a large group of enzymes which function with retention of the anomeric configuration at the hydrolysis site. Accurate three-dimensional (3D) structure data for glucocerebrosidase should help to better understand the molecular bases of Gaucher disease. As such 3D structure data were not available, we used the two-dimensional hydrophobic cluster analysis (HCA) method to make structure predictions for the catalytic domains of clan GH-A glycoside hydrolases. We found that all the enzymes of clan GH-A may share a similar catalytic domain consisting of an (alpha/beta)8 barrel with the critical acid/base and nucleophile residues located at the C-terminal ends of strands beta 4 and beta 7, respectively. In the case of glucocerebrosidase, Glu 235 was predicted to be the putative acid/base catalyst whereas the nucleophile was located at Glu 340. Next, in order to obtain experimental evidence supporting these HCA-based predictions, we used retroviral vectors to express, in murine null cells, E235A and E340A mutant proteins, in which alanine residues unable to participate in the enzymatic reaction replace the presumed critical glutamic acid residues. Both mutants were found to be catalytically inactive although they were correctly folded/processed and sorted to the lysosome. Thus, Glu 235 and Glu 340 do indeed play key roles in the active site of human glucocerebrosidase as predicted by the HCA analysis. In a broader perspective, our work points out that bioinformatics approaches may be highly useful for generating structure-function predictions based on sequence-structure interrelationships, especially in the context of a rapid increase in protein sequence information through genome sequencing.