Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Reliable molecular typing tools are required for a better understanding of the molecular epidemiology of Plasmodium vivax. The genes msp3a and msp1_block5 are highly polymorphic and have been used as markers in many P. vivax population studies. These markers were used to assess the genetic diversity of P. vivax strains from French Guiana (South America) and to develop a molecular typing protocol. METHODS: A total of 120 blood samples from 109 patients (including 10 patients suffered from more than one malaria episode, samples were collected during each episode) with P. vivax infection were genotyped. All samples were analysed by msp3a PCR-RFLP and msp1_b5 gene sequencing was performed on 57 samples. Genotyping protocol applied to distinguish between new infection or relapse from heterologus hypnozoites and treatment failure or relapse from homologus hypnozoites was based on analysing first msp3a by PCR-RFLP and secondly, only if the genotypes of the two samples are identical, on sequencing the msp1_b5 gene. RESULTS: msp3a alleles of three sizes were amplified by PCR: types A, B and C. Eleven different genotypes were identified among the 109 samples analysed by msp3a PCR-RFLP. In 13.8% of cases, a mixed genotype infection was observed. The sequence of msp1_b5 gene revealed 22 unique genotypes and 12.3% of cases with mixed infection. In the 57 samples analysed by both methods, 45 genotypes were found and 21% were mixed. Among ten patients with two or three malaria episodes, the protocol allowed to identify five new infections or relapses from heterologous hypnozoites and six treatment failures of relapses from homologous hypnozoites. CONCLUSION: The study showed a high diversity of msp3a and msp1_b5 genetic markers among P. vivax strains in French Guiana with a low polyclonal infection rate. These results indicated that the P. vivax genotyping protocol presented has a good discrimination power and can be used in clinical drug trials or epidemiological studies.
ISSN: 1475-2875

pasteur-00590981
https://hal-riip.archives-ouvertes.fr/pasteur-00590981
DOI : 10.1186/1475-2875-8-40
PUBMED : 19284592

Éditeur(s) : HAL CCSD Wiley
Résumé :  
The symbiotic interactions between Frankia strains and their associated plants from the Casuarinaceae under controlled conditions are well documented but little is known about these interactions under natural conditions. We explored the symbiotic interactions between eight genotypically characterized Frankia strains and five Casuarinaceae species in long-term field trials. Characterization of strains was performed using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) for the nifD-nifK intergenic transcribed spacer (ITS) and 16S-23S ITS. Assessments of the symbiotic interactions were based on nodulation patterns using nodule dry weight and viability, and on actual N-2 fixation using the delta N-15 method. The PCR-RFLP patterns showed that the analyzed strains belonged to the same genotypic group (CeD group), regardless of the host species and environment of origin. The nodule viability index is introduced as a new tool to measure the viability of perennial nodules and to predict their effectiveness. The host Casuarinaceae species was a key factor influencing both the actual N-2-fixing activity of the associated Frankia strain and the viability of nodules within a location. This is the first study providing information on the symbiotic interactions between genotypically characterized Frankia strains and actinorhizal plants under natural conditions. The results revealed a way to improve a long-term management of the Casuarinaceae symbiosis.
ISSN: 0031-9317

hal-01032134
https://hal.archives-ouvertes.fr/hal-01032134
DOI : 10.1111/j.1399-3054.2007.00856.x

Éditeur(s) : HAL CCSD Wiley
Résumé :  
The chloroplast genome has been widely used to describe genetic diversity in plant species. Its maternal inheritance in numerous angiosperm species and low mutation rate are suitable characters when inferring historical events such as possible recolonization routes. Here we have studied chloroplast DNA variation using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) with seven pairs of primers and four restriction enzymes in 14 populations of Vouacapoua americana (Caesalpiniaceae) a neotropical tree sampled throughout French Guiana. Population diversity (Hs), total gene diversity (Ht) and differentiation among populations (GST) were estimated using Nei's method as 0.09, 0.87 and 0.89, respectively. This is consistent with the limited gene flow associated with synzoochory in this species. The genetic structure observed in the north of French Guiana suggests that historical events such as contractions and recent recolonizations have had a large impact on the distribution of genetic diversity in this species.
ISSN: 0962-1083

hal-01032176
https://hal.archives-ouvertes.fr/hal-01032176
DOI : 10.1046/j.1365-294x.2000.01027.x

Éditeur(s) : Inter-Research
Résumé : The marine environment is of special interest for studying hybridization between closely related taxa because of the high dispersal potential of planktonic larvae, such as those of most bivalve species. The oysters Crassostrea angulata and C. gigas are known to be very close genetically and entirely inter-fertile under controlled conditions. However, hybridization in the wild had not been investigated, mainly due to the lack of nuclear diagnostic markers. In the present paper, we first estimated genetic differentiation between these 2 closely related taxa using 8 microsatellite markers. Interestingly, 5 markers displayed significant differences of allele size between taxa. The subsequent sequencing of alleles of one of these microsatellites showed several mutational events, which suggested null alleles and homoplasy. The presence of 1 insertion/deletion event in its 5' flanking sequence enabled us to design a new bi-allelic ('C' and 'NC') nuclear PCR-restriction fragment length polymorphism (-RFLP) marker (CG44R). This, together with a mitochondrial DNA marker, was used to analyze populations of C. angulata and C. gigas. The CG44R allele frequencies were very different between C. angulata (f[C] = 0.91) and C. gigas (f[NC] = 0.92) populations. This analysis also provided evidence for hybridization between C. angulata and C. gigas in a wild Portuguese population where the 2 taxa are in contact due to recent transportation of C. gigas stocks for aquacultural production. Our results represent the first indication of hybridization between these 2 taxa in the natural environment, and contribute to knowledge of the evolutionary history of the Crassostrea genus.
Marine Ecology Progress Series (0171-8630) (Inter-Research), 2004 , Vol. 272 , P. 141-152

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2004/publication-3355.pdf
http://archimer.ifremer.fr/doc/00000/3355/

Éditeur(s) : HAL CCSD Instituto de Medicina Tropical
Résumé : International audience
Malaria is a major health problem for people who live on the border between Brazil and French Guiana. Here we discuss Plasmodium vivax distribution pattern in the town of Oiapoque, Amapá State using the circumsporozoite (CS) gene as a marker. Ninety-one peripheral blood samples from P. vivax patients have been studied. Of these, 64 individuals were from the municipality of Oiapoque (Amapá State, Brazil) and 27 patients from French Guiana (August to December 2011). DNA extraction was performed, and a fragment of the P. vivax CS gene was subsequently analyzed using PCR/RFLP. The VK210 genotype was the most common in both countries (48.36% in Brazil and 14.28% in French Guiana), followed by the P. vivax-like (1.10% in both Brazil and French Guiana) and VK247 (1.10% only in Brazil) in single infections. We were able to detect all three CS genotypes simultaneously in mixed infections. There were no statistically significant differences either regarding infection site or parasitaemia among individuals with different genotypes. These results suggest that the same genotypes circulating in French Guiana are found in the municipality of Oiapoque in Brazil. These findings suggest that there may be a dispersion of parasitic populations occurring between the two countries. Most likely, this distribution is associated with prolonged and/or more complex transmission patterns of these genotypes in Brazil, bordering French Guiana.
ISSN: 0036-4665

Droits : http://creativecommons.org/licenses/by-nc/
pasteur-01372566
https://hal-pasteur.archives-ouvertes.fr/pasteur-01372566
https://hal-pasteur.archives-ouvertes.fr/pasteur-01372566/document
https://hal-pasteur.archives-ouvertes.fr/pasteur-01372566/file/1678-9946-rimtsp-58-00072.pdf
DOI : 10.1590/S1678-9946201658072

Éditeur(s) : HAL CCSD Instituto de Medicina Tropical
Résumé : International audience
Malaria is a major health problem for people who live on the border between Brazil and French Guiana. Here we discuss Plasmodium vivax distribution pattern in the town of Oiapoque, Amapá State using the circumsporozoite (CS) gene as a marker. Ninety-one peripheral blood samples from P. vivax patients have been studied. Of these, 64 individuals were from the municipality of Oiapoque (Amapá State, Brazil) and 27 patients from French Guiana (August to December 2011). DNA extraction was performed, and a fragment of the P. vivax CS gene was subsequently analyzed using PCR/RFLP. The VK210 genotype was the most common in both countries (48.36% in Brazil and 14.28% in French Guiana), followed by the P. vivax-like (1.10% in both Brazil and French Guiana) and VK247 (1.10% only in Brazil) in single infections. We were able to detect all three CS genotypes simultaneously in mixed infections. There were no statistically significant differences either regarding infection site or parasitaemia among individuals with different genotypes. These results suggest that the same genotypes circulating in French Guiana are found in the municipality of Oiapoque in Brazil. These findings suggest that there may be a dispersion of parasitic populations occurring between the two countries. Most likely, this distribution is associated with prolonged and/or more complex transmission patterns of these genotypes in Brazil, bordering French Guiana.
ISSN: 0036-4665

inserm-01408935
http://www.hal.inserm.fr/inserm-01408935
http://www.hal.inserm.fr/inserm-01408935/document
http://www.hal.inserm.fr/inserm-01408935/file/2016%2C%20Gomes%20-%20Evaluation%20of%20circumsporozoite%20protein%20of%20Plasmodium%20vivax.pdf
DOI : 10.1590/S1678-9946201658072

Résumé : Three species of man.-rove oysters, Crassostrea rhizophorae, C. brasiliana, and C. gasar, have been described along the Atlantic shores of South America and Africa. Because the distribution of these molluscs is of great biological and commercial interest, their taxonomy and distribution deserve further clarification. Therefore, 15 populations were sampled from both continents. Their 16S mitochondrial polymorphism was studied by sequencing and PCR-RFLP analysis. Two haplotypes were identified. Haplotype a was the only one observed in Africa, but it was also observed in South America together with haplotype b. Because C. gasar is the only mangrove oyster identified on the west coast of Africa, haplotype a was attributed to this species, which has thus been shown to occur in South America. Haplotype b is attributed to C. rhizophorae. The karyotypes of specimens of C. gasar, from Africa and from South America, were very similar, and both species were observed at the same location in Brazil. The occurrence of C. gasar in South America adds a third species-in addition to C rhizophorae and C. brasiliana-to the list of species present along these coasts. The predominant surface circulation patterns in this part of the Atlantic Ocean favor the hypothesis that C. gasar was transported from Africa to America. Finally, a phylogenetic tree built with seven 16S sequences from Crassostrea and Saccostrea species showed that C. gasar is intermediate between the American Crassostrea species (C virginica and C. rhizophorae) and the Asian species (C. gigas and C ariakensis).
Biological Bulletin (0006-3185), 2002-06 , Vol. 202 , N. 3 , P. 232-242

Droits : Marine Biological Laboratory.
http://archimer.ifremer.fr/doc/2002/publication-2790.pdf
http://archimer.ifremer.fr/doc/00000/2790/

Résumé : L'étude de la taxonomie des huîtres est longtemps restée basée sur des critères morphologiques (forme de la coquille et description des organes) et géographiques. Ces considérations sont relativement peu fiables en particulier au niveau interspécifique du fait de la plasticité des caractères morphologiques d'une part de des introductions d'espèces étrangères sur les lieux de culture d'autre part. La biologie moléculaire est donc, depuis quelques années, un outil très utilisé pour différencier les espèces d'huîtres. La phylogéographie des huîtres de la région sud-atlantique a ainsi pu être étudiée grâce à différentes méthodes de recherche du polymorphisme réalisées sur le fragment mitochondrial 16S. La PCR-RFLP, la SSCP et le séquençage ont été utilisés pour déterminer les haplotypes de 9 populations d'huîtres creuses du genre Crassostrea provenant du Sénégal, de Guyane, de Martinique et du Brésil. Ceci a permis par extension à d'autres espèces d'apporter des informations complémentaires à la phylogénie de ce genre. Les résultats obtenus par ces 3 méthodes ont permis de montrer que ces 9 populations se différencient en 2 haplotypes : un africain correspondant à l'espèce Crassostrea gasar et un martiniquais correspondant à l'espèce Crassostrea rhizophorae. De plus,C. gasar, huître caractéristique des côtes africaines, est présente dans 2 sites d'Amérique du sud, ont un en sympatrie avec C. rhizophorae au Brésil, ce qui n'a jamais été décrit jusqu'à présent. L'étude d'un point de vue génétique de cette espèce ainsi que la détermination de sa position phylogénétique, sont également une nouveauté. La sympatrie observée au Brésil permet de s'interroger sur l'existence d'une interfécondité possible et d'un flux de gènes entre les 2 espèces. Des études complémentaires à partir d'un échantillonnage plus vaste réalisé sur toute la côte atlantique sud-américaine permettront de confirmer ces résultats. Par ailleurs, la construction d'un arbre phylogénétique à partir des séquences obtenues dans cette étude et de séquences d'autres espèces du même genre, a permis de préciser les positions de ces espèces les unes par rapport aux autres. Ainsi, C. gasar a une position intermédiaire entre les groupes gigas-angulata et virginica-rhizophorae.

Droits : 1999 Univ; La Rochelle, The author
http://archimer.ifremer.fr/doc/00032/14365/11656.pdf
http://archimer.ifremer.fr/doc/00032/14365/