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Kindong R, Wu F, Sarr O, Zhu J. A simulation-based option to assess data-limited fisheries off West African waters. Sci Rep 2023; 13:15290. [PMID: 37714923 PMCID: PMC10504299 DOI: 10.1038/s41598-023-42521-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023] Open
Abstract
Most sophisticated stock assessment models often need a large amount of data to assess fish stocks, yet this data is often lacking for most fisheries worldwide, resulting in the increasing demand for data-limited stock assessment methods. To estimate fish stock status, one class of these data-limited methods uses simply catch time series data and, in other instances, life history information or fishery characteristics. These catch-only methods (COMs) built differently are known to make assumptions about changes in fishing effort and may perform differently under various fishing scenarios. As a case study, this paper used European anchovy (Engraulis encrasicolus) caught in the northwest African waters, though very economically and ecologically important, but still unassessed. Our study investigated the performance of five COMs under different fishing scenarios using as a reference the life-history information of the European anchovy captured in this region of the Atlantic. Hence, the present study developed a simulation approach to evaluate the performance of the five COMs in inferring the stock biomass status (B/BMSY) with consideration of different fishing scenarios under prior information true to anchovy. All five COMs mostly underestimated B/BMSY throughout the simulation period, especially under constant fishing mortality, and in the last five years of the simulation during all fishing scenarios. Overall, these COMs were generally poor classifiers of stock status, however, the state-space COM (SSCOM) generally performed better than the other COMs as it showed possibilities of recovering an overfished stock. When these methods were explored using actual anchovy catch data collected in the northwest African waters, SSCOM yielded results that were deferred from the other COMs. This study being the first to assess this species' stock in this area using a suite of COMs, presents more insights into the species stock status, and what needs to be considered before scientifically putting in place management measures of the stock in the area.
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Affiliation(s)
- Richard Kindong
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China.
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai, 201306, China.
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, China.
- National Engineering Research Centre for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China.
| | - Feng Wu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai, 201306, China
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, China
- National Engineering Research Centre for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Ousmane Sarr
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiangfeng Zhu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China.
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai, 201306, China.
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, 201306, China.
- National Engineering Research Centre for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China.
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Kindong R, Sarr O, Wang J, Xia M, Wu F, Dai L, Tian S, Dai X. Size distribution patterns of silky shark Carcharhinus falciformis shaped by environmental factors in the Pacific Ocean. Sci Total Environ 2022; 850:157927. [PMID: 35963405 DOI: 10.1016/j.scitotenv.2022.157927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Commercial fisheries, especially pelagic longline fisheries targeting tuna and/or swordfish, often land silky sharks (Carcharhinus falciformis), which are currently listed as vulnerable by the International Union for Conservation of Nature (IUCN). Due to increasing fishing effort and the fact that they overlap in habitat with target species, the population trend of silky sharks is declining worldwide. Understanding their relationships with environmental variables that lead to their capture by fisheries is critical for their management and conservation. Nevertheless, little is known about their size distribution in relation to environmental variables in the Pacific Ocean. Using data from the Chinese Observer Tuna Longline fishery from 2010 to 2020, this study developed a species distribution model (SDM) to analyze the relationships between silky shark size distribution patterns and environmental variables and spatio-temporal variability at fishing locations. Observed sizes ranged from 36 to 269 cm fork length (FL). The final model suggests that sea surface temperature (SST), primary production (photosynthetically available radiation, PAR), and ocean surface winds were the key environmental variables shaping size distribution patterns of silky sharks in the Pacific. A high proportion of larger silky sharks has been predicted in areas associated with productive upwelling systems. In addition, the model predicted that larger specimens (>140 cm FL) occur near the equator, and smaller specimens farther from the equator but still in tropical regions. Two regions in the eastern Pacific (the coastal upwelling area off northern Peru and the waters around the Galapagos Islands) seem to be important locations for larger specimens. The size distribution patterns of silky sharks in relation to environmental variables presented in this study illustrate how this species segregates spatially and temporally and presents potential habitat preference areas. The information obtained in the present study is critical in the quest for management and conservation of menaced species such as the silky shark.
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Affiliation(s)
- Richard Kindong
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai 201306, China; Key Laboratory of Oceanic Fisheries Exploitation, Ministry of Agriculture, Shanghai 201306, China; Scientific Observing and Experimental Station of Oceanic Fishery Resources, Ministry of Agriculture, Shanghai 201306, China.
| | - Ousmane Sarr
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jiaqi Wang
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai 201306, China; Key Laboratory of Oceanic Fisheries Exploitation, Ministry of Agriculture, Shanghai 201306, China; Scientific Observing and Experimental Station of Oceanic Fishery Resources, Ministry of Agriculture, Shanghai 201306, China
| | - Meng Xia
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai 201306, China; Key Laboratory of Oceanic Fisheries Exploitation, Ministry of Agriculture, Shanghai 201306, China; Scientific Observing and Experimental Station of Oceanic Fishery Resources, Ministry of Agriculture, Shanghai 201306, China
| | - Feng Wu
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai 201306, China; Key Laboratory of Oceanic Fisheries Exploitation, Ministry of Agriculture, Shanghai 201306, China; Scientific Observing and Experimental Station of Oceanic Fishery Resources, Ministry of Agriculture, Shanghai 201306, China
| | - Libin Dai
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Siquan Tian
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai 201306, China; Key Laboratory of Oceanic Fisheries Exploitation, Ministry of Agriculture, Shanghai 201306, China; Scientific Observing and Experimental Station of Oceanic Fishery Resources, Ministry of Agriculture, Shanghai 201306, China.
| | - Xiaojie Dai
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, Shanghai 201306, China; Key Laboratory of Oceanic Fisheries Exploitation, Ministry of Agriculture, Shanghai 201306, China; Scientific Observing and Experimental Station of Oceanic Fishery Resources, Ministry of Agriculture, Shanghai 201306, China
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Kindong R, Xia M, Pandong NA, Sarr O, Wu F, Tian S, Dai X. All we know about the crocodile shark (Pseudocarcharias kamoharai): Providing information to improve knowledge of this species. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Wu F, Kindong R, Dai X, Sarr O, Zhu J, Tian S, Li Y, Nsangue BTN. Aspects of the reproductive biology of two pelagic sharks in the eastern Atlantic Ocean. J Fish Biol 2020; 97:1651-1661. [PMID: 32892380 DOI: 10.1111/jfb.14526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
This study used data provided by the Chinese Longline Fishery Scientific Observer Programme from the tropical eastern Atlantic Ocean to estimate the reproductive parameters of the blue shark (Prionace glauca) and crocodile shark (Pseudocarcharias kamoharai). Sizes ranged from 80 to 298 cm fork length (FL) for blue sharks and from 48 to 99 cm FL for crocodile sharks. Sexual segregation was observed during different months for both sharks. The sex ratio for blue sharks was 1.38 F:1 M, and 1 F:2.79 M for crocodile sharks. The size of adult blue sharks ranged from 144 to 280 cm for males and from 174 to 298 cm for females; and that of crocodile sharks from 63 to 97 cm for males and 78-99 cm for females. The size at 50% of maturity for blue sharks was estimated at 191.7 cm FL for females and 197.5 cm FL for males, and that of crocodile sharks was assessed at 84.9 cm FL for females and 78.5 cm FL for males. Most sexually matured females were pregnant; their means were 207.2 ± 16.4 cm FL for blue sharks and 89.4 ± 4.3 cm FL for crocodile sharks. Mature sizes for both species were significantly different among months. Embryonic sizes also varied widely among months for crocodile sharks, but a slight change was recorded for those of blue sharks. The observed mean size at birth and litter size were 34.5 cm FL and 37 ± 12 for the blue sharks, and that of the crocodile sharks, 39.5 cm FL and a dominant four embryos in the uterus. Due to the observed increasing catch trend of blue sharks and the slow reproductive cycle of crocodile sharks, this study presents the need of implementing conservation measures to ensure the sustainability of both species in their habitat.
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Affiliation(s)
- Feng Wu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai, China
- Scientific Observing and Experimental Station of Oceanic Fisheries Resources and Environment, Ministry of Agriculture and Rural Affairs, Shanghai, China
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Richard Kindong
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai, China
- Scientific Observing and Experimental Station of Oceanic Fisheries Resources and Environment, Ministry of Agriculture and Rural Affairs, Shanghai, China
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xiaojie Dai
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai, China
- Scientific Observing and Experimental Station of Oceanic Fisheries Resources and Environment, Ministry of Agriculture and Rural Affairs, Shanghai, China
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Ousmane Sarr
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Jiangfeng Zhu
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai, China
- Scientific Observing and Experimental Station of Oceanic Fisheries Resources and Environment, Ministry of Agriculture and Rural Affairs, Shanghai, China
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Siquan Tian
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai, China
- Scientific Observing and Experimental Station of Oceanic Fisheries Resources and Environment, Ministry of Agriculture and Rural Affairs, Shanghai, China
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Yunkai Li
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai, China
- Scientific Observing and Experimental Station of Oceanic Fisheries Resources and Environment, Ministry of Agriculture and Rural Affairs, Shanghai, China
- Key Laboratory of Oceanic Fisheries Exploration, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Bruno T N Nsangue
- College of Marine Sciences, Shanghai Ocean University, Shanghai, China
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Trégarot E, Meissa B, Gascuel D, Sarr O, El Valy Y, Wagne OH, Kane EA, Bal AC, Haidallah MS, Fall AD, Dia AD, Failler P. The role of marine protected areas in sustaining fisheries: The case of the National Park of Banc d’Arguin, Mauritania. Aquaculture and Fisheries 2020. [DOI: 10.1016/j.aaf.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Gning ON, Sarr O, Akpo LE. Richesse de la pharmacopée malinké : rôle médicinal de l’arbre a Khossanto : (Kédougou, Sénégal oriental). ACTA ACUST UNITED AC 2014. [DOI: 10.4314/jab.v74i1.11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Deme AB, Park DJ, Bei AK, Sarr O, Badiane AS, Gueye PEHO, Ahouidi A, Ndir O, Mboup S, Wirth DF, Ndiaye D, Volkman SK. Analysis of pfhrp2 genetic diversity in Senegal and implications for use of rapid diagnostic tests. Malar J 2014; 13:34. [PMID: 24472178 PMCID: PMC3913323 DOI: 10.1186/1475-2875-13-34] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/27/2014] [Indexed: 11/30/2022] Open
Abstract
Background The Senegalese National Malaria Control Programme has recommended use of rapid diagnostic tests (RDTs) that target the histidine-rich protein 2 (HRP2), specific to Plasmodium falciparum, to diagnose malaria cases. The target antigen has been shown to be polymorphic, which may explain the variability in HRP2-based RDT results reported in field studies. The genetic diversity of the pfhrp2 gene has not been investigated in depth in many African countries. The goal of this study is to determine the extent of polymorphism in pfhrp2 among Senegal, Mali and Uganda parasite populations, and discuss the implications of these findings on the utility of RDTs that are based on HRP2 detection. Methods Sequencing data from the pfhrp2 locus were used to analyze the genetic diversity of this gene among three populations, with different transmission dynamics and malaria parasite ecologies. Nucleotide diversity (π) and non-synonymous nucleotide diversity (πNS) were studied in the pfhrp2 gene from isolates obtained in Senegal. Amino acid repeat length polymorphisms in the PfHRP2 antigen were characterized and parameters of genetic diversity, such as frequency and correlation between repeats in these populations, were assessed. Results The diversity survey of the pfhrp2 gene identified 29 SNPs as well as insertion and deletion polymorphisms within a 918 bp region. The Senegal pfhrp2 exhibited a substantial level of diversity [π = 0.00559 and πNS = 0.014111 (πS = 0.0291627)], similar to several polymorphic genes, such as msp1, involved in immune responses, and the gene encoding the SURFIN polymorphic antigen, which are surface exposed parasite proteins. Extensive repeat length polymorphisms in PfHRP2, as well as similar patterns in the number, organization and the type of predicted amino acid repeats were observed among the three populations, characterized by an occurrence of Type 2, Type 4 and Type 7 repeats. Conclusions These results warrant deeper monitoring of the RDT target antigen diversity and emphasize that development of other essential genes as a target for diagnostic tools is critical.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sarah K Volkman
- Broad Institute: The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Miiro GM, Ouwe Missi Oukem-Boyer O, Sarr O, Rahmani M, Ntoumi F, Dheda K, Pym A, Mboup S, Kaleebu P. EDCTP regional networks of excellence: initial merits for planned clinical trials in Africa. BMC Public Health 2013; 13:258. [PMID: 23517572 PMCID: PMC3623728 DOI: 10.1186/1471-2458-13-258] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 03/14/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Achieving the Millennium Development Goals (MDGs) and combating hotspots with escalating but preventable communicable diseases remain major challenges in Africa. The European and Developing Countries Clinical Trials Partnership (EDCTP) intervened to combat poverty-related diseases including malaria, tuberculosis and HIV/AIDS, and to conduct multi-centre clinical trials and multi-disciplinary health research through an innovative model of regional Networks of Excellence (NoEs). METHODS We participated in a quasi-formative evaluation between October and December 2011 on the 4 regional-led research networks. These included the: Central Africa Network on Tuberculosis, HIV/AIDS and Malaria (CANTAM); East African Consortium for Clinical Research (EACCR); West African Network of Excellence for TB, AIDS and Malaria (WANETAM), and the Trials of Excellence for Southern Africa (TESA) launched between 2009 and 2010. We shared a participatory appraisal of field reports, progress reports and presentations from each network to jointly outline the initial experiences of the merits, outputs and lessons learnt. RESULTS The self-regulating democratic networks, with 64 institutions in 21 African countries, have trained over 1, 000 African scientists, upgraded 36 sites for clinical trials, leveraged additional € 24 million and generated 38 peer-reviewed publications through networking and partnerships. CONCLUSIONS The shared initial merits and lessons learnt portray in part the strengthened capacity of these networks for improved research coordination and conduct of planned multi-center clinical trials in Africa. Increased funding by African agencies, governments and international health partners will ensure sustainability of these networks for research capacity development and demonstrate their commitment to achieving the MDGs in Africa.
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Affiliation(s)
- George M Miiro
- EACCR: The East African Consortium for Clinical Research, Uganda Virus Research Institute, Plot 51-59 Nakiwogo, Entebbe, Uganda
| | - Odile Ouwe Missi Oukem-Boyer
- CANTAM: The Central African Network for Tuberculosis HIV/AIDS and Malaria, Fondation Congolaise pour la Recherche Médicale, University Marien Ngouabi, Brazzaville, Republic of Congo
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | - Ousmane Sarr
- WANETAM: The West Africa Network of Excellence for TB, AIDS and Malaria Laboratoire de Bacteriologie-virologie CHU Aristide Le Dantec, Universite Cheikh Anta Diop, Dakar, Senegal
| | - Maerangis Rahmani
- TESA: The Trials of Excellence for Southern Africa, Medical Research Council South Africa- TB Research Unit: Clinical and Biomedical, Durban, South Africa
| | - Francine Ntoumi
- CANTAM: The Central African Network for Tuberculosis HIV/AIDS and Malaria, Fondation Congolaise pour la Recherche Médicale, University Marien Ngouabi, Brazzaville, Republic of Congo
- The Institute for Tropical Medicine, University of Tubingen, Germany
| | - Keertan Dheda
- TESA: The Trials of Excellence for Southern Africa, Medical Research Council South Africa- TB Research Unit: Clinical and Biomedical, Durban, South Africa
| | - Alexander Pym
- TESA: The Trials of Excellence for Southern Africa, Medical Research Council South Africa- TB Research Unit: Clinical and Biomedical, Durban, South Africa
| | - Souleymane Mboup
- WANETAM: The West Africa Network of Excellence for TB, AIDS and Malaria Laboratoire de Bacteriologie-virologie CHU Aristide Le Dantec, Universite Cheikh Anta Diop, Dakar, Senegal
| | - Pontiano Kaleebu
- EACCR: The East African Consortium for Clinical Research, Uganda Virus Research Institute, Plot 51-59 Nakiwogo, Entebbe, Uganda
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Badiane AS, Sarr O, Deme AB, Ahouidi AD, Gueye PEO, Ndiaye M, Seck MC, Diallo M, Bei AK, Duraisingh MT, Wirth D, Ndiaye D, Ndir O, Mboup S. Distribution of erythrocyte binding antigen 175 (EBA-175) alleles and ABO blood groups in a hypoendemic area in Senegal. J Infect Dev Ctries 2012; 6:727-33. [DOI: 10.3855/jidc.2587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 05/02/2012] [Accepted: 06/04/2012] [Indexed: 10/31/2022] Open
Abstract
Introduction: The study was conducted to determine for the first time the association between the erythrocyte binding antigen 175 (EBA-175) alleles and ABO blood groups in malaria patients living in Thies, a hypoendemic area in Senegal. Methodology: In 2007, the EBA-175 alleles and blood group types were determined by nested PCR and the Simonin test respectively in blood samples obtained from uncomplicated Plasmodium falciparum malaria positive patients. Results and conclusion: In total, 129 patients were enrolled in the study. The EBA-175 genotyping showed a prevalence of 67.45% for the F-allele, 27.90% for the C-allele and 4.65% of mixed C+F infection. The distribution of the ABO blood group type showed 59.8% for the O group, 19.7% for the A group, 17.2% for the B group, and 3.3% for the AB group. No correlation was noted between the EBA-175 alleles and either the blood group type or parasitemia.
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Ceesay SJ, Bojang KA, Nwakanma D, Conway DJ, Koita OA, Doumbia SO, Ndiaye D, Coulibaly TF, Diakité M, Traoré SF, Coulibaly M, Ndiaye JL, Sarr O, Gaye O, Konaté L, Sy N, Faye B, Faye O, Sogoba N, Jawara M, Dao A, Poudiougou B, Diawara S, Okebe J, Sangaré L, Abubakar I, Sissako A, Diarra A, Kéita M, Kandeh B, Long CA, Fairhurst RM, Duraisingh M, Perry R, Muskavitch MA, Valim C, Volkman SK, Wirth DF, Krogstad DJ. Sahel, savana, riverine and urban malaria in West Africa: Similar control policies with different outcomes. Acta Trop 2012; 121:166-74. [PMID: 22119584 DOI: 10.1016/j.actatropica.2011.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 11/09/2011] [Accepted: 11/09/2011] [Indexed: 11/26/2022]
Abstract
The study sites for the West African ICEMR are in three countries (The Gambia, Senegal, Mali) and are located within 750 km of each other. In addition, the National Malaria Control Programmes of these countries have virtually identical policies: (1) Artemisinin Combination Therapies (ACTs) for the treatment of symptomatic Plasmodium falciparum infection, (2) Long-Lasting Insecticide-treated bed Nets (LLINs) to reduce the Entomololgic Inoculation Rate (EIR), and (3) sulfadoxine-pyrimethamine for the Intermittent Preventive Treatment of malaria during pregnancy (IPTp). However, the prevalence of P. falciparum malaria and the status of malaria control vary markedly across the four sites with differences in the duration of the transmission season (from 4-5 to 10-11 months), the intensity of transmission (with EIRs from unmeasurably low to 4-5 per person per month), multiplicity of infection (from a mean of 1.0 to means of 2-5) and the status of malaria control (from areas which have virtually no control to areas that are at the threshold of malaria elimination). The most important priority is the need to obtain comparable data on the population-based prevalence, incidence and transmission of malaria before new candidate interventions or combinations of interventions are introduced for malaria control.
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Chen DS, Barry AE, Leliwa-Sytek A, Smith TA, Peterson I, Brown SM, Migot-Nabias F, Deloron P, Kortok MM, Marsh K, Daily JP, Ndiaye D, Sarr O, Mboup S, Day KP. A molecular epidemiological study of var gene diversity to characterize the reservoir of Plasmodium falciparum in humans in Africa. PLoS One 2011; 6:e16629. [PMID: 21347415 PMCID: PMC3036650 DOI: 10.1371/journal.pone.0016629] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 01/06/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The reservoir of Plasmodium infection in humans has traditionally been defined by blood slide positivity. This study was designed to characterize the local reservoir of infection in relation to the diverse var genes that encode the major surface antigen of Plasmodium falciparum blood stages and underlie the parasite's ability to establish chronic infection and transmit from human to mosquito. METHODOLOGY/PRINCIPAL FINDINGS We investigated the molecular epidemiology of the var multigene family at local sites in Gabon, Senegal and Kenya which differ in parasite prevalence and transmission intensity. 1839 distinct var gene types were defined by sequencing DBLα domains in the three sites. Only 76 (4.1%) var types were found in more than one population indicating spatial heterogeneity in var types across the African continent. The majority of var types appeared only once in the population sample. Non-parametric statistical estimators predict in each population at minimum five to seven thousand distinct var types. Similar diversity of var types was seen in sites with different parasite prevalences. CONCLUSIONS/SIGNIFICANCE Var population genomics provides new insights into the epidemiology of P. falciparum in Africa where malaria has never been conquered. In particular, we have described the extensive reservoir of infection in local African sites and discovered a unique var population structure that can facilitate superinfection through minimal overlap in var repertoires among parasite genomes. Our findings show that var typing as a molecular surveillance system defines the extent of genetic complexity in the reservoir of infection to complement measures of malaria prevalence. The observed small scale spatial diversity of var genes suggests that var genetics could greatly inform current malaria mapping approaches and predict complex malaria population dynamics due to the import of var types to areas where no widespread pre-existing immunity in the population exists.
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Affiliation(s)
- Donald S. Chen
- Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Alyssa E. Barry
- Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
- Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, Oxford, United Kingdom
- Centre for Population Health, Burnet Institute, Melbourne, Australia
- Department of Medicine, Central and Eastern Clinical School, Monash University, Victoria, Australia
| | - Aleksandra Leliwa-Sytek
- Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
| | - Terry-Ann Smith
- Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
| | - Ingrid Peterson
- Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
| | - Stuart M. Brown
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, United States of America
| | - Florence Migot-Nabias
- Institut de Recherche pour le Développement, Faculté de Pharmacie, Université Paris 5, Paris, France
| | - Philippe Deloron
- Institut de Recherche pour le Développement, Faculté de Pharmacie, Université Paris 5, Paris, France
| | - Moses M. Kortok
- Kenya Medical Research Institute, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Kevin Marsh
- Kenya Medical Research Institute, Centre for Geographic Medicine Research, Kilifi, Kenya
| | - Johanna P. Daily
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Daouda Ndiaye
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Ousmane Sarr
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Souleymane Mboup
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Karen P. Day
- Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
- Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, Oxford, United Kingdom
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Sarr O, Louveau I, Kalbe C, Metges CC, Rehfeldt C, Gondret F. Prenatal exposure to maternal low or high protein diets induces modest changes in the adipose tissue proteome of newborn piglets1,2. J Anim Sci 2010; 88:1626-41. [DOI: 10.2527/jas.2009-2542] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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13
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Bei AK, Desimone TM, Badiane AS, Ahouidi AD, Dieye T, Ndiaye D, Sarr O, Ndir O, Mboup S, Duraisingh MT. A flow cytometry-based assay for measuring invasion of red blood cells by Plasmodium falciparum. Am J Hematol 2010; 85:234-7. [PMID: 20196166 DOI: 10.1002/ajh.21642] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Variability in the ability of the malaria parasite Plasmodium falciparum to invade human erythrocytes is postulated to be an important determinant of disease severity. Both the parasite multiplication rate and erythrocyte selectivity are important parameters that underlie such variable invasion. We have established a flow cytometry-based method for simultaneously calculating both the parasitemia and the number of multiply-infected erythrocytes. Staining with the DNA-specific dye SYBR Green I allows quantitation of parasite invasion at the ring stage of parasite development. We discuss in vitro and in vivo applications and limitations of this method in relation to the study of parasite invasion.
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Affiliation(s)
- Amy K Bei
- Harvard School of Public Health, Boston, Massachusetts, USA
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14
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Neafsey DE, Schaffner SF, Volkman SK, Park D, Montgomery P, Milner DA, Lukens A, Rosen D, Daniels R, Houde N, Cortese JF, Tyndall E, Gates C, Stange-Thomann N, Sarr O, Ndiaye D, Ndir O, Mboup S, Ferreira MU, Moraes SDL, Dash AP, Chitnis CE, Wiegand RC, Hartl DL, Birren BW, Lander ES, Sabeti PC, Wirth DF. Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence. Genome Biol 2008; 9:R171. [PMID: 19077304 PMCID: PMC2646275 DOI: 10.1186/gb-2008-9-12-r171] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 12/15/2008] [Indexed: 11/10/2022] Open
Abstract
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, inter-population 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.
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Affiliation(s)
- Daniel E Neafsey
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
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15
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Alexandre-Gouabau M, Sarr O, Fança P, Hoebler C, Kaeffer B. SFP-36 – Néonatalogie – Dynamique du protéome des cellules intestinales isolées de nouveau-nés de petits poids de naissance. Validation sur ratons RCIU. Arch Pediatr 2008. [DOI: 10.1016/s0929-693x(08)72103-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Jennings CV, Ahouidi AD, Zilversmit M, Bei AK, Rayner J, Sarr O, Ndir O, Wirth DF, Mboup S, Duraisingh MT. Molecular analysis of erythrocyte invasion in Plasmodium falciparum isolates from Senegal. Infect Immun 2007; 75:3531-8. [PMID: 17470537 PMCID: PMC1932937 DOI: 10.1128/iai.00122-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human malaria parasite, Plasmodium falciparum, utilizes multiple ligand-receptor interactions for the invasion of human erythrocytes. Members of the reticulocyte binding protein homolog (PfRh) family have been shown to be critical for directing parasites to alternative erythrocyte receptors that define invasion pathways. Recent studies have identified gene amplification, sequence polymorphism, and variant expression of PfRh paralogs as mechanisms underlying discrimination between pathways for invasion. In this study, we find considerable heterogeneity in the invasion profiles of clonal, uncultured P. falciparum parasite isolates from a low-transmission area in Senegal. Molecular analyses revealed minimal variation in protein expression levels of the PfRh ligands, PfRh1, PfRh2a, and PfRh2b, and an absence of gene amplification in these isolates. However, significant sequence polymorphism was found within repeat regions of PfRh1, PfRh2a, and PfRh2b. Furthermore, we identified a large sequence deletion ( approximately 0.58 kb) in the C-terminal region of the PfRh2b gene at a high prevalence in this population. In contrast to findings of earlier studies, we found no associations between specific sequence variants and distinct invasion pathways. Overall these data highlight the importance of region-specific elaborations in PfRh sequence and expression polymorphisms, which has important implications in our understanding of how the malaria parasite responds to polymorphisms in erythrocyte receptors and/or evades the immune system.
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Affiliation(s)
- Cameron V Jennings
- Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
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Thiam MH, Faye PL, Ba I, Sarr O, Sy A, Sylla O, Guèye M. [Clinical and psychopathological postpartum depression: eleven Senegalese cases report]. Dakar Med 2007; 52:141-147. [PMID: 19102109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
INTRODUCTION The postpartum depression is a frequent puerperium psychiatric disorder. The authors study the clinical, therapeutic and evolutionary aspects of the postpartum depression among eleven Senegalese women. MATERIAL AND METHOD They examined the medical reports and hospital registers of eleven patients belonging to a sample of 52 women presenting psychic disorders of the puerperality. The diagnosis was made by using the International Classification of the Diseases. RESULTS The symptoms of depression were irritability, bad concentration, multiple somatic complaints, of insomnia of drowsiness, loss of the usual interests. All the patients profited from psychotherapy and have received chemotherapy with antidepressant treatment associated tranquillizing in six cases. They improved from 29 to 43 days after their admission. CONCLUSION The pregnancy and the childbirth, the parity, personal history of the patient, their social environment and the cultural representations of maternity are factors of depression of the postpartum. The antidepressant is always essential in the treatment.
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Affiliation(s)
- M H Thiam
- CHNU de Fann, B.P. 5406, Dakar-Fann, Dakar, Sénégal.
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18
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Volkman SK, Sabeti PC, DeCaprio D, Neafsey DE, Schaffner SF, Milner DA, Daily JP, Sarr O, Ndiaye D, Ndir O, Mboup S, Duraisingh MT, Lukens A, Derr A, Stange-Thomann N, Waggoner S, Onofrio R, Ziaugra L, Mauceli E, Gnerre S, Jaffe DB, Zainoun J, Wiegand RC, Birren BW, Hartl DL, Galagan JE, Lander ES, Wirth DF. A genome-wide map of diversity in Plasmodium falciparum. Nat Genet 2006; 39:113-9. [PMID: 17159979 DOI: 10.1038/ng1930] [Citation(s) in RCA: 242] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 11/02/2006] [Indexed: 11/08/2022]
Abstract
Genetic variation allows the malaria parasite Plasmodium falciparum to overcome chemotherapeutic agents, vaccines and vector control strategies and remain a leading cause of global morbidity and mortality. Here we describe an initial survey of genetic variation across the P. falciparum genome. We performed extensive sequencing of 16 geographically diverse parasites and identified 46,937 SNPs, demonstrating rich diversity among P. falciparum parasites (pi = 1.16 x 10(-3)) and strong correlation with gene function. We identified multiple regions with signatures of selective sweeps in drug-resistant parasites, including a previously unidentified 160-kb region with extremely low polymorphism in pyrimethamine-resistant parasites. We further characterized 54 worldwide isolates by genotyping SNPs across 20 genomic regions. These data begin to define population structure among African, Asian and American groups and illustrate the degree of linkage disequilibrium, which extends over relatively short distances in African parasites but over longer distances in Asian parasites. We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite.
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Affiliation(s)
- Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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19
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Happi CT, Gbotosho GO, Folarin OA, Milner D, Sarr O, Sowunmi A, Kyle DE, Milhous WK, Wirth DF, Oduola AMJ. Confirmation of emergence of mutations associated with atovaquone-proguanil resistance in unexposed Plasmodium falciparum isolates from Africa. Malar J 2006; 5:82. [PMID: 17020611 PMCID: PMC1594577 DOI: 10.1186/1475-2875-5-82] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2006] [Accepted: 10/04/2006] [Indexed: 11/16/2022] Open
Abstract
Background In vitro and in vivo resistance of Plasmodium falciparum to atovaquone or atovaquone-proguanil hydrochloride combination has been associated to two point mutations in the parasite cytochrome b (cytb) gene (Tyr268Ser and Tyr268Asn). However, little is known about the prevalence of codon-268 mutations in natural populations of P. falciparum without previous exposure to the drug in Africa. Methods The prevalence of codon-268 mutations in the cytb gene of African P. falciparum isolates from Nigeria, Malawi and Senegal, where atovaquone-proguanil has not been introduced for treatment of malaria was assessed. Genotyping of the cytb gene in isolates of P. falciparum was performed by PCR-restriction fragment length polymorphism and confirmed by sequencing. Results 295 samples from Nigeria (111), Malawi (91) and Senegal (93) were successfully analyzed for detection of either mutant Tyr268Ser or Tyr268Asn. No case of Ser268 or Asn268 was detected in cytb gene of parasites from Malawi or Senegal. However, Asn268 was detected in five out of 111 (4.5%) unexposed P. falciparum isolates from Nigeria. In addition, one out of these five mutant Asn268 isolates showed an additional cytb mutation leading to a Pro266Thr substitution inside the ubiquinone reduction site. Conclusion No Tyr268Ser mutation is found in cytb of P. falciparum isolates from Nigeria, Malawi or Senegal. This study reports for the first time cytb Tyr268Asn mutation in unexposed P. falciparum isolates from Nigeria. The emergence in Africa of P. falciparum isolates with cytb Tyr268Asn mutation is a matter of serious concern. Continuous monitoring of atovaquone-proguanil resistant P. falciparum in Africa is warranted for the rational use of this new antimalarial drug, especially in non-immune travelers.
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Affiliation(s)
- Christian T Happi
- Malaria Research Laboratories, Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Nigeria
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Grace O Gbotosho
- Malaria Research Laboratories, Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Nigeria
| | - Onikepe A Folarin
- Malaria Research Laboratories, Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Nigeria
| | - Danny Milner
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Ousmane Sarr
- Laboratory of Bacteriology and Virology, Dantec Hospital, Dakar, Senegal
| | - Akintunde Sowunmi
- Malaria Research Laboratories, Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Nigeria
| | - Dennis E Kyle
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Springs, MD, USA
| | - Wilbur K Milhous
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Springs, MD, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Ayoade MJ Oduola
- Special Programme for Research and Training in Tropical Diseases (WHO/TDR), Geneva, Switzerland
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Ndiaye D, Daily J, Sarr O, Ndir O, Gaye O, Mboup S, Roper C, Wirth D. Defining the origin of Plasmodium falciparum resistant dhfr isolates in Senegal. Acta Trop 2006; 99:106-11. [PMID: 16905111 PMCID: PMC2582374 DOI: 10.1016/j.actatropica.2006.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 06/23/2006] [Accepted: 07/04/2006] [Indexed: 11/23/2022]
Abstract
We previously reported a high baseline prevalence of mutations in the dhfr and dhps genes of Plasmodium falciparum throughout Senegal. The highest prevalence of the triple dhfr pyrimethamine associated mutations were found in isolates obtained in the western part of the country near the capital city of Dakar. In this study, we sought out to determine the relatedness of dhfr wild type and mutated strains by analyzing three microsatellite regions upstream of the dhfr locus. Twenty-six of the 31 wild type strains had a unique microsatellite pattern. In contrast, of the 17 isolates containing the triple mutation in dhfr, 11 had an identical microsatellite pattern. Diverse geographical isolates in Senegal containing the triple dhfr mutation have arisen from a limited number of ancestral strains. In addition, we demonstrate that these isolates have shared ancestry with the previously reported triple mutation haplotype found in Tanzania, South Africa, and southeast Asia. This common ancestry may have implications for the malaria control strategy for reducing the spread of sulfadoxine-pyrimethamine resistance in Senegal and elsewhere in Africa.
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Affiliation(s)
- D. Ndiaye
- Department of Parasitology and Mycology, Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - J.P. Daily
- Harvard School of Public Health, Department of Immunology and Infectious Disease, 655 Huntington Avenue, Boston, MA 02115, USA
- Corresponding author. Tel.: +1 617 432 5321; fax: +1 617 432 4766. E-mail address: (J.P. Daily)
| | - O. Sarr
- Laboratory of Bacteriology and Virology, Dantec Hospital, Dakar, Senegal
| | - O. Ndir
- Department of Parasitology and Mycology, Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - O. Gaye
- Department of Parasitology and Mycology, Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - S. Mboup
- Laboratory of Bacteriology and Virology, Dantec Hospital, Dakar, Senegal
| | - C. Roper
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - D.F. Wirth
- Harvard School of Public Health, Department of Immunology and Infectious Disease, 655 Huntington Avenue, Boston, MA 02115, USA
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21
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Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch KG, Sarr O, Ndir O, Mboup S, Batalov S, Wirth DF, Winzeler EA. A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathog 2006; 2:e57. [PMID: 16789840 PMCID: PMC1480597 DOI: 10.1371/journal.ppat.0020057] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 04/28/2006] [Indexed: 11/25/2022] Open
Abstract
Discovering novel genes involved in immune evasion and drug resistance in the human malaria parasite, Plasmodium falciparum, is of critical importance to global health. Such knowledge may assist in the development of new effective vaccines and in the appropriate use of antimalarial drugs. By performing a full-genome scan of allelic variability in 14 field and laboratory strains of P. falciparum, we comprehensively identified ≈500 genes evolving at higher than neutral rates. The majority of the most variable genes have paralogs within the P. falciparum genome and may be subject to a different evolutionary clock than those without. The group of 211 variable genes without paralogs contains most known immunogens and a few drug targets, consistent with the idea that the human immune system and drug use is driving parasite evolution. We also reveal gene-amplification events including one surrounding pfmdr1, the P. falciparum multidrug-resistance gene, and a previously uncharacterized amplification centered around the P. falciparum GTP cyclohydrolase gene, the first enzyme in the folate biosynthesis pathway. Although GTP cyclohydrolase is not the known target of any current drugs, downstream members of the pathway are targeted by several widely used antimalarials. We speculate that an amplification of the GTP cyclohydrolase enzyme in the folate biosynthesis pathway may increase flux through this pathway and facilitate parasite resistance to antifolate drugs. Variability in the genome of the human malaria parasite, Plasmodium falciparum, is key to the parasite's ability to cause disease and overcome therapeutic interventions such as drugs and vaccines. Elucidating the extent of genetic variation in the malaria parasite will therefore be central to decreasing the malaria disease burden. The authors performed a full-genome scan of variability in different strains of P. falciparum and observed a nonrandom distribution of variation. In particular, those genes that are predicted to have roles in evading the host immune response or antimalarial drugs show significantly higher levels of variation. In addition, the authors speculate that a previously unreported genome amplification in the folate biosynthesis pathway correlates with resistance to the antimalarial drug sulfadoxine. Such data enable hypotheses to be made about the function of many of the unknown elements in the parasite's genome, which may permit the identification of new targets that can be investigated for incorporation into a malaria vaccine and may aid in the understanding of how the parasite withstands drug pressure.
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Affiliation(s)
- Claire Kidgell
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Johanna Daily
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Justin O Borevitz
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - David Plouffe
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Jeffrey R Johnson
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Karine G. Le Roch
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Ousmane Sarr
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Omar Ndir
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Soulyemane Mboup
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Serge Batalov
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Elizabeth A Winzeler
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Ndiaye D, Daily JP, Sarr O, Ndir O, Gaye O, Mboup S, Wirth DF. Mutations in Plasmodium falciparum dihydrofolate reductase and dihydropteroate synthase genes in Senegal. Trop Med Int Health 2005; 10:1176-9. [PMID: 16262743 PMCID: PMC2582373 DOI: 10.1111/j.1365-3156.2005.01506.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Senegal recently (2004) switched to sulfadoxine-pyrimethamine (SP) with amodiaquine as first line therapy for malaria in response to increasing chloroquine resistance. In anticipation of emerging resistance to SP as a result of this change in drug pressure, we set out to define the baseline prevalence of SP-associated mutations in the dhfr and dhps genes in Plasmodium falciparum using geographically diverse and longitudinally collected samples. A total of 153 blood samples were analysed from patients (5 years or older) with mild malaria after informed consent was obtained. Longitudinal samples were collected between 2000 and 2003 in Pikine, a suburb of Dakar. Geographically diverse site sampling was carried out in 2003. The mutation prevalence in DHFR codons 51, 59 and 108 is 65%, 61% and 78% in Pikine, 2003. The overall prevalence of the triple mutation that is associated with high-level pyrimethamine resistance is 61%. The mutation prevalence rate in DHPS codons 436 and 437 is 21% and 40%, respectively. There is significant geographic variation in genotypic resistance, as samples from Pikine in 2003 had higher mutation prevalence in the pfdhfr and pfdhps genes compared to samples from Tambacounda (P < 0.015). In summary, this study demonstrates a high background prevalence of SP resistance mutations already present in P. falciparum in Senegal.
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Affiliation(s)
- D Ndiaye
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
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23
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Sarr O, Myrick A, Daily J, Diop BM, Dieng T, Ndir O, Sow PS, Mboup S, Wirth DF. In vivo and in vitro analysis of chloroquine resistance in Plasmodium falciparum isolates from Senegal. Parasitol Res 2005; 97:136-40. [PMID: 15986248 PMCID: PMC2579896 DOI: 10.1007/s00436-005-1406-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2005] [Accepted: 05/06/2005] [Indexed: 11/26/2022]
Abstract
To determine the predictive value of chloroquine (CQ) resistance markers in Senegal, Plasmodium falciparum DNA polymorphisms in pfmdr1and pfcrt were examined in relation to clinical outcome. Despite CQ treatment, 17% of patients had parasitemia after 28 days. Examination of molecular markers of CQ resistance revealed that 64% of all isolates had the T76 resistant allele at the pfcrt locus, while 30% carried the Y86 resistant allele at the pfmdr1 locus. The pfcrt T76 allele was present not only in all in vivo resistant isolates, 89% of in vitro resistant isolates, but also in 35% of in vitro sensitive isolates. The pfmdr1 N86Y polymorphism did not correlate with in vitro or in vivo CQ resistance. Our data suggest that the pfcrt T76 allele alone is required but not a sufficient predictor for in vivo CQ resistance.
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Affiliation(s)
- Ousmane Sarr
- Laboratory of Bacteriology and Virology, Hopital Aristide Le Dantec, Dakar, Senegal, USA
| | - Alissa Myrick
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Johanna Daily
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Bernard M. Diop
- Infectious Diseases Clinic, Fann Hospital, Dakar, Senegal, USA
| | - Therese Dieng
- Laboratory of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal, USA
| | - Omar Ndir
- Laboratory of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal, USA
| | - Pape Salif Sow
- Infectious Diseases Clinic, Fann Hospital, Dakar, Senegal, USA
| | - Souleymane Mboup
- Laboratory of Bacteriology and Virology, Hopital Aristide Le Dantec, Dakar, Senegal, USA
| | - Dyann F. Wirth
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA, E-mail: , Tel.: +1-617-4321563, Fax: +1-617-4324766
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24
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Daily JP, Le Roch KG, Sarr O, Ndiaye D, Lukens A, Zhou Y, Ndir O, Mboup S, Sultan A, Winzeler EA, Wirth DF. In vivo transcriptome of Plasmodium falciparum reveals overexpression of transcripts that encode surface proteins. J Infect Dis 2005; 191:1196-203. [PMID: 15747257 PMCID: PMC2582152 DOI: 10.1086/428289] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Accepted: 10/20/2004] [Indexed: 11/03/2022] Open
Abstract
Infections with the human parasite Plasmodium falciparum continue to present a great challenge to global health. Fundamental questions regarding the molecular basis of virulence and immune evasion in P. falciparum have been only partially answered. Because of the parasite's intracellular location and complex life cycle, standard genetic approaches to the study of the pathogenesis of malaria have been limited. The present study presents a novel approach to the identification of the biological processes involved in host-pathogen interactions, one that is based on the analysis of in vivo P. falciparum transcripts. We demonstrate that a sufficient quantity of P. falciparum RNA transcripts can be derived from a small blood sample from infected patients for whole-genome microarray analysis. Overall, excellent correlation was observed between the transcriptomes derived from in vivo samples and in vitro samples with ring-stage P. falciparum 3D7 reference strain. However, gene families that encode surface proteins are overexpressed in vivo. Moreover, this analysis has identified a new family of hypothetical genes that may encode surface variant antigens. Comparative studies of the transcriptomes derived from in vivo samples and in vitro 3D7 samples may identify important strategies used by the pathogen for survival in the human host and highlight, for vaccine development, new candidate antigens that were not previously identified through the use of in vitro cultures.
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Affiliation(s)
- Johanna P Daily
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
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Myrick A, Sarr O, Dieng T, Ndir O, Mboup S, Wirth DF. Analysis of the genetic diversity of the Plasmodium falciparum multidrug resistance gene 5' upstream region. Am J Trop Med Hyg 2005; 72:182-8. [PMID: 15741555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Recent findings indicating a low level of polymorphism in the Plasmodium falciparum genome have led to the hypothesis that existent polymorphisms are likely to have functional significance. We tested this hypothesis by developing a map of the polymorphism in the P. falciparum multidrug resistance 1 (pfmdr1) gene 5' upstream region and assaying its correlation with drug resistance in a sample of field isolates from Dakar, Senegal. A comparison of six geographically diverse laboratory strains showed that the 1.94-kb 5'-untranslated region is highly monomorphic, with a total of four unique single nucleotide polymorphisms (SNPs) being identified. All of the mutations were localized to a 462-basepair region proximal to the transcription start point. Analysis of this region in field isolates shows the prevalence of one SNP throughout the entire population of parasites, irrespective of drug resistance status. The SNP frequency of the pfmdr1 upstream region is lower than that found in the noncoding region of other genes.
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Affiliation(s)
- Alissa Myrick
- Department of Medicine, San Francisco General Hospital, University of California at San Francisco, 94110, USA
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Daily JP, Le Roch KG, Sarr O, Fang X, Zhou Y, Ndir O, Mboup S, Sultan A, Winzeler EA, Wirth DF. In vivo transcriptional profiling of Plasmodium falciparum. Malar J 2004; 3:30. [PMID: 15296511 PMCID: PMC514566 DOI: 10.1186/1475-2875-3-30] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Accepted: 08/05/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Both host and pathogen factors contribute to disease outcome in Plasmodium falciparum infection. The feasibility of studying the P. falciparum in vivo transcriptome to understand parasite transcriptional response while it resides in the human host is presented. METHODS A custom made oligonucleotide array with probes based on the P. falciparum 3D7 laboratory strain chromosome 2 sequence was used to detect in vivo P. falciparum transcripts. This study analyzed transcripts from total RNA derived from small blood samples of P. falciparum infected patients and compared the in vivo expression profile to the in vitro cultivated 3D7 strain transcriptome. RESULTS The data demonstrated that in vivo transcription can be studied from a small blood sample, despite the abundance of human RNA. The in vivo transcriptome is similar to the 3D7 ring stage transcriptome, but there are significant differences in genes encoding a sexual stage antigen and surface proteins. CONCLUSIONS Whole genome transcription analysis of P. falciparum can be carried out successfully and further studies in selected patient cohorts may provide insight into parasite in vivo biology and defense against host immunity.
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Affiliation(s)
- Johanna P Daily
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Karine G Le Roch
- Genomics Institute of the Novartis Research Foundation, San Diego California, 92121, USA
| | - Ousmane Sarr
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Xuemin Fang
- Department of Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, San Diego California, 92121, USA
| | - Omar Ndir
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Soulyemane Mboup
- Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Ali Sultan
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Elizabeth A Winzeler
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Genomics Institute of the Novartis Research Foundation, San Diego California, 92121, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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Diaw M, Lemordant D, Sock O, Sarr O. Electrochemical behaviour of gold at the carbon paste electrode: application to the gold ore analysis. B CHEM SOC ETHIOPIA 2001. [DOI: 10.4314/bcse.v15i1.71727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Cancré N, Tall A, Rogier C, Faye J, Sarr O, Trape JF, Spiegel A, Bois F. Bayesian analysis of an epidemiologic model of Plasmodium falciparum malaria infection in Ndiop, Senegal. Am J Epidemiol 2000; 152:760-70. [PMID: 11052555 DOI: 10.1093/aje/152.8.760] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plasmodium falciparum has a complex transmission cycle. Public health planning and research would benefit from the ability of a calibrated model to predict the epidemiologic characteristics of populations living in areas of malaria endemicity. This paper describes the application of Bayesian calibration to a malaria transmission model using longitudinal data gathered from 176 subjects in Ndiop, Senegal, from July 1, 1993, to July 31, 1994. The model was able to adequately predict P. falciparum parasitemia prevalence in the study population. Further insight into the dynamics of malaria in Ndiop was provided. During the dry season, the estimated fraction of nonimmune subjects goes down to 20% and then increases up to 80%. The model-predicted time-weighted average incidences contributed by nonimmune and immune individuals are 0.52 cases per day and 0.47 cases per day, respectively. The median times needed to acquire infection (conversion delay) for nonimmune and immune individuals are estimated at 39 days and 285 days, respectively.
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Affiliation(s)
- N Cancré
- Institut Pasteur de Dakar, Senegal
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Tal-Dia A, Toure K, Sarr O, Sarr M, Cisse MF, Garnier P, Wone I. [A baobab solution for the prevention and treatment of acute dehydration in infantile diarrhea]. Dakar Med 1997; 42:68-73. [PMID: 9827122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
OBJECTIVE The purpose of this study was to compare the clinical efficacy of a local solution based on "pain de singe", fruit of baobab (Adansonia digitata), and the WHO standard solution in the treatment of children with acute diarrhea and resulting mild to moderate dehydration. METHODOLOGY A prospective clinical trial comparing the local solution to the standard WHO solution was conducted; in children of 6 months or older (mean age = 16.6 +/- 8.8 months), 79 received the WHO solution and 82 the local solution, and were followed for a period ranging from 4 to 48 hours. Evolution of diarrhea and weight gain were evaluated as variables of interest. RESULTS WHO solution was found to be superior, but not statistically significant in term of duration of diarrhea and weight gain. DISCUSSION The pain de singe based solution presents additional advantages: nutritional, economic and cultural; we recommend it to promote use of TRO at home.
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Affiliation(s)
- A Tal-Dia
- Service de Médecine Préventive et Santé Publique, Faculté de Médecine et Pharmacie, Dakar
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Sarr O, Diop L. I.r. and Raman spectra of M3HP2O7·nH2O (M = Na, Cs; n = 0, 1, 9). Correlation between the POP bridge vibrational frequencies and the POP angle value. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0584-8539(87)80171-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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