Improving microbiological food Safety in peri-urban Mali; an experimental study

Introduction: Twenty years ago, a WHO review of the literature assumed that most food-borne disease transmission in developing countries takes place within the home, and advocated a major programme of interdisciplinary research to develop and test cost-effective interventions to promote food hygiene. Methods: The HACCP approach was applied step by step, to two selected weaning foods prepared by 15 volunteer mothers in peri-urban Mali. After setting Critical Control Points (CCP), actions were taken to control, reduce or eliminate microbial growth at these points. 432 food samples were collected and examined for thermotolerant coliforms in a local laboratory to assess the effectiveness of the approach. Lessons learnt were translated into messages delivered in a pilot study. Results: Traditional cooking was very effective in eliminating faecal contamination; reheating was as effective as cooking when adopted, because there was no significant difference in the temperatures reached in both cases. Behavioural corrective actions were effective in controlling faecal contamination at the other CCPs (serving the child after cooking and after reheating). Conclusion: In conclusion, the HACCP experiment improved significantly the bacterial safety of both types of weaning food studied. © 2011 Elsevier Ltd

Non-livestock value chains. Lateral thinking for the securing of the Sahelian livestock economies

In a rapid rural appraisal conducted in 2012 in the Senegalese Sahel, agropastoralists of Thiel expressed their need for technical and scientific support in peanut value chain development. Value chain analysis assessed the performance of the stakeholders. Multiple correspondence analysis clarified power relationships among them. Social network analysis facilitated the understanding of social and technical relationships inside the particular node of agropastoralists. Results show that the peanut crop is both a source of cash flow (marketing) and a pillar of food (basic consumption) and feed (by-products) security. This paper also highlights a lack of convenient economic environments, mutual assistance, capacity transfer and knowledge sharing on the best agricultural practices among agropastoralists, despite their weak production performance. Agropastoralists have no influence in the peanut value chain and are dependent on decisions from other actors. Technical support and knowledge sharing appear to be key for agropastoralists to control and adopt agricultural innovations. (Résumé d'auteur

Non-livestock value chains. Lateral thinking for the securing of the Sahelian livestock economies

In a rapid rural appraisal conducted in 2012 in the Senegalese Sahel, agropastoralists of Thiel expressed their need for technical and scientific support in peanut value chain development. Value chain analysis assessed the performance of the stakeholders. Multiple correspondence analysis clarified power relationships among them. Social network analysis facilitated the understanding of social and technical relationships inside the particular node of agropastoralists. Results show that the peanut crop is both a source of cash flow (marketing) and a pillar of food (basic consumption) and feed (by-products) security. This paper also highlights a lack of convenient economic environments, mutual assistance, capacity transfer and knowledge sharing on the best agricultural practices among agropastoralists, despite their weak production performance. Agropastoralists have no influence in the peanut value chain and are dependent on decisions from other actors. Technical support and knowledge sharing appear to be key for agropastoralists to control and adopt agricultural innovations

Intégration horticulture ‑ élevage dans les systèmes agricoles urbains de la zone des Niayes (Sénégal)

Les contre‑performances de l'agriculture rurale et le déficit alimentaire encouragent depuis plusieurs décennies le développement d'une activité agricole urbaine et péri urbaine dont les principaux domaines sont l'horticulture et l'élevage. La contribution de cette agriculture urbaine à l'approvisionnement des villes est mal connue au Sénégal. Les rares sources disponibles indiquent que Dakar a lui seul prend 40% de la demande totale de légumes du Sénégal et cette région couvre plus de 60 % d..

Correction to: Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm.

Following publication of the original article [1], the following error was reported: The actin control panel in Fig. 3 of this paper is reproduced from Fig. 7 of Touré et al, 2004 [2] by kind permission of the Genetics Society of America. Touré et al, 2004 used Northern blotting to show that the Y-linked genes Ssty1 and Ssty2 have reduced expression in a range of mouse genotypes with deletions on the Y chromosome long arm. This paper shows that two novel genes, Sly and Asty are also present on mouse Yq and have reduced expression in these deleted genotypes. A further companion paper was published in Human Molecular Genetics (Ellis et al, 2005 [3]) showing that X-linked genes are upregulated in the various deleted genotypes. Since two of the genotypes concerned are sterile and very hard to generate, all the Northern blot experiments in these papers were performed on a single membrane that was stripped and re-probed with a range of different X- and Y-linked genes. The same beta-actin loading control image thus necessarily applies to all the data presented, and was shown in all three papers. We regret that this was not mentioned appropriately in the Methods and figure legends at the time of publication

Mutations in DNAH1, which encodes an inner arm heavy chain dynein, lead to male infertility from multiple morphological abnormalities of the sperm flagella.

International audienceTen to fifteen percent of couples are confronted with infertility and a male factor is involved in approximately half the cases. A genetic etiology is likely in most cases yet only few genes have been formally correlated with male infertility. Homozygosity mapping was carried out on a cohort of 20 North African individuals, including 18 index cases, presenting with primary infertility resulting from impaired sperm motility caused by a mosaic of multiple morphological abnormalities of the flagella (MMAF) including absent, short, coiled, bent, and irregular flagella. Five unrelated subjects out of 18 (28%) carried a homozygous variant in DNAH1, which encodes an inner dynein heavy chain and is expressed in testis. RT-PCR, immunostaining, and electronic microscopy were carried out on samples from one of the subjects with a mutation located on a donor splice site. Neither the transcript nor the protein was observed in this individual, confirming the pathogenicity of this variant. A general axonemal disorganization including mislocalization of the microtubule doublets and loss of the inner dynein arms was observed. Although DNAH1 is also expressed in other ciliated cells, infertility was the only symptom of primary ciliary dyskinesia observed in affected subjects, suggesting that DNAH1 function in cilium is not as critical as in sperm flagellum

Loss-of-Function Mutations in LRRC6, a Gene Essential for Proper Axonemal Assembly of Inner and Outer Dynein Arms, Cause Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is a group of autosomal-recessive disorders resulting from cilia and sperm-flagella defects, which lead to respiratory infections and male infertility. Most implicated genes encode structural proteins that participate in the composition of axonemal components, such as dynein arms (DAs), that are essential for ciliary and flagellar movements; they explain the pathology in fewer than half of the affected individuals. We undertook this study to further understand the pathogenesis of PCD due to the absence of both DAs. We identified, via homozygosity mapping, an early frameshift in LRRC6, a gene that encodes a leucine-rich-repeat (LRR)-containing protein. Subsequent analyses of this gene mainly expressed in testis and respiratory cells identified biallelic mutations in several independent individuals. The situs inversus observed in two of them supports a key role for LRRC6 in embryonic nodal cilia. Study of native LRRC6 in airway epithelial cells revealed that it localizes to the cytoplasm and within cilia, whereas it is absent from cells with loss-of-function mutations, in which DA protein markers are also missing. These results are consistent with the transmission-electron-microscopy data showing the absence of both DAs in cilia or flagella from individuals with LRRC6 mutations. In spite of structural and functional similarities between LRRC6 and DNAAF1, another LRR-containing protein involved in the same PCD phenotype, the two proteins are not redundant. The evolutionarily conserved LRRC6, therefore, emerges as an additional player in DA assembly, a process that is essential for proper axoneme building and that appears to be much more complex than was previously thought

Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm.

BACKGROUND: The male-specific region of the mouse Y chromosome long arm (MSYq) is comprised largely of repeated DNA, including multiple copies of the spermatid-expressed Ssty gene family. Large deletions of MSYq are associated with sperm head defects for which Ssty deficiency has been presumed to be responsible. RESULTS: In a search for further candidate genes associated with these defects we analyzed changes in the testis transcriptome resulting from MSYq deletions, using testis cDNA microarrays. This approach, aided by accumulating mouse MSYq sequence information, identified transcripts derived from two further spermatid-expressed multicopy MSYq gene families; like Ssty, each of these new MSYq gene families has multicopy relatives on the X chromosome. The Sly family encodes a protein with homology to the chromatin-associated proteins XLR and XMR that are encoded by the X chromosomal relatives. The second MSYq gene family was identified because the transcripts hybridized to a microarrayed X chromosome-encoded testis cDNA. The X loci ('Astx') encoding this cDNA had 92-94% sequence identity to over 100 putative Y loci ('Asty') across exons and introns; only low level Asty transcription was detected. More strongly transcribed recombinant loci were identified that included Asty exons 2-4 preceded by Ssty1 exons 1, 2 and part of exon 3. Transcription from the Ssty1 promotor generated spermatid-specific transcripts that, in addition to the variable inclusion of Ssty1 and Asty exons, included additional exons because of the serendipitous presence of splice sites further downstream. CONCLUSION: We identified further MSYq-encoded transcripts expressed in spermatids and deriving from multicopy Y genes, deficiency of which may underlie the defects in sperm development associated with MSYq deletions.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Study of N-acetyltransferase 2 genetic polymorphism in the Senegalese population : preventing toxicity and treatment failure of isoniazid in the treatment of tuberculosis

Un xénobiotique subit plusieurs étapes de biotransformations simultanées ou successives dont les principaux sites sont les tissus situés à l’interface entre l’organisme et le milieu extérieur, à savoir : le tube digestif, l’appareil respiratoire, le rein et le foie. Ce dernier étant fonctionnellement le plus important. Les phases réactionnelles principales constituant les étapes de détoxification, phase I, phase II et phase III, ne sont possibles que par l'intervention de systèmes enzymatiques spécifiques. Etant donné la grande diversité des xénobiotiques auxquels l'organisme est exposé, il existe une multitude d'enzymes présentant des spécificités variées. Les réactions de biotransformation des xénobiotiques s'enchaînent rarement de façon linéaire, car deux voies ou plus prennent souvent naissance à partir d'un métabolite donné. On comprend dès lors que l'existence d'un variant enzymatique défectif pour l'une de ces voies réactionnelles pourra orienter le métabolisme d'une substance donnée vers une autre voie. Cette dernière, généralement mineure, prendra donc une grande importance et les polymorphismes qui la concernent pourront orienter le devenir des métabolites ainsi formés. La famille des N-acétyltransférases (NATs) fait partie des enzymes assurant principalement la réaction de conjugaison de la phase II de détoxification des xénobiotiques. Le polymorphisme des NATS représente l'un des exemples de variation pharmacogénétique décrit, et de l'un des plus documentés, depuis sa découverte au début des années 50, en même temps que la découverte de la grande efficacité de l’isoniazide (INH) dans le traitement de la tuberculose.Les travaux de cette thèse avaient pour objectif d’étudier le profil d’acétylation de la NAT2 dans la population sénégalaise afin de les répartir en acétyleurs lents et en acétyleurs rapides, et de déterminer la cinétique de l’isoniazide chez des sujets tuberculeux en corrélation avec les résultats de génotypage. L’étude des mutations du gène NAT2 a été effectuée par PCR-séquençage directe et a permis de mettre en évidence 11 variants alléliques dans la population sénégalaise.l’activité enzymatique de la NAT2 a été déterminée par utilisation du test à la caféine et le rapport des ratios des métabolites majeurs a permis classer les sénégalais en acétyleurs lents et rapides. La cinétique de l’isoniazide a utilisée la chromatographie UPLC-MS/MS. Ce travail présente les premiers résultats de l’étude de la NAT2 dans la population sénégalaise qui pourront être utilisés pour une meilleur optimisation de l’utilisation de l’INH dans la prise en charge de la tuberculose, maladie à forte prévalence en Afrique.Xenobiotic biotransformation undergoes several stages of simultaneous or successive whose main attractions are the tissues at the interface between the organism and the external environment, namely: digestive, respiratory, kidney and liver. The latter being the most important functionally. The reaction phases constituting the main stages of detoxification, phase I, phase II and phase III, are possible only through the intervention of specific enzyme systems. Given the wide diversity of xenobiotics to which the organism is exposed, there are a multitude of enzymes with various specificities. The biotransformation reactions of xenobiotics are linked linearly rarely, because two or more lanes are often born from a given metabolite. It is therefore understandable that the existence of an enzyme variant defective for one of these reaction pathways can direct the metabolism of a given substance to another track. The latter, usually minor, will therefore important and polymorphisms that concern will guide the fate of metabolites thus formed. The N-acetyltransferases (NATs) is part of enzymes that primarily the conjugation reaction of phase II detoxification of xenobiotics. The polymorphism of NATS is one of the examples of pharmacogenetic variation described, and one of the most documented since its discovery in the early \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'50s, along with the discovery of the high efficacy of isoniazid (INH) in the treatment of tuberculosis. The work of this thesis aimed to study the profile of the NAT2 acetylation in the Senegalese population in order to distribute them in slow acetylators and rapid acetylators, and determine the kinetics of isoniazid in tuberculous subjects correlated with the results of genotyping. The study of mutations of the NAT2 gene was performed by PCR-direct sequencing and allowed to identify 11 allelic variants in the Senegalese population. The enzymatic activity of NAT2 was determined by using caffeine test and the ratios of major metabolites allowed Senegalese classify fast and slow acetylators. The kinetics of isoniazid used UPLC-MS/MS chromatography