Chairman: ..
9h25 - Opening
9h30 - Ecology and evolution of host tumor interactions Justine Boutry---View abstract---
9h55 - Genetic diversity of Indonesian nutmeg Jakty Kusuma---View abstract---
10h20 - Evolution and dynamics of di-symbiotic system in aphids Jeff Rouil---View abstract---
10h45 - Coffee break
11h00 - Incubation period for neuroinvasive cases of Toscana virus infections Lison Laroche---View abstract---
11h25 - Characterization of resistance of sugarcane (Saccharum spp.) to orange rust caused by Puccinia kuehnii and genetic diversity of the pathogen Jordan Dijoux---View abstract---
11h50 - Engineering of resistance by loss of susceptibility : innovating strategies to control bacterial leaf blight of rice in West Africa Coline Sciallano---View abstract---
12h15 - Lunch break
Chairman: ..
13h30 - The root-associated microbiome of rice in a context of infection with phytoparasitic nematodes: ecological, phenotypical and molecular characterizations Anne-Sophie Masson---View abstract---
13h55 - Tool development for the visualization of plant pangenomes Eloi Durant---View abstract---
14h20 - Modulation of jasmonate pathways in rice (Oryza sativa) by the microbiota present in the oral secretions of the Lepidopteran pest Spodoptera frugiperda Laëtitia Leclerc---View abstract---
14h45 - Étude de la dynamique spatio-temporelle de bactéries racinaires bénéfiques pour la croissance et la santé du riz au Burkina Faso Moussa Sondo---View abstract---
15h10 - Coffee break
15h25 - Genetic and epigenetic of the paramutation phenomenon in maize Juliette Aubert---View abstract---
15h50 - Biosynthèse et rôle biologique des diterpènes dans les graines de caféiers Gaelle Antoine---View abstract---
Chairman: ..
9h00 - Opening - GAIA
9h05 - Evaluation of new F1 hybrids of Coffea arabica selected for agroforestry systems in the context of climate change in the North-West of Vietnam Thuan Sarzynski---View abstract---
9h30 - Architecture and growth modelling of savannah agroforestry species native to Côte d’Ivoire Beda Innocent Adji---View abstract---
9h55 - Impacts of forest anthropization on the links between the biodiversity of micrommals hosts, their microbiote and zoonotic danger Marie Bouilloud---View abstract---
10h20 - Impact of biodiversity and its management over the regulation of the disease-pest complex in agroforestry systems Marcos J. Ramos---View abstract---
10h45 - Coffee break
11h00 - L’agrobiodiversité pour renforcer la résilience et réduire les risques faces aux changements climatiques Aby cisse---View abstract---
11h25 - Evaluation de l'impact des mises en valeur agricoles dans la transmission du paludisme à Bouaké, Côte d'ivoire Milossé Mélaine Claudelle Dahoui---View abstract---
11h50 - Analyse géographique des déterminants d'une transmission différenciée du paludisme dans la ville de Bouaké en Côte d'Ivoire Kouassi Arsene Adou---View abstract---
12h15 - Lunch break
Chairman: ..
13h30 - Evolution of Codon Usage Preferences and manipulation of translation fidelity Fanni Borveto---View abstract---
14h00 - Histoire évolutive de l'arbre fuitier Dacryodes edulis : implications pour sa conservation et sa gestion durable PhD defense - Aurore Rimlinger
15h00 - PhD awards
Ecology and evolution of host tumor interactions
...
Genetic diversity of Indonesian nutmeg
My research focuses on the evolutionary history of Indonesian nutmeg species (Myristica fragrans, M. fatua and M. argentea) and more widely on Myristica species. In this aim, I am characterizing the genetic diversity and structure of nutmeg species in their native Indonesian distribution to underpin strategies of conservation and use. These species are food tree species, whom seeds and maces are exploited as spices. Getting information on the distribution of their genetic diversity within and between wild and cultivated populations will help contributing to the conservation, sustainable management and use of these species. To another hand, I will develop a time-calibrated phylogenetic tree, and interpret patterns of Myristica species distribution in light of past geological and climatic events. This will contribute to the understanding of the evolutionary history of tropical flora from South-East Asia.
Characterization of the Interaction between the Magnaporthe oryzae Effector Avr-Pita and the Rice Protein Ptr
Genetic control of phytopathogens is an efficient and resilient management method but requires extensive knowledge of plant immunity. The PhD project will contribute to this by elucidating the molecular mechanisms of resistance to the pathogenic fungus M. oryzae in rice. By investigating a novel type of plant immunity protein, this research will provide new insight into the mechanisms of resistance to fungal diseases, which will be instrumental for the protection of cereal crops.
Evolution and dynamics of di-symbiotic system in aphids.
Aphids feed on the phloem sap of plants, which is poor in amino acid and vitamins, to synthetize these compounds, aphids depend on mutual obligate symbiosis with the bacteria Buchnera aphidicola. Apart from Buchnera, many aphids have found to harbour additional endosymbiotic bacteria. In The aphid subfamily Lachninae, these secondary endosymbionts are obligate and seem to have been acquired and replaced multiple time. By using genomic data and phylogenetic approaches, we try to reconstruct the evolutionary history of this di-symbiotic system. In the same time, we want to describe the dynamic of both endosymbiotic bacteria during aphids’ development.
Incubation period for neuroinvasive cases of Toscana virus infections
Toscana virus (TOSV) is an emerging pathogen in the Mediterranean area transmitted through the bites of female sand flies. TOSV can be neuroinvasive and is a major cause of meningitis and encephalitis in endemic areas during summer. Knowledge on the incubation period of this virus is needed to optimize surveillance and control of these diseases. However, information regarding the incubation period of TOSV is heterogeneous and rarely referenced. In this context, we conducted a systematic review on symptomatic travel-related TOSV infections in order to estimate the incubation period with censored time-to-event models. We found 27 imported cases of TOSV meningoencephalitis infections in 25 case reports. The analyses showed a median incubation period of 12.1 days (95% CI: 10.2–14.2). This evidence-based estimate of the TOSV incubation period allowed us to highlight the need to standardize the data collection for the diagnosis of infected patients.
Characterization of resistance of sugarcane (Saccharum spp.) to orange rust caused by Puccinia kuehnii and genetic diversity of the pathogen
Sugarcane orange rust (SOR), caused by the fungus Puccinia kuehnii, is an emerging disease affecting an increasing number of sugarcane producing countries. SOR has great impact on sugarcane production because numerous cultivars are susceptible to the disease and disease epidemics have a long duration during sugarcane growth. Consequently, SOR is one of the most damaging sugarcane diseases. The use of varietal resistance is the only means to avoid chemical control and the only cost-effective and environmentally viable disease control strategy. However, the genetic support of SOR resistance is poorly understood. Resistance heritability within modern interspecific cultivars (Saccharum officinarum x S. spontaneum) is unknown, as well as the regional and worldwide genetic diversity of the causal agent. This lack of knowledge compromises the efforts of efficient genetic improvement. These improvement efforts can rely on the use of modern interspecific cultivars containing so far uncharacterized sources of resistance, which most likely originated from the wild ancestral species (S. spontaneum) that exhibits higher resistance levels than the domesticated species (S. officinarum). This thesis aims at acquiring key knowledge for resistance breeding by taking advantage of actual progress regarding the understanding of the genome of P. kuehnii and the one, particularly complex (polyploid and highly heterozygous), of modern interspecific cultivars. The thesis will be performed in the frame of scientific collaborations between two research units in Montpellier (UMRs PHIM and AGAP) and one private partner (eRcane) which leads a breeding program in Reunion Island where SOR recently emerged and spread all over the sugarcane production areas. The four main objectives of this thesis are: 1) To study the genetic diversity of P. kuehnii in Reunion Island and in other countries affected by SOR in Africa, the Americas and Asia, in order to identify the source(s) of introduction of the pathogen in Reunion Island and to compare the local and worldwide genetic diversities; 2) To estimate the effect of the disease on agronomic performances (yield and quality of the sugarcane) of commercial cultivars and elite experimental varieties, to improve varietal recommendations and thus limit the risks of economic losses; 3) To characterize the genetic properties of resistance to SOR among current breeding populations to support the management of breeding programs (estimation of the variance components and broad and narrow-sense heritability of the trait, prediction of breeding values of candidate genitors); 4) To study the genetic support of SOR resistance using genome-wide association and genome annotation approaches, and to evaluate genomic selection models to support varietal selection (localization of haplotypes of interest, estimation of their effects, and determination of their ancestral origin).
Engineering of resistance by loss of susceptibility : innovating strategies to control bacterial leaf blight of rice in West Africa
Bacterial Leaf Blight (BLB) which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is a major threat to rice production worldwide, leading up to 50% yield losses in Asia and Africa during severe infections. Xoo pathogenicity relies on the injection into the host cell of Transcription-Activator Like Effectors (TALEs) which are effective transcription factors that hijack the plant transcriptional machinery. TALEs bind to Effector Binding Elements (EBE) in the promoter of susceptibility (S) genes and activate transcription, which is essential for disease development. Clade-III members of the family of SWEET sugar transporters are major BLB susceptibility genes. Naturally occurring polymorphism in the EBEs of SWEET promoters prevent TALE binding and turns these “unresponsive” alleles into recessive resistance genes. Rice lines edited in the EBEs of the three major SWEET genes targeted by Xoo were tested for resistance against a diverse set of strains [1]. While the multi-edited lines are able to defeat Xoo strains of Asian origin, African Xoo strains still maintain some level of virulence. The goal of this thesis is to decipher the virulence strategy of African Xoo. Our main objectives are: i) to understand the dependence of African Xoo toward the use of SWEETs, ii) to investigate the genetic basis for the phenotypic specificity of African Xoo, and iii) to characterise the Xoo populations in Africa.
The root-associated microbiome of rice in a context of infection with phytoparasitic nematodes: ecological, phenotypical and molecular characterizations
The genus Meloidogyne is a group of phytoparasitic nematodes that profoundly affect rice yield especially in the tropical area. The prohibition of the use of synthetic nematicides for public health concerns combined with the evolution of cultural practices (aerobic rice and direct seeding, in particular) led to the increase of their parasitic pressure in the field. In this context, the development of environmentally friendly methods is crucial to maintain global food security and offer a promising alternative for controlling nematode infections. Indeed, the root microbiota plays an important role for plant immunity (Pieterse et al., 2016) and some studies encourage the exploitation of root microbiota to limit the impact of root-knot nematodes in the field (Pereira da Silva et al., 2018 for example). However, we have little knowledge about the interactions between rice, plant parasitic nematodes and root microbiota, especially on the O. sativa - M. graminicola pair in Asian agrosystems. This doctoral work aims to study this interaction at different levels: ecological (description of root-associated communities of infected rice in Vietnam or in different agricultural systems in Cambodia), phenotypic (developmental measures and plant yield after inoculation of candidate bacteria for biocontrol) and molecular (response in the plant and/or in the rhizosphere with a multipartite interaction model). Thus, after having described the microbiome associated with infected roots (the "gallobiome") and determined some factors structuring the microbiome in an agricultural system, the evaluation of bacteria in the field and in the laboratory will make it possible to select a model to be studied more in detail in order to understand the mechanisms of interaction and, in the long term, improve rice immunity in the field.
Tool development for the visualization of plant pangenomes
Single reference genomes are not enough to grasp the diversity within a species (alleles and SNPs, but also structural variations and presence/absence of genes!), which can lead to difficulties during mapping steps for instance. An alternative emerged through the concept of 'pangenome' (from 'pan', all, entirety; and 'genome'), which can have two main definitions, gene-centric or sequence-centric. Such pangenomes may be represented as graphs, which can be really difficult to interpret. My aim is to explore alternative representations and to develop an interactive tool that would allow biologists to work with these novel entities.
Modulation of jasmonate pathways in rice (Oryza sativa) by the microbiota present in the oral secretions of the Lepidopteran pest Spodoptera frugiperda
Spodoptera frugiperda (Lepidoptera: Noctuidae) is an insect pest native to America, which has recently spread throughout the world. Its polyphagous caterpillar attacks a wide variety of host plants, including some of great economic interest such as corn (Zea mays) or rice (Oryza sativa). These plants recognize herbivorous insects thanks to Herbivore Associated Molecular Patterns (HAMPs), such as β‐glucosidase, fatty-acid-amino acid conjugates and inceptins, present in the oral secretions (OS) of the insect. HAMPs will trigger defense molecules synthesis, in particular through the activation of derivatives of the jasmonate (JA) pathway. Our objectives are (i) to study the activation of the JA signaling in rice in response to herbivory, (ii) to evaluate the role of the insect gut microbiota in this plant defense reaction. We mimicked a caterpillar attack by inflicting mechanical injuries on rice leaves followed by addition of laboratory-reared Spodoptera frugiperda caterpillars (6th instar) regurgitation on wounds. First, we observed a significant transcriptional induction of some JA pathway markers (OsJAZ5, OsMyc2 and OsPR10) upon this treatment. When the same experiment was conducted with caterpillar regurgitation from insects that were fed with antibiotics (ampicillin 100μg/mL and erythromycin 400μg/mL), the transcription of the same markers was twice over-induced. We showed that the antibiotic treatment modified the insect intestinal microbiota. Before treatment, we identified the bacterium Enterococcus mundtiiand the yeast Diutina rugosa by plating on nutrient agar medium of both larvae regurgitation and crushed gut. After antibiotic treatment, the bacterium disappeared. In conclusion, our preliminary results suggest that the S. frugiperda OS induce JA-dependent defense pathways in rice and that bacterial microbiota attenuates this reaction.
Étude de la dynamique spatio-temporelle de bactéries racinaires bénéfiques pour la croissance et la santé du riz au Burkina Faso
Dans l’objectif de mettre au point des techniques d’intensification limitant les intrants chimiques, l’étude des micro-organismes des racines, tiges et feuilles des plantes, est de plus en plus prise en compte comme une composante essentielle de la croissance et la santé de la plante. L’analyse de la diversité des communautés microbiennes de la plante, en utilisant l’approche moléculaire (metabarcoding) sur des échantillons suggère que la plante exerce une sévère sélection parmi la diversité de micro-organismes de la rhizosphère (Edward et al., 2015), pour s’associer avec une communauté plus restreinte. En parallèle, des criblages des collections bactériennes cultivables (par inoculation sur la plante en conditions contrôlées et souvent gnotobiotiques) rapportent que des espèces bactériennes, notamment au sein des genres Bacillus, Burkholderia, Herbaspirillum ou encore Pseudomonas (Rascovan N et al. 2016 ; Mansfield J, et al., 2012), peuvent améliorer la croissance des plantes et/ou limiter leurs maladies (effet biocontrôle). Cependant il reste aujourd’hui très difficile de faire le lien entre la découverte des propriétés d’un isolat bactérien et la caractérisation de la diversité microbienne par metabarcoding. Ainsi, les souches bactériennes connues pour avoir des conséquences bénéfiques sur la santé de la plante restent généralement peu décrites en termes de dynamiques spatio-temporelle dans l’agroécosystème, cette information étant pourtant capitale pour comprendre l’effet réel exercé par ces micro-organismes au champ, ainsi que pour évaluer l’efficacité potentielle d’applications par les producteurs. Dans ce contexte, le sujet de notre thèse porte sur l’analyse du microbiome racinaire du riz par l’approche des bactéries cultivables et l’étude des corrélations entre la présence des certaines bactéries bénéfiques et le développement des maladies majeures du riz au Burkina Faso (causé par Magnaporthe oryzae et Xanthomonas oryzae). Les objectifs étant i) isoler les bactéries associées aux racines du riz, ii) sélectionner par le criblage in vitro, in silico et finalement in planta des isolats ayant un effet sur la santé de la plante (croissance et/ou biocontrôle) et iii) étudier le rôle de bactéries bénéfiques dans le microbiome. Afin de réaliser ces objectifs nous avons commencé par l’isolement des bactéries racinaires du riz cultivé en conditions de bas-fond et irrigué. Les résultats de ces travaux incluant i) la caractérisation par le séquençage du fragment ADNr 16S et par le phénotypage in vitro pour les caractéristiques PGPR et ii) l’analyse in silico de la comparaison de la diversité de bactéries cultivables vs la diversité observée par le séquençage barcoding (C. Tollenaere et M. Barro, en rédaction). La compatibilité du lecteur d'écran est activée.
Genetic and epigenetic of the paramutation phenomenon in maize
Paramutation is a rare exception where reprogramming is both mitotically and meiotically stable over many generations. Since its discovery in 1956, only 4 locus of paramutation have been described in Zea mays, all associated with a red pigmentation phenotype: red1 (r1), booster1 (b1), plant color1 (pl1), and pericarp color1 (p1). To our knowledge, no research was conducted to identify paramutable genes that are not involved in a visible phenotype in maize. To determine the importance of paramutation in gene silencing, we crossed independent inbred lines (B73, M37W and M162W) and backcrossed their F1s. We sequenced and analysed leaf messenger RNA from all 4 successive generations, and identified 80 differentially expressed genes in the inbred lines that were stably silenced in the F1s and in all the backcrosses. These alleles meet all criteria of paramutation as their silencing is stable through meiosis, and the newly silenced genes in turn silence active genes in backcrosses. They cover diverse functions in maize, but carry no significant differences in TEs or small-RNA density. With these 80 new candidates to paramutation, we argue that this phenomenon is more common than initially expected in maize, and should not be overlooked when crossing independent lines.
Biosynthèse et rôle biologique des diterpènes dans les graines de caféiers
Les caféiers accumulent de grandes quantités de diterpènes dans leurs graines. Des études récentes leur prêtent des activités anticancéreuses prometteuses. Au sein des caféiers, l’espèce Coffea mauritiana endémique de La Réunion est celle qui accumule le plus de ces métabolites. Malgré l’importance économique du café, le métabolisme des diterpènes est aujourd’hui méconnu, ainsi que le rôle biologique de ces molécules pour la plante. Un objectif majeur de la thèse est donc de combler ces lacunes par des approches combinées de génomique et de chimie analytique en utilisant la diversité chimique présente au sein du genre Coffea et l'espèce Coffea mauritiana comme modèle d'étude. Des approches de réseaux de coexpression génique permettront de déterminer des gènes candidats pour la biosynthèse des diterpènes, qui seront validés fonctionnellement par la suite. Ces approches permettront également d’étudier les liens avec les autres voies de biosynthèse des isoprénoïdes et d’identifier des régulateurs du métabolisme des diterpènes chez les caféiers. Notamment en déterminant la localisation intracellulaire des diterpènes dans la graine par des approches d’imagerie hyperspectrales et de dosage chimique de différentes fractions cellulaires. Le deuxième volet de la thèse s’intéresse aux rôles biologiques des diterpènes dans la défense de la graine et de la jeune plantule contre des ravageurs et pathogènes. Une étude du devenir des diterpènes au cours de la germination sera réalisée par un suivi de la composition chimique des différents tissus de la graine et de la plantule. Enfin, l’activité biologique des diterpènes sera étudiés sur différents pathogènes et ravageurs des cultures. La compatibilité du lecteur d'écran est activée.
Evaluation of new F1 hybrids of Coffea arabica selected for agroforestry systems in the context of climate change in the North-West of Vietnam
Cultivated on 11 millions ha by 50 milllions of small producers in 70 countries in the tropics, coffee (Coffea sp.) is one of the most traded agricultural goods in the world. As many other crops, Coffea arabica (the most cultivated coffee species), is affected by climate change especially by longer droughts and the global increase of average temperatures. These abiotic stresses affect the development and production of the plants which cause social, economic and environmental problems. The creation of new F1 hybrids of C. arabica more resilient and able to face the abiotic stresses related to climate change, and to ensure a high production of beans of high quality, has become an important goal for the sustainability of the coffee industry. In this context, CIRAD, in partnership ECOM, has selected new hybrids of C. arabica for their adaptability to climate change and to the agroforestry systems. In Central America, these hybrids already showed promising agronomical traits such as maintaining high production even under shade. However, the physiological and genetic mechanisms controlling this improved performances are still largely unknown. The goals of Thuan’s thesis is to test these new hybrids in a multilocation trial set in the North-West of Vietnam in the framework of the H2020 BREEDCAFS project supported by EU. In addition, Thuan’s work includes physiological and genetic analyzes carried out in a research trial planted at NOMAFSI station (Son La province) with several hybrids together with local Arabica varieties (used as control) under three contrasted water treatments; namely, rainfed, water supressed, and irrigated. The study of the hybrids tested in these conditions and in the multilocation trials should help to understand what are the optimum environmental conditions for their growth as well as the physiological and genetic mechanisms involved in their higher performances
Architecture and growth modelling of savannah agroforestry species native to Côte d’Ivoire
Reforestation and agroforestr y are the two options favoured by Côte d’Ivoire to restore its forest area and conserve its wood resources. Khaya senegalensis, Pterocarpus erinaceus and Parkia biglobosa are three indigenous savannah forest species with multiple uses. The heavy exploitation of these species exposes them to a loss of diversity that could lead to their eventual extinction. Integrating them into agroforestry programmes is a solution for their conservation and sustainable use. This study is being conducted with the aim of optimising the cultivation of these three species and promoting their agroforestry potential. Architectural analysis (development sequence and morphology of growth units/module) from seedlings to old trees will be carried out. The work will take place along a South-North drought gradient in Côte d’Ivoire in order to understand and determine the intra-specific architectural variability. In a second step, a retrospective analysis of growth will allow the past growth of the trees to be traced using morphological markers left behind by growth stoppages due to dry seasons. In this way, the architectural diagram of each of these species will be established. Finally, organ measurements captured in Multiscale Trees Graph format and analysis of the tops of the three species will be carried out at different ages in the nursery. These measurements will be used to model the growth and development of the target species using the GreenLab structure-function model. Hidden parameters such as organ sourcesink relationships, leaf resistance, common pool and production area will be obtained. These data will guide the choice of progeny or plants for planting, the ideal planting density, the itinerar y and cultivation management of these three species.
Impacts of forest anthropization on the links between the biodiversity of micrommals hosts, their microbiote and zoonotic danger
In recent years, we have observed an increase in the emergence of infectious diseases of zoonotic origin. This phenomenon could be explained by the loss of biodiversity (dilution effect) or by the deregulation of the hosts communities and their pathobiome (microbiome and pathogens) due to global change. The goal of my thesis is to understand the impacts of anthropization on the links between biodiversity and zoonoses in micromammals through the study of host communities and their pathobiome.
Impact of biodiversity and its management over the regulation of the disease-pest complex in agroforestry systems
Within diversified agroecosystems, promoting biodiversity and its associated functions, can become a major leverage for managing the global health of the ecosystem. Because of this, tropical agroforestry systems become the cradle of numerous action pathways, that can be direct or indirect, and that interact for contributing to the regulation and control of diseases and pests within the system. The thesis project aims to determine which are the action pathways that have an impact over the disease and pest complex and understand their effect over the regulation of the complex. This will result in a better understanding of how the system works and allow us to review current management practices and provide recommendations based on our findings.
L’agrobiodiversité pour renforcer la résilience et réduire les risques faces aux changements climatiques
Assurer la sécurité alimentaire face au changement climatique est l'un des plus grands défis sociétaux des années à venir. L’effet de l’agrobiodiversité, en termes d’associations culturales, sur le rendement des agrosystèmes a largement été étudié. A un niveau intraspécifique, le rôle des mélanges variétaux a surtout été abordé du point de vue de la résistance aux pathogènes. Néanmoins, des études récentes semblent indiquer que les mélanges variétaux pourraient impacter positivement le rendement et la résilience des agrosystèmes. En pratique, aussi bien au Niger qu’au Sénégal, nombreux sont les paysans pratiquant les mélanges variétaux, notamment en associant sur une même parcelle des variétés précoces et tardives de mil par exemple. L'objectif de notre étude est d'évaluer le rôle de l’agrobiodiversité et notamment des mélanges variétaux de mil sur le rendement et la stabilité des agrosystèmes. Pour ce faire nous avons utilisé deux approches: 1) nous avons mis en place des essais de mélanges variétaux de mil en milieux paysans et 2) nous avons mené des enquêtes ethnobotaniques auprès des agriculteurs afin d'étudier leur stratégie de semis à la lumière de leur perception du climat. En somme, il est question de tester si : 1) les mélanges variétaux de mil ont un impact sur le rendement et/ou la stabilité du rendement à l’échelle de la parcelle ; 2) si les ménages les plus diversifiés (en termes d’espèces et/ou variétés) ont des rendements meilleurs et/ou plus stables. Cette thèse interdisciplinaire alliant agronomie et ethnobotanie permettra de mettre en lumière le rôle de l’agrobiodiversité sur la sécurité des ménages. Les agriculteurs sont au centre de notre approche, ce qui nous permettra d'éclairer la conception et la mise en œuvre d'une agriculture diversifiée, agronomiquement bénéfique et réaliste pour les agriculteurs.
Evaluation de l'impact des mises en valeur agricoles dans la transmission du paludisme à Bouaké, Côte d'ivoire
L'urbanisation est l'un des phénomènes les plus marquants de ces dernières décennies et touche fortement le continent africain, puisque plus de la moitié de sa population devrait vivre en ville d'ici 2030. Dans le contexte économique actuel difficile, cette tendance à l'urbanisation inéluctable reste mal contrôlée ce qui n'est pas sans conséquence sur le bien-être des populations. De fait les villes sont devenues le berceau des inégalités de tous genres. Les citadins des villes d'Afrique affrontent des difficultés de logement, de transport ou encore de travail. Ils habitent dans des lieux où ils s'exposent à des risques inhérents au manque d'assainissement, aux difficultés d'approvisionnement en eau potable, aux difficultés d’aménagement des espaces. Or, la manière dont les acteurs, les habitants, les autorités locales agissent, s'approprient et transforment leur territoires peuvent avoir un effet sur la santé. Par ailleurs, la croissance des villes impose de réfléchir à l'alimentation de ceux qui les habitent. Or, l'agriculture urbaine peut créer des conditions d'une transmission permanente du paludisme. La ville de Bouaké qui offre à voir un réseau dense de bas-fonds intensément mis en valeur agricole est un site particulièrement adapté à l'analyse des modalités différenciées de cette transmission en lien avec l’occupation agricole. Dans le cadre de cette thèse, il s'agira de s'intéresser à l'alternance des différentes cultures mises en œuvre dans des bas-fonds types et à son impact sur la dynamique des vecteurs du paludisme et sur l'exposition des populations riveraines à la maladie. L’utilisation d’une approche pluridisciplinaire associant l’entomologie (caractérisation des populations vectrices), l’épidémiologie (exposition aux piqûres des populations) et la géographie (SIG, drone) permettra de suivre dans le temps et dans l’espace l’impact des mises en valeur agricoles sur la transmission du paludisme à Bouaké, Côte d’Ivoire. Les données collectées à échelle fine seront ainsi croisées avec les variables environnementales dans l’objectif d’identifier des indicateurs de transmission qui pourront être appliqués à d’autres sites en vue de proposer des scénarios prédictifs du risque de transmission. Les résultats pourront permettre de réfléchir à des stratégies de gestion des espaces agricoles intra urbains permettant de mieux contrôler la transmission du paludisme. La compatibilité du lecteur d'écran est activée.
Analyse géographique des déterminants d'une transmission différenciée du paludisme dans la ville de Bouaké en Côte d'Ivoire
L'hétérogénéité socio-spatiale des espaces urbains a pour conséquence la modulation de la transmission des maladies vectorielles dont le paludisme. A Bouaké, le Projet ANR-COhéSIoN a, dans le cadre de ses activités de recherche, adopté une approche méthodologique d'échantillonnage spatial qui a permis de définir une typologie du tissu urbain afin de conduire des enquêtes biomédicales et géographiques dans 4 quartiers illustratifs de la diversité de son tissu urbain. Les résultats obtenus montrent un lien entre certaines caractéristiques socio-démographiques et l'exposition aux piqûres d'anophèles ainsi que la prévalence du paludisme selon le quartier de résidence.
Evolution of Codon Usage Preferences and manipulation of translation fidelity
Synonymous Codons are not used at random. Codon usage preferences (CUPrefs) vary between organisms, between genes within a genome and between positions along a gene. CUPrefs modulate mRNA translation rate and accuracy, and for some genes or positions may be under selection. We aim at exploring the impact of CUPrefs on the translation machinery, the fitness costs associated to synonymous codons, and the evolutionary solutions to compensate for fitness cost. This project consists of a longterm selection experiment and a series of analysis linked to it. For the experimental part, we designed a set of five genes that have the same amino-acid sequence but use different codons. Human HEK293 cells have been transfected with the different plasmids and cultured under selection of either bleomycin or neomycin, for a long-term evolutionary experiment (~100 generations). We hypothesise that synonymous genes will be differentially expressed according to their match with the avaerage CUPrefs of the cells. These differences may generate variation in cellular fitness, and lead to observing compensation strategies in the transformed cells.