WorldCat Identities

Institut Sophia Agrobiotech (Sophia Antipolis, Alpes-Maritimes)

Overview
Works: 53 works in 53 publications in 2 languages and 53 library holdings
Roles: Other, Performer
Publication Timeline
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Most widely held works by Alpes-Maritimes) Institut Sophia Agrobiotech (Sophia Antipolis
Étude de la régulation du transcriptome de nématodes parasites de plante, les nématodes à galles du genre Meloidogyne by Chinh Nghia Nguyen( )

1 edition published in 2016 in English and held by 1 WorldCat member library worldwide

Les nématodes à galles (RKN) du genre Meloidogyne spp. sont des parasites obligatoires des plantes qui induisent la formation d'un site nourricier spécialisé au sein des racines. Mon projet de thèse a pour objectif d'identifier des gènes spécifiques de ces nématodes qui sont impliqués dans le parasitisme en se focalisant sur des protéines sécrétées ou effecteurs. La technologie de séquençage Illumina a été utilisée pour comparer les transcriptomes de M. incognita au cours de son cycle de vie. A partir de 307 gènes surexprimés dans -au moins- un stade du cycle de vie, nous avons sélectionné 14 candidats d'effecteurs. Des expériences de RT-qPCR, d'hybridation in situ et d'ARN interférence ont permis de confirmer le profil d'expression, de localiser l'expression des effecteurs et d'étudier leur rôle dans la pathogénicité. Ce travail a permis de démontrer le rôle important d'une petite protéine, MiSCR1, dans les stades précoces du parasitisme. Parallèlement, nous avons réalisé l'assemblage de novo du transcriptome de M. enterolobii, qui représente une nouvelle menace pour l'agriculture mondiale du fait de sa capacité à se reproduire sur la majorité des plantes résistantes aux autres RKN. Les premières comparaisons avec d'autres RKN nous ont permis d'identifier, non seulement des effecteurs en commun, mais aussi ceux qui sont spécifiques à certaines espèces de RKN et qui pourraient expliquer des différences de gamme d'hôtes. En conclusion, les analyses de transcriptomes de RKN ont permis de caractériser des nouveaux effecteurs candidats impliqués dans la pathogénicité, et d'apporter de nouvelles connaissances pour le développement de méthodes de lutte contre ces bioagresseurs
Étude de l'implication des mécanismes épigénétiques chez le nématode à galles Meloidogyne incognita by Rahim Hassanaly Goulamhoussen( )

1 edition published in 2021 in French and held by 1 WorldCat member library worldwide

Plant parasitic nematodes of the genus Meloidogyne are crop pests of global importance. As such, M. incognita is the emblematic species as it is present all over the world with a wide spectrum of host plants. Currently, the use of resistant plants is the most effective way to control this nematode. However, the emergence of virulent lines able to bypass the plant resistance requires a better understanding of the biology of this species. M. incognita reproduces asexually by obligate mitotic parthenogenesis. Asexual reproduction is often considered as an evolutionary dead end because in this case, individuals adapt poorly to changing environments, due to the absence of meiosis. Despite this apparent lack of genetic plasticity, this species shows an amazing ability to adapt to adverse environments. An example of this is the bypassing of resistance in response to selection pressure exerted by the tomato Mi-1 resistance gene, with the appearance of virulent phenotypic variants in the progeny. The characteristics of the transmission of this trait over generations suggest a non-Mendelian heritability, thus involving an epigenetic component. In this thesis, the impact of histone post-translational modifications (HPTMs) in the biology of M. incognita was studied. First, the method of chromatin immunoprecipitation in fixed condition was developed and optimized for M. incognita. This optimization, performed for the first time in a parasitic nematode, allowed to show the involvement of five HPTMs in the regulation of genome expression. The conservation of the function of H3K9me3, through its association with transposable elements and low-expressed genes, and of H3K4me3 enriched at the promoter level of highly expressed genes, leads to the hypothesis of the existence of a "histone code" in this species.The dynamics of the chromatin landscape was studied during the development of this nematode, through the analysis of the regulation of the five HPTMs. These dynamics are marked by the expression of specific genes in association with the activating HPTM H3K4me3, during the transition from the egg stage to the L2 juvenile larval stage. At the egg stage, the predicted functions of the genes regulated by this mark concern cell cycle regulation and embryo development, while at the L2 juvenile larval stage, mainly genes involved in stimulus response were identified.The importance of HPTMs in the acquisition of virulence of this nematode was also initiated. The identification of differential enrichment profiles between avirulent and virulent lines of M. incognita showed a virulence polymorphism related to the regulation by HPTMs. At the origin of this polymorphism are a class of genes coding for SKP1 proteins, involved in protein degradation pathways. These candidate genes show overexpression in association with H3K4me3 in avirulent lines and decreased expression associated with loss of this HPTM in virulent lines. The precise role of SKP1 proteins in the acquisition of virulence in M. incognita remains to be determined.All these works contribute to evaluate the importance of epigenetic mechanisms in the adaptation of parthenogenetic organisms to changing environments and to define new control methods against crop pests
Identification de marques épigénétiques chez le nématode à galles parasite de plantes Meloidogyne incognita by Loris Pratx( )

1 edition published in 2017 in French and held by 1 WorldCat member library worldwide

Meloidogyne incognita est le nématode causant le plus de dégâts en agriculture. Sa particularité est d'être un organisme à reproduction asexuée obligatoire. Une femelle engendre des clones a priori 100% identiques génétiquement. Pourtant, M. incognita est capable de faire preuve d'une grande plasticité phénotypique lui permettant de répondre à de nouveaux environnements. Un exemple est le déterminisme du sexe, un phénotype lié aux conditions environnementales et semblant impliquer des régulations chromatiniennes. Un autre exemple est la capacité à contourner les résistances des plantes (virulence), un caractère héréditaire mais non-Mendelien. Dans le cadre de cette thèse, j'ai cherché à tester l'implication des mécanismes épigénétiques dans la plasticité phénotypique en absence de sexe de M. incognita. A ces fins, j'ai évalué la conservation des mécanismes épigénétiques chez les nématodes à galles. Cette approche a permis de pointer que les mécanismes connus chez C. elegans sont conservés chez les nématodes parasites de plantes. Puis, une méthodologie de ChIP-seq a été mise en place afin de comparer les profils d'accumulation des marques d'histones chez M. incognita au cours de la réponse aux conditions environnementales. Cette stratégie a permis la mise en évidence 1- de patrons d'histones modifiées marquant le développement du parasite et 2- de régions génomiques comportant plus de 300 gènes dont des candidats facteurs d'avirulence déjà décrits dans la littérature spécifiquement perdue entre M. incognita (a)virulents. Ces travaux de thèse présentent un intérêt fondamental sur la compréhension de l'évolution d'un organisme en absence de reproduction sexuée
Destin et comportement des spores du groupe Bacillus cereus chez des organismes modèles by Salma Hachfi( )

1 edition published in 2022 in French and held by 1 WorldCat member library worldwide

The Bacillus Cereus (B cereus) group consists of Gram-positive bacteria, commonly isolated from the environment. Members of the B. cereus group are spore-forming bacteria commonly associated with food poisoning and intestinal infections and represent the third cause of food poisoning in Europe and the second in France. The most-studied members of this group are B. anthracis, B. cereus sensu stricto (Bc), and B. thuringiensis (Bt) that are well known for their pathogenic activity. Bt is characterized by the production, during its sporulation, of a crystal containing insecticidal Cry toxins. Thanks to this entomopathogenic activity, bioinsecticides based on spores and crystals of Bt are used to specifically kill lepidopteran pests. Bt bioinsecticides represent more than 50% of the global market share of biopesticides. Upon ingestion of Bt bioinsecticides (spores and toxin crystals), Cry toxins are released from the crystal and destroy the insect gut epithelium allowing spores to invade the internal milieu. Then spores' germination in the hemolymph lead to the pest death by septicemia in less than 3 days. However, the increasing environmental dispersion of Bt products raises the question about their potential risks for non-target animals.Using Drosophila melanogaster (a non-target organism), it has been previously shown that Bt vegetative cells are rapidly cleared from the intestine. This elimination is due to the activation of the local innate immune response. However, few studies suggest that Bt spores can persist in human and rodent intestines. To understand why and how Bt/Bc spores persist in the gut of non-target organisms and the implication of the innate immune response in fighting spores, I have used two powerful models: Drosophila melanogaster and mice. First, I have shown that Bt/Bc spores can persist, after acute ingestion, up to 10 days in the Drosophila midguts and at least 5 days in mice small intestines., Then, using an innovative tool, generated in my lab, consisting of red fluorescent spores that switch in green fluorescent once germinated (corresponding to vegetative bacteria), I have shown that spores accumulate mainly in the posterior midgut of Drosophila and the posterior small intestine of mice where they can further germinate. Then, I confirmed these data using quantitative monitoring of spores vs. vegetative bacteria accumulation in vivo in the intestines of Drosophila and mice. Altogether, my data suggest that, in the posterior regions of the Drosophila midgut (and the small intestine of mice), the innate immune response is inefficient to promptly eliminate spores and germinated bacteriaIn Drosophila midgut, the local innate immune response (i.e. the production of Reactive Oxygen Species (ROS) and Anti-Microbial Peptides (AMPs)) is mainly mounted in the anterior regions. I have shown that, unlike vegetative cells, spores do not trigger ROS and AMPs production. Strikingly, I have even observed that spores inhibit AMPs production. Interestingly, I have found a transcriptional induction of negative regulators (e.g. PGRP-SC1, -SC2, and -LB) of the immune signaling pathways in the posterior region of the midgut in response to spore ingestion. Then, using combinations of mutants of the two immune pathways, Imd and Toll, I have been the first to demonstrate that both immune pathways coexist in the Drosophila midgut, and may contribute either additively or synergistically to fight spore infections
Étude des facteurs écologiques modulant les gammes d'hôtes des parasitoïdes by Lucie Monticelli( )

1 edition published in 2018 in French and held by 1 WorldCat member library worldwide

Parasitoids are insects whose adult females deposit eggs in, on or near hosts and immatures stages develop by host consumption. They are involved in host population regulation and are largely used in biological control to reduce the damages caused by pests in agroecosystems. Their ability to control pest populations mainly depends on their host range i.e., the number of host species enabling offspring production. The parasitoid host range has been largely studied and may depend on its ability to localize, select and sting their hosts (behavioral host range) and/or its ability to consume and circumvent the hosts physiological defenses (physiological host range). However, each ecosystem has his own biotic and abiotic characteristics that can modulate both behavioral and physiological traits of parasitoids but they implication in the host range modulation have rarely been tested. In this context, the objective of my thesis was to evaluate the impact of different ecological factors on parasitoid host ranges. More specifically, I studied the impact of (i) the genetic bottleneck due to the introduction of small parasitoid population in a new area (through classical biological control notably), (ii) the host and host plant phylogenies, (iii) the bottom-up effects of drought stress, (iv) the relationship between the quality of the host and its ability to produce food for the parasitoid and (v) the parasitoid-mediated indirect interactions between unsuitable and suitable hosts, on the aphid parasitoid host range (high implication in biological control). We demonstrated that the aphids and host plant phylogenies are strongly involved in shaping the ecological host range of parasitoids whereas the other factors tested may only modulate the parasitoid fitness and parasitism rate; which may, finally, indirectly modulate the parasitoid host range. Studied the impact of ecological factors on parasitoid host range seems determinant; this thesis enables to better understand some mechanisms involved in parasitoid community functioning and to potentially optimize biological control programs
Diversité génétique du nématode vecteur Xiphinema index sur vigne et application pour optimiser la stratégie de résistance by Van Chung Nguyen( )

1 edition published in 2018 in English and held by 1 WorldCat member library worldwide

The ban of most nematicides renders urgent control alternatives against plant-parasitic nematodes and breeding for resistant plant varieties is promising. In vineyards, the nematode Xiphinema index has a high economical impact by transmitting Grapevine fanleaf virus (GFLV), the main virus of 'Court-noué' disease and the first grapevine viral disease worldwide. Resistant rootstocks are being selected in grapevine, using Muscadinia rotundifolia (muscadine) as a resistance source to the vector, in order to arrest or delay GFLV transmission. In this crop, a previous study had shown that this meiotic parthenogenetic nematode is able to reproduce sexually (rarely) in the field. A preliminary phylogenetic work had allowed to reveal the predominant diversity groups and to select representative populations for the creation of single-female lines. Resistance durability is a real challenge that must consider the key information of the nematode diversity. In this context, the PhD project first completed and deepened our phylogeographical approach using an extended geographic coverage of the worldwide nematode distribution. Our results allow proposing strong hypotheses to locate the native area of X. index in the Middle-East and trace its dissemination routes from the Antiquity. They also highlight the close link since this epoch between dissemination of the nematode and domesticated grapevine by man. The second part of the PhD project has then evaluated the durability of muscadine-derived rootstock material in greenhouse (non viruliferous nematodes on plants aged 3 to 6 years) and field (viruliferous nematodes on plants aged 16 years) conditions. In the greenhouse, F1 and BC1 resistant accessions, previously obtained from both in vitro and hardwood-cutting propagation, were inoculated with 4 mixed representative X. index lines, traceable each with microsatellite markers. We showed that nematodes from plants obtained from in vitro progressively overcame the resistance while the material obtained from cuttings displayed a durable resistance. Nematode progressive multiplication in resistant accessions obtained only from in vitro removes a priori the hypothesis of a nematode genetic adaptation and appears linked to a different architecture of the root system in this propagation type. This type may have induced discrete but durable physiological changes in apical root tissues from where nematodes feed. Nematode microsatellite genotyping allowed detecting a low but increasing rate of hybrid individuals from 4 to 6 years, which confirms data from the vineyard. As the hybrid occurrence appears independent from the propagation type and the resistance status of the plant, our data discard hybridization as the mode of adaptation of the nematode underlying resistance breakdown from in vitro plants. In field conditions, after 16 years, nematodes were almost undetectable on the resistant BC1 accession, also almost unaffected by the viral attacks, while higher numbers were detected on a susceptible control accession, whose plants were by contrast in high majority dead or poorly vigorous. Taken all together, our results show that the muscadine-derived resistance strategy appears durable. This strategy focused on vector control will significantly contribute to reduce the impact of GFLV transmitted by X. index
Gestion durable des nématodes à galles en culture maraîchère par la modélisation et l'optimisation du déploiement de variétés résistantes by Samuel Nilusmas( )

1 edition published in 2020 in French and held by 1 WorldCat member library worldwide

Root-knot nematodes are obligate soil-borne endoparasites of plant roots that cause major yield losses throughout the world. Environmentally-friendly plant protection methods against root-knot nematodes are mainly based on the use of resistant plant cultivars. These cultivars efficiently control nematode populations naturally present in the field, but they favour the emergence of virulent variants that circumvent the resistance genes carried by these cultivars. Since virulence is associated with fitness costs, which limit the virulent nematode ability to infest plant roots or reproduce, susceptible crops counter-select virulent nematodes. The aim of this thesis is to identify effective and sustainable resistance deployment strategies to control root-knot nematodes in horticultural crops. To this end, we developed a semi-discrete epidemiological model describing the nematode dynamics in the soil and in the roots of a resistant or susceptible plant during its growing season, as well as the survival of nematodes in the soil between cropping seasons. The model was fitted to experimental data of within-season infestation of susceptible tomato roots. It was used to determine the rotation strategies alternating susceptible and resistant plants that maximise an average yield proxy, over different time horizons and for different combinations of epidemiological intensity and genetic parameters (mutation rate and virulence costs). Moreover, sensitivity analyses were performed to assess the robustness of the plant resistance deployment strategies. Our results show that carefully designed rotation strategies would not only increase crop yield, but also preserve the sustainability of resistance genes. Sensitivity analyses were performed to evaluate the robustness of our results. This thesis opens both experimental and modelling perspectives for a better control of root-knot nematodes
De la preuve de concept à l'optimisation - l'utilisation d'une espèce d'acarien prédateur pour contrôler la population de la Chrysomèle des racines du Maïs (Diabrotica virgifera virgifera) (LeConte, 1868) by Antoine Pasquier( )

1 edition published in 2021 in English and held by 1 WorldCat member library worldwide

Maize is the most important cereal crop in the world (162 million hectares). It plays a major role in human and animal nutrition and its cultivation occupies about 9% of the useful agricultural area in Europe. Since its arrival in Europe in 1992, the corn rootworm, belonging to the order Coleoptera, has threatened this important crop. The larval stage of this organism is particularly harmful to plants because it attacks the underground parts of this cereal causing yield losses that can reach 80% of the crop's potential in the most critical cases. Chemical pesticides, the use of Bt GMOs and crop rotation alternating soybeans and corn are the main control methods for this pest currently. However, studies have shown that some populations are resistant to these insecticides and are able to (i) persist in the soil longer and (ii) expand their host range by attacking soybean roots. In this context, there is a need to explore new crop protection methods that will allow a more integrated control of this pest. A study recently demonstrated the potential role of soil predatory mites as biological control agents. These organisms are at the top of trophic chains in agricultural systems and have already shown strong abilities to control populations of subterranean pests. The main objective of my thesis is to develop a biological control strategy agronomically and economically viable to control corn rootworm. First, I evaluated the predation capacity of three soil mites (Stratiolaelaps scimitus, Gaeolaelaps aculeifer and Macrocheles robustulus) on the early developmental stages of western corn rootworm in the laboratory. These results were conclusive and one of the three candidates particularly attracted our attention: G. aculeifer. This predatory mite showed a higher predation capacity on the first larval stage of the pest. In a second step, I studied the effect of the presence and the density (100, 500 and 1000 mites per corn plant infested by the pest) of these predatory mites on the western corn rootworm population under semi-controlled conditions.This experiment showed that the mite densities tested were all effective in protecting the maize plant. Finally, and in order to optimize the effectiveness of these predatory mites as a biocontrol agent, I studied the population dynamics of these predators when a low density of predatory mites has been introduced at the time of seeding (Predator-in-first method) and in the presence of alternative food, in a field naturally infested by corn rootworm. These experiments allowed me to identify an application method that would facilitate the introduction of the biological control solution and reduce its cost. My work will provide essential information in understanding the biological control potential of these previously understudied soil organisms
Analyse fonctionnelle des effecteurs nucléaires du parasitisme des nématodes à galle Meloidogyne incognita et caractérisation de leurs cibles végétales by Nhat My Truong( )

1 edition published in 2016 in French and held by 1 WorldCat member library worldwide

The root-knot nematode Meloidogyne incognita is among the most devastating plant pathogens
La biogenèse des galles induites par des phyto-nématodes dépend de l'hyperactivation du cycle cellulaire : études fonctionnelles des nouveaux acteurs du cycle mitotique et de l'endocycle dans les cellules géantes by Danila Cabral do Nascimento( )

1 edition published in 2019 in English and held by 1 WorldCat member library worldwide

Lors des vingt dernières années, l'utilisation d'Arabidopsis thaliana en tant que plante modèle a permis d'accélérer les découvertes biologiques dans l'étude de nombreuses interactions plante-pathogènes tant au niveau moléculaire que cellulaire. Arabidopsis réagis de manière similaire aux plantes cultivées face aux attaques de nombreux pathogènes, y compris les nématodes. Meloidogyne incognita est un nématode endoparasite de la racine des plantes causant de lourdes pertes agronomiques estimées à plusieurs milliards de dollars par an. Afin d'induire la formation de sites nourriciers dans la racine de l'hôte, les nématodes à galles. Ceci a pour effet d'induire la formation de cellules géantes à l'origine des nodosités observées sur la racine de l'hôte communément appelées galles. Lors de la formation des sites nourriciers, les cellules géantes ont pour caractéristiques d'être hypertrophiées et poly-nucléés du fait de l'absence ou de l'interruption de la cytokinèse et de nombreux cycles successifs d'endoreduplication. Ainsi, une caractéristique cruciale du développement du nématode est l'hyper activation du cycle cellulaire dans les galles. Le cycle cellulaire eucaryote est conservé et caractérisé par la phase S (réplication de l'ADN), suivie par la phase mitose (M), la cytokinèse et la division cellulaire. Celles-ci sont entrecoupées par la phase G1 (Gap 1) qui relie la fin de la mitose, et la phase G2 (Gap 2) qui relie la fin de la synthèse de l'ADN. L'endocycle est une variante du cycle cellulaire dans laquelle la réplication se produit sans mitose, induisant le doublement du contenu en ADN cellulaire pour chaque endocycle. L'hyper activation du cycle cellulaire est essentielle pour la biogenèse de la galle induite par les nématodes et un équilibre précis entre les phases mitotiques et endocycliques est essentiel pour la réussite du parasitisme. Dans le cadre de ma thèse de doctorat, nous avons étudié les conditions préalables nécessaires à l'établissement d'une galle fonctionnelle induite par M. incognita. Je me suis particulièrement concentrée sur l'étude fonctionnelle de gènes du cycle cellulaire de la plante jouant un rôle dans la mitose et l'endoreduplication lors de l'interaction plante-nématode. Pour répondre à cette question j'ai réalisé des études fonctionnelles de nouveaux acteurs du cycle cellulaire chez Arabidopsis stimulant (E2F), inhibant (ABAP1 et son-interactor) ou contrôlant (WEE1) le cycle cellulaire des galles. Les résultats obtenus démontrent que les gènes étudiés ici sont essentiels pour la formation et le maintien des sites nourriciers des nématodes. Notre étude fonctionnelle et notre analyse moléculaire montrent que l'absence ou la surexpression de facteurs de transcription E2Fa et E2Fb affectent gravement le développement de la galle et la reproduction des nématodes et perturbent le cycle cellulaire des galles, validant ainsi leur importance pour le développement du site d'alimentation des nématodes. Nous avons également cherché à déterminer si le stress induit par les nématodes déclenche un checkpoint control pendant la progression du cycle cellulaire dans les galles. Par conséquent, une analyse fonctionnelle du facteur de transcription WEE1 a été réalisée et a montré que son absence induit une mitose plus précoce dans les sites nourriciers, affectant ainsi le développement des galles et la reproduction des nématodes. L'utilisation de drogues, d'un marqueur de stress SMR7, ainsi que d'une lignée exprimant un gène rapporteur sous le contrôle du promoteur du gène PARP1 (impliqué dans la réparation de l'ADN) ont suggéré l'activation du checkpoint control G1/S dans les galles. Les données présentées dans cette thèse ont apporté des connaissances fondamentales pour une meilleure compréhension du contrôle du cycle cellulaire lors de la biogenèse de la galle, ainsi que lors du développement de la plante
Le récepteur IOS1 d'Arabidopsis thalisana - modulateur de l'homéostasie protéique du réticulum endoplasmique en réponse au stress biotique by Laïla Giordano( )

1 edition published in 2019 in French and held by 1 WorldCat member library worldwide

Plant cells have a diversifying number of plasma membrane-localized receptors, which are specialized in detecting environmental changes and allow the plant to adapt accordingly. About 200 of these receptors are composed of an extracellular domain with leucine-rich repeats (LRR) and an intracellular kinase domain. We have previously identified a member of this receptor family in Arabidopsis, which contributes to the infection success by biotrophic filamentous pathogens, such as the oomycete Hyaloperonospora arabidopsidis (Hpa). The plant mutant for the receptor gene loses its susceptibility to infection, and according to this phenotype the receptor has been named "Impaired Oomycete Susceptibility 1" (IOS1). IOS1 negatively regulates the abscisic acid (ABA) hormone signaling pathway upon infection. In addition, the receptor has been shown to be part of a plasma membrane receptor complex that detects bacterial infections and triggers innate immunity. The extracellular region of IOS1 harbors an additional so-called Malectin-Like Domain (MLD), which has strong structural similarities to animal malectin. Animal malectin resides in the endoplasmic reticulum (ER), where it interacts with ribophorins from the oligosaccharyltransferase (OST) complex. Proteins from this complex ensure post-translational protein maturation by adding N-glycosylations. Ribophorins monitor the correct folding of neo-synthetized glycoproteins. Environmental changes frequently alter the rate of proteins that are produced and require maturation. If monitoring system is not efficient, neo-synthetized proteins accumulate in the ER and generate the "Unfolded Protein Response" (UPR). The mechanism for controlling glycoprotein maturation and the UPR also exist in plant cells. In order to characterize the functions of the extracellular domain (ED) of IOS1, we show by confocal laser-scanning microscopy that the MLD mediates a retention of the receptor in the ER. Here, the MLD of the receptor attenuates the UPR, which is triggered by the oomycete infection. We identified the plant ribophorin HAP6 and the cell death attenuator Bax-Inhibitor-1 (BI-1) as ER-residing proteins that interact with the ED of IOS1. In functional complementation experiments involving the ios1-1 mutant transformed with individual IOS1 domains, we further evaluated the role of IOS1 and the MLD in the plant responses to ER and ABA stress signaling. We show that the MLD attenuates the UPR during the plant-oomycete interaction, thus promoting successful infection. We also show that ABA signaling correlates positively with the UPR, indicating that the observed IOS1-mediated regulation of hormone signaling is a consequence of interference with the UPR. Taken together, our data suggest that individual domains of the IOS1 receptor target distinct functions in different subcellular compartments
Contrôle biologique par conservation effets des plantes non cultivées sur les communautés d'arthropodes inféodées aux agrosystèmes by Yusha Wang( )

1 edition published in 2020 in English and held by 1 WorldCat member library worldwide

La lutte biologique par conservation manipule l'agro-écosystème et son environnement de manière à améliorer les performances des ennemis naturels (telles que la survie, la fitness ou le comportement) et ainsi optimiser leur efficacité contre les ravageurs. Les plantes non cultivées sont cultivées pour créer un environnement nuisible aux ravageurs et aux maladies et / ou bénéfique aux agents de lutte biologique. L'objectif de ce travail de doctorat était d'étudier comment les plantes non cultivées affectent les interactions entre les plantes cultivées, les herbivores et leurs ennemis naturels à la fois au niveau individuel (traits d'histoire de vie) et de la population (dynamique des populations). Dans un premier temps, nous avons analysé la littérature sur les plantes non cultivées et leur impact sur la performance des ennemis naturels. Les familles des Apiacées, Asteracées, Polygonacées, Brassicacées, Lamiacées and Fabacées sont ressorties comme étant les plus bénéfiques pour les ennemis naturels. Dans un deuxième temps, nous avons mené des études de terrain sur deux agro-systèmes basés sur le blé-maïs et la tomate au champ. Nous avons évalué l'impact de trois niveaux de diversité des plantes non cultivées sur le rendement des cultures des communautés d'insectes et il a été montré un effet fort de la diversité des plantes non cultivées sur le contrôle biologique et sur la dynamique temporelle des interactions naturelles ennemi-ravageur. La diversité des plantes non cultivées a eu un impact positif sur les niveaux trophiques supérieurs (ennemis naturels), la lutte biologique contre les ravageurs, la biodiversité communautaire et la stabilité du réseau trophique. Enfin dans un 3ème temps, nous avons montré par des tests en laboratoire que l'ajout de plantes non cultivées peut améliorer la longévité et / ou la reproduction de Harmonia axyridis, en absence de proies. Ces plantes non cultivées pourraient être des candidats à utiliser pour diversifier les agro-écosystèmes et stimuler le contrôle biologique
Réponse immunitaire de la drosophile à la guêpe endoparasitoïde Leptopilina boulardi : caractérisation d'une réaction de résistance by Chami Kim( )

1 edition published in 2019 in English and held by 1 WorldCat member library worldwide

Drosophila melanogaster is a main model in biology, notably immunity and evolution. Although the Drosophila innate immune processes to fight bacteria and fungi have largely been explored, less is known of the defence against endoparasitoid wasps whose successful development inside the insect host leads to its death. One of the most studied Drosophila - parasitoid wasp interaction involves Leptopilina boulardi that lays eggs inside host larvae and develop at their expense. Once the parasitoid egg has been recognized as a foreign invader, the Drosophila larva can mount a successful immune response, the encapsulation: the egg is surrounded by several layers of hemocytes and there is an increase of a specific types of hemocytes, the lamellocytes. The so-formed capsule is melanised and there is formation of reactive oxygen species, which kills the parasitoid. Alternatively, the immune response can be circumvented thanks to the venom components injected by the female wasp together with the egg. Using two Drosophila strains, resistant and susceptible to L. boulardi, which differ only in a region of chromosome 2R containing a major resistance gene. The resistance was found to be monogenic, with two alleles, the resistance allele being dominant (Rlb+>Rlb). The team previously identified edl/mae (R and S alleles) as a candidate gene. Mae (Modulator of the Activity of ETS) or edl (ETS-domain lacking) was described as a mediator of specific transcription factors of the ETS (E26 transformation-specific) family in Drosophila. Mae interacts with transcription factors trough a SAM (Steril Alpha Domain), a protein - protein interaction domain. Mae is known to regulate yan and pnt P2 transcription factors during the eye development and yan and pnt P2 appear to have a role during haematopoiesis. The objectives of my thesis were to decipher the possible role of edl/mae and identify the molecular and cellular events leading to success or failure of encapsulation. I used various approaches from fly genetics to flow cytometry. The involvement of edl/mae in Drosophila resistance was confirmed by using overexpression and interference of mae expression. The overexpression of the resistant allele in a susceptible background leads to a resistant phenotype. The interference of the expression of the susceptible allele results in an increased rate of parasitoid encapsulation. At the cellular level, an increased in the number of hemocytes after parasitism occurred earlier in the resistant strain than in the susceptible strain. It was also observed that the hematopoietic lymph gland of the resistant larvae busted before the one of the susceptible larvae. At the molecular level, potential interactants of mae were identified in silico and 2 were tested using interference of their expression which led to observing an increase of encapsulation. Overall, a key player in the resistance mechanism of the Drosophila to the parasitic wasp have been identify during this work and it lays the path for future work on regulation mechanism of the response at the molecular level
Distributions des espèces du genre Trichogramma le long d'un gradient altitudinal et adaptations locales aux basses températures chez l'espèce Trichogramma cacoeciae by Michela Ion Scotta( )

1 edition published in 2019 in French and held by 1 WorldCat member library worldwide

All species are facing some environmental heterogeneity in time and / or space and thus with variations in the quality of their local environment. According to their biology (dispersal ability, phenotypic plasticity, local genetic variability, etc.), species respond differently but this heterogeneity usually generates or maintains inter-or intra-specific variations in life history traits. In this context, my thesis focuses on (i) the understanding of the geographical and ecological distributions of Trichogramma species along an altitudinal gradient in a narrow area of the department “Alpes-Maritimes”; (ii) -possible local adaptations to low temperatures in one of the encountered species. For this second part, three types of experiments were conducted from a set of strains from the two contrasted areas along the altitudinal gradient (Meso - and Supra - mediterranean) as well as strains from a more northern geographical area: (i) laboratory comparison of thermal tolerance indices: Ctmin, Chill coma and Recover Activity; (ii) study of diapause capabilities; (iii) study of overwintering modalities in the field. My results first showed that, at the scale of the altitudinal transect studied and with our sampling protocol, T. cacoeciae is the most widely distributed and abundant species. In addition, the Supra - mediterranean strains seem to have genetic differences with regard to the Meso - Mediterranean ones, particularly in their rate of development at low temperatures as well as their propensity to diapause. This genetic differentiation is even more marked in the more northern strains especially for their Chill coma values which are on average lower. Taken as a whole, this study unambiguously concludes that there is intra-specific variability in T. cacoeciae for traits related to adaptation to low temperatures. These results, obtained for a single species and on a small geographical scale, thus open the way towards a more systematic study of these traits and the taking into account/exploitation of their inter and intra-specific variabilities in the evaluation of trichograms as auxiliaries for biological control
Invasion du nématode du pin Bursaphelenchus xylophilus by Sophie Mallez( )

1 edition published in 2014 in French and held by 1 WorldCat member library worldwide

Dans ce projet, nous nous sommes intéressés à l'invasion du nématode du pin, Bursaphelenchus xylophilus, un ver microscopique responsable de la maladie du dépérissement du pin et causant la perte de millions d'arbres annuellement à travers le monde. Notre objectif global était d'affiner nos connaissances sur ce cas d'invasion et particulièrement d'établir l'histoire d'invasion des populations européennes. Nous avons analysé la diversité génétique neutre d'échantillons de populations naturelles de nématode du pin de l'aire native et de différentes zones envahies à l'aide de méthodes de génétique des populations. Ces analyses ont essentiellement mis en évidence que (i) l'aire native du nématode du pin est fortement structurée à fines échelles spatiales et présente une diversité génétique faible à modérée, suggérant un rôle important de la dérive génétique, non compensée par la dispersion, (ii) les populations européennes présentent une diversité génétique extrêmement faible, suggérant un seul évènement d'introduction en Europe, et que (iii) l'Amérique du Nord est la source la plus probable des populations envahissantes européennes, non le Japon et la Chine. Ce projet souligne l'intérêt que les nématologistes et les généticiens des populations ont à collaborer. La génétique des populations a en effet permis de clarifier l'histoire de l'invasion des populations européennes et ce modèle nématode, du fait de son cycle de vie complexe résultant en un cas extrême de faible diversité génétique, a permis de s'interroger sur des méthodes et analyses couramment utilisées en génétique des populations
Analyse fonctionnelle de cibles végétales d'effecteurs du parasitisme du nématode Meloidogyne incognita impliquées dans l'ontogénèse des cellules géantes by Joffrey Mejias( )

1 edition published in 2020 in French and held by 1 WorldCat member library worldwide

Plant parasitic nematodes of the genus Meloidogyne, or root-knot nematodes, are a major phytosanitary problem worldwide. These obligate plant parasites have developed original and complex parasitism strategies. By injecting proteins called "effectors" into the host plant, they induce cell reprogramming and the transformation of root cells into enlarged and polynucleated feeding cells, named "giant cells". However, little is known about the determinism of these newly formed structures in plants. During my thesis, I focused on two proteins secreted by the root-knot nematode M. incognita: the effector 18 encoded by a pioneer gene (MiEFF18) and a protein disulfide isomerase (MiPDI). We have identified the plant protein targeted by the effectors using a yeast two hybrid screen approach and we have studied their roles in the compatible interaction and the formation of giant cells. Immunolocalisation experiments have shown that the protein MiEFF18 is produced in the salivary glands, accumulates in secretory granules indicating that it could be secreted in planta via the stylet. The use of translational fusions between MiEFF18 and GFP has shown that this effector accumulates in the nucleus and nucleolus of plant cells. The SmD1 proteins have been identified as MiEFF18 targets in tomato, Arabidopsis and in N. benthamiana. These SmD1 proteins are conserved and essential components of the spliceosome and the eukaryotic messenger RNA splicing machinery. The sequencing of the transcripts (RNAseq) of wild type plants of Arabidopsis thaliana, plants overexpressing MiEFF18, or mutant plants (knockout) for the AtSmD1b gene, shows that this effector is able to modulate the function of the alternative splicing regulator SmD1 and that its overexpression modifies the expression of genes involved in the giant cell ontogenesis. MiEFF18 also modulates the function of the SmD1 protein in triggering a specific "silencing" pathway called S-PTGS (« sense transgene post-transcriptional gene silencing»). We were able to show that Arabidopsis thaliana, Solanum lycopersicum (tomato) and Nicotiana benthamiana plants in which the expression of SmD1 is affected exhibit increased resistance to root-knot nematodes and that the function of the effector EFF18 is conserved in other Meloidogyne species. EFF18 effectors are therefore able to manipulate the different functions of SmD1 in order to promote the formation of giant cells during infection in Arabidopsis and Solanaceae. In a second part, we were able to demonstrate the secretion of the MiPDI-1 effector in giant cells. A yeast two hybrid strategy made it possible to identify its plant target, the stress-associated protein 12 (SAP12) in tomatoes and A. thaliana. SAP12 is a protein capable of sensing the environment redox state and is involved in plant defense and the response to various abiotic stress. The functional analysis of this effector/target made it possible to show that the manipulation of the SAP12 protein by MiPDI-1 is essential for the parasitic success of M. incognita, in order to (i) protect the larvae of reactive oxygen species produced during the penetration of the host and (ii) to modulate the expression of genes involved in defense and the response to stress during parasitism. This work shows the importance of studying the molecular dialogue between the parasite and the host plant and the characterization of the proteins targeted by these pests for the development of new resistances against these parasites
Impact de la capacité de charge de l'environnement sur les dynamiques d'expansions de métapopulation : théories et applications à un système expérimental hôte-parasitoïde by Marjorie Haond( )

1 edition published in 2019 in French and held by 1 WorldCat member library worldwide

Reaction-diffusion equations are commonly used to describe population propagation dynamics. In particular, they can be used to define two types of dynamics: pulled and pushed. The pulled dynamic results from a colonization led by individuals in small numbers located at the edge of the population, the pushed dynamic results from a colonization led by larger numbers from the core of the population. Biological mechanisms underlying the pushed waves are still poorly described, however, the presence of an Allee effect (characterized by a positive correlation between growth rate and population density for small populations) is known to lead to a pushed dynamic. Other mechanisms generating a dependence between population size and the probability of colonization are also likely to generate pushed waves, but this generalization remains to be confirmed. Few studies have addressed the effects of environmental factors such as carrying capacity on population expansion rates. However, while for a pulled dynamic, the colonization of the few individuals at the front of the wave should not be influenced by the value of the carrying capacity of the environment, in the pushed case, individuals evolving at larger numbers, the carrying capacity could be a limiting factor of the expansion. We have therefore attempted to describe (i) the effects of carrying capacity on population expansion dynamics, particularly through the prism of pulled/pushed dynamics, and (ii) the diversity of demographic mechanisms that can generate high dynamics. For this purpose we used individual-centred modelling approaches and microcosm experimentation on parasitoid hymenoptera, Trichograms. We used a species with a positive density-dependent dispersion resulting in an increase in the individual probability of migrating in large populations, thus leading to potentially high colonization dynamics. Using these two approaches, we first studied the impact of carrying capacity on expansion velocity, validating our hypotheses that the dependence of expansion velocity on carrying capacity could be an indicator of the pushed/puledl nature of expansions. In a second part we studied the phenomena of Range pinning described for populations subjected to Allee effects and we tried to generalize this phenomenon to pushed dynamics in the presence of positive dependent density dispersion. In a third part we studied how a heterogeneous distribution in space of different carrying capacities would influence the dynamics of particularly high expansions
Solution miracle ou coup dans l'eau ? Potentiel et limites de l'utilisation des programmes de lutte biologique en écologie expérimentale by David Muru( )

1 edition published in 2021 in English and held by 1 WorldCat member library worldwide

La lutte biologique (ou biocontrôle) est l'utilisation d'organismes vivants pour lutter contre les populations de ravageurs des cultures en réduisant leur densité et les dommages qu'ils causent. L'auxiliaire de lutte biologique peut interagir, directement ou indirectement avec d'autres organismes en plus du ravageur ciblé et inversement. Le suivi de ses populations, en plus du suivi d'autres variables écologiques, pourrait donc permettre de confirmer ou réfuter des théories écologiques ou découvrir de nouvelles interactions avec les facettes biotiques et abiotiques de l'écosystème. De plus, les aspects méthodologiques de la phase de suivi postlâcher et ceux de l'expérimentation en écologie partagent de fortes ressemblances. Dans ce travail, j'explore comment ces deux disciplines peuvent être conciliées et comment les données qui découlent de la lutte biologique peuvent être optimisées pour leur utilisation en écologie. J'utilise des données issues de programmes de lutte biologique pour traiter des questions en relation avec les dynamiques d'invasion, l'écologie des communautés et l'écologie du paysage. Dans le premier chapitre, je détaille les cas d'études utilisés : (i) l'introduction du parasitoïde Torymus sinensis contre la guêpe galligène Dryocosmus kuriphilus ; (ii) l'introduction de l'ectoparasitoïde Mastrus ridens contre le carpocapse de la pomme Cydia pomonella ; (iii) un inventaire des Trichogramma de France ayant pour objectif de caractériser les zones écologiques de chaque espèce ; (iv) la description des parasitoïdes oophages associés à Iphiclides podalirius à fine échelle temporelle. Le chapitre 2 est centré sur l'étude de la dispersion de T. sinensis à l'échelle de plusieurs zones productrices de châtaignes. Dans ce chapitre, j'utilise des données de suivi sur les sites de lâcher pour en faire un modèle de croissance des populations de T. sinensis et ainsi inférer les dates de colonisations de sites naturellement colonisés. Dans le chapitre 3, je recherche les impacts du succès du contrôle biologique de D. kuriphilus par T. sinensis sur la structure de la communauté de parasitoïdes natifs, récemment associée au ravageur. Le chapitre 4 est dédié aux cas d'études où la valorisation scientifique varie d'un échec complet (primo-introductions de M. ridens), la diffusion de connaissances naturalistes (suivi d'I. podalirius et des parasitoïdes oophages associés) en passant par l'identification de motifs écologiques à l'aide d'outils statistiques spécifiques (suivi des espèces de Trichogrammes à échelle nationale).Enfin, en compilant les connaissances disponibles dans la littérature et mon expérience sur le terrain, je discute ensuite du potentiel et des limites de l'utilisation de la lutte biologique en tant qu'expérimentation en écologie. Je conclue que bien que la lutte biologique fournisse un contexte écologique à l'expérimentation en permettant la manipulation de plusieurs facteurs, le contexte et les organismes impliqués ne peuvent pas être adaptés à n'importe quelle problématique écologique. Par exemple, le parallèle évident entre la biologie de l'invasion et la lutte biologique fait de ce dernier un fort atout pour étudier les procédés qui régissent lesuccès des invasions. Cependant, les facteurs comme les faibles seuils de détectabilité d'un auxiliaire de lutte biologique à faible densité (couplé à la sensibilité des méthodes de suivis) peuvent faire de l'étude des dynamiques et interactions lors des stades précoces de l'invasion, une entreprise périlleuse
Contribution des phytoglobines et des nitrate réductases à la régulation de l'oxyde nitrique et de la fixation de l'azote dans la symbiose Medicago truncatula / Sinorhizobium meliloti by Antoine Berger( )

1 edition published in 2019 in French and held by 1 WorldCat member library worldwide

The nitrogen-fixing symbiosis between legumes and soil bacteria of Rhizobia type reduces atmospheric nitrogen (N2) to ammonia (NH3) through the presence of bacterial nitrogenase in a root organ, called nodule.In the symbiotic model Medicago truncatula / Sinorhizobium meliloti, nitric oxide (NO) is produced throughout the symbiotic process, from the beginning of the interaction between the plant and the bacteria until the senescence of the nodule. The toxic, signal or metabolite effects of NO depend mainly on its concentration at the action site. Its concentration within the nodule cells must be regulated in order to limit its toxic effects and leads its signaling and metabolite functions. In plants, the main sources of NO identified are nitrate reductase (NR) and the mitochondrial electron transfer chain (ETC). In addition, phytoglobins (Phytogb) are known to be involved in the catabolism of NO. According to their sequences homology and affinity for oxygen, three classes of Phytogb have been described in legumes: non-symbiotic Phytogb (Phytogb1), legume-specific leghemoglobin (Lb) and truncated Phytogb (Pgb3).The main objectives of this PhD were, on the one hand, to characterize and study the role of NR and Phytogb in the NO regulation, during the symbiosis between M. truncatula and S. meliloti and, on the other hand, to analyse the role of NO in the development and in mature nodule during the symbiotic process.In M. truncatula, 3 genes code for NR and 17 for Phytogb. The phylogenetic study of M. truncatula Phytogb identified 12 Lb, 3 Phytogb1 and 2 Phytogb3. Analysis of NR and Phytogb gene expression, as well as measurement of total NR activity and NO production, allowed to monitor the level of NO during the N2-finxing symbiosis, and to determine the respective roles of the different NR and Phytogb in the NO regulation. During the symbiotic process, four peaks of NO production were observed, corresponding to four periods of the symbiotic process, during (1) the establishment of the interaction between the plant and the bacteria, (2) at the setup of the nodule organogenesis (3) inside the functioning and mature nodule and (4) at the onset of nodule senescence. During these different periods, the production of NO is particularly correlated with the expression of the NR1 and 2, one Phytogb1 (Phytogb1.1) and one Phytogb3 (Phytogb3.1) genes. The use of various inhibitors of NO synthesis pathways has shown that NO production depends mainly on NR activity and the mitochondrial electron transfer chain. The use of NO donors has shown that, during nodular development, NO induces the expression of Phytogb1 and several defence genes but represses Lb and Phytogb3 genes. Functional analysis of Phytogb1.1, during nodule establishment, functioning and senescence, was initiated via the production of M. truncatula plants overexpressing or silencing this gene. Overexpression and under-expression of this gene resulted, respectively, in a decrease and an increase in the NO level in the nodules, but in both cases resulted in a decrease in the number of nodules per plant. Analysis of the expression of several markers genes of the symbiotic interaction, defence responses, nitrogen metabolism and hypoxia, and analysis of nitrogen fixation in mature nodules highlight the particular role of Phytogb1.1 in the NO regulation during nodule development and during the senescence process
Caractérisation des régulations post-transcriptionnelles intervenant lors de la formation des cellules géantes induites par les nématodes à galles by Yara Noureddine( )

1 edition published in 2021 in English and held by 1 WorldCat member library worldwide

Root-knot nematodes (RKN), genus Meloidogyne, are microscopic plant parasitic worms which infect roots of more than 5 000 cultivated plant species and cause massive crop yield losses worldwide. Within host root, RKN induce the formation of root galls by inducing the dedifferentiation of root vascular cells into giant and multinucleated feeding cells. The formation of feeding cells can be split into two phases: successive nuclear divisions during the first ten days post infection (dpi), then from 10 to 21 dpi feeding cells nuclei undergo extensive endoreduplication and plant growth. These feeding cells supply water and nutrients essential for nematode development. The formation of these feeding cells is the result of an extensive reprogramming of gene expression in targeted root cells as shown by transcriptome analyses. However, few data are available on the regulation of gene expression in these structures. The objective of my PhD thesis was to study small non-coding RNAs, microRNAs, that are key regulators of gene expression. microRNAs act at the post-transcriptional level by inducing the degradation or inhibition of the translation of targeted messenger RNAs (mRNAs). During my PhD thesis, sequencing of small RNAs from tomato (Solanum lycopersicum) galls induced by Meloidogyne incognita RKN and uninfected roots identified 174 microRNAs that are differentially expressed in galls at 7 and/or 14 dpi. mRNAs targeted by microRNAs in tomato galls were then identified by integrating microRNA sequencing data with data from transcriptome analysis and from a specific sequencing of cleaved mRNAs named degradome approach. This integrative analysis built a microRNA-gene regulatory network acting during the formation of galls and feeding cells in tomato roots. Three microRNAs families, miR167, miR398 and miR408, were selected for functional analyses. MiR167 family targets the auxin-response factors ARF8A and ARF8B. These ARFs belong to auxin signaling pathway, a key hormone in plant-RKN interaction. Using tomato lines expressing the two ARF8 promoters fused to GUS reporter gene, I showed a strong activity of both ARF8 promoters in galls at 7 and 14 dpi, confirming the transcriptomic analyzes. Moreover, we analyzed the effect of a CRISPR deletion within ARF8A and ARF8B coding sequences on the infection by M. incognita. Both CRISPR lines showed a significantly increased resistance to nematode infection correlated with defects in feeding cell formation. Altogether, these result showed that ARF8A and ARF8B expression is required for successful tomato-RKN interaction. The two conserved microRNA families, miR398 and miR408, are upregulated in tomato and Arabidopsis thaliana galls. miR398 and miR408 and their targets have been previously described to be involved in the copper signaling pathway. MIR398 and MIR408 expression is activated in response to copper starvation by the SPL7 transcription factor and mature miR398 and miR408 repress expression of genes encoding copper binding proteins non-essential for plant development. By using Arabidopsis lines expressing transcriptional fusion with GUS reporter gene, I showed that both MIR408 and SPL7 were expressed within nematode induced feeding cells. Moreover, infection assays with mir408 and spl7 mutants or lines expressing mutated targets resistant for miR398 cleavage showed an increased resistance of these lines to nematode infection. Finally, watering plants with copper sulfate, at concentration below toxic concentrations for the plants or for the nematodes, induced a strong resistance to nematode infection. Altogether, these results demonstrate the role of the copper signaling through activation of miR398 and miR408 by SPL7 in the formation of giant feeding cells. To conclude, the work presented in this thesis demonstrates the important role of three microRNAs families and their targets in the formation of nematode-induced feeding cells
 
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Centre national de la recherche scientifique (France). Unité mixte de recherche (7254)

Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (France). Unité mixte de recherche (1355)

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