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International audience; Plasmids provide an efficient vehicle for gene sharing among bacterial populations, playing a key role in bacterial evolution. Network approaches are particularly suitable to represent multipartite relationships and are useful tools to characterize plasmid-mediated gene sharing events. The bacterial family Lysobacteraceae includes plant commensal, plant pathogenic and opportunistic human pathogens for which plasmid-mediated adaptation has been reported. We searched for homologues of plasmid gene sequences from this family in the entire diversity of available bacterial genome sequences and built a network of plasmid gene sharing from the results. While plasmid genes are openly shared between the bacteria of the family Lysobacteraceae, taxonomy strongly defined the boundaries of these exchanges, which only barely reached other families. Most inferred plasmid gene sharing events involved a few genes only, and evidence of full plasmid transfers were restricted to taxonomically closely related taxa. We detected multiple plasmid-chromosome gene transfers, including the known sharing of a heavy metal resistance transposon. In the network, bacterial lifestyles shaped substructures of isolates colonizing specific ecological niches and harbouring specific types of resistance genes. Genes associated with pathogenicity or antibiotic and metal resistance were among those that most importantly structured the network, highlighting the imprints of human-mediated selective pressure on pathogenic populations. A massive sequencing effort on environmental Lysobacteraceae is therefore required to refine our understanding of how this reservoir fuels the emergence and the spread of genes among this family and its potential impact on plant, animal and human health.

During AD, tauopathy follows a precise spatio-temporal progression, in correlation with symptoms severity. This progression may be due to the spread of pathological forms of Tau between connected neurons and in which microglia and neuroinflammation could play a role. Our main objective is therefore to develop relevant in vivo models to study the molecular and cellular determinants of Tau propagation which could lead to the identification of new therapeutic targets capable of slowing or even stopping it. We have developed AAV vectors inducing an overexpression of the human Tau protein, which we use to transduce neurons of dentate gyrus of hippocampus and ganglion cells of the retina (RGCs), whose efferent neurons are well characterized . In order to determine the role played by microglia in propagation of pathological species of the Tau protein, we are currently applying this experimental paradigm in Trem2 KO or aged mice in which microglial homeostasis is disturbed. The first analyzes show the presence of hyperphosphorylated Tau protein in the cells transduced by our vectors but also a spreading of Tau protein from the transduced cells towards the neighboring and synapatically connected cells, in the dentate gyrus model only but not in the model within we target ganglion cell in the retina. Preliminary results obtained in Trem2 KO mice indicate that absence of microglia activation seems to protect cells from toxicity induced by the presence of the Tau protein. This deficiency in microglial activation seems to favor intra-neuronal spreading of Tau protein.; Résumé : La tauopathie, une caractéristique majeure de la maladie d’Alzheimer (MA), est due à l’ hyperphosphorylation et l’agrégation intra-neuronale de la protéine Tau. Au cours de la MA, ce phénomène suit une progression spatio-temporelle précise, définie par les stades de Braak, qui corrèle avec la sévérité́ des symptômes. Les données actuelles suggèrent que cette progression est due à la propagation des formes pathologiques de la protéine Tau entre neurones connectés et dans laquelle la microglie et la neuroinflammation pourraient jouer un rôle. Il est donc nécessaire de développer des modèles pertinents permettant d’étudier les mécanismes moléculaires et cellulaires de cette propagation, ce qui pourrait aboutir à l’identification de nouvelles cibles thérapeutiques capables de la ralentir ou même de la stopper. Nous avons développé dans ce but des vecteurs AAV induisant une surexpression de la protéine Tau que nous utilisons pour transduire les neurones du gyrus denté de l'hippocampe ou les cellules ganglionnaires de la rétine, dont les neurones efférents sont bien caractérisés. Afin de déterminer le rôle joué par la microglie dans la propagation des espèces pathologique de la protéine Tau, ces modèles sont ensuite appliqués à des paradigmes expérimentaux dans lesquels l'homéostasie microgliale est perturbée, comme les souris Trem2 KO. Les premières analyses montrent la présence de la protéine Tau hyperphosphorylée dans les cellules transduites par les vecteurs mais aussi une propagation de la protéine Tau des cellules transduites vers les cellules avoisinantes et synaptiquement connectées dans notre modèle gyrus denté mais pas dans le modèle ciblant les neurones de la rétine, au temps étudié. Les résultats préliminaires obtenus chez les souris Trem2 KO indiquent que l’absence d’activation de la microglie semble protéger les neurones transduits de la toxicité liée à présence de la protéine Tau. Cette absence d'activation microgliale semble également favoriser le passage intra-neuronale de la protéine Tau

L'auteur a souhaité limiter l'accès de ce document aux membres de l'Enseignement supérieur français; The progressive increase of multidrug resistance around the world has been recognized as a public health priority. Horizontal gene transfers (HGT) are part of the main causes of the spread of antibiotic resistance genes. This is why it is necessary to understand the mechanisms of transfer within complex communities in order to find counter-measures to limit them. The objective of this study is to optimize an in vivo murine model for studying the transfer of the plasmid pB10 within the intestinal microbiota. This model uses two approaches for the detection and the quantification of the plasmid and its bacterial host: qPCR and flow cytometry. The impact of the matrix (type of sample, mode of preservation, plasmid-donor's inoculum) on the quantification by qPCR must first be studied. Optimization also involves adjusting the flow cytometry protocol using strains harboring different fluorescent labels. Once optimized, this model will open up several leads for studying factors influencing gene transfers in vivo.; La dissémination de l’antibiorésistance représente un enjeu sociétal majeur. Cette dissémination est principalement liée à des phénomènes de transferts horizontaux de gènes (THG) de résistance aux antibiotiques à partir de réservoirs environnementaux mais également animaux, notamment au sein des microbiotes. Il est donc nécessaire de comprendre les mécanismes favorisant ces THG dans les écosystèmes complexes afin d’envisager des solutions de lutte à cette dissémination. L’objectif principal de cette étude est d’optimiser un modèle d’étude des THG in vivo préalablement développé au laboratoire dans un modèle murin. Ce modèle utilise deux approches de détection et quantification des souches donneuses du plasmide cible et des transconjugants, à savoir la qPCR et la cytométrie en flux (CMF). L’optimisation du modèle passe par la détermination de l’effet de la matrice (type d’échantillon, mode de conservation, charge bactérienne en donneuse) sur la quantification des cibles par qPCR. Elle passe également par la mise au point de l’approche de CMF sur des souches ayant différents marquages fluorescents. Une fois optimisé, ce modèle permettra de tester de nombreuses pistes d’étude des facteurs impactant les THG in vivo.

International audience; Rice, the staple food for more than half of humankind and the model monocot crop, was the first cereal in which efficient gene transfer procedures were implemented: 30 years ago, the first transgenic rice plant was regenerated following direct gene transfer to cell suspension-derived protoplasts. Shortly thereafter, transgenic plants were regenerated from zygotic embryo-derived cells following their subjection to micro-projectile acceleration and Agrobacterium-mediated transfection treatments. The high efficiency of transfer deoxyribonucleic acid (T-DNA) integration in seed embryo-derived cells of rice has allowed the transfer of genes of agronomical relevance and the generation of large collections of insertion lines and has provided a key contribution to deciphering the function of more than 2000 rice genes. The high efficiency of T-DNA integration in seed embryo-derived cells of rice also permitted the first implementation of gene targeting and knock-in (KI) events, relying on the albeit very low natural frequency of homology-directed repair (HDR) in the rice genome. In the late 2000s, the advent of site-directed nucleases (SDNs) that induce either single or double-strand breaks at a high frequency and their rapid application to rice permitted routine targeted mutagenesis, which can be multiplexed to simultaneously alter several targets or create deletions, and base and gene editing (e.g. correction of amino acids). Currently, the challenge remains to attain a high frequency of KI and replacement of long stretches of DNA for protein domain or coding sequence swapping. We present herein a historical perspective of the advances that have been readily implemented to determine the function of rice genes and to manipulate traits of agronomical relevance. Two main bottlenecks remain to be alleviated in rice genomic engineering: the low frequency of HDR and the genotype dependence of gene transfer efficiency. Alleviation of these bottlenecks is needed to reach the potential of intra- and interspecific gene replacement and SDN-mediated multiplex editing of alleles in elite materials, which will assist in the breeding and deployment of rice cultivars embedded in sustainable and climate-smart agricultural practices.

Tetrafunctional block copolymers are molecules capable of complexing DNA. Although ineffective in vitro, studies in mice have shown that the tetrafunctional block copolymer 704 is a more efficient lung gene transfer agent than the cationic liposome GL67A, previously used in a phase II clinical trial in cystic fibrosis patients. In the present study, we compared the gene transfer capacity of the 704-DNA formulation and a cationic liposome-DNA formulation equivalent to GL67A in a larger-animal model, the newborn piglet. Our results indicate an efficacy of the 704-DNA formulation well above one order of magnitude higher than that of the cationic liposome-DNA formulation, with no elevated levels of interleukin-6 (IL-6), taken as a marker of inflammation. Transgene expression was heterogeneous within lung lobes, with expression levels that were below the detection threshold in some samples, while high in other samples. This heterogeneity is likely to be due to the bolus injection procedure as well as to the small volume of injection. The present study highlights the potential of tetrafunctional block copolymers as non-viral vectors for lung gene therapy., Graphical Abstract

The integrative mobilizable elements of SGI1-family considerably contribute to the spread of resistance to critically important antibiotics among enteric bacteria. Even though many aspects of SGI1 mobilization by IncA and IncC plasmids have been explored, the basic transfer elements such as oriT and self-encoded mobilization proteins remain undiscovered. Here we describe the mobilization region of SGI1 that is well conserved throughout the family and carries the oriTSGI1 and two genes, mpsA and mpsB (originally annotated as S020 and S019, respectively) that are essential for the conjugative transfer of SGI1. OriTSGI1, which is located in the vicinity of the two mobilization genes proved to be a 125-bp GC-rich sequence with several important inverted repeat motifs. The mobilization proteins MpsA and MpsB are expressed from a bicistronic mRNA, although MpsB can be produced from its own mRNA as well. The protein structure predictions imply that MpsA belongs to the lambda tyrosine recombinase family, while MpsB resembles the N-terminal core DNA binding domains of these enzymes. The results suggest that MpsA may act as an atypical relaxase, which needs MpsB for SGI1 transfer. Although the helper plasmid-encoded relaxase proved not to be essential for SGI1 transfer, it appeared to be important to achieve the high transfer rate of the island observed with the IncA/IncC-SGI1 system.

Adeno-associated viruses (AAVs) are among the most efficient vectors for gene transfer, particularly in the retina. They are used for asking biological questions as well as for gene therapy. Nonetheless, some barriers are still restraining their use. Here, we used a directed evolution method to overcome those barriers and improve the efficiency of AAVs for gene transfer. First, we created three highly diversified viral libraries based on AAV2. Those libraries were based on randomly modified capsids displaying new properties. Then, we did two types of selections. On one hand, we selected our libraries in the retinofugal pathway in order to obtain a capsid with enhanced axonal anterograde trans-synaptic transport capacities, so we could study simultaneously the activity and the connectivity of neuronal networks between the retina and the brain. This selection converged strongly toward a new capsid, named AAV2-7mD, with enhanced axonal anterograde trans-synaptic transport capacities compared to AAV1 and AAV2. On the other hand, we directly selected our viral libraries on human macular explants, to select capsids capable of crossing the human macular inner limiting membrane. Such a capsid would be very useful for retinal gene therapy via intravitreal injections. This library started to converge but we are still waiting to complete the last cycle of selection. In this thesis we discuss the results of these two directed evolution studies on AAV2 to create enhanced gene delivery vectors in the visual system., Les virus adéno-associés (AAVs) font partie des vecteurs les plus efficaces pour le transfert de gène, en particulier dans la rétine. Ils sont utilisés aussi bien pour des études biologiques que pour la thérapie génique. Malgré cela, il reste encore des barrières qui limitent leur utilisation. Nous proposons ici d’utiliser une technique d’évolution dirigée pour surmonter ces barrières et améliorer l’efficacité des AAVs en tant que vecteurs de gènes. Dans un premier temps, nous avons créé trois librairies virales hautement diversifiées basées sur l’AAV2. Ces librairies étaient constituées de capsides modifiées aléatoirement pour leur donner de nouvelles propriétés. Nous avons ensuite réalisé deux types de sélections. D’une part, nous avons sélectionné nos librairies virales dans le système visuel de la souris pour obtenir une capside capable de transport axonal antérograde trans-synaptique afin de pouvoir étudier simultanément l’activité et la connectivité de réseaux neuronaux. Cette sélection a fortement convergée vers une capside nommée AAV2-7mD, dont la capacité de transport axonal antérograde trans-synaptique est plus efficace que les AAVs 1 et 2. D’autre part, nous avons sélectionné nos librairies virales directement sur des explants de maculas de rétine humaine afin découvrir une capside capable de traverser la membrane limitante interne de la macula humaine. Ceci a pour but d’avoir un vecteur efficace pour des traitements de thérapie génique par voie intra-vitréenne. Cette librairie a commencé à converger mais nous sommes toujours en attente du dernier cycle de sélection. Nous traitons donc dans cette thèse des résultats de deux évolutions dirigées sur l’AAV2 afin de créer des vecteurs de gènes plus performants dans le système visuel.

support from the 'Plate-forme Génomique Environnementale et Fonctionnelle' (OSUR: INEE-CNRS) and the Genouest Bioinformatic Plateform (University of Rennes 1); International audience; † Background and Aims To date chloroplast genomes are available only for members of the non-protein amino acidaccumulating clade (NPAAA) Papilionoid lineages in the legume family (i.e. Millettioids, Robinoids and the 'inverted repeat-lacking clade', IRLC). It is thus very important to sequence plastomes from other lineages in order to better understand the unusual evolution observed in this model flowering plant family. To this end, the plastome of a lupine species, Lupinus luteus, was sequenced to represent the Genistoid lineage, a noteworthy but poorly studied legume group. † Methods The plastome of L. luteus was reconstructed using Roche-454 and Illumina next-generation sequencing. Its structure, repetitive sequences, gene content and sequence divergence were compared with those of other Fabaceae plastomes. PCR screening and sequencing were performed in other allied legumes in order to determine the origin of a large inversion identified in L. luteus. † Key Results The first sequenced Genistoid plastome (L. luteus: 155 894 bp) resulted in the discovery of a 36-kb inversion, embedded within the already known 50-kb inversion in the large single-copy (LSC) region of the Papilionoideae. This inversion occurs at the base or soon after the Genistoid emergence, and most probably resulted from a flip-flop recombination between identical 29-bp inverted repeats within two trnS genes. Comparative analyses of the chloroplast gene content of L. luteus vs. Fabaceae and extra-Fabales plastomes revealed the loss of the plastid rpl22 gene, and its functional relocation to the nucleus was verified using lupine transcriptomic data. An investigation into the evolutionary rate of coding and non-coding sequencesamong legume plastomes resulted in the identification of remarkably variable regions. †Conclusions This study resulted in the discovery of a novel, major 36-kb inversion, specific to the Genistoids. Chloroplast mutational hotspots were also identified, which contain novel and potentially informative regions for molecular evolutionary studies at various taxonomic levels in the legumes. Taken together, the results provide new insights into the evolutionary landscape of the legume plastome.

Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICE St3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3′ end of the fda , rpsI , or rpmG gene) with the conjugation module of the ICE St3 subfamily. Sequence analyses also pointed out a recombination occurring at oriT (likely mediated by the relaxase) as a mechanism of ICE evolution. Despite a similar organization in two operons including three conserved genes, the regulation modules show a high diversity (about 50% amino acid sequence divergence for the encoded regulators and presence of unrelated additional genes) with a probable impact on the regulation of ICE activity. Concerning the accessory genes, ICEs of the ICE St3 subfamily appear particularly rich in restriction-modification systems and orphan methyltransferase genes. Other cargo genes that could confer a selective advantage to the cell hosting the ICE were identified, in particular, genes for bacteriocin synthesis and cadmium resistance. The functionality of 2 ICEs of S. salivarius was investigated. Autonomous conjugative transfer to other S. salivarius strains, to S. thermophilus , and to Enterococcus faecalis was observed. The analysis of the ICE- fda border sequence in these transconjugants allowed the localization of the DNA cutting site of the ICE integrase. IMPORTANCE The ICE St3 subfamily of ICEs appears to be widespread in streptococci and targets diverse chromosomal integration sites. These ICEs carry diverse cargo genes that can confer a selective advantage to the host strain. The maintenance of these mobile genetic elements likely relies in part on self-encoded restriction-modification systems. In this study, intra- and interspecies transfer was demonstrated for 2 ICEs of S. salivarius . Closely related ICEs were also detected in silico in other Streptococcus species ( S. pneumoniae and S. parasanguinis ), thus indicating that diffusion of ICE St3 -related elements probably plays a significant role in horizontal gene transfer (HGT) occurring in the oral cavity but also in the digestive tract, where S. salivarius is present.

Vectors derived from the Adeno-associated virus (AAV) have emerged as an efficient system for in vivo gene transfer. However, despite their low immunogenicity and good tolerance in vivo, a better characterization of the host-AAV interaction is required to be able to fully exploit AAV’s potential fora gene therapy or gene vaccination. In this PhD project, we have used an in vitro directed evolution strategy to select an AAV capsid variant able to transduce human dendritic cell (DC), a non-permissive cell type which plays a critical role in the initiation of immune responses and, consequently, on the persistence of the expression of transgene in vivo. This procedure allowed us to identify an AAV variant characterized by a decreased stability of the capsid in vitro. The use of this mutant as a vector to transduce human DC resulted in an improved uncoating of the vector genome in the cell nucleus, thus identifying this step as major barrier toward DC transduction. Interestingly, the selected variant also displayed an increased transduction efficiency not only in DC but also in different primary human and animal cell types, poorly or non-permissive to AAV. Finally, when injected in mice, this AAV variant resulted in a higher expression of the transgene, associated to a low level of immune responses, suggesting the induction of tolerant state. The remarkable features suggest that our selected variant capsid is a promising candidate for medical applications.; Les vecteurs viraux dérivés du virus adéno-associé (AAV) apparaissent depuis deux décennies, comme des outils efficaces pour le transfert de gène in vivo. Cependant, malgré une faible immunogénicité et une absence de toxicité in vivo, leur optimisation requiert encore un effort important vers une meilleure compréhension de leur biologie et, en particulier, de leur interaction avec le système immunitaire. Au cours de ce travail de thèse, nous avons utilisé une méthode de sélection dirigée in vitro dans le but d’obtenir un variant de capside capable de transduire efficacement un type cellulaire non-permissif aux vecteurs AAV : les cellules dendritiques (DC). En effet, ces cellules jouent un rôle primordial dans l’établissement de la réponse immunitaire et, par conséquent, dans la persistance de l’expression du transgène in vivo. Cette technologie, très répandue dans la communauté AAV, a permis de sélectionner un variant de capside aux propriétés très intéressantes. La mutation sélectionnée, caractérisée in vitro comme induisant une instabilité de la capside, a permis d’identifier et de surmonter un point de blocage majeur dans le processus de transduction des DC par les vecteurs AAV consistant dans l’étape de décapsidation du génome du vecteur dans le noyau cellulaire. De manière intéressante, le variant obtenu exhibe un avantage en terme de transduction non seulement dans les DC mais aussi dans différents modèles de cellules primaires humaines (e.g. HUVEC) ou animales (OBC), peu ou pas permissive à l’AAV. De plus, des expériences de transfert de gène in vivo réalisées dans un modèle murin, indiquent que le variant sélectionné conduit à une meilleure expression du transgène, possiblement due à la mise en place d’un processus de tolérisation. Les propriétés remarquables de ce variant de capside, font de lui un candidat intéressant pour des applications médicales.

We have recently isolated the AlSAP (stress-associated protein) gene from the halophyte grass Aeluropus littoralis and demonstrated that AlSAP expression improves tolerance to continuous salt and drought stresses in transgenic tobacco. To extend these findings to an important crop, we generated marker-free transgenic durum wheat plants of the commercial cv. Karim expressing the AlSAP gene. The integration and expression of AlSAP in T3 homozygous plants were ascertained by Southern, Northern and Western blotting respectively. AlSAP wheat lines exhibited improved germination rates and biomass production under severe salinity and osmotic stress conditions. Following a long-term salt or drought stress greenhouse trial, AlSAP lines produced normally filled grains whereas wild-type (WT) plants either died at the vegetative stage under salt stress or showed markedly reduced grain filling under drought stress. Measurements of the RWC (relative water content) and endogenous Na? and K? levels in leaves of AlSAP plants, showed a lower water loss rate and a higher Na? accumulation in senescent-basal leaves, respectively, compared to those of WT plants. Taken together, these results extend to cereals the high potential of the AlSAP gene for engineering effective drought and salt tolerance.

When fused to " Pr AlSAP " promoter, transcripts of gusA exhibited similar accumulation patterns in transgenic rice as AlSAP transcripts in A. littoralis. Pr AlSAP can be used for engineering abiotic stress tolerance. We previously showed that ectopic expression of a stress-associated protein gene from Aeluropus littoralis (AlSAP) enhances tolerance to multiple abiotic stresses in tobacco, wheat and rice. The ortholog of AlSAP in rice is OsSAP9. Here, we demonstrate that AlSAP transcripts accumulate in Aeleuropus in response to multiple abiotic stresses and at a higher level in roots, while those of OsSAP9 are preferentially induced by cold and heat treatments and accumulate preferentially in leaves of rice. In silico analysis of the AlSAP promoter "Pr AlSAP " predicted several cis-acting elements responsible for gene regulation by dehydration, salt, heat, ABA, SA, wounding and tissue-specific expression. The Pr AlSAP promoter was fused to the gusA gene and used to produce transgenic rice plants. Transcripts of gusA exhibited similar accumulation patterns in transgenic rice as AlSAP transcripts in A. littoralis. Indeed, accumulation of gusA transcripts was higher in roots than in leaves and induced by salt, drought, cold and heat treatments. GUS activity was confirmed in roots, coleoptiles, leaves and glumes, but absent in the root cell elongation zone and in dry seeds. A wound treatment strongly induced GUS accumulation in leaves and imbibed seeds. Altogether, these results indicate that the regulatory regions of two ortholog genes "AlSAP" and "OsSAP9" have diverged in the specificity of the signals promoting their induction, but that the trans-acting elements allowing the correct spatiotemporal regulation and stress induction of Pr AlSAP exist in rice. Therefore, the AlSAP promoter appears to be an interesting candidate for engineering abiotic stress tolerance in cereals.

UMR DAP - Equipe DGB; International audience; Plant non-specific lipid transfer proteins (nsLTPs) are encoded by a multigene family and support physiological functions, which remain unclear. We adapted an efficient ligation-mediated polymerase chain reaction (LM-PCR) procedure that enabled isolation of 22 novel Triticum aestivum nsLtp (TaLtp) genes encoding types 1 and 2 nsLTPs. A phylogenetic tree clustered the wheat nsLTPs into ten subfamilies comprising 1-7 members. We also studied the activity of four type 1 and two type 2 TaLtp gene promoters in transgenic rice using the beta-Glucuronidase reporter gene. The activities of the six promoters displayed both overlapping and distinct features in rice. In vegetative organs, these promoters were active in leaves and root vascular tissues while no beta-Glucuronidase (GUS) activity was detected in stems. In flowers, the GUS activity driven by the TaLtp7.2a, TaLtp9.1a, TaLtp9.2d, and TaLtp9.3e gene promoters was associated with vascular tissues in glumes and in the extremities of anther filaments whereas only the TaLtp9.4a gene promoter was active in anther epidermal cells. In developing grains, GUS activity and GUS immunolocalization data evidenced complex patterns of activity of the TaLtp7.1a, TaLtp9.2d, and TaLtp9.4a gene promoters in embryo scutellum and in the grain epicarp cell layer. In contrast, GUS activity driven by TaLtp7.2a, TaLtp9.1a, and TaLtp9.3e promoters was restricted to the vascular bundle of the embryo scutellum. This diversity of TaLtp gene promoter activity supports the hypothesis that the encoded TaLTPs possess distinct functions in planta

A procedure has been established for Agrobacterium tumefaciens-mediated genetic transformation of Hevea brasiliensis embryogenic friable calli. Precultivation of tissues on a CaCl(2)-free maintenance medium dramatically enhanced the transient activity of the reporter gene, gusA encoding beta-glucuronidase (GUS). The increase was first noticed in highly active cells (undifferentiated or/and embryogenic), in tissues precultured for 2-8 weeks. Beyond 8 weeks of preculture, GUS activity increased again, but this time in tissues consisting of differentiated cells accumulating polyphenols. Out of five Agrobacterium strains cocultivated with CaCl(2)-free precultured tissues, only inoculation with EHA105pC2301 led to high transient GUS activity. Paromomycin proved more effective than kanamycin for the selection of transformed cells, as it inhibits the growth of non-transformed cells more radically. Five paromomycin-resistant callus lines were established. The presence of gusA and neomycin phosphotransferase ( nptII) genes in the plant genome was confirmed by DNA amplification, and by Southern hybridization. These results confirmed that A. tumefaciens is an effective system for mediating stable transformation of rubber tree calli with a low copy number of transgenes. Transgenic callus lines constitute a useful tool for studying genes of interest on a cellular level and for regenerating transgenic rubber trees.

Peste des petits ruminants (PPR) is a contagious disease with potential for high economic impacts. Convalescent and vaccinated small ruminants develop a strong and lifelong immunity and are fully protected against re-infection. Consequently, the presence of antibodies, whether they are against a wild virus or a vaccine, is a marker of the host immune protection. Thus, specific antibodies cannot be missed with classical and validated diagnosis assays, such as conventional enzyme-linked immunosorbent assay (ELISA), an alternative testing method to the conventional virus neutralization test (VNT), allowing to monitor vaccination or locate disease outbreaks. Recent insights into the virions' protein composition, development of expression systems, recombinant vectors to express protective antigens, have contributed greatly to update our current knowledge about diagnostics. In the light of this progress, the chapter focuses on PPRV serological tests with particular attention to diagnostic antigen targets and refinement of assays for accurate serodiagnosis of PPRV.

The four salt bridges (Asp(222)-Arg(281), Arg(233)-Glu(288), Arg(234)-Glu(274), and Asp(242)-Arg(265)) linking domains I and II in Cry1Aa were abolished individually in alpha-helix 7 mutants D222A, R233A, R234A, and D242A. Two additional mutants targeting the fourth salt bridge (R265A) and the double mutant (D242A/R265A) were rapidly degraded during trypsin activation. Mutations were also introduced in the corresponding Cry1Ac salt bridge (D242E, D242K, D242N, and D242P), but only D242N and D242P could be produced. All toxins tested, except D242A, were shown by light-scattering experiments to permeabilize Manduca sexta larval midgut brush border membrane vesicles. The three active Cry1Aa mutants at pH 10.5, as well as D222A at pH 7.5, demonstrated a faster rate of pore formation than Cry1Aa, suggesting that increases in molecular flexibility due to the removal of a salt bridge facilitated toxin insertion into the membrane. However, all mutants were considerably less toxic to M. sexta larvae than to the respective parental toxins, suggesting that increased flexibility made the toxins more susceptible to proteolysis in the insect midgut. Interdomain salt bridges, especially the Asp(242)-Arg(265) bridge, therefore contribute greatly to the stability of the protein in the larval midgut, whereas their role in intrinsic pore-forming ability is relatively less important.

International audience; This review deals with the application of antimicrobial agents in veterinary medicine and food animal production and the possible consequences arising from the widespread and multi-purpose use of antimicrobials. The various mechanisms that bacteria have developed to escape the inhibitory effects of the antimicrobials most frequently used in the veterinary field are reported in detail. Resistance of bacteria to tetracyclines, macrolide-lincosamide-streptogramin antibiotics, $\beta$-lactam antibiotics, aminoglycosides, sulfonamides, trimethoprim, fluoroquinolones and chloramphenicol/florfenicol is described with regard to enzymatic inactivation, decreased intracellular drug accumulation and modification/protection/replacement of the target sites. In addition, basic information is given about mobile genetic elements which carry the respective resistance genes, such as plasmids, transposons, and gene cassettes/integrons, and their ways of spreading via conjugation, mobilisation, transduction, and transformation.; Utilisation d'agents antimicrobiens en médecine vétérinaire et mécanismes de résistance. Cette revue présente les différents buts pour lesquels les agents antimicrobiens sont utilisés en médecine vétérinaire, dans les élevages d'animaux entrant dans la chaîne alimentaire et les possibles conséquences de cette large utilisation. Une synthèse est faite des différents mécanismes de résistance développés par les bactéries, comme l'inactivation enzymatique, la diminution de la concentration intracellulaire de l'antibiotique, les modification/protection/déplacement de cible, qui permettent d'échapper à l'action des antibiotiques les plus fréquemment utilisés dans le domaine vétérinaire : tétracyclines, macrolide-lincosamide-streptogramine, $\beta$-lactamines, aminosides, sulfamides, triméthoprime, fluoroquinolones et chloramphénicol/florfénicol. Le rôle d'éléments génétiques mobiles portant les gènes de résistance tels que les plasmides, les transposons ou les cassettes/intégrons, et leur mode de diffusion par conjugaison, mobilisation ou transduction sont présentés.

National audience; La transgenèse permet d’introduire dans le génome d’un animal un fragment d’ADN qui sera ensuite transmis de génération en génération. Elle utilise différentes approches méthodologiques. Certaines, encore limitées à peu d’espèces, permettent des modifications très fines du génome. La transgenèse, associée au développement de la biologie moléculaire, offre des applications multiples tant dans la recherche fondamentale qu’appliquée. Elle est de fait devenue un outil indispensable pour l’analyse de la régulation de l’expression des gènes et la compréhension de leur fonction.

The influence of CaCl2 was investigated on Agrobacterium tumefaciens-mediated gene transfer in Hevea brasiliensis friable calli which are usually proliferated on maintenance medium (MM) containing 9 mM CaCl2. Five A. tumefaciens strains (C58pMP90, C58pGV2260, AGL1, LBA4404 and EHA 105) and two binary vectors (pGIN and pCAMBIA2301) were tested and the strain EHA105pC2301 was selected to conduct further experiments. The calli were precultured on MM containing a range of CaCl2 concentrations, then inoculated with Agrobacterium suspension. Transfer of friable calli from MM containing 9 mM CaCl2 to calcium-free medium significantly enhanced the transient bêta-glucuronidase activity. Interestingly, the use of calcium-free Agrobacterium resuspension medium to inoculate friable calli again dramatically increased the transformation efficiency. Induction of Agrobacterium's virulence with acetosyringone remained an important factor to stimulate transformation.

Almost all the nuclear genes of four Gramineae (maize, wheat, barley, rice) and pea are located in DNA fractions covering only a 1–2% GC range and representing between 10 and 25% of the different genomes. These DNA fractions comprise large gene-rich regions (collectively called the ‘gene space’) separated by vast gene-empty, repeated sequences. In contrast, in Arabidopsis thaliana , genes are distributed in DNA fractions covering an 8% GC range and representing 85% of the genome. Here, we investigated the integration of a transferred DNA (T-DNA) in the genomes of Arabidopsis and rice and found different patterns of integration, which are correlated with the different gene distributions. While T-DNA integrates essentially everywhere in the Arabidopsis genome, integration was detected only in the gene space, namely in the gene-rich, transcriptionally active, regions of the rice genome. The implications of these results for the integration of foreign DNA are discussed.

Nineteen arabica coffee introgression lines (BC1F4) and two accessions derived from a spontaneous interspecific cross (i.e. Timor Hybrid) between #Coffea arabica$ (2n=4x=44) and #C. canephora$ (2n=2x=22) were analysed for the introgression of #C. canephora$ genetic material. The Timor Hybrid-derived genotypes were evaluated by AFLP, using 42 different primer combinations, and compared to 23 accessions of #C. arabica$ and 8 accessions of #C. canephora$. A total of 1062 polymorphic fragments were scored among the 52 accessions analysed. One hundred and seventy-eight markers consisting of 109 additional bands (i.e. introgressed markers) and 69 missing bands distinguished the group composed of the Timor Hybrid-derived genotypes from the accessions of #C. arabica$. AFLP therefore seemed to be an extremely efficient technique for DNA marker generation in coffee as well as for the detection of introgression in #C. arabica$. The genetic diversity observed in the Timor Hybrid-derived genotypes appeared to be approximately double that in #C. arabica$. Although representing only a small proportion of the genetic diversity available in #C. canephora$, the Timor Hybrid obviously constitutes a considerable source of genetic diversity for arabica breeding. Analysis of genetic relationships among the Timor Hybrid-derived genotypes suggested that introgression was not restricted to chromosome substitution but also involved chromosome recombinations. Furthermore, the Timor Hybrid-derived genotypes varied considerably in the number of AFLP markers attributable to introgression. In this way, the introgressed markers identified in the analysed arabica coffee introgressed gentotypes were estimated to represent from 9% to 29% of the #C. canephora$ genome. Nevertheless, the amount of alien genetic material in the introgression arabica lines remains substantial and should justify the development of adapted breeding strategies. (Résumé d'auteur)

The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the disappearance of Neanderthals and the likelihood of cultural and genetic exchange. Serious technical challenges, however, have hindered reliable dating of the period, as the radiocarbon method reaches its limit at 50,000 years ago. Here we apply improved accelerator mass spectrometry 14C techniques to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, ranging from Russia to Spain. Bayesian age modelling was used to generate probability distribution functions to determine the latest appearance date. We show that the Mousterian ended by 41,030–39,260 calibrated years BP (at 95.4% probability) across Europe. We also demonstrate that succeeding ‘transitional’ archaeological industries, one of which has been linked with Neanderthals (Châtelperronian), end at a similar time. Our data indicate that the disappearance of Neanderthals occurred at different times in different regions. Comparing the data with results obtained from the earliest dated AMH sites in Europe, associated with the Uluzzian technocomplex, allows us to quantify the temporal overlap between the two human groups. The results reveal a significant overlap of 2,600–5,400 years (at 95.4% probability). This has important implications for models seeking to explain the cultural, technological and biological elements involved in the replacement of Neanderthals by AMHs. A mosaic of populations in Europe during the Middle to Upper Palaeolithic transition suggests that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.

The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called ‘Florendovirus’, members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of Oryza is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20–34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In Vitis vinifera, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks., Endogenous viral elements have been extensively described in animals but their significance in plants is less well understood. Here, Geering et al. describe a new group of endogenous pararetroviruses, called florendoviruses, which have colonized the genomes of many important crop species.

We have developed an efficient transformation system for the tropical actinorhizal tree #Allocasuarina verticillata$ using #Agrobacterium tumefaciens$ mediated gene transfer. Mature zygotic embryos were inoculated with the disarmed strain C58C1 carrying, in the binary vector BIN19, the nptll gene, providing kanamycin resistance as a selectable marker, and the reporter gene beta-glucuronidase containing an intron. The transformed embryos were cultivated on nutrient medium supplemented with 0,5 microM NAA, 2,5 microM BA, 100 mg/l kanamycin and 250 mg/l cefotaxime. After 2 months, a 21% transformation frequency was obtained. Within 6-9 months, transgenic plants were recovered from 70% of the transformed calli. The presence of the trangenes was demonstrated by PCR analysis and by the expression of the beta-glucuronidase; integration of the T-DNA was confirmed by Southern hybridization. More than 100 transgenic plants from a total of 23 independent events have been successfully established in soil. The possibility to obtain nitrogen-fixing nodules after inoculation of transgenic #A. verticillata$ plants by the actinomycetal strain of Frankia Allo2 was established. (Résumé d'auteur)

Anticancer therapies had, in recent years, an important development that results in an improvement in the quality of life of patients. However, the occurrence of resistance and the significant proportion of untreated cancer force us to consider the development of new anticancer strategies. We have developed a new technique based on the principle of suicide gene using the gene of cytochrome P450 2B6 associated with cyclophosphamide (CPA). This technique involves the transfer of a gene metabolizing an anticancer prodrug within the tumor allowing tumors sensitization to this prodrug. The first objective of this work was to improve the metabolism of the prodrug in building a mutated CYP2B6 fused with the reductase gene essential partner of CYP. In a second step we transferred the CYP2B6TM-RED gene in tumor cells that have been significantly sensitized. These results were confirmed on in vivo models of immunocompetent mice. In addition to the cytotoxic effect, mice were able to develop a specific anti-tumor immunity. This suggests to us that this method can protect against recurrence and metastasis. The good results obtained in the development of this new anticancer strategy, let us hope for a future transition into clinic. For this, new animal models will be developed to definitively validate the method.; Les thérapies anticancéreuses ont connu ces dernières années un développement important ayant pour conséquence une amélioration dans la qualité de vie des patients. Cependant la survenue de résistances et la part significative de cancer sans traitement efficace nous oblige à envisager le développement de nouvelles stratégies anticancéreuses. Nous avons développé une nouvelle technique basée sur le principe du gène suicide en utilisant le gène du cytochrome P450 2B6 associé au cyclophosphamide (CPA). Cette technique qui consiste au transfert d’un gène métabolisant une prodrogue anticancéreuse dans la tumeur permet une sensibilisation des tumeurs à cette prodrogue. Le premier objectif de ce travail a consisté à améliorer le métabolisme de la prodrogue en construisant un gène muté du CYP2B6 en fusion avec la réductase, partenaire indispensable du CYP. Dans un deuxième temps nous avons transféré le gène CYP2B6TM-RED dans des cellules tumorales qui sont devenues sensibles au CPA entrainant une éradication des tumeurs. Ces résultats ont été confirmés in vivo sur des modèles de souris immunocompétentes. Nous avons, en plus de l’effet cytotoxique, mis en évidence un important effet bystander et le développement d’une immunité antitumorale spécifique. Ceci nous laisse penser que cette méthode peut permettre de protéger contre les récidives et les métastases. Les bons résultats obtenus dans le développement de cette nouvelle stratégie anticancéreuse, nous laissent espérer d’un futur passage en clinique. Pour cela de nouveaux modèles animaux devront être mis au point pour optimiser le transfert du transgène dans les tumeurs.

In bacterial genomes, the frequent horizontal gene transfers (HGT) introduce genomic novelties that can promote the diversification of bacterial populations. In opposition, homologous recombination (HR) within populations homogenizes their genotypes, enforcing their cohesion. These processes of genetic exchange, and their patterns of occurrence among and within lineages, must have a great impact on bacterial cladogenesis. Beyond the pattern of exchanges actually occurring between bacteria, the traces of HR and HGT we observe in their genomes reflect what events were fixed throughout their history. This fixation process can be biased regarding the nature of genes or alleles that were introduced. Notably, natural selection can drive the fixation of transferred genes that bring new ecological adaptations. In addition, some mechanical biases in the recombination process itself may lead to the fixation of non-adaptive alleles. We aimed to characterize such adaptive and non-adaptive processes that are shaping bacterial genomes. To this end, several aspects of genome evolution, such as variations of their gene repertoires, of their architecture and of their nucleotide composition were examined in the light of their history of transfer and recombination, Dans les génomes bactériens, les fréquents transferts horizontaux de gènes (HGT) introduisent des innovations génomiques qui peuvent entraîner la diversification des populations bactériennes. À l'inverse, la recombinaison homologue (RH) au sein des populations homogénéise leurs génotypes, et ainsi renforce leur cohésion. Ces processus d'échange génétique, et la fréquence à laquelle ils interviennent au sein et entre les populations, doivent avoir un grand impact sur la cladogénèse bactérienne. Au-delà de la configuration des échanges qui se sont réellement produits entre les bactéries, les traces de RH et de HGT que nous observons dans leurs génomes reflètent les événements qui ont été fixés tout au long de leur histoire. Ce processus de fixation peut être biaisé en ce qui concerne la nature des gènes ou allèles qui ont été introduits. La sélection naturelle peut notamment conduire à la fixation des gènes transférés qui apportent de nouvelles adaptations écologiques. En outre, des biais mécaniques dans le processus de recombinaison lui-même peuvent conduire à la fixation d'allèles non-adaptatifs. Nous avons cherché à caractériser certains de ces processus adaptatifs et non-adaptatifs qui façonnent les génomes bactériens. À cette fin, plusieurs aspects de l'évolution des génomes, comme les variations de leurs répertoires de gènes, de leur architecture et de leur composition en nucléotides ont été examinés à la lumière de leur histoire de transfert et de recombinaison

The occurrence of metastasis in a cancer is generally associated to a bad prognostic for the patient. The formation of metastasis is the result of a complex process in which cell migration plays a key role.Recent studies have shown that the potassium calcium-dependent channel SK3 is expressed in several highly metastatic cancerous cell lines and play a direct role in the migration process. Consequently, this protein is an interesting new therapeutic target to reduce metastasis formation.This PhD thesis work aimed investigating two strategies to reduce SK3 dependent cell migration.Edelfosine, a glycerolipid with a phosphocholine head, was identified as an efficient inhibitor of the SK3 channel activity. However the side effects induced by this molecule (toxicity) led to look for efficient and less toxic analogues. Accordingly, structure-activity studies carried out in our laboratory produced new glyco-glycerolipid including one with a lactose group (ohmline). With the aim of completing this study, we report the synthesis of glyco-glycerolipids and glycophospho-glycerolipids and shown their capacity to inhibit activity of SK3 channel.The second part of this work aims to act at an early stage by using RNAi to block the expression of the SK3 protein. In this way, we have synthesized and formulated, with a cationic lipid used for the transfection, neutral co-lipids functionalized with an anisamide moiety; this motif being recognize sigma receptors which are overexpressed in tumor cell lines that also expressed SK3. First, the synthesis of the lipophosphoramides with an anisamide moiety was described followed by their use in standard transfection experiments (plasmid DNA) to evaluate the effectiveness of the targeting strategy induced by the anisamide moiety.; L’apparition de métastases est souvent le signe d’un mauvais pronostic vital pour les personnes atteintes d’un cancer. Ce processus de formation de métastase est un phénomène complexe dans lequel la migration cellulaire est un facteur clé.De récentes études ont montré que le canal SK3 (canal potassique de faible conductance dont l’activité dépend de la concentration cytosolique en calcium) était exprimé dans des cellules cancéreuses à fort pouvoir métastatique et leur conférait des capacités de migration accrues. Cette protéine constitue donc une nouvelle cible thérapeutique très intéressante pour agir sur la dissémination de cellules cancéreuses.Les objectifs de ces travaux de thèse ont permis de mettre en oeuvre deux stratégies visant à inhiber l’activité de ce canal potassique SK3.L’édelfosine, un glycérolipide à tête phosphocholine, a rapidement été reconnue comme étant un inhibiteur efficace de l’activité de ce canal. Cependant les effets secondaires induits par cette molécule ont conduit à rechercher des analogues moins toxiques et tout aussi efficaces. Des études structures-activité menées au sein du laboratoire ont permis de développer un nouveau glycérolipide à tête lactose, l’ohmline. Dans le but de compléter cette étude, nous avons réalisé la synthèse de glyco-glycérolipides et de glycophospho-glycérolipides et avons montré leur capacité à inhiber la protéine SK3 et à réduire la migration cellulaire SK3 dépendante.Une seconde stratégie vise à l’utilisation possible d’ARN interférents pour bloquer l’expression de la protéine SK3. Dans ce but, nous nous sommes intéressés à la synthèse et à l’incorporation, dans des formulations de lipides cationiques utilisés pour la transfection, de lipides neutres portant des motifs anisamides, ligands spécifiques des récepteurs sigma surexprimés dans des lignées cellulaires de tumeurs exprimant SK3. La synthèse de lipophosphoramides comportant un motif anisamide est présentée suivie de leur utilisation dans des expériences de transfection modèles (vectorisation d’ADN plasmidique) afin d’évaluer l’efficacité du ciblage engendré par le motif anisamide.

Transgenic calli of the tropical tree #Casuarina glauca$ were produced using #Agrobacterium tumefaciens$-mediated gene transfer. Hypocotyls, cotyledons and epicotyls were excised from 30-60-day old #Casuarina$ seedlings and cocultivated with #Agrobacterium$ strain C58C1(pGV2260) containing the binary vector BIN19GUSINT. Transformed calli were selected on nutrient medium supplemented with 0,5 microM NAA, 2,5 microM BA and 50 mg/l kanamycin. Some of the factors influencing T-DNA transfer to #C. glauca$ explants were studied. Optimal transformation rates were obtained when explants from 45-day old seedlings were cocultivated for 3 days in the presence of 25 microM acetosyringone. Transgenic buds differentiated on 10% of the calli grown on transformed epicotyls. Evidence for genetic transformation was obtained by beta-glucuronidase assay, PCR and Southern hybridization. (Résumé d'auteur)

Reliable and long-term expression of transgenes remain significant challenges for gene therapy and biotechnology applications, especially when antibiotic selection procedures are not applicable. In this context, transposons represent attractive gene transfer vectors because of their ability to promote efficient genomic integration in a variety of mammalian cell types. However, expression from genome-integrating vectors may be inhibited by variable gene transcription and/or silencing events. In this study, we assessed whether inclusion of two epigenetic control elements, the human Matrix Attachment Region (MAR) 1-68 and X-29, in a piggyBac transposon vector, may lead to more reliable and efficient expression in CHO cells. We found that addition of the MAR 1-68 at the center of the transposon did not interfere with transposition frequency, and transgene expressing cells could be readily detected from the total cell population without antibiotic selection. Inclusion of the MAR led to higher transgene expression per integrated copy, and reliable expression could be obtained from as few as 2-4 genomic copies of the MAR-containing transposon vector. The MAR X-29-containing transposons was found to mediate elevated expression of therapeutic proteins in polyclonal or monoclonal CHO cell populations using a transposable vector devoid of selection gene. Overall, we conclude that MAR and transposable vectors can be used to improve transgene expression from few genomic transposition events, which may be useful when expression from a low number of integrated transgene copies must be obtained and/or when antibiotic selection cannot be applied.

Le riz ( Oryza sativa L.) a le double statut de céréale la plus consommée par l'homme et d'espèce modèle pour les monocotylédones. Élucider la fonction des gènes sous-tendant les principaux caractères d'intérêt agronomique chez cette plante contribuerait donc à accélérer non seulement l'amélioration variétale du riz mais aussi celle des autres céréales. La transformation génétique est un outil permettant d'accélérer la découverte de la fonction des gènes et l'innovation variétale. La première plante transgénique de riz a été obtenue dès 1988, et, depuis, les technologies ont régulièrement évolué vers plus d'efficacité et de précision. Nous présentons ici les grandes étapes de l'évolution de ces techniques, ainsi que leurs applications pour l'analyse fonctionnelle des gènes. En particulier, les perspectives ouvertes par de nouveaux sauts technologiques en cours, qui permettent à présent une modification ciblée des génomes sans introduction d'acide désoxyribonucléique (ADN) superflu, seront illustrées et discutées.

Depuis l'obtention de la première plante transgénique de riz en 1988, de larges progrès ont été accomplis pour manipuler les caractères d'intérêt agronomique par ingénierie génétique chez cette plante d'importance alimentaire, économique et culturelle majeure. Les caractères concernés vont de la résistance aux insectes ravageurs et aux pathogènes fongiques, bactériens et viraux à la tolérance vis-à-vis des contraintes abiotiques (toxicités et carences minérales, température excessive ou basse, excès ou déficit en eau) en passant par les qualités nutritives ou industrielles du grain. Des portions entières de voies métaboliques peuvent à présent être finement manipulées, permettant par exemple la production de béta-carotène (provitamine A) dans l'albumen du grain, qui en est naturellement dépourvu, ou l'accumulation des enzymes de la photosynthèse C4 dans des tissus foliaires précis. La production de molécules d'intérêt thérapeutique ou industriel dans le grain a aussi été réalisée. Bien que certaines de ces innovations soient prêtes à être transférées dans le champ du riziculteur depuis plusieurs années, les politiques publiques sont encore hésitantes à franchir le pas. Ce retard relatif a été mis à profit pour conduire de nombreuses études sur les impacts alimentaires et environnementaux liés à la consommation et au déploiement de ces nouvelles cultures.

The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Background: With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus Citrus of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated Citrus species. Results: Fifty-four accessions covering the main Citrus species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within C. maxima, C. medica, C. reticulata and C. micrantha. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in C. medica, C. maxima and wild Citrus species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the C. reticulata diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping. Conclusions: A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole Citrus gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around C. maxima, C. medica and C. reticulata as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in Citrus and genetic association in C. reticulata.

Transplantation of mesenchymal stem cells (MSCs) with electrotransferred bone morphogenetic protein-2 (BMP-2) transgene is an attractive therapeutic modality for the treatment of large bone defects: it provides both stem cells with the ability to form bone and an effective bone inducer while avoiding viral gene transfer. The objective of the present study was to determine the influence of the promoter driving the human BMP-2 gene on the level and duration of BMP-2 expression after transgene electrotransfer into rat MSCs. Cytomegalovirus, elongation factor-1 alpha, glyceraldehyde 3-phosphate dehydrogenase, and beta-actin promoters resulted in a BMP-2 secretion rate increase of 11-, 78-, 66- and 36-fold over respective controls, respectively. In contrast, the osteocalcin promoter had predictable weak activity in undifferentiated MSCs but induced the strongest BMP-2 secretion rates in osteoblastically-differentiated MSCs. Regardless of the promoter driving the transgene, a plateau of maximal BMP-2 secretion persisted for at least 21 d after the hBMP-2 gene electrotransfer. The present study demonstrates the feasibility of gene electrotransfer for efficient BMP-2 transgene delivery into MSCs and for a three-week sustained BMP-2 expression. It also provides the first in vitro evidence for a safe alternative to viral methods that permit efficient BMP-2 gene delivery and expression in MSCs but raise safety concerns that are critical when considering clinical applications.

International audience

Tendons are often involved in many musculoskeletal disorders. Knowledge of the different molecules involved in tendons biology allows to consider treatments based on gene therapy. The goal of my work was to evaluate the feasibility of gene transfer in tendons by using two non-viral methods: mesoporous silica nanoparticles and a physical method based on ultrasound-assisted gas microbubbles (sonoporation). In the first study, we showed that mesoporous silica nanoparticles could efficiently transfer genes in rat Achilles tendon. They were used to transfer plasmid DNA encoding PDGF growth factor gene in injured tendons. Data demonstrated that DNA/MSN complexes have improved the healing of injured tendons. In the second study, we used the sonoporation method which has never been applied to the tendons. First, we determined the acoustic parameters for gene transfer in mice Achilles tendon. A stable expression of the transgene was maintained up to 100 days following one local injection of DNA in the presence of gas microbubbles. We then used this method to restore the fibromodulin knocked out gene in a transgenic mouse model having disorganized collagen fibers in tendons. Following the transfer of fibromodulin gene, a remarkable restoration of collagen fibers in these mice was observed. In the last part, we studied the interactions of microbubbles with the plasma membrane and the plasmid DNA internalization into the cells by sonoporation. These studies have identified for the first time a rapid penetration of gas microbubbles inside the cell and an intracellular routing of DNA involving the clathrinmediated endocytosis pathway. In conclusion, both methods of non viral gene transfer led to an efficient gene transfer in tendons. These promising results obtained during this project allow considering their use for therapeutic applications in tendon diseases., Le tendon est un organe impliqué dans de nombreux troubles musculo squelettiques. Les connaissances des différentes molécules impliquées dans la biologie des tendons permettent d’envisager des traitements par thérapie génique. L'objectif de cette thèse a été d'évaluer la faisabilité de transférer des gènes dans les tendons par deux méthodes non virales : une méthode chimique utilisant des nanoparticules de silice mésoporeuses et une méthode physique reposant sur l’utilisation des ultrasons et des microbulles de gaz (sonoporation). Dans une première étude, nous avons montré que des nanoparticules de silice mésoporeuses sont capables de transférer efficacement des gènes dans le tendon d’Achille de rat. Celles-ci ont été utilisées pour transférer le gène du facteur de croissance PDGF dans des tendons lésés. Nos résultats indiquent une accélération de la réparation du tendon lésé. Dans une deuxième étude, nous avons utilisé la sonoporation, technique jamais appliquée aux tendons. Nous avons déterminé les paramètres acoustiques permettant un transfert de gènes efficace dans le tendon d'Achille de souris. Une expression stable d’un transgène a été maintenue pendant 100 jours suite à une injection locale d’ADN en présence de microbulles de gaz. Nous avons ensuite utilisé cette méthode dans un modèle de souris transgénique invalidée pour le gène de la fibromoduline possédant des fibres de collagène anormales. Une restauration remarquable du phénotype de ces souris a été observée suite au transfert du gène de la fibromoduline. Nous avons ensuite étudié les interactions entre les microbulles, la membrane plasmique et le transfert de gènes dans les cellules sous ultrasons. Ces études ont permis d’identifier pour la première fois, une pénétration des microbulles de gaz dans la cellule et un trafic intracellulaire de l’ADN impliquant la voie d’endocytose clathrine dépendante. En conclusion, les deux méthodes de transfert de gènes non virales ont permis de transfecter des gènes efficacement dans les tendons. Ces résultats prometteurs permettent d’envisager leur exploitation pour des applications thérapeutiques dans les pathologies tendineuses.