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Institut Sophia Agrobiotech

Institut Sophia Agrobiotech

Institut Sophia Agrobiotech

UMR INRA - Univ. Nice Sophia Antipolis - Cnrs
Inra PACA
400 route des chappes
BP 167
0690 Sophia Antipolis Cedex
FRANCE
Tel. : +33(0)4 92 38 64 00
Fax : + 33(0)4 92 38 64 01

http://www.paca.inra.fr/institut-sophia-agrobiotech

Publications

Liste des publications

Plateau de biochimie analytique
Plateau de bioinformatique et génomique
Plateau de microscopie

Plateau de biochimie analytique

  • Bidet M, Joubert O, Lacombe B, Nehmé R, Mollat P, Brétillon L, Faure H, Bittman R, Ruat M, and Mus-Veteau I, (2011) The Hedgehog Receptor Patched is involved in Cholesterol Transport, PLoS ONE Sept 08 
  • Hovers J, Potschies M, Polidori A, Pucci B, Bonneté F, Serrano-Vega MJ, Tate CG, Picot D, Pierre Y, Popot JL, Nehmé R, Bidet M, Mus-Veteau I, Bußkamp H, Jung KH, Marx A, Timmins PA, Welte W (2011) A class of mild surfactants that keep integral membrane proteins water-soluble for functional studies and crystallization, Molecular Membrane Biology, DOI 10.3109/09687688.2011.554-2440
  • Nehmé R, Joubert O, Bidet M, Lacombe B, Polidori A, Pucci B, & Mus-Veteau I (2010) Stability Study of the Human G-Protein Coupled Receptor, Smoothened, BBA Biomembrane, 1798: 1100-1110.
  • Joubert O, Nehmé R, Fleury D, De Rivoyre M, Bidet M, Polidori A, Ruat M, Pucci B, Mollat P, & Mus-Veteau I, (2009) Functional studies of membrane-bound and purified human Hedgehog receptor Patched expressed in yeast, BBA Biomembrane, 1788: 1813-1821

Plateau de bioinformatique et génomique

2017
  • Etienne G.J. Danchin, Laetitia Perfus-Barbeoch, Corinne Rancurel, Peter Thorpe, Martine Da Rocha, Simon Bajew, Roy Neilson, Elena Sokolova (Guzeeva), Corinne Da Silva, Julie Guy, Karine Labadie, Daniel Esmenjaud, Johannes Helder, John T. Jones and Sebastian Eves-van den Akker (2017) The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes. Genes (Basel). 8(10): 287.doi:10.3390/genes8100287
  • Nguyen CN, Perfus-Barbeoch L, Quentin M, Zhao J, Magliano M, Marteu N, Da Rocha M, Nottet N, Abad P, Favery B. (2017) A root-knot nematode small glycine and cysteine-rich secreted effector, MiSGCR1, is involved in plant parasitism. New Phytol. 2017 Oct 16. doi: 10.1111/nph.14837.
  • Corinne Rancurel, Ludovic Legrand and Etienne G. J. Danchin. (2017) Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Genes 2017, 8(10), 248; doi:10.3390/genes8100248.
  • Medina C, Da Rocha M, Magliano M, Ratpopoulo A, Revel B, Marteu N, Magnone V, Lebrigand K, Cabrera J, Barcala M, Silva AC, Millar A, Escobar C, Abad P, Favery B, Jaubert-Possamai S. (2017) Characterization of microRNAs from Arabidopsis galls highlights a role for miR159 in the plant response to the root-knot nematode Meloidogyne incognita. New Phytol. 2017 Sep 14. doi: 10.1111/nph.14717.
  • Blanc-Mathieu R, Perfus-Barbeoch L, Aury JM, Da Rocha M, Gouzy J, Sallet E, Martin-Jimenez C, Bailly-Bechet M, Castagnone-Sereno P, Flot JF, Kozlowski DK, Cazareth J, Couloux A, Da Silva C, Guy J, Kim-Jo YJ, Rancurel C, Schiex T, Abad P, Wincker P, Danchin EGJ. (2017). Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLOS Genetics 13, e1006777. doi: 10.1371/journal.pgen.1006777
  • Marie Larousse, Corinne Rancurel, Camille Syska, Ferran Palero, Catherine Etienne, Benoît Industri, Xavier Nesme, Marc Bardin and Eric Galiana. (2017) Tomato root microbiota and Phytophthora parasitica-associated disease. Microbiome 5:56 doi: 10.1186/s40168-017-0273-7
2016
  • Romain Blanc-Mathieu, Laetitia Perfus-Babeoch, Jean-Marc Aury, Martine Da Rocha, Jerome Gouzy, Erika Sallet, Cristina Martin-Jimenez, Philippe Castagnone-Sereno, Jean-Francois Flot, Djampa Kozlowski, Julie Cazareth, Arnaud Couloux, Corinne Da Silva, Julie Guy, Corinne Rancurel, Thomas Schiex, Pierre Abad, Patrick Wincker, Etienne G.J. Danchin (2016). Peculiar hybrid genomes of devastating plant pests promote plasticity in the absence of sex and meiosis. bioRxiv 046805. 2016. doi: 10.1101/046805
  • Marine Pratlong, Corinne Rancurel, Pierre Pontarotti and Didier Aurelle (2016) Monophyly of Anthozoa (Cnidaria): why do nuclear and mitochondrial phylogenies disagree? Zoologica Scripta 46(3),pages 363–371, May 2017;  First published : September 2016. doi: 10.1111/zsc.12208
  • Damiani I., Drain A., Guichard M., Balzergue S., Boscari A., Boyer J-C, Brunaud V., Cottaz S., Rancurel C., Da Rocha M., Fizames C., Fort S., Gaillard I., Danchin E.G.J., Maillol V., Rouached H., Samain E., Su Y-H, Thouin J., Touraine B., Puppo A., Frachisse J-M, Pauly N., Sentenac H. (2016) Nod factor effects on root hair-specific transcriptome of Medicago truncatula: focus on plasma membrane transport systems and reactive oxygen species networks. Frontiers in Plant Science. doi: 10.3389/fpls.2016.00794
  • Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EGJ, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A, Grenier E, Montarry J, Mimee B, Duceppe MO, Boyes I, Marvin JM, Jones LM, Yusup HB, Lafond-Lapalme J, Esquibet M, Sabeh M, Rott M, Overmars H, Finkers-Tomczak A, Smant G, Koutsovoulos G, Blok V, Mantelin S, Cock PJ, Phillips W, Henrissat B, Urwin PE, Blaxter M, Jones JT. (2016). The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biology 17, 124. doi: 10.1186/s13059-016-0985-1
2014
  • Eves-van den Akker S., Lilley C., Danchin E.G.J., Rancurel C., Cock P., Urwin P., Jones J.T. (2014). The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes. Genome Biol. Evol. doi:10.1093/gbe/evu171
  • Pasquier, C., Clément, M., Dombrovsky, A., Penaud, S., Da Rocha, M., Rancurel, C., Ledger, N., Capovilla, M., and Robichon, A. (2014). Environmentally Selected Aphid Variants in Clonality Context Display Differential Patterns of Methylation in the Genome. PLoS ONE 9, e115022. doi: 10.1371/journal.pone.0115022
Before 2014
  • Flot, J.-F., Hespeels, B., Li, X., Noel, B., Arkhipova, I., Danchin, E.G.J., Hejnol, A., Henrissat, B., Koszul, R., Aury, J.-M., et al. (2013). Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature. doi: 10.1038/nature12326
  • Danchin, E.G.J., Arguel, M.-J., Campan-Fournier, A., Perfus-Barbeoch, L., Magliano, M., Rosso, M.-N., Da Rocha, M., Da Silva, C., Nottet, N., Labadie, K., et al. (2013). Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining. PLoS Pathog 9, e1003745. doi: 10.1371/journal.ppat.1003745
  • Jaouannet M, Perfus-Barbeoch L, Deleury E, Magliano M, Engler G, Vieira P, Danchin EG, Da Rocha M, Coquillard P, Abad P, Rosso MN. (2012) A root-knot nematode-secreted protein is injected into giant cells and targeted to the nuclei. New Phytol. Jun;194(4):924-31.
  • Paganini J, Campan-Fournier A, Da Rocha M, Gouret P, Pontarotti P, Wajnberg E, Abad P, Danchin EGJ. Contribution of Lateral Gene Transfers to the Genome Composition and Parasitic Ability of Root-Knot Nematodes. PLoS One (2012)
Communications par affiche
  • Rancurel et al. (2014) Conference: ECCB 2014 : The 13th European Conference on Computational Biology
    Accepted Poster with Abstract F: Evolution and population genomics; F03: Alienness: Rapid detection of horizontal gene transfers in metazoan genomes
  • Da Rocha al., (2012) Does a genome structure in divergent copies allow animal to evolve without sexual reproduction ? JOBIM 2012, poster 25.

Plateau de microscopie

2017
  • Junior, A. de S., Dijair, J., Pierre, O., Coelho, R.R., Grossi-de-Sa, M.F., Engler, G., and de Almeida Engler, J. (2017). Application of Nuclear Volume Measurements to Comprehend the Cell Cycle in Root-Knot Nematode-Induced Giant Cells. Front. Plant Sci. 8. DOI: 10.3389/fpls.2017.00961
  • Ramos Coelho, R., Vieira, P., Antonino de Souza Júnior, J.D., Martin-Jimenez, C., De Veylder, L., Cazareth, J., Engler, G., Grossi-de-Sa, M.F., and de Almeida Engler, J. (2017). Exploiting cell cycle inhibitor genes of the KRP family to control root-knot nematode induced feeding sites in plants. Plant, Cell & Environment. Doi: 10.1111/pce.12912
2016
  • Díaz-Manzano, F.E., Barcala, M., Engler, G., Fenoll, C., de Almeida-Engler, J., and Escobar, C. (2016). A Reliable Protocol for In situ microRNAs Detection in Feeding Sites Induced by Root-Knot Nematodes. Front Plant Sci 7, 966. DOI: 10.3389/fpls.2016.00966
  • Kyndt, T., Goverse, A., Haegeman, A., Warmerdam, S., Wanjau, C., Jahani, M., Engler, G., Engler, J. de A., and Gheysen, G. (2016). Redirection of auxin flow in Arabidopsis thaliana roots after infection by root-knot nematodes. J. Exp. Bot. erw230. DOI: 10.1093/jxb/erw230
2015
  • Albuquerque ÉV, Bezerra CA, Romero JV, Valencia JW, Valencia-Jiménez A, Pimenta LM, Barbosa AE, Silva MC, Meneguim AM, Sá ME, Engler G, de Almeida-Engler J, Fernandez D, Grossi-de-Sá MF (2015) Seed-Specific Stable Expression of the α-AI1 Inhibitor in Coffee Grains and the In Vivo Implications for the Development of the Coffee Berry Borer. Trop Plant Biol. 8:98-107
  • Cabrera, J., Díaz-Manzano, F.E., Barcala, M., Arganda-Carreras, I., de Almeida-Engler, J., Engler, G., Fenoll, C., and Escobar, C. (2015) Phenotyping nematode feeding sites: three-dimensional reconstruction and volumetric measurements of giant cells induced by root-knot nematodes in Arabidopsis. New Phytol. New Phytol. 206(2):868-80
  • Engler, J. de A., Vieira, P., Rodiuc, N., Sa, M.F.G. de, and Engler, G. (2015). The plant cell cycle machinery: usurped and modulated by plant-parasitic nematodes. Advances in Botanical Research 73, 91–118
  • Lourenço-Tessutti IT, Souza Junior JD, Martins-de-Sa D, Viana AA, Carneiro RM, Togawa RC, de Almeida-Engler J, Batista JA, Silva MC, Fragoso RR, Grossi-de-Sa MF (2015) Knock-down of heat-shock protein 90 and isocitrate lyase gene expression reduced root-knot nematode reproduction. Phytopathology. 105(5):628-37
  • Naessens E, Dubreuil G, Giordanengo P, Baron OL, Minet-Kebdani N, Keller H, Coustau C (2015) A Secreted MIF Cytokine Enables Aphid Feeding and Represses Plant Immune Responses. Curr Biol. 25(14):1898-903
  • Paganelli L, Caillaud MC, Quentin M, Damiani I, Govetto B, Lecomte P, Karpov PA, Abad P, Chabouté ME,  Favery B (2015) Three BUB1 and BUBR1/MAD3-related spindle assembly checkpoint proteins are required for accurate mitosis in Arabidopsis.  New Phytol. 205(1):202-15
  • Rodiuc, N., Barlet, X., Hok, S., Perfus-Barbeoch, L., Allasia, V., Engler, G., Séassau, A., Marteu, N., de Almeida-Engler, J., Panabières, F., et al. (2015). Evolutionarily distant pathogens require the Arabidopsis phytosulfokine signalling pathway to establish disease. Plant Cell Environ. DOI: 10.1111/pce.12627
2014
  • Attard A, Evangelisti E, Kebdani-Minet N, Panabières F, Deleury E, Maggio C, Ponchet M, Gourgues M (2014) Transcriptome dynamics of Arabidopsis thaliana root penetration by the oomycete pathogen Phytophthora parasitica. BMC Genomics. 15:538
  • Bernstein, A., Mangeon, A., Almeida-Engler, J., Engler, G., Montagu, M.V., Sachetto-Martins, G., and de Oliveira, D.E. (2014) Functional analysis of an auxin-inducible DNA-binding protein gene. Plant Signal Behav. 10(1):e977706
  • Bezerra, C.A., Macedo, L.L.P., Amorim, T.M.L., Santos, V.O., Fragoso, R.R., Lucena, W.A., Meneguim, A.M., Valencia-Jimenez, A., Engler, G., Silva, M.C.M., et al. (2014). Molecular cloning and characterization of an α-amylase cDNA highly expressed in major feeding stages of the coffee berry borer, Hypothenemus hampei. Gene 553, 7–16. DOI: 10.1016/j.gene.2014.09.050
  • Hopkins J, Pierre O, Kazmierczak T, Gruber V, Frugier F, Clement M, Frendo P, Herouart D, Boncompagni E (2014). MtZR1, a PRAF protein, is involved in the development of roots and symbiotic root nodules in Medicago truncatula. Plant Cell Environ. 37(3):658-69
  • Jezierska, A, Chaux, C, Pesquet, J-C, Talbot, H and Engler, G (2014)  An EM Approach for Time-Variant Poisson-Gaussian Model Parameter Estimation. IEEE Transactions on signal processing. 62(1): 17-30
  • Larousse M, Govetto B, Seassau A, Etienne C, Industri B, Theodorakopoulos N, Deleury E, Ponchet M, Panabieres F, Galiana E (2014) Characterization of PPMUCL1/2/3, three members of a new oomycete-specific mucin-like protein family residing in Phytophthora parasitica biofilm. Protist 165(3):275-92
  • Lipuma J, Cinege G, Bodogai M, Oláh B, Kiers A, Endre G, Dupont L, Dusha I (2014)  A vapBC-type toxin-antitoxin module of Sinorhizobium meliloti influences symbiotic efficiency and nodule senescence of Medicago sativa. Environ. Microbiol. 16(12):3714-29
  • Pierre O, Hopkins J, Combier M, Baldacci F, Engler G, Brouquisse R, Hérouart D, Boncompagni E (2014) Involvement of papain and legumain proteinase in the senescence process of Medicago truncatula nodules. New Phytol. 202(3): 849-63
  • Ribeiro CW, Alloing G, Mandon K, Frendo P (2014) Redox regulation of differentiation in symbiotic nitrogen fixation. Biochim Biophys Acta. 1850(8):1469-78
  • Vieira P, De Clercq A, Stals H, Van Leene J, Van De Slijke E, Van Isterdael G, Eeckhout D, Persiau G, Van Damme D, Verkest A, Antonino de Souza JD, Júnior, Glab N, Abad P, Engler G, Inzé D, De Veylder L, De Jaeger G, Engler JD. (2014) The Cyclin-Dependent Kinase Inhibitor KRP6 Induces Mitosis and Impairs Cytokinesis in Giant Cells Induced by Plant-Parasitic Nematodes in Arabidopsis. Plant Cell 26(6):2633-2647
2013
  • Andrio E, Marino D, Marmeys A, de Segonzac MD, Damiani I, Genre A, Huguet S, Frendo P, Puppo A, Pauly N. (2013) Hydrogen peroxide-regulated genes in the Medicago truncatula–Sinorhizobium meliloti symbiosis. New Phytol. 198:179-89
  • Antonino de Souza Júnior JD, Ramos Coelho R, Tristan Lourenço I, da Rocha Fragoso R, Barbosa Viana AA, Lima Pepino de Macedo L, Mattar da Silva MC, Gomes Carneiro RM, Engler G, de Almeida-Engler J, Grossi-de-Sa MF. (2013) Knocking-down Meloidogyne incognitaproteases by plant-delivered dsRNA has negative pleiotropic effect on nematode vigor . PLoS One. 8(12): e85364
  • Baron OL, van West P, Industri B, Ponchet M, Dubreuil G, Gourbal B, Reichhart JM, Coustau C. (2013) Parental Transfer of the Antimicrobial Protein LBP/BPI Protects Biomphalaria glabrata Eggs against Oomycete Infections. PLoS Pathog. 9(12):e1003792
  • Benyamina SM, Baldacci-Cresp F, Couturier J, Chibani K, Hopkins J, Bekki A, de Lajudie P, Rouhier N, Jacquot JP, Alloing G, Puppo A, Frendo P. (2013) Two Sinorhizobium meliloti glutaredoxins regulate iron metabolism and symbiotic bacteroid differentiation. Environ Microbiol. 15(3):795-810
  • de Almeida Engler J, Gheysen G (2013) Nematode-induced endoreduplication in plant host cells: why and how? Mol Plant Microbe Interact.26(1):17-24
  • Evangelisti E, Govetto B, Minet-Kebdani N, Kuhn ML, Attard A, Ponchet M, Panabières F, Gourgues M. (2013) The Phytophthora parasitica RXLR effector penetration-specific effector 1 favours Arabidopsis thaliana infection by interfering with auxin physiology. New Phytol. 199(2):476-89
  • Firmino AA, Fonseca FC, de Macedo LL, Coelho RR, Antonino de Souza JD Jr, Togawa RC, Silva-Junior OB, Pappas-Jr GJ, da Silva MC, Engler G, Grossi-de-Sa MF. (2013) Transcriptome Analysis in Cotton Boll Weevil (Anthonomus grandis) and RNA Interference in Insect Pests. PLoS One. 8(12):e85079
  • Iberkleid I, Vieira P, de Almeida Engler J, Firester K, Spiegel Y, Horowitz SB. (2013) Fatty acid-and retinol-binding protein, Mj-FAR-1 induces tomato host susceptibility to root-knot nematodes.PLoS One. 8(5): e64586
  • Koch A, Kumar N, Weber L, Keller H, Imani J, et Kogel KH (2013). Host-induced gene silencing of cytochrome P450 lanosterol C14α-demethylase-encoding genes confers strong resistance to Fusarium species. Proc Natl Acad Sci U S A 110, 19324-19329
  • Kyndt T, Vieira P, Gheysen G, de Almeida-Engler J. (2013) Nematode feeding sites: unique organs in plant roots. Planta. 238(5):807-18
  • Pierre, O., Engler, G., Hopkins, J., Brau, F., Boncompagni, E., and Hérouart, D. (2013). Peribacteriod space acidification: a marker of mature bacteroid functioning in Medicago truncatula nodules. Plant Cell Environ. DOI: 10.1111/pce.12116
  • Quentin M, Abad P, Favery B. (2013). Plant parasitic nematode effectors target host defense and nuclear functions to establish feeding cells. Front Plant Sci.  4:53
  • Vieira, P., Engler, G., and de Almeida Engler, J. (2013). Enhanced levels of plant cell cycle inhibitors hamper root-knot nematode-induced feeding site development. Plant Signal Behav. 8(12)
  • Vieira P, Escudero C, Rodiuc N, Boruc J, Russinova E, Glab N, Mota M, De Veylder L, Abad P, Engler G, de Almeida Engler J. (2013)  Ectopic expression of kip-related proteins restrains root-knot nematode-feeding site expansion.  New Phytol. 199 (2): 505-19
2012
  • Ayers K, Mteirek R, Cervantes A, Lavenant-Staccini L, Thérond P and Gallet A. (2012) Dally and Notum regulate the switch between low and high level Hedgehog pathway signalling. Development. 139(17):3168-79
  • Baldacci-Cresp F, Chang C, Maucourt M, Deborde C, Hopkins J, Lecomte P, Bernillon S, Brouquisse R, Moing A, Abad P, Hérouart D, Puppo A, Favery B, Frendo P. (2012) (Homo)glutathione deficiency impairs root-knot. nematode development in Medicago truncatula.PloS Pathog. 8(1):e1002471
  • Cam Y, Pierre O, Boncompagni E, Hérouart D, Meilhoc E, Bruand C. (2012) Nitric oxide (NO): a key player in the senescence of Medicago truncatula root nodules. New Phytol. 196(2):548-60
  • Damiani I, Baldacci-Cresp F, Hopkins J, Andrio E, Balzergue S, Lecomte P, Puppo A, Abad P, Favery B, Hérouart D (2012) Plant genes involved in harbouring symbiotic rhizobia or pathogenic nematodes. New Phytol. 194 (2) : 511-522
  • de Almeida Engler J, Kyndt T, Vieira P, Van Cappelle E, Boudolf V, Sanchez V, Escobar C, De Veylder L, Engler G, Abad P, Gheysen G. (2012) CCS52 and DEL1 genes are key components of the endocycle in nematode induced feeding sites. The Plant Journal. 72(2): 185-198
  • Jaouannet, M., Perfus-Barbeoch, L., Deleury, E., Magliano, M., Engler, G., Vieira, P., Danchin, E.G.J., Da Rocha, M., Coquillard, P., Abad, P. and Rosso, MN.(2012) A root-knot nematode-secreted protein is injected into giant cells and targeted to the nuclei. New Phytologist. 2012: 194: 924-931
  • Ranieri N, Ruel ., Gallet A, Raisin-Tani and Thérond P(2012) Distinct Phosphorylations on Kinesin Costal-2 Mediate Differential Hedgehog Signaling Strength. Dev Cell. 22(2):279-94
  • Schmitz A, Anselme C, Ravallec M, Rebuf C, Simon JC, Gatti JL, Poirié M. (2012). The cellular immune response of the pea aphid to foreign intrusion and symbiotic challenge. PLoS One. 7(7):e42114
  • Thiebaut F, Rojas CA, Almeida KL, Grativol C, Domiciano GC, Lamb CR, Engler Jde A, Hemerly AS, Ferreira PC. (2012). Regulation of miR319 during cold stress in sugarcane. Plant Cell Environ. 35(3):502-12
  • Vieira P, Banora MY, Castagnone-Sereno P, Rosso MN, Engler G, de Almeida Engler J. (2012) An immunocytochemical procedure for protein localization in various nematode life stages combined with plant tissues using methylacrylate-embedded specimens. Phytopathology.102(10):990-6
  • Vieira, P., Engler, G. and de Almeida Engler, J. (2012) Whole-mount confocal imaging of nuclei in giant feeding cells induced by root-knot nematodes in Arabidopsis. New Phytologist. 2012: 195(2): 488-496

Archives 2011-2006 Plateau de Microscopie

Liste des publications 2011-2006
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