2015

mercredi 20 avril 2016

Les publications illustrent les collaborations scientifiques au sein de la FR BioEnviS.
Elles sont portées par au moins 2 unités de la FR et/ou ont bénéficié des services des plateformes de celle-ci.

Belkorchia A., Gasc C., Polonais V., Parisot N., Gallois N., Ribière C., Lerat E., Gaspin C., Pombert J.F., Peyret P. and Peyretaillade E. The prediction and validation of small CDSs expand the gene repertoire of the smallest known eukaryotic genomes. PloS one, 10 (9.)

Billard E., Domaizon I., Tissot N., Arnaud F. and Lyautey E. Multi-scale phylogenetic heterogeneity of archaea, bacteria, methanogens and methanotrophs in lake sediments. Hydrobiologia, 751 : 159–173.

Billoir E., Navratil V. and Blaise B.J. Sample size calculation in metabolic phenotyping studies. Brief. Bioinform., 16, 813-819.

Blavet N., Blavet H., Muyle A., Kafer J., Cegan R., Deschamps C., Zemp N., Mousset S., Aubourg S., Bergero R., Charlesworth D., Hobza R., Widmer A. and Marais G.A. Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia. BMC Genomics, 16 : 546-546.

Borland S., Oudart A., Pringent-Combaret C., Borchier-Armanet C. and Wisniewski-Dyé F. Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum. BMC genomics, 16(1) : 833.

Brault V., Duchon A., Romestaing C., Sahun I., Pothion S., Karout M., Borel C., Dembele D., Bizot J.C., Messaddeq N., Sharp A.J., Roussel D., Antonarakis S.E., Dierssen M. and Hérault Y. Opposite phenotypes of muscle strength and locomotor function in mouse models of partial trisomy and monosomy 21 for the proximal Hspa13-App region. PLoS Genet., 24 ;11(3):e1005062.

Cairey-Remonnay A., Deffaud J., Wesolowski-Louvel M., Lemaire M. and Soulard A. Glycolysis controls plasma-membrane glucose sensors to promote glucose signaling in yeasts. Mol Cell Biol, 35 : 747-757.

Carro L., Pujic P., Alloisio N., Fournier P., Boubakri H., Hay A.E., Poly F., François P., Hocher V., Mergaert P., Balmand S., Rey M., Heddi A. and Normand P. Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia. The ISME Journal, 24 : 2267-2273.

Cayuela H., Quay L., Dumet A., Léna J.P., Miaud C. and Rivière V. Intensive vehicle traffic impacts morphology and endocrine stress response in a threatened amphibian. Fauna & Flora International, 51(1) : 182-188.

Chamam A., Wisniewski-Dyé F., Comte G., Bertrand C. and Prigent-Combaret C. Differential responses of Oryza sativa secondary metabolism to biotic interactions with cooperative, commensal and phytopathogenic bacteria. Planta, 242 : 1439-1452.

Chatagnon A., Veber P., Morin V., Bedo J., Triqueneaux G., Semon M., Laudet V., d’Alche-Buc F. and Benoit G. RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements. Nucleic Acids Res., 43, 4833-4854.

Christina M., Rouifed S., Puijalon S., Vallier F., Meiffren G., Bellvert F. and Piola F. Allelopathic effect of a native species on a major plant invader in Europe. The Science of Nature, 102 : 12.

Cottet M., Piola F., Le Lay Y.F., Rouifed S. and Rivière-Honegger A. How environmental managers perceive and approach the issue of invasive species : the case of Japanese knotweed s.l. (Rhône River, France) . Biological Invasion, 17, 3433–3453.

Dequivre M., Diel B., Villard C., Sismeiro O., Durot M., Coppée J.Y., Nesme X., Vial L. and Hommais F. Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58. Mol Plant Microbe Interact., 28(5) : 580-9.

Desprat J.L., Lengagne T., Dumet A., Desouhant E. and Mondy N. Immunocompetence handicap hypothesis in tree frog : trade-off between sexual signals and immunity ? Behavioral Ecology, 26(4) : 1138–1146.

Dolédec S., Castella E., Forcellini M., Olivier J.-M., Paillex A. and Sagnes P. The generality of changes in the trait composition of fish and invertebrate communities after flow restoration in a large river (French Rhône). Freshwater Biology, 60, 1221-1236.

Dore J., Perraud M., Dieryckx C., Kohler A., Morin E., Henrissat B., Lindquist E., Zimmermann S.D., Girard V., Kuo A., Grigoriev IV., Martin F., Marmeisse R. and Gay G. Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis. New Phytologist, 208 : 1169-1187.

Etienne D., Destas M., Lyautey E., Marti R., Ruffaldi P., Georges-Leroy M., Dambrine E. and Topp E. Two thousand–year reconstruction of livestock production intensity in France using sediment-archived fecal Bacteroidales and source-specific mitochondrial markers. The Holocene, 25 : 1-10.

Faucon F., Dusfour I., Gaude T., Navratil V., Boyer F., Chandre F., Sirisopa P., Thanispong K., Juntarajumnong W., Poupardin R. et al. Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing. Genome Res., 25 : 1347-1359.

Fischer MJC., Rustenhloz C., Leh-Louis V. and Perrière G. Molecular and functional evolution of the fungal diterpene synthase genes. BMC Microbiol,. 15 : 221.

Flandrois J.P., Perrière G. and Gouy M.  leBIBIQBPP : a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences. BMC Bioinformatics, 16(1) : 251.

Freel KC., Krueger MC., Farasin J., Brochier-Armanet C., Barbe V., Andrés J., Cholley PE., Dillies MA., Jagla B., Koechler S., Leva Y., Magdelenat G., Plewniak F., Proux C., Coppée JY., Bertin PN., Heipieper HJ. and Arsène-Ploetze F. Adaptation in Toxic Environments : Arsenic Genomic Islands in the Bacterial Genus Thiomonas. PLoS One, 10(9):e0139011.

Galia W., Mariani-Kurkdjian P., Bastien S., Loukiadis E., Blanquet-Diot S., Leriche F., Brugère H., Shima A., Oswald E., Cournoyer B. and Thevenot-Sergentet D. Correction for Galia et al., genome sequence and annotation of a human infection isolate of Escherichia coli O26:H11 involved in a raw milk cheese outbreak. Genome Announc., 3, e00880-15.

Golanowska M., Galardini M., Bazzicalupo M., Hugouvieux-Cotte-Pattat N., Mengoni A., Potrykus M., Slawiak M., and Lojkowska E. Draft genome sequence of a highly virulent strain of the plant pathogen Dickeya solani, IFB0099. Genome Announc 3(2):e00109-15.

Goubert C., Modolo L., Vieira C., Valiente Moro C., Mavingui P. and Boulesteix M. De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti) . Genome Biology and Evolution, 7(4) : 1192–1205.

Granqvist E., Sun J., Op den Camp R., Pujic P., Hill, L., Normand P., Morris R.J., Downie J.A., Geurts R. and Oldroyd GED. Bacterial-induced calcium oscillations are a common feature of symbiotic signalling in nodulating legumes and non-legumes. New Phytol., 207 : 551-558.

Grimault A., Gendrot G., Chaignon S., Gilard F., Tcherkez G., Thévenin J., Dubreucq B., Depège-Fargeix N. and Rogowsky P.M. Role of B3 domain transcription factors of the AFL family in maize kernel filling. Plant Science, 236 : 116-125.

Guirimand T., Delmotte S. and Navratil V. VirHostNet 2.0 : surfing on the web of virus/host molecular interactions data. Nucleic Acids Res., 43 : D583-587.

Higashi S., Fournier C., Gautier C., Gaspin C. and Sagot MF. Mirinho : An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. BMC Bioinformatics, 16 : 179.

Josserand R., Troïanowski M., Grolet O., Desprat J.L., Lengagne T. and Mondy N. A phytohaemagglutinin challenge test to assess immune responsiveness of European tree frog Hyla arborea. Amphibia-Reptilia, 36 : 111-118.

Kone M., Comte G., Somé M., Zongo I. and Joly P. Comparative performance of sand and coconut substrate in urban wastewater treatment. Performances comparees du sable et du substrat de coco en traitement d’eaux residuaires urbaines. Chemistry & Chemical Engineering, Biotechnology, Food Industry,16 : 1-12.

Lassalle F., Périan S., Bataillon T., Nesme X., Duret L. and Daubin V. GC-content evolution in bacterial genomes : the biased gene conversion hypothesis expands. PLOS Genetics, 11(2):e1004941.

Lengagne T., Gomez T., Josserand R. and Voituron Y. Long Recording Sequences : How to Track the Intra-Individual Variability of Acoustic Signals. PlosOne, 10(5) : e0123828 : 1-11.

Loth K., Costechareyre D., Effantin G., Rahbé Y., Condemine G., Landon C. and da Silva P. New Cyt-like d-endotoxins from Dickeya dadantii : structure and aphicidal activity. Scientific Reports, 5, pp.8791.

Luquet E., Léna J.P., Miaud C. and Plénet S. Phenotypic divergence of the common toad (Bufo bufo) along an altitudinal gradient : evidence for local adaptation. Heredity, 114(1) : 69-79.

Masson F., Moné Y., Vigneron A., Vallier A., Parisot N., Vincent-Monégat C., Balmand S., Carpentier M.C., Zaidman-Rémy A. and Heddi A. Weevil endosymbiont dynamics is associated with a clamping of immunity. BMC Genomics, 16 : 819.

Minard G., Tran F.H., Van Tran Van., Goubert C., Bellet C., Lambert G., Khanh Ly Huynh Kim, Trang Huynh Thi Thuy, Mavingui P. and Valiente-Moro C. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives. Microbial Symbioses, 6 : 970.

Mitchell A., Chang H.Y., Daugherty L., Fraser M., Hunter S., Lopez R., McAnulla C., McMenamin C., Nuka G., Pesseat S. et al. The InterPro protein families database : the classification resource after 15 years. Nucleic Acids Res., 43 : D213-221.

Monternier P.A., Fongy A., Hervant F., Drai J., Collin-Chavagnac D., Rouanet J.L. and Roussel D. Skeletal muscle phenotype affects fasting-induced mitochondrial oxidative phosphorylation flexibility in cold-acclimated ducklings. J Exp Biol., 218(15) : 2427-34.

Naughtin M., Haftek-Terreau Z., Xavier J., Meyer S., Silvain M., Jaszczyszyn Y., Levy N., Miele V., Benleulmi M.S., Ruff M., Parissi V., Vaillant C. and Lavigne M. DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity. PLoS One. 10(6):e0129427.

Orias F., Simon L., Mialdea G., Clair A., Brosselin V. and Perrodin Y. Bioconcentration of 15N-tamoxifen at environmental concentration in liver, gonad and muscle of Danio rerio. Ecotoxicology and Environmental Safety, 120 : 457–462.

Oudot-Canaff J., Bornette G., Vallier F., De Wilde M., Piola F. and Martel, E. Genetic temporal dynamics in restored wetlands : A case of a predominantly clonal species, Berula erecta (Huds.) Coville. Aquatic Botany, 126 : 7-15.

Persson T., Demina I., Battenberg K., Vigil-Stenman T., Vanden Heuvel B., Pujic P., Facciotti M.T., Wilbanks E.G., O’Brien A., Fournier P., Cruz Hernandez M.A., Médigue C., Normand P., Pawlowski K. and Berry A.M. Candidatus Frankia datiscae Dg1, the actinobacterial microsymbiont of Datisca glomerata, uses Nod factors for establishment of symbiosis with its host plant. PLoS One, 10(5):e0127630.

Philippon H., Brochier-Armanet C. and Perriere G. Evolutionary history of phosphatidylinositol- 3-kinases : ancestral origin in eukaryotes and complex duplication patterns. BMC Evol. Biol., 15, 226.

Pozzi A.C., Bautista-Guerrero H., Nouioui I., Cotin-Galvan L., Pepin R., Fournier P., Menu F., Fernandez M.P. and Herrera-Belaroussi A. In-planta sporulation phenotype : a major life history trait to understand the evolution of Alnus-infective Frankia strains. Environ Microbiol., 17 : 3125-38.

Pujic P., Bolotin A., Fournier P., Sorokin A., Lapidus A., Richau K.H., Briolay J., Mebarki F., Normand P. and Sellstedt A. Genome sequence of the atypical symbiotic Frankia R43 strain, a nitrogen-fixing and hydrogen-producing actinobacterium. Genome Announc 3(6) : e01387-15.

Raquin V., Valiente-Moro C., Saucereau Y., Tran F.H., Potier P. and Mavingui P. Native Wolbachia from Aedes albopictus Blocks Chikungunya Virus Infection In Cellulo Bourtzis. PLoS One, 10:e0125066.

René-Martellet M., Valiente Moro C., Chêne G., Bourdoiseau G., Chabanne L. and Mavingui P. Update on epidemiology of canine babesiosis in Southern France. BMC Vet Res, 11:223.

Rey B., Halsey L.G., Hetem R.S., Fuller A., Mitchell D. and Rouanet J.L. Estimating resting metabolic rate by biologging core and subcutaneous temperature in a mammal. Comparative Biochemistry and Physiology, Part A, 183 : 72–77.

Rey B., Pélisson P.F., Bel-Venner M.C., Voituron Y. and Venner S. Revisiting the link between breeding effort and oxidative balance through field evaluation of two sympatric sibling insect species. Evolution, 69(3) : 815–822.

Rousseau D., Widiez T., Di Tommaso S., Rositi H., Adrien J., Maire E., Langer M., Olivier C., Peyrin F. and Rogowsky P. Fast virtual histology using X-ray in-line phase tomography : application to the 3D anatomy of maize developing seeds. Plant Methods, 11 : 55.

Roussel D., Salin K., Dumet A., Romestaing C., Rey B. and Voituron Y. Oxidative phosphorylation efficiency, proton conductance and reactive oxygen species production of liver mitochondria correlates with body mass in frogs. Journal of Experimental Biology, 218 : 3222-3228.

Semeria M., Tannier E. and Gueguen L. Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies. BMC Bioinformatics, 16 Suppl 14 pp.S5-S5

Simonin M., Le Roux X., Poly F., Lerondelle C., Hungate B.A., Nunan N. and Niboyet A. Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply. Microbial Ecology, 70 : 809-818.

Simonin M., Guyonnet JP., Martins JMF., Ginot M. and Richaume A. Influence of soil properties on the toxicity of TiO2 nanoparticles on carbon mineralization and bacterial abundance. Journal of hazardous material, 283 : 529-535.

Troïanowski M., Condette C., Mondy N., Dumet A. and Lengagne T. Traffic noise impact stress and coloration but not calls in the European treefrog (Hyla arborea) . Behaviour, 152 : 821-836.

Yan X., Sivignon A., Alcouffe P., Burdin B., Favre-Bonté S., Bilyy R., Barnich N., Fleury E., Ganachaud F. and Bernard J. Brilliant glyconanocapsules for trapping of bacteria. Chem. Commun, 51(67) 13193-13196.

Youenou B., Favre-Bonté S., Bodilis J., Brothier E., Dubost A., Muller D. and Nazaret S. Comparative genomics of environmental and clinical Stenotrophomonas maltophilia strains with different antibiotic resistance profiles. Genome Biology and Evolution, 7(9):2484-505.


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  • 2015