Experts and Doctors on phylogeny in Lyon, Auvergne Rhône Alpes, France


Locale: Lyon, Auvergne Rhône Alpes, France
Topic: phylogeny

Top Publications

  1. Menard A, Monnez C, Estrada de Los Santos P, Segonds C, Caballero Mellado J, LiPuma J, et al. Selection of nitrogen-fixing deficient Burkholderia vietnamiensis strains by cystic fibrosis patients: involvement of nif gene deletions and auxotrophic mutations. Environ Microbiol. 2007;9:1176-85 pubmed
    ..For 17% of B. vietnamiensis clinical strains, CF lungs appeared to have favoured the selection of mutations or deletions leading to N(2)-fixing deficiencies. ..
  2. Afonso C, Amarasinghe G, Bányai K, Bào Y, Basler C, Bavari S, et al. Taxonomy of the order Mononegavirales: update 2016. Arch Virol. 2016;161:2351-60 pubmed publisher
    ..This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). ..
  3. Schuffenecker I, Ando T, Thouvenot D, Lina B, Aymard M. Genetic classification of "Sapporo-like viruses". Arch Virol. 2001;146:2115-32 pubmed
  4. Waku Kouomou D, Landreau D, Olivier S, Palmyre P, Benoit Catin T, Freymuth F, et al. Molecular characterization of measles virus circulating in the Indian Ocean Islands during 2005-2006 and in France in 2006. J Med Virol. 2007;79:1381-7 pubmed
    ..The knowledge of circulating measles virus will help in documenting measles elimination program. This report also highlights the fact that progress of measles elimination is blighted continually by the phenomenon of measles importation. ..
  5. Glaser P, Martins Simões P, Villain A, Barbier M, Tristan A, Bouchier C, et al. Demography and Intercontinental Spread of the USA300 Community-Acquired Methicillin-Resistant Staphylococcus aureus Lineage. MBio. 2016;7:e02183-15 pubmed publisher
    ..These findings highlight the significance of horizontal gene acquisitions and point mutations in the success of such disseminated clones and illustrate their cyclic and sporadic life cycle. ..
  6. Guo L, Wang D, Zhou H, Wu C, Gao X, Xiao Y, et al. Cross-reactivity between avian influenza A (H7N9) virus and divergent H7 subtypic- and heterosubtypic influenza A viruses. Sci Rep. 2016;6:22045 pubmed publisher
    ..Moreover, serologic diagnoses for H7N9 infections need to consider possible interference from the cross-reactivity of H7N9 with other subtype influenza viruses. ..
  7. Mey C, Metlin A, Duong V, Ong S, In S, Horwood P, et al. Evidence of two distinct phylogenetic lineages of dog rabies virus circulating in Cambodia. Infect Genet Evol. 2016;38:55-61 pubmed publisher
    ..A greater understanding of the molecular epidemiology of rabies in South-East Asia is an important step to monitor progress on the efforts to control canine rabies in the region. ..
  8. Leroux C, Cruz J, Mornex J. SRLVs: a genetic continuum of lentiviral species in sheep and goats with cumulative evidence of cross species transmission. Curr HIV Res. 2010;8:94-100 pubmed
    ..Three classifications have been successively proposed and allowed to refine the SRLV phylogeny over time. Phylogenetic reconstructions support the existence of SRLV cross-species transmission in domestic and wild small ruminants. ..
  9. Bouffaud M, Kyselková M, Gouesnard B, Grundmann G, Muller D, Moënne Loccoz Y. Is diversification history of maize influencing selection of soil bacteria by roots?. Mol Ecol. 2012;21:195-206 pubmed publisher

More Information


  1. Llagonne Barets M, Icard V, Leparc Goffart I, Prat C, Perpoint T, André P, et al. A case of Mayaro virus infection imported from French Guiana. J Clin Virol. 2016;77:66-8 pubmed publisher
  2. Graindorge A, Menard A, Neto M, Bouvet C, Miollan R, Gaillard S, et al. Epidemiology and molecular characterization of a clone of Burkholderia cenocepacia responsible for nosocomial pulmonary tract infections in a French intensive care unit. Diagn Microbiol Infect Dis. 2010;66:29-40 pubmed publisher
    ..Bcc strains from outdoor environments were not related to this clone but indicated the presence of Burkholderia multivorans and Burkholderia vietnamiensis. ..
  3. Butin M, Rasigade J, Martins Simões P, Meugnier H, Lemriss H, Goering R, et al. Wide geographical dissemination of the multiresistant Staphylococcus capitis NRCS-A clone in neonatal intensive-care units. Clin Microbiol Infect. 2016;22:46-52 pubmed publisher
    ..Questions remain regarding the origin and means of international spread, and the reasons for this clone's apparent predilection for neonates. ..
  4. Philippon A, Slama P, Dény P, Labia R. A Structure-Based Classification of Class A β-Lactamases, a Broadly Diverse Family of Enzymes. Clin Microbiol Rev. 2016;29:29-57 pubmed publisher
    ..However, with the exception of PER types, this diversity is poorly represented in existing X-ray crystallographic data. ..
  5. Leroux C, Cadoré J, Montelaro R. Equine Infectious Anemia Virus (EIAV): what has HIV's country cousin got to tell us?. Vet Res. 2004;35:485-512 pubmed
    ..These studies are of interest in the context of HIV and efforts to develop a vaccine. This review will focus on some of the most recent results...
  6. Leroux C, Chastang J, Greenland T, Mornex J. Genomic heterogeneity of small ruminant lentiviruses: existence of heterogeneous populations in sheep and of the same lentiviral genotypes in sheep and goats. Arch Virol. 1997;142:1125-37 pubmed
    ..A phylogenetic tree of pol gene sequences confirmed the presence of a novel genotype of SRLV in France...
  7. B hne A, Darras A, D Cotta H, Baroiller J, Galiana Arnoux D, Volff J. The vertebrate makorin ubiquitin ligase gene family has been shaped by large-scale duplication and retroposition from an ancestral gonad-specific, maternal-effect gene. BMC Genomics. 2010;11:721 pubmed publisher
    ..Comparative expression analysis strongly suggests that the ancestral E3 ubiquitin ligase function of the single copy mkrn gene before duplication in vertebrates was gonad-specific, with maternal expression in early embryos...
  8. Boyer M, Haurat J, Samain S, Segurens B, Gavory F, Gonzalez V, et al. Bacteriophage prevalence in the genus Azospirillum and analysis of the first genome sequence of an Azospirillum brasilense integrative phage. Appl Environ Microbiol. 2008;74:861-74 pubmed
    ..brasilense Cd, and a region of 27.3 kb of phiAb-Cd was found to be duplicated on the 130-kb pRhico plasmid previously sequenced from A. brasilense Sp7, the parental strain of A. brasilense Cd...
  9. Pothier J, Prigent Combaret C, Haurat J, Moënne Loccoz Y, Wisniewski Dyé F. Duplication of plasmid-borne nitrite reductase gene nirK in the wheat-associated plant growth-promoting rhizobacterium Azospirillum brasilense Sp245. Mol Plant Microbe Interact. 2008;21:831-42 pubmed publisher
    ..brasilense Sp245 from a distant relative and underwent subsequent duplication; however, both paralogs remained functional and retained their upregulation by the plant partner. ..
  10. Morvan Dubois G, Le Guellec D, Garrone R, Zylberberg L, Bonnaud L. Phylogenetic analysis of vertebrate fibrillar collagen locates the position of zebrafish alpha3(I) and suggests an evolutionary link between collagen alpha chains and hox clusters. J Mol Evol. 2003;57:501-14 pubmed
    ..An evolutionary scenario is proposed in which phylogenetic relationships of the alpha chains of fibrillar collagens of vertebrates could be related to Hox cluster history. ..
  11. Finet C, Berne Dedieu A, Scutt C, Marl taz F. Evolution of the ARF gene family in land plants: old domains, new tricks. Mol Biol Evol. 2013;30:45-56 pubmed publisher
  12. Chuzeville S, Puymege A, Madec J, Haenni M, Payot S. Characterization of a new CAMP factor carried by an integrative and conjugative element in Streptococcus agalactiae and spreading in Streptococci. PLoS ONE. 2012;7:e48918 pubmed publisher
    ..This work thus describes a CAMP factor that is carried by a mobile genetic element and has spread to different streptococcal species...
  13. Musso D, Gubler D. Zika Virus. Clin Microbiol Rev. 2016;29:487-524 pubmed publisher
    ..There is a high potential for ZIKV emergence in urban centers in the tropics that are infested with competent mosquito vectors such as Aedes aegypti and Aedes albopictus. ..
  14. Sanguin H, Sarniguet A, Gazengel K, Moenne Loccoz Y, Grundmann G. Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture. New Phytol. 2009;184:694-707 pubmed publisher
    ..In conclusion, take-all decline correlated with multiple changes in rhizobacterial community composition, far beyond the sole case of pseudomonads...
  15. Parto S, Lartillot N. Detecting consistent patterns of directional adaptation using differential selection codon models. BMC Evol Biol. 2017;17:147 pubmed publisher
    ..These models can be applied to many other problems, ranging from viral adaptation to evolution of life-history strategies in plants or animals. ..
  16. Kremer N, Charif D, Henri H, Bataille M, Prevost G, Kraaijeveld K, et al. A new case of Wolbachia dependence in the genus Asobara: evidence for parthenogenesis induction in Asobara japonica. Heredity (Edinb). 2009;103:248-56 pubmed publisher
    ..Although dependence should lead to co-divergence between Wolbachia and its hosts, the very few cases of co-speciation observed in host-Wolbachia associations question the stability of these obligatory associations. ..
  17. Castro R, Greenland T, Leite R, Gouveia A, Mornex J, Cordier G. Conserved sequence motifs involving the tat reading frame of Brazilian caprine lentiviruses indicate affiliations to both caprine arthritis-encephalitis virus and visna-maedi virus. J Gen Virol. 1999;80 ( Pt 7):1583-9 pubmed
    ..This may be useful for epizoological tracing of the origin of outbreaks...
  18. Prigent Combaret C, Blaha D, Pothier J, Vial L, Poirier M, Wisniewski Dyé F, et al. Physical organization and phylogenetic analysis of acdR as leucine-responsive regulator of the 1-aminocyclopropane-1-carboxylate deaminase gene acdS in phytobeneficial Azospirillum lipoferum 4B and other Proteobacteria. FEMS Microbiol Ecol. 2008;65:202-19 pubmed publisher
    ..lipoferum 4B. This is the first synteny, phylogenetic, and functional analysis of factors modulating acdS expression in Azospirillum plant growth-promoting rhizobacterium...
  19. Calvignac S, Terme J, Hensley S, Jalinot P, Greenwood A, Hänni C. Ancient DNA identification of early 20th century simian T-cell leukemia virus type 1. Mol Biol Evol. 2008;25:1093-8 pubmed publisher
    ..This represents the first clear evidence that it will be possible to use museum specimens to better characterize simian and human T-tropic retrovirus genetic diversity and analyze their origin and evolution, in greater detail...
  20. Renaud F, Aubel D, Riegel P, Meugnier H, Bollet C. Corynebacterium freneyi sp. nov., alpha-glucosidase-positive strains related to Corynebacterium xerosis. Int J Syst Evol Microbiol. 2001;51:1723-8 pubmed
    ..The name Corynebacterium freneyi sp. nov. is proposed with the type strain ISPB 6695110T (= CIP 106767T = DSM 44506T). ..
  21. Bardet P, Horard B, Robinson Rechavi M, Laudet V, Vanacker J. Characterization of oestrogen receptors in zebrafish (Danio rerio). J Mol Endocrinol. 2002;28:153-63 pubmed
    ..After 48 h after fertilization, all ERs, but predominantly ER alpha, began to be expressed. We conclude that oestrogen signal transduction can operate during zebrafish development only within discrete time windows. ..
  22. Bertrand S, Brunet F, Escriva H, Parmentier G, Laudet V, Robinson Rechavi M. Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems. Mol Biol Evol. 2004;21:1923-37 pubmed
    ..Our results imply that the genes for major receptors such as steroid receptors or thyroid hormone receptors were present in Urbilateria. ..
  23. Brunet F, Roest Crollius H, Paris M, Aury J, Gibert P, Jaillon O, et al. Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol. 2006;23:1808-16 pubmed
    ..These results show that similar mechanisms are at work in fishes as in yeast or plants and provide a framework for future investigation of the consequences of duplication in fishes and other animals. ..
  24. Exposito J, Larroux C, Cluzel C, Valcourt U, Lethias C, Degnan B. Demosponge and sea anemone fibrillar collagen diversity reveals the early emergence of A/C clades and the maintenance of the modular structure of type V/XI collagens from sponge to human. J Biol Chem. 2008;283:28226-35 pubmed publisher
    ..This observation is compatible with the suggested primordial function of type V/XI fibrillar collagens in the initiation of the formation of the collagen fibrils...
  25. Guéhenneux F, Duret L, Callanan M, Bouhas R, Hayette S, Berthet C, et al. Cloning of the mouse BTG3 gene and definition of a new gene family (the BTG family) involved in the negative control of the cell cycle. Leukemia. 1997;11:370-5 pubmed
    ..This family is mainly characterized by the presence of two conserved domains (BTG boxes A and B) of as yet undetermined function which are separated by a non-conserved 20-25 amino acid sequence. ..
  26. Pelandakis M, Serre S, Pernin P. Analysis of the 5.8S rRNA gene and the internal transcribed spacers in Naegleria spp. and in N. fowleri. J Eukaryot Microbiol. 2000;47:116-21 pubmed
    ..8S gene. In addition, it was possible to define species specific primers in ITS regions to rapidly identify N. fowleri...
  27. Mortada H, Vieira C, Lerat E. Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species. J Mol Evol. 2010;71:180-91 pubmed publisher
    ..The higher level of expression found for TE-rich genes in tumor and immune system tissues suggests that TEs play an important role in gene regulation. ..
  28. Nishio S, Gibert Y, Bernard L, Brunet F, Triqueneaux G, Laudet V. Adiponectin and adiponectin receptor genes are coexpressed during zebrafish embryogenesis and regulated by food deprivation. Dev Dyn. 2008;237:1682-90 pubmed publisher
    ..These data indicate that the upstream members of the Adiponectin pathway have complex expression patterns and are regulated by food deprivation in zebrafish. ..
  29. Tavares R, Cagnon M, Negrutiu I, Mouchiroud D. Testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms. BMC Evol Biol. 2010;10:240 pubmed publisher
    ..However, other explanations can be given for the 1:1 ratio that we found. More abundant and more specific (namely carpel and ovule) expression data should be produced in order to further test these theories. ..
  30. Rouault J, Samarut C, Duret L, Tessa C, Samarut J, Magaud J. Sequence analysis reveals that the BTG1 anti-proliferative gene is conserved throughout evolution in its coding and 3' non-coding regions. Gene. 1993;129:303-6 pubmed
    ..These data confirm that BTG1 is phylogenetically highly conserved and that BTG1 and PC3/TIS21 may constitute the first members of a new family of functionally related genes. ..
  31. Leveque N, Amine I, Amine I, Cartet G, Hammani A, Khazraji Y, et al. Two outbreaks of acute hemorrhagic conjunctivitis in Africa due to genotype III coxsackievirus A24 variant. Eur J Clin Microbiol Infect Dis. 2007;26:199-202 pubmed
    ..This is the first report of an epidemic of acute hemorrhagic conjunctivitis due to a coxsackievirus A24 variant in Africa since 1987 and the first ever from Morocco...
  32. Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S, Fernandes D, et al. The genetic history of Ice Age Europe. Nature. 2016;534:200-5 pubmed publisher
    ..These results document how population turnover and migration have been recurring themes of European prehistory. ..
  33. Karaki L, Da Silva P, Rizk F, Chouabe C, Chantret N, Eyraud V, et al. Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. BMC Plant Biol. 2016;16:63 pubmed publisher
  34. Bonneton F, Brunet F, Kathirithamby J, Laudet V. The rapid divergence of the ecdysone receptor is a synapomorphy for Mecopterida that clarifies the Strepsiptera problem. Insect Mol Biol. 2006;15:351-62 pubmed publisher
    ..Protein alignments reveal that eight of 11 synapomorphies support an affinity between Strepsiptera and Coleoptera sequences. The affiliation of Strepsiptera to Diptera should therefore be rejected...
  35. Bardet P, Schubert M, Horard B, Holland L, Laudet V, Holland N, et al. Expression of estrogen-receptor related receptors in amphioxus and zebrafish: implications for the evolution of posterior brain segmentation at the invertebrate-to-vertebrate transition. Evol Dev. 2005;7:223-33 pubmed
  36. Dahmen S, Haenni M, Châtre P, Madec J. Characterization of blaCTX-M IncFII plasmids and clones of Escherichia coli from pets in France. J Antimicrob Chemother. 2013;68:2797-801 pubmed publisher
    ..coli isolates from pets in France. The ST131 clone was rare. However, the predominance of human-like bla(CTX-M) IncFII plasmids suggests exchanges of these plasmids with the human reservoir. ..
  37. Cooper K, Sears K, Uygur A, Maier J, Baczkowski K, Brosnahan M, et al. Patterning and post-patterning modes of evolutionary digit loss in mammals. Nature. 2014;511:41-5 pubmed publisher
    ..Together these data demonstrate remarkable plasticity in the mechanisms of vertebrate limb evolution and shed light on the complexity of morphological convergence, particularly within the artiodactyl lineage. ..
  38. Rodriguez Nava V, Couble A, Molinard C, Sandoval H, Boiron P, Laurent F. Nocardia mexicana sp. nov., a new pathogen isolated from human mycetomas. J Clin Microbiol. 2004;42:4530-5 pubmed
    ..The data obtained indicated that the three clinical strains should be recognized as a new species for which the name Nocardia mexicana sp. nov. is proposed. ..
  39. Valour F, Boisset S, Lebras L, Martha B, Boibieux A, Perpoint T, et al. Clostridium sordellii brain abscess diagnosed by 16S rRNA gene sequencing. J Clin Microbiol. 2010;48:3443-4 pubmed publisher
  40. Pasco Viel E, Charles C, Chevret P, Semon M, Tafforeau P, Viriot L, et al. Evolutionary trends of the pharyngeal dentition in Cypriniformes (Actinopterygii: Ostariophysi). PLoS ONE. 2010;5:e11293 pubmed publisher
    ..Here we provide a further description of this diversity using X-ray microtomography and we map the resulting dental characters on a phylogenetic tree to explore evolutionary trends...
  41. Bonello J, Opsahl Ferstad H, Perez P, Dumas C, Rogowsky P. Esr genes show different levels of expression in the same region of maize endosperm. Gene. 2000;246:219-27 pubmed
  42. Galmès J, Li Y, Rajoharison A, Ren L, Dollet S, Richard N, et al. Potential implication of new torque teno mini viruses in parapneumonic empyema in children. Eur Respir J. 2013;42:470-9 pubmed publisher
    ..This study reports the description of replicative TTMV-LY isolated from parapneumonic effusions of children hospitalised with PPE, suggesting a potential role of the virus in the pathogenesis of pneumonia. ..
  43. Tardy F, Gaurivaud P, Tricot A, Maigre L, Poumarat F. Epidemiological surveillance of mycoplasmas belonging to the 'Mycoplasma mycoides' cluster: is DGGE fingerprinting of 16S rRNA genes suitable?. Lett Appl Microbiol. 2009;48:210-7 pubmed publisher
    ..In this study, we further assessed the suitability of the technique for epidemiological surveillance of mycoplasmas belonging to the 'Mycoplasma mycoides' cluster, a phylogenetic group that includes major ruminant pathogens...
  44. Bérard J, Gueguen L. Accurate estimation of substitution rates with neighbor-dependent models in a phylogenetic context. Syst Biol. 2012;61:510-21 pubmed publisher
    ..Model comparisons within the RN95 + YpR class show the importance of taking into account neighbor-dependent effects. An application of the method to the detection of hypomethylated islands is discussed. ..
  45. Blond J, Beseme F, Duret L, Bouton O, Bedin F, Perron H, et al. Molecular characterization and placental expression of HERV-W, a new human endogenous retrovirus family. J Virol. 1999;73:1175-85 pubmed
    ..1-, and 1.3-kb transcripts was observed, and a putative splicing strategy was described. The apparently tissue-restricted HERV-W long terminal repeat expression is discussed with respect to physiological and pathological contexts. ..
  46. Amarasinghe G, Bao Y, Basler C, Bavari S, Beer M, Bejerman N, et al. Taxonomy of the order Mononegavirales: update 2017. Arch Virol. 2017;162:2493-2504 pubmed publisher
    ..This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). ..
  47. B hne A, Zhou Q, Darras A, Schmidt C, Schartl M, Galiana Arnoux D, et al. Zisupton--a novel superfamily of DNA transposable elements recently active in fish. Mol Biol Evol. 2012;29:631-45 pubmed publisher
    ..To conclude, our analysis has uncovered a new superfamily of DNA transposons with potential roles in genome diversity and evolutionary innovation in fish and other organisms...
  48. Menard A, de los Santos P, Graindorge A, Cournoyer B. Architecture of Burkholderia cepacia complex sigma70 gene family: evidence of alternative primary and clade-specific factors, and genomic instability. BMC Genomics. 2007;8:308 pubmed
    ..aeruginosa and only previously reported to occur among the actinobacteria. ..