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Personne :
Devillers, Rodolphe

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Devillers

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Rodolphe

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Université Laval. Faculté de foresterie, de géographie et de géomatique

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ncf11859861

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Voici les éléments 1 - 9 sur 9
  • PublicationAccès libre
    Conception d'un système multidimensionnel d'information sur la qualité des données géospatiales
    (2004) Devillers, Rodolphe; Bédard, Yvan; Jeansoulin, Robert
    L’information géographique est maintenant un produit de masse fréquemment manipulé par des utilisateurs non-experts en géomatique qui ont peu ou pas de connaissances de la qualité des données qu’ils utilisent. Ce contexte accroît significativement les risques de mauvaise utilisation des données et ainsi les risques de conséquence néfaste résultant de ces mauvaises utilisations. Cette thèse vise à fournir à des utilisateurs experts ou des experts en qualité une approche leur permettant d’évaluer la qualité des données et ainsi être à même de conseiller des utilisateurs non-experts dans leur utilisation des données. Cette approche se base sur une structuration des données de qualité dans une base de données multidimensionnelle et une communication dynamique et contextuelle utilisant des indicateurs de qualité affichés dans un système SOLAP (Spatial On-Line Analytical Processing) combiné à un système d’information géographique.
  • PublicationRestreint
    The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus
    (Wiley-Blackwell, 2014-06-26) Carte, Jason; Devillers, Rodolphe; Christopher, Ross T.; Moineau, Sylvain; Smith, Justin T.; Olson, Sara; Glover, Claiborne; Graveley, Brenton R.; Terns, Rebecca M.; Terns, Michael P.
    CRISPR‐Cas systems are small RNA‐based immune systems that protect prokaryotes from invaders such as viruses and plasmids. We have investigated the features and biogenesis of the CRISPR (cr)RNAs in Streptococcus thermophilus (Sth) strain DGCC7710, which possesses four different CRISPR‐Cas systems including representatives from the three major types of CRISPR‐Cas systems. Our results indicate that the crRNAs from each CRISPR locus are specifically processed into divergent crRNA species by Cas proteins (and non‐coding RNAs) associated with the respective locus. We find that the Csm Type III‐A and Cse Type I–E crRNAs are specifically processed by Cas6 and Cse3 (Cas6e), respectively, and retain an 8‐nucleotide CRISPR repeat sequence tag 5′ of the invader‐targeting sequence. The Cse Type I–E crRNAs also retain a 21‐nucleotide 3′ repeat tag. The crRNAs from the two Csn Type II‐A systems in Sth consist of a 5′‐truncated targeting sequence and a 3′ tag; however, these are distinct in size between the two. Moreover, the Csn1 (Cas9) protein associated with one Csn locus functions specifically in the production of crRNAs from that locus. Our findings indicate that multiple CRISPR‐Cas systems can function independently in crRNA biogenesis within a given organism – an important consideration in engineering coexisting CRISPR‐Cas pathways.
  • PublicationRestreint
    Phage response to CRISPR-encoded resistance in Streptococcus thermophilus
    (American Society for Microbiology, 2008-02-01) Garneau, Josiane; Labonté, Jessica.; Devillers, Rodolphe; Moineau, Sylvain; Fremaux, Christophe; Deveau, Hélène; Boyaval, Patrick; Romero, Dennis A; Horvath, Philippe
    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated genes are linked to a mechanism of acquired resistance against bacteriophages. Bacteria can integrate short stretches of phage-derived sequences (spacers) within CRISPR loci to become phage resistant. In this study, we further characterized the efficiency of CRISPR1 as a phage resistance mechanism in Streptococcus thermophilus. First, we show that CRISPR1 is distinct from previously known phage defense systems and is effective against the two main groups of S. thermophilus phages. Analyses of 30 bacteriophage-insensitive mutants of S. thermophilus indicate that the addition of one new spacer in CRISPR1 is the most frequent outcome of a phage challenge and that the iterative addition of spacers increases the overall phage resistance of the host. The added new spacers have a size of between 29 to 31 nucleotides, with 30 being by far the most frequent. Comparative analysis of 39 newly acquired spacers with the complete genomic sequences of the wild-type phages 2972, 858, and DT1 demonstrated that the newly added spacer must be identical to a region (named proto-spacer) in the phage genome to confer a phage resistance phenotype. Moreover, we found a CRISPR1-specific sequence (NNAGAAW) located downstream of the proto-spacer region that is important for the phage resistance phenotype. Finally, we show through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1.
  • PublicationAccès libre
    CRISPR provides acquired resistance against viruses in prokaryotes
    (American Association for the Advancement of Science, 2007-03-23) Laporte, Mélissa; Fremaux, Christophe; Devillers, Rodolphe; Moineau, Sylvain; Deveau, Hélène; Boyaval, Patrick; Romero, Dennis A.; Horvath, Philippe
    Clustered regularly interspaced short palindromic repeats (CRISPR) are a distinctive feature of the genomes of most Bacteria and Archaea and are thought to be involved in resistance to bacteriophage. We found that following viral challenge, bacteria integrated new spacers derived from phage genomic sequences. Removal or addition of particular spacers modified the phage-resistance phenotype of the cell. Thus, CRISPR, together with associated cas genes, provided resistance against phages, whereby specificity is determined by spacer/phage sequence similarity.
  • PublicationAccès libre
    Immune loss as a driver of coexistence during host-phage coevolution
    (Nature Pub. Group, 2018-01-12) Weissman, Jake L.; Devillers, Rodolphe; Holmes, Rayshawn; Moineau, Sylvain; Fagan, William Frederic; Levin, Bruce R.; Johnson, Philip L. F.
    Bacteria and their viral pathogens face constant pressure for augmented immune and infective capabilities, respectively. Under this reciprocally imposed selective regime, we expect to see a runaway evolutionary arms race, ultimately leading to the extinction of one species. Despite this prediction, in many systems host and pathogen coexist with minimal coevolution even when well-mixed. Previous work explained this puzzling phenomenon by invoking fitness tradeoffs, which can diminish an arms race dynamic. Here we propose that the regular loss of immunity by the bacterial host can also produce host-phage coexistence. We pair a general model of immunity with an experimental and theoretical case study of the CRISPR-Cas immune system to contrast the behavior of tradeoff and loss mechanisms in well-mixed systems. We find that, while both mechanisms can produce stable coexistence, only immune loss does so robustly within realistic parameter ranges.
  • PublicationAccès libre
    The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA
    (Macmillan, 2010-11-03) Garneau, Josiane; Devillers, Rodolphe; Moineau, Sylvain; Romero, Dennis A.; Dupuis, Marie-Ève; Magadán, Alfonso H.; Boyaval, Patrick; Villion, Manuela; Fremaux, Christophe; Horvath, Philippe
    Bacteria and Archaea have developed several defence strategies against foreign nucleic acids such as viral genomes and plasmids. Among them, clustered regularly interspaced short palindromic repeats (CRISPR) loci together with cas (CRISPR-associated) genes form the CRISPR/Cas immune system, which involves partially palindromic repeats separated by short stretches of DNA called spacers, acquired from extrachromosomal elements. It was recently demonstrated that these variable loci can incorporate spacers from infecting bacteriophages and then provide immunity against subsequent bacteriophage infections in a sequence-specific manner. Here we show that the Streptococcus thermophilus CRISPR1/Cas system can also naturally acquire spacers from a self-replicating plasmid containing an antibiotic-resistance gene, leading to plasmid loss. Acquired spacers that match antibiotic-resistance genes provide a novel means to naturally select bacteria that cannot uptake and disseminate such genes. We also provide in vivo evidence that the CRISPR1/Cas system specifically cleaves plasmid and bacteriophage double-stranded DNA within the proto-spacer, at specific sites. Our data show that the CRISPR/Cas immune system is remarkably adapted to cleave invading DNA rapidly and has the potential for exploitation to generate safer microbial strains.
  • PublicationRestreint
    Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus.
    (American Society for Microbiology., 2008-02-01) Horvath, Philippe; Devillers, Rodolphe; Romero, Dennis A.; Moineau, Sylvain; Coûté-Monvoisin, Anne-Claire; Deveau, Hélène; Boyaval, Patrick; Fremaux, Christophe
    Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in prokaryotes that provide acquired immunity against foreign genetic elements. Here, we characterize a novel Streptococcus thermophilus locus, CRISPR3, and experimentally demonstrate its ability to integrate novel spacers in response to bacteriophage. Also, we analyze CRISPR diversity and activity across three distinct CRISPR loci in several S. thermophilus strains. We show that both CRISPR repeats and cas genes are locus specific and functionally coupled. A total of 124 strains were studied, and 109 unique spacer arrangements were observed across the three CRISPR loci. Overall, 3,626 spacers were analyzed, including 2,829 for CRISPR1 (782 unique), 173 for CRISPR2 (16 unique), and 624 for CRISPR3 (154 unique). Sequence analysis of the spacers revealed homology and identity to phage sequences (77%), plasmid sequences (16%), and S. thermophilus chromosomal sequences (7%). Polymorphisms were observed for the CRISPR repeats, CRISPR spacers, cas genes, CRISPR motif, locus architecture, and specific sequence content. Interestingly, CRISPR loci evolved both via polarized addition of novel spacers after exposure to foreign genetic elements and via internal deletion of spacers. We hypothesize that the level of diversity is correlated with relative CRISPR activity and propose that the activity is highest for CRISPR1, followed by CRISPR3, while CRISPR2 may be degenerate. Globally, the dynamic nature of CRISPR loci might prove valuable for typing and comparative analyses of strains and microbial populations. Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes
  • PublicationAccès libre
    Evolution and classification of the CRISPR/Cas systems
    (Nature Publishing Group, 2011-05-09) Makarova, Kira S.; Devillers, Rodolphe; Haft, Daniel H.; Moineau, Sylvain; Brouns, Stan J. J.; Charpentier, Emmanuelle; Horvath, Philippe; Mojica, Francisco Juan Martínez; Wolf, Yuri I.; Yakunin, Alexander F.; Oost, John van der; Koonin, Eugene V.
    The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR–Cas systems and Cas proteins. Three major types of CRISPR–Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR–Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR–cas loci.
  • PublicationAccès libre
    The population and evolutionary dynamics of phage and bacteria with CRISPR–mediated immunity
    (Public Library of Science, 2013-03-14) Levin, Bruce R.; Devillers, Rodolphe; Moineau, Sylvain; Bushman, Mary
    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), together with associated genes (cas), form the CRISPR–cas adaptive immune system, which can provide resistance to viruses and plasmids in bacteria and archaea. Here, we use mathematical models, population dynamic experiments, and DNA sequence analyses to investigate the host–phage interactions in a model CRISPR–cas system, Streptococcus thermophilus DGCC7710 and its virulent phage 2972. At the molecular level, the bacteriophage-immune mutant bacteria (BIMs) and CRISPR–escape mutant phage (CEMs) obtained in this study are consistent with those anticipated from an iterative model of this adaptive immune system: resistance by the addition of novel spacers and phage evasion of resistance by mutation in matching sequences or flanking motifs. While CRISPR BIMs were readily isolated and CEMs generated at high rates (frequencies in excess of 10−6), our population studies indicate that there is more to the dynamics of phage–host interactions and the establishment of a BIM–CEM arms race than predicted from existing assumptions about phage infection and CRISPR–cas immunity. Among the unanticipated observations are: (i) the invasion of phage into populations of BIMs resistant by the acquisition of one (but not two) spacers, (ii) the survival of sensitive bacteria despite the presence of high densities of phage, and (iii) the maintenance of phage-limited communities due to the failure of even two-spacer BIMs to become established in populations with wild-type bacteria and phage. We attribute (i) to incomplete resistance of single-spacer BIMs. Based on the results of additional modeling and experiments, we postulate that (ii) and (iii) can be attributed to the phage infection-associated production of enzymes or other compounds that induce phenotypic phage resistance in sensitive bacteria and kill resistant BIMs. We present evidence in support of these hypotheses and discuss the implications of these results for the ecology and (co)evolution of bacteria and phage.