La divergence adaptative chez le grand corégone (Coregonus clupeaformis, Salmonidae) : portrait intégré de l'évolution de l'expression génique

Au cours des 40 dernières années, il est devenu de plus en plus clair que la divergence d'expression génique est l'un des mécanismes impliqués dans l'émergence de nouvelles espèces. Chez le grand corégone (Coregonus clupeaformis), des expériences réalisées sur puce à ADN ont mené à l'identification de gènes candidats potentiellement impliqués dans l'évolution répétée du corégone nain limnétique, qui est extrêmement différent du corégone normal benthique en termes d'histoire de vie, de morphologie, de métabolisme et de comportement, malgré un temps de divergence de seulement 15 000 ans. Dans ce contexte, le premier objectif de cette thèse était de tester l'hypothèse selon laquelle l'adaptation parallèle à la niche limnétique chez les corégoninés est associée à un parallélisme d'expression des gènes. Une divergence d'expression parallèle entre paires d'espèces de corégone pour trois gènes candidats a été observée, supportant ainsi l'hypothèse selon laquelle la sélection naturelle divergente joue un rôle important dans l'évolution de ces poissons. Le second objectif était d'évaluer la divergence transcriptomique entre nains et normaux telle que mesurée par séquençage à haut débit en plus de tester la corrélation entre la divergence d'expression et de séquence codante. Les résultats ont démontré qu'une telle corrélation était inexistante. Il y aurait donc découplage évolutif des séquences codantes et régulatrices dans la divergence adaptative du grand corégone. Pourtant, certains gènes, tels que la malate déshydrogénase (MDH), avaient une divergence significative d'expression et de séquence. La construction et le criblage d'une banque génomique BAC ont permis de sequencer en entier certains gènes candidats, dont MDH. Le dernier objectif était donc d'identifier des signatures de sélection naturelle dans les séquences codante et régulatrice de ce gène. Alors que sa région codante était clairement sous sélection purificatrice, un site polymorphe dans sa région régulatrice avait des fréquences d'alleles divergentes de façon parallèle parmi plusieurs paires sympatriques de corégones nord-américains et européens. De plus, le génotype pour ce site semblait associé au niveau d'expression de MDH. Ces résultats appuient le rôle de la sélection naturelle dans l'évolution de l'expression génique chez les paires d'espèces de corégone

Tolerancia a falhas em sistemas de agentes moveis

Orientador: Ricardo de Oliveira AnidoDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Agente móvel é um processo que se desloca autonomamente através da rede, executando operações locais à máquina hospedeira. Agentes constituem uma solução alternativa ao paradigma cliente-servidor. A autonomia do agente móvel, entretanto, faz necessária a revisão dos conceitos de tolerância a falhas a fim de garantir confiabilidade em sua operação, evitando que a parada do agente resulte em inconsistências no sistema. Este trabalho apresenta um protocolo para tolerar falhas do tipo falha-e-pára e de comunicaçãoAbstract: Mobile agent is a process capable of roaming autonomously through the network, executing operation locally to a host. Agents can be employed to perform some traditional tasks. In order to enforce dependability in this new paradigm we present a protocol to coordinate a replicated agent system capable of tolerating failstop and communication faultsMestradoCiência da ComputaçãoMestre em Ciência da Computaçã

Visages du slam au Québec histoire et actualisations d'un mouvement poétique et social en émergence

Au sein de la culture lettrée qui est la nôtre, il semble que la littérature soit d'emblée associée à l'écrit. Aussi, les manifestations contemporaines de la littérature orale sont-elles souvent laissées pour compte par les études littéraires, voire dévaluées par l'institution. Or, à une époque où l'on observe une importante résurgence de l'oralité en littérature, il apparaît d'autant plus pertinent de se pencher sur ses nouvelles formes, qui relèvent tout autant de la tradition que d'une modernité caractérisée par l'interdisciplinarité et l'évolution technologique. Dans la mesure où le développement des cultural studies, à la lumière d'une définition extensive de la culture, nous permet de nous intéresser à des pratiques qui n'appartiennent pas à la"haute culture", nous avons pris pour objet le mouvement de slam, qui participe précisément de cette résurgence contemporaine de l'oralité et qui émane, de surcroît, d'une culture"d'en bas". C'est, plus particulièrement, son actualisation québécoise qui constitue le coeur de ce mémoire, bien qu'il ait semblé nécessaire d'en dresser un portrait plus large, vu la méconnaissance relative du phénomène. C'est en 2006 que le mouvement - qui a pris racine au milieu des années 80 aux États-Unis - s'est installé dans la culture francophone du Québec, notamment sous l'impulsion de sa popularisation en France. Il y acquiert rapidement un visage pluriel, fondé sur une ambiguïté quant à la définition même du terme"slam" : s'il désigne à la base un mouvement poétique et social, de même qu'un cadre particulier structurant la pratique de la poésie performée (le slam de poésie), il en vient rapidement à être assimilé à un style, du fait de sa récupération par la culture de masse. Dans un premier chapitre, nous nous attardons à l'histoire du mouvement, ainsi qu'à son évolution aux États-Unis et en France. Dans un deuxième chapitre, nous en retraçons la brève histoire au Québec, avant de dégager les caractéristiques propres de son ancrage québécois. Dans un troisième chapitre, nous analysons la couverture journalistique du slam au Québec, ainsi que sa relation complexe avec l'institution littéraire, et terminons par l'analyse de quatre oeuvres québécoises qui se réclament du slam sans pourtant en adopter le cadre original, afin de cerner leur positionnement en regard du mouvement, de même que les enjeux de la diffusion de l'oralité qu'elles mettent au jour, à l'époque de sa reproductibilité technique

Genomics of antibiotic-resistance prediction in Pseudomonas aeruginosa

Antibiotic resistance is a worldwide health issue spreading quickly among human and animal pathogens, as well as environmental bacteria. Misuse of antibiotics has an impact on the selection of resistant bacteria, thus contributing to an increase in the occurrence of resistant genotypes that emerge via spontaneous mutation or are acquired by horizontal gene transfer. There is a specific and urgent need not only to detect antimicrobial resistance but also to predict antibiotic resistance in silico. We now have the capability to sequence hundreds of bacterial genomes per week, including assembly and annotation. Novel and forthcoming bioinformatics tools can predict the resistome and the mobilome with a level of sophistication not previously possible. Coupled with bacterial strain collections and databases containing strain metadata, prediction of antibiotic resistance and the potential for virulence are moving rapidly toward a novel approach in molecular epidemiology. Here, we present a model system in antibiotic-resistance prediction, along with its promises and limitations. As it is commonly multidrug resistant, Pseudomonas aeruginosa causes infections that are often difficult to eradicate. We review novel approaches for genotype prediction of antibiotic resistance. We discuss the generation of microbial sequence data for real-time patient management and the prediction of antimicrobial resistance

Genes required for free phage production are essential for pseudomonas aeruginosa chronic lung infections

The opportunistic pathogen Pseudomonas aeruginosa causes chronic lung infection in patients with cystic fibrosis. The Liverpool Epidemic Strain LESB58 is highly resistant to antibiotics, transmissible, and associated with increased morbidity and mortality. Its genome contains 6 prophages and 5 genomic islands. We constructed a polymerase chain reaction (PCR)-based signature-tagged mutagenesis library of 9216 LESB58 mutants and screened the mutants in a rat model of chronic lung infection. A total of 162 mutants were identified as defective for in vivo maintenance, with 11 signature-tagged mutagenesis mutants having insertions in prophage and genomic island genes. Many of these mutants showed both diminished virulence and reduced phage production. Transcription profiling by quantitative PCR and RNA-Seq suggested that disruption of these prophages had a widespread trans-acting effect on the transcriptome. This study demonstrates that temperate phages play a pivotal role in the establishment of infection through modulation of bacterial host gene expression

Comparative genomics of isolates of a pseudomonas aeruginosa epidemic strain associated with chronic lung infections of cystic fibrosis patients

Pseudomonas aeruginosa is the main cause of fatal chronic lung infections among individuals suffering from cystic fibrosis (CF). During the past 15 years, particularly aggressive strains transmitted among CF patients have been identified, initially in Europe and more recently in Canada. The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from the United Kingdom and Canada representing different virulence characteristics in order to: (1) associate comparative genomics results with virulence factor variability and (2) identify genomic and/or phenotypic divergence between the two geographical locations. We performed phenotypic characterization of pyoverdine, pyocyanin, motility, biofilm formation, and proteolytic activity. We also assessed the degree of virulence using the Dictyostelium discoideum amoeba model. Comparative genomics analysis revealed at least one large deletion (40-50 kb) in 6 out of the 7 isolates compared to the reference genome of LESB58. These deletions correspond to prophages, which are known to increase the competitiveness of LESB58 in chronic lung infection. We also identified 308 non-synonymous polymorphisms, of which 28 were associated with virulence determinants and 52 with regulatory proteins. At the phenotypic level, isolates showed extensive variability in production of pyocyanin, pyoverdine, proteases and biofilm as well as in swimming motility, while being predominantly avirulent in the amoeba model. Isolates from the two continents were phylogenetically and phenotypically undistinguishable. Most regulatory mutations were isolate-specific and 29% of them were predicted to have high functional impact. Therefore, polymorphism in regulatory genes is likely to be an important basis for phenotypic diversity among LES isolates, which in turn might contribute to this strain's adaptability to varying conditions in the CF lung

Prophage induction reduces Shiga toxin producing \u3ci\u3eEscherichia coli\u3c/i\u3e (STEC) and Salmonella enterica on tomatoes and spinach: A model study

Fresh produce is increasingly implicated in foodborne outbreaks and most fresh produce is consumed raw, emphasizing the need to develop non-thermal methods to control foodborne pathogens. This study investigates bacterial cell lysis through induction of prophages as a novel approach to control foodborne bacterial pathogens on fresh produce. Shiga toxin producing Escherichia coli (STEC) and Salmonella enterica isolates were exposed to different prophage inducers (i.e. mitomycin C or streptonigrin) and growth of the cells was monitored by measuring the optical density (OD600) during incubation at 37C. Beginning at three hours after addition of the inducer, all concentrations (0.5, 1, 2 mg/mL) of mitomycin C, or 2 mg/mL streptonigrin significantly reduced the OD600 in broth cultures, in a concentration dependent manner, relative to cultures where no inducer was added. PCR confirmed bacterial release of induced bacteriophages and demonstrated that a single compound could successfully induce multiple types of prophages. The ability of mitomycin C to induce prophages in STEC O157:H7 and in S. enterica (serovars Typhimurium and Newport) on fresh produce was evaluated by inoculating red greenhouse tomatoes or spinach leaves with 5 x 107 and 5 x 108 colony forming units, respectively. After allowing time for the inoculum to dry on the fresh produce samples, 6 mg/mL mitomycin C was sprayed onto each sample, while control samples were sprayed with water. Following overnight incubation at 4C, the bacterial cells were recovered and plate counts were performed. A 3 log reduction in STEC O157:H7 cells was observed on tomatoes sprayed with mitomycin C compared to those sprayed with water, while a 1 log reduction was obtained on spinach. Similarly, spraying mitomycin C on tomatoes and spinach inoculated with S. enterica isolates resulted in a 1-1.5 log and 2 log reduction, respectively. These findings serve as a proof of concept that prophage induction can effectively control bacterial foodborne pathogens on fresh produce

Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae

The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacteria populations occupying different niches is not well understood. Streptococcus agalactiae is an important bacterial pathogen that has a taxonomically diverse host range making it an excellent model system to study these processes. Here we analyze a global set of 901 genome sequences from nine diverse host species to advance our understanding of these processes. Bayesian clustering analysis delineated twelve major populations that closely aligned with niches. Comparative genomics revealed extensive gene gain/loss among populations and a large pan-genome of 9,527 genes, which remained open and was strongly partitioned among niches. As a result, the biochemical characteristics of eleven populations were highly distinctive (significantly enriched). Positive selection was detected and biochemical characteristics of the dispensable genes under selection were enriched in ten populations. Despite the strong gene partitioning, phylogenomics detected gene spillover. In particular, tetracycline resistance (which likely evolved in the human-associated population) from humans to bovine, canines, seals, and fish, demonstrating how a gene selected in one host can ultimately be transmitted into another, and biased transmission from humans to bovines was confirmed with a Bayesian migration analysis. Our findings show high bacterial genome plasticity acting in balance with selection pressure from distinct functional requirements of niches that is associated with an extensive and highly partitioned dispensable genome, likely facilitating continued and expansive adaptation

O que lembra o paciente com TCE sobre o período de hospitalização?

Traumatic brain injured (TBI) patients with different trauma severity were analyzed about their recollection concerning the period of hospitalization. The study was carried out in the Head Injury Outpatient Clinic at the Central Institute of the FMUSP Hospital including 45 conscious patients able to sustain an interview. Most patients were male, young adults with the major cause of trauma such as traffic accidents and falls. Most patients (86%) reported uncosciouness state of different time duration in their hospitalization period and were unable to remember anything related to that period. The predominant recollection reported by the patients who never had consciousness decreased after the trauma and that ones who had it but awoke during the hospitalization were: seeing, feeling, hearing, and reacting either to sounds and procedures.Se estudiaron los recuerdos que enfermos de TCE de distinta gravedad tienen del periodo de hospitalización. El estudio fue realizado en el servicio de consulta externa de traumatismo del Cráneo del Instituto Central del HC - FMUSP y fueron entrevistados 45 enfermos conscientes y capaces de contestar preguntas. La mayoría de los enfermos eran del sexo masculino, jóvenes y víctimas de accidentes de tránsito y caídas. La mayoría de los enfermos (86%) dijeron no estar despiertos en todos los momentos y que no se recordaban de nada del periodo. Los recuerdos relatados por los que estuvieron despiertos y también por aquellos que se despertaron durante la hospitalización, eran sobre todo mirar, sentir, oír o reaccionar a sonidos y procedimientos.Trata-se da análise das lembranças do período de internação referidas pelos pacientes que sofreram TCE de diferentes gravidades. O estudo foi realizado no ambulatório de Trauma de Crânio do Instituto Central do HC-FMUSP com amostra de 45 pacientes conscientes e capazes de manter entrevista. Predominaram pacientes do sexo masculino, adultos jovens, que tiveram como causas acidentes de trânsito e quedas. A maioria (86,0%) informou ter ficado desacordada em diferentes tempos de duração e nada recordar deste período. Naqueles que sempre estiveram alertas ou que acordaram ainda internados as lembranças relacionaram-se com ter visto, sentido, ouvido ou reagido a sons e procedimentos