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  • 1
    Language: English
    In: Nucleic acids research, 05 May 2017, Vol.45(8), pp.4782-4795
    Description: Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori. We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial expression in H. pylori induces cell death. The synthesis of this toxin is prevented by the transcription of an antitoxin RNA, named IsoA1, expressed on the opposite strand of the toxin gene. We further reveal additional layers of post-transcriptional regulation that control toxin expression: (i) transcription of the aapA1 gene generates a full-length transcript whose folding impedes translation (ii) a 3΄ end processing of this message generates a shorter transcript that, after a structural rearrangement, becomes translatable (iii) but this rearrangement also leads to the formation of two stem-loop structures allowing formation of an extended duplex with IsoA1 via kissing-loop interactions. This interaction ensures both the translation inhibition of the AapA1 active message and its rapid degradation by RNase III, thus preventing toxin synthesis under normal growth conditions. Finally, a search for homologous mRNA structures identifies similar TA systems in a large number of Helicobacter and Campylobacter genomes.
    Keywords: Antitoxins -- Genetics ; Bacterial Proteins -- Genetics ; Bacterial Toxins -- Genetics ; Helicobacter Pylori -- Genetics ; RNA Folding -- Genetics ; RNA, Bacterial -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 2
    Language: English
    In: Nature, March 11, 2010, Vol.463(7286), p.250(6)
    Description: Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differential approach (dRNA-seq) selective for the 5' end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. We discovered hundreds of transcriptional start sites within operons, and opposite to annotated genes, indicating that complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. We also discovered an unexpected number of ~60 small RNAs including the e-subdivision counterpart of the regulatory 6S RNA and associated RNA products, and potential regulators of cis- and trans-encoded target messenger RNAs. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species.
    Keywords: Antisense Rna -- Analysis ; Gene Expression -- Analysis ; Transcription (Genetics) -- Analysis ; Helicobacter Pylori -- Genetic Aspects ; Helicobacter Pylori -- Physiological Aspects
    ISSN: 0028-0836
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  • 3
    In: Nature, 2010, Vol.464(7286), p.250
    Description: Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differential approach (dRNA-seq) selective for the 5' end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. We discovered hundreds of transcriptional start sites within operons, and opposite to annotated genes, indicating that complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. We also discovered an unexpected number of approximately 60 small RNAs including the epsilon-subdivision counterpart of the regulatory 6S RNA and associated RNA products, and potential regulators of cis- and trans-encoded target messenger RNAs. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species.
    Keywords: Gene Expression Profiling ; Genome, Bacterial -- Genetics ; Helicobacter Infections -- Microbiology ; Helicobacter Pylori -- Genetics ; RNA, Bacterial -- Genetics;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 4
    Language: French
    Description: Ces dernières années de nombreuses recherches ont montré l’importance des petits ARN dans la régulation de l’expression des gènes, chez tous les organismes vivants, des bactéries aux mammifères. Le projet de cette thèse était de recherche et d’identifier des petits ARN chez une bactérie pathogène pour l’homme, Helicobacter pylori (Hp). Cette bactérie colonise exclusivement l’estomac humain, un organe qui pendant longtemps a été considéré comme étant stérile, en raison du pH parfois très acide qui y règne. L’infection persistante de l’estomac humain causée par Hp est associée avec plusieurs pathologies gastriques tels que les gastrites, les ulcères peptiques, les cancers gastriques et les lymphomes du MALT. La moitié de la population est infectée par Hp, qui est responsable d’environ 1 million de décès par an à travers le monde, et de 6000 nouveaux cas de cancers gastrique par an en France. Au cours de ma thèse, j’ai travaillé en étroite collaboration avec le groupe du Pr. Jörg Vogel (RNA Biology, MPI, Berlin, Allemagne) pour développer une méthode rapide et efficace d’analyse du transcriptome complet d’Hp, en s’appuyant sur une nouvelle sur une technologie émergente de pyroséquençage haut-débit (HTPS 454 technology, Life Science, USA). Notre méthode de séquençage du transcriptome d’Hp à partir de banques enrichies en transcrits primaires (dRNA-seq), nous a permis d’identifier les sites d’initiation de la transcription (TSS) de milliers de d’ARN. Plus de la moitié de ces TSS ont été associés à des petits ARN non codants, de courte taille (de 50 à 250 nucléotides en moyenne), qui n’avaient jamais été découverts jusqu’alors, et dont les gènes sont localisés dans des régions intergéniques (sRNA) ou en antisens (asRNA) par rapport aux ORF précédemment annotées dans le génome d’Hp. Nos travaux ont également permis de mettre en évidence une forte activité de transcription antisens sur l’ensemble du génome de la bactérie, un phénomène déjà observé chez E. coli et les eucaryotes. Ainsi, au moins un TSS est localisé sur le brin opposé à 46 % des ORF et à 28% des régions « leaders » des précurseurs des ARNr 23S et 16S, et des ARNt. Enfin, l’approche dRNA-seq a permis l’identification de la première famille de toxines de type I (AapA) identifiée à ce jour chez Hp. Dans ces conditions normales de culture, la traduction de ces toxines est constitutivement réprimée par des petits ARN antisens (IsoA) qui ciblent les ARNm aapA par complémentarité de base. Malgré leur homologie avec des modules toxine-antitoxine identifiés chez d’autres bactéries, pour certaines impliquées dans la réponse aux stress, nous n’avons pas encore découvert les conditions dans lesquelles ces peptides aapA seraient exprimées chez Hp, et leur rôle biologique reste à élucider. In the past few years, small regulatory RNAs have emerged as an important class of post-transcriptional regulators of gene expression. Indeed they have been identified and/or predicted to exist in all species ranging from bacteria to mammals. The project of this thesis was to search for small non coding RNAs in a human pathogen: Helicobacter pylori (Hp). This bacterium exclusively colonizes the human stomach, an organ that until recently was thought to be sterile due to its extreme acidity. It is now established that persistent colonization by Hp is associated with various gastric pathologies including gastritis, peptic ulcer, gastric cancer and MALT lymphoma. Half of the human population is infected by Hp that is responsible for about 1 million deaths per year and around 6000 cases of gastric cancer in France. During my thesis we , in a close collaboration with the group of Joerg Vogel (RNA biology, MPI, Berlin, Germany) developed a rapid and efficient method to reveal the whole transcriptome of Hp based on recent advances in high-throughput pyrosequencing technologies (HTPS 454 technology, Life Science, USA). By using specifically enriched libraries in primary transcripts, our strategy allowed us to map thousand (1907) of transcription start sites (TSS) on the Hp genome. More than half of these TSS correspond to new short transcripts (non coding RNAs, between 50 and 250 nucleotides in length) that have never been annotated in this genome and that are localized both in intergenic regions (sRNA) and in regions antisense to annotated ORFs (asRNA). Analysis of associations between primary transcription start sites (pTSS) revealed more complexity in the Hp transcriptome than previously anticipated: around one third (27%) of pTSS belong to antisense transcripts (aTSS). The strikingly high degree of antisense transcription occurs, similar to E. coli and higher eukaryotes, across the entire Hp genome. Overall, at least one aTSS is linked to ~46% of all ORFs, ~28% of tRNAs, and the 5’ leaders of 23S and 16S rRNA precursors. Finally our dRNA-seq approach led us to identify the first family of putative type I toxins (AapA) in the Hp genome. Under normal growth conditions these toxins are constitutively repressed by a sophisticated antisense RNA-mediated (IsoA) mechanism. Despite their homology to other toxin-antitoxin modules previously described in other bacteria, we have not found physiological conditions under which these peptides are expressed and have yet to determine the biological significance (if any ?) of these suicide genes.
    Keywords: Helicobacter Pylori ; Petits Arn Régulateurs ; Séquençage Haut-Débit ; Transcriptome ; Helicobacter Pylori ; Small Regulatory Rna ; High-Throughput Sequencing ; Transcriptome
    Source: Networked Digital Library of Theses and Dissertations
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  • 5
    Language: English
    In: Intensive care medicine, December 2017, Vol.43(12), pp.1942-1943
    Description: Correction to: Intensive Care Med (2017) DOI 10.1007/s00134-017-4891-0.
    Keywords: Ventilation ; Ventilation ; Ventilation ; Weaning;
    ISSN: 03424642
    E-ISSN: 1432-1238
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  • 6
    Language: English
    In: Intensive care medicine, December 2017, Vol.43(12), pp.1793-1807
    Description: The relative merits of immediate extubation versus terminal weaning for mechanical ventilation withdrawal are controversial, particularly regarding the experience of patients and relatives. This prospective observational multicentre study (ARREVE) was done in 43 French ICUs to compare terminal weaning and immediate extubation, as chosen by the ICU team. Terminal weaning was a gradual decrease in the amount of ventilatory assistance and immediate extubation was extubation without any previous decrease in ventilatory assistance. The primary outcome was posttraumatic stress symptoms (Impact of Event Scale Revised, IES-R) in relatives 3 months after the death. Secondary outcomes were complicated grief, anxiety, and depression symptoms in relatives; comfort of patients during the dying process; and job strain in staff. We enrolled 212 (85.5%) relatives of 248 patients with terminal weaning and 190 relatives (90.5%) of 210 patients with immediate extubation. Immediate extubation was associated with airway obstruction and a higher mean Behavioural Pain Scale score compared to terminal weaning. In relatives, IES-R scores after 3 months were not significantly different between groups (31.9 ± 18.1 versus 30.5 ± 16.2, respectively; adjusted difference, -1.9; 95% confidence interval, -5.9 to 2.1; p = 0.36); neither were there any differences in complicated grief, anxiety, or depression scores. Assistant nurses had lower job strain scores in the immediate extubation group. Compared to terminal weaning, immediate extubation was not associated with differences in psychological welfare of relatives when each method constituted standard practice in the ICU where it was applied. Patients had more airway obstruction and gasps with immediate extubation. ClinicalTrials.gov identifier: NCT01818895.
    Keywords: Critical Care ; Ethics ; Immediate Extubation ; Mechanical Ventilation ; Terminal Weaning ; Treatment Limitation ; Airway Extubation -- Methods ; Critical Care -- Methods ; Family -- Psychology ; Stress Disorders, Post-Traumatic -- Psychology ; Ventilator Weaning -- Methods
    ISSN: 03424642
    E-ISSN: 1432-1238
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  • 7
    Language: English
    In: Intensive care medicine, September 2019, Vol.45(9), pp.1252-1261
    Description: Bereavement research has helped to improve end-of-life practices in the ICU. However, few studies have explored bereaved relatives experience of research participation in this context. We aimed to explore the experience of bereaved relatives' participation in the ARREVE study which included three telephone follow-up calls to complete several quantitative tools. Volunteer relatives who participated in the 12-month follow-up call completed a questionnaire about research participation that included ten open-ended questions so that respondents could use their own words and thoughts. These open-ended questions were analyzed using qualitative analysis that examines themes within the data. 175/311 relatives completed the questionnaire. Three themes were derived from the thematic analysis: (1) struggling: reactivation of emotional distress associated with the ICU experience and the loss is frequent, specifically during the 1st follow-up call. (2) Resilience: as time goes by, research participation becomes increasingly positive. The calls are a help both in giving meaning to the relatives' experience and in accepting the loss. (3) Recognition: research calls can compensate for the absence of support during bereavement. Although some emotional difficulties must be acknowledged, bereavement research is overall associated with benefits, by facilitating emotional adjustments, meaning-making and resilience. Lack of support and social isolation during bereavement are frequent experiences, revealing that support strategies for bereaved relatives should be developed after the loss of a loved one in the ICU.
    Keywords: Bereavement Research ; End-of-Life ; Family Experience ; Qualitative Study
    ISSN: 03424642
    E-ISSN: 1432-1238
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  • 8
    Language: English
    In: Critical Care, April 5, 2019, Vol.23(1)
    Description: Background Microaspiration of gastric and oropharyngeal secretions is the main mechanism of entry of bacteria into the lower respiratory tract in intubated critically ill patients. The aim of this study is to determine the impact of enteral nutrition, as compared with...
    Keywords: Clinical Trials – Analysis ; Pneumonia – Care and Treatment ; Respiratory Tract Diseases – Care and Treatment
    ISSN: 1364-8535
    E-ISSN: 1466609X
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  • 9
    Language: English
    In: Annals of Intensive Care, 2017, Vol.7(Supplement 1), pp.1-104
    Keywords: Medicine & Public Health ; Intensive / Critical Care Medicine ; Emergency Medicine ; Anesthesiology ; Medicine;
    E-ISSN: 2110-5820
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  • 10
    In: Critical Care, 2019, Vol.23
    Description: Background Microaspiration of gastric and oropharyngeal secretions is the main mechanism of entry of bacteria into the lower respiratory tract in intubated critically ill patients. The aim of this study is to determine the impact of enteral nutrition, as compared with parenteral nutrition, on abundant microaspiration of gastric contents and oropharyngeal secretions. Methods Planned ancillary study of the randomized controlled multicenter NUTRIREA2 trial. Patients with shock receiving invasive mechanical ventilation were randomized to receive early enteral or parenteral nutrition. All tracheal aspirates were collected during the 48 h following randomization. Abundant microaspiration of gastric contents and oropharyngeal secretions was defined as the presence of significant levels of pepsin (〉 200 ng/ml) and salivary amylase (〉 1685 UI/ml) in 〉 30% of tracheal aspirates. Results A total of 151 patients were included (78 and 73 patients in enteral and parenteral nutrition groups, respectively), and 1074 tracheal aspirates were quantitatively analyzed for pepsin and amylase. Although vomiting rate was significantly higher (31% vs 15%, p  = 0.016), constipation rate was significantly lower (6% vs 21%, p  = 0.010) in patients with enteral than in patients with parenteral nutrition. No significant difference was found regarding other patient characteristics. The percentage of patients with abundant microaspiration of gastric contents was significantly lower in enteral than in parenteral nutrition groups (14% vs 36%, p  = 0.004; unadjusted OR 0.80 (95% CI 0.69, 0.93), adjusted OR 0.79 (0.76, 0.94)). The percentage of patients with abundant microaspiration of oropharyngeal secretions was significantly higher in enteral than in parenteral nutrition groups (74% vs 54%, p  = 0.026; unadjusted OR 1.21 (95% CI 1.03, 1.44), adjusted OR 1.23 (1.01, 1.48)). No significant difference was found in percentage of patients with ventilator-associated pneumonia between enteral (8%) and parenteral (10%) nutrition groups (HR 0.78 (0.26, 2.28)). Conclusions Our results suggest that enteral and parenteral nutrition are associated with high rates of microaspiration, although oropharyngeal microaspiration was more common with enteral nutrition and gastric microaspiration was more common with parenteral nutrition. Trial registration ClinicalTrials.gov, NCT03411447 . Registered 18 July 2017. Retrospectively registered.
    Keywords: Research ; Microaspiration ; Gastric Contents ; Oropharyngeal Secretions ; Pneumonia ; Pathophysiology ; Critical Care
    ISSN: 1364-8535
    E-ISSN: 1466-609X
    Source: U.S. National Library of Medicine (NIH/NLM)
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