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Search Results: 1 - 10 of 3044 matches for " Pascal Barbry "
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Genomotyping of Coxiella burnetii Using Microarrays Reveals a Conserved Genomotype for Hard Tick Isolates
Quentin Leroy, Fabrice Armougom, Pascal Barbry, Didier Raoult
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0025781
Abstract: C. burnetii is a Gram-negative intracellular Y-proteobacteria that causes the zoonotic disease Q fever. Q fever can manifest as an acute or chronic illness. Different typing methods have been previously developed to classify C. burnetii isolates to explore its pathogenicity. Here, we report a comprehensive genomotyping method based on the presence or absence of genes using microarrays. The genomotyping method was then tested in 52 isolates obtained from different geographic areas, different hosts and patients with different clinical manifestations. The analysis revealed the presence of 10 genomotypes organized into 3 groups, with a topology congruent with that obtained through multi-spacer typing. We also found that only 4 genomotypes were specifically associated with acute Q fever, whereas all of the genomotypes could be associated to chronic human infection. Serendipitously, the genomotyping results revealed that all hard tick isolates, including the Nine Mile strain, belong to the same genomotype.
Early Gene Expression in Wounded Human Keratinocytes Revealed by DNA Microarray Analysis
Manal A. Dayem,Chimène Moreilhon,Laurent Turchi,Virginie Magnone,Richard Christen,Gilles Ponzio,Pascal Barbry
Comparative and Functional Genomics , 2003, DOI: 10.1002/cfg.239
Abstract: Wound healing involves several steps: spreading of the cells, migration and proliferation. We have profiled gene expression during the early events of wound healing in normal human keratinocytes with a home-made DNA microarray containing about 1000 relevant human probes. An original wounding machine was used, that allows the wounding of up to 40% of the surface of a confluent monolayer of cultured cells grown on a Petri dish (compared with 5% with a classical ‘scratch’ method). The two aims of the present study were: (a) to validate a limited number of genes by comparing the expression levels obtained with this technique with those found in the literature; (b) to combine the use of the wounding machine with DNA microarray analysis for large-scale detection of the molecular events triggered during the early stages of the wound-healing process. The time-courses of RNA expression observed at 0.5, 1.5, 3, 6 and 15 h after wounding for genes such as c-Fos, c-Jun, Egr1, the plasminogen activator PLAU (uPA) and the signal transducer and transcription activator STAT3, were consistent with previously published data. This suggests that our methodologies are able to perform quantitative measurement of gene expression. Transcripts encoding two zinc finger proteins, ZFP36 and ZNF161, and the tumour necrosis factor α-induced protein TNFAIP3, were also overexpressed after wounding. The role of the p38 mitogen-activated protein kinase (p38MAPK) in wound healing was shown after the inhibition of p38 by SB203580, but our results also suggest the existence of surrogate activating pathways.
Coxiella burnetii Transcriptional Analysis Reveals Serendipity Clusters of Regulation in Intracellular Bacteria
Quentin Leroy,Kevin Lebrigand,Fabrice Armougom,Pascal Barbry,Richard Thiéry,Didier Raoult
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015321
Abstract: Coxiella burnetii, the causative agent of the zoonotic disease Q fever, is mainly transmitted to humans through an aerosol route. A spore-like form allows C. burnetii to resist different environmental conditions. Because of this, analysis of the survival strategies used by this bacterium to adapt to new environmental conditions is critical for our understanding of C. burnetii pathogenicity. Here, we report the early transcriptional response of C. burnetii under temperature stresses. Our data show that C. burnetii exhibited minor changes in gene regulation under short exposure to heat or cold shock. While small differences were observed, C. burnetii seemed to respond similarly to cold and heat shock. The expression profiles obtained using microarrays produced in-house were confirmed by quantitative RT-PCR. Under temperature stresses, 190 genes were differentially expressed in at least one condition, with a fold change of up to 4. Globally, the differentially expressed genes in C. burnetii were associated with bacterial division, (p)ppGpp synthesis, wall and membrane biogenesis and, especially, lipopolysaccharide and peptidoglycan synthesis. These findings could be associated with growth arrest and witnessed transformation of the bacteria to a spore-like form. Unexpectedly, clusters of neighboring genes were differentially expressed. These clusters do not belong to operons or genetic networks; they have no evident associated functions and are not under the control of the same promoters. We also found undescribed but comparable clusters of regulation in previously reported transcriptomic analyses of intracellular bacteria, including Rickettsia sp. and Listeria monocytogenes. The transcriptomic patterns of C. burnetii observed under temperature stresses permits the recognition of unpredicted clusters of regulation for which the trigger mechanism remains unidentified but which may be the result of a new mechanism of epigenetic regulation.
Comparative genomic analysis of Tropheryma whipplei strains reveals that diversity among clinical isolates is mainly related to the WiSP proteins
My-Van La, Nicolas Crapoulet, Pascal Barbry, Didier Raoult, Patricia Renesto
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-349
Abstract: The results revealed a limited genetic variation among the T. whipplei isolates, with at most 2.24% of the probes exhibiting differential hybridization against the Twist strain. The main variation was found in genes encoding the WiSP membrane protein family. This work also demonstrated a 19.2 kb-pair deletion within the T. whipplei DIG15 strain. This deletion occurs in the same region as the previously described large genomic rearrangement between Twist and TW08/27. Thus, this can be considered as a major hot-spot for intra-specific T. whipplei differentiation. Analysis of this deleted region confirmed the role of WND domains in generating T. whipplei diversity.This work provides the first comprehensive genomic comparison of several T. whipplei isolates. It reveals that clinical isolates originating from various geographic and biological sources exhibit a high conservation rate, indicating that T. whipplei rarely interacts with exogenous DNA. Remarkably, frequent inter-strain variations were dicovered that affected members of the WiSP family.Tropheryma whipplei is a Gram positive bacterium responsible for Whipple's disease [1]. This chronic, multisystemic infection is mainly characterized by intestinal malabsorption, but also involves other organs such as the heart and central nervous system and is ultimately fatal without appropriate treatment [2]. T. whipplei infection in human beings is particularly interesting due to the wide range of disease outcomes [3]. While it is known to be associated with the environment [4,5], the natural reservoir of T. whipplei is still unknown.In 2000, the first human isolate of this bacterium was successfully cultured in a fibroblast cell line [6]. This allowed investigators to examine the phenotypic characteristics of the bacterium, about which little had been known [1,7], and made possible the sequencing of the 0.93 Mb genome [8,9]. This major achievement has provided new perspectives on both the diagnosis and treatment of Whipple'
Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis
Laure-Emmanuelle Zaragosi, Brigitte Wdziekonski, Kevin Brigand, Phi Villageois, Bernard Mari, Rainer Waldmann, Christian Dani, Pascal Barbry
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-7-r64
Abstract: We used deep sequencing to identify small RNAs that are differentially expressed during adipogenesis of adipose tissue-derived stem cells. This approach revealed the un-annotated miR-642a-3p as a highly adipocyte-specific miRNA. We then focused our study on the miR-30 family, which was also up-regulated during adipogenic differentiation and for which the role in adipogenesis had not yet been elucidated. Inhibition of the miR-30 family blocked adipogenesis, whilst over-expression of miR-30a and miR-30d stimulated this process. We additionally showed that both miR-30a and miR-30d target the transcription factor RUNX2, and stimulate adipogenesis via the modulation of this major regulator of osteogenesis.Overall, our data suggest that the miR-30 family plays a central role in adipocyte development. Moreover, as adipose tissue-derived stem cells can differentiate into either adipocytes or osteoblasts, the down-regulation of the osteogenesis regulator RUNX2 represents a plausible mechanism by which miR-30 miRNAs may contribute to adipogenic differentiation of adipose tissue-derived stem cells.Obesity, by itself or associated with ancillary disorders such as diabetes and cardiovascular pathologies, represents a major public health issue in developed countries. In severe obesity, as well as in normal development, the growth of adipose tissue is the result of adipocyte hypertrophy and hyperplasia. It is now well established that a pool of multipotent progenitor cells persists in adipose tissue throughout life and is able to differentiate to give rise to adipocytes [1-3]. Certain key events controlling the terminal differentiation of progenitors into adipocytes have been identified. Transcription factors such as CCAAT/enhancer-binding proteins (C/EBPs) and peroxisome proliferator-activated receptors (PPARs) are known to play a critical role in this process [4]. However, the molecular mechanisms controlling the early steps of adipocyte progenitor commitment towards adipocyte d
“Seed-Milarity” Confers to hsa-miR-210 and hsa-miR-147b Similar Functional Activity
Thomas Bertero, Sébastien Grosso, Karine Robbe-Sermesant, Kevin Lebrigand, Imene-Sarah Hénaoui, Marie-Pierre Puisségur, Sandra Fourre, Laure-Emmanuelle Zaragosi, Nathalie M. Mazure, Gilles Ponzio, Bruno Cardinaud, Pascal Barbry, Roger Rezzonico, Bernard Mari
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0044919
Abstract: Specificity of interaction between a microRNA (miRNA) and its targets crucially depends on the seed region located in its 5′-end. It is often implicitly considered that two miRNAs sharing the same biological activity should display similarity beyond the strict six nucleotide region that forms the seed, in order to form specific complexes with the same mRNA targets. We have found that expression of hsa-miR-147b and hsa-miR-210, though triggered by different stimuli (i.e. lipopolysaccharides and hypoxia, respectively), induce very similar cellular effects in term of proliferation, migration and apoptosis. Hsa-miR-147b only shares a “minimal” 6-nucleotides seed sequence with hsa-miR-210, but is identical with hsa-miR-147a over 20 nucleotides, except for one base located in the seed region. Phenotypic changes induced after heterologous expression of miR-147a strikingly differ from those induced by miR-147b or miR-210. In particular, miR-147a behaves as a potent inhibitor of cell proliferation and migration. These data fit well with the gene expression profiles observed for miR-147b and miR-210, which are very similar, and the gene expression profile of miR-147a, which is distinct from the two others. Bioinformatics analysis of all human miRNA sequences indicates multiple cases of miRNAs from distinct families exhibiting the same kind of similarity that would need to be further characterized in terms of putative functional redundancy. Besides, it implies that functional impact of some miRNAs can be masked by robust expression of miRNAs belonging to distinct families.
Innovative approach for transcriptomic analysis of obligate intracellular pathogen: selective capture of transcribed sequences of Ehrlichia ruminantium
Lo?c Emboulé, France Daigle, Damien F Meyer, Bernard Mari, Valérie Pinarello, Christian Sheikboudou, Virginie Magnone, Roger Frutos, Alain Viari, Pascal Barbry, Dominique Martinez, Thierry Lefran?ois, Nathalie Vachiéry
BMC Molecular Biology , 2009, DOI: 10.1186/1471-2199-10-111
Abstract: We successfully adapted the SCOTS method (Selective Capture of Transcribed Sequences) on the model Rickettsiales ER to capture mRNAs. Southern Blots and RT-PCR revealed an enrichment of ER's cDNAs and a diminution of ribosomal contaminants after three rounds of capture. qRT-PCR and whole-genome ER microarrays hybridizations demonstrated that SCOTS method introduced only a limited bias on gene expression. Indeed, we confirmed the differential gene expression between poorly and highly expressed genes before and after SCOTS captures. The comparative gene expression obtained from ER microarrays data, on samples before and after SCOTS at 96 hpi was significantly correlated (R2 = 0.7). Moreover, SCOTS method is crucial for microarrays analysis of ER, especially for early time points post-infection. There was low detection of transcripts for untreated samples whereas 24% and 70.7% were revealed for SCOTS samples at 24 and 96 hpi respectively.We conclude that this SCOTS method has a key importance for the transcriptomic analysis of ER and can be potentially used for other Rickettsiales. This study constitutes the first step for further gene expression analyses that will lead to a better understanding of both ER pathogenicity and the adaptation of obligate intracellular bacteria to their environment.Elucidating molecular mechanisms that drive the adaptation of obligate intracellular pathogens to their host is crucial to understand their pathogenesis. To date, molecular studies on obligate intracellular bacteria can only be performed ex vivo at one time or in vitro in host cells. Thus, RNA extraction from infected cell cultures leads to low quantities of prokaryotic mRNAs with short half-lives and a high amount of contaminant eukaryotic RNAs [1,2]. Moreover, in prokaryotic RNA, ribosomal RNAs (rRNAs) represent more than 80% of total RNA, whereas mRNAs represent only 2% of total RNAs. Therefore, high throughput gene expression analysis of obligate intracellular bacteria depend
Identification of Keratinocyte Growth Factor as a Target of microRNA-155 in Lung Fibroblasts: Implication in Epithelial-Mesenchymal Interactions
Nicolas Pottier, Thomas Maurin, Benoit Chevalier, Marie-Pierre Puisségur, Kevin Lebrigand, Karine Robbe-Sermesant, Thomas Bertero, Christian L. Lino Cardenas, Elisabeth Courcot, Géraldine Rios, Sandra Fourre, Jean-Marc Lo-Guidice, Brice Marcet, Bruno Cardinaud, Pascal Barbry, Bernard Mari
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006718
Abstract: Background Epithelial-mesenchymal interactions are critical in regulating many aspects of vertebrate embryo development, and for the maintenance of homeostatic equilibrium in adult tissues. The interactions between epithelium and mesenchyme are believed to be mediated by paracrine signals such as cytokines and extracellular matrix components secreted from fibroblasts that affect adjacent epithelia. In this study, we sought to identify the repertoire of microRNAs (miRNAs) in normal lung human fibroblasts and their potential regulation by the cytokines TNF-α, IL-1β and TGF-β. Methodology/Principal Findings MiR-155 was significantly induced by inflammatory cytokines TNF-α and IL-1β while it was down-regulated by TGF-β. Ectopic expression of miR-155 in human fibroblasts induced modulation of a large set of genes related to “cell to cell signalling”, “cell morphology” and “cellular movement”. This was consistent with an induction of caspase-3 activity and with an increase in cell migration in fibroblasts tranfected with miR-155. Using different miRNA bioinformatic target prediction tools, we found a specific enrichment for miR-155 predicted targets among the population of down-regulated transcripts. Among fibroblast-selective targets, one interesting hit was keratinocyte growth factor (KGF, FGF-7), a member of the fibroblast growth factor (FGF) family, which owns two potential binding sites for miR-155 in its 3′-UTR. Luciferase assays experimentally validated that miR-155 can efficiently target KGF 3′-UTR. Site-directed mutagenesis revealed that only one out of the 2 potential sites was truly functional. Functional in vitro assays experimentally validated that miR-155 can efficiently target KGF 3′-UTR. Furthermore, in vivo experiments using a mouse model of lung fibrosis showed that miR-155 expression level was correlated with the degree of lung fibrosis. Conclusions/Significance Our results strongly suggest a physiological function of miR-155 in lung fibroblasts. Altogether, this study implicates this miRNA in the regulation by mesenchymal cells of surrounding lung epithelium, making it a potential key player during tissue injury.
The End of Voters in Europe? Electoral Turnout in Europe since WWII  [PDF]
Pascal Delwit
Open Journal of Political Science (OJPS) , 2013, DOI: 10.4236/ojps.2013.31007
Abstract:

Over the past twenty years, the scientific community and politicians in consolidated democracies have been regularly alarmed by political and electoral participation, portrayed as undergoing a brutal and linear decline. Each election is now scrutinized in terms not only of its results but also of its level of electoral turnout. This paper deals with two important issues—the reality of changes in electoral turnout in Europe and the impact of the institutional constraint of compulsory voting in voter turnout levels—through an analysis of 402 elections held in thirty-five States from 1944 until December, the 31st 2009. We do observe a contemporary erosion of voter turnout but at this stage voters are not so impossible to find as some claim they are. Furthermore, the assumption that interest in, and the importance of, compulsory voting as an institutional constraint encouraging voter turnout is confirmed.

 

The Catastrophe Map of a Two Period Production Model with Uncertainty  [PDF]
Pascal Stiefenhofer
Applied Mathematics (AM) , 2013, DOI: 10.4236/am.2013.48A016
Abstract:

This paper shows existence and efficiency of equilibria of a two period production model with uncertainty as a consequence of the catastrophe map being smooth and proper. Its inverse mapping defines a finite covering implying finiteness of equilibria. Beyond the extraction of local equilibrium information of the model, the catastrophe map renders itself well for a global study of the equilibrium set. It is shown that the equilibrium set has the structure of a smooth submanifold of the Euclidean space which is diffeomorphic to the sphere implying connectedness, simple connectedness, and contractibility.

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