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Search Results: 1 - 10 of 10888 matches for " Pierre Fechter "
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Staphylococcus aureus RNAIII Binds to Two Distant Regions of coa mRNA to Arrest Translation and Promote mRNA Degradation
Clément Chevalier,Sandrine Boisset,Cédric Romilly,Benoit Masquida,Pierre Fechter,Thomas Geissmann,Fran?ois Vandenesch ,Pascale Romby
PLOS Pathogens , 2010, DOI: 10.1371/journal.ppat.1000809
Abstract: Staphylococcus aureus RNAIII is the intracellular effector of the quorum sensing system that temporally controls a large number of virulence factors including exoproteins and cell-wall-associated proteins. Staphylocoagulase is one major virulence factor, which promotes clotting of human plasma. Like the major cell surface protein A, the expression of staphylocoagulase is strongly repressed by the quorum sensing system at the post-exponential growth phase. Here we used a combination of approaches in vivo and in vitro to analyze the mechanism used by RNAIII to regulate the expression of staphylocoagulase. Our data show that RNAIII represses the synthesis of the protein through a direct binding with the mRNA. Structure mapping shows that two distant regions of RNAIII interact with coa mRNA and that the mRNA harbors a conserved signature as found in other RNAIII-target mRNAs. The resulting complex is composed of an imperfect duplex masking the Shine-Dalgarno sequence of coa mRNA and of a loop-loop interaction occurring downstream in the coding region. The imperfect duplex is sufficient to prevent the formation of the ribosomal initiation complex and to repress the expression of a reporter gene in vivo. In addition, the double-strand-specific endoribonuclease III cleaves the two regions of the mRNA bound to RNAIII that may contribute to the degradation of the repressed mRNA. This study validates another direct target of RNAIII that plays a role in virulence. It also illustrates the diversity of RNAIII-mRNA topologies and how these multiple RNAIII-mRNA interactions would mediate virulence regulation.
How Many Wolves (Canis lupus) Fit into Germany? The Role of Assumptions in Predictive Rule-Based Habitat Models for Habitat Generalists
Dominik Fechter, Ilse Storch
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0101798
Abstract: Due to legislative protection, many species, including large carnivores, are currently recolonizing Europe. To address the impending human-wildlife conflicts in advance, predictive habitat models can be used to determine potentially suitable habitat and areas likely to be recolonized. As field data are often limited, quantitative rule based models or the extrapolation of results from other studies are often the techniques of choice. Using the wolf (Canis lupus) in Germany as a model for habitat generalists, we developed a habitat model based on the location and extent of twelve existing wolf home ranges in Eastern Germany, current knowledge on wolf biology, different habitat modeling techniques and various input data to analyze ten different input parameter sets and address the following questions: (1) How do a priori assumptions and different input data or habitat modeling techniques affect the abundance and distribution of potentially suitable wolf habitat and the number of wolf packs in Germany? (2) In a synthesis across input parameter sets, what areas are predicted to be most suitable? (3) Are existing wolf pack home ranges in Eastern Germany consistent with current knowledge on wolf biology and habitat relationships? Our results indicate that depending on which assumptions on habitat relationships are applied in the model and which modeling techniques are chosen, the amount of potentially suitable habitat estimated varies greatly. Depending on a priori assumptions, Germany could accommodate between 154 and 1769 wolf packs. The locations of the existing wolf pack home ranges in Eastern Germany indicate that wolves are able to adapt to areas densely populated by humans, but are limited to areas with low road densities. Our analysis suggests that predictive habitat maps in general, should be interpreted with caution and illustrates the risk for habitat modelers to concentrate on only one selection of habitat factors or modeling technique.
Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression
Efthimia Lioliou,Cynthia M. Sharma,Isabelle Caldelari,Anne-Catherine Helfer,Pierre Fechter,Fran?ois Vandenesch,J?rg Vogel ,Pascale Romby
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002782
Abstract: RNA turnover plays an important role in both virulence and adaptation to stress in the Gram-positive human pathogen Staphylococcus aureus. However, the molecular players and mechanisms involved in these processes are poorly understood. Here, we explored the functions of S. aureus endoribonuclease III (RNase III), a member of the ubiquitous family of double-strand-specific endoribonucleases. To define genomic transcripts that are bound and processed by RNase III, we performed deep sequencing on cDNA libraries generated from RNAs that were co-immunoprecipitated with wild-type RNase III or two different cleavage-defective mutant variants in vivo. Several newly identified RNase III targets were validated by independent experimental methods. We identified various classes of structured RNAs as RNase III substrates and demonstrated that this enzyme is involved in the maturation of rRNAs and tRNAs, regulates the turnover of mRNAs and non-coding RNAs, and autoregulates its synthesis by cleaving within the coding region of its own mRNA. Moreover, we identified a positive effect of RNase III on protein synthesis based on novel mechanisms. RNase III–mediated cleavage in the 5′ untranslated region (5′UTR) enhanced the stability and translation of cspA mRNA, which encodes the major cold-shock protein. Furthermore, RNase III cleaved overlapping 5′UTRs of divergently transcribed genes to generate leaderless mRNAs, which constitutes a novel way to co-regulate neighboring genes. In agreement with recent findings, low abundance antisense RNAs covering 44% of the annotated genes were captured by co-immunoprecipitation with RNase III mutant proteins. Thus, in addition to gene regulation, RNase III is associated with RNA quality control of pervasive transcription. Overall, this study illustrates the complexity of post-transcriptional regulation mediated by RNase III.
Escherichia coli Ribosomal Protein S1 Unfolds Structured mRNAs Onto the Ribosome for Active Translation Initiation
Mélodie Duval,Alexey Korepanov,Olivier Fuchsbauer,Pierre Fechter,Andrea Haller,Attilio Fabbretti,Laurence Choulier,Ronald Micura,Bruno P. Klaholz,Pascale Romby ,Mathias Springer,Stefano Marzi
PLOS Biology , 2013, DOI: 10.1371/journal.pbio.1001731
Abstract: Regulation of translation initiation is well appropriate to adapt cell growth in response to stress and environmental changes. Many bacterial mRNAs adopt structures in their 5′ untranslated regions that modulate the accessibility of the 30S ribosomal subunit. Structured mRNAs interact with the 30S in a two-step process where the docking of a folded mRNA precedes an accommodation step. Here, we used a combination of experimental approaches in vitro (kinetic of mRNA unfolding and binding experiments to analyze mRNA–protein or mRNA–ribosome complexes, toeprinting assays to follow the formation of ribosomal initiation complexes) and in vivo (genetic) to monitor the action of ribosomal protein S1 on the initiation of structured and regulated mRNAs. We demonstrate that r-protein S1 endows the 30S with an RNA chaperone activity that is essential for the docking and the unfolding of structured mRNAs, and for the correct positioning of the initiation codon inside the decoding channel. The first three OB-fold domains of S1 retain all its activities (mRNA and 30S binding, RNA melting activity) on the 30S subunit. S1 is not required for all mRNAs and acts differently on mRNAs according to the signals present at their 5′ ends. This work shows that S1 confers to the ribosome dynamic properties to initiate translation of a large set of mRNAs with diverse structural features.
Base Pairing Interaction between 5′- and 3′-UTRs Controls icaR mRNA Translation in Staphylococcus aureus
Igor Ruiz de los Mozos,Marta Vergara-Irigaray,Victor Segura,Maite Villanueva,Nerea Bitarte,Margarida Saramago,Susana Domingues,Cecilia M. Arraiano,Pierre Fechter,Pascale Romby,Jaione Valle,Cristina Solano,I?igo Lasa ,Alejandro Toledo-Arana
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1004001
Abstract: The presence of regulatory sequences in the 3′ untranslated region (3′-UTR) of eukaryotic mRNAs controlling RNA stability and translation efficiency is widely recognized. In contrast, the relevance of 3′-UTRs in bacterial mRNA functionality has been disregarded. Here, we report evidences showing that around one-third of the mapped mRNAs of the major human pathogen Staphylococcus aureus carry 3′-UTRs longer than 100-nt and thus, potential regulatory functions. We selected the long 3′-UTR of icaR, which codes for the repressor of the main exopolysaccharidic compound of the S. aureus biofilm matrix, to evaluate the role that 3′-UTRs may play in controlling mRNA expression. We showed that base pairing between the 3′-UTR and the Shine-Dalgarno (SD) region of icaR mRNA interferes with the translation initiation complex and generates a double-stranded substrate for RNase III. Deletion or substitution of the motif (UCCCCUG) within icaR 3′-UTR was sufficient to abolish this interaction and resulted in the accumulation of IcaR repressor and inhibition of biofilm development. Our findings provide a singular example of a new potential post-transcriptional regulatory mechanism to modulate bacterial gene expression through the interaction of a 3′-UTR with the 5′-UTR of the same mRNA.
A sharp interface method for compressible liquid-vapor flow with phase transition and surface tension
Stefan Fechter,Claus-Dieter Munz,Christian Rohde,Christoph Zeiler
Physics , 2015,
Abstract: The numerical approximation of non-isothermal liquid-vapor flow within the compressible regime is a difficult task because complex physical effects at the phase interfaces can govern the global flow behavior. We present a sharp interface approach which treats the interface as a shock-wave like discontinuity. Any mixing of fluid phases is avoided by using the flow solver in the bulk regions only, and a ghost-fluid approach close to the interface. The coupling states for the numerical solution in the bulk regions are determined by the solution of local multi-phase Riemann problems across the interface. The Riemann solution accounts for the relevant physics by enforcing appropriate jump conditions at the phase boundary. A wide variety of interface effects can be handled in a thermodynamically consistent way. This includes surface tension or mass/energy transfer by phase transition. Moreover, the local normal speed of the interface, which is needed to calculate the time evolution of the interface, is given by the Riemann solution. The interface tracking itself is based on a level-set method. The focus in this paper is the description of the multi-phase Riemann solver and its usage within the sharp interface approach. One-dimensional problems are selected to validate the approach. Finally, the three-dimensional simulation of a wobbling droplet and a shock droplet interaction in two dimensions are shown. In both problems phase transition and surface tension determine the global bulk behavior.
Selective Vulnerability of the Cochlear Basal Turn to Acrylonitrile and Noise
B. Pouyatos,C. A. Gearhart,A. Nelson-Miller,S. Fulton,L. D. Fechter
Journal of Toxicology , 2009, DOI: 10.1155/2009/908596
Abstract: Exposure to acrylonitrile, a high-production industrial chemical, can promote noise-induced hearing loss (NIHL) in the rat even though this agent does not itself produce permanent hearing loss. The mechanism by which acrylonitrile promotes NIHL includes oxidative stress as antioxidant drugs can partially protect the cochlea from acrylonitrile
Bending Fuchsian representations of fundamental groups of cusped surfaces in PU(2,1)
Pierre Will
Mathematics , 2011,
Abstract: We describe a family of representations of $\pi_1(\Sigma)$ in PU(2,1), where $\Sigma$ is a hyperbolic Riemann surface with at least one deleted point. This family is obtained by a bending process associated to an ideal triangulation of $\Sigma$. We give an explicit description of this family by describing a coordinates system in the spirit of shear coordinates on the Teichm\"uller space. We identify within this family new examples of discrete, faithful and type-preserving representations of $\pi_1(\Sigma)$. In turn, we obtain a 1-parameter family of embeddings of the Teichm\"uller space of $\Sigma$ in the PU(2,1)-representation variety of $\pi_1(\Sigma)$. These results generalise to arbitrary $\Sigma$ the results obtained in a previous paper for the 1-punctured torus.
Two Generator groups acting on the complex hyperbolic plane
Pierre Will
Mathematics , 2015,
Abstract: This is an expository article about groups generated by two isometries of the complex hyperbolic plane.
How to Introduce the Cyclic Group and Its Properties Representation with Matlab ? Thanks to Magic Using the Perfect Faro Shuffle  [PDF]
Pierre Schott
Creative Education (CE) , 2011, DOI: 10.4236/ce.2011.21005
Abstract: Why use Magic for teaching arithmetic and geometric suit, additive groups, and algorithmic notions through Matlab? Magicians know that, once the surprise has worn off, the audience will seek to understand how the trick works. The aim of every teacher is to interest their students, and a magic trick will lead them to ask how? And why? And how can I create one myself? In this article we consider a project I presented in 2009. I summarize the project scope, the students' theoretical studies, their approach to this problem and their computer realizations. I conclude using the mathematical complement as well as weak and strong points of this approach. Whatever the student's professional ambitions, they will be able to see the impact that originality and creativity have when combined with an interest in one's work. The students know how to “perform” a magic trick for their family and friends, a trick that they will be able to explain and so enjoy a certain amount of success. Sharing a mathematical / informatics demonstration is not easy and that they do so means that they will have worked on understood and are capable of explaining this knowledge. Isn't this the aim of all teaching?
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