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Search Results: 1 - 10 of 49 matches for " Jihane Amarir-Bouhram "
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Low Efficiency of Homology-Facilitated Illegitimate Recombination during Conjugation in Escherichia coli
Jihane Amarir-Bouhram, Mélodie Goin, Marie-Agnès Petit
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028876
Abstract: Homology-facilitated illegitimate recombination has been described in three naturally competent bacterial species. It permits integration of small linear DNA molecules into the chromosome by homologous recombination at one end of the linear DNA substrate, and illegitimate recombination at the other end. We report that homology-facilitated illegitimate recombination also occurs in Escherichia coli during conjugation with small non-replicative plasmids, but at a low frequency of 3×10?10 per recipient cell. The fate of linear DNA in E. coli is either RecBCD-dependent degradation, or circularisation by ligation, and integration into the chromosome by single crossing-over. We also report that the observed single crossing-overs are recA-dependent, but essentially recBCD, and recFOR independent. This suggests that other, still unknown, proteins may act as mediator for the loading of RecA on DNA during single crossing-over recombination in E. coli.
Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases
Marianne De Paepe ,Geoffrey Hutinet,Olivier Son,Jihane Amarir-Bouhram,Sophie Schbath,Marie-Agnès Petit
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004181
Abstract: Bacteriophages (or phages) dominate the biosphere both numerically and in terms of genetic diversity. In particular, genomic comparisons suggest a remarkable level of horizontal gene transfer among temperate phages, favoring a high evolution rate. Molecular mechanisms of this pervasive mosaicism are mostly unknown. One hypothesis is that phage encoded recombinases are key players in these horizontal transfers, thanks to their high efficiency and low fidelity. Here, we associate two complementary in vivo assays and a bioinformatics analysis to address the role of phage encoded recombinases in genomic mosaicism. The first assay allowed determining the genetic determinants of mosaic formation between lambdoid phages and Escherichia coli prophage remnants. In the second assay, recombination was monitored between sequences on phage λ, and allowed to compare the performance of three different Rad52-like recombinases on the same substrate. We also addressed the importance of homologous recombination in phage evolution by a genomic comparison of 84 E. coli virulent and temperate phages or prophages. We demonstrate that mosaics are mainly generated by homology-driven mechanisms that tolerate high substrate divergence. We show that phage encoded Rad52-like recombinases act independently of RecA, and that they are relatively more efficient when the exchanged fragments are divergent. We also show that accessory phage genes orf and rap contribute to mosaicism. A bioinformatics analysis strengthens our experimental results by showing that homologous recombination left traces in temperate phage genomes at the borders of recently exchanged fragments. We found no evidence of exchanges between virulent and temperate phages of E. coli. Altogether, our results demonstrate that Rad52-like recombinases promote gene shuffling among temperate phages, accelerating their evolution. This mechanism may prove to be more general, as other mobile genetic elements such as ICE encode Rad52-like functions, and play an important role in bacterial evolution itself.
Notch Signaling Activation Suppresses v-Src-Induced Transformation of Neural Cells by Restoring TGF-β-Mediated Differentiation
Samira Amarir,Maria Marx,Georges Calothy
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013572
Abstract: We have been investigating how interruption of differentiation contributes to the oncogenic process and the possibility to reverse the transformed phenotype by restoring differentiation. In a previous report, we correlated the capacity of intracellular Notch (ICN) to suppress v-Src-mediated transformation of quail neuroretina (QNR/v-srcts) cells with the acquisition by these undifferentiated cells of glial differentiation markers.
Distinguishing two-qubit states using local measurements and restricted classical communication
Mark Hillery,Jihane Mimih
Physics , 2002, DOI: 10.1103/PhysRevA.67.042304
Abstract: The problem of unambiguous state discrimination consists of determining which of a set of known quantum states a particular system is in. One is allowed to fail, but not to make a mistake. The optimal procedure is the one with the lowest failure probability. This procedure has been extended to bipartite states where the two parties, Alice and Bob, are allowed to manipulate their particles locally and communicate classically in order to determine which of two possible two-particle states they have been given. The failure probability of this local procedure has been shown to be the same as if the particles were together in the same location. Here we examine the effect of restricting the classical communication between the parties, either allowing none or eliminating the possibility that one party's measurement depends on the result of the other party's. These issues are studied for two-qubit states, and optimal procedures are found. In some cases the restrictions cause increases in the failure probability, but in other cases they do not. Applications of these procedures, in particular to secret sharing, are discussed.
Unambiguous discrimination of special sets of multipartite states using local measurements and classical communication
Jihane Mimih,Mark Hillery
Physics , 2005, DOI: 10.1103/PhysRevA.71.012329
Abstract: We initially consider a quantum system consisting of two qubits, which can be in one of two nonorthogonal states, \Psi_0 or \Psi_1. We distribute the qubits to two parties, Alice and Bob. They each measure their qubit and then compare their measurement results to determine which state they were sent. This procedure is error-free, which implies that it must sometimes fail. In addition, no quantum memory is required; it is not necessary to store one of the qubits until the result of the measurement on the other is known. We consider the cases in which, should failure occur, both parties receive a failure signal or only one does. In the latter case, if the states share the same Schmidt basis, the states can be discriminated with the same failure probability as would be obtained if the two qubits were measured together. This scheme is sufficiently simple that it can be generalized to multipartite qubit and qudit states. Applications to quantum secret sharing are discussed. Finally, we present an optical scheme to experimenatlly realize the protocol in the case of two qubits.
Fuzzy Clustering Based Parallel Cultural Algorithm
Jihane Alami,L. Benameur,Imrani
International Journal of Soft Computing , 2012,
Abstract: This study presents a new method, which combines cultural algorithms and a fuzzy clustering technique to improve the performance of cultural algorithms in multimodal optimization. Based on the metaphor of social environment principles, this model promotes the formation and maintenance of populations and implements the concept of cultural exchanges among them. Computer simulations show good performance for several multimodal test functions.
Heisenberg-limited interferometry with pair coherent states and parity measurements
Christopher C. Gerry,Jihane Mimih
Physics , 2010, DOI: 10.1103/PhysRevA.82.013831
Abstract: After reviewing parity measurement based interferometry with twin-Fock states, which allows for super-sensitivity (Heisenberg-limited) and super-resolution, we consider interferometry with two different superpositions of twin-Fock states, namely two-mode squeezed vacuum states and pair coherent states. This study is motivated by the experimental challenge of producing twin-Fock states on opposite sides of a beam splitter. We find that input two-mode squeezed states, while allowing for Heisenberg-limited sensitivity, do not yield super-resolutions, whereas we that find both are possible with input pair coherent states.
The parity operator in quantum optical metrology
Christopher C. Gerry,Jihane Mimih
Physics , 2010, DOI: 10.1080/00107514.2010.509995
Abstract: Photon number states are assigned a parity of if their photon number is even and a parity of if odd. The parity operator, which is minus one to the power of the photon number operator, is a Hermitian operator and thus a quantum mechanical observable though it has no classical analog, the concept being meaningless in the context of classical light waves. In this paper we review work on the application of the parity operator to the problem of quantum metrology for the detection of small phase shifts with quantum optical interferometry using highly entangled field states such as the so-called N00N states, and states obtained by injecting twin Fock states into a beam splitter. With such states and with the performance of parity measurements on one of the output beams of the interferometer, one can breach the standard quantum limit, or shot-noise limit, of sensitivity down to the Heisenberg limit, the greatest degree of phase sensitivity allowed by quantum mechanics for linear phase shifts. Heisenberg limit sensitivities are expected to eventually play an important role in attempts to detect gravitational waves in interferometric detection systems such as LIGO and VIRGO.
Electrostatic interaction between Interball-2 and the ambient plasma. 2. Influence on the low energy ion measurements with Hyperboloid
M. Hamelin,M. Bouhram,N. Dubouloz,M. Malingre
Annales Geophysicae (ANGEO) , 2003,
Abstract: The measurement of the thermal ion distributions in space is always strongly influenced by the ion motion through the complex 3D electrostatic potential structure built around a charged spacecraft. In this work, we study the related aberrations of the ion distribution detected on board, with special application to the case of the Hyperboloid instrument borne by the Interball-2 auroral satellite. Most of the time, the Interball-2 high altitude auroral satellite is charged at some non-negligible positive potential with respect to the ambient plasma, as shown in part 1; in consequence, the measurement of magnetospheric low energy ions (< 80 eV) with the Hyperboloid instrument can be disturbed by the complex electric potential environment of the satellite. In the case of positive charging, as in previous experiments, a negative bias is applied to the Hyperboloid structure in order to reduce this effect and to keep as much as possible the opportunity to detect very low energy ions. Then, the ions reaching the Hyperboloid entrance windows would have travelled across a continuous huge electrostatic lens involving various spatial scales from ~ 10 cm (detector radius) to ~ 10 m (satellite antennas). Neglecting space charge effects, we have computed the ion trajectories that are able to reach the Hyperboloid windows within their acceptance angles. There are three main results: (i) for given values of the satellite potential, and for each direction of arrival (each window), we deduced the related energy cutoff; (ii) we found that all ions in the energy channel, including the cutoff, can come from a large range of directions in the unperturbed plasma, especially when the solar panels or antennas act as electrostatic mirrors; (iii) for higher energy channels, the disturbances are reduced to small angular shifts. Biasing of the aperture is not very effective with the Hyperboloid instrument (as on previous missions with instruments installed close to the spacecraft body) because the potential environment is driven by effects from the spacecraft. Our results are used to explain some unexpected features of the low energy ion measurements, especially during polar wind events recorded by Hyperboloid. In conclusion, knowing the satellite potential from IESP measurements, we were able to reject any low energy doubtful data and to perform angular corrections for all higher energy ion data. Then the selected and corrected data are a reliable basis for interpretation and estimation of the thermal ion distributions. Key words. Space plasma physics (charged particle motion and a
Electrostatic interaction between Interball-2 and the ambient plasma. 1. Determination of the spacecraft potential from current calculations
M. Bouhram,N. Dubouloz,M. Hamelin,S. A. Grigoriev
Annales Geophysicae (ANGEO) , 2003,
Abstract: The Interball-2 spacecraft travels at altitudes extending up to 20 000 km, and becomes positively charged due to the low-plasma densities encountered and the photoemission on its sunlit surface. Therefore, a knowledge of the spacecraft potential Fs is required for correcting accurately thermal ion measurements on Interball-2. The determination of Fs is based on the balance of currents between escaping photoelectrons and incoming plasma electrons. A three-dimensional model of the potential structure surrounding Interball-2, including a realistic geometry and neglecting the space-charge densities, is used to find, through particle simulations, current-voltage relations of impacting plasma electrons Ie (Fs ) and escaping photoelectrons Iph (Fs ). The inferred relations are compared to analytic relationships in order to quantify the effects of the spacecraft geometry, the ambient magnetic field B0 and the electron temperature Te . We found that the complex geometry has a weak effect on the inferred currents, while the presence of B0 tends to decrease their values. Providing that the photoemission saturation current density Jph0 is known, a relation between Fs and the plasma density Ne can be derived by using the current balance. Since Jph0 is critical to this process, simultaneous measurements of Ne from Z-mode observations in the plasmapause, and data on the potential difference Fs - Fp between the spacecraft and an electric probe (p) are used in order to reverse the process. A value Jph0 ~ = 32 μAm-2 is estimated, close to laboratory tests, but less than typical measurements in space. Using this value, Ne and Fs can be derived systematically from electric field measurements without any additional calculation. These values are needed for correcting the distributions of low-energy ions measured by the Hyperboloid experiment on Interball-2. The effects of the potential structure on ion trajectories reaching Hyperboloid are discussed quantitatively in a companion paper. Key words. Space plasma physics (charged particle motion and acceleration; numerical simulation studies; spacecraft sheaths, wakes, charging)
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