Precise detection of rearrangement breakpoints in mammalian chromosomes

<p>Abstract</p> <p>Background</p> <p>Genomes undergo large structural changes that alter their organisation. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. We developed a method to precisely delimit rearrangement breakpoints on a genome by comparison with the genome of a related species. Contrary to current methods which search for synteny blocks and simply return what remains in the genome as breakpoints, we propose to go further and to investigate the breakpoints themselves in order to refine them.</p> <p>Results</p> <p>Given some reliable and non overlapping synteny blocks, the core of the method consists in refining the regions that are not contained in them. By aligning each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Since this method requires as input synteny blocks with some properties which, though they appear natural, are not verified by current methods for detecting such blocks, we further give a formal definition and provide an algorithm to compute them.</p> <p>The whole method is applied to delimit breakpoints on the human genome when compared to the mouse and dog genomes. Among the 355 human-mouse and 240 human-dog breakpoints, 168 and 146 respectively span less than 50 Kb. We compared the resulting breakpoints with some publicly available ones and show that we achieve a better resolution. Furthermore, we suggest that breakpoints are rarely reduced to a point, and instead consist in often large regions that can be distinguished from the sequences around in terms of segmental duplications, similarity with related species, and transposable elements.</p> <p>Conclusion</p> <p>Our method leads to smaller breakpoints than already published ones and allows for a better description of their internal structure. In the majority of cases, our refined regions of breakpoint exhibit specific biological properties (no similarity, presence of segmental duplications and of transposable elements). We hope that this new result may provide some insight into the mechanism and evolutionary properties of chromosomal rearrangements.</p

A review of elliptical and disc galaxy structure, and modern scaling laws

A century ago, in 1911 and 1913, Plummer and then Reynolds introduced their models to describe the radial distribution of stars in `nebulae'. This article reviews the progress since then, providing both an historical perspective and a contemporary review of the stellar structure of bulges, discs and elliptical galaxies. The quantification of galaxy nuclei, such as central mass deficits and excess nuclear light, plus the structure of dark matter halos and cD galaxy envelopes, are discussed. Issues pertaining to spiral galaxies including dust, bulge-to-disc ratios, bulgeless galaxies, bars and the identification of pseudobulges are also reviewed. An array of modern scaling relations involving sizes, luminosities, surface brightnesses and stellar concentrations are presented, many of which are shown to be curved. These 'redshift zero' relations not only quantify the behavior and nature of galaxies in the Universe today, but are the modern benchmark for evolutionary studies of galaxies, whether based on observations, N-body-simulations or semi-analytical modelling. For example, it is shown that some of the recently discovered compact elliptical galaxies at 1.5 < z < 2.5 may be the bulges of modern disc galaxies.Comment: Condensed version (due to Contract) of an invited review article to appear in "Planets, Stars and Stellar Systems"(www.springer.com/astronomy/book/978-90-481-8818-5). 500+ references incl. many somewhat forgotten, pioneer papers. Original submission to Springer: 07-June-201

Focusing principle of antenna array for localization applications

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Near field focusing circular microstrip antenna array for RFID applications

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Modulation d'intensité optique par interaction acousto-optique sur verre

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Novel integrated polarization analyzer sensor made by ion-exchange in glass

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Acousto-optic intensity modulation on glass-integrated optic

International audienceAn elastic beam of waves in the Megahertz range, generated using a PZT ceramic, crosses one arm of an integrated Mac-Zehnder interferometer realised by ion-exchange in a glass substrate. Elastic waves modify locally the refractive index of glass. A laser beam of 0.83 μm wavelength is injected into the interferometer. For a sine excitation voltage of 7 volts of the piezoelectric transducer, the variation of the optical intensity measured at the interferometer output is greater than 20% of the intensity observed without elastic waves. Refractive index variation of 9.4×10-7 were obtained. The optical intensity observed at the output of the interferometer varies at the frequency of the piezoelectric crystal excitation. A model taking into account the elastic and the optical effects is proposed. This model allows the optimisation of the piezoelectric transducer in order to obtain the maximum of elastic strain at the position of the optical waveguides. The theoretical results obtained with the model are in accordance with the experimental results

Application de l'optique intégrée sur verre à la vélocimétrie laser Doppler pour la mesure de vitesse et de frottement en région pariétale

Un Vélocimètre Laser Doppler entièrement Intégré (VLDI) sur un substrat de verre est présenté dans cet article. Ce nouvel instrument d'investigation est dédié à la mesure de vitesses en proche paroi, dans la sous-couche visqueuse. De la mesure de vitesse faite par ce capteur se déduit directement le frottement entre le fluide et la paroi. Ce capteur peut également être utilisé en micro-fluidique. La tête du capteur est réalisée en une seule étape technologique par diffusion d'ions : Ag+ " Na+. Selon la géométrie choisie, la plaquette de verre de 1 mm d'épaisseur mesure quelques millimètres de large (entre 2 et 8 mm selon les cas) par 3 centimètres de long. La tête du VLDI est alimentée par une diode laser (l0 = 0,8 µm) via une fibre optique monomode. Les signaux Doppler quant à eux sont transmis du capteur vers une diode avalanche par une fibre optique multimode. Une des spécificités de ce capteur de deuxième génération est la production d'un petit volume de mesure : 18 ' 25 ' 10 µm3 selon les axes x, y et z (x est orienté selon l'écoulement du fluide alors que y est la direction perpendiculaire à la paroi.) pour un interfrange de 0,83 µm et de 18 ' 35 ' 18 pour un interfrange de 1,0 µm. Ces mesures sont prises à 1/e2 de l'intensité maximale présente dans le volume de mesure. La focalisation des faisceaux s'effectue grâce à l'intégration de miroirs convergent sur le substrat de verre

Integrated acousto-optic polarization analyzer sensor

International audienceIon-exchange in glass substrate has long been an enabling technology for optical waveguides device manufacturing. Thus, in the last years, hybridization of ion-exchanged glass waveguides components has become a promising method for functional integration. In that context, we propose a Integrated acousto-optic Polarization Analyzer Sensor (IPAS) made by ion-exchange in a glass substrate. The IPAS consists in two Y-junctions that give three different outputs. The first one is simply one output waveguides of the first Y-junction. The two other outputs are the waveguides following the second Y-junction. A piezoelectric plate is placed over the entrance waveguide of the second Y-junction. It creates an artificial anisotropy when it is excited electrically. For each one of the three output signals, a polarizer is inserted between the waveguide's end and a photodetector. The IPAS is a compact hybrid realization insensitive to vibrations and easy to realize. It is capable to determine, with adequate signal processing, the polarization state of a light beam. Experimental results are obtained with a single buried straight waveguide made by low birefringence Ag+↔Na+ ion-exchange. The measured polarization state is compared with a commercial polarization analyzer