Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

BACKGROUND: Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. RESULTS: Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. CONCLUSION: The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL:

Spectroscopy of Colloidal Semiconductor Core/Shell Nanoplatelets with High Quantum Yield

Free standing two-dimensional materials appear as a novel class of structures. Recently, the first colloidal two-dimensional heterostructures have been synthesized. These core/shell nanoplatelets are the first step toward colloidal quantum wells. Here, we study in detail the spectroscopic properties of this novel generation of colloidal nanoparticles. We show that core/shell CdSe/CdZnS nanoplatelets with 80% quantum yield can be obtained. The emission time trace of single core/shell nanoplatelets exhibits reduced blinking compared to core nanoplatelets with a two level emission time trace. At cryogenic temperatures, these nanoplatelets have a quantum yield close to 100% and a stable emission time trace. A solution of core/shell nanoplatelets has emission spectra with a full width half-maximum close to 20 nm, a value much lower than corresponding spherical or rod-shaped heterostructures. Using single particle spectroscopy, we show that the broadening of the emission spectra upon the shell deposition is not due to dispersity between particles but is related to an intrinsic increased exciton–phonon coupling in the shell. We also demonstrate that optical spectroscopy is a relevant tool to investigate the presence of traps induced by shell deposition. The spectroscopic properties of the core/shell nanoplatelets presented here strongly suggest that this new generation of objects will be an interesting alternative to spherical or rod-shaped nanocrystals