École Polytechnique Fédérale de Lausanne

About: École Polytechnique Fédérale de Lausanne is a facility organization based out in Lausanne, Switzerland. It is known for research contribution in the topics: Population & Catalysis. The organization has 44041 authors who have published 98296 publications receiving 4372092 citations. The organization is also known as: EPFL & ETHL.

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Abstract: The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.

Executable cell biology.

Abstract: Computational modeling of biological systems is becoming increasingly important in efforts to better understand complex biological behaviors. In this review, we distinguish between two types of biological models--mathematical and computational--which differ in their representations of biological phenomena. We call the approach of constructing computational models of biological systems 'executable biology', as it focuses on the design of executable computer algorithms that mimic biological phenomena. We survey the main modeling efforts in this direction, emphasize the applicability and benefits of executable models in biological research and highlight some of the challenges that executable biology poses for biology and computer science. We claim that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research. This will drive biology toward a more precise engineering discipline.

Urbach tail of anatase TiO2.

Abstract: The fundamental absorption edge of the anatase phase of ${\mathrm{TiO}}_{2}$ has been studied by performing polarized optical transmission measurements on single crystals at temperatures ranging from 4.2 to 300 K. An Urbach tail has been found that shows an exponential spectral dependence down to liquid-helium temperature. The optical gap of anatase has been estimated to be 3.420 eV in polarization E\ensuremath{\perp}c, and 3.460 eV in polarization E\ensuremath{\parallel}c. Our experimental results can be accounted for in terms of the theory of Toyozawa and co-workers, which ascribes the Urbach tail to the momentary localization of excitons due to phonon interaction. Comparing, in this case, the measured abosrption spectra of anatase and rutile, we conclude that the excitons in anatase are self-trapped while those in rutile are free. This opposite nature of exciton states in anatase and rutile is consistent with the results of previous photoluminescence studies.