Double-pulse-laser volumetric modification of fused silica: the effect of pulse delay on light propagation and energy deposition.

Volumetric modification of dielectrics by ultrashort laser pulses is a complex dynamic phenomenon involving material photoexcitation and associated nonlinear processes. To achieve control over modification, it is necessary to gain a deep insight into the dynamics of laser-excited processes that can be realized using double-laser-pulse experiments with different time separations supported by numerical simulations. In this paper, we apply this approach to investigate fused silica modification with femtosecond laser pulses that provides time-resolved information about the dynamic behavior of the laser-excited bandgap material. It is shown that the laser-generated free-electron plasma causes a shielding effect for the following pulse with a characteristic duration of ∼600 fs after the pulse action. Within this time interval, the second pulse produces a reduced modification as compared to a longer time separation between pulses. For double pulses with different energies, it was found that the volumetric modification is stronger when a lower-energy pulse couples with material first. This is explained by the combination of the effects of the re-excitation of self-trapped excitons, which are generated as a result of free electron recombination and associated light shielding. Experimental results are supported by numerical simulations of double laser pulse propagation in nonlinear media based on Maxwell's equations. Our findings offer a route for better controlling the inscription of 3D photonic structures in bulk optical materials.

Long noncoding RNAs as enhancers of gene expression.

The human genome contains thousands of long noncoding RNAs (ncRNAs) transcribed from diverse genomic locations. A large set of long ncRNAs is transcribed independent of protein-coding genes. We have used the GENCODE annotation of the human genome to identify 3019 long ncRNAs expressed in various human cell lines and tissue. This set of long ncRNAs responds to differentiation signals in primary human keratinocytes and is coexpressed with important regulators of keratinocyte development. Depletion of a number of these long ncRNAs leads to the repression of specific genes in their surrounding locus, supportive of an activating function for ncRNAs. Using reporter assays, we confirmed such activating function and show that such transcriptional enhancement is mediated through the long ncRNA transcripts. Our studies show that long ncRNAs exhibit functions similar to classically defined enhancers, through an RNA-dependent mechanism.

A comparative genome approach to marker ordering.

MOTIVATION: Genome maps are fundamental to the study of an organism and essential in the process of genome sequencing which in turn provides the ultimate map of the genome. The increased number of genomes being sequenced offers new opportunities for the mapping of closely related organisms. We propose here an algorithmic formalization of a genome comparison approach to marker ordering. RESULTS: In order to integrate a comparative mapping approach in the algorithmic process of map construction and selection, we propose to extend the usual statistical model describing the experimental data, here radiation hybrids (RH) data, in a statistical framework that models additionally the evolutionary relationships between a proposed map and a reference map: an existing map of the corresponding orthologous genes or markers in a closely related organism. This has concretely the effect of exploiting, in the process of map selection, the information of marker adjacencies in the related genome when the information provided by the experimental data is not conclusive for the purpose of ordering. In order to compute efficiently the map, we proceed to a reduction of the maximum likelihood estimation to the Traveling Salesman Problem. Experiments on simulated RH datasets as well as on a real RH dataset from the canine RH project show that maps produced using the likelihood defined by the new model are significantly better than maps built using the traditional RH model. AVAILABILITY: The comparative mapping approach is available in the last version of de Givry,S. et al. [(2004) Bioinformatics, 21, 1703-1704, www.inra.fr/mia/T/CarthaGene], a free (the LKH part is free for academic use only) mapping software in C++, including LKH (Helsgaun,K. (2000) Eur. J. Oper. Res., 126, 106-130, www.dat.ruc.dk/keld/research/LKH) for maximum likelihood computation.