Histoire d'une famille de deux générations atteinte par la forme dominante de la maladie de Stargardt, due à une mutation sur le gène ELOVL4 : Case report

Un patient de 22 ans et les membres de sa famille se soumettent à un examen ophtalmique complet, comprenant un examen du fond d'oeil, une autofluorescence, une tomographie à cohérence optique (OCT), un champ visuel et un électrorétinogramme (ERG). De l'ADN génomique est extrait du sang périphérique de ces patients afin de subir une analyse IROme, un « séquençage à haut débit » de 120 gènes, connus pour être impliqués dans diverses maladies rétiniennes héréditaires. Les résultats de cette analyse génétique ont été validés par un séquençage selon Sanger

Phylogenetic Analysis of Cell Types using Histone Modifications

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the differentiation process. In this paper, we present a simple analysis of cell types and differentiation paths using phylogenetic inference based on ChIP-Seq histone modification data. We propose new data representation techniques and new distance measures for ChIP-Seq data and use these together with standard phylogenetic inference methods to build biologically meaningful trees that indicate how diverse types of cells are related. We demonstrate our approach on H3K4me3 and H3K27me3 data for 37 and 13 types of cells respectively, using the dataset to explore various issues surrounding replicate data, variability between cells of the same type, and robustness. The promising results we obtain point the way to a new approach to the study of cell differentiation.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Dihedral-angle Gaussian distribution driving protein folding

The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging from 125 up to 400 amino acids for the different fractions of secondary structure motifs, which dihedral angles were randomly chosen according to narrow Gaussian probability distributions. In order to measure the fractal dimension of proteins three different cases were analyzed. The first contained alpha-helix structures only, the second beta-strands structures and the third a mix of alpha-helices and beta-sheets. The behavior of proteins with alpha-helix motifs are more compacted than in other situations. The findings herein indicate that this model describes some structural properties of a protein and suggest that randomness is an essential ingredient but proteins are driven by narrow angular Gaussian probability distributions and not by random-walk processes.Comment: 9 pages, 4 figures, to be published in Physica

Improved method for determination of waxes in olive oils: Reduction of silica and use of a less hazardous solvent

The evaluation of the content of waxes is request both by IOC Trade Standard and by Regulation (EEC) 2568/91 and its further amendments. The official method uses 15 g of silicic acid and elutes several fractions by using huge volumes of dangerous solvent (n-hexane). The developed method uses 1 g of silicic acid with a different particle size and less than 20 mL of solvent mixture, substituting n-hexane with less toxic isooctane. Briefly, after spiking with a suitable internal standard, oil sample is fractionated by SPE (Solid Phase Extraction) cartridge with 1 g of silica, waxes are eluted with 14 mL of isooctane/ethyl ether 99/1 (6 mL discarded and 8 mL collected), then, after elution sample is reconstitute in 200 \u3bcL of n-heptane and analysed by capillary GC. Data of "In home" validation, (repeatability, accuracy and recovery) and relative chromatograms are reported in this paper

Evaluating synteny for improved comparative studies

Motivation: Comparative genomics aims to understand the structure and function of genomes by translating knowledge gained about some genomes to the object of study. Early approaches used pairwise comparisons, but today researchers are attempting to leverage the larger potential of multi-way comparisons. Comparative genomics relies on the structuring of genomes into syntenic blocks: blocks of sequence that exhibit conserved features across the genomes. Syntenic blocs are required for complex computations to scale to the billions of nucleotides present in many genomes; they enable comparisons across broad ranges of genomes because they filter out much of the individual variability; they highlight candidate regions for in-depth studies; and they facilitate whole-genome comparisons through visualization tools. However, the concept of syntenic block remains loosely defined. Tools for the identification of syntenic blocks yield quite different results, thereby preventing a systematic assessment of the next steps in an analysis. Current tools do not include measurable quality objectives and thus cannot be benchmarked against themselves. Comparisons among tools have also been neglected—what few results are given use superficial measures unrelated to quality or consistency. Results: We present a theoretical model as well as an experimental basis for comparing syntenic blocks and thus also for improving or designing tools for the identification of syntenic blocks. We illustrate the application of the model and the measures by applying them to syntenic blocks produced by three different contemporary tools (DRIMM-Synteny, i-ADHoRe and Cyntenator) on a dataset of eight yeast genomes. Our findings highlight the need for a well founded, systematic approach to the decomposition of genomes into syntenic blocks. Our experiments demonstrate widely divergent results among these tools, throwing into question the robustness of the basic approach in comparative genomics. We have taken the first step towards a formal approach to the construction of syntenic blocks by developing a simple quality criterion based on sound evolutionary principles. Contact: [email protected]