Biomedical subjects

Hubert Charles

Publications and source records attributed to Hubert Charles.

4 recordsLinked to original sources

PubMed2005

SITRANS: a Web Information System for Microarray Experiments.

Microarray experiments aim at analyzing expression levels of genes using DNA probes. The amount of data managed for each experiment is very large. It is thus essential to provide electronic support for the capture and the management of information describing microarray experiments. We present here the SITRANS Web information system, the aim of which is to help research workers storing, browsing, sharing and publishing data.

Database Management Systems↗

PubMed2004

ROSO: optimizing oligonucleotide probes for microarrays.

UNLABELLED: ROSO is software to design optimal oligonucleotide probe sets for microarrays. Selected probes show no significant cross-hybridization, no stable secondary structures and their Tm are chosen to minimize the Tm variability of the probe set. AVAILABILITY: The program is available on the internet. Sources are freely available, for non-profit use, on request to the authors. SUPPLEMENTARY INFORMATION: http://pbil.univ-lyon1.fr/roso

Algorithms↗

PubMed2004

Endosymbiont phylogenesis in the dryophthoridae weevils: evidence for bacterial replacement.

Intracellular symbiosis is widespread in the insect world where it plays an important role in evolution and adaptation. The weevil family Dryophthoridae (Curculionoidea) is of particular interest in intracellular symbiosis evolution with regard to the great economical and ecological features of these invasive insects, and the potential for comparative studies across a wide range of host plants and environments. Here, we have analyzed the intracellular symbiotic bacteria of 19 Dryophthoridae species collected worldwide, representing a wide range of plant species and tissues. All except one (Sitophilus linearis) harbor symbiotic bacteria within specialized cells (the bacteriocytes) assembled as an organ, the bacteriome. Phylogenetic analysis of the 16S rDNA gene sequence of the Dryophthoridae endosymbionts revealed three endosymbiotic clades belonging to gamma3-Proteobacteria and characterized by different GC contents and evolutionary rate. The genus name Candidatus Nardonella was proposed for the ancestral clade infesting Dryophthoridae 100 MYA and represented by five of nine bacterial genera studied. For this clade showing low GC content (40.5% GC) and high evolutionary rate (0.128 substitutions/site per 100 Myr), a single infection and subsequent cospeciation of the host and the endosymbionts was observed. In the two other insect lineage endosymbionts, with relatively high GC content (53.4% and 53.8% GC), competition with ancestral pathogenic bacteria might have occurred, leading to endosymbiont replacement in present-day last insects.

Animals↗

PubMed2004

Assessment of 35mer amino-modified oligonucleotide based microarray with bacterial samples.

Parallel quantification of a large number of messenger RNA transcripts, using microarray technology, promises to provide unsuspected information about many cellular processes. Although experimental protocols on microarray applications are available, only limited methodological information on glass-slide manufacturing and signal interpretation has been published. The aim of this paper is to provide new insights into the practical aspects of the construction and hybridization of oligonucleotide-based microarrays. The intracellular symbiotic bacterium of aphids, Buchnera aphidicola, is used here as a model organism. The first part of the work is devoted to the optimization of procedures for printing slides, labeling of cDNA targets and hybridization. In the second part, based on a statistical analysis of the results, we discuss the influence of the probe attachment chemistry, of the labeling method, of the oligonucleotide position and of the concentration of a spotted oligonucleotide on signal intensity. The problem of signal specificity is also addressed, based on the calculation of the fluorescent ratio for each probe to its corresponding mismatch control probe. Lastly, the selection of internal spiked RNAs appropriate to our bacterial samples and useful for the data normalization step is presented.

Base Pair Mismatch↗