Biomedical subjects

Olivier Andrieu

Publications and source records attributed to Olivier Andrieu.

5 recordsLinked to original sources

PubMed2005

The SuMo server: 3D search for protein functional sites.

UNLABELLED: We provide the scientific community with a web server which gives access to SuMo, a bioinformatic system for finding similarities in arbitrary 3D structures or substructures of proteins. SuMo is based on a unique representation of macromolecules using selected triplets of chemical groups having their own geometry and symmetry, regardless of the restrictive notions of main chain and lateral chains of amino acids. The heuristic for extracting similar sites was used to drive two major large-scale approaches. First, searching for ligand binding sites onto a query structure has been made possible by comparing the structure against each of the ligand binding sites found in the Protein Data Bank (PDB). Second, the reciprocal process, i.e. searching for a given 3D site of interest among the structures of the PDB is also possible and helps detect cross-reacting targets in drug design projects. AVAILABILITY: The web server is freely accessible to academia through http://sumo-pbil.ibcp.fr and full support is available from MEDIT (http://www.medit.fr). CONTACT: mjambon@burnham.org.

Amino Acid Sequence↗

PubMed2005

Combined evidence annotation of transposable elements in genome sequences.

Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1), and we found a substantially higher number of TEs (n = 6,013) than previously identified (n = 1,572). Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1). We also estimated that 518 TE copies (8.6%) are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other species in the genus Drosophila.

Journal Article↗

PubMed2005

Exploring the evolution of Wolbachia compatibility types: a simulation approach.

Wolbachia-induced cytoplasmic incompatibility (CI) is observed when males bearing the bacterium mate with uninfected females or with females bearing a different Wolbachia variant; in such crosses, paternal chromosomes are lost at the first embryonic mitosis, most often resulting in developmental arrest. The molecular basis of CI is currently unknown, but it is useful to distinguish conceptually the male and female sides of this phenomenon: in males, Wolbachia must do something, before it is shed from maturing sperm, that will disrupt paternal chromosomes functionality [this is usually termed "the modification (mod) function"]; in females, Wolbachia must somehow restore embryonic viability, through what is usually called "the rescue (resc) function." The occurrence of CI in crosses between males and females bearing different Wolbachia variants demonstrates that the mod and resc functions interact in a specific manner: different mod resc pairs make different compatibility types. We are interested in the evolutionary process allowing the diversification of compatibility types. In an earlier model, based on the main assumption that the mod and resc functions can mutate independently, we have shown that compatibility types can evolve through a two-step process, the first involving drift on mod variations and the second involving selection on resc variations. This previous study has highlighted the need for simulation-based models that would include the effects of nondeterministic evolutionary forces. This study is based on a simulation program fulfilling this condition, allowing us to follow the evolution of compatibility types under mutation, drift, and selection. Most importantly, simulations suggest that in the frame of our model, the evolution of compatibility types is likely to be a gradual process, with new compatibility types remaining partially compatible with ancestral ones.

Animals↗

PubMed2004

Detection of transposable elements by their compositional bias.

BACKGROUND: Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be used as a tool for detection and analysis of TE sequences. RESULTS: We compared the composition of TE sequences and host gene sequences using probabilistic models of nucleotide sequences. We used hidden Markov models (HMM), which take into account the base composition of the sequences (occurrences of words n nucleotides long, with n ranging here from 1 to 4) and the heterogeneity between coding and non-coding parts of sequences. We analyzed three sets of sequences containing class I TEs, class II TEs and genes respectively in three species: Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. Each of these sets had a distinct, homogeneous composition, enabling us to distinguish between the two classes of TE and the genes. However the particular base composition of the TEs differed in the three species studied. CONCLUSIONS: This approach can be used to detect and annotate TEs in genomic sequences and complements the current homology-based TE detection methods. Furthermore, the HMM method is able to identify the parts of a sequence in which the nucleotide composition resembles that of a coding region of a TE. This is useful for the detailed annotation of TE sequences, which may contain an ancient, highly diverged coding region that is no longer fully functional.

Animals↗

PubMed2003

Hoppel, a P-like element without introns: a P-element ancestral structure or a retrotranscription derivative?

An in silico search for P-transposable-element-related sequences in the Drosophila melanogaster genome allowed us to detect sequences that are similar to P-element transposases. These sequences are located in the central region of 3.4-kb Hoppel elements, a class II transposon. Polymerase chain reaction (PCR) analysis of the insertional polymorphism revealed that these elements are mobile. The 3.4-kb elements are the longest copies of this family ever found. They contain an open reading frame that is long enough to encode a transposase, suggesting that the 3.4-kb elements are the full-length copies of the Hoppel family. Multiple alignments of several P-element transposases from different species and the Hoppel-element-encoded peptide showed that all of the P-element introns and the 5' region of the transposase are absent from the Hoppel sequence. Sequence analysis combined with reverse transcriptase PCR analysis showed that the 3.4-kb Hoppel elements are intronless. P and Hoppel not only share similar amino acid sequences but also have terminal inverted repeats of the same length (31 bp), and their excision footprints present a similar structure, which suggests that their transposases are functionally very similar. Thus, we propose that the Hoppel element family be included in the P-element superfamily. Two evolutionary scenarios are discussed considering the presence /absence of introns within the P-element superfamily.

Amino Acid Sequence↗