Biomedical subjects

H Chiapello

Publications and source records attributed to H Chiapello.

10 recordsLinked to original sources

PubMed2002

Deciphering Arabidopsis thaliana gene neighborhoods through bibliographic co-citations.

In the framework of genome annotation, scientific literature is obviously the major source of biological knowledge. The aim of the work described in this paper is to exploit this source of data for the model plant Arabidopsis thaliana. The first step has consisted in constituting a relevant bibliographic references dataset for plant genomic research. Genes co-citations have then been systematically annotated in this reference dataset, starting from the simple idea that if genes are cited in the same publication, they must probably share some related functional properties. In order to deal with the synonymous gene name problem, a gene name reference list has been constituted starting from A. thaliana SwissProt entries. This list was used to build clusters of co-cited genes by a single linkage procedure such that any gene in a given cluster possesses at least one co-cited partner in the same cluster. Analysis of the clusters demonstrate the biological consistency of this approach, with only very few fortuitous links. As an example, a cluster including genes related to flowering time is more deeply described in the paper. Finally, a graphical representation of each cluster was performed, which provides a convenient way to retrieve the genes (the nodes of the graphs) and the references in which they were co-cited (the edges of the graphs). All the results can be accessed at the URL http://chlora.Igi.infobiogen.fr:1234/bib_arath/.

Arabidopsis↗

PubMed2001

Tnt1 transposition events are induced by in vitro transformation of Arabidopsis thaliana, and transposed copies integrate into genes.

Tissue culture has been shown to induce the transposition of plant transposable elements; their insertion at novel sites results in somaclonal variation. Introduction of the tobacco retrotransposon Tnt1 into Arabidopsis thaliana by co-cultivation of root explants with Agrobacterium tumefaciens induces its transposition at a high frequency, but no transposed copies are found in plants transformed by the in planta procedure. Transposition occurs in the transformed root cells or in the calli derived from them, allowing the regeneration of transformed plants with up to 26 transposed copies of Tnt1. Analysis of Tnt1 integration sites in Arabidopsis shows that the Tnt1 endonuclease does not show any cleavage-site specificity at the sequence level. The insertion sites are unlinked and distributed on all five Arabidopsis chromosomes. The fact that the majority of the integration sites are located in coding regions, and none in repeated sequences, demonstrates the potential of Tnt1 as a tool for gene tagging.

Agrobacterium tumefaciens↗

PubMed2001

SPiD: a subtilis protein interaction database.

MOTIVATION: Protein-protein interactions are a potential source of valuable clues in determining the functional role of as yet uncharacterized gene products in metabolic pathways. Graph-like structures emerging from the accumulation of interaction data make it difficult to maintain a consistent and global overview by hand. Bioinformatics tools are needed to perform this graph visualization while maintaining a link to the experimental data. RESULTS: "SPiD" is an online database for exploring networks of interacting proteins in Bacillus subtilis characterized by the two-hybrid system. Graphical displays of interaction networks are created dynamically as users interactively navigate through these networks. Third party applications can interface the database through a Common Object Request Broker Architecture (CORBA) tier. AVAILABILITY: SPiD is available through its web site at http://www-mig.versailles.inra.fr/bdsi/SPiD, and through an Interoperable Object Reference (IOR) and its associated Interface Definition Language (IDL). CONTACT: hoebeke@versailles.inra.fr

Bacillus subtilis↗

PubMed2000

Detecting localized repeats in genomic sequences: a new strategy and its application to Bacillus subtilis and Arabidopsis thaliana sequences.

A new method for the search of local repeats in long DNA sequences, such as complete genomes, is presented. It detects a large variety of repeats varying in length from one to several hundred bases, which may contain many mutations. By mutations we mean substitutions, insertions or deletions of one or more bases. The method is based on counting occurrences of short words (3-12 bases) in sequence fragments called windows. A score is computed for each window, based on calculating exact word occurrence probabilities for all the words of a given length in the window. The probabilities are defined using a Bernoulli model (independent letters) for the sequence, using the actual letter frequencies from each window. A plot of the probabilities along the sequence for high-scoring windows facilitates the identification of the repeated patterns. We applied the method to the 1.87 Mb sequence of chromosome 4 of Arabidopsis thaliana and to the complete genome of Bacillus subtilis (4.2 Mb). The repeats that we found were classified according to their size, number of occurrences, distance between occurrences, and location with respect to genes. The method proves particularly useful in detecting long, inexact repeats that are local, but not necessarily tandem. The method is implemented as a C program called EXCEP, which is available on request from the authors.

Arabidopsis↗

PubMed1999

Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases.

In spite of many efforts, the prediction of the location of proteins in eukaryotic cells (cytoplasm, mitochondrion or chloroplast) is still far from straightforward. In some cases (e.g. ribosomal proteins and aminoacyl-tRNA synthetases) both the cytoplasmic proteins and their organellar counterparts are encoded by the nuclear genome. A factorial correspondence analysis of the codon usage in yeast and Caenorhabditis elegans shows that the codon usage of those nuclear genes encoding ribosomal proteins or aminoacyl-tRNA synthetases is markedly different, depending on the final location of the proteins (cytoplasmic or mitochondrial). As a consequence, the location of such proteins-whose sequences are now frequently determined by systematic genomic sequencing-can be easily and quickly predicted. A WWW interface has been developed, aimed at providing a user-friendly tool for codon usage pattern analysis. It is available from http://www.genetique.uvsq.fr/afc.html

Amino Acyl-tRNA Synthetases↗

PubMed1998

Codon usage and gene function are related in sequences of Arabidopsis thaliana.

In this paper, the relationship between codon usage and the physiological pattern of expression of a gene is investigated while considering a dataset of 815 nuclear genes of Arabidopsis thaliana. Factorial Correspondence Analysis, a commonly used multivariate statistical approach in codon usage analysis, was used in order to analyse codon usage bias gene by gene. The analysis reveals a single major trend in codon usage among genes in Arabidopsis. At one end of the trend lie genes with a highly G/C biased codon usage. This group contains mainly photosynthetic and housekeeping genes which are known to encode the most abundant proteins of the vegetal cell. At the other extreme lie genes with a weaker A/T-biased codon usage. This group contain genes with various functions which exhibits most of the time a strong tissue-specific pattern of expression in relation, for example, to stress conditions. These observations were confirmed by the detailed analysis of codon usage in the multigene family of tubulins and appear to be general in plant species, even as distant from Arabidopsis thaliana as a monocotyledonous plant such as maize.

Arabidopsis↗

PubMed1998

Evolution of genes, evolution of species: the case of aminoacyl-tRNA synthetases.

All of the aminoacyl-tRNA synthetase (aaRS) sequences currently available in the data banks have been subjected to a systematic analysis aimed at finding gene duplications, genetic recombinations, and horizontal transfers. Evidence is provided for the occurrence (or probable occurrence) of such phenomena within this class of enzymes. In particular, it is suggested that the monomeric PheRS from the yeast mitochondrion is a chimera of the alpha and beta chains of the standard tetrameric protein. In addition, it is proposed that the dimeric and tetrameric forms of GlyRS are the result of a double and independent acquisition of the same specificity within two different subclasses of aaRS. The phylogenetic reconstructions of the evolutionary histories of the genes encoding aaRS are shown to be extremely diverse. While large segments of the population are consistent with the broad grouping into the three Woesian domains, some phylogenetic reconstructions do not place the Archae and the Eucarya as sister groups but, rather, show a gram-negative bacteria/eukaryote clustering. In addition, many individual genes pose difficulties that preclude any simple evolutionary scheme. Thus, aaRS's are clearly a paradigm of F. Jacob's "odd jobs of evolution" but, on the whole, do not call into question the evolutionary scenario originally proposed by Woese and subsequently refined by others.

Amino Acid Sequence↗

PubMed1998

Indigo: a World-Wide-Web review of genomes and gene functions.

The present article describes a genome database reviewing gene-related knowledge of two model bacteria, Bacillus subtilis and Escherichia coli. The database, Indigo, is open through the World-Wide Web (http://indigo.genetique.uvsq.fr). The concept used for organising the data, the concept of neighbourhood, allows one to explore the database content in an efficient although somewhat unusual way. Here, genes are related to each other by a variety of neighbourhoods, including proximity in the chromosome, phylogenetic kinship, participation in a common metabolic pathway, common presence in an article of the literature, or similar use of the genetic code. Several examples illustrate how this concept of neighbourhood permits one to review the available knowledge about a given gene or gene family, and elaborate unexpected, but revealing, analyses about gene functions.

Bacillus subtilis↗

PubMed1993

An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana.

As part of the goal to generate a detailed transcript map for Arabidopsis thaliana, 1152 single run sequences (expressed sequence tags or ESTs) have been determined from cDNA clones taken at random in libraries prepared from different sources of plant material: developing siliques, etiolated seedlings, flower buds, and cultured cells. Eight hundred and ninety-five different genes could be identified, 32% of which showed significant similarity to existing sequences in Arabidopsis and an array of other organisms. These sequences in combination with their positioning on the Arabidopsis genetic map will not only constitute a new set of molecular markers for genome analysis in Arabidopsis but also provide a direct route for the in vivo analysis of their gene products. The sequences have been made available to the public databases.

Animals↗

PubMed1977

[Urea cycle and purinolysis in the embryos and pregnant females of the teleost fish Poecilia reticulata].

The presence of a functional ornithine-urea cycle is evidenced in the embryos of the viviparous Teleost Poecilia reticulata. The activity of the cycle decreases during developmental period but persists in adult tissues. Purinolytic (uricolytic) pathway is another source of urea in both embryos and adults. The implications of these findings are briefly discussed in relation to the problems of ureogenic and ureosmotic phenomena in Teleostean Fishes.

Animals↗