Search results for "insertion"
showing 10 items of 393 documents
Note critique de "De la formation initiale à la vie active. Faciliter les transitions" (OCDE). 2000
2002
International audience
Contribution of insertions and deletions to the variability of hepatitis C virus populations
2007
Little is known about the potential effects of insertions and deletions (indels) on the evolutionary dynamics of hepatitis C virus (HCV). In fact, the consequences of indels on antiviral treatment response are a field of investigation completely unexplored. Here, an extensive sequencing project was undertaken by cloning and sequencing serum samples from 25 patients infected with HCV subtype 1a and 48 patients with subtype 1b. For 23 patients, samples obtained after treatment with alpha interferon plus ribavirin were also available. Two genome fragments containing the hypervariable regions in the envelope 2 glycoprotein and the PKR-BD domain in NS5A were sequenced, yielding almost 16 000 seq…
Clostridium difficile IStron CdISt1: Discovery of a Variant Encoding Two Complete Transposase-Like Proteins
2004
ABSTRACT Screening a Clostridium difficile strain collection for the chimeric element Cd ISt1 , we identified two additional variants, designated Cd ISt1 -0 and Cd ISt1 -III. In in vitro assays, we could prove the self-splicing ribozyme activity of these variants. Structural comparison of all known Cd ISt1 variants led us to define four types of IStrons that we designated Cd ISt1 -0 through Cd ISt1 -III. Since Cd ISt1 -0 encodes two complete transposase-like proteins (TlpA and TlpB), we suggest that it represents the original genetic element, hypothesized before to have originated by fusion of a group I intron and an insertion sequence element.
Impact of Insertion Sequences and RNAs on Genomic Inversions in Pseudomonas aeruginosa
2022
Abstract In this article, a bioinformatics pipeline is proposed that focuses on two types of elements, namely the mobile genetic elements (MGE) and Ribonucleic acids (RNAs). The MGEs are called insertion sequences (ISs) in the prokaryotic domain. The objective of this research work is to study the behaviour of RNAs and MGEs genes, and the effects of their presence around inversions in genome sequences. The proposed pipeline finds the relation between the transposase gene types (e.g., DDE and DEDD) located within insertion sequences according to their IS family and sub-family, and RNAs (tRNA and rRNA) on the one hand, and genomic inversion on the other hand. More precisely, we wonder whether…
Retroposon insertions provide insights into deep lagomorph evolution.
2010
The homogenous mammalian order Lagomorpha comprises about 80 species in two families, Ochotonidae (pikas) and Leporidae (rabbits and hares). However, the phylogenetic relationships among leporids are controversial. Molecular data, particularly from mitochondrial sequences, give highly homoplasious signals. To resolve the controversy between mitochondrial and nuclear data, we analyzed genomic orthologous retroposon insertion sites, a virtually homoplasy-free marker system. From a differential screen of rabbit genomic data for intronic retroposon insertions of CSINE elements, we polymerase chain reaction-amplified and sequenced 11 retroposons in eight representative lagomorphs. We found three…
Epistasis between new mutations and genetic background and a test of genetic canalization.
2001
The importance for fitness of epistatic interactions among mutations is poorly known, yet epistasis can exert important effects on the dynamics of evolving populations. We showed previously that epistatic interactions are common between pairs of random insertion mutations in the bacterium Escherichia coli. In this paper, we examine interactions between these mutations and other mutations by transducing each of twelve insertion mutations into two genetic backgrounds, one ancestral and the other having evolved in, and adapted to, a defined laboratory environment for 10,000 generations. To assess the effect of the mutation on fitness, we allowed each mutant to compete against its unmutated cou…
Plasmid localisation of atrazine-degrading genes in newly described Chelatobacter and Arthrobacter strains
2002
Abstract In a previous study, we isolated a collection of atrazine-degrading bacteria from various soils. The aim of this study was to localise the atrazine-degrading genes in these 25 atrazine-degrading strains. In the case of the Gram-negative strains of Chelatobacter heintzii, six to seven plasmids were observed. The atzABC and trzD genes were located on two or three plasmids with variable molecular masses. For the Gram-positive strains of Arthrobacter crystallopoietes, the atzBC genes were located on a single plasmid of 117 kb. The organisation of atrazine-degrading genes seems to be highly variable between the strains studied. We have shown by a specific PCR the occurrence of IS1071-li…
Transposons Tn916 and Tn925 can transfer from Enterococcus faecalis to Leuconostoc oenos
1996
The streptococcal transposons Tn916 and Tn925 were transferred to several strains of Leuconostoc (Ln.) oenos using the filter mating method. The insertion of both transposons into the chromosome occurred at different sites. Transconjugants of Ln. oenos carrying Tn916 could serve as donors in mating experiments with Lactococcus lactis LM2301. Further analysis of L. lactis LM2301 transconjugants showed that the insertion of the transposon Tn916 into the chromosome was site-specific. These studies establish a basis for the initiation of genetic studies in this Leuconostoc species since there are no efficient conjugal or transformation systems previously described for this microorganism.
Recovery of Fusarium oxysporum Fo47 mutants affected in their biocontrol activity after transposition of the Fot1 element
2002
Trouvelot, S., Olivain, C., Recorbet, G., Migheli, Q., and Alabouvette, C. 2002. Recovery of Fusarium oxysporum Fo47 mutants affected in their biocontrol activity after transposition of the Fot1 element. Phytopathology 92:936-945. To investigate the biocontrol mechanisms by which the antagonistic Fusarium oxysporum strain Fo47 is active against Fusarium wilt, a Fot1 transposon-mediated insertional mutagenesis approach was adopted to generate mutants affected in their antagonistic activity. Ninety strains in which an active Fot1 copy had transposed were identified with a phenotypic assay for excision and tested for their biocontrol activity against F. oxysporum f. sp. lini on flax in greenho…
Deficiency of the Cockayne syndrome B (CSB) gene aggravates the genomic instability caused by endogenous oxidative DNA base damage in mice.
2007
The Cockayne syndrome B protein (CSB) has long been known to be involved in the repair of DNA modifications that block the RNA polymerase in transcribed DNA sequences (transcription-coupled repair). Recent evidence suggests that it also has a more general role in the repair of oxidative DNA base modifications such as 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxoG). In mammalian cells, 8-oxoG is a substrate of the repair glycosylase OGG1. Mice without this enzyme accumulate 8-oxoG in the genome and have elevated spontaneous mutation rates. To elucidate the role of CSB in the prevention of mutations by oxidative DNA base damage, we have generated mice that are deficient in Csb or Ogg1 or both ge…