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Functional analysis and annotation of the virulence plasmid pMUM001 from Mycobacterium ulcerans

Publications associées (35)

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Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae

Melanie Blokesch, David William Adams, Milena Jadwiga Jaskolska

Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability o ...

2022

Natural competence for transformation is an important driver of horizontal DNA exchange between different organisms. This can result in accumulation of dangerous genetic features, such as antibiotic resistance genes, in a single organism. One example of an ...

EPFL2022

New Genome Similarity Measures based on Conserved Gene Adjacencies

Bernard Moret, Shachi Shailesh Deshpande

Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, ...

Mary Ann Liebert2017

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DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from ...

Oxford University Press2015

Computational analysis of ultraconserved non-coding DNA elements in vertebrate genomes

Slavica Dimitrieva Janeva

Recent advancements in DNA sequencing technologies, accompanied by parallel development of sophisticated computational methods, offer an unprecedented opportunity to explore and study the genetic material of many organisms. However, despite the tremendous ...

EPFL2013

MAR-mediated integration of plasmid vectors for in vivo gene transfer and regulation

Andrzej Kulik, Nicolas Mermod, Stefania Puttini, Déborah Ley, Damien Saugy

Background: The in vivo transfer of naked plasmid DNA into organs such as muscles is commonly used to assess the expression of prophylactic or therapeutic genes in animal disease models. Results: In this study, we devised vectors allowing a tight regulatio ...

BioMed Central2013

Several methods are available to manipulate bacterial chromosomes(1-3). Most of these protocols rely on the insertion of conditionally replicative plasmids (e.g. harboring pir-dependent or temperature-sensitive replicons(1,2)). These plasmids are integrate ...

2012

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Comparative analyses of various mammalian genomes have identified numerous conserved non-coding (CNC) DNA elements that display striking conservation among species, suggesting that they have maintained specific functions throughout evolution. CNC function ...

Public Library of Science2011

The Interplay between Cytidine Deaminases, HIV and Domesticated Genetic Parasites

"There is more virus in us than us in us". John Coffin's famous sentence illustrates that particular nucleic acid sequences related to exogenous viruses, called retrotransposons, constitute almost half of the human genome and largely exceeds the amount of ...

EPFL2010