Publications associées à Restriction modification system

Molecular mechanism of plasmid elimination by the DdmDE defense system

Melanie Blokesch, Sandrine Stutzmann, David William Adams, Laurie Righi

Seventh pandemic Vibrio cholerae strains contain two pathogenicity islands that encode the DNA defense modules DdmABC and DdmDE. Here we use cryogenic electron microscopy to reveal the mechanistic basis for plasmid defense by DdmDE. A structure of the DdmD ...

American Association for the Advancement of Science2024

Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA

Gabriela Garcia Rodriguez

The rnlAB toxin-antitoxin operon from Escherichia co/ifunctions as an anti-phage defense system. RnlA was identified as a member of the HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding domain) superfamily of ribonucleases. The activity of the tox ...

OXFORD UNIV PRESS2021

In and out—contribution of natural transformation to the shuffling of large genomic regions

Melanie Blokesch

Naturally competent bacteria can pull free DNA from their surroundings. This incoming DNA can serve various purposes, ranging from acting as a source of nutrients or DNA stretches for repair to the acquisition of novel genetic information. The latter proce ...

Elsevier2017

Construction of pDYN6902, a new Streptomyces integrative expression vector designed for cloning sequences interfering with Escherichia coli viability

Julien Hiblot, Pierre Leblond

We describe here the construction of a new version of the Escherichia coli-Streptomyces shuttle cloning vector pIJ6902, which carries the original thiostrepton-inducible PtipA as well as the integrative and cloning systems, but with the E. coil low copy nu ...

Academic Press Inc Elsevier Science2015

Study of transposon-mediated cell pool and cell line generation in CHO cells

Sowmya Balasubramanian

The goal of this thesis was to evaluate the use of artificial transposon systems for the generation of recombinant cell pools and cell lines with Chinese hamster ovary (CHO) cells as the production host. Transposons are naturally occurring genetic elements ...

EPFL2015

Impact Assessment of Pumping Parameters on Groundwater Bacterial Communities

Christof Holliger, Pierre Rossi, Noam Shani, Guillaume Laulan

Groundwater microbial community samples are traditionally collected using pumping techniques optimized for groundwater chemistry assessment, although the impact of groundwater pumping parameters on apparent bacterial community structures (BCSs) is not real ...

Wiley-Blackwell2013

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Christof Holliger, Julien Maillard, Pierre Rossi, David Gregory Weissbrodt, Jacques Rougemont, Noam Shani, Lucas Sinclair

Background: In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microb ...

BioMed Central2012

Assessing the Bacterial Ecology of Organohalide Respiration for the Design of Bioremediation Strategies

Noam Shani

Groundwater is essential for human activities and is sometimes referred to as a non-renewable resource in the same way as oil and gas. During the past century, precious groundwater reserves worldwide have been threatened by anthropogenic release of chemica ...

EPFL2012

Ecology and Biogeography of Bacterial Communities Associated with Chloroethene-Contaminated Aquifers

Christof Holliger, Pierre Rossi, Noam Shani

Massive usage, along with careless handling, storage, spills, and leakages made chloroethenes (CEs) one of the most abundant classes of groundwater contaminants. Anaerobic organohalide respiring bacteria (OHRB) can couple reductive dechlorination of CEs wi ...

Frontiers Media SA2012

ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites

Giovanna Ambrosini, Christian Iseli, Philipp Bucher

Background: Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specificity is not a ...

BioMed Central2011

Distribution of denitrifying bacterial communities in the stratified water column and sediment-water interface in two freshwater lakes and the Baltic Sea

We have studied the distribution and community composition of denitrifying bacteria in the stratified water column and at the sediment-water interface in lakes Plusee and Schohsee, and a near-shore site in the Baltic Sea in Germany. Although environmental ...

2011

Methane- and ammonia-oxidizing bacteria at the chemocline of Lake Kinneret (Israel)

The vertical distribution of methane- and ammonia-oxidizing bacteria (MOB and AOB, respectively), and the physicochemical conditions in the chemocline of Lake Kinneret (Israel) were studied at a resolution of 10 cm from 16.2 to 17.7 m depth. Profiles of th ...

2010

BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies

Gerardo Turcatti

The tricarboxylate reagent benzene-1,3,5-triacetic acid (BTA) was used to attach 5'-aminated DNA primers and templates on an aminosilanized glass surface for subsequent generation of DNA colonies by in situ solid-phase amplification. We have characterized ...

Oxford University Press2006