A5050840445- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- DNA Repair Mechanisms
- CRISPR and Genetic Engineering
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Antibiotic Resistance in Bacteria
- Gene Regulatory Network Analysis
- DNA and Nucleic Acid Chemistry
- Escherichia coli research studies
- Advanced Fluorescence Microscopy Techniques
- Plant Pathogenic Bacteria Studies
- Genetics, Bioinformatics, and Biomedical Research
- Research Data Management Practices
- Metabolomics and Mass Spectrometry Studies
- Salmonella and Campylobacter epidemiology
- Plant-Microbe Interactions and Immunity
- Scientific Computing and Data Management
- Fungal and yeast genetics research
- Algorithms and Data Compression
- Machine Learning in Bioinformatics
- Nematode management and characterization studies
- Mycobacterium research and diagnosis
- Evolution and Genetic Dynamics
University of Edinburgh
2015-2025
École Normale Supérieure Paris-Saclay
2024-2025
Institute of Cell Biology
2021-2025
Laboratoire de Biologie et Pharmacologie Appliquée
2024
Centre National de la Recherche Scientifique
2024
Wellcome Centre for Cell Biology
2021
Center for Systems Biology
2016-2019
Harvard University
2016-2019
Microbiologie de l’alimentation au service de la santé
2009-2012
Institut National de la Recherche Agronomique
1998-2010
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety commensal and pathogenic strains that diversify by high rates genetic change. We uniformly (re-) annotated genomes 20 E. strain fergusonii (the closest related species), including seven we sequenced to completion. Within approximately 18,000 families orthologous genes, found 2,000 common all strains. Although recombination are much higher than mutation rates, show, both...
The fundamental unit of biological diversity is the species. However, a remarkable extent intraspecies in bacteria was discovered by genome sequencing, and it reveals need to develop clear criteria group strains within Two main types analyses used quantify variation at level are average nucleotide identity (ANI), which detects DNA conservation core genome, content, calculates proportion shared two genomes. Both estimates based on BLAST alignments for definition sequences common pair....
Leading researchers working on synthetic biology and its applications gathered at the University of Edinburgh in May 2018 to discuss latest challenges opportunities field. In addition potential socio-economic benefits biology, they also examined ethics security risks arising from development these technologies. Speakers industry, academia not-for-profit organizations presented their vision for future field provided guidance funding regulatory bodies ensure that research is carried out...
Unlike most bacteria, Vibrio cholerae harbors two distinct, nonhomologous circular chromosomes (chromosome I and II). Many features of chromosome II are plasmid-like, which raised questions concerning its chromosomal nature. Plasmid replication segregation generally not coordinated with the bacterial cell cycle, further calling into question mechanisms ensuring synchronous management II. Maintenance replicons requires resolution dimers created by homologous recombination events. In...
DivIVA is a coiled-coil, tropomyosin-like protein of Gram-positive bacteria. Previous work showed that this targeted to division sites and retained at the cell poles after division. In vegetative cells, sequesters MinCD inhibitor poles, thereby helping direct correct midcell site. We now show has second, quite separate role in sporulating cells Bacillus subtilis . It again acts pole but case interacts with chromosome segregation machinery help position oriC region pole, preparation for polar...
Abstract Many key regulatory proteins in bacteria are present too low numbers to be detected with conventional methods, which poses a particular challenge for single-cell analyses because such can contribute greatly phenotypic heterogeneity. Here we develop microfluidics-based platform that enables single-molecule counting of low-abundance by mechanically slowing-down their diffusion within the cytoplasm live Escherichia coli ( E. ) cells. Our technique also allows automated microscopy at...
Significance Maintaining genomic integrity is crucial for cell survival. In Escherichia coli , RecA-mediated homologous recombination plays an essential role in the repair of DNA double-strand breaks (DSBs). A greater understanding mechanism requires quantitative analysis studies live cells. We have developed a novel method that able to capture these interactions on genome-wide scale by combining ChIP-seq and mathematical modeling interpret patterns RecA–DNA interaction during DSB (DSBR)....
Repairing DNA damage is of primary importance for all living organisms. double-strand breaks (DSBs) are one the most serious types damage, as they lead to loss genetic information and death when not repaired. In E. coli , recognised processed by RecBCD complex, which initiates repair homologous recombination. Although dynamics downstream has been well characterised, it still unclear how long this complex stays attached what triggers its dissociation in vivo . To answer these questions, we...
All living organisms have developed strategies to respond chromosomal damage and preserve genome integrity. One such response is the repair of DNA double-strand breaks (DSBs), one most toxic forms lesions. In Escherichia coli , DSBs are repaired via RecBCD-dependent homologous recombination. RecBCD essential for accurate chromosome maintenance, but its over-expression can lead reduced ability. This apparent paradox suggests that copy numbers may need be tightly controlled within an optimal...
Abstract Cell biology is increasingly dependent on quantitative methods resulting in the need for microscopic labelling technologies that are highly sensitive and specific. Whilst use of fluorescent proteins has led to major advances, they also suffer from their relatively low brightness photo-stability, making detection very abundance using protein-based challenging. Here, we characterize self-labelling protein tag called HaloTag, conjunction with an organic dye, label accurately count...
In natural environments, bacteria are frequently exposed to sub-lethal levels of DNA damage, which leads the induction a stress response (the SOS in Escherichia coli). Natural environments also vary nutrient availability, resulting distinct physiological changes bacteria, may have direct implications on their capacity repair chromosomes. Here, we evaluated impact varying availability expression induced by chronic damage E. coli. We found heterogeneous regulon at single-cell level all growth...
Bacterial biodiversity at the species level, in terms of gene acquisition or loss, is so immense that it raises question how essential chromosomal regions are spared from uncontrolled rearrangements. Protection genome likely depends on specific DNA motifs impose limits undergo recombination. Although most such remain unidentified, they theoretically predictable based their genomic distribution properties. We examined "crossover hotspot instigator," Chi, Escherichia coli, and found its...
Studies of RecBCD–Chi interactions in Escherichia coli have served as a model to understand recombination events bacteria. However, the existence similar has not been demonstrated bacteria unrelated E. . We developed an vivo examine components dsDNA break repair various microorganisms. Here, we identify major exonuclease Lactococcus lactis , Gram-positive organism evolutionarily distant from and provide evidence for exonuclease–Chi interactions. Insertional mutants L. screened...
The Escherichia coli Chi site 5′‐GCTGGTGG‐3′ modulates the activity of powerful dsDNA exonuclease and helicase RecBCD. Genome sequence analyses revealed that is frequent on chromosome oriented with respect to replication E . genome. also present much more frequently than predicted statistically for a random 8‐mer sequence. Although it assumed ubiquitous, there virtually no proof its features are conserved in other microorganisms. We therefore identified analysed an organism which full genome...
Abstract Background Public databases now contain multitude of complete bacterial genomes, including several genomes the same species. The available data offers new opportunities to address questions about genome evolution, a task that requires reliable fine comparison closely related genomes. Recent analyses have shown, using pairwise whole alignments, it is possible segment into common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach...
Bacteria use the global bipolarization of their chromosomes into replichores to control dynamics and segregation genome during cell cycle. This involves protein activities by recognition specific short DNA motifs whose orientation along chromosome is highly skewed. The KOPS act in orienting activity FtsK translocase towards terminal replichore junction. have been identified γ-Proteobacteria Bacillus subtilis as closely related G-rich octamers. We motif Lactococcus lactis , a model bacteria...
Streptococcus pneumoniae is a human pathogen that naturally transformable. In this study major component of the homologous recombination pathway, RexAB exonuclease/helicase, was characterized. rexA and rexB insertional mutants were constructed using mariner mutagenesis found to have identical phenotypes. Both rexAB displayed poor cell viability, reduced double-strand exonuclease activity, UV sensitivity level gene conversion compared wild-type strain. No effect observed on plasmid...
Numerous strategies allowing bacteria to detect and respond oxidative conditions depend on the cell redox state. Here we examined ability of Lactococcus lactis survive aerobically in presence reducing agent dithiothreitol (DTT), which would be expected modify state disable stress response. DTT inhibited L. growth at 37 degrees C aerobic conditions, but not anaerobiosis. Mutants selected as resistant all mapped pstFEDCBA locus, encoding a high-affinity phosphate transporter. Transcription...