A New Integrative and Mobilizable Element Is a Major Contributor to Tetracycline Resistance in subsp. .

Tetracycline resistance in streptococci is mainly due to ribosomal protection mediated by the (M) gene that is usually located in the integrative and conjugative elements (ICEs) of the Tn-family. In this study, we analyzed the genes involved in tetracycline resistance and the associated mobile genetic elements (MGEs) in subsp. (SDSE) causing invasive disease.

ICEscreen: a tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.

Mobile Genetic Elements (MGEs) are integrated in bacterial genomes and key elements that drive prokaryote genome evolution. Among them are Integrative and Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) which are important for bacterial fitness since they frequently carry genes participating in important bacterial adaptation phenotypes such as antibiotic resistance, virulence or specialized metabolic pathways. Although ICEs and IMEs are widespread, they are as yet almost never annotated in public bacterial genomes.

FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs.

Objectives: 'Integrative and Conjugative Elements' (ICEs) and 'Integrative and Mobilizable Elements' (IMEs) are two classes of mobile genetic elements that are complex to detect and delineate. Therefore, they are yet poorly annotated in bacterial genomes. FirmiData provides to the scientific community of microbiologists and bioinformaticians a reference resource of annotated ICEs and of IMEs from Firmicutes.

Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of to the Environment.

is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in genome diversity.

The importance of simulated lung fluid (SLF) extractions for a more relevant evaluation of the oxidative potential of particulate matter.

Particulate matter (PM) induces oxidative stress in vivo, leading to adverse health effects. Oxidative potential (OP) of PM is increasingly studied as a relevant metric for health impact (instead of PM mass concentration) as much of the ambient particle mass do not contribute to PM toxicity. Several assays have been developed to quantify PM oxidative potential and a widely used one is the acellular dithiothreitol (DTT) assay.

New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration.

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus.

Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT.

Motivation: High-throughput sequencing technologies provide access to an increasing number of bacterial genomes. Today, many analyses involve the comparison of biological properties among many strains of a given species, or among species of a particular genus. Tools that can help the microbiologist with these tasks become increasingly important.

Insyght: navigating amongst abundant homologues, syntenies and gene functional annotations in bacteria, it's that symbol!

High-throughput techniques have considerably increased the potential of comparative genomics whilst simultaneously posing many new challenges. One of those challenges involves efficiently mining the large amount of data produced and exploring the landscape of both conserved and idiosyncratic genomic regions across multiple genomes. Domains of application of these analyses are diverse: identification of evolutionary events, inference of gene functions, detection of niche-specific genes or phylogenetic profiling.

CompaGB: An open framework for genome browsers comparison.

Background: Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming.

Findings: To assist in this task, we propose a community-based framework based on two cornerstones: (i) the implementation of industry promoted software qualification method (QSOS) adapted for genome browser evaluations, and (ii) a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations.

Meeting the need to train more doctors: The role of community-based preceptors.

Community-based precepting is becoming a critical component of Canadian medical education. Calls from the public to train increased numbers of physicians have placed more students in community-based settings. Other countries are facing similar situations.