Multiple Comparative Metagenomics using Multiset k-mer Counting

Background. Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole sets of sequences, either do not scale up on ambitious metagenomic projects or do not provide precise and exhaustive results. Methods. These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecological distances by replacing species counts by k-mer counts. Simka scales-up today's metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Results. Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecological distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy or which are based on taxonomic profiling

Influenza vaccine coverage for healthcare workers in geriatric settings in France

Background and aims: Because of a relative lack of efficiency of influenza vaccine in the elderly population, influenza outbreaks in geriatric healthcare settings are probable, despite high influenza vaccination rates in patients. Nosocomial influenza outbreaks, more probably related to healthcare workers, have also been reported. Therefore, vaccination of healthcare workers is considered to be an important preventive policy, to decrease the in- hospital influenza burden during the viral circulation period. Methods: This multicenter study measured influenza vaccine coverage of Health Care Worker in 102 geriatric healthcare settings (acute care, rehabilitation care, long- term care) by a first questionnaire. A second questionnaire assessed main factors associated with vaccine acceptance. Results: 102 geriatric healthcare settings (20%) answered the first questionnaire. Vaccine coverage for physicians (n=187), nurses (n=631) and nurse assistants (n=1487) were 48.4%, 30.5% and 27.9%, respectively. Vaccination rates were correlated between occupational categories according to healthcare settings. Vaccination rates were significantly lower in acute care settings compared with rehabilitation and long- term care settings. Local recommendations was reported for 29.9%, but was not correlated with vaccine coverage. The second questionnaire showed that lack of motivation and knowledge, and organizational problems were the three main reasons for reluctance to be vaccinated. Conclusions: In French geriatric settings, influenza vaccine coverage of healthcare workers is low and highly variable, according to the type of healthcare setting. A group effect was found between occupational categories. However, the reasons for non- acceptance need further evaluation to improve HCW influenza vaccine coverag

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph

International audienceData volumes generated by next-generation sequencing (NGS) technologies is now a major concern for both data storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as the widely used gzip method.We present a novel reference-free method meant to compress data issued from high throughput sequencing technologies. Our approach, implemented in the software LEON, employs techniques derived from existing assembly principles. The method is based on a reference probabilistic de Bruijn Graph, built de novo from the set of reads and stored in a Bloom filter. Each read is encoded as a path in this graph, by memorizing an anchoring kmer and a list of bifurcations. The same probabilistic de Bruijn Graph is used to perform a lossy transformation of the quality scores, which allows to obtain higher compression rates without losing pertinent information for downstream analyses.LEON was run on various real sequencing datasets (whole genome, exome, RNA-seq or metagenomics). In all cases, LEON showed higher overall compression ratios than state-of-the-art compression software. On a C. elegans whole genome sequencing dataset, LEON divided the original file size by more than 20. LEON is an open source software, distributed under GNU affero GPL License, available for download at http://gatb.inria.fr/software/leon/

Case report:Thirty-year progression of an EMPF1 encephalopathy due to defective mitochondrial and peroxisomal fission caused by a novel de novo heterozygous DNM1L variant

Mutations in DNM1L (DRP1), which encode a key player of mitochondrial and peroxisomal fission, have been reported in patients with the variable phenotypic spectrum, ranging from non-syndromic optic atrophy to lethal infantile encephalopathy. Here, we report a case of an adult female patient presenting with a complex neurological phenotype that associates axonal sensory neuropathy, spasticity, optic atrophy, dysarthria, dysphasia, dystonia, and ataxia, worsening with aging. Whole-exome sequencing revealed a heterozygous de novo variant in the GTPase domain of DNM1L [NM_001278464.1: c.176C>A p.(Thr59Asn)] making her the oldest patient suffering from encephalopathy due to defective mitochondrial and peroxisomal fission-1. In silico analysis suggested a protein destabilization effect of the variant Thr59Asn. Unexpectedly, Western blotting disclosed profound decrease of DNM1L expression, probably related to the degradation of DNM1L complexes. A detailed description of mitochondrial and peroxisomal anomalies in transmission electron and 3D fluorescence microscopy studies confirmed the exceptional phenotype of this patient

OryGenesDB: a database for rice reverse genetics

Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB (), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an ‘anchoring’ option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors

Rémy Ollier And Imperial Citizenship

This essay discusses Rémy Ollier’s (1816–45) journalism. As an early claimant of citizenship through (rather than against) the British Empire during the 1840s, Ollier attempted to redress a gap that he perceived between the institutionalization of rights in Britain and Mauritius. Established accounts of Ollier’s political intervention provide a rich narrative of how his efforts are implicated in the development of rights in Mauritius and broader postcolonial nationalisms. However, I argue that facets of his expression of imperial citizenship reside apart from this genealogy. To explore how Ollier uniquely created imperial citizenship, an “acts”-influenced approach to citizenship is adopted. By analyzing his writings in La Sentinelle de Maurice, I reveal how imperial citizenship is generated through a subversive loyalism to Britain and an orientalist portrayal of indentured labourers. I conclude by mobilizing Ollier’s struggle as a challenge to the notion that citizenship realizes itself in teleological fashion