Search results for "sequencing"
showing 10 items of 1087 documents
Natural soil reservoirs for human pathogenic and fecal indicator bacteria
2015
Prod ? EA UB INRA BIOME; International audience; résumé du livre : Environmental microbiology, the study of the roles that microbes play in all planetary environments, is one of the most important areas of scientific research. The The Manual of Environmental Microbiology, Fourth Edition, provides comprehensive coverage of this critical and growing field. Thoroughly updated and revised, the Manuall is the definitive reference for information on microbes in air, water, and soil and their impact on human health and welfare. Written in accessible, clear prose, the manual covers four broad areas: general methodologies, environmental public health microbiology, microbial ecology, and biodegradati…
Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes
2019
γδ T lymphocytes represent ∼1% of human peripheral blood mononuclear cells and even more cells in most tissues of vertebrates. Although they have important anticancer functions, most current single-cell RNA sequencing (scRNA-seq) studies do not identify γδ T lymphocytes because their transcriptomes at the single-cell level are unknown. Here we show that high-resolution clustering of large scRNA-seq datasets and a combination of gene signatures allow the specific detection of human γδ T lymphocytes and identification of their T cell receptor (TCR)Vδ1 and TCRVδ2 subsets in large datasets from complex cell mixtures. In t -distributed stochastic neighbor embedding plots from blood and tumor sa…
Identification of molecular and physiopathologic basis in oral-facial-digital syndromes
2016
Oral-facial-digital syndromes (OFDS) are characterized by the association of oral, facial and digital anomalies. The different modes of inheritance and additional features lead to clinically delineate 13 subtypes. For a long time, only the OFD1 gene, responsible for OFDI subtype and coding for a centrosomal protein, has been known, suggesting the involvement of the primary cilium in OFDS. Mutations have recently been reported in the TMEM216, DDX59, SCLT1, TBC1D32 and TCTN3 genes in anecdotic cases. To identify new genes involved in OFDS, we performed whole-exome sequencing in 24 patients. In 14/24 cases, we identified 5 novel genes (C2CD3, TMEM107, INTU, KIAA0753, IFT57), enlarged the clini…
Genomic characterization of mosaic cutaneous pigmentary disorders
2019
Ntroduction: Mosaic cutaneous dyschromia is strongly evocative of an underlying genetic mosaicism. These post-zygotic events are challenging for conventional diagnostic tools. Thus, genetic basis of mosaic cutaneous dyschromia still remained poorly understood. Materials and Methods: The M.U.S.T.A.R.D. cohort gathers DNA from skin biopsies of patients with mosaic cutaneous dyschromia. After a specialised phenotype analysis, they are referred to either trio exome sequencing (ES) at 200X, or targeted ultra-deep sequencing (60,000X) of candidate genes. Data are analysed with a tailored pipeline, allowing detection of both low-rate nucleotidic variations or chromosomal events. Results: From 2013…
Biodiversité fongique du raisin au vin : impact de l'activité anthropique
2016
The effects of different anthropogenic activities (vineyard, winery) on fungal populations from grape to wine were studied. To characterize these effects, it was necessary to access to the overall diversity of populations (pyrosequencing and spectroscopy FT-IR) but also to intra-specific diversity (FT-IR). Spectroscopy FT-IR has been validated for their ability to characterize the global population and to discriminate the strains for three species of non-Saccharomyces yeasts (NS). For the first time, it is shown that the grape berry is a limited source for NS yeasts while the winery seems to be a significant source; the air is an important vector for dissemination of these yeasts. In additi…
Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil
2013
International audience; Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic compos…
Response of soil bacterial communities to the incorporation of crop residues : influence of agricultural practices and link with the soil biological …
2010
The effect of the location of wheat residues (soil surface vs. incorporated in soil) on their decomposition and on soil bacterial communities was investigated by the means of a field experiment. Bacterial-Automated Ribosomal Intergenic Spacer Analysis (B-ARISA) of DNA extracts from residues, detritusphere (soil adjacent to residues), and bulk soil evidenced that residues constitute the zone of maximal changes in bacterial composition. However, the location of the residues influenced greatly their decomposition and the dynamics of the colonizing bacterial communities. Sequencing of 16S rRNA gene in DNA extracts from the residues at the early, middle, and late stages of degradation confirmed …
Response of soil bacterial communities to the incorporation of crop residues : influence of agricultural practices and link with the soil biological …
2010
The effect of the location of wheat residues (soil surface vs. incorporated in soil) on their decomposition and on soil bacterial communities was investigated by the means of a field experiment. Bacterial-Automated Ribosomal Intergenic Spacer Analysis (B-ARISA) of DNA extracts from residues, detritusphere (soil adjacent to residues), and bulk soil evidenced that residues constitute the zone of maximal changes in bacterial composition. However, the location of the residues influenced greatly their decomposition and the dynamics of the colonizing bacterial communities. Sequencing of 16S rRNA gene in DNA extracts from the residues at the early, middle, and late stages of degradation confirmed …
GnS-PIPE: an optimized bionformatic pipeline to efficiently assess microbial taxonomic diversity of complex environments using high throughput sequen…
2013
International audience; The rRNA genes (16S, 18S, ITS) are widely used to study microbial communities in soils, as they can be easily amplified from metagenomic DNA. Moreover, the recent development of high-throughput sequencing technologies allows the assessment of millions of sequences from a single metagenomic DNA. Some pipelines are already available (e.g. QIIME or Mothur) to efficiently treat such data. However, the development of bioinformatic tools must now be validated by various biological tests. This was particularly true for key steps to appraise microbial diversity and richness. Here, we present a new pipeline named GnS-PIPE, a software application performing bacterial, archaeal…
GnS-PIPE: an optimized bionformatic pipeline to efficiently assess microbial taxonomic diversity of complex environments using high throughput sequen…
2013
International audience; The rRNA genes (16S, 18S, ITS) are widely used to study microbial communities in soils, as they can be easily amplified from metagenomic DNA. Moreover, the recent development of high-throughput sequencing technologies allows the assessment of millions of sequences from a single metagenomic DNA. Some pipelines are already available (e.g. QIIME or Mothur) to efficiently treat such data. However, the development of bioinformatic tools must now be validated by various biological tests. This was particularly true for key steps to appraise microbial diversity and richness. Here, we present a new pipeline named GnS-PIPE, a software application performing bacterial, archaeal…