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KASpOD—a web service for highly specific and explorative oligonucleotide design

Nicolas Parisot, Jérémie Denonfoux, Eric Dugat-Bony, Pierre Peyret, Eric Peyretaillade
2012 Bioinformatics  
KASpOD is a web service dedicated to the design of signature sequences using a k-mer-based algorithm. Such highly specific and explorative oligonucleotides are then suitable for various goals, including Phylogenetic Oligonucleotide Arrays.
doi:10.1093/bioinformatics/bts597 pmid:23047560 fatcat:6prdndhwr5ag5benovustokd64

Detecting unknown sequences with DNA microarrays: explorative probe design strategies

Eric Dugat-Bony, Eric Peyretaillade, Nicolas Parisot, Corinne Biderre-Petit, Faouzi Jaziri, David Hill, Sébastien Rimour, Pierre Peyret
2011 Environmental Microbiology  
Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next-generation sequencing methods. It is now possible to
more » ... take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high-density microarray formats.
doi:10.1111/j.1462-2920.2011.02559.x pmid:21895914 fatcat:3lxrak2jjjhzpeyqst52sdzocm

ASaiM: a Galaxy-based framework to analyze microbiota data

Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret
2018 GigaScience  
doi:10.1093/gigascience/giy057 pmid:29790941 pmcid:PMC6007547 fatcat:guy4ocqx3vhgfn2pk7nd5jmnda

HiSpOD: probe design for functional DNA microarrays

Eric Dugat-Bony, Mohieddine Missaoui, Eric Peyretaillade, Corinne Biderre-Petit, Ourdia Bouzid, Christophe Gouinaud, David Hill, Pierre Peyret
2011 Computer applications in the biosciences : CABIOS  
Motivation: The use of DNA
doi:10.1093/bioinformatics/btq712 pmid:21216777 fatcat:oa57uroeazbhvmtrjb66fx2ccy

ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota [article]

Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret
2017 bioRxiv   pre-print
New generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota
more » ... analyses. ASaiM provides a curated collection of tools to explore and visualize taxonomic and functional information from raw amplicon, metagenomic or metatranscriptomic sequences. To guide different analyses, several customizable workflows are included. All workflows are supported by tutorials and Galaxy interactive tours to guide the users through the analyses step by step. ASaiM is implemented as Galaxy Docker flavour. It is scalable to many thousand datasets, but also can be used a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io/). Based on the Galaxy framework, ASaiM offers sophisticated analyses to scientists without command-line knowledge. ASaiM provides a powerful framework to easily and quickly explore microbiota data in a reproducible and transparent environment.
doi:10.1101/183970 fatcat:ibolunrhlzc4nldbpj2pbof56m

In situTCE degradation mediated by complex dehalorespiring communities during biostimulation processes

Eric Dugat-Bony, Corinne Biderre-Petit, Faouzi Jaziri, Maude M. David, Jérémie Denonfoux, Delina Y. Lyon, Jean-Yves Richard, Cyrille Curvers, Delphine Boucher, Timothy M. Vogel, Eric Peyretaillade, Pierre Peyret
2012 Microbial Biotechnology  
The bioremediation of chloroethene contaminants in groundwater polluted systems is still a serious environmental challenge. Many previous studies have shown that cooperation of several dechlorinators is crucial for complete dechlorination of trichloroethene to ethene. In the present study, we used an explorative functional DNA microarray (DechloArray) to examine the composition of specific functional genes in groundwater samples in which chloroethene bioremediation was enhanced by delivery of
more » ... drogenreleasing compounds. Our results demonstrate for the first time that complete biodegradation occurs through spatial and temporal variations of a wide diversity of dehalorespiring populations involving both Sulfurospirillum, Dehalobacter, Desulfitobacterium, Geobacter and Dehalococcoides genera. Sulfurospirillum appears to be the most active in the highly contaminated source zone, while Geobacter was only detected in the slightly contaminated downstream zone. The concomitant detection of both bvcA and vcrA genes suggests that at least two different Dehalococcoides species are probably responsible for the dechlorination of dichloroethenes and vinyl chloride to ethene. These species were not detected on sites where cis-dichloroethene accumulation was observed. These results support the notion that monitoring dechlorinators by the presence of specific functional biomarkers using a powerful tool such as DechloArray will be useful for surveying the efficiency of bioremediation strategies.
doi:10.1111/j.1751-7915.2012.00339.x pmid:22432919 pmcid:PMC3815876 fatcat:lngzf2l43nabvg56gd2qdibxqu

Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation

Eric Peyretaillade, Olivier Gonçalves, Sébastien Terrat, Eric Dugat-Bony, Patrick Wincker, Robert S Cornman, Jay D Evans, Frédéric Delbac, Pierre Peyret
2009 BMC Genomics  
, Sébastien Terrat, Eric Dugat-Bony, Patrick Wincker, Robert S Cornman, Jay D Evans, Frédéric Delbac, Pierre Peyret To cite this version: Eric Peyretaillade, Olivier Gonçalves, Sébastien Terrat, Eric Dugat-Bony  ...  Bio-analysis strategy for DNA signal identification Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation Eric Peyretaillade, Olivier Gonçalves  ... 
doi:10.1186/1471-2164-10-607 pmid:20003517 pmcid:PMC2803860 fatcat:cnoa62mtljgjppeovamduy34ma

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

Sébastien Terrat, Eric Peyretaillade, Olivier Gonçalves, Eric Dugat-Bony, Fabrice Gravelat, Anne Moné, Corinne Biderre-Petit, Delphine Boucher, Julien Troquet, Pierre Peyret
2010 BMC Bioinformatics  
Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex
more » ... ronments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes. Results: First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently. Conclusions: We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license.
doi:10.1186/1471-2105-11-478 pmid:20860850 pmcid:PMC2955052 fatcat:h6team34s5ggtjsvcycnylvmsm

Functional Characteristics of a Highly Specific Integrase Encoded by an LTR-Retrotransposon

Babacar Faye, Frederick Arnaud, Eric Peyretaillade, Emilie Brasset, Bernard Dastugue, Chantal Vaury, Jean-Nicolas Volff
2008 PLoS ONE  
Citation: Faye B, Arnaud F, Peyretaillade E, Brasset E, Dastugue B, et al. (2008) Functional Characteristics of a Highly Specific Integrase Encoded by an LTR-Retrotransposon. PLoS ONE 3(9): e3185.  ... 
doi:10.1371/journal.pone.0003185 pmid:18784842 pmcid:PMC2527525 fatcat:oppksvjblfhifflfhdyzumsjay

Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms

Cyrielle Gasc, Eric Peyretaillade, Pierre Peyret
2016 Nucleic Acids Research  
The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific
more » ... iomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.
doi:10.1093/nar/gkw309 pmid:27105841 pmcid:PMC4889952 fatcat:ibzxckbn6zc5bdcspsmkubvxvu

Annotation of microsporidian genomes using transcriptional signals

Eric Peyretaillade, Nicolas Parisot, Valérie Polonais, Sébastien Terrat, Jérémie Denonfoux, Eric Dugat-Bony, Ivan Wawrzyniak, Corinne Biderre-Petit, Antoine Mahul, Sébastien Rimour, Olivier Gonçalves, Stéphanie Bornes (+8 others)
2012 Nature Communications  
High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DnA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative
more » ... mic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-associated proteins, which represent good candidates involved in the spore architecture, the invasion process and the microsporidianhost relationships. Furthermore, we find that the ten-fold variation in microsporidian genome sizes is not due to gene number, size or complexity, but instead stems from the presence of transposable elements. such elements, along with kinase regulatory pathways and specific transporters, appear to be key factors in microsporidian adaptive processes.
doi:10.1038/ncomms2156 pmid:23072807 fatcat:xbwjpyany5gc5mlews7vleqyee

PhylArray: phylogenetic probe design algorithm for microarray

Cécile Militon, Sébastien Rimour, Mohieddine Missaoui, Corinne Biderre, Vincent Barra, David Hill, Anne Moné, Geneviève Gagne, Harald Meier, Eric Peyretaillade, Pierre Peyret
2007 Computer applications in the biosciences : CABIOS  
Motivation: Microbial diversity is still largely unknown in most environments, such as soils. In order to get access to this microbial 'black-box', the development of powerful tools such as microarrays are necessary. However, the reliability of this approach relies on probe efficiency, in particular sensitivity, specificity and explorative power, in order to obtain an image of the microbial communities that is close to reality. Results: We propose a new probe design algorithm that is able to
more » ... ect microarray probes targeting SSU rRNA at any phylogenetic level. This original approach, implemented in a program called 'PhylArray', designs a combination of degenerate and nondegenerate probes for each target taxon. Comparative experimental evaluations indicate that probes designed with PhylArray yield a higher sensitivity and specificity than those designed by conventional approaches. Applying the combined PhyArray/GoArrays strategy helps to optimize the hybridization performance of short probes. Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria.
doi:10.1093/bioinformatics/btm392 pmid:17698494 fatcat:7x662o72b5cltgnezmucxh75xe

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota

Clémence Defois, Jérémy Ratel, Sylvain Denis, Bérénice Batut, Réjane Beugnot, Eric Peyretaillade, Erwan Engel, Pierre Peyret
2017 Frontiers in Microbiology  
Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding,
more » ... nscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dosedependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism.
doi:10.3389/fmicb.2017.01562 pmid:28861070 pmcid:PMC5559432 fatcat:c263nd5zivgy5fort7htrkh5jy

Hijacking of Host Cellular Functions by an Intracellular Parasite, the Microsporidian Anncaliia algerae

Johan Panek, Hicham El Alaoui, Anne Mone, Serge Urbach, Edith Demettre, Catherine Texier, Christine Brun, Andreas Zanzoni, Eric Peyretaillade, Nicolas Parisot, Emmanuelle Lerat, Pierre Peyret (+3 others)
2014 PLoS ONE  
Intracellular pathogens including bacteria, viruses and protozoa hijack host cell functions to access nutrients and to bypass cellular defenses and immune responses. These strategies have been acquired through selective pressure and allowed pathogens to reach an appropriate cellular niche for their survival and growth. To get new insights on how parasites hijack host cellular functions, we developed a SILAC (Stable Isotope Labeling by Amino Acids in Cell culture) quantitative proteomics
more » ... . Our study focused on deciphering the cross-talk in a host-parasite association, involving human foreskin fibroblasts (HFF) and the microsporidia Anncaliia algerae, a fungus related parasite with an obligate intracellular lifestyle and a strong host dependency. The host-parasite cross-talk was analyzed at five post-infection times 1, 6, 12 and 24 hours post-infection (hpi) and 8 days post-infection (dpi). A significant up-regulation of four interferon-induced proteins with tetratricopeptide repeats IFIT1, IFIT2, IFIT3 and MX1 was observed at 8 dpi suggesting a type 1 interferon (IFN) host response. Quantitative alteration of host proteins involved in biological functions such as signaling (STAT1, Ras) and reduction of the translation activity (EIF3) confirmed a host type 1 IFN response. Interestingly, the SILAC approach also allowed the detection of 148 A. algerae proteins during the kinetics of infection. Among these proteins many are involved in parasite proliferation, and an over-representation of putative secreted effectors proteins was observed. Finally our survey also suggests that A. algerae could use a transposable element as a lure strategy to escape the host innate immune system.
doi:10.1371/journal.pone.0100791 pmid:24967735 pmcid:PMC4072689 fatcat:3dwrihmghbb5tgrsao2lqolgfq

Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes

Corinne Biderre-Petit, Eric Dugat-Bony, Mickaël Mege, Nicolas Parisot, Lorenz Adrian, Anne Moné, Jérémie Denonfoux, Eric Peyretaillade, Didier Debroas, Delphine Boucher, Pierre Peyret, Paul Jaak Janssen
2016 PLoS ONE  
et al.. Distribution of dehalococcoidia in the anaerobic deep water of a remote meromictic crater lake and detection of dehalococcoidia-derived reductive dehalogenase homologous genes. Abstract Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority
more » ... of 16S rRNA sequences have less than 91% similarity to previously isolated DEH 16S rRNA sequences. To predict the metabolic potential of detected DEH subgroups and to assess if they encode genes to transform halogenated compounds, we enriched DEH-affiliated genomic DNA by using a specific-gene capture method and probes against DEH-derived 16S rRNA genes, reductive dehalogenase genes and known insertion sequences. Two reductive dehalogenase homologous sequences were identified from DEH-enriched genomic DNA, and marker genes in the direct vicinity confirm that gene fragments were derived from DEH. The low sequence similarity with known reductive dehalogenase genes suggests yet-unknown catabolic potential in the anoxic zone of Lake Pavin. (Desulfitobacterium and Dehalobacter), Proteobacteria (e.g. Desulfomonile, Desulfuromonas and Sulfurospirillum) and Chloroflexi (Dehalococcoides, Dehalogenimonas and 'Dehalobium', all affiliated to the class Dehalococcoidia (DEH)) [1] couple reductive dechlorination of organochlorides to energy conservation in a respiratory manner currently referred to as organohalide respiration (OHR). This process has been extensively studied because of its useful application in the bioremediation of soil and groundwater contaminated with chlorinated compounds such as tetrachloroethene (PCE) and trichloroethene (TCE) [2] [3] [4] . All DEH cultured thus far are obligate organohalide respirers and share similar limited metabolic capabilities using hydrogen as an electron donor and organohalogen compounds as electron acceptors [1, 5, 6] . The key enzymes for OHR are the reductive dehalogenases (RDases) (for a review see [7] ). Of all types of dehalogenases discovered over the past few decades, RDases are the most studied due to their often observed capacity to transform highly halogenated compounds. RDases also attract attention because many of them are part of membrane-bound electron transport chains in organohalide-respiring anaerobic bacteria (OHRB) [8] . However, despite the increasing interest on transformation reactions of organochlorides, only a limited number of studies have focused on the degradation of compounds occurring naturally, and little is known about the extent and the ecological role of dechlorination in non-polluted environments [9] [10] [11] . Beyond their importance in the remediation of contaminated environments [3, 12] , the activities of DEH are also of fundamental interest in uncontaminated environments, where up to 2,300 organochlorides have been identified from biotic and abiotic natural sources [13] . Recently, with the advances of molecular methods (such as metagenomics and single-cell genomics), members of the DEH and many reductive dehalogenase homologous genes (rdhA) have been detected in various uncontaminated environments, ranging from soils [11, 14] to sedimentary habitats from marine [10, [15] [16] [17] [18] and freshwater systems [14, 19, 20] . The widespread detection of DEH-affiliated 16S rRNA and rdhA gene sequences in these environments suggests the presence of OHR as an ecologically significant microbial activity. At the same time, the absence of canonical rdhA genes similar to those found in cultivated DEH strains as well as the evidence for additional metabolic lifestyles predicted from some DEH assembled genomes from these pristine environments [16, 17, 19] have shed light on the metabolic versatility of some DEH-related members. This suggests that reductive dehalogenation could be a recently acquired trait, not conserved within all DEH. Therefore, DEH populations might play an important role in the chlorine cycle as well as biogeochemical cycles, including the carbon, within uncontaminated environments [16] . While it is widely believed that microbial dehalogenation plays a significant role in the functioning of the halogen cycle, almost nothing is known about the ecological role and the metabolic characteristics of DEH in lake waters. The only data currently available come from studies aiming to describe the microbial diversity in the stratified waters of two meromictic lakes, Lake Sakinaw (Canada) [21] and Lake Kivu (East Africa) [22] . From these investigations, it has emerged that bacteria affiliated to DEH were widely distributed in the anoxic zone of these uncontaminated ecosystems. In meromictic lakes, the water column stably partitions into an oxic surface water zone (mixolimnion), a redox transition zone (mesolimnion) and an anoxic, often hydrogen sulfide and methane-rich bottom water zone (monimolimnion) [22] . These results suggest that presence of DEH may be an indicator for the monimolimnion. Lake Pavin in the French Massif Central, the subject of our study, is a meromictic lake with permanent redox stratification and no direct industrial inflow [23] . We investigated the presence of DEH in the anoxic water column of Lake Pavin by using a combination of classical molecular approaches -including PCR, qPCR, metabarcoding, and shotgun sequencing-as well as recently established new molecular approaches -including specific-gene capture to isolate Dehalococcoidia in Crater Lake Waters PLOS ONE |
doi:10.1371/journal.pone.0145558 pmid:26734727 pmcid:PMC4703385 fatcat:ogp5fdg64vcxbc6aj6nku7piou
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