A5003525592- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Marine and coastal ecosystems
- Genomics and Phylogenetic Studies
- Marine Biology and Ecology Research
- Environmental DNA in Biodiversity Studies
- Bacteriophages and microbial interactions
- Vector-borne infectious diseases
- RNA and protein synthesis mechanisms
- Plant Virus Research Studies
- Plant and Fungal Interactions Research
- Methane Hydrates and Related Phenomena
- Yersinia bacterium, plague, ectoparasites research
- Molecular Biology Techniques and Applications
- Machine Learning in Bioinformatics
- Insect symbiosis and bacterial influences
- Diatoms and Algae Research
- Parasitic Infections and Diagnostics
- RNA modifications and cancer
- Plant Diversity and Evolution
- Fractal and DNA sequence analysis
- Enzyme Structure and Function
- Marine Toxins and Detection Methods
- Brucella: diagnosis, epidemiology, treatment
- Bacterial biofilms and quorum sensing
Centre National de la Recherche Scientifique
2009-2019
Sorbonne Université
2012-2019
Station Biologique de Roscoff
2011-2019
Adaptation et Diversité en Milieu Marin
2011-2017
Université Paris Cité
2014
Aix-Marseille Université
2009-2011
Institut de Microbiologie de la Méditerranée
2011
Laboratoire Information Génomique et Structurale
1998-2010
Institut de Biologie Structurale
1997-2009
Centre d’Immunologie de Marseille-Luminy
2009
Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, phylogenetic reconstruction graphical representation inferred tree. The Phylogeny.fr platform transparently chains programs automatically perform these tasks. It is primarily designed for biologists with no experience phylogeny, but can also meet needs specialists; first ones will find up-to-date tools chained a phylogeny pipeline...
Genes differentially expressed in different tissues, during development, or specific pathologies are of foremost interest to both basic and pharmaceutical research. “Transcript profiles” “digital Northerns” generated routinely by partially sequencing thousands randomly selected clones from relevant cDNA libraries. Differentially genes can then be detected variations the counts their cognate sequence tags. Here we present first systematic study on influence random fluctuations sampling size...
The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack taxonomically curated reference data sets for targeted genes. Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with taxonomy. mainly consists nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi organelles (mitochondrion, plastid...
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted not accounted for the full range size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone communities collected across tropical temperate oceans during circumglobal Tara Oceans expedition. analyzed 18S ribosomal DNA sequences intermediate plankton-size spectrum smallest unicellular eukaryotes (protists, >0.8 micrometers) to small...
We recently reported the discovery and preliminary characterization of Mimivirus, largest known virus, with a 400-nanometer particle size comparable to mycoplasma. Mimivirus is double-stranded DNA virus growing in amoebae. now present its 1,181,404–base pair genome sequence, consisting 1262 putative open reading frames, 10% which exhibit similarity proteins functions. In addition exceptional size, exhibits many features that distinguish it from other nucleocytoplasmic large viruses. The most...
Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied photic zone interactome using environmental factors organismal abundance profiles found that incomplete predictors community structure. We associations across plankton functional types phylogenetic groups to be nonrandomly distributed on network driven both local global patterns. identified interactions among grazers, primary producers, viruses, (mainly parasitic)...
During a study following pneumonia outbreak in 1992, microorganism growing amoebae and resembling small Gram-positive coccus ([Fig. 1][1]A) was isolated from the water of cooling tower Bradford, England. Despite attempts with various extraction protocols low-stringency polymerase
Acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. This organism was susceptible to most antibiotics the 1970s. It has now become major cause hospital-acquired infections worldwide due its remarkable propensity rapidly acquire resistance determinants wide range antibacterial agents. Here we use comparative genomic approach identify complete repertoire genes exhibited by multidrug-resistant A. strain AYE, which epidemic France, as...
Abstract Background The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality which can have significant impact on final interpretation study. There no single way constructing datasets suitable analysis, because this task intimately depends scientific question we want to address, Moreover, database mining softwares such as BLAST are routinely used searching not specifically optimized task. Results To fill gap, designed...
Significance Diatoms, considered one of the most diverse and ecologically important phytoplanktonic groups, contribute around 20% global primary productivity. They are particularly abundant in nutrient-rich coastal ecosystems at high latitudes. Here, we have explored dataset generated by Tara Oceans from a wide range oceanic regions to characterize diatom diversity patterns on scale. We confirm dominance diatoms as major photosynthetic group identify widespread genera. also provide new...
A group of protist experts proposes a two-step DNA barcoding approach, comprising universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity microbial eukaryotes.
Expresso is a multiple sequence alignment server that aligns sequences using structural information.The user only needs to provide sequences.The runs BLAST identify close homologues of the within PDB database.These structures are used as templates guide original structure-based methods like SAP or Fugue.The final result based on information templates.An advanced mode makes it possible either upload private specify which should be model each sequence.Providing suitable available, delivers...
Rickettsia conorii is an obligate intracellular bacterium that causes Mediterranean spotted fever in humans. We determined the 1,268,755-nucleotide complete genome sequence of R. , containing 1374 open reading frames. This exhibits 804 834 genes previously prowazekii plus 552 supplementary frames and a 10-fold increase number repetitive elements. Despite these differences, two genomes exhibit nearly perfect colinearity allowed clear identification different stages gene alterations with...
Although protists are critical components of marine ecosystems, they still poorly characterized. Here we analysed the taxonomic diversity planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) ribonucleic (RNA) from three size fractions (pico-, nano- micro/mesoplankton), as well dissolved DNA surface sediments were used templates for tag pyrosequencing V4 region 18S ribosomal DNA. Beta-diversity analyses split...
The recently sequenced Rickettsia felis genome revealed an unexpected plasmid carrying several genes usually associated with DNA transfer, suggesting that ancestral rickettsiae might have been endowed a conjugation apparatus. Here we present the sequence of bellii, earliest diverging species known rickettsiae. 1,552,076 base pair-long chromosome does not exhibit colinearity observed between other rickettsia genomes, and encodes complete set putative conjugal transfer most similar to...
Agulhas rings provide the principal route for ocean waters to circulate from Indo-Pacific Atlantic basin. Their influence on global circulation is well known, but their role in plankton transport largely unexplored. We show that, although coarse taxonomic structure of communities continuous across choke point, South diversity altered compared with Indian Ocean source populations. Modeling and situ sampling a young ring indicate that strong vertical mixing drives complex nitrogen cycling,...
We sequenced the genome of Rickettsia felis, a flea-associated obligate intracellular α-proteobacterium causing spotted fever in humans. Besides circular chromosome 1,485,148 bp, R. felis exhibits first putative conjugative plasmid identified among bacteria. This is found short (39,263 bp) and long (62,829 form. contrasts with previously terms many other features, including number transposases, several chromosomal toxin–antitoxin genes, more spoT very large ankyrin-...
Large, publicly available collections of expressed sequence tags (ESTs) have been generated from Arabidopsis thaliana and rice ( Oryza sativa ). A potential, but relatively unexplored application this data is in the study plant gene expression. Other EST data, mainly human mouse, successfully used to point out genes exhibiting tissue- or disease-specific expression, as well for identification alternative transcripts. In report, we go a step further showing that computer analyses can be...
The Rickettsia genus is a group of obligate intracellular α-proteobacteria representing paradigm reductive evolution. Here, we investigate the evolutionary processes that shaped genomes genus. reconstruction ancestral indicates their last common ancestor contained more genes, but already possessed most traits associated with cellular parasitism. differences in gene repertoires across modern are mainly result differential losses from ancestor. We demonstrate using computer simulation...
In an effort to understand how a tick-borne pathogen adapts the body louse, we sequenced and compared genomes of recurrent fever agents Borrelia recurrentis B. duttonii. The 1,242,163-1,574,910-bp fragmented duttonii contain unique 23-kb linear plasmid. This plasmid exhibits large polyT track within promoter region intact variable protein gene telomere resolvase that is Borrelia. genome content characterized by several repeat families, including antigenic lipoproteins. exhibited 20.4% size...
Abstract Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of biosphere. The ongoing environmental metabarcoding revolution opens perspective for holistic biological studies these organisms, particular unicellular microalgae that often lack distinctive morphological characters and complex life cycles. To interpret sequences, necessarily relies on taxonomically curated databases containing reference sequences targeted gene (or barcode) from identified...