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The Ocean Gene Atlas: exploring the biogeography of plankton genes online [article]

Emilie Villar, Thomas Vannier, Caroline Vernette, Magali Lescot, Aurelien Alexandre, Paul Bachelerie, Thomas Rosnet, Eric Pelletier, Shinichi Sunagawa, Pascal Hingamp
2018 biorxiv/medrxiv   pre-print
The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for homology and displaying the abundances of genes in the context of environmental features
more » ... emperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences, and ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes, both produced by the Tara Oceans sequencing effort. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.
doi:10.1101/271882 fatcat:fduxszsqnna5fmnrnyhkwzcqqu

Disruption of Epithelial Integrity Drives Mesendoderm Differentiation in Human Induced Pluripotent Stem Cells by Enabling BMP and ACTIVIN Sensing [article]

Diane Rattier, Thomas Legier, Thomas Vannier, Flavio Maina, Rosanna Dono
2021 bioRxiv   pre-print
ABSTRACTThe processes of primitive streak formation and fate specification in the mammalian epiblast rely on complex interactions between morphogens and tissue organization. Little is known about how these instructive cues functionally interact to regulate gastrulation. We interrogated the interplay between tissue organization and morphogens by using human induced pluripotent stem cells (hiPSCs) down-regulated for the morphogen regulator GLYPICAN-4, in which defects in tight junctions result in
more » ... areas of disrupted epithelial integrity. Remarkably, this phenotype does not affect hiPSC stemness, but impacts on cell fate acquisition processes. Strikingly, cells within disrupted areas become competent to perceive BMP4 and ACTIVIN A/NODAL gastrulation signals and thus, differentiate into mesendoderm. Yet, disruption of epithelial integrity prolongs temporal activation of BMP4 and ACTIVIN A/NODAL downstream effectors and correlates with enhanced hiPSC endoderm/mesoderm differentiation potential. Altogether, our results disclose epithelial cell integrity as a key determinant of TGF-β activity and highlight a new mechanism guiding morphogen sensing and spatial cell fate change within an epithelium.
doi:10.1101/2021.10.22.465459 fatcat:a4wo7pkdcvefvm64ikiids5e2q

Mapping ecosystem services bundles in a heterogeneous mountain region

Clémence Vannier, Rémy Lasseur, Emilie Crouzat, Coline Byczek, Valentine Lafond, Thomas Cordonnier, Pierre-Yves Longaretti, Sandra Lavorel
2019 Figshare  
Recent institutional and policy frameworks prescribe the incorporation of ecosystem services (ES) into land use management and planning, favouring co-production of ES assessments by stakeholders, land planners and scientists. Incorporating ES into land management and planning requires models to map and analyze ES. Also, because ES do not vary independently, many operational issues ultimately relate to the mitigation of ES trade-offs, so that multiple ES and their interactions need to be
more » ... ed. Using a highly accurate LULC database for the Grenoble urban region (French Alps), we mapped twelve ES using a range of models of varied complexity. A specific, fine-grained (less than 1 ha) LULC database at regional scale (4450 km²) added great spatial precision in individual ES models, in spite of limits of the typological resolution for forests and semi-natural areas. We analysed ES bundles within three different socio-ecosystems and associated landscape types (periurban, rural and forest areas). Such type-specific bundles highlighted distinctive ES trade-offs and synergies for each landscape. Advanced approaches combining remote sensing, targeted field data collection and expert knowledge from scientists and stakeholders are expected to provide the significant progress that is now required to support the reduction of trade-offs and enhance synergies between management objectives.
doi:10.6084/m9.figshare.7674188 fatcat:ircuaiys3vf7ri2vcavmfspoiu

The Ocean Gene Atlas: exploring the biogeography of plankton genes online

Emilie Villar, Thomas Vannier, Caroline Vernette, Magali Lescot, Miguelangel Cuenca, Aurélien Alexandre, Paul Bachelerie, Thomas Rosnet, Eric Pelletier, Shinichi Sunagawa, Pascal Hingamp
2018 Nucleic Acids Research  
The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental
more » ... atures (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables nonbioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/oceangene-atlas/.
doi:10.1093/nar/gky376 pmid:29788376 pmcid:PMC6030836 fatcat:raoyacej7ja2fkfzbcafnry2ya

Commet: Comparing and combining multiple metagenomic datasets

Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, Pierre Peterlongo
2014 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and the taxonomical or functional annotations are much smaller than the real biological diversity. This motivated the development of de novo metagenomic read comparison approaches to extract information contained in metagenomic datasets. However, these new
more » ... s do not scale up large metagenomic projects, or generate an important number of large intermediate and result files. We introduce COMMET ("COmpare Multiple METagenomes"), a method that provides similarity overview between all datasets of large metagenomic projects. Directly from non-assembled reads, all against all comparisons are performed through an efficient indexing strategy. Then, results are stored as bit vectors, a compressed representation of read files, that can be used to further combine read subsets by common logical operations. Finally, COMMET computes a clusterization of metagenomic datasets, which is visualized by dendrogram and heatmaps.
doi:10.1109/bibm.2014.6999135 dblp:conf/bibm/MailletCVLP14 fatcat:lxprenti2nfrzptzb72lbf5xnu

The interaction between non-fusogenic Sec22b-Stx complexes and Extended-Synaptotagmins promotes neurite growth and ramification [article]

Alessandra Gallo, Lydia Danglot, Francesca Giordano, Thomas Binz, Christian Vannier, Thierry GALLI
2019 bioRxiv   pre-print
Axons and dendrites are long and often ramified neurites that need particularly intense plasma membrane (PM) expansion during the development of the nervous system. Neurite growth depends on non-fusogenic Sec22b/Stx1 SNARE complexes at endoplasmic reticulum (ER)/PM contacts. Here we show that Sec22b interacts with the endoplasmic reticulum lipid transfer proteins Extended-Synaptotagmins (ESyts) and this interaction depends on the Longin domain of Sec22b. Overexpression of E-Syts stabilizes
more » ... b/Stx1 association, whereas silencing of ESyts has the opposite effect. Overexpression of wild type ESyt2, but not mutants unable to transfer lipids or attach to the ER, increase the formation of axonal filopodia and ramification of neurites in developing neurons. This effect is inhibited by a clostridial neurotoxin cleaving Stx1, expression of Sec22b Longin domain and a Sec22b mutant with extended linker between SNARE and transmembrane domains. We conclude that Sec22b/Stx1 ER/PM contact sites contribute to PM expansion by interacting with lipid transfer proteins such as ESyts.
doi:10.1101/2019.12.24.886648 fatcat:7ixckjq6bnfyrc2g6gf53trdym

Exceptional preservation of eye structure in arthropod visual predators from the Middle Jurassic

Jean Vannier, Brigitte Schoenemann, Thomas Gillot, Sylvain Charbonnier, Euan Clarkson
2016 Nature Communications  
Vision has revolutionized the way animals explore their environment and interact with each other and rapidly became a major driving force in animal evolution. However, direct evidence of how ancient animals could perceive their environment is extremely difficult to obtain because internal eye structures are almost never fossilized. Here, we reconstruct with unprecedented resolution the three-dimensional structure of the huge compound eye of a 160-million-year-old thylacocephalan arthropod from
more » ... he La Voulte exceptional fossil biota in SE France. This arthropod had about 18,000 lenses on each eye, which is a record among extinct and extant arthropods and is surpassed only by modern dragonflies. Combined information about its eyes, internal organs and gut contents obtained by X-ray microtomography lead to the conclusion that this thylacocephalan arthropod was a visual hunter probably adapted to illuminated environments, thus contradicting the hypothesis that La Voulte was a deep-water environment.
doi:10.1038/ncomms10320 pmid:26785293 pmcid:PMC4735654 fatcat:32desghlavh45dihmalyt5dldi

Mapping ecosystem services bundles in a heterogeneous mountain region

Clémence Vannier, Rémy Lasseur, Emilie Crouzat, Coline Byczek, Valentine Lafond, Thomas Cordonnier, Pierre-Yves Longaretti, Sandra Lavorel
2019 Ecosystems and People  
Vannier et al. (2016) and Lefebvre (2014) have described in detail the data sources and methods used to build our LULC database (Table 1 , levels 1, 2, 3).  ...  Their use is therefore only possible in conjunction with other data sources in order to constitute a continuous and exhaustive LULC map at landscape or regional scale (Vannier 2011; Hubert-Moy et al.  ... 
doi:10.1080/26395916.2019.1570971 fatcat:xbawgvp6g5asjfrav3p5jszzyu

Diversity and evolution of bacterial bioluminescence genes in the global ocean

Thomas Vannier, Pascal Hingamp, Floriane Turrel, Lisa Tanet, Magali Lescot, Youri Timsit
2020 NAR Genomics and Bioinformatics  
Although bioluminescent bacteria are the most abundant and widely distributed of all light-emitting organisms, the biological role and evolutionary history of bacterial luminescence are still shrouded in mystery. Bioluminescence has so far been observed in the genomes of three families of Gammaproteobacteria in the form of canonical lux operons that adopt the CDAB(F)E(G) gene order. LuxA and luxB encode the two subunits of bacterial luciferase responsible for light-emission. Our deep
more » ... of public marine environmental databases considerably expands this view by providing a catalog of new lux homolog sequences, including 401 previously unknown luciferase-related genes. It also reveals a broader diversity of the lux operon organization, which we observed in previously undescribed configurations such as CEDA, CAED and AxxCE. This expanded operon diversity provides clues for deciphering lux operon evolution and propagation within the bacterial domain. Leveraging quantitative tracking of marine bacterial genes afforded by planetary scale metagenomic sampling, our study also reveals that the novel lux genes and operons described herein are more abundant in the global ocean than the canonical CDAB(F)E(G) operon.
doi:10.1093/nargab/lqaa018 pmid:33575578 pmcid:PMC7671414 fatcat:6hwo4dggs5addikp6htt4tirwa

Combining the Monthly Drought Code and Paleoecological Data to Assess Holocene Climate Impact on Mediterranean Fire Regime

Marion Lestienne, Christelle Hély, Thomas Curt, Isabelle Jouffroy-Bapicot, Boris Vannière
2020 Fire  
Microscopiques), QMedFire (Quantification et modélisation des régimes des feux méditerranéens), and ENVILEG (Héritage environnemental des grandes transitions socio-écologiques en Europe) led by Boris Vannière  ... 
doi:10.3390/fire3020008 fatcat:utqnqd4xafeqtkjvwoxpidvg34

Cationic helicenes as selective G4 DNA binders and optical probes for cellular imaging

Peter A. Summers, Ajesh P. Thomas, Timothy Kench, Jean-Baptiste Vannier, Marina K. Kuimova, Ramon Vilar
2021 Chemical Science  
Vannier lab's work is supported by the London Institute of Medical Sciences (LMS), which receives its core funding from UKRI (MRC) and by an ERC Starter Grant (637798; MetDNASecStr).  ...  For example, Thomas and co-workers studied the DNA binding properties of the di-ruthenium complex [{Ru(bipy) 2 } 2 (tpphz)] 4+ where each of the two metal centres is in a chiral octahedral environment  ... 
doi:10.1039/d1sc04567a pmid:34881015 pmcid:PMC8580066 fatcat:awshlyheifdpvkstwptnj3z23q

Lung cancer—a fractal viewpoint

Frances E. Lennon, Gianguido C. Cianci, Nicole A. Cipriani, Thomas A. Hensing, Hannah J. Zhang, Chin-Tu Chen, Septimiu D. Murgu, Everett E. Vokes, Michael W. Vannier, Ravi Salgia
2015 Nature Reviews Clinical Oncology  
Fractals are mathematical constructs that show self-similarity over a range of scales and noninteger (fractal) dimensions. Owing to these properties, fractal geometry can be used to efficiently estimate the geometrical complexity, and the irregularity of shapes and patterns observed in lung tumour growth (over space or time), whereas the use of traditional Euclidean geometry in such calculations is more challenging. The application of fractal analysis in biomedical imaging and time series has
more » ... own considerable promise for measuring processes as varied as heart and respiratory rates, neuronal cell characterization, and vascular development. Despite the advantages of fractal mathematics and numerous studies demonstrating its applicability to lung cancer research, many researchers and clinicians remain unaware of its potential. Therefore, this Review aims to introduce the fundamental basis of fractals and to illustrate how analysis of fractal dimension (FD) and associated measurements, such as lacunarity (texture) can be performed. We describe the fractal nature of the lung and explain why this organ is particularly suited to fractal analysis. Studies that have used fractal analyses to quantify changes in nuclear and chromatin FD in primary and metastatic tumour cells, and clinical imaging studies that correlated changes in the FD of tumours on CT and/or PET images with tumour growth and treatment responses are reviewed. Moreover, the potential use of these techniques in the diagnosis and therapeutic management of lung cancer are discussed.
doi:10.1038/nrclinonc.2015.108 pmid:26169924 pmcid:PMC4989864 fatcat:2m24r5xxe5dxzlu5ktpkafysny

Associated data: Indexation, discovery, challenges and roles

Pierre Ocvirk, Gilles Landais, Laurent Michel, Heddy Arab, Sylvain Guehenneux, Thomas Boch, Marianne Brouty, Emmanuelle Perret, François-Xavier Pineau, Tiphaine Pouvreau, Patricia Vannier, S. Lesteven (+3 others)
2018 EPJ Web of Conferences  
Astronomers are nowadays required by their funding agencies to make the data obtained through public-financed means (ground and space observatories and labs) available to the public and the community at large. This is a fundamental step in enabling the open science paradigm the astronomical community is striving for. In other words, tabular data (catalogs) arriving to CDS for ingestion into its databases, in particular VizieR, is more and more frequently accompanied by the reduced observed
more » ... et (spectra, images, data cubes, time series). While the benefits of making this associated data available are obvious, the task is very challenging: in this context "big data" takes the meaning of "extremely heterogeneous data", with a diversity of formats and practices among astronomers, even within the FITS standard. Providing librarians with efficient tools to index this data and generate the relevant metadata is therefore paramount.
doi:10.1051/epjconf/201818602002 fatcat:7bylt5bczvc65lozsbohgvv2aa

Survey of the green picoalga Bathycoccus genomes in the global ocean

Thomas Vannier, Jade Leconte, Yoann Seeleuthner, Samuel Mondy, Eric Pelletier, Jean-Marc Aury, Colomban de Vargas, Michael Sieracki, Daniele Iudicone, Daniel Vaulot, Patrick Wincker, Olivier Jaillon
2016 Scientific Reports  
Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second
more » ... ype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions. Phytoplankton, comprising prokaryotes and eukaryotes, contribute to nearly half of the annual global primary production 1 . Picocyanobacteria of the genera Prochlorococcus and Synechococcus dominate the prokaryotic component 2 . However, small eukaryotes (picoeukaryotes; < 2 μ m) can be major contributors to primary production 3,4 . In contrast to cyanobacteria, the phylogenetic diversity of eukaryotic phytoplankton is wide, with species belonging to virtually all photosynthetic protist groups 5 . Among them, three genera of green algae belonging to the order Mamiellales (class Mamiellophyceae 6 ), Micromonas, Ostreococcus and Bathycoccus are particularly important ecologically because they are found in a wide variety of oceanic ecosystems, from the poles to the tropics 7-12 . The cosmopolitan distribution of these genera raises the questions of their diversity and their adaptation to local environmental conditions. These genera exhibit genetic diversity: for example, there are at least three genetically different clades of Micromonas with different habitat preferences 12,13 . One ecotype of Micromonas seems to be restricted to polar waters 8, 14 . Ostreococcus which is the smallest free-living eukaryotic cell known to date with a cell size of 0.8 μ m 15 can be differentiated into at least four clades. Two Ostreococcus species have been formerly described: O. tauri and O. mediterreanus 15, 16 . Among these Ostreococcus clades, different strains seem to be adapted to different light ranges 17 . However, the ecological preferences of Ostreococcus strains are probably more complex, implying other environmental parameters such as nutrients and temperature 9 . The genus Bathycoccus was initially isolated at 100 m from the deep chlorophyll maximum (DCM) in the Mediterranean Sea 18 and cells with the same morphology (body scales) had been reported previously from the Atlantic Ocean 19 . Bathycoccus has been since found to be widespread in the oceanic environment, in particular in coastal waters 20,21 , and one genome sequence from a coastal strain is available 22 . Metagenomic data have suggested the existence of two Bathycoccus ecotypes 10,11,23 , recently named B1 and B2 11 . These two ecotypes have
doi:10.1038/srep37900 pmid:27901108 pmcid:PMC5128809 fatcat:h4qz3dhc5fetvamdiq5m62edte

An Analysis of Agricultural Systems Modelling Approaches and Examples to Support Future Policy Development under Disruptive Changes in New Zealand

Clémence Vannier, Thomas A. Cochrane, Peyman Zawar Reza, Larry Bellamy
2022 Applied Sciences  
Agricultural systems have entered a period of significant disruption due to impacts from change drivers, increasingly stringent environmental regulations and the need to reduce unwanted discharges, and emerging technologies and biotechnologies. Governments and industries are developing strategies to respond to the risks and opportunities associated with these disruptors. Modelling is a useful tool for system conceptualisation, understanding, and scenario testing. Today, New Zealand and other
more » ... ions need integrated modelling tools at the national scale to help industries and stakeholders plan for future disruptive changes. In this paper, following a scoping review process, we analyse modelling approaches and available agricultural systems' model examples per thematic applications at the regional to national scale to define the best options for the national policy development. Each modelling approach has specificities, such as stakeholder engagement capacity, complex systems reproduction, predictive or prospective scenario testing, and users should consider coupling approaches for greater added value. The efficiency of spatial decision support tools working with a system dynamics approach can help holistically in stakeholders' participation and understanding, and for improving land planning and policy. This model combination appears to be the most appropriate for the New Zealand national context.
doi:10.3390/app12052746 fatcat:lwpzzv7f35drvc45jip7ud6dii
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