Now showing 1 - 10 of 12
  • Publication
    A global ocean atlas of eukaryotic genes
    While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.
    Scopus© Citations 190  162
  • Publication
    A Holistic Approach to Marine Eco-Systems Biology
    The structure, robustness, and dynamics of ocean plankton ecosystems remain poorly understood due to sampling, analysis, and computational limitations. The Tara Oceans consortium organizes expeditions to help fill this gap at the global level.
      99Scopus© Citations 288
  • Publication
    3D-Printed Peptide-Hydrogel Nanoparticle Composites for Surface-Enhanced Raman Spectroscopy Sensing
    Precise control over the arrangement of plasmonic nanomaterials is critical for label-free single-molecule surface-enhanced Raman spectroscopy (SERS)-based sensing applications. SERS templates should provide high sensitivity and reproducibility and be cost-effective and easy to prepare. Additive manufacturing by extrusion-based three-dimensional (3D) printing is an emerging technique for the spatial arrangement of nanomaterials and is a method that may satisfy these SERS template requirements. In this work, we use 3D printing to produce sensitive and reproducible SERS templates using a fluorenylmethyloxycarbonyl diphenylalanine (Fmoc-FF) hydrogel loaded with silver or gold nanoparticles. The Fmoc-FF template allows the detection of low Raman cross-section molecules such as adenine at concentrations as low as 100 pM.
      618Scopus© Citations 21
  • Publication
    End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites
    Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion people worldwide while only a very small percentage have been surveyed. Advances in technology and processing along with affordable underwater cameras and Internet availability gives us the possibility to provide tools and softwares to survey entire coral reefs. Holistic ecological analyses of corals require not only the community view (10s to 100s of meters), but also the single colony analysis as well as corallite identification. As corals are three-dimensional, classical approaches to determine percent cover and structural complexity across spatial scales are inefficient, time-consuming and limited to experts. Here we propose an end-to-end approach to estimate these parameters using low-cost equipment (GoPro, Canon) and freeware (123D Catch, Meshmixer and Netfabb), allowing every community to participate in surveys and monitoring of their coral ecosystem.We demonstrate our approach on 9 species of underwater colonies in ranging size and morphology. 3D models of underwater colonies, fresh samples and bleached skeletons with high quality texture mapping and detailed topographic morphology were produced, and Surface Area and Volume measurements (parameters widely used for ecological and coral health studies) were calculated and analysed. Moreover, we integrated collected sample models with micro-photogrammetry models of individual corallites to aid identification and colony and polyp scale analysis.
    Scopus© Citations 40  181
  • Publication
    Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization
    Background: Compartmentalization is a key feature of eukaryotic cells, but its evolution remains poorly understood. GTPases are the oldest enzymes that use nucleotides as substrates and they participate in a wide range of cellular processes. Therefore, they are ideal tools for comparative genomic studies aimed at understanding how aspects of biological complexity such as cellular compartmentalization evolved. Results: We describe the identification and characterization of a unique family of circularly permuted GTPases represented by the human orthologue of yeast Lsg1p. We placed the members of this family in the phylogenetic context of the YlqF Related GTPase (YRG) family, which are present in Eukarya, Bacteria and Archea and include the stem cell regulator Nucleostemin. To extend the computational analysis, we showed that hLsg1 is an essential GTPase predominantly located in the endoplasmic reticulum and, in some cells, in Cajal bodies in the nucleus. Comparison of localization and siRNA datasets suggests that all members of the family are essential GTPases that have increased in number as the compartmentalization of the eukaryotic cell and the ribosome biogenesis pathway have evolved. Conclusions: We propose a scenario, consistent with our data, for the evolution of this family: cytoplasmic components were first acquired, followed by nuclear components, and finally the mitochondrial and chloroplast elements were derived from different bacterial species, in parallel with the formation of the nucleolus and the specialization of nuclear components.
    Scopus© Citations 47  140
  • Publication
    Spatiotemporally Resolved Heat Dissipation in 3D Patterned Magnetically Responsive Hydrogels
    Multifunctional nanocomposites that exhibit well-defined physical properties and encode spatiotemporally controlled responses are emerging as components for advanced responsive systems, for example, in soft robotics or drug delivery. Here an example of such a system, based on simple magnetic hydrogels composed of iron oxide magnetic nanoflowers and Pluronic F127 that generates heat upon alternating magnetic field irradiation is described. Rules for heat-induction in bulk hydrogels and the heat-dependence on particle concentration, gel volume, and gel exposed surface area are established, and the dependence on external environmental conditions in “closed” as compared to “open” (cell culture) system, with controllable heat jumps, of ∆T 0–12°C, achieved within ≤10 min and maintained described. Furthermore the use of extrusion-based 3D printing for manipulating the spatial distribution of heat in well-defined printed features with spatial resolution <150 µm, sufficiently fine to be of relevance to tissue engineering, is presented. Finally, localized heat induction in printed magnetic hydrogels is demonstrated through spatiotemporally-controlled release of molecules (in this case the dye methylene blue). The study establishes hitherto unobserved control over combined spatial and temporal induction of heat, the applications of which in developing responsive scaffold remodeling and cargo release for applications in regenerative medicine are discussed.
      414Scopus© Citations 20
  • Publication
    Transitional forms between the three domains of life and evolutionary implications
    (The Royal Society, 2011-09-14) ;
    The question as to the origin and relationship between the three domains of life is lodged in a phylogenetic impasse. The dominant paradigm is to see the three domains as separated. However, the recently characterized bacterial species have suggested continuity between the three domains. Here, we review the evidence in support of this hypothesis and evaluate the implications for and against the models of the origin of the three domains of life. The existence of intermediate steps between the three domains discards the need for fusion to explain eukaryogenesis and suggests that the last universal common ancestor was complex. We propose a scenario in which the ancestor of the current bacterial Planctomycetes, Verrucomicrobiae and Chlamydiae superphylum was related to the last archaeal and eukaryotic common ancestor, thus providing a way out of the phylogenetic impasse.
    Scopus© Citations 40  124
  • Publication
    Liquid-phase 3D bioprinting of gelatin alginate hydrogels: influence of printing parameters on hydrogel line width and layer height
    (Springer Science and Business Media LLC, 2019-07-16) ; ; ; ;
    Extrusion-based 3D bioprinting is a direct deposition approach used to create three-dimensional (3D) tissue scaffolds typically comprising hydrogels. Hydrogels are hydrated polymer networks that are chemically or physically cross-linked. Often, 3D bioprinting is performed in air, despite the hydrated nature of hydrogels and the potential advantage of using a liquid phase to provide cross-linking and otherwise functionalize the hydrogel. In this work, we print gelatin alginate hydrogels directly into a cross-linking solution of calcium chloride and investigate the influence of nozzle diameter, distance between nozzle and surface, calcium chloride concentration, and extrusion rate on the dimensions of the printed hydrogel. The hydrogel layer height was generally found to increase with increasing extrusion rate and nozzle distance, according to the increased volume extruded and the available space, respectively. In addition, the hydrogel width was generally found to increase with decreasing nozzle distance and cross-linking concentration corresponding to confinement-induced spreading and low cross-linking regimes, respectively. Width/height ratios of ~ 1 were generally achieved when the nozzle diameter and distance were comparable above a certain cross-linking concentration. Using these relationships, biocompatible 3D multilayer structures were successfully printed directly into calcium chloride cross-linking solution.
      644Scopus© Citations 25
  • Publication
    Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans
    Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.
    Scopus© Citations 67  149
  • Publication
    Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family
    Reconstructing the transition from a single compartment bacterium to a highly compartmentalized eukaryotic cell is one of the most studied problems of evolutionary cell biology. However, timing and details of the establishment of compartmentalization are unclear and difficult to assess. Here, we propose the use of molecular markers specific to cellular compartments to set up a framework to advance the understanding of this complex intracellular process. Specifically, we use a protein family related to ribosome biogenesis, YRG (YlqF related GTPases), whose evolution is linked to the establishment of cellular compartments, leveraging the current genomic data. We analyzed orthologous proteins of the YRG family in a set of 171 proteomes for a total of 370 proteins. We identified ten YRG protein subfamilies that can be associated to six subcellular compartments (nuclear bodies, nucleolus, nucleus, cytosol, mitochondria, and chloroplast), and which were found in archaeal, bacterial and eukaryotic proteomes. Our analysis reveals organism streamlining related events in specific taxonomic groups such as Fungi. We conclude that the YRG family could be used as a compartmentalization marker, which could help to trace the evolutionary path relating cellular compartments with ribosome biogenesis.
    Scopus© Citations 4  206