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Author = Reynaud, Emmanuel G.;
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Displaying Results 1 - 11 of 11 on page 1 of 1
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3D-Printed Peptide-Hydrogel Nanoparticle Composites for Surface-Enhanced Raman Spectroscopy Sensing
(2019)
Almohammed, Sawsan; Alruwaili, Maha; Reynaud, Emmanuel G.; Redmond, Gareth; Rice, James...
3D-Printed Peptide-Hydrogel Nanoparticle Composites for Surface-Enhanced Raman Spectroscopy Sensing
(2019)
Almohammed, Sawsan; Alruwaili, Maha; Reynaud, Emmanuel G.; Redmond, Gareth; Rice, James H.; Rodriguez, Brian J.
Abstract:
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.
Enterprise Ireland
European Commission Horizon 2020
Science Foundation Ireland
The Ministry of Higher Education of Saudi Arabia under the King Abdullah S...
http://hdl.handle.net/10197/10962
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A global ocean atlas of eukaryotic genes
(2020)
Carradec, Quentin; Pelletier, Eric; Da Silva, Corinne; Reynaud, Emmanuel G.; et al.
A global ocean atlas of eukaryotic genes
(2020)
Carradec, Quentin; Pelletier, Eric; Da Silva, Corinne; Reynaud, Emmanuel G.; et al.
Abstract:
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 fo...
http://hdl.handle.net/10197/11794
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A Holistic Approach to Marine Eco-Systems Biology
(2020)
Karsenti, Eric; Acinas, Silvia G.; Bork, Peer; Reynaud, Emmanuel G.; et al.
A Holistic Approach to Marine Eco-Systems Biology
(2020)
Karsenti, Eric; Acinas, Silvia G.; Bork, Peer; Reynaud, Emmanuel G.; et al.
Abstract:
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.
CNRS
EMBL
Genoscope/CEA
VIB
Stazione Zoologica Anton Dohrn
UNIMIB
ANR
FWO
BIO5
http://hdl.handle.net/10197/11790
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End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites
(2020)
Gutierrez-Heredia, Luis; Benzoni, Francesca; Murphy, Emma; Reynaud, Emmanuel G.
End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites
(2020)
Gutierrez-Heredia, Luis; Benzoni, Francesca; Murphy, Emma; Reynaud, Emmanuel G.
Abstract:
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...
http://hdl.handle.net/10197/11787
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Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization
(2020)
Reynaud, Emmanuel G.; Andrade, Miguel A.; Bonneau, Fabien; et al.
Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization
(2020)
Reynaud, Emmanuel G.; Andrade, Miguel A.; Bonneau, Fabien; et al.
Abstract:
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...
http://hdl.handle.net/10197/11788
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Liquid-phase 3D bioprinting of gelatin alginate hydrogels: influence of printing parameters on hydrogel line width and layer height
(2019)
Alruwaili, Maha; Lopez, Jose A.; McCarthy, Kevin; Reynaud, Emmanuel G.; Rodriguez, Bria...
Liquid-phase 3D bioprinting of gelatin alginate hydrogels: influence of printing parameters on hydrogel line width and layer height
(2019)
Alruwaili, Maha; Lopez, Jose A.; McCarthy, Kevin; Reynaud, Emmanuel G.; Rodriguez, Brian J.
Abstract:
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 decre...
http://hdl.handle.net/10197/10925
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Long-term survey of a syringe-dispensing machine needle exchange program: Answering public concerns
(2020)
Duplessy, Catherine; Reynaud, Emmanuel G.
Long-term survey of a syringe-dispensing machine needle exchange program: Answering public concerns
(2020)
Duplessy, Catherine; Reynaud, Emmanuel G.
Abstract:
Background: Syringe-dispensing machines (SDM) provide syringes at any time even to hard-to-reach injecting drug users (IDUs). They represent an important harm reduction strategy in large populated urban areas such as Paris. We analyzed the performance of one of the world's largest SDM schemes based in Paris over 12 years to understand its efficiency and its limitations, to answer public and stakeholder concerns and optimize its outputs. Methods: Parisian syringe dispensing and exchange machines were monitored as well as their sharp disposals and associated bins over a 12-year period. Moreover, mechanical counting devices were installed on specific syringe-dispensing/exchange machines to record the characteristics of the exchange process. Results: Distribution and needle exchange have risen steadily by 202% for the distribution and 2,000% for syringe recovery even without a coin counterpart. However, 2 machines out of 34 generate 50% of the total activity of the scheme. It takes...
http://hdl.handle.net/10197/11784
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Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family
(2020)
Mier, Pablo; Pérez-Pulido, Antonio J.; Reynaud, Emmanuel G.; Andrade, Miguel A.
Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family
(2020)
Mier, Pablo; Pérez-Pulido, Antonio J.; Reynaud, Emmanuel G.; Andrade, Miguel A.
Abstract:
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 eu...
http://hdl.handle.net/10197/11793
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Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans
(2020)
Seeleuthner, Yoann; Mondy, Samuel; Lombard, Vincent; Reynaud, Emmanuel G.; et al.
Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans
(2020)
Seeleuthner, Yoann; Mondy, Samuel; Lombard, Vincent; Reynaud, Emmanuel G.; et al.
Abstract:
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 he...
http://hdl.handle.net/10197/11792
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Taxonomic colouring of phylogenetic trees of protein sequences
(2020)
Palidwor, Gareth; Reynaud, Emmanuel G.; Andrade, Miguel A.
Taxonomic colouring of phylogenetic trees of protein sequences
(2020)
Palidwor, Gareth; Reynaud, Emmanuel G.; Andrade, Miguel A.
Abstract:
Background: Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common. Results: We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissPr...
http://hdl.handle.net/10197/11789
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Transitional forms between the three domains of life and evolutionary implications
(2020)
Reynaud, Emmanuel G.; Devos, Damien P.
Transitional forms between the three domains of life and evolutionary implications
(2020)
Reynaud, Emmanuel G.; Devos, Damien P.
Abstract:
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.
Science Foundation Ireland
EMBL
http://hdl.handle.net/10197/11791
Displaying Results 1 - 11 of 11 on page 1 of 1
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