Emmanuel Reynaud

Emmanuel Reynaud
University College Dublin | UCD · Conway Institute of Biomolecular & Biomedical Research

PhD, MSc, BSc, Knight (Palmes Academiques,France)

About

97
Publications
39,127
Reads
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5,073
Citations
Citations since 2017
20 Research Items
2764 Citations
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20172018201920202021202220230100200300400
20172018201920202021202220230100200300400
Additional affiliations
January 2016 - July 2016
University College Dublin
Position
  • Lecturer
January 2009 - September 2015
University College Dublin
Position
  • Lecturer
September 2001 - January 2009
European Molecular Biology Laboratory
Position
  • EMBO long term Fellow/ Research Scientist

Publications

Publications (97)
Article
Full-text available
Background Harm Reduction (HR) policies for People Who Use Drugs (PWUD) have a significant positive impact on their health. Such approaches limit the spread of infections and reduce opioid overdose mortality. These policies have led to the opening of specialized structures located mainly in big cities and urbanized zones. The COVID-19 pandemic redu...
Preprint
Full-text available
Background: Harm Reduction (HR) policies for People Who Use Drugs (PWUD) have a significant positive impact on their health. Such approaches limit the spread of infections and reduce opioid overdose mortality. These policies have led to the opening of specialized centers located mainly in big cities and urbanized zones. The COVID-19 pandemic reduce...
Cover Page
Full-text available
In article number 2004452, Dermot F. Brougham and co‐workers demonstrate 3D printable responsive magnetic hydrogels composed of magnetic iron oxide nanoflowers and Pluronic polymers that encode spatiotemporally controlled temperature increase and dye release on alternating magnetic field irradiation.
Article
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...
Article
Full-text available
Background: Despite multiple harm reduction (HR) programmes worldwide, there are still an important number of people who use drugs (PWUD) who do not access those services. Their difficulties to obtain HR tools are due to their inability to reach such services (remoteness and/or limited customer service hours), costs, quantitative restrictions, fea...
Article
Full-text available
Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron av...
Preprint
Full-text available
The glass models of invertebrates crafted by Leopold and Rudolf Blaschka were made between 1863 and 1889. Production ceased when the glassmakers turned their attention to what is now known as the Ware Collection of Blaschka Glass Models of Plants, created for the Harvard Museum of Natural History. Nearly 130 years have passed since their last publi...
Article
Full-text available
Additive manufacturing, better known as 3D printing is becoming an easily accessible method to produce 3D objects ranging from medical devices to jet plane parts. However, this implies the creation of an accurate 3D digital model by Computer Assisted Design (CAD) or direct acquisition of a 3D model as well as a correct understanding of the various...
Article
Full-text available
As the production of single use plastic packaging materials is increasing rapidly, the resultant generation of waste material is quickly becoming one of the world’s major environmental issues. These plastic materials are highly stable, with excellent material properties which can allow them to be used beyond their intended single use. To effectivel...
Article
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 physiol...
Article
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Are the answers to biological questions obtained via live fluorescence microscopy substantially affected by phototoxicity? Although a single set of standards for assessing phototoxicity cannot exist owing to the breadth of samples and experimental questions associated with biological imaging, we need quantitative, practical assessments and reportin...
Article
Full-text available
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 cell...
Data
Set of homologous proteins of the YRG protein family. A total of 171 proteomes were used: 32 Bacteria, 93 Archaea and 46 Eukarya. The dash symbol “-” means the absence of the protein in that proteome. If the protein is present in a proteome, the UniProt Accession Number (AC) is shown. (XLSX)
Data
Raw file of the phylogenetic tree obtained with PhyML, with bootstrapping values (0–1000), in Newick format. Each sequence is labeled using the YRG protein, the species name and the taxonomical group it belongs to: YRGprotein_Organism_Phyla. (TXT)
Data
Phylogenetic trees (one per YRG subfamily) obtained with PhyML. Each sequence is labeled using the YRG protein, the species name and the taxonomical group it belongs to: YRGprotein_Organism_Phyla. (PDF)
Data
Set of homologous proteins of the YRG protein family, in FASTA format. Each sequence is labeled using the YRG protein and the species name: YRGprotein_Organism. (FASTA)
Data
Phylogeny of the 370 YRG proteins found in the analyses using an alternative method (RAxML). The sequences are disposed in ten branches, one for each YRG protein subfamily: Gnl3, Gnl3l, Gnl2, Lsg1, Gnl1, YlqF, Mtg1, YjeQ, Noa1 and YAG. Main branches are labeled with a bootstrap support value (0–100), and the lowly supported ones are highlighted in...
Article
Three-dimensional (3D) tissue models are invaluable tools that can closely reflect the in vivo physiological environment. However, they are usually difficult to develop, have a low throughput and are often costly; limiting their utility to most laboratories. The recent availability of inexpensive additive manufacturing printers and open source 3D d...
Article
Full-text available
In vitro cell culture models used to study epithelia and epithelial diseases would benefit from the recognition that organs and tissues function in a three-dimensional (3D) environment. This context is necessary for the development of cultures that more realistically resemble in vivo tissues/organs. Our aim was to establish and characterize biologi...
Preprint
Full-text available
Ocean microbes drive global-scale biogeochemical cycling ¹ , but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories 2–5 . Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surf...
Article
Two polymers, polymethylmethacrylate (PMMA) and cyclic olefin copolymer (COC), containing a range of nano- to micron- roughness surfaces (Ra 0.01, 0.1, 0.4, 1.0, 2.0, 3.2 and 5.0μm) were fabricated using electrical discharge machining (EDM) and replicated using micro injection moulding (μIM). Polymer samples were characterized using optical profilo...
Article
Full-text available
Since the early adoptions of 3DP (3DP) technologies in the late 80's, and more significantly by the rep rap movement in 2005, 3DP has become extremely accessible. There are many different new and exciting methods of 3DP but it the increase in accessibility, through low cost and easy to use formats that has seen 3DP’s diffusion across nearly all sec...
Article
Full-text available
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...
Data
Tables and calculations for analysis (Calculations tables.xlsx). (XLSX)
Data
Echinopora lamellosa, 3D model of complex encrusting colony. (https://vimeo.com/109268768). (MP4)
Article
Full-text available
Between 1863 and 1890 the Blaschka workshop, based in Dresden, produced and distributed glass models of more than 700 species of invertebrates, ranging from anemones to radiolarians. Their unique skills and the quality of their modelling of soft-bodied animals attracted a wealth of orders from across the world. During this period museums and univer...
Article
Full-text available
Ce second article du dossier, écrit par un groupe de travail sous l'égide de la Direction générale de la santé et de la MILDECA, élargit la réflexion à la filtration et propose la création de nouveaux outils, plus efficaces, qui tient compte de la place toujours croissante des médicaments opiacés chez les injecteurs. Swaps accompagne ce débat utile...
Article
Full-text available
The Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater a...
Article
Coral studies rely on comparative research between several reference coral skeletons and living organisms imaged on reefs. However, many of these skeletons are part of collections, making extensive comparative works difficult. Nowadays, imaging technologies and image processing approaches allow acquisition of three-dimensional (3D) datasets that ca...
Article
Full-text available
Ten years of development in light-sheet microscopy have led to spectacular demonstrations of its capabilities. The technology is ready to assist biologists in tackling scientific problems, but are biologists ready for it? Here we discuss the interdisciplinary challenges light-sheet microscopy presents for biologists and highlight available resource...
Article
Full-text available
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...
Chapter
image processing;marine biology;microscopy;optical projection tomography systems;sample preparation
Chapter
Light-sheet fluorescencemicroscopy (LSFM) is a non-invasive opticalmethod for the observation of living specimens. Although this concept was established a century ago it is only during the last decade that instruments suitable for biological applications have been developed, thereby circumventing some of the limitations of established fluorescence...
Chapter
planktonic community analysis;semi-automated;classification;plankton imaging
Chapter
The ocean may have been filled by meteorites bringing water to Earth but its creatures were drawn by men. Sea shells were eaten in caves, dolphins drawn on cave walls. For a long time, though, its surface was the only visible thing, a glittering mirror for the human soul where Gods and Monsters fought over submerged empires, pulling down Atlantis a...
Book
Written by an international team of experts from the Tara Oceans Marine Biology Imaging Platform (TAOMI), this is the first and only compendium on marine imaging technologies, and includes all known underwater as well as on-land techniques. TAOMI is imaging the largest collection of marine organisms in recent history, ranging from viruses to corals...
Conference Paper
Full-text available
Even though the outstanding energy resource provided by ocean surface waves has long been recognized, the extraction of wave power is still in its infancy. Meanwhile, the increased interest in sustainable energy alternatives could lead to large-scale deployments of wave energy convertors (WECs) worldwide in the near future. In this context, the int...
Article
Full-text available
The glass marine invertebrate models produced by Leopold and Rudolf Blaschka represent the most accurate museum artefacts ever made to represent cnidarians, nudibranchs and radiolarians. University College Dublin, originally the Royal College of Science for Ireland, holds a collection of these models, acquired in 1885, some of which continue to be...
Article
Full-text available
Life science research focuses on deciphering the biochemical mechanisms that regulate cell proliferation and function and largely depends on the use of tissue culture methods in which cells are grown on two-dimensional hard plastic or glass surfaces. However, the flat surface of the tissue culture plate represents a poor topological approximation o...
Article
Full-text available
We quantify through simple population-dynamics models the biological growth on wave energy converters (WECs). We also evaluate the effects of the inherently unsteady flow induced by waves and currents on the settlement of various species. Finally, we discuss the impact of the biological growth on the flow pattern around such devices (and consequent...
Article
Full-text available
We designed a widefield frequency domain Fluorescence Lifetime Imaging Microscopy (FLIM)setup, which is based on a Single Plane Illumination Microscope (SPIM). A SPIM provides an inherent optical sectioning capability and reduces photobleaching compared to conventional widefield and confocal fluorescence microscopes. The lifetime precision of the F...
Article
Full-text available
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.
Article
Full-text available
With biology becoming quantitative, systems-level studies can now be performed at spatial scales ranging from molecules to ecosystems. Biological data generated consistently across scales can be integrated with physico-chemical contextual data for a truly holistic approach, with a profound impact on our understanding of life [1]–[5]. Marine ecosyst...
Article
Full-text available
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 an...
Article
Measuring biodiversity in the oceans and its modifications with time or during climate change requires the accurate description of plankton organisms from viruses to fishes. However, our taxonomic knowledge of this 70% of the Earth is extremely limited. The ultimate way to perform large-scale taxonomical analysis is to achieve full 3D imaging of ev...
Article
Full-text available
The Golgi complex has a central role in the secretory pathway of all higher organisms. To explain the synthesis of its unique stacked structure in mammalian cells, two major models have been proposed. One suggests that it is synthesized de novo from the endoplasmic reticulum. The second model postulates a pre-existing Golgi template that serves as...
Article
Full-text available
Bacteria that also have features typical of eukaryotes and archaea may reflect a possible pathway in ancient cellular evolution.
Chapter
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Light Sheet Fluorescence Microscopy (LISH-M) is a true fluorescence optical sectioning technique, first described by Heinrich Siedentopf in 1902 under the name of Ultramicroscopy. Light sheet microscopy utilises a plane of light to optically section samples. This allows deep imaging within transparent tissues and whole organisms.As tissues are expo...
Article
Full-text available
In Jena, at the turn of the century, Richard Zsigmondy (1865-1929), working together with the physicist Heinrich Siedentopf, had the brilliant idea to use a light sheet to illuminate from the side the colloid solution they were investigating [1]. From there the idea of light sheet illumination vanished from the scientific spotlight until it was rev...
Article
Full-text available
The mechanics of the actin cytoskeleton have a central role in the regulation of cells and tissues, but the details of how molecular sensors recognize deformations and forces are elusive. By performing cytoskeleton laser nanosurgery in cultured epithelial cells and fibroblasts, we show that the retraction of stress fibers (SFs) is restricted to the...
Article
To identify the physical and biological factors that influence tissue morphogenesis, 3D imaging tools are essential. However, obtaining quantitative information about the spatial organization of observed objects from the resulting images is not trivial. Often researchers are forced to choose “representative” image regions due to the complexity of a...
Article
Full-text available
Light-sheet-based fluorescence microscopy (LSFM) is a fluorescence technique that combines optical sectioning, the key capability of confocal and two-photon fluorescence microscopes with multiple-view imaging, which is used in optical tomography. In contrast to conventional wide-field and confocal fluorescence microscopes, a light sheet illuminates...
Article
Full-text available
Although cells migrate in a constrained 3D environment in vivo, in-vitro studies have mainly focused on the analysis of cells moving on 2D substrates. Under such conditions, the Golgi complex is always located towards the leading edge of the cell, suggesting that it is involved in the directional movement. However, several lines of evidence indicat...