Caractérisation expérimentale en traction/compression/torsion d'un matériau biosourcé type PHA

National audienceDe nouveaux matériaux polymères biosourcés et biodégradables ont fait leur apparition depuis une dizaine d'années. Ces nouveaux matériaux sont une réponse intéressante aux problèmes de ressource et de recyclage-posés par les polymères classiques provenant de la pétrochimie. Ils présentent le double avantage d'être issus de la biomasse, mais également d'être compostables, c'est-à-dire qu'il ne génère aucun toxique en se dégradant, sous certaines conditions spécifiques d'humidité et de température. Nous nous intéressons dans ce travail à une classe particulière de ces nouveaux matériaux biopolymères produits par des micro-organismes : les PolyHydroxyAlkanoates (ou PHA). Les PHA sont des polymères biosourcés, produits par une grande variété de bactéries (Ralstonia, Pseudomonas,…) en tant que réserve énergétique intracellulaire. Ces matériaux présentent malgré tout un défaut important : leur élaboration reste encore souvent difficile à contrôler conduisant à un coût de production souvent prohibitif et limitant leur dissémination dans des secteurs plus conventionnels comme par exemple celui de l'emballage. Pour que ces matériaux aient une diffusion plus importante dans ce secteur, il s'avère nécessaire d'optimiser la forme et la tenue mécanique de ces produits d'emballage. Cela nécessite une bien meilleure connaissance de leur comportement mécanique encore peu connue pour l'instant. Dans ce contexte, cette étude a pour objectif de caractériser expérimentalement puis numériquement le comportement de nuances de PHA [1]. Le but est ensuite d'aboutir à un outil numérique de calcul, capable de dimensionner et simuler le comportement thermo-mécanique de pièces d'emballages en PHA telles que ceux produits par la société EUROPLASTIQUES, partenaire industriel de ce projet. Parallèlement à ce matériau biosourcé, nous étudions également un polymère plus classique, le polypropylène, avec deux objectifs. Tout d'abord l'idée est de valider la méthodologie d'essai, compte tenu du fait que l'on dispose déjà d'une identification partielle d'une nuance de polypropylène, le PPC7712 [2]. D'autre part, ce polypropylène étant également utilisé en emballage, il permettra des comparaisons finales sur les comportements de structures. Pour la caractérisation mécanique de ces matériaux, un dispositif original a été conçu permettant la réalisation d'essais de cycles multiaxiaux simultanés comprenant des phases de traction, torsion et de compression. Ce dispositif comprend une cellule de force à six axes et d'un montage spécifique pour le serrage et le maintien d'une éprouvette cylindrique (Figure 1). Cette éprouvette est obtenue par injection, elle se compose d'une partie cylindrique et de deux têtes hexagonales (Figure 2). Contrairement, aux essais classiques, où les éprouvettes sont maintenues et entraînées par serrage, l'éprouvette est ici liée par obstacle dans les deux sens des trois directions, sans serrage afin d'éviter, autant que possible, l'apparition de contraintes mécaniques initiales. Un système de mors comprenant des plateaux, des vis et des empreintes hexagonales permettent le blocage total de l'éprouvette, quel que soit l'essai envisagé. Le dispositif prend aussi en compte la dispersion prévisible des dimensions des têtes d'éprouvette par l'intermédiaire de lamelles flexibles entre l'accouplement au vérin et le blocage des têtes. Les déformations sont mesurées directement sur l'échantillon grâce à un dispositif de corrélation d'images en 3D (Aramis 4M, GOM), permettant également de vérifier l'homogénéité de la cinématique. Figure 2: Éprouvette de chargement multiaxial Figure 1: Dispositif d'essais multiaxiaux Ce montage original autorise des cycles de sollicitations successives ou combinées de traction, compression et de torsion (Figure 3), à partir d'une seule géométrie d'éprouvette. Dans la littérature, les essais de traction et de cisaillement sont réalisés habituellement avec des éprouvettes de géométrie spécifique à chaque essai. Dans ce cas, il est difficile d'être sûr d'étudier la même structure de matériau, celle-ci étant fortement dépendante du type d'élaboration et des cinétiques de refroidissement, elles-mêmes directement liées aux dimensions géométriques. Le dispositif expérimental développé ici permet d'effectuer des chemins complexes avec changements de direction et de cycles au cours d'un même essai et sur la même éprouvette, autorisant ainsi l'exploration de tout le plan déviatoire de déformation avec prise en compte de l'histoire du chargement. Pour la simulation du comportement de structures, nous utilisons un modèle de comportement 3D d'Hyper-Visco-Hystérésis (HVH) [2], implanté dans le code de calcul Herezh++ [3]. Il tient sa singularité au fait que le comportement du matériau est décomposé en une contribution additive. Tout en incluant un potentiel hyperélastique, cette loi permet de décrire le phénomène d'hystérésis non-visqueux ainsi qu'une dépendance au temps du matériau. Le protocole d'identification, permettant l'obtention des paramètres utiles à ce modèle, est simple et rapide car il ne nécessite qu'un unique type d'essais de traction/compression relaxation [4]

Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels.

International audienceABSTRACT: BACKGROUND: The deep-sea hydrothermal vent mussel Bathymodiolus azoricus harbors thiotrophic and methanotrophic symbiotic bacteria in its gills. While the symbiotic relationship between this hydrothermal mussel and these chemoautotrophic bacteria has been described, the molecular processes involved in the cross-talking between symbionts and host, in the maintenance of the symbiois, in the influence of environmental parameters on gene expression, and in transcriptome variation across individuals remain poorly understood. In an attempt to understand how, and to what extent, this double symbiosis affects host gene expression, we used a transcriptomic approach to identify genes potentially regulated by symbiont characteristics, environmental conditions or both. This study was done on mussels from two contrasting populations. RESULTS: Subtractive libraries allowed the identification of about 1000 genes putatively regulated by symbiosis and/or environmental factors. Microarray analysis showed that 120 genes (3.5% of all genes) were differentially expressed between the Menez Gwen (MG) and Rainbow (Rb) vent fields. The total number of regulated genes in mussels harboring a high versus a low symbiont content did not differ significantly. With regard to the impact of symbiont content, only 1% of all genes were regulated by thiotrophic (SOX) and methanotrophic (MOX) bacteria content in MG mussels whereas 5.6% were regulated in mussels collected at Rb. MOX symbionts also impacted a higher proportion of genes than SOX in both vent fields. When host transcriptome expression was analyzed with respect to symbiont gene expression, it was related to symbiont quantity in each field. CONCLUSIONS: Our study has produced a preliminary description of a transcriptomic response in a hydrothermal vent mussel host of both thiotrophic and methanotrophic symbiotic bacteria. This model can help to identify genes involved in the maintenance of symbiosis or regulated by environmental parameters. Our results provide evidence of symbiont effect on transcriptome regulation, with differences related to type of symbiont, even though the relative percentage of genes involved remains limited. Differences observed between the vent site indicate that environment strongly influences transcriptome regulation and impacts both activity and relative abundance of each symbiont. Among all these genes, those participating in recognition, the immune system, oxidative stress, and energy metabolism constitute new promising targets for extended studies on symbiosis and the effect of environmental parameters on the symbiotic relationships in B. azoricus

Diversification, evolution and sub-functionalization of 70kDa heat-shock proteins in two sister species of Antarctic krill: differences in thermal habitats, responses and implications under climate change

A comparative thermal tolerance study was undertaken on two sister species of Euphausiids (Antarctic krills) Euphausia superba and Euphausia crystallorophias. Both are essential components of the Southern Ocean ecosystem, but occupy distinct environmental geographical locations with slightly different temperature regimes. They therefore provide a useful model system for the investigation of adaptations to thermal tolerance. Methodology/Principal Finding Initial CTmax studies showed that E. superba was slightly more thermotolerant than E. crystallorophias. Five Hsp70 mRNAs were characterized from the RNAseq data of both species and subsequent expression kinetics studies revealed notable differences in induction of each of the 5 orthologues between the two species, with E. crystallorophias reacting more rapidly than E. superba. Furthermore, analyses conducted to estimate the evolutionary rates and selection strengths acting on each gene tended to support the hypothesis that diversifying selection has contributed to the diversification of this gene family, and led to the selective relaxation on the inducible C form with its possible loss of function in the two krill species. Conclusions The sensitivity of the epipelagic species E. crystallorophias to temperature variations and/or its adaptation to cold is enhanced when compared with its sister species, E. superba. These results indicate that ice krill could be the first of the two species to be impacted by the warming of coastal waters of the Austral ocean in the coming years due to climate change

Transcriptome analyses to investigate symbiotic relationships between marine protists

International audienceRhizaria are an important component of oceanic plankton communities worldwide. A number of species harbor eukaryotic microalgal symbionts, which are horizontally acquired in the environment at each generation. Although these photosymbioses are determinant for Rhizaria ability to thrive in oceanic ecosystems, the mechanisms for symbiotic interactions are unclear. Using high-throughput sequencing technology (i.e., 454), we generated large Expressed Sequence Tag (EST) datasets from four uncultured Rhizaria, an acantharian (Amphilonche elongata), two polycystines (Collozoum sp. and Spongosphaera streptacantha), and one phaeodarian (Aulacantha scolymantha). We assessed the main genetic features of the host/symbionts consortium (i.e., the holobiont) transcriptomes and found rRNA sequences affiliated to a wide range of bacteria and protists in all samples, suggesting that diverse microbial communities are associated with the holobionts. A particular focus was then carried out to search for genes potentially involved in symbiotic processes such as the presence of c-type lectins-coding genes, which are proteins that play a role in cell recognition among eukaryotes. Unigenes coding putative c-type lectin domains (CTLD) were found in the species bearing photosynthetic symbionts (A. elongata, Collozoum sp., and S. streptacantha) but not in the non-symbiotic one (A. scolymantha). More particularly, phylogenetic analyses group CTLDs from A. elongata and Collozoum sp. on a distinct branch from S. streptacantha CTLDs, which contained carbohydrate-binding motifs typically observed in other marine photosymbiosis. Our data suggest that similarly to other well-known marine photosymbiosis involving metazoans, the interactions of glycans with c-type lectins is likely involved in modulation of the host/symbiont specific recognition in Radiolaria

Is geographical variation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima

Background: Kelps (Laminariales, Phaeophyceae) are brown macroalgae of utmost ecological, and increasingly economic, importance on temperate to polar rocky shores. Omics approaches in brown algae are still scarce and knowledge of their acclimation mechanisms to the changing conditions experienced in coastal environments can benefit from the application of RNA-sequencing. Despite evidence of ecotypic differentiation, transcriptomic responses from distinct geographical locations have, to our knowledge, never been studied in the sugar kelp Saccharina latissima so far. Results: In this study we investigated gene expression responses using RNA-sequencing of S. latissima from environments with contrasting temperature and salinity conditions – Roscoff, in temperate eastern Atlantic, and Spitsbergen in the Arctic. Juvenile sporophytes derived from uniparental stock cultures from both locations were pre-cultivated at 8 °C and SA 30. Sporophytes acclimated to 0 °C, 8 °C and 15 °C were exposed to a low salinity treatment (SA 20) for 24 h. Hyposalinity had a greater impact at the transcriptomic level than the temperature alone, and its effects were modulated by temperature. Namely, photosynthesis and pigment synthesis were extensively repressed by low salinity at low temperatures. Although some responses were shared among sporophytes from the different sites, marked differences were revealed by principal component analysis, differential expression and GO enrichment. The interaction between low temperature and low salinity drove the largest changes in gene expression in sporophytes from Roscoff while specimens from Spitsbergen required more metabolic adjustment at higher temperatures. Moreover, genes related to cell wall adjustment were differentially expressed between Spitsbergen and Roscoff control samples. Conclusions: Our study reveals interactive effects of temperature and salinity on transcriptomic profiles in S. latissima. Moreover, our data suggest that under identical culture conditions sporophytes from different locations diverge in their transcriptomic responses. This is probably connected to variations in temperature and salinity in their respective environment of origin. The current transcriptomic results support the plastic response pattern in sugar kelp which is a species with several reported ecotypes. Our data provide the baseline for a better understanding of the underlying processes of physiological plasticity and may help in the future to identify strains adapted to specific environments and its genetic control

Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach

As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the case for the widespread Amoebophrya ceratii species complex, parasites of their dinoflagellate congeners. We used genetic and phenotypic characters, applied to 119 Amoebophrya individuals sampled from the same geographic area, to construct practical guidelines for species delineation that could be applied in DNA/RNA based diversity analyses. Based on the internal transcribed spacer (ITS) regions, ITS2 compensatory base changes (CBC) and genome k-mer comparisons, we unambiguously defined eight cryptic species among closely related ribotypes that differed by less than 97% sequence identity in their SSU rDNA. We then followed the genetic signatures of these parasitic species during a three-year survey of Alexandrium minutum blooms. We showed that these cryptic Amoebophrya species co-occurred and shared the same ecological niche. We also observed a maximal ecological fitness for parasites having narrow tointermediate host ranges, reflecting a high cost for infecting a broader host range. This study suggests that a complete taxonomic revision of these parasitic dinoflagellates is long overdue to understand their diversity and ecological role in the marine plankton

Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids

<p>Abstract</p> <p>Background</p> <p>Heterokont algae, together with cryptophytes, haptophytes and some alveolates, possess red-algal derived plastids. The chromalveolate hypothesis proposes that the red-algal derived plastids of all four groups have a monophyletic origin resulting from a single secondary endosymbiotic event. However, due to incongruence between nuclear and plastid phylogenies, this controversial hypothesis remains under debate. Large-scale genomic analyses have shown to be a powerful tool for phylogenetic reconstruction but insufficient sequence data have been available for red-algal derived plastid genomes.</p> <p>Results</p> <p>The chloroplast genomes of two brown algae, <it>Ectocarpus siliculosus </it>and <it>Fucus vesiculosus</it>, have been fully sequenced. These species represent two distinct orders of the Phaeophyceae, which is a major group within the heterokont lineage. The sizes of the circular plastid genomes are 139,954 and 124,986 base pairs, respectively, the size difference being due principally to the presence of longer inverted repeat and intergenic regions in <it>E. siliculosus</it>. Gene contents of the two plastids are similar with 139-148 protein-coding genes, 28-31 tRNA genes, and 3 ribosomal RNA genes. The two genomes also exhibit very similar rearrangements compared to other sequenced plastid genomes. The tRNA-Leu gene of <it>E. siliculosus </it>lacks an intron, in contrast to the <it>F. vesiculosus </it>and other heterokont plastid homologues, suggesting its recent loss in the Ectocarpales. Most of the brown algal plastid genes are shared with other red-algal derived plastid genomes, but a few are absent from raphidophyte or diatom plastid genomes. One of these regions is most similar to an apicomplexan nuclear sequence. The phylogenetic relationship between heterokonts, cryptophytes and haptophytes (collectively referred to as chromists) plastids was investigated using several datasets of concatenated proteins from two cyanobacterial genomes and 18 plastid genomes, including most of the available red algal and chromist plastid genomes.</p> <p>Conclusion</p> <p>The phylogenetic studies using concatenated plastid proteins still do not resolve the question of the monophyly of all chromist plastids. However, these results support both the monophyly of heterokont plastids and that of cryptophyte and haptophyte plastids, in agreement with nuclear phylogenies.</p

Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen

Biological control using bacteriophages is a promising approach for mitigating the devastating effects of coral diseases. Several phages that infect Vibrio coralliilyticus, a widespread coral pathogen, have been isolated, suggesting that this bacterium is permissive to viral infection and is, therefore, a suitable candidate for treatment by phage therapy. In this study, we combined functional and genomic approaches to evaluate the therapeutic potential of BONAISHI, a novel V. coralliilyticus phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). BONAISHI appears to be strictly lytic for several pathogenic strains of V. coralliilyticus and remains infectious over a broad range of environmental conditions. This candidate has an unusually large dsDNA genome (303 kb), with no genes that encode known toxins or implicated in lysogeny control. We identified several proteins involved in host lysis, which may offer an interesting alternative to the use of whole bacteriophages for controlling V. coralliilyticus. A preliminary therapy test showed that adding BONAISHI to an infected culture of Symbiodinium sp. cells reduced the impact of V. coralliilyticus on Symbiodinium sp. photosynthetic activity. This study showed that BONAISHI is able to mitigate V. coralliilyticus infections, making it a good candidate for phage therapy for coral disease

Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress

The brown alga Ectocarpus siliculosus, unlike terrestrial plants, undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress

First Viruses Infecting the Marine Diatom Guinardia delicatula

The marine diatom Guinardia delicatula is a cosmopolitan species that dominates seasonal blooms in the English Channel and the North Sea. Several eukaryotic parasites are known to induce the mortality of this species. Here, we report the isolation and characterization of the first viruses that infect G. delicatula. Viruses were isolated from the Western English Channel (SOMLIT-Astan station) during the late summer bloom decline of G. delicatula. A combination of laboratory approaches revealed that these lytic viruses (GdelRNAV) are small tailless particles of 35–38 nm in diameter that replicate in the host cytoplasm where both unordered particles and crystalline arrays are formed. GdelRNAV display a linear single-stranded RNA genome of ~9 kb, including two open reading frames encoding for replication and structural polyproteins. Phylogenetic relationships based on the RNA-dependent-RNA-polymerase gene marker showed that GdelRNAV are new members of the Bacillarnavirus, a monophyletic genus belonging to the order Picornavirales. GdelRNAV are specific to several strains of G. delicatula. They were rapidly and largely produced (&lt;12 h, 9.34 × 104 virions per host cell). Our analysis points out the host's variable viral susceptibilities during the early exponential growth phase. Interestingly, we consistently failed to isolate viruses during spring and early summer while G. delicatula developed important blooms. While our study suggests that viruses do contribute to the decline of G. delicatula's late summer bloom, they may not be the primary mortality agents during the remaining blooms at SOMLIT-Astan. Future studies should focus on the relative contribution of the viral and eukaryotic pathogens to the control of Guinardia's blooms to understand the fate of these prominent organisms in marine systems