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informatics

Boxplot of table using ggplot2

Published in , 2017

In R, ggplot2 requires data in a specific format. So, if you want to create a box plot with ggplot2 from a table, you must reshape it.

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publications

2015 - Why fight if you can run Strategies of the brown algal genus Lobophora (Dictyotales, Phaeophyceae) against herbivores.

Published in Vieira thesis 2015, 2015

The brown alga Lobophora represents a major benthic component in tropical coral reefs, capable of dominating large reef areas following coral motality and herbivory declines. The alga, however, has been the object of contradictory observations in terms of susceptibility to herbivory. Unaware of the species-richness of this genus, virtually all the previous studies referred to the single Caribbean species referred to as Lobophora variegata, which was presumably polymorphic, with different chemical compositions and occupying diverse ecological niches. Variation in susceptibility of this single algal species to herbivory have been consequently interpreted as intraspecific variation in terms of morphology and chemical composition as well as differences in herbivore guild compositions and diet across different locations (e.g. habitat, reef, region). Recent taxonomical studies of the genus Lobophora disclosed a high species diversity, which could conceivably explain previous contradictory results. However, the present study, which compared the susceptibility to herbivory of eight different species of Lobophora, which differed in growth form as well as their fine-scale alpha-niche on coral reefs in the southern lagoon in New Caledonia, showed that they were all consumed without outstanding differences. These results suggest that Lobophora strategies in forms of escapes – associational or spatial – have been privileged by this brown tropical alga over defenses – chemical or morphological – against herbivores. Why fight if you can run? Strategies of the brown algal genus Lobophora (Dictyotales, Phaeophyceae) against herbivores. Available from: https://www.researchgate.net/publication/316442155_Why_fight_if_you_can_run_Strategies_of_the_brown_algal_genus_Lobophora_Dictyotales_Phaeophyceae_against_herbivores [accessed Apr 24, 2017].

Recommended citation: Vieira, C., Stenger, PL., Moleana, T., De Clerck, O., & Payri, C. (2015) - working paper - from Vieira Thesis 2015 https://www.researchgate.net/publication/316442155_Why_fight_if_you_can_run_Strategies_of_the_brown_algal_genus_Lobophora_Dictyotales_Phaeophyceae_against_herbivores

2017 - First data on three bivalve species exposed to an intra-harbour polymetallic contamination (La Rochelle, France)

Published in Comparative Biochemistry and Physiology, 2017

Evaluating diffuse sediment contamination in the environment is a major concern with the aim of reaching a good chemical and ecological state of the littoral zone. In this study the risks of chronic chemical contamination and consequences in the bivalves Crassostrea gigas, Mytilus sp. and Mimachlamys varia were evaluated in coastal environments. The objective here was to understand the anthropological phenomena that affect the functioning of themarina of La Rochelle (semi-closed environment). Harbours seeking ecomanagement accreditations (such as the international reference ISO 14001) constitute zones of interest to implement biomonitoring studies. The biological effects of chemical pollution in the Marina of La Rochelle were studied to develop a multi-biomarker biomonitoring approach on specific marine species of this site. Moreover, a genetic (DNA barcoding) approach was applied to validate the species identity of collected bivalves. Of the three species tested the scallop, M. varia, was the most sensitive to metal exposure.

Recommended citation: Breitwieser, M., Viricel, A., Churlaud, C., Guillot, B., Martin, E., Stenger, P. L., ... & Thomas-Guyon, H. (2017). "First data on three bivalve species exposed to an intra-harbour polymetallic contamination (La Rochelle, France)." Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology.. http://ac.els-cdn.com/S1532045617300467/1-s2.0-S1532045617300467-main.pdf?_tid=95d450da-2944-11e7-8f90-00000aacb362&acdnat=1493076200_7fb6e69e9b1793f17049dc23dae9817d

2017 - Package R ImaginR Delimit and Characterize Color Phenotype of the Pearl Oyster

Published in CRAN, 2017

The pearl oyster, Pinctada margaritifera (Linnaeus, 1758), is one of the only bivalves expressing a large varied range of inner shell color, and by correlation, of pearl color. This phenotypic variability is partly under genetic control, but also under environmental influence. This R package allow to to delimit and characterize their color variations (by the HSV color system) with pictures.

Recommended citation: Stenger, P. L. (2017). "Package R ImaginR: Delimit and Characterize Color Phenotype of the Pearl Oyster" CRAN. https://cran.r-project.org/web/packages/ImaginR/ImaginR.pdf

2019 - Colour plasticity in the shells and pearls of animal graft model Pinctada margaritifera through colour quantification with the HSV system

Published in Scientific Reports, 2019

The bivalve Pinctada margaritifera has the capacity to produce the most varied and colourful pearls in the world. Colour expression in the inner shell is under combined genetic and environmental control and is correlated with the colour of pearls produced when the same individual is used as a graft donor. One major limitation when studying colour phenotypes is grader subjectivity, which leads to inconsistent colour qualification and quantification. Through the use of HSV (Hue Saturation Value) colour space, we created an R package named ‘ImaginR’ to characterise inner shell colour variations in P. margaritifera. Using a machine-learning protocol with a training dataset, ‘ImaginR’ was able to reassign individual oysters and pearls to predefined human-based phenotype categories. We then tested the package on samples obtained in an experiment testing the effects of donor conditioning depth on the colour of the donor inner shell and colour of the pearls harvested from recipients following grafting and 20 months of culture in situ. These analyses successfully detected donor shell colour modifications due to depth- related plasticity and the maintenance of these modifications through to the harvested pearls. Besides its potential interest for standardization in the pearl industry, this new method is relevant to other research projects using biological models.

Recommended citation: Stenger, P. L., Vidal-Dupiol, J., Reisser, C., Planes, S., & Ky, C. L. (2019). "Colour plasticity in the shells and pearls of animal graft model Pinctada margaritifera assessed by HSV colour quantification." Scientific reports, 9(1), 1-10.. https://www.nature.com/articles/s41598-019-43777-4

2019 - Limited interspecific variation in grazing susceptibility of the brown alga Lobophora to herbivory

Published in Journal of Experimental Marine Biology and Ecology, 2019

The genus Lobophora is a notable benthic algal component of tropical coral reefs, capable of dominating large reef areas following coral mortality and herbivory declines. The alga, however, has been the object of contradictory observations in terms of susceptibility to herbivory. Unaware of the species-richness of this genus, most studies referred to Lobophora variegata, a species assumed to present various morphotypes and chemotypes, occupying diverse ecological niches. Variation in susceptibility to herbivory has been consequently interpreted as intraspecific variation in terms of morphology and chemical composition as well as differences in herbivore guild compositions and diet across different locations (e.g., habitat, reef, region). Recent taxonomic studies of Lobophora disclosed a high species diversity, which could explain previous conflicting observations. The present study tested the grazing susceptibility of seven species of Lobophora (L. dimorpha, L. hederacea, L. monticola, L. obscura, L. rosacea, L. sonderi and L. undulata), which differ in growth form as well as in their chemical com- position and fine-scale ecological niche on coral reefs in the southern lagoon in New Caledonia, to two important herbivores in New Caledonia, the rabbitfish Siganus lineatus and the sea urchin Diadema setosum using tank, cage, and in situ experiments. All seven Lobophora species were markedly consumed in situ and by the two herbivores. Differences in consumption among the Lobophora species were small but statistically significant. Lobophora rosacea, characterized by a distinct secondary metabolome, was significantly more consumed by the two herbivores. Conversely, L. sonderi was always among the least consumed species. These results point to the possible role of chemical defense, and suggest that L. rosacea may produce less or different chemical deterrents than the other Lobophora species, and that L. sonderi may produce deterrents active over a wider range of herbivores. However, the limited interspecific differences in consumption point to the greater importance of associational and spatial refuges as defense strategies against herbivores over chemical or morphological defenses in the genus Lobophora.

Recommended citation: Vieira, C., Stenger, P. L., Moleana, T., De Clerck, O., & Payri, C. (2019). "Limited interspecific variation in grazing susceptibility of the brown alga Lobophora to herbivory." Journal of Experimental Marine Biology and Ecology, 518, 151175.. https://www.sciencedirect.com/science/article/pii/S0022098118304817?casa_token=t20tBBmPaGwAAAAA:TpiHJITggZFYMztyrQoqNT7KEjHsKIA_aw6GoZCNBFQf-LQ2huIuThXjxxLpBG_DKe7izvtTRMY

2020 - Differential basal expression of immune genes confers Crassostrea gigas resistance to Pacific Oyster Mortality Syndrome

Published in BMC genomics, 2020

As a major threat to the oyster industry, Pacific Oyster Mortality Syndrome (POMS) is a polymicrobial disease affecting the main oyster species farmed across the world. POMS affects oyster juveniles and became panzootic this last decade, but POMS resistance in some oyster genotypes has emerged. While we know some genetic loci associated with resistance, the underlying mechanisms remained uncharacterized. So, we developed a comparative transcriptomic approach using basal gene expression profiles between different oyster biparental families with contrasted phenotypes when confronted to POMS (resistant or susceptible). We showed that POMS resistant oysters show differential expression of genes involved in stress responses, protein modifications, maintenance of DNA integrity and repair, and immune and antiviral pathways. We found similarities and clear differences among different molecular pathways in the different resistant families. These results suggest that the resistance process is polygenic and partially varies according to the oyster genotype. We found differences in basal expression levels of genes related to TLR-NFκB, JAK-STAT and STING-RLR pathways. These differences could explain the best antiviral response, as well as the robustness of resistant oysters when confronted to POMS. As some of these genes represent valuable candidates for selective breeding, we propose future studies should further examine their function.

Recommended citation: De Lorgeril, J., Petton, B., Lucasson, A., Perez, V., Stenger, P. L., Dégremont, L., ... & Leroy, M. (2020). "Differential basal expression of immune genes confers Crassostrea gigas resistance to Pacific oyster mortality syndrome." BMC genomics, 21(1), 1-14. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6471-x

2020 - Contribution of Viral Genomic Diversity to Oyster Susceptibility in the Pacific Oyster Mortality Syndrome

Published in Frontiers in microbiology, 2020

Juvenile Pacific oysters (Crassostrea gigas) are subjected to recurrent episodes of mass mortalities that constitute a threat for the oyster industry. This mortality syndrome named “Pacific Oyster Mortality Syndrome” (POMS) is a polymicrobial disease whose pathogenesis is initiated by a primary infection by a variant of an Ostreid herpes virus named OsHV-1 μVar. The characterization of the OsHV-1 genome during different disease outbreaks occurring in different geographic areas has revealed the existence of a genomic diversity for OsHV-1 μVar. However, the biological significance of this diversity is still poorly understood. To go further in understanding the consequences of OsHV-1 diversity on POMS, we challenged five biparental families of oysters to two different infectious environments on the French coasts (Atlantic and Mediterranean). We observed that the susceptibility to POMS can be different among families within the same environment but also for the same family between the two environments. Viral diversity analysis revealed that Atlantic and Mediterranean POMS are caused by two distinct viral populations. Moreover, we observed that different oyster families are infected by distinct viral populations within a same infectious environment. Altogether these results suggest that the co-evolutionary processes at play between OsHV-1 μVar and oyster populations have selected a viral diversity that could facilitate the infection process and the transmission in oyster populations. These new data must be taken into account in the development of novel selective breeding programs better adapted to the oyster culture environment.

Recommended citation: Delmotte J, Chaparro C, Galinier R, de Lorgeril J, Petton B, Stenger P-L, Vidal-Dupiol J, Destoumieux-Garzon D, Gueguen Y, Montagnani C, Escoubas J-M and Mitta G (2020) Contribution of Viral Genomic Diversity to Oyster Susceptibility in the Pacific Oyster Mortality Syndrome." Front. Microbiol. 11:1579. doi: 10.3389/fmicb.2020.01579 https://www.frontiersin.org/articles/10.3389/fmicb.2020.01579/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Microbiology&id=540521

talks

Internatonal Symposium of Green Chemestry (ISGC 2015) in La Rochelle

Published in Internatonal Symposium of Green Chemestry (ISGC 2015) in La Rochelle, 2052

Testing correlations between genetic diversity and chemical pollution exposure in a bioaccumalting marine bivalve (2015) Speaker: Eric Pante Authors: A. Viricel, PL Stenger, Vanessa Becquet, Eric Pante, Antoine Bonnet, Carine Churlaud, Stéphane Le Floch, Marianne Graber, Marius Pageaud, Hélène Thomas-Guyon