Éditeur(s) : HAL CCSD Wiley
Résumé : 1. Resource control over abundance, structure and functional diversity of soil microbial communities is a key determinant of soil processes and related ecosystem functioning. Copiotrophic organisms tend to be found in environments which are rich in nutrients, particularly carbon, in contrast to oligotrophs, which survive in much lower carbon concentrations. We hypothesized that microbial biomass, activity and community structure in nutrient-poor soils of an Amazonian rain forest are limited by multiple elements in interaction. We tested this hypothesis with a fertilization experiment by adding C (as cellulose), N (as urea) and P (as phosphate) in all possible combinations to a total of 40 plots of an undisturbed tropical forest in French Guiana. After 2years of fertilization, we measured a 47% higher biomass, a 21% increase in substrate-induced respiration rate and a 5-fold higher rate of decomposition of cellulose paper discs of soil microbial communities that grew in P-fertilized plots compared to plots without P fertilization. These responses were amplified with a simultaneous C fertilization suggesting P and C colimitation of soil micro-organisms at our study site. Moreover, P fertilization modified microbial community structure (PLFAs) to a more copiotrophic bacterial community indicated by a significant decrease in the Gram-positive:Gram-negative ratio. The Fungi:Bacteria ratio increased in N fertilized plots, suggesting that fungi are relatively more limited by N than bacteria. Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. In contrast, community level physiological profiles under P fertilization combined with either C or N fertilization or both differed strongly from all other treatments, indicating functionally different microbial communities. While P appears to be the most critical from the three major elements we manipulated, the strongest effects were observed in combination with either supplementary C or N addition in support of multiple element control on soil microbial functioning and community structure. We conclude that the soil microbial community in the studied tropical rain forest and the processes it drives is finely tuned by the relative availability in C, N and P. Any shifts in the relative abundance of these key elements may affect spatial and temporal heterogeneity in microbial community structure, their associated functions and the dynamics of C and nutrients in tropical ecosystems.
ISSN: 0269-8463

hal-01204229
https://hal.archives-ouvertes.fr/hal-01204229
DOI : 10.1111/1365-2435.12329
PRODINRA : 311389

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.
ISSN: 2041-1723

hal-01545322
https://hal.archives-ouvertes.fr/hal-01545322
DOI : 10.1038/ncomms3091

Éditeur(s) : HAL CCSD American Society of Hematology
Résumé : International audience
Sickle cell disease is characterized by painful vaso-occlusive crises during which abnormal interactions between erythroid adhesion molecules and vessel-wall proteins are thought to play a critical role. Hydroxyurea, the only drug with proven benefit in sickle cell disease, diminishes these interactions, but its mechanism of action is not fully understood. We report that, under hydroxyurea, expression of the unique erythroid laminin receptor Lu/BCAM was increased, but red blood cell adhesion to laminin decreased. Because Lu/BCAM phosphorylation is known to activate cell adhesion to laminin, it was evaluated and found to be dramatically lower in hydroxyurea-treated patients. Analysis of the protein kinase A pathway showed decreased intracellular levels of the upstream effector cyclic adenosine monophosphate during hydroxyurea treatment. Using a cellular model expressing recombinant Lu/BCAM, we showed that hydroxyurea led to decreased intracellular cyclic adenosine monophosphate levels and diminished Lu/BCAM phosphorylation and cell adhesion. We provide evidence that hydroxyurea could reduce abnormal sickle red blood cell adhesion to the vascular wall by regulating the activation state of adhesion molecules independently of their expression level.
ISSN: 0006-4971

inserm-00821117
http://www.hal.inserm.fr/inserm-00821117
http://www.hal.inserm.fr/inserm-00821117/document
http://www.hal.inserm.fr/inserm-00821117/file/Bartolucci_Blood_2010.pdf
DOI : 10.1182/blood-2009-12-257444

Éditeur(s) : HAL CCSD
Résumé : International audience
Among the 20 000 human gene products predicted from genome annotation, about 3000 still lack validation at protein level. We developed PepPSy, a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein. PepPSy can also be used by biocurators to revisit the annotation of specific categories of proteins based on the 'omics' data housed by the system. In this study, it was used to prioritize 21 dubious protein-coding genes among the 616 annotated in neXtProt for reannotation.
DATABASE

hal-01342472
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01342472
DOI : 10.1093/database/baw070
PUBMED : 27173522

Éditeur(s) : HAL CCSD Royal Society
Résumé : International audience
Maternal Embryonic Leucine zipper Kinase (MELK) was recently shown to be involved in cell division of Xenopus embryo epithelial cells. The cytokinetic furrow of these cells ingresses asymmetrically and is developmentally regulated. Two subpopulations of xMELK, the mMELK (for "mitotic" xMELK) and iMELK ("interphase" xMELK), which differ in their spatial and temporal regulation, are detected in Xenopus embryo. How cells regulate these two xMELK populations is unknown. In this study we show that, in epithelial cells, xMELK is present at a higher concentration at the apical junctional complex, in contrast to mesenchyme-like cells, which have uniform distribution of cortical MELK. Interestingly, mMELK and iMELK also differ by their requirements towards cell-cell contacts to establish their proper cortical localization both in epithelial and mesenchyme-like cells. Receptor for Activated protein Kinase C (RACK1), which we identified as an xMELK partner, co-localizes with xMELK at the tight junction. Moreover, a truncated RACK1 construct interferes with iMELK localization at cell-cell contacts. Collectively, our results suggest that iMELK and RACK1 are present in the same complex and that RACK1 is involved in the specific recruitment of iMELK at the apical junctional complex in epithelial cells of Xenopus embryos.
ISSN: 2046-6390

hal-00874053
https://hal.archives-ouvertes.fr/hal-00874053
https://hal.archives-ouvertes.fr/hal-00874053/document
https://hal.archives-ouvertes.fr/hal-00874053/file/Cell-cycle_dependent-accepted.pdf
DOI : 10.1242/bio.20136080

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
The benefit of assimilating high spatial and temporal resolution Global Positioning System (GPS) zenith tropospheric delay (ZTD) observations within a high-resolution numerical weather prediction (NWP) system is evaluated during IOP 9 of the Convective and Orographically-induced Precipitation Study (COPS) campaign. In the framework of the international COPS field experiment, which took place from June to August 2007, a dense GPS network was deployed in the Vosges mountain region in eastern France and in the Black Forest region in southwestern Germany. GPS ZTD observations collected during the COPS field campaign, in addition to the European operational GPS data, are assimilated into the AROME/3D-Var system. We investigate the impact of assimilating these GPS ZTD observations on the forecast of convective systems that travelled over eastern France during the three days of COPS IOP 9 (18-20 July 2007). The results show a clear positive impact on short-range quantitative precipitation forecasts when GPS ZTD observations are assimilated. The impact is most important on 19 July 2007 (IOP 9b). The present study benefits from additional validation measurements collected during the COPS campaign. In particular we find that the assimilation of ZTD data induces changes in the low-to-middle tropospheric water vapour vertical structure that are consistent with water vapour measurements from radiosonde and airborne lidar. As most of the improvement is gained by assimilating GPS ZTD observations from the European operational GPS network, this study opens up encouraging horizons for the assimilation of GPS ZTD in new high-resolution operational NWP systems
ISSN: 0035-9009

hal-00424350
https://hal.archives-ouvertes.fr/hal-00424350
DOI : 10.1002/qj.508

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Background Although the French eating model may differ from those of other countries, no studies to date have investigated dietary patterns in a wide age range of adults and at the national level. We aimed to identify dietary patterns (DP) of French adults and assess their associations with demographic, socio-economic and behavioural factors. Methods The present study included 2624 adults (1087 men, 1537 women) aged 18–79 years from the cross-sectional national French INCA2 dietary survey. Dietary data were collected using a 7-day estimated food record. Clusters of DP were derived using principal component analysis and clustering, conjointly. Age-adjusted logistic regression analyses were used to investigate the association between DP and correlates. Results Five DP were identified, namely ‘traditional’, ‘prudent’, ‘diversified’, ‘processed’ and ‘sandwiches’. Men were more likely to follow a traditional diet and women the ‘prudent’ pattern. Members of the ‘processed’ and ‘sandwiches’ patterns were younger compared to non-members. Healthier dietary patterns were overall positively associated with a higher socio-economic position, healthier behaviours (in terms of sedentary behaviours and smoking status) and lower body mass index. Under-reporting of energy intake, restrictive diet to lose weight and dietary supplement consumption were also related to specific DP, although differentially in men and women. Associations with contextual factors (i.e. household composition, agglomeration size and region) were also observed. Conclusions The identification of adults’ dietary patterns and associated behaviours (all modifiable) is important for the conceptualisation of multi-behavioural programs. The additional information on social and environmental correlates is also essential for targeting the most vulnerable population groups in the context of such public health interventions
ISSN: 0952-3871

hal-01299975
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01299975
DOI : 10.1111/jhn.12315
PUBMED : 25233099

Éditeur(s) : HAL CCSD Elsevier
Résumé : Volatile terpenes are among the most diverse class of defensive compounds in plants, and they are implicated in both direct and indirect defense against herbivores. In terpenes, both the quantity and the diversity of compounds appear to increase the efficiency of defense as a diverse blend of compounds provides a more efficient protection against a broader range of herbivores and limits the chances that an enemy evolves resistance. Theory predicts that plant defensive compounds should be allocated differentially among tissues according to the value of the tissue, its cost of construction and the herbivore pressure on it. We collected volatile terpenes from bark and leaves of 178 individual tree belonging to 55 angiosperm species in French Guiana and compare the kind, amount, and diversity of compounds in these tissues. We hypothesized that in woody plants, the outermost part of the trunk should hold a more diverse blend of volatile terpenes. Additionally, as herbivore communities associated with the leaves is different to the one associated with the bark, we also hypothesized that terpene blends should be distinct in the bark vs. the leaves of a given species. We found that the mixture of volatile terpenes released by bark is different and more diverse than that released by leaves, both in monoterpenes and sesquiterpenes. This supports our hypothesis and further suggests that the emission of terpenes by the bark should be more important for trunk defense than previously thought. (c) 2012 Elsevier Ltd. All rights reserved.
ISSN: 0031-9422

hal-01032417
https://hal.archives-ouvertes.fr/hal-01032417
DOI : 10.1016/j.phytochem.2012.07.003

Éditeur(s) : HAL CCSD Wiley
Résumé : While attention on logging in the tropics has been increasing, studies on the long-term effects of silviculture on forest dynamics and ecology remain scare and spatially limited. Indeed, most of our knowledge on tropical forests arises from studies carried out in undisturbed tropical forests. This bias is problematic given that logged and disturbed tropical forests are now covering a larger area than the so-called primary forests. A new network of permanent sample plots in logged forests, the Tropical managed Forests Observatory (TmFO), aims to fill this gap by providing unprecedented opportunities to examine long-term data on the resilience of logged tropical forests at regional and global scales. TmFO currently includes 24 experimental sites distributed across three tropical regions, with a total of 490 permanent plots and 921ha of forest inventories.
ISSN: 1402-2001

hal-01204230
https://hal.archives-ouvertes.fr/hal-01204230
DOI : 10.1111/avsc.12125
PRODINRA : 323838

Éditeur(s) : HAL CCSD
Résumé : 16 p.
National audience
The objective of this paper is to present an approach for experimenting territorial prospective analysis based on spatial modelling. This approach is carried out in the framework of the DESCARTES project which aims at developing a spatial simulation tool to support the design and analysis of different scenarios for land-use allocation in Reunion Island in terms of environmental services. The spatial modelling tool is composed of two complementary applications: (i) the Ocelet modelling language and its land dynamics simulation environment, and (ii) the Margouill@ platform. The first demonstrator, a model of farm land consumption by urbanization, was developed and presented during workshops in order to test the role of the spatial simulation tool in support of a collaborative innovation process among stakeholders, and to foster new research on social learning, spatial simulation of environmental services, and scale change issues.
L'objectif de cet article est de présenter une démarche de construction d'un exercice de prospective territoriale basé sur un outil de modélisation spatiale. Cette démarche est mise en œuvre dans le cadre du projet ANR DESCARTES dont l'objectif est de construire un outil de simulation cartographique pour analyser différents scénarios d'affectation de l'usage des sols à l'Ile de La Réunion, en termes de services environnementaux. La plateforme de simulation cartographique est composée de deux applications complémentaires (i) le langage de modélisation Ocelet et son environnement de simulation de paysages dynamiques, et (ii) la plateforme Margouill@. Le développement puis la présentation, en atelier, d'un premier démonstrateur sur la consommation des terres agricoles par l'urbanisation a permis de tester l'outil cartographique comme support d'un processus d'innovation collective entre les parties prenantes, et d'ouvrir de nouveaux champs de recherche sur l'analyse de la démarche par les apprentissages, la spatialisation et la simulation prospective des services écosystémiques, et la prise en compte du changement d'échelle.
Acte de la Conférence Internationale de Géomatique et d'Analyse Spatiale
Brest, France

cirad-00850243
http://hal.cirad.fr/cirad-00850243
http://hal.cirad.fr/cirad-00850243/document
http://hal.cirad.fr/cirad-00850243/file/SAGEO-Brest2013-version_finale.pdf

Éditeur(s) : HAL CCSD Sociedade Entomológica do Brasil
Résumé : Variations in diel activity among hyperdiverse tropical communities of moths, despite representing a key component of niche partitioning between species, have barely been studied so far. Using light trapping from dawn to sunset over a 1-year period in French Guiana, we investigated these variations within and between two families of moths (Sphingidae and Saturniidae). Our results revealed contrasting patterns in flight activity at night between Sphingidae and Saturniidae. Sphingidae reached their peak in species richness and abundance between 7:00 and 8:00 p.m., followed by a decrease around 11:00 p.m. to midnight, whereas Saturniidae were continuously present throughout the night, with a peak around midnight. In addition, we found changes in diel activity among some of the most common genera in each family, highlighting distinct behavioral, physiological, and functional traits among taxa. Given differences in flight activity at different taxonomic levels, it is strongly recommended to monitor by light trapping throughout the night to effectively sample saturniid and sphingid assemblages, even though the activity of Sphingidae sharply declines after midnight. These results improve the general natural history information of tropical moths and reinforce the need of further research on the ecological and taxonomic consequences of differences in diel activity.
ISSN: 1519-566X

hal-01536447
https://hal.archives-ouvertes.fr/hal-01536447
DOI : 10.1007/s13744-014-0264-3
PRODINRA : 320714

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
To improve a previously constructed broadly neutralizing hepatitis B virus (HBV)-specific preS1 humanized antibody (HzKR127), we further humanized it through specificitydetermining residue (SDR) grafting. Moreover, we improved affinity by mutating two residues in heavy-chain complementarity-determining regions (CDR), on the basis of the crystal structure of the antigen–antibody complex. HzKR127-3.2 exhibited 2.5-fold higher affinity and enhanced virus-neutralizing activity compared to the original KR127 antibody and showed less immunogenic potential than HzKR127. Enhanced virus-neutralizing activity was achieved by the increased association rate, providing insights into engineering potent antibody therapeutics for HBV immunoprophylaxis. HzKR127-3.2 may be a good candidate for HBV immunoprophylaxis.
ISSN: 1873-3468

hal-01110668
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01110668
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01110668/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01110668/file/Enhanced%20humanization_accepted.pdf
DOI : 10.1016/j.febslet.2014.11.046

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.
ISSN: 0737-4038

hal-01544755
https://hal.archives-ouvertes.fr/hal-01544755
DOI : 10.1093/molbev/msu318

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Risk assessment related to the exposure of humans to chemicals released into the environment is a major concern of our modern societies. In this context, toxicology plays a crucial role to characterize the effects of this exposure on health and identify the targets of these molecules. MALDI imaging mass spectrometry (IMS) is an enabling technology for biodistribution studies of chemicals. Although the majority of published studies are presented in a pharmacological context, the concepts discussed in this review can be applied to the toxicological evaluation of chemicals released into the environment. The major asset of IMS is the simultaneous localization and identification of a parent molecule and its metabolites without labeling and without any prior knowledge. Quantification methods developed in IMS are presented with application to an environmental pollutant. IMS is effective in the localization of chemicals and endogenous species. This opens unique perspectives for the discovery of molecular alterations in metabolites and protein biomarkers that could help for a better understanding of toxicity mechanisms. Distribution studies of agrochemicals in plants by IMS can contribute to a better understanding of their mode of action and to a more effective use of these chemicals, avoiding the current concern of environmental damage.
ISSN: 1874-3919

hal-01367141
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367141
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367141/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367141/file/Potential%20of%20MALDI%20imaging.pdf
DOI : 10.1016/j.jprot.2016.05.008

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The development of Plasmodium falciparum within the Anopheles gambiae mosquito relies on complex vector-parasite interactions, however the resident midgut microbiota also plays an important role in mediating parasite infection. In natural conditions, the mosquito microbial flora is diverse, composed of commensal and symbiotic bacteria. We report here the isolation of culturable midgut bacteria from mosquitoes collected in the field in Cameroon and their identification based on the 16S rRNA gene sequencing. We next measured the effect of selected natural bacterial isolates on Plasmodium falciparum infection prevalence and intensity over multiple infectious feedings and found that the bacteria significantly reduced the prevalence and intensity of infection. These results contrast with our previous study where the abundance of Enterobacteriaceae positively correlated with P. falciparum infection (Boissiere et al. 2012). The oral infection of bacteria probably led to the disruption of the gut homeostasis and activated immune responses, and this pinpoints the importance of studying microbe-parasite interactions in natural conditions. Our results indicate that the effect of bacterial exposure on P. falciparum infection varies with factors from the parasite and the human host and calls for deeper dissection of these parameters for accurate interpretation of bacterial exposure results in laboratory settings.
ISSN: 1932-6203

hal-01546172
https://hal.archives-ouvertes.fr/hal-01546172
DOI : 10.1371/journal.pone.0081663

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : International audience
The only symbiotic Mediterranean gorgonian, Eunicella singularis, has faced several mortality events connected to abnormal high temperatures. Since thermotolerance data remain scarce, heat-induced necrosis was monitored in aquarium by morphometric analysis. Gorgonian tips were sampled at two sites: Medes (Spain) and Riou (France) Islands, and at two depths: 15 m and-35 m. Although coming from contrasting thermal regimes, seawater above 28 degrees C led to rapid and complete tissue necrosis for all four populations. However, at 27 degrees C, the time length leading to 50% tissue necrosis allowed us to classify samples within three classes of thermal sensitivity. Irrespectively of the depth, Medes specimens were either very sensitive or resistant, while Riou fragments presented a medium sensitivity. Microsatellite analysis revealed that host and symbiont were genetically differentiated between sites, but not between depths. Finally, these genetic differentiations were not directly correlated to a specific thermal sensitivity whose molecular bases remain to be discovered.
ISSN: 1631-0691

hal-01546168
https://hal.archives-ouvertes.fr/hal-01546168
DOI : 10.1016/j.crvi.2013.06.008

Éditeur(s) : HAL CCSD
Résumé : International audience
BACKGROUND: Numerous chemicals are capable of disrupting androgen production, but the possibility that they might act together to produce effects greater than those of the most effective component in the mixture has not been studied directly in human tissues. Suppression of androgen synthesis in fetal life has been associated with testis maldescent, malformations of the genitalia at birth, and poor semen quality later in life. OBJECTIVES: Our aim was to investigate whether chemicals can act together to disrupt androgen production in human fetal testis explants and to evaluate the importance of mixture effects when characterizing the hazard of individual chemicals. METHODS: We used an organotypic culture system of human fetal testes explants called FEtal Gonad Assay (FEGA) with tissue obtained at 10 and 12 gestational wk (GW 10-12), to screen 27 chemicals individually for their possible anti-androgenic effect. Based on the results of the screen, we selected 11 compounds and tested them as mixtures. RESULTS: We evaluated mixtures composed of four and eight antiandrogens that contained the pharmaceuticals ketoconazole and theophylline and several previously untested chemicals, such as the pesticides imazalil and propiconazole. Mixtures of antiandrogens can suppress testosterone synthesis in human fetal testicular explants to an extent greater than that seen with individual chemicals. This revealed itself as a shift towards lower doses in the dose-response curves of individual antiandrogens that became more pronounced as the number of components increased from four to eight. CONCLUSIONS: Our results with the FEGA provide the foundations of a predictive human mixture risk assessment approach for anti-androgenic exposures in fetal life. https://doi.org/10.1289/EHP1014.
Environmental Health Perspectives

hal-01579609
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01579609
DOI : 10.1289/EHP1014
PUBMED : 28796631