Éditeur(s) : HAL CCSD
Résumé : International audience
Many countries are legally obliged to embrace ecosystem-based approaches to fisheries management. Reductions in bycatch and physical habitat damage are now commonplace, but mitigating more sophisticated impacts associated with the ecological functions of target fisheries species are in their infancy. Here we model the impacts of a parrotfish fishery on the future state and resilience of Caribbean coral reefs, enabling us to view the tradeoff between harvest and ecosystem health. We find that the implementation of a simple and enforceable size restriction of >30 cm provides a win:win outcome in the short term, delivering both ecological and fisheries benefits and leading to increased yield and greater coral recovery rate for a given harvest rate. However, maintaining resilient coral reefs even until 2030 requires the addition of harvest limitations (<10% of virgin fishable biomass) to cope with a changing climate and induced coral disturbances, even in reefs that are relatively healthy today. Managing parrotfish is not a panacea for protecting coral reefs but can play a role in sustaining the health of reefs and high-quality habitat for reef fisheries.
http://hal.univ-reunion.fr/hal-01369752

hal-01369752
http://hal.univ-reunion.fr/hal-01369752
DOI : 10.1073/pnas.1601529113

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is < 2000 mm yr(-1) (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall < 2000 mm yr(-1).
ISSN: 1726-4170

hal-01557759
https://hal.univ-lorraine.fr/hal-01557759
https://hal.univ-lorraine.fr/hal-01557759/document
https://hal.univ-lorraine.fr/hal-01557759/file/bg-13-2537-2016.pdf
DOI : 10.5194/bg-13-2537-2016

Éditeur(s) : HAL CCSD Université des Antilles
Résumé : International audience
In this study, we propose to analyze the limits of mass tourism in the French Antilles, specifically the decline of tourism, economic limits, and ecological degradation). The recognition of these limits is overdue, and signals a need to define another model for tourism development.The popular coastal sector in the south of Martinique has been subject new regulations to protect marine resources. These regulations require the development of new practices and a greater level of awareness for tourists, for example, around coral reefs and mangroves. Ecotourism programs aim to demonstrate to visitors the forests rich natural resources and biodiversity in general. It also features the inclusion of small rural businesses that benefit from additional sources of revenue as a result of ecotourism.The situation in the French Antilles is complex: Urbanization is fraught with serious consequences for the coastline. Tourism products currently being marketed on the island are not competitive (particularly against the political dynamics of the neighbouring island of Dominica). Ecotourism and sustainable tourism are just beginning to develop in such destinations, where tourism has been declining in the last ten years. The situation of the French Antilles is paradoxical in a region that generally has a very favourable tourism. Assessing these limits through the scope of ecotourism helps to highlight the causes of these difficulties and to adapting to new tourism practices.
En el contexto de este estudio, nos proponemos analizar los límites del turismo de masas en las Antillas Francesas (depreciación del turismo, las limitaciones económicas, ecológicas y las molestias). Este reconocimiento de esos límites está en el origen de la conciencia tardía de la necesidad de definir otro modelo de desarrollo turístico.En el sector costero de la más popular, como en el sur de Martinica, se pone en la normativa nuevo lugar para proteger los recursos marinos. Esto requiere el desarrollo de nuevas prácticas y la sensibilización de los turistas, por ejemplo, alrededor de los arrecifes de coral y los manglares.Programas en torno al ecoturismo también tienen como objetivo dar al visitante la riqueza de los recursos forestales y la biodiversidad en general. También incluye las pequeñas empresas rurales que reciben los nuevos ingresos a través del turismo.Pero la situación es compleja en las Antillas francesas: la urbanización está llena de importantes consecuencias para la costa. Productos turísticos que se comercializan actualmente no son competitivos (en particular, contra la dinámica política de la cercana isla de Dominica). Ecoturismo y desarrollo sostenible están empezando a desarrollar en este destino turístico, donde el turismo está en problemas en los últimos diez años.Esta situación es bastante paradójico en un turismo regional muy favorable. Sin lugar a dudas, pensando en el ecoturismo contribuye a identificar los destinos de estos retrasos y dificultades para adaptarse a nuevas prácticas de turismo.
Dans le cadre de cette étude, l’accent est mis sur les limites du tourisme de masse dans les Antilles françaises (dépréciation du tourisme, les contraintes économiques et les nuisances écologiques). La reconnaissance de ces limites est à l'origine de la prise de conscience tardive de la nécessité de définir un autre modèle de développement touristique.Dans le sud de la Martinique, le secteur le plus populaire du littoral, de nouvelles règlementations sont mises en place pour protéger les ressources marines. Cela nécessite le développement de nouvelles pratiques et de sensibilisation des touristes notamment autour des récifs coralliens et les mangroves. Les programmes autour de l'écotourisme visent également à montrer aux visiteurs la richesse des ressources forestières et de la biodiversité en général. Il comprend également les petites entreprises rurales qui reçoivent de nouveaux revenus grâce au tourisme.La situation est complexe dans les Antilles françaises: l'urbanisation est lourde de conséquences importantes sur la côte. Les produits touristiques commercialisés actuellement ne sont pas compétitifs (notamment contre la dynamique politique de l'île voisine de la Dominique). L'écotourisme et le tourisme durable commencent tout juste à se développer dans ces destinations où le tourisme classique est en difficulté depuis une dizaine d’années ; situation assez paradoxale au regard du dynamisme de ce secteur d’activité dans la région.
ISSN: 1779-0980

hal-01624756
https://hal.archives-ouvertes.fr/hal-01624756
DOI : 10.4000/etudescaribeennes.5262

Éditeur(s) : HAL CCSD
Résumé : International audience
STUDY QUESTION: Do freezing and in vitro culture procedures enhance the expression of proteins involved in apoptotic or autophagic pathways in murine pre-pubertal testicular tissue? SUMMARY ANSWER: IVM strongly modified apoptosis- and autophagy-related relative protein levels in mice testicular tissue whereas the impact of cryopreservation procedures was minimal at the end of the culture. WHAT IS KNOWN ALREADY: In vitro spermatogenesis remains a challenging technical issue as it imposes to find a very close balance between survival and death of germ cell natural precursors (i.e. gonocytes and spermatogonia), which will eventually undergo a complete spermatogenesis close to in vivo conditions. The establishment of efficient culture conditions coupled with suitable cryopreservation procedures (e.g. controlled slow freezing [CSF] and solid surface vitrification [SSV]) of pre-pubertal testicular tissue is a crucial step in the fields of fertility preservation and restoration to improve the spermatic yield obtained in vitro. STUDY DESIGN, SIZE, DURATION: Here, we study cryopreservation procedures (i.e. CSF or SSV) and the impact of culture media compositions. A first set of 66 mouse pre-pubertal testes were directly cultured during 30, 36, 38 and 60 days (D) from 2.5 to 6.5-day-old CD-1 mice to evaluate the impact of time-aspect of culture and to endorse the reverse phase protein microarrays (RPPM) technique as an adapted experimental tool for the field of in vitro spermatogenesis. Ninety others fresh, slow-frozen and vitrified pre-pubertal testes were cultured during 30 days for the principal study to evaluate the impact of cryopreservation procedures before and after culture. Thirty-four testes dissected from 2.5, 6.5, 36.5, 40.5, 42.5 and 62.5 days postpartum (dpp) mice, corresponding to the time frames of spermatogenesis orchestrated in vitro, were used as in vivo controls. PARTICIPANTS/MATERIALS, SETTING, METHODS: After in vitro culture, testicular tissue samples originated from 2.5 or 6.5-day-old CD-1 male mice were analyzed using RPPM. This targeted proteomic technique allowed us to assess the expression level of 29 apoptosis- and autophagy-related factors by normalizing blank-corrected signal values. In addition, morphological analyses (e.g. HES, PAS, TRA98 and CREM) and DNA fragmentation in intra-tubular cells (i.e. terminal deoxynucleotidyl transferase dUTP nick end labeling; TUNEL) were assessed for the distinct experimental conditions tested as well as for in vivo control mouse testes. MAIN RESULTS AND THE ROLE OF CHANCE: A validation of the RPPM procedure in the field of in vitro spermatogenesis was completed with assay and array robustness before a principal study concerning the evaluation of the impact of in vitro culture and cryopreservation procedures. The proportion of elongated spermatids and the total cell number per seminiferous tubule tended to be very different between the in vivo and in vitro conditions (P < 0.05), suggesting the presence of a beneficial regulation on the first spermatogenesis wave by intrinsic apoptosis (Caspase₉) and autophagy (Atg5) factors (P < 0.0003 and r2 = 0.74). Concerning the impact of culture media compositions, a basic medium (BM) composed of αMEM plus 10% KnockOut™ serum replacement and gentamicin supplemented with retinol (Rol) and vitamin E (Vit. E) was selected as the best culture medium for fresh 6.5 dpp tissue cultured during 30D with 27.7 ± 8.10% of seminiferous tubules containing elongated spermatids. Concerning the impact of cryopreservation procedures, SSV did not have any impact on the morphological parameters evaluated after culture in comparison to fresh tissue (FT) controls. The proportion of tubules with elongated spermatids on testicular explants cultured with BMRol+Vit. E was not different between SSV (6.6 ± 1.6%) and CSF (5.3 ± 1.9%); however, round spermatids were observed more frequently for SSV (19 ± 6.2%) than CSF (3.3 ± 1.9%, P = 0.0317). Even if the proportion of TUNEL-positive cells for BMRol+Vit. E was higher at D30 after SSV (4.12 ± 0.26%) than CSF (1.86 ± 0.12%, P = 0.0022) and FT (2.69 ± 0.33%, P = 0.0108), the DNA damages observed at the end of the culture (i.e. D30) were similar to respective 6.5 dpp controls. In addition, the relative protein level expression ratio of an apoptotic factor, the phosphorylated FADD on Fas, was reduced by 64-fold in vitrified testes cultured with BMRol+Vit. E. Furthermore, we found in this study that the StemPro®-34 SFM culture medium supplemented with growth factors (e.g. EGF, bFGF, GDNF and LIF) prevented the differentiation of spermatogonial stem cells in favor of a significant proliferation with a better architectural pattern than in vivo 6.5 dpp controls with an increase of seminiferous tubules area for FT (P = 0.0357) and CSF (P = 0.0317). LIMITATIONS REASONS FOR CAUTION: Despite our promising results, the evaluation of apoptotic- and autophagic-related proteins was studied for a limited amount of proteins and on global testicular tissue. WIDER IMPLICATIONS OF THE FINDINGS: The data presented herein will help to improve apoptotic and autophagic understanding during the first spermatogenic wave. Moreover, our findings illustrate for the first time that, using finely-tuned experimental conditions, a testicular in vitro culture combined with proteomic technologies may significantly facilitate the study of cryopreservation procedures and in vitro culture evaluations. This study may also contribute to improve work on testicular tissues from pre-pubertal and adolescent cancer survivors. STUDY FUNDING/COMPETING INTEREST(S): This study was supported by a Ph.D. grant from the Rouen Normandie Université and a financial support from 'la Ligue nationale contre le cancer' (both awarded to L.D.), funding from Institute for Research and Innovation in Biomedicine (IRIB), Agence de la Biomédecine, and co-supported by European Union and Région Normandie. Europe gets involved in Normandie with European Regional Development Fund (ERDF). The authors declare that there is no conflict of interest.
Molecular Human Reproduction

hal-01647081
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01647081
DOI : 10.1093/molehr/gax054
PUBMED : 29040674

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Although niche-based and stochastic processes, including dispersal limitation and demographic stochasticity, can each contribute to community assembly, it is difficult to quantify the relative importance of each process in natural vegetation. Here, we extend Shipley's maxent model (Community Assembly by Trait Selection, CATS) for the prediction of relative abundances to incorporate both trait-based filtering and dispersal limitation from the larger landscape and develop a statistical decomposition of the proportions of the total information content of relative abundances in local communities that are attributable to trait-based filtering, dispersal limitation, and demographic stochasticity. We apply the method to tree communities in a mature, species-rich, tropical forest in French Guiana at 1-, 0.25- and 0.04-ha scales. Trait data consisted of species' means of 17 functional traits measured over both the entire meta-community and separately in each of nine 1-ha plots. Trait means calculated separately for each site always gave better predictions. There was clear evidence of trait-based filtering at all spatial scales. Trait-based filtering was the most important process at the 1-ha scale (34%), whereas demographic stochasticity was the most important at smaller scales (37-53%). Dispersal limitation from the meta-community was less important and approximately constant across scales (similar to 9%), and there was also an unresolved association between site-specific traits and meta-community relative abundances. Our method allows one to quantify the relative importance of local niche-based and meta-community processes and demographic stochasticity during community assembly across spatial and temporal scales.
ISSN: 0012-9658

hal-01032424
https://hal.archives-ouvertes.fr/hal-01032424

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : In this study, we propose to analyze the limits of mass tourism in the French Antilles, specifically the decline of tourism, economic limits, and ecological degradation). The recognition of these limits is overdue, and signals a need to define another model for tourism development.The popular coastal sector in the south of Martinique has been subject new regulations to protect marine resources. These regulations require the development of new practices and a greater level of awareness for tourists, for example, around coral reefs and mangroves. Ecotourism programs aim to demonstrate to visitors the forests rich natural resources and biodiversity in general. It also features the inclusion of small rural businesses that benefit from additional sources of revenue as a result of ecotourism.The situation in the French Antilles is complex: Urbanization is fraught with serious consequences for the coastline. Tourism products currently being marketed on the island are not competitive (particularly against the political dynamics of the neighbouring island of Dominica). Ecotourism and sustainable tourism are just beginning to develop in such destinations, where tourism has been declining in the last ten years. The situation of the French Antilles is paradoxical in a region that generally has a very favourable tourism. Assessing these limits through the scope of ecotourism helps to highlight the causes of these difficulties and to adapting to new tourism practices.
Dans le cadre de cette étude, l’accent est mis sur les limites du tourisme de masse dans les Antilles françaises (dépréciation du tourisme, les contraintes économiques et les nuisances écologiques). La reconnaissance de ces limites est à l'origine de la prise de conscience tardive de la nécessité de définir un autre modèle de développement touristique.Dans le sud de la Martinique, le secteur le plus populaire du littoral, de nouvelles règlementations sont mises en place pour protéger les ressources marines. Cela nécessite le développement de nouvelles pratiques et de sensibilisation des touristes notamment autour des récifs coralliens et les mangroves. Les programmes autour de l'écotourisme visent également à montrer aux visiteurs la richesse des ressources forestières et de la biodiversité en général. Il comprend également les petites entreprises rurales qui reçoivent de nouveaux revenus grâce au tourisme.La situation est complexe dans les Antilles françaises: l'urbanisation est lourde de conséquences importantes sur la côte. Les produits touristiques commercialisés actuellement ne sont pas compétitifs (notamment contre la dynamique politique de l'île voisine de la Dominique). L'écotourisme et le tourisme durable commencent tout juste à se développer dans ces destinations où le tourisme classique est en difficulté depuis une dizaine d’années ; situation assez paradoxale au regard du dynamisme de ce secteur d’activité dans la région.
En el contexto de este estudio, nos proponemos analizar los límites del turismo de masas en las Antillas Francesas (depreciación del turismo, las limitaciones económicas, ecológicas y las molestias). Este reconocimiento de esos límites está en el origen de la conciencia tardía de la necesidad de definir otro modelo de desarrollo turístico.En el sector costero de la más popular, como en el sur de Martinica, se pone en la normativa nuevo lugar para proteger los recursos marinos. Esto requiere el desarrollo de nuevas prácticas y la sensibilización de los turistas, por ejemplo, alrededor de los arrecifes de coral y los manglares.Programas en torno al ecoturismo también tienen como objetivo dar al visitante la riqueza de los recursos forestales y la biodiversidad en general. También incluye las pequeñas empresas rurales que reciben los nuevos ingresos a través del turismo.Pero la situación es compleja en las Antillas francesas: la urbanización está llena de importantes consecuencias para la costa. Productos turísticos que se comercializan actualmente no son competitivos (en particular, contra la dinámica política de la cercana isla de Dominica). Ecoturismo y desarrollo sostenible están empezando a desarrollar en este destino turístico, donde el turismo está en problemas en los últimos diez años.Esta situación es bastante paradójico en un turismo regional muy favorable. Sin lugar a dudas, pensando en el ecoturismo contribuye a identificar los destinos de estos retrasos y dificultades para adaptarse a nuevas prácticas de turismo.
Martinique

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.5262
http://journals.openedition.org/etudescaribeennes/5262

Éditeur(s) : Elsevier
Résumé : A coupled three-dimensional physical-biogeochemical model was developed in order to simulate the ecological functioning of the Rio de la Plata estuary and plume. The biogeochemical model reproduces the nitrogen cycle between five compartments: dissolved inorganic nitrogen, phytoplankton, zooplankton, detritus and dissolved organic nitrogen. The coupling is tested in seasonal climatological configurations and for the particular year 1999. The circulation is forced with Parana and Uruguay rivers discharges, NCEP wind and tide. The biogeochemical model includes loads of inorganic and organic nitrogen from both rivers. The model reproduces the correct tidal amplitudes in the estuary, as well as the most outstanding features of the observed horizontal and vertical structures of the salinity plume. Simulated surface chlorophyll a concentrations exhibit maximum values all year long seaward of the turbidity front, between the 0.5 and 15 isohalines, in agreement with SeaWiFS images of the area. The model simulates well the low primary production in the light-limited highly turbid tidal river (20 gC/m(2)/yr), the high production area in the frontal zone where it can reach 500 gC/m(2)/yr, and the nutrient-limited production in the outer estuary and inner shelf (300 gC/m(2)/yr), with realistic values in each case. According to the 1999 model simulation, the tidal river is the location of organic nitrogen remineralization with a consequent increase of the inorganic pool. At the entrance of the frontal zone, inorganic nitrogen represents about 75% of the whole nitrogen pool, it is reduced to 50% at its sea end-member. The outer estuary has the same sink role for inorganic nitrogen, suggesting that organic nitrogen is the major form exported to the shelf.
Continental Shelf Research (0278-4343) (Elsevier), 2005-03 , Vol. 25 , N. 5-6 , P. 629-653

Droits : 2004 Elsevier Ltd.
http://archimer.ifremer.fr/doc/2005/publication-334.pdf
DOI:10.1016/j.csr.2004.10.003
http://archimer.ifremer.fr/doc/00000/334/

Éditeur(s) : HAL CCSD Nordic Ecological Society
Résumé : Niche differentiation and ecological filtering are primary ecological processes that shape community assembly, but their relative importance remains poorly understood. Analyses of the distributions of functional traits can provide insight into the community structure generated by these processes. We predicted the trait distributions expected under the ecological processes of niche differentiation and environmental filtering, then tested these predictions with a dataset of 4672 trees located in nine 1-ha plots of tropical rain forest in French Guiana. Five traits related to leaf function (foliar N concentration, chlorophyll content, toughness, tissue density and specific leaf area), and three traits related to stem function (trunk sapwood density, branch sapwood density, and trunk bark thickness), as well as laminar surface area, were measured on every individual tree. There was far more evidence for environmental filtering than for niche differentiation in these forests. Furthermore, we contrasted results from species-mean and individual-level trait values. Analyses that took within-species trait variation into account were far more sensitive indicators of niche differentiation and ecological filtering. Species-mean analyses, by contrast, may underestimate the effects of ecological processes on community assembly. Environmental filtering appeared somewhat more intense on leaf traits than on stem traits, whereas niche differentiation affected neither strongly. By accounting for within-species trait variation, we were able to more properly consider the ecological interactions among individual trees and between individual trees and their environment. In so doing, our results suggest that the ecological processes of niche differentiation and environmental filtering may be more pervasive than previously believed.
ISSN: 0030-1299

hal-01032397
https://hal.archives-ouvertes.fr/hal-01032397
DOI : 10.1111/j.1600-0706.2010.19110.x

Éditeur(s) : HAL CCSD Springer International Publishing
Résumé : The intensive farming practices that have been developed over the past 60 years are based mainly on the use of chemical inputs such as fertilisers and pesticides, mechanical tillage and monoculture. The limitations of these methods are now clear: long-term degradation of soil fertility, impacts on the environment and human health, high consumption of fossil fuels, low efficiency of inputs and threats to food security in a context of climate change. Would farming practices that rely on the activation of ecological processes be an alternative to achieve a balance between high productivity and environmental preservation? While many studies suggest a positive relationship between soil biodiversity and ecosystem services, there is considerable debate on the form such agricultural systems should take. This study reviewed the state of current knowledge and identified aspects requiring further research to achieve the aim of sustainable intensification of agriculture. The following major points emerged: 1) Most studies focused on the evaluation of individual practices. However, changes in farmers’ cropping practices to take advantage of soil biodiversity services would need to manage not only the interactions between various practices but also the trade-off between the technical and socio economic constraints of cropping systems. Advances in agricultural system design approaches may help to ensure appropriate trade-offs. 2) More attention should be given to drawing on knowledge from different sources: laboratory studies focusing on the ecological functions of soil biodiversity, experimental surveys on farmers’ fields to rank the farming practices and processes to be included in site-specific models, and on- station experiments to test hypotheses and acquire additional reference material. 3) Whereas advances in technical and scientific knowledge provide an increasing number of relevant indicators for characterizing biodiversity and ecological functions, studies are rarely targeted at the development of indicators that are accessible to farmers or their technical advisors. The lack of indicators accessible to grassroots players for evaluating the impacts of their decisions on soil biodiversity remains a serious obstacle to the development of innovative agro-ecological systems.
Sustainable Agriculture Reviews 14

ISBN : 978-3-319-06015-6
hal-01268743
https://hal.archives-ouvertes.fr/hal-01268743
DOI : 10.1007/978-3-319-06016-3_5
PRODINRA : 270786

Éditeur(s) : Inter-research
Résumé : Environmental conditions experienced by aquatic organisms are archived in biogenic carbonates such as fish otoliths, bivalve shells and coral skeletons. These calcified structures present an accretionary growth and variations in optical properties - color or opacity - that are used to reconstruct time. Full and reliable exploitation of the information extracted from these structures is, however, often limited as the metabolic processes that control their growth and their optical properties are poorly understood. Here, we propose a new modeling framework that couples both the growth of a biogenic carbonate and its optical properties with the metabolism of the organism. The model relies on well-tested properties of Dynamic Energy Budget (DEB) theory. It is applied to otoliths of the Bay of Biscay anchovy (Engraulis encrasicolus) for which a DEB model has been previously developed. The model reproduces well-known otolith patterns and thus provides us with mechanisms for the metabolic control of otolith size and opacity at the scale of an individual lifespan. Two original contributions using this framework are demonstrated. First, the model can be used to reconstruct the temporal variations in the food assimilated by an individual fish. Reconstructing food conditions of past and present aquatic species in their natural environment is key ecological information to better understand population dynamics. Second, we show that non-seasonal checks can be discriminated from seasonal checks, which is a well-recognized problem when interpreting fish otoliths. We discuss further developments of the model and the experimental settings required to test this new promising framework.
Marine Ecology-progress Series (0171-8630) (Inter-research), 2012 , Vol. 447 , P. 151-164

Droits : 2012 Inter-Research
http://archimer.ifremer.fr/doc/00060/17082/14593.pdf
DOI:10.3354/meps09492
http://archimer.ifremer.fr/doc/00060/17082/

Éditeur(s) : HAL CCSD
Résumé : International audience
BACKGROUND AND AIM: The impact of basal core promoter (BCP) and precore (PC) mutants of the hepatitis B virus (HBV) on liver disease severity remains controversial. The aim of the present study was to screen BCP and PC mutations in 252 HBV surface antigen (HBsAg) positive carriers in France and to assess relationships between these mutations and severe fibrosis. METHODS: Direct sequencing of the precore/core gene was used to detect A1762T/G1764A and G1757A mutations in the BCP and G1896A and G1899A mutations in the PC region. RESULTS: The prevalences of A1762T/G1764A, G1757A, G1896A, and G1899A mutations were 34.1%, 38.7%, 54.9%, and 29.3% (P < 0.001), respectively. The independent predictors of severe fibrosis (>/=F3 Metavir) were older age (P < 0.001), male gender (P = 0.012), elevated alanine aminotransferase (P < 0.001), and the double A1762T/G1764A mutant with no other mutations (P = 0.011). Interestingly, the association of the G1899A mutation with the double A1762T/G1764A mutant significantly counteracted the deleterious effect of the sole double A1762T/G1764A mutant (odds ratio [OR] = 0.28 vs. OR = 3.55, respectively, P = 0.028). CONCLUSIONS: Patients with the A1762T/G1764A mutation have a higher risk of severe fibrosis. The G1899A mutation is a protective factor against severe fibrosis that counteracted the deleterious effect of the A1762T/G1764A mutation. Finally, host phenotypic and HBV genotypic markers independently predict fibrosis severity.
Journal of gastroenterology and hepatology

hal-01477209
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01477209
DOI : 10.1111/jgh.13338
PUBMED : 26992056

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September-October (autumn) and lowest in April-May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3-5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. See also the Perspective by Massana
ISSN: 0962-1083

hal-01545321
https://hal.archives-ouvertes.fr/hal-01545321
DOI : 10.1111/mec.13160

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Climatic changes result in an increased in mean temperature and in a higher incidence of extreme weather events such as heat and cold waves. For ectotherms, such as insect parasitoids, the ability to remain active under extreme climatic conditions is a significant key to fitness. The body size of individuals, and in particular their surface to volume ratio, may play a role in their resistance to thermal conditions. The thermal tolerances are investigated of two closely-related sympatric parasitoid species [Aphidius avenae Haliday and Aphidius rhopalosiphi De Stefani-Perez (Hymenoptera: Aphidiinae)] that have a similar ecology but differ in body size and phenologies. The critical thermal limits of individuals are assessed in both sexes of each parasitoid species and the influence of surface-volume ratios on their thermal tolerances. Aphidius avenae is less resistant to low temperatures and more resistant to high temperatures than A. rhopalosiphi. The lower surface to volume ratio of A. avenae individuals may help them to remain active in summer when experiencing heat waves. However, body size is not the sole factor that plays a role in differences of thermal tolerance between species and body size may not be an adaptation to extreme temperatures but rather a by-product of developmental regulation. Closely related sympatric species from the same ecological guild can have different thermal tolerances that may allow them to occur within the same habitat. The present study also highlights the importance of clearly defining how to measure critical thermal limits to determine the thermal tolerance of a species.
ISSN: 0307-6962

hal-00589094
https://hal.archives-ouvertes.fr/hal-00589094
DOI : 10.1111/j.1365-3032.2010.00758.x

Éditeur(s) : HAL CCSD
Résumé : International audience
Background: We examined the association between exposure during pregnancy to trihalomethanes, the most common water disinfection by-products, and birth outcomes in a European cohort study (Health Impacts of Long-Term Exposure to Disinfection By-Products in Drinking Water). We took into account exposure through different water uses, measures of water toxicity, and genetic susceptibility. Methods: We enrolled 14,005 mothers (2002-2010) and their children from France, Greece, Lithuania, Spain, and the UK. Information on lifestyle- and water-related activities was recorded. We ascertained residential concentrations of trihalomethanes through regulatory records and ad hoc sampling campaigns and estimated route-specific trihalomethane uptake by trimester and for whole pregnancy. We examined single nucleotide polymorphisms and copy number variants in disinfection by-product metabolizing genes in nested case-control studies. Results: Average levels of trihalomethanes ranged from around 10 μg/L to above the regulatory limits in the EU of 100 μg/L between centers. There was no association between birth weight and total trihalomethane exposure during pregnancy (β = 2.2 g in birth weight per 10 μg/L of trihalomethane, 95% confidence interval = 3.3, 7.6). Birth weight was not associated with exposure through different routes or with specific trihalomethane species. Exposure to trihalomethanes was not associated with low birth weight (odds ratio [OR] per 10 μg/L = 1.02, 95% confidence interval = 0.95, 1.10), small-for-gestational age (OR = 0.99, 0.94, 1.03) and preterm births (OR = 0.98, 0.9, 1.05). We found no gene-environment interactions for mother or child polymorphisms in relation to preterm birth or small-for-gestational age. Conclusions: In this large European study, we found no association between birth outcomes and trihalomethane exposures during pregnancy in the total population or in potentially genetically susceptible subgroups. © 2016 Wolters Kluwer Health, Inc.
Epidemiology

hal-01392115
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01392115
DOI : 10.1097/EDE.0000000000000544
PUBMED : 27468006

Éditeur(s) : HAL CCSD
Résumé : données, méthodes disponibles auprès de l'auteur
In tropical forest communities, interspecific competition and recruitment limitation by dispersal are two general mecanisms of tree species coexistence. Their role in regeneration remains poorly known, even though it is essential to understand them to better adress the gestion of exploited forests. In this work, environemental conditions and intraspecific relations were taken into account in the analysis of juvenile distribution. Fifteen species were retained according to a gradient of shade-tolerance and various seed dispersal modes. Statistical modelling of local density was used to link the success of installation with environnemental conditions and distances to adults simultaneously. Model prediction evidenced the gradient of shade-tolerance among studied species and revealed different installation curves related to dispersal modes.
Dans les communautés de forêt tropicale humide, la compétition interspécifique et la limitation du recrutement par la dispersion ont généralement invoquées pour expliquer la coexistence de nombreuses espèces d'arbres. Le rôle de ces mécanismes dans la régénération reste peu connu, bien que leur compréhension soit essentielle pour la gestion des forêts exploitées. Dans ce travail, les conditions du milieu et les relations intraspécifiques ont été prises en compte dans l'analyse des distributions de juvéniles. Quinze espèces non pionnières ont été sélectionnées selon un gradient de tolérance à l'ombre et des modes de dispersion variés. La modélisation statistique de la densité locale a permis de relier le succès d'installation des juvéniles aux conditions du milieu et aux distances aux arbres adultes simultanément. Les prédictions des
modèles confirment le gradient de tolérance parmi les espèces étudiées et révèlent des courbes d'installation différentes selon le mode de dispersion.
https://tel.archives-ouvertes.fr/tel-00297707

tel-00297707
https://tel.archives-ouvertes.fr/tel-00297707
https://tel.archives-ouvertes.fr/tel-00297707/document
https://tel.archives-ouvertes.fr/tel-00297707/file/PhD_regeneration_Olivier_Flores.pdf

Éditeur(s) : Universite Montpellier II
Résumé : Since 1980, the expansion of a green macro-alga: Valonia aegagropila (C Agardh) is observed in Salses-Leucate lagoon (France). It is currently distributed in the north of the lagoon with important biomasses (40 gDW/m²) eroding the cover of Zostera noltii. The free form of the alga can be transported with the surface or bottom currents depending on seasons. It multiplies mainly by vegetative reproduction. There are few studies on the ecophysiological capacities of V. aegagropila. This work tries to answer why (physiological adaptation) and how (mechanical process of transport) the alga invaded the lagoon, with an approach including observations, experiments in controlled environment and biological and hydrodynamic models. The growth capacities depend on temperature and light intensities, the nutrients absorption rates and internal nitrogen and phosphorus internal quotas were measured and modelled using a Droop model based on internal quota. Vertically transport was studied with laboratory experiments and measurements of biomass transport were made into the lagoon. The biological model (growth, vertical transport, mortality) was coupled to the MARS 3D hydrodynamic model with a meshgrid of 160m. The results show an adaptation of the alga to low availability of phosphorus and an annual growth of biomass controlled by the availability of nutrient during winter. The alga seems to occupy the whole zones where growth is optimal and the risk of invasion of the southern part of the lagoon is limited. This work opens on research prospects on an ecological model (confronting physiological capacities and competition of V. aegagropila, Zostera noltii, green algae and primary production), new physiological experiments, ecological observations and potential valorisation of V. aegagropila.
Depuis 1980, est observée dans l'étang de Salses-Leucate l'expansion d'une macro-algue verte : Valonia aegagropila (C. Agardh). En 2004, elle était présente sur la presque totalité de la moitié nord de la lagune avec des biomasses importantes (jusqu'à 600 gPS/m²). L'algue envahit et érode également la couverture d'herbiers garant de la biodiversité, de la productivité et de la stabilité de l'écosystème. V. aegagropila se reproduit essentiellement de manière végétative (fragmentation des thalles) et possède la particularité de retenir de l'oxygène de la photosynthèse dans sa structure sphérique. Cet oxygène piégé lui donne la possibilité de mouvement sur la verticale et d'être transportée dans le domaine par les courants. Les conditions physico-chimiques de l'étang présentent de fortes variations saisonnières en salinité, en température et en turbidité, ainsi que des apports nutritifs faibles : la production primaire est principalement limitée par le phosphore. Il existe malheureusement peu d'informations sur V. aegagropila ainsi que trop peu de connaissances sur son écophysiologie. Elle semble vivre dans des milieux plutôt oligotrophe dans des régions tropicales à sub-tropicales. Ce travail basé sur une approche d'observations de terrain, d'expérimentations en milieu contrôlé (en laboratoire) et de modélisation des processus, a permis d'une part d'explorer les capacités adaptatives physiologiques de V. aegagropila aux conditions environnementales de l'étang et d'autre part de mettre à jour les modes de fonctionnement de la dynamique spatio-temporelle de la population. Les capacités de croissance ont été mesurées sur un large spectre de température et de lumière. Les capacités d'absorption des sels nutritifs dans l'eau et les facultés de l'algue à stocker l'azote et le phosphore dans ses tissus ont également été étudiées. D'autre part, un modèle de dynamique des populations a été conceptualisé puis développé. Les processus pris en compte dans ce modèle sont la croissance de l'algue (modèle à quota interne), la flottabilité de l'algue et la mortalité par surdensité. Ces processus ont été paramétrés en majeure partie par des expérimentations réalisées en laboratoire. Ce modèle 0D a par la suite était couplé au modèle hydrodynamique MARS3D (modèle Ifremer) mis en place sur la lagune de Salses-Leucate, utilisant deux grilles de calcul (160m ou de 80m de résolution). Les simulations réalisées permettent d'appréhender les capacités spatio-temporelles de la croissance de l'algue dans l'étang, le turnover annuel de la biomasse totale et les attracteurs de biomasse du système sous différents évènements météorologiques. Ces résultats sont comparés avec les répartitions cartographiques de la population observées in situ en 1999 et 2004 et des flux de biomasses mesurés au cours d'observations de terrain entre juin 2003 et septembre 2004. L'ensemble des résultats montre d'une part une adaptation de l'algue à évoluer dans un milieu pauvre en phosphore et d'autre part une croissance annuelle de la biomasse totale qui est principalement contrôlée par les apports hivernaux en sels nutritifs dans la lagune. Les résultats des simulations montrent également que V. aegagropila semble occuper à présent la majeure partie des zones favorables à sa croissance. Il est également montré que si sa capacité de mouvement peut favoriser la dispersion d'individus dans la lagune et accélérer la croissance de la population pour de faibles biomasses initiales, cette même capacité de mouvement joue plutôt un rôle de régulation de la population lorsque la biomasse totale devient importante. On peut penser que le risque de colonisation de l'herbier à zostère de la partie sud de la lagune (bassin de Salses) est limité. Ce travail ouvre enfin des perspectives de recherche sur l'amélioration du modèle de dynamique des populations de l'espèce, sur de nouvelles expérimentations à réaliser ou encore sur la surveillance écologique du milieu. Des propositions sont faites pour concevoir un modèle écologique confrontant les capacités physiologiques des macrophytes (algues vertes, Valonia et zostères) afin d'apréhender les phénomènes de compétitions et les modes de fonctionnement du réseau trophique de la lagune de Salses- Leucate. Des pistes sur la valorisation de la matière algale de V. aegagropila sont enfin proposées.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/these-2453.pdf
http://archimer.ifremer.fr/doc/00000/2453/

Éditeur(s) : HAL CCSD IWA Publishing
Résumé : International audience
UV spectrophotometry is largely used for water and wastewater quality monitoring. The measurement/estimation of specific and aggregate parameters such as nitrate and dissolved organic carbon (DOC) is possible with UV spectra exploitation, from 2 to multi wavelengths calibration. However, if nitrate determination from UV absorbance is known, major optical interferences linked to the presence of suspended solids, colloids or dissolved organic matter limit the relevance of UV measurement for DOC assessment. A new method based on UV spectrophotometric measurement of raw samples (without filtration) coupling a dual pathlength for spectra acquisition and the second derivative exploitation of the signal is proposed in this work. The determination of nitrate concentration is carried out from the second derivative of the absorbance at 226 nm corresponding at the inflexion point of nitrate signal decrease. A short optical pathlength can be used considering the strong absorption of nitrate ion around 210 nm. For DOC concentration determination the second derivative absorbance at 295 nm is proposed after nitrate correction. Organic matter absorbing slightly in the 270-330 nm window, a long optical pathlength must be selected in order to increase the sensitivity. The method was tested on several hundred of samples from small rivers of two agricultural watersheds located in Brittany, France, taken during dry and wet periods. The comparison between the proposed method and the standardised procedures for nitrate and DOC measurement gave a good adjustment for both parameters for ranges of 2-100 mg/L NO3 and 1 30 mg/L DOC. (C) 2016 Elsevier Ltd. All rights reserved.
ISSN: 0043-1354

hal-01460742
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01460742
DOI : 10.1016/j.watres.2016.11.010
PUBMED : 27838025

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Under physiological conditions, the liver sinusoidal endothelial cells (LSECs) mediate hepatic immune tolerance toward self or foreign antigens through constitutive expression of anti-inflammatory mediators. However, upon viral infection or Toll-like receptor 2 (TLR2) activation, LSECs can achieve proinflammatory functions, but their role in hepatic inflammation during acute viral hepatitis is unknown. Using the highly virulent mouse hepatitis virus type 3 (MHV3) and the attenuated variants 51.6-MHV3 and YAC-MHV3, exhibiting lower tropism for LSECs, we investigated in vivo and in vitro the consequence of LSEC infection on their proinflammatory profiles and the aggravation of acute hepatitis process. In vivo infection with virulent MHV3, in comparison to attenuated strains, resulted in fulminant hepatitis associated with higher hepatic viral load, tissue necrosis, and levels of inflammatory mediators and earlier recruitment of inflammatory cells. Such hepatic inflammatory disorders correlated with disturbed production of interleukin-10 (IL-10) and vascular factors by LSECs. We next showed in vitro that infection of LSECs by the virulent MHV3 strain altered their production of anti-inflammatory cytokines and promoted higher release of proinflammatory and procoagulant factors and earlier cell damage than infection by attenuated strains. This higher replication and proinflammatory activation in LSECs by the virulent MHV3 strain was associated with a specific activation of TLR2 signaling by the virus. We provide evidence that TLR2 activation of LSCEs by MHV3 is an aggravating factor of hepatic inflammation and correlates with the severity of hepatitis. Taken together, these results indicate that preservation of the immunotolerant properties of LSECs during acute viral hepatitis is imperative in order to limit hepatic inflammation and damage. IMPORTANCE Viral hepatitis B and C infections are serious health problems affecting over 350 million and 170 million people worldwide, respectively. It has been suggested that a balance between protection and liver damage mediated by the host's immune response during the acute phase of infection would be determinant in hepatitis outcome. Thus, it appears crucial to identify the factors that predispose in exacerbating liver inflammation to limit hepatocyte injury. Liver sinusoidal endothelial cells (LSECs) can express both anti- and proinflammatory functions, but their role in acute viral hepatitis has never been investigated. Using mouse hepatitis virus (MHV) infections as animal models of viral hepatitis, we report for the first time that in vitro and in vivo infection of LSECs by the pathogenic MHV3 serotype leads to a reversion of their intrinsic anti-inflammatory phenotype toward a proinflammatory profile as well to as disorders in vascular factors, correlating with the severity of hepatitis. These results highlight a new virus-promoted mechanism of exacerbation of liver inflammatory response during acute hepatitis.
ISSN: 0022-538X

hal-01390974
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390974
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390974/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390974/file/Mouse%20Hepatitis%20Virus%20Infection_accepted.pdf
DOI : 10.1128/JVI.01069-16

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Pyrethroids are widely-used chemical insecticides, to which humans are commonly exposed, and known to alter functional expression of drug metabolizing enzymes. Limited data have additionally suggested that drug transporters, that constitute key-actors of the drug detoxification system, may also be targeted by pyrethroids. The present study was therefore designed to analyze the potential regulatory effects of these pesticides towards activities of main ATP-binding cassette (ABC) and solute carrier (SLC) drug transporters, using transporter-overexpressing cells. The pyrethroids allethrin and tetramethrin were found to inhibit various ABC and SLC drug transporters, including multidrug resistance-associated protein (MRP) 2, breast cancer resistance protein (BCRP), organic anion transporter polypeptide (OATP) 1B1, organic anion transporter (OAT) 3, multidrug and toxin extrusion transporter (MATE) 1, organic cation transporter (OCT) 1 and OCT2, with IC50 values however ranging from 2.6 muM (OCT1 inhibition by allethrin) to 77.6 muM (OAT3 inhibition by tetramethrin) and thus much higher than pyrethroid concentrations (in the nM range) reached in environmentally pyrethroid-exposed humans. By contrast, allethrin and tetramethrin cis-stimulated OATP2B1 activity and failed to alter activities of OATP1B3, OAT1 and MATE2-K, whereas P-glycoprotein activity was additionally moderately inhibited. Twelve other pyrethoids used at 100 muM did not block activities of the various investigated transporters, or only moderately inhibited some of them (inhibition by less than 50%). In silico analysis of structure-activity relationships next revealed that molecular parameters, including molecular weight and lipophilicity, are associated with transporter inhibition by allethrin/tetramethrin and successfully predicted transporter inhibition by the pyrethroids imiprothrin and prallethrin. Taken together, these data fully demonstrated that two pyrethoids, i.e., allethrin and tetramethrin, can act as regulators of the activity of various ABC and SLC drug transporters, but only when used at high and non-relevant concentrations, making unlikely any contribution of these transporter activity alterations to pyrethroid toxicity in environmentally exposed humans.
ISSN: 1932-6203

hal-01477206
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01477206
DOI : 10.1371/journal.pone.0169480
PUBMED : 28099443

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Regeneration of artificially induced lesions was monitored in nubbins of the branching coral Acropora muricata at two reef-flat sites representing contrasting environments at Réunion Island (21u079S, 55u329E). Growth of these injured nubbins was examined in parallel, and compared to controls. Biochemical compositions of the holobiont and the zooxanthellae density were determined at the onset of the experiment, and the photosynthetic efficiency (F v /F m) of zooxanthellae was monitored during the experiment. Acropora muricata rapidly regenerated small lesions, but regeneration rates significantly differed between sites. At the sheltered site characterized by high temperatures, temperature variations, and irradiance levels, regeneration took 192 days on average. At the exposed site, characterized by steadier temperatures and lower irradiation, nubbins demonstrated fast lesion repair (81 days), slower growth, lower zooxanthellae density, chlorophyll a concentration and lipid content than at the former site. A trade-off between growth and regeneration rates was evident here. High growth rates seem to impair regeneration capacity. We show that environmental conditions conducive to high zooxanthellae densities in corals are related to fast skeletal growth but also to reduced lesion regeneration rates. We hypothesize that a lowered regenerative capacity may be related to limited availability of energetic and cellular resources, consequences of coral holobionts operating at high levels of photosynthesis and associated growth.
ISSN: 1932-6203

hal-01369712
http://hal.univ-reunion.fr/hal-01369712
http://hal.univ-reunion.fr/hal-01369712/document
http://hal.univ-reunion.fr/hal-01369712/file/journal.pone.0072618.PDF
DOI : 10.1371/journal.pone.0072618