UMR 6249


Partenaires

CNRS
UFC
INRAP INRA
Culture CEA
Europe L'Europe s'engage en Franche-Comté




Rechercher

Sur ce site

Sur le Web du CNRS


Accueil > A noter > HAL : derniers articles publiés

HAL : derniers articles publiés

13 septembre

[hal-01494295] Interpolation of temperatures under forest cover on a regional scale in the French Jura Mountains

23 mars 2017

A network of 48 stations was setup in the Jura Mountains (France) to interpolate temperatures under forest cover, an environment that differs markedly from open sites. The stations were positioned so as to sample all topographical settings. The series analysed consisted of the daily minima and maxima extracted from observations recorded for a year (356 days). Regressions were used to describe relations between temperatures under forest cover (dependent random variables) and a set of explanatory variables: latitudinal and longitudinal variations, distance to the nearest forest edge, and seven variables derived from a digital terrain model by geomatic computation [elevation, slope gradient, sine and cosine of slope aspect, global radiation (g-rad), valley depth, and hump amplitude]. Elevation is the variable that most strongly affects the spatial variation of temperatures under forest cover followed by valley depth, longitudinal variation, and g-rad (for maxima only). Variables that are significant at the 10% level are combined in multiple regressions with a view to estimating temperatures at 50 m resolution. The MAE values are 0.82 and 0.77 °C for minima and maxima, respectively; adjusted R2 values are 0.47 for minima and 0.64 for maxima. Finally, we present four maps of estimated temperature under forest cover.

Lire la suite

[hal-01492347] Investigating Hybridization between the Two Sibling Bat Species Myotis myotis and M. blythii from Guano in a Natural Mixed Maternity Colony.

19 mars 2017

Because they can form seasonal mixed-species groups during mating and maternal care, bats are exciting models for studying interspecific hybridization. Myotis myotis and M. blythii are genetically close and morphologically almost identical, but they differ in some aspects of their ecology and life-history traits. When they occur in sympatry, they often form large mixed maternity colonies, in which their relative abundance can vary across time due to a shift in the timing of parturition. For the first time, we used non-invasive genetic methods to assess the hybridization rate and colony composition in a maternity colony of M. myotis and M. blythii located in the French Alps. Bat guano was collected on five sampling dates spread across the roost occupancy period and was analysed for individual genotype. We investigated whether the presence of hybrids followed the pattern of one of the parental species or if it was intermediate. We identified 140 M. myotis, 12 M. blythii and 13 hybrids among 250 samples. Parental species appeared as genetically well-differentiated clusters, with an asymmetrical introgression towards M. blythii. By studying colony parameters (effective size, sex ratio and proportion of the three bat types) across the sampling dates, we found that the abundances of hybrid and M. blythii individuals were positively correlated. Our study provides a promising non-invasive method to study hybridization in bats and raises questions about the taxonomic status of the two Myotis species. We discuss the contribution of this study to the knowledge of hybrid ecology, and we make recommendations for possible future research to better understand the ecology and behaviour of hybrid individuals.

Lire la suite

[hal-01491118] The interaction between wetland nutrient content and plant quality controls aquatic plant decomposition

16 mars 2017

We conducted an in situ decomposition experiment to better understand how habitat nutrient content controls aquatic plant decomposition and, more precisely, to determine the relative importance of the wetland conditions in decomposition, and the intrinsic degradability of plant tissues. We collected the green leaves of three aquatic plant species with contrasting plant strategies from three wetlands of differing nutrient contents, and allowed them to decompose in seven wetlands along a nutrient gradient. The plant mass loss was higher for competitive and ruderal species collected in nutrient richer wetlands as well as when they were led to decompose in nutrient richer wetlands. Plant water content correlated with mass loss for the competitive and ruderal species, which may explain the increase in mass loss with increasing nutrient content in the collection wetlands. Litter decomposition rate may be enhanced by wetland eutrophication, because of both the modification of wetland decomposition conditions and by changes in plant tissue quality.

Lire la suite

[insu-01341984] Two-stage partial melting during the Variscan extensional tectonics (Montagne Noire, France)

14 mars 2017

One of the striking features that characterise the late stages of the Variscan orogeny is the development of gneiss and migmatite domes, as well a s extensional Late Carboniferous and Permian sedimentary basins . It remains a matter of debate whether the formation of domes was related to the well documented late orogenic extension or to the contractional tectonics that preceded. Migmatization and magmatism are expected to predate extension if the domes are compression - related regional anticlines, but they must both precede and be contemporaneous with extension if they are extensional core complexes. In the Montagne Noire area (s outhern French Massif Central), where migmatization, magmatism and the deformation framework are well documented, the age of the extensional event was unequivocally constrained to 300 - 0 Ma. Therefore , dating migmatization in this area is a key point for discriminating between the two hypotheses and understanding the Late Palaeozoic evolution of this part of the Variscan belt. For this purpose, a migmatite and an associated anatectic granite from the Montagne Noire dome were dated by LA - ICP - MS ( U - Th/Pb on zircon and monazite) and laser probe 40 Ar - 39 Ar ( K - Ar on muscovite). Although zircon did not record any Variscan age unequivocally related to compression (380 - 330Ma) , two age groups were identified from the monazite crystals. A first event, at ca. 319 Ma (U - Th/Pb on monazite) , is interpreted as a first stage of migmatization and as the emplacement age of the granite, respectively. A second event at ca. 298 - 295 Ma, recorded by monazite (U - Th/Pb) and by the muscovite 40 Ar - 39 Ar system in the migmatite and in th e granite, could be interpreted as a fluid - induced event, probably related to a second melting event identified through the syn - extensional emplacement of the nearby Montalet leucogranite ca. 295 Ma ago. The age s of these two events post - date the Variscan compression and agree with an overall extensional context for the development of the Montagne Noire dome - shaped massif. Comparison of these results with published chemical (EPMA) dating of monazite from the same rocks demonstrates that the type of statistical treatment applied to EPMA data is crucial in order to resolve different monazite age populations.

Lire la suite

[hal-01486066] Contribution of long-term hydrothermal experiments for understanding the smectite-to-chlorite conversion in geological environments

9 mars 2017

The smectite-to-chlorite conversion is investigated through long duration experiments (up to 9 years) conducted at 300°C. The starting products were the Wyoming bentonite MX80 (79% smectite), metallic iron, and magnetite in contact with a Na-Ca chloride solution. The predominant minerals in the run-products were an iron-rich chlorite (chamosite-like) and interstratified clays interpreted to be chlorite/smectite and/or corrensite/smectite, accompanied by euhedral crystals of quartz, albite and zeolite. The formation of pure corrensite was not observed in the long duration experiments. The conversion of smectite into chlorite over time appears to take place in several steps and through several successive mechanisms: a solid-state transformation, significant dissolution of the smectite and direct precipitation from the solution, which is over-saturated with respect to chlorite, allowing the formation of a chamosite-like mineral. The reaction mechanisms are confirmed by X-ray patterns and data obtained on the experimental solutions (pH, contents of Si, Mg, Na and Ca). Because of the availability of some nutrients in the solution, total dissolution of the starting smectite does not lead to 100% crystallization of chlorite but to a mixture of two dominant clays – chamosite and interstratified chlorite/smectite and/or corrensite/smectite poor in smectite. The role of Fe/(Fe+Mg) in the experimental medium is highlighted by chemical data obtained on newly-formed clay particles alongside previously published data. The newly-formed iron-rich chlorite has the same composition as that predicted by the geothermometer for diagenetic to low-grade metamorphic conditions, and the quartz + Fe-chlorite + albite experimental assemblage in the 9-year experiment is close to that fixed by water-rock equilibrium.

Lire la suite

[hal-01484169] X!TandemPipeline: a tool to manage sequence redundancy for protein inference and phosphosite identification

7 mars 2017

X!TandemPipeline is a software designed to perform protein inference and to manage redundancy in the results of phosphosite identification by database search. It provides the minimal list of proteins or phosphosites that are present in a set of samples using grouping algorithms based on the principle of parsimony. Regarding proteins, a two-level classification is performed, where groups gather proteins sharing at least one peptide and subgroups gather proteins that are not distinguishable according to the identified peptides. Regarding phosphosites, an innovative approach based on the concept of phosphoisland is used to gather overlapping phosphopeptides. The graphical interface of X!TandemPipeline allows the users to launch X!tandem identification, to inspect spectra and to manually validate their assignment to peptides, to launch the grouping program, and to visualize elementary data as well as grouping and redundancy information. Identification results obtained from other search engines can also be processed. X!TandemPipeline results can be exported as ready-to-use tabulated files or as XML files that can be directly used by the PROTICdb database or by the MassChroQ quantification software. X!TandemPipeline runs fast, is easy to use, and can process hundreds of samples simultaneously. It is freely available under the GNU General Public License v3.0 at http://pappso.inra.fr/bioinfo/xtandempipeline/ .

Lire la suite

[hal-01476062] Polyphase ductile/brittle deformation along a major tectonic boundary in an ophiolitic nappe, Alpine Corsica: Insights on subduction zone intermediate-depth asperities

24 février 2017

In an ophiolitic nappe of Alpine Corsica, a major fault zone superimposes metagabbro over serpentinite and peridotite. Ductile and brittle deformation structures are observed in the fault damage zones. In the metagabbro damage zone, early deformation culminates in blueschist or eclogite facies conditions and consists of west-verging mylonitization alternating with pseudotachylyte-forming faulting with undetermined vergence. This early deformation is likely coeval with west-verging seismic (pseudotachylyte-forming) reverse faulting in the footwall peridotite or with aseismic distributed cataclastic deformation of footwall serpentinite. These early events (aseismic mylonitization or distributed cataclasis and seismic faulting) are interpreted as reverse faulting/shear in an east-dipping subducting oceanic lithosphere in Cretaceous to Eocene times. Late deformation events consist of ductile shear and seismic faulting having occurred under retrograde greenschist conditions. Kinematics of the ductile shear is top-to-the-east. These events are interpreted as the result of syn-to post-collision extension of Alpine Corsica in Eocene to Miocene times. The heterogeneous distribution of pseudotachylyte veins along the fault zone (abundant at peridotite-metagabbro interfaces, rare or absent at serpentinite-metagabbro interfaces) is interpreted as the consequence of contrasted frictional properties of the rocks in contact. High-friction peridotite-metagabbro contacts could correspond to asperities whereas low-friction serpentinite-metagabbro contacts could correspond to creeping zones.

Lire la suite

[hal-01468001] Seismic wave attenuation in the lithosphere of the North Tanzanian divergence zone (East African rift system)

15 février 2017

The seismic effective quality factor (QC) and its frequently dependences or the frequency parameter (n) and attenuation coefficient (δ) for the Earth’s crust and upper mantle of the North Tanzanian divergence zone (East African rift system) were estimated from an analysis of the earthquake coda waves recorded in the SEISMO-TANZ’07 French-Tanzanian seismic experiment. The QC values increase and the n and δ values decrease with increasing frequency and length of the lapse time window. This behavior of the attenuation parameters may be evidence that the degree of heterogeneity of the lithosphere decreases with depth. Comparison of the depth variations in the attenuation coefficient δ and the frequency parameter n with the velocity structure of the region shows that there is a distinct change in the behavior of seismic wave attenuation at velocity discontinuities. The obtained attenuation parameters were compared with the same parameters obtained in our previous studies for other continental rift systems—the Baikal rift system (Eurasia) and the Basin and Range Province (North America).

Lire la suite

[hal-01462849] Couplage de modélisation multi-agents avec un modèle d'équation pour étudier la dynamique spatiale d'une population

9 février 2017

La modélisation explicitement spatiale est essentielle en écologie pour la prise de décision et de gestion. Elle implique la modélisation de l’hétérogénéité du paysage et le fait que les différentes espèces d’agents, représentant les entités du système, sont concernés par plusieurs échelles, ce qui accroît les besoins en matière de données, et oblige à leur intégration précise dans une hiérarchie imbriquée d’échelles spatio-temporelles (local / régional, saisonnier / pluriannuel, etc.) . La modélisation multi-agents (MMA) est un paradigme orienté « spatialement explicite » qui inclut l’hétérogénéité de l’espace (par exemple, des cultures, des prairies, des parcelles de forêt), où les individus (par exemple, les proies, les prédateurs, etc.) se déplacent représentés comme des « agents ». Ces derniers sont des entités autonomes, qui sont situés dans l'espace virtuel et interagissent les uns avec les autres et les patchs environnementaux. Pendant la simulation, les dynamiques émergent et peuvent être observées et quantifiées. Ces modèles mettent en lumière les dynamiques microscopiques et spatiales qui ne peuvent être observées avec les modèles d’équation mathématiques classiques (MME). Le couplage entre MMA et MME est cependant nécessaire pour éviter les limites de calcul lorsque des populations géantes (par exemple des centaines de millions d'individus) sont étudiées pour simuler des phénomènes écologiques tels que traités dans la Zone atelier Arc jurassien à propos des pullulations de campagnols. Les méthodes et résultats préliminaires de cette approche sont présentés ici.

Lire la suite

[hal-01459335] Assessment of Lemna minor (duckweed) and Corbicula fluminea (freshwater clam) as potential indicators of contaminated aquatic ecosystems: responses to presence of psychoactive drug mixtures

7 février 2017

The pharmaceutical products are emerging pollutants continuously released into the environment, because they cannot be effectively removed by the wastewater treatment plants. In recent years, questions have been raised concerning the environmental risks related to these pollutants. The goal of this research was to evaluate the responses in Lemna minor after 7 days and in Corbicula fluminea after differing durations (1, 3, 7, and 19 days) of exposure to the psychoactive drug mixture (valproic acid, citalopram, carbamazepine, cyamemazine, hydroxyzine, oxazepam, norfluoxetine, lorazepam, fluoxetine, and sertraline) in different concentrations (0, 0 + ethanol, drug concentration (DC) 1 = river water concentration, DC2 = effluent concentration, and DC3 = 10× effluent concentration). In this aim, growth parameters of L. minor, gluthathione S-transferase (GSTs), catalase (CAT), ethoxyresorufin-O-deethylase (EROD) and/or gene expressions (pi-gst, cat, cytochrome P450 4 (cyp4), multidrug resistant 1 (mdr1), and superoxide dismutase (sod)) were measured. GST activities increased significantly in L. minor exposed to DC3, but no changes were found in CAT activity. In C. fluminea, EROD activity was induced significantly in both gill and digestive gland tissues after 3 days’ exposure to DC3, while a GST increase was observed only in digestive gland tissues, suggesting that these pharmaceuticals induced an oxidative effect. Gene expression analysis revealed transient transcriptomic responses of cyp4, sod, and mdr1 under drug concentrations 2 or 3 and no change of expression for the other genes (cat and pi-gst) or condition (environmental drug concentration) tested. Finally, the data reported in this study represent important ecotoxicological information, confirming that this enzyme family (cyp4, sod, and mdr1) may be considered as a sensible and early indicator of exposure to drugs and emphasizing the involvement of selected genes in detoxification pathways.

Lire la suite

[hal-01456212] Ecology and Life Cycle Patterns of Echinococcus Species.

5 février 2017

The genus Echinococcus is composed of eight generally recognized species and one genotypic cluster (Echinococcus canadensis cluster) that may in future be resolved into one to three species. For each species, we review existing information on transmission routes and life cycles in different geographical contexts and - where available - include basic biological information of parasites and hosts (e.g., susceptibility of host species). While some Echinococcus spp. are transmitted in life cycles that involve predominantly domestic animals (e.g., dog - livestock cycles), others are wildlife parasites that do or do not interact with domestic transmission. In many cases, life cycle patterns of the same parasite species differ according to geography. Simple life cycles contrast with transmission patterns that are highly complex, involving multihost systems that may include both domestic and wild mammals. Wildlife transmission may be primary or secondary, i.e., resulting from spillovers from domestic animals. For most of the species and regions, existing information does not yet permit a conclusive description of transmission systems. Such data, however, would be highly relevant, e.g., for anticipation of geographical changes of the presence and frequency of these parasites in a warming world, or for initiating evidence-based control strategies.

Lire la suite

[hal-01346160] Subduction zone intermediate-depth seismicity: Insights from the structural analysis of Alpine high-pressure ophiolite-hosted pseudotachylyte (Corsica, France)

20 janvier 2017

Pseudotachylyte in the Cima di Gratera ophiolite, Alpine Corsica, is distributed in the peridotite unit and in the overlying metagabbro unit and was formed under blueschist to eclogite metamorphic facies conditions, corresponding to a 60–90 km depth range. Peridotite pseudotachylyte is clustered in fault zones either beneath the tectonic contact with overlying metagabbros or at short distance from it. Fault zones are either parallel to the contact or make an angle of 55° to it. Displacement sense criteria associated with fault veins indicate top-to-the-west or top-to-the-northwest reverse senses. Cataclasite flanking most veins was formed before or coevally with frictional melting and likely mechanically weakened the peridotite, facilitating subsequent seismic rupture. In the basal part of the metagabbro unit, post-mylonitization pseudotachylyte can be distinguished from pre-mylonitization pseudotachylyte formed earlier. In the equant metagabbro above the mylonitic sole, only one episode of pseudotachylyte formation can be identified. Kinematics associated with metagabbro pseudotachylyte remain unknown. The geometry and kinematics of the pseudotachylyte veins from the peridotite unit and to a lesser extent from the metagabbro unit are similar to modern seismic ruptures of the upper parts of the Wadati-Benioff zones such as in the Pacific plate beneath NE Japan.

Lire la suite

[hal-01437388] High-resolution numerical modelling of the barotropic tides in the Gulf of Gabes, eastern Mediterranean Sea (Tunisia)

17 janvier 2017

A high-resolution 2D barotropic tidal model was developed for the Gulf of Gabes and used to characterise hydrodynamic processes and tidal dynamics. The model is based on the Regional Ocean Modelling System. It is forced at the open boundaries by the semidiurnal M2 and S2 astronomical components while meteorological forcing has been neglected. The model results show good agreement with observations confirming that it reproduces the gulf's main tidal characteristics reasonably well. In fact, the simulated semidiurnal tidal components M2 and S2 generate important sea level variations and coastal currents. Tidal propagation is directed to the gulf's western sector while tidal resonance occurs in its inner sector where the M2 and S2 amplitudes are about 50 and 36 cm, respectively. Phase maxima (170°-185°) are located inside Boughrara Lagoon for both the simulated M2 and S2 tides. The strongest currents are found in shallow coastal regions and at the lagoon's western inlet. During spring tides, currents are around 10-20 cm s-1 in the gulf center and up to 50 cm s-1 inside the lagoon

Lire la suite

[insu-01427249] Groundwater isotopic data as potential proxy for Holocene paleohydroclimatic and paleoecological models in NE Brazil

14 janvier 2017

Holocene paleoclimatic patterns in NE Brazil are recognized to present singular characteristics when compared with the remaining tropical South-America. In particular, isotopic variations in speleothem calcite highlight that in contrast to the rest of tropical SA, NE Brazil experienced humid conditions during lower summer insolation, i.e. throughout the Early-Mid Holocene, and aridity when, as nowadays, summer insolation was high. In parallel, paleobotanical and palynological investigations suggest that these wetter conditions, also associated with colder climate, could have promoted the setting of ecological corridors between the current Amazonian (continental) and Atlantic (littoral) forests. In this context, this work aims at showing how groundwater isotopic data could be used as a complementary proxy to further explain these Holocene paleohydroclimatic and paleoecologic processes. By comparing δ18O, δ2H and d-excess of modern waters with Early-Mid Holocene groundwater in Recife (Pernambuco state, NE Brazil), differences in recharge patterns and moisture origin can be constrained. We find that Early-Mid Holocene waters present higher d-excess than the modern groundwater. Given that the Early-mid Holocene colder and wetter conditions (higher relative humidity) should lead to a reverse trend, i.e. lower d-excess, we hypothesize that the groundwater moisture sources was heavily recycled. Such a hypothesis would be consistent with the presence of a rainforest-type ecosystem, similar to the present Amazonian forest, in the currently arid NE Brazil. These observations highlight the potential added value of the groundwater isotopes proxy to discuss the interrelationships of paleohydrological and paleoecological patterns during the Early-Mid Holocene. These new proxies might allow the spatio-temporal extent of the above-mentioned ecological corridors to be discussed.

Lire la suite

[hal-01435333] Impact of new water systems on healthcare-associated colonization or infection with Pseudomonas aeruginosa

13 janvier 2017

Aim: We aimed to study the impact of new water systems, which were less contaminated with P. aeruginosa, on the incidence of healthcare-associated P. aeruginosa cases (colonizations or infections) in care units that moved to a different building between 2005 and 2014. Methods: Generalized Estimated Equations were used to compare the incidence of P. aeruginosa healthcare-associated cases according to the building. Results: Twenty-nine units moved during the study period and 2,759 cases occurred in these units. No difference was observed when the new building was compared with older buildings overall. Conclusion: Our results did not support our hypothesis of a positive association between water system contamination and the incidence of healthcare-associated P. aeruginosa cases. These results must be confirmed by linking results of water samples and patients' data.

Lire la suite

[hal-01432121] Impacts of several urban-sprawl countermeasures on building (space heating) energy demands and urban heat island intensities. A case study

12 janvier 2017

Controlling the urban development and protecting the natural habitats are major challenges for urban planners. With respect to these challenges, we assess the influence of different spatial planning policies on the urban heat island (UHI) intensity and the energy demand for building space heating in Strasbourg–Kehl urban region (France–Germany). For this purpose, the SLEUTH* urban growth model is coupled off-line with the WRF/urban climate modeling system in order to simulate the impacts of three types of urban development (compact, moderately compact, and sprawling development) combined with ecological preservation rules. Two additional software applications, Graphab and MorphoLim, are used to define the ecological and urban spatial structures, and drive the SLEUTH* simulations. The simulations for the year 2010 are consistent with the existing climate data (mean bias on temperatures less than or equal to 1 °C) and annual energy consumptions for building space heating estimated via a building typology energy assessment approach (discrepancies of 20%). Simulated urban development scenarios for the year 2030 show slight effects on UHI intensities and heating energy demands in buildings. Those results suggest that urban sprawl countermeasures have no significant effect on the UHI intensity and building energy requirements when considering a moderate urban growth and realistic planning scenarios.

Lire la suite

[hal-01429221] Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches

11 janvier 2017

Understanding the factors underlying the co-occurrence of multiple species remains a challenge in ecology. Biotic interactions, environmental filtering and neutral processes are among the main mechanisms evoked to explain species co-occurrence. However, they are most often studied separately or even considered as mutually exclusive. This likely hampers a more global understanding of species assembly. Here, we investigate the general hypothesis that the structure of co-occurrence networks results from multiple assembly rules and its potential implications for grassland ecosystems. We surveyed orthopteran and plant communities in 48 permanent grasslands of the French Jura Mountains and gathered functional and phylogenetic data for all species. We constructed a network of plant and orthopteran species co-occurrences and verified whether its structure was modular or nested. We investigated the role of all species in the structure of the network (modularity and nestedness). We also investigated the assembly rules driving the structure of the plant-orthopteran co-occurrence network by using null models on species functional traits, phylogenetic relatedness and environmental conditions. We finally compared our results to abundance-based approaches. We found that the plant-orthopteran co-occurrence network had a modular organization. Community assembly rules differed among modules for plants while interactions with plants best explained the distribution of orthopterans into modules. Few species had a disproportionately high positive contribution to this modular organization and are likely to have a key importance to modulate future changes. The impact of agricultural practices was restricted to some modules (3 out of 5) suggesting that shifts in agricultural practices might not impact the entire plant-orthopteran co-occurrence network. These findings support our hypothesis that multiple assembly rules drive the modular structure of the plant-orthopteran network. This modular structure is likely to play a key role in the response of grassland ecosystems to future changes by limiting the impact of changes in agricultural practices such as intensification to some modules leaving species from other modules poorly impacted. The next step is to understand the importance of this modular structure for the long-term maintenance of grassland ecosystem structure and functions as well as to develop tools to integrate network structure into models to improve their capacity to predict future changes.

Lire la suite

[hal-01430647] Encaged Chironomus riparius larvae in assessment of trace metal bioavailability and transfer in a landfill leachate collection pond

11 janvier 2017

Household wastes may constitute a vector of environmental contamination when buried, in particular through degradation and production of leachates containing significant trace metal (TM) concentrations that may constitute a serious risk to biota. The objectives of this study were to assess the bioavailability and transfer potential of various TMs present in water and sediments in a reservoir receiving landfill leachates. An active biomonitoring approach was adopted consisting of exposing naive laboratory organisms in cages deployed in the field. Aquatic insects such as Chironomus riparius larvae are good candidates since they represent key organisms in the trophic functioning of aquatic ecosystems. The results show that water, suspended particles, and sediments were significantly contaminated by various TMs (As, Cd, Cu, Ni, Pb, and Zn). Their contribution to the transfer of TMs depends, however, on the specific element considered, e.g., Cd in sediments or Pb in both suspended particles and sediments. The internal fate of TMs was investigated according to their fractionation between an insoluble and a cytosolic fraction. This approach revealed different detoxification strategies capable of preventing the induction of deleterious effects at the individual scale. However, the accumulation of several TMs in C. riparius larvae tissues may also represent a significant load potentially transferable to higher trophic levels

Lire la suite

[hal-01430615] Trace element accumulation and elutriate toxicity in surface sediment in northern Tunisia (Tunis Gulf, southern Mediterranean)

11 janvier 2017

Metal concentrations in sediments were investigated in the Gulf of Tunis, Tunisia, in relation to anthropic activities along the Mejerda River and Ghar El Melh Lagoon, with effluents discharged into the gulf. Distribution of grain size showed that the silty fraction is dominant with 53%, while sand and clay averages are 34 and 12% respectively. Zn concentration increased in the vicinity of the Mejerda River while Pb was at its highest levels at the outlet of Ghar El Mehl Lagoon. Sediment elutriate toxicity, as measured by oyster embryo bioassays, ranged from 10 to 45% abnormalities after 24 h, but no relation was found between metal concentration and sediment toxicity. The AVS fraction that represents monosulfide concentrations in the sediment was higher in the central part of the gulf than in the coastal zone. The results reveal the influence of AVS, TOC and grain size on metal speciation and sediment toxicity

Lire la suite

[hal-01416643] Therapeutic properties in Tunisian hot springs: first evidence of phenolic compounds in the cyanobacterium Leptolyngbya sp. biomass, capsular polysaccharides and releasing polysaccharides

9 janvier 2017

Background: In Tunisia, the use of hot spring waters for both health and recreation is a tradition dating back to Roman times. In fact, thermal baths, usually called “Hammam” are recommended as a therapeutic and prophylactic measure against many types of illness and toxicity. While the chemical concentration of thermal water is admittedly associated with its therapeutic effects, the inclusion in spa waters of efficient bioproduct additives produced by photosynthetic microorganisms and that act against oxidative stress may comprise a significant supplementary value for thermal centers. The aim of this study was to investigate the antioxidant potential of the Tunisian thermophilic cyanobacterium Leptolyngbya sp. and to determine its phytochemical constituents and phenolic profile. Methods: BME (Biomass Methanolic Extract), CME (Capsular polysaccharides Methanolic Extract) and RME (Releasing polysaccharides Methanolic Extract) of Leptolyngbya sp. were examined for their antioxidant activities by means of DPPH, hydroxyl radical scavenging and ferrous ion chelating assays. Their total phenols, flavonoids, carotenoids, Mycosporine-like amino acids (MAAs) and vitamin C contents, as well as their phenolic profiles were also determined. Results: BME has the highest content of phenols (139 ± 1.2 mg/g), flavonoids (34.9 ± 0.32 mg CEQ/g), carotenoids (2.03 ± 0.56 mg/g) and vitamin C (15.7 ± 1.55 mg/g), while the highest MAAs content (0.42 ± 0.03 mg/g) was observed in CME. BME presented both the highest DPPH and hydroxyl radical scavenging ability with an IC50 of 0.07 and 0. 38 mg/ml, respectively. The highest ferrous chelating capacity was detected in CME with an IC50 = 0.59 mg/ml. Phenolic profiles revealed the presence of 25 phenolic compounds with the existence of hydroxytyrosol, oleuropein, resveratrol and pinoresinol. Conclusion: The study demonstrated that the cyanobacterium Leptolyngbya sp. possesses abundant natural antioxidant products which may have prophylactic and therapeutic effects on many types of illness and toxicity. The present findings not only explain and reinforce the rationale behind traditional therapeutic practices in Tunisia in the exploitation of the country’s hot springs, but support the addition of Leptolyngbya to thermal waters as a means to enhance the value and reputation of the curative nature of Tunisian thermal waters.

Lire la suite

[hal-01429226] Ecological Indicator Values of Europe (EIVE) 1.0: a powerful open-access tool for vegetation scientists

8 janvier 2017

Background: Ecological indicator values (EIVs) have a long tradition in vegetation ecological research in Europe. EIVs characterise the ecological optimum of species along major environmental gradients using ordinal scales. Calculating mean indicator values per plot is an effective way of bioindication. Following first systems in Russia and Central Europe, about two dozen EIV systems have been published for various parts of Europe. Aims: As there was no EIV system available at European scale that could be used for broad- scale analyses, e.g. in the context of the European Vegetation Archive (EVA), we develop such a system for the first time for the vascular plants of Europe. Location: Europe. Methods: We compiled all national and major regional EIV systems and harmonized their plant nomenclature with a newly developed contemporary European taxonomic backbone (EuroSL 1.0). Using regression, we rescaled the individual EIV systems for the main parameters to continent-wide quasi-metric scales, ranging from 1 to 99. The data from each individual system were then translated into a probability curve approximated with a normal distribution, weighed with the logarithm of the area represented and summed up across the systems. From the European density curve we extracted then a mean and a variance, which characterise the distribution of this species along this particular ecological gradient. Results and conclusions: Our consensus approach of integrating the expert knowledge of all existing EIV systems allowed deriving the first consistent description of the ecological behaviour for a significant part of the European vascular flora. The resulting Ecological Indicator Values of Europe (EIVE) 1.0 will be published open access to allow bioindication beyond country borders. Future releases of EIVE might contain more parameters, non- vascular plants and regionalisation or could be re-adjusted and extended to hitherto non- covered species through co-occurrence data from EVA.

Lire la suite

[pasteur-01405208] Early diagnosis and monitoring of mucormycosis by detection of circulating DNA in serum: retrospective analysis of 44 cases collected through the French Surveillance Network of Invasive Fungal Infections (RESSIF)

6 janvier 2017

The main objective of this study was to assess the diagnostic performance of a set of three Mucorales quantitative PCR assays in a retrospective multicentre study. Mucormycosis cases were recorded thanks to the French prospective surveillance programme (RESSIF network). The day of sampling of the first histological or mycological positive specimen was defined as day 0 (D0). Detection of circulating DNA was performed on frozen serum samples collected from D-30 to D30, using quantitative PCR assays targeting Rhizomucor, Lichtheimia, Mucor/Rhizopus. Forty-four patients diagnosed with probable (n = 19) or proven (n = 25) mucormycosis were included. Thirty-six of the 44 patients (81%) had at least one PCR-positive serum. The first PCR-positive sample was observed 9 days (range 0-28 days) before diagnosis was made using mycological criteria and at least 2 days (range 0-24 days) before imaging. The identifications provided with the quantitative PCR assays were all concordant with culture and/or PCR-based identification of the causal species. Survival rate at D84 was significantly higher for patients with an initially positive PCR that became negative after treatment initiation than for patients whose PCR remained positive (48% and 4%, respectively; p \textless10(-6)). The median time for complete negativity of PCR was 7 days (range 3-19 days) after initiation of l-AmB treatment. Despite some limitations due to the retrospective design of the study, we showed that Mucorales quantitative PCR could not only confirm the mucormycosis diagnosis when other mycological arguments were present but could also anticipate this diagnosis. Quantification of DNA loads may also be a useful adjunct to treatment monitoring.

Lire la suite

[insu-01424277] Anthropogenic- and natural sources of dust in peatland during the Anthropocene

3 janvier 2017

As human impact have been increasing strongly over the last decades, it is crucial to distinguish human-induced dust sources from natural ones in order to define the boundary of a newly proposed epoch-the Anthropocene. Here, we track anthropogenic signatures and natural geochemical anomalies in the Mukhrino peatland, Western Siberia. Human activity was recorded there from cal AD 1958 (±6). Anthropogenic spheroidal aluminosilicates clearly identify the beginning of industrial development and are proposed as a new indicator of the Anthropocene. In cal AD 1963 (±5), greatly elevated dust deposition and an increase in REE serve to show that the geochemistry of elements in the peat can be evidence of nuclear weapon testing; such constituted an enormous force blowing soil dust into the atmosphere. Among the natural dust sources, minor signals of dryness and of the Tunguska cosmic body (TCB) impact were noted. The TCB impact was indirectly confirmed by an unusual occurrence of mullite in the peat.

Lire la suite

[tel-01421477] Modélisation des interactions trophiques impliquant des transferts de contaminants biologiques et chimiques. Application à Echinococcus multilocularis et aux éléments traces métalliques.

2 janvier 2017

La structure et l'intensité des interactions ressources-consommateurs qui forment les réseaux trophiques régulent une très grande partie des transferts de biomasse mais aussi de contaminants biologiques et chimiques dans les écosystèmes. L’objectif de la thèse est de développer des modèles permettant d’étudier les mécanismes de transport des contaminants et d’évaluer ainsi d’une part la dynamique des maladies infectieuses et des pollutions chimiques, et d’autre part les réponses des réseaux trophiques soumis à ces contaminations. La modélisation des interactions trophiques multi-proies (multi-species functional response : MSFR) ajustée à des données de prédation du renard roux et de la chouette effraie sur des communautés de micromammifères a montré que le changement des préférences alimentaires est une propriété importante ayant deux composantes : l'une en réponse au changement des fréquences relatives des proies, et l'autre en réponse au changement de la densité totale de la communauté des proies. Cela suggère que le prédateur a une image d’ensemble de la communauté des proies, et que ses choix résultent d’un compromis entre la quantité et l'accessibilité des proies disponibles. Les variations de prédation ont des conséquences sur le transfert des contaminants dans les réseaux trophiques. En intégrant les MSFR à la modélisation des dynamiques éco-épidémiologiques du cestode Echinococcus multilocularis (parasite transmis par voie trophique : TTP) entre le renard roux (hôte définitif) et les campagnols des champs et terrestres (hôtes intermédiaires), nous avons identifié et caractérisé les mécanismes de dilution et d’amplification de la transmission du parasite en fonction de la biodiversité des hôtes intermédiaires. Plus particulièrement, la modélisation a permis d’analyser la sensibilité des paramètres des MSFR et des compétences des hôtes sur les risques épidémiques, ainsi que de révéler des mécanismes de dilution densité-dépendants. Nous avons aussi étudié la réponse à une contamination chimique des chaînes trophiques incluant des micromammifères situés à des niveaux trophiques différents (herbivores, omnivores et insectivores) et un top-prédateur (chouette effraie). Le modèle couplant les dynamiques des populations et des concentrations en cadmium (Cd) dans ces populations a permis de caractériser les changements de stabilité des équilibres (les bifurcations) des couples proies-prédateurs en fonction des concentrations de Cd dans le sol et d’autres stresseurs affectant les ressources des proies ou la mortalité du prédateur. L’étude montre ainsi que l’augmentation des ressources, et/ou une diminution de la mortalité des prédateurs, impliquent une déstabilisation des populations qui peut être contrebalancée par l’effet du contaminant sur les populations. Aussi, la contamination combinée à l’augmentation des ressources des proies et une mortalité moyenne des prédateurs peuvent conduire à des zones de bistabilité propices aux basculements soudains de l’état du système, allant d’une coexistence proies-prédateurs à l’extinction des prédateurs. À l’issue de ces travaux, une quatrième étape de la thèse a été d’intégrer les interactions trophiques, les dynamiques des parasites et les impacts des pollutions dans des méta-écosystèmes (i.e. avec dispersions d’individus entre écosystèmes). En utilisant la théorie des matrices aléatoires nous avons établi des mesures des risques d’émergence de parasites que nous avons évalués en fonction des perturbations extérieures. L’étude a ainsi montré que ces perturbations augmentent les risques épidémiques, mais que ces risques pouvaient être réduits par la dispersion des individus (sains et infectés) sous certaines conditions qui sont, par exemple pour les TTP, un nombre d’espèces plus grand que le nombre d’écosystèmes connectés, et un taux de virulence plus faible que le taux de contagion. Ainsi, dans un contexte planétaire d’augmentation des pressions anthropiques sur les écosystèmes, cette thèse de modélisation apporte un ensemble d’outils et de développements conceptuels permettant d’analyser quantitativement et qualitativement les transferts et les impacts des contaminants sur les écosystèmes.

Lire la suite

[hal-01423289] Fungal peptides from pneumonitis hypersensitivity etiologic agents are able to induce specific cellular immune response.

29 décembre 2016

Hypersensitivity pneumonitis (HP) is an immunoallergic disease due to chronic exposure to high quantities of different microorganisms such as Mycobacterium immunogenum (Mi), a mycobacterium, and Lichtheimia corymbifera (Lc), a filamentous fungus. It has recently been demonstrated that the protein DLDH (dihydrolipoyl dehydrogenase), is common to these microorganisms. This study aimed to investigate the immune potential of overlapping peptide pools covering the MiDLDH and LcDLDH.

Lire la suite

[halshs-01420568] Du ciel au territoire, vers une nouvelle perception de l’espace archéologique

22 décembre 2016

Depuis les années 1970, les archéologues utilisent la télédétection aérienne ou par satellite pour repérer des sites archéologiques mais aussi des structures paysagères anciennes encore visibles à la surface de la terre. La télédétection appliquée à l’archéologie n’a donc rien de révolutionnaire, néanmoins les évolutions technologiques depuis les années 2000 ont profondément modifié le rapport des archéologues à ce domaine d’étude. Couplée au développement des systèmes d’information géographique (SIG) et aux techniques de géolocalisation de plus en plus performantes, la télédétection n’est plus une pratique uniquement réservée à quelques spécialistes mais s’est largement diffusée. Au-delà des aspects proprement technologiques, cela a engendré une véritable révolution conceptuelle car les SIG et la télédétection modifient le point de vue des archéologues sur les territoires et paysages du passé.

Lire la suite

[insu-01419190] Geochemistry of the New Caledonia Serpentinites: Evidences for Multiple Serpentinization Events at Various Depths

19 décembre 2016

Studies of serpentine minerals around the world have shown that different varieties can coexist depending on external conditions such as temperature, pressure and chemical exchanges. Identifying serpentine variety can thus provide significant constraints on the geodynamic environment at the time of formation. In the New Caledonia (NC) ophiolite, serpentinization is ubiquitous (>50%). The base of the ophiolite is made of a thick serpentinite sole that recorded multiple serpentinization events. This study aims at deciphering the nature and the origin of fluids involved in serpentinization processes from the characterization of primary minerals and serpentine geochemistry, including: in situ major and trace elements and stable oxygen and hydrogen isotopes. Our results show that lizardite is the main mineral species (~80% of the serpentine). In the serpentinite sole, lizardite is crosscut by multiple serpentine veins ordered as follow: lizardite 1→lizardite 2→antigorite→chrysotile→polygonal serpentine. From the trace elements analysis, we demonstrate that the transition from primary minerals to lizardite 1 occurs almost isochemically. However, serpentine composition in the sole strongly differs from lizardite 1 and show a great enrichment in fluid-mobile elements and an increase of Fe3+/FeT ratio. Stable isotopes show that serpentines display a wide range in δ18O (1.9-14‰) and a narrow range in δD (88-106‰). These results were then modeled based on Monte-Carlo simulations. Fluids in equilibrium with NC serpentines define a linear trend that extends from the meteoric water line to an area defined between 3‰ and 8‰ in δ18O and -80‰ and -60‰ in δD. These compositions are consistent with fluids derived from the dehydration of the altered oceanic crust during the subduction in the South Loyalty Basin at temperatures between 250°C and 400°C. No evidence of sedimentary contribution was observed, suggesting that the serpentinization of the NC ophiolite was complete within few million years after the initiation of the subduction. Low δ18O values indicate that the latest generation of serpentine may derive from the circulation of meteoric fluids at low temperature (<150°C), suggesting that the latest steps of serpentinization started from the beginning of the ophiolite obduction.

Lire la suite

[hal-01417891] Factors associated with 12 week case-fatality in Staphylococcus aureus bacteraemia: a prospective cohort study

17 décembre 2016

Staphylococcus aureus bacteraemia (SAB) is a frequent and deadly disease. Given the lack of a randomized trial, optimal first-line antibiotic treatment is still debated. Our aim was to identify prognostic factors in SAB patients and to analyse the impact of first-line antibiotics. The VIRSTA prospective cohort study was conducted in eight tertiary care centres in France. Consecutive incident adults in whom a blood culture drawn in participating centres grew S. aureus between April 2009 and October 2011 were prospectively followed for 12 weeks. Factors associated with 12-week case-fatality were identified by multivariate logistic regression. We enrolled 2091 patients and analysed survival in 1972 (median age 67.8 years, interquartile range 55.5–78.9; females 692/1972, 35.1%). SAB was nosocomial or healthcare-related in 1372/1972 (69.6%) of cases and the primary focus was unknown in 414/1972 (21.0%) of cases. Week 12 case-fatality rate was 671/1972 (34.0%). The main independent prognostic factors on multivariate analysis were age (adjusted OR by 10-year increment 1.56; 95% CI 1.44–1.69), septic shock (OR 5.11; 95% CI 3.84–6.80), metastatic cancer (OR 4.28; 95% CI 2.88–6.38), and unknown primary focus (OR 2.62; 95% CI 2.02–3.41). In the 1538 patients with methicillin-sensitive S. aureus (MSSA) bacteraemia, first-line empiric antistaphylococcal penicillins (OR 0.40; 95% CI 0.17–0.95) and vancomycin (OR 0.37; 95% CI 0.17–0.83), alone or combined with an aminoglycoside, were associated with better outcome compared with other antibiotics. There are few modifiable prognostic factors for SAB. Initiating empiric antibiotics with antistaphylococcal penicillins or vancomycin may be associated with better outcome in MSSA bacteraemia. © 2016 European Society of Clinical Microbiology and Infectious Diseases

Lire la suite

[hal-01412310] Noise annoyance in urban children: a cross-sectional population-based study

9 décembre 2016

Acoustical and non-acoustical factors influencing noise annoyance in adults have been well-documented in recent years; however, similar knowledge is lacking in children. The aim of this study was to quantify the annoyance caused by chronic ambient noise at home in children and to assess the relationship between these children0s noise annoyance level and individual and contextual factors in the surrounding urban area. A cross sectional population-based study was conducted including 517 children attending primary school in a European city. Noise annoyance was measured using a self-report questionnaire adapted for children. Six noise exposure level indicators were built at different locations at increasing distances from the child0s bedroom window using a validated strategic noise map. Multilevel logistic models were constructed to investigate factors associated with noise annoyance in children. Noise indicators in front of the child0s bedroom (p 0.01), family residential satisfaction (p 0.03) and socioeconomic characteristics of the individuals and their neighbourhood (p 0.05) remained associated with child annoyance. These findings illustrate the complex relationships between our environment, how we may perceive it, social factors and health. Better understanding of these relationships will undoubtedly allow us to more effectively quantify the actual effect of noise on human health.

Lire la suite

[hal-01411184] 3D modeling of phytoplankton seasonal variation and nutrient budget in a southern Mediterranean Lagoon

7 décembre 2016

A 3D coupled physical-biogeochemical model is developed and applied to Bizerte Lagoon (Tunisia), in order to understand and quantitatively assess its hydrobiological functioning and nutrients budget. The biogeochemical module accounts for nitrogen and phosphorus and includes the water column and upper sediment layer. The simulations showed that water circulation and the seasonal patterns of nutrients, phytoplankton and dissolved oxygen were satisfactorily reproduced. Model results indicate that water circulation in the lagoon is driven mainly by tide and wind. Plankton primary production is co-limited by phosphorus and nitrogen, and is highest in the inner part of the lagoon, due to the combined effects of high water residence time and high nutrient inputs from the boundary. However, a sensitivity analysis highlights the importance of exchanges with the Mediterranean Sea in maintaining a high level of productivity. Intensive use of fertilizers in the catchment area has a significant effect on phytoplankton biomass increase.

Lire la suite

[hal-01408475] Couplage de SMA avec des EDO pour simuler les phénomènes écologiques à grande échelle

5 décembre 2016

La modélisation explicitement spatiale est essentielle en écologie pour la prise de décision et de gestion. Elle implique la modélisation de l’hétérogénéité du paysage et le fait que différentes espèces d'agents peuvent se comporter à différentes échelles, ce qui accroît les besoins en matière de données, et oblige à leur intégration précise dans une hiérarchie imbriquée d’échelles spatio-temporelles (local / régional, saisonnier / pluriannuel, etc. . La modélisation multi-agents (MMA est un paradigme orienté « spatialement explicite » qui inclut l’hétérogénéité de l’espace (par exemple, des cultures, des prairies, des parcelles de forêt), où les individus (par exemple, les proies, les prédateurs, etc.) se déplacent représentés comme des « agents ». Ces derniers sont des entités autonomes, qui se déplacent dans l'espace virtuel et interagissent les uns avec les autres et les patchs environnementaux. Pendant la simulation, les dynamiques émergent et peuvent être observées et quantifiées. Ces modèles mettent en lumière les dynamiques microscopiques et spatiales qui ne peuvent être observés avec les modèles d’équation mathématiques classiques, (MME). Le couplage entre MMA et MME est cependant nécessaire pour éviter les limites de calcul lorsque des populations géantes (par exemple des centaines de millions d'individus) sont étudiées pour simuler des phénomènes écologiques tels que traités dans la Zone atelier Arc jurassien à propos des pullulations de campagnols. Les méthodes et résultats préliminaires de cette approche sont présentés ici.

Lire la suite

[hal-01408279] Experimental climate warming alters the relationship between fungal root symbiosis and Sphagnum litter phenolics in two peatland microhabitats

4 décembre 2016

Belowground interactions between plants and microorganisms are involved in numerous ecosystems processes such as carbon and nutrient cycling. Understanding their responses to on-going climate warming is thus of paramount importance to better predict future ecosystem functioning. We hypothesized that climate warming alters the interactions between Sphagnum litter phenolics and the fungal root symbiosis of the Ericale plant Andromeda polifolia in a Jura mountain peatland (France). We initiate a climate warming treatment (+1°C) in April 2008 in two microhabitats (lawns and hummocks). We measured polyphenolic contents, mycorrhizal and dark septate endophyte (DSE) root colonization, phenoloxidase and peroxidase activities in the A. polifolia rhizosphere from 2010 to 2012. We found that four years of warming modulated rhizospheric parameters (fungal root symbiosis and enzyme activities) of A. polifolia, but the response differed between microhabitats. Enzyme activities and fungal root colonization displayed different responses to warming according to the microhabitats. DSE root colonization increased and peroxidase activities decreased in warmed Hummocks while they remained stable in warmed lawns. We found a significant positive correlation between DSE root colonization and litter phenolics recovered in both microhabitats but only under in ambient conditions. On the contrary, significant negative correlation was observed between mycorrhizae and litter phenolics recovered in warmed plots while no relationship was found in control plots. Our work thus provides evidences that interplay between phenolics from Sphagnum litter and fungal symbiosis of an Ericale species in peatlands was affected by climate warming. It highlights different plant biological responses to climate warming according to peatland microhabitats and confirm that belowground activities are crucial to understand the response of peatlands to climate change.

Lire la suite

[hal-01362655] Symptomatic and Asymptomatic Neurological Complications of Infective Endocarditis: Impact on Surgical Management and Prognosis

29 novembre 2016

Objectives:Symptomatic neurological complications (NC) are a major cause of mortality in infective endocarditis (IE) but the impact of asymptomatic complications is unknown. We aimed to assess the impact of asymptomatic NC (AsNC) on the management and prognosis of IE. Methods: From the database of cases collected for a population-based study on IE, we selected 283 patients with definite left-sided IE who had undergone at least one neuroimaging procedure (cerebral CT scan and/or MRI) performed as part of initial evaluation. Results Among those 283 patients, 100 had symptomatic neurological complications (SNC) prior to the investigation, 35 had an asymptomatic neurological complications (AsNC), and 148 had a normal cerebral imaging (NoNC). The rate of valve surgery was 43% in the 100 patients with SNC, 77% in the 35 with AsNC, and 54% in the 148 with NoNC (p<0.001). In-hospital mortality was 42% in patients with SNC, 8.6% in patients with AsNC, and 16.9% in patients with NoNC (p<0.001). Among the 135 patients with NC, 95 had an indication for valve surgery (71%), which was performed in 70 of them (mortality 20%) and not performed in 25 (mortality 68%). In a multivariate adjusted analysis of the 135 patients with NC, age, renal failure, septic shock, and IE caused by S. aureus were independently associated with in-hospital and 1-year mortality. In addition SNC was an independent predictor of 1-year mortality. Conclusions The presence of NC was associated with a poorer prognosis when symptomatic. Patients with AsNC had the highest rate of valve surgery and the lowest mortality rate, which suggests a protective role of surgery guided by systematic neuroimaging results.

Lire la suite

[hal-01403340] Effects of geolocators on hatching success, return rates, breeding movements, and change in body mass in 16 species of Arctic-breeding shorebirds.

25 novembre 2016

Background Geolocators are useful for tracking movements of long-distance migrants, but potential negative effects on birds have not been well studied. We tested for effects of geolocators (0.8–2.0 g total, representing 0.1–3.9 % of mean body mass) on 16 species of migratory shorebirds, including five species with 2–4 subspecies each for a total of 23 study taxa. Study species spanned a range of body sizes (26–1091 g) and eight genera, and were tagged at 23 breeding and eight nonbreeding sites. We compared breeding performance and return rates of birds with geolocators to control groups while controlling for potential confounding variables. Results We detected negative effects of tags for three small-bodied species. Geolocators reduced annual return rates for two of 23 taxa: by 63 % for semipalmated sandpipers and by 43 % for the arcticola subspecies of dunlin. High resighting effort for geolocator birds could have masked additional negative effects. Geolocators were more likely to negatively affect return rates if the total mass of geolocators and color markers was 2.5–5.8 % of body mass than if tags were 0.3–2.3 % of body mass. Carrying a geolocator reduced nest success by 42 % for semipalmated sandpipers and tripled the probability of partial clutch failure in semipalmated and western sandpipers. Geolocators mounted perpendicular to the leg on a flag had stronger negative effects on nest success than geolocators mounted parallel to the leg on a band. However, parallel-band geolocators were more likely to reduce return rates and cause injuries to the leg. No effects of geolocators were found on breeding movements or changes in body mass. Among-site variation in geolocator effect size was high, suggesting that local factors were important. Conclusions Negative effects of geolocators occurred only for three of the smallest species in our dataset, but were substantial when present. Future studies could mitigate impacts of tags by reducing protruding parts and minimizing use of additional markers. Investigators could maximize recovery of tags by strategically deploying geolocators on males, previously marked individuals, and successful breeders, though targeting subsets of a population could bias the resulting migratory movement data in some species.

Lire la suite

[hal-01400212] 2000 Years of Grazing History and the Making of the Cretan Mountain Landscape, Greece

24 novembre 2016

Understanding the processes that led to the recent evolution of Mediterranean landscapes is a challenging question that can be addressed with paleoecological data. Located in the White Mountains of Crete, Asi Gonia peat bog constitutes an exceptional 2000-years-long sedimentary archive of environmental change. In this study, we document the making of the White Mountains landscape and assess human impact on ecosystem trajectories. The paleoenvironmental reconstruction is based on high-resolution analyses of sediment, pollen , dung fungal spores and charcoal obtained from a 6-m core collected from the bog. Multiproxy analyses and a robust chronological control have shed light on anthropogenic and natural processes that have driven ecological changes, giving rise to the present-day Mediterranean ecosystem. Our results suggest that sediment accumulation began during the transition from the Hellenistic to the Roman period, likely due to watershed management. The evolution of the peat bog as well as vegetation dynamics in the surrounding area were linked to past climate changes but were driven by human activities, among which breeding was of great importance. Charcoal analysis reveals that fire was largely used for the construction and maintenance of sylvo-agropastoral areas. Pollen data allow the identification of three main vegetation assemblages: 1) evergreen oak forest (before ca. 850 AD), 2) heather maquis (ca. 850 to 1870 AD), 3) phrygana/steppe landscape. Rapid changes between phases in vegetation development are associated with tipping-points in ecosystem dynamics resulting from anthropogenic impact. The modern ecosystem did not get established until the 20 th century, and it is characterized by biodiversity loss along with a dramatic drying of the peat bog.

Lire la suite

[insu-01397784] Geology of the world-class Kiaka polyphase gold deposit, West African Craton, Burkina Faso

18 novembre 2016

The Kiaka gold deposit is a major resource in West Africa, with measured and indicated resources of 124 Mt at 1.09 g/t Au (3.9 Moz) and inferred resources of 27 Mt at 0.83 g/t Au (0.8 Moz). Located within the Manga-Fada N’Gourma greenstone and plutonic belt in south of the Burkina Faso, the deposit is hosted by a metamorphosed volcano-sedimentary sequence of lithic-, quartz-biotite metagreywacke, aluminosilicate-bearing metapelites and garnet-orthopyroxene-bearing schists and volcanic units. Structural observations indicate four local deformation events: DK1, DK2 and DK3 and DK4. Respectively, these events are linked to regional D1 E-W compression, D2 NW-SE compression and lastly, D3- and D4-related reactivations along D2 shear zones. The S2 foliation and D2-related shear zones are developed during lower amphibolite facies metamorphism whereas retrogression occurs during D3-4 reactivations along these shear zones at upper greenschist facies conditions. The emplacement of a dioritic intrusion, dated at 2140 ± 7 Ma (Concordia U-Pb age on magmatic zircon), is interpreted to be contemporaneous with sinistral displacement along mineralized, NE-trending D2 shear zones. The intersection of these shears zones and the Markoye shear zone (dextral-reverse D1 and sinistral-reverse D2 reactivations) controlled the final geometry of the host rocks and the ore zones. Four subparallel elongated ore bodies are mainly hosted within D2-related shear zones and some are developed in an apparent axial plane of a F2 isoclinal fold. Detailed petrographic studies have identified two main types of hydrothermal alteration associated with two stages of gold mineralization. The stage (1) corresponds to replacement zones with biotite and clinozoisite during the D2 event associated with pyrrhotite ± pyrite, chalcopyrite (disseminated gold stage). The stage (2) occurs during reactivations of the D2-related auriferous shear zones (vein stage) and are characterized by diopside ± actinolite D3 veins and veinlets and D4 pervasive muscovite, ± chlorite, ± calcite in quartz-carbonate vein selvages and associated with pyrrhotite + arsenopyrite ± electrum, ± native gold and tellurobismuthite. The latter stage (2) could be divided into two sub-stages based on mineralogy and crosscutting relationship. A weighted average Re-Os pyrrhotite age at 2157 ± 24 Ma (Re-Os age based on 3 replicates) constraints the timing of the disseminated gold stage and represents the first absolute age for gold mineralization in the Manga Fada N’Gourma area. The timing of gold at Kiaka may be also coeval with one of the two lode gold event at ~ca. 2.16-2.15 Ga and occurred concomitant with tectono-thermal activity during Eo-Eburnean orogeny. The study of the Kiaka gold deposit emphasizes the importance of a multi-scale and multidisciplinary 59 approach (field observations, petrography geothermobarometry and geochronology) to decipher the polyphase character of some Paleoproterozoic gold deposits.

Lire la suite

[hal-01398909] Système régional, paysage et dynamique de la faune sauvage: la notion d'équilibre est elle pertinente, et la santé d'un éco-système modélisable ?

18 novembre 2016

Les pullulations de campagnol terrestre et de campagnol des champs, deux espèces de rongeurs vivant principalement dans les prairies, sont périodiquement d’une actualité préoccupante pour les exploitations agricoles. Les deux espèces sont les proies principales d’un riche cortège de prédateurs qui contribue à la biodiversité régionale et à leur régulation, mais dont les reports de prédation peuvent impacter localement des espèces d’intérêt cynégétique ou patrimonial. Ces systèmes complexes modulent également la transmission d’un certain nombre de zoonoses intéressant la santé publique et vétérinaire. Ils sont étudiés depuis maintenant une trentaine d’année dans la Zone atelier Arc jurassien (http://zaaj.univ-fcomte.fr). Ils conduisent à des jeux d’acteurs subtils par lesquels des points de convergence doivent être trouvés entre des services écosystémiques qui peuvent apparaître contradictoires a priori : protection des cultures et qualité des produits alimentaires, protection des espèces patrimoniales, production cynégétique, santé, voire tourisme. L’objectif de cet exposé est de montrer quels sont les principaux processus en cause et leur dynamique à long terme, et que de nombreux états durables sont possibles pour une communauté donnée d’espèces, avec des avantages et des désavantages qui sont essentiellement perçus d’un point de vue anthropocentriques. Dans de tels anthroposystèmes, la santé des écosystèmes et leur équilibre (dynamique et provisoire) apparaissent plus définis comme un choix de combinaisons de contraintes économiques et un consensus social, parmi une grande variété d’équilibres dynamiques possibles que les composantes non-humaines de l’écosystème pourraient installer « durablement » à un temps donné. Un défi important de la recherche est certainement d’apporter les concepts scientifiques et les voies de modélisation nécessaires à la gestion de tels systèmes multi-potentiels, dans un contexte où l’évolution physique, écologique et darwinienne, dont celle des sociétés humaines, se combinent pour rendre toute gestion statique ou fixiste inappropriée.

Lire la suite

[hal-01397303] Quantification of Saprolegnia parasitica in river water using real-time quantitative PCR: from massive fish mortality to tap drinking water.

16 novembre 2016

Since 2010, the Loue River (Franche-Comté, East of France) has been suffering from massive fish kills infested by Saprolegnia parasitica. The river supplies inhabitants of the city of Besançon in drinking water, raising the question of a potential risk through both water consumption and use. We developed a real-time quantitative PCR (qPCR) to quantify S. parasitica in the Loue River as well as in the drinking water. A weak spatial trend is suggested with greater quantities of S. parasitica observed at the sampling station close to the main pumping station. No S. parasitica DNA was detected in the tap water connected to pumping stations. The use of qPCR, which combines specificity, practicality, speed and reliability, appears to be an effective tool to monitor the spatial and temporal dynamics of this oomycete and identify the risk period for wild salmonid populations in the field, for fishery management or in aquaculture.

Lire la suite

[hal-01390025] Quantitative assessment of the reliability of chironomid remains in paleoecology: effects of count density and sample size

31 octobre 2016

Random distributions for a wide range (1–100,000) of chironomid head capsules (HC) were simulated on a 1-m2 surface. The number of HC found in circular surfaces equivalent to standard core diameters (90 and 63 mm) was estimated 1000 times, over the range of tested densities. For each number of HC found in the samples, the range of simulated densities was estimated using a threshold probability (p > 0.95). This enabled us to develop equations to infer HC density from sample counts. Because of the threshold probability for comparable sample counts, the equations yield higher estimated densities under a random distribution than for a regular distribution. The probability of sampling at least one HC was >0.95 for densities of 900 HC m−2 for the 90-mm core and 1400 HC m−2 for the 63-mm core. For a specific sample count, the range of actual densities was ~10 times higher for the 63-mm core than the 90-mm core. Comparison with field larval densities revealed that most densities were too low to be suitable for annually resolved reconstruction of a quantitative signal, using current corer sizes, although a large number of populations can support sub-decadal analyses. Nonetheless, some lakes exhibit population sizes large enough to reconstruct robust quantitative estimates of past chironomid abundances. This work provides guidance to reconstruct species dynamics and fine-scale time series analyses in paleoecology.

Lire la suite

[insu-01388710] Effets de la subduction d’une dorsale sur la dynamique d’une plaque continentale : apports de la modélisation analogique

28 octobre 2016

Une série de modèles analogiques de subduction d’une plaque océanique sous une plaque continentale ont été reproduits à l’échelle du laboratoire, afin de mieux comprendre les relations entre phénomènes profonds se produisant lors de la subduction d’une dorsale, et la réponse associée en surface. Ces modèles ont été réalisés au sein du laboratoire de modélisation analogique de l’Univ. Rennes 1. Dans ces modèles, l’épaisseur de la plaque océanique augmente en direction de la fosse (plaque en forme de biseau), afin de simuler la variation d’épaisseur de la plaque depuis la dorsale jusqu’à la fosse où elle rentre en subduction. L’objectif de ces expériences est d’observer l’effet de la subduction d’une plaque océanique de plus en plus jeune, et finalement de la subduction d’une dorsale, sur la géométrie de la subduction et la dynamique du système. Un exemple de subduction de dorsale peut être observé actuellement dans les Andes Australes, en Patagonie, où la dorsale du Chili plonge sous le continent sud-américain vers 47S. L’objectif de ce travail est de comprendre l’effet de la subduction de cette dorsale sur la dynamique de la plaque continentale. Plusieurs paramètres (vitesse de convergence, largeur et forme de la plaque plongeante...) ont été testés afin de modéliser leur impact sur la subduction, sur l’évolution du pendage et sur les déformations de la plaque continentale.

Lire la suite

[hal-01388339] Spatial characterization of leachate plume using electrical resistivity tomography in a landfill composed of old and new cells (Belfort, France)

27 octobre 2016

Located near Belfort (France), the Etueffont landfill was in operation from 1976 to 2002 for the disposal and storage of domestic waste produced by 47,650 inhabitants. The site is comprised of the original landfill site called the old landfill (OL), in operation from 1976 to 1999, and a newer section known as the new cell (NC) which operated from 1999 to 2002. The objective of this study is to determine, using electrical resistivity tomography (ERT), the extent of the leachate plume from the OL and to monitor the efficiency of the liner of the NC. The entire Etueffont site was crisscrossed with 21 electrical profile lines which were traced in summer between 2009 and 2011 during a period of dry weather. This investigation allowed visualization of the flow and saturation phenomena within the waste without destructive on-site intervention, and also of leachate infiltration into the substratum. The anomalies of low resistivity extending beneath the base of the OL represent a leachate plume that migrates within the substratum. As the water table ceiling is found at nearly the same level as the base of the waste, leachate infiltration is a source of groundwater pollution. A rising gradient in resistivity values is observed at depth indicating progressive vertical dilution in leachate mineralization. Pollution plume extension is limited both at depth and laterally as it is no longer visible a few dozen meters from the storage zone.

Lire la suite

[hal-01388365] Structuring factors of the spatio-temporal variability of macrozoobenthos assemblages in a southern Mediterranean lagoon: How useful for bioindication is a multi-biotic indices approach?

27 octobre 2016

The authors investigated the impact of the extension of the El Kantra Channel on the composition and structure of macrobenthic assemblages in Boughrara Lagoon (Gulf of Gabes, Tunisia along with the use of 4 biotic indices (AMBI, BENTIX, M-AMBI and TUBI). Thirteen stations were sampled seasonally in 2012–2013. Forty-one species were found in 2012–2013 not recorded in 2009–2010, including 20 species of polychaetes belonging to the trophic groups of deposit-feeders and carnivores which are expected to increase in areas disturbed by organic pollution. During the survey, we recorded a high fish mortality, essentially caused by the development of harmful algal blooms (HAB) which increased organic matter deposition, thus inducing polychaete development. This seems to weaken the bio-indicating power of biotic indices used here which, paradoxically, classified all sampled stations at a high ecological status. A review of these indices and their applicability to all marine environments is recommended.

Lire la suite

[tel-01386786] Mémoire des lacs et mémoire des sociétés du Moyen Âge à nos jours : approche palynologique et historique de la moyenne montagne jurassienne et alpine (lac de Remoray, Doubs ; glissement de Mont Granier, Savoie)

25 octobre 2016

L’objectif principal de cette thèse a été d’établir une histoire précise des interactions sociétés-environnement durant le dernier millénaire dans deux zones de moyenne montagne, territoires particulièrement sensibles aux aléas naturels ainsi qu’aux évènements politiques, économiques et sociaux à travers un jeu de données multiples issues de différentes disciplines. L’étude de deux séquences sédimentaires lacustres de sites jurassien et alpin, grâce à l’outil palynologique - grains de pollen, spores et microfossiles non-polliniques -, particulièrement développé ici avec la haute-résolution, croisé avec l’étude des données historiques et archivistiques nous a permis, en plus de fournir un corpus complémentaire, de tester une approche comparative (données polliniques vs données cadastrales). Au lac de Remoray (Doubs, massif jurassien, 850 m d’altitude), l’étude a précisé le schéma du processus d’occupation de cette partie de la haute vallée du Doubs. Les données du haut Moyen Âge illustrent une fois de plus que l’idée qu’un désert forestier précédant l’arrivée des moines défricheurs est à nuancer. L’installation des communautés religieuses durant les XIème-XIIIème siècles, et l’influence des pouvoirs seigneuriaux sur cette zone stratégique, semblent toutefois l’étape clef dans la mise en place d’un peuplement durable. Les activités économiques se diversifient et prennent leur essor durant les siècles suivants bien que certaines périodes soient marquées de crises socio-politiques et traversées par les effets, plus ou moins ressentis, du Petit Âge Glaciaire. Il faudra attendre la transition XIXème-XXème siècle pour que les paysages sylvo-pastoraux que nous connaissons actuellement se mettent en place. Situé un peu plus au sud (Savoie, massif de la Chartreuse), notre second site d’étude trouve son origine dans ce qui donne à la montagne une autre identité : les risques naturels. Le site est le témoignage d’une zone dévastée en 1248 de notre ère par un immense glissement de terrain suite à la chute d’une partie du Mont Granier (1933 m d’altitude). Cet évènement, privant une partie de la vallée de cinq paroisses et d’un millier d’habitants, a engendré rapidement un nouveau territoire, aussi bien topographique, végétal que socio-économique. L’observation particulière des sédiments du lac Saint-André formé post-éboulement a offert l’occasion de suivre pas à pas cette reconquête végétale et humaine, appuyé par les approches géologiques, géographiques, archéologiques et historiques qui animent la recherche de façon récurrente. Les résultats obtenus témoignent d’une période de recolonisation végétale suivie d’une reconquête agro-pastorale relativement rapide, avec comme particularité la mise en place d’un territoire viticole. L’enregistrement sédimentaire particulier de ce lac a permis de suivre, en plus des indices d’une agriculture vivrière variée jusqu’au début du XXème siècle, le témoignage pollinique particulier de la vigne qui deviendra petit à petit une monoculture.

Lire la suite

[hal-01386113] Enhancement of breathing simulation using individual lobe segmentation

23 octobre 2016

To tackle thorax movement from CT images, we have developed a platform to simulate a customized breathing cycle, where the pulmonary movement has been considered only at the rough border of the whole lung by artificial neural networks (ANN). The goal of this work is to include additional information of the lung lobe. Thus, more ANN will be used and future simulation will be able to take into consideration the impact of tumor on lobe movement. We present a new automatic segmentation algorithm that enables the extraction of lobar contour data using sliding mask and direction estimation. These improvements enhance the overall system performance in which higher precision and more accurate treatments can be expected.

Lire la suite

[hal-01385534] Artificial Intelligence-Virtual Trainer: An educative system based on artificial intelligence and designed to produce varied and consistent training lessons

22 octobre 2016

AI-Virtual Trainer is an educative system using Artificial Intelligence to propose varied lessons to trainers. The agents of this multi-agent system apply case-based reasoning to build solutions by analogy. However, as required by the field, Artificial Intelligence-Virtual Trainer never proposes the same lesson twice, whereas the same objective may be set many times consecutively. The adaptation process of Artificial Intelligence-Virtual Trainer delivers an ordered set of exercises adapted to the objectives and sub-objectives chosen by trainers. This process has been enriched by including the notion of distance between exercises: the proposed tasks are not only appropriate but are hierarchically ordered. With this new version of the system, students are guided towards their objectives via an underlying theme. Finally, the agents responsible for the different parts of lessons collaborate with each other according to a dedicated protocol and decision-making policy since no exercise must appear more than once in the same lesson. The results prove that Artificial Intelligence-Virtual Trainer, however perfectible, meets the requirements of this field.

Lire la suite

[hal-01363732] Ecohealth and the GDRI EHEDE. What’s up ?

21 octobre 2016

The integration of eco-epidemiology in the concept of one-health, the success achieved by systems approach in other science areas (e.g. rodent pest control, conservation biology, etc.) and the fact that disease transmission is increasingly thought to be the result of the (socio-eco) systemic integration of links between the health of all species and that of their environment, the difficult definition of "health" as a general concept, leave open a very fertile field of research. This field of research and application is being popularized in the term "Ecohealth". A basic tenet is that health and well-being cannot be sustained in a resource depleted, polluted and socially unstable planet. This is why Ecohealth scholars and practitioners engage in integrated systems approach to health that sustain ecosystem health services, foster social stability and promote the peaceful interdependence, coexistence and evolution of humans, animals, plants and their environments (see https://ecohealth.net). To do so, it is essential to develop parallel paths, bridges and sustainable long-term interactions, between disciplines that can contribute to these studies. Created in 2013, labeled by the CNRS, this is typically the goal of the GDRI EHEDE. Here we briefly introduce the main research issues of the GDRI EHEDE, and how different lab share experience for a better understanding of environmental issues linked to human, animal and ecosystem health: • Ecology of Cestode transmission in Asia, Europe and North America. The life-cycle of those metazoan parasites ranges from merely sylvatic to merely domestic and offers unique opportunities to understand, in a systems approach, how anthropogenic human disturbance of ecosystems leads to transmission re-enforcement, sustained stability or to extinction in various conditions. • Wildlife ecology and ecosystem health. Here we focus on (1) wildlife human conflicts such as those triggered by small mammal population surges (potentially resulting in increased parasite transmission) as a consequence of landscape and agricultural practice alterations, (2) conservation of the black and white snub-nosed monkey in a context of global warming and increasing agricultural encroachment in high altitude forests (3) management of increasing populations of wild Asian elephants in a mosaic of forest and intensive agriculture. • Permanent workshop on adaptive monitoring, data management and modelling. Here we share experience in long term multi-disciplinary study design and adaptive monitoring in the field of ecosystem health and environmental disease ecology. Moreover, the GDRI EHEDE focusing on integrated systems approaches to health and their practical applications has a special concern about spatially explicit and multiscale modelling.

Lire la suite

[insu-01384716] Effects of experimental climate warming on C sink function in a temperate peatland

21 octobre 2016

Global warming induces complex interactions which could have a positive or a negative feedback on C storage in soils. Peatlands have stored one-third of global C stock of soils because of low rates of plant residue decomposition due to oxygen limitation resulting from flooding which inhibits microbial activities. Given the multiple possible responses of peatlands to global warming, it is presently impossible to predict their future contribution to the global C cycle. Several approaches have attempted to assess the effect of warming on peatlands: mesocosms, latitudinal transects, and in situ field experimental warming. Most of these studies only assessed the warming impact on vegetation and surface gas emissions, and so far, no study to date has addressed the entire range of biodiversity, community structure and ecosystem function responses to increased temperature, particularly in temperate peatlands. Within the PEATWARM project (ANR-07-VUL-010), we investigated the response of a Sphagnum peatland in the Jura Mountains (France) to climate change using an experimental system (Open Top Chambers – OTC’s) to simulate in situ an increase in average temperature. We examined the effects of temperature increase along a narrow fen-bog gradient on the vegetation, above- and belowground gas fluxes (CO2 and CH4), microbial diversity and activity in Sphagnum mosses and in peat, CNS interactions between macro- and microorganisms in the peat biota, and the dynamics of labile and recalcitrant peat organic matter. We showed that warming modifies the C and nutrient cycling of the peatland via changes in above- and belowground interactions. Furthermore, the contrasted responses to warming between the fen and the bog sites suggest that the spatial variability of moisture and hydrochemistry is critical for understanding the impact of global warming on the fate of organic matter and the C cycle in peatlands.

Lire la suite

[insu-01384227] Fossiliferous Holocene tufa of Mende (Lozère, southern France): implication for the Atlantic vegetation of the Causses Basin

19 octobre 2016

Tufas bearing plant macroremains are uncommon in the Causses Basin (southern France). Here, we report a new fossiliferous tufa deposits at Mende, in Lozère. This palaeontological site is the first Quaternary tufa from the northern part of the Causses Basin that yields such an abundance of plant macroremains. The radiocarbon dating shows that these Holocene deposits are related to the Atlantic period. Geomorphology and mineralogy show that the plant-bearing deposit is a calcareous tufa only composed by calcite, deposited near to an outlet of cool water, linked to the karstic hydrological system of the Causse de Mende. The flora exposed in this article is dominated by angiosperms. Leaves and reproductive structures were assigned to Acer platanoides, Corylus sp., Hedera sp., Salix cf. cinerea, and Tilia cordata. This new palaeobotanical data complements our scarcely knowledge of the Atlantic floras from the Causses Basin. During the Atlantic period, and in the northern part of the basin, whereas Pinus-dominated forests and oak groves were probably well-developed, valleys were locally inhabited by diversified wet angiosperm-dominated forests.

Lire la suite

[hal-01381786] Negative impact of urban habitat on immunity in the great tit Parus major.

14 octobre 2016

Urban habitats are described as having an overall negative influence on many fitness-related traits in several bird species, but a vital function such as immunity remains poorly studied. The immune response is strongly linked to individual condition, which partly depends on resource availability and the parasitic context that often differ between urban and natural habitats. A difference between the immunity of populations dwelling in urban areas and populations from more natural habitats can, therefore, be hypothesized. We conducted a 2-year experimental study on great tits (Parus major) in urban and forest areas. We stimulated the constitutive immunity of nestlings and assessed both the inflammatory response by measuring the plasma levels of haptoglobin, an inflammatory marker, and its activation cost through the loss of body mass. In addition, we checked the nestlings for ectoparasites and assessed haemosporidian prevalence in adults. Nestlings from urban sites produced relatively less haptoglobin and lost more body mass than those from forest sites, which suggests that the activation of constitutive immunity is more costly for birds living in urban sites than for those living in the forest. We detected no ectoparasite in birds in both habitats. However, urban adults showed lower haemosporidian prevalence than forest ones, suggesting a reduced exposure to these parasites and their vectors in towns. Overall, our study provides evidence for an immune difference between urban and forest populations. Because immunity is crucial for organism fitness, it is of prime interest to identify causes and processes at the origin of this difference.

Lire la suite

[hal-01380013] Determinism, Probability, and Imprecision in Decision Making

13 octobre 2016

This chapter looks into the decision to move house and the way in which the decision can be formalized by integrating the reflections from the previous chapters. The fact is that the decision-making process is seldom considered in the context of mathematical modelling of residential mobility. The modelling approaches set out in chapter 9 rest essentially on the concept of preferences and investigate the way in which individuals set about classifying criteria or alternatives with respect to residential choice.

Lire la suite

[hal-01380008] Preferences, Utility, Choice, and Attractiveness

13 octobre 2016

The purpose of this chapter is to specify what is meant by preferences, utility, choice, and attractiveness in the context of daily and residential mobility. These notions will be addressed from the angles of economics, geography, and psychology. We are interested in the process of choice leading to a decision and action with spatial consequences, primarily in terms of residential mobility even if factors pertaining to local daily mobility such as modal choice and route choice are evoked.

Lire la suite

[hal-01368336] Asymptomatic subjects with airway obstruction have significant impairment at exercise.

11 octobre 2016

The relevance of screening for airway obstruction in subjects not complaining of COPD symptoms may depend on the definition of airway obstruction. Response to exercise in asymptomatic subjects with persistent airway obstruction as defined by a postbronchodilator FEV1/FVC <5th centile lower limit of normal (LLN) remains unknown. Dyspnoea (Borg scale), exercise tolerance and ventilatory constraints on tidal volume expansion were assessed in 20 consecutive asymptomatic subjects with persistent mild airway obstruction detected by screening (postbronchodilator FEV1/FVC z-score: -2.14±0.29; FEV1 z-score: -1.02±0.64) undergoing incremental cycle cardiopulmonary exercise testing, compared with 20 healthy controls with normal spirometry matched for age, sex, body mass index and smoking history (FEV1/FVC z-score: -0.13±0.57; FEV1 z-score: 0.32±0.67) and with 20 symptomatic patients with COPD matched for the same characteristics (FEV1/FVC z-score: -2.36±0.51; FEV1 z-score: -1.02±0.48). Asymptomatic subjects with airway obstruction had higher dyspnoea ratings than controls during incremental exercise. Asymptomatic subjects with airway obstruction had also peak oxygen consumption and peak power output that were lower than controls, and similar to those observed in patients with COPD. Although less frequent than in COPD, dynamic hyperinflation was more frequent in asymptomatic subjects with airway obstruction than in controls (85%, 50% and 10%, respectively; p=0.01 in asymptomatic subjects vs controls and p=0.04 vs COPD). Although they did not present with chronic activity-related dyspnoea, subjects with a postbronchodilator FEV1/FVC<LLN as detected by screening had poorer exercise tolerance than healthy controls on exertion, and a significant proportion of them had dynamic hyperinflation. These subjects may, therefore, deserve further attention and may warrant regular follow-up.

Lire la suite

[hal-01367899] Habitat fragmentation and conservation of the Black and White Snub-nosed Monkey in Yunnan

11 octobre 2016

Understanding the drivers of habitat distribution patterns and assessing habitat connectivity are crucial for conservation. Habitat fragmentation is considered a major cause of biodiversity loss. It results in interruption of network between habitat patches and subsequent difficulty for gene flow between populations. Maintenance of landscape connectivity can promote populations move between habitat patches, which is essential to biological dispersal and gene flow in mosaic landscapes. In Yunnan, agriculture encroachment upon high altitude forest is one of the major threats to black and white snub-nosed monkey (Rhinopithecus bieti) habitats. In this study, we used maximum entropy distribution modeling (MaxEnt) to identify the climatic and topographic factors driving the distribution of the habitat type of the snub-nosed monkey. We also analyzed potential habitat connectivity between the groups reported in Yunnan, using genetic, least-cost path and Euclidean distance. We show that genetic distance is better explained by human disturbance and land-cover least-cost paths than by Euclidian distance. Furthermore, we used graph theory and least-cost distance to model the ecological network of the Yunnan snub-nosed monkey and to evaluate the connectivity improvement provided by potential measures of reforestation of agricultural lands. This approach was also used to assess the impact of highway development (including tunnels deviating traffic from the mountain roads) on the network connectivity. We show that potential habitat area will be reduced by 15% in total but increases mainly in the north of the distribution range at high altitude (due to tunnels) and decreases at lower altitude (due to habitat fragmentation). Other scenarios were also explored: on the landscape scale, the scenario consisting to reforest with optimal habitat for monkeys provides the biggest increase in connectivity, of course. On patch scale, a patch addition algorithm was applied on 1482 cropland patches to identify the 10 that most increase connectivity at different threshold of (hypothetical) dispersal distances. Graph methods can help modeling connectivity on different scales for species whose habitats are fragmented and thus help planning habitat restoration and conservation measures.

Lire la suite

[hal-01378439] Monastère Saint-Pierre d’Osor (Croatie, île de Cres).

11 octobre 2016

La campagne de fouille 2015 de la Mission franco-croate Saint-Pierre d’Osor a porté sur l’achèvement de la fouille de l’église réduite engagée l’année précédente. L’église réduite du XVe-XVIe siècle correspond à une partie de la nef centrale et du bas-côté nord de l’église du XIe siècle dont elle conserve le mur gouttereau nord. Ce mur a fait l’objet d’une étude du bâti dès la première année de la mission en 2006, qui a permis d’établir le phasage complexe des élévations et de constater la présence d’une phase antérieure au XIe siècle au niveau de l’annexe nord (sacrisitie-memoria) Une première tranchée de sondage avait également été ouverte en 2006, révélant les vestiges du mur-stylobate nord de l’église du XIe siècle. Le sondage avait alors démontré que l’espace intérieur de l’actuelle église Saint-Pierre – qui correspond à l’église réduite – avait été fortement perturbé par des sépultures du bas Moyen Âge et de l’époque moderne. Les sols les plus récents ont été détruits par la mise en culture de la surface de l’église à l’époque contemporaine.

Lire la suite

[hal-01378616] Mercury uptake into poplar leaves

11 octobre 2016

Tailings dumps require mercury stabilization to prevent air pollution by evaporated mercury, which can be achieved through plant covers. Plants are considered a net sink for atmospheric Hg via incorporation into leaf tissues. However, most studies related to Hg uptake by plants have considered plants exposed to only atmospheric Hg, whereas in the case of tailings dumps, plants are potentially exposed to both soil and atmospheric Hg. The goal of this work is to evaluate the relative contributions of root and atmospheric pathways by growing poplar (Populus trichocarpa X Populus maximowiczii/var Skado) cuttings on either control or polluted substrates and under either natural or controlled exposure conditions. We showed that foliar Hg concentrations significantly increased with age, reaching 120 ng g(-1) dry mass when poplars were exposed to Hg-contaminated substrate under natural exposure. Remarkably, we did not observe significantly different Hg concentrations in poplar leaves grown on either the control or polluted substrates when cultivated together in growth chambers. Our set of data prompted us to conclude that Hg entry into poplar leaves is exclusively through an atmospheric pathway. Our results are discussed in line with existing literature.

Lire la suite

[hal-01376775] La forme des villes françaises est-elle déterminée par les morphologies bâties et non bâties qui les environnent ? Éléments de réponse apportés par des analyses multifractales

8 octobre 2016

Des chercheurs en géographie ont montré, depuis les années 90, que les villes contemporaines partagent les caractéristiques morphologiques de certains objets fractals : les bordures urbaines sont très indentées à travers les échelles ; dans chaque ville, le nombre d’agrégats bâti et leur taille suivent une loi de puissance tandis que le nombre d’espaces non bâtis est relié à leur taille selon une autre loi de puissance (Batty & Longley, 1994 ; Frankhauser, 1994). Les dimensions fractales permettent de caractériser au moyen de mesures quantitatives les formes urbaines et ainsi de comparer aussi bien des villes entre elles que des quartiers d’une ville. Nous proposons ici d’explorer, à l’aide d’analyses multifractales, à quel point l’évolution des formes urbaines au cours du temps est déterminée par les formes bâties et non bâties qui les entourent. En effet, la croissance urbaine procède par intégration progressive d’espaces périphériques à la ville. Pour autant, ceci n’implique pas nécessairement la disparition des caractéristiques morphologiques des espaces qui ont été intégrés. Sur cette base, l’hypothèse que nous cherchons à vérifier est que les formes actuelles d’occupation du sol autour de chaque ville permettent d’expliquer la différenciation morphologique des villes entre elles. L’objectif est de mieux comprendre les relations entre les villes et leur environnement. Pour ce faire, nous proposons de mettre en oeuvre des techniques de traitement du signal pour analyser les caractéristiques multifractales du bâti mais aussi de l’ensemble des objets occupant l’espace. Nous utilisons différentes techniques développées pour décrire l’aspect géométrique des d’objets fractals mais aussi les fluctuations présentent au sein de ces objets (Arneodo et al.2000, Pustelnik et al., 2014, Wendt et al., 2009). D’une part, nous proposons de travailler sur des images binaires de bâti. Ces images sont extraites de la BD TOPO de l’IGN, qui fournit sous une forme vectorielle l’emplacement et la forme en 2D de l’ensemble des bâtiments du territoire de France métropolitaine avec une précision métrique. Afin d’identifier différents types de textures bâties à une résolution spatiale fine, nous appliquons une méthode d’analyse que nous avons conçue spécifiquement à cet effet, la Geographically Weighted Fractal Analysis. D’autre part, nous proposons de procéder à une analyse multifractale d’orthophotographies et de faire une segmentation des paysages en fonction de leurs caractéristiques multifractales. Pour cela, nous utilisons la méthode des coefficients Leaders peu coûteuse en temps machine et dont les performances sont bien connues de manière théorique et pratique (Wendt et al., 2009). Les données utilisées sont des ortho-images couleurs recouvrant toute la France, d’une résolution allant de 0.5m à 5m. Ces images sont issues de la source BD ORTHO de l’IGN. Pour chaque département, l’IGN propose des orthophotographies actualisées selon un cycle quinquennal avant 2014 et triennal ensuite. Ainsi la France est entièrement couverte par des ortho-images dont les années de prise de vue changent d’un département à l’autre avec un maximum de 5 ans entre deux départements. Dans un troisième temps, ces différentes typologies de textures bâties et d’occupation du sol sont comparées entre elles et comparées aux délimitations morphologiques des agglomérations urbaines identifiées au moyen de la méthodologie fractale proposée par Tannier et al. (2011). Avec cette méthode, qui considère le bâti à résolution spatiale fine, la frontière urbain-rural est choisie pour maximiser la différence morphologique entre l’intérieur et l’extérieur de la ville, sans fixer a priori de seuil de distance inter-bâtiments qui distinguerait une configuration du bâti urbaine d’une configuration rurale. Ce travail est réalisé dans le cadre du projet Lecture multifractale de la forme des villes en relation avec la forme des espaces qui les entourent, dirigé par Stéphane Roux et financé par l’Institut des systèmes complexes rhône-alpin IXXI (2015-2016).

Lire la suite

[insu-01375648] Erosion under climate and human pressures: An alpine lake sediment perspective

5 octobre 2016

We review the scientific efforts over the last decades to reconstruct erosion from continuous alpine lake sediment records. We focused both on methodological issues, showing the growing importance of non-destructive high resolution approaches (XRF core-scanner) as well as progresses in the understanding of processes leading to the creation of an “erosion signal” in lakes. We distinguish “continuous records” from “event-records”. Both provide complementary information but need to be studied with different approaches. Continuous regionally-relevant records proved to be particularly pertinent to document regional erosion patterns throughout the Holocene, in particular applying the source to sink approach. Event-based approaches demonstrated and took advantage of the strong non-linearity of sediment transport in high altitude catchment areas. This led to flood frequency and intensity reconstructions, highlighting the influence of climate change upon flood dynamics in the mountain. The combination of different record types, both in terms of location (high vs. low elevation), sedimentology (high vs. low terrigenous contribution) and significance (local vs. regional) is one of the main outputs of this paper. It allows the establishment of comprehensive histories of NW French Alps erosion, but also and consequently, soil dynamics and hydrological patterns throughout the Holocene. We also discuss the influence of glacier dynamics, one of the major agents of erosion in the Alps. A major feature is the growing human influence upon erosion at a local scale since at least the middle of the Bronze Age (3500 cal. BP). However and according to the regional record from Lake Bourget, only few periods of rising erosion at local scales generated a regional record that can be discriminated from wetter climatic periods. Among them, the period between 200 BCE and 400 AD appeared to be marked by a generalised rise in human-triggered erosion at local scales in the northern French Alps. This review highlights the importance of modern high-resolution and interdisciplinary studies of lake sediments, in order to better understand the complex relationships between humans, climate and the Earth system in general. We strongly argue that regional integration of data is now required to move a step further. Such an integration is easier with cost- and time-effective methods as well as after a better definition of approaches and their limits. This should lead to a stronger collaboration between paleo-data producers and modellers in the near future.

Lire la suite

[hal-01370183] Carbon emission along a eutrophication gradient in temperate riverine wetlands: effect of primary productivity and plant community composition

28 septembre 2016

1. Eutrophication increases primary productivity and favours the predominance of floating vegetation in wetlands. Carbon (C) fluxes in wetlands are strongly driven by primary productivity and can differ by vegetation type. However, to the best of our knowledge, the role of eutrophication in C fluxes has rarely been assessed. 2. Consequently, we aimed to measure the seasonal variation in carbon dioxide (CO2) and methane (CH4) fluxes at six aquatic sites in four temperate wetlands, ranging along a gradient of sediment total phosphorus content, and determine whether C fluxes correlate with above-ground net primary productivity (ANPP) and plant community composition along this eutrophication gradient. 3. Daytime CO2 emissions were significantly and negatively correlated with wetland net primary productivity as a result of the greater C fixation by photosynthesis during the peak of production. Conversely, CH4 emissions were significantly and positively correlated with wetland ANPP, possibly due to higher litter production and anaerobic decomposition. 4. The highest CH4 emissions were observed above floating vegetation, which favoured hypoxic conditions in the water column. CH4 emissions including ebullition were higher above macroalgal belts than above vascular plants with floating leaves. CH4 emissions without ebullition (i.e. resulting from plant transport and diffusion) better correlated with the abundance of macroalgae than with the abundance of vascular plants with floating leaves. 5. Our results suggest that eutrophication may greatly modify CO2 and CH4 emissions from wetlands through changes in vegetation type and productivity.

Lire la suite

[hal-01371832] Agriculture et campagnols : quels impacts sur les écosystèmes franguignons ?

27 septembre 2016

Les pullulations de campagnol terrestre et de campagnol des champs, deux espèces de rongeurs vivant principalement dans les prairies, sont périodiquement d’une actualité préoccupante pour les exploitations agricoles. Les deux espèces sont les proies principales d’un riche cortège de prédateurs qui contribue à la biodiversité régionale et à leur régulation, mais dont les reports de prédation peuvent impacter localement des espèces d’intérêt cynégétique ou patrimonial. Ces systèmes complexes modulent également la transmission d’un certain nombre de zoonoses intéressant la santé publique et vétérinaire. Ils sont étudiés depuis maintenant une trentaine d’année dans la Zone atelier Arc jurassien (http://zaaj.univ-fcomte.fr). Ils conduisent à des jeux d’acteurs subtils par lesquels des points de convergence doivent être trouvés entre des services écosystémiques qui peuvent apparaître contradictoires a priori : protection des cultures et qualité des produits alimentaires, protection des espèces patrimoniales, production cynégétique, santé, voire tourisme. Ces questions ne concernent plus seulement les zones d’altitude du massif du Jura, mais aussi le Morvan et les zones de grande culture de basse altitude où techniques culturales simplifiées et semis direct se popularisent. L’objectif de cet exposé est de montrer quels sont les principaux processus en cause et leur dynamique à long terme, qui, de plusieurs manières, portent conséquences sur la faune et la flore régionale des espaces dits « naturels » bourguicomtois, dont la quasi-totalité sont en fait anthropogènes, c’est-à-dire le résultat transitoire d’économies agricole et forestière adaptatives, dans un contexte biogéographique donné.

Lire la suite

[hal-01368326] Is the lesser horseshoe bat (Rhinolophus hipposideros) exposed to causes that may have contributed to its decline? A non-invasive approach

23 septembre 2016

While the lesser horseshoe bat (Rhinolophus hipposideros) was common in most western and Central Europe, this species endured a dramatic decline in the 1950s–1970s. The causes are thought to comprise the extensive spread of chemical pollutants affecting both bat and prey populations, changes in landscape composition and structure leading to population fragmentation or roost deterioration, and infectious diseases. While lesser horseshoe bat populations recently increased after nearly thirty years of decline in the Franche-Comté region (eastern France), it is unclear whether bats are currently confronted with causes that may have contributed to former demographic disturbances. Although stressors are generally studied separately, we simultaneously measured several variables directly or indirectly reflecting the supposed causes of bat decline: availability of woodland habitats around bat roosts, genetic differentiation amongst colonies, and exposure to chemical pollutants and to a protozoan parasite, Eimeria hessei. Twenty maternity colonies were sampled using a non-invasive approach based on droppings. Maternity roosts were located in buildings mainly surrounded by woodland and shrubland (48% of a 2500 m radius

Lire la suite

[hal-01368318] Fatal acute respiratory distress by Toxoplasma gondii in a toxoplasma seronegative liver transplant recipient.

20 septembre 2016

The risk of Toxoplasma gondii infection in solid organ transplant recipients is well known but mainly after heart transplantation. We discuss a case of acute respiratory distress caused by Toxoplasma gondii on Day 32 after liver transplantation. The reported case, which is extremely rare, emphasizes how direct examination and Quantitative Polymerase Chain Reaction (QPCR) in broncholaveolar lavage help to diagnose the infection. Given Trimethoprim/Sulfamethoxazole toxicity, systematic prescription of Toxoplasma gondii chemoprophylaxis is not commonly approved in liver transplantation.

Lire la suite

[hal-01368320] Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria.

20 septembre 2016

In Algeria, previous studies investigated genotypes of Echinococcus granulosus sensu lato in animals and identified E. granulosus sensu stricto (s.s.) genotypes G1 and G3 whereas Echinococcus canadensis genotype G6 was only reported from dromedary cysts. Molecular data on human cystic echinococcosis (CE) were limited. We implemented a large genotyping study of hydatid cysts from humans and livestock animals to specify CE's molecular epidemiology and the genetic diversity in Algeria. Fifty-four human CE cysts from patients predominantly admitted in surgical units from Mustapha Hospital, Algiers, and 16 cysts from livestock animals gathered in two geographically distinct slaughterhouses, Tiaret and Tamanrasset, were collected. Molecular characterization was performed using sequencing of two mitochondrial genes, cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit I (NDI). In humans, G1 of E. granulosus s.s. was the main genotype (90.7 %); four samples (7.4 %) were characterized as E. granulosus s.s. G3 and one cyst as E. canadensis G6 (1.8 %). This molecular confirmation of E. canadensis G6 human infection in Algeria was observed in a Tuareg female living in a desertic area in Tamanrasset. All cysts from sheep, cattle, and goat were identified as E. granulosus s.s. G1 and the two cysts originating from dromedary as E. canadensis G6. Twenty concatenated haplotypes (COI + NDI) were characterized. Among E. granulosus s.s., one haplotype (HL1) was highly predominant in both humans and animals cysts (71.6 %). This study revealed main occurrence of E. granulosus s.s. in humans and livestock animals, with description of a predominant shared haplotype corresponding to the main worldwide observed haplotype E.granulosus s.s. G1. E. canadensis G6 was limited to South Algeria, in dromedary as well as in human.

Lire la suite

[hal-01368319] Positive fungal quantitative PCR and Th17 cytokine detection in bronchoalveolar lavage fluids: Complementary biomarkers of hypersensitivity pneumonitis?

20 septembre 2016

Interstitial lung disease (ILD) is a large group of diseases, including hypersensitivity pneumonitis (HP), idiopathic pulmonary fibrosis (IPF) and sarcoidosis. In this study, we aimed to identify bronchoalveolar lavage fluid (BALF) biomarkers which could be contributive for HP diagnosis. We analyzed 39 BALF samples from 12 ILD patients with sarcoidosis, 11 with IPF and 16 with HP. We determined the levels of 10 cytokines and carried out quantitative PCR for 10 microorganisms involved in farm-associated or domestic forms of HP. IL-8, IL-6, TNFα, IL-17 and IL-23 levels were significantly higher in BALF samples from HP patients (p<0.05, one-way Kruskal-Wallis analysis). QPCR tests for Eurotium amstelodami and Wallemia sebi were positively significantly more frequently for HP patients (p<0.05, one-way Kruskal-Wallis). The biomarkers identified here can be detected in BALF, which could be routinely obtained as complementary analysis in ILD diagnosis.

Lire la suite

[hal-01368327] Hypersensitivity pneumonitis in a beautician.

20 septembre 2016

A radioimmunoassay for guanosine-5'-diphosphate-3'-diphosphate (ppGpp) and adenosine-5'-triphosphate-3'-diphosphate (pppApp) has been developed. The assay method is based on competition of an unlabeled highly phosphorylated nucleotide with 3H-labeled highly phosphorylated nucleotide for binding sites on a specific antibody. Antibodies to ppGpp and pppApp were obtained by immunizing rabbits with the antigen prepared by conjugating ppGpp with human serum albumin using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide, and with the antigen prepared by conjugating 8-(6-aminohexyl)amino-adenosine-5'-triphosphate-3'-diphosphate with human serum albumin using glutaraldehyde, respectively. Antibody-bound 3H-labeled highly phosphorylated nucleotides were separated from the free 3H-labeled highly phosphorylated nucleotides by selective adsorption on dextran-coated charcoal. Displacement plots were linear over a concentration range of 5-1,000 pmol/assay tube in a log-probit percentage plot. Application of this method to biological systems offers improved accuracy and convenience compared with the previous 32PO4-labeling technique.

Lire la suite

[hal-01368330] Enhanced T helper 1 and 2 cytokine responses at birth associate with lower risk of middle ear infections in infancy.

20 septembre 2016

Respiratory tract infectious symptoms and illnesses are frequent during early childhood, but their risk factors, including the effect of early immune regulation, are less known. Aim of the study was to analyse whether stimulated cord blood cytokine production is associated with the frequency of respiratory tract infectious symptoms or infections during the first year of life. The study population consisted of children of mothers from farm or non-farm rural environment from Austria, Finland, Germany and Switzerland who participated in a prospective birth cohort study (PASTURE: Protection against Allergy - study in Rural Environments) (N=550). Cord blood samples were stimulated with the combination of phorbol ester and ionomycin (P/I) for 24 hours and the production of IL-5, IL-10, TNF-α and IFN-γ was determined by using ELISA. Information about infectious morbidity was collected using weekly diaries. P/I stimulated production of IL-5 (adjusted risk ratio (aRR) for ≤median production, 0.37; 95% Confidence Interval (CI), 0.25-0.55, aRR for >median production, 0.41; 95%CI, 0.27-0.61 vs. production <detection limit) and IFN-γ (aRR for ≤median production, 0.62; 95%CI, 0.40-0.95, aRR for >median production, 0.39; 95% CI, 0.25-0.62 vs. production <detection limit) in cord blood were associated with lower number of weeks with reported middle ear infection. There was a tendency towards positive association with P/I stimulated TNF-α production and middle ear infections. Our results suggest that increased Th2- and Th1-associated cytokine responses at birth may provide protection from later middle ear infections. This article is protected by copyright. All rights reserved.

Lire la suite

[hal-01368338] IL-33 polymorphisms are associated with increased risk of hay fever and reduced regulatory T cells in a birth cohort.

20 septembre 2016

IL-33 polymorphisms influence the susceptibility to asthma. IL-33 indirectly induces Th2-immune responses via dendritic cell activation, being important for development of atopic diseases. Furthermore, IL-33 upregulates regulatory T cells (Tregs), which are critical for healthy immune homeostasis. This study investigates associations between IL-33 polymorphisms during the development of childhood atopic diseases and underlying mechanisms including immune regulation of Tregs. Genotyping of IL-33-polymorphisms (rs928413, rs1342326) was performed by MALDI-TOF-MS in 880 of 1133 PASTURE/EFRAIM children. In 4.5-year-old German PASTURE/EFRAIM children (n = 99), CD4(+) CD25(high) FOXP3(+) Tregs were assessed by flow cytometry following 24-h incubation of PBMCs with PMA/ionomycin, LPS or without stimuli (U). SOCS3, IL1RL1, TLR4 mRNA expression and sST2 protein levels ex vivo were measured in PASTURE/EFRAIM children by real-time PCR or ELISA, respectively. Health outcomes (hay fever, asthma) were assessed by questionnaires at the age of 6 years. rs928413 and rs1342326 were positively associated with hay fever (OR = 1.77, 95%CI = 1.02-3.08; OR = 1.79, 95%CI = 1.04-3.11) and CD4(+) CD25(high) FOXP3(+) Tregs (%) decreased in minor allele homozygotes/heterozygotes compared to major allele homozygotes (p(U) = 0.004; p(LPS) = 0.005; p(U) = 0.001; p(LPS) = 0.012). SOCS3 mRNA expression increased in minor allele homozygotes and heterozygotes compared with major allele homozygotes for both IL-33-polymorphisms (p(rs928413) = 0.032, p(rs1342326) = 0.019) and negatively correlated to Tregs. IL-33-polymorphisms rs928413 and rs1342326 may account for an increased risk of hay fever with the age of 6 years. Lower Tregs and increased SOCS3 in combined heterozygotes and minor allele homozygotes may be relevant for hay fever development, pointing towards dysbalanced immune regulation and insufficient control of allergic inflammation.

Lire la suite

[hal-01367363] Non-invasive genetic tools to study wildlife populations

19 septembre 2016

The past three decades have witnessed the development of molecular tools, resulting in the successful integration of genetic methods into studies of wildlife populations. Genomic DNA can be obtained from a variety of sources including blood or tissues, but also sources which do not necessarily depend on handling or observing animals, like feces, urine, hair, or shed skin. These non-invasive samples can then be used to identify individuals, gender, and species. Genetic data can also be used to assess mating systems, hybridization, gene flow, and effective population size. Conservation biology can benefit of genetic data to define management units and to provide insights into demographic patterns. We describe some applications of genetic data in the study of European bat populations, based exclusively on non-invasive samplings. The populations of many European bat species experienced a dramatic decline in the latter half of the twentieth century, and most of them are currently considered to be vulnerable or endangered species. Many aspects of bat ecology are still unknown, and genetic data provide a powerful tool, especially regarding difficulties to catch and/or observe individuals. Based on bat feces, we investigated population genetics, effective population size and parasite prevalence in the lesser horseshoe bat (Rhinolophus hipposideros). Combined with ecotoxicological data, results provided important insights on the current exposure of this bat species to several disruptors that may have contributed to its former decline. A similar sampling strategy was applied to study hybridization between two sibling cryptic bat species: the greater mouse-eared bat (Myotis myotis) and the lesser mouse-eared bat (M. blythii). These two species often form large mixed-species groups in maternity roosts, where visual counting is impossible because the two species are morphologically almost identical. Genotyping analysis and molecular sexing were used to highlight hybridization cases between the two bat species and to assess the composition of a mixed-species group. Non-invasive sampling and molecular methods were also used in archeological samples to separate DNA mixtures and identify species present at each stratum of guano cores collected in bat roosts. Finally, we present preliminary tests realized on the Yunnan snub-nosed monkey (Rhinopithecus bieti) feces samples collected in Yunnan (China). We discuss how genetic data could help future research on the ecology and conservation of the Yunnan snub-nosed monkey and other species.

Lire la suite

[hal-01367362] Coupling agent based with equation based models for studying explicitly spatial population dynamics

17 septembre 2016

Agent Based Modeling (ABM) is a spatially explicit oriented paradigm that models space as a heterogeneous environment (e.g. crop, grassland, forest patches), where individuals (e.g. predators, preys, etc.) move, all represented as “agents”. The latter are autonomous entities, which move on the virtual space and interact with each other and the environmental patches. During simulation, dynamics emerge and can be observed and quantified. Agent based modeling is versatile and keeps proximity with the real system: data such as Geographical Information System (GIS) could be easily included in the model; model architecture is close to the ecological expert knowledge; operational outputs can be tracked and explored for, e.g., decision making. Agent based modeling permits to produce large-scale models composed of several hundred thousand interacting agents. These models bring to light microscopic and spatial dynamics that could not be observed with Equation Based Model (EBM). Nevertheless, computational limits are often overflowed. This problem is frequent in ecology where giant populations (e.g. hundreds of thousand millions of individuals) are at stake. Here we propose to couple ABM to EBM in a multiscale model to overcome this limit and simulate the spreading of a montane water vole population in the Haute-Romanche valley (France). The colonization of an Alpine valley where the species was absent before was observed from 1998 to 2010 (Halliez et al. 2015) reaching peaks of 500-1000 voles/ha, and a total population estimated at more than 2,500,000 individuals. EBM allow quantifying the growth of such a large population but cannot take spatial heterogeneity (land use, soil, elevation) and individual vole dispersal into account. Vole are usually sedentary and establish themselves in the near vicinity (some 10 meters) where they are born, but sometimes, when juvenile individuals suffer of neighborhood stress, they move away on long distance (some hundred meters or kilometers). This specific behavior can be modeled using ABM. A grid was built from a GIS, altitude data imported and slopes computed. Each cell (30m X 30m) describes an age-structured population of voles, based on a logistic model. When the population exceeds a threshold, agents are created to model short distance and long distance individual dispersers. Each agent moves according to the topology within a distance range as long as they do not find a cell with a population below the threshold. There, the agent is aggregated in the population. Additionally, survival as a function of age in the population, of status (e.g. moving agent) and reproduction season length can be parametrized. The next step will be to simulate density dependent mortality (e.g. predators and diseases) in this system in order to explore the conditions by which travelling waves can occur.

Lire la suite

[hal-01367365] Methods in genetics to investigate E. multilocularis transmission patterns

17 septembre 2016

Echinococcus multilocularis is a common tapeworm in foxes and rodents in the northern hemisphere and the causal agent of Alveolar Echinococcosis (AE). Epidemiological discontinuities are known: highly endemic in China, in expansion in Europe and rarely described in North America. In this context, a part of the European project EchinoRisk aimed to focus on genetic diversity to explain the discrepancy amongst European foci. Moreover genetic analyses were performed to identify the parasite circulation amongst hosts in the environment on different spatial scales. A highly discriminant molecular marker was thus designed. It took ten years from the first description to the assessment of its discrimination power amongst E. multilocularis isolates from different geographical scales. The microsatellite EmsB was confirmed as a tandemly repeated sequence of about 250 bp present in about 40 copies in the parasite genome. Its original profile indicated high power of discrimination. First, regional E. multilocularis profiles were described by the analysis of EmsB in Europe, America and Asia. In Europe, the marker has permitted to distinguish a historical area surrounded by newly endemic areas. Moreover an Arctic origin was described for E. multilocularis recently discovered in Svalbard Island (Norway). In order to better understand its transmission pathway to human, a genotyping project on European AE has been started. The first results suggest a contamination in the close environment of the patient. In this context, an international EmsB database has been implemented in the EWET project (“EmsB Website for Echinococcus Typing”), comprising about 1200 genotyped E. multilocularis samples, to compare a new isolate to a reference collection. The next step after EmsB, will focus on large screening in the parasite genome. As regards to performances in Next Generation Sequencing technologies, whole-genome sequencing first based on EmsB profiles previously described have to be performed to highlight genes or groups of genes presenting variations and potentially could explain the different phenotypes or forms of pathogenicity encountered in intermediate hosts, among a European panel of samples tested. This panel can be also tested for phylogenetic studies in Europe to challenge EmsB.

Lire la suite

[hal-01367367] New approaches to description and modeling of trophic interactions: reliable allies to study trophically-transmitted parasites?

17 septembre 2016

Trophic interactions, eg predation and herbivory, are one of the main biotic interactions driving the composition and functioning of terrestrial and aquatic food webs as they sustain energy and matter flows among organisms. The relationship between a resource availability and its consumption rate by a predator or herbivore, the functional response, is complex since often non-linear in shape and likely to depend upon the availability of other resources. Trophic interactions also nest the transmission of a large variety of multi-hosts parasites (ie trophically-transmitted parasites, TTP) within food webs. Moreover, the capacity to acquire, develop and transmit a parasite, called competence, vary among host species. The use of mathematical approaches, such as mechanistic dynamic models, to explore the transmission dynamics of TTP have often ignore the complexity of functional response and the variation in host competence. However, a prerequisite for understanding and modeling the ecology of TTP is to identify hosts species that are involved in transmission, ie the consumption of which ensures the parasite to step from the larval to the adult stage. This translates into the simple question “who is eating whom?”. Traditional techniques for investigating feces or stomach content based on macro- or microscopic identification of food remains fail to achieve fine taxonomic resolution identification of ingested items. Recently, DNA-based techniques such as metabarcoding have arisen as a powerful approach for the simultaneous taxonomic identification of several food items in feces or stomach content with high taxonomic resolution. We built a “one predator-two prey” eco-epidemiological model using a system of ordinary differential equations which allows for complex predation patterns. Using parameters related to Echinococcus multilocularis transmission in wildlife in Eastern France, we analyzed to what extent variations in prey diversity, total density and competence to transmit the parasite impact the basic reproductive number R0, which is a measure of disease outbreak risk. In parallel, we developed a molecular metabarcoding approach to investigate the diet of dog and red fox in rural settings of Eastern France, Gansu and Kyrgyzstan where E. multilocularis is endemic. Preliminary results, advantages and limitations, as well as perspectives of these recent developments will be presented.

Lire la suite

[hal-01367643] Well GeHP detector calibration for environmental measurements using reference materials

17 septembre 2016

A well-type detector installed in the Modane underground Laboratory (LSM) can combine both low background and high detection efficiency and it is well suited for the analysis of small amounts of environmental samples. Reference materials such as IAEA-447 (moss-soil), IAEA-RG-Th1 and IAEA-RG-U1 were used for the detector calibration, owing to a chemical composition close to those of the environmental samples. Nevertheless , the matrix effects and the true coincidence summing effects must be corrected from the full energy peak efficiency (FEPE). The FEPE was performed for a wide range of energy by a semi-empirical method using Monte Carlo simulation (MCNP6), intended for environmental measurements such as lake sediments dating. In the well geometry, the true coincidence summing effects could be very important and correction factors have been computed in three different ways.

Lire la suite