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Chapot-Chartier M.-P.,French National Institute for Agricultural Research | Chapot-Chartier M.-P.,Agro ParisTech
Frontiers in Microbiology | Year: 2014

Lactic acid bacteria (LAB) are Gram positive bacteria widely used in the production of fermented food in particular cheese and yoghurts. Bacteriophage infections during fermentation processes have been for many years a major industrial concern and have stimulated numerous research efforts. Better understanding of the molecular mechanisms of bacteriophage interactions with their host bacteria is required for the development of efficient strategies to fight against infections. The bacterial cell wall plays key roles in these interactions. First, bacteriophages must adsorb at the bacterial surface through specific interactions with receptors that are cell wall components. At next step, phages must overcome the barrier constituted by cell wall peptidoglycan (PG) to inject DNA inside bacterial cell. Also at the end of the infection cycle, phages synthesize endolysins able to hydrolyze PG and lyse bacterial cells to release phage progeny. In the last decade, concomitant development of genomics and structural analysis of cell wall components allowed considerable advances in the knowledge of their structure and function in several model LAB. Here, we describe the present knowledge on the structure of the cell wall glycopolymers of the best characterized LAB emphasizing their structural variations and we present the available data regarding their role in bacteria-phage specific interactions at the different steps of the infection cycle. © 2014 Chapot-Chartier.

Renard P.,University of Neuchatel | Allard D.,French National Institute for Agricultural Research
Advances in Water Resources | Year: 2013

Understanding the role of connectivity for the characterization of heterogeneous porous aquifers or reservoirs is a very active and new field of research. In that framework, connectivity metrics are becoming important tools to describe a reservoir. In this paper, we provide a review of the various metrics that were proposed so far, and we classify them in four main groups. We define first the static connectivity metrics which depend only on the connectivity structure of the parameter fields (hydraulic conductivity or geological facies). By contrast, dynamic connectivity metrics are related to physical processes such as flow or transport. The dynamic metrics depend on the problem configuration and on the specific physics that is considered. Most dynamic connectivity metrics are directly expressed as a function of an upscaled physical parameter describing the overall behavior of the media. Another important distinction is that connectivity metrics can either be global or localized. The global metrics are not related to a specific location while the localized metrics relate to one or several specific points in the field. Using these metrics to characterize a given aquifer requires the possibility to measure dynamic connectivity metrics in the field, to relate them with static connectivity metrics, and to constrain models with those information. Some tools are already available for these different steps and reviewed here, but they are not yet routinely integrated in practical applications. This is why new steps should be added in hydrogeological studies to infer the connectivity structure and to better constrain the models. These steps must include specific field methodologies, interpretation techniques, and modeling tools to provide more realistic and more reliable forecasts in a broad range of applications. © 2011 Elsevier Ltd.

Peay K.G.,Stanford University | Baraloto C.,French National Institute for Agricultural Research | Fine P.V.A.,University of California at Berkeley
ISME Journal | Year: 2013

The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant-fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity. © 2013 International Society for Microbial Ecology.

Lobet G.,Catholic University of Louvain | Pages L.,French National Institute for Agricultural Research | Draye X.,Catholic University of Louvain
Plant Physiology | Year: 2011

We present in this paper a novel, semiautomated image-analysis software to streamline the quantitative analysis of root growth and architecture of complex root systems. The software combines a vectorial representation of root objects with a powerful tracing algorithm that accommodates a wide range of image sources and quality. The root system is treated as a collection of roots (possibly connected) that are individually represented as parsimonious sets of connected segments. Pixel coordinates and gray level are therefore turned into intuitive biological attributes such as segment diameter and orientation as well as distance to any other segment or topological position. As a consequence, user interaction and data analysis directly operate on biological entities (roots) and are not hampered by the spatially discrete, pixel-based nature of the original image. The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements. The use of the software is illustrated with a time-lapse analysis of cluster root formation in lupin (Lupinus albus) and an architectural analysis of the maize (Zea mays) root system. The software, SmartRoot, is an operating system-independent freeware based on ImageJ and relies on cross-platform standards for communication with data-analysis software. © 2011 American Society of Plant Biologists. All Rights Reserved.

Forrest M.J.,University of California at San Diego | Schlaepfer M.A.,New York University | Schlaepfer M.A.,French National Institute for Agricultural Research
PLoS ONE | Year: 2011

Dramatic declines and extinctions of amphibian populations throughout the world have been associated with chytridiomycosis, an infectious disease caused by the pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd). Previous studies indicated that Bd prevalence correlates with cooler temperatures in the field, and laboratory experiments have demonstrated that Bd ceases growth at temperatures above 28°C. Here we investigate how small-scale variations in water temperature correlate with Bd prevalence in the wild. We sampled 221 amphibians, including 201 lowland leopard frogs (Rana [Lithobates] yavapaiensis), from 12 sites in Arizona, USA, and tested them for Bd. Amphibians were encountered in microhabitats that exhibited a wide range of water temperatures (10-50°C), including several geothermal water sources. There was a strong inverse correlation between the water temperature in which lowland leopard frogs were captured and Bd prevalence, even after taking into account the influence of year, season, and host size. In locations where Bd was known to be present, the prevalence of Bd infections dropped from 75-100% in water <15°C, to less than 10% in water >30°C. A strong inverse correlation between Bd infection status and water temperature was also observed within sites. Our findings suggest that microhabitats where water temperatures exceed 30°C provide lowland leopard frogs with significant protection from Bd, which could have important implications for disease dynamics, as well as management applications. There must be quite a few things a hot bath won't cure, but I don't know many of them - Sylvia Plath, "The Bell Jar" (1963). © 2011 Forrest, Schlaepfer.

Choumert J.,French National Center for Scientific Research | Combes Motel P.,French National Center for Scientific Research | Dakpo H.K.,French National Institute for Agricultural Research
Ecological Economics | Year: 2013

Although widely studied, deforestation remains a common research topic. The relationship between economic development and deforestation is still in question. This paper presents a meta-analysis of Environmental Kuznets Curve (EKC) studies for deforestation. Using 69 studies, offering 547 estimations, we shed light on why EKC results differ. We investigate the incidence of choices made by authors (such as econometric strategy, measure of deforestation, geographical area, and presence of control variables) on the probability of finding an EKC. After a phase of work corroborating the EKC, we find a turning point after the year 2001. Building on our results, we conclude that the EKC story will not fade until theoretical alternatives are provided. © 2013 Elsevier B.V.

Reynaud A.,French National Institute for Agricultural Research
International Journal of Water Resources Development | Year: 2013

This paper reports an investigation of the impact of price policies (PP) and non-price policies (NPP) on residential water demand. Using a sample of US water utilities located in Wisconsin, residential water demand was estimated by taking into account the fact that some of the characteristics of local communities that determine PP and NPP choices may also influence residential water consumption levels. It is fi{ligature}rst shown that neglecting endogeneity of PP or NPP may lead to biased parameter estimates. Second, it is demonstrated that the policy mix (PP or NPP) may be as important as the level of prices for determining water consumption. Lastly, evidence is provided that dissemination efforts made by local communities to promote NPP drive the effectiveness of those policies. © 2013 Copyright Taylor and Francis Group, LLC.

Remy J.-J.,French National Institute for Agricultural Research
Current Biology | Year: 2010

Sensory imprinting produces life-long attachment to environmental features experienced during a critical period of early development. Imprinting of this kind is highly conserved in evolution and is an important form of adaptive behavioral plasticity [1]. The nematode Caenorhabditis elegans undergoes such adaptation to new environments through imprinting: attractive odorants, when present during the first larval stage, produce life-long olfactory imprints that enhance attraction and egg-laying rates in the adults [2]. Here I report evidence that the olfactory imprint can be transmitted to the next generation. If the imprint is generated successively over more than four generations, it is not just transmitted through one further generation, but rather, it is stably inherited through many following generations. While the transient nature of the inheritance suggests the existence of resetting mechanisms, stable trans-generational inheritance of the kind reported here raises the possibility that a behavioral alteration produced by an environmental change might be genetically assimilated after a limited number of generations. © 2010 Elsevier Ltd. All rights reserved.

Aykut S.C.,French National Institute for Agricultural Research
Wiley Interdisciplinary Reviews: Climate Change | Year: 2016

Attention in the literature on global climate politics has recently turned from a focus on intergovernmental negotiations to conceptualizing climate governance 'beyond' or 'outside' the UN regime. However, this literature differs on three key aspects: the underlying research paradigms, what is identified as the heart of the problem, and proposed solutions. One group of scholars calls for an attention shift from the 'tip of the iceberg' of climate governance to its much larger 'hidden parts,' conceptualized through notions such as the 'climate change regime complex,' a 'fragmented climate governance architecture,' and 'transnational climate governance.' A second set of authors points to the 'elephant in the room,' namely underlying power structures and material configurations in the international system that block effective responses to the climate crisis. A third group has argued that instead of looking at the individual 'trees' of climate negotiations, research should focus on the 'forest' of climate governance, made up of framings, norms, and emerging 'climate governmentalities.' The article proposes the concept of a 'schism of reality' as a means to overcome this fragmentation of the literature. This notion offers a new way of understanding interactions between the climate regime and its wider environment by focusing on discrepancies and contradictions. It accommodates different theoretical perspectives and provides common ground for future research: on how paradoxes and contradictions are dealt with in climate governance; how they can be overcome; how current developments in climate governance reduce the schism; and where and why aspects of the schism persist. © 2016 Wiley Periodicals, Inc.

Tardieu F.,French National Institute for Agricultural Research | Tuberosa R.,Viale Fanin
Current Opinion in Plant Biology | Year: 2010

Plants have acquired a variety of whole-plant protection mechanisms in response to abiotic stresses, often at the expenses of performance. Hence, a given trait can have positive, negative or no effect depending on the stress scenario. A new approach has emerged that dissects yield and integrative traits that influence stress tolerance into heritable traits (e.g. sensitivity parameters or architectural traits) by using phenotyping platforms with model-assisted methods. The genetic and physiological mechanisms accounting for the variability of these traits and their effects on yield are considered in a second step. Effects of traits on yield are analysed via a combination of modelling and field experiments, which allows identification of the stress scenarios where a given allele has favourable effects. © 2010 Elsevier Ltd. All rights reserved.

Roques L.,French National Institute for Agricultural Research | Cristofol M.,Aix - Marseille University
Nonlinearity | Year: 2010

This paper is devoted to the analysis of some uniqueness properties of a classical reaction-diffusion equation of the Fisher-KPP type, coming from population dynamics in heterogeneous environments. We work in a one-dimensional interval (a, b) and we assume a nonlinear term of the form u (μ(x) - γu) where μ belongs to a fixed subset of C0([a, b]). We prove that the knowledge of u at t = 0 and of u, ux at a single point x0 and for small times t ∈ (0, ε) is sufficient to completely determine the couple (u(t, x), μ(x)) provided γ is known. Additionally, if uxx(t, x0) is also measured for t ∈ (0, ε), the triplet (u(t, x), μ(x), γ) is also completely determined. Those analytical results are completed with numerical simulations which show that, in practice, measurements of u and ux at a single point x0 (and for t ∈ (0, ε)) are sufficient to obtain a good approximation of the coefficient μ(x). These numerical simulations also show that the measurement of the derivative ux is essential in order to accurately determine μ(x). © 2010 IOP Publishing Ltd and London Mathematical Society.

Lebourgeois F.,Agro ParisTech | Rathgeber C.B.K.,French National Institute for Agricultural Research | Ulrich E.,Office National des Forets
Journal of Vegetation Science | Year: 2010

Questions: (1) How do extreme climatic events and climate variability influence radial growth of conifers (silver fir, Norway spruce, Scots pine)? (2) How do elevation and soil water capacity (SWC) modulate sensitivity to climate? Location: The sampled conifer stands are in France, in western lowland and mountain forests, at elevations from 400 to 1700 m, and an SWC from 50 to 190 mm. Methods: We established stand chronologies for total ring width, earlywood and latewood width for the 33 studied stands (985 trees in total). Responses to climate were analysed using pointer years and bootstrapped response functions. Principal component analysis was applied to pointer years and response function coefficients in order to elucidate the ecological structure of the studied stands. Results: Extreme winter frosts are responsible for greater growth reductions in silver fir than in Norway spruce, especially at the upper elevation, while Scots pine was the least sensitive species. Exceptional spring droughts caused a notable growth decrease, especially when local conditions were dry (altitude<1000 m and SWC<100 mm for silver fir, western lowlands for Scots pine). Earlywood of silver fir depended on previous September and November and current-year February temperature, after which current June and July water supply influenced latewood. Earlywood of Norway spruce was influenced by previous September temperature, after which current spring and summer droughts influenced both ring components. In Scots pine, earlywood and latewood depended on the current summer water balance. Local conditions mainly modulated latewood formation. Conclusions: If the climate becomes drier, low-elevation dry stands or trees growing in western lowlands may face problems, as their growth is highly dependent on soil moisture availability. © 2009 International Association for Vegetation Science.

Genetically modified (GM) herbicide-tolerant (HT) crops have been largely adopted where they have been authorized. Nevertheless, they are fiercely criticized by some, notably because of the herbicide use associated with them. However, how much herbicide is applied to GMHT crops compared to conventional crops, and what impacts does the use of herbicide have? The paper first presents some factors explaining the predominance of GMHT crops. Then, trends in the use of herbicide for GM crops are studied in the case of the most widespread HT crop: HT soybean in the USA. The trends in the toxicity of herbicides applied to HT soybean are also addressed, as well as the appearance of glyphosate-resistant (GR) weeds. Lastly, the paper examines the spread of GR weeds and its impact. How are farmers, weed scientists, and the industry coping with this development, and what are the prospects of glyphosate-tolerant crops given weed resistance? In conclusion, some issues of sustainability and innovation governance raised by genetically modified herbicide-tolerant crops are discussed. © 2011 by the authors.

Croson R.,University of Texas at Arlington | Treich N.,French National Institute for Agricultural Research
Environmental and Resource Economics | Year: 2014

Environmental issues provide a rich ground for identifying the existence and consequences of human limitations. In this paper, we present a growing literature lying at the interface between behavioral and environmental economics. This literature identifies alternative solutions to traditional economic instruments in environmental domains that often work imperfectly. But it also faces a set of challenges, including the difficulty of computing welfare effects, and the identification of a robust environmental policy based on context-dependent (socio-) psychological effects. We illustrate our critical discussion with two behavioral schemes that have been widely implemented: "green nudges" and "corporate environmental responsibility." © 2014 Springer Science+Business Media Dordrecht.

Rey O.,French National Institute for Agricultural Research
Proceedings. Biological sciences / The Royal Society | Year: 2013

Androgenesis is the production of an offspring containing exclusively the nuclear genome of the fathering male via the maternal eggs. This unusual mating system is generally considered a male trait, giving to androgenetic males a substantial fitness advantage over their sexually reproducing relatives. We here provide the first empirical study of the evolutionary outcomes of androgenesis in a haplo-diploid organism: the invasive ant Wasmannia auropunctata. Some of the populations of this species have a classical haplo-diploid sexual mating system. In other populations, females and males are produced through parthenogenesis and androgenesis, respectively, whereas workers are produced sexually. We conducted laboratory reciprocal-cross experiments with reproductive individuals from both types of populations and analysed their progenies with genetic markers, to determine the respective contribution of males and females to the production of androgenetic males. We found that androgenesis was a parthenogenetic female trait. A population genetic study conducted in natura confirmed the parthenogenetic female origin of androgenesis, with the identification of introgression events of sexual male genotypes into androgenetic/parthenogenetic lineages. We argue that by producing males via androgenesis, parthenogenetic queen lineages may increase and/or maintain their adaptive potential, while maintaining the integrity of their own genome, by occasionally acquiring new male genetic material and avoiding inbreeding depression within the sexually produced worker cast.

Dinant S.,French National Institute for Agricultural Research | Lemoine R.,University of Poitiers
Comptes Rendus - Biologies | Year: 2010

The phloem is a central actor in plant development and nutrition, providing nutrients and energy to sink organs and integrating interorgan communication. A comprehensive picture of the molecules trafficking in phloem sap is being made available, with recent surveys of proteins, RNAs, sugars, and other metabolites, some of which are potentially acting as signals. In this review, we focus on recent breakthroughs on phloem transport and signalling. A case study was phloem loading of sucrose, acting both as a nutrient and as a signal, whose activity was shown to be tightly regulated. Recent advances also described actors of macromolecular trafficking in sieve elements, including chaperones and RNA binding proteins, involved potentially in the formation of ribonucleoprotein complexes. Likewise, long distance signalling appeared to integrate electrical potential waves, calcium bursts and potentially the generation of reactive oxygen species. The ubiquitin-proteasome system was also proposed to be on action in sieve elements for signalling and protein turnover. Surprisingly, several basic processes of phloem physiology are still under debate. Hence, the absence in phloem sap of reducing sugar species, such as hexoses, was recently challenged with observations based on an analysis of the sap from Ranunculaceae and Papaveraceae. The possibility that protein synthesis might occur in sieve elements was again questioned with the identification of components of the translational machinery in Pumpkin phloem sap. Altogether, these new findings strengthen the idea that phloem is playing a central role in interorgan nutrient exchanges and communication and demonstrate that the ways by which this is achieved can obey various patterns among species. © 2010 Académie des sciences.

Ahmed I.,French Institute of Health and Medical Research | Sarazin A.,French Institute of Health and Medical Research | Bowler C.,French Institute of Health and Medical Research | Colot V.,French Institute of Health and Medical Research | Quesneville H.,French National Institute for Agricultural Research
Nucleic Acids Research | Year: 2011

Transposable elements (TEs) and their relics play major roles in genome evolution. However, mobilization of TEs is usually deleterious and strongly repressed. In plants and mammals, this repression is typically associated with DNA methylation, but the relationship between this epigenetic mark and TE sequences has not been investigated systematically. Here, we present an improved annotation of TE sequences and use it to analyze genome-wide DNA methylation maps obtained at single-nucleotide resolution in Arabidopsis. We show that although the majority of TE sequences are methylated, ∼26 are not. Moreover, a significant fraction of TE sequences densely methylated at CG, CHG and CHH sites (where H=A, T or C) have no or few matching small interfering RNA (siRNAs) and are therefore unlikely to be targeted by the RNA-directed DNA methylation (RdDM) machinery. We provide evidence that these TE sequences acquire DNA methylation through spreading from adjacent siRNA-targeted regions. Further, we show that although both methylated and unmethylated TE sequences located in euchromatin tend to be more abundant closer to genes, this trend is least pronounced for methylated, siRNA-targeted TE sequences located 5′ to genes. Based on these and other findings, we propose that spreading of DNA methylation through promoter regions explains at least in part the negative impact of siRNA-targeted TE sequences on neighboring gene expression. © 2011 The Author(s).

Bohn-Courseau I.,French National Institute for Agricultural Research
Comptes Rendus - Biologies | Year: 2010

Plant development is characterized by the continuous initiation of tissues and organs. The meristems, which are small stem cell populations, are involved in this process. The shoot apical meristem produces lateral organs at its flanks and generates the growing stem. These lateral organs are arranged in a stereotyped pattern called phyllotaxis. Organ initiation in the peripheral zone of the meristem involves accumulation of the plant hormone auxin. Auxin is transported in a polar way by influx and efflux carriers located at cell membranes. Polar localization of the PIN1 efflux carrier in meristematic cells generates auxin concentration gradients and PIN1 localization depends, in turn, on auxin gradients: this feedback loop generates a dynamic auxin distribution which controls phyllotaxis. Furthermore, PIN-dependent local auxin gradients represent a common module for organ initiation, in the shoot and in the root. © 2010 Académie des sciences.

Hirsch E.C.,University Pierre and Marie Curie | Hirsch E.C.,French National Institute for Agricultural Research | Hirsch E.C.,French National Center for Scientific Research | Jenner P.,Kings College London | Przedborski S.,Columbia University
Movement Disorders | Year: 2013

Parkinson's disease is a common adult-onset neurodegenerative disorder whose pathogenesis remains essentially unknown. Currently, it is believed that the neurodegenerative process in Parkinson's disease is a combination of both cell-autonomous and non-cell-autonomous mechanisms. Proposed cell-autonomous mechanisms include alterations in mitochondrial bioenergetics, dysregulation of calcium homeostasis, and impaired turnover of mitochondria. As for the proposed non-cell-autonomous mechanisms, they involve prion-like behavior of misfolded proteins and neuroinflammation. This suggests that cell death in Parkinson's disease is caused by a multifactorial cascade of pathogenic events and argues that effective neuroprotective therapy for Parkinson's disease may have to rely on multiple drug interventions. © 2013 Movement Disorders Society.

Pages L.,French National Institute for Agricultural Research
Annals of Botany | Year: 2014

Background and Aims Root branching, and in particular acropetal branching, is a common and important developmental process for increasing the number of growing tips and defining the distribution of their meristem size. This study presents a new method for characterizing the results of this process in natura from scanned images of young, branched parts of excavated roots. The method involves the direct measurement or calculation of seven different traits. MethodsYoung plants of 45 species of dicotswere sampled fromfields and gardens with uniform soils.Rootswere separated, scanned and then measured using ImageJ software to determine seven traits related to root diameter and interbranch distance. Results The traits exhibited large interspecific variations, and covariations reflecting trade-offs. For example, at the interspecies level, the spacing of lateral roots (interbranch distance along the parent root) was strongly correlated to the diameter of the finest roots found in the species, and showed a continuum between two opposite strategies: making dense and fine lateral roots, or thick and well-spaced laterals. Conclusions A simple method is presented for classification of branching patterns in roots that allows relatively quick sampling and measurements to be undertaken. The feasibilty of the method is demonstrated for dicotyledonous species and it has the potential to be developed more broadly for other species and a wider range of enivironmental conditions. © 2014 The Author.

Perga M.-E.,French National Institute for Agricultural Research
Journal of Paleolimnology | Year: 2010

Stable isotope analyses on cladoceran subfossil exoskeletons retrieved from sediment cores could allow the reconstruction of past changes in lake food webs provided the δ13C and δ15N values of the exoskeletons reflect those of the organisms' whole body. The relationships between the C and N stable isotope compositions of the exoskeletons and those of the whole body were investigated for two freshwater cladoceran taxa (Bosmina sp. and Daphnia sp.) from modern samples. The C and N stable isotope compositions of the exoskeleton and those of the whole body were strongly correlated. Exoskeleton δ13C was similar to the whole body δ13C for both taxa. Daphnia exoskeletons were strongly depleted in 15N (-7. 9‰) compared to the whole body. Stable isotope analyses were thereafter performed on cladoceran remains from five downcore samples from Lake Annecy, France. Results showed that Bosmina δ15N values increased by more than 4‰, between the early twentieth and twenty first centuries. Such changes might be the result of changes in nitrogen sources or cycling in the lake and/or of major shifts in Bosmina trophic position within the lake food web. This study sets up the potential of stable isotope analyses performed on cladoceran subfossil remains for paleo-ecological purposes. © 2009 Springer Science+Business Media B.V.

Tadonleke R.D.,French National Institute for Agricultural Research
Limnology and Oceanography | Year: 2010

Using 31-yr data from measurements in a lake that has experienced change in eutrophication status, I showed that the effects of global warming on chlorophyll a (Chl a)-normalized maximum rates of photosynthesis (Pmax : Chl a) may be positive, nonsignificant, or negative, depending on nutrient availability. The magnitude of Pmax : Chl a change in response to warming showed hyperbolic relationships with phosphorus concentrations; it was positive and constant when total phosphorus (TP) in the lake water exceeded 22 μg P L -1 (eutrophic conditions) but was negative when TP was lower (nutrient-poor conditions), indicating direct negative effects of warming on primary productivity (PP) under phosphorus scarcity. Vertically integrated PP responses corroborate those of Pmax : Chl a. These data also showed long-term seasonal variations in the sensitivity of phytoplankton productivity to temperature. The observed hyperbolic curves strongly suggest that the "limiting-nutrient cell quota"-based mechanism reported so far only in laboratories (by studies analyzing temperature-nutrient effects on microalgal growth or photosynthesis) operates in nature and plays a key role in determining phytoplankton response to warming of waters. The present findings provide insight on how phytoplankton productivity may respond to future warming in lakes of differing eutrophication status. © 2010, by the American Society of Limnology and Oceanography, Inc.

Meuret M.,French National Institute for Agricultural Research | Provenza F.D.,Utah State University
Rangeland Ecology and Management | Year: 2015

Landscapes are complex creative systems that continually transform due to ever-changing relationships among environments and organisms including human beings. During the past half-century, those who study these relationships and those who manage them have become increasingly isolated from one another in their attempts to understand and manage landscapes. As we have come to rely on experimental science to understand principles, we have diminished the importance of experiential knowledge in understanding and implementing practices. In this paper, we discuss convergence of the knowledge of herders from Southeastern France with the science of foraging behavior. We review insights of researchers gained through interviews with herders, surveys, and in situ recordings of the foraging behavior of closely herded sheep and goats. Though years of hands-on experience, herders have come to understand processes involved in food and habitat selection. Using a conceptual model of four steps, which represent four intertwined processes for a given herder-herd-fodder resource, we describe how herders 1) teach their animals to use the full range of forages, 2) train the herd to respect the boundaries of grazing areas, 3) modulate what they call the "temporary palatability scoring" of forages, and 4) establish daily grazing circuits to stimulate appetite and intake through meal sequencing. This knowledge is also valuable when the objective is to boost appetite for particular forages, such as coarse grasses, scrub, and invasive species. The practices of herders are consistent with scientific studies that show the importance of plant biodiversity for enabling animals to select nutritious diets and the significance of animal learning and culture on nutrition, production, and health. We conclude by highlighting implications for furthering the exchange between herders and scientists and by providing implications for managing grazing on pastures and rangelands, with or without shepherds and dogs, and targeting grazing on particular plants and habitats. © 2015 Society for Range Management. Published by Elsevier Inc. All rights reserved.

Solymosi K.,A.P.S. University | Schoefs B.,French National Institute for Agricultural Research
Photosynthesis Research | Year: 2010

Chloroplast development is usually regarded as proceeding from proplastids. However, direct or indirect conversion pathways have been described in the literature, the latter involving the etioplast or the etio-chloroplast stages. Etioplasts are characterized by the absence of chlorophylls (Chl-s) and the presence of a unique inner membrane network, the prolamellar body (PLB), whereas etio-chloroplasts contain Chl-s and small PLBs interconnected with chloroplast thylakoids. As etioplast development requires growth in darkness for several days, this stage is generally regarded as a nonnatural pathway of chloroplast development occurring only under laboratory conditions. In this article, we have reviewed the data in favor of the involvement of etioplasts and etio-chloroplasts as intermediary stage(s) in chloroplast formation under natural conditions, the molecular aspects of PLB formation and we propose a dynamic model for its regulation. © 2010 Springer Science+Business Media B.V.

Genin S.,French National Institute for Agricultural Research
New Phytologist | Year: 2010

Ralstonia solanacearum is regarded as one of the world's most important bacterial plant pathogens because of its aggressiveness., large host range, broad geographical distribution and long persistence in soil and water environments. This root pathogen is an attractive model to investigate the question of host adaptation as it exhibits a remarkably broad host range, being able to infect numerous plant species belonging to different botanical families. Several effector proteins transiting through the type III secretion system have been shown to restrict or extend specifically the host range of the bacterium. Recent investigations on the mechanisms that coordinate changes in gene expression during the passage between saprophytism and life within host tissues have allowed the identification of other molecular determinants implicated in the adaptation of R. solanacearum to its hosts and pathogenesis. Among these determinants are genes involved in chemotaxis, secondary metabolic pathways and the detoxification of various antimicrobial compounds, and genes directing the biosynthesis of phytohormones or adherence factors. The regulation of many of these genes is coordinated by the master pathogenicity regulator HrpG. These hrpG-dependent genes control major steps during the interaction with plant cells, and probably determine the ecological behaviour of the microorganism, being required for the establishment of pathogenesis or mutualism. © The Author (2010). [Correction added after first online publication on 6 August 2010: the copyright line was corrected from 'no claim to original French government works' to '© The Author (2010)'.] Journal compilation © New Phytologist Trust (2010).

Lairon D.,French National Institute for Agricultural Research
Agronomy for Sustainable Development | Year: 2010

Food security, nutritional quality and safety vary widely around the world. Reaching these three goals is one of the major challenges for the near future. Up to now, industrialized production methods have clearly shown severe limitations such as a worldwide contamination of the food chain and water by persistent pesticide residues, and reduced nutrient and flavor contents through low-cost intensive food production and/or processing. In line with several published literature reviews, the French Agency for Food Safety (AFSSA) performed under my coordination an up-to-date exhaustive and critical evaluation of the nutritional and sanitary quality of organic food. This review is based on the AFSSA report issued and recently published studies. The major points are: 1/ organic plant products contain more dry matter and minerals (Fe, Mg); and contain more anti-oxidant micronutrients such as phenols and salicylic acid, 2/ organic animal products contain more polyunsaturated fatty acids, 3/ data on carbohydrate, protein and vitamin levels are insufficiently documented, 4/ 94-100% of organic food does not contain any pesticide residues, 5/ organic vegetables contain far less nitrates, about 50% less; and 6/ organic cereals contain overall similar levels of mycotoxins as conventional ones. Thus, organic agricultural systems have already proved able to produce food with high quality standards. I propose also improvements of organic production to achieve sustainable food production for humans in the near future. © 2010 INRA, EDP Sciences.

Clepet C.,French National Institute for Agricultural Research
PLoS ONE | Year: 2011

Background: In the genome era, characterizing the structure and the function of RNA molecules remains a major challenge. Alternative transcripts and non-protein-coding genes are poorly recognized by the current genome-annotation algorithms and efficient tools are needed to isolate the less-abundant or stable RNAs. Results: A universal RNA-tagging method using the T4 RNA ligase 2 and special adapters is reported. Based on this system, protocols for RACE PCR and full-length cDNA library construction have been developed. The RNA tagging conditions were thoroughly optimized and compared to previous methods by using a biochemical oligonucleotide tagging assay and RACE PCRs on a range of transcripts. In addition, two large-scale full-length cDNA inventories relying on this method are presented. Conclusion: The RNA Captor is a straightforward and accessible protocol. The sensitivity of this approach was shown to be higher compared to previous methods, and applicable on messenger RNAs, non-protein-coding RNAs, transcription-start sites and microRNA-directed cleavage sites of transcripts. This strategy could also be used to study other classes of RNA and in deep sequencing experiments. © 2011 Christian Clepet.

Rimet F.,French National Institute for Agricultural Research
Hydrobiologia | Year: 2012

The first studies of diatoms and river pollution were carried out 60 years ago, and the suitability of these micro-algae as bioassessment indicators for monitoring river quality was quickly demonstrated. The objective of this review is to describe the state of the art of the study of diatoms and river pollution between 1999 and 2009. The objective was to group the publications homogeneously according to subject and to indicate which subjects never overlap. To this end a lexical analysis was conducted on the abstract structure of these publications and seven K-means clusters were defined. Most of the items in this area were found to have been published in Hydrobiologia. One group (group 6) comprises publications about a discipline (ecotoxicology); several others group publications on the basis of the same approaches, for example species (group 3), basin (group 7), or spatial approaches (group 2). Other publications are brought together because the studies used a common method of using data, namely predictive models (group 1) or biotic indices (group 4). One group of publications was of studies performed in the same area-South Africa (group 5). Several remarks can be made. First, ecotoxicological studies are mostly experimental and restricted to small study areas. To answer society's demand for new assessment tools for micropollutant assessment, the next step would be to have more in-situ tests on larger spatial scales. Second, diatom biomonitoring uses the word "species" extensively, because this is the basis for establishing the lists of flora which are used extensively in such subject areas. Species is closely related to taxonomy; nevertheless this discipline is very rarely addressed in the papers. Third, phylogeny is never addressed in the publications. This is significant because phylogenetic studies for freshwater macroinvertebrates enable appropriate definition of taxonomic aggregations that can be used as accurate indicators of particular environmental stressors. © 2011 Springer Science+Business Media B.V.

Andrey P.,French National Institute for Agricultural Research
PLoS computational biology | Year: 2010

In eukaryotes, the interphase nucleus is organized in morphologically and/or functionally distinct nuclear "compartments". Numerous studies highlight functional relationships between the spatial organization of the nucleus and gene regulation. This raises the question of whether nuclear organization principles exist and, if so, whether they are identical in the animal and plant kingdoms. We addressed this issue through the investigation of the three-dimensional distribution of the centromeres and chromocenters. We investigated five very diverse populations of interphase nuclei at different differentiation stages in their physiological environment, belonging to rabbit embryos at the 8-cell and blastocyst stages, differentiated rabbit mammary epithelial cells during lactation, and differentiated cells of Arabidopsis thaliana plantlets. We developed new tools based on the processing of confocal images and a new statistical approach based on G- and F- distance functions used in spatial statistics. Our original computational scheme takes into account both size and shape variability by comparing, for each nucleus, the observed distribution against a reference distribution estimated by Monte-Carlo sampling over the same nucleus. This implicit normalization allowed similar data processing and extraction of rules in the five differentiated nuclei populations of the three studied biological systems, despite differences in chromosome number, genome organization and heterochromatin content. We showed that centromeres/chromocenters form significantly more regularly spaced patterns than expected under a completely random situation, suggesting that repulsive constraints or spatial inhomogeneities underlay the spatial organization of heterochromatic compartments. The proposed technique should be useful for identifying further spatial features in a wide range of cell types.

Valentin D.,French National Institute for Agricultural Research
Chemosensory Perception | Year: 2011

Numerous cross-modal associations bearing on food perception and evaluation have been highlighted. Some of them hold between apparently disconnected features like musical instruments and basic tastes, or pitches and flavors, raising questions regarding their perceptual grounding. In the present study, we investigated whether there are any such cross-modal correspondences between shapes and flavors of liquids, as suggested by the reports that certain beverages taste round or sharp, which bypass the associations made on the basis of visual characteristics of the products or their names. Participants took part in a blind matching task in order to measure the consistency of the association between samples of beer presenting different flavor characteristics and a large set of images of 2D and 3D shapes. Participants were then asked to provide descriptors for the perceived flavor characteristics of the tasted samples. Analysis of the participants' responses revealed no overall dominance of 2D or 3D shapes but highlighted the existence of a significant correspondence between sweetness, voluminousness, and roundness and between bitterness, thinness, and angular shapes. The study suggests that a perceptual correspondence, rather than a purely linguistic association, is at stake. Hypotheses and guidelines for future investigation are offered to understand better the nature of this correspondence. © Springer Science+Business Media, LLC 2011.

Pro-inflammatory cytokines like macrophage migration inhibitory factor (MIF), IL-1β and TNF-α predominate in inflammatory bowel diseases (IBD) and TNBS colitis. Increased levels of serine proteases activating protease-activated receptor 2 (PAR-2) are found in the lumen and colonic tissue of IBD patients. PAR-2 activity and pro-inflammatory cytokines impair epithelial barrier, facilitating the uptake of luminal aggressors that perpetuate inflammation and visceral pain. Soy extracts contain phytoestrogens (isoflavones) and serine protease inhibitors namely Bowman-Birk Inhibitors (BBI). Since estrogens exhibit anti-inflammatory and epithelial barrier enhancing properties, and that a BBI concentrate improves ulcerative colitis, we aimed to evaluate if a fermented soy germ extract (FSG) with standardized isoflavone profile and stable BBI content exert cumulative or synergistic protection based on protease inhibition and estrogen receptor (ER)-ligand activity in colitic rats. Female rats received orally for 15 d either vehicle or FSG with or without an ER antagonist ICI 182.780 before TNBS intracolonic instillation. Macroscopic and microscopic damages, myeloperoxidase activity, cytokine levels, intestinal paracellular permeability, visceral sensitivity, faecal proteolytic activity and PAR-2 expression were assessed 24 h, 3 d and 5 d post-TNBS. FSG treatment improved the severity of colitis, by decreasing the TNBS-induced rise in gut permeability, visceral sensitivity, faecal proteolytic activity and PAR-2 expression at all post-TNBS points. All FSG effects were reversed by the ICI 182.780 except the decrease in faecal proteolytic activity and PAR-2 expression. In conclusion, the anti-inflammatory properties of FSG treatment result from two distinct but synergic pathways i.e an ER-ligand and a PAR-2 mediated pathway, providing rationale for potential use as adjuvant therapy in IBD.

Tremillon N.,French National Institute for Agricultural Research
PloS one | Year: 2012

Protein folding in the envelope is a crucial limiting step of protein export and secretion. In order to better understand this process in Lactococcus lactis, a lactic acid bacterium, genes encoding putative exported folding factors like Peptidyl Prolyl Isomerases (PPIases) were searched for in lactococcal genomes. In L. lactis, a new putative membrane PPIase of the cyclophilin subfamily, PpiA, was identified and characterized. ppiA gene was found to be constitutively expressed under normal and stress (heat shock, H(2)O(2)) conditions. Under normal conditions, PpiA protein was synthesized and released from intact cells by an exogenously added protease, showing that it was exposed at the cell surface. No obvious phenotype could be associated to a ppiA mutant strain under several laboratory conditions including stress conditions, except a very low sensitivity to H(2)O(2). Induction of a ppiA copy provided in trans had no effect i) on the thermosensitivity of an mutant strain deficient for the lactococcal surface protease HtrA and ii) on the secretion and stability on four exported proteins (a highly degraded hybrid protein and three heterologous secreted proteins) in an otherwise wild-type strain background. However, a recombinant soluble form of PpiA that had been produced and secreted in L. lactis and purified from a culture supernatant displayed both PPIase and chaperone activities. Although L. lactis PpiA, a protein produced and exposed at the cell surface under normal conditions, displayed a very moderate role in vivo, it was found, as a recombinant soluble form, to be endowed with folding activities in vitro.

Hofte H.,French National Institute for Agricultural Research | Hofte H.,Agro ParisTech
Plant and Cell Physiology | Year: 2015

Understanding how developmental and environmental signals control plant cell expansion requires an intimate knowledge of the architecture of the primary cell wall and the chemo-rheological processes that underlie cell wall relaxation. In this review I discuss recent findings that reveal a more prominent role than previously suspected for covalent bonds and pectin cross-links in primary cell wall architecture. In addition, genetic studies have uncovered a role for receptor kinases in the control of cell wall homeostasis in growing cells. The emerging view is that, upon cell wall disruption, compensatory changes are induced in the cell wall through the interplay between the brassinosteroid signaling module, which positively regulates wall extensibility and receptor kinases of the CrRLKL1 family, which may act as negative regulators of cell wall stiffness. These findings lift the tip of the veil of a complex signaling network allowing normal homeostasis in walls of growing cells but also crisis management under stress conditions. © The Author 2014.

Le Corre V.,CNRS Agroecology Lab | Kremer A.,French National Institute for Agricultural Research | Kremer A.,University of Bordeaux 1
Molecular Ecology | Year: 2012

Most adaptive traits are controlled by large number of genes that may all together be the targets of selection. Adaptation may thus involve multiple but not necessarily substantial allele frequency changes. This has important consequences for the detection of selected loci and implies that a quantitative genetics framework may be more appropriate than the classical 'selective sweep' paradigm. Preferred methods to detect loci involved in local adaptation are based on the detection of 'outlier' values of the allelic differentiation F ST. A quantitative genetics framework is adopted here to review theoretical expectations for how allelic differentiation at quantitative trait loci (F STQ) relates to (i), neutral genetic differentiation (F ST) and (ii), phenotypic differentiation (Q ST). We identify cases where results of outlier-based methods are likely to be poor and where differentiation at selected loci conveys little information regarding local adaptation. A first case is when neutral differentiation is high, so that local adaptation does not necessitate increased differentiation. A second case is when local adaptation is reached via an increased covariance of allelic effects rather than via allele frequency changes, which is more likely under high gene flow when the number of loci is high and selection is recent. The comparison of theoretical predictions with observed data from the literature suggests that polygenic local adaptation involving only faint allele frequency changes are very likely in some species such as forest trees and for climate-related traits. Recent methodological improvements that may alleviate the weakness of F ST-based detection methods are presented. © 2012 Blackwell Publishing Ltd.

Noctor G.,French National Institute for Agricultural Research | Foyer C.H.,University of Leeds
Plant Physiology | Year: 2016

Recent years have witnessed enormous progress in understanding redox signaling related to reactive oxygen species (ROS) in plants. The consensus view is that such signaling is intrinsic to many developmental processes and responses to the environment. ROS-related redox signaling is tightly wedded to compartmentation. Because membranes function as barriers, highly redox-active powerhouses such as chloroplasts, peroxisomes, and mitochondria may elicit specific signaling responses. However, transporter functions allow membranes also to act as bridges between compartments, and so regulated capacity to transmit redox changes across membranes influences the outcome of triggers produced at different locations. As well as ROS and other oxidizing species, antioxidants are key players that determine the extent of ROS accumulation at different sites and that may themselves act as signal transmitters. Like ROS, antioxidants can be transported across membranes. In addition, the intracellular distribution of antioxidative enzymes may be modulated to regulate or facilitate redox signaling appropriate to the conditions. Finally, there is substantial plasticity in organellar shape, with extensions such as stromules, peroxules, and matrixules playing potentially crucial roles in organelle-organelle communication. We provide an overview of the advances in subcellular compartmentation, identifying the gaps in our knowledge and discussing future developments in the area. © 2016 American Society of Plant Biologists. All rights reserved.

Roosen J.,TU Munich | Marette S.,French National Institute for Agricultural Research
European Review of Agricultural Economics | Year: 2011

This article shows how experiments revealing information about food quality and safety can contribute to regulatory debates on food and health. After detailing the motivations of regulation for the food sector, we underline the limits of theoretical welfare analysis. Despite challenges from behavioural economics, cost-benefit analysis using experimental results can complement theoretical analysis. In a brief review of laboratory and field experiments with food, we discuss their relative strengths and weaknesses and suggest an analytical approach of how to integrate experimental data into welfare analysis. An empirical application quantifies and compares the welfare impact of health information and a subsidy for fish. © Oxford University Press and Foundation for the European Review of Agricultural Economics 2011; all rights reserved.

Gaucherel C.,French National Institute for Agricultural Research
International Journal of Climatology | Year: 2010

Most climate fluctuations may be modulated by a variety of periodic or quasi-periodic deterministic forcing (e.g. diurnal, seasonal or Milankovitch cycles). These process modulations often induce cyclostationary (CS) behaviour defined as periodic correlations. I proposed here that quasi-periodic correlations may appear when the inertia (memory) of a process is modulating its pure CS property. This effect of the phenomenon memory led to CS behaviour 'in average' both in time and frequency domains, called Extended CycloStationarity (ECS) and being rigorously defined in this paper. A new statistical tool has been developed to analyse ECS in a time series with the help of a comfortable time-frequency visualization technique (called DXM). This tool has been applied to the quantification of ENSO interannual ECS quasi-cycles, taking into account the possible ENSO memory. ECS property searched in the SOI and SST (Niño-3) indices perfectly confirmed the well-known interannual periodicities (the quasi-biennial, 28 months, and the quasi-quadrennial, 45 months) and their evolutions discussed in the literature. The main result presented here was that these significant quasi-cycles were the only ones detected throughout the 50-year datasets, suggesting that various periodicities were detected in the past because ECS quasi-cycles were not taken into account. This result led to the hypothesis that the quasi-biennial cycle belonged to the atmospheric component and that the quasi-quadrennial cycle belonged to the oceanic component of ENSO only. Both quasi-cycle evolutions were significantly (p < 0.01) correlated (r 2 = 0.62), with a delayed action (30-month time lag) of the atmosphere upon the ocean. This observation highlighted the nature of the strong coupling between the two components and suggested a possible influence of Pacific atmospheric processes on oceanic processes. © 2009 Royal Meteorological Society.

Loisel P.,French National Institute for Agricultural Research
Journal of Forest Economics | Year: 2011

The impact of the presence of risk of destructive event on the silvicultural practice of a forest stand is investigated. For that, we consider a model of population dynamics. This model has allowed us to make the comparison without and with risk, and highlight the influence of the presence of risk of destructive event on optimal thinning and optimal rotation period. © 2011 Department of Forest Economics, SLU Umeå, Sweden.

Goulet E.,Institute Francais Of La Vigne Et Du Vin | Morlat R.,French National Institute for Agricultural Research
Land Use Policy | Year: 2011

Studies of terroir have been increasingly developed during the last two decades, in different vineyards all around the world. The indigenous knowledge and the know-how of wine growers is an important part of the French terroir concept which must be taken into account in terroir studies. In the middle-Loire Valley (France) results of terroir studies were made readily accessible to all the wine growers through cartographic atlases, including maps of terroir units and their components as well as advisory maps. In this paper, the authors use different kinds of surveys among wine growers for the knowledge of terroir and show the interest of this approach. Surveys among farmers, performed at their home were developed within the framework of terroir studies carried out in the Anjou, Chinon and Sarthe vineyards in the middle-Loire Valley (France). A first category of surveys (59) led at the farm scale were used to characterise different vineyards at the socio-economic level. A second category of surveys (439) carried out at the plot scale have allowed to obtain a knowledge about agro-viticultural practices, and to study the viticultural and grape quality potentials of terroir units, in the regions studied. Finally, telephone surveys among 244 growers in the Anjou region were used to assess the level of perception of terroir studies and their impact through directive and semi-directive questionnaires, Socio-economic surveys at the wine farm scale made it possible to establish a general typology of studied vineyards, to identify their characteristics. Results allowed to distinguish between Chinon and Sarthe vineyards, in terms of operating structure, production potential, and typology of growers. Surveys showed large differences in terms of socio-economic aspects between the two studied vineyards. Agro-viticultural surveys, at the plot scale, provided significant differences for grape varieties, rootstocks and soil management practices, between the Chinon and Sarthe vineyards. Crossed with soils properties, these surveys allowed to identify the plant behaviour in terms of timing of the growth cycle, water supply and vine vigour and the potential for grape quality in different terroir units within an experimental area in Anjou vineyards. In these same vineyards, surveys about the perception and the acceptance of terroir studies by growers have shown that terroir studies and cartographic atlases, readily available to wine growers, were known by a large number of producers and used fairly frequently by some of them. Results of surveys indicated that about one quarter of growers were really influenced in their agro-viticultural practices by terroir studies. The rigorous and systematic use of adapted surveys bodes well for the rapid development of terroir studies in different vineyards. They make it possible to significantly alleviate classic studies without decreasing their relevance and they constitute an active contribution of wine growers to the characterization of terroir units. In addition, surveys can allow to assess the level of adaptation of agro-viticultural practices in use in the vineyards. © 2011 Elsevier Ltd.

Rothwell J.A.,French National Institute for Agricultural Research
Database : the journal of biological databases and curation | Year: 2012

Phenol-Explorer, launched in 2009, is the only comprehensive web-based database on the content in foods of polyphenols, a major class of food bioactives that receive considerable attention due to their role in the prevention of diseases. Polyphenols are rarely absorbed and excreted in their ingested forms, but extensively metabolized in the body, and until now, no database has allowed the recall of identities and concentrations of polyphenol metabolites in biofluids after the consumption of polyphenol-rich sources. Knowledge of these metabolites is essential in the planning of experiments whose aim is to elucidate the effects of polyphenols on health. Release 2.0 is the first major update of the database, allowing the rapid retrieval of data on the biotransformations and pharmacokinetics of dietary polyphenols. Data on 375 polyphenol metabolites identified in urine and plasma were collected from 236 peer-reviewed publications on polyphenol metabolism in humans and experimental animals and added to the database by means of an extended relational design. Pharmacokinetic parameters have been collected and can be retrieved in both tabular and graphical form. The web interface has been enhanced and now allows the filtering of information according to various criteria. Phenol-Explorer 2.0, which will be periodically updated, should prove to be an even more useful and capable resource for polyphenol scientists because bioactivities and health effects of polyphenols are dependent on the nature and concentrations of metabolites reaching the target tissues. The Phenol-Explorer database is publicly available and can be found online at http://www.phenol-explorer.eu. Database URL: http://www.phenol-explorer.eu.

Wery N.,French National Institute for Agricultural Research
Frontiers in cellular and infection microbiology | Year: 2014

Bioaerosols generated at composting plants are released during processes that involve the vigorous movement of material such as shredding, compost pile turning, or compost screening. Such bioaerosols are a cause of concern because of their potential impact on both occupational health and the public living in close proximity to such facilities. The biological hazards potentially associated with bioaerosol emissions from composting activities include fungi, bacteria, endotoxin, and 1-3 β-glucans. There is a major lack of knowledge concerning the dispersal of airborne microorganisms emitted by composting plants as well as the potential exposure of nearby residents. This is due in part to the difficulty of tracing specifically these microorganisms in air. In recent years, molecular tools have been used to develop new tracers which should help in risk assessments. This review summarizes current knowledge of microbial diversity in composting aerosols and of the associated risks to health. It also considers methodologies introduced recently to enhance understanding of bioaerosol dispersal, including new molecular indicators and modeling.

Fardet A.,French National Institute for Agricultural Research | Fardet A.,Clermont University
Nutrition Research Reviews | Year: 2010

Epidemiological studies have clearly shown that whole-grain cereals can protect against obesity, diabetes, CVD and cancers. The specific effects of food structure (increased satiety, reduced transit time and glycaemic response), fibre (improved faecal bulking and satiety, viscosity and SCFA production, and/or reduced glycaemic response) and Mg (better glycaemic homeostasis through increased insulin secretion), together with the antioxidant and anti-carcinogenic properties of numerous bioactive compounds, especially those in the bran and germ (minerals, trace elements, vitamins, carotenoids, polyphenols and alkylresorcinols), are today well-recognised mechanisms in this protection. Recent findings, the exhaustive listing of bioactive compounds found in whole-grain wheat, their content in whole-grain, bran and germ fractions and their estimated bioavailability, have led to new hypotheses. The involvement of polyphenols in cell signalling and gene regulation, and of sulfur compounds, lignin and phytic acid should be considered in antioxidant protection. Whole-grain wheat is also a rich source of methyl donors and lipotropes (methionine, betaine, choline, inositol and folates) that may be involved in cardiovascular and/or hepatic protection, lipid metabolism and DNA methylation. Potential protective effects of bound phenolic acids within the colon, of the B-complex vitamins on the nervous system and mental health, of oligosaccharides as prebiotics, of compounds associated with skeleton health, and of other compounds such as -linolenic acid, policosanol, melatonin, phytosterols and para-aminobenzoic acid also deserve to be studied in more depth. Finally, benefits of nutrigenomics to study complex physiological effects of the whole-grain package, and the most promising ways for improving the nutritional quality of cereal products are discussed. © 2010 The Author.

Small ruminant production is the main source of income of farmers living in arid and semiarid regions. Sheep and goats raised in these areas are generally confronted with severe nutritional deficits during food scarcity period which exacerbate disease and health problems and consequently low productive and reproductive performances. These areas are characterized by rainfall seasonality and scarcity resulting in a low fodder potential. Therefore, native rangelands are degrading due to overgrazing, high stocking rates and mismanagement. Options to improve small ruminant-based production systems include i) innovative technologies targeting the increase of feed resources availability, rumen manipulation using natural compounds to boost microbial activity, improving diets' quality, alleviation of feeding cost, and better control of livestock watering. Although this paper is focussing on the benefits from these technical options, we should bear in mind that i) the organization of local institutions for better adoption of these technologies and for protecting the main natural resources (rangelands and water) and ii) the participatory approach involving all partners concerned with the improvement of farmer's income and livelihood are key tools for promoting livestock sector in the target areas. A set of simple, inexpensive and environmentally friendly options that could ameliorate small ruminant production in the semiarid regions are discussed in this paper. © 2010 Sociedade Brasileira de Zootecnia.

Castagnone-Sereno P.,French National Institute for Agricultural Research
Nematology | Year: 2012

Meloidogyne enterolobii (= M. mayaguensis), the root-knot nematode of the pacara earpod tree, belongs to the group of tropical root-knot nematodes and is considered as one of the most damaging species, due to its wide host range, pathogenicity and ability to develop and reproduce on several crops carrying resistance genes. Moreover, recent reports indicate that the geographic distribution of the parasite tends to extend beyond tropical areas, and the risk of its establishment and spread in Mediterranean regions and southern Europe is now highly probable. Recently, molecular markers have been developed that allow the specific identification of this pest, a prerequisite for the implementation of efficient control strategies. In that respect, plant resistance and biological control are currently being actively investigated but a huge amount of research and development is still required to ensure the successful use of such methods in the field. © 2012 Koninklijke Brill NV, Leiden, The Netherlands.

Cotte V.,French National Institute for Agricultural Research
Vector borne and zoonotic diseases (Larchmont, N.Y.) | Year: 2010

In Europe, Ixodes ricinus ticks are vectors of many emerging pathogens, including Borrelia burgdorferi sensu lato (sl), Anaplasma phagocytophilum, spotted fever group Rickettsia sp., Babesia sp., and very likely Bartonella sp. In this study, we looked for the presence of DNA of these microorganisms in 572 ticks from two forests in the west of France. DNA extraction and polymerase chain reaction (PCR) amplification were performed on individual nymphal, male, and female I. ricinus ticks. Amplification from 1 tick among the 572 samples (0.2%) resulted in PCR products with Bartonella-specific primers. Sequence analysis of the amplified fragment did not lead to species identification. Two ticks (0.3%) carried A. phagocytophilum-specific DNA. Eight ticks (1.4%) were positive with spotted fever group Rickettsia-specific primers, and all PCR fragments were related to Rickettsia helvetica. Thirty-five ticks (6.1%) were positive with B. burgdorferi sl-specific primers; the sequences were all related to Borrelia garinii or Borrelia afzelii, except one that was related to Borrelia carolinensis, a newly described species never reported in Europe so far. Thirty-five ticks (6.1%) carried Babesia sp. DNA. Female adults were more infected by B. burgdorferi sl than male adults. The prevalence of B. burgdorferi sl and Babesia sp. was significantly different between the two forests, with a higher prevalence of B. burgdorferi sl in ticks from the forest of Princé and a higher prevalence of Babesia sp. in ticks from the forest of Gâvre. To our knowledge, this is the first study that has detected all five pathogens in questing I. ricinus in the west of France and the first report of B. carolinensis DNA in ticks in Europe.

Cebo C.,French National Institute for Agricultural Research
Food Technology and Biotechnology | Year: 2012

Lipids are released in milk as fat globules, which are droplets of apolar lipids surrounded by a complex membrane deriving from the mammary epithelial cell (MEC) and called the milk fat globule membrane (MFGM). The structure of the MFGM is highly complex and closely related to the mechanisms of milk fat globule secretion in the mammary epithelial cell. Indeed, MFGM is composed of two biological membranes, a phospholipid monolayer, deriving from the endoplasmic reticulum, and a phospholipid bilayer, which originates from the apical plasma membrane of the MEC, with variable amounts of cytoplasm trapped between. Biochemical techniques (i.e. sodium dodecyl sulphate-polyacrylamide gel electrophoresis followed by different staining procedures) have been employed historically to characterize major MFGM proteins, namely MUC-1, fatty acid synthase, xanthine oxidase, butyrophilin, lactadherin, and adipophilin. However, recent advances in the field of proteomics (mostly development of one-dimensional gel electrophoresis approach coupled with tandem mass spectrometry) have led to the identification of hundreds of proteins associated with the MFGM. Surprisingly, newly identified MFGM proteins were not only involved in lipid metabolic or exocytosis-related biological processes, but also in cell signalling, translation, or host defense-related mechanisms. Therefore, the milk fat globule should no longer be viewed as an inert structure only devoted to the delivery of lipids to the newborn, but rather as a dynamic and informative compartment which can contribute to the improvement of our comprehension of the mammary gland biology.

Genin S.,French National Institute for Agricultural Research | Genin S.,French National Center for Scientific Research | Denny T.P.,University of Georgia
Annual Review of Phytopathology | Year: 2012

Ralstonia solanacearum is a major phytopathogen that attacks many crops and other plants over a broad geographical range. The extensive genetic diversity of strains responsible for the various bacterial wilt diseases has in recent years led to the concept of an R. solanacearum species complex. Genome sequencing of more than 10 strains representative of the main phylogenetic groups has broadened our knowledge of the evolution and speciation of this pathogen and led to the identification of novel virulence-associated functions. Comparative genomic analyses are now opening the way for refined functional studies. The many molecular determinants involved in pathogenicity and host-range specificity are described, and we also summarize current understanding of their roles in pathogenesis and how their expression is tightly controlled by an intricate virulence regulatory network. © 2012 by Annual Reviews. All rights reserved.

Blesbois E.,French National Institute for Agricultural Research
Journal of Poultry Science | Year: 2012

Male gamete biology shows specific features in birds that contribute to the reproductive strategy of flying animals adapted to highly variable environmental conditions. In this paper, we review the main characteristics of bird sperm, their selectionand storage in the highly specialized female oviduct, specific features of polyspermic fertilization, and the consequences of these biological adaptations on semen biotechnology. Among other features, the storage of sperm in specific oviducal glands is a key factor to increase reproductive "freedom" but is also a critical point for the success of semeninvitro storage.

Wajnberg E.,French National Institute for Agricultural Research
Journal of Animal Ecology | Year: 2012

Animals foraging for resources are under a variety of selective pressures, and separate optimality models have been developed predicting the optimal reproductive strategies they should adopt. In most cases, the proximate behavioural mechanisms adopted to achieve such optimality goals have been identified. This is the case, for example, for optimal patch time and sex allocation in insect parasitoids. However, behaviours modelled within this framework have mainly been studied separately, even though real animals have to optimize some behaviours simultaneously. For this reason, it would be better if proximate behavioural rules were designed to attain several goals simultaneously. Despite their importance, such multi-objective proximate rules remain to be discovered. Based on experiments on insect parasitoids that simultaneously examine their optimal patch time and sex allocation strategies, it is shown here that animals can adopt multi-objective behavioural mechanisms that appear consistent with the two optimal goals simultaneously. Results of computer simulations demonstrate that these behavioural mechanisms are indeed consistent with optimal reproductive strategies and have thus been most likely selected over the course of the evolutionary time. © 2011 The Author. Journal of Animal Ecology © 2011 British Ecological Society.

Fady B.,French National Institute for Agricultural Research
Annals of Forest Science | Year: 2012

Context: Mediterranean pines share many common lifehistory traits. They are found at almost all altitudinal levels around the Mediterranean Basin, from sea level to highelevation mountains, and from hot and dry to wet and cold bioclimates. Their distribution ranges from widespread to regional and narrow, and from dense extensive populations to small populations of scattered individuals. They have been extensively used by human civilizations for millennia. Aims: I show which are the main phylogenetic, ecological, and climatic factors explaining the patterns of within and among-population genetic diversity in Mediterranean pines. Methods: I use a narrative synthesis approach and multiple examples from the literature on pine species from the Mediterranean Basin and California. Results: While Mediterranean pines have the highest levels of differentiation worldwide, their genetic diversity increases from west to east and is significantly reduced in low-elevation species. Factors such as ancestral adaptation to wildfire, reduction of effective population size during the Last Glacial Maximum, long distance dispersal during the Holocene, and more recent adaptation to patchy environmental conditions could explain these patterns. Conclusion: Because of contrasted ecological, demographic, historical, and geographical processes, and despite their common biological attributes, pines of the Mediterranean Basin display complex biogeographic patterns at neutral gene level that can help retrace their evolutionary history. Although individual species often represent unique case studies that make generalizations risky, locating habitats of significantly high and low genetic diversity is key for detecting and understanding the major factors affecting gene diversity and may prove useful for profiling areas of high conservation value in the Mediterranean. © INRA /Springer-Verlag France 2012.

Meunier G.,French National Institute for Agricultural Research
Energy Economics | Year: 2013

This article analyzes the effect of risk and risk-aversion on the long-term equilibrium technology mix in an electricity market. It develops a model where firms can invest in baseload plants with a fixed variable cost and peak plants with a random variable cost, and demand for electricity varies over time but is perfectly predictable. At equilibrium the electricity price is partly determined by the random variable cost and the returns from the two kinds of plants are negatively correlated. When the variable cost of the peak technology is high the return of peak plants is low but the return to baseload plants is high. Risk-averse firms reduce the capacity of the riskiest technology and develop the capacity of the other, compared to risk-neutral firms. In the particular case where a risk-neutral firm invests heavily in baseload technology and only sparely in peak capacity, a risk-averse firm would invest less in baseload, increase peak capacity, and increase total installed capacity. © 2013 Elsevier B.V.

Walrand S.,French National Institute for Agricultural Research
Journal of Nutrition, Health and Aging | Year: 2010

Our current knowledge on the causes of sarcopenia is still fragmentary. One of the most evident candidates to explain muscle loss in elderly includes imbalance in protein turnover, i.e. decreased muscle protein synthesis rate, notably in the post-prandial state. Nutritional strategies such as leucine supplementation, use of fast digested proteins or a pulse protein intake have been show to enhance the synthesis rate of muscle proteins in older individuals. Ornithine alpha-ketoglutarate (OKG) is a precursor of amino acids such as glutamine, arginine and proline, and increases the secretion of anabolic hormones, i.e. insulin and growth hormone. A beneficial anabolic action of OKG has been demonstrate in several pathological conditions associated with muscle loss. Therefore, OKG may be of a potential interest to modulate muscle protein metabolism and to maintain muscle mass during aging. © 2010 Serdi and Springer Verlag France.

This H.,French National Institute for Agricultural Research
Journal of Culinary Science and Technology | Year: 2011

Molecular Gastronomy (MG) has been developing in France since the very beginning of this scientific discipline, largely due to the fact that one of its co-founders resides in the country. Since 1995, a French group of molecular gastronomists has been promoting the discipline in France, as well as other countries throughout the world. It should come as no surprise, then, given the large scope of MG, that activities in the field of, or related to, MG are numerous. © Taylor & Francis Group, LLC.

Ragsdale D.W.,University of Minnesota | Landis D.A.,Michigan State University | Brodeur J.,University of Montreal | Heimpel G.E.,University of Minnesota | Desneux N.,French National Institute for Agricultural Research
Annual Review of Entomology | Year: 2011

The soybean aphid, Aphis glycines Matsumura, has become the single most important arthropod pest of soybeans in North America. Native to Asia, this invasive species was first discovered in North America in July 2000 and has rapidly spread throughout the northcentral United States, much of southeastern Canada, and the northeastern United States. In response, important elements of the ecology of the soybean aphid in North America have been elucidated, with economic thresholds, sampling plans, and chemical control recommendations widely adopted. Aphid-resistant soybean varieties were available to growers in 2010. The preexisting community of aphid natural enemies has been highly effective in pressing aphid populations in many situations, and classical biological control efforts have focused on the addition of parasitoids of Asian origin. The keys to sustainable management of this pest include understanding linkages between the soybean aphid and other introduced and native species in a landscape context along with continued development of aphid-resistant varieties. © 2011 by Annual Reviews. All rights reserved.

Tardieu F.,French National Institute for Agricultural Research
Journal of Experimental Botany | Year: 2012

Most traits associated with drought tolerance have a dual effect, positive in very severe scenarios and negative in milder scenarios, or the opposite trend. Their effects also depend on other climatic conditions such as evaporative demand or light, and on management practices. This is the case for processes associated with cell protection and with avoidance, but also for the maintenance of growth or photosynthesis, high water use efficiency, large root systems or reduced abortion rate under water deficit. Therefore, spectacular results obtained in one drought scenario may have a limited interest for improving food security in other geographical areas with water scarcity. The most relevant questions on drought tolerance are probably, 'Does a given allele confer a positive effect on yield in an appreciable proportion of years/scenarios in a given area or target population of environment (TPE)?'; 'In a given site or TPE, what is the trade-off between risk avoidance and maintained performance?'; and 'Will a given allele or trait have an increasingly positive effect with climate change?' Considerable progress has already occurred in drought tolerance. Nevertheless, explicitly associating traits for tolerance to drought scenarios may have profound consequences on the genetic strategies, with a necessary involvement of modelling. © 2011 The Author(s).

Endale Ahanda M.L.,French National Institute for Agricultural Research
PloS one | Year: 2012

THE SLA (swine leukocyte antigen, MHC: SLA) genes are the most important determinants of immune, infectious disease and vaccine response in pigs; several genetic associations with immunity and swine production traits have been reported. However, most of the current knowledge on SLA is limited to gene coding regions. MicroRNAs (miRNAs) are small molecules that post-transcriptionally regulate the expression of a large number of protein-coding genes in metazoans, and are suggested to play important roles in fine-tuning immune mechanisms and disease responses. Polymorphisms in either miRNAs or their gene targets may have a significant impact on gene expression by abolishing, weakening or creating miRNA target sites, possibly leading to phenotypic variation. We explored the impact of variants in the 3'-UTR miRNA target sites of genes within the whole SLA region. The combined predictions by TargetScan, PACMIT and TargetSpy, based on different biological parameters, empowered the identification of miRNA target sites and the discovery of polymorphic miRNA target sites (poly-miRTSs). Predictions for three SLA genes characterized by a different range of sequence variation provided proof of principle for the analysis of poly-miRTSs from a total of 144 M RNA-Seq reads collected from different porcine tissues. Twenty-four novel SNPs were predicted to affect miRNA-binding sites in 19 genes of the SLA region. Seven of these genes (SLA-1, SLA-6, SLA-DQA, SLA-DQB1, SLA-DOA, SLA-DOB and TAP1) are linked to antigen processing and presentation functions, which is reminiscent of associations with disease traits reported for altered miRNA binding to MHC genes in humans. An inverse correlation in expression levels was demonstrated between miRNAs and co-expressed SLA targets by exploiting a published dataset (RNA-Seq and small RNA-Seq) of three porcine tissues. Our results support the resource value of RNA-Seq collections to identify SNPs that may lead to altered miRNA regulation patterns.

Marc D.,French National Institute for Agricultural Research
Frontiers in Bioscience | Year: 2010

A misfolded isoform of the prion protein (PrP) is the essential component of the prion diseases' agent. The prion concept has progressively gained acceptance, in a large part thanks to the realization that it played a role not only in the transmissible spongiform encephalopathies, but also in the non-Mendelian propagation of self-perpetuating phenotypes of the yeast Saccharomyces cerevisiae. Uncertainties about the nature of the agent and the function of PrP have fostered searches of nucleic acid ligands of the protein. In vitro methods of nucleic acid evolutions have been used to identify RNAs or DNAs that bind PrP, towards the triple objective of i) setting up new diagnostic tools, ii) identifying nucleic acids with which PrP may interact, as part of its physiological or pathological function, and iii) elucidating the pathological transconformation of PrP. This review will focus on these studies, their methods, the knowledge acquired from them about the prion protein, and the possibilities that they offer in the areas of diagnosis and therapy of prion diseases.

Boichard D.,French National Institute for Agricultural Research | Brochard M.,Institute Of Lelevage
Animal | Year: 2012

Cattle production faces new challenges regarding sustainability with its three pillars - economic, societal and environmental. The following three main factors will drive dairy cattle selection in the future: (1) During a long period, intensive selection for enhanced productivity has deteriorated most functional traits, some reaching a critical point and needing to be restored. This is especially the case for the Holstein breed and for female fertility, mastitis resistance, longevity and metabolic diseases. (2) Genomic selection offers two new opportunities: as the potential genetic gain can be almost doubled, more traits can be efficiently selected; phenotype recording can be decoupled from selection and limited to several thousand animals. (3) Additional information from other traits can be used, either from existing traditional recording systems at the farm level or from the recent and rapid development of new technologies and precision farming. Milk composition (i.e. mainly fatty acids) should be adapted to better meet human nutritional requirements. Fatty acids can be measured through a new interpretation of the usual medium infrared spectra. Milk composition can also provide additional information about reproduction and health. Modern milk recorders also provide new information, that is, on milking speed or on the shape of milking curves. Electronic devices measuring physiological or activity parameters can predict physiological status like estrus or diseases, and can record behavioral traits. Slaughterhouse data may permit effective selection on carcass traits. Efficient observatories should be set up for early detection of new emerging genetic defects. In the near future, social acceptance of cattle production could depend on its capacity to decrease its ecological footprint. The first solution consists in increasing survival and longevity to reduce replacement needs and the number of nonproductive animals. At the individual level, selection on rumen activity may lead to decreased methane production and concomitantly to improved feed efficiency. A major effort should be dedicated to this new field of research and particularly to rumen flora metagenomics. Low input in cattle production is very important and tomorrow's cow will need to adapt to a less intensive production environment, particularly lower feed quality and limited care. Finally, global climate change will increase pathogen pressure, thus more accurate predictors for disease resistance will be required. © 2011 The Animal Consortium.

Cabaret J.,French National Institute for Agricultural Research
Anti-Infective Agents in Medicinal Chemistry | Year: 2010

Anthelmintic resistance in humans has been suspected but remains until now anecdotic compared to the extension of the phenomenon in helminths of livestock or Plasmodium in humans. Human mass drug treatment has been offered against several filarial diseases, schistosomiasis and soil-transmitted nematode infections, thus the appearance of resistance is expected. Up to now the used drugs remain active but a follow up of their efficacy is needed. A poor observed efficacy is not always due to resistance and cases of false resistance are recorded or suspected. In such cases, the quality of the drug may be faulty since many of the proposed drugs on shelf are counterfeit in poor countries; in other countries the unregulated internet pharmacies may also propose counterfeit drugs. The quality drug may also have a poor absorption or metabolisation due to diet or to concomitant treatments of the patients. False resistance observation may arise from poor diagnostic or misdiagnosis and then diagnostic improvement is the main solution to be proposed. The evaluations of resistance in the field are mostly derived from in vivo efficacy assessments based in majority on before and after treatment measurements. The use of control group when feasible and more refined statistical tools should be implemented. When the resistance mechanisms are partly known (several classes of drugs in malaria or benzimidazole resistance of nematodes) molecular tests on parasites would be the best instrument for a follow up of resistance. The last cause of false resistance could also be simply poor compliance of drug use, particularly when the drug exerts unpleasant side effects or when the duration of treatment is long. The assessment of resistance is not always easy in field conditions due to all these confounding effects and false resistance should be an issue to be considered in most cases. © 2010 Bentham Science Publishers Ltd.

Boissonnas C.C.,University of Paris Descartes | Jouannet P.,University of Paris Descartes | Jammes H.,French National Institute for Agricultural Research
Fertility and Sterility | Year: 2013

Objective: To provide a link between epigenetics and male subfertility at the DNA, histone-protamine, and RNA levels and its consequences on fertilization and embryo development. Design: Review of the relevant literature. Setting: University-based clinical and research laboratories. Patient(s): Fertile and infertile men. Intervention(s): None. Main Outcome Measure(s): Critical review of the literature. Result(s): Epigenetic markers can be modified in infertile patients. Epigenetic modifications include methylation loss or gain on the global level and on imprinted genes, high levels of histone retention in spermatozoa, and deficiencies in some transcripts involved in spermatogenesis. Interestingly, these abnormalities are all linked together, because DNA methylation maintenance depends on DNA histone-protamine configuration which itself is stabilized by spermatozoal RNAs. Conclusion(s): The paternal genome has long been considered to be silent and passive in embryo formation. The epigenetic processes associated with the paternal DNA genome highlights its importance in male fertility as well as for embryo development. ©2013 by American Society for Reproductive Medicine.

Hamel L.-P.,Universite de Sherbrooke | Nicole M.-C.,Universite de Sherbrooke | Duplessis S.,French National Institute for Agricultural Research | Ellis B.E.,University of British Columbia
Plant Cell | Year: 2012

Mitogen-activated protein kinases (MAPKs) are evolutionarily conserved proteins that function as key signal transduction components in fungi, plants, and mammals. During interaction between phytopathogenic fungi and plants, fungal MAPKs help to promote mechanical and/or enzymatic penetration of host tissues, while plant MAPKs are required for activation of plant immunity. However, new insights suggest that MAPK cascades in both organisms do not operate independently but that they mutually contribute to a highly interconnected molecular dialogue between the plant and the fungus. As a result, some pathogenesis-related processes controlled by fungal MAPKs lead to the activation of plant signaling, including the recruitment of plant MAPK cascades. Conversely, plant MAPKs promote defense mechanisms that threaten the survival of fungal cells, leading to a stress response mediated in part by fungal MAPK cascades. In this review, we make use of the genomic data available following completion of whole-genome sequencing projects to analyze the structure of MAPK protein families in 24 fungal taxa, including both plant pathogens and mycorrhizal symbionts. Based on conserved patterns of sequence diversification, we also propose the adoption of a unified fungal MAPK nomenclature derived from that established for the model species Saccharomyces cerevisiae. Finally, we summarize current knowledge of the functions of MAPK cascades in phytopathogenic fungi and highlight the central role played by MAPK signaling during the molecular dialogue between plants and invading fungal pathogens. © 2012 American Society of Plant Biologists. All rights reserved.

Wolf S.,French National Institute for Agricultural Research | Greiner S.,Center for Organismal Studies Heidelberg
Protoplasma | Year: 2012

Plant cell growth is controlled by the balance between turgor pressure and the extensibility of the cell wall. Several distinct classes of wall polysaccharides and their interactions contribute to the architecture and the emergent features of the wall. As a result, remarkable tensile strength is achieved without relinquishing extensibility. The control of growth and development does not only require a precisely regulated biosynthesis of cell wall components, but also constant remodeling and modification after deposition of the polymers. This is especially evident given the fact that wall deposition and cell expansion are largely uncoupled. Pectins form a functionally and structurally diverse class of galacturonic acid-rich polysaccharides which can undergo abundant modification with a concomitant change in physicochemical properties. This review focuses on homogalacturonan demethylesterification catalyzed by the ubiquitous enzyme pectin methylesterase (PME) as a growth control module. Special attention is drawn to the recently discovered role of this process in primordial development in the shoot apical meristem. © 2012 Springer-Verlag.

Robaglia C.,Aix - Marseille University | Thomas M.,University Paris - Sud | Meyer C.,French National Institute for Agricultural Research
Current Opinion in Plant Biology | Year: 2012

The perception of nutrient and energy levels inside and outside the cell is crucial to adjust growth and metabolism to available resources. The signaling pathways centered on the conserved TOR and SnRK1/Snf1/AMPK kinases have crucial and numerous roles in nutrient and energy sensing and in translating this information into metabolic and developmental adaptations. In plants evidence is mounting that, like in other eukaryotes, these signaling pathways have pivotal and antagonistic roles in connecting external or intracellular cues to many biological processes, including ribosome biogenesis, regulation of translation, cell division, accumulation of reserves and autophagy. Data on the plant TOR pathway have been hitherto rather scarce but recent findings have shed new light on its roles in plants. Moreover, the distinctive energy metabolism of photosynthetic organisms may reveal new features of these ancestral eukaryotic signaling elements. © 2012 Elsevier Ltd.

Yoshimoto K.,French National Institute for Agricultural Research | Yoshimoto K.,Agro ParisTech
Plant and Cell Physiology | Year: 2012

Autophagy is an evolutionarily conserved intracellular process for the vacuolar degradation of cytoplasmic components. There is no doubt that autophagy is very important to plant life, especially because plants are immobile and must survive in environmental extremes. Early studies of autophagy provided our first insights into the structural characteristics of the process in plants, but for a long time the molecular mechanisms and the physiological roles of autophagy were not understood. Genetic analyses of autophagy in the yeast Saccharomyces cerevisiae have greatly expanded our knowledge of the molecular aspects of autophagy in plants as well as in animals. Until recently our knowledge of plant autophagy was in its infancy compared with autophagy research in yeast and animals, but recent efforts by plant researchers have made many advances in our understanding of plant autophagy. Here I will introduce an overview of autophagy in plants, present current findings and discuss the physiological roles of self-degradation. © The Author 2012. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

Zitt M.,French National Institute for Agricultural Research
Scientometrics | Year: 2012

J. K. Vanclay's article is a bold attempt to review recent works on the journal impact factor (JIF) and to call for alternative certifications of journals. The too broad scope did not allow the author to fulfill all his purposes. Attempting after many others to organize the various forms of criticism, with targets often broader than the JIF, we shall try to comment on a few points. This will hopefully enable us to infer in which cases the JIF is an angel, a devil, or a scapegoat. We shall also expand on a crucial question that Vanclay could not really develop in the reduced article format: the field-normalization. After a short recall on classical cited-side or ex post normalization and of the powerful influence measures, we will devote some attention to the novel way of citing-side or ex ante normalization, not only for its own interest, but because it directly proceeds from the disassembling of the JIF clockwork. © 2012 Akadémiai Kiadó, Budapest, Hungary.

Marino D.,French National Institute for Agricultural Research | Marino D.,French National Center for Scientific Research | Marino D.,University of Nice Sophia Antipolis | Dunand C.,CNRS Plant Research Laboratory | And 2 more authors.
Trends in Plant Science | Year: 2012

Reactive oxygen species (ROS) are highly reactive molecules able to damage cellular components but they also act as cell signalling elements. ROS are produced by many different enzymatic systems. Plant NADPH oxidases, also known as respiratory burst oxidase homologues (RBOHs), are the most thoroughly studied enzymatic ROS-generating systems and our understanding of their involvement in various plant processes has increased considerably in recent years. In this review we discuss their roles as ROS producers during cell growth, plant development and plant response to abiotic environmental constraints and biotic interactions, both pathogenic and symbiotic. This broad range of functions suggests that RBOHs may serve as important molecular 'hubs' during ROS-mediated signalling in plants. © 2011 Elsevier Ltd.

Tomas J.,French National Institute for Agricultural Research
Animal health research reviews / Conference of Research Workers in Animal Diseases | Year: 2012

The mammalian intestine harbors a large and diverse community of micro-organisms, known as the intestinal microbiota. Recent developments in molecular profiling methods, mainly based on microbial 16S ribosomal RNA gene sequencing, have provided unprecedented insights into the make-up and diversity of intestinal microbial communities. Using these culture-independent analyses, gut microbiota of several mammals including laboratory rodents, have been revisited. The laboratory rat is one of the major species bred and kept for scientific research. Although this animal is bred in confined environments and subjected to procedures for satisfying health requirements that hamper natural colonization, some major features of mammalian gut microbiota are conserved. However, the gut microbiota varies according to the breeding conditions of the rats and this could impact reproducibility of the experimental models. Determining the non-pathogenic microbial community might be relevant in standards of quality control of laboratory animals. Molecular profiling techniques could be applied to document this information.

Lannou C.,French National Institute for Agricultural Research
Annual Review of Phytopathology | Year: 2012

The first section presents the quantitative traits of pathogenicity that are most commonly measured by plant pathologists, how the expression of those traits is influenced by environmental factors, and why the traits must be taken into account for understanding pathogen evolution in agricultural systems. Particular attention is given to the shared genetic control of these traits by the host and the pathogen. Next, the review discusses how quantitative traits account for epidemic development and how they can be related to pathogen fitness. The main constraints that luence the evolution of quantitative traits in pathogen populations are detailed. Finally, possible directions for research on the management of pathogen virulence (as defined by evolutionists) and host quantitative resistance are presented. The review evaluates how the theoretical corpus developed by epidemiologists and evolutionists may apply to plant pathogens in the context of agriculture. The review also analyzes theoretical papers and compares the modeling hypotheses to the biological characteristics of plant pathogens. © 2012 by Annual Reviews. All rights reserved.

Fauvel M.,French National Institute for Agricultural Research | Chanussot J.,CNRS GIPSA Laboratory | Benediktsson J.A.,University of Iceland
Pattern Recognition | Year: 2012

Classification of remotely sensed images with very high spatial resolution is investigated. The proposed method deals with the joint use of the spatial and the spectral information provided by the remote-sensing images. A definition of an adaptive neighborhood system is considered. Based on morphological area filtering, the spatial information associated with each pixel is modeled as the set of connected pixels with an identical gray value (flat zone) to which the pixel belongs: The pixels neighborhood is characterized by the vector median value of the corresponding flat zone. The spectral information is the original pixels value, be it a scalar or a vector value. Using kernel methods, the spatial and spectral information are jointly used for the classification through a support vector machine formulation. Experiments on hyperspectral and panchromatic images are presented and show a significant increase in classification accuracies for peri-urban area: For instance, with the first data set, the overall accuracy is increased from 80% with a conventional support vectors machines classifier to 86% with the proposed approach. Comparisons with other contextual methods show that the method is competitive. © 2011 Elsevier Ltd. All rights reserved.

Mzoughi N.,French National Institute for Agricultural Research
Ecological Economics | Year: 2014

We examine the relationship between organic farming and subjective well-being or life satisfaction. Applying an ordered probit model to a sample of French farmers located in the Provence-Alpes-CÔte d'Azur (PACA) area (Southeast), we find that organic farmers report higher levels of life satisfaction, compared to the conventional ones. Moreover, this positive relationship holds for both recently-converted and earlier-converted farmers. Our findings also show that subjective well-being is positively associated with income, profitability, satisfaction at work, social recognition, and good health. © 2014 Elsevier B.V.

Chauvel B.,French National Institute for Agricultural Research
Weed Biology and Management | Year: 2011

Common ragweed (Ambrosia artemisiifolia L.) is one of the annual plants that were described recently as invasive weeds in Europe. This species is described as an invasive plant that produces seeds that are highly variable. Its production of variably sized seeds is regarded as promoting its spread in different environments. Experiments were carried out to determine the influence of the seed weight and temperature on germination and the influence of the seed weight and burial depth on seedling emergence. The seeds were divided into a number of classes of weight and the seed weight effect on germination was evaluated by Petri dish assays. In another experiment, the seeds were buried at different depths in a clay soil/sand mix to estimate the burial effect on germination and seedling emergence. The germination level of A. artemisiifolia was high overall, between 76.8% and 94.2%. The seed germination was modified by temperature but it was not influenced by the seed weight. The amounts of germination and seedling emergence were greater for the seeds on the soil surface and decreased with an increasing burial depth, from 2 to 8cm. No germination or emergence was observed for the seeds that were buried at 10 and 12cm. The lightest seeds were more sensitive to burial. A greater level of seedling emergence for those seeds that were placed near the soil surface could explain the success of this species in open habitats, where the probability of deeper burial is low. After high seed production, the management of A. artemisiifolia in fields could be partly achieved through soil tillage, burying seeds below 10cm, and not carrying out deep soil tillage the following year. © 2011 AgroSup Dijon. Weed Biology and Management © 2011 Weed Science Society of Japan.

Vignon M.,University of Pau and Pays de lAdour | Vignon M.,French National Institute for Agricultural Research
Journal of Experimental Marine Biology and Ecology | Year: 2012

Otolith morphometrics has been shown to provide a practical basis for stock discrimination and ageing. This approach has been extensively used by fisheries scientists over the last decades. However, the determinants of otolith shape are not fully understood and shape apparently results from the synergistic action of various confounding factors. In this study, I used a geometric morphometric approach to quantitatively investigate the concomitant effect of local environmental conditions and ontogeny on otolith shape. I specifically focused on the ontogenetic trajectories of otolith shape in a coral reef fish (Lutjanus kasmira) during an ontogenetic shift in habitat use, from juveniles settled in the estuary to adults inhabiting either the channel or the outer-reef off French Polynesia. Data emphasize that both ontogeny and environmental conditions influence otolith shape in an interactive way, potentially mediated by growth rate. More specifically, during the early life stages living in the estuary, otolith shape is mainly linked to fish size, indicating an ontogenetically determined development that induces an overall reshaping of the otoliths. In contrast, the transition from the estuarine to the reef life is considered as a crucial phase in fish life history, as revealed by an important change in the ontogenetic rate and direction of the otolith development for both habitats. After the shift in habitat use, otolith demonstrated divergent ontogenetic growth patterns, not in terms of heterochrony but in the magnitude and direction of morphological changes. This indicates that growth axis can be completely reshaped by environmental conditions, with respect to allometric component. This information is fundamental if otolith shape is to be used in fisheries management as an effective tool for modeling age-structured populations and stocks as a function of the use made of the habitat during life span. © 2012 Elsevier B.V.

Plumecocq G.,French National Institute for Agricultural Research
Ecological Economics | Year: 2014

This paper examines the discourse produced in the academic journal Ecological Economics from its inception in 1989, and compares this discourse with that of the field of environmental economics. I used methods for discourse analysis (Alceste and Iramuteq) on 6308 abstracts of papers published in four journals - namely Ecological Economics, the Journal of Environmental Economics and Management, Environmental Values, and Environmental and Resource Economics, published between 1989 and 2013. The results suggest that the discourses of ecological economics and environmental economics have grown closer over time. The semantic classification of co-occurrent terms used in Ecological Economics indicates increasing significance of the notions of ecosystem services and of monetary valuation. I argue that this trend is parallel to Costanza's career-path, which suggests the rise of a tacit recognition of the New Environmental Pragmatic scientific approach. I conclude with some of the implications for EE of promoting this kind of discourse to such an extent. © 2014 Elsevier B.V.

Boval M.,French National Institute for Agricultural Research | Dixon R.M.,University of Queensland
Animal | Year: 2012

The global importance of grasslands is indicated by their extent; they comprise some 26% of total land area and 80% of agriculturally productive land. The majority of grasslands are located in tropical developing countries where they are particularly important to the livelihoods of some one billion poor peoples. Grasslands clearly provide the feed base for grazing livestock and thus numerous high-quality foods, but such livestock also provide products such as fertilizer, transport, traction, fibre and leather. In addition, grasslands provide important services and roles including as water catchments, biodiversity reserves, for cultural and recreational needs, and potentially a carbon sink to alleviate greenhouse gas emissions. Inevitably, such functions may conflict with management for production of livestock products. Much of the increasing global demand for meat and milk, particularly from developing countries, will have to be supplied from grassland ecosystems, and this will provide difficult challenges. Increased production of meat and milk generally requires increased intake of metabolizable energy, and thus increased voluntary intake and/or digestibility of diets selected by grazing animals. These will require more widespread and effective application of improved management. Strategies to improve productivity include fertilizer application, grazing management, greater use of crop by-products, legumes and supplements and manipulation of stocking rate and herbage allowance. However, it is often difficult to predict the efficiency and cost-effectiveness of such strategies, particularly in tropical developing country production systems. Evaluation and on-going adjustment of grazing systems require appropriate and reliable assessment criteria, but these are often lacking. A number of emerging technologies may contribute to timely low-cost acquisition of quantitative information to better understand the soil-pasture-animal interactions and animal management in grassland systems. Development of remote imaging of vegetation, global positioning technology, improved diet markers, near IR spectroscopy and modelling provide improved tools for knowledge-based decisions on the productivity constraints of grazing animals. Individual electronic identification of animals offers opportunities for precision management on an individual animal basis for improved productivity. Improved outcomes in the form of livestock products, services and/or other outcomes from grasslands should be possible, but clearly a diversity of solutions are needed for the vast range of environments and social circumstances of global grasslands. © 2012 The Animal Consortium.

Trystram G.,French National Institute for Agricultural Research
Journal of Food Engineering | Year: 2012

Modelling is an important task in food engineering and numerous approaches are possible. Based on the massy experience the paper discusses the challenge, interest and difficulties of modelling of food and food processes. Some key points are specifically discussed mainly on the base of heat processing operation. Heat and mass transfer and their consequences on structure evolution and on the building of the chemical content of food are discussed. Different kind of modelling approaches are also discussed considering control, optimisation and design objective. The coming challenge is as a conclusion presented on two main questions. The building of parameters that are necessary for simulation, mainly using molecular modelling approaches and the challenges related with scales description and the way a continuous understanding becomes probably possible in the future between all the scales. © 2011 Elsevier Ltd. All rights reserved.

Ramayo-Caldas Y.,French National Institute for Agricultural Research
ISME Journal | Year: 2016

The ecological interactions within the gut microbial communities are complex and far from being fully understood. Here we report the first study that aims at defining the interaction network of the gut microbiota in pigs and comparing it with the enterotype-like clustering analysis. Fecal microbiota of 518 healthy piglets was characterized by 16S ribosomal RNA gene sequencing. Two networks were constructed at the genus and operational taxonomic unit levels. Within-network interactions mirrored the human gut microbiota relationships, with a strong co-exclusion between Prevotella and Ruminococcus genera, and were consistent with the two enterotype-like clusters identified in the pig microbiota. Remarkably, the cluster classification of the individuals was significantly associated with the body weight at 60 days of age (P=0.005) and average daily gain (P=0.027). To the best of our knowledge, this is the first study to provide an integrated overview of the porcine gut microbiota that suggests a conservation of the ecological community interactions and functional architecture between humans and pig. Moreover, we show that the microbial ecosystems and porcine growth traits are linked, which allows us to foresee that the enterotype concept may have an important role in the animal production industry.The ISME Journal advance online publication, 13 May 2016; doi:10.1038/ismej.2016.77. © 2016 International Society for Microbial Ecology

Nguyen-The C.,French National Institute for Agricultural Research | Nguyen-The C.,University of Avignon
LWT - Food Science and Technology | Year: 2012

The contribution of fruit and vegetables to the burden of foodborne diseases has increased since the end of the eighties, stressing the need to control biological hazards in processed products. Salmonella, verotoxigenic Escherichia coli and foodborne viruses were the main pathogens transmitted by fruit, vegetables and product thereof, except for heat-treated products which mostly transmitted pathogenic Clostridium and Bacillus. Pathogenic Clostridium and Bacillus need to multiply to high numbers, or produce toxins, in the processed fruit and vegetables to cause diseases, in contrast to some Salmonella, verotoxigenic E. coli and viruses. Heat resistance of hepatitis A virus in fruits products is presented and compared to the stability of fruit enzymes such as PME. In the case of high hydrostatic pressure, the efficacy to kill E. coli and Salmonella in fruit and vegetables juices is strongly affected by the juice matrix. Challenge tests showed that botulinum toxin production is possible during refrigerated storage of heat processed vegetables, but the risk that it would occur in real conditions remains unknown. In the case of Bacillus cereus a recent reassessment of the phylogeny permitted to improve assessment of the risk in cooked chilled courgette purée. © 2012 Elsevier Ltd.

Bossy R.,French National Institute for Agricultural Research
BMC bioinformatics | Year: 2012

We present the BioNLP 2011 Shared Task Bacteria Track, the first Information Extraction challenge entirely dedicated to bacteria. It includes three tasks that cover different levels of biological knowledge. The Bacteria Gene Renaming supporting task is aimed at extracting gene renaming and gene name synonymy in PubMed abstracts. The Bacteria Gene Interaction is a gene/protein interaction extraction task from individual sentences. The interactions have been categorized into ten different sub-types, thus giving a detailed account of genetic regulations at the molecular level. Finally, the Bacteria Biotopes task focuses on the localization and environment of bacteria mentioned in textbook articles. We describe the process of creation for the three corpora, including document acquisition and manual annotation, as well as the metrics used to evaluate the participants' submissions. Three teams submitted to the Bacteria Gene Renaming task; the best team achieved an F-score of 87%. For the Bacteria Gene Interaction task, the only participant's score had reached a global F-score of 77%, although the system efficiency varies significantly from one sub-type to another. Three teams submitted to the Bacteria Biotopes task with very different approaches; the best team achieved an F-score of 45%. However, the detailed study of the participating systems efficiency reveals the strengths and weaknesses of each participating system. The three tasks of the Bacteria Track offer participants a chance to address a wide range of issues in Information Extraction, including entity recognition, semantic typing and coreference resolution. We found common trends in the most efficient systems: the systematic use of syntactic dependencies and machine learning. Nevertheless, the originality of the Bacteria Biotopes task encouraged the use of interesting novel methods and techniques, such as term compositionality, scopes wider than the sentence.

Ratkovic Z.,French National Institute for Agricultural Research
BMC bioinformatics | Year: 2012

Bacteria biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications (e.g., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data.

Marze S.,French National Institute for Agricultural Research
Food and Function | Year: 2015

Despite the considerable number of in vivo and in vitro studies on the digestive fate of lipophilic nutrients, micronutrients, and bioactives, the effects of the structure and composition of foods on the physicochemical mechanisms of luminal digestion are still poorly understood. Studying them is indeed complex because the number of parameters is high and many of them are interdependent. To solve this problem, an in silico simulation based on a multi-agent system was recently proposed to study the intestinal bioaccessibility of lipophilic nutrients and micronutrients from a single oil droplet. The roles of lipolysis and solubilization in bile salt were included. The effects of several food and digestion parameters were in line with those reported in the experimental literature. The goal of the research reported in this new article was to include more digestion parameters in the simulation in order to make it more realistic against complex cases. This was done in one specific digestion condition reflecting in vitro experiments, using droplets of tricaprylin or triolein containing vitamin A. The structure and principles of the original model were kept, with independent local modifications in order to study each factor separately. First, a gastric step was added where lipolysis took place, and only a marginal effect on the following intestinal step was found. Then, the chemical form of vitamin A, either non-hydrolyzed retinyl ester or retinyl ester instantly hydrolyzed into retinol, was investigated by considering different localizations in the droplet, resulting in a higher bioaccessibility for the retinol. The case of a mixture of tricaprylin and triolein indicated an influence of the oil phase viscosity. The consideration of mixed micelles compared to simple bile salt micelles was also investigated, and resulted in a higher vitamin A bioaccessibility, especially with triolein. Finally, a full model including the most influential parameters was tested to simulate the digestion of triglyceride-limonene mixtures, giving bioaccessibility trends in very good agreement with the literature. This journal is © The Royal Society of Chemistry 2015.

Bazinet R.P.,University of Toronto | Laye S.,French National Institute for Agricultural Research | Laye S.,University of Bordeaux 1
Nature Reviews Neuroscience | Year: 2014

The brain is highly enriched with fatty acids. These include the polyunsaturated fatty acids (PUFAs) arachidonic acid and docosahexaenoic acid, which are largely esterified to the phospholipid cell membrane. Once PUFAs are released from the membrane, they can participate in signal transduction, either directly or after enzymatic conversion to a variety of bioactive derivatives ('mediators'). PUFAs and their mediators regulate several processes within the brain, such as neurotransmission, cell survival and neuroinflammation, and thereby mood and cognition. PUFA levels and the signalling pathways that they regulate are altered in various neurological disorders, including Alzheimer's disease and major depression. Diet and drugs targeting PUFAs may lead to novel therapeutic approaches for the prevention and treatment of brain disorders. © 2015 Macmillan Publishers Limited.

Sadras V.O.,South Australian Research And Development Institute | Lemaire G.,French National Institute for Agricultural Research
Field Crops Research | Year: 2014

The nitrogen economy of the crop is a critical driver of biomass and grain production, and its importance is reflected in a large, worldwide research effort to link nitrogen, growth and yield. Particular research questions require measurement of specific traits, hence the need to quantify multiple, often complementary traits including crop nitrogen uptake, nitrogen use efficiency and its components, nitrogen concentration in the crop and its parts, down to relevant enzymes (e.g. nitrate reductase) and other products of gene expression. Nitrogen uptake, however, is co-regulated by both soil nitrogen availability and crop biomass accumulation; hence, crop nitrogen uptake or shoot nitrogen concentration reflect univocally crop nitrogen status only if comparisons are made at similar biomass. Although the allometric relationships between biomass and nitrogen uptake have been established for over two decades, many studies still report results in terms of nominal treatments, e.g. high vs low nitrogen, which are uninformative; curves relating yield and fertiliser rate, which are of local interest but provide little insight on the underlying processes and have low generic value; and nitrogen-related traits that are incomplete or inadequate to quantify crop nutrition status. Often, the allometric relationships between nitrogen and biomass are overlooked. In this opinion paper, we summarise the already well established concepts of dilution curves and nitrogen nutrition index, outline the standard partitioning of nitrogen use efficiency, and highlight the confounded effects in nitrogen use efficiency when the allometric relationship between nitrogen uptake and biomass is ignored. A sample of recent papers is used to survey the most common approaches to characterise nitrogen related traits. We illustrate the application of dilution curves and nitrogen nutrition index in the assessment and interpretation of crop responses to agronomic practices and comparisons of wheat cultivars and maize hybrids. © 2014 Elsevier B.V.

Biacchesi S.,French National Institute for Agricultural Research
Veterinary Research | Year: 2011

Aquaculture has expanded rapidly to become a major economic and food-producing sector worldwide these last 30 years. In parallel, viral diseases have emerged and rapidly spread from farm to farm causing enormous economic losses. The most problematic viruses encountered in the field are mainly, but not exclusively, RNA viruses belonging to the Novirhabdovirus, Aquabirnavirus, Alphavirus and Betanodavirus genera. The recent establishment of reverse genetics systems to recover infectious fish RNA viruses entirely from cDNA has made possible to genetically manipulate the viral genome. These systems have provided powerful tools to study all aspects of the virus biology and virus-host interactions but also gave the opportunity to use these viruses as live vaccines or as gene vectors. This review provides an overview on the recent breakthroughs achieved by using these reverse genetics systems in terms of viral protein function, virulence and host-specificity factor, vaccine development and vector design. © 2011 Biacchesi; licensee BioMed Central Ltd.

Beaujean N.,French National Institute for Agricultural Research
Reproduction, Fertility and Development | Year: 2015

It is very important for embryologists to understand how parental inherited genomes are reprogrammed after fertilisation in order to obtain good-quality embryos that will sustain further development. In mammals, it is now well established that important epigenetic modifications occur after fertilisation. Although gametes carry special epigenetic signatures, they should attain embryo-specific signatures, some of which are crucial for the production of healthy embryos. Indeed, it appears that proper establishment of different epigenetic modifications and subsequent scaffolding of the chromatin are crucial steps during the first cleavages. This 'reprogramming' is promoted by the intimate contact between the parental inherited genomes and the oocyte cytoplasm after fusion of the gametes. This review introduces two main epigenetic players, namely histone post-translational modifications and DNA methylation, and highlights their importance during early embryonic development. © IETS 2015.

Debierre-Grockiego F.,French National Institute for Agricultural Research
Trends in Parasitology | Year: 2010

Induction of sterilizing immunity by vaccination is extremely difficult because of the evasion mechanisms developed by parasites, and identification of new targets for therapy is therefore important. Glycosylphosphatidylinositols (GPIs) of parasites are glycolipids that participate in pathogenicity of parasitic diseases. Studies of Plasmodium falciparum and Trypanosoma brucei indicate that GPIs are good candidates for developing vaccines against malaria and sleeping sickness, respectively. By contrast, fatty acids isolated from P. falciparum and Toxoplasma gondii can inhibit the production of inflammatory cytokines induced by the GPIs in macrophages. GPIs are considered to be toxins that, if present in large amounts, induce irreversible damages to the host, and treatment with fatty acids could reduce this effect. © 2010 Elsevier Ltd.

Trayer V.,French National Institute for Agricultural Research
General and comparative endocrinology | Year: 2013

Cortisol is a pleiotropic glucocorticoid hormone that acts through the intracellular glucocorticoid receptors (GR). Cortisol affects many important biological functions in mammals, including immune function, behavior, stress, metabolism, growth and organogenesis. In fishes, cortisol has an additional function in the osmoregulatory activity of ionocytes (ICs). Although much progress has been made toward understanding cortisol action at the levels of adult osmoregulatory tissues, the developmental functions of cortisol and its receptors in ICs remain to be clarified. We first analyzed the total contents of both cortisol and corticosteroid receptor mRNAs (GR1, GR2 and MR) during medaka development. Although low levels of cortisol were detected during development of the medaka embryo, maternal GR1, GR2 and MR transcripts were detected at higher levels than zygotic transcripts. We investigated the effect of exogenous cortisol on IC number during medaka embryogenesis. We observed that cortisol treatment induced an earlier expansion of the IC population but did not modify the final IC number. Using functional genomic approaches, we also tested the involvement of GR1, GR2 and mineralocorticoid receptor (MR) in IC development by systematic knock-down with translation-blocking morpholinos. Only GR2 knock-down led to a reduction of the total number of ICs in the epidermis. In addition, a GR2 splice-blocking morpholino did not have any effect on the biogenesis of ICs, underscoring the importance of maternally inherited GR2 mRNAs. We propose that maternal GR2, but not GR1 or MR, is a major pathway in the IC biogenesis in medaka most likely through cortisol activation, and that cortisol exposition fine-tunes their developmental timing. These findings provide a framework for future research on the regulatory functions of corticosteroids in euryhaline fishes and provide medaka as an advantageous model to further elucidate the underlying molecular regulatory mechanisms of IC development. Copyright © 2013 Elsevier Inc. All rights reserved.

Dusko Ehrlich S.,French National Institute for Agricultural Research
Gastroenterologie Clinique et Biologique | Year: 2010

A major challenge in the human metagenomics field is to identify associations of the bacterial genes and human phenotypes and act to modulate microbial populations in order to improve human health and wellbeing. MetaHIT project addresses this ambitious challenge by developing and integrating a number of necessary approaches within the context of the gut microbiome. Among the first results is the establishment of a broad catalog of the human gut microbial genes, which was achieved by an original application of the new generation sequencing technology. The catalog contains 3.3 million non-redundant genes, 150-fold more than the human genome equivalent and includes a large majority of the gut metagenomic sequences determined across three continents, Europe, America and Asia. Its content corresponds to some 1000 bacterial species, which likely represent a large fraction of species associated with humankind intestinal tract. The catalog enables development of the gene profiling approaches aiming to detect associations of bacterial genes and phenotypes. These should lead to the speedy development of diagnostic and prognostic tools and open avenues to reasoned approaches to the modulation of the individual's microbiota in order to optimize health and well-being. © 2010 Elsevier Masson SAS.

Timmers A.C.,French National Institute for Agricultural Research
Journal of Microscopy | Year: 2016

Plants are ideal organisms for light microscopical studies of cellular mechanisms controlling cell organisation and cell functioning. However, most plant organs are not transparent to light which prevents high resolution imaging deep within plant tissues. Classically, access into plant organs is achieved by sectioning or whole-mount tissue clearing. Until recently, the protocols for clearing destroyed the signal from fluorescent markers which prevented the imaging of the distribution of fluorescent proteins and the three-dimensional reconstruction from optical slices of whole plant organs. From 2011, a number of protocols have been developed for whole brain and whole organism imaging for animal studies. Now, these protocols have been adapted for in-depth imaging of whole plant organs. Here, I present an overview of clearing techniques of plant organs and highlight the latest developments of plant tissue clearing in combination with high resolution fluorescence microscopy. © 2016 Royal Microscopical Society.

Marze S.,French National Institute for Agricultural Research
Food and Function | Year: 2014

The digestion of lipophilic nutrients and micronutrients requires numerous and simultaneous processes of chemical, physical and biological nature. Studying these processes experimentally is challenging, explaining why there is only little information about the mechanisms and interactions involved. Nevertheless, the bioaccessibility of lipophilic micronutrients is poorly understood so new investigation approaches are needed, all the more when digestion of lipophilic nutrients is also involved. In this article, the development of a coarse-grained simulation with no adjustable parameter is reported, enabling the study of the chemical and physical processes controlling bioaccessibility in such systems. The intestinal digestion of a droplet of a pure triglyceride containing a lipophilic vitamin was simulated to obtain their bioaccessibility kinetics (via lipolysis and/or solubilization in bile salt). The parameters examined here were the type of triglyceride, the type of vitamin, the digestive fluid amount, the droplet size, and different digestion conditions reflecting the in vitro or in vivo cases. Among these structure and composition parameters, the type of triglyceride and the digestion conditions had the greatest effects on bioaccessibility. An interplay between triglyceride digestion and micronutrient bioaccessibility kinetics was evidenced, highlighting the roles of the different parameters, in agreement with the experimental literature. This new approach is shown to be relevant to both nutrition and pharmacology. © 2014 The Royal Society of Chemistry.

Pieri P.,French National Institute for Agricultural Research
Ecological Modelling | Year: 2010

Row crops like vineyards undergo various and significant manipulations of training system and cultural practices, which strongly influence the quality of products. Variations of water vapour fluxes from the soil surface and the leaves in the row volume are closely linked to the ratio of energy available to each compartment. A physically realistic model of available energy partition between the rows and the soil surface is therefore a key factor towards optimization of such systems, and must be included in canopy models. A number of available models were not directly validated. The purpose of the study was therefore to design a model of net radiation partition and check it directly. The model of net radiation partition between rows (Rnv), considered as a whole, and intervening soil surface (Rns) of a row-crop canopy was developed from physically realistic yet simple assumptions:-global solar (short wave) radiation partition was calculated by a previously validated geometric model;-long-wave radiative fluxes between the soil surface, the rows and the atmosphere were calculated from the corresponding view factors, which only depended on canopy geometry;-atmospheric radiation was estimated by a simple empirical relation based on air temperature as the only input variable;-air temperature in the vicinity of leaves replaced leaf surface temperatures as a more convenient input variable, with little loss of information. The input variables were incoming direct and diffuse solar radiation, soil surface mean temperature and air temperature near the leaves. The main parameters were soil and leaf albedos, row porosity and dimensions. A direct validation of the model was attempted by measuring net radiation above the canopy and at five positions above the soil surface in a vineyard of the Bordeaux area. The reliability of soil surface net radiation measurements was estimated by thorough error propagation analysis. When found significant, errors were corrected and finally soil surface net radiation data were corrected only for delay in direct downward solar radiation striking net radiometers, because canopy was discontinuous and height of net radiometers was not negligible compared to canopy height. In these conditions, model calculations were in agreement with measurements, although the model slightly underestimated Rns and therefore overestimated Rnv. As the mean error was about 20 W m-2, and therefore compatible with instrument accuracy, the results were considered satisfactory. This available energy partition model is able to estimate radiative balance in various canopy systems and in various thermal environment conditions, leading to easier simulations of energy balance and water fluxes. It could therefore be a useful tool for optimizing row-crop canopies, taking fully into account any kind of present or future thermal environment. © 2009 Elsevier B.V. All rights reserved.

Gerdeaux D.,French National Institute for Agricultural Research
Hydrobiologia | Year: 2011

In France, the Arctic charr (Salvelinus alpinus) is native in only two lakes (Lakes Bourget and Geneva), in the most southerly part of its distribution area. It is a profundal morph living at depths of between 30 and 100 m in Lake Geneva. Following considerable stocking of Lake Geneva with juvenile Arctic charr and some good results during the 1980s, catches are currently declining. Several hypotheses have been proposed to explain this decrease, but the potential influence of warming of the lake in the 1990s has not been considered. This article studies the relationship between the strength of the cohorts and the temperature in Lake Geneva from 1992 to 2002, and discusses the various potential causes of the population collapse observed. The findings reveal close correlation between water temperature and the strength of the cohorts. It is concluded that the recent warming of Lake Geneva may have a significant direct or indirect impact on the Arctic charr population. © Springer Science+Business Media B.V. 2010.

Delagrange S.,University of Quebec at Montreal | Delagrange S.,French National Institute for Agricultural Research
Environmental and Experimental Botany | Year: 2011

Processes involved in leaf photosynthetic acclimation to light and throughout the growing season were investigated in two hardwood species (Acer saccharum and Betula alleghaniensis), which differed in their level of shade-tolerance. For both species, variation in traits related to (i) leaf morphology (LMA, leaf mass:area ratio), (ii) leaf N content (NA, leaf nitrogen content on an area basis and NM, N concentration in leaf dry mass), (iii) leaf N partitioning among photosynthetic functions (Pr, N allocated to Rubisco, and Pb, N allocated to bioenergetics), and (iv) leaf photosynthetic capacity (Vcmax, maximal carboxylation rates, and Jmax, maximal light-driven electron flow) were assessed at three different times during the growing season (early, mid- and late summer) and under four contrasting light regimes (40, 17, 6 and 2% of full sunlight). For both species, light-driven variation in most traits was greater than their seasonally driven variation. Furthermore, results showed for both species the pre-eminence of LMA changes in the light-driven acclimation of NA. Importance of NM to variation in NA was restricted to seasonal acclimation, especially for the less shade-tolerant species, B. alleghaniensis. Similarly, for both species, light-driven acclimation of leaf photosynthetic capacities was tightly related to variation in NA, which was related to LMA changes. However, variation in Pr and Pb better explained seasonally driven variation in Vcmax and Jmax, specifically under lower light levels, where NA was low. Thus, the great variability observed for leaf activity in response to contrasting light environments was related to efficient morphological adjustments, regardless of species level of shade-tolerance. Finally, physiological adjustments were mainly involved in fine-scale changes observed during seasonally driven acclimation of leaves, when LMA was constrained to a slight range of variation. © 2010 Elsevier B.V.

Wallach D.,French National Institute for Agricultural Research
Agronomy Journal | Year: 2011

It is common practice to calibrate crop models. This involves estimating some of the model parameters to give a better fit of the model to data. The purpose of this study was to investigate the statistical treatment of crop model calibration, which has not previously been done and is important to better understand the properties of the calibrated model. We considered the case where there is only a single type of variable measured, in the limit of a very large amount of data, and where estimation is based on least squares. We supposed that the individual process models that make up a crop model are such that, for the true parameter values, model error has expectation zero and is independent of the explanatory variables. We show that even in this case, the crop model does not have these properties (i.e., it is misspecified). Based on the structure of crop models and a simulation study, we argue that misspecification is oft en quite important for crop models. Under misspecification, calibration still tends to minimize prediction error but only for the variable and sampled population used for calibration. There is no assurance that calibration improves prediction for other variables or other populations. © 2011 by the American Society of Agronomy. All rights reserved.

Poultry production has been widely criticized for its negative environmental impact related to the quantity of manure produced and to its nitrogen and phosphorus content. In this study, we investigated which traits related to excretion could be used to select chickens for lower environmental pollution.The genetic parameters of several excretion traits were estimated on 630 chickens originating from 2 chicken lines divergently selected on apparent metabolisable energy corrected for zero nitrogen (AMEn) at constant body weight. The quantity of excreta relative to feed consumption (CDUDM), the nitrogen and phosphorus excreted, the nitrogen to phosphorus ratio and the water content of excreta were measured, and the consequences of such selection on performance and gastro-intestinal tract (GIT) characteristics estimated. The genetic correlations between excretion, GIT and performance traits were established. Heritability estimates were high for CDUDM and the nitrogen excretion rate (0.30 and 0.29, respectively). The other excretion measurements showed low to moderate heritability estimates, ranging from 0.10 for excreta water content to 0.22 for the phosphorus excretion rate. Except for the excreta water content, the CDUDM was highly correlated with the excretion traits, ranging from -0.64 to -1.00. The genetic correlations between AMEn or CDUDM and the GIT characteristics were very similar and showed that a decrease in chicken excretion involves an increase in weight of the upper part of the GIT, and a decrease in the weight of the small intestine. In order to limit the environmental impact of chicken production, AMEn and CDUDM seem to be more suitable criteria to include in selection schemes than feed efficiency traits.

Derrien D.,French National Institute for Agricultural Research | Amelung W.,University of Bonn
European Journal of Soil Science | Year: 2011

Soils contain the largest carbon (C) reservoir on Earth, but the mean residence time (MRT) of soil C is often poorly estimated, despite its importance for assessing the efficiency with which soils may serve as a sink for atmospheric C. The objective of this study was to evaluate how the structure of simple models of soil C dynamics affects the MRT determined from isotope-mixing experiments, using data from field studies with either artificial labelling (FACE) or C3/C4 vegetation change. We first highlighted theoretically how non-steady-state conditions and the model structure (one single, two successive, or two parallel C pools) can have an impact on the MRT assessment. We then tested these different model structures against published data on the dynamics of different soil organic matter separates and their constituents. Our findings indicated that many of the reviewed studies assumed wrongly that the system was at steady state or could be described by a single-pool approach. To select the correct model, exact knowledge of C input rates and several data points are needed from the beginning of the experiment. For steady-state conditions an apparent temporal change of MRT computed from a single-pool model is thus a clear indicator that a two-pool approach must be chosen. The errors made by the wrong choice of model varied with the length of the experiment and usually resulted in an over-estimate of MRT by a factor of 1.15 for some data published on physical size separates, but by a factor of up to 11 for individual microbial biomarkers such as muramic acid. © 2011 The Authors. Journal compilation © 2011 British Society of Soil Science.

Lamine C.,French National Institute for Agricultural Research
Journal of Rural Studies | Year: 2011

The growing criticism of intensive agricultural practices that lead to a deterioration of natural resources and a decrease of biodiversity has progressively led to more environmental constraints being put on agricultural activities through an "ecologization" of agricultural policies. The aims of these policies have been to protect environmentally sensitive areas, to improve groundwater quality and, more recently, to develop organic farming and/or reduce pesticide use. However, these efforts are still a far cry from a robust ecologization of agricultural practices. In order to identify the conditions for the implementation of such an ecologization, the changes in practices from conventional agriculture towards organic farming and integrated pest management (IPM) are investigated using a sociological study of farmers' trajectories, coupled with the ESR (Efficiency-Substitution-Redesign) framework developed by biological and agricultural scientists. This combined approach reveals that a robust ecologization of agricultural practices requires us to take into account the specific and variable tempo of farmers' trajectories and to redesign not only technical agricultural systems but also interactions within larger agrifood systems. © 2011 Elsevier Ltd.

Small livestock (goats, sheep, llamas, camels...) like other agricultural activities could have to face dramatic social, economical and environmental challenges. These challenges are identified underlining that these activities are often important and well present in countries with low incomes or in less favored areas. Although they are often low input production systems with lower environmental impacts, they face desertification and less water availability, genetic erosion, soil degradation and degradation of rangelands, competitions for land use. The needs of policy on more research, education, micro credits, organization and extension are enhanced. A global review of publications in the main scientific journals shows that relatively few works are still dedicated to marketing, Economic development, management and productions systems. The main subjects related to these challenges are the control of emergent diseases and parasites, the improvement of nutrition in harsh conditions, the genetic characterization of local breeds. But these results confirm that most articles have few links with the demand for innovation. The several journals in social science publish relatively few works on these livestock activities. To face these challenges, the discussion proposes new forms of governance in which priority is given to the participation of all stakeholders and the confrontation between local and scientific knowledge. This would have consequences on educational programs and training. The awareness of the public powers on these questions has to be improved by a coordinated and argued active communication. At short term, new types of events and conferences at local and international levels have to be created to manage innovation and transitions towards the necessary destabilizing changes. © 2011 Elsevier B.V.

Marze S.,French National Institute for Agricultural Research
Food and Function | Year: 2015

Digestion is an important process, the first one in the conversion of food to energy. From this angle, digestion of nutrients was extensively studied, and this process was found to be very efficient. Nevertheless, many molecules contained in food do not bring energy but are essential as they allow maintaining normal body functions. These are the micro-nutrients, including vitamins and minerals. On top of that, recent nutrition research identified many other bioactive molecules (termed micro-constituents as they only represent a small part of the food) playing a role in the health status, e.g. contributing to the prevention of chronic diseases. However, it was shown that their digestion is much less efficient, especially that of lipophilic micro-constituents (such as lipophilic vitamins, carotenoids, cholesterol and other steroids) depending on food structure and composition. Enhancing their health effects through optimal absorption and bioavailability thus requires a comprehensive knowledge of their release from food within the gastrointestinal tract. To study this step, of which the endpoint is termed bioaccessibility, in vitro digestion methods proved to be well adapted to fundamental research. This review reports the effects of the physicochemical parameters controlling the bioaccessibility of various lipophilic micro-constituents from emulsion. Notably, it appears that this bioaccessibility is related to the bioaccessibility of lipid nutrients, as their kinetics are interrelated. This knowledge will enable the formulation of food in terms of structure and composition to obtain optimal bioaccessibility. As the latter likely controls bioavailability, prevention of some metabolic disorders could be targeted in the long term. © The Royal Society of Chemistry 2015.

Macek B.,University of Tubingen | Mijakovic I.,French National Institute for Agricultural Research
Proteomics | Year: 2011

Protein phosphorylation on serine, threonine and tyrosine is established as an important regulatory modification in bacteria. A growing number of studies employing mass spectrometry-based proteomics report large protein phosphorylation datasets, providing precise evidence for in-vivo phosphorylation that is especially suitable for functional follow-up. Here, we provide an overview of the strategies currently used in bacterial phosphoproteomics, with an emphasis on gel-free proteomics and approaches that enable global detection of phosphorylation sites in bacterial proteins. The proteomics technology has matured sufficiently to permit routine characterization of phosphoproteomes and phosphopeptides with high sensitivity; we argue that the next challenge in the field will be the large-scale detection of protein kinase and phosphatase substrates and their integration into regulatory networks of the bacterial cell. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sakr N.,French National Institute for Agricultural Research
Archives of Phytopathology and Plant Protection | Year: 2011

Relationship between aggressiveness and zoosporangia viability was studied in seven Plasmopara halstedii (sunflower downy mildew) isolates of races 100, 300, 304, 314, 710, 704 and 714. Aggressiveness criteria including latent period and sporulation density were analysed on sunflower inbred line showing a high level of quantitative resistance. There were significant differences between pathogen isolates for the two aggressiveness criteria. Viability analyses were performed on oval and spheric zoosporangia. The number of zoospores released from oval zoosporangia was significantly higher than those released from spheric ones. The oval zoosporangia for more aggressive isolates of races 100 and 3xx produced more zoospores than the oval ones for less aggressive isolates of races 7xx. There was a significant correlation between aggressiveness criteria and the number of zoospores released from oval zoosporangia and vice versa for zoospores released from spheric ones. It is concluded that the relationship between aggressiveness and oval zoosporangia viability may be established in P. halstedii. © 2011 Taylor & Francis.

Quiniou S.M.A.,U.S. Department of Agriculture | Boudinot P.,French National Institute for Agricultural Research | Bengten E.,University of Mississippi Medical Center
Immunogenetics | Year: 2013

A comprehensive survey of channel catfish Toll-like receptors (TLRs) was undertaken following a genomic PCR approach based on degenerate primers. Twenty different TLRs were identified in channel catfish. Channel catfish TLR sequences were characterized by phylogenetic analysis based on their conserved Toll/interleukin-1 receptor domain and by in-depth analysis of leucine-rich repeat (LRR) motifs of the ligand binding extracellular domain (ECD). The catfish have representatives of all the TLR types defined in vertebrates with the exception of TLR6, TLR10, TLR11, TLR12, TLR13, TLR15, TLR23, and TLR24. Additionally, two new types were discovered: TLR25 and TLR26. TLR25 is also present in cyprinids, cichlids, plecoglossids, and adrianichthyids, suggesting its presence early in fish evolution. To date, TLR26 was found only in channel catfish. Like TLR18-23, TLR25 and TLR26 were not found in any other vertebrate classes and appear to be fish specific. Data mining using the catfish TLR sequences revealed that in addition to ictalurids and cyprinids, TLR4 is also present in salmonids. TLR19 and TLR20 were both found in ictalurids, cyprinids, and salmonids, demonstrating a wider range than previously known. The LRR structure within ECDs appeared generally well conserved. TLR7 demonstrated a very high identity to human TLR7 strongly suggesting that ligand specificity maybe conserved. Finally, expression profiling confirmed that most TLRs are widely expressed in a diversity of tissues and revealed marked differences of expression level. © 2013 Springer-Verlag Berlin Heidelberg (outside the USA).

Teychene B.,National Polytechnic Institute of Toulouse | Guigui C.,French National Institute for Agricultural Research | Cabassud C.,French National Center for Scientific Research
Water Research | Year: 2011

For membrane bioreactors (MBR) applied to wastewater treatment membrane fouling is still the prevalent issue. The main limiting phenomena related to fouling is a sudden jump of the transmembrane pressure (TMP) often attributed to the collapse of the fouling layer. Among existing techniques to avoid or to delay this collapse, the addition of active particles membrane fouling reducers (polymer, resins, powdered activated carbon (PAC), zeolithe...) showed promising results.Thus the main objective of this work is to determine if fouling can be reduced by inclusion of inert particles (500 nm and inert compared to other fouling reducers) and which is the impact on filtration performances of the structuring of the fouling. Those particles were chosen for their different surface properties and their capability to form well structured layer.Results, obtained at constant pressure in dead end mode, show that the presence of particles changes foulant deposition and induces non-compressible fouling (in the range of 0.5-1 bar) and higher rejection values compared to filtration done on supernatant alone. Indeed dead end filtration tests show that whatever interactions between biofluid and particles, the addition of particles leads to better filtration performances (in terms of rejection, and fouling layer compressibility). Moreover results confirm the important role played by macromolecular compounds, during supernatant filtration, creating highly compressible and reversible fouling.In conclusion, this study done at lab-scale suggests the potential benefit to engineer fouling structure to control or to delay the collapse of the fouling layer. Finally this study offers the opportunities to enlarge the choice of membrane fouling reducers by taking into consideration their ability to form more consistent fouling (i.e. rigid, structured fouling). © 2010 Elsevier Ltd.

Fahrig L.,Carleton University | Baudry J.,French National Institute for Agricultural Research | Brotons L.,Center Tecnologic Forestal Of Catalonia | Burel F.G.,University of Rennes 1 | And 5 more authors.
Ecology Letters | Year: 2011

Ecology Letters (2011) 14: 101-112 Biodiversity in agricultural landscapes can be increased with conversion of some production lands into 'more-natural'- unmanaged or extensively managed - lands. However, it remains unknown to what extent biodiversity can be enhanced by altering landscape pattern without reducing agricultural production. We propose a framework for this problem, considering separately compositional heterogeneity (the number and proportions of different cover types) and configurational heterogeneity (the spatial arrangement of cover types). Cover type classification and mapping is based on species requirements, such as feeding and nesting, resulting in measures of 'functional landscape heterogeneity'. We then identify three important questions: does biodiversity increase with (1) increasing heterogeneity of the more-natural areas, (2) increasing compositional heterogeneity of production cover types and (3) increasing configurational heterogeneity of production cover types? We discuss approaches for addressing these questions. Such studies should have high priority because biodiversity protection globally depends increasingly on maintaining biodiversity in human-dominated landscapes. © 2010 Blackwell Publishing Ltd/CNRS.

Mazenc F.,French National Institute for Agricultural Research | Malisoff M.,Louisiana State University
IEEE Transactions on Automatic Control | Year: 2010

We provide new techniques for building explicit global strict Lyapunov functions for broad classes of periodic time varying nonlinear systems satisfying LaSalle conditions. We illustrate our work using the Lotka-Volterra model, which plays a fundamental role in bioengineering. We use our strict Lyapunov constructions to prove robustness of the Lotka-Volterra tracking dynamics to uncertainty in the death rates. © 2006 IEEE.

Jacquin-Joly E.,French National Institute for Agricultural Research
International journal of biological sciences | Year: 2012

Chemical senses are crucial for all organisms to detect various environmental information. Different protein families, expressed in chemosensory organs, are involved in the detection of this information, such as odorant-binding proteins, olfactory and gustatory receptors, and ionotropic receptors. We recently reported an Expressed Sequence Tag (EST) approach on male antennae of the noctuid moth, Spodoptera littoralis, with which we could identify a large array of chemosensory genes in a species for which no genomic data are available.Here we describe a complementary EST project on female antennae in the same species. 18,342 ESTs were sequenced and their assembly with our previous male ESTs led to a total of 13,685 unigenes, greatly improving our description of the S. littoralis antennal transcriptome. Gene ontology comparison between male and female data suggested a similar complexity of antennae of both sexes. Focusing on chemosensation, we identified 26 odorant-binding proteins, 36 olfactory and 5 gustatory receptors, expressed in the antennae of S. littoralis. One of the newly identified gustatory receptors appeared as female-enriched. Together with its atypical tissue-distribution, this suggests a role in oviposition. The compilation of male and female antennal ESTs represents a valuable resource for exploring the mechanisms of olfaction in S. littoralis.

Castagneyrol B.,French National Institute for Agricultural Research | Jactel H.,University of Bordeaux 1
Ecology | Year: 2012

In the face of unprecedented loss of biodiversity, cross-taxon correlates have been proposed as a means of obtaining quantitative estimates of biodiversity for identifying habitats of important conservation value. Habitat type, animal trophic level, and the spatial extent of studies would be expected to influence the strength of such correlations. We investigated these effects by carrying out a meta-analysis of 320 case studies of correlations between plant and animal species richnesses. The diversity of arthropods, herps, birds, and mammals significantly increased with plant diversity regardless of species habitat. However, correlations were stronger when plant and animal species richnesses were compared between habitats (γ diversity) than within single habitats (α diversity). For arthropods, both the coefficient of correlation and the slope of the regression line were also greater for primary than for secondary consumers. These findings substantiate the use of plant species richness as an indicator of the diversity of animal taxa over space. © 2012 by the Ecological Society of America.

Bonny S.,French National Institute for Agricultural Research
Cahiers Agricultures | Year: 2011

Over the last several years, indeed over several decades, a number of voices have called for a change in agriculture and its model of production because of their limitations and changes in the context. They have put forward several proposals for new directions. These include particularly ecologically intensive agriculture, which is examined here. The objective of this paper is to contribute to analyzing the possible pathways to and socioeconomic challenges facing ecologically intensive agriculture, founded upon the sustainable use of natural processes and ecosystem functions while achieving a good level of yield. Firstly, the notion of ecological intensification by comparison/opposition with conventional forms of agricultural intensification is presented. The positions of the various actors, in relationship to the concept of ecologically intensive agriculture, are then examined. If this movement towards ecological intensification is apparently garnering a rather good consensus, there are in fact many hurdles to the implementation of these practices. Finally, we analyze some opportunities, barriers and facing the development of ecologically intensive agriculture. Such an evolution notably requires a context in agreement with it.

Zhang C.,French National Institute for Agricultural Research
ISME Journal | Year: 2016

Resident gut microbes co-exist with transient bacteria to form the gut microbiota. Despite increasing evidence suggesting a role for transient microbes on gut microbiota function, the interplay between resident and transient members of this microbial community is poorly defined. We aimed to determine the extent to which a host’s autochthonous gut microbiota influences niche permissivity to transient bacteria using a fermented milk product (FMP) as a vehicle for five food-borne bacterial strains. Using conventional and gnotobiotic rats and gut microbiome analyses (16S rRNA genes pyrosequencing and reverse transcription qPCR), we demonstrated that the clearance kinetics of one FMP bacterium, Lactococcus lactis CNCM I-1631, were dependent on the structure of the resident gut microbiota. Susceptibility of the resident gut microbiota to modulation by FMP intervention correlated with increased persistence of L. lactis. We also observed gut microbiome configurations that were associated with altered stability upon exposure to transient bacteria. Our study supports the concept that allochthonous bacteria have transient and subject-specific effects on the gut microbiome that can be leveraged to re-engineer the gut microbiome and improve dysbiosis-related diseases. © 2016 International Society for Microbial Ecology

Bouche N.,French National Institute for Agricultural Research
Plant Signaling and Behavior | Year: 2010

We recently identified a new target of microRNA398 (miR398), a conserved miRNA in plants. In Arabidopsis, miR398 targets the mRNAs of two copper/zinc superoxide dismutases (Cu/Zn SODs) by triggering their cleavage or repressing their translation. We analyzed the transcriptomes of mutants impaired in miR398 production, revealing that the mRNAs encoding the chaperone (CCS1), essential for copper delivering to the Cu/Zn SODs of Arabidopsis and to generate the mature proteins, were undiscovered targets of miR398. It is likely that CCS1 was not identiied by previous bioinformatic predictions because of the number of mismatches between the mRNA and its target. Since CCS1 has four mismatches and one GU wobble, it would have been excluded by the majority of prediction algorithms. miR398 directs the post-transcriptional regulation of CCS1 mRNAs by cleavage and ARGONAUTE10 (AGO10)-mediated translational repression. Indeed, CCS1 protein accumulate in zwille (ago10) mutants while both miR398 and CCS1 mRNAs levels remain identical to the Landsberg erecta WT plants. Moreover, since AGO10 is a negative regulator of AGO1, the CCS1 protein is more abundant in a double agol-27 ago10-3 Col mutant compared to the single hypo-morphic ago1-27 mutant, as previously shown for CSD2. © 2010 Landes Bioscience.

Pobel D.,Isara Lyon | Robin J.,Isara Lyon | Humbert J.-F.,French National Institute for Agricultural Research
Water Research | Year: 2011

Sampling cyanobacteria in freshwater ecosystems is a crucial aspect of monitoring programs in both basic and applied research. Despite this, few papers have dealt with this aspect, and a high proportion of cyanobacteria monitoring programs are still based on monthly or twice-monthly water sampling, usually performed at a single location. In this study, we conducted high frequency spatial and temporal water sampling in a small eutrophic shallow lake that experiences cyanobacterial blooms every year. We demonstrate that the spatial and temporal aspects of the sampling strategy had a considerable impact on the findings of cyanobacteria monitoring in this lake. In particular, two peaks of Aphanizomenon flos-aquae cell abundances were usually not picked up by the various temporal sampling strategies tested. In contrast, sampling once a month was sufficient to provide a good overall estimation of the population dynamics of Microcystis aeruginosa. The spatial frequency of sampling was also important, and the choice in the location of the sampling points around the lake was very important if only two or three sampling points were used. When four or five sampling points were used, this reduced the impact of the choice of the location of the sampling points, and allowed to obtain fairly similar results than when six sampling points were used. These findings demonstrate the importance of the sampling strategy in cyanobacteria monitoring, and the fact that it is impossible to propose a single universal sampling strategy that is appropriate for all freshwater ecosystems and also for all cyanobacteria. © 2010 Elsevier Ltd.

Bedoussac L.,INPT | Justes E.,French National Institute for Agricultural Research
Plant and Soil | Year: 2010

In a previous paper [Bedoussac L, Justes E (2009) Plant Soil, doi: 10.1007/s11104-009-0082-2, we showed that intercropping of durum wheat and winter pea increased the yield and protein concentration of durum wheat when early N availability was less than 120 kg N ha-1. The aim of the present work was to understand these results by analysing intercrop species dynamics for growth, light and N acquisition. A 2-year field experiment was carried out in southwest France with different fertilizer-N levels in order to compare wheat (Triticum turgidum L.) and pea (Pisum sativum L.) grown as sole crops and as an intercrop in a row substitutive design. The advantages of intercropping in low N conditions were due mainly to: (1) better light use (up to 10%), thanks to species dynamic complementarity for leaf area index and height; (2) growth complementarity over time (higher growth rate of wheat until pea flowering and then of pea until wheat flowering); and (3) dynamic complementary N acquisition associated with better wheat N status throughout growth. Disadvantages, underlining poorer complementarity within the intercrop stand, were observed with ample available N in early growth. This induced higher cereal growth during winter, which led to increase interspecies competition by reducing pea light absorption and, consequently, its biomass production. © Springer Science+Business Media B.V. 2010.

Bonneau M.,French National Institute for Agricultural Research
Animal | Year: 2010

The use of an anti-gonadotropin-releasing hormone vaccine for immunocastration of male pigs has been recently approved in the European Union. This technique is potentially useful for avoiding both castration-associated pain for the animal and boar taint in pork. However, some animals may escape immunocastration and be slaughtered as entire males, potentially exhibiting boar taint. Therefore, it is important to check the efficacy of immunocastration on the slaughter line. To achieve that, the currently proposed method, based on testis weight, is not fully reliable because there is some overlap in the distributions of testis weight between immunocastrates and entire males. On the basis of literature data on the effect of immunocastration on the development of accessory sex glands, this paper provides evidence that the weight of seminal vesicles might be a much better criterion for checking the efficacy of immunocastration, because their size decreases more rapidly, and to a greater extent, than that of the testis. © 2010 The Animal Consortium.

Bedoussac L.,Toulouse 1 University Capitole | Justes E.,French National Institute for Agricultural Research
Plant and Soil | Year: 2010

Grain protein concentration of durum wheat is often too low, particularly in low-N-input systems. The aim of our study was to test whether a durum wheat-winter pea intercrop can improve relative yield and durum wheat grain protein concentration in low-N-input systems. A 2-year field experiment was carried out in SW France with different fertilizer-N levels to compare wheat (Triticum turgidum L., cv. Nefer) and pea (winter pea, Pisum sativum L., cv. Lucy) grown as sole crops or intercrops in a row-substitutive design. Without N fertilization or when N was applied late (N available until pea flowering less than about 120 kg N ha-1), intercrops were up to 19% more efficient than sole crops for yield and up to 32% for accumulated N, but were less efficient with large fertilizer N applications. Wheat grain protein concentration was significantly higher in intercrops than in sole crops (14% on average) because more N was remobilized into wheat grain due to: i) fewer ears per square metre in intercrops and ii) a similar amount of available soil N as in sole crops due to the high pea N2 fixation rate in intercrops (88% compared to 58% in sole crops). © Springer Science + Business Media B.V. 2009.

Choubert G.,French National Institute for Agricultural Research
Aquaculture Nutrition | Year: 2010

Rainbow trout with an average initial weight of 160 g were fed during 42 days diets containing varied keto-carotenoids astaxanthin (Ax)/canthaxanthin (Cx) ratio, as follows: Ax 100%: Cx 0%; Ax 75%: Cx 25%; Ax 50%: Cx 50%; Ax 25%: Cx 75% and Ax 0%: Cx 100%. Muscle colour and carotenoid muscle retention were studied. Colour parameter values for mixed astaxanthin-canthaxanthin-fed fish were intermediate between those obtained for Ax 0%: Cx 100% fed fish group and for Ax 100%: Cx 0% fed fish group. Concerning muscle carotenoid retention, it has been observed that as the level of canthaxanthin in diet increased, the muscle total carotenoid retention decreased. In the mean time, as the level of canthaxanthin in diet increased, the muscle astaxanthin retention decreased while that of canthaxanthin increased. The results reported here provide further evidence of non-beneficial effects in terms of muscle colour and muscle carotenoid retention of the use of varying dietary astaxanthin/canthaxanthin ratio for feeding rainbow trout compared to values obtained for astaxanthin-only feed. © 2009 Blackwell Publishing Ltd.

Bertheau C.,University of Orleans | Brockerhoff E.G.,New Zealand Forest Research Institute | Roux-Morabito G.,University of Orleans | Lieutier F.,University of Orleans | Jactel H.,French National Institute for Agricultural Research
Ecology Letters | Year: 2010

The translocation of species beyond their native range is a major threat to biodiversity. Invasions by tree-feeding insects attacking native trees and the colonization of introduced trees by native insects result in new insect-tree relationships. To date there is uncertainty about the key factors that influence the outcome of these novel interactions. We report the results of a meta-analysis of 346 pairwise comparisons of forest insect fitness on novel and ancient host tree species from 31 publications. Host specificity of insects and phylogenetic relatedness between ancient and novel host trees emerged as key factors influencing insect fitness. Overall, fitness was significantly lower on novel host species than on ancient hosts. However, in some cases, fitness increased on novel hosts, mainly in polyphagous insects or when close relatives of ancient host trees were colonized. Our synthesis enables greatly improved impact prediction and risk assessment of biological invasions. © 2010 Blackwell Publishing Ltd/CNRS.

Passos F.,Polytechnic University of Catalonia | Uggetti E.,Polytechnic University of Catalonia | Carrere H.,French National Institute for Agricultural Research | Ferrer I.,Polytechnic University of Catalonia
Bioresource Technology | Year: 2014

Microalgae have been intensively studied as a source of biomass for replacing conventional fossil fuels in the last decade. The optimization of biomass production, harvesting and downstream processing is necessary for enabling its full-scale application. Regarding biofuels, biogas production is limited by the characteristics of microalgae, in particular the complex cell wall structure of most algae species. Therefore, pretreatment methods have been investigated for microalgae cell wall disruption and biomass solubilization before undergoing anaerobic digestion. This paper summarises the state of the art of different pretreatment techniques used for improving microalgae anaerobic biodegradability. Pretreatments were divided into 4 categories: (i) thermal; (ii) mechanical; (iii) chemical and (iv) biological methods. According to experimental results, all of them are effective at increasing biomass solubilization and methane yield, pretreatment effect being species dependent. Pilot-scale research is still missing and would help evaluating the feasibility of full-scale implementation. © 2014 Elsevier Ltd.

Baraloto C.,French National Institute for Agricultural Research | Couteron P.,Institute pour la Recherche et le Developpement
Biotropica | Year: 2010

We examined fine-scale heterogeneity of environmental conditions in a primary rain forest in French Guiana to describe variation in microhabitats that plants may experience during establishment. We characterized both the range as well as the spatial structuring of 11 environmental factors important for seedling establishment in six hexagonal sampling grids, one each in gap and understory sites at three points representing the predominant geomorphic units in this primary forest. Each grid contained 37 sampling points separated by 31 cm-20 m. Monte-Carlo tests of semivariograms against complete spatial randomness indicated that for many variables in all six sampling grids, spatial dependence did not exceed 1 m. A principal component analysis of all sampling points revealed a lack of spatial microhabitat structure, rather than homogeneous patches associated with canopy structure or geomorphology. Our results suggest that ample fine-scale spatial heterogeneity exists to support the coexistence of plant species with differential abiotic requirements for regeneration. © 2010 The Author(s). Journal compilation © 2010 by The Association for Tropical Biology and Conservation.

Hocquette J.F.,French National Institute for Agricultural Research
Animal | Year: 2010

Muscle metabolism (in interaction with other organs and tissues, including adipose tissue) plays an important role in the control of growth and body composition. Muscle ontogenesis has been described in different genotypes of cattle for myofibres, connective tissue and intramuscular depots. The ontogenesis or the action of putatively important factors controlling muscle development (IGF-II expression, IGF receptors, growth hormone (GH) receptor, myostatin, basic fibroblast growth factor, transforming growth factor-β1, insulin and thyroid hormones) has also been studied on bovine foetal muscle samples and satellite cells. The glucose/insulin axis has been specifically studied in both the bovine adipose tissue and heart. Clearly, cattle, like sheep, are mature species at birth based on their muscle characteristics compared to other mammalian or farm animal species. The different myoblast generations have been well characterised in cattle, including the second generation which is liable to be affected by foetal undernutrition at least in sheep. Interesting genotypes, for example, double-muscled genotype, have been characterised by an altered metabolic and endocrine status associated with a reduced fat mass, specific muscle traits and different foetal characteristics. Finally, the recent development of genomics in cattle has allowed the identification of novel genes controlling muscle development during foetal and postnatal life. Generally, a high muscle growth potential is associated with a reduced fat mass and a switch of muscle fibres towards the glycolytic type. The possibility and the practical consequences of manipulating muscle growth and, hence, body composition by nutritional and hormonal factors are discussed for bovines based on our current biological knowledge. Copyright © 2010 The Animal Consortium.

Genty A.,CEA Saclay Nuclear Research Center | Pot V.,French National Institute for Agricultural Research
Transport in Porous Media | Year: 2012

The 3D description of the soil structure at the pore scale level can help to elucidate the biological functioning of soil. The water-air distribution in the 3D-pore space is of particular interest because it determines the diffusion pathways of nutrients and the localisation of active soil microorganisms. We used the Shan-Chen interparticle-potential approach to simulate spontaneous phase separation in complex academic and real 3D-porous media using the advanced TRT lattice Boltzmann scheme. The equation of state and phase diagram were calculated and the model was verified using hydrostatic laws. The 3D pattern of water/air interface in two complex academic pore geometries was accurately computed. Finally, 3D maps of static liquid-gas distribution were simulated in a real 3D X-ray computed tomography image obtained from an undisturbed soil column sampled in a silty clay loam soil. The simulated soil sample of 1.7 cm3 was described at a voxel-resolution of 60 μm. The range of the simulated saturations (from 0.5 to 0.9) was in a good agreement with the expected saturations calculated from the phase diagram. © 2012 Springer Science+Business Media Dordrecht.

Stitt M.,Max Planck Institute of Molecular Plant Physiology | Gibon Y.,French National Institute for Agricultural Research
Trends in Plant Science | Year: 2014

Information about the abundance and biological activities of proteins is essential to reveal how genes affect phenotypes. Over the past decade, mass spectrometry (MS)-based proteomics has revolutionized the identification and quantification of proteins, and the detection of post-translational modifications. Interpretation of proteomics data depends on information about the biological activities of proteins, which has created a bottleneck in research. This review focuses on enzymes in central metabolism. We examine the methods used for measuring enzyme activities, and discuss how these methods provide information about the kinetic and regulatory properties of enzymes, their turnover, and how this information can be integrated into metabolic models. We also discuss how robotized assays could enable the genetic networks that control enzyme abundance to be analyzed. © 2013 Elsevier Ltd.

Charmet G.,French National Institute for Agricultural Research
Comptes Rendus - Biologies | Year: 2011

Wheat was one of the first crops to be domesticated more than 10,000 years ago in the Middle East. Molecular genetics and archaeological data have allowed the reconstruction of plausible domestication scenarios leading to modern cultivars. For diploid einkorn and tetraploid durum wheat, a single domestication event has likely occurred in the Karacadag Mountains, Turkey. Following a cross between tetraploid durum and diploid T. tauschii, the resultant hexaploid bread wheat was domesticated and disseminated around the Caucasian region. These polyploidisation events facilitated wheat domestication and created genetic bottlenecks, which excluded potentially adaptive alleles. With the urgent need to accelerate genetic progress to confront the challenges of climate change and sustainable agriculture, wild ancestors and old landraces represent a reservoir of underexploited genetic diversity that may be utilized through modern breeding methods. Understanding domestication processes may thus help identifying new strategies. © 2011 Académie des sciences.

Winter ecology of natural enemies has a great influence on the level and efficiency of biological control at spring. The hoverfly Episyrphus balteatus (DeGeer) (Diptera: Syrphidae) is one of the most important natural predators of crop aphids in Europe. Three different overwintering strategies coexist in this species which makes it a good model in order to study ecologically-based speciation processes. The purpose of this study was to determine whether E. balteatus populations with alternative overwintering strategies are genetically differentiated. To that aim, we developed 12 specific microsatellite markers and evaluated the level of neutral genetic differentiation between E. balteatus field populations that overwinter in the three different ways described in this species (i.e. migration, local overwintering at a pre-imaginal stage, and local overwintering at adult stage). Results showed a lack of neutral genetic differentiation between individuals with different overwintering strategies although there are strong ecological differences between them. All pair-wise FST values are below 0.025 and non-significant, and Bayesian clustering showed K=1 was the most likely number of genetic clusters throughout our sample. The three overwintering strategies form one unique panmictic population. This suggests that all the individuals may have genetic material for the expression of different overwintering phenotypes, and that their commitment in one particular overwintering strategy may depend on environmental and individual factors. Consequently, the prevalence of the different overwintering strategies would be potentially modified by landscape engineering and habitat management which could have major implications for biological control.

Acloque H.,French National Institute for Agricultural Research
PloS one | Year: 2013

In mammals, the non-random organization of the sperm nucleus supports an early function during embryonic development. Altering this organization may interfere with the zygote development and reduce fertility or prolificity. Thus, rare studies on sperm cells from infertile patients described an altered nuclear organization that may be a cause or a consequence of their respective pathologies. Thereby, chromosomal rearrangements and aneuploidy can be studied not only for their adverse effects on production of normal/balanced gametes at meiosis but also for their possible impact on sperm nuclear architecture and the epigenetic consequences of altered chromosome positioning. We decided to compare the global architecture of sperm nuclei from boars, either with a normal chromosome composition or with a Robertsonian translocation involving chromosomes 13 and 17. We hypothesized that the fusion between these chromosomes may change their spatial organization and we examined to what extend it could also modify the global sperm nuclear architecture. Analysis of telomeres, centromeres and gonosomes repartition does not support a global nuclear disorganization. But specific analysis of chromosomes 13 and 17 territories highlights an influence of chromosome 17 for the positioning of the fused chromosomes within the nucleus. We also observed a specific clustering of centromeres depending of the chromosome subtypes. Altogether our results showed that chromosome fusion does not significantly alter sperm nucleus architecture but suggest that centromere remodelling after chromosome fusion locally impacts chromosome positioning.

Bedoussac L.,National Polytechnic Institute of Toulouse | Justes E.,French National Institute for Agricultural Research
Field Crops Research | Year: 2011

There are many indices available to evaluate the potential advantages of intercrops and species interactions but correct choice of index is crucial in making accurate interpretations. This study compared and evaluated the relevance in understanding intercrop functioning of some well-known indices (aggressivity, AG; cumulative relative efficiency index, REIc; land equivalent ratio, LER) and other potentially useful indices (change in contribution, CC; interspecific and intraspecific interaction index, IE and IA; comparative absolute growth rate, CGR).Data collected from a two-year field experiment in SW France with different fertiliser N levels comparing wheat (Triticum turgidum L., cv. Nefer) and pea (winter pea, Pisum sativum L., cv. Lucy) grown as sole crops or intercrops in a row substitutive design were used to calculate, compare and evaluate the relevance of the selected indices for understanding intercrop functioning.It was found that AG indices (calculated with or without considering sowing density or actual plant density) did not provide the information generally claimed in the literature (i.e. whether a crop is dominant or dominated). Consequently, their use is clearly unadvisable except when analysed jointly with partial land equivalent ratios. The LER index proved to be clearly relevant, versatile and helpful in illustrating the pattern of competitive outcomes in intercropping experiments, in particular when plotting partial LER values of wheat as a function of those of pea. However, LER cannot identify intraspecific and interspecific interactions. To do so we suggest using the intraspecific and interspecific interaction indices, which can also reveal possible facilitation phenomena and allow description of species change in the contribution index (CC). Interaction dynamics between crops that determine the final balance and the outcome of all competitive interactions occurring between the two crops can be evaluated using the CGR index, which is preferable to REIc, particularly when crops differ greatly in their dry weight.Careful choice of index and interpretation of the results are thus essential in correctly understanding species interactions (globally and dynamically) and intercrop efficiency compared with sole crops. Such indices can help highlight and reveal cereal and legume traits suited to intercropping and also appropriate cropping sequences and management techniques, allowing efficient intercropping. However, the results must always be related to actual data values (yield, dry weight or N accumulated) because the indices used cannot evaluate intrinsically quantitative performance but only the relative performance of intercrops compared with that of sole crops. © 2011 Elsevier B.V.

Mijakovic I.,Chalmers University of Technology | Deutscher J.,French National Center for Scientific Research | Deutscher J.,French National Institute for Agricultural Research
Frontiers in Microbiology | Year: 2015

The discovery of tyrosine-phosphorylated proteins in Bacillus subtilis in the year 2003 was followed by a decade of intensive research activity. Here we provide an overview of the lessons learned in that period. While the number of characterized kinases and phosphatases involved in reversible protein-tyrosine phosphorylation in B. subtilis has remained essentially unchanged, the number of proteins known to be targeted by this post-translational modification has increased dramatically. This is mainly due to phosphoproteomics and interactomics studies, which were instrumental in identifying new tyrosine-phosphorylated proteins. Despite their structural similarity, the two B. subtilis protein-tyrosine kinases (BY-kinases), PtkA and PtkB (EpsB), seem to accomplish different functions in the cell. The PtkB is encoded by a large operon involved in exopolysaccharide production, and its main role appears to be the control of this process. The PtkA seems to have a more complex role; it phosphorylates and regulates a large number of proteins involved in the DNA, fatty acid and carbon metabolism and engages in physical interaction with other types of kinases (Ser/Thr kinases), leading to mutual phosphorylation. PtkA also seems to respond to several activator proteins, which direct its activity toward different substrates. In that respect PtkA seems to function as a highly connected signal integration device. © 2015 Mijakovic and Deutscher.

Robert L.,French National Institute for Agricultural Research | Robert L.,Agro ParisTech | Robert L.,University Pierre and Marie Curie
Frontiers in Microbiology | Year: 2015

Bacteria proliferate by repetitive cycles of cellular growth and division. The progression into the cell cycle is admitted to be under the control of cell size. However, the molecular basis of this regulation is still unclear. Here I will discuss which mechanisms could allow coupling growth and division by sensing size and transmitting this information to the division machinery. Size sensors could act at different stages of the cell cycle. During septum formation, mechanisms controlling the formation of the Z ring, such as MinCD inhibition or Nucleoid Occlusion (NO) could participate in the size-dependence of the division process. In addition or alternatively, the coupling of growth and division may occur indirectly through the control of DNA replication initiation. The relative importance of these different size-sensing mechanisms could depend on the environmental and genetic context. The recent demonstration of an incremental strategy of size control in bacteria, suggests that DnaA-dependent control of replication initiation could be the major size control mechanism limiting cell size variation. © 2015 Robert.

Ramarao N.,French National Institute for Agricultural Research
Journal of visualized experiments : JoVE | Year: 2012

The study of bacterial virulence often requires a suitable animal model. Mammalian models of infection are costly and may raise ethical issues. The use of insects as infection models provides a valuable alternative. Compared to other non-vertebrate model hosts such as nematodes, insects have a relatively advanced system of antimicrobial defenses and are thus more likely to produce information relevant to the mammalian infection process. Like mammals, insects possess a complex innate immune system(1). Cells in the hemolymph are capable of phagocytosing or encapsulating microbial invaders, and humoral responses include the inducible production of lysozyme and small antibacterial peptides(2,3). In addition, analogies are found between the epithelial cells of insect larval midguts and intestinal cells of mammalian digestive systems. Finally, several basic components essential for the bacterial infection process such as cell adhesion, resistance to antimicrobial peptides, tissue degradation and adaptation to oxidative stress are likely to be important in both insects and mammals(1). Thus, insects are polyvalent tools for the identification and characterization of microbial virulence factors involved in mammalian infections. Larvae of the greater wax moth Galleria mellonella have been shown to provide a useful insight into the pathogenesis of a wide range of microbial infections including mammalian fungal (Fusarium oxysporum, Aspergillus fumigatus, Candida albicans) and bacterial pathogens, such as Staphylococcus aureus, Proteus vulgaris, Serratia marcescens Pseudomonas aeruginosa, Listeria monocytogenes or Enterococcus faecalis(4-7). Regardless of the bacterial species, results obtained with Galleria larvae infected by direct injection through the cuticle consistently correlate with those of similar mammalian studies: bacterial strains that are attenuated in mammalian models demonstrate lower virulence in Galleria, and strains causing severe human infections are also highly virulent in the Galleria model(8-11). Oral infection of Galleria is much less used and additional compounds, like specific toxins, are needed to reach mortality. G. mellonella larvae present several technical advantages: they are relatively large (last instar larvae before pupation are about 2 cm long and weight 250 mg), thus enabling the injection of defined doses of bacteria; they can be reared at various temperatures (20 °C to 30 °C) and infection studies can be conducted between 15 °C to above 37 °C(12,13), allowing experiments that mimic a mammalian environment. In addition, insect rearing is easy and relatively cheap. Infection of the larvae allows monitoring bacterial virulence by several means, including calculation of LD50(14), measurement of bacterial survival(15,16) and examination of the infection process(17). Here, we describe the rearing of the insects, covering all life stages of G. mellonella. We provide a detailed protocol of infection by two routes of inoculation: oral and intra haemocoelic. The bacterial model used in this protocol is Bacillus cereus, a Gram positive pathogen implicated in gastrointestinal as well as in other severe local or systemic opportunistic infections(18,19).

Leroy G.,Agro ParisTech | Leroy G.,French National Institute for Agricultural Research
Veterinary Journal | Year: 2011

Pedigree analysis constitutes a classical approach for the study of the evolution of genetic diversity, genetic structure, history and breeding practices within a given breed. As a consequence of selection pressure, management in closed populations and historical bottlenecks, many dog breeds have experienced considerable inbreeding and show (on the basis of a pedigree approach) comparable diversity loss compared to other domestic species. This evolution is linked to breeding practices such as the overuse of popular sires or mating between related animals. The popular sire phenomenon is the most problematic breeding practice, since it has also led to the dissemination of a large number of inherited defects. The practice should be limited by taking measures such as restricting the number of litters (or offspring) per breeding animal. © 2011 Elsevier Ltd.

Blesbois E.,French National Institute for Agricultural Research
Avian Biology Research | Year: 2011

Semen cryopreservation is an important tool for the storage of reproductive cells used for the ex situ management of genetic diversity in birds. Recent advances in poultry semen cryopreservation technology have resulted in the emergence of cryobanking, which is now being developed in an increasing number of countries. In addition, semen freezing methods are now effective for various domestic and wild bird species, although species such as guinea fowls are still highly affected by the process. The methods of freezing avian semen now use a small number of cryoprotectants, (mainly glycerol, dimethyl or N-methylacetamide) and cell packaging (such as straws or pellets). Temperature curves of freezing and thawing remain the most variable points as very slow or very rapid curves are sometimes used in the same species. Specific features of bird reproductive physiology are very important for sperm cryopreservation and application. The characteristics of initial semen quality, including cell membrane properties, mobility capacity and ability to undergo the acrosome reaction are critical points. The specific features of the oviparity system of reproduction and the internal fertilization process affect the conditions of semen use. The in vivo storage of spermatozoa in the sperm storage tubules of the female genital tract, and the conditions of the drastic selection of sperm in the highly specialized female oviduct constitute major factors that are highly species-specific. These constraints involve adaptations of the semen media used for freezing and of the zootechnical parameters of semen use. This review highlights the main factors that are critical for the success of semen cryopreservation in bird species.

Parent B.,Australian Center for Plant Functional Genomics | Tardieu F.,French National Institute for Agricultural Research
New Phytologist | Year: 2012

Rates of tissue expansion, cell division and progression in the plant cycle are driven by temperature, following common Arrhenius-type response curves. We analysed the genetic variability of this response in the range 6-37°C in seven to nine lines of maize (Zea mays), rice (Oryza spp.) and wheat (Triticum aestivum) and in 18 species (17 crop species, different genotypes) via the meta-analysis of 72 literature references. Lines with tropical or north-temperate origins had common response curves over the whole range of temperature. Conversely, appreciable differences in response curves, including optimum temperatures, were observed between species growing in temperate and tropical areas. Therefore, centuries of crop breeding have not impacted on the response of development to short-term changes in temperature, whereas evolution over millions of years has. This slow evolution may be a result of the need for a synchronous shift in the temperature response of all developmental processes, otherwise plants will not be viable. Other possibilities are discussed. This result has important consequences for the breeding and modelling of temperature effects associated with global changes. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Sicard D.,University Paris - Sud | Legras J.-L.,French National Institute for Agricultural Research
Comptes Rendus - Biologies | Year: 2011

Yeasts of the Saccharomyces sensu stricto species complex are able to convert sugar into ethanol and CO2 via fermentation. They have been used for thousands years by mankind for fermenting food and beverages. In the Neolithic times, fermentations were probably initiated by naturally occurring yeasts, and it is unknown when humans started to consciously add selected yeast to make beer, wine or bread. Interestingly, such human activities gave rise to the creation of new species in the Saccharomyces sensu stricto complex by interspecies hybridization or polyploidization. Within the S. cerevisiae species, they have led to the differentiation of genetically distinct groups according to the food process origin. Although the evolutionary history of wine yeast populations has been well described, the histories of other domesticated yeasts need further investigation. © 2011 Académie des sciences.

Chaboureau A.-C.,University of Versailles | Sepulchre P.,University of Versailles | Donnadieu Y.,University of Versailles | Franc A.,French National Institute for Agricultural Research
Proceedings of the National Academy of Sciences of the United States of America | Year: 2014

In 1879, Charles Darwin characterized the sudden and unexplained rise of angiosperms during the Cretaceous as an "abominable mystery." The diversification of this clade marked the beginning of a rapid transition among Mesozoic ecosystems and floras formerly dominated by ferns, conifers, and cycads. Although the role of environmental factors has been suggested [Coiffard C, Gómez B (2012) Geol Acta 10(2):181-188], Cretaceous global climate change has barely been considered as a contributor to angiosperm radiation, and focus was put on biotic factors to explain this transition. Here we use a fully coupled climate model driven by Mesozoic paleogeographic maps to quantify and discuss the impact of continental drift on angiosperm expansion and diversification. We show that the decrease of desertic belts between the Triassic and the Cretaceous and the subsequent onset of long-lasting humid conditions during the Late Cretaceous were driven by the breakup of Pangea and were contemporaneous with the first rise of angiosperm diversification. Positioning angiosperm-bearing fossil sites on our paleobioclimatic maps shows a strong match between the location of fossilrich outcrops and temperate humid zones, indicating that climate change from arid to temperate dominance may have set the stage for the ecological expansion of flowering plants.

Bellini C.,Umea University | Bellini C.,French National Institute for Agricultural Research | Pacurar D.I.,Umea University | Perrone I.,Umea University
Annual Review of Plant Biology | Year: 2014

In addition to its role in water and nutrient uptake, the root system is fundamentally important because it anchors a plant to its substrate. Although a wide variety of root systems exist across different species, all plants have a primary root (derived from an embryonic radicle) and different types of lateral roots. Adventitious roots, by comparison, display the same functions as lateral roots but develop from aerial tissues. In addition, they not only develop as an adaptive response to various stresses, such as wounding or flooding, but also are a key limiting component of vegetative propagation. Lateral and adventitious roots share key elements of the genetic and hormonal regulatory networks but are subject to different regulatory mechanisms. In this review, we discuss the developmental processes that give rise to lateral and adventitious roots and highlight knowledge acquired over the past few years about the mechanisms that regulate adventitious root formation. Copyright © 2014 by Annual Reviews.

Ricard A.,French National Institute for Agricultural Research
Genetics Selection Evolution | Year: 2015

Background: Recently, a mutation was discovered in the DMRT3 gene that controls pacing in horses. The mutant allele A is fixed in the American Standardbred trotter breed, while in the French trotter breed, the frequency of the wild-type allele C is still 24%. This study aimed at measuring the effect of DMRT3 genotypes on the performance of French trotters and explaining why the polymorphism still occurs in this breed. Using a mixed animal model, genetic parameters and environmental effects on performance traits were estimated from data on 173 176 French trotter races. The effect of the DMRT3 gene was then estimated by the effect of genotype at the highly linked SNP BIEC2-620109 (C-C, A-T) for 630 horses. A selection scheme that included qualification and racing performances was modeled to (1) verify if the observed superiority of heterozygous CT horses at this SNP could be explained only by selection and (2) understand why allele C has not disappeared in French trotters. Results: Heritability of racing performance traits was high for qualification test (0.56), moderate for annual earnings per finished race (0.26 to 0.31) and low for proportion of disqualified races (0.06 to 0.09). Genotype CC was always unfavorable compared to genotype TT for qualification: the probability to be qualified was 20% for CC vs. 48% for TT and earnings were -0.96 sy lower for CC than for TT. Genotype CT was also unfavorable for qualification (40%) and earnings at 3 years (-0.21 sy), but favorable for earnings at ages greater than 5 years: +0.41 sy (P = 7.10-4). Selection on qualification could not explain more than 19% of the difference between genotypes CC and CT in earnings at ages greater than 5 years. Only a scenario for which genotype CT has a favorable effect on the performance of horses older than 5 years could explain that the polymorphism at the DMRT3 gene still exists in the French trotter breed. Conclusions: The use of mature horses in the French racing circuit can explain that the CA genotype is still present in the French trotter horses. © 2015 Ricard.

Danchin E.G.,French National Institute for Agricultural Research
Frontiers in cellular and infection microbiology | Year: 2012

It is now accepted that lateral gene transfers (LGT), have significantly contributed to the composition of bacterial genomes. The amplitude of the phenomenon is considered so high in prokaryotes that it challenges the traditional view of a binary hierarchical tree of life to correctly represent the evolutionary history of species. Given the plethora of transfers between prokaryotes, it is currently impossible to infer the last common ancestral gene set for any extant species. For this ensemble of reasons, it has been proposed that the Darwinian binary tree of life may be inappropriate to correctly reflect the actual relations between species, at least in prokaryotes. In contrast, the contribution of LGT to the composition of animal genomes is less documented. In the light of recent analyses that reported series of LGT events in nematodes, we discuss the importance of this phenomenon in the evolutionary history and in the current composition of an animal genome. Far from being neutral, it appears that besides having contributed to nematode genome contents, LGT have favored the emergence of important traits such as plant-parasitism.

Duveiller G.,Catholic University of Louvain | Baret F.,French National Institute for Agricultural Research | Defourny P.,Catholic University of Louvain
Remote Sensing of Environment | Year: 2011

Information on vegetation status can be retrieved from satellite observations by modelling and inverting canopy radiative transfer. Agricultural monitoring and yield forecasting could greatly benefit from such techniques by coupling crop growth models with crop specific information through data assimilation. An indicator which would be particularly interesting to obtain from remote sensing is the total surface of photosynthetically active plant tissue, or green area index (GAI). Currently, the major limitation is that the imagery that can be used operationally and economically over large areas with high temporal frequency has a coarse spatial resolution. This paper demonstrates how it is possible to characterise the regional crop specific GAI range along with its temporal dynamic using MODIS imagery by controlling the degree at which the observation footprints of the coarse pixels fall within the crop-specific mask delineating the target. This control is done by modelling the instrument's point spread function and by filtering out less reliable GAI estimations in both the spatial and temporal dimensions using thresholds on 3 variables: pixel purity, observation coverage and view zenith angle. The difference in performance between MODIS and fine spatial resolution to estimate the median GAI of a given crop over a 40×40km study region can be reduced to a RMSE of 0.053m2/m2. The consistency between fine and coarse spatial resolution GAI estimations suggests a possible instrument synergy whereby the high temporal resolution of MODIS provides the general GAI trajectory and while high spatial resolution can be used to estimate the local GAI spatial heterogeneity. © 2011 Elsevier Inc.

Drogue S.,French National Institute for Agricultural Research | DeMaria F.,University of Calabria
Food Policy | Year: 2012

In this paper we study the impact of the regulations on Maximum Residue Levels (MRLs) of pesticides on the trade of apples and pears and related processed products with the aim of understanding how their similarity (or dissimilarity) affect trade. Most studies investigate the impact of sanitary regulations introducing directly in the analysis the MRL put in force in the importing country. They introduce in the analysis the level of the regulation in the importing country without taking into account the rule in force in the exporting country. Rather than focusing on a particular pesticide we take into account the entire list of substances set out by the various regulations. We then build a similarity index and introduce it into a gravity equation to assess the impact of the differences in MRL of pesticides on trade. Results suggest that the differences between regulations matter and may, in some case, hinder trade. © 2012 Elsevier Ltd.

Perga M.-E.,French National Institute for Agricultural Research
Journal of Paleolimnology | Year: 2011

I addressed the effects of taphonomic and early diagenetic processes on the isotope composition of cladoceran remains, using both experimental and field approaches. An experiment was designed to mimic the conditions encountered by cladoceran remains when they settle through the water column and are buried in the sediment. Cladoceran exoskeletons were incubated for 4 months in oxic or anoxic water, and in sediment. Changes in their carbon (C) and nitrogen (N) content and isotope compositions were measured. Most changes in isotope composition of exoskeletons took place when they settled through the water column. Once buried in the sediment, however, the δ13C and δ15N values of cladoceran exoskeletons did not undergo further change. Taphonomic processes resulted in an increase in δ13C and δ15N of the cladoceran remains and this was related to microbial degradation, which selectively removed isotopically light C and N compounds from the remains. For δ13C, changes were minimal (<1‰) and occured within the first 3 months. Taphonomic effects on δ15N were larger, from +2 to +5‰, and occurred within the first 2-3 weeks. These effects depended on incubation conditions and were greater in anoxic waters than under oxic conditions. Monthly changes in the isotope composition of sedimenting cladoceran exoskeletons were also recorded in the field using sediment traps, and were compared to the isotope composition of the living cladoceran community. The isotope composition of sedimenting remains displayed values consistent with those that might be expected, considering the effects of taphonomic processes observed in the experiment. Because C and N in cladoceran exoskeletons might involve a different isotope routing, the δ15N value of the remains provides an annual record of the value in the parent community, with a 1-month delay, while δ13C of remains essentially reflects that of the parent community during the period of lake thermal stratification. These findings provide insights into paleolimnological interpretation of isotopic changes in cladoceran remains from sediment cores. © 2011 Springer Science+Business Media B.V.

Nicaise V.,French National Institute for Agricultural Research | Nicaise V.,University of Bordeaux 1
Cell Host and Microbe | Year: 2015

Plant viruses depend on the host translational machinery to establish their infectious cycle. In a recent Nature publication, Zorzatto et al. (2015) highlight the suppression of the protein synthesis process as an antiviral defense mechanism in plants. © 2015 Elsevier Inc.

Yvan-Charvet L.,Columbia University | Quignard-Boulange A.,French National Institute for Agricultural Research | Quignard-Boulange A.,Agro ParisTech
Kidney International | Year: 2011

Obesity is a leading cause of death worldwide because of its associated inflammatory disorders such as hypertension, cardiovascular and kidney diseases, dyslipidemia, glucose intolerance, and certain types of cancer. Adipose tissue expresses all components of the renin-angiotensin system necessary to generate angiotensin (Ang) peptides for local function. The angiotensin type 1 (AT1) and type 2 (AT2) receptors mediate the effect of Ang II and recent studies have shown that both receptors may modulate fat mass expansion through upregulation of adipose tissue lipogenesis (AT2) and downregulation of lipolysis (AT1). Thus, both receptors may have synergistic and additive effects to promote the storage of lipid in adipose tissue in response to the nutrient environment. The production of angiotensinogen (AGT) by adipose tissue in rodents also contributes to one third of the circulating AGT levels. Increased adipose tissue AGT production in the obese state may be responsible in part for the metabolic and inflammatory disorders associated with obesity. This supports the notion that besides the traditional role of Ang II produced by the liver in the control of blood pressure, Ang II produced by the adipose tissue may more accurately reflect the role of this hormone in the regulation of fat mass and associated disorders. © 2011 International Society of Nephrology.

Rainard P.,French National Institute for Agricultural Research
Clinical and Vaccine Immunology | Year: 2010

Concentrations of the chemoattractants CXCL1, CXCL2, CXCL3, CXCL8, and C5a in milk were reduced by the preparation of milk whey by high-speed centrifugation or with rennet. About half of the chemoattractants (35 to 65%) were associated with the casein micelle sediment, except when whey was prepared by acidification. Consequently, quantification of chemoattractants should be carried out preferentially with skimmed milk samples or, whenever whey is needed, with acidic whey samples. The interference of milk or milk whey with the enzyme-linked immunosorbent assays (ELISAs) used to quantify the chemoattractants was moderate, as long as tetramethylbenzidine (TMB), not ABTS [2,2′-azino-bis-(3-ethylbenzthiazoline-sulfonate)], was used as the substrate of peroxidase. These considerations will help to assess more precisely a component of the immune response of the mammary gland to infection. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

Canonne J.,French National Institute for Agricultural Research
Plant signaling & behavior | Year: 2012

In order to promote virulence, Gram-negative bacteria have evolved the ability to inject so-called type III effector proteins into host cells. The plant cell nucleus appears to be a subcellular compartment repeatedly targeted by bacterial effectors. In agreement with this observation, mounting evidence suggests that manipulation of host transcription is a major strategy developed by bacteria to counteract plant defense responses. It has been suggested that bacterial effectors may adopt at least three alternative, although not mutually exclusive, strategies to subvert host transcription. T3Es may (1) act as transcription factors that directly activate transcription in host cells, (2) affect histone packing and chromatin configuration, and/or (3) target host transcription factor activity. Here, we provide an overview on how all these strategies may lead to host transcriptional re-programming and, as a result, to improved bacterial multiplication inside plant cells.

Trotier D.,French National Institute for Agricultural Research
European Annals of Otorhinolaryngology, Head and Neck Diseases | Year: 2011

For many organisms, pheromonal communication is of particular importance in managing various aspects of reproduction. In tetrapods, the vomeronasal (Jacobson's) organ specializes in detecting pheromones in biological substrates of congeners. This information triggers behavioral changes associated, in the case of certain pheromones, with neuroendocrine correlates. In human embryos, the organ develops and the nerve fibers constitute a substrate for the migration of GnRH-secreting cells from the olfactory placode toward the hypothalamus. After this essential step for subsequent secretion of sex hormones by the anterior hypophysis, the organ regresses and the neural connections disappear. The vomeronasal cavities can still be observed by endoscopy in some adults, but they lack sensory neurons and nerve fibers. The genes which code for vomeronasal receptor proteins and the specific ionic channels involved in the transduction process are mutated and nonfunctional in humans. In addition, no accessory olfactory bulbs, which receive information from the vomeronasal receptor cells, are found. The vomeronasal sensory function is thus nonoperational in humans. Nevertheless, several steroids are considered to be putative human pheromones; some activate the anterior hypothalamus, but the effects observed are not comparable to those in other mammals. The signaling process (by neuronal detection and transmission to the brain or by systemic effect) remains to be clearly elucidated. © 2011 Elsevier Masson SAS. All rights reserved.

Loeuille N.,University Pierre and Marie Curie | Loeuille N.,French National Institute for Agricultural Research
Ecology Letters | Year: 2010

In randomly assembled communities, diversity is known to have a destabilizing effect. Evolution may affect this result, but our theoretical knowledge of its role is mostly limited to models of small food webs. In the present article, I introduce evolution in a two-species Lotka-Volterra model in which I vary the interaction type and the cost constraining evolution. Regardless of the cost type, evolution tends to stabilize the dynamics more often in trophic interactions than for mutualism or competition. I then use simulations to study the effect of evolution in larger communities that contain all interaction types. Results suggest that evolution usually stabilizes the dynamics. This stabilizing effect is stronger when evolution affects trophic interactions, but happens for all interaction types. Stabilization decreases with diversity and evolution becomes destabilizing in very diverse communities. This suggests that evolution may not counteract the destabilizing effect of diversity observed in random communities. © 2010 Blackwell Publishing Ltd/CNRS.

Fameau A.-L.,French National Institute for Agricultural Research | Zemb T.,CNRS Marcoule Institute for Separative Chemistry
Advances in Colloid and Interface Science | Year: 2014

Fatty acids can self-assemble under various shapes in the presence of amines or cationic components. We assemble and compare these types of self-assembly leading toward a catanionic system either with a cationic surfactant or with an amine component playing the role of counter-ion. First, we focus on the molar ratio as a key driving parameter. Known and yet un-known values from other quantities governing the colloidal properties of these systems such as structural surface charge, osmotic pressure, molecular segregation, rigidity, in plane colloidal interactions and melting transition are discussed. We include also recent results obtained on the interfacial and foaming properties of these systems. We will highlight the specificity of these self-assemblies leading to unusual macroscopic properties rich of robust applications. © 2013 Elsevier B.V.

Michel L.,French National Institute for Agricultural Research
PloS one | Year: 2013

The world's population is predicted to exceed nine billion by 2050 and there is increasing concern about the capability of agriculture to feed such a large population. Foresight studies on food security are frequently based on crop yield trends estimated from yield time series provided by national and regional statistical agencies. Various types of statistical models have been proposed for the analysis of yield time series, but the predictive performances of these models have not yet been evaluated in detail. In this study, we present eight statistical models for analyzing yield time series and compare their ability to predict wheat yield at the national and regional scales, using data provided by the Food and Agriculture Organization of the United Nations and by the French Ministry of Agriculture. The Holt-Winters and dynamic linear models performed equally well, giving the most accurate predictions of wheat yield. However, dynamic linear models have two advantages over Holt-Winters models: they can be used to reconstruct past yield trends retrospectively and to analyze uncertainty. The results obtained with dynamic linear models indicated a stagnation of wheat yields in many countries, but the estimated rate of increase of wheat yield remained above 0.06 t ha-1 year-1 in several countries in Europe, Asia, Africa and America, and the estimated values were highly uncertain for several major wheat producing countries. The rate of yield increase differed considerably between French regions, suggesting that efforts to identify the main causes of yield stagnation should focus on a subnational scale.

Baillet A.,EPHE Paris | Mandon-Pepin B.,French National Institute for Agricultural Research
Molecular and Cellular Endocrinology | Year: 2012

Over the past 50 years, the ovary development has been subject of fewer studies as compare to the male pathway. Nevertheless due to the advancement of genetics, mouse ES cells and the development of genetic models, studies of ovarian differentiation was boosted. This review emphasizes some of new progresses in the research field of the mammalian ovary differentiation that have occurred in recent years with focuses of the period around prophase I of meiosis and of recent roles of small non-RNAs in the ovarian gene expression. © 2011 Elsevier Ireland Ltd.

Berger N.,French National Institute for Agricultural Research | Dubreucq B.,Agro ParisTech
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms | Year: 2012

Chromatin-associated proteins (CAP) play a crucial role in the regulation of gene expression and development in higher organisms. They are involved in the control of chromatin structure and dynamics. CAP have been extensively studied over the past years and are classified into two major groups: enzymes that modify histone stability and organization by post-translational modification of histone N-Terminal tails; and proteins that use ATP hydrolysis to modify chromatin structure. All of these proteins show a relatively high degree of sequence conservation across the animal and plant kingdoms. The essential Drosophila melanogaster GAGA factor (dGAF) interacts with these two types of CAP to regulate homeobox genes and thus contributes to a wide range of developmental events. Surprisingly, however, it is not conserved in plants. In this review, following an overview of fly GAF functions, we discuss the role of plant BBR/BPC proteins. These appear to functionally converge with dGAF despite a completely divergent amino acid sequence. Some suggestions are given for further investigation into the function of BPC proteins in plants. © 2012 Elsevier B.V.

Even P.C.,French National Institute for Agricultural Research | Nadkarni N.A.,Agro ParisTech
American Journal of Physiology - Regulatory Integrative and Comparative Physiology | Year: 2012

In this article, we review some fundamentals of indirect calorimetry in mice and rats, and open the discussion on several debated aspects of the configuration and tuning of indirect calorimeters. On the particularly contested issue of adjustment of energy expenditure values for body size and body composition, we discuss several of the most used methods and their results when tested on a previously published set of data. We conclude that neither body weight (BW), exponents of BW, nor lean body mass (LBM) are sufficient. The best method involves fitting both LBM and fat mass (FM) as independent variables; for low sample sizes, the model LBM + 0.2 FM can be very effective. We also question the common calorimetry design that consists of measuring respiratory exchanges under free-feeding conditions in several cages simultaneously. This imposes large intervals between measures, and generally limits data analysis to mean 24 h or day-night values of energy expenditure. These are then generally compared with energy intake. However, we consider that, among other limitations, the measurements of V̇O2, V̇CO2, and food intake are not precise enough to allow calculation of energy balance in the small 2-5% range that can induce significant long-term alterations of energy balance. In contrast, we suggest that it is necessary to work under conditions in which temperature is set at thermoneutrality, food intake totally controlled, activity precisely measured, and data acquisition performed at very high frequency to give access to the part of the respiratory exchanges that are due to activity. In these conditions, it is possible to quantify basal energy expenditure, energy expenditure associated with muscular work, and response to feeding or to any other metabolic challenge. This reveals defects in the control of energy metabolism that cannot be observed from measurements of total energy expenditure in free feeding individuals. © 2012 the American Physiological Society.

Al-Gubory K.H.,French National Institute for Agricultural Research
International Journal of Biochemistry and Cell Biology | Year: 2012

Mitochondria are the main organelles that produce reactive oxygen species (ROS). Overproduction of ROS induces oxidative damage to macromolecules, including lipids, and can damage cellular membrane structure and functions. Mitochondria, the main target of ROS-induced damage, are equipped with a network of antioxidants that control ROS production. Dietary intake of omega-3 polyunsaturated fatty acids (ω3PUFAs) and consequently the increase in ω3PUFA content of membrane lipids may be disadvantageous to the health because ROS-induced oxidative peroxidation of ω3PUFAs within membrane phospholipids can lead to the formation of toxic products. Mitochondrial control of lipid peroxidation is one of the mechanisms that protect cell against oxidative damage. This review discusses the role of mitochondria in ROS generation and the mechanisms by which it regulates ROS production. The susceptibility to peroxidation of PUFAs by ROS raises the question of the adverse effects of ω3PUFA dietary supplementation on embryonic development and prenatal developmental outcomes. © 2012 Elsevier Ltd.

Fortin M.,French National Institute for Agricultural Research
Canadian Journal of Forest Research | Year: 2013

Data in forestry are often spatially and (or) serially correlated. In the last two decades, mixed models have become increasingly popular for the analysis of such data because they can relax the assumption of independent observations. However, when the relationship between the response variable and the covariates is nonlinear, as is the case in generalized linear mixed models (GLMMs), population-averaged predictions cannot be obtained from the fixed effects alone. This study proposes an estimator, which is based on a five-point Gauss-Hermite quadrature, for population-averaged predictions in the context of GLMM. The estimator was tested through Monte Carlo simulation and compared with a regular generalized linear model (GLM). The estimator was also applied to a real-world case study, a harvest model. The results showed that GLM predictions were unbiased but that their confidence intervals did not achieve their nominal coverage. On the other hand, the proposed estimator yielded unbiased predictions with reliable confidence intervals. The predictions based on the fixed effects of a GLMM exhibited the largest biases. If statistical inferences are needed, the proposed estimator should be used. It is easily implemented as long as the random effect specification does not contain multiple random effects for the same hierarchical level.

Alcazar R.,Max Planck Institute for Plant Breeding Research | Reymond M.,French National Institute for Agricultural Research | Schmitz G.,University of Munster | De Meaux J.,University of Munster
Current Opinion in Plant Biology | Year: 2011

There is now ample evidence that plant development, responses to abiotic environments, and immune responses are tightly intertwined in their physiology. Thus optimization of the immune system during evolution will occur in coordination with that of plant development. Two alternative and possibly complementary forces are at play: genetic constraints due to the pleiotropic action of players in both systems, and coevolution, if developmental changes modulate the cost-benefit balance of immunity. A current challenge is to elucidate the ecological forces driving evolution of quantitative variation for defense at molecular level. The analysis of natural co-variation for developmental and immunity traits in Arabidopsis thaliana promises to bring important insights. © 2011 Elsevier Ltd.

Legarra A.,French National Institute for Agricultural Research
Genetics research | Year: 2011

Empirical experience with genomic selection in dairy cattle suggests that the distribution of the effects of single nucleotide polymorphisms (SNPs) might be far from normality for some traits. An alternative, avoiding the use of arbitrary prior information, is the Bayesian Lasso (BL). Regular BL uses a common variance parameter for residual and SNP effects (BL1Var). We propose here a BL with different residual and SNP effect variances (BL2Var), equivalent to the original Lasso formulation. The λ parameter in Lasso is related to genetic variation in the population. We also suggest precomputing individual variances of SNP effects by BL2Var, to be later used in a linear mixed model (HetVar-GBLUP). Models were tested in a cross-validation design including 1756 Holstein and 678 Montbéliarde French bulls, with 1216 and 451 bulls used as training data; 51 325 and 49 625 polymorphic SNP were used. Milk production traits were tested. Other methods tested included linear mixed models using variances inferred from pedigree estimates or integrated out from the data. Estimates of genetic variation in the population were close to pedigree estimates in BL2Var but not in BL1Var. BL1Var shrank breeding values too little because of the common variance. BL2Var was the most accurate method for prediction and accommodated well major genes, in particular for fat percentage. BL1Var was the least accurate. HetVar-GBLUP was almost as accurate as BL2Var and allows for simple computations and extensions.

Briet A.,French National Institute for Agricultural Research
ISME Journal | Year: 2016

Antibiotic resistance genes (ARGs) are pervasive in gut microbiota, but it remains unclear how often ARGs are transferred, particularly to pathogens. Traditionally, ARG spread is attributed to horizontal transfer mediated either by DNA transformation, bacterial conjugation or generalized transduction. However, recent viral metagenome (virome) analyses suggest that ARGs are frequently carried by phages, which is inconsistent with the traditional view that phage genomes rarely encode ARGs. Here we used exploratory and conservative bioinformatic strategies found in the literature to detect ARGs in phage genomes, and experimentally assessed a subset of ARG predicted using exploratory thresholds. ARG abundances in 1181 phage genomes were vastly overestimated using exploratory thresholds (421 predicted vs 2 known), due to low similarities and matches to protein unrelated to antibiotic resistance. Consistent with this, four ARGs predicted using exploratory thresholds were experimentally evaluated and failed to confer antibiotic resistance in Escherichia coli. Reanalysis of available human- or mouse-associated viromes for ARGs and their genomic context suggested that bona fide ARG attributed to phages in viromes were previously overestimated. These findings provide guidance for documentation of ARG in viromes, and reassert that ARGs are rarely encoded in phages.The ISME Journal advance online publication, 21 June 2016; doi:10.1038/ismej.2016.90. © 2016 International Society for Microbial Ecology

Pan Ke Shon J.-L.,French National Institute for Agricultural Research
Urban Studies | Year: 2012

Many poor neighbourhoods, home to both socially disadvantaged populations and to foreigners, are characterised by a strong perception of insecurity. The purpose of this article is determine the origin of this perception. To do so, two possible causes are dissociated: racial prejudice and racial proxy (the ethnic minorities are perceived in terms of the negative social characteristics that are often associated with them). More specifically, it is shown that the 'ethnic' variable captures the effects of an overconcentration of poverty, approximated here by the concentration of unemployment, but that these two variables act separately. This result should be taken into account in the policies implemented by public authorities and local actors. In this study, an original methodology is applied based simultaneously on individual geocoded data, the proportion of foreigners, the unemployment rate at the neighbourhood level and an indirect indicator of perceived insecurity. © 2011 Urban Studies Journal Limited.

Arnan X.,Autonomous University of Barcelona | Gaucherel C.,French National Institute for Agricultural Research | Andersen A.N.,CSIRO
Oecologia | Year: 2011

The role of competitive exclusion is problematic in highly diverse ant communities where exceptional species richness occurs in the face of exceptionally high levels of behavioural dominance. A possible non-niche-based explanation is that the abundance of behaviourally dominant ants is highly patchy at fine spatial scales, and subordinate species act as insinuators by preferentially occupying these gaps-we refer to this as the interstitial hypothesis. To test this hypothesis, we examined fine-scale patterns of ant abundance and richness according to a three-tiered competition hierarchy (dominants, subdominants and subordinates) in an Australian tropical savanna using pitfall traps spaced at 2 m intervals. Despite the presence of gaps in the fine-scale abundance of individual species, the combined abundance of dominant ants (species of Iridomyrmex, Papyirus and Oecophylla) was relatively uniform. There was therefore little or no opportunity for subordinate species to preferentially occupy gaps in the foraging ranges of dominant species, and we found no relationship between the abundance of dominant ants and nondominant species richness at fine spatial scales. However, we found a negative relationship between subdominant and subordinate ants, a negative relationship between dominant and subdominant ants, and a positive relationship between dominant and subordinate ants. These results suggest that dominant species actually promote species richness by neutralizing the effects of subdominant species on subordinate species. Such indirect interactions have very close parallels with three-tiered trophic cascades in food webs, and we propose a "competition cascade" where the interactions are through a competition rather than trophic hierarchy. © 2011 Springer-Verlag.

Mericq J.-P.,Toulouse 1 University Capitole | Laborie S.,French National Institute for Agricultural Research | Cabassud C.,French National Center for Scientific Research
Water Research | Year: 2010

Seawater desalination by Reverse Osmosis (RO) is an interesting solution for drinking water production. However, because of limitation by the osmotic pressure, a high recovery factor is not attainable. Consequently, large volumes of brines are discharged into the sea and the flow rate produced (permeate) is limited. In this paper, Vacuum Membrane Distillation (VMD) is considered as a complementary process to RO to further concentrate RO brines and increase the global recovery of the process. VMD is an evaporative technology that uses a membrane to support the liquid-vapour interface and enhance the contact area between liquid and vapour in comparison with conventional distillation. This study focuses on VMD for the treatment of RO brines. Simulations were performed to optimise the operating conditions and were completed by bench-scale experiments using actual RO brines and synthetic solutions up to a salt concentration of 300 g L-1. Operating conditions such as a highly permeable membrane, high feed temperature, low permeate pressure and a turbulent fluid regime allowed high permeate fluxes to be obtained even for a very high salt concentration (300 g L-1). For the membrane studied, temperature and concentration polarisation were shown to have little effect on permeate flux. After 6 to 8 h, no organic fouling or biofouling was observed for RO brines. At high salt concentrations, scaling occurred (mainly due to calcium precipitation) but had only a limited impact on the permeate flux (24% decrease for a permeate specific volume of 43L m-2 for the highest concentration of salt). Calcium carbonate and calcium sulphate precipitated first due to their low solubility and formed mixed crystal deposits on the membrane surface. These phenomena only occurred on the membrane surface and did not totally cover the pores. The crystals were easily removed simply by washing the membrane with water. A global recovery factor of 89% can be obtained by coupling RO and VMD. © 2010 Elsevier Ltd.

Nicolai M.,French National Institute for Agricultural Research
Genetics and molecular research : GMR | Year: 2012

Genetic markers based on single nucleotide polymorphisms (SNPs) are in increasing demand for genome mapping and fingerprinting of breeding populations in crop plants. Recent advances in high-throughput sequencing provide the opportunity for whole-genome resequencing and identification of allelic variants by mapping the reads to a reference genome. However, for many species, such as pepper (Capsicum annuum), a reference genome sequence is not yet available. To this end, we sequenced the C. annuum cv. "Yolo Wonder" transcriptome using Roche 454 pyrosequencing and assembled de novo 23,748 isotigs and 60,370 singletons. Mapping of 10,886,425 reads obtained by the Illumina GA II sequencing of C. annuum cv. "Criollo de Morelos 334" to the "Yolo Wonder" transcriptome allowed for SNP identification. By setting a threshold value that allows selecting reliable SNPs with minimal loss of information, 11,849 reliable SNPs spread across 5919 isotigs were identified. In addition, 853 single sequence repeats were obtained. This information has been made available online.

Foulongne-Oriol M.,French National Institute for Agricultural Research
Applied Microbiology and Biotechnology | Year: 2012

Genetic mapping is a basic tool for eukaryotic genomic research. Linkage maps provide insights into genome organization and can be used for genetic studies of traits of interest. A genetic linkage map is a suitable support for the anchoring of whole genome sequences. It allows the localization of genes of interest or quantitative trait loci (QTL) and map-based cloning. While genetic mapping has been extensively used in plant or animal models, this discipline is more recent in fungi. The present article reviews the current status of genetic linkage map research in fungal species. The process of linkage mapping is detailed, from the development of mapping populations to the construction of the final linkage map, and illustrated based on practical examples. The range of specific applications in fungi is browsed, such as the mapping of virulence genes in pathogenic species or the mapping of agronomically relevant QTL in cultivated edible mushrooms. Future prospects are finally discussed in the context of the most recent advances in molecular techniques and the release of numerous fungal genome sequences. © Springer-Verlag 2012.

Kellermeier F.,University of Glasgow | Chardon F.,French National Institute for Agricultural Research | Amtmann A.,University of Glasgow
Plant Physiology | Year: 2013

Root architecture is a highly plastic and environmentally responsive trait that enables plants to counteract nutrient scarcities with different foraging strategies. In potassium (K) deficiency (low K), seedlings of the Arabidopsis (Arabidopsis thaliana) reference accession Columbia (Col-0) show a strong reduction of lateral root elongation. To date, it is not clear whether this is a direct consequence of the lack of K as an osmoticum or a triggered response to maintain the growth of other organs under limiting conditions. In this study, we made use of natural variation within Arabidopsis to look for novel root architectural responses to low K. A comprehensive set of 14 differentially responding root parameters were quantified in K-starved and Kreplete plants. We identified a phenotypic gradient that links two extreme strategies of morphological adaptation to low K arising from a major tradeoff between main root (MR) and lateral root elongation. Accessions adopting strategy I (e.g. Col-0) maintained MR growth but compromised lateral root elongation, whereas strategy II genotypes (e.g. Catania-1) arrested MR elongation in favor of lateral branching. K resupply and histochemical staining resolved the temporal and spatial patterns of these responses. Quantitative trait locus analysis of K-dependent root architectures within a Col-0 X Catania-1 recombinant inbred line population identified several loci each of which determined a particular subset of root architectural parameters. Our results indicate the existence of genomic hubs in the coordinated control of root growth in stress conditions and provide resources to facilitate the identification of the underlying genes. © 2013 American Society of Plant Biologists. All Rights Reserved.

Ranc N.,French National Institute for Agricultural Research
G3 (Bethesda, Md.) | Year: 2012

Genome-wide association mapping is an efficient way to identify quantitative trait loci controlling the variation of phenotypes, but the approach suffers severe limitations when one is studying inbred crops like cultivated tomato (Solanum lycopersicum). Such crops exhibit low rates of molecular polymorphism and high linkage disequilibrium, which reduces mapping resolution. The cherry type tomato (S. lycopersicum var. cerasiforme) genome has been described as an admixture between the cultivated tomato and its wild ancestor, S. pimpinellifolium. We have thus taken advantage of the properties of this admixture to improve the resolution of association mapping in tomato. As a proof of concept, we sequenced 81 DNA fragments distributed on chromosome 2 at different distances in a core collection of 90 tomato accessions, including mostly cherry type tomato accessions. The 81 Sequence Tag Sites revealed 352 SNPs and indels. Molecular diversity was greatest for S. pimpinellifolium accessions, intermediate for S. l. cerasiforme accessions, and lowest for the cultivated group. We assessed the structure of molecular polymorphism and the extent of linkage disequilibrium over genetic and physical distances. Linkage disequilibrium decreased under r(2) = 0.3 within 1 cM, and minimal estimated value (r(2) = 0.13) was reached within 20 kb over the physical regions studied. Associations between polymorphisms and fruit weight, locule number, and soluble solid content were detected. Several candidate genes and quantitative trait loci previously identified were validated and new associations detected. This study shows the advantages of using a collection of S. l. cerasiforme accessions to overcome the low resolution of association mapping in tomato.

Jacquemond M.,French National Institute for Agricultural Research
Advances in Virus Research | Year: 2012

Cucumber mosaic virus (CMV) is an important virus because of its agricultural impact in the Mediterranean Basin and worldwide, and also as a model for understanding plant-virus interactions. This review focuses on those areas where most progress has been made over the past decade in our understanding of CMV. Clearly, a deep understanding of the role of the recently described CMV 2b gene in suppression of host RNA silencing and viral virulence is the most important discovery. These findings have had an impact well beyond the virus itself, as the 2b gene is an important tool in the studies of eukaryotic gene regulation. Protein 2b was shown to be involved in most of the steps of the virus cycle and to interfere with several basal host defenses. Progress has also been made concerning the mechanisms of virus replication and movement. However, only a few host proteins that interact with viral proteins have been identified, making this an area of research where major efforts are still needed. Another area where major advances have been made is CMV population genetics, where contrasting results were obtained. On the one hand, CMV was shown to be prone to recombination and to show high genetic diversity based on sequence data of different isolates. On the other hand, populations did not exhibit high genetic variability either within plants, or even in a field and the nearby wild plants. The situation was partially clarified with the finding that severe bottlenecks occur during both virus movement within a plant and transmission between plants. Finally, novel studies were undertaken to elucidate mechanisms leading to selection in virus population, according to the host or its environment, opening a new research area in plant-virus coevolution. © 2012 Elsevier Inc.

Leroy G.,French National Institute for Agricultural Research
Animal Genetics | Year: 2014

Inbreeding, by virtue of its consequence on traits of interest, is a topic of major interest for geneticists and animal breeders. Based on meta-analysis conducted on 57 studies and seven livestock species considering a wide variety of selected traits, it was estimated that inbreeding depression corresponds to on average a decrease of 0.137 percent of the mean of a trait per 1 percent of inbreeding. The decrease was larger for production traits (reduction of 0.351%) than for other trait categories. For populations raised as purebreds, inbreeding depression may impact the economic income of breeders. There is a need for studies assessing the existence of an inbreeding purge phenomenon as well as the impact of inbreeding on adaptation capacities of livestock species. Promises brought by the development of dense genotyping as well as functional genomics will increase the capacities to improve our understanding and management of the phenomenon. © 2014 Stichting International Foundation for Animal Genetics.

Meynial-Denis D.,French National Institute for Agricultural Research
Nutrition Reviews | Year: 2016

Glutamine, reviewed extensively in the last century, is a key substrate for the splanchnic bed in the whole body and is a nutrient of particular interest in gastrointestinal research. A marked decrease in the plasma glutamine concentration has recently been observed in neonates and adults during acute illness and stress. Although some studies in newborns have shown parenteral and enteral supplementation with glutamine to be of benefit (by decreasing proteolysis and activating the immune system), clinical trials have not demonstrated prolonged advantages such as reductions in mortality or risk of infections in adults. In addition, glutamine is not able to combat the muscle wasting associated with disease or age-related sarcopenia. Oral glutamine supplementation initiated before advanced age in rats increases gut mass and improves the villus height of mucosa, thereby preventing the gut atrophy encountered in advanced age. Enterocytes from very old rats continuously metabolize glutamine into citrulline, which allowed, for the first time, the use of citrulline as a noninvasive marker of intestinal atrophy induced by advanced age. © The Author(s) 2016. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved.

Thedrez A.,French National Institute for Agricultural Research
Arteriosclerosis, Thrombosis, and Vascular Biology | Year: 2016

OBJECTIVE—: Proprotein convertase subtilisin kexin type 9 (PCSK9) inhibitors lower low-density lipoprotein (LDL) cholesterol in the vast majority of patients with autosomal dominant familial hypercholesterolemia. Will PCSK9 inhibition with monoclonal antibodies, in particular alirocumab, be of therapeutic value for patients with autosomal recessive hypercholesterolemia (ARH)? APPROACH AND RESULTS—: Primary lymphocytes were obtained from 28 genetically characterized ARH patients and 11 controls. ARH lymphocytes treated with mevastatin were incubated with increasing doses of recombinant PCSK9 with or without saturating concentrations of alirocumab. Cell surface LDL receptor expression measured by flow cytometry and confocal microscopy was higher in ARH than in control lymphocytes. PCSK9 significantly reduced LDL receptor expression in ARH lymphocytes albeit to a lower the extent than in control lymphocytes (25% versus 76%, respectively), an effect reversed by alirocumab. Fluorescent LDL cellular uptake, also measured by flow cytometry, was reduced in ARH lymphocytes compared with control lymphocytes. PCSK9 significantly lowered LDL cellular uptake in ARH lymphocytes, on average by 18%, compared with a 46% reduction observed in control lymphocytes, an effect also reversed by alirocumab. Overall, the effects of recombinant PCSK9, and hence of alirocumab, on LDL receptor expression and function were significantly less pronounced in ARH than in control cells. CONCLUSIONS—: PCSK9 inhibition with alirocumab on top of statin treatment has the potential to lower LDL cholesterol in some autosomal recessive hypercholesterolemia patients. © 2016 American Heart Association, Inc.

Poulsen C.,Copenhagen University | Vaucheret H.,French National Institute for Agricultural Research | Brodersen P.,Copenhagen University
Plant Cell | Year: 2013

RNA silencing refers to a collection of gene regulatory mechanisms that use small RNAs for sequence specific repression. These mechanisms rely on ARGONAUTE (AGO) proteins that directly bind small RNAs and thereby constitute the central component of the RNA-induced silencing complex (RISC). AGO protein function has been probed extensively by mutational analyses, particularly in plants where large allelic series of several AGO proteins have been isolated. Structures of entire human and yeast AGO proteins have only very recently been obtained, and they allow more precise analyses of functional consequences of mutations obtained by forward genetics. To a large extent, these analyses support current models of regions of particular functional importance of AGO proteins. Interestingly, they also identify previously unrecognized parts of AGO proteins with profound structural and functional importance and provide the first hints at structural elements that have important functions specific to individual AGO family members. A particularly important outcome of the analysis concerns the evidence for existence of Gly-Trp (GW) repeat interactors of AGO proteins acting in the plant microRNA pathway. The parallel analysis of AGO structures and plant AGO mutations also suggests that such interactions with GW proteins may be a determinant of whether an endonucleolytically competent RISC is formed. © 2013 American Society of Plant Biologists. All rights reserved.

McKown A.D.,University of California at Los Angeles | Cochard H.,French National Institute for Agricultural Research | Cochard H.,University Blaise Pascal | Sack L.,University of California at Los Angeles
American Naturalist | Year: 2010

Leaf venation architecture is tremendously diverse across plant species. Understanding the hydraulic functions of given venation traits can clarify the organization of the vascular system and its adaptation to environment. Using a spatially explicit model (the program K-leaf), we subjected realistic simulated leaves to modifi-cations and calculated the impacts on xylem and leaf hydraulic conductance (K x and Kleaf, respectively), important traits in determining photosynthesis and growth.We tested the sensitivity of leaves to altered vein order conductivities (1) in the absence or (2) presence of hierarchical vein architecture, (3) to major vein tapering, and (4) to modification of vein densities (length/leaf area). The K x and Kleaf increased with individual vein order conductivities and densities; for hierarchical venation systems, the greatest impact was from increases in vein conductivity for lower vein orders and increases in density for higher vein orders. Individual vein order conductivities were colimiting of K x and Kleaf, as were their densities, but the effects of vein conductivities and densities were orthogonal. Both vein hierarchy and vein tapering increased K x relative to xylem construction cost. These results highlight the important consequences of venation traits for the economics, ecology, and evolution of plant transport capacity. © 2010 by The University of Chicago.

Hirt H.,French National Institute for Agricultural Research
Plant signaling & behavior | Year: 2011

More than 100,000 publications demonstrate that AGC kinases are important regulators of growth, metabolism, proliferation, cell divison, survival and apoptosis in mammalian systems. Mutation and/or dysregulation of these kinases contribute to the pathogenesis of many human diseases, including cancer and diabetes. Although AGC kinases are also present in plants, little is known about their functions. We demonstrated that the AGC kinase OXIDATIVE SIGNAL-INDUCIBLE 1 (OXI1/AGC2-1) regulate important developmental processes and defense responses in plants. The summary of recent progress also demonstrates that we are only beginning to understand the role of this kinase pathway in plants.

Zitt M.,French National Institute for Agricultural Research
Scientometrics | Year: 2011

A new family of citation normalization methods appeared recently, in addition to the classical methods of "cited-side" normalization and the iterative measures of intellectual influence in the wake of Pinski and Narin influence weights. These methods have a quite global scope in citation analysis but were first applied to the journal impact, in the experimental Audience Factor (AF) and the Scopus Source-Normalized Impact per Paper (SNIP). Analyzing some properties of the Garfield's Journal Impact Factor, this note highlights the rationale of citing-side (or source-level, fractional citation, ex ante) normalization. © 2011 Akadémiai Kiadó, Budapest, Hungary.

Ravet K.,Colorado State University | Ravet K.,French National Institute for Agricultural Research | Pilon M.,Colorado State University
Antioxidants and Redox Signaling | Year: 2013

Significance: Photosynthesis, the process that drives life on earth, relies on transition metal (e.g., Fe and Cu) containing proteins that participate in electron transfer in the chloroplast. However, the light reactions also generate high levels of reactive oxygen species (ROS), which makes metal use in plants a challenge. Recent Advances: Sophisticated regulatory networks govern Fe and Cu homeostasis in response to metal ion availability according to cellular needs and priorities. Molecular remodeling in response to Fe or Cu limitation leads to its economy to benefit photosynthesis. Fe toxicity is prevented by ferritin, a chloroplastic Fe-storage protein in plants. Recent studies on ferritin function and regulation revealed the interplay between iron homeostasis and the redox balance in the chloroplast. Critical Issues: Although the connections between metal excess and ROS in the chloroplast are established at the molecular level, the mechanistic details and physiological significance remain to be defined. The causality/effect relationship between transition metals, redox signals, and responses is difficult to establish. Future Directions: Integrated approaches have led to a comprehensive understanding of Cu homeostasis in plants. However, the biological functions of several major families of Cu proteins remain unclear. The cellular priorities for Fe use under deficiency remain largely to be determined. A number of transcription factors that function to regulate Cu and Fe homeostasis under deficiency have been characterized, but we have not identified regulators that mediate responses to excess. Importantly, details of metal sensing mechanisms and cross talk to ROS-sensing mechanisms are so far poorly documented in plants. © 2013, Mary Ann Liebert, Inc.

Philippot L.,French National Institute for Agricultural Research | Philippot L.,University of Burgundy | Hallin S.,Swedish University of Agricultural Sciences
Trends in Plant Science | Year: 2011

Agriculture is an important source of anthropogenic emissions of the greenhouse gases (GHG), methane (CH 4) and nitrous oxide (N 2O), and crops can affect the microbial processes controlling these emissions in many ways. Here, we summarize the current knowledge of plant-microbe interactions in relation to the CH 4 and N 2O budgets and show how this is promoting new gIPCCenerations of crop cultivars that have the potential to mitigate GHG emissions for future agricultural use. The possibility of breeding low GHG-emitting cultivars is a paradigm shift towards sustainable agriculture that balances climate change and food and bioenergy security. © 2011 Elsevier Ltd.

Haegeman A.,Ghent University | Jones J.T.,SCRI | Danchin E.G.J.,French National Institute for Agricultural Research
Molecular Plant-Microbe Interactions | Year: 2011

The origin of plant parasitism within the phylum Nematoda is intriguing. The ability to parasitize plants has originated independently at least three times during nematode evolution and, as more molecular data has emerged, it has become clear that multiple instances of horizontal gene transfer (HGT) from bacteria and fungi have played a crucial role in the nematode's adaptation to this new lifestyle. The first reported HGT cases in plant-parasitic nematodes were genes encoding plant cell wall-degrading enzymes. Other putative examples of HGT were subsequently described, including genes that may be involved in the modulation of the plant's defense system, the establishment of a nematode feeding site, and the synthesis or processing of nutrients. Although, in many cases, it is difficult to pinpoint the donor organism, candidate donors are usually soil dwelling and are either plant-pathogenic or plant-associated microorganisms, hence occupying the same ecological niche as the nematodes. The exact mechanisms of transfer are unknown, although close contacts with donor microorganisms, such as symbiotic or trophic interactions, are a possibility. The widespread occurrence of horizontally transferred genes in evolutionarily independent plant-parasitic nematode lineages suggests that HGT may be a prerequisite for successful plant parasitism in nematodes. © 2011 The American Phytopathological Society.

Tena G.,Harvard University | Boudsocq M.,Harvard University | Boudsocq M.,French National Institute for Agricultural Research | Sheen J.,Harvard University
Current Opinion in Plant Biology | Year: 2011

In plants and animals, innate immunity is triggered through pattern recognition receptors (PRRs) in response to microbe-associated molecular patterns (MAMPs) to provide the first line of inducible defense. Plant receptor protein kinases (RPKs) represent the main plasma membrane PRRs perceiving diverse MAMPs. RPKs also recognize secondary danger-inducible plant peptides and cell-wall signals. Both types of RPKs trigger rapid and convergent downstream signaling networks controlled by calcium-activated PKs and mitogen-activated PK (MAPK) cascades. These PK signaling networks serve specific and overlapping roles in controlling the activities and synthesis of a plethora of transcription factors (TFs), enzymes, hormones, peptides and antimicrobial chemicals, contributing to resistance against bacteria, oomycetes and fungi. © 2011 Elsevier Ltd.

Girard A.L.,French National Institute for Agricultural Research
The Plant cell | Year: 2012

The plant cuticle consists of cutin, a polyester of glycerol, hydroxyl, and epoxy fatty acids, covered and filled by waxes. While the biosynthesis of cutin building blocks is well documented, the mechanisms underlining their extracellular deposition remain unknown. Among the proteins extracted from dewaxed tomato (Solanum lycopersicum) peels, we identified GDSL1, a member of the GDSL esterase/acylhydrolase family of plant proteins. GDSL1 is strongly expressed in the epidermis of growing fruit. In GDSL1-silenced tomato lines, we observed a significant reduction in fruit cuticle thickness and a decrease in cutin monomer content proportional to the level of GDSL1 silencing. A significant decrease of wax load was observed only for cuticles of the severely silenced transgenic line. Fourier transform infrared (FTIR) analysis of isolated cutins revealed a reduction in cutin density in silenced lines. Indeed, FTIR-attenuated total reflectance spectroscopy and atomic force microscopy imaging showed that drastic GDSL1 silencing leads to a reduction in ester bond cross-links and to the appearance of nanopores in tomato cutins. Furthermore, immunolabeling experiments attested that GDSL1 is essentially entrapped in the cuticle proper and cuticle layer. These results suggest that GDSL1 is specifically involved in the extracellular deposition of the cutin polyester in the tomato fruit cuticle.

Bouillaud F.,University of Paris Descartes | Blachier F.,French National Institute for Agricultural Research
Antioxidants and Redox Signaling | Year: 2011

Sulfide is a molecule with toxicity comparable to that of cyanide. It inhibits mitochondrial cytochrome oxidase at submicromolar concentrations. However, at even lower concentrations, sulfide is a substrate for the mitochondrial electron transport chain in mammals, and is comparable to succinate. This oxidation involves a sulfide quinone reductase. Sulfide is thus oxidized before reaching a toxic concentration, which explains why free sulfide concentrations are very low in mammals, even though sulfide is constantly released as a result of cellular metabolism. It has been suggested that sulfide has signaling properties in mammals like two other gases, NO and CO, which are also cytochrome oxidase inhibitors. The oxidation of sulfide by mitochondria creates further complexity in the description/use of sulfide signaling in mammals. In fact, in the many studies reported in the literature, the sulfide concentrations that have been used were well within the range that affects mitochondrial activity. This review focuses on the relevance of sulfide bioenergetics to sulfide biology and discusses the case of colonocytes, which are routinely exposed to higher sulfide concentrations. Finally, we offer perspectives for future studies on the relationship between the two opposing aspects of this Janus-type molecule, sulfide. © Copyright 2011, Mary Ann Liebert, Inc.

Chateigner-Boutin A.-L.,French National Institute for Agricultural Research | Small I.,University of Western Australia
Wiley Interdisciplinary Reviews: RNA | Year: 2011

RNA editing is a term used for a number of mechanistically different processes that alter the nucleotide sequence of RNA molecules to differ from the gene sequence. RNA editing occurs in a wide variety of organisms and is particularly frequent in organelle transcripts of eukaryotes. The discontiguous phylogenetic distribution of mRNA editing, the mechanistic differences observed in different organisms, and the nonhomologous editing machinery described in different taxonomic groups all suggest that RNA editing has appeared independently several times. This raises questions about the selection pressures acting to maintain editing that are yet to be completely resolved. Editing tends to be frequent in organisms with atypical organelle genomes and acts to correct the effect of DNA mutations that would otherwise compromise the synthesis of functional proteins. Additional functions of editing in generating protein diversity or regulating gene expression have been proposed but so far lack widespread experimental evidence, at least in organelles. © 2011 John Wiley & Sons, Ltd.

Citti C.,National Veterinary School of Toulouse | Blanchard A.,University of Bordeaux 1 | Blanchard A.,French National Institute for Agricultural Research
Trends in Microbiology | Year: 2013

Commonly known as mycoplasmas, bacteria of the class Mollicutes include the smallest and simplest life forms capable of self replication outside of a host. Yet, this minimalism hides major human and animal pathogens whose prevalence and occurrence have long been underestimated. Owing to advances in sequencing methods, large data sets have become available for a number of mycoplasma species and strains, providing new diagnostic approaches, typing strategies, and means for comprehensive studies. A broader picture is thus emerging in which mycoplasmas are successful pathogens having evolved a number of mechanisms and strategies for surviving hostile environments and adapting to new niches or hosts. © 2013 Elsevier Ltd.

Lesage F.,French National Institute for Agricultural Research | Lesage F.,University of Nice Sophia Antipolis | Barhanin J.,University of Nice Sophia Antipolis
Physiology | Year: 2011

Background K 2P channels are tightly regulated by different stimuli including variations of external and internal pH. pH sensitivity relies on proton-sensing residues that influence channel gating and activity. Gene inactivation in the mouse is a revealing implication of K 2P channels in many physiological functions ranging from hormone secretion to central respiratory adaptation. Surprisingly, only a few phenotypic traits of these mice have yet been directly related to the pH sensitivity of K 2P channels. © 2011 by the American Physiological Society.

Coma V.,French National Institute for Agricultural Research
Polimeros | Year: 2013

Active packaging is one of the responses to the recent food-borne microbial outbreaks and to the consumer's demand for high quality food and for packaging that is more advanced and creative than what is currently offered. Moreover, with the recent increase in ecological awareness associated with the dramatic decrease in fossil resources, research has turned towards the elaboration of more natural materials. This paper provides a short review of biomaterials exhibiting antimicrobial and antioxidant properties for applications in food preservation. The two main concepts of active biopackaging materials are briefly introduced. The different polysaccharides potentially used in packaging materials are then presented associated with a brief overview of research works related to biopackaging, exhibiting notably antimicrobial or antioxidant properties. Finally, future trends such as the release-on-demand of bioactive agents are discussed.

Budar F.,French National Institute for Agricultural Research
Plant signaling & behavior | Year: 2011

That organellar genome variation can play a role in plant adaptation has been suggested by several lines of evidence, including cytoplasm capture, cytoplasm effects in local adaptation, and positive selection in a chloroplast gene. In-depth analysis and better understanding of the genetic basis of plant adaptation is becoming a main objective in plant science. Arabidopsis thaliana has all the required characteristics to be used as a model for obtaining knowledge on the mechanisms underlying the role of organelles in plant adaptation. The availability of the appropriate tools and materials for assessing organelle genetic variation will open up new opportunities for developing novel breeding strategies.

Poirier M.,CNRS Center of Evolutionary and Functional Ecology | Durand J.-L.,French National Institute for Agricultural Research | Volaire F.,CNRS Center of Evolutionary and Functional Ecology
Global Change Biology | Year: 2012

Extreme climatic events are expected to increase in frequency and magnitude as a consequence of global warming. Grasslands cover a large proportion of the European continent and contribute to both agricultural production and ecosystem services through inter and intraspecific genetic variability. This study analysed the effects of summer droughts and heat waves on the persistence and production of perennial forage grasses. Mediterranean and temperate populations of Dactylis glomerata L. and Festuca arundinacea (Schreb.) were compared at both Mediterranean and temperate sites in France. By manipulating canopy temperatures and water availability, grass swards in the field were subjected to cumulative summer and spring water deficits (CSSWD) ranging from 329 to 707 mm to test different projected climatic conditions and extreme summer events. Under controlled summer heat waves (6-21 days at a mean daily canopy temperature higher than 30-35 °C), there was no increase in membrane damage to surviving aerial tissues. Plant stress was thus mainly generated through greater soil water deficit. Under the greatest CSSWD, annual biomass production was reduced on average by 60% and 30% with temperate and Mediterranean populations, respectively. Thresholds for a significant increase in summer tiller mortality were seen at CSSWD higher than 450 mm for temperate populations and 550 mm for Mediterranean populations. The latter displayed lower predawn leaf water potentials in summer and recovered through intense tillering in the subsequent seasons. Under the most extreme CSSWD, fewer than 20% of tillers of temperate populations survived and their nitrogen uptake ability was drastically altered. The higher potential productivity of Mediterranean populations in winter was associated with greater frost sensitivity. The identification of thresholds for vulnerability and the determination of the role of genetic diversity will improve the management of plant resilience and the design of new plant material to cope with climate change. © 2012 Blackwell Publishing Ltd.

Zitt M.,French National Institute for Agricultural Research
Journal of Informetrics | Year: 2010

The principle of a new type of impact measure was introduced recently, called the " Audience Factor" (AF). It is a variant of the journal impact factor where emitted citations are weighted inversely to the propensity to cite of the source. In the initial design, propensity was calculated using the average length of bibliography at the source level with two options: a journal-level average or a field-level average. This citing-side normalization controls for propensity to cite, the main determinant of impact factor variability across fields. The AF maintains the variability due to exports-imports of citations across field and to growth differences. It does not account for influence chains, powerful approaches taken in the wake of Pinski-Narin's influence weights. Here we introduce a robust variant of the audience factor, trying to combine the respective advantages of the two options for calculating bibliography lengths: the classification-free scheme when the bibliography length is calculated at the individual journal level, and the robustness and avoidance of ad hoc settings when the bibliography length is averaged at the field level. The variant proposed relies on the relative neighborhood of a citing journal, regarded as its micro-field and assumed to reflect the citation behavior in this area of science. The methodology adopted allows a large range of variation of the neighborhood, reflecting the local citation network, and partly alleviates the " cross-scale" normalization issue. Citing-side normalization is a general principle which may be extended to other citation counts. © 2010 Elsevier Ltd.

Wolf S.,Center for Organismal Studies Heidelberg | Hofte H.,French National Institute for Agricultural Research
Plant Cell | Year: 2014

Despite an increasingly detailed understanding of endogenous and environmental growth-controlling signals and their signaling networks, little is known on how these networks are integrated with the cell expansion machinery. Members of the CrRLK1L family control cell wall properties and cell expansion in a variety of developmental and environmental contexts. Two recent reports provide exciting new insights into the mode of action of these RLKs. One study shows that one family member, FERONIA (FER), is required for the production of hydroxyl radicals in the female gametophyte, which causes pollen tube rupture and sperm cell release during fertilization. Another study shows that FER is a receptor for a signaling peptide (Rapid Alkalinization Factor 1 [RALF1]) that triggers cell wall alkalinization and growth arrest, possibly through the inhibition of plasma membrane H+-ATPase activity. RALF1 belongs to a large gene family, with a wide range of expression patterns. Other CrRLK1L family members therefore may also be receptors for RALF-like peptides. These findings have important implications for our understanding of the control of cell wall integrity during growth and raise new intriguing questions. © 2014 American Society of Plant Biologists. All rights reserved.

Braybrook S.A.,University of Bern | Braybrook S.A.,University of Cambridge | Peaucelle A.,University Paris Diderot | Peaucelle A.,French National Institute for Agricultural Research
PLoS ONE | Year: 2013

How instructive signals are translated into robust and predictable changes in growth is a central question in developmental biology. Recently, much interest has centered on the feedback between chemical instructions and mechanical changes for pattern formation in development. In plants, the patterned arrangement of aerial organs, or phyllotaxis, is instructed by the phytohormone auxin; however, it still remains to be seen how auxin is linked, at the apex, to the biochemical and mechanical changes of the cell wall required for organ outgrowth. Here, using Atomic Force Microscopy, we demonstrate that auxin reduces tissue rigidity prior to organ outgrowth in the shoot apex of Arabidopsis thaliana, and that the de-methyl-esterification of pectin is necessary for this reduction. We further show that development of functional organs produced by pectin-mediated ectopic wall softening requires auxin signaling. Lastly, we demonstrate that coordinated localization of the auxin transport protein, PIN1, is disrupted in a naked-apex produced by increasing cell wall rigidity. Our data indicates that a feedback loop between the instructive chemical auxin and cell wall mechanics may play a crucial role in phyllotactic patterning. © 2013 Braybrook, Peaucelle.

Storlie E.,Colorado State University | Charmet G.,French National Institute for Agricultural Research
Plant Genome | Year: 2013

Cross-validation (CRV) methods were designed to simulate genomic selection (GS) for yield in a wheat (Triticum aestivum L.) breeding program wiThdata of 318 genotypes grown over an 11-yr period at six locations in France. Two methods, CVSWO (cross-validation-specific without location as factor) and CVSW (cross-validation-specific wiThlocation as factor), included 11 folds, each comprising genotypes grown during a specific year and each representing target populations, while the remaining folds comprising genotypes grown during the other 10 yr represented training populations. These methods were compared with CVRWO (cross-validation-random without location as factor) and CVRW (cross-validation-random wiThlocation as factor), designed to simulate standard CRV while retaining the structure of the first two CRV methods; the same 318 genotypes were used to create 11 folds, each comprising randomly selected genotypes. Results suggest the accuracy of the CRV methods using specifically selected genotypes (correlation coefficient between (marker based) estimate of breeding value and observed phenotype [rM] = 0.20) based on years grown were significantly less than methods using randomly selected genotypes (rM = 0.40-0.50). These results imply wheat yield is more difficult to predict for unknown, futuristic years than standard CRV methods suggest. An alternative measure of accuracy based on predicted genotypic ranks, termed predicted rank conversion (PRC), was implemented for the purpose of improving accuracies and reducing the differences between CRV methods. © Crop Science Society of America.

Vercken E.,French National Institute for Agricultural Research | Kramer A.M.,University of Georgia | Tobin P.C.,Northern Research Station | Drake J.M.,University of Georgia
Ecology Letters | Year: 2011

Ecology Letters (2011) 14: 179-186 Allee effects are important dynamical mechanisms in small-density populations in which per capita population growth rate increases with density. When positive density dependence is sufficiently severe (a 'strong' Allee effect), a critical density arises below which populations do not persist. For spatially distributed populations subject to dispersal, theory predicts that the occupied area also exhibits a critical threshold for population persistence, but this result has not been confirmed in nature. We tested this prediction in patterns of population persistence across the invasion front of the European gypsy moth (Lymantria dispar) in the United States in data collected between 1996 and 2008. Our analysis consistently provided evidence for effects of both population area and density on persistence, as predicted by the general theory, and confirmed here using a mechanistic model developed for the gypsy moth system. We believe this study to be the first empirical documentation of critical patch size induced by an Allee effect. © 2010 Blackwell Publishing Ltd/CNRS.

Ghestem M.,Agro ParisTech | Sidle R.C.,French National Institute for Agricultural Research | Stokes A.,U.S. Environmental Protection Agency
BioScience | Year: 2011

Although research has explained how plant roots mechanically stabilize soils, in this article we explore how root systems create networks of preferential flow and thus influence water pressures in soils to trigger landslides. Root systems may alter subsurface flow: Hydrological mechanisms that promote lower pore-water pressures in soils are beneficial to slope stability, whereas those increasing pore pressure are adverse. Preferential flow of water occurs in the following types of root channels: (a) channels formed by dead or decaying roots, (b) channels formed by decayed roots that are newly occupied by living roots, and (c) channels formed around live roots. The architectural analysis of root systems improves our understanding of how roots grow initially, develop, die, and interconnect. Conceptual examples and case studies are presented to illustrate how root architecture and diverse traits (e.g., diameter, length, orientation, topology, sinuosity, decay rate) affect the creation of root channels and thus affect preferential flow. © 2011 by American Institute of Biological Sciences. All rights reserved.

Kadam V.S.,University of Maine, France | Nicol E.,University of Maine, France | Gaillard C.,French National Institute for Agricultural Research
Macromolecules | Year: 2012

A triblock poly(2-methacryloyloxyethyl acrylate)-b-poly(ethylene oxide)-b-poly(2-methacryloyloxyethyl acrylate) (PMEA-b-PEO-b-PMEA) copolymer bearing polymerizable groups on the hydrophobic blocks was synthesized and self-assembled in water. The transient micellar structures formed in selective solvent were permanently fixed by cross-linking the methacrylate moieties in the micelles cores under UV light. The structures obtained after cross-linking were characterized by static and dynamic light scattering (SLS and DLS), size exclusion chromatography (SEC), and electron microscopy (TEM and cryoTEM). SLS measurements showed an increase of the aggregation number of the micelles during the photo-cross-linking process. This result was discussed in terms of competition between the micelles polymerization rate and the unimers exchange rate. At low concentration, mainly flower-like architectures were obtained. As the concentration of the cross-linked solutions increased, more complex aggregates, in which the "flower" is the basic unit, were obtained. © 2011 American Chemical Society.

Distribution of energy at the soil surface in a row-crop influences mainly soil temperature and water content, and therefore root activity, nitrogen mineralization and within canopy air temperature, which all affect plant physiology. In the case of a vineyard, it is also closely related to the energy available to the berries and therefore most influential for fruit quality. The aim of this study was to develop a simplified model of available energy distribution at the soil surface and at the bottom of the rows, where most of the clusters are located. Such a model would be helpful for optimising some aspects of row-crop management like training system choice, row geometry, leaf area density, and soil surface maintenance practices. The model simulated radiation balance at the soil surface, split up into downward and upward short- and long-wave fluxes. Row shadows were calculated at any point of the inter-row space, in interaction with actual row geometry and simplified porosity distribution within row volume. All hemispheric radiations (long-wave and diffuse solar radiation) were calculated according to view factors between the row and soil surfaces. Input variables were therefore incoming solar radiation over the canopy, air temperatures near the row walls and soil surface temperatures. Parameters were row geometry, dimensions and porosities. The model was validated in a 7 years old Merlot vineyard in the Médoc area, by comparing model predictions to measured net radiation (Rns) at five positions above the inter-row soil surface. Along the row sampling was achieved by a moving device carrying the net-radiometers. Structure of the vegetation was kept constant during the experiment and gap fraction parameters were derived from pictures of shadows at the soil surface. Since Rns measurements are impracticable directly at the soil surface and horizontal distribution of Rns is heterogeneous, comparison was performed by calculating net radiation at the actual measurement height which was close to average cluster height. Model prediction agreed with field measurement in most conditions, which suggests that all short- and long-wave radiation fluxes, as well as interactions with the canopy structure, were well described. Rns, energy available to clusters, and soil surface temperature variations were all mainly driven by shading due to the rows. Coupling the model to soil heat transfer and convective fluxes to the atmosphere models will help forecasting soil temperature distribution at the surface and in depth as well as canopy microclimate. The model will also be an essential part of a more elaborate model of cluster microclimate, a key determinant of berry quality. © 2009 Elsevier B.V. All rights reserved.

Lombard V.,CNRS Architecture and Functions of Biological Macromolecules Lab | Lombard V.,Aix - Marseille University | Golaconda Ramulu H.,CNRS Architecture and Functions of Biological Macromolecules Lab | Golaconda Ramulu H.,Aix - Marseille University | And 6 more authors.
Nucleic Acids Research | Year: 2014

The Carbohydrate-Active Enzymes database (CAZy; http://www.cazy.org) provides online and continuously updated access to a sequence-based family classification linking the sequence to the specificity and 3D structure of the enzymes that assemble, modify and breakdown oligo- and polysaccharides. Functional and 3D structural information is added and curated on a regular basis based on the available literature. In addition to the use of the database by enzymologists seeking curated information on CAZymes, the dissemination of a stable nomenclature for these enzymes is probably a major contribution of CAZy. The past few years have seen the expansion of the CAZy classification scheme to new families, the development of subfamilies in several families and the power of CAZy for the analysis of genomes and metagenomes. This article outlines the changes that have occurred in CAZy during the past 5 years and presents our novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes. © 2013 The Author(s). Published by Oxford University Press.

Teil G.,French National Institute for Agricultural Research
Science Technology and Human Values | Year: 2012

The sociology of science has shown that the scientific quest for truth, framed by the search for objectivity was granting objects of knowledge the form of independent and autonomous things, "data" already given and preexisting their observation. But do "real" objects only fit the form of data or things? If not, to which other form and objectivity do they fit? The author considers the question by examining the dispute between scientists and vintners on the issue of terroir, a complex combination of viticulture and wine-making practices and agro-climactic factors, which gives wines a particular taste, or terroir typicity. For scientists who are unable to reduce it to a stable list of determining factors, terroir is an unfounded notion, an imaginary social construction, and an economic barrier. Producers, on the other hand, along with the wider distribution network of terroir wines, consider terroir as a real object, although one whose manifestations cannot be evaluated using the same procedures as those of scientists. By analyzing how proof of terroir is implemented, the author uncovers a regime of existence of objects different from the scientific regime: a pluralist one governed by critical discussion from which objects emerge as distributed results of a production process. © The Author(s) 2012.

Cossart P.,Institute Pasteur Paris | Cossart P.,French National Institute for Agricultural Research | Helenius A.,ETH Zurich
Cold Spring Harbor Perspectives in Biology | Year: 2014

Of the many pathogens that infect humans and animals, a large number use cells of the host organism as protected sites for replication. To reach the relevant intracellular compartments, they take advantage of the endocytosis machinery and exploit the network of endocytic organelles for penetration into the cytosol or as sites of replication. In this review, we discuss the endocytic entry processes used by viruses and bacteria and compare the strategies used by these dissimilar classes of pathogens. © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Kim E.,Catholic University of Daegu | Coelho D.,University of Sao Paulo | Blachier F.,French National Institute for Agricultural Research
Nutrition Research | Year: 2013

The incidence of colorectal cancer (CRC) is rapidly increasing in developing countries, especially among populations that are adopting Western-style diets. Several, but not all, epidemiological and experimental studies suggest that a high intake of meat, especially red and processed meat, is associated with increased CRC risk. Potential reasons for the association between high red and processed meat intake and CRC risk include the content of the meat (e.g. protein, heme) and compounds generated by the cooking process (e.g. N-nitroso compounds, heterocyclic amines). These factors can affect the large intestine mucosa with genotoxicity and metabolic disturbances. Increased bacterial fermentation (putrefaction) of undigested protein and production of bacterial metabolites derived from amino acids may affect colon epithelial homeostasis and renewal. This correlates with the fact that most colonic cancers are detected in the distal colon and rectum where protein fermentation actively occurs. However, there are still large controversies on the relationship between red meat consumption and CRC risk. Therefore, the purpose of this review is to enhance the current understanding on the association between high red and processed meat intakes with CRC risk. A principal focus of this review will be to discuss the meat-related components, such as proteins in the meat, heme, N-nitroso compounds, and heterocyclic amines, and the effects they have upon the large intestine mucosa and the intestinal gut microbiota. © 2013 Elsevier Inc.

Vlad D.,French National Institute for Agricultural Research
PLoS genetics | Year: 2010

A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 x Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent--but still functional-combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation polymorphisms using high-throughput sequencing, because it remains challenging to distinguish allelic from paralogous variation at this scale.

Valiente A.G.,University of Oviedo | Beall E.,French National Institute for Agricultural Research | Garcia-Vazquez E.,University of Oviedo
Global Change Biology | Year: 2010

Populations at the edge of species distributions are especially vulnerable to climate change. Genetic changes as well as modification of their population structure are expected as reactions to global warming. Atlantic salmon (Salmo salar) inhabiting south France has been chosen as a model for studying the effect of global warming in marginal populations during the last 15 years. Increased gene flow between neighboring populations and dichotomy of maturation age between sexes have been identified as two main population changes significantly associated with high values of the North Atlantic Oscillation index, a global climate indicator. Although occurrence of isolated populations in each river (or even tributary) is a paradigm for this species, at least in northern areas, increased gene flow between rivers is forecasted as long as climate warming increases, favoring metapopulations at regional level. © 2009 Blackwell Publishing Ltd.

Glemin S.,French National Center for Scientific Research | Ronfort J.,French National Institute for Agricultural Research
Evolution | Year: 2013

Evolution of selfing from outcrossing recurrently occurred in many lineages, especially in flowering plants. Evolution of selfing induces dramatic changes in the population genetics functioning but its consequences on the dynamics of adaptation have been overlooked. We studied a simple one-locus model of adaptation where a population experiences an environmental change at a given time. We first determined the effect of the mating system on the genetic bases and the speed of adaptation, focusing on the dominance of beneficial mutations and the respective part of standing variation and new mutations. Then, we assumed that the environmental change is associated with population decline to determine the effect of the mating system on the probability of population extinction. Extending previous results, we found that adaptation is more efficient and extinction less likely in outcrossers when beneficial mutations are dominant and codominant and when standing variation plays a significant role in adaptation. However, given adaptation does occur, it is usually more rapid in selfers than in outcrossers. Our results bear implications for the evolution of the selfing syndrome, the dynamics of the domestication process, and the dead-end hypothesis that posits that selfing lineages are doomed to extinction on the long run. © 2012.

Rouger R.,French National Institute for Agricultural Research
Heredity | Year: 2016

Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).Heredity advance online publication, 20 July 2016; doi:10.1038/hdy.2016.52. © 2016 Macmillan Publishers Limited, part of Springer Nature.

Reynaud A.,Toulouse 1 University Capitole | Couture S.,French National Institute for Agricultural Research
Theory and Decision | Year: 2012

We compare two different elicitationmethods formeasuring risk attitudes on a sample of French farmers.We consider the lottery tasks initially proposed by Holt and Laury (Econ Rev 92:1644-1655, 2002) and by Eckel and Grossman (Evol Hum Behav 23:281-295, 2002; J Econ Behav Org 68:1-7, 2008). The main empirical result from this within-subject study is that risk preference measures are affected by the type of mechanism used.We first show that this risk preference instability can be related to non-expected utility preferences of farmers. Using a risk-taking psychometric questionnaire, we then demonstrate that risk preferences of farmers are context-dependent. This may be another explanation of the observed risk preference instability. © 2012 Springer Science+Business Media New York.

Masson P.,French National Institute for Agricultural Research
Spectrochimica Acta - Part B Atomic Spectroscopy | Year: 2014

Plants take up and store elements according to the environment in which they are growing. Because plants are at the base of the food chain, the determination of essential elements or toxic elements in plant materials is of importance. However, it is assumed that the element content determined on selected tissues may provide more specific information than that derived from the whole plant analysis. In this work, we assessed the feasibility of solid sampling-electrothermal vaporization-inductively coupled plasma-optical emission spectrometry analyses for quantitative imaging of Cd and Mg in plant leaves. Leaves of tobacco (Nicotiana tabacum) were selected to be used as samples. To produce a two dimensional image, sections cut from leaf samples were analyzed. Cellulose doped with multi-element solution standards was used as calibration samples. Two certified reference materials (NIST SRM 1547 Peach Leaves and NIST SRM 1573a Tomato leaves) were used to verify the accuracy of measurements with good agreement between the measured concentrations and the certified values. Quantitative imaging revealed the inhomogeneous distribution of the selected elements. Excess of Cd and Mg tended to be focused on peripheral regions and the tip of the leaf. © 2014 Elsevier B.V. All rights reserved.

Meurens F.,French National Institute for Agricultural Research | Summerfield A.,Institute of Virology and Immunoprophylaxis IVI | Nauwynck H.,Ghent University | Saif L.,Ohio State University | Gerdts V.,University of Saskatchewan
Trends in Microbiology | Year: 2012

An animal model to study human infectious diseases should accurately reproduce the various aspects of disease. Domestic pigs (Sus scrofa domesticus) are closely related to humans in terms of anatomy, genetics and physiology, and represent an excellent animal model to study various microbial infectious diseases. Indeed, experiments in pigs are much more likely to be predictive of therapeutic treatments in humans than experiments in rodents. In this review, we highlight the numerous advantages of the pig model for infectious disease research and vaccine development and document a few examples of human microbial infectious diseases for which the use of pigs as animal models has contributed to the acquisition of new knowledge to improve both animal and human health. © 2011 Elsevier Ltd.

Marc D.,French National Institute for Agricultural Research | Marc D.,University of Tours
Journal of General Virology | Year: 2014

Most viruses express one or several proteins that counter the antiviral defences of the host cell. This is the task of non-structural protein NS1 in influenza viruses. Absent in the viral particle, but highly expressed in the infected cell, NS1 dramatically inhibits cellular gene expression and prevents the activation of key players in the IFN system. In addition, NS1 selectively enhances the translation of viral mRNAs and may regulate the synthesis of viral RNAs. Our knowledge of the virus and of NS1 has increased dramatically during the last 15 years. The atomic structure of NS1 has been determined, many cellular partners have been identified and its multiple activities have been studied in depth. This review presents our current knowledge, and attempts to establish relationships between the RNA sequence, the structure of the protein, its ligands, its activities and the pathogenicity of the virus. A better understanding of NS1 could help in elaborating novel antiviral strategies, based on either live vaccines with altered NS1 or on small-compound inhibitors of NS1. © 2014 The Authors.

Chastant-Maillard S.,French National Institute for Agricultural Research | Chastant-Maillard S.,National Polytechnic Institute of Toulouse
Transboundary and Emerging Diseases | Year: 2015

Bovine herpesvirus 4 (BoHV-4) is increasingly considered as responsible for various reproductive troubles. This virus infects blood mononuclear cells and displays a specific tropism for vascular endothelia, mammary tissue, endometrium and foetal tissues. Viral multiplication can be reactivated by corticosteroids or stress, both factors present at calving. BoHV-4 has been isolated in a large variety of clinical cases, primarily metritis, vaginitis and mastitis, but also endometritis, abortion and orchitis. Its impact on reproductive performance has been suggested by several epidemiological studies: seroprevalence against BoHV-4 is higher in aborted females and in repeat breeders. Nevertheless, its intrinsic pathogenic power seems low, symptoms developing only when BoHV-4 cooperates with bacteria: within the uterus or mammary gland. BoHV-4 is rather currently considered as a cofactor for the development of an inflammatory reaction initiated by bacteria. © 2013 Blackwell Verlag GmbH.

Federici F.,University of Cambridge | Dupuy L.,James Hutton Institute | Laplaze L.,French National Institute for Agricultural Research | Heisler M.,Developmental Biology Unit | And 2 more authors.
Nature Methods | Year: 2012

We present the coupled use of specifically localized fluorescent gene markers and image processing for automated quantitative analysis of cell growth and genetic activity across living plant tissues. We used fluorescent protein markers to identify cells, create seeds and boundaries for the automatic segmentation of cell geometries and ratiometrically measure gene expression cell by cell in Arabidopsis thaliana. © 2012 Nature America, Inc. All rights reserved.

Segura V.,Austrian Academy of Sciences | Segura V.,French National Institute for Agricultural Research | Vilhjalmsson B.J.,Austrian Academy of Sciences | Vilhjalmsson B.J.,University of Southern California | And 7 more authors.
Nature Genetics | Year: 2012

Population structure causes genome-wide linkage disequilibrium between unlinked loci, leading to statistical confounding in genome-wide association studies. Mixed models have been shown to handle the confounding effects of a diffuse background of large numbers of loci of small effect well, but they do not always account for loci of larger effect. Here we propose a multi-locus mixed model as a general method for mapping complex traits in structured populations. Simulations suggest that our method outperforms existing methods in terms of power as well as false discovery rate. We apply our method to human and Arabidopsis thaliana data, identifying new associations and evidence for allelic heterogeneity. We also show how a priori knowledge from an A. thaliana linkage mapping study can be integrated into our method using a Bayesian approach. Our implementation is computationally efficient, making the analysis of large data sets (n > 10,000) practicable. © 2012 Nature America, Inc. All rights reserved.

Moury B.,French National Institute for Agricultural Research
Molecular Plant Pathology | Year: 2010

Potato virus Y (PVY) is one of the rare plant viruses for which some biological traits (host range and symptomatology) are highly correlated with phylogeny, allowing the reconstruction of the evolutionary history of these traits. In this article, a new lineage of PVY isolates from Chile is described, showing unique genomic and biological properties. This lineage was found to be the sister group of all other PVY isolates and helped in the reconstruction of the ancestral traits and evolutionary history of PVY, suggesting that veinal necrosis in tobacco is an ancestral state and that adaptation to pepper (Capsicum spp.) and potato (Solanum tuberosum) has been modified several times during PVY history. © 2009 Blackwell Publishing Ltd.

Lamichhane J.R.,French National Institute for Agricultural Research
Advances in Agronomy | Year: 2015

Diseases caused by plant pathogenic bacteria have attained great concern worldwide as they are responsible for severe economic losses throughout the cultivated areas. Although studies performed in experimental conditions have provided many new insights into chemical and molecular signaling between plants and bacterial pathogens during pathogenesis, little is known about the factors that interact in natural field conditions. In particular, a wide gap exists between these two systems in terms of disease occurrence and severity. This review attempts to highlight the possible reasons that make natural field conditions different from the experimental ones, which might be useful to bridge the current gap and to facilitate the development of adequate control measures. © 2015 Elsevier Inc.

Roques A.,French National Institute for Agricultural Research
New Zealand Journal of Forestry Science | Year: 2010

This paper examines the effects of changing world trends on the introduction, establishment and spread of exotic insects associated with woody plants. Three aspects are considered: (i) commercial trade; (ii) tourism and consumer behaviour; and (iii) climate change. The current literature indicates that there are two key pest pathways: movement of wood ( (including solid-wood packaging), and the ornamental plant trade. The number of pests introduced along these routes is positively correlated with the volume and source of imports. It is likely, therefore, that improvements in regulation of the movement of wood will lead to a decrease in pest entry via this pathway. However, complexities associated with the ornamental plant trade will ensure that it remains a high risk route. There is evidence to suggest that numbers of interceptions at airports are positively related to the volume of air traffic from the countries from which passengers originate. Shifts in climatic conditions are likely to affect the survival, fecundity, development and dispersal of native insect species. However, it is difficult to entirely disentangle the effect of climate change from that of other physical or chemical factors, and/or other biotic causes. Improved monitoring of imports/exports, more knowledge about possible pests, and the impacts of climate change are needed to prevent the arrival of foreign pests in the future. © 2010 New Zealand Forest Research Institute Limited, trading as Scion.

D'Ischia M.,University of Naples Federico II | Napolitano A.,University of Naples Federico II | Ball V.,University of Strasbourg | Ball V.,French National Institute for Agricultural Research | And 2 more authors.
Accounts of Chemical Research | Year: 2014

Polydopamine (PDA), a black insoluble biopolymer produced by autoxidation of the catecholamine neurotransmitter dopamine (DA), and synthetic eumelanin polymers modeled to the black functional pigments of human skin, hair, and eyes have burst into the scene of materials science as versatile bioinspired functional systems for a very broad range of applications. PDA is characterized by extraordinary adhesion properties providing efficient and universal surface coating for diverse settings that include drug delivery, micro fluidic systems, and water-treatment devices. Synthetic eumelanins from dopa or 5,6-dihydroxyindoles are the focus of increasing interest as UV-absorbing agents, antioxidants, free radical scavengers, and waterdependent hybrid electronic-ionic semiconductors. Because of their peculiar physicochemical properties, eumelanins and PDA hold considerable promise in nanomedicine and bioelectronics, as they are biocompatible, biodegradable, and exhibit suitable mechanical properties for integration with biological tissues. Despite considerable similarities, very few attempts have so far been made to provide an integrated unifying perspective of these two fields of technology-oriented chemical research, and progress toward application has been based more on empirical approaches than on a solid conceptual framework of structure-property relationships. The present Account is an attempt to fill this gap. Following a vis-à-vis of PDA and eumelanin chemistries, it provides an overall view of the various levels of chemical disorder in both systems and draws simple correlations with physicochemical properties based on experimental and computational approaches. The potential of large-scale simulations to capture the macroproperties of eumelanin-like materials and their hierarchical structures, to predict the physicochemical properties of new melanin-inspired materials, to understand the structure-property-function relationships of these materials from the bottom up, and to design and optimize materials to achieve desired properties is illustrated. The impact of synthetic conditions on melanin structure and physicochemical properties is systematically discussed for the first time. Rational tailoring strategies directed to critical control points of the synthetic pathways, such as dopaquinone, DAquinone, and dopachrome, are then proposed, with a view to translating basic chemical knowledge into practical guidelines for material manipulation and tailoring. This key concept is exemplified by the recent demonstration that varying DA concentration, or using Tris instead of phosphate as the buffer, results in PDA materials with quite different structural properties. Realizing that PDA and synthetic eumelanins belong to the same family of functional materials may foster unprecedented synergisms between research fields that have so far been apart in the pursuit of tailorable and marketable materials for energy, biomedical, and environmental applications. (Chemical Equation Presented). © 2014 American Chemical Society.

Moisan M.-P.,French National Institute for Agricultural Research
Molecular and Cellular Endocrinology | Year: 2010

Corticosteroid-binding globulin (CBG) is a plasma glycoprotein discovered more than 60 years ago for its high-affinity for glucocorticoids. Although its molecular structure and its biochemical properties have been described, its various biological roles and its importance are not yet fully understood. This review focuses first on studies that have used no-hypothesis-driven genetic approaches in animal models to reveal the higher than expected importance of CBG in particular in glucocorticoid stress responses. Then the dissection of some CBG physiological roles in an animal model of genetic CBG deficiency is reported. Finally, studies on the role of CBG genetic variability in human obesity traits are reviewed and discussed. © 2009 Elsevier Ireland Ltd. All rights reserved.

Aubin J.,French National Institute for Agricultural Research
CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources | Year: 2013

Fish production is facing increasing worldwide demand while fish landings are plateauing. Fish production is the only kind of animal production that is still dominated by extractive activity, endangered because of overexploitation of natural resources and a rearing activity with a rapid expansion. Life Cycle Assessment (LCA), which estimates local- to global-scale environmental impacts, has been adapted to seafood production systems. Scientific publications increasingly propose methodological improvements and case-study applications of LCA in the fishery and aquaculture sectors, with the combined objectives of better describing and understanding their biophysical interactions with the environment and supporting decision-making and eco-labelling of seafood products. In particular, the development of innovative indicators better defines impacts of fisheries on the marine ecosystem (e.g., benthos damage, by-catch, biotic resource use). Nevertheless, the lack of consensus about methodological questions (e.g., co-product allocation rules, system boundary definition) weakens comparisons between studies and limits the generalization of results and dissemination of methods. This paper reviews published applications of LCA to farmed and wild-caught fish. © CAB International 2013.

Pitrat M.,French National Institute for Agricultural Research
Plant Biotechnology | Year: 2013

Like many crops, cultivated melons present a very large phenotypic polymorphism compared with the low phenotypic polymorphism of wild melons. Domestication has not been intensively studied and the genetic control of domestication traits is still poorly understood. The results of the subsequent diversification and selection processes are the present day types of melons. Genetic control of a majority of the diversification traits is under recessive genetic control: sex expression, fruit shape, sutures, number of placentas, gelatinous sheath around the seeds, white flesh colour and so on. Other phenotypic traits are dominant (orange flesh colour, netting, yellow colour of mature fruit in the Amarillo type and so on) as are most of the disease resistances. Presence of the same traits in very different botanical groups can be the result of parallel evolution but also of intercrossing between groups and selection of preferred alleles. New results (genome sequencing) and methods will allow a better understanding of the genetic control of domestication and diversification.

Gough C.,French National Institute for Agricultural Research | Gough C.,French National Center for Scientific Research | Jacquet C.,CNRS Plant Research Laboratory
Trends in Plant Science | Year: 2013

Plant plasma membrane-bound receptors with extracellular lysin motif (LysM) domains participate in interactions with microorganisms. In Medicago truncatula, the LysM receptor-like kinase gene nodulation (Nod) factor perception (NFP) is a key gene that controls the perception of rhizobial lipochitooligosaccharide (LCO) Nod factors for the establishment of the Rhizobium-legume symbiosis. In this article, we review recent data that have refined our understanding of this function and that have revealed a role for NFP in the perception of arbuscular mycorrhizal (AM) symbiotic signals and plant pathogenic microorganisms. The dual role of NFP in symbiosis and immunity suggests that this receptor protein controls the perception of different signals and the activation of different downstream signalling pathways. These advances provide new insights into the evolution and functioning of this versatile plant protein. © 2013 Elsevier Ltd.

De Almeida Engler J.,French National Institute for Agricultural Research | Gheysen G.,Ghent University
Molecular Plant-Microbe Interactions | Year: 2013

Plant-parasitic root-knot and cyst nematodes have acquired the ability to induce remarkable changes in host cells during the formation of feeding sites. Root-knot nematodes induce several multinucleate giant cells inside a gall whereas cyst nematodes provoke the formation of a multinucleate syncytium. Both strategies impinge on the deregulation of the cell cycle, involving a major role for endoreduplication. This review will first describe the current knowledge on the control of normal and aberrant cell cycles. Thereafter, we will focus on the role of both cell-cycle routes in the transformation process of root cells into large and highly differentiated feeding sites as induced by the phytoparasitic root-knot and cyst nematodes. © 2013 The American Phytopathological Society.

Etienne A.,CIRAD - Agricultural Research for Development | Genard M.,French National Institute for Agricultural Research | Lobit P.,Universidad Michoacana de San Nicolas de Hidalgo | Mbeguie-A-Mbeguie D.,CIRAD - Agricultural Research for Development | Bugaud C.,CIRAD - Agricultural Research for Development
Journal of Experimental Botany | Year: 2013

Fleshy fruit acidity is an important component of fruit organoleptic quality and is mainly due to the presence of malic and citric acids, the main organic acids found in most ripe fruits. The accumulation of these two acids in fruit cells is the result of several interlinked processes that take place in different compartments of the cell and appear to be under the control of many factors. This review combines analyses of transcriptomic, metabolomic, and proteomic data, and fruit process-based simulation models of the accumulation of citric and malic acids, to further our understanding of the physiological mechanisms likely to control the accumulation of these two acids during fruit development. The effects of agro-environmental factors, such as the source:sink ratio, water supply, mineral nutrition, and temperature, on citric and malic acid accumulation in fruit cells have been reported in several agronomic studies. This review sheds light on the interactions between these factors and the metabolism and storage of organic acids in the cell. © 2013 The Authors.

Boudsocq M.,French National Institute for Agricultural Research | Sheen J.,Harvard University
Trends in Plant Science | Year: 2013

Ca2+ has long been recognized as a conserved second messenger and principal mediator in plant immune and stress responses. How Ca2+ signals are sensed and relayed into diverse primary and global signaling events is still largely unknown. Comprehensive analyses of the plant-specific multigene family of Ca2+-dependent protein kinases (CDPKs) are unraveling the molecular, cellular and genetic mechanisms of Ca2+ signaling. CDPKs, which exhibit overlapping and distinct expression patterns, sub-cellular localizations, substrate specificities and Ca2+ sensitivities, play versatile roles in the activation and repression of enzymes, channels and transcription factors. Here, we review the recent advances on the multifaceted functions of CDPKs in the complex immune and stress signaling networks, including oxidative burst, stomatal movements, hormonal signaling and gene regulation. © 2012 Elsevier Ltd.

Marze S.,French National Institute for Agricultural Research
Critical Reviews in Food Science and Nutrition | Year: 2013

Many food systems are dispersed systems, that is, they possess at least two immiscible phases. This is generally due to the coexistence of domains with different physicochemical properties separated by many interfaces which control the apparent thermodynamic equilibrium. This feature was and is still largely studied to design pharmaceutical delivery systems. In food science, the recent intensification of in vitro digestion tests to complement the in vivo ones holds promises in the identification of the key parameters controlling the bioaccessibility of nutrients and micronutrients. In this review, we present the developments of in vitro digestion tests for dispersed food systems (mainly emulsions, dispersions and gels). We especially highlight the evidences detailing the roles of the constituting multiscale structures. In a perspective section, we show the potential of structured interfaces to allow controlled bioaccessibility. © 2013 Copyright Taylor and Francis Group, LLC.

Ronceret A.,French National Institute for Agricultural Research | Pawlowski W.P.,Cornell University
Cytogenetic and Genome Research | Year: 2010

Early stages of meiotic prophase are characterized by complex and dramatic chromosome dynamics. Chromosome behavior during this period is associated with several critical meiotic processes that take place at the molecular level, such as recombination and homologous chromosome recognition and pairing. Studies to characterize specific patterns of chromosome dynamics and to identify their exact roles in the progression of meiotic prophase are only just beginning in plants. These studies are facilitated by advances in imaging technology in the recent years, including development of ultra-resolution three-dimensional and live microscopy methods. Studies conducted so far indicate that different chromosome regions exhibit different dynamics patterns in early prophase. In many species telomeres cluster at the nuclear envelope at the beginning of zygotene forming the telomere bouquet. The bouquet has been traditionally thought to facilitate chromosome pairing by bringing chromosome ends into close proximity, but recent studies suggest that its main role may rather be facilitating rapid movements of chromosomes during zygotene. In some species, including wheat and Arabidopsis, there is evidence that centromeres form pairs (couple) before the onset of pairing of chromosome arms. While significant advances have been achieved in elucidating the patterns of chromosome behavior in meiotic prophase I, factors controlling chromosome dynamics are still largely unknown and require further studies. Copyright © 2010 S. Karger AG, Basel.

Ball V.,French National Institute for Agricultural Research | Ball V.,University of Strasbourg
Colloids and Surfaces A: Physicochemical and Engineering Aspects | Year: 2010

The deposition of dopa-melanin films from dopamine solutions in oxidative conditions may offer new opportunities in surface coating methods. After having demonstrated that such films become impermeable to ferrocyanide anions after having reached a thickness of a few nanometers (F. Bernsmann, A. Ponche, C. Ringwald, J. Hemmerle, J. Raya, B. Bechinger, J.C. Voegel, P. Schaaf, V. Ball, Characterization of Dopamine-Melanin Growth on Silicon Oxide, Journal of Physical Chemistry C 113 (2009) 8234-8242) and after the determination of their zeta potential in the same pH conditions as those used for the film deposition we wish now to investigate the impedance spectra and zeta potential titration curve of such thin films. These properties are important to understand the electrical properties and surface chemistry of the melanin films, respectively. Such an investigation will hence allow to improve future applications of dopa-melanin films. The impedance spectra show that the films charge transfer and mass transfer resistance increase rapidly as the film deposits in parallel to a decrease of their permeability to ferrocyanide anions. The zeta potential versus pH titration curves display two inflexion points at pH values close to 6 and 9 which can be related to the titration of quinone-imine and catechol groups respectively. For the first time we show that dopa-melanin prepared in these conditions has an isoelectric point close to 4. The relevance of this finding is discussed. © 2010 Elsevier B.V.

Govind A.,French National Institute for Agricultural Research
International Journal of Biometeorology | Year: 2014

The nature of canopy radiative transfer mechanism (CRTM) describes the amount of beam penetration through a canopy and governs the nature of canopy illumination, i.e. the abundance of sunlit and shaded portions. Realistic representation of canopy illumination is critical for simulating various canopy biophysical processes associated with vegetated land surfaces. The adequate representation of CRTM can be attributed to the parameterizations of the two main canopy characteristics: the foliage projection (G-function) and the clumping effect (Ω function). Herein, using various types of G and Ω functions developed in a previous study, I tested 15 CRTM scenarios that combine different types of G and Ω functions to predict the dynamics of sunlit fraction (ε) of canopies having a wide range of plant area index (Ptotal) at various solar zenith angles (SZAs). It was observed that, for a given Ptotal, ε decreases as the SZA increases. However, ε significantly changed in accordance with the type of G and Ω functions used. Scenarios that employed random distribution of elements in space (S-4, S-9, and S-14) consistently returned larger ε values even at lower SZAs. This means that ignoring the clumping behavior of canopies could result in greater proportion of sunlit elements thereby reducing the beam penetration deeper into the canopy as opposed to those canopies where the elements are more aggregated. Beyond 70° SZA, almost all the scenarios returned similar ε values for a given Ptotal, which implied that the methods used is less sensitive at higher SZAs. The values of ε calculated by all the scenarios were significantly different from the S-6 (the ideal case). This observation highlights the importance of explicitly describing the G and Ω functions to adequately depict canopy illumination conditions. © 2013, ISB.

Cossart P.,Institute Pasteur Paris | Cossart P.,French Institute of Health and Medical Research | Cossart P.,French National Institute for Agricultural Research | Roy C.R.,Yale University
Current Opinion in Cell Biology | Year: 2010

Subversion of host membrane machinery is important for the uptake, survival, and replication of bacterial pathogens. Understanding how pathogens manipulate host membrane transport pathways provides mechanistic insight into how infection occurs and is also revealing new information on biochemical processes involved in the functioning of eukaryotic cells. In this review we discuss several of the canonical host pathways targeted by bacterial pathogens and emerging areas of investigation in this exciting field. © 2010 Elsevier Ltd.

Katerji N.,French National Institute for Agricultural Research | Campi P.,Italian Agricultural Research Council | Mastrorilli M.,Italian Agricultural Research Council
Agricultural Water Management | Year: 2013

The FAO AquaCrop model has been conceived as a tool for simulating, on a daily scale, the canopy cover (CC), biomass and the actual evapotranspiration and for simulating, on a seasonal scale, the final biomass, the harvested yield, the cumulate actual evapotranspiration, and the crop water use efficiency. This performance was analysed after a series of tests carried on 12 crop cycles, concerning corn and tomato grown in the Mediterranean region, and having three levels of plant water stress: absence of plant water stress (control), moderately stressed and severely stressed. The results highlight the effects of three factors affecting the AquaCrop performances: the species, the level of plant water stress during the crop cycle and the output variable to simulate.The AquaCrop adequately simulates the daily canopy cover (CC) in control treatments of tomato and corn, and in moderate stress treatment of corn. In the severe stressed treatment of corn, the simulated values of CC were close to the measured values only from sowing to 60 days after sowing, after that the simulated values do not fit the measurements.The AquaCrop model adequately simulates the daily biomass accumulation under all treatments in tomato and under non-stressed and moderate stressed treatments in corn. However, the simulated biomass outputs were generally overestimated during the late stages of the crop cycles and, consequently, the yield also exhibited a tendency to be overestimated. Nevertheless, the yield overestimation can be retained as acceptable because the normalised differences (D) between the simulations and measured values were less than 15% on average. An exception was the tomato yield simulated in the severely stressed treatment, for which D was greater than 30%. In contrast, in the case of the severely stressed treatment in corn, AquaCrop did not exhibit any aptitude for simulating the biomass or the grain yield. In fact, the model predicts the absence of any