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Compagnie Gervais Danone and French National Institute for Agricultural Research | Date: 2015-04-15

The present invention provides the use of Lactobacillus rhamnosus, for maintaining or increasing the intestinal microbiota diversity in a subject.

Compagnie Gervais Danone and French National Institute for Agricultural Research | Date: 2015-04-15

The present invention provides the use of Lactobacillus paracasei, for maintaining or increasing the intestinal microbiota diversity in a subject having dysbiosis.

French National Institute for Agricultural Research, French National Conservatory of Arts, Crafts, Institute Science Industries Vivant Et Environnement Agroparistech, Brodart and French National Center for Scientific Research | Date: 2015-03-04

The use of a composition including at least one saturated free fatty acid and at least one unsaturated free fatty acid as additive, for modifying the mechanical properties of a thermoplastic polymer material. An additivated thermoplastic polymer material and a process for producing same are also described.

French National Institute for Agricultural Research | Date: 2015-03-27

The invention relates to a method for increasing the frequency of meiotic recombination in plants, by inhibiting the RECQ4 or TOP3A protein, especially by mutagenesis or extinction of the RECQ4 or TOP3A gene coding for said protein. The invention can be used especially in the field of plant breeding and genetic mapping.

Kallistem, French National Center for Scientific Research, French National Institute for Agricultural Research and Ecole Normale Superieure de Lyon | Date: 2014-12-19

The present invention relates to a process for in vitro spermatogenesis from male germinal tissue comprising conducting maturation of testicular tissue comprising germ cells in a bioreactor which is made of a biomaterial and comprises at least one cavity wherein the germinal tissue is placed, and recovering elongated spermatids and/or spermatozoa.

French National Institute for Agricultural Research and French National Center for Scientific Research | Date: 2017-03-15

The present invention relates to novel fusion polypeptides and the uses thereof. The invention particularly relates to conjugated coat proteins derived from nepoviruses, virus-like particles made with such proteins, and the uses thereof. The particles of the invention can expose and/or encage molecules of interest and have utility in various fields such as the pharmaceutical, agro, or veterinary areas.

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

Aumeier C.,French National Institute for Agricultural Research
Nature Cell Biology | Year: 2016

The dynamic instability of microtubules is characterized by slow growth phases stochastically interrupted by rapid depolymerizations called catastrophes. Rescue events can arrest the depolymerization and restore microtubule elongation. However, the origin of these rescue events remains unexplained. Here we show that microtubule lattice self-repair, in structurally damaged sites, is responsible for the rescue of microtubule growth. Tubulin photo-conversion in cells revealed that free tubulin dimers can incorporate along the shafts of microtubules, especially in regions where microtubules cross each other, form bundles or become bent due to mechanical constraints. These incorporation sites appeared to act as effective rescue sites ensuring microtubule rejuvenation. By securing damaged microtubule growth, the self-repair process supports a mechanosensitive growth by specifically promoting microtubule assembly in regions where they are subjected to physical constraints. © 2016 Nature Publishing Group

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.

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.

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.

Vignon M.,University of Pau and Pays de l'Adour | 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.

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.

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.

Capron I.,French National Institute for Agricultural Research | Cathala B.,French National Institute for Agricultural Research
Biomacromolecules | Year: 2013

Cellulose nanocrystals (CNCs) are rod-like colloidal particles that irreversibly adsorb at the oil-water interface to produce ultrastable emulsions. When the internal phase fraction is increased, these CNCs can produce gel-like oil-in-water high internal phase emulsions (HIPEs) in which more than 90% of the hydrophobic phase is stabilized by less than 0.1% wt. of CNCs. However, a one-step preparation of HIPEs is not possible, and incorporation of the high internal phase fraction requires the prior preparation of Pickering emulsions. We propose that this two-step process to create CNC HIPEs relies on a swelling process of the droplets that does not desorb the CNCs from the interface, decreasing the coverage ratio of the droplets and leading to coalescence. As a result, this process leads to a drops deformation and a new interfacial networking organization as revealed by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) images. © 2013 American Chemical Society.

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

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.

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.

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.

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.

Disdier A.-C.,French National Institute for Agricultural Research | Marette S.,French National Institute for Agricultural Research
American Journal of Agricultural Economics | Year: 2010

This article explores the link between gravity and welfare frameworks for measuring the impact of nontariff measures. First, an analytical approach suggests how to combine a gravity equation with a partial equilibrium model to determine the welfare impact of nontariff measures. Second, an empirical application focuses on the effects of a standard that caps antibiotic residues in crustaceans in the United States, the European Union, Canada, and Japan. While the econometric estimation of the gravity equation reports a negative impact on imports, welfare evaluations show that in most cases, a stricter standard leads to an increase in both domestic and international welfare. © The Author (2010).

Maumus F.,French National Institute for Agricultural Research | Quesneville H.,French National Institute for Agricultural Research
PLoS ONE | Year: 2014

Eukaryotic genomes contain highly variable amounts of DNA with no apparent function. This so-called junk DNA is composed of two components: repeated and repeat-derived sequences (together referred to as the repeatome), and nona-nnotated sequences also known as genomic dark matter. Because of their high duplication rates as compared to other genomic features, transposable elements are predominant contributors to the repeatome and the products of their decay is thought to be a major source of genomic dark matter. Determining the origin and composition of junk DNA is thus important to help understanding genome evolution as well as host biology. In this study, we have used a combination of tools enabling to show that the repeatome from the small and reducing A. thaliana genome is significantly larger than previously thought. Furthermore, we present the concepts and results from a series of innovative approaches suggesting that a significant amount of the A. thaliana dark matter is of repetitive origin. As a tentative standard for the community, we propose a deep compendium annotation of the A. thaliana repeatome that may help addressing farther genome evolution as well as transcriptional and epigenetic regulation in this model plant. © 2014 Maumus, Quesneville.

Buscaill P.,French National Institute for Agricultural Research | Rivas S.,French National Center for Scientific Research
Current Opinion in Plant Biology | Year: 2014

Mounting of efficient plant defence responses depends on the ability to trigger a rapid defence reaction after recognition of the invading microbe. Activation of plant resistance is achieved by modulation of the activity of multiple transcriptional regulators, both DNA-binding transcription factors and their regulatory proteins, that are able to reprogram transcription in the plant cell towards the activation of defence signalling. Here we provide an overview of recent developments on the transcriptional control of plant defence responses and discuss defence-related hormone signalling, the role of WRKY transcription factors during the regulation of plant responses to pathogens, nuclear functions of plant immune receptor proteins, as well as varied ways by which microbial effectors subvert plant transcriptional reprogramming to promote disease. © 2014 Elsevier Ltd.

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.

Bellini C.,Umeå University | Bellini C.,French National Institute for Agricultural Research | Pacurar D.I.,Umeå University | Perrone I.,Umeå 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.

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.

van Aarle I.M.,French National Institute for Agricultural Research | Plassard C.,French National Institute for Agricultural Research
Soil Biology and Biochemistry | Year: 2010

Several ectomycorrhizal fungi, including Hebeloma cylindrosporum, actively release large quantities of phosphatase enzymes into their growth medium. We fractionated the phosphatase activity of the ectomycorrhizal association between H. cylindrosporum and its host plant, Pinus pinaster, with the aim to quantify its spatial and temporal variation in response to contrasting soil phosphorus conditions. Seedlings were grown in mini-rhizoboxes and the phosphomonoesterase activity of rhizosphere soil, released by roots, surface-bound to roots or mycelium was determined spectrophotometrically with the p-nitrophenyl phosphate method or microscopically with the ELF-method as a function of culture time. We showed that acid phosphatase activity of the soil and the root increased with mycorrhizal association. We also observed that the phosphatase activity associated with ectomycorrhizal plants was related to soil type. All phosphatase fractions decreased over culture time, except the proportion of hyphae exhibiting phosphatase activity in the extramatrical mycelium, which increased over time. The specific fractions of phosphatase activity associated with the mycorrhizal plants were clearly related to the soil phosphorus type and content. Soils showed an increase in acid phosphomonoesterase activity with mycorrhizal association, supporting a role for this enzyme in the degradation of soil bound phosphorus. The gradually increasing proportion of hyphae in the extramatrical mycelium exhibiting alkaline phosphatase activity, particularly under low phosphorus conditions, indicates an induction of alkaline phosphatase activity by phosphorus limitation. © 2009 Elsevier Ltd. 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.

Kalashnikova I.,French National Institute for Agricultural Research | Bizot H.,French National Institute for Agricultural Research | Cathala B.,French National Institute for Agricultural Research | Capron I.,French National Institute for Agricultural Research
Biomacromolecules | Year: 2012

Neutral cellulose nanocrystals dispersed in water were shown in a previous work to stabilize oil/water interfaces and produce Pickering emulsions with outstanding stability, whereas sulfated nanocrystals obtained from cotton did not show interfacial properties. To develop a better understanding of the stabilization mechanism, amphiphilic properties of the nanocrystals were modulated by tuning the surface charge density to investigate emulsifying capability on two sources of cellulose: cotton linters (CCN) and bacterial cellulose (BCN). This charge adjustment made it possible to determine the conditions where a low surface charge density, below 0.03 e/nm 2, remains compatible with emulsification, as well as when assisted by charge screening regardless of the source. This study discusses this ability to stabilize oil-in-water emulsions for cellulose nanocrystals varying in crystalline allomorph, morphology, and hydrolysis processes related to the amphiphilic character of nonhydrophobized cellulose nanocrystal. © 2011 American Chemical Society.

Barakat A.,French National Institute for Agricultural Research | Monlau F.,French National Institute for Agricultural Research | Steyer J.-P.,French National Institute for Agricultural Research | Carrere H.,French National Institute for Agricultural Research
Bioresource Technology | Year: 2012

Hydrolysates resulting from the lignocellulosic biomass pretreatment in bioethanol production may be used to produce biogas. Such hydrolysates are rich in xylose but also contain lignin polymers or oligomers as well as phenolic and furan compounds, such as syringaldehyde, vanillin, HMF, furfural. The aim of this study was to investigate the impact of these byproducts on biomethane production from xylose. The anaerobic digestion of the byproducts alone was also investigated. No inhibition of the anaerobic digestion of xylose was observed and methane was obtained from furans: 430mLCH 4/g of furfural and 450mLCH 4/g of HMF; from phenolic compounds: 453mLCH 4/g of syringaldehyde and 105mLCH 4/g of vanillin; and, to a lesser extent, from lignin polymers: from 14 to 46mLCH 4/gMV. The use of different natural polymers (lignosulfonates, organosolv and kraft lignins) and synthetic dehydrogenative polymers showed that higher S/G ratios and lower molecular weights in lignin polymers led to greater methane production. © 2011 Elsevier Ltd.

Avice J.-C.,University of Caen Lower Normandy | Avice J.-C.,French National Institute for Agricultural Research | Etienne P.,University of Caen Lower Normandy | Etienne P.,French National Institute for Agricultural Research
Journal of Experimental Botany | Year: 2014

Despite its worldwide economic importance for food (oil, meal) and non-food (green energy and chemistry) uses, oilseed rape has a low nitrogen (N) use efficiency (NUE), mainly due to the low N remobilization efficiency (NRE) observed during the vegetative phase when sequential leaf senescence occurs. Assuming that improvement of NRE is the main lever for NUE optimization, unravelling the cellular mechanisms responsible for the recycling of proteins (the main N source in leaf) during sequential senescence is a prerequisite for identifying the physiological and molecular determinants that are associated with high NRE. The development of a relevant molecular indicator (SAG12/Cab) of leaf senescence progression in combination with a 15N-labelling method were used to decipher the N remobilization associated with sequential senescence and to determine modulation of this process by abiotic factors especially N deficiency. Interestingly, in young leaves, N starvation delayed senescence and induced BnD22, a water-soluble chlorophyll-binding protein that acts against oxidative alterations of chlorophylls and exhibits a protease inhibitor activity. Through its dual function, BnD22 may help to sustain sink growth of stressed plants and contribute to a better utilization of N recycled from senescent leaves, a physiological trait that could improve NUE. Proteomics approaches have revealed that proteolysis involves chloroplastic FtsH protease in the early stages of senescence, aspartic protease during the course of leaf senescence, and the proteasome 1 subunit, mitochondria processing protease and SAG12 (cysteine protease) during the later senescence phases. Overall, the results constitute interesting pathways for screening genotypes with high NRE and NUE. © 2014 The Author.

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.

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.

Block M.A.,French National Institute for Agricultural Research | Jouhet J.,French National Institute for Agricultural Research
Current Opinion in Cell Biology | Year: 2015

Glycerolipid synthesis in plant cells is characterized by an intense trafficking of lipids between the endoplasmic reticulum (ER) and chloroplasts. Initially, fatty acids are synthesized within chloroplasts and are exported to the ER where they are used to build up phospholipids and triacylglycerol. Ultimately, derivatives of these phospholipids return to chloroplasts to form galactolipids, monogalactosyldiacylglycerol and digalactosyldiacylglycerol, the main and essential lipids of photosynthetic membranes. Lipid trafficking was proposed to transit through membrane contact sites (MCSs) connecting both organelles. Here, we review recent insights into ER-chloroplast MCSs and lipid trafficking between chloroplasts and the ER. © 2015 Elsevier Ltd.

Madzak C.,French National Institute for Agricultural Research
Applied Microbiology and Biotechnology | Year: 2015

The oleaginous yeast Yarrowia lipolytica has become a recognized system for expression/secretion of heterologous proteins. This non-conventional yeast is currently being developed as a workhorse for biotechnology by several research groups throughout the world, especially for single-cell oil production, whole cell bioconversion and upgrading of industrial wastes. This mini-review presents established tools for protein expression in Y. lipolytica and highlights novel developments in the areas of promoter design, surface display, and host strain or metabolic pathway engineering. An overview of the industrial and commercial biotechnological applications of Y. lipolytica is also presented. © 2015, Springer-Verlag Berlin Heidelberg.

Revers F.,French National Institute for Agricultural Research | Revers F.,University of Bordeaux 1 | Garcia J.A.,Autonomous University of Madrid
Advances in Virus Research | Year: 2015

Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses. © 2015 Elsevier Inc.

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.

Tardieu F.,French National Institute for Agricultural Research | Parent B.,French National Institute for Agricultural Research | Caldeira C.F.,French National Institute for Agricultural Research | Welcker C.,French National Institute for Agricultural Research
Plant Physiology | Year: 2014

The sensitivity of expansive growth to water deficit has a large genetic variability, which is higher than that of photosynthesis. It is observed in several species, with some genotypes stopping growth in a relatively wet soil, whereas others continue growing until the lower limit of soil-available water. The responses of growth to soil water deficit and evaporative demand share an appreciable part of their genetic control through the colocation of quantitative trait loci as do the responses of the growth of different organs to water deficit. This result may be caused by common mechanisms of action discussed in this paper (particularly, plant hydraulic properties). We propose that expansive growth, putatively linked to hydraulic processes, determines the sink strength under water deficit, whereas photosynthesis determines source strength. These findings have large consequences for plant modeling under water deficit and for the design of breeding programs. © 2014 American Society of Plant Biologists. All rights reserved.

Fady B.,French National Institute for Agricultural Research | Conord C.,French National Institute for Agricultural Research
Diversity and Distributions | Year: 2010

Aim We address the question of whether broad scale biogeographical structure of species diversity (SD) matches that of genetic diversity (GD) of vascular plants. Location The Mediterranean basin. Methods We normalized vascular plant species richness (SD) estimates per country using the Med-Checklist taxonomic database. We used a linear regression analysis to correlate normalized country estimates with country longitudinal position. We also compiled published and geo-referenced within-population GD data for tree species, which had populations in the Mediterranean. We normalized GD estimates for each population across species. Again, we used a linear regression analysis to correlate GD with population longitudinal position. We then compared the populations' geographical and bioclimatic trends for GD with Last Glacial Maximum (LGM) palaeo-climate data and the species current ecological requirements. Results The eastern Mediterranean and the coast of former Yugoslavia had higher SD than other regions. There was no overall spatial structure of SD in the Mediterranean, whereas there was an east-west trend of decreasing GD. This trend for GD tended to covary with an east-west warm/wet-cold/dry trend detected during the LGM. Low elevation xerothermic pine species displayed significantly less GD than higher elevation mesothermic or mountain pine species. Main conclusions We suggest that LGM climate may have significantly shaped the current longitudinal and altitudinal patterns of GD we observed in woody taxa across the Mediterranean, although it did not affect comparable SD patterns. In particular, colder LGM summer temperatures in the western Mediterranean may have reduced population sizes significantly more than in the eastern Mediterranean. As plant species richness and GD did not covary, SD and GD may not be used as surrogates of one another in the Mediterranean basin. As they contain comparatively less GD, conservation priorities in the Mediterranean should focus on hot spots of endemism and Western Mediterranean populations and species. © 2009 Blackwell Publishing Ltd.

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.

Tixador P.,French National Institute for Agricultural Research
PLoS pathogens | Year: 2010

Prions are unconventional infectious agents thought to be primarily composed of PrP(Sc), a multimeric misfolded conformer of the ubiquitously expressed host-encoded prion protein (PrP(C)). They cause fatal neurodegenerative diseases in both animals and humans. The disease phenotype is not uniform within species, and stable, self-propagating variations in PrP(Sc) conformation could encode this 'strain' diversity. However, much remains to be learned about the physical relationship between the infectious agent and PrP(Sc) aggregation state, and how this varies according to the strain. We applied a sedimentation velocity technique to a panel of natural, biologically cloned strains obtained by propagation of classical and atypical sheep scrapie and BSE infectious sources in transgenic mice expressing ovine PrP. Detergent-solubilized, infected brain homogenates were used as starting material. Solubilization conditions were optimized to separate PrP(Sc) aggregates from PrP(C). The distribution of PrP(Sc) and infectivity in the gradient was determined by immunoblotting and mouse bioassay, respectively. As a general feature, a major proteinase K-resistant PrP(Sc) peak was observed in the middle part of the gradient. This population approximately corresponds to multimers of 12-30 PrP molecules, if constituted of PrP only. For two strains, infectivity peaked in a markedly different region of the gradient. This most infectious component sedimented very slowly, suggesting small size oligomers and/or low density PrP(Sc) aggregates. Extending this study to hamster prions passaged in hamster PrP transgenic mice revealed that the highly infectious, slowly sedimenting particles could be a feature of strains able to induce a rapidly lethal disease. Our findings suggest that prion infectious particles are subjected to marked strain-dependent variations, which in turn could influence the strain biological phenotype, in particular the replication dynamics.

Gonzalez-Fernandez C.,French National Institute for Agricultural Research | Sialve B.,Naskeo Environnement | Bernet N.,French National Institute for Agricultural Research | Steyer J.P.,French National Institute for Agricultural Research
Bioresource Technology | Year: 2012

Ultrasound at 20. Hz was applied at different energy levels (Es) to treat Scenedesmus biomass, and organic matter solubilization, particle size distribution, cell disruption and biochemical methane potential were evaluated. An Es of 35.5 and 47.2. MJ/kg resulted in floc deagglomeration but no improvement in methane production compared to untreated biomass. At an Es of 128.9, cell wall disruption was observed together with a 3.1-fold organic matter solubilization and an approximately 2-fold methane production in comparison with untreated biomass. Thermal pretreatment at 80. °C caused cell wall disruption and improved anaerobic biodegradability 1.6-fold compared to untreated biomass. Since sonication caused a temperature increase in samples to as high as 85. °C, it is likely that thermal effects accounted for much of the observed changes in the biomass. Given that ultrasound treatment at the highest Es studied only increased methane production by 1.2-fold over thermal treatment at 80. °C, the higher energy requirement of sonication might not justify the use of this approach over thermal treatment. © 2012 Elsevier Ltd.

Fanciullino A.L.,French National Institute for Agricultural Research | Bidel L.P.R.,French National Institute for Agricultural Research | Urban L.,University of Avignon
Plant, Cell and Environment | Year: 2014

Carotenoids play an important role in plant adaptation to fluctuating environments as well as in the human diet by contributing to the prevention of chronic diseases. Insights have been gained recently into the way individual factors, genetic, environmental or developmental, control the carotenoid biosynthetic pathway at the molecular level. The identification of the rate-limiting steps of carotenogenesis has paved the way for programmes of breeding, and metabolic engineering, aimed at increasing the concentration of carotenoids in different crop species. However, the complexity that arises from the interactions between the different factors as well as from the coordination between organs remains poorly understood. This review focuses on recent advances in carotenoid responses to environmental stimuli and discusses how the interactions between the modulation factors and between organs affect carotenoid build-up. We develop the idea that reactive oxygen species/redox status and sugars/carbon status can be considered as integrated factors that account for most effects of the major environmental factors influencing carotenoid biosynthesis. The discussion highlights the concept of carotenoids or carotenoid-derivatives as stress signals that may be involved in feedback controls. We propose a conceptual model of the effects of environmental and developmental factors on carotenoid build-up in fruits. This review presents an assessment of the current understanding of how the different environmental factors and their interactions influence carotenoid accumulation at the organ level. We develop the idea that environmental factors converge to modulate reactive oxygen species (ROS)/redox status (influenced by oxidative stress), and sugars/carbon status (which results from the balance between carbon gains and losses, and allocation between competing organs) and in this way regulate carotenoid accumulation. The discussion highlights the concept of carotenoids or carotenoid-derivatives as stress signals that may be involved in feedback controls. We propose a conceptual model of the effects of environmental and developmental factors that accounts for the known roles played by ROS and sugars on carotenoid build-up in fruits. © 2013 John Wiley & Sons Ltd.

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.

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.

Sorel M.,French National Institute for Agricultural Research | Garcia J.A.,Autonomous University of Madrid | German-Retana S.,French National Institute for Agricultural Research
Molecular Plant-Microbe Interactions | Year: 2014

A unique feature shared by all plant viruses of the Potyviridae family is the induction of characteristic pinwheelshaped inclusion bodies in the cytoplasm of infected cells. These cylindrical inclusions are composed of the viralencoded cylindrical inclusion helicase (CI protein). Its helicase activity was characterized and its involvement in replication demonstrated through different reverse genetics approaches. In addition to replication, the CI protein is also involved in cell-to-cell and long-distance movements, possibly through interactions with the recently discovered viral P3N-PIPO protein. Studies over the past two decades demonstrate that the CI protein is present in several cellular compartments interacting with viral and plant protein partners likely involved in its various roles in different steps of viral infection. Furthermore, the CI protein acts as an avirulence factor in gene-for-gene interactions with dominant-resistance host genes and as a recessive-resistance overcoming factor. Although a significant amount of data concerning the potential functions and subcellular localization of this protein has been published, no synthetic review is available on this important multifunctional protein. In this review, we compile and integrate all information relevant to the current understanding of this viral protein structure and function and present a mode of action for CI, combining replication and movement. © 2014 The American Phytopathological Society.

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.

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.

Lalles J.-P.,French National Institute for Agricultural Research
Nutrition Reviews | Year: 2014

Important protective roles of intestinal alkaline phosphatase (IAP) - including regulation of intestinal surface pH, absorption of lipids, detoxification of free nucleotides and bacterial lipopolysaccharide, attenuation of intestinal inflammation, and possible modulation of the gut microbiota - have been reviewed recently. IAP is modulated by numerous nutritional factors. The present review highlights new findings on the properties of IAP and extends the list of its protective functions. Critical assessment of data suggests that some IAP properties are a direct result of dephosphorylation of proinflammatory moieties, while others (e.g., gut barrier protection and microbiota shaping) may be secondary to IAP-mediated downregulation of inflammation. IAP and tissue-nonspecific alkaline phosphatase isoforms characterize the small intestine and the colon, respectively. Gastrointestinal administration of exogenous IAP ameliorates gut inflammation and favors gut tissue regeneration, whereas enteral and systemic IAP administration attenuates systemic inflammation only. Finally, the IAP gene family has a strong evolutionary link to food-driven changes in gastrointestinal tract anatomy and microbiota composition. Therefore, stimulation of IAP activity by dietary intervention is a goal for preserving gut homeostasis and health by minimizing low-grade inflammation. © 2013 International Life Sciences Institute.

Masclaux-Daubresse C.,French National Institute for Agricultural Research | Chardon F.,French National Institute for Agricultural Research
Journal of Experimental Botany | Year: 2011

Nineteen Arabidopsis accessions grown at low (LOW N) and high (HIGH N) nitrate supplies were labelled using 15N to trace nitrogen remobilization to the seeds. Effects of genotype and nutrition were examined. Nitrate availability affected biomass and yield, and highly modified the nitrogen concentration in the dry remains. Surprisingly, variations of one-seed dry weight (DW1S) and harvest index (HI) were poorly affected by nutrition. Nitrogen harvest index (NHI) was highly correlated with HI and showed that nitrogen use efficiency (NUE) was increased at LOW N. Nitrogen remobilization efficiency (NRE), as 15N partitioning in seeds (15NHI), was also higher at LOW N. The relative specific abundance (RSA) in seeds and whole plants indicated that the 14NO3 absorbed post-labelling was mainly allocated to the seeds (SEEDS) at LOW N, but to the dry remains (DR) at HIGH N. Nitrogen concentration (N%) in the DR was then 4-fold higher at HIGH N compared with LOW N, whilst N% in seeds was poorly modified. Although NHI and 15NHI were highly correlated to HI, significant variations in NUE and NRE were identified using normalization to HI. New insights provided in this report are helpful for the comprehension of NUE and NRE concepts in Arabidopsis as well as in crops and especially in Brassica napus. © 2010 The Author(s).

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.

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.

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.

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.

Vignaud T.,French National Institute for Agricultural Research | Blanchoin L.,French National Institute for Agricultural Research | Thery M.,French National Institute for Agricultural Research
Trends in Cell Biology | Year: 2012

The cytoskeleton architecture supports many cellular functions. Cytoskeleton networks form complex intracellular structures that vary during the cell cycle and between different cell types according to their physiological role. These structures do not emerge spontaneously. They result from the interplay between intrinsic self-organization properties and the conditions imposed by spatial boundaries. Along these boundaries, cytoskeleton filaments are anchored, repulsed, aligned, or reoriented. Such local effects can propagate alterations throughout the network and guide cytoskeleton assembly over relatively large distances. The experimental manipulation of spatial boundaries using microfabrication methods has revealed the underlying physical processes directing cytoskeleton self-organization. Here we review, step-by-step, from molecules to tissues, how the rules that govern assembly have been identified. We describe how complementary approaches, all based on controlling geometric conditions, from in vitro reconstruction to in vivo observation, shed new light on these fundamental organizing principles. © 2012 Elsevier Ltd.

Attaix D.,French National Institute for Agricultural Research | Taillandier D.,French National Institute for Agricultural Research
Cell Metabolism | Year: 2012

FoxO3 regulates the transcription of autophagy-related genes that induce mitophagy in muscle wasting. In this issue of Cell Metabolism, Lokireddy et al. (2012) now show that the mitochondrial ubiquitin protein ligase 1 (Mul1) polyubiquitinates the mitochondrial fusion protein Mfn2 and is necessary for FoxO3- and lysosomaldependent mitophagy in muscle atrophy. © 2012 Elsevier Inc.

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.

Burute M.,French National Institute for Agricultural Research | Thery M.,French National Institute for Agricultural Research
Current Opinion in Cell Biology | Year: 2012

Cell-cell adhesion (CCA) and cell-matrix adhesion (CMA) play determinant roles in the architecture and function of epithelial cells. CCA and CMA are supported by transmembrane molecular complexes that dynamically interact with the extracellular environment and the cell cytoskeleton. Although those complexes have distinct functions, they are involved in a continuous crosstalk. In epithelia, CCA and CMA segregate in distinct regions of the cell surface and thereby take part in cell polarity. Recent results have shown that the two adhesion systems exert negative feedback on each other and appear to regulate actin network dynamics and mechanical force production in different ways. In light of this, we argue that the interplay between these regulatory mechanisms plays an important role in the spatial separation of cell-cell and cell-matrix adhesions components in distinct regions of the cell surface. © 2012 Elsevier Ltd.

Mostowy S.,Institute Pasteur Paris | Mostowy S.,French Institute of Health and Medical Research | Mostowy S.,French National Institute for Agricultural Research | Mostowy S.,Imperial College London | And 3 more authors.
Nature Reviews Molecular Cell Biology | Year: 2012

Septins belong to a family of proteins that is highly conserved in eukaryotes and is increasingly recognized as a novel component of the cytoskeleton. All septins are GTP-binding proteins that form hetero-oligomeric complexes and higher-order structures, including filaments and rings. Recent studies have provided structural information about the different levels of septin organization; however, the crucial structural determinants and factors responsible for septin assembly remain unclear. Investigations on the molecular functions of septins have highlighted their roles as scaffolds for protein recruitment and as diffusion barriers for subcellular compartmentalization in numerous biological processes, including cell division and host-microorganism interactions. © 2012 Macmillan Publishers Limited. All rights reserved.

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.

Danan S.,French National Institute for Agricultural Research | Veyrieras J.,French National Institute for Agricultural Research | Lefebvre V.,French National Institute for Agricultural Research
BMC Plant Biology | Year: 2011

Background: Integrating QTL results from independent experiments performed on related species helps to survey the genetic diversity of loci/alleles underlying complex traits, and to highlight potential targets for breeding or QTL cloning. Potato (Solanum tuberosum L.) late blight resistance has been thoroughly studied, generating mapping data for many Rpi-genes (R-genes to Phytophthora infestans) and QTLs (quantitative trait loci). Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits.Results: Nineteen QTL publications for late blight resistance were considered, seven of them reported maturity QTLs. Twenty-one QTL maps and eight reference maps were compiled to construct a 2,141-marker consensus map on which QTLs were projected and clustered into meta-QTLs. The whole-genome QTL meta-analysis reduced by six-fold late blight resistance QTLs (by clustering 144 QTLs into 24 meta-QTLs), by ca. five-fold maturity QTLs (by clustering 42 QTLs into eight meta-QTLs), and by ca. two-fold QTL confidence interval mean. Late blight resistance meta-QTLs were observed on every chromosome and maturity meta-QTLs on only six chromosomes.Conclusions: Meta-analysis helped to refine the genomic regions of interest frequently described, and provided the closest flanking markers. Meta-QTLs of late blight resistance and maturity juxtaposed along chromosomes IV, V and VIII, and overlapped on chromosomes VI and XI. The distribution of late blight resistance meta-QTLs is significantly independent from those of Rpi-genes, resistance gene analogs and defence-related loci. The anchorage of meta-QTLs to the potato genome sequence, recently publicly released, will especially improve the candidate gene selection to determine the genes underlying meta-QTLs. All mapping data are available from the Sol Genomics Network (SGN) database. © 2011 Danan et al; licensee BioMed Central Ltd.

Boitard S.,French National Institute for Agricultural Research | Rocha D.,French National Institute for Agricultural Research
Animal Genetics | Year: 2013

Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection and therefore could help in identifying mutations responsible for improved traits. We used genotyping data generated using Illumina's BovineSNP50 Genotyping BeadChips to identify selection signatures in the Blonde d'Aquitaine breed, a well-muscled French beef breed. For this purpose, we employed a hidden Markov model-based test, which detects selection by studying local variations in the allele frequency spectrum along the genome, within a single population. Three regions containing selective sweeps were identified. Annotation of genes located within these regions revealed interesting candidate genes. For example, myostatin (also known as GDF8), a known muscle growth factor inhibitor, is located within the selection signature region found on chromosome 2. In addition, we have identified chromosomal regions that show some evidence of selection within QTL regions for economically important traits. The results of this study could help to better understand the mechanisms related to the selection of the Blonde d'Aquitaine breed. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

Dun E.A.,University of Queensland | Germain A.S.,French National Institute for Agricultural Research | Rameau C.,French National Institute for Agricultural Research | Beveridge C.A.,University of Queensland
Plant Physiology | Year: 2012

Cytokinin (CK) has long been implicated as a promoter of bud outgrowth in plants, but exactly how this is achieved in coordination with other plant hormones is unclear. The recent discovery of strigolactones (SLs) as the long-sought branchinhibiting hormone allowed us to test how CK and SL coordinately regulate bud outgrowth in pea (Pisum sativum). We found that SL-deficient plants are more sensitive to stimulation of bud growth by low concentrations of locally applied CK than wildtype plants. Furthermore, in contrast with SL mutant plants, buds of wild-type plants are almost completely resistant to stimulation by CK supplied to the vasculature. Regardless of whether the exogenous hormones were supplied locally or to the xylem stream, SL and CK acted antagonistically on bud outgrowth. These data suggest that SLs do not affect the delivery of CK to axillary buds and vice versa. Rather, these data combined with dose-response experiments suggest that SLs and CK can act directly in buds to control their outgrowth. These hormones may converge at a common point in the bud outgrowth regulatory pathway. The expression of pea BRANCHED1, a TCP transcription factor expressed strongly in buds and thought to act downstream of SLs in shoot branching, is regulated by CK and SL without a requirement for protein synthesis and in a manner that correlates with observed bud growth responses. © 2011 American Society of Plant Biologists. 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.

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.

Marchione R.,Joseph Fourier University | Leibovitch S.A.,French National Institute for Agricultural Research | Lenormand J.-L.,Joseph Fourier University
Cellular and Molecular Life Sciences | Year: 2013

The regulation of the protein synthesis has a crucial role in governing the eukaryotic cell growth. Subtle changes of proteins involved in the translation process may alter the rate of the protein synthesis and modify the cell fate by shifting the balance from normal status into a tumoral or apoptotic one. The largest eukaryotic initiation factor involved in translation regulation is eIF3. Amongst the 13 factors constituting eIF3, the f subunit finely regulates this balance in a cell-type-specific manner. Loss of this factor causes malignancy in several cells, and atrophy in normal muscle cells. The intracellular interacting partners which influence its physiological significance in both cancer and muscle cells are detailed in this review. By delineating the global interaction network of this factor and by clarifying its intracellular role, it becomes apparent that the f subunit represents a promising candidate molecule to use for biotherapeutic applications. © 2013 The Author(s).

Kerboeuf D.,French National Institute for Agricultural Research | Guegnard F.,French National Institute for Agricultural Research
Antimicrobial Agents and Chemotherapy | Year: 2011

P glycoproteins (Pgp), members of the ABC transporter superfamily, play a major role in chemoresistance. In nematodes, Pgp are responsible for resistance to anthelmintics, suggesting that they are Pgp substrates, as they are in mammalian cells. However, their binding to nematode Pgp and the functional consequences of this interaction have not been investigated. Our study showed that levamisole and most of the macrocyclic lactones (MLs) are Pgp substrates in nematodes. Ivermectin, although a very good substrate in mammalian cells, is poorly transported. In contrast to their inhibitory effect on mammalian Pgp, these drugs had a stimulatory effect on the transport activity of the reference Pgp substrate rhodamine 123 (R123) in the nematode. This may be due to a specific sequence of nematode Pgp, which shares only 44% identity with mammalian Pgp. Other factors, such as the affinity of anthelmintics for Pgp and their concentration in the Pgp microenvironment, could also differ in nematodes, as suggested by the specific relationship observed between the octanol-water partition coefficient (log P) of MLs and R123 efflux. Nevertheless, some similarities were also observed in the functional activities of the mammalian and nematode Pgp. As in mammalian cells, substrates known to bind the H site (Hoechst 33342 and colchicine) activated the R site, resulting in an increased R123 efflux. Our findings thus show that ML anthelmintics, which inhibit Pgp-mediated efflux in mammals, activate transport activity in nematodes and suggest that several substituents in the ML structure are involved in modulating the stimulatory effect. Copyright © 2011, American Society for Microbiology. All Rights Reserved.

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.

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.

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.

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.

Corbel S.,French National Institute for Agricultural Research | Mougin C.,French National Institute for Agricultural Research | Bouaicha N.,CNRS Ecology, Systematic and Evolution Laboratory
Chemosphere | Year: 2014

The occurrence of harmful cyanobacterial blooms in surface waters is often accompanied by the production of a variety of cyanotoxins. These toxins are designed to target in humans and animals specific organs on which they act: hepatotoxins (liver), neurotoxins (nervous system), cytotoxic alkaloids, and dermatotoxins (skin), but they often have important side effects too. When introduced into the soil ecosystem by spray irrigation of crops they may affect the same molecular pathways in plants having identical or similar target organs, tissues, cells or biomolecules. There are also several indications that terrestrial plants, including food crop plants, can bioaccumulate cyanotoxins and present, therefore, potential health hazards for human and animals. The number of publications concerned with phytotoxic effects of cyanotoxins on agricultural plants has increased recently. In this review, we first examine different cyanotoxins and their modes of actions in humans and mammals and occurrence of target biomolecules in vegetable organisms. Then we present environmental concentrations of cyanotoxins in freshwaters and their fate in aquatic and soil ecosystems. Finally, we highlight bioaccumulation of cyanotoxins in plants used for feed and food and its consequences on animals and human health. Overall, our review shows that the information on the effects of cyanotoxins on non-target organisms in the terrestrial environment is particularly scarce, and that there are still serious gaps in the knowledge about the fate in the soil ecosystems and phytotoxicity of these toxins. © 2013 Elsevier Ltd.

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.

Novak S.M.,French National Institute for Agricultural Research | Fiorelli J.L.,French National Institute for Agricultural Research
Agronomy for Sustainable Development | Year: 2010

Dairy production systems represent a significant source of air pollutants such as greenhouse gases (GHG), that increase global warming, and ammonia (NH3), that leads to eutrophication and acidification of natural ecosystems. Greenhouse gases and ammonia are emitted both by conventional and organic dairy systems. Several studies have already been conducted to design practices that reduce greenhouse gas and ammonia emissions from dairy systems. However, those studies did not consider options specifically applied to organic farming, as well as the multiple trade-offs occurring between these air pollutants. This article reviews agricultural practices that mitigate greenhouse gas and ammonia emissions. Those practices can be applied to the most common organic dairy systems in northern Europe such as organic mixed crop-dairy systems. The following major points of mitigation options for animal production, crop production and grasslands are discussed. Animal production: the most promising options for reducing greenhouse gas emissions at the livestock management level involve either the improvement of animal production through dietary changes and genetic improvement or the reduction of the replacement rate. The control of the protein intake of animals is an effective means to reduce gaseous emissions of nitrogen, but it is difficult to implement in organic dairy farming systems. Considering the manure handling chain, mitigation options involve housing, storage and application. For housing, an increase in the amounts of straw used for bedding reduces NH3 emissions, while the limitation of CH4 emissions from deep litter is achieved by avoiding anaerobic conditions. During the storage of solid manure, composting could be an efficient mitigation option, depending on its management. Addition of straw to solid manure was shown to reduce CH4 and N2O emissions from the manure heaps. During the storage of liquid manure, emptying the slurry store before late spring is an efficient mitigation option to limit both CH4 and NH3 emissions. Addition of a wooden cover also reduces these emissions more efficiently than a natural surface crust alone, but may increase N2O emissions. Anaerobic digestion is the most promising way to reduce the overall greenhouse gas emissions from storage and land spreading, without increasing NH3 emissions. At the application stage, NH3 emissions may be reduced by spreading manure during the coolest part of the day, incorporating it quickly and in narrow bands. Crop production: the mitigation options for crop production focus on limiting CO2 and N2O emissions. The introduction of perennial crops or temporary leys of longer duration are promising options to limit CO2 emissions by storing carbon in plants or soils. Reduced tillage or no tillage as well as the incorporation of crop residues also favour carbon sequestration in soils, but these practices may enhance N2O emissions. Besides, the improvement of crop N-use efficiency through effective management of manure and slurry, by growing catch crops or by delaying the ploughing of leys, is of prime importance to reduce N2O emissions. Grassland: concerning grassland and grazing management, permanent conversion from arable to grassland provides high soil carbon sequestration while increasing or decreasing the livestock density seems not to be an appropriate mitigation option. From the study of the multiple interrelations between gases and between farm compartments, the following mitigation options are advised for organic mixed crop-dairy systems: (1) actions for increasing energy efficiency or fuel savings because they are beneficial in any case, (2) techniques improving efficiency of N management at field and farm levels because they affect not only N2O and NH3 emissions, but also nitrate leaching, and (3) biogas production through anaerobic digestion of manure because it is a promising efficient method to mitigate greenhouse gas emissions, even if the profitability of this expensive investment needs to be carefully studied. Finally, the way the farmer implements the mitigation options, i.e.his practices, will be a determining factor in the reduction of greenhouse gas and NH3 emissions. © 2009 INRA, EDP Sciences.

Zub H.W.,French National Institute for Agricultural Research | Brancourt-Hulmel M.,French National Institute for Agricultural Research
Agronomy for Sustainable Development | Year: 2010

The European Union recommends the use of lignocellulosic biomass to produce biofuels in order to reduce greenhouse gas emissions. Miscanthus × giganteus, a C4 perennial and rhizomatous plant, has been identified as a good candidate for biomass production because of its high potential yield, of up to 49 t DM.ha-1 for autumn harvest and 26 t DM.ha-1 for winter harvest, under low input levels. Here, we review current knowledge on the biomass production in Europe of M × giganteus and its two parental species, M. sinensis and M. sacchariflorus, under different stress conditions. This review identifies two key areas where M. giganteus crops could be improved: (i) tolerance to frost during winter or early spring is essential, mainly in Northern Europe, in order to ensure overwintering and protect young shoots following early emergence. Susceptibility to winter frost at temperatures below -3.5 °C for rhizomes and -8 °C for young shoots of M. × giganteus can lead to significant plant losses and lower yields, and (ii) a good water supply is necessary to ensure good establishment rates and satisfactory biomass production. Reductions of up to 84% in above-ground dry matter production because of a lack of water for the autumn harvest, and up to 26% for the winter harvest have been observed. M. sinensis, which displays greater genetic variability than M. giganteus, will provide the necessary genetic resources for frost and water stress tolerance. It is also necessary to either identify genotypes among M. sinensis species that are able to produce an above-ground biomass yield close to the biomass production of M. giganteus under limited water supplies and/or low temperatures, or to generate new interspecific hybrids of M. giganteus with greater tolerance. Particular attention should be paid to nitrogen response; although no response to nitrogen supply has been observed in M. giganteus, M. sinensis produces higher levels of biomass with nitrogen inputs. © 2009 INRA, EDP Sciences.

Blein T.,French National Institute for Agricultural Research | Hasson A.,French National Institute for Agricultural Research | Laufs P.,French National Institute for Agricultural Research
Current Opinion in Plant Biology | Year: 2010

Formation of dissected compound leaves involves the transient maintenance of an indeterminate environment and the generation of new growth axes that will generate leaflets. Recent work has revealed additional multi-layered mechanisms controlling the activities of the KNOXI homeodomains factors that play a prominent role in the control of indeterminacy associated with compound leaf development. Patterning and individualisation of the leaflets has been shown to involve gradients of the phytohormone auxin and the contribution of the NAM/CUC3 boundary genes. Identification of these novel actors governing compound leaf development opens the opportunity for further comparative studies aimed at understanding the molecular basis of leaf shape evolution. © 2009 Elsevier Ltd. All rights reserved.

Pata M.O.,French National Institute for Agricultural Research | Hannun Y.A.,Medical University of South Carolina | Ng C.K.-Y.,University College Dublin
New Phytologist | Year: 2010

Contents Summary Sphingolipids are a ubiquitous class of lipids present in a variety of organisms including eukaryotes and bacteria. In the last two decades, research has focused on characterizing the individual species of this complex family of lipids, which has led to a new field of research called 'sphingolipidomics'. There are at least 500 (and perhaps thousands of) different molecular species of sphingolipids in cells, and in Arabidopsis alone it has been reported that there are at least 168 different sphingolipids. Plant sphingolipids can be divided into four classes: glycosyl inositol phosphoceramides (GIPCs), glycosylceramides, ceramides, and free long-chain bases (LCBs). Numerous enzymes involved in plant sphingolipid metabolism have now been cloned and characterized, and, in general, there is broad conservation in the way in which sphingolipids are metabolized in animals, yeast and plants. Here, we review the diversity of sphingolipids reported in the literature, some of the recent advances in our understanding of sphingolipid metabolism in plants, and the physiological roles that sphingolipids and sphingolipid metabolites play in plant physiology. © 2009 New Phytologist.

Davison J.,French National Institute for Agricultural Research
Plant Science | Year: 2010

The EU has the probably strictest regulations in the world for the presence of GMOs in food and feed. These require the labeling of food and feed where the level of approved GMO exceeds 0.9% of unintentional adventitious presence. For non-approved GMOs the threshold is 'zero' and thus requires that cargoes containing GMOs non-approved GMOs are returned to the port of origin or are destroyed. The process of GMO safety approval is slow and subject to extensive political interference. However outside of Europe, new GMOs are being created, approved and cultivated at a rate exceeding that of EU approvals. Since current methods of cultivation, storage and transport do not permit complete segregation of GMO and non-GMO crops, some co-mingling must be expected. This leads to a peculiar situation where the EU is dependent on imports (particularly soybean for animal feed) from North and South America and yet, legally, must reject these imports since they contain low levels of unauthorized GMOs. Several authorative European reports indicate that this is not a sustainable situation and must result in feed shortages and price increases of meat and poultry. The solution is to either to modify EU regulations or to synchronize GMOs approvals on an international level. The USA has constantly criticized the EU for its unscientific GMO regulations which it says amounts to trade protectionism. Very recently however, the USA has realized that other countries are now producing and cultivating their own GMOs, and that these are not authorized in the USA. The USA is thus proposing to set up its own system of GMO regulations which may bear a close similarity to those in Europe. © 2010 Elsevier Ireland Ltd. All rights reserved.

Kaushik S.J.,French National Institute for Agricultural Research | Seiliez I.,French National Institute for Agricultural Research
Aquaculture Research | Year: 2010

Optimising the amino acid supply in tune with the requirements and improving protein utilization for body protein growth with limited impacts on the environment in terms of nutrient loads is a generic imperative in all animal production systems. With the continued high annual growth rate reported for global aquaculture, our commitments should be to make sure that this growth is indeed reflected in provision of protein of high biological value for humans. The limited availability of fish meal has led to some concerted efforts in fish meal replacement, analysing all possible physiological or metabolic consequences. The rising costs of plant feedstuffs make it necessary to strengthen our basic knowledge on amino acid availability and utilization. Regulation of muscle protein accretion has great significance with strong practical implications. In fish, despite low muscle protein synthesis rates, the efficiency of protein deposition appears to be high. Exploratory studies on amino acid flux, inter-organ distribution and particularly of muscle protein synthesis, growth and degradation and the underlying mechanisms as affected by dietary factors are warranted. Research on specific signalling pathways involved in protein synthesis and degradation have been initiated in order to elucidate the reasons for high dietary protein/amino acid supply required and their utilization. © 2010 The Authors. Journal Compilation © 2010 Blackwell Publishing Ltd.

Patry C.,French National Institute for Agricultural Research | Ducrocq V.,French National Institute for Agricultural Research
Genetics Selection Evolution | Year: 2011

Background: In future Best Linear Unbiased Prediction (BLUP) evaluations of dairy cattle, genomic selection of young sires will cause evaluation biases and loss of accuracy once the selected ones get progeny. Methods. To avoid such bias in the estimation of breeding values, we propose to include information on all genotyped bulls, including the culled ones, in BLUP evaluations. Estimated breeding values based on genomic information were converted into genomic pseudo-performances and then analyzed simultaneously with actual performances. Using simulations based on actual data from the French Holstein population, bias and accuracy of BLUP evaluations were computed for young sires undergoing progeny testing or genomic pre-selection. For bulls pre-selected based on their genomic profile, three different types of information can be included in the BLUP evaluations: (1) data from pre-selected genotyped candidate bulls with actual performances on their daughters, (2) data from bulls with both actual and genomic pseudo-performances, or (3) data from all the genotyped candidates with genomic pseudo-performances. The effects of different levels of heritability, genomic pre-selection intensity and accuracy of genomic evaluation were considered. Results: Including information from all the genotyped candidates, i.e. genomic pseudo-performances for both selected and culled candidates, removed bias from genetic evaluation and increased accuracy. This approach was effective regardless of the magnitude of the initial bias and as long as the accuracy of the genomic evaluations was sufficiently high. Conclusions: The proposed method can be easily and quickly implemented in BLUP evaluations at the national level, although some improvement is necessary to more accurately propagate genomic information from genotyped to non-genotyped animals. In addition, it is a convenient method to combine direct genomic, phenotypic and pedigree-based information in a multiple-step procedure. © 2011 Patry and Ducrocq; licensee BioMed Central Ltd.

Chakir R.,French National Institute for Agricultural Research | Le Gallo J.,University of Franche Comte
Ecological Economics | Year: 2013

Predictions of future land use areas are an important issue as land use patterns significantly impact environmental conditions (biodiversity, water pollution, soil erosion, and climate change) as well as economic and social welfare. In order to improve the prediction accuracy of aggregated land use share models, we propose in this paper a methodological contribution by controlling for both unobserved individual heterogeneity and spatial autocorrelation. Our model is a land use shares model applied to aggregated data in France. Our dataset is a panel which covers both time series observations from 1992 to 2003 and cross-sectional observations by Département (equivalent to NUTS3 regions). We consider four land use classes: (1) agriculture, (2) forest, (3) urban and (4) other use. We investigate the relation between the areas in land in different alternative uses and economic and demographic factors influencing land use decisions. Based on the comparison of prediction accuracy of different model specifications, our findings are threefold: First, controlling for both unobserved individual heterogeneity and spatial autocorrelation outperforms any other specification in which spatial autocorrelation and/or individual heterogeneity are ignored. Second, accounting for cross-equation correlations does not seem to improve the prediction performances and finally, ignoring individual heterogeneity introduces substantial loss in prediction accuracy. © 2012 Elsevier B.V.

Maunoury N.,French National Institute for Agricultural Research | Vaucheret H.,French National Institute for Agricultural Research
PLoS ONE | Year: 2011

Background: In Arabidopsis, AGO1 and AGO2 associate with small RNAs that exhibit a Uridine and an Adenosine at their 5′ end, respectively. Because most plant miRNAs have a 5′U, AGO1 plays many essential roles in miRNA-mediated regulation of development and stress responses. In contrast, AGO2 has only been implicated in antibacterial defense in association with miR393*, which has a 5′A. AGO2 also participates in antiviral defense in association with viral siRNAs. Principal Findings: This study reveals that miR408, which has a 5′A, regulates its target Plantacyanin through either AGO1 or AGO2. Indeed, neither ago1 nor ago2 single mutations abolish miR408-mediated regulation of Plantacyanin. Only an ago1 ago2 double mutant appears compromised in miR408-mediated regulation of Plantacyanin, suggesting that AGO1 and AGO2 have redundant roles in this regulation. Moreover, the nature of the 5′ nucleotide of miR408 does not appear essential for its regulatory role because both a wildtype 5′A-MIR408 and a mutant 5′U-MIR408 gene complement a mir408 mutant. Conclusions/Significance: These results suggest that miR408 associates with both AGO1 and AGO2 based on criteria that differ from the 5′ end rule, reminiscent of miR390-AGO7 and miR165/166-AGO10 associations, which are not based on the nature of the 5′ nucleotide. © 2011 Maunoury, Vaucheret.

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.

Zytnicki M.,French National Institute for Agricultural Research | Quesneville H.,French National Institute for Agricultural Research
PLoS ONE | Year: 2011

High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. S-MART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci. © 2011 Zytnicki, Quesneville.

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.

Pitaval A.,Institute Of Recherche En Science Et Technologies Pour Le Vivant | Tseng Q.,French National Institute for Agricultural Research | Bornens M.,University Pierre and Marie Curie | Thery M.,French National Institute for Agricultural Research
Journal of Cell Biology | Year: 2010

In most lineages, cell cycle exit is correlated with the growth of a primary cilium. We analyzed cell cycle exit and ciliogenesis in human retinal cells and found that, contrary to the classical view, not all cells exiting the cell division cycle generate a primary cilium. Using adhesive micropatterns to control individual cell spreading, we demonstrate that cell spatial confinement is a major regulator of ciliogenesis. When spatially confined, cells assemble a contractile actin network along their ventral surface and a protrusive network along their dorsal surface. The nucleus-centrosome axis in confined cells is oriented toward the dorsal surface where the primary cilium is formed. In contrast, highly spread cells assemble mostly contractile actin bundles. The nucleus-centrosome axis of spread cells is oriented toward the ventral surface, where contractility prevented primary cilium growth. These results indicate that cell geometrical confinement affects cell polarity via the modulation of actin network architecture and thereby regulates basal body positioning and primary cilium growth. © 2010 Pitaval et al.

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.

Orseau L.,French National Institute for Agricultural Research
Theoretical Computer Science | Year: 2013

Finding the universal artificial intelligent agent is the old dream of AI scientists. Solomonoff Induction was one big step towards this, giving a universal solution to the general problem of sequence prediction by defining a universal prior distribution. Hutter defined the AIXI model, which extends the latter to the reinforcement learning framework, where almost all if not all AI problems can be formulated. However, new difficulties arise because the agent is now active, whereas it is only passive in the sequence prediction case. This makes proving AIXI's optimality difficult. In fact, we prove that the current definition of AIXI can sometimes be suboptimal in a certain sense, but that this behavior is still the most rational one, hence emphasizing the difficulty of universal reinforcement learning. © 2012 Elsevier B.V. All rights reserved.

Berton-Carabin C.C.,Wageningen University | Ropers M.-H.,French National Institute for Agricultural Research | Genot C.,French National Institute for Agricultural Research
Comprehensive Reviews in Food Science and Food Safety | Year: 2014

More polyunsaturated fats in processed foods and fewer additives are a huge demand of public health agencies and consumers. Consequently, although foods have an enhanced tendency to oxidize, the usage of antioxidants, especially synthetic antioxidants, is restrained. An alternate solution is to better control the localization of reactants inside the food matrix to limit oxidation. This review establishes the state-of-the-art on lipid oxidation in oil-in-water (O/W) emulsions, with an emphasis on the role of the interfacial region, a critical area in the system in that respect. We first provide a summary on the essential basic knowledge regarding (i) the structure of O/W emulsions and interfaces and (ii) the general mechanisms of lipid oxidation. Then, we discuss the factors involved in the development of lipid oxidation in O/W emulsions with a special focus on the role played by the interfacial region. The multiple effects that can be attributed to emulsifiers according to their chemical structure and their location, and the interrelationships between the parameters that define the physicochemistry and structure of emulsions are highlighted. This work sheds new light on the interpretation of reported results that are sometimes ambiguous or contradictory. © 2014 Institute of Food Technologists®.

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.

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.

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.

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.

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.

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.

Serrano I.,French National Institute for Agricultural Research | Audran C.,French National Institute for Agricultural Research | Rivas S.,French National Institute for Agricultural Research
Journal of Experimental Botany | Year: 2016

The major role played by chloroplasts during light harvesting, energy production, redox homeostasis, and retrograde signalling processes has been extensively characterized. Beyond the obvious link between chloroplast functions in primary metabolism and as providers of photosynthesis-derived carbon sources and energy, a growing body of evidence supports a central role for chloroplasts as integrators of environmental signals and, more particularly, as key defence organelles. Here, we review the importance of these organelles as primary sites for the biosynthesis and transmission of pro-defence signals during plant immune responses. In addition, we highlight interorganellar communication as a crucial process for amplification of the immune response. Finally, molecular strategies used by microbes to manipulate, directly or indirectly, the production/function of defence-related signalling molecules and subvert chloroplast-based defences are also discussed. © 2016 The Author.

Orseau L.,French National Institute for Agricultural Research
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2011

From a point of view of Artificial General Intelligence, RL learners like Hutter's universal, Pareto optimal, incomputable AIXI heavily rely on the definition of the rewards, which are necessarily given by some "teacher" to define the tasks to solve. AIXI, as is, cannot therefore be said to be a fully autonomous agent. Furthermore, it has recently been shown that AIXI can converge to a suboptimal behavior in certain situations, hence showing the intrinsic difficulty of RL, with its non-obvious pitfalls. We propose a new model of intelligence, the Knowledge-Seeking Agent (KSA), halfway between Solomonoff Induction and AIXI, that defines a completely autonomous agent that does not require a teacher. The goal of this agent is not to maximize arbitrary rewards, but "simply" to entirely explore its world in an optimal way. A proof of strong asymptotic optimality for a class of horizon functions shows that this agent, unlike AIXI in its domain, behaves according to expectation. Some implications of such an unusual agent are proposed. © 2011 Springer-Verlag.

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.

Barakat A.,French National Institute for Agricultural Research | Rouau X.,French National Institute for Agricultural Research
Biotechnology for Biofuels | Year: 2014

Background: Today, most of pretreatments used to convert biomass into biofuels are based on expensive chemical processes that not only do not keep the major components intact after separation, but also consume water and generate many effluents. However, dry fractionation technologies are an important step for future biomass biorefineries since they do not require chemicals and do not generate wastewater. Therefore, the aim of the present study was to evaluate the feasibility of using milling combined with an electrostatic fractionation (ES) of wheat straw (WS) as a way to separate fractions that are enriched in cellulose and more enzymatically accessible, from recalcitrant tissues enriched in lignin-hemicelluloses, in order to produce biofuels.Results: After milling, WS particles are introduced into a tribo-electrostatic separator, where they are positively or negatively charged by tribo-electricity. Then they are introduced into a separation cell comprising two electrodes (+ and -). The negative electrode attracts the positively charged particles and the positive electrode attracts the negatively charged particles. Results show that amorphous cellulose rich particles were clearly more abundant in positively charged fractions (F+), and loose crystalline cellulose, lignin-xylan and ash-containing material were more abundant in negatively charged fractions (F-). Indeed, positively charged fractions (F+) are more accessible upon enzymatic hydrolysis, which resulted, for example, in sugars yield of 43.5% glucose (254 gKg-1) for F2B + compared to 25.2% (103 gKg-1) for F2A-, and 26.3% (130 gKg-1) for unfractionated WS F0, respectively.Conclusions: The combination strategy of milling and ES fractionation could improve the economic feasibility by low energy consumption (10.5 WhKg-1) and it produces reactive lignocelluloses particles with different physicochemical structures, which can be converted easily into biofuels and biomaterials without generating toxic effluents. © 2014 Barakat and Rouau.

Soussana J.-F.,French National Institute for Agricultural Research
Journal of Cleaner Production | Year: 2014

Recognizing that research for sustainable agri-food systems will be essential to meet global and European challenges in the coming decades, European countries participate in two Joint Programming Initiatives (JPIs): Agriculture, Food Security and Climate Change (FACCE) and Healthy Diet for Healthy Life (HDHL). Mission oriented research agendas have been developed and are focused on delivering key outputs. For FACCE these are: i) to sustainably intensify European agriculture, ii) to operate agriculture within greenhouse gas, energy, biodiversity and contaminant limits and iii) to build resilience to climatic change in agricultural and food systems. HDHL focuses on: i) determinants of diet and physical activity, ii) developing healthy, high-quality, safe and sustainable foods, iii) diet-related chronic diseases. The role of life cycle assessment (LCA) in the context of these research priorities is discussed. Bridging nature capital, on the one hand, and health issues, on the other, with the assessment of the life cycle may lead to breakthroughs in the sustainability assessment of food systems. © 2014 Elsevier Ltd. All rights reserved.

Rimet F.,French National Institute for Agricultural Research | Bouchez A.,French National Institute for Agricultural Research
Ecological Indicators | Year: 2011

The persistence of pesticides in the environment and their effects are a cause of concern to more and more people, and so in 2009 the French government announced plans to reduce pesticide use in agriculture over the next 10 years. Water managers are to monitor the beneficial impact of this reduction on aquatic environments. It has been suggested that diatoms may be good indicators of pesticides, and more particularly of herbicides, in water. Diatoms have been routinely used to assess organic and nutrient pollution for more than 10 years. The general approach is to develop a diatom-based tool to assess pesticide contamination. Diatom indices are usually based on specific pollution sensitivity. Other metrics, such as life-forms, ecological guilds, or cell size offer other advantages. For instance, the relationships between trends in these metrics and environmental gradients are more robust, and make it easier to establish ecological hypotheses. We have therefore opted for this approach. To develop such a tool, outdoor, lotic mesocosm experiments lasting about 2 months were conducted from 2006 to 2008. Herbicides (diuron) and fungicides (azoxystrobin, tebuconazole) were tested at environmental concentrations (sum of pesticides concentrations from 1.11 to3.01 μgL-1 for chronic pollutions and from 20.25 to 29.50 μgL-1 for short-term acute pollutions). Diatom communities in artificial channels were analyzed by light microscopy using standard European methods. The various parameters structuring diatom communities were assessed, and colonization time appeared to be the most important. However, pesticide contamination was the second most important, and had a more significant impact on the composition of ecological guilds than on species composition. Some metrics did not display any significant trends (benthic/planktonic, colonial, pedunculate, pioneer), but others looked promising for use in pesticide contamination assessment: the abundances of motile guild, low-profile guild and mucous tubule diatoms all increased in contaminated channels, whereas high-profile diatoms showed the opposite trend. Some possible explanations, such as a protective effect of the exopolysaccharide matrix, can be advanced: diatoms living inside a mucous tubule may be shielded from dissolved pesticides, as are motile diatoms, which have a micro-habitat preference for thick matrices which also allows them to withstand higher levels of water contamination. In the same way, high-profile guild diatoms are exposed to dissolved pesticides to a greater extent, and this could explain their lower abundance in contaminated channels. © 2010 Elsevier Ltd. All rights reserved.

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

Dupuy J.-L.,French National Institute for Agricultural Research | Marechal J.,French National Institute for Agricultural Research
International Journal of Wildland Fire | Year: 2011

Two series of 16 and 18 laboratory fire experiments were conducted to explore the respective roles of radiation and convection heat transfer in slope effect on fire spread. The first series attempts to measure fuel temperature and gas temperature simultaneously and at the same location using an infrared camera and thermocouples respectively. The second series measures the incident radiant heat flux as would be received by a small fuel bed volume ahead of the fire line. These measurements are used to compute a fuel bed heat balance for each slope angle (0°, 10°, 20° and 30°). Overall, radiative heating is found to be the heat transfer mechanism that dominates in the slope effect between 0° and 20°, but close to the fire line (<10cm), the flux due to convective heating is also significant, reaching one-third of the net heat flux at a 20° slope angle. When the slope angle increases from 20° to 30°, the rate of spread rises by a factor of 2.5 due to a marked increase in convective heating, while radiative heating no longer increases. Far from the fire line, cooling by convection is found to be substantial except at the 30° slope angle. © IAWF 2011.

Merian P.,French National Institute for Agricultural Research | Lebourgeois F.,French National Institute for Agricultural Research
Canadian Journal of Forest Research | Year: 2011

Existing literature investigates the effect of the number of cored trees per plot (N) on chronology statistics. The present study sought to highlight (i) the effect of N on the reliability of both chronology and climate-growth relationships and (ii) its variability across five European tree species with differentiated ecophysiological patterns. Fifty-eight pure, evenaged forests were sampled across France. For each plot, dendroecological investigations were carried out using chronologies built from 28 to three trees. Chronology reliability was studied using the mean intertree correlation (rbt) and the expressed population signal (EPS), whereas the climate-growth relationships were evaluated through the bootstrapped correlation coefficients (BCC). The accuracy of the dendroecological investigations decreased with decreasing N: EPS and BCC approached zero, implying that the signal common to all trees weakened. Thus, most of the significant correlations became nonsignificant when the sample size decreased from 28 to three trees per plot. Differences were found between species. For a given sample size, the shade-intolerant species Quercus petraea and Pinus sylvestris displayed lower intertree differences in growth-index series (higher rbt) and higher EPS than the shade-tolerant species Abies alba, Fagus sylvatica, and Picea abies. These latter species also displayed a greater sensitivity to sample size decrease, with a stronger BCC weakening and a higher proportion of changes in correlation significance. The EPS threshold of 0.85 was reached for around six to 10 trees for shade-intolerant species versus 20-30 for the shade-tolerant ones and generally corresponded to a mean correlation precision of around 0.06. We finally propose a general method to estimate this precision.

Merian P.,French National Institute for Agricultural Research | Lebourgeois F.,French National Institute for Agricultural Research
Forest Ecology and Management | Year: 2011

In most dendrochronological studies, climate-growth relationships are established on dominant trees to minimize non-climatic signals. However, response to environmental factors may be affected by tree-size, which begs the question of the representativeness of dominant trees on the stand level. To highlight the variations in climate-growth relationships among sizes and species, under a wide range of ecological conditions (climate and soil properties), 61 pure even-aged stands were sampled across France. At each stand, two tree-ring chronologies were established from 10 big- to 10 small-diameter trees. Our objectives were, (1) to assess variations in climate sensitivity between the two size-diameter classes, and (2) to investigate the role of species and ecological conditions on these variations. The climate-growth relationships were evaluated from 122 tree-ring chronologies (1. 220 trees) through extreme growth years and correlation function analyses. Sensitivity to climate of shade-intolerant and moderately shade-tolerant species (Picea abies (L.) Karst., Pinus sylvestris L. and Quercus petraea (Matt.) Liebl.) remained constant between the size-diameter classes for both temperature and hydric balance, while the shade-tolerant species Abies alba Mill. and Fagus sylvatica L. displayed significant differences, with larger trees being more sensitive to summer drought than smaller trees. This difference increased with increasing climatic xericity. Our results suggest that, for shade-tolerant species, (1) big trees could be more sensitive to climatic change especially under xeric climate, and (2) future tree ring studies should include trees stratified by size to produce unbiased estimation of sensitivity to climate. © 2011 Elsevier B.V.

Porcher J.,French National Institute for Agricultural Research
Journal of Agricultural and Environmental Ethics | Year: 2011

Animal production, especially pork production, is facing growing international criticism. The greatest concerns relate to the environment, the animals' living conditions, and the occupational diseases. But human and animal conditions are rarely considered together. Yet the living conditions at work and the emotional bond that inevitably forms bring the farm workers and the animals to live very close, which leads to shared suffering. Suffering does spread from animals to human beings and can cause workers physical, mental, and also moral suffering, which is all the more harmful due to the fact that it is concealed. The conceptual tools used to conceal suffering ("animal welfare," stress, pain) suggest that the industrial system can be improved, whereas for farmers it is by definition incompatible with animal husbandry. © 2010 Springer Science+Business Media B.V.

Picheny V.,French National Institute for Agricultural Research
Journal of Machine Learning Research | Year: 2014

Using statistical emulators to guide sequential evaluations of complex computer experiments is now a well-established practice. When a model provides multiple outputs, a typical objective is to optimize one of the outputs with constraints (for instance, a threshold not to exceed) on the values of the other outputs. We propose here a new optimization strategy based on the stepwise uncertainty reduction paradigm, which offers an efficient trade-off between exploration and local search near the boundaries. The strategy is illustrated on numerical examples.

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.

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.

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.

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.

Mellin J.R.,Institute Pasteur Paris | Mellin J.R.,French Institute of Health and Medical Research | Mellin J.R.,French National Institute for Agricultural Research | Cossart P.,Institute Pasteur Paris | And 2 more authors.
Trends in Genetics | Year: 2015

Bacterial riboswitches are elements present in the 5'-untranslated regions (UTRs) of mRNA molecules that bind to ligands and regulate the expression of downstream genes. Riboswitches typically regulate the expression of protein-coding genes. However, mechanisms of riboswitch-mediated regulation have recently been shown to be more diverse than originally thought, with reports showing that riboswitches can regulate the expression of noncoding RNAs and control the access of proteins, such as transcription termination factor Rho and RNase E, to a nascent RNA. Riboswitches are also increasingly used in biotechnology, with advances in the engineering of synthetic riboswitches and the development of riboswitch-based sensors. In this review we address the emerging roles and mechanisms of riboswitch-mediated regulation in natura and recent progress in the development of riboswitch-based technology. © 2015 Elsevier Ltd.

Rimet F.,French National Institute for Agricultural Research | Bouchez A.,French National Institute for Agricultural Research
Ecological Indicators | Year: 2012

Benthic diatoms are routinely used to assess river pollution. Most of the tools based on these organisms exploit the differences of pollution sensitivity between species; as such, species level identification is required. Accurate determination of diatom species requires rigorous training due to the extreme diversity of the group. The level of taxonomic resolution for biomonitoring is still debated. We tested the influence of taxonomic resolution on diatom bioassessment in an ecoregional framework. We used a database of 1967 diatom samples from biomonitoring programs in two French river basins, that reported three kinds of data for each site: (a) taxa abundance, expressed with 6 separate level of taxonomic resolution: species, genus, family, order, class or subdivision level; (b) physical and chemical characterization; (c) ecoregion and river-size class memberships. Mantel tests showed that the influence of taxonomic resolution on assemblage composition description was weak from species to order level. Mantel tests between chemical parameters and diatom assemblages showed that there was an increase in correlation from subdivision to genera resolution. But species and genus resolutions showed equivalent correlations with chemical parameters. Predictive models using diatom data to reconstruct nutrients, organic matter and major-ions content showed an increasing performance from sub-division to species resolution. Nevertheless their performances did not follow the exponential increase of taxa number from sub-division to species: models performances improved only by 12-23% from genus to species depending on the parameter reconstructed whereas number of taxa was multiplied by 10. Finally, we observed that the more precise the taxonomic resolution, the better the correspondence with ecoregion classification. This can be partly explained by diatom endemism and cosmopolitanism which is mostly observed to species level, rarely to genus level and never above.For a quick and robust assessment of river pollution coarse identification is sufficient. Hypotheses to explain such results are that: (1) many species are too rare to describe their ecological requirements with certainty; (2) more environmental descriptors are necessary to explain the presence of some species; (3) the dataset is compromised by identification errors, particularly at the species level. On the other hand, a precise ecoregional bioassessment requires a fine taxonomic resolution; this must be stressed for the European Water Framework Directive which requires an assessment in an ecoregion classification. © 2011 Elsevier Ltd. All rights reserved.

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.

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.

Nicaise V.,French National Institute for Agricultural Research
Frontiers in Plant Science | Year: 2014

Viruses cause epidemics on all major cultures of agronomic importance, representing a serious threat to global food security. As strict intracellular pathogens, they cannot be controlled chemically and prophylactic measures consist mainly in the destruction of infected plants and excessive pesticide applications to limit the population of vector organisms. A powerful alternative frequently employed in agriculture relies on the use of crop genetic resistances, approach that depends on mechanisms governing plant-virus interactions. Hence, knowledge related to the molecular bases of viral infections and crop resistances is key to face viral attacks in fields. Over the past 80 years, great advances have been made on our understanding of plant immunity against viruses. Although most of the known natural resistance genes have long been dominant R genes (encoding NBS-LRR proteins), a vast number of crop recessive resistance genes were cloned in the last decade, emphasizing another evolutive strategy to block viruses. In addition, the discovery of RNA interference pathways highlighted a very efficient antiviral system targeting the infectious agent at the nucleic acid level. Insidiously, plant viruses evolve and often acquire the ability to overcome the resistances employed by breeders. The development of efficient and durable resistances able to withstand the extreme genetic plasticity of viruses therefore represents a major challenge for the coming years. This review aims at describing some of the most devastating diseases caused by viruses on crops and summarizes current knowledge about plant-virus interactions, focusing on resistance mechanisms that prevent or limit viral infection in plants. In addition, I will discuss the current outcomes of the actions employed to control viral diseases in fields and the future investigations that need to be undertaken to develop sustainable broad-spectrum crop resistances against viruses. © 2014 Nicaise.

Briat J.-F.,French National Institute for Agricultural Research | Dubos C.,French National Institute for Agricultural Research | Gaymard F.,French National Institute for Agricultural Research
Trends in Plant Science | Year: 2015

One of the grand challenges in modern agriculture is increasing biomass production, while improving plant product quality, in a sustainable way. Of the minerals, iron (Fe) plays a major role in this process because it is essential both for plant productivity and for the quality of their products. Fe homeostasis is an important determinant of photosynthetic efficiency in algae and higher plants, and we review here the impact of Fe limitation or excess on the structure and function of the photosynthetic apparatus. We also discuss the agronomic, plant breeding, and transgenic approaches that are used to remediate Fe deficiency of plants on calcareous soils, and suggest ways to increase the Fe content and bioavailability of the edible parts of crops to improve human diet. © 2014 Elsevier Ltd.

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.

Mallory A.,French National Institute for Agricultural Research | Vaucheret H.,French National Institute for Agricultural Research
Plant Cell | Year: 2010

Both transcriptional (TGS) and posttranscriptional gene silencing (PTGS) are conserved eukaryotic gene regulatory mechanisms, integral for taming exogenous (viruses and bacteria) or endogenous (repetitive elements and transposons) invasive nucleic acids to minimize their impact on genome integrity and function. TGS and PTGS also are essential for controlling the expression of protein coding genes throughout development or in response to environmental stimuli. In plants and animals, at least one memberof the conserved ARGONAUTE(AGO) protein family comprises the catalytic engine of the silencing complex, which is guided by sequence-specific small RNA to cognate RNA. In this review, we present general features of plant and animal AGO proteins and detail our knowledge on the 10 Arabidopsis thaliana AGOs. © 2010 American Society of Plant Biologists.

Allaire G.,French National Institute for Agricultural Research
Agricultural Economics | Year: 2010

This article reviews the concept of the "market" and questions the standard view of the "market" developed by orthodox economic theory. The article highlights how Economic Sociology and Convention Theory is more useful in understanding markets and appreciating markets as social constructs, which are governed by institutions and social orders. This adjustment in the analytical framework to study markets and especially food markets, is useful in unpacking the various dimensions of "quality" in food products and illustrating that "quality" is an institution that is shaped by society and by culture. © 2010 International Association of Agricultural Economists.

Bournet P.-E.,Agrocampus Ouest | Boulard T.,French National Institute for Agricultural Research
Computers and Electronics in Agriculture | Year: 2010

Ventilation processes inside the greenhouse strongly affect air renewal and internal climatic conditions, which themselves interact with the growth and homogeneity of the crop. Natural ventilation is often chosen since it is the most economic method available.Studies of internal distributed climate induced by ventilation have been taking place for the past 25 years. Experimental studies have pointed out the impact of vent configurations on airflow pattern, particularly when the wind is the main driving force. However, the development of computational fluid dynamics (CFDs) has only recently provided the opportunity to simulate the climate inside greenhouses for known vent configurations, and to test a wide range of geometries with different vent combinations under different climatic conditions.In this article, the main factors governing air movements inside the greenhouse are first analysed. The characteristics of the laboratory scale models and field experiments are reviewed, with particular focus on the technologies implemented. The principles of CFD, the main modelling approach, together with its adaptations to greenhouse climate simulation, are then described in detail. Conclusions of studies concerning ventilation efficiency inside greenhouses are reviewed with respect to greenhouse geometry and opening arrangements. Other parameters affecting ventilation, such as wind speed and direction, the addition of insect-proof or shading screens, and interactions with the crop, are also discussed. © 2010 Elsevier 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).

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.

Colbach N.,French National Institute for Agricultural Research
Plant Science | Year: 2010

Managing crop pests (weeds, insects, pathogens, etc.) to limit both crop production loss and environmental impacts is a major challenge of agriculture. Because of the large number of factors and the complexity of interactions, models are invaluable tools to synthesize our knowledge on pests and to quantify the effects of cropping systems on pest dynamics. These models must be able to rank candidate cropping systems as a function of pest frequency and severity, and to account for variability in effects to estimate the risk of success or failure of a particular system. Two contrasting approaches are possible. Mechanistic models describe variability with process-based, usually deterministic sub-models quantifying interactions between cropping system components and environmental conditions. Empirical models directly relate observations to input variables, using few parameters, and usually quantify variability with probabilistic (stochastic) functions. The present paper critically evaluates these a priori contradictory approaches, i.e. deterministic vs. stochastic and mechanistic vs. empirical representations of cropping system effects in pest dynamics models, relative to model objectives and scales, pest species, scientific disciplines and knowledge level. We do not attempt to be exhaustive but analyse a small number of contrasting models to identify their advantages, disadvantages and complementarities. The paper concludes that models using a mechanistic representation of the cropping system × environment interactions are best for quantifying effects and accounting for their variability, combined with a subsequent transformation with in silico experiments into empirical models of the major cropping system components. © 2010 Elsevier Ireland Ltd.

Soussana J.-F.,French National Institute for Agricultural Research | Graux A.-I.,French National Institute for Agricultural Research | Tubiello F.N.,European Commission - Joint Research Center Ispra
Journal of Experimental Botany | Year: 2010

Projections of climate change impacts on global food supply are largely based on crop and pasture modelling. The consistency of these models with experimental data and their ability to simulate the effects of elevated CO 2 and of increased climate variability has been debated. The effects of high temperatures, of increased climate variability and of several limiting factors which interact with elevated CO2 such as soil nutrients, pests and weeds are neither fully understood nor well implemented in leading models. Targeted model developments will be required based on experimental data concerning: (i) the role of extreme climatic events, (ii) the interactions between abiotic factors and elevated CO2, (iii) the genetic variability in plant CO2 and temperature responses, (iv) the interactions with biotic factors, and (v) the effects on harvest quality. To help make better use of the available knowledge, it is envisioned that future crop and pasture modelling studies will need to use a risk assessment approach by combining an ensemble of greenhouse gas emission (or stabilization) scenarios, of regional climate models and of crop and pasture models, as well as an ensemble of adaptation options concerning both management practices and species/varieties. © 2010 The Author.

Piou C.,French National Institute for Agricultural Research | Prevost E.,French National Institute for Agricultural Research
Ecological Modelling | Year: 2012

Predicting the persistence and adaptability of natural populations to climate change is a challenging task. Mechanistic models that integrate biological and evolutionary processes are helpful toward this aim. Atlantic salmon, Salmo salar (L.), is a good candidate to assess the effect of environmental change on a species with a complex life history through an integrative modelling approach due to (i) a large amount of knowledge concerning its biology and (ii) extensive historical data sets that can be used for model validation. This paper presents an individual-based demo-genetic model developed to simulate S. salar population dynamics in southern European populations: IBASAM (Individual-Based Atlantic SAlmon Model). The model structure is described thoroughly. A parameterization exercise was conducted to adjust the model to an extensive set of demographic data collected over 15 years on the Scorff River, Brittany, France. A sensitivity analysis showed that two parameters determining mean and variability of juvenile growth rates were crucial in structuring the simulated populations. Additionally, realistic microevolutionary patterns of different aspects of life history were predicted by the model, reproducing general knowledge on S. salar population biology. The integration into IBASAM of a demo-genetic structure coupled with the explicit representation of individual variability and complex life histories makes it a cohesive and novel tool to assess the effect of potential stressors on evolutionary demography of Atlantic salmon in further studies. © 2012 Elsevier B.V.

Jean P.,French National Institute for Agricultural Research | Jean-Christophe S.,French National Institute for Agricultural Research
Ecological Entomology | Year: 2010

1. Host-specialised races of plant-feeding insects are particularly informative models in the study of ecological speciation, that is, the evolution of reproductive isolation through divergent natural selection. However, within the enormous diversity of phytophagous insects, the mechanisms of ecological divergence have been elucidated in few host race systems. 2. Here we review the literature covering speciation through host-plant specialisation in a well-studied model, the pea aphid complex, Acyrthosiphon pisum, which encompasses numerous biotypes that parasitise different legume host species worldwide. 3. Published results are consistent with ecologically promoted reproductive isolation. Divergent host-induced selection is pronounced across biotypes, and reflects genetic trade-offs preventing the optimal use of multiple host plants. While these genetic trade-offs may partly explain the unfitness of hybrids between biotypes, hybridisation occurring on plants is also limited by genetically-based host preference, and by selection against migrants that chose unfavourable hosts. The continuum of genetic divergence displayed by 11 races and species of the pea aphid complex suggests that host races constitute an intermediate step in the speciation process, and that host specialisation may indeed lead to complete speciation. Uncertainties remain on the contribution of non-ecological reproductive barriers to biotype divergence and on the physiological and molecular bases of host specialisation. © 2010 The Royal Entomological Society.

Network R.P.,French National Institute for Agricultural Research
Trends in Plant Science | Year: 2016

Pesticide resistance is a crucial factor to be considered when developing strategies for the minimal use of pesticides while maintaining pesticide efficacy. This goal requires monitoring the emergence and development of resistance to pesticides in crop pests. To this end, various methods for resistance diagnosis have been developed for different groups of pests. This review provides an overview of biological, biochemical, and molecular methods that are currently used to detect and quantify pesticide resistance. The agronomic, technical, and economic advantages and drawbacks of each method are considered. Emerging technologies are also described, with their associated challenges and their potential for the detection of resistance mechanisms likely to be selected by current and future plant protection methods. © 2016 Elsevier Ltd

Heberden C.,French National Institute for Agricultural Research
Nutrition Research Reviews | Year: 2016

Three areas in the brain continuously generate new neurons throughout life: the subventricular zone lining the lateral ventricles, the dentate gyrus in the hippocampus and the median eminence in the hypothalamus. These areas harbour neural stem cells, which contribute to neural repair by generating daughter cells that then become functional neurons or glia. Impaired neurogenesis leads to detrimental consequences, such as depression, decline of cognitive abilities and obesity. Adult neurogenesis is a versatile process that can be modulated either positively or negatively by many effectors, external or endogenous. Diet can modify neurogenesis both ways, either directly by ways of food-borne molecules, or possibly by the modifications induced on gut microbiota composition. It is therefore critical to define dietary strategies optimal for the maintenance of the stem cell pools. Copyright © The Author 2016

Tepfer M.,French National Institute for Agricultural Research
GM crops & food | Year: 2013

When applying risk assessment and the broader process of risk analysis to decisions regarding the dissemination of genetically modified organisms (GMOs), the process has a tendency to become remarkably complex. Further, as greater numbers of countries consider authorising the large-scale dissemination of GMOs, and as GMOs with more complex traits reach late stages of development, there has been increasing concern about the burden posed by the complexity of risk analysis. We present here an improved approach for GMO risk analysis that gives a central role to problem formulation. Further, the risk analysis strategy has been clarified and simplified in order to make rigorously scientific risk assessment and risk analysis more broadly accessible to diverse stakeholder groups.

Cheynier V.,French National Institute for Agricultural Research
Phytochemistry Reviews | Year: 2012

Phenolic compounds are a large class of plant secondary metabolites, showing a diversity of structures, from rather simple structures, e.g. phenolic acids, through polyphenols such as flavonoids, that comprise several groups, to polymeric compounds based on these different classes. Phenolic compounds are important for the quality of plant based foods: they are responsible for the colour of red fruits, juices and wines and substrates for enzymatic browning, and are also involved in flavour properties. In particular, astringency is ascribed to precipitation of salivary proteins by polyphenols, a mechanism possibly involved in defence against their anti-nutritional effects. Finally, phenolic compounds are considered to contribute to the health benefits associated to dietary consumption of fruits and vegetables. During food processing and storage, plant phenolics are converted to a variety of derived compounds. While methods to analyse lower molecular weight phenolic compounds are well developed, analysis of polymeric compounds remains a challenge. Indeed, strong interactions of polymeric phenolics with plant cell wall material limit their extraction. Besides, their polydispersity results in poor resolution and detection, especially of derived structures such as oxidation products. However, recent advances of the analytical techniques have allowed some progress in their structural characterisation. This review summarizes the current knowledge on methods to analyse polyphenols. It presents their reactions in foods and beverages and the resulting structures, and highlights some aspects related to their impact on colour, flavour and health properties, with examples taken mostly from wine research. © 2012 Springer Science+Business Media B.V.

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.

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.

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.

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.

Cubillos F.A.,French National Institute for Agricultural Research | Coustham V.,French National Institute for Agricultural Research | Loudet O.,French National Institute for Agricultural Research
Current Opinion in Plant Biology | Year: 2012

Even if considerable progress has been achieved towards the understanding of natural variation in plant systems, the contribution of transcript abundance variation to phenotypic diversity remains unappreciated. Over the last decade, efforts to characterise the genome-wide expression variation in natural accessions, structured populations and hybrids have improved our knowledge of the contribution of non-coding polymorphisms to gene expression regulation. Moreover, new studies are helping to unravel the role of expression polymorphisms and their orchestrated performance. Recent advances involving classical linkage analysis, GWAS and improved eQTL mapping strategies will provide a greater resolution to determine the genetic variants shaping the broad diversity in plant systems. © 2012 Elsevier Ltd.

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.

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.

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.

Shukat R.,French National Institute for Agricultural Research | Relkin P.,French National Institute for Agricultural Research
Colloids and Surfaces B: Biointerfaces | Year: 2011

Twelve oil-in-water nano-emulsions were prepared using a melt high-pressure homogenisation process (HPH) at 300, 800 or 1200. bar. The resulting emulsions containing 20. wt% palm oil in the absence or presence of α-tocopherol were stabilised by whey proteins alone or in mixture with lecithin. Lipid nanoparticles in these emulsions were characterized for their particle size, surface charge and protein surface concentration (PSC) in relation to their stability against aggregation and coalescence, and to their ability for encapsulation and protection of α-tocopherol against chemical degradation. Increasing HPH values were accompanied by the formation of lipid nanoparticles with decreasing size and PSC, but increasing long-term stability against aggregation and coalescence in parallel with an increase in α-tocopherol degradation (up to 15. wt% for 1200. bar). Presence of α-tocopherol, led to increasing (or decreasing) PSC values with increasing (or decreasing) HPH values for lipid nanoparticles stabilised by proteins alone (or in mixture with lecithins). In addition to these structural properties, the ability for α-tocopherol long-term stability of nanoparticles in emulsions was shown to differ more depending on their adsorbed materials (protein alone, or in mixture with lecithin) than on their particle size values. After 2 months storage, α-tocopherol in emulsions prepared at 300, 800 or 1200. bar was protected against chemical degradation at 79, 77, 67. wt%, respectively, when whey proteins were used alone, instead of 66, 63, 48. wt% when proteins were used in mixture with lecithins.These results indicated the dominant role of adsorbed proteins on the protection of vitamin models by nanoemulsions. They are of a great technological importance for production of lipid nanoparticles presenting a high volume-to-diameter ratio values and consequently high exchange surfaces between the matrix carrier and water and oxygen environmental factors. © 2011 Elsevier B.V.

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.

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.

Dulermo T.,French National Institute for Agricultural Research | Nicaud J.-M.,French National Institute for Agricultural Research
Metabolic Engineering | Year: 2011

The oleaginous yeast Yarrowia lipolytica can accumulate up to 38% of its dry weight (DW) as lipids. Factors involved in lipid accumulation, particularly triglycerides, are not well identified. Using different mutations in the glycerol-3-phosphate (G3P) shuttle pathway (δgut2 affecting the anabolic dehydrogenase or overexpressing GPD1 affecting the catabolic dehydrogenase), we were able to modulate G3P concentration. We show that in a Po1d genetic background, GPD1 overexpression, GUT2 inactivation or both mutations together result in 1.5, 2.9, and 5.6-fold respective increases in the level of G3P leading to an increase of triacylglyceride (TAG) accumulation. Moreover, our results indicate that each strain with an increased concentration of G3P, also presented a decreased concentration of glycerol. Analysis of the different genes involved in glycerol metabolism indicated that Y. lipolytica does not possess a gene for glycerol-3-phosphatase. These findings suggest that Y. lipolytica has a modified and unique metabolism of glycerol that is dedicated to G3P synthesis (and also to TAG synthesis) which may contribute to its oleaginous character. Furthermore, coupling the G3P shuttle disorders to a deficient Β-oxidation pathway (by inactiving POX1-6 or MFE1 genes) increased TAG and free fatty acids content. Finally, we obtained strains that accumulated up to 65-75% of their DW as lipid. Transcriptional analysis in these strains, revealed that the high levels of lipids resulted from over-expression of genes involved in TAG synthesis (SCT1, encoding a sn-1 acyltransferase; and DGA1, encoding an acylCoA diacylglycerol acyltransferase) and the repression of genes involved in the degradation of TAG (TGL3 and TGL4, encoding triacylglycerol lipases). These findings indicate that TAG synthesis is limited by the availability of G3P and fatty acids, and that the expression of genes involved in TAG homeostasis is regulated by the G3P shuttle and the Β-oxidation pathway. Finally, the synergistic contribution of acyltransferase gene expression to G3P synthesis is required for high levels of TAG synthesis and lipid accumulation in Y. lipolytica. © 2011 Elsevier Inc.

Levasseur A.,French National Institute for Agricultural Research | Drula E.,CNRS Architecture and Functions of Biological Macromolecules Lab | Lombard V.,CNRS Architecture and Functions of Biological Macromolecules Lab | Coutinho P.M.,CNRS Architecture and Functions of Biological Macromolecules Lab | Henrissat B.,CNRS Architecture and Functions of Biological Macromolecules Lab
Biotechnology for Biofuels | Year: 2013

Background: Since its inception, the carbohydrate-active enzymes database (CAZy;) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category. Results: Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name "Auxiliary Activities" in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). Conclusions: The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery. © 2013 Levasseur et al.; licensee BioMed Central Ltd.

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.

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.

Gautier M.,French National Institute for Agricultural Research | Naves M.,French National Institute for Agricultural Research
Molecular Ecology | Year: 2011

Admixed populations represent attractive biological models to study adaptive selection. Originating from several waves of recent introduction from European (EUT), African (AFT) and zebus (ZEB) cattle, New World Creole cattle allow investigating the response to tropical environmental challenges of these three ancestries. We here provide a detailed assessment of their genetic contributions to the Creole breed from Guadeloupe (CGU). We subsequently look for footprints of selection by combining results from tests based on the extent of haplotype homozygosity and the identification of excess/deficiency of local ancestry. To tackle these issues, 140 CGU individuals and 25 Brahman zebus from Martinique were genotyped at 44 057 SNPs. These data were combined to those available on 23 populations representative of EUT, AFT or ZEB. We found average proportions of 26.1%, 36.0% and 37.9% of EUT, AFT and ZEB ancestries in the CGU genome indicating a higher level of African and zebu ancestries than suggested by historical records. We further identified 23 genomic regions displaying strong signal of selection, most of them being characterized by an excess of ZEB local ancestry. Among the candidate gene underlying these regions, several are associated with reproductive functions (RXFP2, PMEPA1, IGFBP3, KDR, PPP1R8, TBXA2R and SLC7A5) and metabolism (PDE1B and CYP46A1). Finally, two genes (CENTD3 and SAMD12) are involved in cellular signalization of immune response. This study illustrates the relevance of admixed populations to identify footprints of selection by combining several tests straightforward to implement on large data sets. © 2011 Blackwell Publishing Ltd.

Pages L.,French National Institute for Agricultural Research
Plant, Cell and Environment | Year: 2011

We designed a simple dynamic and stochastic architectural model with six parameters to link the foraging performance of root systems to their developmental processes. Soil foraging was quantified by the volume enveloping the roots until a given uptake distance. Many simulated architectures were obtained by combining four different values for each parameter. The rate of soil colonization was mainly defined by individual root elongation rates and interbranch distances. Less intuitively, we showed that differentiation of elongation rates among the roots increased this colonization rate. Uptake efficiency - the ratio of the actual colonized volume to the volume of a unique cylinder with the same length and a radius corresponding to the uptake distance - declined with root system size. Nevertheless, large variations in efficiency existed among root systems for a given size, typically in a 4- to 10-fold range. Therefore, the 'efficiency gain' was defined as the deviation from the average trend in efficiency versus size. Between-root differentiation in elongation rates increased this gain. The level of hierarchy between mother and lateral roots, as well as the variation of elongation rates among lateral roots, was also shown to contribute to this optimization. Several parameter combinations could lead to similar efficiency gains. The aim of our work is to bridge knowledge between root structure and function at the root and root system scales. A very simple simulation model of the root system architecture was designed to represent root developmental processes and study the integrated uptake performance of virtual root systems. Extensive simulations demonstrated the importance of inter-branch distances, whose optimal values depended on the mobility of the considered soil resource. Growth differentiation between roots also appeared as a key point for optimizing foraging. © 2011 Blackwell Publishing Ltd.

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.

Theodorou V.,French National Institute for Agricultural Research
Neurogastroenterology and Motility | Year: 2013

Despite high prevalence, the precise irritable bowel syndrome (IBS) pathophysiology remains poorly understood likely due to the heterogeneity of IBS populations and the multifactorial etiology of this disorder. Among risk factors, genetic predisposition and early life trauma have been reported. In this context, the debate on genetic or environmental influences in the IBS pathogenesis is still open. The study by van der Wijngaard et al., reporting for the first time that susceptibility to stress-induced visceral hypersensitivity in maternally separated rats can be transferred to the next generation without any further exposure of F2 individuals to maternal separation, supports the importance of environmental influence in the IBS phenotype. Epigenetic mechanisms such as hypermethylation in the promoter region of the glucocorticoid receptor gene mediating the long-term and transgenerational behavioral effects of maternal care on the development have been shown in some but not in all studies. Van der Wijngaard et al. incriminated maternal care in the transmitted susceptibility to stress-induced visceral hypersensitivity, but not changes in glucocorticoid receptor protein expression in the brain. This finding opens a broad field of future directions aimed at evaluating the mechanisms involved in the transmission across generations of the digestive features of IBS, including, for example, on the role of gut microbiota changes in vertical transmission or epigenetic modifications of intestinal mast cells and the junctional region of intestinal epithelial cells in vertical transfer. © 2013 John Wiley & Sons Ltd.

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.

Chun Y.J.,Korea Research Institute of Bioscience and Biotechnology | Le Corre V.,French National Institute for Agricultural Research | Bretagnolle F.,French National Institute for Agricultural Research
Molecular Ecology | Year: 2011

The impact of natural selection on the adaptive divergence of invasive populations can be assessed by testing the null hypothesis that the extent of quantitative genetic differentiation (QST) would be similar to that of neutral molecular differentiation (FST). Using eight microsatellite loci and a common garden approach, we compared QST and FST among ten populations of an invasive species Ambrosia artemisiifolia (common ragweed) in France. In a common garden study with varying water and nutrient levels, we measured QST for five traits (height, total biomass, reproductive allocation, above-to belowground biomass ratio, and days to flowering). Although low FST indicated weak genetic structure and strong gene flow among populations, we found significant diversifying selection (QST > FST) for reproductive allocation that may be closely related to fitness. It suggests that abiotic conditions may have exerted selection pressure on A. artemisiifolia populations to differentiate adaptively, such that populations at higher altitude or latitude evolved greater reproductive allocation. As previous studies indicate multiple introductions from various source populations of A. artemisiifolia in North America, our results suggest that the admixture of introduced populations may have increased genetic diversity and additive genetic variance, and in turn, promoted the rapid evolution and adaptation of this invasive species. © 2011 Blackwell Publishing Ltd.

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.

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.

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.

Cordella C.B.Y.,French National Institute for Agricultural Research | Bertrand D.,French National Institute for Agricultural Research
TrAC - Trends in Analytical Chemistry | Year: 2014

The SAISIR Toolbox for MATLAB, OCTAVE and SCILAB is a freely available collection of functions and algorithms for modeling physicochemical, sensorial and multidimensional data with a large range of bilinear and multilinear models. The SAISIR toolbox can be freely downloaded at http://www.chimiometrie.fr/saisirdownload.html. SAISIR contains many functions for loading, saving, manipulating or displaying data. It is well equipped with more than 200 chemometric functions for regression, multidimensional analysis, discrimination and multiblock analysis. © 2013 Elsevier Ltd.

Ming R.,University of Illinois at Urbana - Champaign | Bendahmane A.,French National Institute for Agricultural Research | Bendahmane A.,King Saud University | Renner S.S.,Ludwig Maximilians University of Munich
Annual Review of Plant Biology | Year: 2011

Sex chromosomes in land plants can evolve as a consequence of close linkage between the two sex determination genes with complementary dominance required to establish stable dioecious populations, and they are found in at least 48 species across 20 families. The sex chromosomes in hepatics, mosses, and gymnosperms are morphologically heteromorphic. In angiosperms, heteromorphic sex chromosomes are found in at least 19 species from 4 families, while homomorphic sex chromosomes occur in 20 species from 13 families. The prevalence of the XY system found in 44 out of 48 species may reflect the predominance of the evolutionary pathway from gynodioecy towards dioecy. All dioecious species have the potential to evolve sex chromosomes, and reversions back from dioecy to various forms of monoecy, gynodioecy, or androdioecy have also occurred. Such reversals may occur especially during the early stages of sex chromosome evolution before the lethality of the YY (or WW) genotype is established. Copyright © 2011 by Annual Reviews. All rights reserved.

Moury B.,French National Institute for Agricultural Research | Simon V.,French National Institute for Agricultural Research
Molecular Biology and Evolution | Year: 2011

The dN/dS ratio between nonsynonymous and synonymous substitution rates has been used extensively to identify codon positions involved in adaptive processes. However, the accuracy of this approach has been questioned, and very few studies have attempted to validate experimentally its predictions. Using the coat protein (CP) of Potato virus Y (PVY; genus Potyvirus, family Potyviridae) as a case study, we identified several candidate positively selected codon positions that differed between clades. In the CP of the N clade of PVY, positive selection was detected at codon positions 25 and 68 by both the softwares PAML and HyPhy. We introduced nonsynonymous substitutions at these positions in an infectious cDNA clone of PVY and measured the effect of these mutations on virus accumulation in its two major cultivated hosts, tobacco and potato, and on its efficiency of transmission from plant to plant by aphid vectors. The mutation at codon position 25 significantly modified the virus accumulation in the two hosts, whereas the mutation at codon position 68 significantly modified the virus accumulation in one of its hosts and its transmissibility by aphids. Both mutations were involved in adaptive trade-offs. We suggest that our study was particularly favorable to the detection of adaptive mutations using dN/dS estimates because, as obligate parasites, viruses undergo a continuous and dynamic interaction with their hosts that favors the recurrent selection of adaptive mutations and because trade-offs between different fitness traits impede (or at least slow down) the fixation of these mutations and maintain polymorphism within populations. © 2011 The Author.

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.

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.

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).

Baldazzi V.,French National Institute for Agricultural Research | Bertin N.,French National Institute for Agricultural Research | de Jong H.,French Institute for Research in Computer Science and Automation | Genard M.,French National Institute for Agricultural Research
Trends in Plant Science | Year: 2012

One of the ambitions of 'crop systems biology' is to combine information from molecular biology with a broader view of plant development and growth. In the context of modeling, this calls for a multiscale perspective that focuses on the interplay between cellular and macroscopic studies. With this in mind, in this review we aim to draw attention to a panel of approaches that were developed in the context of systems biology and are used for analyzing and describing the behavior of cellular networks. Ultimately, insights obtained from these methods can be exploited to refine the description of plant processes, leading to integrated plant-cellular models. © 2012 Elsevier Ltd.

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.

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.

Gohin A.,French National Institute for Agricultural Research | Chantret F.,French National Institute for Agricultural Research
Energy Policy | Year: 2010

The world prices of some food and energy products have followed similar large swings in recent years. We investigate the long-run relationship between these prices using a world Computable General Equilibrium model with detailed representations of food and energy markets. Particular attention is paid to specifying macro-economic linkages which have often been overlooked in recent analysis and debate. We find that the omission of these macro-economic linkages has a substantial bearing on this relationship. A positive relationship due to the cost push effect has been identified in most analysis, but we find that the introduction of the real income effect may indeed imply a negative relationship between world food and energy prices. © 2009 Elsevier Ltd. All rights reserved.

Lu Y.,Chinese Academy of Agricultural Sciences | Wu K.,Chinese Academy of Agricultural Sciences | Jiang Y.,National Agro Technical Extension and Service Center | Guo Y.,Chinese Academy of Agricultural Sciences | Desneux N.,French National Institute for Agricultural Research
Nature | Year: 2012

Over the past 16 years, vast plantings of transgenic crops producing insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) have helped to control several major insect pests and reduce the need for insecticide sprays. Because broad-spectrum insecticides kill arthropod natural enemies that provide biological control of pests, the decrease in use of insecticide sprays associated with Bt crops could enhance biocontrol services. However, this hypothesis has not been tested in terms of long-term landscape-level impacts. On the basis of data from 1990 to 2010 at 36 sites in six provinces of northern China, we show here a marked increase in abundance of three types of generalist arthropod predators (ladybirds, lacewings and spiders) and a decreased abundance of aphid pests associated with widespread adoption of Bt cotton and reduced insecticide sprays in this crop. We also found evidence that the predators might provide additional biocontrol services spilling over from Bt cotton fields onto neighbouring crops (maize, peanut and soybean). Our work extends results from general studies evaluating ecological effects of Bt crops by demonstrating that such crops can promote biocontrol services in agricultural landscapes. © 2012 Macmillan Publishers Limited. All rights reserved.

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.

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.

Sosnowski O.,French National Institute for Agricultural Research | Charcosset A.,French National Institute for Agricultural Research | Joets J.,French National Institute for Agricultural Research
Bioinformatics | Year: 2012

Summary: Compilation of genetic maps combined to quantitative trait loci (QTL) meta-analysis has proven to be a powerful approach contributing to the identification of candidate genes underlying quantitative traits. BioMercator was the first software offering a complete set of algorithms and visualization tool covering all steps required to perform QTL meta-analysis. Despite several limitations, the software is still widely used. We developed a new version proposing additional up to date methods and improving graphical representation and exploration of large datasets. © The Author(s) 2012. Published by Oxford University Press.

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.

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.

Meuret M.,French National Institute for Agricultural Research | Provenza F.,Utah State University
Animal Production Science | Year: 2015

European rangelands have rugged terrain with highly diverse patchworks of vegetation communities. They are mostly public lands that were abandoned for more than 50 years, because they served no purpose at the time of animal husbandry modernisation. The European Union's policy now promotes the reintroduction of grazing on rangelands to prevent wildfires and to restore habitats for biodiversity conservation. Facing the lack of knowledge to implement such a policy, researchers, nature managers, and pastoral advisors began working closely with shepherds and goat herders in France, who had persisted in using rangelands. The research presented here is part of this collective effort to understand and assess the experiential knowledge and feeding practices that herders use for livestock. The study required in situ and simultaneous recording of several types of information at different levels of organisation - herder, herd, individual animal - using methods from scientific disciplines ranging from ethnology to animal behavioural ecology and landscape ecology. The results for herded animals were surprising; they had daily intake levels often twice those observed in controlled studies with forages of similar nutritive values. The reason became clear when we learned that herders use grazing circuits that sequence a meal into a succession of contrasting and complementary grazing 'sectors' that boost appetite and intake. Our modelling of this practice in MENU, a model conceived and developed with experienced herders, shows how a herder can use understanding of complementarities among sectors to sequence meals that increase appetite and intake and ensure renewal of resources at the landscape level, or conversely, to apply more intensive grazing impact on particular target sectors. © CSIRO 2015.

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.

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.

Simon C.,French National Institute for Agricultural Research | Etienne M.,French National Institute for Agricultural Research
Environmental Modelling and Software | Year: 2010

To assist the Société Civile des Terres du Larzac (SCTL) in its effort to develop alternative forest management plans, a group of researchers and extension officers proposed applying a companion modelling approach. The objective was to support forest owners and livestock farmers while they worked out a solution to their forest management problems. The approach was based on the co-construction and use of an agent-based model providing a shared representation of the current management of farms and providing multiple view points on alternative forest management scenarios. The validation of the model allowed the development of a shared representation of the territory. The use of the model as an exploratory tool empowered local stakeholders to elaborate alternative management strategies for their renewable resources (forage, timber, firewood). It also expanded the discussion on forest management to a multi-scale level where managers assumed progressively a role of land administrators. When playing this role, they compared their forest policy orientations and forest harvesting decisions with farmers' individual situations and interests. Participants became aware of how spatial and temporal scales of management overlap and they progressively worked out a compromise between livestock breeding concerns of farmers and forest dynamics concerns of SCTL managers. © 2009 Elsevier Ltd.

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.

Pantin F.,French National Institute for Agricultural Research | Simonneau T.,French National Institute for Agricultural Research | Muller B.,French National Institute for Agricultural Research
New Phytologist | Year: 2012

Contents: Summary 349 I. Leaf growth: volume, structures, water and carbon 349 II. Coupling water and carbon limitations through the Lockhart model? 350 III. ABA signalling pathway as a hub to coordinate water and carbon relations 353 IV. Leaf venation: just a two-way pipe network? 354 V. Leaf ontogeny orchestrates the actors involved in the control of leaf growth 355 VI. The growing leaf in a changing world 360 VII. Conclusion 361 Acknowledgements 362 References 362 Summary: Leaf growth is the central process facilitating energy capture and plant performance. This is also one of the most sensitive processes to a wide range of abiotic stresses. Because hydraulics and metabolics are two major determinants of expansive growth (volumetric increase) and structural growth (dry matter increase), we review the interaction nodes between water and carbon. We detail the crosstalks between water and carbon transports, including the dual role of stomata and aquaporins in regulating water and carbon fluxes, the coupling between phloem and xylem, the interactions between leaf water relations and photosynthetic capacity, the links between Lockhart's hydromechanical model and carbon metabolism, and the central regulatory role of abscisic acid. Then, we argue that during leaf ontogeny, these interactions change dramatically because of uncoupled modifications between several anatomical and physiological features of the leaf. We conclude that the control of leaf growth switches from a metabolic to a hydromechanical limitation during the course of leaf ontogeny. Finally, we illustrate how taking leaf ontogeny into account provides insights into the mechanisms underlying leaf growth responses to abiotic stresses that affect water and carbon relations, such as elevated CO2, low light, high temperature and drought. © 2012 New Phytologist Trust.

Murgue C.,French National Institute for Agricultural Research | Therond O.,French National Institute for Agricultural Research | Leenhardt D.,French National Institute for Agricultural Research
Land Use Policy | Year: 2015

One of the great challenges of developing sustainable water management is to integrate water and land use issues, and to favor stakeholders' involvement in the process of designing a solution to the specific issues of water basins. This study aims to help reach these objectives: we present the outcomes of a methodology that aims to design, with stakeholders of a watershed facing quantitative water management issues, alternative agricultural landscapes that they each consider as potential solutions. Our design approach combines (1) facilitation of participatory workshops for designing changes in cropping systems and their spatial distributions at the landscape level with (2) formalization of these alternatives in a GIS. The formalized alternatives provide precise information about fields, farms and areas concerned by the designed changes. We present two sample results of this methodology implemented in a 840km2 irrigated landscape located in a water-deficient watershed in southwestern France. We discuss how our design approach may be useful for a wider design-and-assessment methodology involving researchers and stakeholders with conflicting interests. We show that our co-design approach provides fertile ground for the emergence of salient, credible and legitimate change options. © 2015 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.

Chardon F.,French National Institute for Agricultural Research | Noel V.,ARVALIS Institute du Vegetal | Masclaux-Daubresse C.,French National Institute for Agricultural Research
Journal of Experimental Botany | Year: 2012

There is evidence that crop yields are showing a trend of stagnation in many countries. This review aims to make an inventory of the last decade's crop productions and the associated economic and environmental challenges. Manipulating nitrogen use efficiency in crops appears to be the best way to conciliate global food security, respecting environmental policies, and the need to produce biofuels. In such a context, the specifications of ideal plants for the future are discussed with regards to human needs and taking into account current physiological and genetic knowledge. The approaches undertaken so far to design an ideal crop and to find suitable new germplasms are discussed. The interest in using model plants in agronomic research is illustrated through the recent data provided by studies exploring natural variation in Arabidopsis thaliana. Efficient Arabidopsis ideotypes are proposed and discussed. © 2012 The Author.

Hamel L.-P.,Université de Sherbrooke | Nicole M.-C.,Université 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.

Borel P.,French National Institute for Agricultural Research | Borel P.,French Institute of Health and Medical Research | Borel P.,Aix - Marseille University
Molecular Nutrition and Food Research | Year: 2012

As shown in most clinical studies dedicated to carotenoids, there is a huge interindividual variability in absorption, and blood and tissue responses, of dietary carotenoids. The recent discovery that several proteins are involved in carotenoid metabolism in humans has prompted a possible explanation for this phenomenon: genetic variants in genes encoding for these proteins may affect their expression or activity, and in turn carotenoid metabolism and carotenoid status. The proteins clearly identified so far are (i) the carotene oxygenases β,β-carotene-15,15′-monooxygenase (BCMO1) and β,β-carotene-9′,10′-oxygenase (BCDO2), which are involved in carotenoid cleavage, (ii) scavenger receptor class B type I (SR-BI), cluster determinant 36 (CD36), and Niemann Pick C1-like 1 (NPC1L1), which are involved in carotenoid uptake by cells, and (iii) glutathione S-transferase Pi 1 (GSTP1) and human retinal lutein-binding protein (HR-LBP), which are involved in the transport of xanthophylls in the retina. Other proteins, such as ATP-binding cassette subfamily G member 5 (ABCG5) and the fatty acid-binding proteins (FABPs) are also apparently involved although firmer evidence is still required. A genome-wide association study, as well as several candidate gene association studies, has shown that groups of subjects bearing different alleles in single nucleotide polymorphisms located in or near several of the above-mentioned genes display different blood and/or tissue concentrations of carotenoids. Further studies are needed to identify all the proteins involved in carotenoid metabolism and assess whether other types of genetic variation, e.g. copy number variants and epigenetic modifications, can modulate carotenoid status. One potential application of such research could be personalized dietary guidelines for carotenoids according to individual genetic characteristics. © 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Monteil C.L.,French National Institute for Agricultural Research | Bardin M.,French National Institute for Agricultural Research | Morris C.E.,French National Institute for Agricultural Research
ISME Journal | Year: 2014

Clarifying the role of precipitation in microbial dissemination is essential for elucidating the processes involved in disease emergence and spread. The ecology of Pseudomonas syringae and its presence throughout the water cycle makes it an excellent model to address this issue. In this study, 90 samples of freshly fallen rain and snow collected from 2005-2011 in France were analyzed for microbiological composition. The conditions favorable for dissemination of P. syringae by this precipitation were investigated by (i) estimating the physical properties and backward trajectories of the air masses associated with each precipitation event and by (ii) characterizing precipitation chemistry, and genetic and phenotypic structures of populations. A parallel study with the fungus Botrytis cinerea was also performed for comparison. Results showed that (i) the relationship of P. syringae to precipitation as a dissemination vector is not the same for snowfall and rainfall, whereas it is the same for B. cinerea and (ii) the occurrence of P. syringae in precipitation can be linked to electrical conductivity and pH of water, the trajectory of the air mass associated with the precipitation and certain physical conditions of the air mass (i.e. temperature, solar radiation exposure, distance traveled), whereas these predictions are different for B. cinerea. These results are pertinent to understanding microbial survival, emission sources and atmospheric processes and how they influence microbial dissemination. © 2014 International Society for Microbial Ecology All rights reserved.

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.

Zhong X.,French National Institute for Agricultural Research | Jacquet S.,French National Institute for Agricultural Research
Environmental Microbiology | Year: 2014

Little is known about Phycodnavirus (or double-stranded DNA algal virus) diversity in aquatic ecosystems, and virtually, no information has been provided for European lakes. We therefore conducted a 1-year survey of the surface waters of France's two largest lakes, Annecy and Bourget, which are characterized by different trophic states and phytoplanktonic communities. We found complementary and contrasting diversity of phycodnavirus in the lakes based on two genetic markers, the B family DNA polymerase-encoding gene (polB) and the major capsid protein-encoding gene (mcp). These two core genes have already been used, albeit separately, to infer phylogenetic relationships and genetic diversity among members of the phycodnavirus family and to determine the occurrence and diversity of these genes in natural viral communities. While polB yielded prasinovirus-like sequences, the mcp primers yielded sequences for prasinoviruses, chloroviruses, prymnesioviruses and other groups not known from available databases. There was no significant difference in phycodnavirus populations between the two lakes when the sequences were pooled over the full year of investigation. By comparing Lakes Annecy and Bourget with data for other aquatic environments around the world, we show that these alpine lakes are clearly distinct from both other freshwater ecosystems (lakes and rivers) and marine environments, suggesting the influence of unique biogeographic factors. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Ragsdale D.W.,University of Minnesota | Landis D.A.,Michigan State University | Brodeur J.,University of Montréal | 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.

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.

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.

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.

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.

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.

Dore J.,French National Institute for Agricultural Research | Blottiere H.,French National Institute for Agricultural Research
Current Opinion in Biotechnology | Year: 2015

Man is an intimate symbiosis between 10 trillion human cells and some 100 trillion bacteria, most of which inhabit the intestine where they constitute an extremely dense and diverse microbiota. This symbiotic balance that has to be established within each newborn is key to the maintenance of health and well being. Its development is markedly influenced by microbial exposure encountered very early in life. Mode of infant feeding, and the post-weaning transition to habitual diet will further shape the microbiota. Recent studies support the concept that diet should be viewed as a means to prevent potentially durable alterations of symbiosis observed in immune-mediated metabolic and inflammatory diseases. Non-digestible dietary fiber will play a major role in this context. © 2015 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.

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.

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.

In most organisms, storage lipids are packaged into specialized structures called lipid droplets. These contain a core of neutral lipids surrounded by a monolayer of phospholipids, and various proteins which vary depending on the species. Hydrophobic structural proteins stabilize the interface between the lipid core and aqueous cellular environment (perilipin family of proteins, apolipoproteins, oleosins). We developed a genetic approach using heterologous expression in Saccharomyces cerevisiae of the Arabidopsis thaliana lipid droplet oleosin and caleosin proteins AtOle1 and AtClo1. These transformed yeasts overaccumulate lipid droplets, leading to a specific increase in storage lipids. The phenotype of these cells was explored using synchrotron FT-IR microspectroscopy to investigate the dynamics of lipid storage and cellular carbon fluxes reflected as changes in spectral fingerprints. Multivariate statistical analysis of the data showed a clear effect on storage carbohydrates and more specifically, a decrease in glycogen in our modified strains. These observations were confirmed by biochemical quantification of the storage carbohydrates glycogen and trehalose. Our results demonstrate that neutral lipid and storage carbohydrate fluxes are tightly connected and co-regulated.

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.

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.

Liao C.-Y.,Wageningen University | Smet W.,Wageningen University | Brunoud G.,French National Institute for Agricultural Research | Yoshida S.,Wageningen University | And 3 more authors.
Nature Methods | Year: 2015

The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species. © 2015 Nature America, Inc.

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.

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.

Zeller B.,French National Institute for Agricultural Research | Dambrine E.,French National Institute for Agricultural Research
Soil Biology and Biochemistry | Year: 2011

Forest soils contain a variable amount of organic N roughly repartitioned among particles of different size, microbial biomass and associated with mineral compounds. All pools are alimented by annual litter fall as main input of organic N to the forest floor. Litter N is further subject to mineralization/stabilization recognized as the crucial process for the turnover of litter N. Although it is well documented that different soil types have different soil N stocks, it is presently unknown how different soil types affect the turnover of recent litter N. Here, we compared the potential mineralization of the total soil organic N with that of recent litter-released N in three beech forests varying in their soil properties. Highly 15N-labelled beech litter was applied to stands located at Aubure, Ebrach, Collelongo, which differ in humus type, soil type and soil chemistry. After 4-5 years of litter decomposition, the upper 3 cm of the organo-mineral A horizon was sampled and the net N mineralization was measured over 112 days under controlled conditions. The origin of mineralized N (litter N versus soil organic N) was calculated using 15N labeling. In addition, soils were fractionated according to their particle size (>2000 μm, 200-2000 μm, 50-200 μm, <50 μm) and particulate organic matter (POM) was separated from the mineral fraction in size classes, except the <50 μm fraction. Between 41 and 69% of soil organic N was recovered as POM. Litter-released 15N was mainly to be found in the coarse POM fractions >200 μm. On a soil mass basis, N mineralization was two-fold higher at Aubure and Collelongo than at Ebrach, but, on a soil N basis, N mineralization was the lowest at Collelongo and the highest at Ebrach. On a soil N (or 15N) basis, mineralization of litter 15N was two to four-fold higher than mineralization of the average soil N. Furthermore, the δ15N of the mineral N produced was closer to that of POM than to that of the mineral-bound fraction (<50 μm). Highest rates of 15N mineralization happened in the soil with the lowest N content, and we found a negative relationship between accumulations of N in the upper A horizon and the mineralization of 15N from the litter. Our results show that mineral N is preferentially mineralized from POM in the upper organo-mineral soil irrespective of the soil chemistry and that the turnover rate of litter N is faster in soils with a low N content. © 2010 Elsevier Ltd.

Leroux P.,French National Institute for Agricultural Research | Walker A.-S.,French National Institute for Agricultural Research
Pest Management Science | Year: 2011

Background: Sterol 14α-demethylation inhibitors (DMIs) have been widely used in many European countries to control septoria leaf blotch, which is caused by Mycosphaerella graminicola (Fückel) J Schrot (anamorph Septoria tritici Berk & MA Curtis). However, treatment efficacy has declined, and significant shifts in population susceptibility have occurred in recent years, with the isolation of particularly highly resistant strains from French, English and Irish populations. The present aim was to determine the phenotypic characteristics of these field isolates and to identify the possible resistance mechanisms.Results: Target alteration, linked to 11 possible changes in the gene encoding 14α-demethylase (Cyp51), was the basic resistance mechanism in weakly, moderately and highly resistant strains. Changes in Cyp51 combined with the overexpression of drug efflux transporters probably result in multidrug resistance in some of the most resistant phenotypes. Finally, some moderately or highly resistant isolates were found to harbour an insertion in the Cyp51 promoter and/or new combinations of known mutations in the target gene.Conclusion: An updated overview of M. graminicola field strains displaying low to high resistance to DMIs is provided here. The management of field resistance and efficacy should be adapted to take these findings into account. © 2010 Society of Chemical Industry.

Sauviac L.,French National Institute for Agricultural Research | Bruand C.,French National Institute for Agricultural Research
Journal of Bacteriology | Year: 2014

The EcfG-type sigma factor RpoE2 is the regulator of the general stress response in Sinorhizobium meliloti. RpoE2 activity is negatively regulated by two NepR-type anti-sigma factors (RsiA1/A2), themselves under the control of two anti-anti-sigma factors (RsiB1/B2) belonging to the PhyR family of response regulators. The current model of RpoE2 activation suggests that in response to stress, RsiB1/B2 are activated by phosphorylation of an aspartate residue in their receiver domain. Once activated, RsiB1/B2 become able to interact with the anti-sigma factors and release RpoE2, which can then associate with the RNA polymerase to transcribe its target genes. The purpose of this work was to identify and characterize proteins involved in controlling the phosphorylation status of RsiB1/B2. Using in vivo approaches, we show that the putative histidine kinase encoded by the rsiC gene (SMc01507), located downstream from rpoE2, is able to both positively and negatively regulate the general stress response. In addition, our data suggest that the negative action of RsiC results from inhibition of RsiB1/B2 phosphorylation. From these observations, we propose that RsiC is a bifunctional histidine kinase/phosphatase responsible for RsiB1/B2 phosphorylation or dephosphorylation in the presence or absence of stress, respectively. Two proteins were previously proposed to control PhyR phosphorylation in Caulobacter crescentus and Sphingomonas sp. strain FR1. However, these proteins contain a Pfam: HisKA_2 domain of dimerization and histidine phosphotransfer, whereas S. meliloti RsiC harbors a Pfam:HWE_HK domain instead. Therefore, this is the first report of an HWE_HK-containing protein controlling the general stress response in Alphaproteobacteria. © 2014, American Society for Microbiology.

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.

Simon A.,French National Institute for Agricultural Research | Biot E.,French National Institute for Agricultural Research
Bioinformatics | Year: 2010

Summary: ANAIS is a user-friendly web-based tool for the processing of NimbleGen expression data. The interface reads single-channel microarray files generated by NimbleGen platforms and produces easily interpretable graphical and numerical results. It provides biologists six turnkey analysis modules-normalization, probe to gene, quality controls, differential expression, detection, queries and clustering-to explore quickly, freely and without the need for computer programming, NimbleGen transcriptome data. © The Author 2010. Published by Oxford University Press. All rights reserved.

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.

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.

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.

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).

Macek B.,University of Tübingen | 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.

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.

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.

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.

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.

Tardieu F.,French National Institute for Agricultural Research | Granier C.,French National Institute for Agricultural Research | Muller B.,French National Institute for Agricultural Research
Current Opinion in Plant Biology | Year: 2011

Water deficit affects plant growth via reduced carbon accumulation, cell number and tissue expansion. We review the ways in which these processes are co-ordinated. Tissue expansion and its sensitivity to water deficit may be the most crucial process, involving tight co-ordination between the mechanisms which govern cell wall mechanical properties and plant hydraulics. The analyses of sensitivities, time constants and genetic correlations suggest that tissue expansion is loosely co-ordinated with cell division and carbon accumulation which may have limited direct effects on growth under water deficit. We therefore argue for essentially uncoupled mechanisms with feedbacks between them, rather than for a co-ordinated re-programming of all processes. Consequences on plant modelling and plant breeding in dry environment are discussed. © 2011 Elsevier Ltd.

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.

Wolf S.,French National Institute for Agricultural Research | Hematy K.,French National Institute for Agricultural Research | Hofte H.,French National Institute for Agricultural Research
Annual Review of Plant Biology | Year: 2012

Plant cell walls have the remarkable property of combining extreme tensile strength with extensibility. The maintenance of such an exoskeleton creates nontrivial challenges for the plant cell: How can it control cell wall assembly and remodeling during growth while maintaining mechanical integrity? How can it deal with cell wall damage licted by herbivores, pathogens, or abiotic stresses? These processes likely require mechanisms to keep the cell ormed about the status of the cell wall. In yeast, a cell wall integrity (CWI) signaling pathway has been described in great detail; in plants, the existence of CWI signaling has been demonstrated, but little is known about the signaling pathways involved. In this review, we first describe cell wall-related processes that may require or can be targets of CWI signaling and then discuss our current understanding of CWI signaling pathways and future prospects in this emerging field of plant biology. © 2012 by Annual Reviews. All rights reserved.

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.

Murray J.A.H.,University of Cardiff | Jones A.,University of Cardiff | Godin C.,French National Institute for Agricultural Research | Traas J.,French National Institute for Agricultural Research
Plant Cell | Year: 2012

The shoot apical meristem (SAM) is a small population of stem cells that continuously generates organs and tissues. This review covers our current understanding of organ initiation by the SAM in Arabidopsis thaliana. Meristem function and maintenance involves two major hormones, cytokinins and auxins. Cytokinins appear to play a major role in meristem maintenance and in controlling meristematic properties, such as cell proliferation. Self-organizing transport processes, which are still only partially understood, lead to the patterned accumulation of auxin at particular positions, where organs will grow out. A major downstream target of auxin-mediated growth regulation is the cell wall, which is a determinant for both growth rates and growth distribution, but feedbacks with metabolism and the synthetic capacity of the cytoplasm are crucial as well. Recent work has also pointed at a potential role of mechanical signals in growth coordination, but the precise mechanisms at work remain to be elucidated. © 2012 American Society of Plant Biologists. All rights reserved.

Deslandes L.,French National Institute for Agricultural Research | Deslandes L.,French National Center for Scientific Research | Rivas S.,French National Institute for Agricultural Research | Rivas S.,French National Center for Scientific Research
Trends in Plant Science | Year: 2012

To suppress plant defense responses and favor the establishment of disease, phytopathogenic bacteria have gained the ability to deliver effector molecules inside host cells through the type III secretion system. Inside plant cells, bacterial effector proteins may be addressed to different subcellular compartments where they are able to manipulate a variety of host cellular components and molecular functions. Here we review how the recent identification and functional characterization of plant components targeted by bacterial effectors, as well as the discovery of new pathogen recognition capabilities evolved in turn by plant cells, have significantly contributed to further our knowledge about the intricate molecular interactions that are established between plants and their invading bacteria. © 2012 Elsevier 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.

Leroy G.,Agro ParisTech | 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.

Soussana J.-F.,French National Institute for Agricultural Research | Lemaire G.,French National Institute for Agricultural Research
Agriculture, Ecosystems and Environment | Year: 2014

The C sequestration capacity of grassland soils depends on both the net primary production of the ecosystem that determines the C flows from atmosphere to vegetation and soil, and on the mean residence time of C within the different compartments. Within grassland ecosystems, C and N cycles are strongly coupled by elemental stoichiometry of plant autotrophy and of soil microbial heterotrophy. Plasticity in plant form and function, plant species diversity and regulation of biological N fixation all contribute to stabilize the C:N ratio of organic matter inputs to soil. Soil processes such as the priming effect and nitrate leaching tend to restore stoichiometry by releasing elements in excess. Nevertheless, domestic herbivores tend to uncouple the C and N cycles, by releasing digestible C as CO2 and CH4, and by returning digestible N at high concentrations in urine patches. At low stocking density, herbivores enhance soil N cycling and net primary productivity, leading to an increased soil C sequestration, which however declines at high stocking density. Assuming no overgrazing, the environmental impacts of grassland intensification are therefore controlled by a trade-off between increased C-N coupling by vegetation and increased C-N decoupling by animals. Stimulation of vegetation by adequate N and P fertilizer applications increases the C flows from the atmosphere to the soil, while increasing stocking density reduces mean C residence time within the system.Intensification of grassland productivity by manipulation of both primary production and stocking density leads to complex responses in terms of environmental impacts: as intensification increases, positive impacts, such as C sequestration are progressively impaired by negative impacts linked to excessive active N forms. Hence, in each unique environmental setting, a threshold level of grassland intensification can be determined above which any additional animal production would be associated with unacceptable environmental risks. Improved grassland management and integration with crop systems may help minimize the harmful environmental effects of C-N decoupling by domestic herbivores, thereby enhancing synergies among food production, biodiversity and various other ecosystem services. © 2013 Elsevier B.V.

Lalles J.-P.,French National Institute for Agricultural Research
Nutrition Reviews | Year: 2010

The diverse nature of intestinal alkaline phosphatase (IAP) functions has remained elusive, and it is only recently that four additional major functions of IAP have been revealed. The present review analyzes the earlier literature on the dietary factorsmodulating IAP activity in light of these new findings. IAP regulates lipid absorption across the apical membrane of enterocytes, participates in the regulation of bicarbonate secretion and of duodenal surface pH, limits bacterial transepithelial passage, and finally controls bacterial endotoxin-induced inflammation by dephosphorylation, thus detoxifying intestinal lipopolysaccharide. Many dietary components, including fat, protein, and carbohydrate, modulate IAP expression or activity and may be combined to sustain a high level of IAP activity. In conclusion, IAP has a pivotal role in intestinal homeostasis and its activity could be increased through the diet. This is especially true in pathological situations (e.g., inflammatory bowel diseases) in which the involvement of commensal bacteria is suspected and when intestinal AP is too low to detoxify a sufficient amount of bacterial lipopolysaccharide. © 2010 International Life Sciences Institute.

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.

Fameau A.-L.,French National Institute for Agricultural Research | Arnould A.,French National Institute for Agricultural Research | Saint-Jalmes A.,Rennes Institute of Physics
Current Opinion in Colloid and Interface Science | Year: 2014

Fatty acids are anionic surfactants under their deprotonated forms. They are surfactants with both biodegrability and low toxicity. Fatty acid molecules can self-assemble under various shapes in an aqueous solution. These self-assembled structures can respond to stimuli such as pH, CO2 and temperature due to changes occurring at the molecular level. These specificities make them surfactants of special interest to tune the properties at a macroscopic scale. The aim of this article is to review the recent advances in the creation and in the understanding of responsive self-assemblies obtained from fatty acid molecules in an aqueous solution. The links between the microscopic, mesoscopic and macroscopic scales are described. The alkyl chain melting phenomenon triggered by temperature at the molecular level leading to thermoresponsive interfaces and foams at the macroscopic scale is highlighted. © 2014 Elsevier Ltd.

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.

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.

Lasselin J.,French National Institute for Agricultural Research | Capuron L.,French National Institute for Agricultural Research
NeuroImmunoModulation | Year: 2014

The ability of cytokines to influence cerebral functions and to induce the development of behavioral alterations is well established in conditions of acute or chronic high-grade activation of the innate immune system. Recent evidence suggests that the release of these immune mediators during chronic low-grade endogenous inflammatory processes may also contribute to the development of behavioral alterations. Metabolic disorders, including obesity, type 2 diabetes and the metabolic syndrome, represent examples of those conditions which are both characterized by a chronic low-grade inflammatory state and an increased prevalence of behavioral disorders. In metabolic disorders, the increased production of acute-phase proteins and cytokines (e.g. C-reactive protein, interleukin-6 and tumor necrosis factor-α), but at relatively low levels, may promote and contribute to the development of behavioral symptoms, including depressive symptoms, cognitive impairment, fatigue, sleep problems and pain. This hypothesis is supported by a growing literature referring both to experimental and clinical findings that will be reviewed here. © 2014 S. Karger AG, Basel.

Renier S.,French National Institute for Agricultural Research | Hebraud M.,French National Institute for Agricultural Research | Desvaux M.,French National Institute for Agricultural Research
Environmental Microbiology | Year: 2011

The opportunistic and facultative intracellular pathogenic bacterium Listeria monocytogenes causes a rare but severe foodborne disease called listeriosis, the outcome of which can be fatal. The infection cycle and key virulence factors are now well characterized in this species. Nonetheless, this knowledge has not prevented the re-emergence of listeriosis, as recently reported in several European countries. Listeria monocytogenes is particularly problematic in the food industry since it can survive and multiply under conditions frequently used for food preservation. Moreover, this foodborne pathogen also forms biofilms, which increase its persistence and resistance in industrial production lines, leading to contamination of food products. Significant differences have been reported regarding the ability of different isolates to form biofilms, but no clear correlation can be established with serovars or lineages. The architecture of listerial biofilms varies greatly from one strain to another as it ranges from bacterial monolayers to the most recently described network of knitted chains. While the role of polysaccharides as part of the extracellular matrix contributing to listerial biofilm formation remains elusive, the importance of eDNA has been demonstrated. The involvement of flagella in biofilm formation has also been pointed out, but their exact role in the process remains to be clarified because of conflicting results. Two cell-cell communication systems LuxS and Agr have been shown to take part in the regulation of biofilm formation. Several additional molecular determinants have been identified by functional genetic analyses, such as the (p)ppGpp synthetase RelA and more recently BapL. Future directions and questions about the molecular mechanisms of biofilm formation in L. monocytogenes are further discussed, such as correlation between clonal complexes as revealed by MLST and biofilm formation, the swarming over swimming regulation hypothesis regarding the role of the flagella, and the involvement of microbial surface components recognizing adhesive matrix molecules in the colonization of abiotic and biotic surfaces. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

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.

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.

Gough C.,French National Institute for Agricultural Research | Cullimore J.,French National Institute for Agricultural Research
Molecular Plant-Microbe Interactions | Year: 2011

The arbuscular mycorrhizal (AM) and the rhizobia-legume (RL) root endosymbioses are established as a result of signal exchange in which there is mutual recognition of diffusible signals produced by plant and microbial partners. It was discovered 20 years ago that the key symbiotic signals produced by rhizobial bacteria are lipo-chitooligosaccharides (LCO), called Nod factors. These LCO are perceived via lysin-motif (LysM) receptors and activate a signaling pathway called the common symbiotic pathway (CSP), which controls both the RL and the AM symbioses. Recent work has established that an AM fungus, Glomus intraradices, also produces LCO that activate the CSP, leading to induction of gene expression and root branching in Medicago truncatula. These Myc-LCO also stimulate mycorrhization in diverse plants. In addition, work on the nonlegume Parasponia andersonii has shown that a LysM receptor is required for both successful mycorrhization and nodulation. Together these studies show that structurally related signals and the LysM receptor family are key components of both nodulation and mycorrhization. LysM receptors are also involved in the perception of chitooligosaccharides (CO), which are derived from fungal cell walls and elicit defense responses and resistance to pathogens in diverse plants. The discovery of Myc-LCO and a LysM receptor required for the AM symbiosis, therefore, not only raises questions of how legume plants discriminate fungal and bacterial endosymbionts but also, more generally, of how plants discriminate endosymbionts from pathogenic microorganisms using structurally related LCO and CO signals and of how these perception mechanisms have evolved. © 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.

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.

Baeza E.,French National Institute for Agricultural Research | Le Bihan-Duval E.,French National Institute for Agricultural Research
Animal | Year: 2013

Divergent selection of chickens for low or high abdominal fat (AF) but similar BW at 63 days of age was undertaken in 1977. The selection programme was conducted over seven successive generations. The difference between lines was then maintained constant at about twice the AF in the fat line as in the lean line. The aims of the first studies on these divergent chicken lines were to describe the growth, body composition and reproductive performance in young and adult birds. The lines were then used to improve the understanding of the relationship between fatness and energy and protein metabolism in the liver, muscle and adipose tissues, as well as the regulation of such metabolism at hormonal, gene and hypothalamic levels. The effects on muscle energy metabolism in relation to meat quality parameters were also described. This paper reviews the main results obtained with these lines. Copyright © The Animal Consortium 2013.

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.

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.

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.

Chun Y.J.,French National Institute for Agricultural Research | van Kleunen M.,University of Bern | Dawson W.,University of Bern
Ecology Letters | Year: 2010

An explanation for successful invasion is that invasive alien species sustain less pressure from natural enemies than co-occurring native species. Using meta-analysis, we examined whether invasive species: incur less damage, exhibit better performance in the presence of enemies, and tolerate damage more than native species. Invasive alien species did not incur less damage than native species overall. The performance of invasive alien species was reduced compared to natives in the presence of enemies, indicating the invasive alien species were less tolerant to damage than native species. However, there was no overall difference in performance of invasive alien and native species with enemies present. The damage and degree of reduction in performance of invasive alien relative to native species did not depend on relatedness to natives. Our results suggest aliens may not always experience enemy release, and enemy release may not always result in greater plant performance. © 2010 Blackwell Publishing Ltd/CNRS.

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.

Morris C.E.,French National Institute for Agricultural Research | Monteil C.L.,French National Institute for Agricultural Research | Berge O.,French National Institute for Agricultural Research
Annual Review of Phytopathology | Year: 2013

The description of the ecology of Pseudomonas syringae is moving away from that of a ubiquitous epiphytic plant pathogen to one of a multifaceted bacterium sans frontières in fresh water and other ecosystems linked to the water cycle. Discovery of the aquatic facet of its ecology has led to a vision of its life history that integrates spatial and temporal scales spanning billions of years and traversing catchment basins, continents, and the planet and that confronts the implication of roles that are potentially conflicting for agriculture (as a plant pathogen and as an actor in processes leading to rain and snowfall). This new ecological perspective has also yielded insight into epidemiological phenomena linked to disease emergence. Overall, it sets the stage for the integration of more comprehensive contexts of ecology and evolutionary history into comparative genomic analyses to elucidate how P. syringae subverts the attack and defense responses of the cohabitants of the diverse environments it occupies. © Copyright ©2013 by Annual Reviews. All rights reserved.

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.

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.

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.

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.

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.

Guesnet P.,French National Institute for Agricultural Research | Alessandri J.-M.,French National Institute for Agricultural Research
Biochimie | Year: 2011

The accretion of docosahexaenoic acid (DHA) in membranes of the central nervous system is required for the optimum development of retina and brain functions. DHA status is determined by the dietary intake of n-3 polyunsaturated fatty acids (PUFA), both the metabolic precursor α-linolenic acid (α-LNA) and DHA. Clinical studies have shown that feeding term or premature infants with formula low in total n-3 PUFA may alter the maturation of visual acuity. Moreover, feeding infants over the first 6 mon of life with formula containing adequate α-LNA, but no DHA, did not sustain the same cerebral accretion of DHA as that of breast-fed infants. Whether lower DHA accretion in brain of formula-fed term infants impairs neurophysiological performances is not clearly established. Contradictory data have been published, possibly owing to confounding factors such as maternal intakes and/or genetic variations in PUFA metabolism. Nevertheless, a large corpus of data is in favor of the recommendation of regular dietary intakes of DHA (during at least the first 6 mon of life) and suggest that DHA should be added in formulas at the level generally found in human milk (0.2-0.3 wt% of total fatty acids). The maternal intake of n-3 PUFA during pregnancy and lactation is also crucial, since the n-3 PUFA are provided during perinatal development through placental transfer and maternal milk, which determines the DHA status of the newborn and consequently impacts on post-natal development of brain and visual functions. Whether more clinical studies are needed to control and improve the impact of DHA maternal intakes on the progeny's neurodevelopment, several commissions recommended by precaution that DHA average intake for pregnant and lactating women should be of 200-300 mg/day. 2009 Elsevier Masson SAS. All rights reserved.

Haeussler M.,French National Institute for Agricultural Research | Joly J.-S.,French National Institute for Agricultural Research
Developmental Biology | Year: 2011

A major prerequisite for the investigation of tissue-specific processes is the identification of cis-regulatory elements. No generally applicable technique is available to distinguish them from any other type of genomic non-coding sequence. Therefore, researchers often have to identify these elements by elaborate in vivo screens, testing individual regions until the right one is found. Here, based on many examples from the literature, we summarize how functional enhancers have been isolated from other elements in the genome and how they have been characterized in transgenic animals. Covering computational and experimental studies, we provide an overview of the global properties of cis-regulatory elements, like their specific interactions with promoters and target gene distances. We describe conserved non-coding elements (CNEs) and their internal structure, nucleotide composition, binding site clustering and overlap, with a special focus on developmental enhancers. Conflicting data and unresolved questions on the nature of these elements are highlighted. Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communities and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers. The review is accompanied by a list of general guidelines for such a project. © 2010 Elsevier Inc.

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.

Vieux F.,Aix - Marseille University | Soler L.-G.,French National Institute for Agricultural Research | Touazi D.,French National Institute for Agricultural Research | Darmon N.,Aix - Marseille University | Darmon N.,French Institute of Health and Medical Research
American Journal of Clinical Nutrition | Year: 2013

Background: Healthy diets are supposed to be more environmentally friendly because they rely mainly on plant-based foods, which have lower greenhouse gas emissions (GHGEs) per unit weight than do animal-based foods. Objectives: The objectives were to estimate the GHGEs associated with the consumption of self-selected diets in France and to analyze their relation with the nutritional quality of diets. Design: For each adult in the national dietary Individual and National Survey on Food Consumption (n = 1918), the GHGEs of his or her diet were estimated based on the GHGEs of 391 foods. Highestnutritional- quality diets were defined as those having simultaneously 1) an energy density below the median, 2) a mean adequacy ratio (MAR) above the median, and 3) a mean excess ratio (MER, percentage of maximum recommended values for nutrients for which intake should be limited) below the median. Results: MAR was positively correlated and MER was negatively correlated with diet-related GHGEs. High-nutritional-quality diets contained more plant-based foods, notably fruit and vegetables, and fewer sweets and salted snacks than did low-quality diets. After adjustment for age, sex, and energy intake, the consumption of sweets and salted snacks was negatively correlated with diet-related GHGEs, whereas the consumption of animal products and of fruit and vegetables was positively associated with them. After adjustment for energy intake, high-nutritional- quality diets had significantly higher GHGEs (+9% and +22% for men and women, respectively) than did lownutritional- quality diets. Conclusion: Despite containing large amounts of plant-based foods, self-selected diets of the highest nutritional quality are currently not those with the lowest diet-related GHGEs. © 2013 American Society for Nutrition.

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.

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.

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.

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.

Bourlieu C.,French National Institute for Agricultural Research | Michalski M.-C.,French National Institute for Agricultural Research
Current Opinion in Clinical Nutrition and Metabolic Care | Year: 2015

PURPOSE OF REVIEW: The complex biochemical composition and physical structure of the milk fat globule (MFG) are presented as a basis for its paradoxical metabolic fate: MFG is a rapid conveyor of energy through its triacylglycerol (TAG) core but contains some low-digestible bioactive complex lipids and proteins, which influence lipid metabolism and contribute to intestinal and systemic health. RECENT FINDINGS: MFG structure modulates gastrointestinal lipolysis, postprandial lipemia and even the postprandial fate of ingested fatty acids. Proof-of-concept of the nutritional programming induced by early consumption of an emulsion biomimetic of MFG compared with a typical infant formula was published in an animal model (mice). The metabolic response to a high-fat diet during adulthood was improved following neonatal exposure to the biomimetic emulsion. SUMMARY: MFG TAG are tailored with a unique regiodistribution delivering in priority short to medium-chain fatty acids in gastric phase, an important amount of quickly metabolizable oleic acid and protecting palmitic acid in sn-2 position. MFG digestion may not only trigger rapid TAG and chylomicron plasma peaks with fast clearance but also the luminal release of nonhydrolysable bioactive compounds (glycosylated compounds and sphingomyelin), which contribute to intestinal and systemic health by shaping the microbiota and modulating the immune system. These bioactive compounds form self-assembled structures, protect specific micronutrients and lower cholesterol absorption. The health benefits of MFG consumption or of some of its fractions (MFGM) under specific structures are steadily being demonstrated with still much unsolved questions especially for populations with high nutritional needs (e.g. elderly, infants). Copyright © 2015 Wolters Kluwer Health, Inc. All rights reserved.

Fardet A.,French National Institute for Agricultural Research | Boirie Y.,French National Institute for Agricultural Research
Nutrition Reviews | Year: 2014

Associations between food and beverage groups and the risk of diet-related chronic disease (DRCD) have been the subject of intensive research in preventive nutrition. Pooled/meta-analyses and systematic reviews (PMASRs) aim to better characterize these associations. To date, however, there has been no attempt to synthesize all PMASRs that have assessed the relationship between food and beverage groups and DRCDs. The objectives of this review were to aggregate PMASRs to obtain an overview of the associations between food and beverage groups (n=17) and DRCDs (n=10) and to establish new directions for future research needs. The present review of 304 PMASRs published between 1950 and 2013 confirmed that plant food groups are more protective than animal food groups against DRCDs. Within plant food groups, grain products are more protective than fruits and vegetables. Among animal food groups, dairy/milk products have a neutral effect on the risk of DRCDs, while red/processed meats tend to increase the risk. Among beverages, tea was the most protective and soft drinks the least protective against DRCDs. For two of the DRCDs examined, sarcopenia and kidney disease, no PMASR was found. Overweight/obesity, type 2 diabetes, and various types of cardiovascular disease and cancer accounted for 289 of the PMASRs. There is a crucial need to further study the associations between food and beverage groups and mental health, skeletal health, digestive diseases, liver diseases, kidney diseases, obesity, and type 2 diabetes. © 2014 International Life Sciences Institute.

Blanchoin L.,French National Institute for Agricultural Research | Blanchoin L.,University Pierre and Marie Curie | Blanchoin L.,French National Center for Scientific Research | Boujemaa-Paterski R.,French National Institute for Agricultural Research | And 8 more authors.
Physiological Reviews | Year: 2014

Tight coupling between biochemical and mechanical properties of the actin cytoskeleton drives a large range of cellular processes including polarity establishment, morphogenesis, and motility. This is possible because actin filaments are semi-flexible polymers that, in conjunction with the molecular motor myosin, can act as biological active springs or "dashpots" (in laymen's terms, shock absorbers or fluidizers) able to exert or resist against force in a cellular environment. To modulate their mechanical properties, actin filaments can organize into a variety of architectures generating a diversity of cellular organizations including branched or crosslinked networks in the lamellipodium, parallel bundles in filopodia, and antiparallel structures in contractile fibers. In this review we describe the feedback loop between biochemical and mechanical properties of actin organization at the molecular level in vitro, then we integrate this knowledge into our current understanding of cellular actin organization and its physiological roles. © 2014 the American Physiological Society.

Cerf-Bensussan N.,University of Paris Descartes | Cerf-Bensussan N.,French National Institute for Agricultural Research | Gaboriau-Routhiau V.,University of Paris Descartes | Gaboriau-Routhiau V.,French National Institute for Agricultural Research
Nature Reviews Immunology | Year: 2010

The mammalian intestine is home to a complex community of trillions of bacteria that are engaged in a dynamic interaction with the host immune system. Determining the principles that govern host-microbiota relationships is the focus of intense research. Here, we describe how the intestinal microbiota is able to influence the balance between pro-inflammatory and regulatory responses and shape the host's immune system. We suggest that improving our understanding of the intestinal microbiota has therapeutic implications, not only for intestinal immunopathologies but also for systemic immune diseases. © 2010 Macmillan Publishers Limited. All rights reserved.

Etile F.,French National Institute for Agricultural Research | Jones A.M.,University of York
Journal of Health Economics | Year: 2011

Post-war expansion of education in France transformed the distribution of schooling for the cohorts born between the 1940s and the 1970s. However, throughout this expansion the proportion with the highest levels of qualifications remained stable, providing a natural control group. We evaluate the impact of schooling on smoking, for the beneficiaries of the post-war expansion, by comparing changes in their outcomes across birth cohorts with changes within the control group. We uncover robust evidence that educational expansion contributed to a decline in smoking prevalence of 2.9 points of percentage for men and 3.2 points for women at the turn of the 21st century. Our results also suggest that the persistence of the schooling-smoking gradient is better explained by differences in the education-related opportunity costs of smoking than by differences in information about smoking dangers. © 2011 Elsevier B.V.

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.

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.

Millock K.,Paris-Sorbonne University | Nauges C.,French National Institute for Agricultural Research
Environmental and Resource Economics | Year: 2010

Using survey data of around 10,000 households from 10 OECD countries, we identify the driving factors of household adoption of water-efficient equipment by estimating Probit models of a household's probability to invest in such equipment. The results indicate that environmental attitudes and ownership status are strong predictors of adoption of water-efficient equipment. In terms of policy, we find that households that were both metered and charged for their water individually had a much higher probability to invest in water-efficient equipment compared to households that paid a flat fee. © 2010 Springer Science+Business Media B.V.

Villard P.,Institut Universitaire de France | Malausa T.,French National Institute for Agricultural Research
Molecular Ecology Resources | Year: 2013

SP-Designer is an open-source program providing a user-friendly tool for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. SP-Designer selects PCR primer pairs for the amplification of DNA from a target species on the basis of several criteria: (i) primer specificity, as assessed by interspecific sequence polymorphism in the annealing regions, (ii) the biochemical characteristics of the primers and (iii) the intended PCR conditions. SP-Designer generates tables, detailing the primer pair and PCR characteristics, and a FASTA file locating the primer sequences in the original sequence alignment. SP-Designer is Windows-compatible and freely available from http://www2.sophia.inra.fr/urih/sophia_mart/sp_designer/info_sp_designer.php. © 2013 John Wiley & Sons Ltd.

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.

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.

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.

Pauloin A.,French National Institute for Agricultural Research | Chanat E.,French National Institute for Agricultural Research
Biochimica et Biophysica Acta - Molecular Cell Research | Year: 2012

The aim of the present study is to estimate the role played by cortisol, prolactin (PRL) and epidermal growth factor (EGF) in the synthesis of adipocyte differentiation-related protein (ADRP) as compared to the well-studied regulation of[U+F020] β-casein synthesis by these hormones in the mammary epithelial cell line HC11. This comparison between a cytoplasmic lipid droplet-associated protein, which is strictly specific to both lipid accumulation and secretion by lactating mammary epithelial cells, and an archetypal milk protein is useful for evaluating the extent to which a mechanistic relationship exists between biosynthesis, transport and secretion of these two major milk components. We found that cortisol inhibits PRL-stimulated ADRP synthesis, as opposed to its known stimulating effect on β-casein synthesis. The involvement of PRL and EGF in ADRP synthesis was explored by means of a battery of inhibitors. The Jak2 inhibitor AG490 provoked a stimulation of ADRP synthesis whereas it totally suppressed that of β-casein. The use of AG1478, a specific inhibitor of EGF receptor phosphorylation, or of PD98059, a specific MEK inhibitor, revealed that the Ras/Raf/MEK/ERK1/2 pathway has no significant influence on ADRP levels. Inhibition of JNK was also ineffective. In contrast, incubation of the cells with SB 203580, a specific inhibitor of p38, slightly stimulated ADRP synthesis and induced a proportional dose-response inhibition of PRL-induced β-casein synthesis. Finally, cell treatment with wortmannin or LY294002 revealed that both PRL and EGF positively regulate ADRP and β-casein synthesis through PI3-kinase signaling. Because both the Akt inhibitor MK-2206 and the mTOR inhibitor rapamycin provoked a strong diminution of PRL-induced synthesis of the two proteins, and because oleate induced phosphorylation of Akt, we concluded that, in the mammary epithelial cell line HC11, the PI3-kinase/Akt/mTOR signaling pathway strongly participates in β-casein synthesis and is a main regulator of ADRP expression. © 2012 Elsevier B.V..

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.

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.

Treich N.,French National Institute for Agricultural Research
Journal of Environmental Economics and Management | Year: 2010

The paper shows that ambiguity aversion increases the value of a statistical life if the marginal utility of an increase in wealth is larger if one is alive rather than dead. Intuitively, ambiguity aversion has a similar effect as an increase in the perceived baseline mortality risk, and thus operates as the "dead anyway" effect. A numerical example suggests, however, that ambiguity aversion cannot justify the substantial "ambiguity premium" apparently embodied in environmental policy-making. The paper also shows that ambiguity aversion decreases the marginal cost of individual self-protection effort but may well decrease its marginal benefit, so that the total effect of ambiguity aversion on self-protection is unclear. © 2009 Elsevier Inc. All rights reserved.

Flutre T.,University of Chicago | Flutre T.,French National Institute for Agricultural Research | Wen X.,University of Michigan | Pritchard J.,University of Chicago | And 2 more authors.
PLoS Genetics | Year: 2013

Mapping expression Quantitative Trait Loci (eQTLs) represents a powerful and widely adopted approach to identifying putative regulatory variants and linking them to specific genes. Up to now eQTL studies have been conducted in a relatively narrow range of tissues or cell types. However, understanding the biology of organismal phenotypes will involve understanding regulation in multiple tissues, and ongoing studies are collecting eQTL data in dozens of cell types. Here we present a statistical framework for powerfully detecting eQTLs in multiple tissues or cell types (or, more generally, multiple subgroups). The framework explicitly models the potential for each eQTL to be active in some tissues and inactive in others. By modeling the sharing of active eQTLs among tissues, this framework increases power to detect eQTLs that are present in more than one tissue compared with "tissue-by-tissue" analyses that examine each tissue separately. Conversely, by modeling the inactivity of eQTLs in some tissues, the framework allows the proportion of eQTLs shared across different tissues to be formally estimated as parameters of a model, addressing the difficulties of accounting for incomplete power when comparing overlaps of eQTLs identified by tissue-by-tissue analyses. Applying our framework to re-analyze data from transformed B cells, T cells, and fibroblasts, we find that it substantially increases power compared with tissue-by-tissue analysis, identifying 63% more genes with eQTLs (at FDR = 0.05). Further, the results suggest that, in contrast to previous analyses of the same data, the majority of eQTLs detectable in these data are shared among all three tissues. © 2013 Flutre et al.

Desneux N.,University of Minnesota | Desneux N.,French National Institute for Agricultural Research | Blahnik R.,University of Minnesota | Delebecque C.J.,Harvard University | Heimpel G.E.,University of Minnesota
Ecology Letters | Year: 2012

Ecology Letters (2012) 15: 453-460 The host range of insect parasitoids and herbivores is influenced by both preference-related traits which mediate host choice behaviour, and performance-related traits which mediate the physiological suitability of the consumer-resource interaction. In a previous study, we characterised the influence of preference- and performance-related traits on the host range of the aphid parasitoid Binodoxys communis (Hymenoptera: Braconidae) and herein we build upon those data sets by mapping a series of these traits onto the phylogeny of the (aphid) host species. We found a strong effect of host phylogeny on overall parasitoid reproduction on the 20 host species tested, but no effect of the phylogeny of host plants of the aphids. We found an effect of aphid phylogeny on host acceptance and sting rates (related to preference) from behavioural observations and for pupal survivorship (related to performance), showing that both classes of traits show phylogenetic conservatism with respect to host species. © 2012 Blackwell Publishing Ltd/CNRS.

Cresswell J.E.,University of Exeter | Desneux N.,French National Institute for Agricultural Research | vanEngelsdorp D.,Pennsylvania State University
Pest Management Science | Year: 2012

Background: Honey bees are important pollinators of both crops and wild plants. Pesticide regimes that threaten their sustainability should therefore be assessed. As an example, evidence that the agricultural use of neonicotinoid pesticides is a cause of the recently observed declines in honey bees is examined. The aim is to define exacting demographic conditions for a detrimental factor to precipitate a population decline, and Hill's epidemiological 'causality criteria' are employed as a structured process for making an expert judgement about the proposition that trace dietary neonicotinoids in nectar and pollen cause population declines in honey bees. Results: In spite of the absence of decisive experimental results, the analysis shows that, while the proposition is a substantially justified conjecture in the context of current knowledge, it is also substantially contraindicated by a wide variety of circumstantial epidemiological evidence. Conclusion:It is concluded that dietary neonicotinoids cannot be implicated in honey bee declines, but this position is provisional because important gaps remain in current knowledge. Avenues for further investigations to resolve this longstanding uncertainty are therefore identified. © 2012 Society of Chemical Industry.

Collinet C.,French National Institute for Agricultural Research | Lecuit T.,French National Institute for Agricultural Research
Progress in Molecular Biology and Translational Science | Year: 2013

Adherens junctions display dual properties of robustness and plasticity. In multicellular organisms, they support both strong cell-cell adhesion and rapid cell-cell contact remodeling during development and wound healing. The core components of adherens junctions are clusters of cadherin molecules, which mediate cell-cell adhesion through homophilic interactions in trans. Interactions of cadherins with the actin cytoskeleton are essential for providing both stability and plasticity to adherens junctions. Cadherins regulate the turnover of actin by regulating its polymerization and anchor tensile actomyosin networks at the cell cortex. In turn, actin regulates cadherin turnover by regulating its endocytosis and actomyosin networks exert forces driving remodeling of cell-cell contacts. The interplay between adherens junctions and contractile actomyosin networks has striking outcomes during epithelial morphogenesis. Their integrated dynamics result in different morphogenetic patterns shaping tissues and organs. © 2013 Elsevier Inc.

Brusini J.,French National Institute for Agricultural Research | Brusini J.,University of Florida | Robin C.,French National Institute for Agricultural Research | Franc A.,French National Institute for Agricultural Research
Ecology Letters | Year: 2011

In fungi, horizontal transmission of deleterious cytoplasmic elements is reduced by the vegetative incompatibility system. This self/non-self recognition system may select for greater diversity of fungal incompatibility phenotypes in a frequency-dependent manner but the link between the diversity of fungal phenotypes and the virulence of cytoplasmic parasites has been poorly studied. We used an epidemiological model to show that even when transmission between incompatibility types is permitted, parasite pressure can lead to high levels of polymorphism for vegetative incompatibility systems. Moreover, high levels of polymorphism in host populations can select for less virulent cytoplasmic parasites. This feedback mechanism between parasite virulence and vegetative incompatibility system polymorphism of host populations may account for the general avirulence of most known mycoviruses. Furthermore, this mechanism provides a new perspective on the particular ecology and evolution of the host/parasite interactions acting between fungi and their cytoplasmic parasites. © 2011 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.

Le Bissonnais Y.,French National Institute for Agricultural Research
European Journal of Soil Science | Year: 2016

Crusting and erosion of cultivated soils result from aggregate breakdown and the detachment of soil fragments by rain, and the susceptibility of soil to these processes is often inferred from measurements of aggregate stability. Here, theories of aggregate breakdown are reviewed and four main mechanisms (i.e. slaking, breakdown by differential swelling, mechanical breakdown by raindrop impact and physico-chemical dispersion) are defined. Their relative importance depends on the nature of the rain, as well as on the soil's physical and chemical properties. The relations between aggregate breakdown, crusting and water erosion are analysed, and existing methods for the assessment of aggregate stability are reviewed. A unified framework for the measurement of aggregate stability is proposed to assess a soil's susceptibility to crusting and erosion. It combines three treatments having various wetting conditions and energies (fast wetting, slow wetting, and stirring after pre-wetting) and measures the resulting fragment size distribution after each treatment. It is designed to compare different soils, or different climatic conditions for a given soil, not to compare time-dependent changes in that soil. © 2016 British Society of Soil Science.

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.

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.

Federici F.,University of Cambridge | Dupuy L.,James Hutton Institute | Laplaze L.,French National Institute for Agricultural Research | Heisler M.,European Molecular Biology Laboratory | 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.