Showing papers by "Agrocampus Ouest published in 2008"

FactoMineR: An R Package for Multivariate Analysis

Abstract: In this article, we present FactoMineR an R package dedicated to multivariate data analysis. The main features of this package is the possibility to take into account different types of variables (quantitative or categorical), different types of structure on the data (a partition on the variables, a hierarchy on the variables, a partition on the individuals) and finally supplementary information (supplementary individuals and variables). Moreover, the dimensions issued from the different exploratory data analyses can be automatically described by quantitative and/or categorical variables. Numerous graphics are also available with various options. Finally, a graphical user interface is implemented within the Rcmdr environment in order to propose an user friendly package.

Transcriptome profiling of the feeding-to-fasting transition in chicken liver

Abstract: Starvation triggers a complex array of adaptative metabolic responses including energy-metabolic responses, a process which must imply tissue specific alterations in gene expression and in which the liver plays a central role. The present study aimed to describe the evolution of global gene expression profiles in liver of 4-week-old male chickens during a 48 h fasting period using a chicken 20 K oligoarray. A large number of genes were modulated by fasting (3532 genes with a pvalue corrected by Benjamini-Hochberg < 0.01); 2062 showed an amplitude of variation higher than +/- 40% among those, 1162 presented an human ortholog, allowing to collect functional information. Notably more genes were down-regulated than up-regulated, whatever the duration of fasting (16 h or 48 h). The number of genes differentially expressed after 48 h of fasting was 3.5-fold higher than after 16 h of fasting. Four clusters of co-expressed genes were identified by a hierarchical cluster analysis. Gene Ontology, KEGG and Ingenuity databases were then used to identify the metabolic processes associated to each cluster. After 16 h of fasting, genes involved in ketogenesis, gluconeogenesis and mitochondrial or peroxisomal fatty acid beta-oxidation, were up-regulated (cluster-1) whereas genes involved in fatty acid and cholesterol synthesis were down-regulated (cluster-2). For all genes tested, the microarray data was confirmed by quantitative RT-PCR. Most genes were altered by fasting as already reported in mammals. A notable exception was the HMG-CoA synthase 1 gene, which was up-regulated following 16 and 48 h of fasting while the other genes involved in cholesterol metabolism were down-regulated as reported in mammalian studies. We further focused on genes not represented on the microarray and candidates for the regulation of the target genes belonging to cluster-1 and -2 and involved in lipid metabolism. Data are provided concerning PPARa, SREBP1, SREBP2, NR1H3 transcription factors and two desaturases (FADS1, FADS2). This study evidences numerous genes altered by starvation in chickens and suggests a global repression of cellular activity in response to this stressor. The central role of lipid and acetyl-CoA metabolisms and its regulation at transcriptional level are confirmed in chicken liver in response to short-term fasting. Interesting expression modulations were observed for NR1H3, FADS1 and FADS2 genes. Further studies are needed to precise their role in the complex regulatory network controlling lipid metabolism.

Spatial sensitivity of maize gene-flow to landscape pattern: a simulation approach

Abstract: Pollen dispersal is a critical process defining connectivity among plant populations. In the context of genetically modified (GM) crops in conventional agricultural systems, strategies based on spatial separation are promoted to reduce functional connectivity between GM and non-GM crop fields. Field experiments as well as simulation studies have stressed the dependence of maize gene flow on distances between source and receptor fields and on their spatial configuration. However, the influence of whole landscape patterns is still poorly understood. Spatially explicit models, such as MAPOD-maize, are thus useful tools to address this question. In this paper we developed a methodological approach to investigate the sensitivity of cross-pollination rates among GM and non-GM maize in a landscape simulated with MAPOD-maize. The influence of landscape pattern on model output was studied at the landscape and field scales, including interactions with other model inputs such as cultivar characteristics and wind conditions. At the landscape scale, maize configuration (proportion of and spatial arrangement in a given field pattern) was shown to be an important factor influencing cross-pollination rate between GM and non-GM maize whereas the effect of the field pattern itself was lower. At the field scale, distance to the nearest GM maize field was confirmed as a predominant factor explaining cross-pollination rate. The metrics describing the pattern of GM maize in the area surrounding selected non-GM maize fields appeared as pertinent complementary variables. In contrast, field geometry and field pattern resulted in little additional information at this scale.

Sacrifice ratio dispersion within the Euro Zone: what can be learned about implementing a single monetary policy?

Abstract: This article focuses on the comparison of sacrifice ratios as an indicator for structural dispersion within the euro area over the period 1972–2003. Estimates of the sacrifice ratio, defined as the cumulative output cost arising from permanent inflation reduction, are obtained using structural VAR models. Results from sub‐period analysis as well as 10‐year‐period rolling estimates lead to two main conclusions. First, empirical evidence displays a recent increase in the average sacrifice ratio, which can be linked to the simultaneous decrease in the average inflation rate: this negative relationship between the initial level of inflation and the cost of disinflation can be seen as a justification for the choice of an inflation objective close to 2% for the European Central Bank (ECB) rather than a target of perfect price stability, potentially very damaging. Second, we cannot provide evidence of any reduction in European sacrifice ratio dispersion, which would suggest that the nominal convergence triggered...

Systèmes alimentaires territorialisés : les circuits courts comme vecteurs de développement territorial

Abstract: Systemes alimentaires territorialises : les circuits courts comme vecteurs de developpement territorial

European Union’s preferential trade agreements in agricultural sector: a gravity approach

Abstract: The European Union (EU) is the first target market for developing countries’ and Least Developed Countries’ agricultural exports. Preferential trade agreements, either reciprocal or not, play a central role in forming trade opportunities for numerous developing countries. Our objective is to measure the impact of eleven regional trade agreements (RTA) on European agricultural imports with an expanded gravity model. Also, in order to compare these RTAs and their effects we calculate the implied tariff equivalent. Results indicate that a large number of EU’s RTAs support the agricultural exports of developing countries to the EU market. Thus, RTAs are generally an attractive alternative for countries wishing to speed up the move towards multilateral free trade in agriculture. Nevertheless, two most important and unilateral RTAs (Generalized System of Preference expanded by Everything But Arms) and the agreement with Mexico have the negative effect over agricultural exports to EU. We attempt to explain the reasons of their failure.

Efficacité économique de systèmes laitiers herbagers en agriculture durable (RAD) : une comparaison avec le RICA

Abstract: Un echantillon de 74 exploitations du Reseau Agriculture Durable (RAD), specialisees en bovins laitiers, economes et autonomes maximisant le pâturage et pratiquant la reduction d’intrants, est compare a un echantillon de 374 exploitations specialisees bovins lait de l’echantillon RICA. L'analyse fine des resultats economiques moyens met en valeur l'efficacite economique des exploitations du RAD : la reduction de 50% des charges de concentres, d'engrais, de produits phytosanitaires, de semences, permet de degager un resultat courant et une valeur ajoutee superieurs meme si le chargement est legerement inferieur (1,4 au lieu de 1,7 UGB/ha). Ces economies sont realisees grâce au pâturage et aux surfaces fourrageres (prairies d'associations de longue duree). D'autres differences sont soulignees entre les 2 echantillons : une repartition des aides PAC differente, moins d'amortissements et frais financiers, de charges de mecanisation mais plus de charges de main d'œuvre pour les exploitations du RAD… Ces systemes presentent des avantages economiques, sociaux, environnementaux, mais ils ne sont pas forcement transposables. C’est plutot la demarche de recherche d’autonomie et d’efficience du processus de ces agriculteurs qu'il faut chercher a generaliser.

Modélisation du transfert de l'eau et des sels dans les casiers rizicoles du delta du fleuve sénégal

Abstract: La salinisation des sols constitue un risque majeur du developpement de l’irrigation dans le monde. Dans le Delta du Fleuve Senegal, l’existence d’une nappe phreatique salee et proche de la surface du sol accentue ce risque. Une modelisation des transferts hydriques a ete realisee pour mieux evaluer ce risque. Elle a ete faite a partir du code Hydrus sur l’ensemble du cycle cultural et a pris en compte deux types de sol et deux modes de culture de cette region : la simple et la double culture. Elle a permis d’estimer les flux hydriques descendants pendant la phase d’irrigation par submersion, et les flux hydriques et salins ascendants pendant la phase d’irrigation et de non-irrigation. Cette modelisation indique que : i) le toit de la nappe salee remonte d’environ 50 cm pendant la phase d’irrigation; ii) une zone non saturee de faible epaisseur subsiste entre la surface inondee et la nappe; iii) l’infiltration cumulee est deux fois plus forte en double qu’en simple culture; et iv) la forte evaporation durant la phase de non-irrigation peut faire remonter entre 5,5 a 6 t de sels par ha et par an, selon les sols et les conditions de culture. Cette modelisation, qui s’appuie sur des mesures in situ des parametres hydrodynamiques, devra etre confrontee a des observations in situ de flux. Elle devra integrer des processus non pris a ce stade tel que le piegeage d’air. Les releves piezometriques depuis dix ans montrent, par ailleurs, un leger relevement du niveau de la nappe salee. L’ensemble de ces resultats est suffisamment preoccupant pour preconiser, dans le cas d’une irrigation par submersion, la mise en place d’un drainage superficiel pour eviter le relevement de la nappe et assurer l’evacuation des sels hors de la nappe et, par la, la perennisation de l’agriculture dans cette region du Delta du fleuve Senegal

Diversification des activités de pêche en Bretagne : acceptabilité et conditions de développement

Abstract: Le sujet de l'etude « Diversification des activites de peche et de cultures marines en Bretagne : acceptabilite et conditions de developpement » est issu d'une reflexion sur la multifonctionnalite des peches et des cultures marines, menee par le Pole halieutique d'AGROCAMPUS OUEST, en preparation des Assises de la Peche et de l'Aquaculture menees par la Region Bretagne en 2005-2006. Ce rapport presente une synthese des travaux realises dans le cadre de la premiere partie de l'etude portant sur la peche. La majorite des informations contenues sont issues des enquetes et des entretiens realises aupres des professionnels.

Armington elasticities and tariff regime: an application to European Union rice imports

Abstract: Most of the European Union’s (EU) import sources for rice are in developing countries and the least-developed countries (LDCs). The EU has moreover made a commitment to allow duty-free and quota-free access to rice imports originating in the LDCs from September 2009 onward. The purpose of this article is to answer two questions – First: Does the inclusion of import tariffs in the specification lead to different estimated Armington elasticities? Second: When a discriminating tariff is introduced, what happens to the market share of large rice exporters to the EU, especially to the market share of poor countries? Consequently, we present the Armington model, derived from a constant elasticity of substitution (CES) utility function, and a non-homothetic CES utility functional form, which is more flexible. Then, we estimate the Armington model, with and without the inclusion of a tariff, and we compare the elasticities. Lastly, we model five scenarios with different discriminating import tariff rates to calculate the changes in the market access of large rice exporters to the EU. Our empirical results show that it is worthwhile to consider non-homothetic preferences and import tariffs. When the model is estimated, ignoring the import tariffs and the non-homothetic parameter, results may be biased and of uncertain validity. Furthermore the simulation findings demonstrate that in spite of a large difference between import tariff rate of Suriname and other countries (scenario V), its market access would not change greatly. This may be caused by supply side problems like poor infrastructures, weak technology and small capacity production in LDCs.

Assessing the freshwater distribution of yellow eel

Abstract: In the global context of the decline in wild species, modeling the distribution of populations is a crucial aspect of ecological management. This can be a major challenge, especially for species, such as the European eel, that have complex life cycles, exhibit cryptic behavior, or migrate over long distances. A review of the literature suggests that eel size data could be used to assess and analyze freshwater distribution of eel. We argue that analyses based on small yellow eels (≤ 300 mm) along the longitudinal course of rivers could provide a valuable tool for population monitoring. We propose a standardized catchment recruitment index and a colonization index based on the probability of occurrence (presence/absence data) using logistic models for different size classes. The model developed here provides a convenient guide for assessing yellow eel stages in freshwater areas, and should have concrete applications for management of the species.

Economie et politique de la chasse : constat, analyse et idées pour l'action

Abstract: L’article comporte deux parties. La premiere partie donne une explication, en termes d’incitation et de valeur, des inefficacites qui affectent la pratique du loisir chasse et les ressources naturelles qui le supportent. Elle debouche sur une analyse economique des politiques cynegetiques. D'autre part, la gestion des ressources cynegetiques s'inscrivant dans un cadre territorial, il est egalement necessaire de faire appel aux apports de l'economie regionale et territoriale pour expliciter, dans une deuxieme partie, les relations pas toujours evidentes entre ressources cynegetiques et developpement territorial dans un cadre d'analyse global.

La gestion du sanglier : modèle bioéconomique, dégâts agricoles et prix des chasses en forêt

Abstract: Le sanglier est a la fois une ressource et une peste : gibier valorise par les chasseurs et responsable de dommages collectifs, notamment agricoles. La population optimale serait celle correspondant a la maximisation de la richesse collective liee a la presence du sanglier. La valeur collective a maximiser est le flux actualise sur un horizon infini du consentement a payer des chasseurs diminue des dommages agricoles. L’optimum economique compare consentement a payer marginal au dommage marginal en tenant compte de la perte de bienetre d’une reduction des populations supportee par tous les chasseurs. Nous nous sommes servis des donnees sur les degâts agricoles pour reconstruire la dynamique des populations de sanglier. L’analyse des prix des adjudications des chasses en foret domaniale a permis de reveler la demande de chasse au sanglier. Nous avons utilise pour cela la methode des prix hedonistes. Nous avons mis en evidence des differences de consentement a payer marginal selon les departements (entre 80 et 300 €). Plusieurs optima sont calcules, ils ne correspondent pas forcement a ce que l’on observe, mais permettent d’apporter un eclairage sur la politique optimale de conservation ou non des populations de sanglier.

Analyse factorielle multiple de données mixtes : application à la comparaison de deux codages

Abstract: The multiple factor analysis (MFA) is applied to a whole of scale variables considered both as quantitative and qualitative variables. One thus illustrates a way of taking into account these two types of variables simultaneously as active in a factor analysis.

Postgenomic analysis of desiccation tolerance

Abstract: Desiccation tolerance is the capacity to survive complete drying. It is an ancient trait that can be found in prokaryotes, fungi, primitive animals (often at the larval stages), whole plants, pollens and seeds. In the dry state, metabolism is suspended and the duration that anhydrobiotes can survive ranges from years to centuries. Whereas genes induced by drought stress have been successfully enumerated in tissues that are sensitive to cellular desiccation, we have little knowledge as to the adaptive role of these genes in establishing desiccation tolerance at the cellular level. This paper reviews postgenomic approaches in a variety of desiccation tolerant organisms in which the genetic responses have been investigated when they acquire the capacity of tolerating extremes of dehydration or when they are dry. Accumulation of non-reducing sugars, LEA proteins and a coordinated repression of metabolism appear to be the essential and universal attributes that can confer desiccation tolerance. The protective mechanisms of these attributes are described. Furthermore, it is most likely that other mechanisms have evolved since the function of about 30% of the genes involved in desiccation tolerance remains to be elucidated. The question of the overlap between desiccation tolerance and drought tolerance is briefly addressed.

Organisation du contrôle des pêches maritimes en France

Abstract: HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Organisation du contrôle des pêches maritimes en France Marie Lesueur, Nicolas Roncin, Bertrand Le Gallic, Carole Ropars-Collet

Diversification des activités de cultures marines en Bretagne : acceptabilité et conditions de développement

Abstract: Le sujet de l'etude « Diversification des activites de peche et de cultures marines en Bretagne : acceptabilite et conditions de developpement » est issu d'une reflexion sur la multifonctionnalite des peches et des cultures marines menee par le Pole halieutique d'AGROCAMPUS OUEST, en preparation des Assises de la Peche et de l'Aquaculture menees par la Region Bretagne en 2005-2006 (Lesueur, Boude, Le Goffe, 2007).

Including dynamic fishermen behaviour in a fisheries simulation model to assess the impact of environmental changes

Abstract: Vermard, Y., Mahevas, S., Marchal, P., and Thebaud, O. 2008 A fleet dynamic model of the Bay of Biscay pelagic fleet simulating metiers’ choice. Canadian Journal of Fisheries and Aquatic Sciences, In Press. The aim is to obtain a realistic modelling of fishermen adaptative response to spatial management options under various environmental scenarios to enable management assessment. Perspectives Fleet dynamic model simulating metiers choices using Random Utility Model (Model Fit) (Vermard et al. 2008) Prediction of effort reallocation by the fleet in response to the fishing ban in 2005 using RUMs coefficients (Vermard et al. 2008) ifremer ifremer