Thiverval-Grignon, France
Thiverval-Grignon, France

AgroParisTech is a French university-level institution, also known as a "Grande Ecole". It was founded on January 1, 2007, by the merger of three graduate institutes of science and engineering: Institut national agronomique Paris-Grignon , founded in 1826 École nationale du génie rural, des eaux et des forêts , known in English as the French National School of Forestry, established in 1964 École nationale supérieure des industries agricoles et alimentaires , founded in 1893AgroParisTech is a member of the UniverSud Paris and the Paris Institute of Technology . The latter is a consortium of ten graduate institutes of science and engineering.AgroParisTech is also part of 'The Life and Environmental Science and Technology Hub' of the Paris region, together with INRA, Cemagref, AFSSA, the Ecole nationale vétérinaire d'Alfort, and the Versailles National School of Landscape architecture.Leader in life science and agronomy, AgroParisTech is one of the foremost and most prestigious Grandes Ecoles.AgroParisTech is one of the founding members of the Université Paris-Saclay cluster, which will be the largest European multidisciplinary campus. AgroParisTech will consequently be moving to the Plateau de Saclay in 2018. Wikipedia.


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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.


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.


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.


Rigottier-Gois L.,French National Institute for Agricultural Research | Rigottier-Gois L.,Agro ParisTech
ISME Journal | Year: 2013

The healthy intestine is characterized by a low level of oxygen and by the presence of large bacterial communities of obligate anaerobes. Dysbiosis of the gut microbiota has been reported in patients suffering from inflammatory bowel diseases (IBDs), but the mechanisms causing this imbalance remain unknown. Observations have included a decrease in obligate anaerobes of the phylum Firmicutes and an increase in facultative anaerobes, including members of the family Enterobacteriaceae. The shift of bacterial communities from obligate to facultative anaerobes strongly suggests a disruption in anaerobiosis and points to a role for oxygen in intestinal dysbiosis. Proposals to evaluate this hypothesis of a role for oxygen in IBD dysbiosis are provided. If this hypothesis is confirmed, decreasing oxygen in the intestine could open novel means to rebalance the microbiota and could provide novel preventative or therapeutic strategies for IBD patients in whom current treatments are ineffective. © 2013 International Society for Microbial Ecology All rights reserved.


Patent
French Institute of Health, Medical Research, University Paris Est Creteil, Assistance Publique Hopitaux De Paris and Agro ParisTech | Date: 2013-05-07

The present invention relates to methods and compositions for the prevention or treatment of chronic obstructive pulmonary disease.


Moyano F.E.,French National Center for Scientific Research | Manzoni S.,Duke University | Chenu C.,Agro ParisTech
Soil Biology and Biochemistry | Year: 2013

Soil moisture strongly affects the dynamics of soil organic matter and is an important environmental variable in all models predicting changes in soil carbon stocks from site to global scales. Despite this, the mechanisms determining the response of heterotrophic soil respiration to soil moisture remain poorly quantified, being represented in most current carbon cycle models as simple empirical functions. With the aim of providing an overview and new insights into the mechanisms involved, here we review the observations and theory behind the respiration-moisture relationship. We start by calculating best estimates of average empirical relationships using published data and comparing the results for contrasting soil types. The theoretical linkages between substrate and gas diffusivity in soil pores and heterotrophic respiration are then explored as a function of temperature and textural properties. Based on this theoretical model we interpret the variability of moisture effects observed in previous empirical studies. Transient CO2 efflux-moisture relationships are discussed next, reviewing the theory and models developed in the last years with particular emphasis on the 'Birch effect'. We continue by giving an overview of recent pore-scale models and consider how these can be used to gain a more mechanistic understanding of carbon storage and stabilization in variably saturated soils. From this review we conclude that current empirical models are useful but limited approximations, with questionable predictive capacity. Significant efforts are still necessary to represent the full range of soil moisture responses in a unifying model with a sound theoretical basis that can help identify common underlying processes. Equations present here, combining diffusion, texture and substrate to model respiration, are a step forward in this direction. © 2013 Elsevier Ltd.


BACKGROUND: To identify the key elements controlling grain production in maize, it is essential to have an integrated view of the responses to alterations in the main steps of nitrogen assimilation by modification of gene expression. Two maize mutant lines (gln1.3 and gln1.4), deficient in two genes encoding cytosolic glutamine synthetase, a key enzyme involved in nitrogen assimilation, were previously characterized by a reduction of kernel size in the gln1.4 mutant and by a reduction of kernel number in the gln1.3 mutant. In this work, the differences in leaf gene transcripts, proteins and metabolite accumulation in gln1.3 and gln1.4 mutants were studied at two key stages of plant development, in order to identify putative candidate genes, proteins and metabolic pathways contributing on one hand to the control of plant development and on the other to grain production.RESULTS: The most interesting finding in this study is that a number of key plant processes were altered in the gln1.3 and gln1.4 mutants, including a number of major biological processes such as carbon metabolism and transport, cell wall metabolism, and several metabolic pathways and stress responsive and regulatory elements. We also found that the two mutants share common or specific characteristics across at least two or even three of the "omics" considered at the vegetative stage of plant development, or during the grain filling period.CONCLUSIONS: This is the first comprehensive molecular and physiological characterization of two cytosolic glutamine synthetase maize mutants using a combined transcriptomic, proteomic and metabolomic approach. We find that the integration of the three "omics" procedures is not straight forward, since developmental and mutant-specific levels of regulation seem to occur from gene expression to metabolite accumulation. However, their potential use is discussed with a view to improving our understanding of nitrogen assimilation and partitioning and its impact on grain production.


Boccard J.,Agro ParisTech | Rutledge D.N.,Agro ParisTech
Analytica Chimica Acta | Year: 2013

Omics approaches have proven their value to provide a broad monitoring of biological systems. However, as no single analytical technique is sufficient to reveal the full biochemical content of complex biological matrices or biofluids, the fusion of information from several data sources has become a decisive issue. Omics studies generate an increasing amount of massive data obtained from different analytical devices. These data are usually high dimensional and extracting knowledge from these multiple blocks is challenging. Appropriate tools are therefore needed to handle these datasets suitably. For that purpose, a generic methodology is proposed by combining the strengths of established data analysis strategies, i.e. multiple kernel learning and OPLS-DA to offer an efficient tool for the fusion of Omics data obtained from multiple sources. Three real case studies are proposed to assess the potential of the method. A first example illustrates the fusion of mass spectrometry-based metabolomic data acquired in both negative and positive electrospray ionisation modes, from leaf samples of the model plant Arabidopsis thaliana. A second dataset involves the classification of wine grape varieties based on polyphenolic extracts analysed by two-dimensional heteronuclear magnetic resonance spectroscopy. A third case study underlines the ability of the method to combine heterogeneous data from systems biology with the analysis of publicly available data related to NCI-60 cancer cell lines from different tissue origins, which include metabolomics, transcriptomics and proteomics.The fusion of Omics data from different sources is expected to provide a more complete view of biological systems. The proposed method was demonstrated as a relevant and widely applicable alternative to handle efficiently the inherent characteristics of multiple Omics data, such as very large numbers of noisy collinear variables. © 2013 Elsevier B.V.


Desquilbet L.,Agro ParisTech | Mariotti F.,Agro ParisTech
Statistics in Medicine | Year: 2010

Taking into account a continuous exposure in regression models by using categorization, when non-linear dose-response associations are expected, have been widely criticized. As one alternative, restricted cubic spline (RCS) functions are powerful tools (i) to characterize a dose-response association between a continuous exposure and an outcome, (ii) to visually and/or statistically check the assumption of linearity of the association, and (iii) to minimize residual confounding when adjusting for a continuous exposure. Because their implementation with SAS® software is limited, we developed and present here an SAS macro that (i) creates an RCS function of continuous exposures, (ii) displays graphs showing the dose-response association with 95 per cent confidence interval between one main continuous exposure and an outcome when performing linear, logistic, or Cox models, as well as linear and logistic-generalized estimating equations, and (iii) provides statistical tests for overall and non-linear associations. We illustrate the SAS macro using the third National Health and Nutrition Examination Survey data to investigate adjusted dose-response associations (with different models) between calcium intake and bone mineral density (linear regression), folate intake and hyperhomocysteinemia (logistic regression), and serum high-density lipoprotein cholesterol and cardiovascular mortality (Cox model). Copyright © 2010 John Wiley & Sons, Ltd.

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