Construction d'un modèle sémantique pour organiser les connaissances dédiées à l'agroécologie. Le cas d'Agro-PEPS/GECO

International audienceIn 2008, the RMT SdCi (Joint Technological Network on Innovative Cropping Systems) launched the develop-ment of a collaborative web tool, named Agro-PEPS, in response to the needs to redesign the mode of agricul-tural production. This tool aims to help practitioners to design, pilot, manage and learn innovative and efficient cropping systems. In 2015, the Ministry in charge of Agriculture decided to develop GECO within the framework of the ECOPHYTO plan. GECO is a collaborative knowledge management tool dedicated to agroecology. It is built up in using Agro-PEPS as a prototype. The necessarily systemic and complex nature of this type of knowledge leads us to develop a semantic model. This model allows the search engine to provide more accurate answers to queries and to sort them depending on their relevance. We present the first version of this model in this article. GECO will be online in a beta version in early 2017.Face aux besoins de reconception des modes de production agricoles, le Réseau Mixte Technologique SdCi (Systèmes de Culture Innovants) a lancé, dès 2008, le développement d'un outil web collaboratif, Agro-PEPS, pour aider les acteurs du terrain à concevoir, piloter, gérer et faire l'apprentissage de systèmes de culture innovants et performants. En 2015, le ministère en charge de l'agriculture a décidé, dans le cadre du plan Ecophyto, de développer GECO, dispositif de GEstion des COnnaissances, en utilisant Agro-PEPS comme prototype. GECO est un outil web collaboratif de gestion des connaissances dédiées à l'agroécologie. Le caractère nécessairement systémique et complexe de ce type de connaissances nous a conduits à développer un modèle sémantique. Ce modèle, dont une première version est présentée dans cet article, permet au moteur de recherche de fournir des réponses aux requêtes plus précises et dont la pertinence est hiérarchisée. GECO sera mis en ligne dans sa version béta début 2017

Integrating new memories into the hippocampal network activity space

By investigating the topology of neuronal co-activity, we found that mnemonic information spans multiple operational axes in the mouse hippocampus network. High-activity principal cells form the core of each memory along a first axis, segregating spatial contexts and novelty. Low-activity cells join co-activity motifs across behavioral events and enable their crosstalk along two other axes. This reveals an organizational principle for continuous integration and interaction of hippocampal memories

Giving new sorghum variety options to resource-poor farmers in Nicaragua through participatory varietal selection

In the dry areas of Nicaragua, white-grain sorghum is an important subsistence crop for resource-poor farmers. From 2002 to 2007, participatory varietal selection (PVS) was implemented in three regions with the aim of identifying new varieties matching small farmers' needs. This paper describes the general approach, the partnership and the methods used to identify farmers' selection criteria (FSC), as well as the evaluation of new germplasm using the scoring method. Data analysis involved relating farmers' evaluation data to agronomic data and farmers' selection decisions (FSD), using Spearman correlations and the chi-square test. In the three regions, higher grain yield and good grain quality for making tortillas were identified as the two main FSCs for both the 'tortillero' and 'millón' sorghum types; the ranking of the other important FSC differed between the sites and the sorghum types. Our data shows that farmers' scores for earliness were highly correlated with breeder's observations while farmers' assessments of grain yield were correlated with measured yield in half the cases, depending on their knowledge of the crop. The study shows that in evaluating grain quality the farmers used several specific traits which were not considered by breeders. Overall appreciation, grain yield and grain quality were the key farmers' criteria that contributed to FSD. The PVS work enabled breeders to obtain a better understanding of farmers' criteria as well as identifying new progenitors, which should be useful for the sorghum breeding schemes in Central America in the future. Furthermore, by exploring wide genetic diversity, it was possible to release several farmer-preferred and high-performing varieties within a fairly short period

New sources of resistance to sorghum midge in Burkina Faso

New sources of midge (Stenodiplosis sorghicola) resistance among local Sorghum bicolor cultivars were determined in experiments carried out from 1996-99 in Burkina Faso. Two hundred local landraces from Burkina Faso and other West African countries were screened for midge resistance. The 40 best cultivars were tested with resistant and susceptible controls during the 1999 rainy seasons, in midge-infested sites Kouaré and Farako-Bâ. The average percentage of midge-damaged spikelets in Kouaré varied from 0% in ICSV 745 to 45.3% in susceptible landrace 439. At Farako-Bâ, the percentage of damaged spikelets varied from 0.4% in ICSV 745 to 31.8% on the susceptible control Sariaso 10. Cultivar Tenlopieno had the highest percentage of damaged spikelets in both locations, but showed low visual midge damage scores

The histone demethylase JMJD2A/KDM4A links ribosomal RNA transcription to nutrients and growth factors availability

The interplay between methylation and demethylation of histone lysine residues is an essential component of gene expression regulation and there is considerable interest in elucidating the roles of proteins involved. Here we report that histone demethylase KDM4A/JMJD2A, which is involved in the regulation of cell proliferation and is overexpressed in some cancers, interacts with RNA Polymerase I, associates with active ribosomal RNA genes and is required for serum-induced activation of rDNA transcription. We propose that KDM4A controls the initial stages of transition from 'poised', non-transcribed rDNA chromatin into its active form. We show that PI3K, a major signalling transducer central for cell proliferation and survival, controls cellular localization of KDM4A and consequently its association with ribosomal DNA through the SGK1 downstream kinase. We propose that the interplay between PI3K/SGK1 signalling cascade and KDM4A constitutes a mechanism by which cells adapt ribosome biogenesis level to the availability of growth factors and nutrients

Time-dependent release of growth factors from implant surfaces treated with plasma rich in growth factors

Abstract: Plasma rich in growth factors (PRGFs) technology is an autologous platelet-rich plasma approach that provides a pool of growth factors and cytokines that have been shown to increase tissue regeneration and accelerate dental implant osseointegration. In this framework, the spatiotemporal release of growth factors and the establishment of a provisional fibrin matrix are likely to be key aspects governing the stimulation of the early phases of tissue regeneration around implants. We investigated the kinetics of growth factor release at implant surfaces functionalized either with PRGFs or platelet-poor plasma and correlated the results obtained with the morphology of the resulting interfaces. Our main finding is that activation and clot formation favors longer residence times of the growth factors at the interfaces studied, probably due to their retention in the adsorbed fibrin matrix. The concentration of the platelet-derived growth factors above the interfaces becomes negligible after 2-4 days and is significantly higher in the case of activated interfaces than in the case of nonactivated ones, whereas that of the plasmatic hepatocyte growth factor is independent of platelet concentration and activation, and remains significant for up to 9 days. Platelet-rich plasma preparations should be activated to permit growth factor release and thereby facilitate implant surface osseointegration. V C 2012 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 00A:000-000, 2012

A New Isoform of the Histone Demethylase JMJD2A/KDM4A Is Required for Skeletal Muscle Differentiation

In proliferating myoblasts, muscle specific genes are silenced by epigenetic modifications at their promoters, including histone H3K9 methylation. Derepression of the promoter of the gene encoding the myogenic factor myogenin (Myog) is key for initiation of muscle differentiation. The mechanism of H3K9 demethylation at the Myog promoter is unclear, however. Here, we identify an isoform of the histone demethylase JMJD2A/KDM4A that lacks the N-terminal demethylase domain (ΔN-JMJD2A). The amount of ΔN-JMJD2A increases during differentiation of C2C12 myoblasts into myotubes. Genome-wide expression profiling and exon-specific siRNA knockdown indicate that, in contrast to the full-length protein, ΔN-JMJD2A is necessary for myotube formation and muscle-specific gene expression. Moreover, ΔN-JMJD2A promotes MyoD-induced conversion of NIH3T3 cells into muscle cells. ChIP-on-chip analysis indicates that ΔN-JMJD2A binds to genes mainly involved in transcriptional control and that this binding is linked to gene activation. ΔN-JMJD2A is recruited to the Myog promoter at the onset of differentiation. This binding is essential to promote the demethylation of H3K9me2 and H3K9me3. We conclude that induction of the ΔN-JMJD2A isoform is crucial for muscle differentiation: by directing the removal of repressive chromatin marks at the Myog promoter, it promotes transcriptional activation of the Myog gene and thus contributes to initiation of muscle-specific gene expression

Bone Marrow Mesenchymal Stem Cells for Improving Hematopoietic Function: An In Vitro and In Vivo Model. Part 2: Effect on Bone Marrow Microenvironment

The aim of the present study was to determine how mesenchymal stem cells (MSC) could improve bone marrow (BM) stroma function after damage, both in vitro and in vivo. Human MSC from 20 healthy donors were isolated and expanded. Mobilized selected CD34+ progenitor cells were obtained from 20 HSCT donors. For in vitro study, long-term bone marrow cultures (LTBMC) were performed using a etoposide damaged stromal model to test MSC effect in stromal confluence, capability of MSC to lodge in stromal layer as well as some molecules (SDF1, osteopontin,) involved in hematopoietic niche maintenance were analyzed. For the in vivo model, 64 NOD/SCID recipients were transplanted with CD34+ cells administered either by intravenous (IV) or intrabone (IB) route, with or without BM derived MSC. MSC lodgement within the BM niche was assessed by FISH analysis and the expression of SDF1 and osteopontin by immunohistochemistry. In vivo study showed that when the stromal damage was severe, TP-MSC could lodge in the etoposide-treated BM stroma, as shown by FISH analysis. Osteopontin and SDF1 were differently expressed in damaged stroma and their expression restored after TP-MSC addition. Human in vivo MSC lodgement was observed within BM niche by FISH, but MSC only were detected and not in the contralateral femurs. Human MSC were located around blood vessels in the subendoestal region of femurs and expressed SDF1 and osteopontin. In summary, our data show that MSC can restore BM stromal function and also engraft when a higher stromal damage was done. Interestingly, MSC were detected locally where they were administered but not in the contralateral femur

Consolidation of an Olfactory Memory Trace in the Olfactory Bulb Is Required for Learning-Induced Survival of Adult-Born Neurons and Long-Term Memory

Background: It has recently been proposed that adult-born neurons in the olfactory bulb, whose survival is modulated by learning, support long-term olfactory memory. However, the mechanism used to select which adult-born neurons following learning will participate in the long-term retention of olfactory information is unknown. We addressed this question by investigating the effect of bulbar consolidation of olfactory learning on memory and neurogenesis. Methodology/Principal Findings: Initially, we used a behavioral ecological approach using adult mice to assess the impact of consolidation on neurogenesis. Using learning paradigms in which consolidation time was varied, we showed that a spaced (across days), but not a massed (within day), learning paradigm increased survival of adult-born neurons and allowed long-term retention of the task. Subsequently, we used a pharmacological approach to block consolidation in the olfactory bulb, consisting in intrabulbar infusion of the protein synthesis inhibitor anisomycin, and found impaired learning and no increase in neurogenesis, while basic olfactory processing and the basal rate of adult-born neuron survival remained unaffected. Taken together these data indicate that survival of adult-born neurons during learning depends on consolidation processes taking place in the olfactory bulb. Conclusion/Significance: We can thus propose a model in which consolidation processes in the olfactory bulb determine both survival of adult-born neurons and long-term olfactory memory. The finding that adult-born neuron survival durin

The E1A-Associated p400 Protein Modulates Cell Fate Decisions by the Regulation of ROS Homeostasis

The p400 E1A-associated protein, which mediates H2A.Z incorporation at specific promoters, plays a major role in cell fate decisions: it promotes cell cycle progression and inhibits induction of apoptosis or senescence. Here, we show that p400 expression is required for the correct control of ROS metabolism. Depletion of p400 indeed increases intracellular ROS levels and causes the appearance of DNA damage, indicating that p400 maintains oxidative stress below a threshold at which DNA damages occur. Suppression of the DNA damage response using a siRNA against ATM inhibits the effects of p400 on cell cycle progression, apoptosis, or senescence, demonstrating the importance of ATM–dependent DDR pathways in cell fates control by p400. Finally, we show that these effects of p400 are dependent on direct transcriptional regulation of specific promoters and may also involve a positive feedback loop between oxidative stress and DNA breaks since we found that persistent DNA breaks are sufficient to increase ROS levels. Altogether, our results uncover an unexpected link between p400 and ROS metabolism and allow deciphering the molecular mechanisms largely responsible for cell proliferation control by p400