Evaluation of modelling approaches for predicting the spatial distribution of soil organic carbon stocks at the national scale

Soil organic carbon (SOC) plays a major role in the global carbon budget. It can act as a source or a sink of atmospheric carbon, thereby possibly influencing the course of climate change. Improving the tools that model the spatial distributions of SOC stocks at national scales is a priority, both for monitoring changes in SOC and as an input for global carbon cycles studies. In this paper, we compare and evaluate two recent and promising modelling approaches. First, we considered several increasingly complex boosted regression trees (BRT), a convenient and efficient multiple regression model from the statistical learning field. Further, we considered a robust geostatistical approach coupled to the BRT models. Testing the different approaches was performed on the dataset from the French Soil Monitoring Network, with a consistent cross-validation procedure. We showed that when a limited number of predictors were included in the BRT model, the standalone BRT predictions were significantly improved by robust geostatistical modelling of the residuals. However, when data for several SOC drivers were included, the standalone BRT model predictions were not significantly improved by geostatistical modelling. Therefore, in this latter situation, the BRT predictions might be considered adequate without the need for geostatistical modelling, provided that i) care is exercised in model fitting and validating, and ii) the dataset does not allow for modelling of local spatial autocorrelations, as is the case for many national systematic sampling schemes

Environmental Assessment of Soil for Monitoring: Volume IIb Survey of National Networks

The ENVASSO Project (Contract 022713) was funded 2006-8, under the European Commission 6th Framework Programme of Research, with the objective of defining and documenting a soil monitoring system appropriate for soil protection at continental level. The ENVASSO Consortium, comprising 37 partners drawn from 25 EU Member States, reviewed almost 300 soil indicators, identified existing soil inventories and monitoring programmes in the Member States, designed and programmed a database management system to capture, store and supply soil profile data, and drafted procedures and protocols appropriate for inclusion in a European soil monitoring network of sites that are geo-referenced and at which a qualified sampling process is or could be conducted. This volume (IIb), a Survey of National Networks, is the second of two reports that together constitute the most comprehensive study to date of the soil inventory and monitoring activities in the European Union. It contains comprehensive fact sheets for each national network, listing the purpose, sampling strategy adopted, analytical methods used and the number of monitoring sites.JRC.H.7-Climate Risk Managemen

Fertilité des sols: conclusions du rapport sur l'état des sols de France

Les sols constituent une ressource naturelle non renouvelable. Leurs usages et leur devenir représentent un enjeu collectif majeur, tant pour les activités agricoles ou sylvicoles que pour la préservation de la qualité de notre environnement. Après dix ans de travaux, le Groupement d’Intérêt Scientifique sur les sols, le Gis Sol, a dressé le premier bilan scientifiquement quantifié de l’état des sols de France métropolitaine et d’Outre-mer dans un rapport sur l’état des sols de France publié en 2011. Ce rapport relève des points positifs mais également un certain nombre de préoccupations du point de vue de la fertilité. Les sols agricoles ne présentent pas d’évolution mesurable de leur acidité, ce quiindique une bonne gestion du pH à l’échelle nationale. Le rapport fait en revanche état de teneurs en phosphore relativement faibles pour de nombreux sols, et à l’inverse de situations d’excédents très préoccupantes en raison de son impact sur la qualité des eaux et l’eutrophisation des milieux. Il pose ainsi la question de la durabilité à long terme du système agricole actuel et celle d’une meilleure valorisation des effluents d’élevage. D’assez nombreuses situations pourraient également être susceptibles de provoquer des carences en oligo-éléments pour des cultures exigeantes. Enfin, une inquiétude majeure concerne la progression de l’artificialisation des sols, qui s’est accélérée durant la dernière décennie et occasionne des pertes importantes de sols agricoles.Soils are a non-renewable, natural resource. Their uses and their future represent, therefore, a collective issue for agricultural and forestry production, as well as for the preservation of our environment. After ten years of work, the “Groupement d’intérêt scientifique sur les sols”, the Gis Sol (Soils Scientific Interest Group) has presented the first appraisal of soil quality in mainland France and its overseas territories in a report on the state of the soils in France published in 2011. This appraisal shows evidence for positive points but also highlights some concerns regarding soil fertility. Agricultural soils do not show a measurable change in their acidity, thus indicating an efficient management of pH at a national level. On the other hand, the report shows relatively low phosphorus levels for numerous soils, and inversely situations of structural excess which remain very worrying due to its impact on water quality and on the eutrophication of the environments. It also raises the questionsof the long-term sustainability of current cultivation systems and of a better treatment of effluents from livestock farming. Numerous situations also seem to be incompatible, for certain oligo-elements, with demanding cultures. At last, a major concern is the development of soil sealing, which has accelerated over the last decade and is responsible for the loss of large areas of agricultural soils

Interaction between O-GlcNAc Modification and Tyrosine Phosphorylation of Prohibitin: Implication for a Novel Binary Switch

Prohibitin (PHB or PHB1) is an evolutionarily conserved, multifunctional protein which is present in various cellular compartments including the plasma membrane. However, mechanisms involved in various functions of PHB are not fully explored yet. Here we report for the first time that PHB interacts with O-linked β-N-acetylglucosamine transferase (O-GlcNAc transferase, OGT) and is O-GlcNAc modified; and also undergoes tyrosine phosphorylation in response to insulin. Tyrosine 114 (Tyr114) and tyrosine 259 (Tyr259) in PHB are in the close proximity of potential O-GlcNAc sites serine 121 (Ser121) and threonine 258 (Thr258) respectively. Substitution of Tyr114 and Tyr259 residues in PHB with phenylalanine by site-directed mutagenesis results in reduced tyrosine phosphorylation as well as reduced O-GlcNAc modification of PHB. Surprisingly, this also resulted in enhanced tyrosine phosphorylation and activity of OGT. This is attributed to the presence of similar tyrosine motifs in PHB and OGT. Substitution of Ser121 and Thr258 with alanine and isoleucine respectively resulted in attenuation of O-GlcNAc modification and increased tyrosine phosphorylation of PHB suggesting an association between these two dynamic modifications. Sequence analysis of O-GlcNAc modified proteins having known O-GlcNAc modification site(s) or known tyrosine phosphorylation site(s) revealed a strong potential association between these two posttranslational modifications in various proteins. We speculate that O-GlcNAc modification and tyrosine phosphorylation of PHB play an important role in tyrosine kinase signaling pathways including insulin, growth factors and immune receptors signaling. In addition, we propose that O-GlcNAc modification and tyrosine phosphorylation is a novel previously unidentified binary switch which may provide new mechanistic insights into cell signaling pathways and is open for direct experimental examination

Development of an Agricultural Primary Productivity Decision Support Model: A Case Study in France

Agricultural soils provide society with several functions, one of which is primary productivity. This function is defined as the capacity of a soil to supply nutrients and water and to produce plant biomass for human use, providing food, feed, fiber, and fuel. For farmers, the productivity function delivers an economic basis and is a prerequisite for agricultural sustainability. Our study was designed to develop an agricultural primary productivity decision support model. To obtain a highly accurate decision support model that helps farmers and advisors to assess and manage the provision of the primary productivity soil function on their agricultural fields, we addressed the following specific objectives: (i) to construct a qualitative decision support model to assess the primary productivity soil function at the agricultural field level; (ii) to carry out verification, calibration, and sensitivity analysis of this model; and (iii) to validate the model based on empirical data. The result is a hierarchical qualitative model consisting of 25 input attributes describing soil properties, environmental conditions, cropping specifications, and management practices on each respective field. An extensive dataset from France containing data from 399 sites was used to calibrate and validate the model. The large amount of data enabled data mining to support model calibration. The accuracy of the decision support model prior to calibration supported by data mining was ~40%. The data mining approach improved the accuracy to 77%. The proposed methodology of combining decision modeling and data mining proved to be an important step forward. This iterative approach yielded an accurate, reliable, and useful decision support model for the assessment of the primary productivity soil function at the field level. This can assist farmers and advisors in selecting the most appropriate crop management practices. Embedding this decision support model in a set of complementary models for four adjacent soil functions, as endeavored in the H2020 LANDMARK project, will help take the integrated sustainability of arable cropping systems to a new level

Early maternal mirroring predicts infant motor system activation during facial expression observation.

Processing facial expressions is an essential component of social interaction, especially for preverbal infants. In human adults and monkeys, this process involves the motor system, with a neural matching mechanism believed to couple self- and other-generated facial gestures. Here, we used electroencephalography to demonstrate recruitment of the human motor system during observation and execution of facial expressions in nine-month-old infants, implicating this system in facial expression processing from a very young age. Notably, examination of early video-recorded mother-infant interactions supported the common, but as yet untested, hypothesis that maternal mirroring of infant facial gestures is central to the development of a neural matching mechanism for these gestures. Specifically, the extent to which mothers mirrored infant facial expressions at two months postpartum predicted infant motor system activity during observation of the same expressions at nine months. This suggests that maternal mirroring strengthens mappings between visual and motor representations of facial gestures, which increases infant neural sensitivity to particularly relevant cues in the early social environment

Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism

Variants in ribosomal protein (RP) genes drive Diamond-Blackfan anemia (DBA), a bone marrow failure syndrome that can also predispose individuals to cancer. Inherited and sporadic RP gene variants are also linked to a variety of phenotypes, including malignancy, in individuals with no anemia. Here we report an individual diagnosed with DBA carrying a variant in the 5'UTR of RPL9 (uL6). Additionally, we report two individuals from a family with multiple cancer incidences carrying a RPL9 missense variant. Analysis of cells from these individuals reveals that despite the variants both driving pre-rRNA processing defects and 80S monosome reduction, the downstream effects are remarkably different. Cells carrying the 5'UTR variant stabilize TP53 and impair the growth and differentiation of erythroid cells. In contrast, ribosomes incorporating the missense variant erroneously read through UAG and UGA stop codons of mRNAs. Metabolic profiles of cells carrying the 5'UTR variant reveal an increased metabolism of amino acids and a switch from glycolysis to gluconeogenesis while those of cells carrying the missense variant reveal a depletion of nucleotide pools. These findings indicate that variants in the same RP gene can drive similar ribosome biogenesis defects yet still have markedly different downstream consequences and clinical impacts