Documentation of baseline and policy scenarios to be assessed with prototypes 2 and 3

This report describes the construction of baseline and policy scenarios in Test Case 1 and 2 for the second and third prototypes of SEAMLESS-IF. It provides details of the methodology used in SEAMLESS-IP to build scenarios, and the data and parameters needed for the implementation of these scenarios in SEAMLESS-IF. These scenarios will be used to test the second and third prototypes of the integrated framework and its individual tools, especially the two backbone model chains: Data-base-APES-FSSIM-Indicators and Databases- APES-FSSIM-EXPAMOD-CAPRI-Indicators

RPG Explorer: A new tool to ease the analysis of agricultural landscape dynamics with the Land Parcel Identification System

International audienceIn the early 2000s a Land Parcel Identification System (LPIS) was set up by each member state of theEuropean Union, to manage agricultural subsidies. These databases describe field geometry and landcover,and provide information on farm characteristics. LPIS data could therefore be used to describe agriculturallandscape dynamics, but are seldom put to this purpose by scientists and local stakeholdersbecause it requires the use of GIS software and programming skills. The objective of this paper is thusto present RPG Explorer, a new tool that we developed to analyze agricultural landscape dynamics withLPIS data. RPG Explorer doesn’t require any specific skills in GIS and programming allowing non specialistto deal with complex data.RPG Explorer includes a first module which computes the changes in crop proportions and farm characteristics(numbers of farm, farm area, farm type). A second module computes crop sequences on eachfarmer block of LPIS data. We also included a crop rotation model in a third module.We illustrated the use of RPG Explorer for two example neighboring catchments located in westernFrance, the Vivier catchment (16,000 ha) and the Courance catchment (15,000 ha). For example, RPGExplorer easily revealed the evolution of crop proportions, such as the increase of temporary grasslandsin the Courance catchment (from 7.2% of the Utilized Agricultural Area (UAA) in 2007 to 11.7% in 2013).The number of farms was also shown to vary a lot: from 230 in 2007 to 207 in 2013 for the Vivier catchment,with a subsequent increase of their mean UAA (from 101 ha to 119 ha). RPG Explorer also showedthat more than half of the Vivier catchment UAA (59%) was occupied by only 50 farms in 2013.Concerning crop sequences, the sunflower ! winter wheat sequence was the most frequent 2-yearsequence in both catchments, but some differences appeared with for example, a higher proportion ofwinter wheat ! winter wheat sequence in the Courance catchment (7.2% against 3.6%). Crop rotationmodeling indicated that the rapeseed !winter wheat!sunflower!winter wheat, sunflower !winterwheat and maize monoculture were the three main crop rotations.Finally, these examples illustrate well the ability for scientist and local stakeholders to easily describesome major agricultural landscape dynamics with RPG Explorer

Impact of mutations within the [Fe-S] cluster or the lipoic acid biosynthesis pathways on mitochondrial protein expression profiles in fibroblasts from patients

International audienceLipoic acid (LA) is the cofactor of the E2 subunit of mitochondrial ketoacid dehydrogenases and plays a major role in oxidative decarboxylation. De novo LA biosynthesis is dependent on LIAS activity together with LIPT1 and LIPT2. LIAS is an iron-sulfur (Fe-S) cluster-containing mitochondrial protein, like mitochondrial aconitase (mt-aco) and some subunits of respiratory chain (RC) complexes I, II and III. All of them harbor at least one [Fe-S] cluster and their activity is dependent on the mitochondrial [Fe-S] cluster (ISC) assembly machinery. Disorders in the ISC machinery affect numerous Fe-S proteins and lead to a heterogeneous group of diseases with a wide variety of clinical symptoms and combined enzymatic defects. Here, we present the biochemical profiles of several key mitochondrial [Fe-S]-containing proteins in fibroblasts from 13 patients carrying mutations in genes encoding proteins involved in either the lipoic acid (LIPT1 and LIPT2) or mitochondrial ISC biogenesis (FDX1L, ISCA2, IBA57, NFU1, BOLA3) pathway. Ten of them are new patients described for the first time. We confirm that the fibroblast is a good cellular model to study these deficiencies, except for patients presenting mutations in FDX1L and a muscular clinical phenotype. We find that oxidative phosphorylation can be affected by LA defects in LIPT1 and LIPT2 patients due to excessive oxidative stress or to another mechanism connecting LA and respiratory chain activity. We confirm that NFU1, BOLA3, ISCA2 and IBA57 operate in the maturation of [4Fe-4S] clusters and not in [2Fe-2S] protein maturation. Our work suggests a functional difference between IBA57 and other proteins involved in maturation of [Fe-S] proteins. IBA57 seems to require BOLA3, NFU1 and ISCA2 for its stability and NFU1 requires BOLA3. Finally, our study establishes different biochemical profiles for patients according to their mutated protein