30 ans après, le "journalisme d’exposition" vu par Science Actualités

L’article disponible en ligne sur www.ocim.fr (rubrique La Lettre de l’OCIM) montrait comment les centres de science peuvent porter un autre regard sur l’actualité scientifique, différent de celui des autres organes de presse. "Pourquoi et comment traiter l’actualité scientifique quand on n’est pas un organe de presse ?" : telle était la question posée en 2004 dans un numéro spécial de La Lettre de l’OCIM consacré à la place de l’actualité dans les centres de science. Aujourd’hui, la Cité de..

Soil biodiversity: functions, threats and tools for policy makers

Human societies rely on the vast diversity of benefits provided by nature, such as food, fibres, construction materials, clean water, clean air and climate regulation. All the elements required for these ecosystem services depend on soil, and soil biodiversity is the driving force behind their regulation. With 2010 being the international year of biodiversity and with the growing attention in Europe on the importance of soils to remain healthy and capable of supporting human activities sustainably, now is the perfect time to raise awareness on preserving soil biodiversity. The objective of this report is to review the state of knowledge of soil biodiversity, its functions, its contribution to ecosystem services and its relevance for the sustainability of human society. In line with the definition of biodiversity given in the 1992 Rio de Janeiro Convention, soil biodiversity can be defined as the variation in soil life, from genes to communities, and the variation in soil habitats, from micro-aggregates to entire landscapes. Bio Intelligence Service, IRD, and NIOO, Report for European Commission (DG Environment

Étude numérique des premières étapes d'agrégation du peptide amyloïde GNNQQNY, impliqué dans une maladie à prion

Les protéines amyloïdes sont impliquées dans les maladies neurodégénératives comme Alzheimer, Parkinson et les maladies à prions et forment des structures complexes, les fibres amyloïdes. Le mécanisme de formation de ces fibres est un processus complexe qui implique plusieurs espèces d’agrégats intermédiaires. Parmi ces espèces, des petits agrégats, les oligomères, sont reconnus comme étant l’espèce amyloïde toxique, mais leur mécanisme de toxicité et d’agrégation sont mal compris. Cette thèse présente les résultats d’une étude numérique des premières étapes d’oligomérisation d’un peptide modèle GNNQQNY, issu d’une protéine prion, pour des systèmes allant du trimère au 50-mère, par le biais de simulations de dynamique moléculaire couplée au potentiel gros-grain OPEP. Nous trouvons que le mécanisme d’agrégation du peptide GNNQQNY suit un processus complexe de nucléation, tel qu’observé expérimentalement pour plusieurs protéines amyloïdes. Nous observons aussi que plusieurs chemins de formation sont accessibles à l’échelle du 20-mère et du 50-mère, ce qui confère aux structures un certain degré de polymorphisme et nous sommes capable de reproduire, dans nos simulations, des oligomères protofibrillaires qui présentent des caractéristiques structurelles observées expérimentalement chez les fibres amyloïdes.Amyloid proteins are involved in neurodegenerative diseases such as Alzheimer’s, Parkinson’s and prion diseases and form complex structures called amyloid fibrils. The fibril formation mechanism is a complex process, which involves several intermediary species. Among these species, small early aggregates, called oligomers, are thought to be the toxic amyloid species but their toxicity and aggregation mechanisms are poorly understood. This thesis aims at presenting the results of a numerical study of the first oligomerization steps of the model peptide GNNQQNY, from a prion protein, for system sizes ranging from the trimer to the 50-mer, via molecular dynamics simulations using the OPEP coarse-grained potential. We find that GNNQQNY’s assembly follows a complex nucleation process, as observed experimentally for numerous amyloid proteins. We also observe that the 20-mer and 50-mer systems form polymorphic structures that are the byproducts of different formation pathways. We further report the spontaneous formation of protofibrillar oligomers with structural characteristics typical of experimentally determined amyloid fibril structures

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided

L’outil scientifique comme instrument d’objectivation de la communication environnementale : Discussion d’un usage de L’Analyse de Cycle de Vie (ACV)

Nous discutons de l'usage d'un outil d'évaluation environnementale : l'analyse de cycle de vie (ACV), dans le cadre d'une communication grand public du fabricant d’emballages alimentaires Tetra Pak. La première partie de l’intervention montre que cet outil, qui est porté par une communauté scientifique, s’inscrit dans un cadre normé et apporte aux entreprises des données stratégiques et « propositionnelles ». La deuxième partie discute de l’usage de l’ACV en communication. Dans le cas de Tetra Pak, la communication sur une ACV suscite une forte polémique. Elle apporte cependant un soutien pérenne à l’entreprise, tandis que le débat suscité fait progresser l’outil scientifique dans le milieu de l’emballage. Cette communication s’achève par une ouverture sur les développements méthodologiques de l’outil à mettre en place pour faciliter son emploi dans le domaine de la communication environnementale des entreprises.Nous discutons de l'usage d'un outil d'évaluation environnementale : l'analyse de cycle de vie (ACV), dans le cadre d'une communication grand public du fabricant d’emballages alimentaires Tetra Pak. La première partie de l’intervention montre que cet outil, qui est porté par une communauté scientifique, s’inscrit dans un cadre normé et apporte aux entreprises des données stratégiques et « propositionnelles ». La deuxième partie discute de l’usage de l’ACV en communication. Dans le cas de Tetra Pak, la communication sur une ACV suscite une forte polémique. Elle apporte cependant un soutien pérenne à l’entreprise, tandis que le débat suscité fait progresser l’outil scientifique dans le milieu de l’emballage. Cette communication s’achève par une ouverture sur les développements méthodologiques de l’outil à mettre en place pour faciliter son emploi dans le domaine de la communication environnementale des entreprises

Synthesis, Crystal Structure and Interaction With DNA of N,N′-(Butane-1,4-Diyl)Bis(Guanidinium) Tetrachloroplatinate (II)

The design, synthesis, crystal structure and interaction with DNA of the N,N′-(butane-1,4-diyl)bis(guanidinium) tetrachloroplatinate(ll) are described. Crystal data: a = 8.152(1), b = 8.889(4), c = 10.700(3) Å , α = 81.59(3), β = 87.99(5), γ = 78.48(6)°, V = 752(1) Å3, Z = 2 , space group P-1. The structure was refined to R = 0.039 and Rw = 0.046 from 1853 reflections (I > 3σ(I)). This compound, named PtC4Gua, does not exhibit a center of symmetry and the center linker chain C(2) - C(3) - C(4) - C(5) is in gauche conformation. The cation is bisprotonated with the H+ attached to the imine group of each terminal guanidinium function. The presence of the platinum moiety reinforces the binding of the butane(bis)guanidinium structure with double stranded DNA as judged from thermal denaturation studies and DNA unwinding experiments

A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35

ABSTRACT: The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided

Ternary Copper(II) Complexes With Indomethacin, a Potent Non-Steroidal Antiinflammatory Drug. Crystal Structure of Bis (Dimethylformamide)-Tetrakis[1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1-H-Indole-3-Acetato]Dicopper(II). Antiinflammatory Properties and Prevention of Gastrointestinal Side Effects by Nanocapsules

Two ternary copper(ll) complexes of indomethacin [1-(4-chlorobenzoyl)-5-methoxy-2- methyl-1-H-indole-3-acetic acid] called hereafter lndo, were prepared and characterized by single crystal X-ray diffraction. The first complex Cu2(Indo)4(DMF)2 I crystallizes in space group P-1 (a = 10.829(2), b = 13.379(2), c = 16.491(3) Å; α = 105.58(2), β = 101.06(2), γ = 106.96(2)°; V= 2104.6(6) Å3, Z= 1). The title molecule is a centrosymmetric binuclear complex, with Cu atoms bridged by the carboxylate moieties of four indomethacinate ligands. The four nearest O atoms around each Cu atom form a square planar arrangement with the square pyramidal coordination completed by the O atom of N,N′-dimethylformamide. Daily administration for seven days of 1 mg/kg of indomethacin, I and I encapsulated into liposomes induces a weak inflammation of rat gastrointestinal tract. I was less inflammatory than indomethacin but the better protection was brought by encapsulation of the compound. This might be of interest in sustained therapies of chronic inflammatory diseases

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-ray crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and [alpha]-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a [beta]-sheet arrangement reminiscent of the [beta]-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods