Understanding new expectations for democratic environmental governance

This paper is based at the nodal points of several phenomena, including political distrust in France, a European trend supporting public participation, a failed experiment of citizen assembly in France, and the organisation of a citizen collective to advocate for a replication of a similar citizen assembly, at the regional level, by environmental activists. In this context, I have conducted a policy analysis focusing particularly on the activist movement with the aim to provide insights into new expectations for democratic governance of environmental resources. This research introduces a new approach to the study of the dynamics of democracy. By applying a power- and subjectivity-sensitive policy analysis framework to an activist movement, I argue that much can be learned about the grounds and sense-making of this movement, which holds a great potential in facilitating dialogue between the civil society and political governance institutions, and democratising governance. The analysis revealed that the current model of French governmental policymaking is criticised on the grounds of its unwillingness to include external knowledge, perspectives, and actors. The rationale for replicating a citizen assembly then, stood both in the process and in the outcome. The process of the CCC-AURA project enables for a subjectivity-sensitive form of governance to take place, based on principles of inclusion, the valuation of all knowledges, and the specific attention to lived experiences and subjectivities created, and in which citizens reclaim decision-making power. This holds implications in terms of the agency, and subjectivities created by the policy, but also for future governance: the CCC-AURA comes in as a project to re-align environmental governance practices to the democratic expectations held by citizens and creates a momentum that can be harnessed to challenge and redefine what democratic governance means in practice

Association between the squat lobster Gastroptychus formosus and cold-water corals in the North Atlantic

Although there are no previous descriptions of the habits of chirostylids in the North Atlantic, it is likely that species in the genera Uroptychus, Eumunida and Gastroptychus have close ecological ties with deep-sea corals since they have all been recorded in trawl samples containing corals from ∼200m depth. We analysed in situ distribution of Gastroptychus formosus and potential hosts using a ROV at a range of north-eastern Atlantic sites and found that this species forms a close association with deep-sea corals that resembles the chirostylid-anthozoan associations reported in shallow Indo-Pacific waters. We update the known distribution for G. formosus, confirming that it is an amphiatlantic species that occurs along the Mid-Atlantic Ridge at least as far south as the Azores and along continental margins from the Canary Islands to Scotland at depths of 600-1700m. The adults have very specific habitat preferences, being only found on gorgonian and antipatharian corals with a strong preference for Leiopathes sp. as a host. This highly restricted habitat preference is likely to render chirostylids vulnerable to the impacts of demersal fishing both directly, as by-catch, and indirectly through habitat loss. © 2010 Marine Biological Association of the United Kingdom

Fpocket: An open source platform for ligand pocket detection

<p>Abstract</p> <p>Background</p> <p>Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compounds. For SBVS, the identification of candidate pockets in protein structures is a key feature, and the recent years have seen increasing interest in developing methods for pocket and cavity detection on protein surfaces.</p> <p>Results</p> <p>Fpocket is an open source pocket detection package based on Voronoi tessellation and alpha spheres built on top of the publicly available package Qhull. The modular source code is organised around a central library of functions, a basis for three main programs: (i) Fpocket, to perform pocket identification, (ii) Tpocket, to organise pocket detection benchmarking on a set of known protein-ligand complexes, and (iii) Dpocket, to collect pocket descriptor values on a set of proteins. Fpocket is written in the C programming language, which makes it a platform well suited for the scientific community willing to develop new scoring functions and extract various pocket descriptors on a large scale level. Fpocket 1.0, relying on a simple scoring function, is able to detect 94% and 92% of the pockets within the best three ranked pockets from the holo and apo proteins respectively, outperforming the standards of the field, while being faster.</p> <p>Conclusion</p> <p>Fpocket provides a rapid, open source and stable basis for further developments related to protein pocket detection, efficient pocket descriptor extraction, or drugablity prediction purposes. Fpocket is freely available under the GNU GPL license at <url>http://fpocket.sourceforge.net</url>.</p

Développement de méthodes et d’outils chémoinformatiques pour l’analyse et la comparaison de chimiothèques

Some news areas in biology ,chemistry and computing interface, have emerged in order to respond the numerous problematics linked to the drug research. This is what this thesis is all about, as an interface gathered under the banner of chimocomputing. Though, new on a human scale, these domains are nevertheless, already an integral part of the drugs and medicines research. As the Biocomputing, his fundamental pillar remains storage, representation, management and the exploitation through computing of chemistry data. Chimocomputing is now mostly used in the upstream phases of drug research. Combining methods from various fields ( chime, computing, maths, apprenticeship, statistics, etc…) allows the implantation of computing tools adapted to the specific problematics and data of chime such as chemical database storage, understructure research, data visualisation or physoco-chimecals and biologics properties prediction.In that multidisciplinary frame, the work done in this thesis pointed out two important aspects, both related to chimocomputing : (1) The new methods development allowing to ease the visualization, analysis and interpretation of data related to set of the molecules, currently known as chimocomputing and (2) the computing tools development enabling the implantation of these methods.De nouveaux domaines ont vu le jour, à l’interface entre biologie, chimie et informatique, afin de répondre aux multiples problématiques liées à la recherche de médicaments. Cette thèse se situe à l’interface de plusieurs de ces domaines, regroupés sous la bannière de la chémo-informatique. Récent à l’échelle humaine, ce domaine fait néanmoins déjà partie intégrante de la recherche pharmaceutique. De manière analogue à la bioinformatique, son pilier fondateur reste le stockage, la représentation, la gestion et l’exploitation par ordinateur de données provenant de la chimie. La chémoinformatique est aujourd’hui utilisée principalement dans les phases amont de la recherche de médicaments. En combinant des méthodes issues de différents domaines (chimie, informatique, mathématique, apprentissage, statistiques, etc.), elle permet la mise en oeuvre d’outils informatiques adaptés aux problématiques et données spécifiques de la chimie, tels que le stockage de l’information chimique en base de données, la recherche par sous-structure, la visualisation de données, ou encore la prédiction de propriétés physico-chimiques et biologiques.Dans ce cadre pluri-disciplinaire, le travail présenté dans cette thèse porte sur deux aspects importants liés à la chémoinformatique : (1) le développement de nouvelles méthodes permettant de faciliter la visualisation, l’analyse et l’interprétation des données liées aux ensembles de molécules, plus communément appelés chimiothèques, et (2) le développement d’outils informatiques permettant de mettre en oeuvre ces méthodes

Floral vascular patterns of the double-flowered and wild-type morphs of Nigella damascena L. (Ranunculaceae)

The perianth of the double-flowered morph of Nigella damascena L. consists of spirally inserted petaloid sepals and sepal-like organs, similar in shape and colour to the petaloid sepals of the wild-type flower. It is devoid of petals. We compare the vascularization of each organ category of the double flower with that of the wild-type. We show that the vascular patterns of the sepal-like organs and of the petals are identical, and found an inverse relationship between the number of bracts and the number of sepals in the double-flowered morph. These two surprising findings will influence the future evo-devo studies on this plant model

Specific duplication and dorsoventrally asymmetric expression patterns of Cycloidea-like genes in zygomorphic species of Ranunculaceae.

Floral bilateral symmetry (zygomorphy) has evolved several times independently in angiosperms from radially symmetrical (actinomorphic) ancestral states. Homologs of the Antirrhinum majus Cycloidea gene (Cyc) have been shown to control floral symmetry in diverse groups in core eudicots. In the basal eudicot family Ranunculaceae, there is a single evolutionary transition from actinomorphy to zygomorphy in the stem lineage of the tribe Delphinieae. We characterized Cyc homologs in 18 genera of Ranunculaceae, including the four genera of Delphinieae, in a sampling that represents the floral morphological diversity of this tribe, and reconstructed the evolutionary history of this gene family in Ranunculaceae. Within each of the two RanaCyL (Ranunculaceae Cycloidea-like) lineages previously identified, an additional duplication possibly predating the emergence of the Delphinieae was found, resulting in up to four gene copies in zygomorphic species. Expression analyses indicate that the RanaCyL paralogs are expressed early in floral buds and that the duration of their expression varies between species and paralog class. At most one RanaCyL paralog was expressed during the late stages of floral development in the actinomorphic species studied whereas all paralogs from the zygomorphic species were expressed, composing a species-specific identity code for perianth organs. The contrasted asymmetric patterns of expression observed in the two zygomorphic species is discussed in relation to their distinct perianth architecture

Transcriptomic response to divergent selection for flowering times reveals convergence and key players of the underlying gene regulatory network

International audienceArtificial selection experiments are designed to investigate phenotypic evolution of complex traits and its genetic basis. Here we focused on flowering time, a trait of key importance for plant adaptation and life-cycle shifts. We undertook divergent selection experiments from two maize inbred lines. After 13 generations of selection, we obtained a time-lag of roughly two weeks between Early-and Late-populations. We used this material to characterize the genome-wide transcriptomic response to selection in the shoot apical meristem before, during and after floral transition in field conditions during two consecutive years. We validated the reliability of performing RNA-sequencing in uncontrolled conditions. We found that roughly half of maize genes were expressed in the shoot apical meristem, 59.3% of which were differentially expressed. We detected a majority of genes with differential expression between inbreds and across meristem status, and retrieved a subset of 2,451 genes involved in the response to selection. Among these, we found a significant enrichment for genes with known function in maize flowering time. Furthermore, they were more often shared between inbreds than expected by chance, suggesting convergence of gene expression. We discuss new insights into the expression pattern of key players of the underlying gene regulatory network including the Zea mays genes CENTRORADIALIS (ZCN8), RELATED TO AP2.7 (RAP2.7), MADS4 (ZMM4), KNOTTED1 (KN1), GIBBERELLIN2-OXIDASE1 (GA2ox1), as well as alternative scenarios for genetic convergence

fpocket: online tools for protein ensemble pocket detection and tracking

Computational small-molecule binding site detection has several important applications in the biomedical field. Notable interests are the identification of cavities for structure-based drug discovery or functional annotation of structures. fpocket is a small-molecule pocket detection program, relying on the geometric α-sphere theory. The fpocket web server allows: (i) candidate pocket detection—fpocket; (ii) pocket tracking during molecular dynamics, in order to provide insights into pocket dynamics—mdpocket; and (iii) a transposition of mdpocket to the combined analysis of homologous structures—hpocket. These complementary online tools allow to tackle various questions related to the identification and annotation of functional and allosteric sites, transient pockets and pocket preservation within evolution of structural families. The server and documentation are freely available at http://bioserv.rpbs.univ-paris-diderot.fr/fpocket

Study of ferroelectric/dielectric multilayers for tunable stub resonator applications at microwaves

International audienceTunable coplanar waveguide stub resonators deposited on various ferroelectric/dielectric heterostructures are studied in the 10-GHz band. A frequency tunability of up to ~ 45% is achieved under a moderate biasing field (Ebias < 100 kV/cm) when the resonator is printed on KTa0.5Nb0.5O3 (KTN) ferroelectric thin film alone: this comes from the large permittivity agility of the KTN material (εr(KTN) varies from ~ 700 to ~ 200). Nevertheless this also leads to significant insertion loss due to the dielectric loss of the ferroelectric material itself (tanδr(KTN) ≈ 0.15-0.30 at 10 GHz). In this paper, an original route has been considered to reduce the device loss while keeping up a high frequency tunability. It consists in associating the KTN film with a dielectric film to elaborate ferroelectric/dielectric multilayers. The Bi1.5Zn0.9Nb1.5O7−δ (BZN) oxide material is selected here for two main reasons, namely its low dielectric loss (tanδr(BZN) ≈ 0.005-0.0075) and its moderate relative permittivity (εr(BZN) ≈ 95-125) at 12.5 GHz. The relevance of this approach is studied numerically and experimentally. We compare numerically two different heterostructures for which the ferroelectric film is grown on the dielectric film (KTN/BZN), or vice versa (BZN/KTN). A stub resonator printed on the most relevant heterostructure has been fabricated, and experimental data are discussed and compared to the numerical results

Loss reduction technique in ferroelectric tunable devices by laser micro-etching. Application to a CPW stub resonator in X-band

International audienceFerroelectric materials are known to be lossy at microwaves. A local microetching technique based on laser ablation is implemented here to reduce the insertion loss of highly tunable devices fabricated on KTa1-xNbxO3 (KTN) ferroelectric thin films. The relevance of this approach is studied in X-band by comparing numerically and experimentally the performance of a frequency-tunable coplanar waveguide stub resonator before and after KTN microetching. The experimental data demonstrate a large loss reduction (by a factor 3.3), while keeping a high-frequency tunability (47%) under a moderate biasing static electric field (80 kV/cm). This approach paves the way for the design of ferroelectric reconfigurable devices with attractive performance in X-band and even beyond