Mise au point interactive de programmes dans un atelier de genie logiciel

SIGLECNRS T 57144 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Mise au point interactive de programmes dans un atelier de génie logiciel

Université : Université scientifique et médicale de GrenobleCette thése présente différents types de metteurs au point, puis elle essaie d'apporter une solution à ce problème en présentant le metteur au point PASCAL réalisé au sein de l'environnement de programmation ADELE. Pour cela, elle décrit l'interpréteur réalisé dans le cadre de ce projet; cet interpréteur travaille sur une représentation interne de l'arbre abstrait des programmes. Nous montrons ensuite comment est exploité cet outil pour réaliser les différentes fonctions de mise au point offertes à l'utilisateu

Conjugated protein domains as engineered scaffold proteins

Assembly of proteins into higher-order complexes generates specificity and selectivity in cellular signaling. Signaling complex formation is facilitated by scaffold proteins that use modular scaffolding domains, which recruit specific pathway enzymes. Multimerization and recombination of these conjugated native domains allows the generation of, libraries of, engineered multi-domain scaffold proteins. Analysis of these engineered proteins has provided molecular insight into the regulatory mechanism of the native scaffold proteins and the applicability of these synthetic variants. This topical review highlights the use of engineered, conjugated multi-domain scaffold proteins on different length scales in the context of synthetic signaling pathways, metabolic engineering, liquid-liquid phase separation and hydrogel formation

Hypergraph Based Data Model for Complex Health Data Exploration and Its Implementation in PREDIMED Clinical Data Warehouse

International audienceWithin the PREDIMED Clinical Data Warehouse (CDW) of Grenoble Alpes University Hospital (CHUGA), we have developed a hypergraph based operational data model, aiming at empowering physicians to explore, visualize and qualitatively analyze interactively the complex and massive information of the patients treated in CHUGA. This model constitutes a central target structure, expressed in a dual form, both graphical and formal, which gathers the concepts and their semantic relations into a hypergraph whose implementation can easily be manipulated by medical experts. The implementation is based on a property graph database linked to an interactive graphical interface allowing to navigate through the data and to interact in real time with a search engine, visualization and analysis tools. This model and its agile implementation allow for easy structural changes inherent to the evolution of techniques and practices in the health field. This flexibility provides adaptability to the evolution of interoperability standards

EVASEP: A Noninterventional Study Describing the Perception of Neurologists, Patients, and Caregivers on Caregivers’ Role in the Support of Patients Suffering from Multiple Sclerosis Treated with Subcutaneous Interferon Beta 1a

Background. The perception of the role of caregivers for people with multiple sclerosis (MS) is important but poorly studied, particularly in patients with low levels of disability. Objectives. To describe the perceptions of the role of caregivers from the perspective of the caregiver, the patient, and neurologists. Methods. This observational study was conducted in France on patients with relapsing remitting MS treated with subcutaneous (SC) interferon-β-1a (IFN-β-1a) for more than 24 months. Results. Caregiver, patients, and neurologists all considered providing moral support and fighting against the disease as the most important role of the care provider. Moral support was considered significantly more important by caregivers than the patients and neurologists (p=0.002) and caregivers considered their role in helping patients to fight disease more important than did the neurologists (p=0.006). Knowledge of disease and available treatments were less important among support providers than patients (p=0.007 and p=0.001). Conclusion. There are many unmet needs in the perception of the role of caregivers for people with MS which need to be addressed to deliver the most effective care package for patients and to support the needs of the support provider

Switchable Control of Scaffold Protein Activity via Engineered Phosphoregulated Autoinhibition

Scaffold proteins operate as organizing hubs to enable high-fidelity signaling, fulfilling crucial roles in the regulation of cellular processes. Bottom-up construction of controllable scaffolding platforms is attractive for the implementation of regulatory processes in synthetic biology. Here, we present a modular and switchable synthetic scaffolding system, integrating scaffold-mediated signaling with switchable kinase/phosphatase input control. Phosphorylation-responsive inhibitory peptide motifs were fused to 14-3-3 proteins to generate dimeric protein scaffolds with appended regulatory peptide motifs. The availability of the scaffold for intermolecular partner protein binding could be lowered up to 35-fold upon phosphorylation of the autoinhibition motifs, as demonstrated using three different kinases. In addition, a hetero-bivalent autoinhibitory platform design allowed for dual-kinase input regulation of scaffold activity. Reversibility of the regulatory platform was illustrated through phosphatase-controlled abrogation of autoinhibition, resulting in full recovery of 14-3-3 scaffold activity

Modular bioengineered kinase sensorsviascaffold protein-mediated split-luciferase complementation

Phosphorylation is a key regulation event in cellular signaling. Sensing the underlying kinase activity is of crucial importance for its fundamental understanding and for drug development. For this, modular kinase activity sensing concepts are urgently needed. We engineered modular serine kinase sensors based on complementation of split NanoBiT luciferase on protein assembly platforms generated from the scaffold protein 14-3-3. The bioengineered platforms are modular and easy adaptable as exemplary shown using novel sensors for the kinases PKA, PKB, and CHK1. Two designs were conceptualized, both relying on binding of defined mono- or bivalent kinase recognition motifs to the 14-3-3 platform upon phosphorylation, resulting in reconstitution of active split-luciferase. Especially the design based on double phosphorylation and bivalent 14-3-3 binding exhibits high efficiency for signal amplification (>1000-fold) and sensitivity to specific kinases, including in cellular lysates

Protease-activatable scaffold proteins as versatile molecular hubs in synthetic signaling networks

Protease signaling and scaffold-induced control of protein-protein interactions represent two important mechanisms for intracellular signaling. Here we report a generic and modular approach to control the activity of scaffolding proteins by protease activity, creating versatile molecular platforms to construct synthetic signaling networks. Using 14 3 3 proteins as a structurally well-characterized and important class of scaffold proteins, three different architectures were explored to achieve optimal protease-mediated control of scaffold activity, fusing either one or two monovalent inhibitory ExoS peptides or a single bivalent ExoS peptide to T14 3 3 using protease-cleavable linkers. Analysis of scaffolding activity before and after protease-induced cleavage revealed optimal control of 14-3-3 activity for the system that contained monovalent ExoS peptides fused to both the N-and C-terminus, each blocking a single T14 3 3 binding site. The protease-activatable 14 3 3 scaffolds were successfully applied to construct a three-step signaling cascade in which dimerization and activation of FGG-caspase-9 on an orthogonal supramolecular platform resulted in activation of a 14 3 3 scaffold, which in turn allowed 14-3-3-templated complementation of a split-luciferase. In addition, by combining 14 3 3-templated activation of caspase-9 with a caspase-9-activatable 14 3 3 scaffold the first example of a synthetic self-activating protease signaling network was created. Protease-activatable 14 3 3 proteins thus represent a modular platform whose properties can be rationally engineered to fit different applications, both to create artificial in vitro synthetic molecular networks and as a novel signaling hub to re-engineer intracellular signaling pathways

Small molecule-induced and cooperative enzyme assembly on a 14-3-3 scaffold

\u3cp\u3eScaffold proteins regulate cell signalling by promoting the proximity of putative interaction partners. Although they are frequently applied in cellular settings, fundamental understanding of them in terms of, amongst other factors, quantitative parameters has been lagging behind. Here we present a scaffold protein platform that is based on the native 14-3-3 dimeric protein and is controllable through the action of a small-molecule compound, thus permitting study in an in vitro setting and mathematical description. Robust small-molecule regulation of caspase-9 activity through induced dimerisation on the 14-3-3 scaffold was demonstrated. The individual parameters of this system were precisely determined and used to develop a mathematical model of the scaffolding concept. This model was used to elucidate the strong cooperativity of the enzyme activation mediated by the 14-3-3 scaffold. This work provides an entry point for the long-needed quantitative insights into scaffold protein functioning and paves the way for the optimal use of reengineered 14-3-3 proteins as chemically inducible scaffolds in synthetic systems.\u3c/p\u3