Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression

<p>Abstract</p> <p>Background</p> <p>Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (<it>Spadella cephaloptera</it>) and to use them in phylogenetic studies.</p> <p>Results</p> <p>This analysis has allowed us to determine the complete primary structures of 23 out of 32 RPs from the small ribosomal subunit (SSU) and 32 out of 47 RPs from the large ribosomal subunit (LSU). Ten proteins are partially determined and 14 proteins are missing. Phylogenetic analyses of concatenated RPs from six animals (chaetognath, echinoderm, mammalian, insect, mollusc and sponge) and one fungal taxa do not resolve the chaetognath phylogenetic position, although each mega-sequence comprises approximately 5,000 amino acid residues. This is probably due to the extremely biased base composition and to the high evolutionary rates in chaetognaths. However, the analysis of chaetognath RP genes revealed three unique features in the animal Kingdom. First, whereas generally in animals one RP appeared to have a single type of mRNA, two or more genes are generally transcribed for one RP type in chaetognath. Second, cDNAs with complete 5'-ends encoding a given protein sequence can be divided in two sub-groups according to a short region in their 5'-ends: two novel and highly conserved elements have been identified (5'-TAATTGAGTAGTTT-3' and 5'-TATTAAGTACTAC-3') which could correspond to different transcription factor binding sites on paralog RP genes. And, third, the overall number of deduced paralogous RPs is very high compared to those published for other animals.</p> <p>Conclusion</p> <p>These results suggest that in chaetognaths the deleterious effects of the presence of paralogous RPs, such as apoptosis or cancer are avoided, and also that in each protein family, some of the members could have tissue-specific and extra-ribosomal functions. These results are congruent with the hypotheses of an allopolyploid origin of this phylum and of a ribosome heterogeneity.</p

Similarities and dissimilarities between safety levels and security levels

International audienceThe paper proposes a comparative analysis of the notions of Safety Levels and Security Levels as defined (under various names) by the relevant standards. This comparison is a basis for the elaboration of a harmonised process to develop and validate embedded systems having to comply with both safety and security requirements (including related certification requirements when applicable), which is the objective of the French collaborative project SEISES. An important case corresponds to systems for which security requirements come from safety needs i.e., the necessity to preserve safety properties even in case of security threats. In such a case it is necessary to identify clearly the dependencies between the Safety and the Security Levels of the system

Joint use of static and dynamic software verification techniques: a cross-domain view in safety critical system industries

International audienceHow different are the approaches to combining formal methods (FM) and testing in the safety standards of the automotive, aeronautic, nuclear, process, railway and space industries? This is the question addressed in this paper by a cross-domain group of experts involved in the revision committees of ISO 26262, DO-178C, IEC 60880, IEC 61508, EN 50128 and ECSS-Q-ST-8OC. First we review some commonalities and differences regarding application of formal methods in theaforementioned standards. Are they mandatory or recommended only? What kind of properties are they advised to be applied to? What is specified in the different standards regarding coverage (both functional and structural) if testing and formal methods are used jointly?We also account for the return on experience of the group members in the six industrial domains regarding state of the art practice of joint use of formal methods and testing. Where did formal methods actually prove to outperform testing? Then we discuss verification coverage, and more specifically the role of structural coverage. Does structural coverage play the same role in all the standards? Is it specific to testing and irrelevant for formal methods? What verification terminationcriteria is applicable in case FM-test mix? We conclude on some prospective views on how software safety standards may evolve to maximize the benefits of joint use of dynamic (testing) and static (FM) verification methods

Security and Safety Assurance for Aerospace Embedded Systems

International audienceThe paper starts with the list of basic principles that guided the development of the SEISES security and safety assurance framework. Then we present the SEISES structure and we provide some examples of assurance objectives and related assurance activities. We detail the convergence between safety and security assurance activities that we have identified. Finally, we introduce the three demonstrators and we summarize the main lessons learnt from these experimentations. We conclude the paper by summarizing the results of the SEISES project, by comparing these results with other approaches dealing with joint safety and security assurance and by listing promising directions for further research

Multi-domain comparison of safety standards

International audienceThis paper presents an analysis of safety standards and their implementation in certification strategies from different domains such as aeronautics, automation, automotive, nuclear, railway and space. This work, performed in the context of the CG2E ("Club des Grandes Entreprises de l'Embarqué"), aims at identifying the main similarities and dissimilarities, for potential cross-domain harmonization. We strive to find the most comprehensive 'trans-sectorial' approach, within a large number of industrial domains. Exhibiting the 'true goals' of their numerous applicable standards, related to the safety of system and software, is a first important step towards harmonization, sharing common approaches, methods and tools whenever possible

Ecofriendly recycled aggregate concrete and bioreceptivity

Nowadays, it becomes essential to limit environmental impact of building materials and to consider the life cycle of materials used. Recycling of materials from demolition has the dual objective of preserving natural resources and limiting the number of storage sites. The study presented here aims to develop the use of recycled aggregate issued of concrete in total replacement of natural materials (sand and gravel). This work has to be done upstream the studies on bio-corrosion or bio-receptivity of these concrete composed of recycled aggregates. Following an experimental analysis of physical, mechanical and mineralogical properties of recycled aggregates,the influence of these characteristics on choosing formulation parameters of concrete and mortar was studied. It was shown that the use of superplasticizers is necessary to reach satisfactory properties of concrete. The next step of this work will be toanalyse the bio-receptivity of these concrete and compatibilitywith bio-admixture used to decrease bio-receptivity and bio-corrosion; and to develop bio-superplasticizers to replace chemical ones

Conception d'un support de communication sûr de fonctionnement pour systèmes de surveillance et de sécurité : REBECCA

CE MEMOIRE EST CONSACRE A LA CONCEPTION D'UN SUPPORT DE COMMUNICATION SUR DE FONCTIONNEMENT, A TEMPS D'ACCES BORNE ET FAIBLE, POUR SYSTEMES DISTRIBUES DE SURVEILLANCE ET SECURITE. L'ANALYSE EFFECTUEE CONDUIT A UNE APPROCHE PAR DOUBLE DECOMPOSITION INTEGRANT LA VALIDATION PROGRESSIVE DES CHOIX: LA CONCEPTION EST MENEE PAR AFFINEMENTS SUCCESSIFS, CONJOINTEMENT SUR PLUSIEURS NIVEAUX D'ABSTRACTION AFIN DE PRENDRE EN COMPTE L'ENSEMBLE DES CONTRAINTES ET DE LEURS INTERACTIONSIndisponibl

Dependability engineering of complex computing systems

International audienceThis paper presents a development model focused on the production of dependable systems. Three classes of processes are distinguished: 1) the system creation process which builds on the classical development steps (requirements, design, realization, integration); 2) dependability processes (i.e., fault prevention, fault tolerance, fault removal and fault forecasting); and 3) other supporting processes such as quality assurance and certification. The proposed approach relies on the identification of basic activities for the system creation process and for the dependability processes, and then on the analysis of the interactions among the activities of each process and with the other processes. Finally, to support the development of dependable systems, we define for each system creation activity, a checklist that specifies the key issues related to fault prevention, fault tolerance, fault removal, and fault forecasting, that need to be addressed

System Level Integrated Failure Analysis

International audienc

A CROSS-DOMAIN COMPARISON OF SYSTEMATIC ERRORS CONTROL STRATEGIES

International audienceAll domain specific safety frameworks account for controlling introduction of systematic errors and mitigating their effect on system mission and environment. However they exhibit differences according to application sectors. The position of safety standards regarding systematic failures quantification is also variable and reveals significant differences deserving some further analysis. In this paper, we analyse how different standards account, or not, for the contribution of systematic errors to overall failures rates. We describe how different strategies for systematic error control have an impact on system engineering. We expose the underlying approach of each sector and explore the specific aspects of systematic errors control at item level versus system level.Toutes les normes de sécurité prennent en compte le contrôle des erreurs systématiques et la limitation de leurs effets sur la mission et l'environnement d'un système. Cependant on note des différences d'approche des normes de sécurité vis-à-vis de la quantification des défaillances systématiques est également variable et révèle des différences méritant une analyse plus approfondie. Nous analysons dans cet article comment différentes normes prennent en compte la contribution des erreurs systématiques aux taux de défaillances globaux des systèmes. Nous décrivons comment différentes stratégies de contrôle des erreurs systématiques ont un impact sur les exigences d'ingénierie des systèmes. Nous explorons les aspects spécifiques du contrôle des erreurs systématiques au niveau des items par rapport au niveau du système